General Biology Textbook

Getting Started

The word biology means, "the science of life", from the Greek bios, life, and logos, word or knowledge. Therefore, Biology is the science of Living Things. That is why Biology is sometimes known as Life Science.

The science has been divided into many subdisciplines, such as botany, bacteriology, anatomy, zoology, histology, mycology, embryology, parasitology, genetics, molecular biology, systematics, immunology, microbiology, physiology, cell biology, cytology, ecology, and virology. Other branches of science include or are comprised in part of biology studies, including paleontology, taxonomy, evolution, phycology, helimentology, protozoology, entomology, biochemistry, biophysics, biomathematics, bio engineering, bio climatology and anthropology.

Characteristics of life

Not all scientists agree on the definition of just what makes up life. Various characteristics describe most living things. However, with most of the characteristics listed below we can think of one or more examples that would seem to break the rule, with something nonliving being classified as living or something living classified as nonliving. Therefore we are careful not to be too dogmatic in our attempt to explain which things are living or nonliving.

Living things are composed of matter structured in an orderly way where simple molecules are ordered together into much larger macromolecules.

An easy way to remember this is GRIMNERD C All organisms; - Grow, Respire, Interact, Move, Need Nutrients, Excrete (Waste), Reproduce,Death, Cells (Made of)

Living things are sensitive, meaning they are able to respond to stimuli.
Living things are able to grow, develop, and reproduce.
Living things are able to adapt over time by the process of natural selection.
All known living things use the hereditary molecule, DNA.
Internal functions are coordinated and regulated so that the internal environment of a living thing is relatively constant, referred to as homeostasis.

Living things are organized in the microscopic level from atoms up to cells. Atoms are arranged into molecules, then into macromolecules, which make up organelles, which work together to form cells. Beyond this, cells are organized in higher levels to form entire multicellular organisms. Cells together form tissues, which make up organs, which are part of organ systems, which work together to form an entire organism. Of course, beyond this, organisms form populations which make up parts of an ecosystem. All of the Earth's ecosystems together form the diverse environment that is the earth.

Example:-

sub atoms, atoms, molecules, cells, tissues, organs, organ systems, organisms, population, community, eco systems, biosphere

Emergent property is viewed in the biological organization of life, ranging from the subatomic level to the entire biosphere. Emergent properties are not unique to life, but biological systems are far more complex, making the emergent properties of life difficult to study.

Systems biology is a biology-based inter-disciplinary field of study that focuses on complex interactions within biological systems, using a holistic approach.

Biologists study properties of life, with reductionist approach and holistic approach.

Nature of science

Science is a methodology for learning about the world. It involves the application of knowledge.

The scientific method deals with systematic investigation, reproducible results, the formation and testing of hypotheses, and reasoning.

Reasoning can be broken down into two categories, induction (specific data is used to develop a generalized observation or conclusion) and deduction (general information leads to specific conclusion). Most reasoning in science is done through induction.

Science as we now know it arose as a discipline in the 17th century.

Scientific method

The scientific method is not a step by step, linear process. It is an intuitive process, a methodology for learning about the world through the application of knowledge. Scientists must be able to have an "imaginative preconception" of what the truth is. Scientists will often observe and then hypothesize the reason why a phenomenon occurred. They use all of their knowledge and a bit of imagination, all in an attempt to uncover something that might be true. A typical scientific investigation might go like so:

You observe that a room appears dark, and you ponder why the room is dark. In an attempt to find explanations to this curiosity, your mind unravels several different hypotheses. One hypothesis might state that the lights are turned off. Another hunch might be that the room's lightbulb has burnt out. Worst yet, you could be going blind. To discover the truth, you experiment. You feel your way around the room and find a light switch and turn it on. No light. You repeat the experiment, flicking the switch back and forth. Still nothing. That means your initial hypothesis, the room is dark because the lights are off, has been rejected. You devise more experiments to test your hypotheses, utilizing a flashlight to prove that you are indeed not blind. In order to accept your last remaining hypothesis as the truth, you could predict that changing the light bulb will fix the problem. If all your predictions succeed, the original hypothesis is valid and is accepted. In some cases, however, your predictions will not occur, in which you'll have to start over. Perhaps the power is off.

**How Science is Done**
A diagram that illustrates scientific investigation

Scientists first make observations that raise a particular question. In order to explain the observed phenomenon, they develop a number of possible explanations, or hypotheses. This is the inductive part of science, observing and constructing plausible arguments for why an event occurred. Experiments are then used to eliminate one or more of the possible hypotheses until one hypothesis remains. Using deduction, scientists use the principles of their hypothesis to make predictions, and then test to make sure that their predictions are confirmed. After many trials (repeatability) and all predictions have been confirmed, the hypothesis then may become a theory.

Quick Definitions

Observation - Quantitative and qualitative measurements of the world.

Inference - Deriving new knowledge based upon old knowledge.

Hypotheses - A suggested explanation.

Rejected Hypothesis - An explanation that has been ruled out through experimentation.

Accepted Hypothesis - An explanation that has not been ruled out through excessive experimentation and makes verifiable predictions that are true.

Experiment - A test that is used to rule out a hypothesis or validate something already known.

Scientific Method - The process of scientific investigation.

Theory - A widely accepted hypothesis that stands the test of time. Often tested, and usually never rejected.

The scientific method is based primarily on the testing of hypotheses by experimentation. This involves a control, or subject that does not undergo the process in question. A scientist will also seek to limit variables to one or another very small number, single or minimum number of variables. The procedure is to form a hypothesis or prediction about what you believe or expect to see and then do everything you can to violate that, or falsify the hypotheses. Although this may seem unintuitive, the process serves to establish more firmly what is and what is not true.

A founding principle in science is a lack of absolute truth: the accepted explanation is the most likely and is the basis for further hypotheses as well as for falsification. All knowledge has its relative uncertainty.

Theories are hypotheses which have withstood repeated attempts at falsification. Common theories include evolution by natural selection and the idea that all organisms consist of cells. The scientific community asserts that much more evidence supports these two ideas than contradicts them.

Charles Darwin

Charles Darwin is most remembered today for his contribution of the theory of evolution through natural selection.

The seeds of this theory were planted in Darwin's mind through observations made on a five-year voyage through the New World on a ship called the Beagle. There, he studied fossils and the geological record, geographic distribution of organisms, the uniqueness and relatedness of island life forms, and the affinity of island forms to mainland forms.

Upon his return to England, Darwin pondered over his observations and concluded that evolution must occur through natural selection. He declined, however, to publish his work because of its controversial nature. However, when another scientist, Wallace, reached similar conclusions, Darwin was convinced to publish his observations in 1859. His hypothesis revolutionized biology and has yet to be falsified by empirical data collected by mainstream scientists.

After Darwin

Since Darwin's day, scientists have amassed a more complete fossil record, including microorganisms and chemical fossils. These fossils have supported and added subtleties to Darwin's theories. However, the age of the Earth is now held to be much older than Darwin thought. Researchers have also uncovered some of the preliminary mysteries of the mechanism of heredity as carried out through genetics and DNA, areas unknown to Darwin. Another growing area is comparative anatomy including homology and analogy.

Today we can see a bit of evolutionary history in the development of embryos, as certain (although not all) aspects of development recapitulate evolutionary history.

The molecular biology study of slowly mutating genes reveal considerable evolutionary history consistent with fossil and anatomical record.

Challenges to Darwin

Darwin and his theories have been challenged many times in the last 150 years. The challenges have been primarily religious based on a perceived conflict with the preconceived notion of creationism. Many of those who challenge Darwin have been adherents to the young earth hypothesis that says that the Earth is only some 6000 years old and that all species were individually created by a god. Some of the proponents of these theories have suggested that chemical and physical laws that exist today were different or nonexistent in earlier ages. However, for the most part, these theories are either not scientifically testable and fall outside the area of attention of the field of biology, or have been disproved by one or more fields of science.

References

Matter

Matter is defined as anything that has mass (an amount of matter in an object) and occupies space (which is measured as volume).

Particles, from smallest to largest and amal is the greatest
1. Subatomic particles
2. Atoms
3. Molecules
4. Macromolecules
Origin of matter
1. Big Bang, about 13.7 billion years ago
2. Hydrogen, helium
3. Heavier elements formed in suns, super nova
  - Earth's matter predates formation of sun, 4.5 billion years ago
All matter consists of atoms, which are composed of : electrons, protons, neutrons

The atom

Example: Hydrogen
- The simplest element
- One proton (+)
- One electron in orbit (-)
Built by adding one proton (and one electron) at a time
Number of protons determines atomic number and number of electrons
Neutrons
- Neutral charge
- Contribute mass
- May decay
Oxygen
- 8 protons (mass)
- 8 electrons
- 8 neutrons (mass)

Mass and isotopes

Atomic mass
- Sum of masses of protons and neutrons
- Measured in daltons or AMU (Atomic Mass Unit)
- An AMU is 1/12 the mass of Carbon-12
- proton ~1 AMU or dalton
- 6.024 x 10²³ daltons/gram
Atoms with same atomic number belong to same element
Isotopes
- Same atomic number but different atomic mass
- Some are radioactive
- Uses of isotopes
  - Radioactive: 3H, 14C, 32P, 35S
    - Tracers in biochemical reactions
    - Detection of molecules in recombinant DNA technology (genetic engineering)
    - Half-life: dating of rocks, fossils
  - Non-radioactive (N, C, O)
    - Diet of organisms (including fossils)
    - Biochemical tracers

Electrons

Negative charge
Held in orbit about nucleus by attraction to positively charged nucleus
Atom may gain or lose electron, altering charge
- Cation: loses electron, positive charge
  - Na⁺
- Anion: gains electron, negative charge
  - Cl^-
Determine chemical properties of atoms
- Number
- Energy level

Chemical bonds

Form molecules
Enzymes: make, break, rearrange chemical bonds in living systems
Ionic
Covalent
- Sharing of one or more pairs of electrons
  - Called single, double, or triple
- No net charge (as in ionic bonds)
- No free electrons
- Give rise to discrete molecules
- Hydrogen

Chemical reactions

Formation and breaking of chemical bonds
Shifting arrangement of atoms
Reactants -> products
Reactions are influenced by:
- Temperature
- Concentration of reactants, products
- Presence of catalysts (enzymes)
Oxidation:reduction

Water

Essential for life
~75% earth's surface is water
Life evolved in water
Solvent for many types of solutes
High specific heat
High polarity
- Creates a slightly negative Oxygen and a Slightly positive hydrogen
- allows formation of Hydrogen Bonds

Hydrogen bonding

A type of polar interaction
Critical for:
- Protein structure
- Enzymatic reactions
- Movement of water in plant stems
Weak and transient
Powerful cumulative effect
- Solubility of many compounds
- Cohesion (capillary action)
- Lower density of ice
Formed between molecules other than water
- Protein structure
- DNA, RNA structure

Water organizes nonpolar molecules

Nonpolar molecules: no polarity (+/-) charges
Hydrophobic: exclude water because they don't form hydrogen bonds with it
Consequences:
- Membranes
- Protein structure
Hydrophilic: polar substances associate with water

Ionization of water: H₂O -> H⁺ + OH^-

Forms a Hydrogen ion (H⁺), hydroxide ion (OH^-)
Due to spontaneous breakage of covalent bond
At 25 °C, 1 liter of water contains 10-7 moles of H⁺ ions: 10-7 moles/liter

pH

A convenient way of indicating H⁺ concentration
pH = -log[H⁺]
For water, pH = -log[10-7] = 7
Since for each H⁺ in pure water, there is one OH^-, pH of 7 indicates neutrality
Logarithmic scale

Buffer

Reservoir for H⁺
Maintains relatively constant pH over buffering range

References

Building blocks of life

Carbon based: organic molecules
Carbohydrates: CHO
Lipids: CHO, water insoluble
Proteins: CHONS, structure/function in cells
Nucleic acids: CHONP, hereditary (genetic) information

Carbon

Can make 4 covalent bonds
- Chains
  - Straight
  - Branched
  - Ring
- Hydrocarbons (C, H): store energy
- Functional groups
  - Attach to carbon
  - Alter chemical properties
  - Form macromolecules
  - Sapoteton

Carbohydrates

Principally CHO (rare N, S and P)
- 1C:2H:1O ratio
- Energy rich (many C-H bonds)
Monosaccharides (principal: glucose)
- Simple sugars
- Principle formula: C₆H₁₂O₆
- Form rings in water solution
Disaccharides (sucrose, lactose)
Polysaccharides (starch, glycogen, cellulose, chitin)

Stereoisomers

Bond angles of carbon point to corners of a tetrahedron
When 4 different groups are attached to a carbon, it is asymmetric, leading to various types of isomerism
- Stereoisomers: (D, L)
Same chemical properties
Different biological properties
D sugars, L amino acids

Lipids

C-H bonds (nonpolar) instead of C-OH bonds as in carbohydrates
- High energy
- Hydrophobic (insoluble in water)
Categories
- Fats: glycerol and three fatty acids
- Phospholipids: primary component of membranes
- Prostaglandins: chemical messengers (hormones)
- Steroids: membrane component; hormones
- Terpenes: pigments; structure

Fatty acids

Hydrocarbon chain
- Even number of C, 14->20
- Terminates in carboxyl group
Saturated: contain maximum number of hydrogens (all single bonds); maximum energy
Unsaturated: one or more double bonds
- Usually higher melting point
- Many common oils are polyunsaturated

Proteins

Polymer of amino acids
- 21 different amino acids found in proteins
- Sequence of amino acids determined by gene
Amino acid sequence determines shape of molecule
- Linked by peptide bond (covalent)
Functions
- regulate chemical reactions and cell processes [enzymes]
- form bone and muscle; various other tissues
- facilitate transport across cell membrane [carrier proteins]
- fight disease [antibodies]
Motifs: folding patterns of secondary structure
Domains: structural, functional part of protein often independent of another part; often encoded by different exons
Shape determines protein's function

Amino acids

21 commonly found in proteins
- 21st is selenocysteine, not mentioned in text
Common structure
- Amino group: NH₂
- Carboxyl group: COOH
- R group- 4 different kinds of R groups
  - acidic
  - basic
  - hydrophilic (polar)
  - hydrophobic (nonpolar)
Confer individual properties on amino acids
List of amino acids

Structure

Primary structure: the amino acid sequence
- Determines higher orders of structure
- Critical for structure and function of protein
Secondary: stabilized by intramolecular hydrogen bonding
- helix
- sheet
Tertiary: folding, stabilized by ionic bonds (between R groups), hydrogen bonding, van der Waal's forces, hydrophobic interactions
Quaternary: _ 2 polypeptides

Function

Requires proper folding, cofactors, pH, temperature, etc.
Proteins are often modified after synthesis
- Chemical modification
- Addition of heme groups (hemoglobin, cytochrome)
Denatured proteins can not function properly
Proteins are degraded by proteosome as part of constant turnover of cell components

Hereditary (Genetic) information

Nucleic acids
- DNA: deoxyribonucleic acid
Hereditary information of all cells
Hereditary information for many viruses
- RNA: ribonucleic acid
Hereditary information of certain viruses (HIV)
Intermediate in gene expression
Composed of nucleotides
- Ribonucleotides
- Deoxyribonucleotides

RNA DNA origin

Which came first?
Paradox: DNA encodes protein necessary for its own replication
Discovery of catalytic RNA by Cech and Altman suggested that RNA might have been first self-replicating molecule
DNA evolved as more stable type of storage molecule

Proteins: Their building block is amino acids. The bond connecting 2 of the amino acids together are called peptide bonds. One of these bonds makes a monopeptide, two a dipeptide, and any more than that makes a polypeptide.

References

Properties of life

Organization: Being structurally composed of one or more cells, which are the basic units of life.
- prokaryote: no nucleus
- eukaryote: membrane bound nucleus.
Sensitivity: respond to stimuli.
Energy Processing
Growth and Development
Reproduction
- hereditary mechanisms to make more of self; DNA based.
Regulation, including homeostasis.
Evolution.

Origin of life: 3 hypotheses

Extraterrestrial origin (panspermia): meteor, comet borne from elsewhere in universe
- evidence of amino acids and other organic material in space (but often both D & L forms)
- questionable bacterial fossils in Martian rock

-However, this would imply that some other origin of life was likely because it would have had to happen elsewhere before it could be transported here, and the only difference would be that life did not originate on Earth.

Spontaneous origin on earth: primitive self-replicating macromolecules acted upon by natural selection ((macro)Evolution is one example of this)

-This is often criticized for the improbability of life being produced by a chemical reaction caused by lightning, along with the ability of any produced DNA to be in a sequence that could reproduce a working life model. It is also attacked for religious reasons, as it bypasses things like the idea of a supreme being directly creating humans. It also seems unlikely to some that such huge changes are possible in evolution without evidence of a credible "in-between” stage. Many of the stages of man are disputed due to their somewhat shaky grounds. For example, bones from other animals or species have been mistaken for humanoid while complete skeletons have been put together from a limited number of bones.

Special creation: religious explanations (Intelligent Design is one popular example of this.) These explanations contend that life was created by God (or perhaps some other Intelligent Designer).
- Proponents of Intelligent design suggest that the vast complexity of life could only have been intentionally designed while other creationists cite biblical support.

-This is often attacked for many of the same reasons that religion is attacked, and is often regarded as superstitious and/or unscientific.

It is debated whether schools should teach one hypothesis over another when discussing the origin of life. However, since they are all accepted hypotheses in some respect, this wikibook will include both of them without favoring one over the other.

The early earth

It is believed that the Earth was formed about 4.5 billion years ago.

Heavy bombardment by rubble ceased about 3.8 billion years ago.
Reducing atmosphere: much free H
- also H₂O, NH₃, CH₄
- little, if any, free O₂
- with numerous H electrons, require little energy to form organic compounds with C
Warm oceans, estimated at 49-88 °C
Lack of O₂ and consequent ozone (O₃) meant considerable UV energy

Chemical reactions on early earth

UV and other energy sources would promote chemical reactions and formation of organic molecules
Testable hypothesis: Miller-Urey experiment
- simulated early atmospheric conditions
- found amino acids, sugars, etc., building blocks of life
- won Nobel prize for work
- experiment showed prebiotic synthesis of biological molecules was possible

Issues

Miller later conceded that the conditions in his experiments were not representative of what is currently thought to be those of early earth
He also conceded that science has no answer for how amino acids could self-organize into replicating molecules and cells
In the 50 years since Miller-Urey, significant issues and problems for biogenesis have been identified. This is a weak hypothesis at this time.
Conclusion: Life exists, we don't know why.

Origin of cells

Cells are very small and decompose quickly after death. As such, fossils of the earliest cells do not exist. Scientists have had to form a variety of theories on how cells (and hence life) was created on Earth.

Bubble hypothesis
- A. Oparin, J.B.S. Haldane, 1930’s
Primary abiogenesis: life as consequence of geochemical processes
Protobionts: isolated collections of organic material enclosed in hydrophobic bubbles
- Numerous variants: microspheres, protocells, protobionts, micelles, liposomes, coacervates
Other surfaces for evolution of life
- deep sea thermal vents
- ice crystals
- clay surfaces
- tidal pools

The RNA world?

DNA → RNA → polypeptide (protein)
Catalytic RNA: ribozyme
- discovered independently by Tom Cech and Sid Altman (Nobel prize)
- catalytic properties: hydrolysis, polymerization, peptide bond formation, etc.
Self-replicating RNA molecule may have given rise to life
- consistent with numerous roles for RNA in cells as well as roles for ribonucleotides (ATP)
- relationship to bubble-like structures is uncertain

The earliest cells

Microfossils
- ~3.5 by
- resemble bacteria: prokaryotes
- biochemical residues
- stromatolites
Archaebacteria (more properly Archaea)
- extremophiles: salt, acid, alkali, heat, methanogens
- may not represent most ancient life
Eubacteria
- cyanobacteria: photosynthesis
atmospheric O₂; limestone deposits
chloroplasts of eukaryotes

Cyanobacteria

Major steps in evolution of life

Prebiotic synthesis of macromolecules
Self replication
- RNA? (primitive metabolism)
DNA as hereditary material
1st cells
Photosynthesis
Aerobic respiration
Multicellularity (more than once)

References

This text is based on notes very generously donated by Dr. Paul Doerder, Ph.D., of the Cleveland State University.

Cells

Cell structure

What is a cell? The word cell comes from the Latin word "cella", meaning "small room", and it was first coined by a microscopist observing the structure of cork. The cell is the basic unit of all living things, and all organisms are composed of one or more cells. Cells are so basic and critical to the study of life, in fact, that they are often referred to as "the building blocks of life". Organisms - bacteria, amoebae and yeasts, for example - may consist of as few as one cell, while a typical human body contains about a trillion cells.

According to Cell Theory, first proposed by Schleiden and Schwann in 1839, all life consists of cells. The theory also states that all cells come from previously living cells, all vital functions (chemical reactions) of organisms are carried out inside of cells, and that cells contain necessary hereditary information to carry out necessary functions and replicate themselves. It is the basis of human life.

All cells contain:

Lipid bilayer boundary (plasma membrane)
Cytoplasm
DNA (hereditary information)
Ribosomes for protein synthesis

Eukaryotic cells also contain:

At least one nucleus
Mitochondria for cell respiration and energy

Cells may also contain:

Lysosomes
Peroxisomes
Vacuoles
Cell walls

Concepts

Plasma Membrane: Phospholipid bilayer, which contains great amount of proteins, the most important functions are the following:

It selectively isolates the content of the cell of the external atmosphere.
It regulates the interchange of substances between the cytoplasm and the environment.
Communicates with other cells.

Model of the fluid mosaic: Describes the structure of the plasma membrane, this model was developed in 1972 by cellular biologists J. Singer and L. Nicholson.
Phospholipid bilayer: Is in the plasma membrane and produces the fluid part of membranes.
Proteins: Long chains of amino acids.
Glucose proteins: Proteins together with carbohydrates in the plasma membrane, mostly in the outer parts of the cell.
Functions of proteins: Transport oxygen, they are components of hair and nails, and allow the cell interact with its environment.
Transport Proteins: Regulate the movement of soluble water molecules, through the plasma membrane. Some transport proteins called channel proteins form pores or channels in the membrane so that water soluble molecules pass.
Carrying proteins: Have union sites that can hold specific molecules.
Reception proteins: They activate cellular responses when specific molecules join.
Proteins of recognition: They work as identifiers and as place of union to the cellular surface.
Fluid: It is any substance that can move or change of form.
Concentration: Number of molecules in a determined unit of volume.
Gradient: Physical difference between two regions of space, in such a way that the molecules tend to move in response to the gradients.
Diffusion: Movement of the molecules in a fluid, from the regions of high concentration to those of low concentration.
Passive transport: Movement of substances in a membrane that doesn’t need to use energy.
Simple diffusion: Diffusion of water, gases or molecules across the membrane.
Facilitated diffusion: Diffusion of molecules across the membranes with the participation of proteins.
Osmosis: Diffusion of the water across a membrane with differential permeability.
Transport that needs energy: Movement of substances across a membrane generally in opposition to a gradient of concentration with the requirement of energy.
Active transport: Movement of small molecules using energy (ATP).
Endocytosis: Movement of big particles towards the interior of the cell using energy. The cells enclose particles or liquids.
Pinocytosis: (Literally cell drinking) Form in which the cell introduces liquids.
Phagocytosis: Way of eating of the cells. It feeds in this case of big particles or entire microorganisms.
Pseudopodia: False feet (the amoeba).
Exocytosis: Movement of materials out of the cell with the use of energy. It throws waste material.
Isotonic: The cytoplasm fluid of the interior of the cells is the same that the outer.
Hypertonic solution: The solutions that have a higher concentration of dissolved particles than the cellular cytoplasm and that therefore water of the cells goes out with osmosis.
Hypotonic: The solutions with a concentration of dissolved particles lower than the cytoplasm of a cell and that therefore do that water enters the cell with osmosis.
Swelling: Pressure of the water inside the vacuole.
Endoplasmic Reticulum: It is the place of the synthesis of the cellular membrane.

Structure and function of the cell

Rudolf Virchow: Zoologist, who proposed the postulates of the cellular theory, observes that the living cells could grow and be in two places at the same time, he proposed that all the cells come from other equal cells and proposed 3 postulates:

Every living organism is formed from one or more cells
The smallest organisms are unicellular and these in turn are the functional units of the multicellular organisms.
All the cells come from preexisting cells.

Common characteristics of all the cells

Molecular components: Proteins, amino acids, lipids, sweeten, DNA, RNA.
Structural components: Plasmatic membrane, cytoplasm, ribosomes.
Robert Hooke: He postuled for the first time the term cell
Prokaryotes: Their genetic material is not enclosed in a membrane ex. Bacterias
Eukaryotes: Their genetic material is contained inside a nucleus closed by a membrane

History of cell knowledge

The optical microscope was first invented in 17th century. Shortly thereafter scientists began to examine living and dead biological tissues in order to better understand the science of life. Some of the most relevant discovery milestones of the time period include:

The invention of the microscope, which allowed scientists for the first time to see biological cells
Robert Hooke in 1665 looked at cork under a microscope and described what he called cork "cells"
Anton van Leeuwenhoek called the single-celled organisms that he saw under the microscope "animalcules"
Matthias Jakob Schleiden, a botanist, in 1838 determined that all plants consist of cells
Theodor Schwann, a zoologist, in 1839 determined that all animals consist of cells
Rudolf Virchow proposed the theory that all cells arise from previously existing cells

In 1838, the botanist Matthias Jakob Schleiden and the physiologist Theodor Schwann discovered that both plant cells and animal cells had nuclei. Based on their observations, the two scientists conceived of the hypothesis that all living things were composed of cells. In 1839, Schwann published 'Microscopic Investigations on the Accordance in the Structure and Growth of Plants and Animals', which contained the first statement of their joint cell theory.

Cell Theory

Schleiden and Schwann proposed spontaneous generation as the method for cell origination, but spontaneous generation was later disproven. Rudolf Virchow famously stated "Omnis cellula e cellula"... "All cells only arise from pre-existing cells." The parts of the theory that did not have to do with the origin of cells, however, held up to scientific scrutiny and are widely agreed upon by the scientific community today.

The generally accepted portions of the modern Cell Theory are as follows: (1) The cell is the fundamental unit of structure and function in living things. (2) All organisms are made up of one or more cells. (3) Cells arise from other cells through cellular division. (4) Cells carry genetic material passed to daughter cells during cellular division. (5) All cells are essentially the same in chemical composition. (6) Energy flow (metabolism and biochemistry) occurs within cells.

Microscopes

Allow greater resolution, can see finer detail
Eye: resolution of ~ 100 μm
Light microscope: resolution of ~ 200 nm
Limited to cells are larger organelles within cells
Confocal microscopy: 2 dimension view
Electron microscope: resolution of ~0.2 nm
Laser tweezers: move cell contents

Cell size

One may wonder why all cells are so small. If being able to store nutrients is beneficial to the cell, how come there are no animals existing in nature with huge cells? Physical limitations prevent this from occurring. A cell must be able to diffuse gases and nutrients in and out of the cell. A cell's surface area does not increase as quickly as its volume, and as a result a large cell may require more input of a substance or output of a substance than it is reasonably able to perform. Worse, the distance between two points within the cell can be large enough that regions of the cell would have trouble communicating, and it takes a relatively long time for substances to travel across the cell.

That is not to say large cells don't exist. They are, once again, less efficient at exchanging materials within themselves and with their environment, but they are still functional. These cells typically have more than one copy of their genetic information, so they can manufacture proteins locally within different parts of the cell.

Key concepts: Cell size:

Is limited by need for regions of cell to communicate
Diffuse oxygen and other gases
Transport of mRNA and proteins
- Surface area to volume ratio limited
Larger cells typically:
- Have extra copies of genetic information
- Have slower communication between parts of cell

Structure of Eukaryotic cells

Eukaryotic cells feature membrane delimited nucleii containing two or more linear chromosomes; numerous membrane-bound cytoplasmic organelles: mitochondria, RER, SER, lysosomes, vacuoles, chloroplasts; ribosomes and a cytoskeleton. Also, plants, fungi, and some protists have a cell wall.

Structure of the nucleus

The nucleus is the round object in the cell that holds the genetic information (DNA) of the cell. It is surrounded by a nuclear envelope and has a nucleolus inside.

Nuclear envelope

The nuclear envelope is a double-layered plasma membrane like the cell membrane, although without membrane proteins. To allow some chemicals to enter the nucleus, the nuclear envelope has structures called Nuclear pores. The nuclear envelope is continuous with the endoplasmic reticulum.

Nucleolus

The nucleolus appears in a microscope as a small dark area within the nucleus. The nucleolus is the area where there is a high amount of DNA transcription taking place.

Chromatin

Chromosomes consist of chromatin. This is made up of strings of DNA, which typically measure centimeters in length if stretched out. This DNA is wound around a histone core and organized into nucleosomes.

The chromatin must be uncoiled for gene expression and replication. Chromosome micrograph

Endoplasmic reticulum

The endoplasmic reticulum is a cellular organelle made up of a series of extended folded intracellular membranes. It is continuous with the nuclear membrane.

There are two main types of endoplasmic reticulum:

RER: rough endoplasmic reticulum (site of protein synthesis) associated with ribosomes
SER: smooth endoplasmic reticulum (site of lipid synthesis)

Rough Endoplasmic Reticulum

Proteins are directed to the RER by a signal sequence of a growing polypeptides on the ribosome. This is recognised by a signal recognition particle which brings the ribosome/polypeptide complex to a channel on the RER called a translocon. At the translocon, the signal sequence and ribosome/polypeptide complex interact with the translocon to open it. The signal sequence becomes attached to the translocon. The ribosome can continue to translate the polypeptide into the lumen of the RER. As synthesis continues, 2 processes can happen.

If the protein is destined to become a membrane bound protein then the protein synthesis will continue until termination. The ribosome can then dissociate, allowing protein folding within the RER lumen to occur and continuation to the golgi apparatus for processing of the polypeptide.
If the protein is destined for storage for later secretion after stimulation or for continuous secretion then a protease -an enzyme which cuts proteins at the peptide bond- can cut the signal sequence from the growing polypeptide. Continuation to the golgi etc. can then occur.

When produced, proteins are then exported to one of several locations. The proteins are either modified for extracellular membrane insertion or secretion. Note, this is in contrast with ribosomes which do not associate with the RER and produce proteins which will become cytosolic enzymes for example.

Smooth Endoplasmic Reticulum

Smooth endoplasmic reticulum produces enzymes for lipid and carbohydrate biosynthesis and detoxification RER

Sarcoplasmic Reticulum

This is a specialised form of endoplasmic reticulum found in some muscle cell types-particularly striated, skeletal muscle. Its main function is different from the other 2 types in that is mainly acts as a storage of calcium. This reticulum has voltage gated channels which respond to signals from 'motor neurones' to open and release calcium into the cytoplasm. This can then bring about the next part in muscle contraction.

Figure 1 : Image of nucleus, endoplasmic reticulum and Golgi apparatus.

Nucleus.
Nuclear pore.
Rough endoplasmic reticulum (RER).
Smooth endoplasmic reticulum (SER).
Ribosome on the rough ER.
Proteins that are transported.
Transport vesicle.
Golgi apparatus.
Cis face of the Golgi apparatus.
Trans face of the Golgi apparatus.
Cisternae of the Golgi apparatus.

The Golgi apparatus

The golgi apparatus is made up of multiple stacks of bilipid membranes.

Proteins made on the RER are modified and then sorted
Formation of secretory vesicles
Formation of lysosomes (intracellular digestion)

Other membrane-bound cytoplasmic organelles include:

Microbodies (generic term)
Glyoxysome (transforms fat into carbohydrate in plants)
Peroxisome (uses oxidative metabolism to form hydrogen peroxide and is destroyed by catalase)

Ribosomes

Ribosomes are the site of protein synthesis. Ribosomes themselves are synthesized in the cell nucleoli and are structured as two subunits, the large and the small. These parts are composed of RNA and protein.

Prokaryotic and eukaryotic ribosomes are different, the eukaryotic ones being larger and more complicated.

DNA-containing organelles

Mitochondria

Double membrane
Aerobic metabolism, internal membrane
DNA, ribosomes
Give rise to new mitochondria

Chloroplast

Double membrane
Photosynthesis, internal membrane
DNA, ribosomes
Give rise to new chloroplasts

Centrioles

Microtubule organizing centers
- Animal cells and many protists
- Pair constitutes the centrosome
- Give rise to flagellum during spermatogenesis
Consist of 9 triplet microtubules
Mitosis, meiosis

Cytoskeleton

Cytoskeleton is a collective term for different filaments of proteins that can give physical shape within the cell and are responsible for the 'roads' which organelles can be carried along.

Gives the cell shape
Anchors other organelles
Vital to intracellular transport of large molecules

The cytoskeleton is composed of 3 main types of filaments:

Actin filaments (7 nm)
Microtubules: (25 nm) polymer of tubulin; 13/ring.
Intermediate Filaments

Both actin and microtubules can have associated motor proteins.

Intermediate Filaments

These are rope like filaments, 8-10 nm in diameter and tend to give the structural stability to cells. Examples include Vimentin, neurofilaments and keratin. It is keratin which principly makes up hair, nails and horns.

Actin Filaments

Growth

These filaments are 2-stranded and composed of dimeric subunits called G-Actin. They contain a GTP molecule in order to bind (polymerise). As GTP is hydrolysed then the structure becomes unstable and depolymerisation occurs. The growth of actin filaments is concentration dependant-that is, the higher the concentration of free G-actin, the greater the polymerisation. The are also polar, having a + and a - end (not related to charge) and polymerisation tends to happen faster at the + end.

Cilia and flagella are threads of microtubules that extend from the exterior of cells and used to move single celled organisms as well as move substances away from the surface of the cell. motor proteins-move, wave motion General Biology | Getting Started | Cells | Genetics | Classification | Evolution | Tissues & Systems | Additional Material

Biological membranes

Biological membranes surround cells and serve to keep the insides separated from the outsides. They are formed of phospholipid bilayers, which by definition are a double layer of fatty acid molecules (mostly phospholipids, lipids containing lots of phosphorus).

Proteins serve very important functions in cellular membranes. They are active transports in and out of the cell, acting as gatekeepers. They relay signals in and out of the cell. Proteins are the site of many enzymatic reactions in the cell, and play a role in regulation of cellular processes.

Phospholipid

Phospholipid bilayer

basis of biological membranes and cellular organisms
contains a charged, hydrophilic (attracted to water) head and two hydrophobic (repelled by water) hydrocarbon tails
In presence of water, phospholipids form bilayer
- maximize hydrogen bonds between water
- creates barrier to passage of materials
- fluid mosaic model shows horizontal (common) and "flip-flop" (rare) movement of phospholipids

Fluid mosaic model

Current model of membrane
Phospholipid bilayer
- Phospholipids
Move freely in lipid layer, but rarely switch layers
Different phospholipids in each layer in different organelles
- Glycolipids
- Sterols (cholesterol in animals)
Transmembrane proteins "float" in fluid lipid bilayer
- also called intrinsic, integral proteins
Exterior (extrinsic, peripheral) proteins

Membrane proteins

Transport channels
Enzymes
Cell surface receptors
Cell surface identity markers
Cell adhesion proteins
Attachments to cytoskeleton

Integral membrane proteins

Anchoring to membrane
- Protein has attached phosphatidylinositol (GPI) linkage, anchors protein in outer layer (no picture)
- Protein has one or more hydrophobic transmembrane domains
-helix
-sheet

Channel protein Transport across membranes * Diffusion

- From higher concentration to lower concentration
- Membranes are selectively permeable
Ions diffuse through membrane channels
- Selective
- Movement determined by diffusion and voltage differences
Facilitated diffusion
- Carrier protein, physically binds transported molecule
Osmosis
Diffusion of water down concentration gradient
In cell: various solutes (amino acids, ions, sugars, etc.)
- interact with water, e.g., hydration shells
Water moves through aquaporin channels into cell
Depends upon the concentration of all solutes in solution
- Hyperosmotic solution: higher concentration of solutes
- Hypoosmotic solution: lower concentration of solutes
- Isoosmotic solution: solute concentrations equal
Water moves from hypoosmotic solution to hyperosmotic solution

Osmotic pressure Bulk transport

Endocytosis: energy requiring
- Phagocytosis
Solid material, typically food
- Pinocytosis
Primarily liquid

** Receptor-mediated endocytosis

Pits on cell surface coated with clathrin and receptors
Bind specific proteins
Exocytosis
- Discharge of materials from vesicle at cell surface

Receptor-mediated endocytosis

Active transport

Energy required (usuallyننةىة
Highly selective
Works against concentration gradient
Many examples, e.g., Na⁺/K⁺ pump

Cotransport (coupled transport)

Does not use ATP directly
Molecule is transported in connection with another molecule that is moving down a concentration gradient
- Example: Na⁺ gradient is established by a Na⁺ pump, with higher concentration on outside of cell. Cotransport channel carries Na+ and another molecule (e.g. glucose) into cell
May involve proton (H⁺) pumps (chemiosmosis - ATP production)

Cell-cell interactions

Cells interact with the environment and with each other.

Cell signaling

Signaling requires
- Signal
- Cell receptor (usually on the surface of a membrane)
Signaling is important in:
- Response to environmental stimuli
- Sex
- Development
Major area of research in biology today

Types of signaling

Direct contact (e.g., gap junctions between cells)
Paracrine: Diffusion of signal molecules in extracellular fluid; highly local
Endocrine: Signal (hormone) molecule travels through circulatory system
Synaptic: neurotransmitters

Types of signal molecules

Hormones: chemically diverse
- Steroid
- Polypeptide
- Vitamin/amino acid derived
Cell surface proteins/glycoproteins
Ca²⁺, NO
Neurotransmitter
- Several hundred types
- Some are also hormones e.g. Estrogen, progesterone

Receptor molecules

Intracellular
- Protein that binds signal molecule in cytoplasm
- Bound receptor may act as:
Gene regulator
Enzyme
Cell surface
- Gated ion channels (neurotransmitter receptor)
- Enzymic receptors
- G protein-linked receptors

Cell surface protein

Tissue identity
- glycolipids
- MHC proteins
Immune systems
- distinguish self from not-self
Intercellular adhesion
- permanent contact
- help form sheets of cells, tissues
- may permit signaling

Example: G proteins

Transmembrane surface receptor binds signal molecule
Conformational change allows binding of G protein on cytoplasmic side
G protein binds GTP, becomes activated
G protein activates intracellular signal cascade
- Change in gene expression
- Secrection
- Many other possible consequences

Communicating junctions

Gap junctions
- animals
- small molecules and ions may pass
Plasmodesmata
- plants
- lined with plasma membrane
- permit passage of water, sugars, etc.

Gap junctions

Energy

The capacity to do work.
- Kinetic energy: energy of motion (ex. jogging).
- Potential energy: stored energy (ex. a lion that is about to leap on its prey).
Many forms of energy: e.g.,
- Heat
- Sound
- Electric current
- Light
- All convertible to heat
Most energy for biological world is from sun
Heat (energy of random molecular motion, thermal energy)
- Convenient in biology
- All other energy forms can be converted to heat
- Thermodynamics: study of thermal energy
Heat typically measured in kilocalories
- Kcal: 1000 calories
- 1 calorie: amount of heat required to raise the temperature of one gram of water one degree Celsius (°C)
Heat plays major role in biological systems
- Ecological importance
- Biochemical reactions

Oxidation–Reduction

Energy flows into biological world from sun
Light energy is captured by photosynthesis
- Light energy raises electrons to higher energy levels
- Stored as potential energy in covalent C-H bonds of sugars
Strength of covalent bond is measured by amount of energy required to break it
- 98.8 kcal/mole of C-H bonds
In chemical reaction, energy stored in covalent bonds may transfer to new bonds. When this involves transfer of electrons, it is oxidation–reduction reaction
Always take place together
- Electron lost by atom or molecule through oxidation is gained by another atom or molecule through reduction
- Potential energy is transferred from one molecule to another (but never 100%)
Often called redox reactions
- Photosynthesis
- Cellular Respiration
- Chemiosynthesis
- Autotrophs
- Heterotrophs

NAD⁺

Common electron acceptor/donor in redox reactions
Energetic electrons often paired with H⁺

Free energy

Energy required to break and subsequently form other chemical bonds
- Chemical bonds: sharing of electrons, tend to hold atoms of molecule together
- Heat, by increasing atomic motion, makes it easier to break bonds (entropy)
Energy available to do work in a system
In cells, G = H - TS
- G = Gibbs’ free energy
- H = H (enthalpy) energy in molecule’s chemical bonds
- TS (T, temperature in °K; S, entropy)
Chemical reactions break and make bonds, producing changes in energy
Under constant conditions of temperature, pressure and volume, ΔG = ΔH - TΔS
ΔG, change in free energy
- If positive (+), H is higher, S is lower, so there is more free energy; endergonic reaction, does not proceed spontaneously; require input of energy (e.g., heat)
- If negative (–), H is lower, S is higher. Product has less free energy; exergonic; spontaneous

Activation energy

Reactions with –ΔG often require activation energy
- e.g., burning of glucose
- Must break existing bonds to get reaction started
Catalysts lower activation energy

Enzymes

Biological catalysts
- Protein
- RNA (ribozyme)
Stabilizes temporary association between reactants (substrates) to facilitate reaction
- Correct orientation
- Stressing bonds of substrate
Lower activation energy
Not consumed (destroyed) in reaction

Carbonic anhydrase

Important enzyme of red blood cells
CO₂ + H₂O → H₂CO₃ -> HCO₃ + H⁺
Carbonic anhydrase catalyzes 1st reaction
- Converts water to hydroxyl
- Orients the hydroxyl and CO₂

Enzyme mechanism

One or more active sites which bind substrates (reactants)
- Highly specific
Binding may alter enzyme conformation, inducing better fit

Factors affecting enzyme activity

Substrate concentration
Product concentration
Cofactor concentration
Temperature
pH
Inhibitors
- Competitive: bind to active site
- Noncompetitive: bind to 2nd site, called allosteric site; changes enzyme conformation
Activators
- Bind to allosteric sites, increase enzyme activity

Cofactors

Required by some enzymes
Positively charged metal ions
- e.g., ions of Zn, Mo, Mg, Mn
- Draw electrons away from substrate (stress chemical bonds)
Non-protein organic molecules (coenzymes)
- E.g., NAD⁺, NADP⁺, etc.
- Major role in oxidation/reduction reactions by donating or accepting electrons

ATP

Adenosine triphosphate
Major energy currency of cells, power endergonic reactions
Stores energy in phosphate bonds
- Highly negative charges, repel each other
Makes these covalent bonds unstable
- Low activation energy
When bonds break, energy is transferred
ATP → ADP + Pi + 7.3 kcal/mole

Biochemical pathways

Metabolism: sum of chemical reactions in cell/organism
Many anabolic and catabolic reactions occur in sequences (biochemical pathways)
Often highly regulated

Evolution of biochemical pathways

Protobionts or 1st cells likely used energy rich substrates from environment
Upon depletion of a substrate, selection would favor catalyst which converts another molecule into the depleted molecule
By iteration, pathway evolved backward

References

Glucose + O₂ → CO₂ + H₂O + ATP

Energy

Energy is primarily in C-H bonds (C-O too)
Chemical energy drives metabolism
- Autotrophs: harvest energy through photosynthesis or related process (plants, algae, some bacteria)
- Heterotrophs: live on energy produced by autotrophs (most bacteria and protists, fungi, animals)
Digestion: enzymatic breakdown of polymers into monomers
Catabolism: enzymatic harvesting of energy
Respiration: harvesting of high energy electrons from glucose

Respiration

Transfer of energy from high energy electrons of glucose to ATP
Energy depleted electron (with associated H⁺) is donated to acceptor molecule
- Aerobic respiration: oxygen accepts electrons, forms water
- Anaerobic respiration: inorganic molecule accepts hydrogen/electron
- Fermentation: organic molecule accepts hydrogen/electron

Respiration of glucose

C₆H₁₂O₆ + 6 O₂ → 6 CO₂ + 6 H₂O + energy
ΔG = -720 kcal/mole under cellular conditions
Largely from the 6 C-H bonds
Same energy whether burned or catabolized
In cells, some energy produces heat, most is transferred to ATP

Alternative anaerobic respiration

Methanogens (Archaebacteria).
- CO₂ is electron acceptor, forming CH₄
Sulfur bacteria
- SO₄ reduced to H₂S
- Formation of H₂S set stage for evolution of photosynthesis (H₂S as electron donor before H₂O)
- About 2.7 by, based on ratio of 32S/34S, where only biological processes produce 32S enrichment

Glycolysis overview

Glycolysis accounting

Oxidation
- Two electrons (one proton) are transferred from each G3P to NAD⁺ forming NADH

2NADH

Substrate level phosphorylation
- G3P to pyruvate forms 2 ATP molecules

4 ATP (from 2 G3P)

–2 ATP (priming)

 2 ATP (net gain)

Summary: The net input of glycolysis is 2 ATP molecules which are used to split one glucose molecule. The net yield of this step is 2 ATP and 2 pyruvate.

Regeneration of NAD⁺

Reduction of NAD⁺ to NADH can deplete NAD⁺ supply; it must be regenerated
Two pathways, coupled to fate of pyruvate
- With oxygen: enter electron transport chain, forming water (and ATP)
- Without oxygen: fermentation
lactate
ethanol

Alcohol fermentation

Lactate formation

Either lactic acid or alcohol can be formed as a result of anaerobic respiration in cells.

Krebs cycle: overview

Matrix of mitochondrion
Priming steps
- Joining of acetyl-CoA to oxaloacetate
- Isomerization reactions
Energy extraction steps in Krebs cycle
- Per glucose
6 NADH
2 FADH₂
2 ATP (from GTP)
4 CO₂

ATP production

Chemiosmosis (Mitchell)
H⁺ (from NADH and FADH₂) is pumped against a gradient into the intermembranal space of the mitochondrion (creates voltage potential)
Diffusion back into matrix through ATP synthase channels drives synthesis of ATP (ADP + Pi → ATP)
ATP exits mitochondrion by facilitated transport

Evolution of aerobic respiration

Preceded by evolution of photosynthesis (O2 needed; also, prior evolution of electron transport and chemiosmosis)
High efficiency of ATP production compared to glycolysis
- Fostered evolution of heterotrophs
- Fostered evolution of mitochondria by endosymbiosis in eukaryotes

6 CO₂ + 6 H₂O → C₆H₁₂O₆ + 6 O₂

One of most important reactions in history of life:
- source of atmospheric O₂
- ultimately led to aerobic respiration and eukaryotes
Responsible for bulk of glucose production
Early experiments showed that mass of plant must be derived from substances in the air, not the soil
Experiments with isotopes showed that liberated oxygen comes from water
Experiments also showed that light is essential but that some reactions (e.g., reduction of CO₂) continue in the dark
Plants do two big, important things during photosynthesis: gain energy (absorb light) and build sugar (glucose).
Photosynthesis can be divided into two series of chemical reactions: the light (light-dependent) reactions and the dark (light-independent) reactions. In light reactions, light is absorbed; in dark reactions, sugar is built.
Occurs when plants, algae, and autotrophic bacteria absorb light energy and build glucose.

Light Reactions

Part of the electromagnetic spectrum
Consists of units of energy called photons
Photons at UV end of spectrum have more energy than those at the red end
Occur on the surface of thylakoid disks
Chlorophyll and other plant pigments differentially absorb photons
- Chlorophyll a: light to chemical energy
- Chlorophyll b: accessory chlorophyll
- Chlorophylls absorb primarily blue and red (green reflected back, hence the green color of plants)

Accessory pigments

Chlorophyll is a major light gathering pigment
- Absorbs light with considerable efficiency (i.e., retaining energy)
Accessory pigments
- Chlorophyll b
- Carotenoinds
capture light of wavelengths not captured by chlorophylls
Confer other colors to plant leaves (autumn colors too)

Photosynthetic steps

Primary photoevent: light photon captured by photosystem and energy transferred to electron donated by water
Electron transport: excited electron is shuttled along imbedded series of electron carriers to proton pump and electron is transferred to acceptor
Chemiosmosis: transport of protons back into chloroplast drives synthesis of ATP

The Even More Detailed Light Reactions

What the Light Reactions Do:

The light reactions of photosynthesis occur in chloroplasts in and on the thylakoid disks. During the light reactions, light energy charges up ATP molecules. More specifically, light turns the chloroplast into an acid battery, and this battery charges up ATP.

How the "Chloroplast-Battery" Charges ATP:

The stroma is the fluid inside of the chloroplasts, and it carries a negative charge. This means that it contains about a "gazillion" extra electrons. The solvent of stroma is water.

The fluid inside the thylakoid disks is positively charged because it contains a lot of hydrogen (H+) ions. The pH here is low, making the fluid very acidic. The solvent of thylakoid disk fluid is water.

A chloroplast acts like a battery, because it has separated a strong positive charge and a strong negative charge in two different compartments. Energy is released when H+ ions (free protons) flow from the inside of a thylakoid disk to the stroma. This is electrical energy, since it is a flow of charged particles.

The protons pass through special channels (made of protein) in the thylakoid membrane; this reaction is 'exothermic.' The energy that is given off is used to fuel this reaction (Pi is the phosphate ion):

                    ADP + Pi --> ATP

The proton can go to the negative stroma, but only if it uses its energy to charge up ATP. Since one reaction wants to go, and the other one doesn't, and since the first reaction releases energy and the second one absorbs energy, the two reactions are known to be 'coupled' together so that the first fuels the second. Of course, a special enzyme must be involved for this to happen.

Chlorophyll Molecules on a Thylakoid Disk:

Hundreds of chlorophyll molecules cover the surface of a thylakoid disk, making the disk green. The nonpolar "tails" of the chlorophyll molecule are embedded in the membrane of the thylakoid.

“Dark” reactions

ATP drives endergonic reactions
NADPH provides hydrogens for reduction of CO₂ to carbohydrate (C-H bonds)
Occur in the stroma
First step in carbon fixation

The Detailed Dark Reactions

What the Dark Reactions Do:

The dark reactions build sugar from carbon dioxide gas (CO2), water (H2O), and energy from ATP molecules that were charged up during the light reactions. The dark reactions occur in the stroma of a chloroplast. Dark reactions usually occur in the light, but they don't have to. They'll occur in the dark until the chloroplast's supply of ATP runs out (usually about 30 seconds).

The Calvin Cycle:

The Calvin Cycle is the fancy name for the metabolic pathway that builds sugar. This means that it involves a whole lot of chemical reactions, and it uses a lot of different enzymes to catalyze the reactions.

Carbon dioxide gas is stable, therefore the bonds that hold the carbon and oxygen atoms are strong. Therefore it takes a lot of energy to break the bonds and separate the carbon atoms from the oxygen atoms. The energy needed to do this comes from ATP molecules.

When inorganic carbon (like from CO2) is being added to an organic molecule (such as sugar), this is called carbon fixation.

It takes 2 complete turns of the Calvin Cycle to make a glucose molecule.

References

How cells divide

Prokaryote cell division

Binary fission
- Doubling of cell contents, including DNA
- Fission to divide contents
Segregation of replicated genomes by growth of membrane between attachment points
Partitioning of cytoplasmic components
Escherichia coli
- Capable of cell division every 20 minutes under optimal conditions (DNA in continuous state of replication)
- Model organism of bacterial cell division

Bacterial DNA replication

Replication follows rules of base pairing, with each polynucleotide chain serving as template for synthesis of its complement.
Genetic evidence showed that the bacterial chromosome is circular long before there was corroborating physical evidence.

Eukaryotic chromosomes

Discovered by Walther Fleming in 1882 in dividing cells of salamander larvae, following improvements in microscopes and staining technology
- He called division mitosis (mitos = “thread”)
Chromosome number is constant in a species
- Ranges from 2 to >500 (46 in human somatic cells)
- Homologous pairs, one contributed by each parent
- Change in number is cause and consequence of speciation
Chromosome constancy and their precise division in mitosis and meiosis led biologists to postulate that they were carriers of hereditary information

Chromosome number

1N = number of chromosomes in gamete
1N = haploid chromosome number
2N = number of chromosomes in somatic cells (cells that are not egg or sperm)
2N = diploid
Deviations from N or 2N are usually lethal in animals

Chromosome numbers

Eukaryotic chromosomes

Consist of chromatin
- DNA and associated proteins, mainly histones
- Nucleosomal organization
- Euchromatin: unwound chromatin, in basic nucleosomal configuration; genes available for expression
- Heterochromatin: highly condensed except during replication
Karyotype: array of chromosomes an individual possesses
- Clinical importance (Down syndrome; cancer)
- Evolutionary importance (speciation)

Chromosome organization

Human karyotype stained by chromosome painting

Chromosomes

Homologous pairs
- Inherited one from each parent
- Identical in length and position of centromere
- Contain identical or similar genes
- Homologous pair = homologs
Morphology
- After replication, consist of two sister chromatids attached to a centromere

Human chromosomes

Diploid number = 2n = 46 = 23 pairs of homologs
Haploid number = 23 (gametes)
Each replicated chromosome contains 2 sister chromatids = 92 chromatids

Cell cycle

Growth and division cycle of cells
Precisely controlled by biochemical and gene activity, except in cancer
Phases
- G1: primary growth phase
- S: DNA replication; chromosome replication
- G2: second growth phase; preparation for mitosis
- M: mitosis; nuclear division
- C: cytoplasmic division

Mitotic cell cycle

Cells exiting the cell cycle are said to be in G0
Cell cycle time varies with stages of life cycle and development, with G1 the most variable
DNA replication occurs during S phase of the cell cycle following G1.

 - at this point the chromosomes are composed of two sister chromatids connected by a common centromere.

Replicated human chromosomes

Mitosis

Nuclear division
- equational division of replicated chromosomes
- chromatids move to opposite poles
Continuous process
- prophase
- metaphase
- anaphase
- telophase
Driven by motors and microtubules
No change in chromosome number
- N → N by mitosis
- 2N → 2N by mitosis
May be accompanied by cytokinesis

Kinetochore Microtubules attach to kinetochores. Metaphase

Momentary alignment of chromosomes in center of cell

Anaphase

Plant mitosis

Similar to animal mitosis
New cell wall formed between cells from membrane partition

Cell cycle control

Cell cycle events are regulated by protein complexes and checkpoints
Discovered by microinjection of proteins in to eggs, by mutational analysis and by techniques of molecular biology

Molecular control of cell cycle: Cdk and cyclin

Cyclin dependent protein kinase (Cdk)
- Phosphorylate serine/threonine of target regulatory proteins
- Function only when bound to cyclin
Cyclin: short-lived proteins that bind to cdks

Controlling the cell cycle

External signals initiate cell division in multicellular organisms
Growth factors: extracellular regulatory signals
- Usually soluble; bind to cell surface receptor
- Sometimes membrane bound, requiring cell-cell contact with receptor
- E.g., upon wound, platelets release PDGF which stimulates fibroblasts to enter cell cycle (exit G0), to heal wound

Cancer

Unregulated cell proliferation
Cancer cells have numerous abnormalities
- >46 chromosomes
- Mutations in proto-oncogenes
Encode proteins stimulating the cell cycle
May be regulated by phosphorylation
Often over expressed in cancer cells
- Mutations in tumor-suppressor genes
Encode proteins inhibiting the cell cycle
- Often bind to products of proto-oncogenes
May be regulated by phosphorylation

Mutations and cancer

References

Sexual

Exclusively eukaryotes
Fusion of two haploid genomes
- Fertilization (= syngamy)
- Forms new individuals in multicellular organisms as result of fusion of egg and sperm
Plants
Animals
Meiosis yields haploid genomes at some point in life cycle

Sexual life cycle

Typical animal life cycle

Meiosis occurs in germ line cells in gonads producing haploid gametes
All other cells are somatic cells
Alternation of generations
Sexual intercourse

Meiosis

Gives rise to genetic variation
Reduction division: 2n to n
Preceded by one round of DNA (chromosome) replication
Two rounds of nuclear (& usually cell) division
- Meiosis I
Synapsis of homologs
Segregation of homologs
Reduction division, 2n to n
- Meiosis II
No chromosome replication
Segregation of sister chromatids
Formation of 4 haploid (n) cells
Two nuclear divisions, usually 2 cell divisions, only one round of replication
Meiosis I
- Prophase: synapsis and crossing over
- Metaphase
- Anaphase: chromosome segregation
- Telophase
Meiosis II (mitosis-like)
- Prophase
- Metaphase
- Anaphase: sister chromosome segregation
- Telophase

Prophase I: synapsis

Complete alignment of replicated homologs
Synapsis occurs throughout the entire length of a pair of homologs
Key to chromosome segregation
Synapsis, crossing over
Subdivided into 5 continuous stages

Crossing over

Reciprocal, physical exchange between nonsister chromatids
Type of recombination; mixes maternal and paternal genes
Visual evidence: chiasmata

Microtubules and anaphase I

During prophase microtubules attach to kinetochores on one side of centromere
The metaphase checkpoint insures proper attachment
A phosphorylation event initiates motor activity and anaphase

Meiosis II

Cytologically similar to mitosis
- No preceding DNA replication
- Chromatids segregate and move to opposite poles as chromosomes
- 4 haploid cells produced
In animals, these cells differentiate into gametes
In plants and many other organisms, these cells divide by mitosis, followed some time later by gamete formation

Evolution of sex

Asexual reproduction: all offspring genetically identical to parent
Sex: recombination destroys advantageous combinations
So why sex?
- Many hypotheses
- Effect repair of genetic damage?
Much pachytene repair as well as gene conversion
Some protists form diploid cells in response to stress
- Recombination breaks up combinations of genes favoring parasites, thus reducing parasitism?

Consequences of sex

Recombination: generates genetic diversity
- Crossing over
- Independent assortment
Random fertilization
- Qualities of gamete usually do NOT reflect qualities of genes enclosed in gamete

References

This text is based on notes very generously donated by Paul Doerder, Ph.D., of the Cleveland State University.

Genetics

Charles Darwin, for all he contributed to the science of biology, never knew about the mechanism by which living things inherit traits from previous generations, or how new traits arise.

As any schoolchild can tell you, this mechanism of interitance has since been found to be DNA, or deoxyribonucleic acid. DNA allows for stable inheritance of traits: the code in each strand of DNA is replicated precisely through the pairing of basic units along each strand. The error rate in this replication is amazingly low; not even one base pair in a million matches out of sequence.

However, when even one base pair is added to a new strain of DNA in an order differently than in the parent chain, it can be the basis of a mutation. These changes in DNA sequences are the microscopic origin of changes in traits of all studied living things. Even the smallest difference in a strand of DNA can result in a change in traits that can cost the life of the organism. Mutations can produce proteins with a new or altered function. In humans, the example of Sickle cell anemia is commonly given as its origin is a difference of only one base pair in a section of DNA that encodes red blood cells.

Individual sequences of DNA that encode for specific proteins are called genes and are the units of heredity. Each one has a set nucleotide, and together all of the genes (and some sequence of DNA that apparently do not code for any biologically important functions) together make up the entire chromosome

Mendel

Discovered principle of genetic segregation via numerous experiments utilizing pea plants
Inferred the existence of genes through segregation of phenotypes
Used quantitative methods: counted; ratios
Work is model of scientific method
In particular, observed the F2 progeny, which lead to the discovery of dominant and recessive traits
Published work in 1866, went unnoticed
In 1900 his scientific paper was “rediscovered”
Mendel is acknowledged as founder of Genetics
- still used alphabet letters to designate genes
- still refer to dominant and recessive genes
- still refer to segregation of alleles in meiosis
- principle of segregation applies to all sexually reproducing organisms; Mendel’s results were immediately applied to humans in 1900

Mendel’s experiments

1856, began experiments with the garden pea, Pisum sativum
1865, presented results to the Bruno natural history society, which he helped found
1866, published his results in proceedings of the society
Naegeli encouraged Mendel to reproduce results in another species, which failed because the species did not undergo true fertilization
discrete traits in Pisum sativum
- pure-breeding lines
- dominant/recessive alleles
alleles are two alternate versions of a gene
- gametes contain hybridized chromosomes that are formed during meiosis
- homozygous has two of the same allele
- heterozygous has two different alleles
reciprocal F1 crosses (all exhibiting dominant phenotypes); F2; F3
counted offspring, noted ratios
inferred genotypes from phenotypes
tested hypotheses with testcrosses
attempted to repeat with another species

Mendel’s seven pairs of traits

Seed form (round or wrinkled)
Cotyledon color (green or yellow)
Seed coat color (white or colored)
Pod form (inflated or constricted)
Pod color (green or yellow)
Flower position (axial or terminal)
Plant heights (tall or short)

Locus

The location of a specific gene within a chromosome

Modern Y chromosome

Y-chromosome is the most evolved chromosome. Generally it is thought that if Y- chromosome is present in an individual then he will be male. But if mutation occurs at sex determining region or zinc factor then it will not code for testis determining factor, and results in normal female. This type of female's frequency is 1/250000.

Chromosome phenomena

X-chromosome inactivation
- Barr bodies
Nondisjunction: failure of chromosome segregation at meiosis or mitosis
- Results in 2N ± 1 chromosome number
Trisomy 2N + 1
- Usually lethal. Trisomy 21 (Down) exception
Monosomy 2N ** 1
- Lethal except XO
- Usually maternal origin in humans

X-chromosome inactivation

In females, one X-chromosone is randomly switched off forming a Barr body.

Barr body

Dense region in the nucleus formed by the inactive X-chromosome.

Human genetic disorders

Down's Syndrome (Mongolism)

Down's Syndrome is usually produced by the nondisjunction of chromosome 21 during oogenesis and sometimes during spermatogenesis. The individual suffering from this type of syndrome has 47 chromosomes instead of the normal 46. The extra chromosome is not a sex chromosome but an autosome.

Most cases of mongolism were found to occur in children born by women in their forties. The affected children, called mongoloids, show mental retardation and have a shorter life expectancy. Their most prominent feature is the Mongolian folds in their eyes; hence, the term mongolism.

Klinefelter's Syndrome

When an XY-bearing sperm unites with an X-bearing egg, the resulting condition is called Klinefelter's Syndrome, or sexually undeveloped male. Individuals having the syndrome show the following characteristics:

testes are small
sperms are never produced
breasts are enlarged
body hair is sparse
individuals are mentally defective

The same abnormal meiotic division may occur in females. They produce eggs with XX or no sex chromosomes. Such egg, when fertilized by a Y-bearing sperm, will not develop (YO). This is because YO is lethal—it wil cause death to the offspring. General Biology | Getting Started | Cells | Genetics | Classification | Evolution | Tissues & Systems | Additional Material

DNA

DNA stands for Deoxyribose Nucleic Acid. That is, a nucleic acid with two sugars. DNA is the hereditary material of cells and is considered the blueprint of life. DNA is found in all kingdoms of life. Even most viruses have DNA. A molecule of DNA is chemically stable (it does not have a 2-prime alcohol group.)

When someone says DNA, they may be referring to one's genetic material on multiple levels: They may be speaking about a single deoxyribose nucleic acid molecule, a section of a double helix, a section of a chromosome, or one's entire hereditary composition.

antiparallel
Double helix
- Semiconservative replication
- Sequence of nucleotides encodes functional RNA or polypeptide

Historical perspective

Mitosis and meiosis
- Regular distribution of chromosomes suggested that they contain hereditary information
- Bridges/Morgan, using Drosophila melanogaster showed that genes are on chromosomes (1910s)
Hammerling: nucleus contains hereditary information (1930s)
Griffith: transformation of bacteria (1928)
Avery, MacLeod, McCarty: transforming substance is DNA (1944)
Hershey, Chase: DNA is hereditary material of viruses (1952)
Rosalind Franklin
Watson and Crick: structure of DNA (1953)

Hershey-Chase Experiment

Two batches of isotopically labeled bacteriophage T2 particles were prepared. One was labeled with 32P in the phosphate groups of the DNA, the other with 35S in the sulfur-containing amino acids of the protein coats (capsids). (Note that DNA contains no sulfur and viral protein contains no phosphorus.) The two batches of labeled phage were then allowed to infect separate suspensions of unlabeled bacteria. Each suspension of phage-infected cells was agitated in a blender to shear the viral capsids from the bacteria. The bacteria and empty viral coats (called “ghosts”) were then separated by centrifugation. The cells infected with the 32P-labeled phage were found to contain 32P, indicating that the labeled viral DNA had entered the cells; the viral ghosts contained no radioactivity. The cells infected with 35S-labeled phage were found to have no radioactivity after blender treatment, but the viral ghosts contained 35S. Progeny virus particles (not shown) were produced in both batches of bacteria some time after the viral coats were removed, indicating that the genetic message for their replication had been introduced by viral DNA, not by viral protein.

DNA/RNA components

Miescher: discovered DNA, 1869

Structure of DNA

DNA is in a double helix structure made up of nucleotides. The "backbone" of the double helix is composed of phosphates connected to a five-carbon sugar called deoxyribose. The "rungs" are composed of organic compounds, purines and pyrimidines. Purines contain Adenine(A) and Guanine(G) and have two rings in their structures. Pyrimidines contain Cytosine(C) and Thymine (T) and have one ring in their structures.

Chemical structure of DNA

Polynucleotide
- Phosphodiester bonds between nucleotides
- 5’-pGpTpCpGpTpApApTp-OH 3’
Chargaff’s rules, in DNA: equimolar amounts
- A = T
- G = C

3D structure of DNA

James Watson and Francis Crick (1953)
- Nucleotide
- Keto and amino forms of bases
- Chargaff’s rules
- X-ray crystallographic data (Rosalind Franklin)

Franklin

X-ray diffraction of DNA crystals
revealed regular pattern explained by antiparallel double helix

DNA model

Double helix of polynucleotides
- antiparallel
- 3’-5’ phosphodiester bonds
Base pairs held by hydrogen bonds
- AT
- GC
There are about 10 base pairs per turn of helix
model has predictive power
- mode of DNA replication
- encoding of genetic information

DNA replication

Conservative model
- One double helix of both old strands
- One double helix of two new strands
Dispersed
- Each strand mixture of old new
Semiconservative
- Meselson-Stahl experiment confirmed its viability over the previous two
  - grew E. coli bacterium in a culture containing 15N (a heavy isotope of nitrogen)
  - bacterium assimilated the 15N into their DNA
  - a similar process was then done using 14N, a lighter isotope
  - following centrifugation, the densities were observed to be that of combined in the middle, and 14N on top, thereby confirming the semiconservative model

DNA replication

Semiconservative
New nucleotides added to 3’ –OH
Replication fork
- Replication complex
DNA polymerase
Associated enzymes/proteins
- Energy from phosphate bonds of triphosphate nucleotide substrates (dNTP)

DNA polymerases

Prokaryotes, E. coli
- 3 DNA polymerases
- III is main enzyme for DNA replication
- ~1000 nt/sec
Eukaryotes
- 6 DNA polymerases
Add nucleotide to 3’ –OH end
All require primer, i.e., free 3’ –OH

DNA replication complex

Helicase "unzips" the DNA double helix
Primase: synthesize RNA primer
Single-strand binding proteins
DNA gyrase (topoisomerase)
DNA polymerase III
DNA polymerase I (remove primer, fill gaps)

DNA replication

5’ → 3’ replication
- Nucleotide addition at 3’ –OH
- No exceptions
New strands are oriented in opposite direction due to 5’ → 3’ constraint
- Leading strand: continuous replication
- Lagging strand: discontinuous replication
  - contains multiple Okazaki fragments
Joined by DNA ligase

DNA replication fork

primer required by all DNA polymerases

Replication units

Replicon

A region of DNA that is replicated from a single origin.

What is gene?

Garrod
- “inborn errors of metabolism”
- Alkaptonuria: enzyme deficiency
Beadle and Tatum
- One gene one enzyme
- Genetic and biochemical analysis in Neurospora
Today: gene is sequence of nucleotides encoding functional RNA molecule or the amino acid sequence of a polypeptide

References

Flow of genetic information

DNA → mRNA → polypeptide
Transcription: DNA → mRNA
- RNA polymerase
- Nucleus in eukaryotes
- Transcription also makes rRNA and tRNA
Translation: mRNA → polypeptide
- Ribosomes: protein and rRNA
- Genetic code and tRNA

“Central Dogma”

The Genetic Code

Triplet codon
- 64 triplet codons (43)
- Experimentally deciphered in 1961
Nearly universal
- Implies common ancestor to all living things
- Minor exceptions: certain ciliates, mitochondria, chloroplasts
Still evolving

Transcription

RNA polymerase
- NTP substrates
- Synthesizes single stranded RNA complementary to template strand of DNA
- New nucleotides to 3’ end
Begins at promoter site
- no primer necessary
Ends at terminator site
Much posttranscriptional modification in eukaryotes

Transcription bubble

Promoter site

Prokaryotes
- -10 nt, TATA box
- -35 nt, additional signal
Eukayotes
- -25, TATAAA box
- Additional signals upstream
Promoters may be strong or weak
In eukaryotes, access to promoter depends upon state of chromatin coiling

Eukaryote mRNA

Synthesized as pre-mRNA, processed in nucleus
5’ end: GTP cap placed in inverted position
- Essential for ribosome recognition
3’ end: poly-A tail; non-templated addition of ~50-250 A nucleotides; stability
Introns: intervening sequences removed

Translation

Requires:
- mRNA
- tRNA
- ribosomes
- translation factors (various proteins)
In prokaryotes, takes place on growing mRNA
In eukaryotes, in cytoplasm on free ribosomes and RER
AUG start codon to stop codon

Translation in bacteria

tRNA

Transfer RNA
Two important parts
- Anticodon
Hydrogen bonds with mRNA codon
- 3’ end
Accepts amino acid (using energy of ATP)
Aminoacyl-tRNA synthetase

Aminoacyl tRNA synthase

Enzyme used to bind amino acid from the cytoplasm to tRNA, which then transfers that amino acid to the ribosome for polypeptide formation

Ribosome structure

Large ribosome subunit

Translation

Initiation complex
- Small ribosomal subunit
- mRNA
- fMet-tRNA (prokaryotes only; met-tRNA in eukaryotes)
- Initiation factors
Elongation
- Ribosome
- mRNA
- tRNAs
- Elongation factors

Initiation complex

Elongation, translocation

incoming tRNA enters the A site
rRNA catalyzes peptide bond formation. Note that growing peptide is attached to what was incoming tRNA at P site after translocation.
empty tRNA leaves via E site; recycled
A site ready for next charged tRNA

Introns/exons

In eukaryotes, coding regions of gene may be interrupted by introns, noncoding regions of DNA (RNA)
Introns
- 22- >10,000 nt in length
- 5’ GU … 3’ AG removal sequence
- Not essential to genes
- May constitute >90% of gene
removed from pre-mRNA to form mRNA
Exon: often codes for functional domain of protein
- translatable mRNA

References

Not all genes are expressed in a cell
Gene expression can be turned on and off
Multiple levels of regulation gene function
- Transcription initiation
State of chromatin
Transcription factors
- Post-transcriptional
mRNA processing
mRNA half-life
Translational
Post-translational
- Protein modification

Transcriptional control

State of chromatin
- Euchromatin: transcriptionally active
- Heterochromatin: transcriptionally inactive
- Chemical modification of histones
- Methylation of bases
Transcription factors
- Bind to DNA at promoter or other regulatory sites (enhancers)
Recognize base sequence through major and minor grooves
- Recruit RNA polymerase

DNA grooves

Categories of transcription factors in eukaryotes

Helix-turn-helix
- Two small "-helices
- Fit into DNA groove
Homeodomain
- Highly conserved helical domains
- ~60 amino acids
Zinc finger motif
- Zn atom bound
Leucine zipper
- dimer

Regulatory proteins

Activity may depend upon allosteric binding of small molecules
- cAMP
- Co-repressors
- Inhibitors
Binding to promoter region may “bend” DNA, making it accessible to other regulatory proteins

Lac operon of E. coli

Single promoter region for cluster of genes
Regulated and transcribed as a single unit
Operons typical in prokaryotes
Repressor: turns OFF gene expression

lac repressor

Turns off transcription by blocking access by RNA polymerase
repressor in activated by allosteric binding of lactose

Regulation in eukaryotes

Both proximal (promoter) and distal (enhancer) to gene
Typically transcription unit encodes a single polypeptide
Promoter
- TATA box
- Other elements (regulatory sequences) may be present
Enhancers
- Work upstream, downstream, close, far from gene
- Bend DNA

Alternative splicing

Single transcript gives rise to 2 or more mature mRNAs
- encode different polypeptides with shared domains
- tissue and developmentally specific

References

A mutation is a permanent change to an organism's genetic material (DNA or RNA). Mutations are a rare but significant biological process, since they provide the variation on which evolution acts and are also the source of cancer.

An organism's genetic material is made up of polymers (chains) of four different nucleotides, like a recipe book written in a language of only four letters. A mutation event is when the order of the nucleotides in DNA change, usually when the DNA is being copied.

Mutations come in a number of forms:

Point Mutations

Point mutations are all mutations which involve a single nucleotide. These come in the form of substitutions, insertions and deletions:

Substitution

Substitution Mutations: In substitution mutations, a nitrogenous base of a triplet codon of DNA is replaced by another nitrogen base or some derivative of the nitrogen base, changing the codon. The altered codon codes for a different amino acid substitution.The substitution mutations are of two types:

1.Transitions: It is the replacement of one purine in a polynucleotide chain by another purine(A by G or G by A) or one pyrimidine by another pyrimidine(T by C or C by T)

2.Transversions:A base pair substitution involving the substitution of a purine by pyrimidine or pyrimidine by a purine is called transversion.

Insertion

Deletion

Larger mutations

Larger mutations which involve more than one nucleotide also include insertions and deletions, but can also include inversions, rearrangement of nucleotides and duplication of entire genes:

Inversion

Rearrangement

Gene/Exon Duplications

Transposition

Retrotransposition

Chromosomal mutations

Chromosomal mutations involve changes to entire chromosomes. These mutations are particularly rare:

Translocation

Fusion

Fission

Segmental Duplication

Chromosomal Duplication

Genome Duplication

Causes of mutations

Effects of mutations

Mutations can have a variety of different effects depending on the type of mutation, the significance of the piece of genetic material affected and whether the cells affected are germ-line cells. Only mutations in germ-line cells can be passed on to children, while mutations elsewhere can cause cell-death or cancer.

Mutations can be classified by their effects:

Silent Mutation

Silent Mutations are DNA mutations that do not result in a change to the amino acid sequence or a protein. They may occur in a non-coding region (outside of a gene or within an intron), or they may occur within an exon in a manner that does not alter the final amino acid chain.

Frameshift

Missense Mutation

Missense mutations are types of point mutations where a single nucleotide is changed to cause substitution of a different amino acid. This in turn can render the resulting protein nonfunctional. Such mutations are responsible for diseases such as Epidermolysis bullosa.

Nonsense Mutation

Original notes

“Rare” change in nucleotide sequence
- Somatic vs germline
only those in germline are heritable
- Point mutation
Single nucleotide change
- Change in gene position
Transposition
Chromosomal rearrangement
Mutagenic agents
Raw material for evolutionary change

Point mutation

Ionizing radiation
- UV light induces thymine dimers
Reparable
Error during DNA synthesis
Movement of transposons
- McClintock
Chemical mutagens
May alter
- Properties of promoter, enhancer
- Amino acid sequence of polypeptide

Acquisition of genetic variability

Mutation
Sex (fusion of genomes)
Recombination
- Crossing over
Reciprocal (may result in gene conversion)
Unequal (gives rise to gene families)
- Independent segregation
Transposition by transposons
Conjugation in bacteria
- One way transfer from donor to recipient

Eukaryote genome

Thousands of transposons
Millions of transposon derived elements
- LINES, SINES
Above may constitute largest portion of genome
Pseudogenes
Tandem clusters (rRNA genes; nucleolus)
Multigene families
Single-copy genes (one copy per 1n)

Barbara McClintock

Discovered transposons in perhaps greatest and ultimately most important intellectual endeavors in genetics
- Maize
- Worked alone
Transposons: likely responsible for considerable evolution in eukaryotic genomes
Likely origin of viruses

References

This text is based on notes very generously donated by Paul Doerder, Ph.D., of the Cleveland State University.

Recombinant DNA technology

Revolutionized modern biology
- Ability to manipulate genes in vitro
Hybrid genes, including combining genes of different species
Detailed study of gene function
- Determine nucleotide sequences of genes and their regulators (deduce amino acid sequences of proteins)
Genome projects: complete nucleotide sequence of >40 genomes, including human
Made possible by convergence of:
- discovery of restriction enzymes
- genetics of bacteria and their plasmids

Recombinant DNA technology

Uses
- Detailed study of gene function
Homeostasis, response to stress
Development (birth defects)
- Evolution of genes informs on evolution of life
Human betterment
- Medicine
Identification, treatment of genetic disorders
Molecular medicine: from deduced amino acid sequences, design better drugs
- Foods
Improve crop yield, resistance to disease
Improve nutritional value
- Forensics
DNA fingerprinting: guilt or innocence

Restriction endonucleases

Originally found in bacteria to prevent invasion of viral DNA, cuts double stranded DNA that is unmethylated, will not cut newly synthesized DNA since hemi-methylated, a product of semi-conservative replication of DNA

sever phosphodiester bonds of both polynucleotide strands in order to combine foreign DNA
- create restriction fragments (restriction digestion)
- 5’ phosphate and 3’ –OH at ends
usually nucleotide specific target sequence
- 4-6 bp most common, the more bases, then the more specific for recombination
- cuts in or near sequence
- ends
sticky=overhanging ends, 5’ or 3’
blunt ends - straight cut, will anneal with any other blunt end in the presence of high ligase
Hundreds of know restriction endonucleases, usually named after the bacteria that it was found in
- e.g. EcoR1, Alu1, BamHI, HindIII

Restriction endonucleases

Gene cloning

Cloning:
- Restriction digestion of DNA
- insertion of restriction fragment into cloning vector
Bacterial plasmid
Bacterial virus
Yeast artificial chromosomes
Transformation of bacteria with recombinant plasmid, virus
Screening for clone of interest by using reporter genes or resistance upon exposure to anti-biotic

Uses of cloned gene

Determine nucleotide sequence and deduce amino acid sequence from genetic code
- Submit to GenBank (available on WWW)
Manipulate gene to study function
- In vitro
- In vivo
Transgenic (recombinant) organisms
Knockout organisms
Medical and commercial uses

Other molecular procedures

Polymerase chain reaction (Mullis)
- Amplifies target DNA without cloning
- Target amount can be single molecule
- Amplified DNA can be sequenced, cloned, etc.
Southern blotting
- Used to identify restriction fragments carrying particular gene
- Also used for DNA fingerprinting and RFLP analysis
cDNA construction
- Reverse transcription from mRNA template

RFLP(restriction fragment length polymorphism) analysis

Basis of DNA fingerprinting using SNP - single nucleotide polymorphisms and repeats of DNA sequence
Many uses
- Criminal cases using multiple probes
- Parentage
- Species identification
- Gene evolution
- Species evolution

Sanger DNA sequencing

Uses dideoxynucleotides (ddNTP), a template strand, DNA polymerase 1 (Also known as Kornberg enzymes) and dNTPs
- Missing 3’-OH for nulceopjilic attack for elongation
- DNA synthesis stops after one is incorporated into DNA fragment
- ratio of ddNTP to dNTP determines likelihood of termination
Manual method with 32P-labeled ddATP and 4 test tubes - ddATP, ddCTP, ddGTP, ddTTP
Automated method using ddNTPs labeled with fluorescent dyes in capillary tube
- Often done commercially

Automated sequencing

Typical machine

- 2 hour sequencing run
- 600-1000 bases per sample
- multiple samples
Up to 500,000 bases per day (12 hr)
Data processed by computer
In big labs, sequencing reactions also are automated

Genome projects

Determine entire nucleotide sequence of genome
>40 genomes sequenced
- Helicobacter pylori
- Escherichia coli
- Saccharomyces cerevisiae
- Caenorhabditis elegans
- Drosophila melanogaster
- Homo sapiens (first rough draft)
Computer identifies all genes, based on properties of genes (e.g., start/stop codons, introns, etc.).

Biochips

Microarray of DNA fragments, size of postage stamp; can be expensive, but has decreased in cost

Microarray chips contain wells of DNA that code for specific genes that uses the concept of hybridization with the gene of interest to see if a gene is expressed or is present.

Designed to detect:
- mutated genes (SNPs)
- expressed genes
Instant DNA profile (“GATTACA”)

DNA chip controversies

Medicine
- Risks and informed consent for gene replacement therapy
- Alteration of human gene pool
- Parental choice
- Privacy
Genetically modified foods
- Safety
- Labeling
Forensics
- Mandatory tests
- Reliability standards

Gene patenting

Techniques to study and manipulate genes are patented (e.g., cloning and PCR)
Should genes be patented?
- Are they the intellectual property of the discoverer?
- Don’t they belong to all of us?
- Should indigenous peoples be compensated for useful genes extracted from their local plants and fungi?

Stem cells

Totipotent cells from early embryo
- grow into any tissue or cell type
Recombinant genes can be introduced
Considerable use in analyzing gene expression in mice
Possible therapeutic use in humans
Very controversial

This text is based on notes very generously donated by Paul Doerder, Ph.D., of the Cleveland State University.

Classification of Living Things

Fundamental classification

Classification of Living Things and Naming of Organisms

In science, the practice of classifying organisms is called taxonomy (Taxis means arrangement and nomos mean method). The modern taxonomic system was developed by the Swedish botanist Carolus Linnaeus (1707-1778). He used simple physical characteristics of organisms to identify and differentiate between different species and is based on genetics.

Linnaeus developed a hierarchy of groups for taxonomy. To distinguish different levels of similarity, each classifying group, called taxon (pl. taxa) is subdivided into other groups. To remember the order, it is helpful to use a mnemonic device. The taxa in hierarchical order:

Domain - Archaea, Eubacteria, Eukaryote
Kingdom - Plantae, Animalia, Fungi, Protista, Eubacteria (Monera), Archaebacteria
Phylum - Invertebrates, Vertebrates
Class - Fish, Bird, Mammal, Amphibian
Order - The Organism get its Energy?
Family - Special characteristics of the Organism and its relatives
Genus - First name of Organism
Species - Last name of Organism

The domain is the broadest category, while species is the most specific category available. The taxon Domain was only introduced in 1990 by Carl Woese, as scientists reorganise things based on new discoveries and information. For example, the European Hare would be classified as follows:

Eukaryote --> Animalia --> Chordata --> Mammalia --> Lagomorpha --> Leporidae --> Lepus --> Lepus europaeus.

Eukaryote is just one of the classes inside of the main class Phyla

Binomial nomenclature

Binomial nomenclature is used to name an organism, where the first word beginning with a capital is the genus of the organism and the second word beginning with lower-case letter is the species of the organism. The name must be in italics and in Latin, which was the major language of arts and sciences in the 18th century. The scientific name can be also abbreviated, where the genus is shortened to only its first letter followed by a period. In our example, Lepus europaeus would become L. europaeus.

Taxonomy and binomial nomenclature are both specific methods of classifying an organism. They help to eliminate problems, such as mistaken identity and false assumptions, caused by common names. An example of the former is the fact that a North American robin is quite different from the English robin. An example of the latter is the comparison between crayfish and catfish, where one might believe that they both are fish when in fact, they are quite different.

Nomenclature is concerned with the assignment of names to taxonomic groups in agreement with published rules. To study for a test these are the best words to know taxonomist, biologist, chemist, geologist, unicellular, multicellular, bilateral symmetry, radial symmetry, chlorophyll, photosynthesis, respiration, reproduction, vertebrates, endoskeleton, exoskeleton, consumers, decomposers, heterotroph, autotroph, vascular, non-vascular. These are all part of classifying things.

Eukaryotes and Prokaryotes

There are two basic types of cells: eukaryotes and prokaryotes.

Eukaryotes are more complex in structure, with nuclei and membrane-bound organelles. Some characteristics of eukaryotes are:

Unicellular or multicellular
Small to large, with lengths from about 1μm (Ostreococcus) to 30m (the blue whale)
DNA in nucleus, bounded by nuclear envelope
Genome consists of several chromosomes
Cell division by mitosis or meiosis; sexual reproduction is common
Mitochondria and other organelles are present

Prokaryotes refer to the smallest and simplest type of cells, without a true nucleus and no membrane-bound organelles. Bacteria fall under this category. Some characteristics:

Unicellular only, although some form filaments or colonies
Small, with lengths from about 0.1 to 5 μm (excluding filaments or colonies)
DNA is circular, and unbounded by a membrane
Genome consists of single chromosome, but there may be additional plasmids
Asexual reproduction, although plasmid transfer may occur
No membrane-bound organelles

Three Domains and Six Kingdoms

The three domains are organized based on the difference between eukaryotes and prokaryotes. Today's living prokaryotes are extremely diverse and different from eukaryotes. This fact has been proven by molecular biological studies (e.g. of RNA structure) with modern technology. The three domains are as follows:

Archaea (Archaebacteria) consists of archaebacteria, bacteria which live in extreme environments. The kingdom Archaea belongs to this domain.

Eubacteria consists of more typical bacteria found in everyday life. The kingdom Eubacteria belongs to this domain.

Eukaryote encompasses most of the world's visible living things. The kingdoms Protista, Fungi, Plantae, and Animalia fall under this category.

The Six Kingdoms

Under the three domains are six kingdoms in taxonomy:

Animalia, contains general animals and is the largest kingdom with over 1 000 000 species.

Plantae, contains all plants on Earth.

Protista, the third kingdom, was introduced by the German biologist Ernst Haeckel in 1866 to classify micro-organisms which are neither animals nor plants. Since protists are quite irregular, this kingdom is the least understood and the genetic similarities between organisms in this kingdom are largely unknown. For example, some protists can exhibit properties of both animals and plants.

Fungi are organisms that obtain food by absorbing materials in their bodies. Mushrooms and molds belong in this kingdom. Originally, they were part of the plant kingdom but were recategorized when they were discovered not to photosynthesize.

Eubacteria are bacteria, made up of small cells, which differ in appearance from the organisms in the above kingdoms. They lack a nucleus and cell organelles. They have cell walls made of peptidoglycan.

Archae (or Archaebacteria) are bacteria that live in extreme environments, such as salt lakes or hot, acidic springs. These bacteria are in their own category as detailed studies have shown that they have unique properties and features (ex. unusual lipids that are not found in any other organism) which differ them from other bacteria and which allow them to live where they live. Their cell walls lack peptidoglycan.

Origins of Diversity

The diversity in our planet is attributed to diversity within a species. As the world changed in climate and in geography as time passed, the characteristics of species diverged so much that new species were formed. This process, by which new species evolve, was first described by British naturalist Charles Darwin as natural selection.

For an organism to change, genetic mutations must occur. At times, genetic mutations are accidental, as in the case of prokaryotes when they undergo asexual reproduction. For most eukaryotes, genetic mutations occur through sexual reproduction, where meiosis produces haploid gametes from the original parent cells. The fusion of these haploid gametes into a diploid zygote results in genetic variation in each generation. Over time, with enough arrangement of genes and traits, new species are produced. Sexual reproduction creates an immense potential of genetic variety.

One goal of taxonomy is to determine the evolutionary history of organisms. This can be achieved by comparing species living today with species in the past. The comparison in anatomy and structure is based on data from development, physical anatomy, biochemistry, DNA, behaviour, and ecological preferences. The following are examples of how such data is used:

Anatomy:

Although a horse and a human may look different, there is evidence that their arm structures are quite similar. Their arms' sizes and proportions may be different, but the anatomical structures are quite similar. Such evidence reveals that animals in different taxa may not be that different. Biological features from a common evolutionary origin are known as homologous.

Development

Biochemistry:

Biochemical analysis of animals similar in appearance have yielded surprising results. For example, although guinea pigs were once considered to be rodents, like mice, biochemistry led them to be in their taxon of their own.

Phylogeny, Cladistics, and Cladograms

Modern taxonomy is based on many hypotheses' of the evolutionary history of organisms, known as phylogeny. As with the Scientific Method, scientists develop a hypothesis on the history of an animal and utilise modern science and technology to prove the phylogeny.

Cladistics is a classification system which is based on phylogeny. Expanding on phylogeny, cladistics is based on the assumption that each group of related species has one common ancestor and would therefore retain some ancestral characteristics. Moreover, as these related species evolve and diverge from their common ancestor, they would develop unique characteristics. Such characteristics are known as derived characteristics

The principles of phylogeny and cladistics can be expressed visually as a cladogram, a branching diagram which acts as a family (phylogenetic) tree for similar species. A cladogram can also be used to test alternative hypotheses for an animal's phylogeny. In order to determine the most likely cladogram, the derived characteristics of similar species are matched and analysed.

Classification of Living Things Practice Questions

1. If taxonomists had to select an existing kingdom to reclassify, which of the six would most likely be chosen? Why?

2. Complete the following without consulting external sources:

a) The species caudatum is in the family Paramecidae. What would be the binomial name of this organism?

b) Give the abbreviation of the binomial name.

3.

a) Irish moss belongs to the genus Chondrus. The name for this species is crispus. Give the binomial name.

b) Give the abbreviation of the binomial name.

4. Humans and chimpanzees are alike. Which of the following data would most accurately prove this correct?

a) biochemistry

b) DNA

c) appearance

d) development

e) A, B, C

5. Which of the following is out of order?

a) Kingdom --> Phylum --> Class

b) Class --> Family --> Order

c) Family --> Order --> Genus

d) Genus --> Species

e) A, C

f) A, B, D

g) B, C

6. A taxonomist discovers Organism A and Organism B and wishes to classify them. Which of the following choices is the most informative?

a) Both organisms are brown.

b) Both organisms have a tail.

c) Both organisms have ears.

d) Both organisms are nocturnal.

7. DNA analysis is usually done using DNA found in a cell's mitochondria, and not in a cell's nucleus. From your knowledge of mitosis, explain why this is so.

1. Archaebacteria 3.a) Chondrus crispus b) C. cripus 4. B 5. G 6. B

Introduction

Viruses are the smallest biological particle (the tiniest are only 20 nm in diameter). However, they are not biological organisms so they are not classified in any kingdom of living things. They do not have any organelles and cannot respire or perform metabolic functions. Viruses are merely strands of DNA or RNA surrounded by a protective protein coat called a capsid. Viruses only come to life when they have invaded a cell. Outside of a host cell, viruses are completely inert.

Since first being identified in 1935, viruses have been classified into more than 160 major groups. Viruses are classified based on their shape, replication properties, and the diseases that they cause. Furthermore, the shape of a virus is determined by the type and arrangement of proteins in its capsid. Viruses pathogenic to humans are currently classified into 21 groups.

Viruses can also attack bacteria and infect bacterial cells. Such viruses are called bacteriophages.

Viral Replication

As previously stated, viruses are not a biological life form so they cannot reproduce by themselves. They need to take over a functioning eukaryotic or prokaryotic cell to replicate its DNA or RNA and to make protein coat for new virus particles.

In order to enter a cell, a virus must attach to a specific receptor site on the plasma membrane of the host cell. The proteins on the surface of the virus act as keys which fit exactly into a matching glycoprotein on the host cell membrane. In some viruses, the attachment protein is not on the surface of the virus but is in the capsid or in the envelope.

There are two forms of viral replication: the lytic cycle and the lysogenic cycle.

Lytic Cycle

Attachment: The virus binds to specific receptors on the host cell.
Entry: There are two ways in which a virus can enter cells. Firstly, the virus can inject its nucleic acid into the host cell. Secondly, if a virus is contained in an envelope, the host cell can phagocytosise the entire virus particle into a vacuole. When the virus breaks out of the vacuole, it then releases its nucleic acid into the cell.
Replication: The virus's nucleic acid instructs the host cell to replicate the virus's DNA or RNA.
Assembly: New virus particles are assembled.
Lysis and Release: The virus directs the production of an enzyme which damages the host cell wall, causing the host cell to swell and burst. The newly formed virus particles are now released.

Lysogenic Cycle

Attachment: Similar to Lytic Cycle
Entry: Similar to Lytic Cycle
Incorporation: The viral nucleic acids is not replicated, but instead integrated by genetic combination (crossing over) into the host cell's chromosome. When integrated in a host cell this way, the viral nucleic acid as part of the host cell's chromosome is known as a prophage.
Host Cell Reproduction: The host cell reproduces normally. Subsequent cell divisions, daughter cells, contain original father cell's chromosome embedded with a prophage.
Cycle Induction: Certain factors now determine whether the daughter cell undergoes the lytic or lysogenic cycle. At any time, a cell undergoing the lysogenic cycle can switch to the lytic cycle.

The reproduction cycle of viruses with RNA and no DNA is slightly different. A notable example of a RNA-based virus is HIV, a retrovirus.

Retrovirus reproductive cycle

The retrovirus force RNA into cell, by either one of the two methods of entry (See above).
In the retrovirus are reverse transcriptase enzymes, which catalyses the synthesis of a DNA strand complementary to the viral RNA.
Reverse transcriptase catalyses a second DNA strand complementary to the first. With these two strands, the double-stranded DNA can be created.
DNA is then incorporated into the host cell's chromosomes. Similar to the concept of a prophage, this incorporated DNA is called a provirus. However, the provirus never leaves the host cell, unlike a prophage.
The infected host cell undergoes the lytic or lysogenic cycle.

Viral Genome

The genome of a virus consists of DNA or RNA, whose size and configuration vary. The entire genome can exist as a single nucleic acid molecule or several nucleic acid segments. Also, the DNA or RNA may be single-stranded or double-stranded, and either linear or circular.

Not all viruses can reproduce in a host cell by themselves. Since viruses are so small, the size of their genome is limiting. For example, some viruses have coded instructions for only making a few different proteins for the viruses' capsid. On the other hand, the human genome codes for over 30,000 different proteins. Therefore, the lack of coded instructions cause some viruses to need the presence of other viruses to help them reproduce themselves. Such viruses are called replication defective.

Lastly, it is worthy to note that 70% of all viruses are RNA viruses. As the process of RNA replication (with enzymes and other organelles of the host cell) is more prone to errors, RNA viruses have much higher mutation rates than do DNA viruses.

Viruses Practice Questions

As the name implies, the Tomato Spotted Wilt Virus targets tomatoes. Would it be possible for this virus to target other fruits as well? Explain.
Many people have had cold sores, which are caused by infection with the herpes simplex virus. One characteristic of cold sores is that after a period of inactivity, they will reappear many times during the course of a person's life. Which cycle would the herpes simplex virus undergo?
Chicken pox is a common, non-fatal disease usually acquired in adolescence and caused by the varicella zoster virus. In adulthood, many people suffer from shingles, an altered form of the varicella zoster virus. Which cycle would the varicella zoster virus have undergone?
Would an antibiotic work for a person suffering from a cold of flu? Explain.

Answers to Viruses Practice Questions For Eubacteria, please visit General Biology/Classification of Living Things/Eubacteria.

Archaea

Proposed as separate group from (eu)bacteria by Carl Woese
- based on structure and metabolic pathways
- inhabit extreme environments
- unique branched lipids in membrane
Share traits with both eukaryotes and eubacteria, e.g., RNA polymerase, introns
Biochemically diverse
Economically important
- Taq polymerase used in PCR

Types

Methanogens
Halophiles
Thermophiles

Underground bacteria

Metabolism
- built around inorganic energy sources
e.g., basalt reacts with H₂O to release hydrogen which is catalytically combined with CO₂ to form carbohydrate (akin to photosynthesis)
may result in deposit of minerals
Unresolved problems
- Did bacteria move downward from surface or did they first evolve there, protected from harsh surface conditions?
- Could bacteria be ejected into space in rocks?

Prokaryote evolution

Tentative, subject to change
Derived largely from molecular systematics (rRNA sequences)
Note: most bacteria can’t be cultured, thus hard to study! (Studied by PCR of water/soil samples)

Domains of life: characteristics

This text is based on notes very generously donated by Paul Doerder, Ph.D., of the Cleveland State University.

Introduction

Out of the six kingdoms, Protista is the most diverse. This is the kingdom of organisms with strange, atypical characteristics. In essence, this kingdom is designated for organisms which do not belong in any other kingdom. The majority of protists are microscopic.

Classification of Protists

There are three phyla of protists, based on their type of nutrition.

1. Protozoa (animal-like protists) are heterotrophs that ingest or absorb their food and helps.

2. Algae (plant-like protists) are autotrophs they get nutrition from photosythesis.

3. Slime moulds and water moulds (fungus-like protists) are also heterotrophs, like protozoa.

Protozoa

As heterotrophs, protozoa scavenge materials from their surroundings. Others are predators which actively hunt or ambush small organisms such as bacteria and other protozoa for a source of nutrition. Protozoa can be parasitic as well; they may live inside larger organisms, like humans. Most protozoa live as single cells, although a few form colonies.

Protozoa are generally difficult to identify due to their varied shape. They may appear as jelly-like blobs, spherical sunbursts, or a flattened leaf. Tiny blood parasites may be only 2 μm long. On the other hand, shell-covered marine may be 5 cm or more in diameter.

Furthermore, different protozoans have their own complex life cycles. The complexity has led certain organisms to be mistakenly classified for other species.

Nevertheless, protozoa can move, and so, they are classified based on their methods of locomotion.

Characteristics of Protozoa :

About 30,000 species known

About 10,000 species are pathogenic, including some of the worst human diseases

heterotrophic

highly variable in form and life cycle

mostly unicellular

range in size from 0.005 mm to 50 mm

lack cell walls

they love environment and each other..............

Algae

Algae are much simpler than protozoa. They are aquatic and contain chlorophyll. Algae can exist as a single cell or as giant seaweeds 60 m in length. Formerly, algae were classified as plants but this was incorrect as algae lack parts of true plants: leaves, stems, roots, xylem, and phloem (though some plants, such as mosses, also lack all of these parts). Since algae belong in the kingdom Protista, algae is a broad term used to denote all aquatic eukaryotes which photosynthesise; algae can differ in size and shape as well.

There are six phyla of algae: chlorophytes (green algae), phaeophytes (brown algae), rhodophytes (red algae), chrysophytes (diatoms), pyrrophytes (dinoflagellates), and euglenophytes (euglenoids).

Chlorophytes

Chlorophytes resemble plants the most. Like plants, their cell walls contain cellulose and they store food in reserve as starch. Chlorophytes can be unicellular or multicellular. Most chlorophytes use flagellae for some locomotion.

Phaeophytes

Phaeophytes are nearly all multicellular marine organisms, which are known to us as seaweeds. They have cell walls composed of cellulose and alginic acid (a substance similar to pectin). The cellulose and alginic acid help to retain water and prevent seawood from drying out when exposed to air at low tide.

Since phaeophytes live in a tidal environment, they have large, flat fronds (a large leaf) which can withstand pounding by waves. Their bases strongly anchor the algae to the rocky seabed and prevent them from being washed out to sea. Phaeophytes are usually found in areas of cold water.

Rhodophytes

Rhodophytes are typically found in warmer seawater, and are more delicate and smaller than brown algae (phaeophytes). Rhodophytes are also able to grow at deeper depths in the ocean, since red algae absorb green, violet, and blue light, the wavelengths of which penetrate the deepest below the water surface. They also have mucilaginous material to resist drying.

Chryosophytes

Chryosophytes are the most abundant unicellular algae in the oceans. They are also one of the biggest components of plankton, a free-floating collection of microorganisms, eggs, and larvae. As photosynthetic organisms, they produce a significant amount of atmospheric oxygen.

The reproduction cycle of chrysophytes is particularly interesting. Note that diatoms reproduce both asexually and sexually. Since diatoms have a rigid cell wall with an outer layer of silica (found in sand and glass), the daughter cells produced by mitosis must fit inside the original cell wall. Therefore, each generation of diatoms is smaller than the one before. The reduction in size continues until the diatoms produce sexually, producing a zygote which eventually grows to the original size as it matures.

Pyrrophytes

Pyrrophytes are unicellular, photosynthetic, and mostly aquatic. They have protective coats composed of stiff cellulose. They are more easily identifiable, due to the presence of two flagellae. The longer flagellae propels the dinoflagellate, while the second shorter, flatter flagellae functions as a rudder.

Some species of pyrrophytes are zooxanthellae. Since they lack cellulose plates, they make their home in coral reefs and animals, such as sea anemones, and molluscs. In returning the favour of sheltering them, dinoflagellates provide carbohydrates to their host through photosynthesis. This is why there are nutrient-rich coral reefs in malnutritions water.

A negative aspect of pyrrophytes is that under certain conditions, species of dinoflagellates reproduce rapidly to form a harmful algal bloom (HAB), known as a red tide if dinoflagellates are the cause. Such pyrrophytes can produce toxins which may injure or kill wildlife, and additionally any consumers of contaminated wildlife.

Euglenophytes

Like pyrrophytes, euglenophytes are small unicellular freshwater organisms with two flagella. They are mainly autotrophic or heterotrophic, depending if they have a red, light-sensitive structure called an eyespot.

Slime molds & Water molds

There are two phyla of slime moulds and one phylum of water moulds.

Oomycotes (Water moulds)

Oomycotes are filamentous organisms which resemble fungi, in that they live as saprotrophs. Oomycotes differ from other moulds with the presence of spores and their sexual life cycle.

Myxomycetes (Plasmodial slime moulds)

Myxomycetes are visible to the naked eye as tiny slug-like organisms which creep over decayed and dead matter. This streaming blob containing many nuclei is called a plasmodium.

Acrasiomycetes (Cellular slime moulds) and its reproductive cycle

Acrasiomycetes exist as individual amoeboid cells with one nucleus each. When in unfavourable conditions, each acrasiomycota cell gathers together to form a pseudoplasmodium.

Reproductive Cycle:

1. One acrasiomycota cell joins with others to form a pseudoplasmodium.

2. The pseudoplasmodium shrinks and forms a smaller plasmodium.

3. The plasmodium migrates to a suitable environment.

4. The plasmodium develops a sporangia, where original parental nuclei has divided by meiosis into haploid spores to be germinated.

5. When favourable conditions arise, the spores germinate and are carried away by animals or the wind.

6. Cycle repeats.

Protists Practice Questions

1. Which of the following adjectives describe the major food source of protozoa?

a) chemoautotrophic

b) photoheterotrophic

c) chemoheterotrophic

d) heterotrophic

e) A, C, D

f) C, D

2. The protozoan Giardia lamblia can inhabit a human body's intestinal tract and cause gastroenteritis.

a) Give the abbreviated binomial name of this protozoan.

b) Would the relationship between this protozoan and human being be mutualistic, commensalistic, or parasitic?

3. Found in many products, such as Petri dishes, agar is made from mucilaginous material in seaweed. Of the six phyla of algae, which phyllum/phyla would agar be made from?

4. Which of the following adjectives describe the major food source of Euglenophytes without an eyespot?

a) photoautotrophic

b) photoheterotrophic

c) chemoautotrophic

d) chemoheterotrophic

e) B or C

f) C or D

Multicellular Photosynthetic Autotrophs

Plants

Multicellular
Cellulose cell walls
Chlorophylls a and b
Develop from embryophyte
Alternation of generations
Major food source for terrestrial life
Atmospheric O2 and CO2 balance
Coal deposits
Intimate association with mycorrhizal fungi
>250,000 species (~500,000?)
Taxonomy
- State of flux
DNA sequencing
Developmental studies
- Division (old literature) = phylum (new literature)
- ~12 phyla, 9 of which are vascular plants

Plant phyla

Phyla are 12 groupings

Plant evolution

Evolved from green algae, likely related to charophytes
Evidence
- DNA sequences
- homologous chloroplasts: chlorophyll b and beta-carotene; thylakoids in grana;
- Cellulose in both groups; also peroxisomes
- Mitosis and cytokinesis similar
- Sperm ultrastructure

Terrestrial adaptations

Stomata: pores in leaves for exchange of gases; prevent desiccation
Secondary metabolites:
- cuticle: waxy coating to prevent H2O loss
- lignin: hardens wood
- sporopollenin: resistant polymer; coats pollen
- predator defenses
Embryonic development
- gametangia in early plants
- spores; seeds
Mycorrhizae
Water/food conducting systems

Plant phylogeny

Plant life cycles

Alternation of generations
Sporophyte
- diploid
- produces spores in sporangia
Gametophyte
- develops from spore
- haploid
- produces gametes in gametangia
Haplodiplontic life cycle

Moss life cycle

Moss has no vascular tissues or flowers. It is a thallus plant (it does not have true roots,stem and leaves). It does not produce seeds like the angiosperm.

Vascular plants

Most have roots
Aerial shoot systems
Vascular tissue
- xylem: water, mineral transport
- phloem: food transport
Lignin
Branched sporophyte is dominant stage
- amplified production of spores
- evolution of complex plant bodies
Dominated Carboniferous (360 my)

Vascular plant life cycles

Homosporous (single type of spore)
Heterosporous (two types of spore)

Pterophyta (ferns)

Non-seed plant
Sporophyte conspicuous (vascular tissue)
Rhizome: ground stem, roots
Fronds: leaves
Sori: clusters of sporangia
Motile sperm require external water for fertilization
Originated in Devonian, 350 my

Tree fern Fern life cycle

Non-seed plants, continued

Lycophyta: club mosses
- E.g., Lycopodium (“ground pine”)
- Many species became extinct 270 my, once dominant (coal formations)
- Gametophyte non-photosynthetic, nourished by fungi
Arthrophyta: horsetails
- Equisitum
- Some fossil forms (300 my) were tree-size (coal)
- Photosynthetic stems, no leaves
- Silica deposits in epidermal cells

Seed plants

1st appeared in Devonian, 360 my
Seed develops from ovule, protects embryo
- withstands drought
- dispersal is enhanced
- no immediate need for water for germination
Heterosporous
- male gametophyte: arise from microspores
- female gametophyte: arise from megaspores in ovule in ovary
Two groups
- gymnosperms
- angiosperms

plant

Sporophyte/gametophyte

Megasporangium (nucellus)

Key to seed development
Nucellus: solid, fleshy, surrounded by integuments derived from sporophyte (seed coat)
Entire structure called ovule
Flower may have many ovules

Pollen

Develop from microspores, become male gametophyte
Protected by sporopellenin
In most plants, sperm lack flagella (loss)
Many mechanisms to transport pollen
- wind
- insects, birds,

Gymnosperms

“naked seed”
- ovule not fully enclosed by sporophyte at time of pollination
Conifers, cycads, gnetophytes, Ginkgo
Small, inconspicuous plants to giants like sequoia
Conifers: to carry cones fv
- male cones, Female conesvv
- evergreen

Pine life cycle

Other Coniferophyta

Cycadophyta: cycads
- tropical, subtropical
- flagellated sperm
Gnetophyta
- e.g., Ephedra, Mormon Tea
Ginkgophyta: Ginkgo
- only one surviving species
- diecious (separate % and &trees)

Other gymnosperms

Angiosperms

Flowering plants, Anthophyta
- monocots- single seed leaf (grasses, lilies, etc.)
- dicots- two seed leaves (roses, pulses, maples)
More specialized xylem (water transport)
- vessel elements
- fiber cells
Fossils date to 130 my
Animal (e.g., insect) coevolution

Monocots vs dicots

Earliest angiosperm

What is earliest angiosperm?
Recent analysis of nucleotide and amino acid sequences suggests that Amborella, a tropical plant found only on the island of New Caledonia, is closest relative to flowering plants

Angiosperm flower

Angiosperm life cycle

This text is based on notes very generously donated by Paul Doerder, Ph.D., of the Cleveland State University.

Introduction

Although you may not recognise fungi, they are just as prevalent as plants and animals. Their spores are in the air which we breathe, fungi allow us to make bread, and mushrooms (a type of fungi) are eaten by us. A few types of fungi are unicellular. For example, yeasts live as individual oval or cylindrical cells. However, the majority of fungi are multicellular. Their bodies are composed of hyphae, a network of fine filaments. In a mushroom, the hyphae are densely packed so it is difficult to see the individual structures when a mushroom is eaten. However, a mushroom is only a specialised reproductive part of the whole fungus. The main part of the fungi is underground in a whole web of hyphae, called a mycelium.

In the mycelium, each fungal cell is separated from each other by a septum. Each fungal cell may have one or more nuclei and remains connected to the mycelium because the septa are porous, allowing cytoplasm to flow through the hyphae and fungal cell walls, made of a hard material called chitin. Some fungi do not have septa, and they appear to be large, branching, multinucleate cells.

Nutrition

Fungi are saprophytes. When they find a source of food (e.g. dead wood, orange peel) , they decompose it and digest it. The enzymes break down larger organic molecules in the substrate into smaller molecules. These smaller molecules diffuse into the fungus, where they are used to allow growth and repair.

Fungi which feed on living cells are parasitic. For example, athlete's foot grows on the human foot. These kinds of fungi produce hyphae called haustoria, which can penetrate host cells without immediately killing them.

However, they are friendlier species of fungi. Many fungi live symbiotically with plants or animals. For example, most trees have fungi living in close contact with their roots. In this relationship, known as a mycorrhiza, there are many benefits:

Growing around the plant roots and often entering plant cells, the hyphae absorb minerals from the soil and release them in the roots. The fungi gets its source of food (organic nutrients) while delivering food to the plant.

The mycelium here would increase the surface area, thus the absorptive surface, of the plant roots.

The fungal cells help to maintain air and water flow in the soil around the roots.

The fungi may prevent other potentially pathogenic fungi to attack the tree.

Fungal Reproduction

Fungi can reproduce in two ways. Firstly, they may asexually produce through fragmentation. This occurs when pieces of hyphae are broken off, which then grow into new mycelia.

The second method is by spores. Spores are lightweight structures and windblown designed to be transported over long distances and by many mediums, such as on the bodies of insects and birds. They are additionally light enough to be blown away for hundreds of kilometers. Spores may be asexual and sexual. Their sexual properties can be analysed to classify the four phylla of fungi.

Types of Fungi

Zygospore Fungi (Zygomycetes)

This phylum includes bread molds and other saprotrophs. Comparable to bacteria, this phylum prefers asexual reproduction over sexual reproduction.

1. Two haploid hyphae of opposite types, also known as mating strain + and mating strain -, combine and fuse together.

2. Plasmogamy, the union of the two parent hyphae, occurs and results in the creation of a heterokaryotic (n + n) zygosporangium or zygospore. Note that the zygospore is NOT diploid yet; the haploid nuclei are simply clumped together.

3. Immediately, a thick wall develops around the zygospore to protect it from drying and other hazards. The zygospore becomes dormant.

4. When conditions are favourable, the zygospore absorbs water and undergoes karyogamy (n + n = 2n), where the haploid nuclei contributed by the two parents fuse to produce diploid zygosporangia.

5. The now diploid zygosporangium then undergoes meiosis to form haploid sporangia.

6. Through asexual reproduction of fungi (See above for more information), the spores from the sporangia germinate and grow into new mycelia.

7. Back to step #1.

Club Fungi (Basidiomycetes)

This phylum increases mushrooms and shelf fungi. In many ways, the reproduction stages of this phylum is similar to that of zygomycetes.

1. Two haploid hyphae of opposite types, also known as mating strain + and mating strain -, combine and fuse together.

2. Plasmogamy takes place, and a dikaryotic mycelium forms. The dikaryotic mycelium grows faster than the haploid parental mycelia.

3. Environmental factors cause the dikaryotic mycelium to form compact masses which develop into basidiocarps, short-lived reproductive structures. An example is the mushroom.

4. The basidiocarp gills are lined with terminal dikaryotic cells called basidia, which then undergo karyogamy.

5. The basidia are now diploid. They undergo meiosis to develop haploid basidiospores, a term referring to a basidiomycete's spores.

6. Still remaining on the basidiocarp, the haploid basidiospores eject, fall from the basidiocarp, and are dispersed by the wind when mature.

7. In a favourable environment, the basidiospores germinate and grow into short-lived haploid mycelia.

Key Terms

synapomorphy

Introduction

What makes an animal an animal?

If animals are a monophyletic taxon, then animals should be able to be defined by synapomorphies, (shared, derived characteristics). Ideally, we would NOT define this or any taxon using symplesiomorphies (shared ancestral or primitive characteristics) or homoplastic characters (the independent evolution of similarity, or "convergent evolution"). See pages 654 - 656 and Fig. 32.6 in your text to review these concepts. As you consider the characteristics listed below, ask yourself whether or not each is a synapomorphy.

Characteristics of an Animal

There is no one universally accepted definition of an animal. The following treatment follows your text, beginning on page 876.
- Animals:
  - Are multicellular, heterotrophic eukaryotes …
  - Lack the distinctive cell walls of plants & fungi
  - Share unique characteristics …
  - Share certain reproductive characteristics …
  - Other commonly used definitions …

Animals are multicellular heterotrophic eukaryotes

Unfortunately, none of these traits is exclusive to animals:
- Plants, fungi, and some algae are multicellular.
- Many bacteria, protists, and all fungi are heterotrophic.
- Everything other than bacteria and archaea are eukaryotic.
Moreover, all three of these characteristics also apply to fungi.
- However, there is a difference here between animals and fungi. Animals generally take in their food through ingestion, or eating and swallowing something. Fungi are absorptive heterotrophs; they secrete their digestive enzymes onto their food, and then absorb the resulting nutrients.

Animals share unique characteristics

Only animals have muscle tissue and nervous tissue.
Only animals have collagen, a structural protein
Only animals have the following types of intercellular junctions: (See pages 135 - 139, Figure 7.15 in your text for more information on these junctions.)
- Tight junctions (sealing function)
- Desmosomes (anchoring function)
- Gap junctions (communication function)

Animals share certain reproductive characteristics

Most animals reproduce sexually, with the diploid stage dominating.
In most animals, a small, haploid, flagellated, motile sperm fertilizes a larger, haploid, nonmotile egg to form a diploid zygote.
Mitotic division of the zygote yields a blastula stage, followed by a gastrula stage. A synapomorphy? This feature could be another "unique characteristic" shared by animals.
Development may be direct to adult form, or there may be a sexually immature stage (or stages) that are morphologically & ecologically distinct from the adult called a larva (plural: larvae).

Other commonly used definitions or characterizations

It is surprisingly difficult to find two texts that agree on a precise definition of an animal. Here are a few perspectives from some other texts.
- Animals are multicellular eukaryotes; they are chemosynthetic heterotrophs that ingest their food.
- Animals are motile, though many are secondarily sessile. Gametes usually are produced in multicellular sex organs, and the zygote passes through embryonic stages that include a blastula.
- Animals are organisms that are multicellular, with more than one type of cell. They are heterotrophic. They reproduce sexually (at least sometimes), with a zygote formed from two different haploid gametes. They go through a developmental stage called a blastula.
- Animals are not photosynthetic, have no cell wall, and no hyphae or mycelia. (What would a cladist think of this definition of the taxon Animalia?)

What kinds of animals are there?

Kingdom Animalia generally is recognized to have approximately 30 phyla ...
- There is relatively little dispute over the number of phyla recognized; however, the phylogenetic relationships among the phyla are hotly debated.
- Molecular techniques for assess similarity based on nucleotide sequences in nucleic acids are providing valuable new perspectives on this question.
Remember that two animals in different phyla generally are considered to be more different from each other than are animals within one phylum (e.g., nematodes are more different from annelids than humans are from sharks).

Introduction to animal phyla

There currently are almost 40 recognized phyla.

Phylum — Number of Species — Common Name

Placozoa — 1
Monoblastozoa — 1
Rhombozoa — 50
Orthonectida — 50
Porifera — 9,000 — sponges (figures)
Cnidaria — 9,000 — corals (figures)
Ctenophora — 100 — comb jellies
Platyhelminthes — 20,000 — flatworms (figures)
Nemertea — 900 — ribbon worms (figures)
Rotifera — 1,800 — rotifers (figures)
Gastrotricha — 450 — gastrotrichs
Kinorhyncha — 150 — kinorhynchids
Nematoda — 12,000 — roundworms (figures)
Nematomorpha — 230 — horsehair worms
Priapula — 15
Acanthocephala — 700 — (figures)
Entoprocta — 150
Gnathostomulida — 80
Loricifera — 35
Annelida — 15,000 — segmented worms (figures)
Sipuncula — 250 — peanut worms (figures)
Echiura — 135
Pogonophora — 145 — beard worms
Vestimentifera — 8 — beard worms
Arthropoda — 957,000 — arthropods (figures)
Onychophora — 80
Tardigrada — 400 — water bears
Pentastomida — 95 — tongue worms
Mollusca — 100,000 — molluscs (figures)
Phoronida — 15
Ectoprocta — 4,500 — sessile zooids
Brachiopoda — 335 — lampshells
Echinodermata — 7000 — echinoderms (figures)
Chaetognatha — 100 — arrow worms (figures)
Hemichordata — 85 — acorn worms
Chordata — 50,000 — chordates (figures)

Phylum Porifera

The name Porifera means "pore-bearing".

This phylum is commonly called sponges. The number of species is estimated to be between 5,000 and 10,000. All are aquatic and almost all are marine.

Animals in this phyla have no true tissues, which means, for example, that they have no nervous system or sense organs. Although sponges are multicellular, they are described as being essentially at a cellular level of organization. They are sessile as adults, but have a free swimming larva.

Their bodies are porous. They are filter feeders; water flows in through many small openings (ostia), and out through fewer, large openings (osculum). They have inner and outer cell layers, and a variable middle layer. The middle layer often is gelatinous with spiny skeletal elements (called spicules) of silica or calcium carbonate, and fibres made of spongin (a form of collagen). Choanocytes are flagellated cells lining the inside of the body that generate a current, and trap and phagocytize food particles.

Their cells remain totipotent, or developmentally flexible: they can become any type of cell at any point in the sponge's development. This allows for the great regenerative power sponges have.

Sponges are an ancient group, with fossils from the early Cambrian (ca. 540 mya) and possibly from the Precambrian. Sponges often are abundant in reef ecosystems. They somehow are protected from predators (spicules? bad taste?).

Many organisms are commensals of sponges, living inside them. Some sponges harbor endosymbiotic cyanobacteria or algae (dinoflagellates, a.k.a. "zooxanthellae").

Phylum Cnidaria

Name comes from the Greek knide- meaning "nettle".

This phylum formerly known as phylum coelenterata consists of the jellyfish, hydra, sea anemones, corals, sea pens, sea wasps, sea whips and box jellyfish. There are about 9,000 species. Almost all are marine. This is another ancient group, with fossils perhaps reaching back to 700 mya.

Cnidarians exhibit radial symmetry. Their basic body plan is a sac with a gastrovascular cavity, or a central digestive system. They have one opening, which serves as both mouth and anus. The body wall has an outer ectoderm, an inner endoderm, and a variable undifferentiated middle layer called mesoglea or mesenchyme that may be jelly-like. The mesoglea is NOT considered to be true mesoderm and so the Cnidaria are described as diploblastic. Tentacles usually extend from the body wall around the mouth/anus.

There are two basic body plans: the polyp and the medusa. The polyp is sessile and attaches to substrate by the aboral end (i.e., the end away from the mouth). The medusa ("jellyfish") is a floating form, and looks like an upside-down version of the polyp. Some cnidarians only have the polyp stage, some have only the medusa stage, and others have both.

The typical life cycle of a cnidarian involves what is called "alternation of generations": an alternation between an asexual polyp stage and a sexual medusa stage.

The tentacles are armed with cnidae (or nematocysts), small intracellular "harpoons" that function in defense and prey capture. When fired, the cnidae deliver a powerful toxin that in some cases is dangerous to humans. The phylum is named after the cnidae.

Cnidarians have no head, no centralized nervous system, and no specialized organs for gas exchange, excretion, or circulation. They do have a "nerve net" and nerve rings (in jellyfish).

Many cnidarians have intracellular algae living within them in a mutualistic symbiotic relationship (Dinoflagellates = zooxanthellae). This combination is responsible for much of the primary productivity of coral reefs.

There are three main classes in the phylum

Class Hydrozoa (hydras and Portuguese man-of-war are well-known but atypical examples of this Class)
Class Scyphozoa (jellyfish)
- The medusa stage is dominant and the polyp stage often is reduced.
Class Anthozoa (sea anemones, most corals)
- No medusa (jellyfish) stage, so sexual reproduction occurs in the polyp stage in this group. The polyps also can reproduce asexually, which is how individual "corals" grow.

Phylum Platyhelminthes

Name means "flat worm"

Most members of this phylum are parasitic (flukes and tapeworms), but some are free living (e.g., planaria). There are about 20,000 species.

They are dorsoventrally compressed (i.e., "flat").

Animals in this phylum are acoelomate, triploblastic, bilaterally symmetrical, and unsegmented. Platyhelminths have a simple anterior "brain" and a simple ladder-like nervous system. Their gut has only one opening. Flatworms have NO circulatory or gas exchange systems. They do have simple excretory/osmoregulatory structures (protonephridia or "flame cells").

Platyhelminths are hermaphroditic, and the parasitic species often have complex reproductive (life) cycles.

There are four main classes of platyhelminths:

Class Turbellaria (mostly free living flatworms, e.g., planaria)
Class Monogenea (parasitic flukes)
Class Trematoda (parasitic flukes, e.g., liver fluke and the human blood fluke, Schistosoma)
Class Cestoda (tapeworms)
- Cestodes are endoparasitic in the gut of vertebrates. They do not have a mouth or digestive system.

Phylum Rotifera

The Rotifers. The name means "wheel bearing," a reference to the corona, a feeding structure (see below).

They are triploblastic, bilaterally symmetrical, and unsegmented. They are considered pseudocoelomates.

Most less than 2 mm, some as large as 2 – 3 mm.

Rotifers have a three part body: head, trunk, and foot. The head has a ciliary organ called the corona that, when beating, looks like wheels turning, hence the name of the phylum. The corona is a feeding structure that surrounds the animal's jaws. The gut is complete (i.e., mouth & anus), and regionally specialized. They have protonephridia but no specialized circulatory or gas-exchange structures.

Most live in fresh water, a very few are marine or live in damp terrestrial habitats. They typically are very abundant. There are about 2,000 species.

Parthenogenesis, where females produce more females from unfertilized but diploid eggs, is common. Males may be absent (as in bdelloid rotifers) or reduced. When males are present, sexual and asexual life cycles alternate. Males develop from unfertilized haploid eggs and are haploid. Males produce sperm by mitosis which can fertilize haploid eggs, yielding a diploid zygote that develops into a diploid female. Sexual reproduction occurs primarily when living conditions are unfavorable.

Most structures in rotifers are syncytial ("a mulitnucleate mass of protoplasm not divided into separate cells," or "a multinucleated cell") and show eutely (here, "constant or near-constant number of nuclei").

Phylum Nematoda

Name from the Greek for "thread".

This phylum consists of the round worms. There are about 12,000 named species but the true number probably is 10 - 100 times this!

These animals are triploblastic, bilaterally symmetrical, unsegmented pseudocoelomates. They are vermiform, or wormlike.

In cross-section, they are round, and covered by a layered cuticle (remember this cuticle !!). Probably due to this cuticle, juveniles in this phylum grow by molting. The gut is complete. They have a unique excretory system but they lack special circulatory or gas-exchange structures. The body has only longitudinal muscle fibers. The sexes are separate.

Nematodes can be incredibly common, widespread, and of great medical and economic importance. They are parasites of humans and our crops. They can live pretty much anywhere.

In one rotting apple, there can be up to 90,000 nematodes, and in one tablespoon of coastal mud, there can be 236 species of nematodes!

Nematodes can be free living or important parasites of our crops, or of humans and other animals. They have become very important in development studies, especially the species Caenorhabditis elegans, presumably due to its small size and constancy of cell number (eutely - 959 cells in C. elegans).

Phylum Annelida

Name means "ringed", from the Greek annulatus.

This phylum consists of earthworms, leeches, and various marine worms given many different names (e.g., sand worms, tube worms). There are about 12,000 - 15,000 species.

Animals in this phylum are triploblastic, bilaterally symmetrical, segmented coelomates. Development is typically protostomous. They have a complete circulatory system, and a well-developed nervous system. Typically, each segment has paired epidermal "bristles" (setae or chaetae).

Most are marine but they are successful occupants of almost anywhere sufficient water is available. They can be free living, parasitic, mutualistic, or commensalistic.

Major advances of this phylum include the true coelom, segmentation, both longitundinal and circular muscles, a closed circulatory system and, for most, a more advanced excretory system (metanephridia).

There are three main classes of Annelids

Class Oligochaeta (earthworms)
Class Polychaeta (marine worms, fan worms, sand worms, paddle worms)
Class Hirudinea (leeches)

Phylum Arthropoda

Name means "jointed feet".

This phylum consists of spiders, ticks, mites, insects, lobsters, crabs, and shrimp, and is the largest of all the phyla. So far, over 1 million species have been named, and it is likely that the true number out there is 10 - 100 times greater.

This phylum also includes the extinct trilobites, which were prevalent in the Paleozoic era. Because of their exoskeletons, these animals fossilized well and over 4000 species have been named.

These animals are triploblastic, bilaterally symmetrical, segmented, protostome coelomates. The coelom is generally reduced to portions of the reproductive and excretory systems. They have an open circulatory system.

The most notable advancement of this phylum is a rigid exoskeleton. It has major implications in these organisms' locomotion, flexibility, circulatory systems, gas exchange systems, and growth. It also was partially responsible for the ability of the arthropods to move on to land.

There are several major groupings of arthropods:

Major subgroups include:

The chelicerates (eurytperids, horseshoe crabs, scorpions, spiders, ticks) have clawlike feeding appendages. They lack antennae and usually have simple eyes.
The Trilobites...they get their own grouping
The uniramians (centipedes, millipedes, insects) have one pair of antennae and unbranched (uniramous) appendages.
The crustaceans (crabs, shrimp, lobsters, barnacles and many others) have two pairs of antennae and branched (biramous) appendages.

Major Classes Include

Class Arachnida (mites, scorpions, spiders, ticks)
Class Diplopoda (millipedes)
Class Chilopoda (centipedes)
Class Insecta (insects)
Class Crustacea (crabs, crayfish, lobsters, shrimp)

Phylum Mollusca

Name means "soft".

This phylum consists of snails, slugs, bivalves, chitons, squids, octopus, and many others. About 110,000 species

All molluscs have a similar body plan:

A muscular foot, usually used for movement.
A visceral mass, containing most of the internal organs.
A mantle, a fold of tissue that drapes over the visceral mass and secretes the shell, if present.
Most have a radula, or a rasping organ to scrape food.

Molluscs are bilaterally symmetrical, or secondarily asymmetrical. They are coelomates, but the coelom generally has been greatly reduced; the main body cavity is a hemocoel. Development is typically protostomous. The gut is complete with marked regional specialization. Large, complex, metanephridia (excretion).

Many molluscan life cycles include a trochophore larva. This stage also is characteristic of annelids.

There are several major classes of molluscs:

Class Polyplacophora (chitons)
Class Gastropoda (snails, limpets, conchs, slugs, nudibranchs)
Class Bivalvia (clams, mussels, scallops, oysters)
Class Cephalopoda (squids, octopus, nautilus, cuttlefish)
Class Scaphopoda (tusk shells)

Phylum Echinodermata

Name means "spiny skin"

This phylum consists of sea stars, brittle stars, sea urchins, and sea cucumbers.

Echinoderms are mostly sessile or very slow moving animals.

As adults, they are radially symmetrical, but in the larval stage, they are bilaterally symmetrical. They are considered deuterostomes.

Echinoderms are unique in that they have a water vascular system composed of a system of fluid-filled canals. These canals branch into the tube feet, which function in feeding, locomotion, and gas exchange.

There are six major classes of echinoderms:

Class Asteroidea (sea stars)
Class Ophiuroidea (brittle stars)
Class Echinoidea (sea urchins, sand dollars)
Class Crinoidea (sea lilies and sea feathers)
Class Holothuroidea (sea cucumber)

Phylum Chordata

Name means "the chordates", i.e., these animals have a notochord at some stage in their lifecycle.

This phylum consists of tunicates, lancelets, and the vertebrates.

There are four major features that characterize the phylum Chordata.

A notochord, or a longitudinal, flexible rod between the digestive tube and the nerve cord. In most vertebrates, it is replaced developmentally by the vertebral column. This is the structure for which the phylum is named.
A dorsal hollow nerve cord which develops from a plate of ectoderm that rolls into a tube located dorsal to the notochord. Other animal phyla have solid nerve cords ventrally located. A chordate nerve cord splits into the central nervous system: the brain and spinal cord.
Pharyngeal slits, which allow water that enters through the mouth to exit without continuing through the entire digestive tract. In many of the invertebrate chordates, these function as suspension feeding devices; in vertebrates, they have been modified for gas exchange, jaw support, hearing, and other functions.
A muscular, postanal tail which extends posterior to the anus. The digestive tract of most nonchordates extends the length of the body. In chordates, the tail has skeletal elements and musculature, and can provide most of the propulsion in aquatic species.

Chordates have a segmented body plan, at least in development. This segmentation evolved independently from the segmentation of annelids.

Three subphyla make up the phylum Chordata:

Subphylum Urochordata (tunicates): the adults are enclosed in a tunic made of a carbohydrate much like cellulose. They squirt water out of an excurrent siphon. Urochordates are characterized by errant (mobile and active) larvae and sessile adults. All are filter feeders. The only "chordate" characteristics retained in adult life are the pharyngeal slits. Larval urochordates look more like adult cephlochordates & adult vertebrates than adult urochordates.
Subphylum Cephalochordata: Cephalochordates are known as lancelets because of their blade-like shape; they are also known as amphioxus. They are marine animals and usually live on the bottom, but can swim.
Subphylum Vertebrata (vertebrates) ...

Formally, the phyla Urochordata and Cephalochordata are considered invertebrates.

Subphylum Vertebrata

Vertebrata refers to the presence of vertebrae and a vertebral column.

This subphylum includes most of the animals with which most people are familiar.

Vertebrates show extreme cephalization.

The notochord generally is replaced by the cranium & vertebral column in adults.

Neural Crest Cells

Later in development, these give rise to many cells of the body, including some cartilage cells, pigment cells, neurons & glial cells of the peripheral nervous systems, much of the cranium, and some of the cells of the endocrine system.

Some scientists would like to classify the neural crest as the fourth germ layer.

The phylum Chordata includes three subphyla. These include vertebrates and invertebrate chordates.

Shared characteristics

Notochord: The flexible, hydrostatic (non-collapsible), rod-shaped supporting axis wrapped in tough connective tissue that is found dorsal to the gut/coelom and below the nervous system of the embryos of all chordates, including vertebrates. As bone does not compress, muscles tensed on one side result in body movement instead of shortening the animal. This allows for much better locomotion than do cilia for larger animals in water, a crucial victory for later success.
Pharyngeal slits: Slits in the pharynx originally used to gather food. Water enters the mouth, passes through the pharynx and exits through gill-like slits, passing through a cavity called the atrium, and then expelled from the body. In humans, they are present only during the embryonic stage of development.
Dorsal nerve cord: A neural tube dorsal to the notochord.
Postanal tail: Elongation of the body and notochord, nerve cord and muscles past the anus into a mobile, external appendage on the same axis; its contribution to early locomotive function led to success.

Non-synapomorphic characteristics (not limited to chordates):

Bisymmetrical (bilateral symmetry)
Segmented muscles and bones

Subphylum Urochordata

The tunicates are located in this subphylum. Along with the subphylum Cephalochordata, these two subphyla make up the invertebrate chordates. Only the tunicate larvae have notochords, nerve cords, and postanal tails. Most adult tunicates are sessile, filter-feeders which retain their pharyngeal slits. Adult tunicates also develop a sac, called a tunic, which gives tunicates their name. Cilia beating within the tunicate cause water to enter the incurrent siphon. The water enters the body, passes through the pharyngeal slits, and leaves the body through the excurrent siphon. Undigested food is removed through the anus. Tunicates are hermaphrodites and can reproduce asexually through budding. In urochordates notochord is confined to larval tail.

Characteristics

Lack a cranium
Have an open type of circulatory system
Excretion is by neural gland (nephrocytes)
Have two siphons through which water enters and exits the body
Have a tubular heart
Have a tough outer covering (e.g. Accidia)

Subphylum Cephalochordata

The lancelets are located in this subphylum. Along with the subphylum Urochordata, these two subphyla make up the invertebrate chordates. Lancelets receive their name from their blade-like shape. They resemble fish, but they are actually scale-less chordates only a few centimeters long. They spend most of their time buried in the sand with their mouths protruding. Fossils of lancelets have been found to be over 550 million years old. Dropped out sessile stage, what was the larval stage is now sexually reproductive. Includes Branchiostoma (“amphioxus”).

Subphylum Vertebrata

This group gets its name from the Latin verb vertere, meaning "to turn." They are characterized by separate bones or cartilage blocks firmly joined as a backbone. The backbone supports and protects a dorsal nerve cord. Vertebrates have tissues which are organized into organs which in turn are organized into organ systems.

Characteristics

All vertebrates share the following characteristics:

are segmented
a true coelom
bilateral symmetry
cephalization
a backbone
a bony skull
a closed circulatory system
a multi-chambered heart
two pairs of jointed appendages
tissues organized into organs with specialized functions

The vertebrate organ systems are broadly categorized into:

Neurological
Circulatory
Digestive
Respiratory
Reproductive
Excretory

The vertebral column is not present in higher vertebrate organisms that have reached maturity. (In humans, the gel-like, spongy core of the vertebral column is the only remainder; ruptured or herniated discs are an injury to this.) The cranium is a composite structure of bone and cartilage that serves two primary functions:

protect and orient the sensory organs of the head, and
enclose or partially enclose the brain

What evolutionary relationship could we imagine between sessile echinoderms and the higher chordate animals?

Paedomorphic (child-form) hypothesis: basically, evolution of sexual reproduction in what had previously been a larval life stage, or the retention of at least one juvenile characteristic into the adult (capable of sexual reproduction) stage. Some scientists believe that this occurred in a proto-chordate animal lineage. Maybe chordates (and vertebrates) arose from sessile (attached) ancestors. Selection in these proto-chordates maybe began to favor more time in the larval stage, as feeding was more successful or mortality lower in this stage. As larvae got bigger physics shows that the cilia become less efficient for locomotion, favoring the undulating motion allowed by a notochord.

Is this hypothesis crazy? A similar example of this today is Ephemeroptera, the mayfly, which has almost abandoned its adult stage. Its one-year lifespan is mostly larval with just a brief day of reproduce-and-die as an adult, which doesn't even have usable mouthparts.

Tunicate (sea squirt) larva has all four chordate characteristics, although adult sessile (“attached”).

Class Agnatha

"jawless fish"

Ostracoderms: extinct Agnathans which had primitive fins and massive plates of bony tissue on their body.
Cyclostomes: "circle mouth" - a group of Agnathans which is still alive in the form of lampreys and hagfish.

Appeared approximately 500 million years ago and dominated the oceans for about 100 million years. The first group of fish to appear. They had neither jaws, paired fins, nor scales, but they were the first organisms with a backbone.

Class Acanthodia

"spiny fish" Appeared about 430 million years ago. An extinct class of fish that developed jaws with bony edges. They had internal skeletons made of cartilage and some bone.

Class Placodermi

Appeared about 410 million years ago, dominated the sea for about 50 million years. An extinct class of fissive heads.

Class Chondrichthyes

"cartilaginous fish" Appeared about 400 million years ago with bony fish. Includes sharks, skates and rays, and chimaeras. Their skeletons are made of cartilage strengthened by the mineral calcium carbonate.

The main characteristics and distinguishing features of this class: - gills - single-loop blood circulation - vertebral column - presence of placoid scales on their bodies - internal skeleton of cartilage - paired, fleshy pectoral and pelvic fins - asymmetrical tail fin prevents sinking - fatty liver provides neutral buoyancy - visceral clefts present as separate and distinct gills - no external ear - oviparous - internal fertilization - ectoderms - cold blooded

Class Osteichthyes

"bony fish" Appeared about 400 million years ago with cartilaginous fish. Includes about 95% of today's fish species.

Subclass Sarcopterygii

fleshy-finned fishes. Fins have bones and muscles, homologous to our limbs.

Order Dipnoi

lung fishes, two groups isolated when continents separated

Order Crossopterygii

includes coelacanths and rhipodistians, gave rise to amphibians, had lungs which evolved into a swim bladder in bony fishes, and labyrinthodont teeth, characterized by complex folding of enamel.

• Skeleton made of bone, jaws, fins, most with scales, two-chambered heart.

Class Amphibia

means “both lives”, aquatic larvae, terrestrial adult Amphibians: - Legs - Lungs - Double-Loop Circulation - Partially Divided Heart - Cutaneous Respiration (Breathes through Skin)

Order Salientia

frogs (jumping) (aka Anura)

Order Urodela

salamanders (tailed)

Labyrinthodont amphibians: oldest known amphibians, inherited characteristic teeth from crossopterygii ancestor, had stocky, aquatic larvae.

Amphibians have limbs instead of fins. Girdles and vertebral column now more substantial and connected, support body on legs.

Lisamphybia: no scales, “smooth”, eggs with no shell, laid in water (water-reliant).

Amphibians gave rise to cotylosaurs, from which arose dinosaurs, turtles, lizards, and therapsids.

Class Reptilia

amniotic egg allowed freedom from water, shelled egg. (Amnion: protection). Reptiles have four extra-embryonic membranes:

Amnion: supports aquatic environment inside egg in fluid sac.
Allantois: allows gas exchange and elimination of wastes.
Chorion: gas exchange
Yolk sac: only one of the four left over from amphibian ancestor

Reptiles are cold-blooded, or ectothermic, meaning that their heat come from their environment. Sometimes defined as all amniotes that are not birds or mammals.

Reptiles can be classified by skull structure into four groups:

Anapsid
Synapsid
Diapsid
Euryasid

Refers to number of holes in the skull. Cotylosaurs had Anapsid skull

Dermatocranium: from bony outer skull structure, precursor to human cranium.

Subclass Anapsidia

Subclass Testudinata

turtles, terrapins

Subclass Diapsida

dinosaurs, snakes, most stuff

Subclass Synapsida

Order Therapsids

Subclass Diapsida

includes Ichthyosaurs, marine reptiles convergent on dolphins; Plesiosaurs, ancient sea monsters; Squamates, including lizards and snakes; and Thecodonts, which gave rise to

birds
dinosaurs
crocodilians

Dinosaurs: broken into two groups, based on hip structure

Saurischia: lizard hips (gave rise to birds [!]), ancestrally bipedal
Ornithischian: bird hips, ancestrally quadripedal

Crocodilians: come from archosaurs, the only extant (still living today) archosaur descendant. Ancestrally bipedal, secondarily quadripedal.

Synapsids: refers to joined (Greek syn-, together with) parts of skull. Led eventually to mammals. Synapsid pelycosaur >> therapsid >> mammals

Pelycosaur: Sail-backed dinosaur, legs not spread out like lizard but more pillar-like and under body, allowing greater activity and competence in motion, pendulum like rather than constant push-up. Teeth differentiated into different types, for pre-processing of food needed by higher metabolism. Skull changes, bone histology, suggestions of warm-bloodedness.

Class Aves

arose late Jurassic, early Cretaceous. Feathers, skeleton modified for flight. Feathers: epidermal derivative, made of keratin (like fingernails). Carpometacarpis: bears primary flight feathers, parallel to hand parts. Keeled sternum: breastbone, powerful one needed to support flight muscles. Strong, light, occasionally hollow bones. All birds lay eggs (as contrasted to reptiles, which have developed live birthing over 100 independent times.) Why are there no live-bearing birds? Early birds had teeth, lost them. With mammals, only exothermic animals.

Archaeopteryx: “ancient wing”, Jurassic bird-reptile, very dinosaur-like. Good fossils found in Zolenhoffen, German sandstone mine with fine sand, shows feathers clearly, found shortly after Darwin’s publication and used to support his hypothesis. Thick, heavy bones and no sternum, bony tail, not a good flyer but did have primary flight feathers.

Archaeornithes: includes archaeopteryx.

Paleognathae: gave rise to Australian flightless birds.

Neognathae: remaining live birds.

Class Mammalia

Two unique characteristics, or synapomorphies:

Hair
Mammary glands

(don't fossilize well)

Three skeletal characteristics (fossilize)

Lower jaw only one bone, the dentary (several in reptiles)
Three bones in middle ear: malleus, incus, stapes (reptiles have one or two, never three)
Joint between upper and lower jaws between dentary and squamosal of skull (in reptiles this joint is between other bones)

Mammals basically have a synapsid skull design inherited from ancestor

Non diagnostic characteristics (not unique to mammals):

Warm-blooded
Skin glands: sweat glands and oil-producing sebaceous glands
Large nasal cavities (because of high metabolism) Clean, warm and humidify air
Heterodonty (differentiated teeth)
Diphiodonty: two sets of teeth: baby and adult (“deciduous” teeth, drop out) (reptile teeth are continually replaced)

Subclass Protheria

monotremes (Greek mon-, one; and trema, hole), or egg-laying mammals, have one opening for excretion and urination.

Subclass Theria

Metatheria: Marsupials (opossum, kangaroo…) Eutheria: Placental mammals (all common mammals)

Marsupium: (from Greek marsypion, purse or pouch). Gestation period much shorter than in Eutherian mammals, but after leaving the uterus the tiny offspring crawls into a pouch where it completes development latched onto a teat.

Recent molecular (read: genetic) evidence suggests that two different mammal groups may have developed live-bearing ability separately. Instead of being a “rough draft” for placental-style live bearing, perhaps the marsupial pouch approach is another solution to the same problem. Advantage: in tough times the parent can pitch out the offspring and increase its own chance of survival.

Tissues and Systems

Epithelial tissue

Comes from various sources, ectodermal or endodermal material. Cell sheet lines a surface or body cavity. One side, called freesurface or Apical, is exposed to

animal interior (forming the lumen) or
exterior of its body cavity.

The other side rests on the basal layer.

Epithelial tissue is not penetrated by blood vessels.

Two categories:

sheets
glands

Classified on two features:

simple, (a single layer of cells),
stratified, (more than one cell layer.)

Cell shape at free surface:

squamous (broad and flat)
cuboidal (spherish)
columnar (tall and thin)

Simple squamous epithelium: usually lines body cavities and vessels,alveoli, glomeruli of kidney; in blood and lymph vessels called endothelium; in body cavities called mesothelium (serosae): parietal serous membranes line body wall, visceral serous membranes cover organ
Simple cuboidal epithelium: in ducts like kidney and salivary glands.
Simple columnar epithelium: nonciliated type lines digestive tract, ciliated type lines some regions of uterine tubes and lungs
Stratified squamous epithelium: (important) lines mouth, esophagus,and vagina. Cells sometimes dead, flat and keratinized, making them resistant to abrasion. Stratified squamous epithelium changes to columnar squamous epithelium progressively down esophagus to the stomach.
Epidermis: from epithelium. Below this is dermis, thicker and with blood vessels.

Two specialized epithelia:

pseudostratified
transitional

Pseudostratified epithelia: lines the trachea (where it is ciliated)and the male urethra (where it is non ciliated), looks stratified but not.
Transitional epithelia: found only in bladder and urinary system. As it stretches it appears to go from 6 to 3 cell layers deep.
Glandular epithelia: (gland: group of cells that excretes something.. mostly derived from epithelium. Glands are classified into endocrine and exocrine by where they excrete.
Endocrine glands: secrete hormones into the blood without use of ducts.
Exocrine glands: secrete onto the body surface or into a cavity, thru a duct. Exocrine substances include sweat, mucous, oil, and saliva. An exocrine gland is the liver, which secretes bile.

Connective tissue

This is a “grab bag” category of diverse tissue types. Functions include binding and supporting. Types include bone, cartilage, fibrous connective tissue, blood and adipose (fat) tissue.

If you took away everything in the body except the connective tissue, you'd still be able to see the basic form of the body.

Form: distinctive cells surrounded by a cell matrix made of extra-cellular fiber grounded in a ground substance (excluding blood)

Types:
1. connectile connective tissues (can be 1. loose or 2. dense)
2. special connective tissue (includes blood, bones and cartilage).

Fibroblasts form connective tissue proper;
chondoroblasts form cartilage;
asdasdasdasdasdasdads osteoblasts form bone;
and blood is formed from various sources.

Ground substance: “unstructured” material that fills space between cells and contains fibers. Made of
1. interstitial fluid (bathes cells)
2. proteoglycans (protein core with attached polysaccharides, glycoaminoglycans or GAGs such as chondroitin sulfate, keratin sulfate, and hyalronic acid, whose consistency is syrupy to gelatin-like)
3. cell-adhesion proteins (connect connective tissue cells to the fibers).

Fibers of connective tissue:
1. Collagen (flexible protein resistant to stretching, tensile strength, most abundant protein in animals, white)
2. elastin (rubbery, resilient protein, in dermis, lungs, blood vessels, yellow when fresh)
3. andreticulin (like collagen).

Loose connective tissue: found beneath skin, anchors muscles,nerves etc. Include fibroblasts, macrophages, mast cells,and adipose cells. Fibers include collagen and elastic fibers. Ground substance is “syrupy”. Adipose included.

Dense connective tissue: largely densely packed fibers of collagen or elastin regularly or irregularly arranged. Forms tendons and ligaments, coverings of muscles, capsules around organs and joints, and dermis of skin.

Cartilage vs. bone

Feature	Bone	Cartilage
cell type	osteocytes	chondrocytes
ground substance	calcium phosphate	chondroitin sulfate
vascularization	vascular	avascular
micro architecture	highly ordered	less organized
units called	osteons
fibrous sheath	peristeum	perichondrium

Cartilage: There are three cartilage types:
1. hyaline cartilage
2. fibrocartilage (fibrous cartilage)
3. elastic cartilage

Hyaline cartilage: most widespread cartilage type, in adults forms articular surfaces of long bones, rib tips, rings of trachea, and parts of skull. Mostly collagen, name refers to glassy appearance. In embryo, bones form first as hyaline cartilage, later ossifies. Found in tracheal rings. Few collagen fibers.

Fibrous cartilage: have lots of collagen fibers. Found in intervertebral discs, pubic symphesis. Grades into dense tendon and ligament tissue.

Elastic cartilage: springy and elastic. Found in internal support of external ear and in epiglottis, yellow when fresh.

Chondrocites (cartilage cells) rely on diffusion for nutrients, as cartilage has no direct blood supply, and no enervation (nerves). Can be loaded with calcium salts.

Bone: Specialized connective tissue, calcium phosphate arranged in highly ordered unit called osteon, or Hyvercian system. Concentric rings around central canal with blood vessels and enervation (nerves). Bone varied, not all vertebrate bone is even cellular. Our concern: simple pattern for mammals.

Lacuna (spaces in which osteocytes found); canaliculi (little canals) bigger diagonal cells, layers of bone called lamellae.

Three types of bone cells, ending in
-blast, (mend bone)
-cyte (fortify bone)
-clast (tear down bone)

Classified by
1. appearance (spongy vs. hard)
2. where found (outside or inside)
3. how it is formed (endochondral cartilage model forms first and then is ossified, and entramembranous, bone forms directly without cartilage precursor)

Example of endochondral bone formation: long bone begins to ossify from center shaft, calcified region expands and cuts off diffusion of nutrients as bone replaces cartilage. In young mammals, secondary ossification centers then form at bone ends, growth has stopped by sexual maturity as all primary bone is ossified. In other animals, bones continue growing throughout their lifetime.

Three types of intramembrous bone:
1. dermal bone
2. sessamoid bone
3. perichondral bone.

Dermal bone forms skull, shoulder/pectoral girdle, and integument, descended from dermal armor of ancestor. Comes from mesoderm, in dermis of skin.

Sessamoid bones: form directly in tendons. Example: kneecap, also in wrist. Deals with stress.

Perichondral bone means “around cartilage,” forms around cartilage or bone. Functions in bone repair and in ossification of endochondral bone.

Bone remodeling and repair: bone has mineral structure, and develops tiny fractures, which, under stress, can lead to larger fractures. To combat this, bone is constantly replaced. Osteoclasts channel through existing bone, tear down and leave behind osteoblasts and lacuna, leaving osteocytes. Continually resets mineral structure of bone, and is preventative maintenance.

Muscle tissue

Mesodermal in origin, muscle has several functions: supply force for movement, restrain movement, proper posture, act on viscera (internal organs) for peristalsis (moving food down digestive tract), give body shape, form sphincters, (such as in esophagus, between stomach and intestine, large and small intestine, in anus), in sheets of muscles, affect air flow in and out of lungs, line blood vessels and play vital role in circulation.

Secondary roles: heat production (shivering a specialized heat production to supplement metabolism).

Muscles co-opted to other non-original functions: sharks detect electrical field created by fish muscles. Some fish formed electric organs, create current strong enough to repel predators or stun prey. Other fish can use field as “radar” to see things and communicate with other animals. (Evolved independently in different groups).

Different classifications: by color, (red or white) location, nature of nervous system control (voluntary or involuntary), embryonic origin, or by general microscopic appearance (striated, smooth, and cardiac.)

Striated muscle (or skeletal muscle): under voluntary control. Individual cells called fibers, grouped into fascicle. Myofibrils founding one cell made of even smaller myofilaments. Each striated cell very long and multi-nucleated. Fibers joined end to end to form longer composite fibers. Sarcomeres: repeating units make up myofibrils. Two kinds of myofilaments, thick kind made up of myosin and thin of actin. Striations visible in light microscope, smaller part only with electron microscope.

Cardiac muscle: occurs only in heart. Light banding visible under light microscope. Each band short, principally mononucleate (occasionally dinucleate) often branched, joined together with intercollated discs. Involuntary. Waves of contraction spread through intercollated discs. Initiated by nerve stimulation or can originate in the heart itself (useful in heart transplants.)

Smooth muscle: no striations visible with light microscope. Almost entirely visceral function: digestion, sphincters, urogenital tracts, piloerectory muscles (make hairs stand up), lungs. Non-voluntary control. Slow and sustained action. Each cell mononucleate, short, fusiform (spindly) in shape, cells usually uniform in size.

Striated muscle contraction: Muscle broken into units called fascicles, in units of myofibrils. Repeating units called sarcomeres, consisting of two kinds of myofilaments:
1. thick, myosin filament
2. thin, actin filament.

Sarcomere: Thick and thin filaments interspersed in ordered grid.

Sliding filament theory: thick and thin filaments move past each other in opposite direction, shortening length. Longer muscles contract more rapidly than short ones (see cell bio for details).

Myosin molecule: two polypeptides twisted together with two globular heads at end.

Myosin filament: many slender myosin molecules together.

Actin filament: chain of actin single, tropomyosin strands with repeated globular troponin, and with actin. All play role in muscle contraction. Myocin heads have sites that bind to actin. Actin filaments have many regular sites that can bind to myosin.

Troponin has four sites:
1. one to bind myosin
2. one for actin
3. one for tropomyocin
4. one for calcium ions

Nerve signal reaches muscle, triggers release of chemical signal called neurotransmitter, that diffuses across cell membrane (sarcolimic reticulum) and binds to receptors in it. Receptor is acetylcholine, ACH. When there is enough nerve signal, the message travels through t-line to sarcoplasmic reticulum to release calcium ions.

Lacking calcium, tropomyosin site blocked. In calcium, myosin binding sites exposed and heads bind to actin molecules, delivering force to move fibers in relation to each other. Myocin head then interacts with ATP to get “recocked”, if myosin still exposed then it fires again and results in further muscle contration. If there is no further nerve signal, sarcoplasmic reticulum sequesters Ca+ ions again and no recocking occurs.

Quirari (or curare): known from movies, used in South America, blocks acetylcholine receptors in cell and causes skeletal paralysis. Victim dies of asphyxiation because he can’t breathe.

Duchenne's muscular dystrophy: degeneration of sarcolema, plasma membrane of muscle cell unable to release signal and quickly atrophies.

Fast and slow twitch fibers: vertebrate muscle fiber. Terms relative within one group of animals. Differences related to differences in enervation, type of myocin, and actin activation.

Two parts of force generated by muscle: 1. active component 2. elastic component (energy stored in muscle when stretched by gravity or another force. Stored in muscle elastic tissue around tendons. Especially important in limb oscillation, like running, or trunk twisting, like fish swimming. Up to 90% of stored elastic energy can be recovered.)

How does a muscle match its power to its job? Two ways:
1. rate modulation, derived from frequency of nervous stimulation of muscle, force increases as frequency of stimulation increases up to point of tetanus.
2. selective involvement of motor units, a given neuron enervates a fixed number of muscle cells, (a motor unit), and force is increased by recruiting more motor units. Motor units may be small, such as in eye, or larger, like in leg muscle.

How do muscles grow stronger?
1. add more myofilaments, increases cross sectional area by up to 50%, more little ratchets working
2. proliferation in blood vessels and connective tissue around muscle

Muscle strength is relative to cross sectional area, not length. Not always feasible to add more cross sectional area.

Pinnate fibers: oriented obliquely (Y-shaped) to minimize muscle mass, in certain circumstances, like calf muscle. Spreads muscle out.

Velocity of shortening greater in long muscle than short. Why? Contraction tied to relation between fibers, and to total length of muscle. Both long and short muscles reach same percentage of contraction in same unit time, but distance covered by the longer muscle is greater.

Synergist muscles: muscles work together to produce motion in same general direction. Bicep shares work with brachialis.

Antagonist muscles: muscles that oppose each other. Bicep pulls forearm in, triceps pulls it back out.

Origin vs. insertion: origin is the end of the muscle that more fixed in its attachment to the body. The more movable end called insertion.

Fixators: muscles that act to stabilize a joint or lever system. Like upper arm when you clench your fist hard.

Flexors and extensors: applied mainly to limbs. Flexor bends one part relative to another about limb, extensor straightens it.

Vertebrate digestive system

Functions to break down food into molecules small enough to absorb, or pass across digestive membrane.

Digestive tract: tube extending from lips of mouth to anus or cloacae in bird, reptile or monotreme.

Lumanal glands: empty into inner body cavity (lumen: inner surface).

Tract divided into three main regions:
1. buccal cavity
2. pharynx
3. alimentary canal

Alimentary canal divided into four regions:
1. esophagus
2. stomach
3. small intestine
4. large intestine

Accessory digestive glands, outside digestive tract proper, secrete into lumen of tract through ducts. Includes the salivary glands, liver and pancreas.

Buccal cavity, which includes palate and tongue, develops from infolding of stomadeum, or second opening of blastula, whereas the rest of the digestive tract develops from the primitive gut.

Teeth: capture and hold prey. In mammals in particular further process and break down food into small particles, increasing surface area available for enzymatic action.

Tooth anatomy:
1. crown projects above gum,
2. root below gum,
3. enamel is outer coating of crown, hardest surface in body, of epideral origin
4. dentin, below enamel, bone-like and forms bulk of tooth, is harder than bone and contains nerves and blood vessels. (Remember that mammals are heterodontic, with different types of teeth).

Pharynx: air passage for adult, gill slits in embryo. Important in lower vertebrates, site of gills. Features derived from pharyngeal region: first pharyngeal pouch gives rise to parts of the ear, other pouches give rise to various other structures.

Alimentary canal: epithelium lines lumen, glands secrete into lumen, longitudinal and circular muscles help digestive movements (peristalsis).

Esophagus: tube carries food from mouth to stomach. Expands to fit large bolus (lump of chewed food). Secretes mucus for lubrication. Birds have crop for storage, enlargement of esophagus.

Epiglottis: keeps food out of air tube, an evolutionary “kludge,” or fix.

Stomach. Absorbs water, alcohol, nutrients, uses gastric juice with enzymes, mucous, HCl, released by chief and parietal cells (release protein enzymes) in gastric pits. Rugae: folds of stomach, disappear when full. Sphincter at both ends of stomach, control food passage.

Chyme: semi-digested food released to small intestine.

Small intestine: three regions, duodenum, jejunum, and ileum.

Duodenum site of most intestinal digestion. Jejunum and ileum do most of intestinal absorption. Ileum ends with another sphincter, ileocolic valve or ileosecal valve. Structure: Circular folds covered with villi (singular is villus).

Villi: finger-like cellular projections, covered with microvilli, tiny projections which increase surface area. Increases surface area by 900x, speeds digestion (break down) and absorption (taking in nutrients).

Large intestine: larger diameter, shorter length than small intestine. No villi. In mammals, forms large gentle loop, colon, empties into straight region, rectum, empties into outside world through anal sphincter. Colon: absorbs water left over, also absorbs vitamins released by bacteria which live there (vitamin K).

Food: made up of 1. proteins, 2. fats, 3. carbohydrates 4. fibrous material.

Digestive system breaks foods down. Proteins must be broken to amino acids to be absorbed. Polysaccharides to monosaccharides, lipids to fatty acids and monoglycerides to absorb.

Salivary glands in mouth, saliva contains mucous, salt and a few enzymes (amalase, begins starch breakdown). Snake venom from oral gland, mixture of toxins and digestive enzymes. Breaks down blood vessels and disables nervous system.

Stomach enzymes: released in inactive form, zymogene, converts to active form in lumen of gut. Transformation is triggered by another enzyme, or the stomach’s low pH. Pepsin secreted as pepsinogen (-ogen means primitive form). Stomach glands secrete up to two or three liters a day of gastric juice, which is reabsorbed.

Chyme released to duodenum.

Small intestine has two major accessory glands:
1. pancreas
2. liver

Pancreas has endocrine and exocrine functions, releases large amounts of carbonate to neutralize acidic chyme, as intestinal enzymes work in neutral pH, and stuff to break down lipids and starch (zymogens, like tripsin)

Liver releases bile. Bile made from cholesterol, stored in gall bladder', released in duodenum, emulsifies fats.'

Emulsify: keeps fats in tiny drops, which are suspended, increasing surface area and action of lipases. Protein and carbohydrates absorbed in intestine, taken to liver for processing. Fatty acids go to lymphatic system

Appendix: vestigial remnant. Much variation in digestive systems within mammals: herbivore, carnivore, insectivore, non-ruminant herbivore.

Rumen: four-chambered stomach of animals like cows (ruminant herbivores). Cellulose resistant to digestion, rely on microorganisms to break down cellulose. Some bacteria, protists and fungi can break down cellulose, almost no animals can. Bacteria break down cellulose in rumen, to be taken back to the mouth to chew their cud (ruminate). Later cow swallows to proceed with digestion. (Horses not like this).

Circulatory system

Circulatory system functions

1. Transportation

 a. Respiration: gas exchange (O2 and CO2), overcomes limited rate of

diffusion

 b. Nutrition:

 c. Excretory: (remove metabolic wastes)

2. Regulation

 a. Transport hormones

 b. Regulate body temperature

 c. Protection

    i.  Blood clotting

    ii.  Immune system (carries white blood cells)

Vasodilation: allows heat loss across epidermis, as seen in elephant ears, takes more blood to surface of body, sweating may accompany

Countercurrent heat exchange: used by dolphins in fins to conserve heat in cold water. Veins surround an artery, and blood returning to body absorbs heat from blood traveling out from body to fin, minimizing heat loss. Used by dogs in feet, etc.

Blood made of
1. plasma and
2. formed cellular elements (red and white blood cells, and platelets).

Plasma makes up 55% of blood volume. Cellular elements make up the other 45%.

Plasma makeup: 90% water, 7-8% soluble proteins (albumin maintains blood osmotic integrity, others clot, etc.) 1% electrolytes 1% elements in transit

Red blood cell (erythrocyte): contains hemoglobin, functions in oxygen transport. In mammals, red blood cells lose nuclei on maturation, and take on biconcave, dimpled, shape. No self repair, live 120 days. About 1000x more red blood cells than white blood cells. About 7-8 micrometers in diameter.

Hematocrit: proportion of blood volume that is occupied by cells, about 43% in humans on average. 48% for men and 38% for women.

White blood cells (leukocytes): Nucleated, about 10-14 micrometers in diameter, commonly amoeboid, escape circulatory system in capillary beds. Include basophils, eosinophils, neutrophils, monocytes, B- and T-cell lymphocytes.

Platelets (thrombocytes) Membrane bound cell fragments in mammals, no nucleus. In non-mammals, platelet role replaced by nucleated cells. Accumulate at site of broken blood vessels, form clots. Bud off special cells in bone marrow. 1-2 micrometers in diameter. 7-8 day life span, 1/10 or 1/20 as abundant as white blood cells.

Arteries: carry blood away from heart. Smallest tubes called arterioles, feed blood to capillaries.

Veins: return blood to heart. Smallest veins called venules.

Structure of arteries and veins, listed from inside (lumen) out:
1. epithelium (endothelium),
2. elastic connective tissue fibers,
3. smooth muscle,
4. connective tissue. Arteries have thicker elastic layer than do veins.

Capillaries, where exchange of materials occurs, are very thin and narrow, and red blood cells pass through single file. Capillaries are tiny but numerous, and their total volume is greater than that of supplying arteries.

Blood velocity drops in capillaries, picks back up in veins. Pressure highest in arteries, lower in capillaries and arteries.

Osmotic pressure draws interstitial fluid from blood in arterioles, but replaces it in venules.

One-way valves mean that blood can flow only one way, works with residual blood pressure and compression by skeletal muscles. Low pressure in thoracic cavity caused by breathing also helps move blood.

Lymphatic system: part of the immune system, a one-way, or open, system. Takes up interstitial fluid not taken up by venules.

Lymphatic structures:
1. lymphatic capillaries
2. lymphatic vesicles
3. lymph nodes
4. lymphatic organs (spleen and thymus)

Lymph: movement in mammals through one-way valves, similar to blood movement in veins. (Some non-mammals have lymphatic hearts of unknown embryonic origin. Frogs and salamanders have several.) Lymph rejoins cardiovascular system into a large vein near the heart via single large thoracic duct.

As lymph passes through system, passes lymphocytes, second part of immune system.

Heart: pumps blood, design varies between animals. In adult mammal,four chambers form two separate circulations
1. pulmonary circulation to and from lungs and
2. systemic circulation to and from tissues of body.

Everything in the heart comes in pairs: 2 atria, 2 ventricles (left and right).

Diagrams usually drawn as though animal were on its back.

Pattern of blood flow through heart: blood returning from major veins (vena cava) enters right atrium, contraction there delivers blood to right ventricle through a tricuspid valve, one of atrial ventricular valves (AV valve). Contraction of right ventricle drives blood through semi lunar valve into pulmonary circuit and to lungs.Blood return to heart in pulmonary veins, is oxygenated. Goes to left atrium, which contracts and delivers blood to left ventricleby way of aortic semi-lunar valve, then goes to systemic circulation.

Both atria and ventricles contract in unison, left is more powerful than right (to all system vs. just lungs).

Systole: heart contraction, diastole: heart relaxed

Timing of heart contraction: ventricles rebound to relaxed shape (diastole), and semi-lunar valves close. Both atria(singular: atrium) fill with blood coming from pulmonary and systemic circulations.Pressure rises in the atria and blood begins to move into the ventricles.The atria then contract, forcing more blood into the ventricles. There is a pause, then ventricles contract. This raises ventricle pressure, atrio-ventricular(AV) valves shut and semi-lunar valves open, forcing blood from the left ventricle into the major arteries and from the right ventricle into the aorta.

Control for this action doesn’t rely on nervous stimulation, has intrinsic rhythmicity, called myogenic. This is the case in mammal as well as in mollusk hearts. Other animals have neurogenic hearts that rely on nervous stimulation for heart action, originating in the cardiac ganglion.

The rhythmicity of mammalian heart relies on the sino-atrial (SA)node, or pacemaker. This is a phylogenic (based on evolutionary history) remnant of an early vertebrate heart that had one more chamber than modern hearts.

How the heart contracts: waves of depolarization start in SA node and spread through atria. Connectile tissue pauses the spread of depolarization at the atrial ventricular node. Signal continued by bundle branches to lower ventricle, begins to stimulate heart to contract. Contraction starts at bottom of heart at heart apex,then signals spread through heart.

Medulla (in the brain) controls autonomic nervous system. (The medulla is part of the brain, is continuous with the spinal cord, and controls involuntary actions of the body). Sympathetic cardiac acceleratorconnects to spinal cord, uses norepinephrine to signal. Parasympathetic cardio-inhibitory center reaches heart through Vagus nerve, usesacetylcholine to signal. Hyperpolarizes membrane to inhibit heart contraction. (Autonomic nervous system: two parts working in contra to control from both sides.) Dominant effect here is inhibitory. If we cut Vagus nerve, heart rate promptly rises about 25 bpm.

Respiratory system

In humans and other animals, for example, the anatomical features of the respiratory system include airways, lungs, and the respiratory muscles.

Other animals, such as insects, have respiratory systems with very simple anatomical features, and in amphibians even the skin plays a vital role in gas exchange.

Plants also have respiratory systems but the directionality of gas exchange can be opposite to that in animals. The respiratory system in plants also includes anatomical features such as holes on the undersides of leaves known as stomata.

In mammals, the diaphragm divides the body cavity into the

  abdominal cavity: contains the viscera (e.g., stomach and intestines)

  thoracic cavity: contains the heart and lungs.

Respiratory tree: terminates in alveolus, alveoli. Respiratory bronchioles branch into alveolar ducts and into alveoli. Alveolus: microscopic air sacs, 300 million of these in human lungs. Total surface area large. Gas diffuses micrometer, very tiny distance. Nervous System

Composed of tissues designed to integrate sensory information and direct a coordinated response to the environment.

Basic unit of the nervous system is the neuron, a highly specialized cell that uses both electrical and chemical processes to communicate. Neurons "listen" to sensory organs or other neurons, and can simultaneously "hear" from 1 to hundreds of inputs simultaneously. Likewise, a neuron can "talk" to other neurons or cells that can create an action, like muscle cells or glands.

Neurons are outnumbered in the nervous system by glia. Glia were once thought to only play a supportive role in helping neurons survive; today we know that they also are important participants in the communication process. Glial cells include astrocytes, ependymal cells, and a cell that has a macrophage like function. There are also oligodendocytes and Schwann cells that provide a myelin sheath.

Neuron structure

Dendrite will receive information from other axons
Stoma is the neuron body and contains typical cell parts including the mitochondria and nucleus. This is where neurotransmitters are synthesized.
Axon hillock is where the cell body and the axon meet.
Axon is surrounded by myelin.
- Contains nodes of Ranvier

Types of axons include unipolar, bipolar, pseudopolar.

Action potentials results from excitatory stimuli received from the dendrites that results in a signal that travels down the axon. On the cellular level, there is a Na+ influx via channels causing a depolarization of the cell. Once those channels close, the slower opening K+ channels will open resulting in hyperpolarization by the cell.

Synapses

Neurotransmitters allow a chemical signal to be sent from one neuron to the other. Neurotransmitters must bypass a physical gap called the synapse. Examples of neurotransmitters include acetylcholine, epinephrine, and glutamate.

Example : Neuromuscular synapses

Circuits / Nuclei / Ganglia

Central nervous system

Central nervous system includes the brain and the spinal cord.

Brain There are four lobes of the brain.

Frontal lobe - decision making
Parietal lobe
Temporal lobe
Occipital lobe - vision

The areas of the brain are also dedicated to different functions.

Precentral gyrus
Postcentral gyrus

Protection The CNS is protected by three layers - the pia mater, the arachnoid mater, and the dura mater. Protection also comes from the circulation of cerebral spinal fluid (CSF). CSF helps to float the brain and also provide nutrients to both the brain and the spinal cord. CSF is synthesized from the choroid plexus of the lateral ventricles. In total, there are four ventricles - 2 lateral ventricles, a 3rd, and 4th ventricle.

Peripheral nervous system

The peripheral nervous system is broken down into two sub-systems, the somatic nervous system and the autonomic nervous system.

ANS - Autonomic Nervous System The ANS has two components - parasympathetic and sympathetic.

The sympathetic nervous system is the "fight or flight" or fright response and results in an increased heart rate, increased rate of breathing, and an elevated blood glucose level. There is also decreased digestion. The second neurotransmitter is epinephrine. In this case, the first neuron is short and the second neuron is long.

The parasympathetic nervous system is the rest and digest system.

Drugs must be able to pass the blood brain barrier to have an effect on the CNS. Drugs act by affecting the neuron and how likely it is to fire an action potential.

Sensory systems

Categorized by

nature of stimulus, such as mechanical, chemicalor light stimulus, and
where stimulus received, such as outside (exteroceptors,such as the eye and skin temp receptors) or insidebody (interoceptors, such as blood body temperature receptors).

Transduction of sensory input into signal. Means to “carry across”, signal transduced, or carried, from environment into nervous signal.

Three sensory processes we cover

taste and smell (chemoreception)
gravity and movement
light

Taste and smell (chemoreception)

Found in mammal nose and mouth, fly feet, fish bodies, moth antennae.

Papilla: bumps on tongue, contain taste buds down between. Sweet, sour, salty and bitter. Some act directly by ion channels, others act indirectly. Other “taste” sensations really smell.

Smell: received in nasopharynx. Airborne molecules go into solution on moist epithelial surface of nasal passage. Approximately 1000 genescode for sensory neuron receptors. “Fried onions” odor not one receptor but a mixture of many odors registered in our mind as one. Very sensitive, habituates rapidly (don’t notice a smell after a bit). Odor sensation has relatively unfiltered root to higher brain centers.

Snakes more chemosensory focused than us.

Response to gravity and movement

Registered in inner ear. Three semicircular canals loop in three planes at right angles to each other, responsible for transduction of movement messages. Method: hair cells deformed by gelatinous membrane. Vestibular apparatus, gives us perception of gravity and movement. Due to physical response, not chemical binding.

Cochlea: bony, coil shaped part of inner ear, where hearing occurs.

Sound enters through auditory canal, vibrates tympanic membrane,moving three bones of middle ear (malleus, incus, and stapes)against oval window opening in front of cochlea. Cochlea has three fluid filled ducts, one of these the organ of Corti. Sound waves in air go to vibration in organ of Corti; fluid tickles hair cells, which register the movement along basilar membrane in cochlea. Different sound frequencies move different portions of basilar membrane. Hearing loss due to loss of hair cells.Humans normally smell more than 300 odors in a day(Facts and Truth).

Transduction of sound accomplished through physical deformation,not chemical binding.

Vision

Light enters pupil, focused by lens onto retina.

Sclera: hardened part behind retina.

Optic nerves and neurons attached to retina. Blind spot where optic nerve attaches, has no receptors.

Two types of photoreceptors

rods - black and white low-light vision, 100 million in each retina in humans.
cones - color vision, work best under better illumination. 3 million in each retina.

Fovia: region of most acute vision, has most of the cones, few rods.

Transduction process of light to signal a molecular change, to light absorbing molecule called photopigment. Located in outer parts of rods and cones in pigment discs. The rod photopigment is called rhodopsin,cone has three photopigments, called photopsins. This molecular change initiates pathways to result in action potential in downstream neuron leading to vision center in brain.Parul Godika

Each of the three photopsins has a different peak of sensitivity: blue,green or red, and changes isometric form (from cisto trans) based on light from a particular wavelength range. Color blindness:inherited lack of one or more types of these cones. Gene carried on X chromosome, therefore more common in men than women.

Homeostasis

Is a very important part of everyone's and everything's lives. Defined as dynamic constancy of internal environment, maintenance of a relatively stable environment inside an organism usually involving feedback regulation.

Homeostasis is maintained in face of

a varying external environment, or
a non-ideal, constant external environment (as with the penguin).

Deals with temperature, pH, chemical concentrations,pressure, oxygen levels.

Occurs through negative feedback loops.

Various forms: simple thermostat in house turns off heater when above a certain temperature and on when below a certain temperature Involves stimulus, sensor,integrating center, effector and response.

More efficient control has two sensors and two effectors. Can be antagonistic to each other, such as, one cools, the other heats.

Precise control through proportional control, not all-or-none, furnace comes on a little bit if the house a bit cold. Examples in humans: vasoconstriction, change in metabolic rate, shivering. Physiological responses for high body temp: blood goes to body surface, sweating, behavioral changes (get out of sun).

Positive feedback loop: effector increases deviation from set point. Amplifies reaction. Like blood clotting process, uterine contraction during childbirth. Negative feedback must exist at some point for control.

Osmotic environments and regulations

Marine invertebrates
1. fully marine invertebrates (not intertidal or estuarine) osmoconformers (set internal environment same as environment, no net flow of ions) in a stenohaline (narrow non-changing salt level) environment
2. Coastal, intertidal, estuarine (ion levels fluctuate) invertebrates.Partly osmoconfomers, partly osmoregulators in a euryhaline (wide salt level variation) environment (ex: shore crab, regulates sometimes when salt levels in environment get real low).
Freshwater animals. Here, environment has lower solute concentrations than do living organisms so water tends to flow in and solutes out.
1. Freshwater fish (bony) dilute urine, and gills actively take up ions (NaCl)
2. Freshwater invertebrates: same situation as freshwater fish but with different structures
3. Freshwater amphibians: active uptake of salts across their skin
Marine fishes: Here the environment has a higher solute concentration than does the organism so water tends to flow out and ions in.
1. Bony fishes: actively secrete salts (NaCl) across gills, absorb water across gut wall, their kidney (unlike mammalian kidney) is unable to generate concentrated urine so glomerulus is reduced, active tubular secretion of MgSO₄
2. cartilaginous fishes (and coelacanth): blood retains urea and trimethylamineoxide to increase its osmolality to that of seawater
Terrestrial animals: here problem is loss of water to a drier environment, and regulation of salt levels.
1. water loss adaptations
2. concentrated exception of salts and nitrogenous wastes

Hypoosmotic: having less osmotic potential than nearby fluid

Hyperosmotic: having more osmotic potential than nearby fluid

Isoosmotic: having equal osmotic potential than nearby fluid

Glomerulus: reduces volume of kidney

Fish started in salt water, spread to fresh water, later reinvaded salt-water environment.

Terrestrial animal water sources:
1. drinking
2. moist foods
3. from breakdown of metabolic molecules like fats. (Desert kangaroo rats get 90% of their water from metabolism.)

Secretion of nitrogenous wastes: from metabolism of amino acids, amino group has to be removed in one of three basically interchangeable chemical forms:
1. ammonia (aquatic life)
2. urea (mammals)
3. uric acid (birds)

Ammonia very toxic, soluble, and cheap to produce. Easy to expel for bony fishes.

Urea: low toxicity, good solubility, more costly to lose as it contains other groups on it. Must be released in solution, water cost.

Uric acid (white part of bird poo) low toxicity, insoluble, secreted with little water loss, more costly side groups lost than the others.

Mammalian kidney: Structure: fist-sized organ in lower back. About 1/5 of blood from aorta at any time is passing through kidneys. Blood passes through kidney many times a day.

Nephron: structural and functional unit of kidney.

Bowmans capsule: funnel-like opening, contains primary filter, the glomerulus.

Proximal convoluted tubule: receives stuff from Bowmans capsule.

Loop of Henle: descends and ascends.

Vasa recta: capillaries that surround the Loop of Henle.

Glomerulus: main filter of the nephron, located within the Bowman's capsule

Kidney properties and processes important to its function

1. Active transport of solutes from one fluid to another against a concentration gradient, Na⁺ actively transported out of filtrate by cells of the thick ascending loop of Henley into the interstitial fluid
2. Passive movement of solutes and water from one fluid to another(down a concentration gradient), movement of water and NaCl out of descending loop of Henley into interstitial fluid.
3. Differential permeability of cells in different regions of the nephron to movement of water and solutes, ascending thick look is impermeable to water, descending portion is permeable to water
4. Hormonal control of that permeability, antidiuretic hormone(ADH) increases permeability of collecting due to water, resulting in reduced volume of filtrate and thus more concentrated urine.
5. Increasing solute concentration in the interstitial fluid of the kidney, from the cortex to the deepest medulla, maintained by a countercurrent multiplier mechanism

Additional material

Francis Crick chemist and molecular biologist, discovered structure of DNA molecule
Charles Darwin the father of the science of evolutionary biology
Richard Dawkins zoologist and biology populariser
Stephen Jay Gould paleontologist and science populariser
J.B.S. Haldane geneticist and evolutionary biologist, founded population genetics and the modern synthesis
Bill Hamilton formulated theory of inclusive fitness and kin selection
Thomas Huxley "Darwin's Bulldog", early evolutionary biologist and science populariser
Lynn Margulis introduced the theory of eukaryotic cell origin through endosymbiosis
Barbara McClintock geneticist and molecular biologist, discovered transposons
Gregor Mendel discovered the basic rules of heredity
Ernst Mayr evolutionary biologist and science populariser
Mark Ridley science populariser
Fred Sanger founder of DNA and protein sequencing techniques
John Maynard Smith evolutionary biologist and science populariser
Alfred Russel Wallace evolutionary biologist
James Watson molecular biologist, discovered structure of DNA molecule
Edward Wilson founded "sociobiology"

This book is intended as a compilation of biographies describing the lives and work of influential biologists.

External Links

EvoWiki: List of Biologists

Glossary

Autotroph: an organism which can make its own energy
Cell: Fundamental structural unit of all living things
Ether:noun

1. CHEMISTRY a pleasant-smelling, colorless, volatile liquid that is highly flammable. It is used as an anesthetic and as a solvent or intermediate in industrial processes. any organic compound with a structure similar to ether, having an oxygen atom linking two alkyl or other organic groups. plural noun: ethers "methyl t -butyl ether"

2. literary the clear sky; the upper regions of air beyond the clouds. "nasty gases and smoke disperse into the ether"

Eukaryote: an organism with a nucleus
Exoenzyme: an enzyme used to break down organic molecules outside the body
Glycerol: noun; a colorless, sweet, viscous liquid formed as a byproduct in soap manufacture. It is used as an emollient and laxative, and for making explosives and antifreeze.
Heterotroph: an organism which can not make its own energy
Hydrocarbon: an organic compound that contains carbon and hydrogen only.
Lipid: fatty acid esters which form the basis of cell membranes
Nucleus: Membrane-bound organelle which contains the chromosomes
Prokaryote: an organism with no nucleus
Seed: noun

1. a flowering plant's unit of reproduction, capable of developing into another such plant. synonyms: pip, stone, kernel; ovule "apple seeds" a quantity of these. "grass seed" the cause or latent beginning of a feeling, process, or condition. "the conversation sowed a tiny seed of doubt in his mind" synonyms: genesis, source, origin, root, starting point, germ, beginnings, potential (for); More archaic (chiefly in biblical use) a person's offspring or descendants. synonyms: descendants, heirs, successors, scions; More a man's semen. a small crystal introduced into a liquid to act as a nucleus for crystallization. noun: seed crystal; plural noun: seed crystals a small container for radioactive material placed in body tissue during radiotherapy. 2. any of a number of stronger competitors in a sports tournament who have been assigned a specified position in an ordered list with the aim of ensuring that they do not play each other in the early rounds. "he knocked the top seed out of the championships" verb verb: seed; 3rd person present: seeds; past tense: seeded; past participle: seeded; gerund or present participle: seeding 1. sow (land) with seeds. "the shoreline is seeded with a special grass" sow (a particular kind of seed) on or in the ground. cause (something) to begin to develop or grow. "severance payouts that help seed their new businesses" place a crystal or crystalline substance in (something) in order to cause crystallization or condensation (especially in a cloud to produce rain). 2. (of a plant) produce or drop seeds. "mulches encourage many plants to seed freely"

Flower: noun

1. the seed-bearing part of a plant, consisting of reproductive organs (stamens and carpels) that are typically surrounded by a brightly colored corolla (petals) and a green calyx (sepals). synonyms: bloom, blossom, floweret, floret "blue flowers" a brightly colored and conspicuous example of the flower of a plant together with its stalk, typically used with others as a decoration or gift. "I stopped to buy Bridget some flowers" the state or period in which a plant's flowers have developed and opened. "the roses were just coming into flower" 2. the finest individuals out of a number of people or things. "the flower of college track athletes" synonyms: best, finest, pick, choice, cream, crème de la crème, elite "the flower of the nation's youth" antonyms: dregs the period of optimum development. "a young policeman in the flower of his life gunned down" verb verb: flower; 3rd person present: flowers; past tense: flowered; past participle: flowered; gerund or present participle: flowering 1. (of a plant) produce flowers; bloom. "these daisies can flower as late as October" induce (a plant) to produce flowers. 2. be in or reach an optimum stage of development; develop fully and richly. "it is there that the theory of deconstruction has flowered most extravagantly"

Tracheid: a type of water-conducting cell in the xylem that lacks perforations in the cell wall.
Haploid: A cell with a single set of chromosomes (23 in humans), in humans this is usually in gametes. This is commonly represented by n.
Diploid: A cell with two sets of chromosomes (46 in humans). This is commonly represented by 2n.
Sporangium: (in ferns and lower plants) a receptacle in which asexual spores are formed.

The majority of the modules making up this book are based on notes very generously donated by Paul Doerder, Ph.D. and Ralph Gibson, Ph.D. both currently of the Cleveland State University.

The book was initiated by Karl Wick, who donated many of his own class notes for other modules, and who is fleshing out the outline format of Dr. Doerder's notes into text.

Users

Alsocal

Darren Hess MD/PhD recent grad, enjoys teaching, hopes to help work up the Nervous System Tissue section.

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Contents

General Biology Textbook

Getting Started

Characteristics of life

Nature of science

Scientific method

Charles Darwin

After Darwin

Challenges to Darwin

References

Mass and isotopes

Electrons

Chemical bonds

Chemical reactions

Hydrogen bonding

References

Stereoisomers

Structure

Function

Hereditary (Genetic) information

RNA DNA origin

References

Properties of life

Origin of life: 3 hypotheses

The early earth

Origin of cells

The RNA world?

The earliest cells

Major steps in evolution of life

References

Cells

Cell structure

Concepts

Structure and function of the cell

Common characteristics of all the cells

History of cell knowledge

Cell Theory

Microscopes

Cell size

Structure of Eukaryotic cells

Structure of the nucleus

Nuclear envelope

Nucleolus

Chromatin

Endoplasmic reticulum

Rough Endoplasmic Reticulum

Smooth Endoplasmic Reticulum

Sarcoplasmic Reticulum

The Golgi apparatus

Ribosomes

DNA-containing organelles

Cytoskeleton

Intermediate Filaments

Actin Filaments

Growth

Biological membranes

Phospholipid

Fluid mosaic model

Membrane proteins

Receptor-mediated endocytosis

Cell-cell interactions

Cell signaling

Types of signaling

Types of signal molecules

Receptor molecules

Cell surface protein

Example: G proteins

Communicating junctions

Gap junctions

Energy

Oxidation–Reduction

NAD+

Free energy

Activation energy

Enzymes

Carbonic anhydrase

Enzyme mechanism

Factors affecting enzyme activity

Cofactors

ATP

NAD⁺

Regeneration of NAD⁺