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Experimental Design and Biochemistry

  • Helpful Videos and Animations:

    • Bozeman Science: Biological Molecules, tinyurl.com/bmanbiomol
    • Bozeman Science: Nucleic Acids, tinyurl.com/bmannucac
    • Bozeman Science: Lipids, tinyurl.com/bmanlip
    • Bozeman Science: Carbohydrates, tinyurl.com/bmancarb
    • Bozeman Science: Proteins, tinyurl.com/bmanprotein
    • Bozeman Science: Polymers, tinyurl.com/bmanpoly
    • Bozeman Science: Gibbs Free Energy, tinyurl.com/bmangibbs
    • Bozeman Science: Life Requires Free Energy, tinyurl.com/bmanlifereq
    • Bozeman Science: Coupled Reactions, tinyurl.com/bmancoupled
    • Bozeman Science: Enzymes, tinyurl.com/bmanenzyme

  • Relevant Objectives:

    • Difference between monomer and polymer.
    • Name the four main classes of macromolecules and their monomers.
    • Describe dehydration synthesis and hydrolysis reactions.
    • Explain the properties of water and why they are essential to life.
    • Describe the levels of protein structure.
    • Explain the difference between polar and nonpolar molecules.
    • Know and explain the steps of the scientific method.
    • Know the components of a valid experiment.
    • Explain the function of an enzyme and describe how an enzyme works.
    • Explain factors influencing enzyme activity.
    • Determine the rate of an enzyme catalyzed reaction from a graph or data table and compare and contrast rates.
    • Explain how activators and inhibitors affect enzyme activity.
    • Differentiate between different types of inhibitors – competitive, noncompetitive.

  • Basic Background Information:

    • Experimental Design:
      • Control group: Baseline for comparison.
      • Independent variable: Manipulated/changed by researcher.
      • Dependent variable: Effect being measured.
    • CHNOPS: Most common elements in living matter.
    • Bonds:
      • Ionic: Transfer electrons.
      • Covalent: Sharing electrons.
        • Polar: Unequal sharing.
        • Non-polar: Equal sharing.
      • Hydrogen: Weak bonds between hydrogen and negatively charged items.
      • Hydrophobic interactions: Non-polar compounds congregate together (lipids).
    • pH:
      • Acid-base scale: 0-14, determined by # of H ions; logarithmic.
      • Example: pH 3 = 10^{-3} = 1/1000.
      • Blood: 7.4, Stomach: 2, Small intestine: 8. Enzymes are specific to pH.
    • Water properties:
      • Polarity, cohesion, adhesion, low density when frozen, versatile solvent, high heat of fusion/vaporization, surface tension.

  • Organic molecules:

    • Monomers are simplest form; join via dehydration synthesis (loss of water) to make polymers.
    • Polymers broken down via hydrolysis (input of water).
      • A. Carbohydrates- CHO 1:2:1 ratio, monomer = monosaccharides, 2 = disaccharides, 3 or more = polysaccharides
        • Used for energy (cell respiration)
        • Examples
          • glucose- immediate energy to make ATP
          • starch- stored energy in plants
          • glycogen- stored energy in animals (stored in liver)
          • cellulose- plant cell wall
      • B. Lipids – C, H, O (not a 1:2:1 ratio) *P only in phospholipids
        • fats, waxes, oils and sterols
        • Saturated fats have single bonds between carbons, unsaturated fats have at least one double bond between carbons (kinky); plants make polyunsaturated; animals make monounsaturated
        • Phospholipids make up cell membranes (double layer) and are amphipathic- hydrophilic and hydrophobic
        • Uses- in all membranes; stored energy, protection, insulation, myelin sheath of nerves
      • C. Proteins- C, H, O, N (may have other elements in R group)
        • Monomer- amino acids (20 total types), 2=dipeptide, 3 or more= polypeptide
        • Parts of amino acid= carboxyl group (COOH) on one end, amino group on the other end (NH2), central carbon and variable R group (can be hydrophobic or hydrophilic) which determines chemical properties.
        • Protein Folding- shape determines function; primary= a.a. chain; secondary= beta pleated sheet or alpha helix( hydrogen bonds); tertiary=globular; folds in on itself (disulfide bridges, hydrogen bonds, hydrophobic interactions; ionic bonding); quartenary= more than one polypeptide.
        • Uses- protein carriers in cell membrane, antibodies, hemoglobin, enzymes, most hormones
      • D. Nucleic acids – C, H, O, N
        • Monomer= nucleotide, 2 = dinucleotide, 2 or more polynucleotide
        • Nucleotide made up of sugar, phosphate and base.
        • Used to store genetic information
        • DNA is double stranded, has deoxyribose, A, G, C, T.
        • RNA is single stranded, has ribose, A, G, C, U
        • mRNA- copies genetic message; rRNA- attaches mRNA and makes up ribosomes (most common);tRNA- carries amino acids; DNA- carries genetic code

  • Enzymes

    • Biological catalysts (made of protein) speed up rate of chemical reactions by lowering activation energy required for reaction.
    • Enzyme has active site (exposed R groups) where reaction occurs.
    • Enzymes can break down (catabolic) or build up (anabolic) substances.
    • Enzyme/substrate complex is formed.
    • Substrate is what enzyme acts on.
    • Rate is determined by collisions between substrate and enzyme.
    • Ends in –ase, named after substrate often.
    • Enzyme is specific to substrate; substrate must be complementary to surface properties (shape and charge) of active site (made up of R groups with specific chemistry, i.e. hydrophobic).
    • Enzyme rate affected by:
      • pH (optimal for each enzyme).
      • Temperature (optimal for each enzyme but increased temperature increases collisions so rate goes up initially; too much heat can denature enzyme).
      • Enzyme concentration (more enzyme faster rate or vice versa).
      • Substrate concentration (more substrate faster rate; vmax is fastest enzyme can work when saturated).
    • Inhibition
      • Competitive inhibition: Something competes for active site; overcome with more substrate.
      • Non-competitive inhibition: Attaches at allosteric site, changes enzyme shape so it is not functional; can not be overcome with more substrate.

Cells

  • Cell Types:
    • Prokaryotic (Bacteria)
      • No membrane-bound organelles
      • No nucleus (single; circular DNA)
      • Free ribosomes and cell wall
    • Eukaryotic (all other living things)
      • Membrane-bound organelles, ex. Chloroplasts and nucleus
      • Multiple linear DNA
      • Histones on DNA
  • Cell organelles
    • Nucleus- holds DNA and nucleolus(where ribosomal subunits are made)
    • Mitochondria- double membrane; outer is smooth and inside is folded with enzymes to make ATP (site of cellular respiration (glucose breakdown)
    • Ribosome- site of translation- protein synthesis; made of rRNA and protein
    • E.R.- connected to nucleus; allows for reactions, membranous; smooth= lipids; rough=proteins
    • Golgi complex- packaging in membrane and signals for export
    • Cytoskeleton: Microfilaments- contractile protein, gives shape, movement within cell; Microtubules- centrioles, cilia, flagella, spindle fibers
    • vacuoles/vesicles- water and solutes; large and central in plants
    • ANIMAL
      • Lysosomes- contain enzymes; used for intracellular digestion and apoptosis
      • Centrioles- used in cell division
    • PLANT
      • Chloroplast- double membrane; site of photosynthesis (glucose synthesis)
      • Cell wall- middle lamella- pectin; primary cell wall- cellulose; secondary cell wall- lignin
    • Endosymbiont theory- all eukaryotic cells came from bacterial cells that lived together; proof= all chloroplasts and mitochondria have own DNA and are autonomous
  • Cell membrane (separates the internal environment of cell from external environment).
    • Phospholipid bilayer (selectively permeable; amphipathic)
    • Fluid mosaic model (in motion; proteins, cholesterol, glycoproteins and glycolipids among phospholipids). Membrane is hydrophilic on inside and outside, hydrophobic within membrane
    • Simple diffusion- from high to low concentration- small and uncharged move freely through phospholipids ex. CO2, O2 (passive; no energy; no protein carrier)
    • Facilitated diffusion- large or charged from high to low, passive; with protein carrier: ex. glucose, K+
    • Active transport- from low to high concentration; uses ATP; uses a protein
    • Endocytosis- phagocytosis (solid) and pinocytosis (liquid); membrane surrounds and forms vesicles; receptor mediated endocytosis has receptors on surface
    • Exocytosis- release of material using vesicles fusing with membrane
    • Osmosis- diffusion of water using a selectively permeable membrane; passive; no proteins
    • Water potential= pressure potential plus pressure potential; water moves from high water potential to low water potential; solutes always lower water potential; pressure can increase or decrease depending on if it is negative or positive.
    • Plant cells have pressure related to cell wall and vacuole; turgor pressure
    • Hypertonic (high solute), hypotonic (low solute), and isotonic solutions(equal concentration)
    • High surface area : volume ratio increases rate at which food can be taken in a waste expelled
  • Nervous System
    • function: sensory input, motor function, regulation
    • structure: neuron, axon, dendrites, synapse
    • Polarized neuron: Na+ outside, K+ and Cl- inside
    • Depolarization moves Na into neuron, generating an action potential
    • Repolarization exchanges Na+ and K+ through the sodium-potassium pump
    • At synapse, calcium channels open to allow calcium to rush in, stimulating release of neurotransmitters
    • Neurotransmitters released into synapse to generate action potential for motor neuron or muscle cell

Energy and Metabolism

  • Energy
    • Organisms use free energy for organization, growth, and reproduction. Loss of order or free energy flow results in death.
    • More free energy (ex. Food) than needed stored for growth (roots, glycogen, fat, etc.).
    • Matter and energy are not created but change form (1st law of thermo, ex. Sun energy to bond energy in glucose) and entropy is increasing in disorganization of energy (i.e. heat released by cell respiration). More organized or built up compounds have more free energy and less entropy (i.e. glucose) and less organized have less free energy and more entropy (i.e. carbon dioxide).
    • Reactions can be coupled to maintain a system, ex. Photosynthesis and cell respiration
  • Cellular respiration C6H{12}O6 + 6O2 \rightarrow 6CO2 + 6H2O
    • Makes ATP for cell use; uses glucose and oxygen makes waste products of carbon dioxide and water; occurs in mitochondria; NADH is electron carrier used
    • Glycolysis
      • occurs in cytoplasm; anaerobic
      • rearranges the bonds in glucose molecules, releasing free energy to form ATP from ADP through substrate-level phosphorylation resulting in the production of pyruvate.
    • Kreb’s cycle
      • occurs in mitochondrial matrix
      • also called the citric acid cycle
      • occurs twice per molecule of glucose
      • Pyruvate is oxidized further and carbon dioxide is released ; ATP is synthesized from ADP and inorganic phosphate via substrate level phosphorylation and electrons are captured by coenzymes (NAD+ and FAD).
      • NADH and FADH2 carry electrons to the electron transport chain.
    • Electron Transport Chain and Chemiosmosis
      • The electron transport chain captures electrons, pumping H+ ions into the inter- membrane space of the mitochondria.
      • Electrons are accepted by O2 molecule forming H2O
      • Concentration of H+ builds up within inter-membrane space lowering the pH and ions rush through ATP synthase into the mitochondria matrix. Rush of ions “spins” ATP synthase protein, causing ADP and Pi to join forming ATP by oxidative phosphorylation
  • Photosynthesis 6CO2 + 6H2O \rightarrow C6H{12}O6 + 6O2
    • Photosynthetic organisms capture free energy present in sunlight and use water and carbon dioxide to make carbon products and free oxygen.
    • Light-dependent reactions- photophosphorylation
      • Photosystems I and II (chlorophyll and proteins) are embedded in the internal membranes of chloroplasts (thylakoids of the grana). They pass electrons through an electron transport chain (ETC). When electrons are passed they allow hydrogen ions (protons) across the thykaloid membrane. The formation of the proton gradient powers the process of ATP synthesis to add a phosphate ADP to ATP (chemiosmosis).
      • Electrons are passed to NADP+ to make NADPH (electron carrier)
      • H2O is used and O2 released as by-product
      • Red and blue light works best (green is reflected typically)
      • Energy converted from sun into chemical energy of ATP and NADPH to be used in building of sugar (Calvin Cycle)
    • Light-independent reactions- Calvin Cycle
      • carbon fixation occurs (carbons of CO2 used to make sugar)
      • occurs in stroma of chloroplasts
      • ATP and NADPH generated by light-dependent reactions are used to assemble glucose
  • Anaerobic Fermentation
    • No oxygen; cell only goes through glycolysis followed by fermentation
    • Fermentation recycles NAD needed to restart glycolysis
    • alcohol fermentation ex. yeast cells- glucose → ethyl alcohol + CO2+ NAD+
    • lactic acid fermentation ex. muscle cells- glucose → lactic acid + NAD+
    • Fermentation does not make ATP but glycolysis does- 2ATP; very inefficient; sufficient for microorganisms

The Cell Cycle and Heredity

  • Cell cycle
    • Reason for division- as cells increase in volume, the surface area decreases and demand for material resources increases which limits cell size
    • Smaller cells have a more favorable surface area-to-volume ratio for exchange of materials with the environment (diffusion, etc.). High SA:V ratio is favorable. Ex. 6:1 is better than 6:5
    • Cell cycle switches between interphase and cell division.
    • Interphase has three phases: growth (G1), synthesis of DNA (S) and preparation for mitosis (G2).
    • During mitosis duplicated chromosomes line up in center with spindle fibers attached to help pull them apart. Duplicated chromosomes are pulled apart by spindle fibers.
    • Cytokinesis-division of cytoplasm and reformation of cell membrane. Animal cell- pinches in (cleavage) using microfilaments; plant cell- form cell plate reforms cell wall.
    • The cell cycle is directed by internal controls or checkpoints. Internal (enzymes and promoting factors) and external signals (growth factors) provide stop and- go signs at the checkpoints. Ex. Mitosis-promoting factor (MPF)
    • Cancer results from disruptions in cell cycle control (too much division, defective tumor suppressor genes, overactive genes) which are a result of DNA damage to proto- oncogenes (regulatory genes) which make products like cyclins and cyclin-dependent kinases.
    • Cells spend different amounts of time in interphase or division. Nondividing cells may exit the cell cycle; or hold at a particular stage in the cell cycle.
    • Mitosis is used for growth and repair in animals; plants use mitosis to make gametes and for growth or repair.
    • Mitosis usually begins with 1 cell, makes 2 identical cells or clones; maintains chromosome number; 1n→1n or 2n→2n.
    • Meiosis (occurs after interphase) takes diploid cells and reduces the chromosome number to haploid. 2n→1n.
    • During meiosis, homologous chromosomes are paired (one from mom and one from dad) and line up in the center of the cell randomly. The homologues are pulled apart and separated in meiosis I. A second division occurs in which the duplicated chromosomes are pulled apart.
    • Variation occurs in gametes during “crossing over,” and fertilization because of all possible combinations of homologous chromosomes aligning during metaphase I.
  • Mendel’s Laws (remember he laid groundwork for genetics but these rules can all be broken looking at chromosome theory and molecular genetics)
    • Law of Dominance- one allele will be expressed over another (ex. Aa – if big A is purple it will be seen over little a which is white)
    • Law of Segregation- alleles pairs separate from each other during meiosis
    • Law of Independent Assortment- alleles assort independently during meiosis IF they are on separate chromosomes (i.e. AaBb can make gametes AB, Ab, aB or ab)
  • Probability, Patterns and Exceptions to Mendel’s Rules
    • product rule- multiply chance of one event happening by the chance of another event happening to get the chance of both events occurring together
    • autosomal vs. sex-linked (on the X or Y chromosome)
    • monohybrid cross; one trait; 3:1 (Aa x Aa); 1:1 (Aa x aa) or 4:1 (AA x_), (aa x aa)
    • dihybrid cross; 9:3:3:1 genotype (AaBb x AaBb) or test cross 1:1:1:1(AaBb x aabb)
    • Thomas Hunt Morgan- fruit flies, X- linked traits
      • male- heterozygous XY; Y chromosome is very small in mammals and fruit flies with few genes
      • female- homozygous XX
      • single gene mutations on X chromosome cause disease such as hemophilia or colorblindness
      • sex limited traits are dependent on sex of individual like milk production or male patterned baldness
    • incomplete dominance- red X white → pink; both protein product are expressed and blended
    • codominance- red x white → red and white; both protein products are equally expressed ex.AB blood types
    • epistasis- one gene affects expression of another
    • linked genes- genes on same chromosome that are inherited together (can be unlinked by crossing over); recombination frequency calculated by recombinants/total; used for chromosome mapping; genes further apart cross over more often
    • gene/environment- phenotypes affect by environment, Siamese cat, flower color with soil pH, seasonal color in arctic animals, human height and weight
    • polygenic- continuous variation, many genes affect one trait- height, color
  • Human Genetics
    • karyotype- 22 pair autosomes & 1 pair sex chromosomes + 46 total chromosomes
    • Chromosomal Mutations (occur during gamete formation)
      • deletion, inversion, addition of genes as a result of crossing over mistakes
      • chromosomal number abnormalities → nondisjunction is failure of chromosomes to separate at anaphase of meiosis

Molecular Genetics

  • DNA Structure
    • Discovery
      • Avery-MacLeod- Marty- 1944 isolated DNA from Griffith’s transformation experiment
      • Hershey-Chase- 1952 elegant experiment with virus and bacteria showing DNA was injected not protein
      • Watson, Crick, Wilkins, and Franklin- 1953 W and C published work showing structure of DNA (used Wilkins and Franklins work to do so)
    • Structure of DNA
      • Deoxyribose nucleic acid
      • Double helix (two twisted strands) made of nucleotides (monomers)
      • Nucleotide = phosphate + 5C deoxyribose sugar + nitrogen base
      • Antiparallel strands- one runs 3’ to 5’ the other runs 5’ to 3’,sides of phosphates and sugars (backbone), rungs of paired bases with hydrogen bonds in between
      • Purines (adenine,guanine; double rings) pair with Pyrimidines (cytosine, uracil, thymine; single ring)
      • A - T- double H bond
      • C – G- triple H bond
    • Location
      • In eukaryotes DNA is found in nucleus on multiple linear chromosomes (a chromosome IS a strand of DNA with proteins etc. associated).
      • In prokaryotes DNA is not in a nucleus and is usually a single circular chromosome
      • Prokaryotes, viruses, and eukaryotes (yeast) can contain plasmids (small extra- chromosomal DNA that is double stranded DNA)
  • DNA replication
    • Process of making exact copies of DNA (i.e. for mitosis or meiosis)
    • Process is semi conservative (original strand is copied)
    • Steps
      • Enzyme (helicase) unzip strands by breaking hydrogen bonds
      • “Spare” nucleotides are added bidirectionally to bond complementarily with use of DNA polymerases (DNA pol)
      • DNA pol only can add to the 3’ to 5’ side and new DNA is made in the 5’ to 3’direction
      • Replication bubbles open up and a replication fork is created because bubble is in half and it has one side 3/5 and one 5/3
      • RNA primers must be laid down to start process (RNA primase makes primers)
      • Leading strand makes DNA continuously (3/5)
      • Lagging strand makes DNA discontinuously (5/3), Okazaki fragments
      • Lagging strand requires enzyme (ligase) to fuse fragments
  • RNA
    • Ribonucleic acid
    • Single stranded, different sugar called ribose, different base called uracil INSTEAD of thymine
    • Base pair rules in RNA, A-U and C-G
    • messenger RNA or mRNA carries information from DNA to the ribosome
    • transfer RNA or tRNA bind amino acids and are used in translation at ribosome
    • ribosomal RNA or rRNA are part of ribosomes that have catalytic function
    • RNAi are molucules that are used for regulation of gene expression (turn on or off)
  • Transcription
    • making mRNA in nucleus
    • enzyme RNA pol reads the DNA in 3’ to 5’ direction and synthesizes complementary mRNA
    • Ex. 3’ to 5’ DNA is ATG CAT then the 5’ to 3’ mRNA made will be UAC GUA
    • Steps
      • TATA Box where RNA pol binds and begins
      • Transcription Factors (proteins that enhance transcription and help RNA pol into correct shape)
      • Elongation (adding of RNA nucleotides- does not stay attached to DNA)
      • Termination, ends when RNA pol reaches a termination sequence
  • mRNA editing
    • introns are excised (cut out)
    • exons are left and spliced together using spliceosomes (snRNP’s)
    • add polyA tail to 3’
    • add GTP cap to 5’
    • each 3 are called a codon
    • go to ribosome (free or in RER)
  • Translation
    • mRNA code is read and matched with tRNA (brings amino acids) to construct a polypeptide using the ribosome
    • Ex. mRNA codon is AAA then tRNA anticodon will be UUU and will have a corresponding amino acid for that codon of mRNA
    • Initiation: 5’ end of mRNA attaches to small ribosome, tRNA with anticodon UAC attaches to start codon AUG ; large ribosomal subunit binds and tRNA is in P site
    • Elongation: new tRNA enters A site; peptide bond forms when a.a. is transferred from tRNA in P site to A site; translocation occurs and tRNA in A site moves to P
    • Termination: Ribosome encounters stop codon (UAA, UAG, UGA)
    • If in ER then: polypeptide is released into ER, then to Golgi complex, vesicle to cell membrane, then exocytosis (may be given signals for exit/destination)
    • Free ribosomes typically make products for the cell and are not exported
  • Mutations
    • any change of DNA sequence, can be inheritable if it is in egg or sperm
    • point mutations- one nucleotide error; substitutions (i.e. A instead of G)
    • frame shift mutations- one or more bases deleted or inserted
    • silent mutations can occur, i.e. substitution codes for same a.a. or deletion/insertion is of three nucleotides

Regulation

  • Feedback
    • Negative feedback mechanisms maintain dynamic homeostasis for a particular condition (variable) by regulating physiological processes, returning the changing condition back to its target set point.
    • Positive feedback mechanisms amplify responses and processes in biological organisms. The condition initiating the response is moved farther away from the initial set-point. Amplification occurs when the stimulus is further activated which, in turn, initiates an additional response that produces system change.
  • Cell-to-cell communication
    • Cells receive or send inhibitory or stimulatory signals from other cells, organisms or the environment.
    • In single-celled organisms, it is response to its environment.
    • In multicellular organisms, signal transduction pathways coordinate the activities within individual cells. Ex. Epinephrine stimulation of glycogen breakdown in mammals
    • Cells communicate by cell-to-cell contact. Ex Immune cells interact by cell-cell contact, antigen- presenting cells (APCs), helper T-cells and killer T cells or plasmodesmata between plant cells that allow material to be transported from cell to cell.
    • Cells communicate over short distances by using local regulators that target cells in the vicinity of the emitting cell. Ex. Neurotransmitters, plant immune response
    • Signals released by one cell type can travel long distances to target cells of another cell type. Ex. Hormones
    • A receptor protein recognizes signal molecules, causing the receptor protein’s shape to change, which initiates transduction of the signal. Ex. G-protein linked receptors, ligand- gated ion channels, tyrosine kinase receptors.
    • Signal transduction is the process by which a signal is converted to a cellular response. Signaling cascades relay signals from receptors to cell targets, often amplifying the incoming signals, with the result of appropriate responses by the cell.
    • Second messengers inside of cells are often essential to the function of the cascade.
    • Many signal transduction pathways include: Protein modifications or phosphorylation cascades in which a series of protein kinases add a phosphate group to the next protein in the cascade sequence.
  • Gene Regulation
    • Prokaryotes
      • Inducers (turn genes on) and repressors (turn genes off) are small molecules that interact with regulatory proteins and/or regulatory sequences.
      • Regulatory proteins inhibit gene expression by binding to DNA and blocking transcription (negative control).
      • Regulatory proteins stimulate gene expression by binding to DNA and stimulating transcription (positive control) or binding to repressors to inactivate repressor function.
    • Eukaryotes
      • Transcription factors bind to DNA sequences and other regulatory proteins
      • Some of these transcription factors are activators (increase expression), while others are repressors (decrease expression).
      • The combination of transcription factors binding to the regulatory regions at any one time determines how much, if any, of the gene product will be produced.
  • Immunity
    • Plants, invertebrates and vertebrates have multiple, nonspecific immune responses, ex: phagocytes engulf and digest pathogens with the help of lysosomes
    • Mammals use specific immune responses triggered by natural or artificial agents that disrupt dynamic homeostasis.
      • The mammalian immune system includes two types of specific responses: cell mediated and humoral.
      • In the cell-mediated response, cytotoxic T cells, a type of lymphocytic white blood cell, target‖intracellular pathogens when antigens are displayed on the outside of the cells.
      • In the humoral response, B cells, a type of lymphocytic white blood cell, produce antibodies against specific antigens.
      • Antigens are recognized by antibodies to the antigen.
      • Antibodies are proteins produced by B cells, and each antibody is specific to a particular antigen.
      • A second exposure to an antigen results in a more rapid and enhanced immune response.
  • Viruses
    • Replication
      • Viruses inject DNA or RNA into host cell
      • Viruses have highly efficient replicative capabilities that allow for rapid evolution
      • Viruses replicate via the lytic cycle, allowing one virus to produce many progeny simultaneously
      • Virus replication allows for mutations to occur through usual host pathways.
      • RNA viruses lack replication error-checking mechanisms, and thus have higher rates of mutation.
      • Related viruses can combine/recombine information if they infect the same host cell.
      • Some viruses are able to integrate into the host DNA and establish a latent (lysogenic) infection
      • HIV is a well-studied system where the rapid evolution of a virus within the host contributes to the pathogenicity of viral infection.
      • Genetic information in retroviruses is a special case and has an alternate flow of information: from RNA to DNA, made possible by reverse transcriptase, an enzyme that copies the viral RNA genome into DNA. This DNA integrates into the host genome and becomes transcribed and translated for the assembly of new viral progeny.

Evolution

  • Natural Selection
    • Major mechanism of change over time – Darwin’s theory of evolution
    • There is variation among phenotypes – genetic mutations play a role in increasing variation
    • Competition for resources results in differential survival, with individuals with the most favorable traits surviving to reproduce offspring
    • An adaptation is a genetic variation that is favored by selection and is manifested as a trait that provides an advantage to an organism in a particular environment.
    • Fitness is the ability to survive and reproduce
  • Hardy-Weinberg Equilibrium
    • A mathematical model used to calculate changes in allele frequency, providing evidence for the occurrence of evolution in a population.
    • 5 conditions must be met for a population to be in HW equilibrium – conditions are seldom met
      • Large population
      • No migration
      • No mutations
      • Random mating
      • No natural selection
    • Equations
      • p = the frequency of dominant alleles in a population
      • q = the frequency of recessive alleles in a population
      • p^2 = the frequency of homozygous dominant individuals in a population
      • q^2 = the frequency of homozygous recessive individuals in a population
      • 2pq=the frequency of heterozygous individuals in a population
      • p + q = 1
      • p^2 + 2pq + q^2 = 1
  • Speciation
    • An evolutionary process by which 2 or more species arise from 1 species and 2 new species can no longer breed and reproduce successfully
    • Many mechanisms by which it can occur
      • Geographic isolation
        • Species separated by physical barrier
      • Reproductive isolation
        • Different behaviors limit mating
        • Different habitats limit mating
        • Different mating seasons limit mating
        • Different anatomical structures limit mating
    • Can take place over millions of years or rapidly (after extinction events, for example)
  • Evidence for Evolution
    • Fossils can be dated by a variety of methods that provide evidence for evolution. These include the age of the rocks where a fossil is found, the rate of decay of isotopes including carbon-14, the relationships within phylogenetic trees, and the mathematical calculations that take into account information from chemical properties and/or geographical data.
    • Morphological homologies represent features shared by common ancestry. Vestigial structures are remnants of functional structures, which can be compared to fossils and provide evidence for evolution.
    • Biochemical and genetic similarities, in particular DNA nucleotide and protein sequences, provide evidence for evolution and ancestry.
  • Origin of Life
    • Primitive Earth provided inorganic precursors from which organic molecules could have been synthesized due to the presence of available free energy and the absence of a significant quantity of oxygen.
    • Chemical experiments have shown that it is possible to form complex organic molecules from inorganic molecules in the absence of life.
    • These complex reaction sets could have occurred in solution (organic soup model) or as reactions on solid reactive surfaces.
    • The RNA World hypothesis proposes that RNA could have been the earliest genetic material.
  • Phylogenetic Trees
    • Phylogenetic trees and cladograms can represent traits that are either derived or lost due to evolution.
    • Phylogenetic trees and cladograms illustrate speciation that has occurred, in that relatedness of any two groups on the tree is shown by how recently two groups had a common ancestor.
    • Phylogenetic trees and cladograms can be constructed from morphological similarities of living or fossil species, and from DNA and protein sequence similarities.
    • Phylogenetic trees and cladograms are dynamic, constantly changing due to current and emerging knowledge.

Ecology

  • Populations
    • group of individuals of same species living in same area (size, density, distribution/dispersion)
    • habitat (type of area organism lives) vs. niche (role in ecosystem)
    • competition for resources
    • age structure (rapid growth vs. declining vs. stable populations)
    • population growth
      • density dependent limiting factors (competition for resources, parasites & diseases, waste products, stress, predation)
      • density independent limiting factors (climate = temperature & rainfall, natural disaster)
      • exponential growth (J-shaped, unlimited) vs. logistic growth curve (S-shaped, limited)
      • carrying capacity = maximum population supported by habitat
      • populations can cycle
    • Population ability to respond to changes in the environment is affected by genetic diversity. Species and populations with little genetic diversity are at risk for extinction.
  • Communities
    • measured and described in terms of species composition and species diversity
    • symbiosis = species interaction
      • mutualism +/+ (acacia tree & ants; lichens, N-fixing bacteria & legume plants)
      • commensalism +/0 (egrets & cattle)
      • parasitism +/– (tapeworm, cowbird)
      • predation +/– (carnivores &