AP Biology Review Notes

How to Design an Experiment

• Identify the question.
• Identify the tool for measurement (color change, absorbance, movement, specific test).
• Control:
  • Negative control: Should not work (absence of enzyme/substrate/placebo).
  • Positive control: Should work (addition of enzyme/correct temp/absence of inhibitor).
  • Control is required for comparison and identification of significant results.
• Constants in the experiment.
• Analysis of data:
  • Tables
  • Standard error calculation
  • Graphs: Line graph for continuous data; bar graph for discontinuous data.
  • Standard error drawn in the graph ($\pm$ 1 SE or $\pm$ 2 SE)
  • Null hypothesis stated
  • Chi-squared calculations and degree of freedom ($n-1$, where n is the number of variables)
  • Biological systems usually use a p-value of 0.05 unless specified otherwise.
• Results: Stating your analysis
• Discussion: Explaining your analysis of data

Water

• Polar covalent compound
• Hydrogen bonding
• Solvent
• Surface tension: Allows insects to walk on water.
• Cohesion and adhesion: Allows movement of water from roots to leaves.
• Low density of ice: Maintains 4°C below and protects aquatic organisms beneath ice.
• Latent heat of vaporization: Allows evaporative cooling.
• High specific heat: Maintains internal body temperature.

Biomolecules

• Dehydration (condensation): Makes polymer.
• Hydrolysis: Breaks polymer.
• Carbohydrates: CHO; isomers; linear or ring structure; numbering of C atoms is important.
• Glycosidic linkage to form polymers.
• The isomer of monosaccharide and the C atom involved defines the structure and therefore the function of the polymer.
• Starch made of amylose (alpha 1-4 linkage) and amylopectin (branched; alpha 1-4 and alpha 1-6 at the branches).
• Glycogen similar to amylopectin.
• Starch and Glycogen are storage carbohydrates.
• Cellulose: Beta 1-4 linkages; sheet-like structures; protection and supportive role.
• Glycosylation is the addition of carbohydrates to lipids or proteins.
• Transport of glucose into the cell is through secondary active transport or specific protein channels.
• Transport of glucose is regulated, and cells receive a signal to transport glucose.
• Glucose is broken down in the cell through the process of cellular respiration.

Biomolecules - Lipids

• Lipids: CHO, no polymer, fats, steroids, cholesterol, waxes, phospholipids
• Fats made of fatty acids and glycerol through ester linkages
• Saturated fatty acids: single bond- straight chain-increases intermolecular interactions-can be stacked.
• Unsaturated fatty acids: double bond- bends in structure- cis or trans isomer- decreased intermolecular interactions- cannot be stacked.
• Unsaturated lipids have a lower melting temperature than saturated lipids
• Phospholipids: amphipathic-polar head and non-polar tails-assemble into micelles in water.
• Membrane is a phospholipid bilayer-saturated and unsaturated present- fluid ( allows for movement)- mosaic- has proteins ( peripheral or integral).
• Fluidity in bacteria is controlled by switching from unsaturated to saturated and vice versa with respect to changing temperature.
• Fluidity in eukaryotes is controlled by cholesterol.
• Membrane is semi-permeable.
• Proteins present play multiple roles

Biomolecules - Proteins

• Proteins: CHON (Sulfur present in cysteine amino acid)- play multiple roles
• Made of amino acids; R groups (side chains) of amino acid determine if amino acids are charged/polar/non-polar-this can determine interactions
• Amino acids form peptide bonds between the carboxyl group of the 1st amino acid and the amino group of the second amino acid- protein has directionality: N to C
• Sequence of amino acids determined by the gene.
• Primary structure: sequence of aa.
• Protein folds because of interactions that happen within the backbone of amino acids – leads to H bonds (secondary structure) and interactions between R groups (Tertiary structure)
• Types of secondary structure: alpha helix and beta sheets. Some aa have a propensity to form alpha helix and some will form beta sheets, some do not form any.
• Tertiary structure determines final conformation-important for function.
• Changes to amino acids will affect tertiary structure and thereby the function.
• Protein misfolding can lead to decreased functionality.
• The amino acid residues exposed/ surface ones will be involved in interactions with other molecules.
• Some proteins require a quaternary structure- many subunits form a large protein- each subunit may be coded for by the same gene.

Biomolecules - Nucleic Acids

• Nucleic acid: CHONP-monomer-nucleotide- 3 parts: ribose sugar, phosphate, and base
• Polymer-phosphodiester linkages make the sugar-phosphate backbone.
• DNA-deoxyribose sugar, base(A,T,G,C) and phosphate, mostly double-stranded, H-bonds between bases in two strands; antiparallel, has directionality 5’Phosphate and 3’ hydroxyl
• A and T have 2 H bonds, and G and C have 3 H bonds. The melting temperature ($T_m$) is the temperature at which 50% of ds DNA is converted to ss DNA- higher if DNA is rich in G-C sequences
• The sugar-phosphate backbone gives the DNA a negative charge, so it can be separated using gel electrophoresis.
• DNA-binding proteins identify specific sequences on DNA to which they bind.
• DNA gets packaged into higher-order structures. Histones (eukaryotes) and Histone-like proteins (prokaryotes) package the DNA.
• DNA is also methylated at specific sites (CpG islands)-methylation regulates gene expression.
• Restriction enzymes bind to a specific site in DNA and cut the DNA.
• Exonucleases can chew up the DNA either from the 5’ end or 3’ end
• Endonucleases cut the DNA in between

Cell Structure

• Endosymbiotic theory
• Know the function of the different organelles.
• Know the structure of the plasma membrane.
• Know the types of junctions between cells.
• Endomembrane system
• The number of organelles can be different based on the cell’s function.
• Mitochondrial and chloroplast genes are maternally inherited.

Transport

• SA/V ratio high to increase the efficiency of the cell.
• Cells/organelles can increase surface area by folds in the membrane.
• Passive transport- movement with the gradient and no energy required.
• Diffusion- no help required- small nonpolar molecules-temperature and concentration difference can affect the rate of diffusion- specific channels or carrier for specific molecule-rate of diffusion using carrier proteins slower than rate using a channel because the carrier protein has to change conformation.
• Facilitated diffusion- needs protein carrier or channel (for polar molecules)
• Osmosis –movement of water. Depends on water potential.
• Water moves from an area of high water potential to an area of low water potential.
• Water potential is calculated by: $\Psi<em>{system} = \Psi</em>{total} = \Psi<em>s + \Psi</em>p$
• Solute potential = $\Psi_s= -iCRT$ (i= ionization constant) – if more solute, then low water potential.
• Cells control the movement of water by adjusting their solute concentrations.
• Isotonic, hypotonic, and hypertonic solutions (plant cells have a cell wall that leads to turgor pressure-plasmolysis and turgidity in plant cells)
• Guard cells actively transport ions inside the cell to increase solute potential so that water can move in. Once water moves in, they become turgid, and the stomata open.

Transport - Active

• Active transport-movement against the concentration gradient so requires energy.
• Primary transport-protein pumps- uses ATP to move ions/molecules against concentration gradient.
• Uniporters, Symporters, and antiporters
• A mutation in the protein would disrupt transport.
• Disruptions in a cell that affect the production of ATP will have an effect on the active transport mechanism.
• Examples include: Sodium/Potassium ATPase channel moves ions against the gradient, creating an electrochemical gradient.
• Secondary transport- as ions move back across the membrane, they can transport glucose and other molecules against their concentration gradient.

Transport - Bulk

• Bulk transport- endocytosis:
  • phagocytosis,
  • pinocytosis
  • receptor-mediated endocytosis
• Bulk transport-exocytosis.
• Methods of Transport, Energy Requirements, and Types of Material Transported

Cellular Energetics

• All organisms follow the laws of thermodynamics.
• $\Delta G = \Delta H - T\Delta S$; $\Delta G$ is negative- reaction is spontaneous
• Biological system-energy coupling- ATP hydrolysis (ATP hydrolysis spontaneous-energy in the last phosphate bond-if not coupled, energy is lost as heat)
• Endergonic reaction-energy higher in product than in reactants-anabolic reactions
• Exergonic reaction-energy lower in product than in reactants-catabolic reactions.
• Reactants must get over activation barrier to form products- must have enough activation energy.
• Catalysts lower activation energy without changing $\Delta G$.
• Enzymes are catalysts of biological systems

Cellular Energetics - Enzymes

• Enzymes- mostly proteins except for ribozyme (involved in spliceosome complex).
• Highly specific-Induced fit model-site of substrate binding is the active site.
• Enzyme activity curve-can reach a plateau when all substrate is consumed.
• Rate of enzyme reaction-amount of substrate consumed or product formed over time.
• Changes in amino acids that form part of the active site will change enzyme activity.
• Changes in enzyme structure will affect enzyme activity.
• Sites other than active site-Allosteric sites on enzymes- allosteric activators and inhibitors of enzymes
• pH can change the charge on the amino acids and thereby the structure of the enzyme- denaturation.
• Temperature can break bonds and thereby change the structure – denaturation.
• Some enzymes need to be activated-phosphorylation; binding of activator.
• Competitive inhibitors-bind to active site- can overcome inhibition by adding more substrate
• Non-competitive inhibitors- bind to a site other than the active site- cannot be overcome by adding more substrate.
• Enzymes are highly regulated, end-product inhibition; other molecules can also regulate.
• Enzyme compartmentalization benefits
  • Concentration of enzymes.
  • Increased concentration of intermediates through a selectively permeable diffusion barrier.
  • Maintenance of a chemical microenvironment essential for enzymatic function.
  • Protection of enzymes from molecules from deactivators or competitors.
  • Isolation of toxic enzymes of intermediates from the cell.

Cellular Energetics - Respiration

• Cellular respiration-breakdown of glucose to make ATP
• Anaerobic (facultative and obligate) and aerobic cellular respiration
• Anaerobic-Glycolysis and fermentation (lactate or ethanol)
• Aerobic-Glycolysis, Kreb’s cycle (citrate cycle)-oxidative phosphorylation
• Glycolysis- in all organisms-cytoplasm-does not require oxygen- only 2 ATP and 2 NADH ( high energy electron carrier)-end product is pyruvate. ATP generated through substrate-level phosphorylation
• Glycolysis regulation-all irreversible steps are regulated- Hexokinase; Phosphofructokinase; pyruvate kinase are the enzymes that are highly regulated- High levels of ATP, Citrate, Glucose-6-phosphate are inhibitors. AMP and ADP are activators.
• Absence of oxygen-pyruvate converted to lactate( or ethanol) and NADH is oxidized back to NAD. No ATP formed.
• Lactate produced due to hypoxia( low Oxygen levels) is transported by the blood to the liver where it is converted to pyruvate.
• Net gain of anaerobic respiration is only 2 ATP molecules.
• Presence of oxygen-pyruvate converted to acetyl coA-irreversible step –enzyme pyruvate dehydrogenase allosterically regulated.

Cellular Energetics - Aerobic Respiration

• Occurs in mitochondria -some mitochondrial genes code for the proteins that play a role in the Kreb’s cycle and oxidative phosphorylation.
• Kreb’s cycle-mitochondrial matrix-acetyl coA enters the cycle to form citrate- key enzymes are inhibited by ATP, NADH, citrate
• Kreb’s cycle generates NADH, FADH2 (high energy electron carriers), and ATP(GTP)
• NADH and FADH2 go through oxidative phosphorylation to make ATP.
• Oxidative phosphorylation/ETC-mitochondrial membrane- large protein complexes involved in the redox reaction- NAD and FAD are oxidized by complexes while pumping protons (hydrogen ions) into intermembrane space.
• The final electron acceptor is oxygen- Oxygen is reduced to water- if an electron is not transferred to oxygen-oxygen is not consumed.
• Electron transfer-Hydrogen ion (proton) transport- electrochemical gradient created- protons move back in through ATPase -ATP formation.
• If proton gradient disrupted –ATP synthesis affected- increase in pH (low H ions) in intermembrane space- low ATP production
• If no electron transported-no proton gradient created-no ATP –no oxygen consumed.
• Uncouplers- allow hydrogen ions to move back through either pores or act as channels to allow protons back in- uncouple electron transport from ATP synthesis-no ATP but oxygen is consumed. Cells start using fats for energy.
• Uncouplers present in cell are regulated.

Cellular Energetics - Photosynthesis

• Chloroplast-endosymbiosis; maternal inheritance
• Photoautotrophs, chemoautotrophs, water, or other chemical used?
• Conversion of light energy to chemical energy by chlorophyll.
• 2 parts-light dependent and light independent.
• Light-dependent – photosystem 2 and photosystem 1- complexes of chlorophyll molecule and proteins- chlorophyll absorbs red and blue wavelengths of light-activated electrons transfer energy through ETC.
• Photosystem 2- activated electron transported through ETC to PS 1-as electrons transported –H ions are pumped out -creation of chemical gradient-movement of ions back in through ATP synthase –ATP made.
• Lost electrons of PS 2 replaced by photolysis of water to form H ions and oxygen.
• PS 1 activated electrons transferred through ferrodoxin complex to NADP-NADP reduced to NADPH-final electron acceptor in photosynthesis is NADP.
• Change in protein complexes in PS 2 or PS 1 affects light absorption.
• Transfer of electrons from PS 2 to PS 1 to NADP-non-cyclic photophosphorylation
• Cyclic photophosphorylation-some bacteria and sometimes plants-high NADPH levels-PS1 electrons go through ETC to make ATP instead of reducing more NADP.
• The rate of the light-dependent reaction is affected by-wavelength of light; temperature, NADPH levels

Cellular Energetics - Calvin Cycle

• NADPH-high energy electron carrier-glyceraldehyde 3-phosphate-Calvin cycle.
• Carbon dioxide fixation by RUBISCO-first step in the Calvin cycle-rubisco catalyzes the addition of $CO_2$ oxaloacetate to form a 6 C compound that is broken down to a 3 C compound-C 3 plants
• Rubisco-higher affinity for oxygen than $CO_2$ – leads to photorespiration-not useful to make glucose.
• Abiotic factors (high temp/aridity/ high humidity) can affect the rate of photosynthesis-plants overcome this by compartmentalizing-C 4 ($CO<em>2$ fixed to form a 4 C compound) and CAM ($CO</em>2$ fixation at night to form a 4 C compound)-reduces photorespiration by Rubisco by increasing Carbon di oxide presented to Rubisco.
• Biotic factors also control photosynthesis-cell signaling to open stomata

Cell Signaling

• Important for communication between cells- autocrine, paracrine, and endocrine.
• Quorum signaling in bacteria-sensing of the same species as well as other species in the neighborhood.
• Yeast mating factors- alpha and
• Development of the embryo- signaling to form a specific cell type-only certain genes are activated and expressed.
• During growth and other metabolic activities-signal-specific cells (tissue-specific expression)
• Signaling involves-reception-transduction-response
• Reception-hydrophobic signaling molecules- intracellular receptors; polar molecules- cell surface receptors-enzyme linked (tyrosine kinase) or G protein-coupled or ion channel receptors.
• Signal transduction- phosphorylation or second messengers-cAMP; Calcium ion; Inositol phosphate.
• Response-activation of transcription factors; cellular metabolism, cell growth, or cell death/apoptosis
• Termination of signal-phosphatases/degradation of ligands/ phosphodiesterase and calcium pumps.
• The same ligand binding to different receptors can elicit different responses.
• Different ligands binding to different receptors can bring about the same response.
• Mutations that change the receptor or the formation of a second messenger will affect response.
• Chemicals that directly compete for the binding site with a ligand or allosterically affect the receptor will affect the response
• Feedback regulation-negative and positive

Feedback Regulation

• Positive feedback-childbirth and blood clotting

• Idealized Negative Feedback Loop

  • Input: Information
  • sent along afferent
  • pathway to Receptor (sensor)
  • Change detected by receptor
  • Control center
  • Stimulus: Produces change
  • in variable
  • Imbalance
  • Variable (in homeostasis)
  • Imbalance
  • Information sent
  • Output: along efferent
  • pathway to Nerve
  • impulses
  • happen
  • Effector
  • Response of effector feeds
  • back to influence
  • magnitude of stimulus and
  • returns variable
  • to homeostasis

• Positive Feedback Loop-Fruit Ripening

Cell Cycle

• Cell cycle-interphase and mitosis
• Interphase-G1, S (DNA replication), and G2; G 0 is entered by certain cells that are differentiated (nerve cell, cardiac muscle cells) or waiting for a signal to enter G 1
• Cell cycle checkpoints-regulated by cyclin-cdk levels-Cdk (cyclin-dependent kinase) is always present but activated when bound to cyclin-activated cyclin-cdk complex phosphorylates other factors to drive the cell to enter a certain phase.
• Positive regulators-cyclins and cdk; negative regulators-p53, p21 –check for damage to DNA and stop cell from continuing with cell division till damage is fixed.
• Mutations to either positive or negative regulators will affect the cell cycle.
• Mutations to negative regulators-increased division of cells with accumulated mutations-tumors.
• The cell cycle is also regulated by external signals/environmental cues and by contact inhibition
• Cells undergoing uncontrolled division are not restricted by contact inhibition.

Cell Cycle Regulation - Positive and Negative

• Negative regulators act on the positive regulators.
• Examples: Rb, P53, P21, etc

Cell Cycle - Mitosis

• Somatic cells- 2 identical daughter cells with the same number of chromosomes as the parent cell.
• Required for growth and repair
• Regulated by signaling molecules/hormones
• Phases- prophase, metaphase, anaphase, telophase, and cytokinesis.
• Chromosome packaging and segregation are important.
• Non-disjunction when spindle fibers do not attach to kinetochores and separate the chromosomes.
• Factors/chemicals that affect spindle formation can arrest the cell at metaphase.
• Different cells undergo different rates of mitosis.

Cell Cycle - Meiosis

• Meiosis-reduction division-germ cells- 4 non-identical haploid cells (half the number of chromosomes as the parent cell).
• Meiosis 1- prophase 1-crossing over or recombination happens between non-sister chromatids- tetrads are formed, and DNA is exchanged at the chiasmata.
• Meiosis 1- metaphase 1 –random alignment of homologous pairs of chromosomes.
• Meiosis 1- anaphase 1-random segregation of the homologous pairs of chromosomes-leads to some daughter haploid cell getting a mix of maternal and paternal chromosomes.
• Meiosis 2- no interphase before the start of meiosis 2-no crossing over in prophase 2- separation of sister chromatids- results in 4 haploid non-identical cells,
• 4 daughter cells formed have a mix of maternal and paternal chromosomes (because of random segregation) and are not identical to the parent cell because of recombination.
• Some genes that are placed close together on the chromosome are not recombined and are said to be linked-linkage maps are used to determine the placement of genes on the chromosome.
• Non-disjunction of chromosomes either in meiosis 1 or 2 can lead to an unequal distribution of chromosomes to daughter cells.

Mendelian Genetics

• Allele-alternate form of a gene- homozygous recessive; homozygous dominant; heterozygous.
• P –parent generation; F1 (filial/child); true breeding-homozygous recessive or dominant
• Back cross-cross F1 to parent; test cross-cross with homozygous recessive
• Monohybrid ratio (by Mendel’s laws: F1 all heterozygous; F2-3:1 if true breeding parents)- one allele dominant over another
• Dihybrid ratio-true breeding for two different traits-F1 all heterozygous for both traits-F2 at 9:3:3:1- law states that each allele(trait) segregates independently of the other.
• To use probability to determine gametes or genotype- if use word AND- multiply; if use word OR-then add

Non-Mendelian Genetics

• Incomplete dominance- fusion of phenotype (1:2: 1 phenotype ratio)
• Co-dominance- both alleles dominant
• Multiple alleles responsible for a phenotype-sickle cell allele/ blood group
• Homeotic genes- developmental genes
• Pleiotropy-one gene affecting multiple characteristics
• Lethal allele-results in death
• Linked genes –sex-linked genes- autosomal linked genes
• Epistasis-one gene can control the expression of another gene –fur color

Molecular Biology

• Central dogma-DNA to RNA to Protein; RNA virus is the only one to oppose this-RNA to DNA to RNA to protein.
• DNA in prokaryotes is circular; also has extrachromosomal elements such as plasmids.
• DNA in eukaryotes is linear, large, and packaged into euchromatin (loosely packaged-ready for replication and transcription) and heterochromatin
• DNA replication-semi-conservative- directional-5’ to 3’- occurs during S phase.
• DNA replication starts at the origin of replication (one in pro and many in eukaryotes) and is bidirectional
• Basic facts of replication are the same in pro and eu- the enzymes are more complex in eukaryotes.
• DNA polymerase III in prokaryotes needs a primer to provide a 3’ OH end so it can catalyze the formation of a phosphodiester linkage between nucleotides.
• Primase provides DNA pol with an RNA primer to start the synthesis.
• DNA is antiparallel, and synthesis can happen only in the 5’ to 3’ direction, so one strand is continuously synthesized, and the other is discontinuous (Okazaki fragments).
• Order of enzymes-Helicase to unwind-ssb-topoisomerase to release torque behind the replication fork-primase-DNA Pol 111- DNA Pol 1 (checks for error)- ligase.
• DNA pol has high fidelity, i.e., low error
• Termination of replication when the replication forks meet in prokaryotes and in eukaryotes when replication forks collide or when they reach a terminal sequence
• PCR uses the same concept but uses an enzyme that can work at high temp (Taq polymerase) to amplify a segment of DNA

Molecular Biology - Telomeres

• Replication of ends of eukaryotic chromosomes- telomeres.
• Telomeres-repetitive sequences present at the end of chromosomes that play a protective role- they shorten with each round of replication
• Telomeres can be copied only with the help of telomerase
• Telomerase is present only in germ cells and some tumor cells.

Molecular Biology - Transcription

• Making the message from DNA
• RNA polymerase –directional-5’ to 3’ direction-highly regulated.
• RNA pol is not as high fidelity as DNA pol
• Upstream of the gene to be transcribed lies the promoter-the sequence of DNA to which RNA polymerase binds- transcription factors control the binding of RNA pol to the promoter,
• Genes may have more than 1 promoter.
• Transcription-initiation complex including RNA pol-elongation (catalysis of phosphodiester linkage between nucleotides) –termination.
• Prokaryotic transcription happens in the cytoplasm-termination by either rho protein or rho independent termination.
• Prokaryotic transcription is coupled with translation

Molecular Biology - Eukaryotic Transcription

• The nucleus is the site of transcription-directional 5’ to 3’- highly regulated- multiple promoters can be present-enhancers (nucleotide sequences 1000 bp upstream can regulate transcription)
• Termination of transcription by multiple means based on RNA made
• Pre mRNA has both exons (coding regions) and introns (non-coding regions) - has to undergo processing to remove introns-the spliceosome recognizes the beginning and the end sequence of introns and excises it out and splices the exons together. If a mutation in the middle of an intron, it will not affect the protein- if a mutation at the end of the introns, then the intron may not be spliced, and you will have a mutant protein.
• Processing also involves – addition of 5’cap and poly A tail.
• Only mature mRNA leaves the nucleus

Molecular Biology - Translation

• Site of protein synthesis - ribosomes
• 1st amino acid to be added met or f-met
• tRNA has the anticodon-wobble hypothesis-allows a little wobble in terms of pairing of the third nucleotide- allowing multiple codons for the same amino acid.

Molecular Biology - Protein Folding

• Once proteins are made, they fold to form their correct tertiary structure.
• Chaperones exist to help those proteins that cannot fold spontaneously.
• Proteins that need to be glycosylated or further processed are sent to the ER.
• They are recognized by the presence of a signal peptide.

Gene Expression - Prokaryotes

• Operons are present-classic examples-lac operon and trp operon.
• In the absence of tryptophan, the repressor dissociates
  from the operator, and RNA synthesis proceeds.
• When tryptophan is present, the trp repressor binds the operator, and RNA synthesis is blocked.
• Proteins that bind to the operator silence trp expression.

Gene Expression - CAP

• Proteins that bind the promoter in order to activate gene expression
• Proteins that activate or repress transcription Activation/repression depends on the local environment and the needs of the cell.

Gene Expression - Lac Operon

• In the absence of lactose, the lac repressor
  binds to the operator, and transcription is
  blocked.
• In the presence of lactose, the lac repressor
  is released from the operator, and
  transcription proceeds at a slow rate.
• Activation/repression depends on the local
  environment and the
  needs of the cell.
• The inducible operon is exploited in biotechnology. The gene of interest can be cloned downstream of the promoter element of the inducible operon- the expression of the cloned gene can be regulated by the presence or absence of the inducer molecule ( IPTG =similar to lactose)

Gene Expression - Eukaryotes

• Eukaryotic gene expression is more complex than in prokaryotes:
  • Transcription and translation are physically separated.
  • Regulation can occur at many levels.
  • 1st level begins with control of access to the DNA epigenetic regulation - and occurs
  • before transcription begins.
  • Transcription factors are proteins that
  • control the transcription of genetic
  • information from DNA to RNA
• Chemical tags are added to histones and DNA Phosphate, methyl, acetyl groups serve as tags. Tags are not permanent - can be added or removed Acts as signals to tell histones if a region of the chromosome should be open or closed

Gene Expression Eukaryotes

• Epigenetic regulation - "around genetics" temporary
• changes to nuclear proteins and DNA that do not alter
• nucleotide sequence but do alter gene expression
• When nucleosomes are spaced closely together (top), transcription
• factors cannot bind and gene expression is turned off.
• When the nucleosomes are spaced far apart (bottom), the DNA is
• exposed.
• With the DNA exposed,
• transcription factors can bind to it,
• allowing gene expression to occur.
• Methylation of DNA and histones cause nucleosomes
• to pack tightly together, Transcription factors cannot
• bind the DNA, and genes are not expressed
• DEVELOPMENT FROM IN UTERO, CHILDHOOD
• ENVIRONMENTAL CHEMICALS
• DRUGS PHARMACEUTICALS
• AGING
• DIET
• ALTER EXPRESSION OF VARIOUS GENES
• TRANSCRIPTION
• MRNA STABILITY
• TRANSLATION
• EPIGENETIC ACCESSIBILITY
  *. Histone acetylation results in loose packing of nucleo-
  somes. Transcription factors can bind the DNA and genes are expressed.

Gene Expression Eukaryotes Translation

• TRANSLATION IS CONTROLLED BY
• FACTORS THAT BIND THE TRANSLATION INITIATION
• COMPLEX
• When elF-2 is phosphorylated, a conformation change occurs When GTP cannot bind elF-2: Translation cannot occur
• CHEMICAL MODIFICATIONS AFFECT PROTEIN ACTIVITY
• Proteins can be chemically modified - chemicals added or. These chemical changes regulate protein activity or length: Translation cannot occur: 1. Translation controlled by proteins that bind and initiate process (formation of initiation complex). Factors That Bind The Translation Initiation:
• Complex. 1st protein to bind and to these chemical changes regulate protein activity or length to the cell
• When Elfa phosphate cannot to the cell, to the cell

Virus

• VIRUS
• Lytic and lysogenic cycles
• Transduction-variation in bacteria

Bacteria

• Variations in bacteria-mutations; conjugation, and transformation
• Used in biotechnology-can manipulate plasmids-insert gene of choice
• Go through notes about replication, transcription and translation and gene expression.

Biotech Tools

• Reading the DNA code - Sanger dideoxynucleotide sequencing

Biotech Tools - Gel Electrophoresis

• DNA has a negative charge and will move towards a positive pole in an electrical field.
• DNA fragments are loaded into a gel that is electrified.
• The gel acts as a sieve sorting fragments by size.
• Small fragments move more easily through the pores of the gel than do large ones.
• The result is that smaller fragments move faster

Biotech Tools - PCR

• Step 1: denaturing
• Step 2: annealing
• Step 3: synthesizing

Biotech Tools - cDNA Library

• mRNA is used
• collection of cDNA library of actively transcribed genes
  *. White colonies have plasmids with the foreign insert.
• Blue colonies have plasmids without an insert. Molecular Cloning Both foreign DNA and a plasmid are cut with the same restriction enzyme.
• The restriction site occurs only once in the plasmid in the middle of a gene for an enzyme (lacZ). The restriction enzyme leaves
• complementary sticky ends on the foreign DNA fragment and the plasmid. This allows the foreign
• DNA to be inserted into the plasmid
  when the sticky ends anneal. Adding
  DNA ligase reattaches the DNA
  backbones. These are recombinant plasmids.
  Bacteria may take up plasmid with or without the insert, or may not take up plasmid at all.

Evolution

• How is Evolution defined? Change in allele frequency.
• What are the mechanisms of Evolution?
  • Gene flow
  • Genetic drift
  • Natural selection
  • Mutation
• How does variation arise in a population?
• What is Fitness?
• How does Natural selection work?
• Different types of selection.
• How can we predict if a population is evolving?
• What are the factors necessary for a population to be stable and not evolving?

Evolution - Hardy-Weinberg

• What is the Hardy-Weinberg equilibrium and how is it calculated?
• Identify which is p and q. Know what $p^2$ and $q^2$ and $2pq$ mean.
• Know how to use the H-W equation to identify an evolving population.
• Chi-squared analysis using p and q to predict/show factors that can affect a population.
• What are the different pieces of evidence of evolution?
  • Anatomical
  • Analogous structure
  • Homologous structure
  • Vestigeal structures
  • Embryological
  • Fossil
  • Biogeographical
  • Molecular evidence (conserved nucleotide sequence for important genes or conserved amino acid sequence for important proteins)
• Difference between convergent and divergent evolution.
• What are phylogenetic trees?
• How to read and draw a cladogram?

Evolution - Speciation

• Define species.
• How do new species arrive?
• Factors that can lead to speciation.
• Allopatric and Sympatric speciation
• What is Extinction?
• Origin of species-experiment
• How did early earth support the formation of biomolecules?

Ecology

• Animal behavior-Types of communication and reasons for behavior.
  *