AP Biology Midterm Review Sheet Diagrams

2 - Biochemistry

· What are the life processes?

· What causes the different types of bonds (Nonpolar Covalent, Polar Covalent, Ionic, Hydrogen)?

· Electronegativity

· Mass # = protons + neutrons

· Atomic # = protons

· Protons (mass, +1, nucleus), neutron (mass, +0, nucleus), electron (no mass, -1, orbitals, valence e- involved in bonds)

Description: 04_04OrganicValences_L.jpg

Description: 02-12-CovalentBonding-L.gif

Description: 02-14-IonicBonding-L.gif

3 – Water -

· What types of bonds do you find within a water molecule? “ “ “ between water molecules?

· What atom in water is very electronegative?

· Properties: excellent solvent, high heat capacity—moderating influence, evaporative cooling, ice floats, strong cohesion & surface tension, strong adhesion

· PH scale 0-14 acid = 0-(7) high [H+], low [OH-] neutral = 7 base (7)-14, low [H+], high [OH-]

Description: 02-13-PolarBond-L.gif

Description: 03-01-WaterMolecules-L.gif

Description: 03_08pHScale_L.jpg

4 – Carbon / Organic Molecules

· What are some properties of the carbon (organic) atom?

· Functional Groups: structural formulas, properties, and examples of molecules they are found in:

o Amino, central carbonyl, terminal carbonyl, carboxyl, hydroxyl, methyl, phosphate, sulfhydryl

· Isomers = same number of atoms, different properties

Description: 04T-01-OrganicCompounds-L.gif

Description: 04-06-OrganicIsomers-L.gif

5- Macromolecules

· What is the difference between dehydration/condensation synthesis and hydrolysis?

o C6H12O6 + C6H12O6 = C12H22O11 (disaccharide) + H2O

· Know macromolecule monomers vs. polymers, bonds, and examples:

o Carbohydrates: monosaccharides, disaccharides, polysaccharides, sugars, starch, glycogen, cellulose, chitin, glycosidic linkage bonds

o Proteins - structure, transport, defense, enzymes, amino acids, dipeptides, polypeptides, proteins, peptide bonds, 1°, 2°, 3°, 4° levels of structure

o Lipids - energy storage, structure, hormones, groups: triglycerides (fats, saturated C-C, unsaturated/kinky C=C), phospholipids, steroids, (cholesterol, sex hormones), ester linkage bonds

o Nucleic acids- genetic information storage, structure: nucleotides (pentose sugar, nitrogenous base (A,T,C,G,U), negatively charged phosphate groups, DNA, RNA, hydrogen bonds between bases, covalent bonds in backbone

Description: 05-03-Monosaccharides-L.gif

Description: 05-05-Disaccharides-L.gif

Description: 05-07-PolysaccharidesArt-L.gif

Description: 05-10-FatStructure-L.gif

Description: 05-11-SaturatedUnsatFats-L.jpg

Description: 05-12-PhospholipidSruct-L.gif

Description: 05-14-Cholesterol-L.gif

Description: 05-15a-NonpolarAminoAcid-L.gif

Description: 05-15b-PolarAminoAcids-L.gif

Description: 05-24-ProteinStructure-L.gif

Description: 18_13PrionPropagation_L.jpg

Description: 05-30-DNADoubleHelix-L.gif

6 - Enzymes/ Metabolism

· What do the first and second laws of thermodynamics state?

· What is the structure and purpose of ATP?

· What happens when high-energy phosphate bonds are broken in ATP?

· Δ G Reaction (Change in Energy of Reaction) = G products (Energy of Products) – G reactants (Energy of Reactants)

· Define: Catabolism, Hydrolysis, Exergonic, Negative Delta G

· What macromolecule are enzymes made of? What do they do to a substrate? Can they be reused? What do enzymes do to the activation energy of a reaction?

· Function: metabolic catalysts, lock & key model, induced fit model, “-ase”, substrate specific

· Factors affecting enzyme action: pH, temperature, coenzymes, cofactors, substrate concentration, enzyme concentration

· Activators (ex: allosteric) vs. inhibitors (ex: competitive or non-competitive)

· Allosteric site vs. active site

· Negative feedback loop / feedback inhibition

· Be able to label & interpret a Rates of Reaction Diagram:

Description: 08_09ATPHydrolysis_L.jpg

Description: 08_19EnzymeInhibition_L.jpg

7 - The Cell

· What are the names, functions, and locations of the following organelles?

o Nucleus, nucleolus, ribosomes, SER, RER, golgi apparatus, mitochondria, chloroplast, lysosome, peroxisome, cytoskeleton, microtubules, flagella, cilia, microfilaments, intermediate filaments, centrosome, centrioles, large central vacuole / tonoplast, vesicles, vacuole, cell wall, cell junctions (desmosomes, tight junctions, gap junctions, plasmodesmata)

· Explain some differences & similarities between plant, animal (Eukaryotic) and bacterial (Prokaryotic) cells:

o eukaryotes: nucleus & membrane-bound organelles

o plants: cell wall, chloroplasts, central vacuole

o animals: lysosomes, centrioles

o prokaryotes (bacteria): naked circular DNA, ribosomes, no nucleus or membrane-bound organelles, sometimes cell wall (peptidoglycans)

· What are viruses composed of and why are they exception to the Cell Theory?

Description: 07-04-ProkaryoticCell-L.jpg

Description: 07-07-AnimalCell-L.jpg

Description: 07-08-PlantCell-L.jpg

Description: 07-10-Ribosomes-L.jpg

Description: 07-16-Endomembranes-L.gif

8 - Membranes

· Explain Passive Transport (Diffusion, Osmosis, & Facilitated Diffusion) vs. Active Transport

· Define: Isotonic, Hypotonic, Hypertonic

· Define turgid plant cell, plasmolysed plant cell, lysed animal cell

· vesicular transport: exocytosis, endocytosis (phagocytosis, pinocytosis)

· Know the functions of the components of a cell membrane / phospholipid bilayer/ fluid mosaic model:

o Phosopholipids - hydrophilic heads, hydrophobic tails (amphipathic)

o proteins – amphipathic, integral & transmembrane, ion channel, transport, electron transfer, peripheral,

o glycoproteins - recognition, receptor, adhesion

o cholesterol - fluidity

· What types of materials can pass through a selectively permeable membrane and why?

· What types of materials cannot pass through a selectively permeable membrane and why?

· What types of cells have membranes and what are they composed of?

· Plant Cells vs. Animal Cells Placed in solutions of different Molarities (M)

Description: 08-06-PlasmaMembrane-L.jpg

Description: 08-11-Osmosis-L.gif

Description: 08-12-CellWaterBalance-L.gif

Description: 08-16-Transport-L.gif

Description: http://teacher2.smithtown.k12.ny.us/epaulik/congrad1.gif

Description: Hypertonic/hypotonic solutions

The solution in the bag contains less solute than the solution in the beaker. The solution in the bag is hypotonic (lower solute concentration) to the solution in the beaker. The solution in the beaker is hypertonic (higher solute concentration) to the one in the bag. Water will move from the hypotonic solution into the hypertonic solution.

9 – Respiration

· Net Equation: C6H12O6 + 6 O2 à 6 CO2 + 6 H2O + energy

· Aerobic Respiration: Know the locations, reactants, products of:

o Glycolysis

§ 1 glucose  -> 2 pyruvate, net 2 ATP(substrate-level phosphorylation), 2 NADH

§ all aerobic & anaerobic organisms, most widespread pathway, cytosol

o Kreb’s Cycle / Citric Acid Cycle

§ PreKrebs: 2 pyruvate --> 2 acetyl CoA + 2 NADH

§ 2 rounds of Krebs Cycle: 2 ATP (substrate-level phosphorylation), 6 NADH, 2 FADH2

§ Aerobic only, matrix of mitochondria

o Electron Transport Chain / Oxidative Phosphorylation / Chemiosmosis)

§ NADH & FADH2 donate electrons to ETC, cytochrome carrier proteins in membrane,

§ pump H+ ions to intermembrane space, H+ flow down concentration gradient through ATP synthase, phosphorylate ADP à ATP, O2 is final electron acceptor

§ yield: 36-38 ATP

§ Aerobic only, folded inner membrane of mitochondria aka cristae (lots of surface area)

· Anaerobic Respiration: Know the locations, reactants, products of:

o Lactic Acid Fermentation (mammalian muscle cells, bacteria), no CO2 produced

o Alcohol Fermentation (bacteria, yeast), CO2 produced

o both start with Glycolysis (the most widespread pathway)

Description: 07-17-Mitochondrion-L.jpg

Description: 09-16-CellRespirReview-L.gif

Description: 09_08GlycolysisEnergy_L.jpg

Description: 09-10-ConvertToAcetylCoA-L.gif

Description: 09-11-KrebsCycle-L4.gif

Description: 09_15Chemiosmosis_L.jpg

Description: 09-17a-Fermentation-L.gif

Description: 09-17b-Fermentation-L.gif

10 – Photosynthesis

· Net Equation: light + 6 H2O + 6 CO2 --> C6H12O6 + 6 O2

· LEO the “RED-OX” says GER: Redox reactions: Lose Electrons = Oxidation, Gain Electrons = Reduction

· Know the locations, reactants and products of:

o Light Reactions AKA Light Dependent Reactions (“Nerf Ball Game”)

§ How is chemiosmosis associated with the light reactions?

§ Chloroplast: thylakoid membrane, grana

§ noncyclic photophosphorylation

• photosystem II (P680), photolysis, primary electron acceptor, electron transport chain, ADP à ATP (phosphorylation)

• photosystem I (P700), primary electron acceptor, electron transport chain, NADP -->NADPH

§ why does cyclic photophosphorylation occur?

o Calvin Cycle AKA Dark Reactions AKA Light – Independent Reactions

§ Chloroplast: stroma

§ carbon fixation: inorganic CO2 + RuBP -- enzyme Rubisco -> organic PGA (3C)

§ 6 “turns” = 6 CO2 input = 1 glucose (6C) output

· What is photorespiration?

o C3: can undergo photorespiration, b/c of inefficiency of Rubisco in high [O2], Ex: wheat, rice

o C4: minimizes photorespiration, separate 2 steps of carbon fixation anatomically = 2 different cells, PEP carboxylase in outer ring of mesophyll cells, 4C "storage" compounds, (oxaloacetate, malate)., passes carbon by regenerating CO2 in inner bundle sheath cells to Calvin Cycle and Rubisco. Ex: crabgrasses, corn, sugar cane

o CAM: minimizes photorespiration, separate 2 steps of carbon fixation temporally = 2 different times, fix carbon at night with PEP carboxylase (when stomates open), put it in “storage” compounds (organic acids: malic acid, isocitric acid), then in day (when stomates closed), release CO2 from “storage” compounds to Calvin cycle with Rubisco. Ex: cacti, succulents, pineapple

· AP Lab 4: What does DPIP replace? What color change occurs when DPIP is reduced (gains electrons)?

Description: 10-02-Chloroplast-L.gif

Description: 10-04-PhotosynOverview-L3.gif

Description: 10_13NoncyclicElectron_5_L.jpg

Description: 10_15CyclicElectronFlow_L.jpg

Chemiosmosis

Description: 10-15-ChemiosmosisCompar-L.gif

Description: 10_17ThylakoidMembrane_L.jpg

Description: 10-17-CalvinCycleArt-L3.gif

Description: 10-18-C4Pathway-L.gif

Description: 10-19-C4andCAMphotosyn-L.jpg

Description: http://teacher2.smithtown.k12.ny.us/epaulik/ap_bio4.jpgDescription: http://teacher2.smithtown.k12.ny.us/epaulik/ap_bio5.jpg

11- Cell Communication

· Signal transduction pathway: reception, transduction, response

· Cell junctions (gap junctions, plasmodesmata) vs. Cell-to-cell recognition (glycoproteins)

Description: 11_05CellSignalingOver_L.jpg

12 – Mitosis

· What is the purpose of mitosis? (clones, asexual reproduction, growth, repair)

· Haploid vs. diploid

· Know specifics about Interphase (G1, S, G2), Prophase, Metaphase, Anaphase, Telophase, Cytokinesis (animal cleavage furrow vs. plant cell plate)

· Purpose of Checkpoints, mutation prevention, no signal at G1 checkpoint / “restriction point” à G0 – nerves, muscle cells

· Chromosomes vs. chromatids, centromere, complementary strands

· cell division triggered by growth (surface to volume ratio), density dependent inhibition

· What are the differences between mitosis in plant cells vs. animal cells?

· How do bacteria asexually reproduce?

· Cancer = unregulated cell division

Description: 12-06-MitoticSpindle-L.jpg

Description: 12-05a-MitosisArtLeft-L.jpg

Description: 12-05b-MitosisArtRight-L.jpg

Description: 12-08-Cytokinesis-L.jpg

Description: 12-10-BinaryFission-L3.gif

13 – Meiosis

· What is the purpose of meiosis? “reduction division”, haploid gamete (sex cell) production, genetic variation & recombination

· What are the differences between mitosis and meiosis? What are the differences between Meiosis I vs. Meiosis II?

· What is chromatin? What are kinetochore vs. nonkinetochore microtubules?

· Interphase I, Prophase I (synapsis, tetrad, chiasmata, crossing over), Metaphase I (independent assortment), Anaphase I (separates homologous pairs), Telophase I (diploid 2n --> haploid 1n), Cytokinesis I

Interphase II / Interkinesis (rest), Prophase II, Metaphase II, Anaphase II (separates sister chromatids), Telophase II (haploid 1n-->  haploid  1n), Cytokinesis II

Description: 13-07a-MeiosisArtLeft-L.gif

Description: 13-07b-MeiosisArtRight-L.gif

Description: 13-08a-MitosisMeiosis-L.gif

14 - Mendelian Genetics

· Using Punnett squares to determine genotypes of parents and offspring

· Testcross

· locus, gene, allele, homologous pairs, dominant, recessive, phenotype, genotype, homozygous, heterozygous, monohybrid cross, dihybrid cross; P, F1, F2 generations,

· Multiple alleles : Blood type determination (ex: cross: IAIB x ii)

· Incomplete dominance (pink flowers) vs. Codominance (roan cow)

· Use a pedigree to determine the inheritance pattern of an autosomal Mendelian trait.

· Law of Segregation: random segregation of alleles to separate gametes

· Law of Independent Assortment: chromosomes segregate separately from other nonhomologous chromosomes

· Epistasis

· Pleiotropy

· Polygenic inheritance

Description: 14-06-Testcross-L.gif

Description: 14-07-DihybridCross-L.gif

Description: 14_02ABObloodGroup_T.jpg

Description: 14-09-IncompletDominance-L.gif

Description: 14-14-PedigreeAnalysis-L.jpg

15 - Chromosomal Basis of Inheritance

· List some examples of sex-linked (X-linked) traits.

· Use a pedigree to determine the inheritance pattern of a sex-linked trait.

· As the distance between 2 linked genes increases, what happens to the crossover frequency?

· Use crossover frequencies (map units) to determine a linkage map of the locations of genes on a chromosome.

· What are some chromosomal mutations? (non-disjunction, deletion, duplication, translocation, inversion)

X-inactivation

Description: 15-05b-RecombOffspring-L.gifDescription: http://teacher2.smithtown.k12.ny.us/epaulik/ap_bio6.jpg

Description: 15_11XChromInactivation_CL.jpgDescription: http://ghr.nlm.nih.gov/handbook/illustrations/normalkaryotype.jpg

Description: 15-13-ChromAlterations-L.gif

16 - DNA & DNA Replication

· Griffith – Bacterial Transformation (+ Avery, McCarthy, MacLeod’s contribution)

· Hershey and Chase – T2 bacteriophage (Viral Replication)

· Meselson and Stahl – Semiconservative DNA replication

· Chargaff: A-T, C-G

· Watson and Crick – DNA Double Helix shape

· What does a DNA nucleotide consist of? “ “ “ RNA nucleotide consist of?

· Explain the steps in semiconservative DNA replication/ (know the enzymes!) template DNA strand, DNA polymerase, leading strand, lagging strand, helicase, replication fork, single stranded binding proteins, DNA ligase, Okazaki fragments, RNA primase, RNA primer, new DNA made 5’ à 3, new nucleotides added onto the free 3’ end

mutations: deletion, substitution, insertion, frame shift

Description: 16-01-BacterialTransform-L.gif

Description: http://www.accessexcellence.org/RC/VL/GG/ecb/ecb_images/05_04_Avery_MacLeod.jpg

Description: 16-02b-PhageAttachGenes-L.gif

Description: 16-05-DoubleHelix-L.jpg

Description: 16-08-ReplicationModels-L.gif

Description: 16-09-MeselsonStahlExp-L4.gif

Description: 16-15-DNAEnzymes-L.gif

Description: 16-16-DNAReplication-L.gif

17 - Protein Synthesis

· Beadle and Tatum: one-gene-one-enzyme hypothesis, one-gene-one-polypeptide hypothesis

· How are the terms codon and anticodon related to each other?

· Converting Genetic “Languages”: 3’ DNA Template 5’ à 5’ mRNA 3’ à 3’ tRNA 5’ à Amino Acid Sequence

· Transcription (RNA polymerase makes 5’à 3’ pre-mRNA from DNA template strand in nucleus)

· RNA Processing (introns spliced out with snRNPs, exons will be expressed , 5’ cap, poly-A tail, in nucleus)

Translation (mRNA codon matches with tRNA anticodon, rRNA, ribosome, small ribosomal subunit, large ribosomal subunit, P site, A site, wobble, stop codon, start codon (Met), initiation, elongation, termination, in cytoplasm)

Description: 17-01-GeneEnzymeHypothes-L.gif

Description: 17-03-TripletCode-L.gif

Description: 17-02-TranscriptTranslat-L5.gif

Description: 17-25-EukarTranscrTransl-L.gif

Description: 17_24BasePairSubstitution_L.jpg

Description: 17_25FrameshiftMutation_L.jpg

Description: 17_23PointMutation_L.jpg

18 - Genetics of Viruses & Bacteria ****

· (Bacterio)phages – capsids + genome

· viral reproduction: lytic (host cell bursts), lysogenic (phage DNA circularizes into prophage), retrovirus (reverse transcription)

· bacteria: transformation, transduction, conjugation, plasmid

· operons (regulatory gene, repressor protein, promoter, RNA polymerase, operator, structural genes)

· inducible enzyme: lac operon, when lactose present binds to repressor & induces it to release DNA

· repressible enzyme: trp operon, when tryptophan (corepressor) present binds to repressor & triggers it to bind to DNA

Description: 18_10HIVReproduction_CL.jpg

Description: 18_07LamdaLyticLysoCycle_L.jpg

Description: 18_16Transduction_2_L.jpg

Description: 18_18ConjRecombination_4_L.jpg

Description: 18_21bTrpOperon_2_L.jpg

Description: 18_22bLacOperon_L.jpg

19 - Organization of Eukaryotic Genomes ****

· Chromatin (Hetero- vs. Eu-), histone proteins, nucleosome, “beads on a string”

· transposons

Description: 19_02ChromatinPacking_L.jpg

20 – DNA Technology ****

· genetic engineering: plasmids, restriction enzymes, sticky / blunt ends, DNA ligase

· Polymerase Chain Reaction (primers, DNA polymerase, nucleotides, heat break H bonds, cool form H bonds)

· Agarose Gel Electrophoresis (shorter DNA fragments (-) migrate towards (+) end faster than larger fragments)

Description: 20_04GeneCloning_3_L.jpg

Description: 20-07-PolymeraseChain-L.gif

Description: 20-08-GelElectrophoresis-L.gif

21 – Genetic Basis of Development ****

· Cloning, multipotent cells, totipotent cells

Description: 21_09StemsCells_L.jpg

22 - Darwinian Evolution

· Speciation = formation of a new species

· What does “homologous structures” mean and why are they evidence of evolution?

· What does “analogous structures” mean and how is convergent evolution related to it?

· Rates of evolution (Gradualism, Punctuated Equilibrium aka Catatrophism, etc)

· Lamarckian evolution and Theory of Inheritance of Acquired Characteristics.

· Darwinian evolution and Theory of natural selection (over-production, inherited variation, competition, adaptations, fitness, “survival of the fittest”, accumulation of advantageous traits)

· What is artificial selection

· What are analogous structures?

· Evidence for Evolution (comparative anatomy, embryology, biogeography, Vestigial structures, homologous structures, molecular biology / biochemical comparison, etc)

Description: 22-01-DarwinHistorContext-L.gif

Description: 22-14-HomologousStruct-L.gif

23 - Hardy-Weinberg Equlibrium vs. Microevolution

· Requirements for Hardy Weinberg Genetic Equilibrium: infinitely large population (no genetic drift, no founder effect, no bottleneck effect), no natural selection, no mutations, no gene flow (no migration), random mating,

· Memorize frequency of alleles formula: p + q = 1

· Memorize frequency of genotypes or individuals formula: p 2 + 2pq + q2 = 1

· What does each of the following terms represent? p, q, p 2, 2pq, q2

p = the frequency of the dominant allele (represented here by A)
q = the frequency of the recessive allele (represented here by a)

p2 = frequency of AA (homozygous dominant)
2pq = frequency of Aa (heterozygous)
q2 = frequency of aa (homozygous recessive)

p + q = 1

p2 + 2pq + q2 = 1

Description: 23-12-ModesOfSelection-L.gif