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AP Bio Exam Review. Molecular Biology Importance of molecules and bonding Bonds: Ionic – transfer of electrons, results in charged atoms or ions Covalent.

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Presentation on theme: "AP Bio Exam Review. Molecular Biology Importance of molecules and bonding Bonds: Ionic – transfer of electrons, results in charged atoms or ions Covalent."— Presentation transcript:

1 AP Bio Exam Review

2 Molecular Biology Importance of molecules and bonding Bonds: Ionic – transfer of electrons, results in charged atoms or ions Covalent – sharing of electrons; most common in organic molecules

3 Types of covalent bonds Polar – results if one element is more grabby for the electrons (oxygen, nitrogen) ex – Oxygen in the H 2 O molecule Nonpolar – electrons are shared equally, no areas of charge Important in shape of molecules

4 Bonds between molecules Hydrogen bonding- attraction between H of one molecule and an electronegative element in another molecule

5 Van der Waal forces: is the sum of the attractive or repulsive forces between molecules molecules

6 Organic chemistry – the chemistry of Carbon compounds Most biochemical macromolecules are polymers (units linked together) For the exam, think about what elements are found in the various macromolecules.

7 Carbohydrates Main energy source Made of monosaccharides many H and OH In water, forms rings

8 Can link together to form disaccharides or polysaccharides (starches) with the loss of a water molecule (dehydration synthesis or condensation reaction)

9 When polysaccharides are taken apart, water has to be added back in: Hydrolysis

10 Important polysaccharides These are made of glucose units. Glycogen – animal starch, stored in liver and muscles Cellulose – plant starch (animal cant digest) Amylose – plant starch

11 Dont forget when figuring out formula for the polysaccharides to subtract the water molecules! Linking 6 glucose (C 6 H 12 O 6 ) units:

12 Proteins Made of amino acids (20) Used for structure, enzymes, hormones, transport molecules, etc. Shape very important

13 R groups? Make each amino acid unique Can confer polarity to the protein Can be hydrophobic or hydrophilic Important in secondary and tertiary folding

14 Amino acids are linked by peptide bonds in a condensation (dehydration) reaction Orientation is important – Carboxyl group joined to amino group

15 Three levels of protein structure Primary: chain of amino acids Secondary: Beta pleats and alpha helix due to hydrogen bonding Tertiary: interactions betweenR groups due to ionic attractions, polarity, disulfide bridges, etc. Quaternary: attractions between chains


17 Lipids Used for insulation, energy Nonpolar (do not dissolve in water) Contain fats, oils, waxes, steroids such as cholesterol

18 Structure of a fat – glycerol and 3 fatty acids unsaturated

19 Phospholipids make up cell membranes

20 Steroids, such as cholesterol, ring structure Also important in cell membranes

21 Nucleic Acids DNA, RNA Made of nucleotides Each nucleotide has a sugar, phosphate, and a nitrogenous base (A,T,C,G) Nucleotides also found in ATP and GTP, energy transfer molecules


23 Enzymes Protein catalysts Very specific Affected by temp, pH, competing molecules Rate can be altered by amount of substrate/enzyme Usually named by what they work on

24 Enzyme Lab Catalase – breaks down hydrogen peroxide into water and oxygen Used sulfuric acid to stop reaction Titration using KMnO 4 to measure amt of H 2 O 2 left. Measured rate

25 The rate can be defined as the amount of product formed in a period of time. Or it can be defined as the amount of substrate used in a period of time.

26 Allosteric Interactions Another molecule can bind and cause the enzyme to change shape

27 Difference in Eukaryotic and Prokaryotic Cells Prokaryotic cells do not have membrane-bound organelles such as nuclei, ER, Golgi, etc. Their energy reactions are carried on in sections of their cell membrane. They do have ribosomes, DNA and some have cell walls.

28 Developing the eukaryotic cell Think about importance of an endomembrane system (endocytosis) and endosymbiosis.

29 Cell Organelles Nucleus – control via DNA making proteins Nucleolus – stores ribosomes ER – rough – site of ribosome attachment - smooth – lipid metabolism, toxin removal Lysosomes – digestive vacuoles Golgi – packages, modifies proteins Mitochondria – energy (ATP) via aerobic cell. resp Chloroplasts – photosynthesis Cytoskeletal elements – microtubules, microfilaments, support, make up other structures (centrioles, flagella, etc.) Centrioles – cell division (animal cells), anchor spindle fibers

30 Cell Membrane Made of phospholipids and integral and peripheral proteins (act as carrier molecules, enzymes, gates etc) Cholesterol – maintains fluidity Have glycoproteins and glycolipids as surface markers (receptors, MHCs etc) Hydrophobic on inside, hydrophilic on outside


32 Differences in cells Cell walls in plant, fungi, bacterial cells Cell wall composition varies - fungi: chitin - plants: cellulose - bacteria: peptidoglycan Chloroplasts in photosynthetic cells

33 Connections between cells Gap junctions – animals Plasmodesmata – plant cells

34 Movement of materials in and out of cells Surface area to volume ratio important in determining the movement of materials Smaller cells better!

35 Types of transport Diffusion (facilitated uses carrier molecules/channels) – passive Osmosis – Water movement – passive Active Transport: against conc gradient, - uses energy and carrier molecules, also includes endocytosis and exocytosis


37 Osmolarity Direction of water flow depends on solute conc WATER ALWAYS MOVES INTO A HYPERTONIC (HYPEROSMOTIC) SITUATION! Look at solute concentration to gauge water movement.

38 Water Potential Equation for water potential (osmotic potential) Ψ = Ψ P + Ψ s pressure potential + solute potential (+ or -) (always -) Ψ = 0 MPa for pure water As you add solute, the wp becomes more negative

39 Our lab: Diffusion Used bags of different molarities; weighed water gain Determined the solute potential SP of potato cells Where graph crossed line (no gain or loss of water) gave molar concentration - Use SP = -iCRT (to figure out solute potential; C = molar conc)

40 Cell Cycle controlled by checkpoints, CDK, cyclin

41 Mitosis Keeps chromosome no. constant, no genetic diversity 2 identical cells Stages: PMAT Think about what is happening to the DNA during the stages.

42 Prophase, metaphase, anaphase, telophase

43 cytokinesis Actual division of cytoplasm Forms cell plate in plant cells Cleavage furrow in animal cells

44 Meiosis Purpose: to divide chromosome number in half (diploid – haploid) and to promote diversity. Results in 4 NONIDENTICAL cells due to crossing over, different arrangement of chromosomes at Metaphase I. Meiosis I: cuts chrom no in half Meiosis II: divides chromatids


46 When does crossing- over occur? Tetrads

47 Meiosis is used to make gametes Some organisms such as fungi have complete bodies made of haploid cells

48 Genetics Remember ratios. One trait F 2 3:1 (Aa x Aa) Two trait – Remember each organisms has two alleles for each trait! ex: tall, green plant TtGg Each gamete gets ONE of each allele pair. Think of all possibilities. ex: TG, Tg, tG, tg F 2 9:3:3:1 (AaBb x AaBb)

49 Be able to relate crosses to Mendels laws: Law of Segregation – alleles separate during formation of gametes

50 Law of Independent Assortment: each allele separates independently of other allele in pair (ie chromosomes in Metaphase I of meiosis)

51 Test cross (backcross): use homozygous recessive to determine the genotype of an organism expressing the dominant trait to see if it is heterozygous. ex – AA or AA, mate with aa Sex-linked: REMEMBER TO USE SEX- CHROMOSOMES….NOTHING ON THE Y. Probability: use what you expect from individual crosses ex: AaBb x AABb probability of getting AABB?

52 Pedigrees: If skips a generation anywhere, recessive If more in males, may be sex-linked If dominant, has to appear in one parent Type of inheritance?

53 Linked genes will not give expected ratios Determined by amount of crossing-over resulting in recombinations of parent-types Can use to make chromosome maps - closer genes are, less recombinations or cross-overs

54 Other things Pleiotropy: one gene, many effects Polygenic Inheritance: many genes determining phenotype, additive effect Epistasis: one gene controlling expression of another gene Incomplete dominance Codominance

55 Genetic diseases May be caused by chromosome abnormalities (number and structural) Turners 45 female XO Klinefelters 47 male XXY Downs trisomy 21 - may be caused by nondisjunction during cell division May be caused by gene mutations

56 Nondisjunction Failure of chromosomes to separate normally

57 Structural abnormalities

58 Karyotypes can discern chromosome abnormalities

59 Our lab: Fruit Flies Chi-square test used to test validity of results Formulas will be given to you on the exam.

60 This number or lower to consider your data fits your prediction.

61 Importance of Free Energy Ability to do work in the cell

62 Energy Transformations Laws of thermodynamics: 1 st energy, 2 nd entropy (confusion) ATP – energy carrier molecule substrate level phosphorylation – transferring a phosphate from ATP to a molecule to activate it oxidative phosphorylation – using the movement of electrons to attach a phosphate to ADP to make ATP

63 What to expect on the exam…. You need to know general outcomes, places in the cell these occur, importances, etc. Pathways will probably be given for you to interpret.

64 Photosynthesis vs Cell Respiration Photosynthesis – anabolic Cellular respiration – catabolic 6CO 2 + 6H 2 O C 6 H 12 O 6 + 6H 2 O photo cell resp Do not memorize steps. Diagrams are usually given on the AP exam for interpretation.

65 Cellular respiration deriving energy (ATP) from food we eat Three parts: glycolysis (in cytoplasm); Krebs Cycle (matrix of mitochondria); ETC (cristae membrane) in eukaryotes. Prokaryotes carry on these processes in specialized membranes near the cell membrane.

66 Glycolysis – Glucose to 2 Pyruvates, needs 2ATP to start, makes 4 ATP, net yield 2 ATP If aerobic: pyruvate changes to acetyl Co-A (after releasing CO 2 ) to enter the Krebs Cycle Krebs Cycle generates (per turn, 2 turns per glucose) 1 ATP, 3 NADH, 1 FADH, 2 CO 2 Krebs cycle generates many intermediaries used in other pathways NADH and FADH are electron/H carriers


68 If anaerobic (no oxygen), fermentation occurs and pyruvate is changed to - lactic acid in muscle cells - alcohol and CO 2 in yeast cells No more ATP generated, but does recycle NADH to NAD + a to be used in glycolysis.


70 Electron Transport Chain Basis: electrons (along with H atoms) are passed from one energy level to next by NADH and FADH 2. Final acceptor of electrons is OXYGEN! Forms water (with H atoms)

71 How does this make ATP? Chemiosmosis: reactions pump H + into space between mitochondrial inter membrane space. As protons flow back across the inner membrane, ATP is phosphorylated.


73 Same type of ETC in photosynthesis in the chloroplasts (different direction of e flow)

74 All organisms carry on some phase of cell respiration – maybe only glycolysis!

75 Photosynthesis Occurs in the chloroplast

76 Two parts: Light-dependent (in thylakoid membranes of the grana) – light separates electrons from chlorophyll and those are passed through a series of carriers to generate ATP and eventually picked up by NADP (P in plants) Water is split generating oxygen as a waste product. The purpose of splitting water is to supply electrons to those lost in chlorophyll! ATP and NADPH go to the Calvin Cycle (light independent part)


78 Calvin Cycle – use ATP and NADPH and CO 2 to make glucose

79 Our labs Using DPIP as an electron-acceptor (replaces NADP) in the light-dependent reaction, changes color. Cell respiration: germinating vs nongerminating pea seeds, measured oxygen uptake in respirometers

80 Cell Respiration Lab

81 Some typical results

82 Photosynthesis Lab

83 Graph from Photosynthesis Lab: % Transmission of light by chloroplasts in various conditions

84 Leaf Float Lab

85 Rate Calculations How do you calculate rate? Change in product divided by change in time.

86 Molecular Genetics DNA vs RNA sugars (deoxyribose in DNA, ribose RNA structure (double strand DNA, single RNA) bases (DNA thymine) RNA (uracil) Base pairs 3 bonds more stable

87 DNA replication – semiconservative (Meselsohn-Stahl – used N14 and N15)

88 Enzymes involved: (supposedly do not need to know for exam) helicase – unwinds single-stranded binding proteins – keeps strands apart topoisomerase – allows strands to unravel RNA primase – attach RNA primers DNA polymerase – add new DNA bases Ligase – joins Okasaki fragments Chromosomes are protected by telomeres during replication.

89 Leading and lagging strands DNA polymerase moves in 3-5 direction One side copied in one piece Other side in pieces called Okasaki fragments Pieces joined by ligase

90 Notice the replication proceeds in opposite directions. DNA polymerase moves in 3-5 direction

91 Protein Synthesis Central dogma: DNA – RNA – protein Two steps Transcription – mRNA made from DNA in nucleus Translation – mRNA (codons) match to tRNA (anticodons) with their amino acids at the ribosomes EPA sites (probably too specific for exam) Amino acids joined by peptide bonds


93 Transcription steps 1) initiation – RNA polymerase attaches to promoter regions (TATA box) unzips DNA 2) elongation – by RNA polymerase 5 – 3 3) termination – RNA processing: introns removed by snRNPs exons stay end modification; Poly A tail, 5 cap (from GTP)

94 Translation – same steps initiation – small ribosomal subunit attaches to mRNA tRNA carrying methionine attaches P site next tRNA comes into A site continues, original tRNA goes to E site stops at termination (stop codon) Energy provided by GTP In prokaryotes, both processes occur in the cytoplasm of the cell; no RNA processing

95 What happens to the proteins that are made? Those that are made on attached ribosomes: Those that are made on free ribosomes:

96 Mutations Point – change in nucleotide - silent mutation – does not change amino acid - missense mutation – different amino acid - nonsense mutation - changes aa to stop codon Frame Shift – deletion, addition throws reading frame off.

97 DNA organization DNA packaged with proteins (histones) to form chromatin in beads called nucleosomes Euchromatin – DNA loosely bound, can be transcribed Heterochromatin – DNA tightly bound, due to methylation Chromatin becomes chromosomes during cell division.

98 Viruses Consist of protein coat and nucleic acid Not considered living, need a host cell Have lytic and lysogenic cycles Can be used as vectors to carry genes Bacteriophages – used by Hershey and Chase to prove DNA was genetic material Retroviruses – contain reverse transcriptase for RNA DNA

99 Unfortunately DNA from retroviruses such as HIV is not proof-read so many mutations may occur.


101 Bacterial Genetics Bacteria contain plasmids Most reproduce by binary fission (asex) Ways for genetic variation conjugation with sex pili transduction – during lytic phase of viral infection, some bacterial/viral DNA is mixed transformation - DNA taken up from surroundings

102 Conjugation can result with bacterial cells gaining R plasmids for antibiotic resistance.

103 Transduction brings new genetic combinations

104 Binary Fission asexual

105 Gene Regulation All cells in an organism have the same DNA, but not all of it is turned on In prokaryotes, have operons that direct a particular pathway Remember RPOG RNA polymerase binds here Regulator – Promoter – Operator – Genes Codes for repressor which can bind to the operator

106 Lac operon – inducible lactose acts as an inducer

107 Tryp operon – repressible - produces enzymes for synthesis of tryptophan; presence of tryptophan in cell cuts it off

108 Remember! Inducible operons (lac) are off and are turned on by available substrate in the cell to code for enzymes to break down the substrate Repressible operons (tryp) are on and are turned off by the product which acts as a corepressor.

109 Epigenetics changes in gene expression or cellular phenotype, caused by mechanisms other than changes in the underlying DNA sequence, some of which are heritable.gene expressioncellular phenotype DNA heritable Examples of such modifications are DNA methylation and histone modification DNA methylationhistone modification can modify the activation of certain genes

110 Examples of epigenetics in Development Somatic epigenetic inheritance through epigenetic modifications, particularly through DNA methylation and chromatin remodeling, is very important in the development of multicellular eukaryotic organisms. Cells differentiate into many different types, which perform different functions, and respond differently to the environment and intercellular signalling. epigenetic modifications

111 Epigenetic changes have been observed to occur in response to environmental exposurefor example, mice given some dietary supplements have epigenetic changes affecting expression of the agouti gene, which affects their fur color, weight, and propensity to develop canceragouti gene

112 MicroRNA and RNAis Non-coding RNAs that downregulate mRNAs by causing the decay of the targeted mRNA some downregulation occurs at the level of translation into protein.

113 DNA technology Recombinant DNA – use restriction enzymes to cut DNA and gene of interest to be inserted Gel electrophoresis – sort fragments by size and charte DNA fingerprinting – people have different size fragment RFLPS


115 Plasmid Maps Be able to read and create one.

116 Complementary DNA or cDNA made from mRNA using reverse transcriptase PCR

117 Our Labs DNA electrophoresis of restriction enzyme fragments -how to plot graph and read size of fragments Transformation experiment with pGLO, inserting plasmid with GFP into E.coli cells. - calculate transformation efficiency

118 Evolution Darwinian evolution – by means of natural selection based on heritable traits Remember populations evolve, not individuals Evidences for: homologies, biogeography, fossil record, molecular evidence (DNA, proteins)

119 Evolution of Populations Microevolution – looking at changes in allele frequencies Hardy Weinberg Equilibrium says gene frequencies WILL NOT CHANGE if conditions are met: - no natural selection - random mating - large populations - no gene flow (migration, immigration)

120 You have to know how to do this! p = frequency of recessive allele (can be obtained by taking the square root of the number of recessive individuals in the population) r = frequency of dominant allele (subtract p from 1) p + q = 1

121 Substitute in equation

122 Types of selection Directional – drifts to either side Stabilizing – stays same Disruptive – middle NOT favored Sexual (can be combined with other three)


124 Speciation populations have to be reproductively isolated (cannot interbreed and produce fertile offspring) Allopatric – geographical isolation Sympatric – reproductive barriers exist in same location

125 Allopatric Speciation

126 Reproductive barriers Pre-zygotic - different mating rituals, mismatch genitals, time of mating, etc. Post-zygotic - failure of zygote to thrive or failure of offspring or grand-offspring to survive and reproduce


128 Hybrids Can complicate the issue of determining if different species If hybrids can interbreed with either parent, probably not new species Polyploidy (allo and auto) lead to new species in plants

129 History of Life on Earth Hypotheses of how life arose RNA hypothesis Metabolism first hypothesis At some time though abiotic synthesis probably did occur - Miller, Urey experiment - protobionts, coacervates

130 Endosymbiosis Important in explaining the origin of eukaryotic cells, particularly mitochondria and chloroplast

131 endosymbiosis and tree of life

132 Mass Extinctions Be able to interpret diagrams and charts

133 Do not need to memorize, just interpret


135 Phylogeny and systematics Phylogeny – evolutionary history Systematics – classifying and determining evolutionary relationships KNOW how to interpret and create cladograms. Expect lots of these! Use Bioinformatics (computer programs such as BLAST) to infer phylogeny

136 Cladogram Analysis Look for outgroups (those that have the most differences) Those with the least differences are the closest together.

137 outgroup


139 Derived characters

140 Different ways to set-up

141 Use of parsimony in cladisticscladistics The set-up that involves the least amount of evolutionary changes It is considered more likely that trait B evolved only once (right hand cladogram) rather than twice (left-hand cladogram).trait

142 Looking at ancestry Polyphyletic - A group that does not share a common ancestor,groupcommon ancestor Paraphyletic - groups that have a common ancestry but that do not include all descendants Monophyletic - includes the most recent common ancestor of a group of organisms, and all of its descendents

143 What is this one?

144 What about convergent evolution? Traits evolved due to inhabiting similar environments or needed for similar situations. Do not infer ancestry.

145 Convergent evolution


147 Three domains

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