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 H2O 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

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 can’t digest)
Amylose – plant starch

11. Don’t forget when figuring out formula for the polysaccharides to subtract the water molecules!
Linking 6 glucose (C6H12O6) 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 KMnO4 to measure amt of H2 O2 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, MHC’s 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 pressure potential + solute potential
Equation for water potential (osmotic potential)
Ψ = ΨP + Ψs
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
F2 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
F2 9:3:3:1 (AaBb x AaBb)

49. Be able to relate crosses to Mendel’s 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. If skips a generation anywhere, recessive
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
Down’s 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:
1st energy, 2nd 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 H2O C6H12O H2O
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 CO2) to enter the Krebs Cycle
Krebs Cycle generates (per turn, 2 turns per glucose) 1 ATP, 3 NADH, 1 FADH, 2 CO2
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 CO2 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 FADH2.
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 CO2 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 snRNP’s
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 RNA polymerase Regulator – Promoter – Operator – Genes
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.
Examples of such modifications are DNA methylation and histone 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.

111. Epigenetic changes have been observed to occur in response to environmental exposure—for 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 cancer

112. MicroRNA and RNAi’s
Non-coding RNA’s 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 cladistics
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).

142. Looking at ancestry
Polyphyletic - A group that does not share a common 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