Tuesday, March 14, 2000

Final Exam

Biology 113

Name: _____________________________________

 

Œ   Place your name at the top of each page.

   There are 17 non-comprehensive and 17 comprehensive questions

Ž   Each question is worth the same amount

   Remember to distinguish compared items by linking descriptions with terms (e.g., the sky isblue).

   Unless requested, do not multiply out expressions (e.g., stop at 2*5003 rather than 2.5x108).

‘   I encourage you to ask questions during the exam, but do so discretely.

’   Remember to use safe, i.e., unambiguous & well-articulated answers whenever possible.

“   Above all, avoid jumping to profoundly incorrect conclusions: make sure you actually read a question (all of it) before you answer, and then make sure you are actually answering what is being asked.

 

(1) Beginning at the point where DNA has already been separated via gel electrophoresis, describe the Southern blotting procedure. I’d say that there are basically two key steps that you need to include in this description.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

A: Southern blotting involves the transfer (blotting) of the DNA to (nitrocellulose) paper followed by the probing of that DNA with tagged DNAs of specific sequence; note that in for this to occur the transferred DNA must be denatured to the single-stranded state, and that the probes, too, must be single stranded (i.e., the entire procedure is based on the propensity for complementary DNAs to hydrogen bond to form double helices) (from chapter 20)

(2) Describe how/why DNA ligase is employed in gene cloning procedures.

 

 

 

A: There are a variety of possible answers including: DNA ligase is employed to close gaps between adjacent nucleotides in DNA molecules making up one-half of double-helices; DNA ligase is employed to attach DNA pieces to plasmids into which the pieces have been inserted; DNA ligase covalently attaches DNAs that adhere via sticky ends, or even that adhere (transiently) via blunt ends (from chapter 20)

(3) In gel electrophoresis, contrast the physical characteristics of molecules that migrate rapidly from ones that migrate more slowly. Ignore considerations of charge differences between the molecules.

 

More-slowly migrating:

 

More-rapidly migrating:

 

A: More-slowly migrating molecules tend to be larger and more diffuse than more-rapidly migrating molecules; the reason for this slower migration is that greater size increases the duration of and propensity for interactions between the molecule and the gel matrix (from chapter 20)

(4) In Griffith’s (1928) experiment, the technical term for the uptake of DNA by Streptococcus is __________.

 

A: Transformation (from chapter 18)

(5) In terms of chromatin structure, what is a common means by which control of gene expression is effected? That is, what general chromatin state of being correlates with less gene expression? With more gene expression?

 

 

 

 

 

 

A: Generally, more-condenced DNA (heterochromatin) is less available to RNA polymerase and therefore less-well expressed, whereas less condenced DNA (euchromatin) is more available to RNA polymerase and therefore expressed to a greater degree (from chapter 19)

(6) Infection by a virus with a __________ life cycle obligately ends with the destruction of the host cell.

 

A: Lytic (from chapter 18)

(7) Lambda (l) virus is an example of a bacteriophage that, unlike bacteriophage T4, can exhibit a __________life cycle.

 

A: lysogenic (from chapter 18)

(8) Matching: (a) allolactose (a lactose derivative), (b) cAMP (c) tryptophan.

(i) Corepressed operon: __________

(ii) Inducible operon: __________

(iii) Positive control: __________

 

A: (i) (c) tryptophan, (ii) (a) allolactose, (iii) (b) cAMP (from chapter 18)

(9) All operons consist of three major components. Name them. Recall that an operon is basically just a sequence of DNA (i.e., there are no protein components).

 

 

 

 

A: Operator, promoter, structural genes (from chapter 18)

(10) The expression of nuclear genes is controlled primarily at the level of __________.

(a) mRNA modification

(b) Ribosome binding

(c) Protein degradation

(d) Transcription

(e) Translation

 

A: (d) Transcription (from chapter 19)

(11) What do enhancers enhance?

 

A: Eukaryotic gene transcription (from chapter 19)

(12) What does RFLP stand for?

 

A: Restriction Fragment Length Polymorphism (from chapter 20)

 

(13) What enzymes are employed to cut genes out of an organism’s genome prior to the cloning of these genes?

 

A: Restriction endonucleases/enzymes (from chapter 20)

 

(14) What is conjugation?

 

 

 

 

 

 

A: Conjugation is the passage of DNA from one bacteria to a second bacteria to which the first bacteria is directly connected via a sex pili (from chapter 18)

 

(15) What is the cofactor employed in the regulation of the trp operon?

 

A: Trp (from chapter 18)

 

(16) What chemical reaction is catalyzed by reverse transcriptase? (note that you can be reasonably non-specific in your answer, i.e., I am not looking for all substrates and products, just the particularly important ones that distinguish this chemical reaction from those better-associated with the central dogma of molecular genetics)

 

 

 

A: RNA à DNA, i.e., RNA-templated DNA polymerization (from chapter 18)

 

(17) Which means of protein regulation generally allows the most rapid phenotypic adaptation?

(a) mRNA degradation

(b) mRNA activation/inactivation

(c) Protein activation/inactivation

(d) Protein degradation

(e) Transcriptional control

A: (c) Protein activation/inactivation (from chapter 19)

 

(1) A typical cell from a given genotypically and phenotypically normal male mammal harbors 2n = 50 chromosomes. How many pairs of homologous autosomes does that imply?

 

A: 24 (i.e., X and Y are not homologous pairs nor autosomes) (from chapter 13)

(2) Complete this reaction of glycolysis: C3-P + NAD+ + __________ à __________ + NADH + H+

 

 

A: Pi, P-C3-P (from chapter 9 & midterm exam #2)

(3) Considering both substrate-level phosphorylation and the oxidative phosphorylation that eventually occurs, how many ATPs does one turn of the Kreb’s cycle generate? (assume standard ATP estimations from chemiosmosis)

 

A: 3 NADH, 1 FADH2, and one substrate-level phosphorylation per turn of the Kreb’s cycle, for a total of 3x3 + 1x2 + 1 ATP = 12 (from chapter 9 & midterm exam #2)

 

(4) Name a viable human monosomy.

 

A: XO, i.e., Turner syndrome (from chapter 15)

(5) Name an organelle that is found within the matrix of mitochondria (matrix, cytoplasm, inner membrane, and cristae are all not correct answers).

 

A: ribosome as well as chromosome are correct answers (from chapter 7)

(6) Name four structures or complexes that make up the mitotic spindle in animals. I’m looking for answers other than cytoskeleton, chromsome, centromere, chromatid, or metaphase plate. Even excluding the above, by my count there are at least seven possible answers to this question.

 

 

 

 

 

A: Microtubules, tubulin, kinetochore microtubules, non-kinetochore microtubules, centrioles, centrosomes, spindle fibers, aster (from chapter 12)

(7) Name one substrate of the enzyme primase.

 

A: Answers include: the DNA template, the RNA triphosphates, and the growing RNA primer (from chapter 16)

(8) Name the three intervening steps, in order, that occur during the majority of oxidative phosphorylations on the path from substrate to ATP generation. Note that glycolysis, the Kreb’s cycle, etc. serve to generate the already mentioned substrates so they and their ilk are not answers. Note also that the first of these steps is a chemical reaction while the last two are more complicated than that (i.e., are complex chemical and physical processes… and no, while a proton-motive force is certainly a component of these processes, it is not one of the three answers). Please try to employ the common names for these last two processes rather than a complicated description.

 

 

 

 

 

 

A: NADH + H+ à electron transport chain à chemiosmosis (from chapter 9)

(9) On average, how many hydrogen bonds is a water molecule participating in at any given time in liquid water? (note that you do not know the exact answer to this question plus I have not supplied sufficient information for anybody to answer this question exactly, but nevertheless the question does have a relatively straightforward, not terrible difficult answer—hint: the answer is a very simple algebraic expression rather than a whole or even a fractional number)

 

 

A: Less than four or, algebraically, x < 4 where x is the average number of hydrogen bonds a water molecule is participating in at any given instant in liquid water; 4, of course, is the maximum (not average) number of hydrogen bonds a water molecule can form with water neighbors (a number better approximated by ice than by liquid water which, almost by definition, is a substance in which the maximum number of hydrogen bonds is not continuously maintained) (from chapter 3)

(10) Order the following from most-reduced (most associated energy) carbon-based group to least-reduced (least associated energy) carbon-based group: carbonyl group, carboxyl group, hydroxyl group, and methyl group (a hydrocarbon group, i.e., -CH3).

 

A: methyl (C-CH3), hydroxyl (C-OH), carbonyl (C=O), carboxy (C-COOH) (from chapter 4)

 

(11) Proteins are costly for a cell to produce and if a protein is responsible for catalyzing an endergonic physical or chemical process, then proteins are also costly for a cell to operate. Given both of these costs, arrange the following processes in order going from most-costly to a cell to least-costly to a cell: active transport, facilitated diffusion, and passive transport. Briefly justify your answer.

 

 

 

 

 

 

 

A: Active transport (requires proteins and is costly to run), facilitated diffusion (requires proteins but is not costly to run), and passive transport (does not require proteins and it not costly to run) (from chapter 8)

(12) Suppose that an individual plant is known to be heterozygous at 15 different independently assorting loci.  Considering only these loci, how many possible genotypic combinations of gametes can this individual produce?

 

 

 

 

 

 

 

A: 215 (i.e., two different for gametes for every loci: 2 x 2 x 2 x 2 x 2 x 2 x 2 x 2 x 2 x 2 x 2 x 2 x 2 x 2 x 2 = 215) (from chapter 14)

(13) What general name does one use to describe that broad class of proteins that function in metabolic processes to lower the activation energy required to initiate specific chemical reactions?

 

A: Enzyme (from chapter 6)

(14) What is the difference between amylose and amylopectin?

 

 

 

A: Amylopectin is branched; amylose is not (from chapter 5)

(15) What is the first step of signal transduction, i.e., that is directly and immediately induced by ligand binding at the surface of a cell?

 

 

A: Conformational change of the receptor protein is typically the first step of signal transduction following ligand binding (from chapter 11)

(16) What is the significance of “AUG”?

 

A: AUG is the start codon (from chapter 17)

(17) Where, specifically (structurally), in chloroplasts are the photosynthesis photosystems found? I want you to zoom in as far as you can, i.e., be as specific as you can.

 

A: the membranes of the thylakoids (from chapter 10)