Download Name SIS # 1 Introductory Biochemistry BI 28 Third Midterm

Name
SIS #
Introductory Biochemistry
BI 28
Third Midterm Examination
May 1, 2007
Make sure that your name or SIS # is on every page. This is the only way we have of
matching you with your exam after grading it. Please work independently. Read each question
carefully before answering. Unless otherwise indicated, there is only one correct answer for each
multiple choice question. Points are indicated by the question within brackets [ ]. There are no
calculators or other electronic devices needed or allowed on this exam. Exams will be
photocopied before being returned on Thursday. Please note: All regrade requests for this exam are
due by Thursday May 10th at 5 pm. Regrades can lead to an overall lower score on the exam.
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Extra Credit__________/3
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1) [3] Difluoromethylornithine (DFMO) is an inhibitor of the enzyme
__________________________, which is involved in the synthesis of the polyamines
________________ and _____________________.
2) [3] Tetrapyrroles are derived from ____________________ and
_________________________________ in animals, fungi, and some bacteria and from
______________________ in plants, algae, and most bacteria.
3) [2] Degradation of heme by the enzyme ____________________________ yields
______________________.
4) [2] The synthesis of purine and pyrimidine nucleotides differ in that:
A) ATP is required in the synthesis of purines but not in the synthesis of pyrimidines.
B) purine biosynthesis starts with the formation of PRPP, whereas pyrimidines incorporate the
PRPP near the end of the pathway.
C) purine formation requires a THF derivative, whereas pyrimidine formation does not.
D) pyrimidine biosynthesis is tightly regulated in the cell, whereas purine biosynthesis is not.
E) pyrimidines go through many steps, adding a single carbon or nitrogen each time, whereas
the basic skeleton for purines is formed by two main precursors.
Circle the correct answer.
5) [2] Which of the following is not true of the reaction catalyzed by ribonucleotide reductase?
A) Glutathione is part of the path of electron transfer.
B) It acts on nucleoside diphosphates.
C) Its mechanism involves formation of a free radical.
D) There is a separate enzyme for each nucleotide (ADP, CDP, GDP, UDP).
E) Thioredoxin acts as an essential electron carrier.
Circle the correct answer
6.) [4] The name of molecule A in the box below is ______________, and molecule B is
_______________. Molecule A is the _____________(substrate/product) and molecule B is the
__________ (substrate/product) of the enzyme _______________________________.
A
B
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7.) [4] Write the correct name of the nucleoside portion under each molecule given below.
Name:
8) [6] Using the structures above, draw just the four bases in the space provided below in the correct
base-pairing orientation and indicate hydrogen bonds between the two bases with dashed lines.
(Must be completely correct to receive credit).
9) [2] Topoisomerases can:
A) change the linking number (Lk) of a DNA molecule.
B) change the number of base pairs in a DNA molecule.
C) change the number of nucleotides in a DNA molecule.
E) convert D isomers of nucleotides to L isomers.
F) interconvert DNA and RNA.
Circle the correct answer
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10) [2] Histones are _______ that are usually associated with _________.
A) acidic proteins; DNA
B) acidic proteins; RNA
C) basic proteins; DNA
D) basic proteins; RNA
E) coenzymes derived from histidine; enzymes
Circle the correct answer
11) [2] The Meselson-Stahl experiment established that:
A) DNA polymerase has a crucial role in DNA synthesis.
B) DNA synthesis in E. coli proceeds by a conservative mechanism.
C) DNA synthesis in E. coli proceeds by a semiconservative mechanism.
D) DNA synthesis requires dATP, dCTP, dGTP, and dTTP.
E) newly synthesized DNA in E. coli has a different base composition than the preexisting
DNA.
Circle the correct answer
12) [3] A suitable substrate for DNA polymerase is shown below. Label the primer and template,
and indicate which end of each strand must be 3' or 5'.
13) [2] Indicate whether the following statements are true or false by circling T or F for each
question.
T/F
T/F
In E. coli replication begins at the origin of replication and proceeds in one direction until
the entire circular DNA molecule has been copied.
Prokaryotic DNA replication occurs in two steps. First, ATP provides a phosphate to the
growing DNA chain. This is followed by addition of a nucleoside.
14) [4] All known DNA polymerases can only elongate a preexisting DNA chain (i.e., require a
primer), but cannot initiate a new DNA chain. Nevertheless, during semiconservative DNA
replication in the cell, entirely new daughter DNA chains are synthesized. Explain the process
that occurs in the cell that allows for the synthesis of daughter chains by DNA polymerase.
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15) [4] The high fidelity of DNA replication is due primarily to immediate error correction by the 3'
—> 5' exonuclease (proofreading) activity of the DNA polymerase. Some incorrectly paired
bases escape this proofreading, and further errors can arise from challenges to the chemical
integrity of the DNA. List the four classes of repair mechanisms that the cell can use to help
correct such errors.
1.
2.
3.
4.
16) [2] RNA polymerase:
A) binds tightly to a region of DNA thousands of base pairs away from the DNA to be
transcribed.
B) can synthesize RNA chains de novo (without a primer).
C) has a subunit called λ (lambda), which acts as a proofreading ribonuclease.
D) separates DNA strands throughout a long region of DNA (up to thousands of base pairs),
then copies one of them.
E) synthesizes RNA chains in the 3' → 5' direction.
Circle the correct answer
17) [2] Enzymes that synthesize RNA from an RNA template are called __________________,
whereas enzymes that synthesize DNA from and RNA template are called
_____________________________.
18) [2] Introns:
A) are frequently present in prokaryotic genes but are rare in eukaryotic genes.
B) are spliced out before transcription.
C) are translated but not transcribed.
D) can occur many times within a single gene.
E) encode unusual amino acids in proteins.
Circle the correct answer
19) [4] Describe the sequence of events in the initiation of transcription by E. coli RNA polymerase.
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20) [4] Describe the mechanistic difference that distinguishes the splicing of group I introns from
that of group II introns.
21) [2] Which of the following are features of the wobble hypothesis?
A) A naturally occurring tRNA exists in yeast that can read both arginine and lysine codons.
B) A tRNA can recognize only one codon.
C) Some tRNAs can recognize codons that specify two different amino acids, if both are
nonpolar.
D) The “wobble” occurs only in the 5’ base of the anticodon.
E) The 3’ base in a codon always forms a normal Watson-Crick base pair.
Circle the correct answer
22) [2] Which of the following is true about the sorting pathway for proteins destined for
incorporation into the plasma membrane of eukaryotic cells?
A) Binding of SRP to the signal peptide and the ribosome temporarily accelerates protein
synthesis.
B) The newly synthesized polypeptides include a signal peptide at their carboxyl termini.
C) The signal peptide is cleaved off inside the mitochondria by signal peptidase.
D) The signal recognition particle (SRP) binds to the signal peptide soon after it appears
outside the ribosome.
E) The signal sequence is added to the polypeptide in a posttranslational modification reaction.
Circle the correct answer
23) [2] Ubiquitin-mediated protein degradation is a complex process, and many of the signals
remain unknown. One known signal involves recognition of amino acids in a processed protein
that are either stabilizing (Ala, Gly, Met, Ser, etc.) or destabilizing (Arg, Asp, Leu, Lys, Phe,
etc.), and are located at:
A) a helix-turn-helix motif in the protein.
B) a lysine-containing target sequence in the protein.
C) a zinc finger structure in the protein.
D) the amino-terminus of the protein.
E) the carboxy-terminus of the protein.
Circle the correct answer
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24) [4] In 1961, Howard Dintzis carried out an experiment that defined the direction of polypeptide
chain growth during protein synthesis in cells. The experiment involved the analysis of
hemoglobin molecules that were being synthesized in reticulocytes in the presence of
radioactive amino acids. Describe this experiment precisely and how it demonstrated the
direction of polypeptide chain growth, including in your answer the observed direction of this
growth.
25) [3] Polypeptide chain elongation in E. coli occurs by the cyclical repetition of three steps. What
are these steps and what cellular factors (if any) that are necessary for each of them to occur?
Step 1:
Step 2:
Step 3:
26) [2] The binding of CRP (cAMP receptor protein of E. coli) to DNA in the lac operon:
A) assists RNA polymerase binding to the lac promoter.
B) is inhibited by a high level of cAMP.
C) occurs in the lac repressor region.
D) occurs only when glucose is present in the growth medium.
E) prevents repressor from binding to the lac operator.
Circle the correct answer
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27) [2] The diagram below represents a hypothetical operon in the bacterium E. coli. The operon
consists of two structural genes (A and B), which code for the enzymes A-ase and B-ase,
respectively, and also includes P (promoter) and O (operator) regions as shown.
When a certain compound (X) is added to the growth medium of E. coli, the separate enzymes
A-ase and B-ase are both synthesized at a 50-fold higher rate than in the absence of X. (X has a
molecular weight of about 200.) Which of the following statements is true of the operon
decribed above?
A) All four genes (A, B, O, and P) will be transcribed into an mRNA that will then be
translated into four different proteins.
B) The 3' end of the mRNA from the operon will correspond to the left end of the operon as
drawn.
C) The 5' end of the messenger from this operon will correspond to the right end of the operon
as drawn.
D) The repressor for this operon binds just to the right of A.
E) When RNA polymerase makes mRNA from this operon, it begins RNA synthesis just to the
left of gene A.
Circle the correct answer
28) [2] Attenuation in the trp operon of E. coli:
A) can adjust transcription of the structural genes upwards when tryptophan is present.
B) can fine-tune the transcription of the operon in response to small changes in Trp availability.
C) is a mechanism for inhibiting translation of existing (complete) trp mRNAs.
D) results from the binding of the Trp repressor to the operator.
E) results from the presence of short leader peptides at the 5' end of each structural gene.
Circle the correct answer
29) [4] In prokaryotes such as E. coli, many operons that encode enzymes involved in amino acid
biosynthesis begin with a sequence coding for a leader peptide. This peptide has no known
enzymatic function and is rich in the amino acid that is synthesized by the enzymes coded for in
the operon. What is the function of this leader peptide?
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30) [2] Which one of the following types of eukaryotic regulatory proteins interact with enhancers?
A) Basal transcription factors
B) Coactivators
C) Repressors
D) TATA-binding proteins
E) Transactivators
Circle the correct answer
31) [2] Which one of the following is not involved in steroid hormone action?
A) Cell surface receptors
B) Hormone-receptor complexes
C) Specific DNA sequences
D) Transcription activation and repression
E) Zinc fingers
Circle the correct answer
32) [2] The E. coli recombinant plasmid pBR322 has been widely utilized in genetic engineering
experiments. pBR322 has all of the following features except:
A) a number of conveniently located recognition sites for restriction enzymes.
B) a number of palindromic sequences near the EcoRI site, which permit the plasmid to
assume a conformation that protects newly inserted DNA from nuclease degradation.
C) a replication origin, which permits it to replicate autonomously.
D) resistance to two different antibiotics, which permits rapid screening for recombinant
plasmids containing foreign DNA.
E) small overall size, which facilitates entry of the plasmid into host cells by transformation.
Circle the correct answer
33) [4] A scientist wishes to produce a mammalian protein in E. coli. The protein is a glycoprotein
with a molecular weight of 40,000. Approximately 20% of its mass is polysaccharide. The
isolated protein is usually phosphorylated and contains three disulfide bonds. The cloned gene
contains no introns.
(a) What sequences or sites will be required in the vector to get this gene regulated, transcribed, and
translated in E. coli?
(b) List two problems in E. coli that might arise in producing a protein identical to that isolated
from mammalian cells and describe each problem in no more than two sentences.
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34) [2] Which of the following statements about type II restriction enzymes is false?
A) Many make staggered (off-center) cuts within their recognition sequences.
B) Some cut DNA to generate blunt ends.
C) They are part of a bacterial defense system in which foreign DNA is cleaved.
D) They cleave and ligate DNA.
E) They cleave DNA only at recognition sequences specific to a given restriction enzyme.
Circle the correct answer
35) [2] The technique known as two hybrid analysis for detecting interacting gene products depend
on:
A) activation of DNA polymerase by the nearby binding of hybridizing protein complexes.
B) direct binding of a Gal4p activation domain to a DNA sequence in the promoter region.
C) an intact transactivator protein fused to only one of two interacting proteins
D) hybridization of DNA segments corresponding to the two genes being examined.
E) stimulation of trasncription by interaction of two Gal4p domains via fused protein
sequences.
Circle the correct answer
36) Explain how each of the following is used in cloning in a plasmid:
(a) [2] antibiotic resistance genes (You must state two different reasons for full credit):
(b) [1] origin of replication:
(c) [1] polylinker region:
Extra Credit:
37) [3] Nucleotide polymerization appears to be a thermodynamically balanced reaction (because
one phosphodiester bond is broken and one is formed). Nevertheless, the reaction proceeds
efficiently both in a test tube and in the cell. Explain.
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