Download Chapter 12: Nucleotides and Nucleic Acids

NAME ________________________________
EXAM IV
November 25, 2002
Biochemistry I
I.
__________________/28
II.
__________________/4
III.
__________________/17
IV.
__________________/8
V.
__________________/6
VI.
__________________/37
TOTAL
/100
I. MULTIPLE CHOICE. (28 points; 2 points each)
Choose the BEST answer to the question by circling the appropriate letter.
1.
Which of the following is a palindromic sequence?
A.
2.
C.
D.
E.
B.
C.
D.
C.
GAATCC
D.
AGGTCC
E.
CCTTCC
the two strands are parallel.
sequences rich in A-T base pairs are more difficult to denature than
those rich in G-C pairs.
the structure is compatible only with a right-handed (never a
left-handed) helix.
the two strands have complementary sequences.
the sequence of bases has no effect on the overall structure.
B-form DNA predominates in aqueous solution; dehydration favors the
A form.
Z-form DNA has a helical sense (left-handed) that is opposite that
for A-form DNA.
The sugar pucker is either 2' or 3'.
Nucleotide sequence has little or no effect on which form DNA takes.
Prokaryotic DNA polymerase III:
A.
B.
C.
D.
5.
GTATCC
Which of these statements about alternate forms of DNA is false?
A.
4.
B.
In double-stranded DNA:
A.
B.
3.
GGATCC
contains a 5' ® 3' proofreading activity to improve the fidelity of
replication.
synthesizes DNA 3' ® 5'.
has a b subunit that acts as a circular clamp to greatly improve the
processivity of DNA synthesis.
synthesizes only the leading strand; DNA polymerase I synthesizes
the lagging strand.
Common lesions found in DNA after exposure to ultraviolet light are __.
A.
B.
C.
D.
E.
pyrimidine dimers
single strand breaks
AP-sites
deamination of cytosine
purine dimers
Page 1
NAME ________________________________
6.
Which of the following statements about aminoacyl-tRNA synthetases is
false?
A.
B.
C.
There is a different synthetase for every amino acid.
The enzyme attaches an amino acid to the 3' end of a tRNA.
The enzyme splits ATP to AMP + PPi.
D.
The enzyme will use any tRNA species, but is highly specific for a
given amino acid.
Some of the enzymes have an editing/proofreading capacity.
E.
7.
Which of the following statements about the polymerase chain reaction
(PCR) is false?
A.
B.
C.
D.
E.
8.
Which of the following is true about a circular double-stranded DNA
genome that is determined by chemical means to be 21% adenosine?
A.
B.
C.
D.
E.
9.
The genome is 10.5% guanosine.
The genome is 21% guanosine.
The genome is 29% guanosine.
The genome is 58% guanosine.
The base percent composition of guanosine in the genome cannot be
determined from the information given.
Which of the following is most likely to lead to a loss of gene
function?
A.
B.
C.
D.
E.
10.
DNA is amplified at random points when using genomic DNA as
template.
The boundaries of the amplified DNA segment are determined by the
synthetic oligonucleotides used to prime DNA synthesis.
The technique is useful for site-directed mutagenesis.
Newly synthesized DNA must be denatured with heat before the next
round of DNA synthesis begins.
DNA amplified by PCR can be cloned.
A missense mutation (coding a different amino acid) in the open
reading frame
A change from a TAA codon to a TAG codon (see page 7) in the protein
coding region
A change from T to C in the promoter region
A frameshift mutation in the coding region
A sequence change in the 3'UTR
Which of the following is NOT involved in the processing of mRNA
precursors in eukaryotic cells?
A.
B.
C.
D.
E.
Capping of the 5'-end
Addition of poly-A
Excision of introns
Splicing of exons
Transport of the pre-mRNA to the cytoplasm
Page 2
NAME ________________________________
11.
The ribosome is involved in all of the following EXCEPT
A.
B.
C.
D.
E.
12.
Which of the following in NOT a potential problem associated with
expressing a eukaryotic, protein-encoding gene in prokaryotic cells?
A.
B.
C.
D.
E.
13.
Lack of an intron-splicing mechanism in prokaryotes
Differences in the translation initiation codon used by eukaryotic
cells and prokaryotic cells
Susceptibility of the protein product to prokaryotic proteases
Stability of mRNA in prokaryotic cells
Differences in transcriptional signals between eukaryotic cells and
prokaryotic cells
All of the following contribute to promoter binding by RNA polymerase
in E. coli EXCEPT the
A.
B.
C.
D.
E.
14.
peptide bond formation
aminoacylation of tRNA
binding of protein factors during elongation
binding of aminoacyl tRNA to mRNA
binding of mRNA at an initiation codon
rho factor
-10 consensus sequence
-35 consensus sequence
b' subunit of RNA polymerase
b subunit of RNA polymerase
In a bacterial cell, a mutation in an aminoacyl-tRNA synthetase leads
to charging of the entire tRNASer population with alanine. Which of the
following describes the result of using these aminoacyl tRNAs for
protein synthesis in the cell?
A.
B.
C.
D.
E.
The alanyl-tRNASer will not function in protein synthesis.
Proteins synthesized using the alanyl-tRNASer will contain neither
alanine nor serine.
Proteins synthesized using the alanyl-tRNASer will contain only
serine where alanine would normally occur.
Proteins synthesized using the alanyl-tRNASer will contain only
alanine where serine would normally occur.
Proteins synthesized using the alanyl-tRNASer will randomly contain
either alanine or serine where serine would normally occur.
II. BASE PAIRS.
15.
(4 points)
Draw the rare tautomeric form of guanosine. Place arrow(s) pointing to
those hydrogen-bond donors or acceptors that might change due to the
tautomeric shift.
Page 3
NAME ________________________________
III. MATCHING (17 points)
Follow directions to each problem.
16. Match the type of bond with the role below:
(a)
(b)
(c)
(d)
17.
Bond type
phosphodiester
N-glycosidic
phosphate ester
hydrogen
Match the factor or enzyme at right with the stage(s) of protein
synthesis at which it acts. If a factor or enzyme participates
in two stages of protein synthesis, indicate all of them.
___
___
___
___
18.
Role
___ links base to pentose in a nucleotide
___ joins adjacent nucleotides in one strand
___ joins complementary nucleotides in two
strands
___ difference between a nucleoside and a
nucleotide.
amino acid activation
initiation
elongation
synthetase termination
(a)
(b)
(c)
(d)
RF1
EF-Tu
AA-tRNA synthetase
Shine-Dalgarno sequence
Match each feature of the plasmid pBR322 (at left) with one appropriate
description presented (at right) (see picture of pBR322 below).
Descriptions may be used more than once.
EcoRI
BamHI
PstI
(amp R ) (tet R )
SalI
(ori)
PvuII
____
____
____
____
____
ampR sequence
ori sequence
tetR
BamHI sequence
PstI sequence
(a) permits selection of bacteria containing
the plasmid
(b) a sequence required for packaging
recombinant plasmids into bacteriophage
(c) origin of replication
(d) cleavage of the plasmid here does not
affect the antibiotic resistance genes
(e) insertion of foreign DNA here permits
selection of bacteria containing
recombinant plasmids
Page 4
NAME ________________________________
19.
For each of the following statements, indicate with a P if the
statement applies only to prokaryotes, an E if the statement applies
only to eukaryotes, and an E & P if the statement applies to both
eukaryotes and prokaryotes.
___ A single RNA polymerase transcribes genes that encode mRNAs,
tRNAs, and rRNA.
___ RNA processing/stability is a level at which gene expression can
be regulated.
___ Sigma (s) subunit detaches from RNA polymerase shortly after
transcription has initiated.
___ The 5' end of the mature mRNA begins with a triphosphate.
IV. Fill in the Blanks. (8 points)
Write the appropriate word or words in each blank provided.
20.
DNA replication in E. coli begins at a site in the DNA called the
(a) ___________. At the replication fork the (b) ___________ strand is
synthesized continuously while the (c) _________ strand is synthesized
discontinuously. On the strand synthesized discontinuously, the short
pieces are called (d) ____________ fragments. An RNA primer for each
of the fragments is synthesized by an enzyme called (e) __________, and
this RNA primer is removed after the fragment is synthesized by the
enzyme (f) ___________, using its (g) _____________ activity. The
nicks left behind in this process are sealed by the enzyme
(h) _____________.
V. TRUE/FALSE. (6 points)
Choose the BEST answer to the question by circling the appropriate letter.
T
F
21.
The A-form and B-form DNA are right-handed helices, but Z-form DNA is a
left-handed helix found only in single-stranded DNA.
T
F
22.
The linking number (Lk) of DNA can be changed only by breaking one or
both strands of constrained DNA.
T
F
23.
All tRNAs have the sequence -CCA at their 5' terminus.
T
F
24.
Some tRNAs contain G=U base pairs.
T
F
25.
Ribosomes contain many separate proteins.
T
F
26.
The three ribosomal RNAs in a bacterial ribosome are distributed in
three separate large ribosomal subunits.
VI. SHORT ANSWER (37 points)
Give a very brief answer as directed to each problem or question below.
27.
What is the approximate length of a DNA molecule in mmeters (in the B
form) containing 10,000 base pairs? (2 pts)
28.
Describe the composition and structure of a nucleosome. (3 pts)
Page 5
NAME ________________________________
29.
Why does lowering the ionic strength of a solution of double-stranded
DNA permit the DNA to denature more readily (for example, to denature
at a lower temperature than at a higher ionic strength)? (2 pts)
30.
Transfer RNAs have several bases in addition to the normal four found
in RNA. How are these rare bases incorporated into the tRNA molecule?
(2 pts)
31.
Below is a piece of DNA that is giving rise to an RNA molecule.
Indicate the 5' and 3' ends of the RNA molecule and of the strand of
DNA that is complementary to the RNA molecule. In which direction is
synthesis occurring (i.e., which end will be getting longer)? (4 pts)
32.
List one basic property that distinguishes RNA polymerases from DNA
polymerases, and list one basic property they share. (4 pts)
33.
A new antibiotic named ericamycin was recently discovered by a
brilliant graduate student. This antibiotic works by inhibiting
prokaryotic protein synthesis. In the presence of ericamycin protein
synthesis can initiate, but only dipeptides that remain bound to the
ribosome are formed. What specific step of protein synthesis is likely
to be blocked by this antibiotic? (3 pts)
34.
In a certain organism, the gene for hexokinase has 20,000 base pairs.
The molecular weight of hexokinase is 100,000. Is the organism likely
to be a eukaryote or a prokaryote? Explain your answer (do any
calculations on the back). (2 pts)
35.
In protein synthesis, 61 codons specify the 20 amino acids. Base
pairing between the codon and the tRNA anticodon assures that the
correct amino acid will be inserted into the nascent polypeptide chain.
Why then does the cell require only 32 different tRNAs to recognize 61
different codons? (3 pts)
Page 6
NAME ________________________________
36.
The Standard Genetic Code
UCU
Ser
UAU
Tyr
UCC
Ser
UAC
Tyr
UCA
Ser
UAA
Stop
UCG
Ser
UAG
Stop
UUU
UUC
UUA
UUG
Phe
Phe
Leu
Leu
UGU
UGC
UGA
UGG
Cys
Cys
Stop
Trp
CUU
CUC
CUA
CUG
Leu
Leu
Leu
Leu
CCU
CCC
CCA
CCG
Pro
Pro
Pro
Pro
CAU
CAC
CAA
CAG
His
His
Gln
Gln
CGU
CGC
CGA
CGG
Arg
Arg
Arg
Arg
AUU
AUC
AUA
AUG
Ile
Ile
Ile
Met
ACU
ACC
ACA
ACG
Thr
Thr
Thr
Thr
AAU
AAC
AAA
AAG
Asn
Asn
Lys
Lys
AGU
AGC
AGA
AGG
Ser
Ser
Arg
Arg
GUU
GUC
GUA
GUG
Val
Val
Val
Val
GCU
GCC
GCA
GCG
Ala
Ala
Ala
Ala
GAU
GAC
GAA
GAG
Asp
Asp
Glu
Glu
GGU
GGC
GGA
GGG
Gly
Gly
Gly
Gly
The template strand of a segment of double-stranded DNA contains the
sequence:
(5')CTT TGA TAA GGA TAG CCC TTC
(a) What is the base sequence of the mRNA that can be transcribed from
this strand (list in 5'® 3' direction)? (b) What amino acid sequence
could be coded by the mRNA base sequence in (a), using only the first
reading frame starting at the 5' end? (Refer to the genetic code
table.) (c) Suppose the other (complementary) strand is used as a
template for transcription. What is the amino acid sequence of the
resulting peptide, again starting from the 5' end and using only the
first reading frame? (6 pts)
37.
What is the basis of the separation on your cellulose acetate strips in
the laboratory? Draw the expected pattern of bands you would expect
from a zymogram run at pH 8.8 loaded with an enzyme composed of two
isozymes (a & b). Each isozyme has a trimeric quaternary structure and
can associate with itself and each other. One isozyme has a net charge
of +3/subunit and the other has a net charge of 0 at pH 8.8. Be sure
to label the origin (or point of loading) and the anode and the
cathode. (6 pts)
Page 7
Answer Sheet for Exam 4
11/25/2002
Test
Correct
Question Answer
Multiple Choice
1
A
2
D
3
D
4
C
5
A
6
D
7
A
8
C
9
D
10
E
11
B
12
B
13
A
14
D
Base Pairs
15
OH
N
6
7
N1
5
N
3
HO-CH 2
N
H
Enol
9
4
2
H N
8
O
ribose
O
H
H N
N
6
7
N1
5
4
2
H
9
N
3
N
Keto
8
HO-CH 2
O
ribose
---Matching
16
17
18
19
Fill in the Blanks
20
b;
c;
a;
P;
a; d; c
d; b; a
c; a; e; e
E & P; P; P
(a) origin; (b) leading; (c) lagging; (d) Okazaki;
(e) primase; (f) DNA pol I; (g) 5'® 3' exonuclease;
(h) DNA ligase
Test
Correct
Question Answer
True/False
21
F
22
T
23
T
24
T
25
T
26
F
Short Answer
27
28
29
30
Å
10,000 bp @10 bp/turn = 1000 turns @34 Å/turn = 34,000
= 3,400 nm = 3.4 mm
A nucleosome consists of double-stranded DNA wound
around a core of 8 histones. The octomer consists of 2
each of histone H2A, H2B, H3 and H4. Each nucleosome
involves about 150 base pairs of DNA, and nucleosomes
are spaced along a DNA molecule at intervals of about
200 base pairs.
Lower ionic strength reduces the screening of the
negative charges on the phosphate groups by positive
ions in the medium. The result is stronger chargecharge repulsion between the phosphate, which favors
strand separation.
The unusual bases in tRNA are added by enzymatically
modifying specific nucleotide residues in the pre-tRNA
molecule.
31
3'
5'
3'
direction of
synthesis
5'
32
33
34
Among the distinguishing characteristics:
RNA polymerase does not require a primer, but DNA
polymerase does; RNA polymerase lacks the 3'®5'
proofreading exonuclease activity present in DNA
polymerase.
Among the shared properties:
both enzymes use nucleoside triphosphates as substrates,
require Mg2+, Zn2+, produce an antiparallel complement to
the template, and synthesize nucleic acids in the
direction 5'® 3'.
Ericamycin probably blocks translocation.
The organism is a eukaryote.
-20,000 base pairs can encode a sequence of up to about
6700 amino acids. An enzyme of Mr 100,000 has about 900
amino acids (each amino acid residue contributes an
average of 110 to the total molecular weight). The gene
is therefore about seven times longer than needed to
encode the enzyme; six-sevenths of the gene sequence
must be introns, which are very rare in prokaryotes, but
common in eukaryotes.
Page 2
Test
Correct
Question Answer
35
36
37
In each recognized codon, there is a standard anticodoncodon base pair with the first two bases of the codon;
in the third base pair a "wobble base" exists that
allows one tRNA to read three different codons.
Similarly, tRNAs with U or G in the first anticodon
position also exhibit a wobble effect that permits
pairing with two different codons. For example, certain
tRNAs have the unusual nucleotide inosinate in the first
anticodon position. Because inosinate can base pair
with A, U, or C, a tRNA containing hypoxanthine can
recognize three different codons.
(a) (5')GAA GGG CUA UCC UUA UCA AAG
(b) Glu-Gly-Leu-Ser-Leu-Ser-Lys
(c) The codons translate to Leu-Stop-Stop. No peptide
would be produced, because of the stop codons.
The basis of the separation is by the charge on the
protein trimer. One trimer would have a net charge of
+9, another +6, another +3, and the last (the one that
does not move off the origin) is 0.
origin
anode
----
Page 3
a3
a2b
ab 2
b3
cathode