Download Chapter 4

BIOCHEMISTRY 461
DR. BOURQUE
Chapter 4 Study Questions Key
Fall 2010
[4 pts] The pentanucleotide, pACCGAp, can be either an RNA or a DNA molecule of 5 bases in
length, depending on whether the sugars are ribose or deoxyribose.
a) If it is an RNA, the pentanucleotide will have a total of __5____ free ribose OH group(s).
b) If it is a DNA, the pentanucleotide will have a total of
group(s).
[10 pts]
___0___ free deoxyribose OH
Answer the following questions:
a) Name two important required features of a template - primer complex for DNA polymerase
to function in DNA replication. (4 pts)
Answer: any two of these
- base-pairing of primer with template
- base pairing of incoming nucleotide with template
- free 3'-OH group
b) What is the DNA polymerase reaction mechanism. Be sure to name the attacking group
and its target. (4 pts)
- nucleophilic attack by negatively charged unpaired electrons of primer 3'OH on alpha phosphate of incoming NTP
c) Name the functional groups involved and the driving force for DNA synthesis by DNA
polymerase. (2 pts)
!
!
[6 pts]
PPi is leaving group
its hydrolysis to 2Pi by pyrophosphatase is the driving force for net RNA
synthesis
What characteristics are common to DNA synthesis, RNA synthesis, and the first
committed step in purine biosynthesis? Circle the correct choices:
[Circle the correct answers]
Reactions are actually ( reversible, irreversible ).
Reactions in cells are driven to ( synthesis, no synthesis ).
Reactions in cells are driven by ( breakdown, synthesis ) of product pyrophosphate
(PPi).
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[18 pts]
Answer the following questions which relate to this DNA sequence and the
genetic code:
3'
-TACCGTTTTTAAAAGACT -5'
Using this DNA as a template for transcription, show the base sequence of the mRNA for which it
codes: [6 pts]
Answer: 5'-AUG GCA AAA AUU UUC UGA-3'
What is the polypeptide for which this mRNA codes? [6 pts]
Answer: Met-Ala-Lys-Ile-Phe
What single base change in the mRNA will
alter the last (3') codon to a trytophan (Trp)
codon? [2 pts]
Answer:-UGA to UGG (change A to G)
What single base change in the mRNA will
alter the second codon (from the 5'-end) to a
serine (Ser) codon? [2pts]
Answer:
CA to UCA(change G to U)
In human mitochondria, UGA codes for tryptophan. What would the sequence of the polypeptide be if
the mRNA was translated in human mitochondria? [2pts]
Answer: Met-Ala-Lys-Ile-Phe-Trp
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[16 pts] Write in the blanks the most important characteristic features of protein synthesis and
transcription associated with the questions in the left-hand column.
Protein Synthesis
Transcription
What are start
signal(s)?
AUG codon
promoter: has two conserved
sequences 5' to start of
transcription
What are stop
signal (s)?
stop codons
the RNA transcript has a
hairpin loop with GC base
pairs and followed at 3' end
by several U’s
Need for primer?
(yes or no)
no
no
Compare
procaryotic and
eucaryotic
sequence signals
procaryotic: a sequence on
mRNA aligns with ribosome
eucaryotic: ribosome searches
for 1st AUG from 5' end
both types of promoters have
two conserved sequence
elements 5' to start of
transcription. eucaryotic ones
are farther away from start
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[22 pts] ANSWER TRUE OR FALSE:
T
A complementary DNA copy of its RNA genome is synthesized by a retrovirus as part of its life
cycle.
T
In the DNA-B double helix, both polynucleotide chains have the opposite phosphodiester bond
polarity.
F
RNA polymerase synthesizes RNA in the 3' to 5' direction by attaching each new, correctly
base-paired, ribonucleotide to a free 5'-OH group of the terminal ribose.
F
DNA replication occurs by a mechanism in which one daughter DNA molecule has both intact
parent DNA strands and the other daughter molecule has two newly synthesized DNA strands.
T
Portions of most RNA molecule can form a base-paired hybrid RNA-RNA double helix.
T
The temperature (Tm) at which 50% of the base pairs of a DNA molecule are separated is
directly related to the %GC base pairs of the DNA.
F(T) In double-stranded DNA-RNA hybrids, base pairing occurs between A and T [True if A is in
the RNA strand and T is in the DNA strand; False if A is in the DNA strand, since it would
base-pair with U in the RNA strand]
F
Experiments with tobacco mosaic virus showed that the coat protein of the infecting virus
determines the RNA sequence tha is transmitted from one virus particle to its progeny.
T
The total length of DNA in your body is more than a billion base pairs.
T
Radioisotope labeling experiments proved that mRNA for T2 bacteriophage is complementary to
T2 DNA, with which it can form double-stranded base-paired structures.
F Each amino acid is coded by more than one codon in the Universal Genetic Code.
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Multiple Choice Questions
How does a nucleotide differ from a nucleoside?
A)
B)
C)
D)
E)
Nucleosides are found in DNA, whereas nucleotides are found in RNA.
Purines are only found in nucleotides.
Nucleosides contain only deoxyribose sugars.
A nucleotide is a nucleoside with a phosphate ester linked to the sugar .
None of the above.
Ans: D
What is the nucleotide sequence on the DNA template strand that yields the CUA codon for leucine?
A)
AUC D)
GAT
B)
TAG E)
CUA
C)
CTA
Ans: B
The technique(s) used by Franklin and Wilkins to deduce the structure of DNA was
A)
absorbance spectrophotometry. D)
All of the above.
B)
electron microscopy.
E)
None of the above.
C)
X-ray diffraction.
Ans: C
The feature(s) of DNA deduced by Watson and Crick included
A)
two antiparallel polynucleotide chains coiled in a helix around a common axis.
B)
the pyrimidine and purine bases lie on the inside of the helix.
C)
the bases are nearly perpendicular to the axis.
D)
All of the above.
E)
None of the above.
Ans: D
What is the approximate error rate in DNA replication?
A) 1 ´ 10-8 B) 1 ´ 10-6 C) 1 ´ 10-15 D) 1 ´ 10-10
Ans: A
E) None of the above.
What are the common promoter regions found in bacterial genes?
A)
a Pribnow box about –10 and a –35 region
B)
a TATA box about –25 and a CAAT box about –75
C)
a Pribnow box about –10 and a TATA box about –25
D)
a TATA box about –25 and a –35 region
E)
None of the above.
Ans: A
Which of the following is correct concerning the adaptor molecule tRNA?
A)
tRNA contains an anticodon sequence that is the mRNA template recognition site.
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B)
C)
D)
E)
The amino acid is attached to the 5' end of tRNA.
tRNA contains a poly A tail at the 3' end.
tRNA is the smallest RNA in the cell.
tRNA serves as the gene in some viruses.
Ans: A
Features of the genetic code include
A)
a codon is defined by three bases.
B)
the code overlaps. E)
a and b.
C)
the code is degenerate.
Ans: D
The first amino acid in bacterial proteins is
A) Met. B) fGly. C) fMet. D) Gly.
Ans: C
D)
a and c.
E) None of the above.
In which codon position(s) do most synonyms differ?
A)
first position D)
a and c
B)
second position
E)
None of the above
C)
third position
Ans: C
The sites for intron splicing consensus sequences are often
A)
AC-------------------AAAA. D)
All of the above.
B)
GU-------------------AG.
E)
None of the above.
C)
AU-------------------GC.
Ans: B
Ribosomes are composed of”
A) DNA. B) rRNA. C) protein.
Ans: E
D) All of the above.
E) b and c.
Draw two nucleotides in DNA showing the linkage between the sugars linked.
Ans: The 3' oxygen of one nucleotide is linked to a phosphorous atom, which is linked
to the oxygen on the 5' carbon on the next sugar. Two extra oxygens should be
attached to the phosphorus atom, and the phosphate should be shown ionized at
neutral pH. There should be no oxygen at the 2' position of the sugar.
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Describe the DNA helix proposed by Watson and Crick.
Ans: The DNA model proposed by Watson and Crick contains two DNA polymer
strands coiled around a common axis. The strands are orientated in opposite directions
from 5' to 3' (antiparallel), and the two strands are twisted in a right-handed coil. The
sugar-phosphate backbone is located on the outside. The base pairs are stacked in the
center of the helix and are stabilized by specific hydrogen bonds between AT and GC
base pairs. The base pairs lie perpendicular to the axis, and there are 10 base pairs per
turn with a helical repeat of 34 angstroms.
Draw the Hydrogen bonded base pairs of A to T.
Answer: See figures in notes and tet.
Briefly describe the Meselson and Stahl experiment that indicated that DNA replication is
semiconservative
Ans: Meselson and Stahl grew bacteria in the presence of 15N, or "heavy" nitrogen.
They rapidly replaced the 15N media with 14N, or light nitrogen. DNA was extracted at
various time intervals during the growth of the bacteria, representing different stages of
replication (generations). They examined the DNA using density-gradient equilibrium
sedimentation and observed that no "heavy" DNA was present in the first generation,
but that the DNA was intermediate between light and heavy. After the second
generation, there were equal amounts of intermediate and light. This confirmed that
one strand of the parent DNA is present in each daughter strand of replicated DNA.
What is nucleic acid (DNA-DNA, DNA-RNA or RNA-RNA) hybridization?
Ans: DNA hybridization is the process whereby strands of nearly complimentary DNA
from different organisms or one strand of DNA and one strand of RNA base pair to form
a helix.
Draw a template-primer comlex and show how the dNTP is added to a DNA strand at the 3' end?
Ans: The drawing should indicate clearly how the 3'OH oxygen attacks the phosphate
on the incoming dNTP with the displacement of pyrophosphate.
How does RNA polymerase differ from DNA polymerase?
Ans: Although similar in many respects to DNA polymerase, RNA polymerase does not
require a primer, nor does it have the nuclease "proofreading" capacity.
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What is a consensus sequence?
Ans: A consensus sequence is a common sequence motif found in a number of genes
or DNA regions. While all the sequences may not be exactly alike, and may differ in one
or several bases, the sequences have a very similar structure, and implied common
function.
What are two features of eukaryotic mRNA that are unique as compared to prokaryotic mRNA.
Ans: Eukaryotic mRNA has a special nucleotide "cap" at the 5' end and a poly A tail at
the 3' end.
What is an advantage of codon degeneracy?
Ans: Changes in the third position often have no effect on the final amino acid used in
translation. Thus, degeneracy minimizes the deleterious effect of DNA mutations.
The genetic code is not universal. Where are exceptions found?
Ans: Exceptions are found in several places. The most notable are those in
mitochondria. Ciliated protozoans also have some unique codons.
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