Basic Molecular Genetic Mechanisms - Lodish Ch4

Question 1

The percentage of G·C base pairs in a DNA molecule is related to the Tm of that molecule because

a. the stability of G·C and A·T base pairs is intrinsically different.
b. A·T base pairs require a higher temperature for denaturation.
c. the triple bonds of G·C base pairs are less stable than the double bonds of A·T base pairs.
d. the G·C content equals the A·T content.

Answer 1

a. the stability of G·C and A·T base pairs is intrinsically different.

Question 2

An investigator would be able to distinguish a solution containing RNA from one containing DNA by

a. heating the solutions to 82.5°C and measuring the absorption of light at 260 nm.
b. comparing the Tm of each solution.
c. monitoring the change in absorption of light at 260 nm while elevating the temperature.
d. measuring the absorption of light at 260 nm.

Answer 2

c. monitoring the change in absorption of light at 260 nm while elevating the temperature.

Question 3

What happens to a supercoiled, circular DNA molecule if it becomes nicked?

a. Torsional stress increases.
b. Torsional stress decreases.
c. A relaxed circle forms.
d. A linear molecule forms.

Answer 3

b. Torsional stress decreases.

c. A relaxed circle forms.

Question 4

Which of the following are used by RNA polymerase in the process of transcription?

a. DNA template
b. ribonucleotide triphosphates
c. deoxyribonucleotide triphosphates
d. inorganic phosphate

Answer 4

a. DNA template

b. ribonucleotide triphosphates

Question 5

What protein factors are required for transcription?

a. general transcription factors
b. RNA polymerase
c. DNA polymerase
d. ribosome

Answer 5

a. general transcription factors
b. RNA polymerase
d. ribosome

Question 6

Alternative splicing can result in which of the following?

a. production of different mRNA molecules from the same gene
b. production of different proteins from the same gene
c. production of two or more proteins that differ in their function
d. production of novel peptide domains

Answer 6

a. production of different mRNA molecules from the same gene
b. production of different proteins from the same gene
c. production of two or more proteins that differ in their function
d. production of novel peptide domains

Question 7

Which of the following statements is (are) true of bacterial genes?

a. They can be alternatively spliced.
b. They are organized into operons.
c. They are transcribed by RNA polymerase.
d. They have long 5´ and 3´ untranslated regions.

Answer 7

b. They are organized into operons.

c. They are transcribed by RNA polymerase.

Question 8

Each of the 20 different aminoacyl-tRNA synthetases

a. links an amino acid to the 3´ terminus of a tRNA molecule.
b. recognizes multiple amino acids.
c. requires ATP to catalyze reactions.
d. sometimes make mistakes.

Answer 8

a. links an amino acid to the 3´ terminus of a tRNA molecule.
c. requires ATP to catalyze reactions.
d. sometimes make mistakes.

Question 9

The ribosome

a. is an enzyme complex made entirely of protein molecules.
b. directs elongation of polypeptides.
c. is organized into two subunits whose sizes are designated in svedberg (S) units.
d. is not used by cells that secrete large amounts of protein.

Answer 9

b. directs elongation of polypeptides.

c. is organized into two subunits whose sizes are designated in svedberg (S) units.

Question 10

Which of the following occur(s) when the eukaryotic translational machinery encounters the TAG codon?

a. The bound preinitiation complex stops scanning and positions the Met-tRNAiMet at this site.
b. The termination factors recognize this codon and translation ends.
c. This codon is recognized by the corresponding anticodon of an empty tRNA molecule that is not linked to an amino acid.
d. This codon is not recognized by any factors that ultimately cause the translational machinery to stop.

Answer 10

b. The termination factors recognize this codon and translation ends.

Question 11

DNA replication

a. requires a DNA template, deoxynucleotides, primers, and DNA polymerase.
b. can be initiated de novo.
c. requires the addition of de-oxynucleotides to the 5´ free hydroxl group.
d. occurs on only 1 strand of DNA.
e. utilizes Okazaki fragments on the leading strand.

Answer 11

a. requires a DNA template, deoxynucleotides, primers, and DNA polymerase.

Question 12

Which of the following DNA repair mechanisms can repair double-stranded DNA breaks in eukaryotes?

a. base excision repair
b. homologous recombination
c. mismatch excision repair
d. nonhomologous end joining
e. nucleotide excision repair

Answer 12

b. homologous recombination

d. nonhomologous end joining

Question 13

DNA viral genomes encode the virus’s own

a. DNA polymerase.
b. transcriptional machinery.
c. translational machinery.
d. none of the above

Answer 13

a. DNA polymerase.

Question 14

If the adenine content of DNA from an organism is 36 percent, what is the guanine content?

Answer 14

Since A = T, the A + T content = 72 percent and G + C content = 28 percent. Since G = C, the content of G is 14 percent.

Question 15

Which of the common Watson-Crick base pairs in DNA is most stable? Why? How does this property affect the melting temperature of DNA?

Answer 15

Guanine-cytosine (G·C) base pairs are more stable than adenine-thymine (A·T) pairs because G and C form three hydrogen bonds, whereas A and T form only two. The greater stability conferred by the additional hydrogen bonds in G·C pairs means that DNA rich in G·C pairs requires more energy for denaturation than does DNA rich in A·T pairs. Thus, the melting (denaturation) temperature of G-C-rich DNA is higher than that of A·T-rich DNA.

Question 16

What is the major difference in the genome organizations of prokaryotic and eukaryotic genes?

Answer 16

In prokaryotes, genes devoted to a single metabolic goal are most often found in a contiguous array called an operon. These operons are regulated as a unit from a single promoter. In eukaryotes, this clustering of genes does not occur, and such genes are most often physically separated in the DNA. Each gene is transcribed from its own promoter producing single RNA molecules. In addition, eukaryotes have a significant amount of noncoding DNA present in their genomes. Prokaryotes genes are closely packed with very few noncoding gaps. Lastly, eukaryotic genes can contain noncoding sequences called introns within their coding regions. Prokaryotic genes do not contain introns.

Question 17

Describe three features of eukaryotic transcripts that generally are not shared with prokaryotic transcripts.

Answer 17

Unprocessed eukaryotic transcripts contain introns which must be spliced out before translation occurs. Eukaryotic transcripts also are modified at the 5´ and 3´ ends. The 5´ end contains a 7-methylguanylate cap that is connected to the terminal nucleotide of the RNA molecule. In addition, processing at the 3´ end produces a free hydroxyl group to which a string of adenylic acid residues is added. This is called the poly(A) tail. While some prokaryotic transcripts do contain a poly(A) tail, this is still considered a hallmark of eukaryotic mRNA transcripts.

Question 18

What is one conclusion that can be drawn from the observation that the genetic code is nearly identical in all cells on earth?

Answer 18

A strong conclusion from this observation is that life on earth evolved only once.

Question 19

What is one possible reason why nonstandard base pairing (wobble) is allowed during protein synthesis?

Answer 19

Wobble may speed up protein synthesis by allowing the use of alternative tRNAs. If only one codon-anticodon pair were permitted for each amino acid insertion, protein synthesis might be temporarily halted until a reasonable level of that particular activated tRNA was regenerated. In fact, a slowdown of protein synthesis, due to the lack of a particular aminoacyl tRNA, is used to regulate the levels of enzymes involved in synthesis of some amino acids. This process is called attenuation.

Question 20

What purpose is served by having mRNA, aminoacyl-tRNAs, and various enzymes associated with a large, complicated structure (the ribosome) during protein synthesis?

Answer 20

The highly specific chemical reactions of translation take place at a much higher rate if the individual components (mRNA, aminoacyl-tRNAs, and the appropriate enzymes) are confined by mutual binding to a common structure, the ribosome. This interaction limits diffusion of one component away from the rest and enables protein synthesis to proceed at the rate of nearly 1 million peptide bonds per second in the average mammalian cell. (Similarly, electron donors and acceptors, in a highly organized array, such as that found in the inner membrane of the mitochondrion or the plasma membrane of a bacterium, can operate much more efficiently than they would if diffusion in three dimensions occurred.) Ribosomes not only provide a site at which the necessary components for protein synthesis are assembled, but at least one ribosomal component, the (prokaryotic) 23S rRNA, is involved in catalyzing the formation of peptide bonds.

Question 21

DNA replication is always 5´ to 3´. Explain what “5´ to 3´” means with respect to nucleotide subunits. What activity of DNA polymerase necessitates that replication is 5´ to 3´ rather than 3´ to 5´?

Answer 21

5´ to 3´ means that the 5´ phosphate of the nucleotide being added to the chain forms a phosphodiester bond with the 3´ hydroxyl of the nucleotide last added to the chain. Replication must be 5´ to 3´ because of the proofreading capabilities of DNA polymerase. If replication were 3´ to 5´ (and exonuclease activity 5´ to 3´) there would be no high-energy phosphate bond available after proofreading to provide energy for the addition of the correct base.

Question 22

Why is DNA synthesis discontinuous—that is, why is DNA ligase needed to join fragments of one strand of DNA?

Answer 22

DNA synthesis is discontinuous because the double helix consists of two antiparallel strands and DNA polymerase can synthesize DNA only in the 5´ to 3´ direction. Thus one strand is synthesized continuously at the growing fork, but the other strand is synthesized in fragments that are joined by DNA ligase.

Question 23

Why might a double-stranded break in DNA caused by ionizing radiation be considered more harmful that a thymine dimer caused by ultraviolet radiation?

Answer 23

When a double-stranded break occurs in DNA, there is no information on either strand to prevent ligation of DNA from different chromosomes or from different parts of a chromosome. This causes a mutation that will be perpetuated in future cell generations. Thymine dimers are repaired by mechanisms that remove nucleotide from only one of the two complementary strands, leaving the other strand as a template for DNA polymerase to fill in the correct bases.

Question 24

Why did the discovery of reverse transcriptase go against the so-called central dogma? Which organism was utilized in the discovery of reverse transcriptase? Why is this enzyme crucial to this organism’s life cycle?

Answer 24

The central dogma states that information flows from DNA to RNA. The discovery of reverse transcriptase goes against the central dogma because this enzyme catalyzes the synthesis of DNA from a viral RNA template. Reverse transcriptase was first identified in retroviruses, viruses that contain an RNA genome. Retroviruses need reverse transcriptase to copy the viral genome into double-stranded DNA complementary to the virion RNA. This DNA is integrated into the chromosomal DNA of the infected cell. This DNA is then transcribed by the cell’s own machinery into RNA, which is either translated into viral proteins or is packaged within the virion coat proteins to form progeny.

Question 25

How can one estimate melting temperatures for PCR primers?

Answer 25

For short sequences of DNA, the Tm can be estimated by 4°C(# G + C) + 2°C(# A + T). The melting temperatures estimated by this formula are shown.

Question 26

For each tRNA, there may be:

a. more than one amino acid
b. only one amino acid
c. more than one codon
d. only one codon
e. no available codons

Answer 26

b. only one amino acid
c. more than one codon

The genetic code is degenerate but unambiguous. This means that each codon codes for a single amino acid, and each tRNA carries only one amino acid, but there can be more than one codon that specifies a particular amino acid.

Question 27

In which order are the following enzymatic activities required for DNA replication on the lagging strand in eukaryotes? Each activity may be used more than once or not at all.

a. DNA polymerase
b. RNA polymerase
c. DNase
d. RNase
e. DNA ligase

Answer 27

1. RNA polymerase (b)
2. DNA polymerase (a)
   3 RNase (d)
3. DNA polymerase (a)
4. DNA ligase (e)

Question 28

Which type of DNA damage is considered the most deleterious to the stability of the genome?

a. abasic sites
b. double-stranded breaks
c. point mutations
d. single-stranded breaks
e. thymine dimers

Answer 28

b. double-stranded breaks

Unlike the other types of damage, for double-stranded breaks there is no template on the complementary strand to ensure accurate repair. Double-stranded breaks require repair by DNA ligase, and often the ends will be ligated to other strands, rather than to each other.

Question 29

What creates the 5’ to 3’ directionality of double-stranded DNA?

Answer 29

Phosphodiester linkages

Question 30

Each turn of a double helix has how many nucleotides?

Answer 30

10 nucleotides or 3.4 nm

Question 31

What causes the major and minor grooves?

Answer 31

Slight offset between the bond of the sugar and bases, the glycosidic bonds. Create a curve.

Question 32

What is the core mechanism underlying nucleic acid thermodynamics?

Answer 32

Hydrogen bonding

Question 33

Define melting temperature (Tm).

Answer 33

The temperature at which 50% of db-stranded DNA parade into ss-DNA.

G:C has a higher melting temperature (almost 2X) compared to A:T.

Question 34

Why do many PCR assays contain a protein digestion step?

Answer 34

Proteins such as histones may bind and prevent access for primers or probes to DNA. This is especially true for heterochromatin, tightly condensed areas of DNA.

Question 35

Why is DNA replication considered semi-conservative?

Answer 35

Each double-stranded DNA strand consists of an old and a new strand.

Question 36

What is the processivity rate of most polymerases?

Answer 36

1,000 bases per minute

Question 37

The fidelity of a polymerase refers to…

Answer 37

The accuracy of the enzyme to incorporate the correct complimentary base in the newly synthesized DNA strand.

Question 38

What are the bases of a start codon?

Answer 38

AUG, methionine

Question 39

What are the triplet base cods for a stop codon?

Answer 39

UAG
UGA
UAA