Question 1

The role of the Dam methylase is to:

Accepted Answer

A)  add a methyl group to uracil, converting it to thymine. 
B)  modify the template strand for recognition by repair systems. 
C)  remove a methyl group from thymine. 
D)  remove a mismatched nucleotide from the template strand. 
E)  replace a mismatched nucleotide with the correct one. 
A)  add a methyl group to uracil, converting it to thymine. 
B)  modify the template strand for recognition by repair systems. 
C)  remove a methyl group from thymine. 
D)  remove a mismatched nucleotide from the template strand. 
E)  replace a mismatched nucleotide with the correct one. B

Question 2

What distinguishes the simple from the complex class of bacterial transposon?

Accepted Answer

Bacterial transposons, also known as transposable elements, are segments of DNA that can move from one location to another within a genome. They play a significant role in the evolution of bacterial genomes by facilitating genetic variation and horizontal gene transfer. Transposons are classified into two main categories based on their structure and mechanism of transposition: simple transposons and complex transposons.

Simple Transposons:
Simple transposons, also known as insertion sequences (IS elements), are the most basic form of transposable elements. They typically consist of a single gene that encodes the transposase enzyme, which is required for the cut-and-paste mechanism of transposition. This gene is flanked by short inverted repeat sequences that are recognized by the transposase. The simple transposons do not carry additional genes other than those necessary for transposition. Due to their simplicity, they are usually smaller in size compared to complex transposons.

Complex Transposons:
Complex transposons, on the other hand, contain additional genes beyond the transposase and the inverted repeats. These additional genes often include those that confer antibiotic resistance or other traits beneficial to the bacteria. Complex transposons may also contain more than one gene involved in the transposition process, such as a resolvase that helps resolve cointegrate structures formed during transposition. They are larger than simple transposons and can carry a significant amount of genetic material from one location to another.

In summary, the key distinctions between simple and complex bacterial transposons are:

1. Gene Content: Simple transposons contain only the genes necessary for transposition, while complex transposons carry additional genes, often conferring advantageous traits like antibiotic resistance.

2. Size: Simple transposons are generally smaller due to their limited gene content, whereas complex transposons are larger because they include extra genes.

3. Structural Complexity: Simple transposons have a straightforward structure with a transposase gene flanked by inverted repeats. Complex transposons have a more elaborate structure that can include multiple genes and regulatory sequences.

Understanding the differences between simple and complex transposons is crucial for comprehending how genetic elements contribute to the adaptability and evolution of bacterial species.

Question 3

Which statement is FALSE regarding the DNA ligase mechanism?

Accepted Answer

A)  The mechanism is an example of covalent catalysis. 
B)  Either ATP or NAD+ may contribute an adenyl group to the reaction. 
C)  Energy from a phosphoanhydride bond is used to make a phosphodiester bond. 
D)  One of the products of the reaction is ADP. 
E)  A lysine is found in the active site of the enzyme. 
A)  The mechanism is an example of covalent catalysis. 
B)  Either ATP or NAD+ may contribute an adenyl group to the reaction. 
C)  Energy from a phosphoanhydride bond is used to make a phosphodiester bond. 
D)  One of the products of the reaction is ADP. 
E)  A lysine is found in the active site of the enzyme. D

Question 4

List two proteins or enzymes, other than DNA polymerase III, that are found at the replication fork in E. coli. Describe each of their functions with no more than one sentence.

Accepted Answer

1. Helicase - Helicase is responsible fo

Question 5

The high fidelity of DNA replication is due primarily to immediate error correction by the 3' $\rightarrow$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.

Accepted Answer

1. Mismatch repair: This mechanism corre

Question 6

Which eukaryotic DNA polymerase carries out replication in a manner analogous to E. coli DNA polymerase III?

Accepted Answer

A)  DNA polymerase $\alpha$(alpha) 
B)  DNA polymerase $\beta$ (beta) 
C)  DNA polymerase $\gamma$ (gamma) 
D)  DNA polymerase  $\delta$  (delta) 
E)  DNA polymerase $\varepsilon$ (epsilon) 
A)  DNA polymerase $\alpha$(alpha) 
B)  DNA polymerase $\beta$ (beta) 
C)  DNA polymerase $\gamma$ (gamma) 
D)  DNA polymerase  $\delta$  (delta) 
E)  DNA polymerase $\varepsilon$ (epsilon)

Question 7

What concept does NOT generally apply to bacterial transposons?

Accepted Answer

A)  Transposons are sometimes referred to as "jumping genes." 
B)  Transposons contain segments of repeating DNA at either end. 
C)  Insertion of a transposon followed by excision results in damage to the sequence at the insertion site. 
D)  "Transposases" are the enzymes involved in transposition. 
E)  Transposition is a homologous-recombination process. 
A)  Transposons are sometimes referred to as "jumping genes." 
B)  Transposons contain segments of repeating DNA at either end. 
C)  Insertion of a transposon followed by excision results in damage to the sequence at the insertion site. 
D)  "Transposases" are the enzymes involved in transposition. 
E)  Transposition is a homologous-recombination process.

Question 8

Which statement is FALSE regarding the E. coli DNA unwinding element (DUE)?

Accepted Answer

A)  This sequence appears in tandem. 
B)  The sequence is part of the origin of replication. 
C)  This sequence binds to DnaA. 
D)  This sequence is where the helicase binds during initiation of replication. 
E)  This sequence will be hemi-methylated after replication begins. 
A)  This sequence appears in tandem. 
B)  The sequence is part of the origin of replication. 
C)  This sequence binds to DnaA. 
D)  This sequence is where the helicase binds during initiation of replication. 
E)  This sequence will be hemi-methylated after replication begins.

Question 9

An alternative repair system by error-prone translesion DNA synthesis can result in a high mutation rate because:

Accepted Answer

A)  alternative modified nucleotides can be incorporated more readily. 
B)  interference from the RecA and SSB proteins hinders the normal replication accuracy. 
C)  replication proceeds much faster than normal, resulting in many more mistakes. 
D)  the DNA polymerases involved cannot facilitate base-pairing as well as DNA polymerase III. 
E)  the DNA polymerases involved lack exonuclease proofreading activities. 
A)  alternative modified nucleotides can be incorporated more readily. 
B)  interference from the RecA and SSB proteins hinders the normal replication accuracy. 
C)  replication proceeds much faster than normal, resulting in many more mistakes. 
D)  the DNA polymerases involved cannot facilitate base-pairing as well as DNA polymerase III. 
E)  the DNA polymerases involved lack exonuclease proofreading activities.

Question 10

In homologous recombination in E. coli, the protein that moves along a double-stranded DNA, unwinding the strands ahead of it and degrading them, is:

Accepted Answer

A)  chi. 
B)  DNA ligase. 
C)  RecA protein. 
D)  RecBCD enzyme. 
E)  RuvC protein (resolvase). 
A)  chi. 
B)  DNA ligase. 
C)  RecA protein. 
D)  RecBCD enzyme. 
E)  RuvC protein (resolvase).

Question 11

List the four enzymes involved in base-excision repair, in order of their activity, when uracil is incorporated into DNA and briefly outline their function.

Accepted Answer

The four enzymes involved in base-excisi

Question 12

Briefly explain the difference between base-excision repair and nucleotide-excision repair.

Accepted Answer

Base-excision repair (BER) and nucleotid

Question 13

Which protein does NOT contribute in some fashion to the low rate of errors in DNA replication in E. coli?

Accepted Answer

A)  MutS 
B)  DNA Pol III 
C)  Dam methylase 
D)  DnaG 
E)  UvrD 
A)  MutS 
B)  DNA Pol III 
C)  Dam methylase 
D)  DnaG 
E)  UvrD

Question 14

In base-excision repair, the first enzyme to act is:

Accepted Answer

A)  AP endonuclease. 
B)  Dam methylase. 
C)  DNA glycosylase. 
D)  DNA ligase. 
E)  DNA polymerase. 
A)  AP endonuclease. 
B)  Dam methylase. 
C)  DNA glycosylase. 
D)  DNA ligase. 
E)  DNA polymerase.

Question 15

Which phrase describes a role for E. coli DNA Pol III?

Accepted Answer

A)  lagging strand synthesis only 
B)  base excision repair only 
C)  mismatch repair only 
D)  both lagging strand synthesis and mismatch repair 
E)  All of these are roles for DNA Pol III. 
A)  lagging strand synthesis only 
B)  base excision repair only 
C)  mismatch repair only 
D)  both lagging strand synthesis and mismatch repair 
E)  All of these are roles for DNA Pol III.

Question 16

In humans, what repair mechanism is used to correct thymine dimers?

Accepted Answer

A)  base-excision repair 
B)  nucleotide-excision repair 
C)  mismatch repair 
D)  photolyase 
E)  both nucleotide-excision repair and photolyase 
A)  base-excision repair 
B)  nucleotide-excision repair 
C)  mismatch repair 
D)  photolyase 
E)  both nucleotide-excision repair and photolyase

Question 17

Which sequences are palindromic?

Accepted Answer

A)  DNA unwinding elements (DU
E)  
B)  terminator sequences (Ter) 
C)  EcoRI restriction sites 
D)  both DUE and Ter 
E)  None of these sequences is palindromic. 
A)  DNA unwinding elements (DU
E)  
B)  terminator sequences (Ter) 
C)  EcoRI restriction sites 
D)  both DUE and Ter 
E)  None of these sequences is palindromic.

Question 18

What role does AP endonuclease have in the base-excision repair system?

Accepted Answer

A)  It removes the damaged base from the nucleic acid. 
B)  It cleaves the phosphodiester backbone after base removal. 
C)  It removes nucleotides from the broken strand of the nucleic acid. 
D)  It adds new nucleotides to replace the excised ones. 
E)  It creates a new phosphodiester bond to repair the backbone. 
A)  It removes the damaged base from the nucleic acid. 
B)  It cleaves the phosphodiester backbone after base removal. 
C)  It removes nucleotides from the broken strand of the nucleic acid. 
D)  It adds new nucleotides to replace the excised ones. 
E)  It creates a new phosphodiester bond to repair the backbone.

Question 19

The 5' $\rightarrow$3' exonuclease activity of E. coli DNA polymerase I is involved in:

Accepted Answer

A)  formation of a nick at the DNA replication origin. 
B)  formation of Okazaki fragments. 
C)  proofreading of the replication process. 
D)  removal of RNA primers by nick translation. 
E)  sealing of nicks by ligase action. 
A)  formation of a nick at the DNA replication origin. 
B)  formation of Okazaki fragments. 
C)  proofreading of the replication process. 
D)  removal of RNA primers by nick translation. 
E)  sealing of nicks by ligase action.

Question 20

Which recombination or repair mechanism does NOT generally conserve the original DNA sequence?

Accepted Answer

A)  recombinational DNA repair 
B)  site-specific recombination 
C)  nonhomologous end joining 
D)  photolyase repair 
E)  nucleotide-excision repair 
A)  recombinational DNA repair 
B)  site-specific recombination 
C)  nonhomologous end joining 
D)  photolyase repair 
E)  nucleotide-excision repair

Exam 25: DNA Metabolism

The role of the Dam methylase is to:

What distinguishes the simple from the complex class of bacterial transposon?

Which statement is FALSE regarding the DNA ligase mechanism?

List two proteins or enzymes, other than DNA polymerase III, that are found at the replication fork in E. coli. Describe each of their functions with no more than one sentence.

Which eukaryotic DNA polymerase carries out replication in a manner analogous to E. coli DNA polymerase III?

What concept does NOT generally apply to bacterial transposons?

Which statement is FALSE regarding the E. coli DNA unwinding element (DUE)?

An alternative repair system by error-prone translesion DNA synthesis can result in a high mutation rate because:

In homologous recombination in E. coli, the protein that moves along a double-stranded DNA, unwinding the strands ahead of it and degrading them, is:

List the four enzymes involved in base-excision repair, in order of their activity, when uracil is incorporated into DNA and briefly outline their function.

Briefly explain the difference between base-excision repair and nucleotide-excision repair.

Which protein does NOT contribute in some fashion to the low rate of errors in DNA replication in E. coli?

In base-excision repair, the first enzyme to act is:

Which phrase describes a role for E. coli DNA Pol III?

In humans, what repair mechanism is used to correct thymine dimers?

Which sequences are palindromic?

What role does AP endonuclease have in the base-excision repair system?

The 5' →\rightarrow→ 3' exonuclease activity of E. coli DNA polymerase I is involved in:

Which recombination or repair mechanism does NOT generally conserve the original DNA sequence?

The Foundations of Biochemistry

Water

Amino Acids, Peptides, and Proteins

The Three-Dimensional Structure of Proteins

Protein Function

Enzymes

Carbohydrates and Glycobiology

Nucleotides and Nucleic Acids

DNA-Based Information Technologies

Lipids

Biological Membranes and Transport

Biosignaling

Bioenergetics and Biochemical Reaction Types

Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway

Principles of Metabolic Regulation

The Citric Acid Cycle

Fatty Acid Catabolism

Amino Acid Oxidation and the Production of Urea

Oxidative Phosphorylation and Photophosphorylation

Carbohydrate Biosynthesis in Plants and Bacteria

Lipid Biosynthesis

Biosynthesis of Amino Acids, Nucleotides, and Related Molecules

Hormonal Regulation and Integration of Mammalian Metabolism

Genes and Chromosomes

RNA Metabolism

Protein Metabolism

Regulation of Gene Expression

Filters

The 5' $\rightarrow$ 3' exonuclease activity of E. coli DNA polymerase I is involved in: