11.E: Mechanisms of Microbial Genetics (Exercises)

11.1: What Are Genes?

A gene is composed of DNA that is “read” or transcribed to produce an RNA molecule during the process of transcription. One major type of RNA molecule, called messenger RNA (mRNA), provides the information for the ribosome to catalyze protein synthesis in a process called translation. The processes of transcription and translation are collectively referred to as gene expression.

Multiple Choice

DNA does all but which of the following?

1. serves as the genetic material passed from parent to offspring
2. remains constant despite changes in environmental conditions
3. provides the instructions for the synthesis of messenger RNA
4. is read by ribosomes during the process of translation

Answer

D

According to the central dogma, which of the following represents the flow of genetic information in cells?

1. protein to DNA to RNA
2. DNA to RNA to protein
3. RNA to DNA to protein
4. DNA to protein to RNA

Answer

B

True/False

Cells are always producing proteins from every gene they possess.

Answer

False

Fill in the Blank

The process of making an RNA copy of a gene is called ________.

Answer

transcription

A cell’s ________ remains constant whereas its phenotype changes in response to environmental influences.

Answer

genotype or genome

Short Answer

Can two observably different cells have the same genotype? Explain.

Critical Thinking

A pure culture of an unknown bacterium was streaked onto plates of a variety of media. You notice that the colony morphology is strikingly different on plates of minimal media with glucose compared to that seen on trypticase soy agar plates. How can you explain these differences in colony morphology?

11.2: DNA Replication

The DNA replication process is semiconservative, which results in two DNA molecules, each having one parental strand of DNA and one newly synthesized strand. In bacteria, the initiation of replication occurs at the origin of replication, where supercoiled DNA is unwound by DNA gyrase, made single-stranded by helicase, and bound by single-stranded binding protein to maintain its single-stranded state.

Multiple Choice

Which of the following is the enzyme that replaces the RNA nucleotides in a primer with DNA nucleotides?

1. DNA polymerase III
2. DNA polymerase I
3. primase
4. helicase

Answer

B

Which of the following is not involved in the initiation of replication?

1. ligase
2. DNA gyrase
3. single-stranded binding protein
4. primase

Answer

A

Which of the following enzymes involved in DNA replication is unique to eukaryotes?

1. helicase
2. DNA polymerase
3. ligase
4. telomerase

Answer

D

Which of the following would be synthesized using 5′-CAGTTCGGA-3′ as a template?

1. 3′-AGGCTTGAC-4′
2. 3′-TCCGAACTG-5′
3. 3′-GTCAAGCCT-5′
4. 3′-CAGTTCGGA-5′

Answer

C

Fill in the Blank

The enzyme responsible for relaxing supercoiled DNA to allow for the initiation of replication is called ________.

Answer

DNA gyrase or topoisomerase II

Unidirectional replication of a circular DNA molecule like a plasmid that involves nicking one DNA strand and displacing it while synthesizing a new strand is called ________.

Answer

rolling circle replication

True/False

More primers are used in lagging strand synthesis than in leading strand synthesis.

Answer

True

Short Answer

Why is primase required for DNA replication?

What is the role of single-stranded binding protein in DNA replication?

Below is a DNA sequence. Envision that this is a section of a DNA molecule that has separated in preparation for replication, so you are only seeing one DNA strand. Construct the complementary DNA sequence (indicating 5’ and 3’ ends).

DNA sequence: 3’-T A C T G A C T G A C G A T C-5’

Critical Thinking

Review Figure 11.2.1 and Figure 11.2.2. Why was it important that Meselson and Stahl continue their experiment to at least two rounds of replication after isotopic labeling of the starting DNA with ¹⁵N, instead of stopping the experiment after only one round of replication?

If deoxyribonucleotides that lack the 3’-OH groups are added during the replication process, what do you expect will occur?

11.3: RNA Transcription

During the process of transcription, the information encoded within the DNA sequence of one or more genes is transcribed into a strand of RNA, also called an RNA transcript. The resulting single-stranded RNA molecule, composed of ribonucleotides containing the bases adenine, cytosine, guanine, and uracil, acts as a mobile molecular copy of the original DNA sequence. Transcription in prokaryotes and in eukaryotes requires the DNA double helix to partially unwind in the region of RNA synthesis.

Multiple Choice

During which stage of bacterial transcription is the σ subunit of the RNA polymerase involved?

1. initiation
2. elongation
3. termination
4. splicing

Answer

A

Which of the following components is involved in the initiation of transcription?

1. primer
2. origin
3. promoter
4. start codon

Answer

C

Which of the following is not a function of the 5’ cap and 3’ poly-A tail of a mature eukaryotic mRNA molecule?

1. to facilitate splicing
2. to prevent mRNA degradation
3. to aid export of the mature transcript to the cytoplasm
4. to aid ribosome binding to the transcript

Answer

A

Mature mRNA from a eukaryote would contain each of these features except which of the following?

1. exon-encoded RNA
2. intron-encoded RNA
3. 5’ cap
4. 3’ poly-A tail

Answer

B

Fill in the Blank

A ________ mRNA is one that codes for multiple polypeptides.

Answer

polycistronic

The protein complex responsible for removing intron-encoded RNA sequences from primary transcripts in eukaryotes is called the ________.

Answer

Spliceosome

Short Answer

What is the purpose of RNA processing in eukaryotes? Why don’t prokaryotes require similar processing?

Below is a DNA sequence. Envision that this is a section of a DNA molecule that has separated in preparation for transcription, so you are only seeing the antisense strand. Construct the mRNA sequence transcribed from this template.

Antisense DNA strand: 3’-T A C T G A C T G A C G A T C-5’

Critical Thinking

Predict the effect of an alteration in the sequence of nucleotides in the –35 region of a bacterial promoter.

11.4: Protein Synthesis (Translation)

The synthesis of proteins consumes more of a cell’s energy than any other metabolic process. In turn, proteins account for more mass than any other macromolecule of living organisms. They perform virtually every function of a cell, serving as both functional (e.g., enzymes) and structural elements. The process of translation, or protein synthesis, the second part of gene expression, involves the decoding by a ribosome of an mRNA message into a polypeptide product.

Multiple Choice

Which of the following is the name of the three-base sequence in the mRNA that binds to a tRNA molecule?

1. P site
2. codon
3. anticodon
4. CCA binding site

Answer

B

Which component is the last to join the initiation complex during the initiation of translation?

1. the mRNA molecule
2. the small ribosomal subunit
3. the large ribosomal subunit
4. the initiator tRNA

Answer

C

During elongation in translation, to which ribosomal site does an incoming charged tRNA molecule bind?

1. A site
2. P site
3. E site
4. B site

Answer

A

Which of the following is the amino acid that appears at the N-terminus of all newly translated prokaryotic and eukaryotic polypeptides?

1. tryptophan
2. methionine
3. selenocysteine
4. glycine

Answer

B

When the ribosome reaches a nonsense codon, which of the following occurs?

1. a methionine is incorporated
2. the polypeptide is released
3. a peptide bond forms
4. the A site binds to a charged tRNA

Answer

B

Fill in the Blank

The third position within a codon, in which changes often result in the incorporation of the same amino acid into the growing polypeptide, is called the ________.

Answer

wobble position

The enzyme that adds an amino acid to a tRNA molecule is called ________.

Answer

aminoacyl-tRNA synthetase

True/False

Each codon within the genetic code encodes a different amino acid.

Answer

False

Short Answer

Why does translation terminate when the ribosome reaches a stop codon? What happens?

How does the process of translation differ between prokaryotes and eukaryotes?

What is meant by the genetic code being nearly universal?

Below is an antisense DNA sequence. Translate the mRNA molecule synthesized using the genetic code, recording the resulting amino acid sequence, indicating the N and C termini.

Antisense DNA strand: 3’-T A C T G A C T G A C G A T C-5’

Critical Thinking

Label the following in the figure: ribosomal E, P, and A sites; mRNA; codons; anticodons; growing polypeptide; incoming amino acid; direction of translocation; small ribosomal unit; large ribosomal unit.

Prior to the elucidation of the genetic code, prominent scientists, including Francis Crick, had predicted that each mRNA codon, coding for one of the 20 amino acids, needed to be at least three nucleotides long. Why is it not possible for codons to be any shorter?

11.5: Mutations

A mutation is a heritable change in the DNA sequence of an organism. The resulting organism, called a mutant, may have a recognizable change in phenotype compared to the wild type, which is the phenotype most commonly observed in nature. A change in the DNA sequence is conferred to mRNA through transcription, and may lead to an altered amino acid sequence in a protein on translation.

Multiple Choice

Which of the following is a change in the sequence that leads to formation of a stop codon?

1. missense mutation
2. nonsense mutation
3. silent mutation
4. deletion mutation

Answer

B

The formation of pyrimidine dimers results from which of the following?

1. spontaneous errors by DNA polymerase
2. exposure to gamma radiation
3. exposure to ultraviolet radiation
4. exposure to intercalating agents

Answer

C

Which of the following is an example of a frameshift mutation?

1. a deletion of a codon
2. missense mutation
3. silent mutation
4. deletion of one nucleotide

Answer

D

Which of the following is the type of DNA repair in which thymine dimers are directly broken down by the enzyme photolyase?

1. direct repair
2. nucleotide excision repair
3. mismatch repair
4. proofreading

Answer

A

Which of the following regarding the Ames test is true?

1. It is used to identify newly formed auxotrophic mutants.
2. It is used to identify mutants with restored biosynthetic activity.
3. It is used to identify spontaneous mutants.
4. It is used to identify mutants lacking photoreactivation activity.

Answer

B

Fill in the Blank

A chemical mutagen that is structurally similar to a nucleotide but has different base-pairing rules is called a ________.

Answer

nucleoside analog

The enzyme used in light repair to split thymine dimers is called ________.

Answer

photolyase

The phenotype of an organism that is most commonly observed in nature is called the ________.

Answer

wild type

True/False

Carcinogens are typically mutagenic.

Answer

True

Short Answer

Why is it more likely that insertions or deletions will be more detrimental to a cell than point mutations?

Critical Thinking

Below are several DNA sequences that are mutated compared with the wild-type sequence: 3’-T A C T G A C T G A C G A T C-5’. Envision that each is a section of a DNA molecule that has separated in preparation for transcription, so you are only seeing the template strand. Construct the complementary DNA sequences (indicating 5’ and 3’ ends) for each mutated DNA sequence, then transcribe (indicating 5’ and 3’ ends) the template strands, and translate the mRNA molecules using the genetic code, recording the resulting amino acid sequence (indicating the N and C termini). What type of mutation is each?

Mutated DNA Template Strand #1: 3’-T A C T G T C T G A C G A T C-5’ Complementary DNA sequence: mRNA sequence transcribed from template: Amino acid sequence of peptide: Type of mutation:

Mutated DNA Template Strand #2: 3’-T A C G G A C T G A C G A T C-5’ Complementary DNA sequence: mRNA sequence transcribed from template: Amino acid sequence of peptide: Type of mutation:

Mutated DNA Template Strand #3: 3’-T A C T G A C T G A C T A T C-5’ Complementary DNA sequence: mRNA sequence transcribed from template: Amino acid sequence of peptide: Type of mutation:

Mutated DNA Template Strand #4: 3’-T A C G A C T G A C T A T C-5’ Complementary DNA sequence: mRNA sequence transcribed from template: Amino acid sequence of peptide: Type of mutation:

Why do you think the Ames test is preferable to the use of animal models to screen chemical compounds for mutagenicity?

11.6: How Asexual Prokaryotes Achieve Genetic Diversity

How do organisms whose dominant reproductive mode is asexual create genetic diversity? In prokaryotes, horizontal gene transfer (HGT), the introduction of genetic material from one organism to another organism within the same generation, is an important way to introduce genetic diversity. HGT allows even distantly related species to share genes, influencing their phenotypes.

Multiple Choice

Which is the mechanism by which improper excision of a prophage from a bacterial chromosome results in packaging of bacterial genes near the integration site into a phage head?

1. conjugation
2. generalized transduction
3. specialized transduction
4. transformation

Answer

C

Which of the following refers to the uptake of naked DNA from the surrounding environment?

1. conjugation
2. generalized transduction
3. specialized transduction
4. transformation

Answer

D

The F plasmid is involved in which of the following processes?

1. conjugation
2. transduction
3. transposition
4. transformation

Answer

A

Which of the following refers to the mechanism of horizontal gene transfer naturally responsible for the spread of antibiotic resistance genes within a bacterial population?

1. conjugation
2. generalized transduction
3. specialized transduction
4. transformation

Answer

A

Fill in the Blank

A small DNA molecule that has the ability to independently excise from one location in a larger DNA molecule and integrate into the DNA elsewhere is called a ________.

Answer

transposon or transposable element

________ is a group of mechanisms that allow for the introduction of genetic material from one organism to another organism within the same generation.

Answer

Horizontal gene transfer

True/False

Asexually reproducing organisms lack mechanisms for generating genetic diversity within a population.

Answer

False

Short Answer

Briefly describe two ways in which chromosomal DNA from a donor cell may be transferred to a recipient cell during the process of conjugation.

Describe what happens when a nonsense mutation is introduced into the gene encoding transposase within a transposon.

11.7: Gene Regulation - Operon Theory

Genomic DNA contains both structural genes, which encode products that serve as cellular structures or enzymes, and regulatory genes, which encode products that regulate gene expression. The expression of a gene is a highly regulated process. Whereas regulating gene expression in multicellular organisms allows for cellular differentiation, in single-celled organisms like prokaryotes, it ensures that a cell’s resources are not wasted making proteins that the cell does not need at that time.

Multiple Choice

An operon of genes encoding enzymes in a biosynthetic pathway is likely to be which of the following?

1. inducible
2. repressible
3. constitutive
4. monocistronic

Answer

B

An operon encoding genes that are transcribed and translated continuously to provide the cell with constant intermediate levels of the protein products is said to be which of the following?

1. repressible
2. inducible
3. constitutive
4. activated

Answer

C

Which of the following conditions leads to maximal expression of the lac operon?

1. lactose present, glucose absent
2. lactose present, glucose present
3. lactose absent, glucose absent
4. lactose absent, glucose present

Answer

A

Which of the following is a type of regulation of gene expression unique to eukaryotes?

1. attenuation
2. use of alternate σ factor
3. chemical modification of histones
4. alarmones

Answer

C

Fill in the Blank

The DNA sequence, to which repressors may bind, that lies between the promoter and the first structural gene is called the ________.

Answer

operator

The prevention of expression of operons encoding substrate use pathways for substrates other than glucose when glucose is present is called _______.

Answer

catabolite repression

Short Answer

What are two ways that bacteria can influence the transcription of multiple different operons simultaneously in response to a particular environmental condition?

Critical Thinking

The following figure is from Monod’s original work on diauxic growth showing the growth of E. coli in the simultaneous presence of xylose and glucose as the only carbon sources. Explain what is happening at points A–D with respect to the carbon source being used for growth, and explain whether the xylose-use operon is being expressed (and why). Note that expression of the enzymes required for xylose use is regulated in a manner similar to the expression of the enzymes required for lactose use.