Deck 8: Transcription, Translation, and Bioinformatics

Question 1

A consensus sequence of any genetic element is

A) sequences that are rarely found in nature.
B) the sequence with the most likely base (or bases) at each position.
C) hairpins in RNA to slow down or stop transcription.
D) sequences to which ribosomes bind.
E) primer sequences used to initiate transcription.

Answer 1

B

Question 2

Which of the following is normally read as a stop codon but encodes tryptophan in vertebrate mitochondria?

A) AUG
B) UCA
C) UAC
D) UGA
E) UAG

Answer 2

D

Question 3

In the figure below, which label represents the promoter?

A) A
B) B
C) C
D) D
E) -35

Answer 3

A

Question 4

DNA-dependent ________ polymerase makes a copy of DNA that is then used for translation. The process carried out by this enzyme is called ________.

A) RNA; transformation
B) protein; transcription
C) DNA; transcription
D) RNA; transcription
E) protein; transposition

Question 5

The average half-life for mRNA in a typical bacterium such as E. coli is

A) 1-3 seconds.
B) 10-30 seconds.
C) 1-3 minutes.
D) 1-3 hours.
E) 1-3 days.

Question 6

During transcription of the ________ genes, normal, unmodified bases are incorporated, but specific enzymes modify some of these later.

A) tRNA
B) tmRNA
C) mRNA
D) sRNA
E) catalytic RNA

Question 7

The process of taking a DNA template and making a complementary RNA molecule is called

A) transposition.
B) transertion.
C) replication.
D) translation.
E) transcription.

Question 8

Which of the following is NOT part of initiation of transcription?

A) -10 and -35 sequences
B) binding of RNA polymerase to the beginning of the gene
C) melting of the helix
D) binding of sigma factor to promoter followed by binding of core RNA polymerase
E) base pairing of the first nucleotide of the RNA

Question 9

The unusual bases found in tRNA are poor substrates for

A) proteases.
B) polymerases.
C) ribosomes.
D) ribozymes.
E) RNases.

Question 10

The RpoD sigma-70 factor of E. coli recognizes promoters for

A) stress-response genes.
B) motility and chemotaxis genes.
C) "housekeeping" genes.
D) heat shock-induced genes.
E) genes for nitrogen metabolism.

Question 11

Molecules of sRNA do not encode proteins but are used to ________ the stability or translation of specific mRNAs into proteins.

A) start
B) regulate
C) stop
D) speed up
E) slow down

Question 12

Which drug intercalates into DNA and inhibits transcription in both prokaryotes and eukaryotes?

A) streptomycin
B) actinomycin D
C) chloramphenicol
D) rifampin
E) tetracycline

Question 13

Using the genetic code shown below, find the correct start and stop codons. Which of the following peptides might this message code for?
5'-GAGUUAUGCACGGGUUCUAUGUGUAG-3'

A) GLU-LEU-CYS-MET-GLY-SER-MET-CYS
B) MET-GLY-SER-MET-CYS
C) MET-HIS-GLY-PHE-TYR-VAL
D) MET-CYS-ILE-LEU-GLY-THR-TYR
E) ASP-VAL-TYR-LEU-GLY-TYR-VAL-LEU

Question 14

Which of the following is NOT true of initiation of transcription?

A) The RNA polymerase holoenzyme binds.
B) GTP hydrolysis catalyzes bubble formation.
C) The promoter unwinds.
D) The first rNTP is usually a purine.
E) Position +1 marks the start of the gene.

Question 15

Most tRNA molecules begin with a 5' ________ and all end with a 3' ________, to which the amino acids attach.

A) phosphate; hydroxyl
B) C; GGA
C) G; CCA
D) A; TTA
E) C; AAT

Question 16

In the figure below, which label represents the Shine Delgarno site?

A) A
B) B
C) C
D) D
E) -35

Question 17

The figure below shows subunits of a structure in a bacterial cell. This structure is

A) a type I secretion system.
B) RNA polymerase.
C) a ribosome.
D) aminoacyl-tRNA synthetase.
E) sigma factor and RNA polymerase.

Question 18

In the absence of Rho, what can bring about transcription termination?

A) stem and loop and stretches of uridines
B) stem and loop only
C) GC-rich region near the 3¢ terminus
D) GC-rich region near the 3¢ terminus followed by four to eight uridines
E) stem and loop followed by a GC-rich region

Question 19

A researcher is studying transcription and has added a chemical to a transcription experiment using both E. coli and mammalian cells. This chemical inhibits both systems. The chemical is most likely

A) streptomycin.
B) rifamycin.
C) erythromycin.
D) rifampin.
E) actinomycin D.

Question 20

________ RNA polymerase plus sigma factor together are called ________.

A) Transcription; translation
B) Holoenzyme; core
C) Translation; transcription
D) Core; holoenzyme
E) Ribosome; rRNA

Question 21

E. coli is being used in order to study various agents that inhibit protein synthesis. An agent will bind the 16S RNA of the 30S subunit and block aminoacyl tRNA from entering the ribosome. This agent is most likely related to

A) chloramphenicol.
B) streptomycin.
C) puromycin.
D) tetracycline.
E) erythromycin.

Question 22

What does it mean to say that the genetic code is redundant?

A) There is more than one kind of amino acid in proteins.
B) More than one rRNA can bind to the ribosome at the same time.
C) A codon is composed of more than one nucleotide.
D) More than one codon can specify the same amino acid.
E) All products of translation contain a certain minimum number of mistakes, called mutations.

Question 23

Which form of RNA has the task of unsticking stuck ribosomes?

A) mRNA
B) rRNA
C) sRNA
D) tmRNA
E) tRNA

Question 24

The significance of the Shine-Dalgarno sequence is that it is the site where

A) RNA polymerase binds to begin transcription.
B) a ribosome binds so that it can initiate translation.
C) DNA polymerase binds to begin chromosome replication.
D) the tRNA binds to the mRNA in translation.
E) DNA polymerase begins synthesis of the Okazaki fragments on the lagging strand.

Question 25

The energy source utilized by the elongation factors EF-G and EF-Tu is

A) proton motive force.
B) ATP hydrolysis.
C) GTP hydrolysis.
D) phosphoenolpyruvate hydrolysis.
E) No energy source is required.

Question 26

In the figure shown below, the RfaH protein is undergoing a change from ________ as a result of binding to ________.

A) beta-sheet to alpha-helix; a promoter to initiate transcription
B) alpha-helix to beta-sheet; a promoter to initiate translation
C) beta-sheet to alpha-helix; RNAP and thus being able to bind ribosomal protein
D) alpha-helix to beta-sheet; RNAP and thus being able to bind ribosomal protein
E) beta-sheet to alpha-helix; RNAP to initiate translation

Question 27

Resistance to the protein synthesis antibiotics can be carried out by all of the following EXCEPT

A) the use of an acetyltransferase to destroy activity.
B) immediate metabolization to gain ATP.
C) efflux pumps to move it out of the cell.
D) the use of phosphotransferases to chemically modify the antibiotic.
E) mutations in genes for the bacterial target so antibiotics can no longer bind.

Question 28

After ________, each polypeptide must be properly folded and placed at the correct cellular or extracellular location.

A) replication
B) transcription
C) translation
D) degradation
E) conjugation

Question 29

Post-translational modification to achieve function does NOT involve

A) adenylation.
B) phosphorylation.
C) acetylation.
D) removal of formylmethionine.
E) ubiquitination.

Question 30

After tmRNA releases an mRNA and aberrant polypeptide from a stuck ribosome,

A) clpX tags the peptide for destruction.
B) sspB tags the peptide for destruction.
C) tmRNA then destroys the peptide.
D) tmRNA ubiquitinates the peptide.
E) sspB recognizes a proteolysis tag and delivers the peptide to clpX for degradation.

Question 31

Both codons and anticodons

A) are part of tRNA.
B) are sequences of DNA three nucleotides long.
C) are identical RNA sequences.
D) are complementary RNA sequences.
E) interact with tmRNA in order to function.

Question 32

Different ________ can bind simultaneously to the start of each gene within a polygenic mRNA.

A) genes
B) proteins
C) polymerases
D) ribosomes
E) RNases

Question 33

A ________ mRNA is a single mRNA molecule that contains information from several contiguous genes.

A) cistronic
B) transfer
C) polygenic
D) ribosomal
E) small

Question 34

The importance of the stop codon UAG is that it

A) tells the DNA polymerase to stop replicating the chromosome.
B) tells the RNA polymerase to stop transcribing the chromosome.
C) tells the tRNA to stop transcribing the DNA.
D) tells the ribosome to stop translating the mRNA.
E) signals the end of the operon.

Question 35

The typical bacterial ribosome is composed of

A) 16 RNAs and a variety of proteins.
B) an 80S (30S + 50S) component made of RNA and proteins.
C) 80S subunits along with several RNAs and at least 50 proteins.
D) two subunits made of three RNAs and at least 50 proteins.
E) three subunits containing both RNA and proteins.

Question 36

Which of the following may serve as a molecular clock that measures the approximate time since two related species diverged?

A) tRNA
B) mRNA
C) rRNA
D) sRNA
E) tmRNA

Question 37

E. coli is being used to study various agents that inhibit protein synthesis. One agent binds the 23S rRNA of the 50S subunit and prevents peptide bond formation. No new proteins are produced. To which antibiotic is this agent likely related?

A) chloramphenicol
B) streptomycin
C) puromycin
D) tetracycline
E) erythromycin

Question 38

Which of the following are required for the termination of translation?

A) sRNAs
B) degrons
C) TolC proteins
D) release factors
E) ubiquitins

Question 39

The charging of tRNAs is carried out by a set of enzymes called ________ synthetases.

A) ribozymes
B) aminoacyl-tRNA
C) peptidyl
D) proteases
E) polymerases

Question 40

Which RNA species is a component of the 30S subunit of the ribosome?

A) 5S RNA
B) 16S RNA
C) 23S RNA
D) tRNA
E) mRNA

Question 41

The term "________" is used to describe movement of a protein from one compartment to another.

A) export
B) import
C) translocation
D) transport
E) secretion

Question 42

Beta-lactamases are proteins found in many bacteria that can degrade beta-lactam antibiotics such as ampicillin. Families of these proteins are coded by genes with similar sequences even though they are found in a variety of bacteria. These genes would be considered to be

A) paralog.
B) orthologs.
C) open reading frames (ORFs).
D) introns.
E) aligned sequences.

Question 43

The general secretion complex known as the SecYEG translocon is found in the

A) nucleus.
B) inner membrane.
C) cell wall.
D) periplasmic space.
E) outer membrane.

Question 44

How do sigma factors in a bacterium such as E. coli regulate major physiological responses?

Question 45

The figure below shows a diagram of a DNA and a process. This microorganism is a(n) ________, and the process being diagrammed is ________.

A) archaea; exon removal
B) bacteria; splicing
C) eukaryote; splicing
D) bacteria; exon removal
E) eukaryote; exon removal

Question 46

Certain proteins in a bacterial cell are short-lived and are labeled with a leucine, phenylalanine, tryptophan, or tyrosine at the N-terminal end. These proteins are degraded by

A) GroEL and GroES.
B) DnaK and DnaJ.
C) clpAP protease.
D) Sec A.
E) ubiquitin.

Question 47

Signal sequences are found where?

A) in the 30S ribosomal subunit
B) in the 50S ribosomal subunit
C) at the N-terminal end of a protein
D) at the C-terminal end of a mRNA
E) upstream of the promoter

Question 48

SRP stands for ________, and it plays a role in ________.

A) secretion recognition particle; refolding
B) secretion ribosomal particle; refolding
C) signal recognition particle; refolding
D) secretion ribosomal particle; secretion
E) signal recognition particle; secretion

Question 49

The role of ExPortal in Streptococci is to

A) serve as a secretion system and a chaperone.
B) mark proteins for destruction.
C) secrete proteins to the periplasm.
D) anchor proteins in the cytoplasmic membrane.
E) form -S-S- bonds needed for protein structure.

Question 50

How have bioinformatic approaches been helpful in designing growth media for intestinal bacteria such as Faecalibacterium prausnitzii?

A) Genes encoding enzymes for fermentation and production of butyrate have been found.
B) The genome is similar to other bacteria and thus the media for those other bacteria can now be used.
C) Bioinformatics has indicated genes for metabolism of sugars that can now be added to the growth medium.
D) Bioinformatics has revealed that this bacterium can make its own amino acids and thus they are not needed in the growth medium.
E) Bioinformatics has revealed that biosynthetic genes for certain amino acids and vitamins are absent. Now these can be added to growth medium and the bacterium will grow.

Question 51

Explain the processes of Rho-dependent and Rho-independent termination of transcription.

Question 52

Which of the following terms refers to an interdisciplinary field that uses computer programs to compare genes of different species?

A) annotation
B) bioinformatics
C) open reading frames (ORFs)
D) sequence homology
E) computer analysis

Question 53

How does mRNA compare to the template and nontemplate DNA strand?

Question 54

Describe how Marshal Nirenberg and Heinrich Matthaei utilized an E. coli cell lysate to figure out the genetic code.

Question 55

Increased levels of chaperones increase heat resistance of bacteria by

A) destroying damaged proteins so the amino acids can be recycled.
B) refolding proteins damaged by heat so they function again.
C) secreting damaged proteins into the periplasm.
D) labeling damaged proteins for destruction by clp proteases.
E) adding N-formylmethionine to damaged proteins.

Question 56

Which of the following is NOT an example of a heat-shock protein?

A) trigger factor
B) GroES
C) GroEL
D) Clp protease
E) DnaK

Question 57

Genes that have arisen from a duplication within a species and have evolved to carry out different functions are referred to as

A) homologs.
B) orthologs.
C) paralogs.
D) homogenous.
E) synonymous.

Question 58

What are the functions of the different types of RNA molecules?

Question 59

Explain the process of transcription initiation.

Question 60

Gram-negative microbes are surrounded by two layers of ________, between which lies ________.

A) membrane; periplasm
B) membrane; periplasmic space and lipopolysaccharide
C) membrane; periplasmic space and peptidoglycan
D) lipopolysaccharide; periplasmic space and peptidoglycan
E) lipopolysaccharide; peptidoglycan

Question 61

At times a ribosome may get stuck with an mRNA that has been damaged so that there is no stop codon. What happens to this ribosome to fix this problem?

Question 62

Why is protein degradation necessary to maintain cellular health?

Question 63

Name two antibiotics that affect transcription and explain their mode of action.

Question 64

Every mRNA has three possible reading frames. How does the ribosome find the correct reading frame?

Question 65

How are folded and unfolded proteins moved from the cytoplasm to the periplasm?

Question 66

Where is fMet used as the N-terminal amino acid? What does that mean for the human immune response?

Question 67

Explain how a type I secretion system works. Are the secreted proteins ever in periplasmic space?

Question 68

What does it mean to annotate a genome? Explain the goals.

Question 69

Examine the DNA sequence shown below. How many possible reading frames does this piece of DNA have? Explain where they are. Which one can be used and how do you know?
5'-AGTCGATCGAACGGTCATCG-3'
3'-TCAGCTAGCTTGCCAGTAGC-5'

Question 70

Name two antibiotics that affect translation and explain their modes of action.

Question 71

A variety of online software tools are available to aid with analyzing DNA and protein sequences. Name any three and explain what they can be used for.

Question 72

Define "half-life" in terms of mRNA. Biologically, why is it important that the half-life of mRNA be the shortest of the RNAs? What chemically leads to a longer half-life for tRNAs and rRNAs?

Question 73

Where is the Shine-Dalgarno sequence located and what is it responsible for?

Question 74

What feature of eukaryotes makes annotation more difficult?

Question 75

Since ribosomes do not translate to the end of the mRNA, what causes translation to end?

Question 76

As a peptide is produced on a ribosome, describe two methods used to get the protein into its proper shape.