Deck 8: Transcription, Translation, and Bioinformatics

Question 1

The RpoH 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

Answer 1

C

Question 2

Which drug interferes with transcription in prokaryotes?

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

Answer 2

C

Question 3

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
D) GC-rich region followed by four to eight uridines
E) stem and loop followed by a GC-rich region

Answer 3

D

Question 4

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 5

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 6

During transcription of the __________ genes, normal, unmodified bases are incorporated, but some of these are modified later by specific enzymes.

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

Question 7

A consensus sequence consists of:

A) the region to which sigma factors can bind
B) 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

Question 8

Transcription occurs in the __________ and translation occurs in the __________ of a eukaryotic cell.

A) nucleoid; cytoplasm
B) cytoplasm; cytoplasm
C) nucleus; cytoplasm
D) nucleus; nucleus
E) nucleoid; nucleoid

Question 9

The function of rho requires:

A) a stretch of uridines
B) GC-rich region followed by uridines
C) pause sites and GC-rich regions
D) pause sites and stretches of uridines
E) a helicase to unwind it from the RNA

Question 10

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 11

Without __________, the core RNA polymerase binds and releases DNA at random.

A) initiation factor
B) Shine-Dalgarno sequence
C) sigma factor
D) peptidyltransferase
E) release factor

Question 12

Actinomycin D is produced by actinomycetes, and it:

A) prevents the mRNA from exiting RNA polymerase
B) prevents binding of RNA polymerase to DNA
C) inhibits transcription in both prokaryotes and eukaryotes
D) binds the beta subunit of RNA polymerase, blocking the exit channel
E) can inhibit translation and replication as well as transcription

Question 13

An enzyme complex called RNA polymerase is also known as DNA-dependent RNA polymerase because:

A) DNA codes for the subunits of this protein
B) DNA serves as a template for translation
C) hydrolysis of DNA provides the energy for RNA polymerase
D) DNA serves as a template for transcription
E) DNA is required as a primer for this polymerase

Question 14

The unusual bases found in tRNA are poor substrates for:

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

Question 15

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 16

__________ is normally read as a stop codon but encodes tryptophan in vertebrate mitochondria.

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

Question 17

Molecules of sRNA do not encode proteins, but are used to __________ the translation of specific mRNAs into proteins.

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

Question 18

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 19

The charging of tRNAs is carried out by a set of enzymes called __________ transferases.

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

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

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) none is required

Question 22

Which of the following is a ribozyme?

A) Clp protease
B) release factor
C) trigger factor
D) peptidyl transferase
E) aminoacyl-tRNA transferase

Question 23

What is the significance of the Shine-Dalgarno sequence?

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

Question 24

Peptidyl transferase is present in the __________ ribosomal subunit.

A) 30S
B) 50S
C) 5S
D) 16S
E) 80S

Question 25

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 26

What do codons and anticodons have in common?

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

Question 27

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

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

Question 28

The typical bacterial ribosome is comprised of:

A) 16 RNAs and a variety of proteins
B) a 80s (30s + 50s) component made of RNA and proteins
C) 70s subunits along with several RNAs and several proteins
D) Two subunits made of three RNAs and at least 50 proteins
E) Three subunits containing both RNA and proteins

Question 29

A __________ RNA is a single RNA molecule that contains information from several contiguous genes.

A) cistronic
B) transfer
C) polycistronic
D) ribosomal
E) messenger

Question 30

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 31

Peptide bond formation effectively transfers the peptide from the tRNA in the __________ to tRNA in the __________.

A) P-site; E-site
B) E-site; A-site
C) E-site; P-site
D) P-site; A-site
E) A-site; P-site

Question 32

Different __________ can bind simultaneously to the start of each cistron within a polycistronic mRNA.

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

Question 33

What is the importance of the stop codon UAG?

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

Question 34

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 35

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

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

Question 36

Post-translational modification to achieve function does not involve:

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

Question 37

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

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

Question 38

The __________ of transcription and translation helps microbes rapidly adjust gene expression to changes in their environment.

A) pausing
B) separation
C) processes
D) slowing
E) coupling

Question 39

__________ may serve as a molecular clock that measures the approximate time since two closely related species diverged.

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

Question 40

Several different antibiotics have been isolated from:

A) E. coli
B) Streptomyces
C) Mycoplasma
D) Mycobacterium
E) Streptococcus

Question 41

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

Question 42

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

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

Question 43

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

Question 44

Describe the experiment utilizing an E. coli cell lysate that was used to figure out the genetic code.

Question 45

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

Question 46

Which of the following uses the proton motive force as its energy source?

A) signal recognition particle
B) SecYEG translocon
C) SecA ATPase
D) twin arginine translocase
E) type I protein secretion

Question 47

Explain the process of transcription initiation.

Question 48

How do sigma factors regulate major physiological responses?

Question 49

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 50

Similar genes within the same organism that have different functions are referred to as:

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

Question 51

Which of the following terms refers to a discipline involving comparison of genes of different species?

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

Question 52

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

Question 53

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

Question 54

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 55

__________ controls protein turnover by closely regulating the degradation of specific proteins.

A) Ubiquitination
B) Half-life
C) Amino acid sequence
D) Tertiary structure
E) Protease

Question 56

Signal sequences are found:

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 57

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

Question 58

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 59

In eukaryotes, protein degradation occurs through organelles called:

A) proteases
B) lysosomes
C) RNases
D) proteasomes
E) vacuoles

Question 60

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 61

What specifically about eukaryotes makes bioinformatic analysis more complicated?

Question 62

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

Question 63

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 64

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

Question 65

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

Question 66

Why is protein degradation necessary to maintain cellular health?

Question 67

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

Question 68

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

Question 69

Eukaryotes and the archaea contain proteasomes. Compare and contrast these proteasomes in terms of structure and function.

Question 70

What does it mean to say that transcription and translation are coupled, and what are some of the potential problems with this?