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BIOC4332: Biochemistry II > Exam II Review > Flashcards

Exam II Review Flashcards

1
Q

Among the distinct epigenetic modifications that regulate the genome which one involves changes directly to the DNA?

A. Imprinting
B. Acetylation
C. Phosphorylation
D. Histone methylation

A

A. Imprinting

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2
Q

Which of the following is true regarding genomic imprinting?

A. None of these
B. For imprinted genes both parental alleles are methylated
C. It requires histone methylation
D. Imprinted genes are induced
E. Imprinted genes are acetylated

A

A. None of these

The repressed allele is methylated, while the active allele is unmethylated

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3
Q

Which of the following is a function of the transcription factor subunit TBP?

A. Recognition of the TATA box
B. Recruitment of RNA capping factors
C. Recognition of the BRE element
D. DNA unwinding to initiate transcription
E. Histone demethylation

A

A. Recognition of the TATA box

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4
Q

Compared to the human genome, the genome of yeast typically has:

A. A higher fraction of coding DNA
B. Longer chromosomes
C. More introns
D. Longer genes
E. More repetitive DNA

A

A. A higher fraction of coding DNA

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5
Q

A bacterial activator binds to:

A. None of these
B. The operon gene cluster
C. The initiator sequence
D. The BRE element
E. The operator

A

A. None of these

Promoter

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6
Q

Which of these proteins are NOT part of the nucleosome core histones?

A. H2AX
B. H2B
C. H4
D. H3

A

A. H2AX

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7
Q

Indicate which of the statements below regarding DNA methylation in humans is true:

A. Cytosine methylation often occurs within a 5′-CG-3′ sequence
B. Methylation of adenines is the most common DNA methylation in humans
C. DNA methylation at the promoter is an indication of active transcription
D. DNA methylation is removed by histone demethylases
E. Depends on histone methylases

A

A. Cytosine methylation often occurs within a 5′-CG-3′ sequence

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8
Q

Under which of the following conditions is the Lac operon in Escherichia coli fully turned on?

A. Low glucose but high lactose levels
B. Low glucose and lactose levels
C. High glucose but low lactose levels
D. High glucose and lactose levels
E. Low cAMP and high glucose levels

A

A. Low glucose but high lactose levels

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9
Q

The chromatin remodeling complexes play an important role in chromatin regulation in the nucleus. They…

A. All of these are correct
B. Can slide nucleosomes on DNA
C. Can interact with histone chaperones
D. Can remove or exchange core histone subunit

A

A. All of these are correct

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10
Q

Which is major histone tail modification associated with transcriptional activation?

A. Acetylation
B. Phosphorylation
C. Methylation
D. None of these

A

A. Acetylation

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11
Q

Transcription regulation has similarities and differences in bacteria and in eukaryotes. Which of the following is correct?

A. Both bacteria and eukaryotes have consensus promoter sequences
B. Most bacterial genes are regulated individually, whereas most eukaryotic genes are regulated in clusters
C. DNA looping for gene regulation is the rule in bacteria but the exception in eukaryotes
D. Transcription regulators in both bacteria and eukaryotes bind exclusively to RNA polymerase
E. The default state of both bacterial and eukaryotic genomes is transcriptionally active

A

A. Both bacteria and eukaryotes have consensus promoter sequences

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12
Q

Which is the protein domain that recognizes histone methylation?

A. Chromodomain
B. Bromodomain
C. Zinc finger domain
D. Carboxy Terminal Domain
E. None of these

A

A. Chromodomain

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13
Q

In which step of the prokaryote transcription a stable hairpin loop is formed?

A. Termination
B. Initiation
C. Elongation
D. Promoter cleareance
E. Sigma factor dissociation

A

A. Termination

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14
Q

The Trp operon in Escherichia coli encodes the components necessary for tryptophan biosynthesis. In the presence of the amino acid in a bacterium:

A. the tryptophan operator is bound to the tryptophan repressor
B. the tryptophan repressor is bound to bacterial RNA polymerase
C. the expression of the tryptophan repressor is shut off
D. the operon genes are expressed
E. All of these

A

A. The tryptophan operator is bound to the tryptophan repressor

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15
Q

For a bacterial gene that is positively regulated, which of the following is true?

A. An activator is required to increase RNA polymerase binding
B. In absence of any regulator factors, the gene is transcribed
C. A repressor is always bound to the operon
D. A repressor activates RNA polymerase

A

A. An activator is required to increase RNA polymerase binding

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16
Q

What is the CRISPR genome editing component that provides target site specificity?

A

sgRNA

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17
Q

What is the conserved sequence specific of eukaryotic promoters?

A

BRE

18
Q

What is the transcriptional regulation in which a gene is actively transcribed in absence of regulatory factors?

A

Negative regulation

19
Q

What interacts with the -10 and -35 boxes?

A

Sigma factor

20
Q

What is the technique for identifying binding sites of specific proteins?

A

DNA footprinting

21
Q

What’s a method to identify DNA methylation?

A

Bisulfite sequencing

22
Q

What are epigenetic marks?

A

Covalent modifications of histones or DNA

23
Q

What are histone writer enzymes?

A

Acetyl transferases

24
Q

What do code readers do?

A

Recognize histone modifications

25
Q

What’s the gene sequence that codes for a protein?

A

CDS

26
Q

What’s the transcription factor that unwinds DNA?

A

TFIIH

27
Q

What transcription factor recognizes the BRE?

A

TFIIB

28
Q

What forms a hairpin loop to terminate transcription?

A

GC inverted repeat

29
Q

What recognizes the poly-A tail of RNAs?

A

Poly-A-binding proteins

30
Q

What transcription factor is required to allow the recycling of RNA Pol II for further transcription cycles?

A

CTD phosphatase

31
Q

What’s it called when multiple genes are transcribed into a single transcript?

A

Polycistronic

32
Q

True or false? In eukaryotes most genes are regulated in clusters.

A

False

33
Q

True or false? The TATA box and the BRE element are sequences of the prokaryotic promoters that are located upstream the transcription start sites.

A

False

Downstream

34
Q

True or false? Nucleosome remodeling in eukaryotic cells can provide a more accessible DNA for the transcription machinery.

A

True

35
Q

True or false. The TATA box sequence is transcribed into the RNA molecule during transcription in eukaryotes.

A

False

36
Q

True or false? A difference between transcription and DNA replication in eukaryotes is that transcription does not require to open the DNA double helix to initiate.

A

False

Both require open DNA

37
Q

True or false? The maintenance methylase DNMT1 causes gene silencing by promoting the binding of bromodomain-containing proteins to DNA.

A

False

Bromodomain recognizes acetylation (Expression not silencing)

38
Q

True or false? All bacteria promoters contain a consensus sequence that exactly matches the ideal binding sequence of sigma factor.

A

False

Not ALL

39
Q

True or false? The phosphorylation status of the C-terminal domain of RNA polymerase II regulates recruitment of capping and polyadenylation factors.

A

True

40
Q

True or false? mRNA capping consists in the addition of a 7-methylguanosine at the 3’ end of nascent transcript to protect them from degradation in prokaryotes.

A

False

It’s at the 5’ end (5’ cap)

41
Q

True or false? A chromodomain binds to DNA sequences that contain methylated Cytosines in dinucleotides 5’-CG.

A

False

Chromodomain recognizes histone methylation, not DNA

BIOC4332: Biochemistry II (7 decks)

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