Exam 2 : 5-7

Which of the following is not true about RNA structure

RNA helices are left handed

A hairpin loop in the 5′ untranslated region of an mRNA may function as what?

Inhibitor of translation.

tRNA molecules have how many hairpin loops?

Three hairpin loops that function in amino acid attachment and recognition.

The T-arm of a tRNA is important for what?

Recognition by the ribosome

Why are non-base-paired nucleotides in a hairpin loop functionally important?

They allow interactions with other biomolecules.

Which of the following is NOT a feature of an RNA hairpin loop?

Thymine

You discover a new nucleic acid that forms a helix with approximately 11 nucleotides per helical turn. Which helical form is it most likely to adopt?

A-form.

RNA helices typically adopt which helical form?

A-form.

Which of the following is true about the differences between A-form and B-form helices?

A. A-form helices contain approximately 11 base pairs per turn, while B-form helices contain approximately 10 base pairs per turn.
B. A-form produces a wider and shorter or flatter right-handed helix than B-form.
C. The phosphate groups are positioned closer to the helical axis in A-form than in B-form.

What type of bond is crucial for base pairing in the stems of RNA stem-loops?

Hydrogen bonds.

RNA sugars commonly have which type of sugar pucker?

RNA sugars commonly have a C3'-endo sugar pucker, which significantly influences the conformation and stability of RNA structures.

A hairpin is an example of which level of RNA structure?

Secondary structure.

Which of the following names are commonly used to describe the strand of DNA with a sequence that matches a transcribed mRNA sequence?

coding strand, sense strand, and non-template strand

High levels of histone deacetylase (HDAC) expression in cells might have which of the following effects on transcription?

Inhibit transcription

DNA/RNA polymerase synthesizes RNA in what direction?

5′ → 3′

Transcription factors bind to which of the following?

Enhancer sequences

α-Amanitin inhibits which RNA polymerase?

RNA polymerase II

Elongation of transcription requires which of the following events?

Phosphorylation of RNA polymerase/transcription factor components

The product of RNA polymerase II during transcription is:

Pre-mRNA

Rifampicin is an inhibitor of bacterial RNA polymerase. Which subunit does rifampicin bind?

Beta (β) subunit

Which of the following best describes a promoter?

A specific DNA sequence 5′ to a gene that participates in regulating gene expression

Termination of transcription involves which of the following?

A. Release of mRNA from RNA polymerase
B. Endoribonuclease cleavage of the RNA transcript (in some cases)
C. Transcription terminator sequences in DNA

In transcription, which of the following best describes the antisense strand?

The DNA strand read by RNA polymerase

Eukaryotic RNA polymerase II synthesizes which of the following RNA molecules?

mRNA

Which of the following can occur simultaneously in eukaryotes?

Translation and protein folding

Protein folding is template-driven.

False

You isolate a protein and place it in a buffer that mimics conditions inside a cell. What conformation will the protein most likely adopt?

Native structure

The translocon is a complex of proteins involved in membrane protein folding. Which of the following is true?

The translocon is slightly open on one side to allow hydrophobic amino acids to partition into the membrane.

A protein you are studying becomes reduced while proteins are folding. What is the likely role of your protein?

A chaperone involved in disulfide bond formation

Why is it important to degrade misfolded proteins?

They can aggregate and become toxic to cells.

Disulfide bonds are formed between which two amino acids?

Two cysteines

When proteins misfold, they are commonly labeled with what to target them to the proteasome?

Ubiquitin

Protein folding begins co-translationally.

true

When cells are placed under stressful conditions, newly synthesized proteins may have difficulty folding. What mechanism helps cells overcome this problem?

Express chaperones to help folding

Calnexin is a chaperone protein that binds what?

Sugar modifications

Protein disulfide isomerase (PDI) reduces disulfide bonds and, in the process, becomes:

oxidized

Protein folding is driven only by thermodynamics.

False

An inducer molecule functions to do what in an inducible operon system?

Binds to the repressor to inhibit the action of the repressor, allowing transcription to proceed.

Methylation at which lysine residue is generally associated with gene repression?

H3K27

Which of the following protein domains binds modified histones?

Bromodomain

Divalent cations such as zinc facilitate transcription by which mechanism?

Binding to transcription factors/DNA-binding proteins to stabilize their structure.

Which of the following is a cofactor for HDAC enzymes?

Divalent cations

A co-repressor functions to do what in a repressible operon system?

Allows the repressor to bind the operator.

Which of the following is NOT an example of a domain in a transcription factor?

Promoter sequence

Phosphorylation of CREB occurs in response to changes in which molecule?

cyclic AMP (cAMP) and calcium ions

Regulation of gene expression in prokaryotes occurs primarily at the level of transcription because:

A. Transcription and translation occur in the same location.
B. Transcription and translation occur simultaneously.
C. Prokaryotes do not have a nucleus.

What enzyme catalyzes the phosphorylation of CREB?

PKA (Protein Kinase A)

Which biomolecule acts as the methyl donor for histone methyltransferase enzymes?

S-adenosylmethionine (SAM)

When high concentrations of tryptophan are present in a bacterium containing the trp operon, what happens to expression of the trp operon genes?

Decreases

In an operon diagram, a gene located upstream of the promoter encodes what type of molecule?

Repressor protein

Which of the following is NOT a mechanism of gene regulation in eukaryotes?

Operons

If you are expressing a protein that is toxic to bacteria, which operon system should you use?

Inducible system

cAMP promotes transcription in eukaryotes through which type of protein regulator?

Transcription factor

Which of the following is an example of a protein structure found in a transcription factor?

Helix-turn-helix