xuanhoang

xuanhoang

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QUESTION 1

Which of the following occur(s) during Pol II transcription preinitiation complex formation? (More than one correct answer possible. Mark all that apply).

A) TFIIB unwinds the DNA.

B) TFIIB contacts both TATA box-binding factor and the DNA.

C) DNA bends.

D) TFIIA binds to TFIIB.

Question 2

An enhancer (select all that apply)

A) is a DNA element that interacts directly with general transcription factors to enhance or repress transcription.

B) is a protein that binds to a promoter and enhances its activity.

C) is a protein that binds to RNA polymerase and enhances transcription.

D) interacts with repressor proteins to enhance transcriptional repression.

E) is a DNA control element that can be located at a great distance upstream or downstream of a promoter.

F) acts as a binding site for RNA polymerase.

QUESTION 3

An important early step before transcription initiation that leads to gene expression is

A) Rapid packaging of DNA into condensed chromatin assuring the activity of all the genes in eukaryotic cells except those whose transcription is repressed by specific negative regulatory mechanisms.

B) relief of transcription repression by chromatin remodeling and the removal of neucleosomes to transiently expose promoter DNA.

C) the coiling of DNA around a set of eight histones in the nucleosome.

D) DNA binding by TATA binding protein (TBP).

QUESTION 4

The activation domains of transcriptional activators

A) can be swapped with another activation domain to create a new chimeric transcription factor.

B) can interact directly with the promoter.

C) can facilitate transcription by catalyzing RNA polymerization

D)can bind to DNA.

QUESTION 5

The mediator complex

A) can form a molecular bridge between activators of transcription and DNA replication machinery.

B) can function to maintain nucleosomes at promoter regions in a hypoacetylated state (facilitating nucleosome stability and chromatin condensation).

C) transduces regulatory signals between activation (and repression) domains of transcription factors bound to distal DNA elements (e.g. enhancers) and RNA polymerase II by binding directly to both.

D) is a small, a 30-residue long protein that forms a molecular bridge between activation domains of transcription factors and their DNA binding domains.

QUESTION 6

Transcription factors can do all of the following EXCEPT

A) Synthesize RNA.

B) undergo conformational changes which alter activity.

C) act to repress transcription of transcription factor genes.

D) exist as heterodimers.

E) respond to extracellular signals.

QUESTION 7

Which of the following statements concerning the Mediator is correct?

A) Some of the mediator subunits bind to the DNA at distal sites and at enhancers while other subunits simultaneously bind the DNA at promoter proximal sequences.

B) Most of the yeast Mediator subunits are unique and have no homologs

in cells of higher eukaryotes (e.g. flies and humans).

C) The mediator acts as a bridge between transcription factors binding at distal sites and enhancers on the one hand and the basal transcription initiation machinery including RNA pol II at promoter sites.

D) The major mediator subunits can trace their evolutionary origin to bacterial σ factors.

E) All of the statements, including this one, are true.

Answer: QUESTION 1 B) TFIIB contacts both TATA box-binding factor and the DNA....

QUESTION 1

One major challenge for the eukaryotic transcription machinery not faced by its prokaryotic counterpart is

A) transcribing complex transcription units into polycistronic mRNA as compared to the simple, typically monocistronic transcription units of prokaryotes.

B) is dealing with the fact that eukaryotic DNA is packaged into neucleosomes and higher-order forms of chromatin structure, while prokaryotic DNA is not.

C) is the need to engage transcription activators and disengage transcription repressors.

D) is unwinding the DNA to allow RNA polyemerase to transcribe the template-strand.

QUESTION 2

Which is the first factor to bind at the promoter of eukaryotic genes?

A) TFIIA

B) TATA box-binding protein

C) RNA polymerase

D) TFIIB

E) TFIIH

QUESTION 3

The fidelity of RNA pol II refers to

A) the enzyme's ability to identify the correct promoter from which to initiate transcription.

B) the enzyme's ability to initiate transcription without the need for a preexisting primer.

C) the enzyme's ability to proceed along the DNA while sequentially catalyzing the addition of new NTPs to the growing RNA chain, without detaching prematurely from the DNA.

D) the enzyme's ability to select the correct nucleotide to add to the growing RNA chain.

QUESTION 4

Are the following components of transcription regulation in eukaryotes cis-acting elements or trans-acting factors? (a.cis-acting element or b.trans-acting factor)

A) TATA-box

B) general transcription factors

C) enhancer

D) initiator

E) mediator

F) TATA-binding protein

Answer: QUESTION 1 B) is dealing with the fact that eukaryotic DNA is packaged...
Answer: The correct answer is: e) TFIIH
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1. The prokaryotic cells most commonly used to study transcription and translation are from

a. E. coli.

b. B. subtilis.

c. S. cerevisiae.

d. D. discoidium.

2. Eukaryotic RNA polymerase I genes code for

a. mRNAs.

b. tRNAs.

c. small nuclear RNAs and small cytoplasmic RNAs.

d. ribosomal RNAs.

3. Mitochondrial genes are transcribed by

a. RNA polymerase I.

b. RNA polymerase II.

c. RNA polymerase III.

d. a separate mitochondrial RNA polymerase.

4. The first step in the formation of a transcription complex for mRNA transcription is the binding of _______ to the TATA box.

a. TFIA

b. TFIIA

c. TFIIIA

d. TFIID

5. The large multi-subunit complex that links the general transcription factors to the gene-specific transcription factors is called

a. the transcription complex.

b. Mediator.

c. the operator.

d. TBP.

6. Release of RNA polymerase II to initiate transcription appears to be the direct result of the

a. binding of TAFs to the polymerase.

b. unwinding of the DNA by helicases.

c. phosphorylation of RNA polymerase by a protein kinase.

d. removal of the nucleosome occupying the promoter site.

7. A major difference between eukaryotic and prokaryotic RNA polymerases is that eukaryotic polymerases

a. use a set of transcription factors to bind to and initiate transcription.

b. use sigma (s) factors to initiate transcription.

c. start from promoters.

d. start from origins of replication.

8. Enhancers usually are _______ sequences that require _______ to regulate a gene.

a. cis-acting; other cis-acting sequences

b. cis-acting; trans-acting factors

c. trans-acting; trans-acting factors

d. Both a and b

9. Steroid hormone receptors recognize and bind to specific DNA sequences by _______ domains.

a. zinc finger

b. helix-loop-helix

c. helix-turn-helix

d. leucine zipper

10. Helix-turn-helix transcription factor proteins are found

a. only in insects.

b. only in eukaryotes.

c. only in prokaryotes.

d. in both prokaryotes and eukaryotes.

11. DNA sequences that prevent enhancers from acting on promoters located in adjacent domains are called

a. insulators.

b. isolators.

c. repressors.

d. boundaries.

12. Aminoacyl tRNA synthetases are enzymes that

a. synthesize transfer RNAs.

b. attach amino acids to specific transfer RNAs.

c. connect amino acids while they are held in place on ribosomes by transfer RNAs.

d. attach the terminal CCA sequence to transfer RNAs.

13. E. coli contains about _______ different tRNAs that code for _______ different amino acids.

a. 62; 40

b. 62; 20

c. 50; 20

d. 40; 20

14. The capacity for some tRNAs to recognize more than one codon in mRNA is explained by a phenomenon called

a. redundancy.

b. wobble.

c. a reading frameshift.

d. degeneracy.

15. Translation always occurs on which of the following structures?

a. Ribosomes

b. Endoplasmic reticulum

c. Nuclear envelope

d. Mitochondria

16. The combined sizes of prokaryotic and eukaryotic ribosomes are

a. the same.

b. 30S and 50S, respectively.

c. 40S and 60S, respectively.

d. 70S and 80S, respectively.

17. Which of the following statements is true and provides evidence that a certain component of the ribosome catalyzes protein synthesis?

a. Ribosomes are inactive after protease digestion.

b. Ribosomes are inactive after RNase digestion.

c. Structural analysis shows that proteins occupy the catalytic site where peptide bonds are formed.

d. Structural analysis shows that mRNA occupies the catalytic site where peptide bonds are formed.

18. In translation, mRNAs are read in the _______ direction, and polypeptide chains are synthesized from the _______ends.

a. 5ʹ to 3ʹ; carboxyl to the amino

b. 5ʹ to 3ʹ; amino to the carboxyl

c. 3ʹ to 5ʹ; carboxyl to the amino

d. 3ʹ to 5ʹ; amino to the carboxyl

19. During translation, the codons on the mRNA are recognized by complementary base pairing to the anticodon on the

a. ribosome.

b. transfer RNA.

c. small cytoplasmic RNA.

d. aminoacyl tRNA synthetase.

20. Eukaryotic ribosomes recognize and initially bind to what structure on the mRNA?

a. A Shine-Dalgarno sequence

b. The 7-methylguanosine cap

c. A TATA sequence

d. A CCAAT sequence

21. The factor that escorts the amionacyl tRNA to the eukaryotic ribosome and then releases it with GTP hydrolysis following the correct codon–anticodon base pairing is

a. eIF-1.

b. eRF-1.

c. eIF-2.

d. eEF-1a.

22. Signaling by the steroid hormone estrogen is an example of _______ signaling.

a. autocrine

b. endocrine

c. paracrine

d. direct cell-to-cell

23. Signaling by neurotransmitters is an example of _______ signaling.

a. autocrine

b. endocrine

c. paracrine

d. direct cell-to-cell

24. Stimulation of T lymphocytes, leading to their synthesis of a growth factor resulting in T lymphocyte proliferation, is an example of _______ signaling.

a. autocrine

b. endocrine

c. paracrine

d. direct cell-to-cell

25. Steroid hormones usually act via receptors that

a. are coupled to G proteins that activate adenylyl cyclase.

b. activate tyrosine kinases.

c. bind to DNA.

d. activate phospholipase C.

26. Which of the following signal molecules binds to nuclear receptors?

a. Thyroid hormone

b. Vitamin D3

c. Retinoic acid

d. Estrogen

27. Neurotransmitters act by binding to receptors that are

a. ligand-gated ion channels.

b. located in the cytoplasm.

c. tyrosine-kinase receptors.

d. not coupled to G proteins.

28. Peptide hormones and growth factors act on target cells by binding to cell surface and _______ receptors.

a. endoplasmic reticulum

b. cytosolic

c. nuclear

d. soluble extracellular

29. The G protein that activates adenylyl cyclase is a

a. monomeric G protein in the Ras family that binds GTP.

b. dimeric G protein that separates into a and b subunits.

c. heterotrimeric G protein that separates into a and bg subunits.

d. heterotrimeric G protein that separates into ab andg subunits.

30. The GTP on the G protein that is linked to adenylyl cyclase is split to GDP and Pi

a. in the inactive state.

b. in the process of subunit separation.

c. upon activation by the receptor.

d. by the active a subunit.

31. The major function of cAMP in animal cells is to activate

a. adenylyl cyclase.

b. protein kinase A.

c. protein kinase C.

d. tyrosine kinases.

32. Which of the following is not considered a second messenger?

a. cAMP

b. IP3

c. Calcium

d. Ecdysone

33. Which of the following correctly describes how protein kinase A can activate genes?

a. Nuclear protein kinase A is activated by cAMP to phosphorylate general transcription factors.

b. Cytosolic protein kinase A is activated by cAMP to release the catalytic subunits, which move into the nucleus and phosphorylate CREB.

c. Cytosolic protein kinase A is activated by cAMP to release the catalytic subunits, which move into the nucleus and phosphorylate general transcription factors.

d. Nuclear protein kinase A is activated by cAMP to phosphorylate CREB.

34. Rhodopsin in the vertebrate retinal photoreceptor cells results in a change in the second messenger _______, leading to the opening of ion channels in the plasma membrane and the production of a nerve impulse.

a. Ca2+

b. cAMP

c. cGMP

d. IP3

35. The first step in growth factor pathway activation is

a. receptor dimerization.

b. receptor phosphorylation.

c. Ras activation.

d. the binding of SH2-containing proteins.

Answer: (a) E. coli. (d) Ribosomal RNAs. (d) a separate mitochondrial RNA poly...

  1. You are studying a steroid hormone-binding protein in mice. Youhave isolated two proteins that have similar but not identicalamino acid sequences from a mixed tissue homogenate (prepared frombrain, muscle, liver, ovary, adrenal gland and kidney of a mixedpopulation of adult mice). There are at least three differentmolecular mechanisms that can give rise to similar butnon-identical proteins. List and explain two of these.

2. The differentiation of muscle cellsin the developing embryo is controlled by myogenin, ahelix-loop-helix (HLH) gene regulatory protein that functions as aheterodimer with another HLH protein. The activity of myogenin mustbe carefully controlled so it does not trigger premature expressionof muscle cell differentiation. The myogenin gene isturned on in advance of the time when it is needed, but myogenin isprevented from functioning by its tight binding to Id, an HLHprotein that lacks a DNA-binding domain, and by phosphorylation ofits DNA-binding domain. Explain how dimerization with Id andphosphorylation of the DNA-binding domain might act to keepmyogenin non-functional.

3. Imprinting occurs only in mammals,and why it should exist at all is a mystery. One gene that isimprinted in most mammalian species is Igf2 gene, whoseproduct � insulin-like growth factor-2 � is required for prenatalgrowth. Most mammalian females can mate with multiple males,generating multiple embryos with different fathers in each litter.If one father had an Igf2 allele that caused more rapidprenatal growth, embryos carrying his genes, it would prosper atthe expense of the other embryos. While this would be good for thefather�s genes (in an evolutionary sense), it would drain theresources of the mother, potentially putting her life at risk (notgood for her genes). Thus, it is in the mother�s interest tocounter these paternal effects with maternal changes that limit thegrowth of the embryo. Based on this scenario, decide whether theIgf2 gene is more likely to be imprinted in the male or inthe female.

Answer: Molecular Mechanisms for Generating Similar but Non-Identical Proteins...

3. The activity of myogenin must be carefully controlled lest it trigger premature expression of the gene essential for cell differentiation. The myogenin gene is turned ON in before it is actually needed (and myogenin is expressed), but myogenin is prevented from functioning by phosphorylation of its DNA-binding domain AND by its tight binding to Id, a helix-loop-helix protein that lacks the DNA binding domain.

A. What types of interactions would hold the heterodimer together and you expect them to be the same as those that are necessary for Id binding? Where would you find these bonds/interactions (use the figure).

B. Explain how phosphorylation of the DNA binding domain and dimerization with Id might act to keep myogenin nonfunctional.

Extra credit. Why might this method of protein regulation be preferred over transcriptional control in this case?

4. Aminoacyl-tRNA synthetases attach specific amino acids to their appropriate tRNAs. The synthetase that attaches valine to tRNAval must be able to discriminate valine from threonine. Valyl-tRNA synthetase achieves this discrimination in two steps. In the first, it uses a binding pocket whose contours allow only valine and threonine to bind, but the binding of valine is preferred. This site is responsible for coupling the amino acid to the tRNA. In the second step, the enzyme checks the newly made aminoacyl-tRNA using a second binding site that is very specific for threonine and hydrolyses it from the tRNA. How do you suppose it is that the second binding site can be very specific for threonine, whereas the first binding site has only a moderate specificity for valine?

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