mol bio practice exam #2

c. 5'--AATTGCCTAGCTGGAATC--3'

If an mRNA has the sequence, 5'GAUUCCAGCUAGGCAAUU, the sequence of its DNA template strand will be

a. 5'--GATTCCAGCTAGGCAATT--3'
b. 3'--CTAAGGTCGATCCGTTAA--5'
c. 5'--AATTGCCTAGCTGGAATC--3'
d. 3'--CUAAGGUCGAUCCGUUAA--5'
e. 5'--TTAACGGATCGACCTTAG--3'

e. The sequence of the region between the -10 element and -35 box

Which of the following is relatively unimportant for the recognition of the promoter by sigma factor?

a. The -35 box
b. The length of the region between the -10 element and -35 box
c. The -10 element
d. The sequence surrounding the start point
e. The sequence of the region between the -10 element and -35 box

b. requires transcription of the sequences signaling termination.

In general, termination of transcription in E. coli:

a. requires many accessory proteins.
b. requires transcription of the sequences signaling termination.
c. is unaffected by sequences that are not in proximity to the termination site.
d. is triggered by RNA polymerase's interaction with DNA sequences.

d. A sample with a high Ct value has more starting material (cDNA) than one with a lower Ct value.

Which is NOT a true statement about the quantitative PCR (qPCR) method?

a. It can be used to determine the amount of mRNA in a sample.
b. It involves reverse transcription of mRNA.
c. Measurement of a Ct value.
d. A sample with a high Ct value has more starting material (cDNA) than one with a lower Ct value.
e. Fluorescence from the dye, SYBRGreen can be used to measure the amount of PCR product.

a. 2, 4, 1, 3.

Place the steps of conducting a microarray assay in the correct order.
1. Hybridize to DNA fragments representative of genes of interest.
2. Purify RNA
3. Construct heat map
4. Make fluorescent tagged cDNA

a. 2, 4, 1, 3.
b. 2, 3, 1, 4.
c. 4, 2, 3, 1.
d. 1, 3, 4, 2.

e. 4, 3, 2, 1

A. To reflect the degree to which several samples share the same expression pattern.

What function might a heat map serve?

A. To reflect the degree to which several samples share the same expression pattern.
B. The change in temperature as genes are expressed in different regions of a tumor.
C. To compare the sequence identity of two genomes.

d. housekeeping genes.

Genes with promoters that are expressed in all cells are called:

a. universal genes.
b. silencer genes.
c. activator genes
d. housekeeping genes.
e. enhancer genes.

a. They are a binding site for RNA polymerase.

Which of the following is NOT a function of transcription factors that bind enhancers?

a. They are a binding site for RNA polymerase.
b. They bind enhancers and interact with the basal transcription apparatus.
c. They change the structure of DNA, typically by bending it.
d. Their binding can affect expression of either upstream or downstream genes.

b. number and size of exons

The length of genes in a gene family often varies; this variation is most often determined by:

a. length of the 5,’untranslated region.
b. number and size of exons
c. number and size of introns.
d. length of the 3,untranslated region.

d. both the 5' and 3' ends have been modified in mRNA and the fact that all introns have been spliced out in the mRNA

The difference between a pre-mRNA and a mature eukaryotic mRNA is:

a. the 5' and 3' ends have been modified in mRNA.
b. the removal of the leader sequence from the pre-mRNA.
c. the fact that all introns have been spliced out in the mRNA.
d. both the 5' and 3' ends have been modified in mRNA and the fact that all introns have been spliced out in the mRNA

b. Genes with a TATA DNA sequence in their promoter and those without a TATA DNA sequence in their promoters.

TATA-binding protein (TBP) is required for initiation by:

a. Genes which depend on TFIIH.
b. Genes with a TATA DNA sequence in their promoter and those without a TATA DNA sequence in their promoters.
c. Genes with a TATA DNA sequence in their promoter but not those without a TATA DNA sequence in their promoters.

a. 5' cap with a 5' - 5' linkage

Pre-mRNA splicing does NOT involve which of the following structural features?

a. 5' cap with a 5' - 5' linkage
b. branch site
c. 3' splice site

d. 5' splice site
e. All of these structural features are involved in pre-mRNA splicing.

Promoters are DNA sequences that serve as binding sites for RNA polymerase and transcription factors, playing a crucial role in initiating transcription. They contain three different sites
1. Binding Sites for RNA Polymerase where RNA polymerase binds to initiate transcription. In prokaryotes, this sequence is called the -10 and -35 regions, while in eukaryotes, it's often the TATA box or other promoter elements.
2. Transcription Factor Binding Sites which can either enhance or repress transcription by interacting with the promoter region.
3. Binding site for Regulatory Elements like enhancer or silencer which can modulate transcriptional activity. These elements can be in proximally or distally to the core promoter and interact with transcription factors to regulate gene expression.

What is characteristic of promoters in both prokaryotes and eukaryotes?

α Subunit (2 copies) which are involved in the assembly and stability of the RNA polymerase complex.

β Subunit contains the active site responsible for catalyzing the formation of phosphodiester bonds between ribonucleotides during RNA synthesis. It binds to the DNA template strand and the incoming ribonucleoside triphosphates (NTPs) used for RNA synthesis.

β' subunit binds to the DNA template strand and plays a role in DNA melting and RNA synthesis. It is involved in the elongation of transcription. The β' subunit helps maintain the stability of the RNA polymerase complex.

ω subunit stabilizes the core enzyme complex of RNA polymerase. It is not essential for the core catalytic activity of RNA polymerase, but it contributes to the stability and assembly of the enzyme complex

What is the role of the four main subunits of bacterial RNA polymerase?

The conserved features are the start point (usually a purine), the –10 element (TATAAT), the –35 box (TTGACA), and the distance separating the -10 and –35 sequences. The UP element is sometimes a feature as well.

What are the conserved features of a bacterial promoter?

The promoter, start point, and terminator sequences define the transcription unit, which constitutes a stretch of DNA expressed via the production of a single RNA molecule.

What DNA sequence elements define a transcription unit and how do they relate to the RNA that is produced?

The three main stages of the transcription reaction are: (1) template recognition, which occurs when RNA polymerase binds double-stranded DNA at a promoter, and initiation, which occurs when the first nucleotide bonds in RNA are synthesized; (2) elongation, which occurs when RNA polymerase moves along the DNA and extends the RNA chain; and (3) termination, which occurs when the formation of RNA stops and the transcription complex comes apart.

What are the three main stages of the transcription reaction?

This is determined by the strand that has the specific sequences recognized by sigma factor. Although contact points with the protein are found on both strands, the two strands are distinguished by different contact points

When RNA polymerase binds to a promoter, how does it choose which strand is the template strand?

A-T base pairs are held together by two hydrogen bonds and are easier to denature than G-C base pairs, which have three hydrogen bonds. The promoter must be denatured to allow the RNA polymerase to transcribe the template strand, and the higher A-T content facilitates this denaturation.

Why is the −10 box A-T rich? What is the effect of this fact with regard to the function of the sequence

The sigma factor has general affinity for DNA and higher affinity for specific sequences. It is likely that the sigma factor binds nonspecifically to DNA then rapidly exchanges bound sequences until it binds to a high-affinity promoter site. Also, Sigma factor binding gives holoenzyme a drastically reduced ability to bind random DNA sequences and confers the ability to recognize specific binding sites

What effect does the sigma factor have on how the RNA polymerase binds to DNA?

Sigma factors are replaced with others that direct transcription of a new set of genes. A cascade of sigma factors is used to complete the transcription program. Most vegetative genes continue to be expressed.

How does transcription of sporulation genes in B. subtilis involve different sigma factors?

RNA pol I - Ribosomal RNA
RNA pol II - Pre-mRNA; ncRNA; snRNA; miRNA
RNA pol III - tRNA; 5S-rRNA; U6 snRNA; RNase P RNA; a few miRNAs

What groups of genes are transcribed by each of the eukaryotic RNA polymerases?

TATA Box is a conserved DNA sequence located around 25 to 30 base pairs upstream of the transcription start site. It is recognized by the TATA-binding protein (TBP).

CAAT Box is typically located further upstream of the transcription start site compared to the TATA box. and helps to enhance transcriptional activity.

GC Box is a DNA sequence motif rich in guanine (G) and cytosine (C) nucleotides. It is located near the transcription start site. The GC box is recognized by transcription factors such as Sp1 and can contribute to the regulation of gene expression.

However, not all promoters contain all three elements, and the presence and arrangement of these elements can vary depending on the specific gene and its regulatory requirements.

What are the three major promoter elements that are each found in many, but not all, promoters for RNA polymerase II?

Type 1 Promoters are found upstream of genes encoding tRNAs and 5S rRNA. They consist of two conserved sequence elements: the A box and the B box, also known as the internal promoter elements.

Type 2 Pol III promoters are found upstream of genes encoding small nuclear RNAs (snRNAs) and some other noncoding RNAs. They are characterized by a TATA box-like sequence, known as the TATA-less promoter.

Type 1 and type 2 Pol III promoters bind to specific transcription factors (TFIIIC for type 1 and TFIIIB for type 2) to help the recruitment of RNA polymerase III and the initiation of transcription.

What are the two main types of promoters recognized by RNA polymerase III, and how do they work to facilitate proper transcription initiation?