BIOL 3450 exam 2

You would expect a potential 3' splice acceptor site (AG dinucleotide) to occur in a random DNA sequence once in every _____ nucleotides.

16

Following is the order of packaging of eukaryotic DNA into chromosomes. What belongs in the blank? DNA double helix → 'beads-on-a-string' form of chromatin → (____) → extended scaffold associated form → condensed scaffold associated form → metaphase chromosome

30 nm chromatin fiber

What sequences are present at the beginning and end of an intron?

GU at the 5' end of an intron and AG at the 3' end of the intron.

This is the structure of ibuprofen. It has limited solubility in water (21 mg/L at pH 7) and has a pKa of approximately 5. You have a headache but you have to study for the Cell Bio midterm, and you decide to take an ibuprofen pill. How does it get from your gastrointestinal tract into your bloodstream?

In the stomach, with pH 1, ibuprofen is protonated, uncharged, and able to cross the lipid bilayer membranes of the intestinal epithelial cells. Once it gets to the bloodstream, at pH 7, it is deprotonated, negatively charged, and able to circulate in the blood.

Which mobile genetic elements encode a reverse transcriptase?

LTR retrotransposons and LINEs

Coenzyme Q, an intermediate electron carrier in the mitochondrial electron transport chain, has a redox potential close to zero. What are the redox potentials of NADH and O2?

NADH has a negative redox potential; O2 has a positive redox potential

Which of these molecules would most rapidly cross cell membranes via simple diffusion?

O2

Only RNA Polymerase II, which transcribes nuclear pre-mRNAs, has an extended carboxy-terminal domain (CTD) with 26 (in yeast) to 52 copies (in vertebrates) of a repeated peptide sequence: Tyr-Ser-Pro-Thr-Ser-Pro-Ser. Which of these amino acids have a hydroxyl group in their side chain, allowing it to be phosphorylated

Y (tyr) S (ser) T (thr)

Which of the following can be metabolized to/from pyruvate (assuming the necessary co-substrate/cofactors are available for the enzyme that makes the interconversion)?

alanine and lactate

In addition to GU and AG at the 5' and 3' ends, what other DNA sequence elements determine what potential splice sites are actually used?

an A nucleotide at the branch point a pyrimidine-rich region near the 3' end of the intron exonic splice enhancers

A membrane-localized protein that transports lipids or lipophilic drugs out of the cell using the energy from ATP hydrolysis is most likely a:

an ABC superfamily transporter

You wish to create a yeast plasmid that is replicated once each cell cycle and segregates to both daughter cells during mitosis. What DNA sequence elements must be present on the plasmid?

an origin of DNA replicationb. a centromeric sequencec. a telomeric sequence

The Na+/K+ ATPase is a___

antiport transporter, a P-type ATPase

The figure at the right shows what type of transcription factor?

basic helix-loop-helix proteins

PRC1 complex subunit Pc

binds to methylated H3K27, and dimerize to bring nucleosomes closer

PRC1 complex

binds to multiple Pc proteins to condense the chromatin and maintains H3K27 methylation

rRNA

catalyzes peptide bond formation during protein synthesis

snRNAs

catalyzes pre-mRNA splicing to remove introns

What would be the consequence(s) to a cell of a loss of telomeric sequences from the ends of its chromosomes

chromosomes will shorten at the ends with each round of DNA replication chromosomes will randomly join end-to-end during interphase, but then break during anaphase of mitosis

Which of these post-translational modifications occur in the lumen of the ER?

cleavage of the signal sequence Addition of GPI anchors to the C-terminus Isomerization of disulfide bonds binding of chaperones (BiP, calnexin, calreticulin) and protein folding Addition of N-linked oligosaccharides

If you align the components of the mitochondrial electron transport pathway in order of the standard reduction potentials for the individual steps, they follow the predicted pattern—i.e., from

components with the more negative redox potentials to those with more positive redox potentials

CpG island

genes with bidirectional transcription from promoter

Histones can neutralize the negative charge on DNA because

histones have a positive charge that ion pairs with the negative charge on DNA

Compared to genes expressed at low levels, highly expressed genes will have promoter regions that are

hypomethylated at CpG sites and packaged in nucleosomes with acetylated histones

Which proteins contain a signal sequence that is recognized by the signal recognition particle (SRP)?

integral membrane proteins destined for the plasma membrane secreted proteins ER lumen proteins

When a protein has an NLS sequence and is bound by importin, it is tagged to be transported ____.

into the nucleus

The destruction of bacteria by phagocytosis involves vacuolar ATPase proton pump(s). Its (their) function is to pump protons ______.

into the phagosome so its (the phagosome) pH will decrease

Which histone modification leads to greater condensation, characteristic of heterochromatin?

methylation

Put the following events in order as you would expect them to occur after addition of tunicamycin to cells in culture. Order the events as follows: Event 1 < Event 2 < no addition of N-acetylglucosamine to dolichol phosphate no N-linked glycosylation of proteins translation of Hac1 transcription factor mRNA increased transcription of ER chaperones and protein folding catalysts accumulation of unfolded or mis-folded proteins in the ER lumen dimerization of IRE1

no addition of N-acetylglucosamine to dolichol phosphate < no N-linked glycosylation of proteins < accumulation of unfolded or mis-folded proteins in the ER lumen < dimerization of IRE1 < translation of Hac1 transcription factor mRNA < increased transcription of ER chaperones and protein folding catalysts

Which of the pre-mRNA processing steps shown is (are) truly post-transcriptional, meaning that they occur after RNA Pol II falls off the DNA template and the transcript is released?

none, they are all co transcriptional

What are the minimum structural or functional elements required for a eukaryotic chromosome

telomeres centromere origin of DNA replication

What transporter is primarily responsible for generating and maintaining a mammalian cell's plasma membrane potential?

the Na+/K+ ATPase

Which region(s) of a protein-coding gene are transcribed in the nucleus, but are not present in the mRNA that is exported to the cytoplasm?

the introns

When a mitochondrion is "uncoupled" it means:

the mitochondrion is leaky to protons so the pH gradient generated by the electron transport chain isn't used to make ATP

This figure is part of Fig 4-24, showing a key step in translational initiation. Using the information in this figure and also from chapter 10 text, what would happen to an mRNA with no 5' cap?

would not be translated, or translated very poorly It would be degraded rapidly by a 5' exonuclease

Will benzo(a)pyrene diffuse freely across a cell membrane?

yes

What are common domains in transcription factors that bind to DNA

zinc-finger leucine zipper basic helix-loop-helix (bHLH)

What is the free energy change, expressed as kcal/mol, for efflux of K+ ions given that the membrane potential of the cell is -70 mV, and the K+ ion concentrations are 150 mM in the cytoplasm and 15 mM outside the cell? Be sure to indicate whether the deltaG is positive or negative. Use 2.3 RT = 1.4 kcal/mol under physiological conditions. Enter just the number with + or - sign (e.g. -1.4); kcal/mol will be assumed. Your Answer (Incorrect)

0.21 deltaGm = nFV Both K+ and Na+ have single positive charge, so n = +1 for both. Given the membrane potential of -70 mV, the efflux of K+ is against the membrane potential; so deltaGm will have the same magnitude as for Na+ influx, but opposite in sign: +1.61 kcal/mol. The efflux of K+ down the K+ concentration gradient then, can be calculated as: deltaGc = -2.3 RT log{[K+in]/[K+out]} = -2.3 RT log(10) = -2.3 RT (1) = -1.4 kcal/mol Adding the two terms, overall deltaG = deltaGm + deltaGc = 1.61 kcal/mol - 1.4 kcal/mol = 0.21 kcal/mol

Which of these happens first? 5' cap addition 3' polyadenylation splicing to remove introns export from the nucleus to the cytoplasm initiation of translation

5' cap addition

The polyadenylation (Poly-A) consensus sequences is 5' ______ 3':

AAUAAA

Which type of promoter often generates bidirectional transcription by RNA pol II?

CpG islands

Which of the following is a commonly used component for both miRNA and RNA interference?

DICER

Recruitment of which enzyme(s) to a region of chromatin would cause it to become more condensed?

DNA methyl transferase (DNMT) b. histone deacetylase (HDAC)

Dicer

Endonuclease that cuts double-stranded RNA; processes pre-microRNAs

Argonaute

Endonuclease that is part of RISC complex; uses short RNA fragments as guide RNA to cleave complementary mRNAs

For the simplified diagram here for the F0F1 complex, the region that allows protons to move through the complex and induce a conformation change is labeled ____ and the portion where ATP is generated from ADP + Pi is labeled

F0; F1

Proteins that are imported into mitochondria are:

First translated in the cytosol, then bind to a receptor on the outer mitochondrial membrane

The TATA box is one of the major promoters eukaryotes use in transcription. If we delete 10 nucleotides between the TATA box and the transcription start site (e.g. -20 to -11), where will transcription start from

It will start from +11. Because transcription will occur 25 bp downstream of TATA box. This is determined by the size and binding of RNA pol II and the associated machinery to TATA box

Which of the following is a superoxide anion (the substrate of superoxide dismutase, SOD)?

O2•-

Which of the following statements about pyruvate are true? Select all that are true.

Pyruvate is the end-product of glycolysis Pyruvate can be fermented to lactic acid or ethanol Pyruvate can be converted to alanine and vice versa Pyruvate enters mitochondria to be further metabolized to carbon dioxide via pyruvate oxidation and the TCA cycle

Which sequence element(s) is or are present in promoters of genes that are transcribed at high levels?

TATA box

What is the immediate effect of TBP binding to the DNA? How might that be important for transcription initation by RNA Pol II?

TBP binding bends the DNA. The DNA bending may bring transcription factors bound upstream and downstream of TBP together so they can form a complex that helps RNA polymerase initiate transcription.

Which of the following explains tissue specific gene expression (the same gene is expressed in one or more specific cell types) ?

There are different transcription factors expressed in each tissue and some can bind to enhancer of the gene and promote transcription

Enhancers are considered transcription-control elements that regulate the expression of eukaryotic genes. Which one of the following is true regarding these elements

They generally range in length from about 50-200 base pairs

For import of proteins into the mitochondria, the proteins that recognize the mitochondria localization signal and transport the polypeptide through the membrane are named

Toms and Tims

TATA box

a promoter-proximal element for genes with high levels of transcription

Which transposons encode a reverse transcriptase?

a. LINEsb. LTR-retrotransposons

What is (are) the role(s) of general pol II transcription factors (TFIIA,B,D,E,F, and H)?

a. They bind to transcription factors such as TBPb. They recruit RNA polymerase IIc. They bind to mediatord. They phosphorylate the carboxy terminal domain of RNA pol II

Which of the following pre-mRNA processing steps occurs first?

addition of the 7-methyl guanosine at the 5' end

Eukaryotic genes that are expressed at low levels, including most "housekeeping" genes, lack TATA boxes or Initiator sequences, but have a promoter region that is relatively rich in CG dinucleotides. In regions of the genome other than promoters, these CG dinucleotides in promoter regions are methylated at the cytosine base. In promoter regions, the CG dinucleotides are not methylated (hypo-methylated). Transcription begins at a variable distance downstream of the hypomethylated CG-rich "islands". Recall that deamination of methylated cytosines results in a uracil, and creates a U-A mismatch in the DNA. Which DNA repair system repairs this mismatch?

base excision repair

The Warburg effect, also called aerobic glycolysis, is found in many cancer cells. If most of the pyruvate generated from glycolysis is not respired in the mitochondria, what other compounds would be produced from pyruvate?

both alanine and lactic acid

What is the role of the 3' polyA tail on an mRNA?

it stabilizes the mRNA from degradation it increases translational efficiency it mediates circularization of the mRNA via interaction of PABP with eIF4

What would happen to an mRNA that loses its poly(A) tail?

it would be rapidly degraded

tRNA

matches codons in the mRNA to their amino acids

PRC2 complex

methylates histone H3 at lysine 27

Which RNA polymerase transcribes 18S and 28S ribosomal RNAs?

pol 1

miRNA

post-transcriptional regulation of gene expression

In the absence of mitochondria, what molecules will cells be unable to metabolize for energy to make ATP?

pyruvate fatty acids amino acids

enhancer

regulatory DNA sequence elements that may be either upstream or downstream of the transcription start site, often many thousands of base-pairs distant

snoRNA

required for processing rRNAs in the nucleolus

What DNA element can jump (relocate) and proliferate in the genome by a "copy and paste" mechanism?

retrotransposons

Telomerase contains an RNA template and has

reverse transcriptase activity

RNA pol 3

synthesizes 5S RNA, tRNAs and other small RNAs

How much energy does it take to pump a proton across the mitochondrial inner membrane, from the matrix to the intermembrane space? The membrane potential across the inner membrane is +150 mV (the intermembrane space is more positive than the matrix). There is 1 pH unit difference between the mitochondrial matrix and the intermembrane space (which has the higher proton concentration?). F = 23 kcal/(mol*volt) 2.3 RT = 1.4 kcal/mol at 37 deg C Express your answer as deltaG, in kcal/mol - enter just the numerical value.

4.85 For movement of ions across a membrane, the deltaG has 2 components: deltaGc = 2.3 RT log([H+]in/[H+]out) = 2.3 RT = 1.4 kcal/mol deltaGm = FE = 23 kcal/(mol*volt) * .15 volt = 3.45 kcal/mol Note that we are pumping protons against the concentration gradient, and against the membrane potential, so the signs are positive for both terms. So deltaG = 1.4 kcal/mol + 3.45 kcal/mol = 4.85 kcal/mol

Which of the pre-mRNA processing steps shown occur in the nucleus?

5' capping 3' polyadenylation RNA splicing

Chromatin is isolated from a eukaryotic cell, and then digested to completion with micrococcal nuclease (cuts naked DNA). The DNA is then purified away from bound proteins and electrophoresed on an agarose gel. What size DNA fragments would you expect to see?

A blob of DNA fragments at around 140-150 nucleotides

Add a 3rd plot (line or curve) to this figure that represents the expected uptake of glucose by simple diffusion, into a cell with no glucose transporter.

A straight line with a very shallow slope, indicating very low transport into the cell, even at high concentrations of external glucose. Cell membranes are relatively impermeable to glucose.

What sequence in the pre-mRNA signals polyadenylation?

AAUAAA

Which of the following statement regarding heterochromatin is correct?

After DNA dyes staining, heterochromatin looks darker than euchromatin. The DNA of heterochromatin is more highly condensed than that of euchromatin. Heterochromatin is associated with inactive genes.

Above is an image of an agarose gel stained with ethidium bromide. Lane 2 contains a sample of DNA purified from chromatin that has been partially digested with micrococcal nuclease. Lane 1 has a 100 bp DNA ladder. Explain the banding pattern of the nuclease-digested chromatin sample in lane 2.

The nuclease is cutting the DNA between nucleosomes. DNA wrapped around the nucleosomes is protected from nuclease digestion. Since about 150 bp of DNA is wrapped around a single nucleosome, the smallest DNA fragment is about 150 bp. Other fragments represent 2 nucleosomes (150 bp + 200 bp), 3 nucleosomes, etc.

GAL4 is a transcriptional activator protein that binds to a motif within the UASGAL Interpret the experimental results shown in part b. What do these experiments and results say about the parts of the GAL4 protein that are necessary and sufficient for transcriptional activation of a downstream gene? ​

These results indicate that the DNA-binding domain (residues 1-74) and the activation domain (residues 738-823) of the GAL4 protein are necessary and sufficient for transcriptional activation. The amino acids in between are not necessary, because deleting them still results in transcriptional activation. Elimination of residues 1-74 prevents binding to the UAS (promoter) site in the DNA. Elimination of residues 738-823) results in proteins that can bind to UAS, but cannot activate transcription.

The so-called "initiator sequence" is poorly defined: (5′) Y-Y-A+1-N-T/A-Y-Y-Y (3′) Y is any pyrimidine. Which DNA bases are pyrimidines?

cytosine and thymine

What is the target of the maintenance DNA methylase, DNMT1?

cytosines that are 5' to a guanine, where the partner DNA strand has methylated cytosine

What is the most common pathway for mRNA degradation?

deadenylation-dependent pathway

most vertebrate mRNAs are degraded by which of these pathways?

deadenylation-dependent pathway

What enzyme cleaves double-stranded RNA to generate both miRNAs and siRNAs?

dicer

Which post-translational processes occur in the ER lumen?

disulfide bond formation addition of N-linked oligosaccharides protein folding with assistance from chaperones

Which of the following is NOT one of the three principal types of DNA sequences present in eukaryotic promoters? TATA box initiator enhancers CpG islands

enhancers

The SR proteins in the cross-exon recognition complex bind what sequences in the pre-mRNA?

exonic splice enhancers (ESEs)

This figure represents the primary structure of a plasma membrane protein, with the transmembrane domain and signal-anchor sequence shown as a red helix. The +++ indicates the location of positively charged amino acid side chains. Will the N-terminus of this protein be on the cytosolic side or the exoplasmic side of the ER membrane?

exoplasmic side

There was once a careless graduate student who had a tendency to leave cells in culture in our incubators so long that some of the water evaporated from the dishes, causing the NaCl concentration to rise above the usual physiologic level (~150 mM). For awhile, the cells were able to survive by maintaining a relatively normal intracellular Na+ concentration. This situation (higher concentrations of ions outside the cell than inside) would be described as:

hypertonic

One of the major reasons that ion channels are used to propagate an action potential down an axon rather than to move the ions across the membrane with another type of transporter (such as a Na+/K+ antiporter) is

ion channels are much faster

Match the compartment to the protein trafficking mechanism A. secreted proteins 1. N-terminal hydrophobic signal peptide B. mitochondrial matrix 2. N-terminal amphipathic helix C. nuclear proteins 3. clusters of positively charged amino acid residues D. cytosolic proteins 4. proteins with no localization signals E. peroxisomal proteins 5. ser-lys-leu (SKL) at C-terminus

secreted proteins - N-terminal hydrophobic signal peptide mitochondrial matrix - N-terminal amphipathic helix nuclear proteins - clusters of positively charged amino acid residues cytosolic proteins - proteins with no localization signals peroxisomal proteins - ser-lys-leu (SKL) at C-terminus

Which of the following small RNA molecules is present in spliceosomes?

snRNA

The key components of a spliceosome are:

snRNAs that base-pair with the 5' splice donor and 3' splice acceptor junctions

Which of the following non-coding RNAs never exit the nucleus? Select all that apply. A. rRNAs B. tRNAs C. snoRNAs D. snRNAs E. miRNAs

snoRNAs and snRNAs

The transporter shown in this diagram would be categorized as _____.

symporter

RNA pol 2

synthesizes pre-mRNA

RNA pol 1

synthesizes rRNA

The diagram below shows the steps in the transport of Ca2+ by the Ca2+ ATPase in the sarcoplasmic reticulum membrane of skeletal smooth muscle cells. What is happening in the step of the cycle that is designated by the question mark ("?") ?

the transporter will hydrolyze the enzyme-P bond