Cell Molecular Exam 3

You are studying a set of mouse genes whose expression increases when cells are exposed to the hormonecortisol, and you believe that the same cortisol-responsive transcriptional activator regulates all of thesegenes. Which of the following statements below should be true if your hypothesis is correct?

The cortisol-responsive genes share a DNA sequence in their regulatory regions that binds the cortisol-responsive transcriptional activator.

Which of the following processes do not take place in the mitochondrion?

Glycogen Breakdown

Cholesterol serves several essential functions in mammalian cells. Which of the following properties of themembrane is not influenced by cholesterol?

Membrane thickness

Which of the following statements is false?

RNA has a uracil base and a ribose sugar

Transcription in bacteria differs from transcription in a eukaryotic cell in that

RNA polymerase (along with its sigma subunit) can initiate transcription on its own.

Match the following types of RNA with the main polymerase that transcribes them: most rRNA genes

RNA polymerase I

Match the following types of RNA with the main polymerase that transcribes them: Protein coding genes, mRNA genes

RNA polymerase II

Match the following types of RNA with the main polymerase that transcribes them: tRNA genes, 55 rRNA genes

RNA polymerase III

Which of the following reactions is catalyzed by ribozymes?

RNA splicing

Which of the following statements about RNAi is true?

RNAi is induced when double-stranded, foreign RNA is present in the cell.

Which of the following antibiotics targets RNA polymerase?

Rifamycin

Where are proteins of the electron transport chain, ATP synthase, and membrane transport protein for pyruvate located in the mitochondria?

inner membrane

Which of the following is not true of glycolysis?

it oxidizes glucose to carbon dioxide

In anaerobic conditions,skeletal muscle produces:

lactate only

Cell membranes are fluid and thus proteins can diffuse laterally within the lipid bilayer most likely accompanied by specific lipids. This association of proteins and lipids is called

lipid raft

Which amino acid would you expect a tRNA with the anticodon 5′-CUU-3′ to carry?

lysine

Total nucleic acids are extracted from a culture of yeast cells and are then mixed with resin beads to whichthe polynucleotide 5'-TTTTTTTTTTTTTTTTTTTTTTTTT-3' has been covalently attached. After a shortincubation, the beads are then extracted from the mixture. When you analyze the cellular nucleic acids thathave stuck to the beads, which of the following is most abundant?

mRNA

Where is the mitochondrial genome and the citric acid cycle enzymes located?

matrix

These mechanisms all allow for cell ________, a property involving the maintenance of gene expression patterns important for cell identity.

memory

In mammals, individuals with two X chromosomes are female, and individuals with an X and a Y chromosome are male. It had long been known that a gene located on the Y chromosome was sufficient to induce the gonads to form testes, which is the main male-determining factor in development, and researchers sought the product of this gene, the so-called testes-determining factor (TDF). For several years, the TDF was incorrectly thought to be a zinc finger protein encoded by a gene called BoY. Which of the following observations would most strongly suggest that BoY might not be the TDF? Explain your answer.

Some XY individuals that develop into females have mutations in a different gene, SRY, but are normal at BoY.

Telomeres serve as caps at the ends of linear chromosomes. Which of the following is not true regarding the replication of telomeric sequences?

The leading strand doubles back on itself to form a primer for the lagging strand.

Which of the following statements is not an accurate statement about thymidine dimers?

Thymidine dimers are covalent links between thymidines on opposite DNA strands.

Anaerobically growing yeast further metabolizes the pyruvate produced by glycolysis to CO2 and ethanol aspart of a series of fermentation reactions. A physiological role of fermentation, other than the production ofsmall amounts of ATP, is to regenerate NAD+.

True

Pumps are transporters that are able to harness energy provided by other components in the cells to drive the movement of solutes across membranes, against their concentration gradient. This type of transport is called _____________.

active transport

MicroRNAs ____________________.

are produced from a precursor miRNA transcript

Find the mismatched pair regarding broad spectrum antibiotics

kanamycin - inhibitor of NAD+ biosynthesis

During strenuous exercise, hypoxic (low oxygen) muscle cells convert pyruvate to:

lactate

A neuron and a white blood cell have very different functions. For example, a neuron can receive andrespond to electrical signals while a white blood cell defends the body against infection. This is because

the neuron expresses some mRNAs that the white blood cell does not.

Another way to inherit chromatin structures involves DNA_________,

methylation

Where is porin located in the mitochondria?

outer membrane

A bacterium is suddenly expelled from a warm human intestine into the cold world. Which of the following adjustments might the bacterium make to maintain the same level of membrane fluidity?

produce lipids with hydrocarbon tails that are shorter and have more double bonds

The sigma subunit of bacterial RNA polymerase:

recognizes promoter sites in the DNA.

The classic experiments conducted by Meselson and Stahl demonstrated that DNA replication is accomplished by a ________________ mechanism.

semiconservative

A mutation in the tRNA for the amino acid lysine results in the anticodon sequence 5′-UAU-3′ (instead of 5′-UUU-3′). Which of the following aberrations in protein synthesis might this tRNA cause?

substitution of lysine for isoleucine

Consider the apical location of protein A expressed in epithelial cells, illustrated in panel (A) of the figure above. Which type of defect described below is the most likely to cause the redistribution of protein A around the entire cell, shown in panel (B)?

the deletion of a protein in the tight junction

Define proteome

the entire complement of proteins that is or can be expressed by a cell, tissue, or organism:

Define genome

the haploid set of chromosomes in a gamete or microorganism, or in each cell of a multicellular organism.

Define transcriptome

the sum total of all the messenger RNA molecules expressed from the genes of an organism.

Define Metabolome

the total number of metabolites present within an organism, cell, or tissue:

The distinct characteristics of different cell types in a multicellular organism result mainly from the differential regulation of

transcription of genes transcribed by RNA polymerase II.

Human beings with the inherited disease xeroderma pigmentosum have serious problems with lesions ontheir skin and often develop skin cancer with repeated exposure to sunlight. What type of DNA damage isnot being recognized in the cells of these individuals?

ultraviolet irradiation damage

The figure above shows a simple scheme by which three transcription regulators are used duringdevelopment to create eight different cell types. How many cell types could you create, using the samerules, with four different transcription regulators?

16

The classical point of view is that, during mitochondrial respiration, three ATP molecules can be generatedfrom one molecule of NADH + H+ and only two from FADH2. When factoring in the cytosolic NADH + H+, themaximum number of molecules of ATP per glucose generated by the electron transport system is _____.

38

You have a piece of DNA that includes the following sequence:5'-ATAGGCATTCGATCCGGATAGCAT-3'3'-TATCCGTAAGCTAGGCCTATCGTA-5'Which of the following RNA molecules could be transcribed from this piece of DNA?

5'-AUAGGCAUUCGAUCCGGAUAGCAU-3'

Which of the following molecules of RNA would you predict to be the most likely to fold into a specificsecondary structure due to intramolecular base pairing?

5'CCCUAAAAAAAAAAAAAAAAUUUUUUUUUUUUUUUUAGGG-3'

Below is the sequence from the 3′ end of an mRNA.5′-CCGUUACCAGGCCUCAUUAUUGGUAACGGAAAAAAAAAAAAAA-3′If you were told that this sequence contains the stop codon for the protein encoded by this mRNA, what isthe anticodon on the tRNA in the P site of the ribosome when release factor binds to the A site?

5′ -CCA-3′

Which is the anticodon in tRNA Met?

5′-CAU-3′

What kind of ribosomes would you find in chloroplasts?

70S ribosomes

What kind of ribosomes would you find in mitochondria?

70S ribosomes

What kind of ribosomes would you find in the cytoplasm of a plant cell?

80S ribosomes

What kind of ribosomes would you find in the cytoplasm of an animal cell or a fungal cell?

80S ribosomes

On a DNA strand that is being used as a template, where is the copying occurring relative to the replication origin—3′ of the origin, 5′, or both?

Both, as a result of the bidirectional nature of chromosomal replication.

In oxidative phosphorylation, ATP production is coupled to the events in the electron-transport chain. Whatis accomplished in the final electron transfer event in the electron-transport chain?

O2 is reduced to H2O

The figure above shows a highly schematized bacterial DNA molecule during replication. Find the wrong label:

Order of synthesis of Okazaki Fragments

There are several reasons why the primase used to make the RNA primer for DNA replication is not suitablefor gene transcription. Which of the statements below is not one of those reasons?

Primase can initiate RNA synthesis without the need for a base-paired primer.

Find the mismatched pair

Produced under anaerobic conditions by several microbial groups—cholesterol

Three different membrane components are shown in the figure below. Using the list below identify the three molecules, and label the chemical groups indicated.

Sterol polar head group Sterol Phospholipid

The following is incorrect regarding the statement "A small amount of ATP is made in glycolysis":

Substrate-level phosphorylation depends on a DpH and a voltage gradient.

In eukaryotic cells, general transcription factors are required for the activity of all promoters transcribed byRNA polymerase II. The assembly of the general transcription factors begins with the binding of the factor__________________ to DNA, causing a dramatic local distortion in the DNA. This factor binds at the DNAsequence called the ___________, which is typically located 25 nucleotides upstream from the transcriptionstart site.

TFIID, TATA box

On a DNA strand that is being synthesized, which end is growing—the 3′ end, the 5′ end, or both ends? Explain your answer.

The 3′ end. DNA polymerase can add nucleotides only to the 3′-OH end of a nucleic acid chain.

Which of the following choices best describes how transcription occurs?

The bottom strand is the template strand; RNA polymerase moves along this strand from 3' to 5'

We can estimate the relative mobility of a population of molecules along the surface of a living cell byfluorescently labeling the molecules of interest, bleaching the label in one small area using laser, and thenmeasuring the speed of signal recovery as molecules migrate back into the bleached area. What is this method called?

FRAP

During glycolysis, glucose molecules are broken down to ultimately yield CO2 and H2O.

False

In the generation of ATP by oxidative phosphorylation inorganic phosphate (Pi) binds directly to ADP via adehydration reaction (i.e., ADP + Pi ⇌ ATP).

False

The cleavage of fructose 1,6-bisphosphate yields two molecules of glyceraldehyde 3-phosphate.

False

The transcription start site sequence on DNA is equivalent to the translation start site in RNA.

False

Which of the following does not occur before a eukaryotic mRNA is exported from the nucleus?

The ribosome binds to the mRNA.

Indicate which of the following statements regarding DNA damage is incorrect.

After damaged DNA has been repaired, nicks in the phosphate backbone are maintained as a way to identify the strand that was repaired.

Which of the following organisms will have the highest percentage of unsaturated phospholipids in their membranes?

Antarctic fish

Which of the following membrane lipids does not contain fatty acid tails?

Cholesterol

Which of the following is not a good example of a housekeeping protein?

DNA repair enzymes

If the genome of the bacterium Escherichia coli requires about 20 minutes to replicate itself, how can the genome of the fruit fly Drosophila be replicated in only 3 minutes?

Drosophila DNA contains more origins of replication than E. coli DNA.

The MyoD transcriptional regulator is normally found in differentiating muscle cells andparticipates in the transcription of genes that produce muscle-specific proteins, such as thoseneeded in contractile tissue. Amazingly, expression of MyoD in fibroblasts causes these cellsderived from skin connective tissue to produce proteins normally only seen in muscles.However, some other cell types do not transcribe muscle-specific genes when MyoD isexpressed in them. Which of the following statements below is the best explanation of whyMyoD can cause fibroblasts to express muscle-specific genes

During their developmental history, fibroblasts have accumulated sometranscriptional regulators in common with differentiating muscle cells.

Some animal cells have a layer of carbohydrates on the external (noncytosolic) surface of the plasmamembrane, that is, oligosaccharide side chains are attached to membrane glycolipids and glycoproteins (cf.Fig. 11-35). What is the name of this sugar coat?

Glycocalyx

In mammals, glycogen is a more useful food storage molecule than fat because:

Glycogen can be used to produce ATP under anaerobic conditions whereas fat cannot

Which of the following statements about DNA methylation in eukaryotes is false?

Immediately after DNA replication, each daughter helix contains one methylated DNA strand, which corresponds to the newly synthesized strand.

Which of the following statements is false?

In eukaryotes, all membrane-enclosed organelles are surrounded by one lipid bilayer.

Which of the following statements about RNA splicing is false?

In order for a gene to function properly, exons must be removed from the primary transcript.

Most cells in the body of an adult human lack the telomerase enzyme because its gene is turned off and is therefore not expressed. An important step in the conversion of a normal cell into a cancer cell, which circumvents normal growth control, is the resumption of telomerase expression. Explain why telomerase might be necessary for the ability of cancer cells to divide over and over again.

In the absence of telomerase, the life-span of a cell and its progeny cells is limited. With each round of DNA replication, the length of telomeric DNA will shrink, until finally all the telomeric DNA has disappeared. Without telomeres capping the chromosome ends, the ends might be treated like breaks arising from DNA damage, or crucial genetic information might be lost. Cells whose DNA lacks telomeres will stop dividing or die.However, if telomerase is provided to cells, they may be able to divide indefinitely because their telomeres will remain a constant length despite repeated rounds of DNA replication.

A pregnant mouse is exposed to high levels of a chemical. Many of the mice in her litter are deformed, butwhen they are interbred with each other, all their offspring are normal. Which two of the following statements could explain these results?

In the deformed mice, somatic cells but not germ cells were mutated. The toxic chemical affects development but is not mutagenic

What purpose does the phosphorylation of glucose to glucose 6-phosphate by the enzyme hexokinase serve as the first step in glycolysis?

It helps drive the uptake of glucose from outside the cell.

Where does oxidative phosphorylation take place in the animal cell and what other processes are requiredfor this to occur?

It takes place in the mitochondrion and follows the production of NADH + H+ and FADH2.

You have discovered an exo- mutant of DNA polymerase. The enzyme's 3′-to-5′ exonuclease function has been destroyed but the ability to join nucleotides together is unchanged. Which of the following properties do you expect the mutant polymerase to have?

It will be more likely to generate mismatched base pairs.

The general transcription factors and RNA polymerase are not sufficient to initiate transcription in the celland are affected by proteins bound thousands of nucleotides away from the promoter. Proteins that link thedistantly bound gene regulatory proteins to RNA polymerase and the general transcription factors include the large complex of proteins called ___

Mediator

Observe the figure below and find the incorrect statement

The figure represents a eukaryotic message.

In the course of evolution, a large number of genes from mitochondria and chloroplasts (originally bacterial endosymbionts) have become incorporated into the nucleus. What kind of gene expression controls the production of the proteins encoded by such genes?

The genes originally in the organelles are now regulated by mechanisms in the nucleus.

Which of the following statements about the genetic code is correct?

The genetic code is redundant.

Which of the following statements about the genetic code is incorrect?

The genetic code is universally present across the domains of life and organelles

Which of the following statements about mRNA half-life is false?

The half-life of most eukaryotic-cell mRNAs is >24 hours.

Which one of the following is the main reason that a typical eukaryotic gene is able to respond to a fargreater variety of regulatory signals than a typical prokaryotic gene or operon?

The transcription of a eukaryotic gene can be influenced by proteins that bind far from the promoter.

Plasma membranes are extremely thin and fragile, requiring an extensive support network of fibrous proteins. This network is called the ______.

cytoskeleton

New membrane phospholipids are synthesized by enzymes bound to the _____________ side of the_________________ membrane.

cytosolic, endoplasmic reticulum

Which statement is false?

When DNA is being replicated inside a cell, local heating occurs, allowing the two strands to separate.

Three phospholipids X, Y, and Z are distributed in the plasma membrane as indicated in the figure on theleft. For which of these phospholipids does a flippase probably exist?

X and Y

Beside the distortion in the DNA backbone caused by a mismatched base pair, what additional mark is thereon eukaryotic DNA to indicate which strand needs to be repaired?

a nick in the new strand

The piece of RNA below includes the region that codes for the binding site for the initiator tRNA needed intranslation.5′-GUUUCCCGUAUACAUGCGUGCCGGGGGC-3′Which amino acid will be on the tRNA that is the first to bind to the A site of the ribosome?

arginine

Sickle-cell anemia is an example of an inherited disease. Individuals with this disorder have misshapen(sickle-shaped) red blood cells caused by a change in the sequence of the β-globin gene. What is the nature of the change?

base-pair change

How are most eukaryotic transcription regulators able to affect transcription when their binding sites are far from the promoter?

by looping out the intervening DNA between their binding site and the promoter

As pyruvate is completely broken down in the TCA (Krebs) cycle, some of its energy is

conserved in NADH + H+ and FADH2.

Some genes are expressed all the time , e.g. actin (cytoskeleton) and are called "house-keeping" genes (_______ expressed). In contrast, genes that are expressed only temporarily and/or in a certain are called ________.

constitutively, inducible genes

Operons

contain a cluster of genes transcribed as a single mRNA.

DNA replication is considered semiconservative because ____________________________.

each daughter DNA molecule consists of one strand from the parent DNA molecule and one new strand

the transmission of information important for gene regulation from parent to daughter cell, without altering the actual nucleotide sequence, is called _______ inheritance.

epigenetic

Gene transcription patterns can also be transmitted across generations through positive_________ looks that can involve a transcription regulator activating its own transcription in addition in addition to other genes.

feedback

The CRISPR-Cas9 system is used by certain bacteria as a specific defense mechanism against certain viruses. Although therapeutic uses are in the works, CRISPR-Cas9 has been adapted for research, specifically in

gene editing

this type of inheritance is seen with the inheritance of the covalent modifications on________ proteins bound to dna ;

histone

A biochemist has synthesized a drug that blocks phosphofructokinase. This drug would not be a goodantibacterial treatment for human use because

human cells also perform glycolysis so the drug might also poison them

DNA polymerase catalyzes the joining of a nucleotide to a growing DNA strand. What prevents this enzyme from catalyzing the reverse reaction?

hydrolysis of PPi to Pi + Pi

You are collaborating with several illustrators in creating the figures for a molecular biology textbook. They got at least one label wrong on the figure above and want you to make sure that they are labeling things properly. Help them find the incorrect label:

ii—DNA ligase