Lecture 1 A Quiz

Question 1

True or False: Only eukaryotes replicate their DNA by templated polymerization.

Answers: True
False
Question 2

Which of the following is characteristic of all cells?

Answers: a. binary fission

b. plasma membrane
c. peptidoglycan cell wall

d. smaller than 5 m in diameter

Question 3

A The Latin phrase omnis cellula e cellula refers to a cellular principle. Which of the following statements is the
best interpretation of this phrase?

Answers: a. Tissues are composed of similar cells.

b. Cells generally are found in clusters.

c. All cells arise only from preexisting cells.

d. Organs are composed of tissues and cells.

e. The cell is the basic unit of structure.

Question 4

Which of the following processes that happens inside a cell DOES NOT normally require
consumption of free energy by the cell?

Answers: a. Replication of the genetic material

b. Import of nutrients from the environment

c. Diffusion of small molecules within the cell

d. Regulation of gene expression

e. Synthesis of enzymes that catalyze cellular reactions

Question 5
 Imagine a segment of DNA (within a gene) encoding a certain amount of information in its nucleotide sequence.
When this segment is fully transcribed into mRNA and then translated into protein, in general,

Answers: a. the protein sequence would carry more information compared to the DNA and mRNA sequences,
because its alphabet has 20 letters.
b. the protein sequence would carry less information compared to the DNA and mRNA sequences,
because several codons can correspond to one amino acid.
c. the amount of information in the mRNA sequence is lower than DNA, because the mRNA has
been transcribed using only one of the DNA strands as the template.
d. the amount of information in the mRNA sequence is higher than DNA, because several mRNA
molecules can be transcribed from one DNA molecule.

Lecture 1B quiz
Question 1

In which of the following properties are the archaea more similar to eukaryotes than they are to bacteria?

Answers: a. size

b. microtubules and microfilaments

c. translation initiation
d. mode of cell division
e. both translation initiation and mode of cell division

Question 2

Fill in the blanks in the following paragraph with either

A - Archaea
B - Bacteria
E - Eukaryotes

Methanococcus jannaschii is an anaerobic thermophilic microbe that belongs to the domain _______ and is
found in extreme environments such as hydrothermal vents. It lives at temperatures near the boiling point of
water and at pressures over 200 times higher than at sea level. Its genome sequence, identified in 1996, revealed
that most of its metabolic processes are similar to those
in ______, while its genetic machinery is more similar to that of _______.

Answers: a. BEA

b. EBA
c. AEB
 d. ABE

e. BAE
Question 3

Mitochondria are thought to have evolved from ancient bacteria. Which characteristics of a free-living bacteria
have mitochondria lost over time?

Answers: a. an independent genome

b. ribosomes

c. phospholipid membranes

d. motility

e. ribosomes, phospholipid membranes, motility, and an independent genome

Question 4

Based on the variation of genome size and gene number in the organisms presented in the following graph,
which organism has the highest number of genes per unit length of their genome? (Note the logarithmic scale.)

Answers: a. H. sapiens
 b. M. musculus

c. A. thaliana
d. C. elegans

e. E. coli

Lecture 1C Quiz

Which of the following pairs correctly matches the monomer with its polymer?

Answers: a. peptides; proteins

b. amino acids; polysaccharides

c. glucose; proteins
d. terpenes; nucleic acids

e. nucleotides; nucleic acids

Question 2

Which of the following has the greatest number of glycosidic bonds?

Answers: a. glucose

b. triacylglycerol

c. amylose

d. DNA
e. vitamin A
Question 3

The bond energies associated with noncovalent attractions in the cell are too weak to resist disruption by thermal
motion. However, cellular macromolecules can interact specifically AND strongly with each other (or fold by
themselves) merely via such interactions. How is this possible?

Answers: a. The bond energies increase radically when two interacting molecules approach each other.

b. The interacting molecules also fortify their binding via covalent bonds to keep them from
dissociation.
c. Many weak bonds together in a complementary geometry can afford a strong binding.

d. The cell lowers its internal temperature to reduce thermal motion of molecules and enhance the
weak attractions.
Question 4
 The amino acid serine has an R group which contains a hydroxyl. Which of the following better represents the
structure of this amino acid at neutral pH?

Answers: a. A

b. B

c. C

d. D

e. E
Question 5

Macromolecules in the cell can be made from their monomers using one of two polymerization schemes. One is
called head polymerization, in which the reactive bond required for polymerization is carried on the end of the
growing polymer. In contrast, in tail polymerization, the reactive bond is carried by each monomer for its own
incorporation. In the figure, indicate the polymerization scheme and the type of macromolecule.
 Answers: a. Head polymerization of a protein

b. Tail polymerization of a protein

c. Head polymerization of a polysaccharide

d. Head polymerization of a nucleic acid

e. Tail polymerization of a nucleic acid

Lecture 1D Quiz
Question 1

The observation that proteins can renature into their original conformations after they have been unfolded by
denaturing solvents implies that

Answers: a.the information needed to specify the three-dimensional shape of a protein is encoded in its amino
acid sequence.

b. the cell does not need molecular chaperones for survival.

c. the final folded structure of a protein is usually NOT the one with the lowest free energy.
 d. each protein folds into several different conformations inside the cell.

e. All of the above.

Question 2

Protein secondary structure elements such as helices and sheets constitute the major regular folding patterns
in proteins. With regard to these elements,

Answers: a.hydrogen-bonding between the amino acid side chains defines the type of secondary structure.

b. a certain short amino acid sequence always adopts the same secondary structure.

c. only a few specific amino acid sequences can adopt these repetitive structures.

d. the folding patterns result from hydrogen-bonding between the NH and C=O groups in the
polypeptide backbone.

e. All of the above.

Question 3

The R group or side chain of the amino acid threonine is CH(OH)CH3. The R group or side chain of the amino
acid alanine is CH3. Where would you expect to find these amino acids in a globular protein in aqueous
solution?
Answers: a. Both threonine and alanine would be on the exterior of the globular protein.

b. threonine would be in the interior, and alanine would be on the exterior of the globular protein

c. Both threonine and alanine would be in the interior of the globular protein.

d. Both threonine and alanine would be in the interior and on the exterior of the globular protein.

e. alanine would be in the interior, and threonine would be on the exterior of the globular protein.

Question 4

Proline is referred to as the "helix breaker" because

Answers: a. its only found in the L form, which is incompatible with helical protein structure.
 b. it lacks the hydrogen atom needed for hydrogen bonding.

c. it lacks a charged functional groups for ionic bonding.

d. it is hydrophobic.

e. it has a polar functional group.

Question 5

You've just sequenced a new protein found in mice and observe that sulfur-containing cysteine residues occur at
regular intervals. What is the significance of this finding?

Answers: a. Cysteine residues are required for the formation of -helices and -pleated sheets.

b. It will be important to include cysteine in the diet of the mice.

c. Cysteine residues are involved in disulfide bridges that help form tertiary structure

d. Cysteine causes bends, or angles, to occur in the tertiary structure of proteins.

e. Cysteine residues are only found in the unstructured loops of proteins, so this protein has minimal
tertiary structure.

Lecture 2A Quiz
Question 1

Identify which numbered feature (1 to 5) in the schematic drawing below of the DNA double helix corresponds
to each of the following terms in sequential order (1 5).
 Answers: a. nitrogenous base; covalent linkage; phosphate group; hydrogen bond; deoxyribose sugar

b. deoxyribose sugar; nitrogenous base; hydrogen bond; covalent linkage; phosphate group

c. phosphate group; deoxyribose sugar; covalent linkage; hydrogen bond; nitrogenous base

d. nitrogenous base; phosphate group; covalent linkage; hydrogen bond; deoxyribose sugar

e. deoxyribose sugar; phosphate group; hydrogen bond; covalent linkage; nitrogenous base

Question 2

The polarity of double-stranded DNA arises from

Answers: a. negative charges on the backbone phosphates

b. the presence of 5 phosphate on one end of each strand, and 3 hydroxyl on the other end of each
strand

c. base pairing

d. the sequence of bases, which is strand-specific

Question 3

Which of the following statements regarding a DNA double helix is always true?

Answers: a. The amount of adenine is equal to the amount of uracil, and the amount of guanine is equal to the
amount of cytosine.

b. The amount of adenine is equal to the amount of cytosine, and the amount of guanine is equal to
the amount of thymine.

c. The amount of adenine is equal to the amount of guanine, and the amount of thymine is equal to
the amount of cytosine.

d. The amount of adenine is equal to the amount of thymine, and the amount of guanine is equal to
the amount of cytosine.

Question 4
 The base composition in DNA isolated from cow liver cells is 28% adenine; what percent of the bases are
cytosine?

Answers: a. 14%

b. 22%

c. 28%

d. 36%

e. 56%

Question 5

Avery, MacLeod, and McCarty (1944) demonstrated that DNA was the genetic material by treating heat-
killed Streptococcus pneumoniae S (smooth) strain with DNase, thereby preventing transfer of the "transforming
substance" from the killed S strain to the live R (rough) strain when the two were mixed together and injected
into mice. Another way that one could demonstrate transformation in bacteria would be to extract DNA from

Answers: a. an R strain and mix it with cells of an S strain.

b. both S and R strains and mix it to allow recombination to take place.

c. an ampicillin-sensitive strain and mix it with cells of an ampicillin-resistant strain.

d. an S strain and mix it with cells of an R strain.

e. None of the above are correct.

Lecture 2B/2C Quiz

Question 1

The eukaryotic chromosomes are organized inside the nucleus with a huge compaction ratio of several-
thousand-fold. What is responsible for such a tight packaging?

Answers: a. The various chromatin proteins that wrap and fold the DNA

b. The nuclear envelope which encapsulates the chromosomes

c. The nuclear matrix that provides a firm scaffold

 d. All of the above

Question 2

The acetylation of lysines on the histone tails

Answers: a. loosens the chromatin structure because it adds positive charges to the histones.

b. recruits the heterochromatin protein HP1, resulting in the establishment of heterochromatin.

c. can be performed on methylated lysines only after they are first demethylated.

d. is a covalent modification and is thus irreversible.

Question 3

In assembling a nucleosome, normally the ___(1) histone dimers first combine to form a tetramer, which then
further combines with two ___(2) histone dimers to form the octamer.

Answers: a. 1: H1H3; 2: H2AH2B

b. 1: H3H4; 2: H2AH2B

c. 1: H2AH2B; 2: H1H3

d. 1: H2AH2B; 2: H3H4

e. 1: H1H2; 2: H3H4

Question 4

Which of the following is the correct order of the levels of DNA packaging in eukaryotic chromosomes?

Answers: a. nucleosome chromatin fiber looped domains heterochromatin

b. nucleosome looped domains chromatin fiber heterochromatin

c. heterochromatin nucleosome chromatin fiber looped domains

d. chromatin fiber heterochromatin nucleosome looped domains

 e. chromatin fiber nucleosome looped domains heterochromatin

Question 5

The position effect variegation (PEV) phenotype described in chapter 4 can be used to identify new genes that
regulate heterochromatin formation. For instance, strains of Drosophila melanogaster with the White
variegation phenotype have been subjected to mutagenesis to screen for dominant mutations (in other genes)
that either enhance or suppress PEV, meaning the mutations result in either lower or higher red pigment
production, respectively. Which of the following mutations is expected to be an enhancer of variegation?

Answers: a. A mutation that results in the loss of function of the flys HP1 (heterochromatin protein 1) gene.

b. A loss-of-function mutation in a gene encoding a histone deacetylase that deacetylates lysine 9

on histone H3.

c. A gain-of-function mutation in a gene encoding a histone methyl transferase that trimethylates

lysine 9 on histone H3, resulting in a hyperactive form of the enzyme.

d. A gain-of-function mutation in a gene encoding a histone acetyl transferase that normally

acetylates lysine 9 on histone H3, resulting in higher expression of the protein.

Lecture 2D Quiz
Question 1

The DNA polymerase reaction occurs in the ________ as incoming nucleotides are added to ________ end(s) of
the growing DNA chain.

Answers: a. 5' 3' direction; the 3'-hydroxyl

b. 5' 3' direction; the 3'-phosphate

c. 3' 5' direction; the 5'-hydroxyl

d. 3' 5' direction; the 5'-phosphate

e. 5' 3' direction or 3' 5' direction; both

Question 2
 DNA strand elongation occurs only in the 5' to 3' direction because

Answers: a. Okazaki fragments prevent elongation in the 3 to 5 direction.

b. replication must move away from the replication fork.

c. the polarity of the DNA molecule prevents addition of nucleotides at the 5 end.

d. DNA polymerase can only add nucleotides to the free 3 end.

Question 3

At the replication fork, the template for the lagging strand is thought to loop around. This looping would allow
the lagging-strand polymerase to move along with the rest of the replication fork instead of in the opposite
direction. The single-strand part of the loop is bound by the single-strand DNA-binding (SSB) proteins. As each
Okazaki fragment is synthesized toward completion, how does the size of the loop change? What about the size
of the SSB-bound part of the loop?

Answers: a. Increases; decreases.

b. Increases; increases.

c. Decreases; increases.

d. Decreases; decreases.

e. Decreases; does not change.

Question 4

An isolate of a mutant bacterium appears to grow more slowly than the wild-type population from which it was
isolated. Further studies showed that the slower growth was due to a markedly reduced DNA polymerase I
activity. From this information, one would expect that this organism would also be deficient in the activity of
DNA

Answers: a. excision repair.

b. recombination.

c. transcription.

d. translation.
 e. unwinding.

Question 5

In Escherichia coli, replication of DNA can occur throughout the cell cycle while the cell is
also actively transcribing its genes. This means collisions between replication forks and RNA
polymerases are inevitable. Depending on the orientation of the genes, collisions can be rear-
end (when both machines are traveling in the same direction) or head-on (when they are
traveling in opposite directions). In the following paragraph, match each of the letters (A to
D) to one appropriate number below. Do not use a number more than once. Your answer
would be a four-digit number composed of digits 1 to 5 only, e.g. 1253.

Typically, in a rear-end collision, the (A) of RNA polymerase collides with the (B) in the
replication fork. In contrast, in a head-on collision, the (C) of RNA polymerase hits the (D) in
the fork.

1. front edge (of RNA polymerase)

2. rear edge (of RNA polymerase)
3. DNA helicase
4. leading-strand DNA polymerase
5. lagging-strand DNA polymerase

Answers: a. 1,3,4,2

b. 2,4,1,3

c. 3,1,5,4

d. 1,3,2,4

e. 2,3,4,1

Lecture 2E Quiz
Question 1

Which of the following is involved in proofreading during DNA replication?

Answers: a. 5' to 3' exonuclease activity of DNA polymerase

 b. 3' to 5' exonuclease activity of DNA polymerase

c. 5' to 3' endonuclease activity of DNA polymerase

d. 3' to 5' endonuclease activity of DNA polymerase

e. RNA polymerase

Question 2

Mismatch repair targets improperly paired nucleotides. In prokaryotes, the incorrect member of an abnormal
base pair can be differentiated from the correct member because

Answers: a. the incorrect member has undergone a hydroxylation reaction.

b. newly synthesized DNA contains uracil.

c. the incorrect member doesn't match the surrounding bases.

d.the original strand of DNA contains methylated bases while newly synthesized DNA does not;
thus the correct member is in the methylated strand.

e. the correct member has been deaminated.

Question 3

Which statement is not true about the enzyme methyltransferase?

Answers: a. A sulfhydryl group of a cysteine residue in the enzyme accepts a methyl group.

b. The enzyme mediates direct reversal of DNA damage.

c. After accepting a methyl group from methylguanine, the enzyme can be used again.

d. The enzyme is present in organisms ranging from E. coli to humans.

Question 4

DNA repair in eukaryotes and prokaryotes

 Answers: a. relies on DNA polymerases to correct all mutations.

b. relies on completely different mechanisms.

c. is accomplished by multiple specialized pathways.

d. can only repair abnormal nucleotides such as pyrimidine dimers and depurinated nucleotides.

e. is very ineffective.

Question 5

DNA ligases are used in both DNA replication and repair to seal breaks in the DNA. But DNA damage can
result in single- or double-strand breaks that are not normal ligase substrates. These need to be processed first
before a ligase can act on them. One of the enzymes that is recruited to some of such breaks is called PNK. It
has two separate activities on the DNA, both of which can help provide a canonical ligase substrate. Which of
the following activities would you expect PNK to have in this context?

Answers: a. 5 kinase (phosphorylation of a free 5-OH group) and 3 kinase

b. 5 phosphatase (dephosphorylation to create a free 5-OH group) and 3

phosphatase

c. 3 kinase and 3 phosphatase

d. 5 phosphatase and 3 kinase

e. 5 kinase and 3 phosphatase

Lecture 3A/3B Quiz

Question 1

DNA and RNA polymerase differ in all of the following EXCEPT...

Answers: a. the nucleotide substrates they incorporate.

 b. their requirement for a primer.

c. their error rate.

d. the type of chemical reaction they catalyze.

e. their processivity.

Question 2

This general transcription factor recognizes the TATA box in RNA polymerase II promoters. It is

Answers: a. the only single-subunit general transcription factor.

b. able to introduce a rather sharp kink in the double helix upon binding to DNA.

c. responsible for the phosphorylation of the RNA polymerase CTD during transcription initiation.

d. also responsible for the recognition of the BRE element in the promoter.

e. All of the above.

Question 3

RNA polymerase II differs from RNA polymerase I and III by having

Answers: a. fewer amino acids at the N-terminus.

b. additional amino acids at the N-terminus.

c. fewer amino acids at the C-terminus.

d. additional amino acids at the C-terminus.

e. different amino acids, but all three RNA polymerases are the same size

Question 4

TFIID is one of the basal transcription factors to bind the promoter during the assembly of the pre-initiation
complex, which of the following statements about TFIID is false?
 Answers: a. TFIID distorts the DNA duplex when it binds.

b. TFIID binds the TATA box in promoters

c. TFIID binds the DNA only after basal transcription factors have bound the promoter region.

d. TFIID is composed of TBP and other TATA box binding proteins associated factors (TAFs).

Question 5

A new antibiotic is able to bind the rho () factor associated with some transcription processes. As a result, this
antibiotic would affect

Answers: a. initiation of transcription.

b. elongation of transcription.

c. binding of the RNA polymerase.

d. termination of all transcription.

e. termination of some transcription.

Lecture 3C Quiz
Question 1

The following schematic drawing represents the activation of transcription for a eukaryotic gene (gene X).
Indicate what component (A to D) in the drawing corresponds to each of the following in order from A to D.

Mediator
cis-Regulatory sequence
A general transcription factor
Spacer DNA that may encode lncRNAs
 Answers: a. BCAD

b. ADBC

c. CBAD

d. DBAC

e. ACDB

Question 2

In analysis using two-dimensional gel electrophoresis of the proteins expressed in different cell types, the
number of spots that are different in different cells usually exceeds the number of common spots, and even the
common spots can still have different intensities. The spots representing which of the following proteins would
you expect to be among the common spots when compared across several cell types?

Answers: a. RPL10 (a ribosomal protein)

b. HBA1 (a hemoglobin subunit)

c. Insulin (a hormone)

d. Tyrosine aminotransferase (a metabolic enzyme)

 e. All of the above

Question 3

Transcription regulation has similarities and differences in bacteria and in eukaryotes. Which of the following is
correct in this regard?

Answers: a. Most bacterial genes are regulated individually, whereas most eukaryotic genes are regulated in
clusters.

b. The rate of transcription for a eukaryotic gene can vary in a much wider range than for a bacterial
gene

c. DNA looping for gene regulation is the rule in bacteria but the exception in eukaryotes.

d. Transcription regulators in both bacteria and eukaryotes usually bind directly to RNA
polymerase.

e. The default state of both bacterial and eukaryotic genomes is transcriptionally active

Question 4

Studying the expression of a transcription regulatory protein in two cell types, you have performed experiments
showing that the mRNA encoding the protein is present at comparable levels in the cytosol of both cell types.
However, based on the expression of its target genes, you suspect that the protein activity might be significantly
different in the two cell types. Which of the following steps in expression of the gene encoding this protein is
more likely to be differentially controlled in these cell types?

Answers: a. Transcription

b. Translation

c. mRNA transport

d. mRNA degradation

Question 5

A DNA-binding protein recognizes a specific eight-nucleotide sequence in DNA. Assuming that its binding is
perfectly specific, how many binding sites are expected to exist for it in human genomic DNA, which is
composed of about 6 109 nucleotide pairs? What about if the protein forms a homodimer? Note that the target
sequence can be oriented either way in the double-stranded DNA.
 Answers: a. About 200,000; about 30,000

b. About 2000; about 300

c. About 200; about 30

d. About 200,000; about 300

e. About 200,000; about 3

Lecture 3D Quiz
Question 1

Which of the following is directed by transcription activators in eukaryotic cells in order to provide a more
accessible DNA for the transcription machinery?

Answers: a. Nucleosome remodeling

b. Histone removal

c. Histone replacement

d. Histone modifications

e. All of the above

Question 2

Which of the following DNA-binding motifs uses sheets to recognize DNA bases?

Answers: a. The helixturnhelix motif

b. The leucine zipper

c. The zinc finger motif

 d. The helixloophelix motif

e. None of the above

Question 3

The basic leucine zipper (bZIP) motif has all of the following characteristics, except:

Answers: a. it is a DNA-binding domain that directly contacts DNA in the major groove

b. is a stretch of amino acids that fold into a long alpha-helix with leucines in every seventh position

c. it facilitates dimerization of two similar polypeptide chains

d. it is not as common as the zinc finger motif

Question 4

You create a chimeric protein that contains the DNA binding domain of the Fork head transcription factor and
the transactivation domain of the Sp1 transcription factor. Which of the following predictions would you make
concerning the activity of your chimeric protein?

Answers: a. It would bind the transcription of genes normally activated by Fork head.

b. It would bind the transcription of genes normally activated by Sp1.

c. It would activate the transcription of genes normally activated by both Fork head and Sp1.

d. It would not activate the transcription of any genes.

Question 5

To prevent spurious transcription from a gene, acetylation of histoneswhich is carried out by histone acetyl
transferases ahead of a moving RNA polymerase IIis quickly reversed by histone deacetylases and histone
methyl transferases in the wake of the polymerase, leaving a trail of specific methylated histones. Which of the
following curves do you think better represents the distribution of this specific histone methylation mark with
respect to a gene?
 Answers: a. A

b. B

c. C

d. D

Lecture 4A/4B Quiz

Question 1

To ensure that RNA polymerase is only released after it has transcribed a gene to its end, termination is
mechanistically linked to

Answers: a. 5 capping

b. excision of the lariat RNA

c. alternative splicing

d. 3 end formation

Question 2
 For some pre-mRNAs, splicing is regulated by

Answers: a. RNA polymerase stalling

b. splicing enhancer sequences

c. localization of the pre-mRNA to subnuclear speckles

d. transcription termination

Question 3

The mechanism for nuclear pre-mRNA splicing is similar to the splicing mechanism of

Answers: a. Group I introns

b. Group II introns

c. Archael introns

d. nuclear tRNA introns

Question 4

One way to detect alternative splicing of a given gene is to compare:

Answers: a. the relative rate of transcription of the alternatively spliced gene with
another gene

b. the sequence of the alternatively spliced gene to that of another gene.

c. the size and frequency of different pre-mRNAs transcribed from this gene.

d. the size and sequence of mature mRNAs produced from this gene.

Question 5
 Which of the following is true about the molecule shown in the following drawing?

Answers: a. Its gene is transcribed by RNA polymerase I.

b. There are about 50 genes in our genome encoding this type of molecule.

c. This molecule normally undergoes various covalent modifications.

d. It is normally composed of about 20 monomers.

e. Its gene transcript normally undergoes alternative splicing.

Lecture 4C Quiz
Question 1

Aminoacyl-tRNA synthetases are enzymes that

Answers: a. catalyze loading of an anticodon onto the 3 end of a tRNA.

b. catalyze loading of an amino acid onto the 3 end of a tRNA.

c. catalyze loading of an amino acid onto the anticodon loop of a tRNA.

d. act as chaperones to fold tRNA into its functional L-shaped tertiary structure.

Question 2

Which step of translation requires mRNA decoding by a protein?

Answers: a. Initiation
 b. Elongation

c. Termination

d. A and C

Question 3

Which of the following processes takes place in the nucleoli within the eukaryotic nucleus?

Answers: a. Ribosome assembly

b. rRNA gene transcription

c. Telomerase assembly

d. tRNA processing

e. All of the above

Question 4

Which of the following features is common between the bacterial and eukaryotic ribosomes in translation
initiation?

Answers: a. They both use an initiator tRNA that carries formylmethionine.

b. They both bind to the 5' end of the mRNA and move forward to find the start codon.

c. They both recognize the start codon by interacting with the ShineDalgarno sequence.

d. They both interact with various translation initiation factors.

e. All of the above.

Lecture 4D Quiz
Question 1
 Transfer RNAs are thought to improve the fidelity of mRNA translation by

Answers: a. preventing translocation if an incorrect amino acid is present in the peptidyl transferase center.

b. increasing the rate of GTP hydrolysis by EF-Tu upon accurate codon-anticodon pairing.

c. activating proofreading activity of eEF2.

d. linking codon-anticodon mispairing in the P site to translation termination.

Question 2

Which of the following does not need to occur for translation to terminate?

Answers: a. cleavage of the polypeptide from the tRNA in the P-site

b. recognition of the stop codon by a release factor

c. translocation by eEF2

d. binding of a tRNA to the A-site

Question 3

An elongating ribosome is bound to appropriate tRNAs in both the A and the P sites and is ready for peptidyl
transfer. What happens next?

Answers: a. The carboxyl end of the polypeptide chain is released from the P-site tRNA and joined to the free
amino group of the amino acid linked to the A-site tRNA.

b. The amino end of the polypeptide chain is released from the P-site tRNA and joined to the free
carboxyl group of the amino acid linked to the A-site tRNA.

c. The carboxyl end of the amino acid is released from the A-site tRNA and joined to the free amino
group of the polypeptide chain linked to the P-site tRNA.

d. The amino end of the amino acid is released from the A-site tRNA and joined to the free
carboxyl group of the polypeptide chain linked to the P-site tRNA.

Question 4
 Read the following to answer questions 4-7:
When unfolded proteins accumulate in the lumen of the endoplasmic reticulum due to
inefficient folding conditions, a membrane-bound protein kinase is activated and
phosphorylates a subunit of the translation initiation factor eIF2. Indicate which of the
following events would (Y) or would not (N) occur as a result.

eIF2 binds tightly to the ribosome.

Answers: a. Yes

b. No

Question 5

Translation initiation is stimulated.

Answers: a. Yes

b. No

Question 6

The GDP-bound form of eIF2 accumulates.

Answers: a. Yes

b. No

Question 7

eIF2B is activated.

Answers: a. Yes

b. No

Question 8
 When the translation initiation factor eIF2 is phosphorylated in response to a sudden temperature increase or
viral infection, translation can be greatly inhibited. In this case, phosphorylated eIF2 is under _______________
control, and the phosphorylation of eIF2 leads to global (general or widespread) _____________ control.

Answers: a. translational; post-translational

b. post-translational; translational

c. post-translational; transcriptional

d. translational; transcriptional

Lecture 5A Quiz
Question 1

In which of the following microscopy techniques are oblique rays of light focused on the specimen?

Answers: a. Bright-field microscopy

b. Dark-field microscopy

c. Phase-contrast microscopy

d. Differential-interference-contrast microscopy

Question 2

For Questions 2-5:

Indicate true (T) and false (F) statements below regarding light and light microscopy. Your answer would be a
four-letter string composed of letters T and F only, e.g. FFFF.

Two light waves of the same amplitude and frequency will completely cancel each other out if not perfectly in
phase.

Answers: True

False

Question 3
 If the refractive index of a medium is 1.1, light travels in a vacuum 1.1 times faster than it does in the medium.

Answers: True

False

Question 4

The limit of resolution for conventional light microscopy is approximately 0.4 m, corresponding to the
wavelength of violet light.

Answers: True

False

Question 5

A fluorescent particle can be detected but not clearly observed with a light microscope even if it is several times
smaller than the resolution limit of the microscope.

Answers: True

False

Question 6

A scientist wants to magnify a pollen grain 8,000 times and examine the ridges and pores on its surface. Which
one of the following instruments would be best?

Answers: a. a transmission electron microscope

b. a scanning electron microscope

c. a fluorescence confocal microscope

d. a phase contrast light microscope

Question 7

Which of the following is not a property of green fluorescent protein (GFP)?

 Answers: a. GFP can be detected directly in living cells.

b. GFP requires addition of a cofactor for light production.

c. GFP contains an intrinsic peptide fluorophore.

d. Following excitation with ultraviolet light, GFP emits green light.

Question 8

Two segments (S1 and S2) in a viral protein are suspected to be responsible for the nuclear localization of the
protein in infected human cells. You have engineered a plasmid to encode the green fluorescent protein (GFP)
fused to either or both of these peptide segments, and have introduced the plasmid into human cells. After the
expression of the fusion protein is induced, you visualize the cells using a fluorescence microscope equipped
with filters appropriate for detection of GFP. Your results are presented in the following schematic drawings in
which the GFP signal is represented in green. Which of the following is more consistent with these
observations?

Answers: a. Both S1 and S2 are required for nuclear localization.

b. S1 is required and sufficient for nuclear localization.

c. S2 is required and sufficient for nuclear localization.

d. S1 is required but not sufficient for nuclear localization.

Lecture 5B Quiz
Question 1
 At its isoelectric point

Answers: a. a protein has a positive charge

b. a protein has a negative charge

c. a protein has no net charge

d. whether a protein has a positive or negative charge depends on the particular protein

Question 2

Which of the following techniques separates proteins based only on their size?

Answers: a. SDS-PAGE (SDSpolyacrylamide gel electrophoresis)

b. mass spectrometry

c. ion-exchange chromatography

d. two-dimensional gel electrophoresis

e. SDS-PAGE and mass spectrometry

Question 3

During the process of two-dimensional PAGE

Answers: a. the first dimension separates proteins by isoelectric point and the second dimension separates
them by size.

b. the first dimension separates proteins by size and the second dimension separates them by
isoelectric point.

c. the first dimension separates proteins by size and the second dimension separates them by shape.

d. the first dimension separates proteins by shape and the second dimension separates by
size.

Question 4
 In purifying proteins by column chromatography, elution can be performed in different ways, depending on the
type of matrix. For example, bound proteins can be eluted by gradually increasing or decreasing salt
concentration in the solution applied to the column. For which of the following matrices do you think increasing
and decreasing salt concentration, respectively, are used for elution?

Answers: a. Ion-exchange; hydrophobic

b. Affinity; ion-exchange

c. Hydrophobic; affinity

d. Hydrophobic; ion-exchange

e. Ion-exchange; gel-filtration

Lecture 5C Quiz
Question 1

Production of recombinant proteins in bacteria involves the cloning of the cDNA encoding the desired protein
into an expression vector that contains a(n)

Answers: a. promoter

b. enhancer

c. intron

d. start codon

Question 2

Whole genome or shotgun sequencing requires

Answers: a. the creation of a cDNA library.

b. the creation of overlapping DNA fragments whose sequences can be aligned into large
contiguous fragments (contigs) using computer algorithms.
 c. large contiguous fragments (contigs) cloned into yeast artificial chromosomes (YACs) in an
ordered fashion.

d. very large amounts of DNA from the organism whose genome is being sequenced.

e. the use of a gene gun to propel DNA-coated particles at high velocities into cells.

Question 3

The following schematic graph shows temperature change over time in a cycle of a PCR assay. Which steps (A
to C) in the cycle correspond to hybridization (annealing), strand separation (denaturation), and DNA synthesis
(extension), respectively? Your answer would be a three-letter string composed of letters A to C, e.g. ACB.

Answers: a. B, C, A

b. C, B, A

c. A, C, B

d. B, A, C

e. C, A, B

Question 4

A piece of DNA has been sequenced by automated dideoxy sequencing, in which each dideoxyribonucleoside
triphosphate was labeled with a fluorescent tag of a different color. The data corresponding to a small segment
 with the sequence 5-TGCCACA-3 is shown in the following diagram. Knowing that ddGTP has been labeled
with green fluorescence, what color do you think was the fluorescent tag used to label ddTTP in the sequencing
experiment?

Answers: a. Blue

b. Green

c. Red

d. Yellow

Question 5

You have constructed a genomic library of Felis catus (domestic cat) in E. coli. You extract the plasmid DNA
from the clones, digest the plasmid with restriction enzymes, separate the resulting fragments by gel
electrophoresis, and transfer the fragments to a nylon membrane by the Southern blot procedure. You then use a
fluorescently labeled probe that is complementary to a gene of interest that may be involved in feline lymphoma.
The DNA corresponding to one clone yields a single fluorescent DNA band after probing the Southern blot.
Based on this information

Answers: a. all of the clones tested, except the one described, have the gene of interest.

b. only the one clone described has the gene of interest.

c. the gene of interest is located entirely on the fluorescent DNA band.

d. the part of the gene complementary to the probe is located on the fluorescent DNA band.

e. only the one clone described contains the part of the gene complementary to the probe on the
fluorescent DNA band.

Lecture 5D Quiz
Question 1
 Bacterial artificial chromosomes (BACs)

Answers: a. are derived from the E. coli chromosome.

b. are present in high copy numbers per cell.

c. can maintain DNA sequences of 100-300 Kb

d. are generally not stable.

e. All of the above.

Question 2

You are interested in studying the expression of a gene associated with human cancer during fetal development
using a mouse model. Which of the following might be useful to study the expression of this gene over time?

Answers: a. DNA microarrays

b. genome-wide association studies

c. Southern blot analysis

d. in situ hybridization

e. DNA microarrays and in situ hybridization

Question 3

You have carried out a genetic screen in a species of fish, and have identified a new gene in this organism. You
have cloned and sequenced the gene, but do not know anything about the biochemical function of the gene
product. Which of the following is the most sensible next step in order to get clues about the function?

Answers: a. Purifying the protein product and determining its structure by x-ray diffraction

b. Screening for small molecules that perturb gene function

c. Using the BLAST algorithm to scan sequence databases for similar sequences
 d. Using MS/MS to sequence the gene product without the need for purification

e. Mutating the gene and performing reverse genetics

Question 4

You have studied mutations in a transcription regulatory protein from Bacillus subtilis by an in vivo reporter
gene assay carried out in Escherichia coli. The cis-regulatory sequence that the protein normally recognizes was
inserted upstream of a gene encoding an enzyme that can produce a visible blue product. E. coli cells were then
transformed with the reporter construct along with the gene encoding one of the various mutant forms of the
transcription regulatory protein. Since the transcription regulatory protein is an inhibitor, the colonies turn blue
only when the mutant protein is nonfunctional and unable to inhibit gene expression. Interestingly, you have
identified a number of cold-sensitive loss-of-function mutations that show the mutant phenotype at 22C but
not at 37C. Which of the following correctly describes the phenotype of these cold-sensitive mutants?

Answers: a. Their colonies turn blue at permissive (low) temperatures.

b. Their colonies turn blue at permissive (high) temperatures.

c. Their colonies turn blue at nonpermissive (low) temperatures.

d. Their colonies turn blue at nonpermissive (high) temperatures.

Lecture 6A Quiz
Question 1

Glycolipids are never found on the cytoplasmic face of plasma membranes in living cells.

Answers: True

False

Question 2

Cholesterol

Answers: a. is found in abundance in prokaryotic cell membranes.

b. buffers membrane fluidity by increasing fluidity at low temperature and decreasing fluidity at
high temperature.
 c. increases permeability for Ca2+.

d. increases permeability for small polar molecules.

e. All of the above are correct.

Question 3
Many cells store lipids in droplets of varying sizes. These droplets

Answers: a. are enclosed by a phospholipid monolayer (instead of a bilayer).

b. mostly store cholesterol and phospholipids.

c. are produced by and released from the Golgi apparatus.

d. have mostly protein-free bilayer membranes.

e.

are composed primarily of charged amphiphilic lipids.

Question 4

Arctic fish probably have ______________ in their plasma membranes than tropical fish

Answers: a. fewer transmembrane proteins

b. more phospholipids with unsaturated fatty acids

c. more amphipathic phospholipids

d. more phosholipids with longer hydrocarbon tails

e. more phospholipids with saturated fatty acids

Question 5

Why do liposomes not fuse with one another spontaneously when suspended in an aqueous environment?

Answers: a. Because fusion requires a large number of flip-flops, which are very rare.

b. Because the hydration shell of the polar head groups of the lipids needs to be removed.

c. Because fusion requires micelle formation.

 d. Because of the rapid lateral diffusion and rotation of the lipid molecules.

Lecture 6B Quiz
Question 1

The two monolayers of the plasma membrane in a human red blood cell

Answers: a. have different overall electrical charges, with negatively charged phospholipids normally
enriched in the inner monolayer.
b. have the same abundance of phosphatidylinositol.
c. exchange phospholipids only through spontaneous flip-flops.

d. both contain glycolipids.

e. both contain gangliosides.

Question 2

Match the membrane lipid group on the left with the correct type of membrane lipid on the right.

Question Correct Match

Phosphosphingolipids b. Sphingomyelin

Glycosphingolipids c. Cerbrosides

Sterols a. Cholesterol

Phosphoglycerides d. Phosphatidylserine

Glycoglycerolipids e. Monogalactosyldiacylglycerol (MGDG)

Question 3

Gorter and Grendel extracted lipids from human red blood cells. They calculated the total surface area for these
red blood cells and found it to be 72 2. How much surface area would these lipids cover once they were spread
across the surface of water?
 Answers: a. 182

b. 362

c. 1442

d. 722

Question 4

Which of the following changes would you expect to increase the phase transition temperature of a synthetic
bilayer composed of phosphatidylserine?

Answers: a. Incorporation of phospholipids with longer fatty acid chains.

b. Introduction of double bonds in the fatty acids.

c. Addition of cholesterol.

d. Removal of serine from the head group.

e. None of the above.

Question 5

A colleague gives you two tubes containing membrane fractions from an animal cell lysate. One tube contains
the plasma membrane fraction, and the other tube contains the mitochondrial inner membrane fraction, but the
tubes are not labeled. When you analyze the macromolecule composition of the samples, you are confident that
the second tube contains the mitochondrial fraction, because the sample has

Answers: a. a higher ratio of cholesterol to phospholipids.

b. a higher protein to lipid ratio.

c. a lower protein to lipid ratio.

d. more carbohydrate in glycoproteins.

e. more GPI-anchored proteins.

 Lecture 6C Quiz
Question 1

What do all -barrel transmembrane proteins have in common?

Answers: a. The number of strands.

b. The diameter of the barrel.

c. The number of negative peaks in their hydropathy plots.

d. The structural rigidity compared to -helical transmembrane proteins.

Question 2

Integrins are single-pass integral membrane proteins in the plasma membrane of animal cells and are involved in
the interaction of the cell with the surrounding extracellular matrix. Which of the following descriptions do you
think matches the transmembrane part of an integrin molecule?

Answers: a. It forms a barrel.

b. It is an helix that is bent in the middle.

c. It is about 10 amino acids long, with every other amino acid side chain being hydrophobic.

d. It folds in a conformation with maximal intrachain hydrogen-bonding.

e. It is about 100 amino acids long.

Question 3

Which of the following types of protein would be most easily removed from a membrane by changing pH or
ionic strength?

Answers: a. GPI-anchored protein

 b. fatty acid-anchored protein

c. integral protein

d. peripheral protein

e. glycosylated integral protein

Question 4

For each membrane protein in the following schematic drawings, indicate whether the cytoplasmic side of the
membrane is more likely to be on the left (L) or on the right (R).

Answers: a. RLRR

b. RLRL

c. LLRL

d. LRLL

e. LRRL

Question 5

In the schematic drawing below, a protein is present on one side of a membrane in a high-enough quantity to
induce curvature in this region of the membrane. In each of the following scenarios, indicate whether the protein
would induce positive (P) or negative (N) curvature in the membrane. Your answer would be a three-letter string
composed of letters P and N only, e.g. PPP.
 The protein inserts a hydrophobic domain into the membrane leaflet that is facing it.
The protein is a phospholipase that cleaves the head group in specific phospholipids.
The protein binds cooperatively to multiple phospholipids with very large head groups.

Answers: a. NNP

b. NPN

c. PPN

d. PNP

e. PNN

Lecture 7A Quiz
Question 1

Water moves across the plasma membrane into or out of a cell by osmosis when

Answers: a. there is an equal solute concentration on both sides of the membrane.

b. water diffuses through a semipermeable membrane toward a higher solute concentration.

c. water diffuses through a semipermeable membrane toward a lower solute concentration.

d. a high solute concentration opens an aquaporin channel.

e. ATP hydrolysis drives aquaporin transport.

Question 2
 For which of the following ions is the cytosolic concentration typically higher than the extracellular
concentration?

Answers: a. Sodium

b. Calcium

c. Magnesium

d. Potassium

e. Chloride

Question 3

Imagine a small synthetic vesicle made from pure phospholipids enclosing an interior lumen containing 1 mM
glucose and 1 mM sodium chloride. If the vesicle is placed in pure water, which of the following happens
faster?

Answers: a. Na+ diffuses out.

b. Cl diffuses out.

c. H2O diffuses in.

d. Glucose diffuses out.

e. Sodium chloride diffuses out.

Question 4

Because the procedure you are using to modify plants requires their cell membranes to be pulled away from the
cell walls by plasmolysis, you place the cells in a(n)

Answers: a. acid solution.

b. hypotonic solution.

c. isotonic solution.

d. basic solution.
 e. hypertonic solution.

Question 5

A researcher is interested in the modes of transport across the cell membrane of three different substances: A, B,
and C. Her data are reported in the graphs associated with the following question. The graph above shows the
initial rate of transport for each substance when the cells are placed in solutions of different concentrations of A,
B, and C. Based on these data, substance A is transported via
Selected Answer: d.

simple diffusion.
Answers: a. active transport.

b. facilitated transport.

c. passive transport.

d. simple diffusion.

e. symport.

Lecture 7B Quiz
Question 1
 In contrast to transporters, the channel proteins in cellular membranes

Answers: a. interact strongly with the solute(s) that they transport.

b. undergo a conformational change every time they transport a solute.

c. can only mediate passive transport.

d. form pores that are always open.

Question 2

A potassium channel conducts K+ ions several orders of magnitude better than Na + ions, because

Answers: a. the Na+ ion is too large to pass through the channel pore

b. the hydrated Na+ ion occupies a larger volume compared to the hydrated K+ ion, and is too large
to pass through the channel pore

c. the Na+ ion is too small to interact with the channel in a way that facilitates the loss of water
from the ion

d. the Na+ ion cannot bind to the high-affinity K+-binding sites in the channel pore

Question 3

An ion channel

Answers: a. always mediates passive transport.

b. is ion-selective.

c. is typically several orders of magnitude faster than a transporter.

d. is usually gated.

e. All of the above.

Question 4
 Aquaporin has a pair of key asparagine residues located on the wall almost halfway through its pore. These
residues simultaneously bind to the oxygen atom of a passing water molecule, rendering it unavailable for
hydrogen-bonding. As a result,

Answers: a. the channel can conduct negatively charged (but not positively charged) ions

b. the channel can conduct glycerol as well as water

c. the channel cannot conduct protons

d. the channel cannot conduct chloride ions

Question 5

A potassium channel conducts K+ ions several orders of magnitude better than Na+ ions, because

Answers: a. the Na+ ion is too large to pass through the channel pore.

b. the hydrated Na+ ion occupies a larger volume compared to the hydrated K+ ion, and is too large
to pass through the channel pore.

c. the Na+ ion is too small to interact with the channel in a way that facilitates the loss of water
from the ion.

d. the Na+ ion cannot bind to the high-affinity K+-binding sites in the channel pore.

Lecture 7C Quiz
Question 1

This family of ATPases is structurally related to the turbine-like pumps that acidify lysosomes and vesicles;
however, they usually function in reverse, generating ATP from ADP and Pi using proton gradients across
membranes. What are they called?

Answers: a. P-type pumps

b. ABC transporters

c. V-type pumps

d. F-type pumps
 e. Permeases

Question 2

In the schematic drawing of the structure of ATP synthase, determine whether each of the numbered
components of the machine (from 1 to 5, respectively) is rotary or stationary

Answers: a. All 5 are rotary

b. 1, 4, and 5 are rotary

c. Only 1 and 5 are rotary

d. Only 1 and 4 are rotary

e. Only 1 and 2 are rotary

Question 3

Choose the item in column 2 that best matches each item in column 1. You may use an item
from column 2 more than once.

Question Correct Match

Requires direct ATP hydrolysis a. Primary active transport

 Driven by an ion gradient e. Secondary active transport

Transports glucose across membranes b. Primary and secondary active transport

Na+/glucose symport e. Secondary active transport

Na+/K+ ATPase pump a. Primary active transport

Question 4

Which of the following transporters mediates primary active transport when transporting the solutes in the directions
indicated? The concentration of both solutes (shown as small circles and squares) is higher outside of the cell.

Answers: a. A

b. B

c. C

d. D

e. E

Question 5

Most eukaryotic ABC transporters are involved in exporting small molecules from the cytosol. In this subset of
the ABC transporters, does the small molecule bind better to the ATP-bound or the ATP-free transporter?
Answers: a. ATP-bound

b. ATP-free