BME 553/753 Cell and Tissue Biology Exam I Fall 2010

Closed Book, Closed Notes.

Name___________________________
1.

By definition, procaryotic cells do not possess (select one):

(a)
a nucleus
(b)
replication machinery
(c)
ribosomes
(d)
membrane bilayers

2.

Use the list of structures, and the schematic drawing of an animal cell in the figure. For each
term below, write the corresponding number from the figure.
A.____plasma membrane
B. ____nuclear envelope
C. ____cytosol
D. ____Golgi apparatus
E. ____endoplasmic reticulum
F. ____mitochondrion
G. ____transport vesicles

3. The nucleus confines the __________, keeping them separated from other components of the cell.
(a)
lysosomes
(b)
chromosomes
(c)
peroxisomes
(d)
ribosomes

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4.
A.
B.
C.
D.
E.
F.
G.
H.
I.

Match each term related to the structure of nucleic acids (AI) with one of the
descriptions provided.
base
glycosidic bond
nucleoside
nucleotide
phosphoanyhydride bond
phosphoester bond
ribose
phosphodiester bond
deoxyribose

____
____
____
____
____

the linkage between two nucleotides

the nitrogen-containing aromatic ring
five-carbon sugar found in DNA
sugar linked to a base and a phosphate
five-carbon sugar found in RNA

5.

True or False?
(a) T F Twenty-two amino acids are commonly found in proteins.
(b) T F Most of the amino acids used in protein biosynthesis have charged side chains.
(c) T F Amino acids are often linked together to form branched polymers.
(d) T F All amino acids contain an NH2 and a COOH group
(e) T F ATP is a storage form for electrons
(f) T F ATP is sometimes called the universal currency in the energy economy of cells.
(g) T F ATP can be incorporated into DNA.
(h) T F ATP can be hydrolyzed to release energy to power hundreds of reactions in cells.
(i) T F ATP comprises a sugar, phosphate groups, and a nitrogenous base.
(j) T F NADH is a short-term storage form of energy
(k) T F In terms of amount of energy stored per weight, glycogen is a more effective
storage form of energy than lipids.

6.

What is the principal force that holds the two strands of DNA together? (select one)
(a)
ionic interactions
(b)
hydrogen bonds
(c)
covalent bonds
(d)
van der Waals interactions

7. Chemical reactions carried out by living systems depend on the ability of some organisms to
capture and use atoms from nonliving sources in the environment. The specific subset of these
reactions that breakdown nutrients in food can be described as _(select one) :
(a)
metabolic
(b)
catabolic
(c)
anabolic
(d)
biosynthetic

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8.

You are trying to make a synthetic copy of a particular protein but accidentally join the amino
acids together in exactly the reverse order. One of your classmates says the two proteins must
be identical, and bets you $20 that your synthetic protein will have exactly the same
biological activity as the original. What particular feature of a polypeptide chain makes you
sure that the two proteins are not identical?

9.

The second law of thermodynamics states that the disorder in any system is always increasing.
In simple terms, you can think about dropping NaCl crystals into a glass of water. The
solvation and diffusion of ions is favored because there is an increase in (select one):
a)
pH
(b)
entropy
(c)
stored energy

10.

The energy used by the cell to generate specific biological molecules and highly ordered
structures is stored in the form of (select one):
(a)
Brownian motion
(b)
heat
(c)
light waves
(d)
chemical bonds

11.

Generally, the atom that is oxidized will experience which of the following with respect to the
electrons in its outer shell (select one):?
(a)
a net gain
(b)
a net loss
(c)
no change

12.

Arrange the following molecules in order with respect to their relative levels of oxidation
(assign 5 to the most oxidized and 1 to the most reduced).
_______ CH2O (formaldehyde)
_______ CH4 (methane)
_______ CHOOH (formic acid)
_______ CH3OH (methanol)
_______ CO2 (carbon dioxide)

13.

Which reaction below is likely to proceed forward, at standard conditions? Select all that apply.

(a)
(b)
(c)
(d)

ADP + Pi ATP
glucose 1-phosphate glucose 6-phosphate
glucose + fructose sucrose
glucose CO2 + H2O

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G = +7.3 kcal/mole
G = 1.7 kcal/mole
G = +5.5 kcal/mole
G = 686 kcal/mole

14.

For each of the following sentences, fill in the blanks with the best word or phrase selected
from the list below. Not all words or phrases will be used; each word or phrase should be used
only once.
By definition, catalysis allows a reaction to occur more __________________.
Chemical reactions occur only when there is a loss of __________________
energy. Enzymes act more __________________ than other catalysts. A
catalyst decreases the __________________ energy of a reaction.
activation
chemical bond
completely
selectively

15.

free
kinetic
rapidly

slowly
unfavorable
favorable

The figure below is an energy diagram for the reaction XY. Which equation below provides
the correct calculation for the amount of free-energy change when X is converted to Y?
(select one)
(a)
(b)
(c)
(d)

a+b c
a b
a c
c a

16.

For the reaction YX at standard conditions with [Y] = 1 M and [X] = 1 M, G is initially a
large negative number. As the reaction proceeds, [Y] decreases and [X] increases until the
system reaches an equilibrium. How do the values of G and G change as the reaction
equilibrates? (select one)
(a)
G becomes less negative and G stays the same.
(b)
G becomes positive and G becomes positive.
(c)
G stays the same and G becomes less negative.
(d)
G reaches zero and G becomes more negative.

17.

True or false?
(a) T F Peptide bonds are the only covalent bonds that can link together two amino acids in
proteins.
(c) T F Nonpolar amino acids tend to be found in the interior of proteins.
(d) T F The sequence of the atoms in the polypeptide backbone varies between different
proteins.

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18.

On the basis of the two reactions below, decide which of the following statements are true and
which are false. If a statement is false, explain why it is false.
1:
2:

ATP + Y Y-P + ADP

Y-P + A B

G = 100 kcal/mole
G = 50 kcal/mole

A. T F Reaction 1 is favorable because of the large negative G associated with the

hydrolysis of ATP.
B, T F

Reaction 2 is an example of an unfavorable reaction.

C. T F Reactions 1 and 2 are coupled reactions, and when they take place together,
reaction 2 will proceed in the forward direction.
D. T F
19.

Reaction 2 can be used to drive reaction 1 in the reverse direction.

You are studying a biochemical pathway that requires ATP as an energy source. To your
dismay, the reactions soon stop, partly because the ATP is rapidly used up and partly because
an excess of ADP builds up and inhibits the enzymes involved. You are about to give up when
the following table from a biochemistry textbook catches your eye.

Which of the following reagents are most likely to revitalize your reaction? (select one)
(a)
a vast excess of ATP
(b)
glucose 6-phosphate and enzyme E
(c)
creatine phosphate and enzyme A
(d)
pyrophosphate
20.

Indicate whether the following statements are true or false. If a statement is false, explain why
it is false.
A. T F Generally, the total number of nonpolar amino acids has a greater effect on protein
structure than the exact order of amino acids in a polypeptide chain.
B. T F The polypeptide backbone refers to all atoms in a polypeptide chain, except for
those that form the peptide bonds.
C. T F The chemical properties of amino acid side chains include charged, uncharged polar,
and nonpolar.

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D. T F Enzymes alter the equilibrium point of a reaction.

E. T F Vmax can be determined by measuring the amount of product accumulated late in the
reaction.
F. T F Competitive inhibitors bind irreversibly to the enzyme active site, lowering Vmax.

21.

For each of the following sentences, fill in the blanks with the best word or phrase selected
from the list below. Not all words or phrases will be used; each word or phrase should be used
only once.
The helices and sheets are examples of protein __________________
structure. A protein such as hemoglobin, which is composed of more than one
protein __________________, has __________________ structure. A proteins
amino acid sequence is known as its __________________ structure. The
three-dimensional conformation of a protein is its __________________
structure. Proteins such as collagen tend to be constructed mainly of _______
allosteric
sheets
helices

ligand
primary
quaternary

secondary
subunit
tertiary

22. Collagen is an example of (select one):

a) globular protein
b) fibrous protein
c) enzyme
d) hormone
23.

Indicate whether the following statements are true or false. If a statement is false, explain why
it is false.
(a) T F Disulfide bonds are formed by the cross-linking of methionine residues.
(b) T F Disulfide bonds stabilize but do not change a proteins final conformation.
(c) T F Agents such as mercaptoethanol can break disulfide bonds through oxidation.
d ) T F The amino acids in the interior of a protein do not interact with the ligand and do not
play a role in selective binding.
e ) T F Antibodies are Y shaped and are composed of six different polypeptide chains.
f ) T F ATPases generate ATP for the cell.

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24.

Lysozyme is an enzyme that specifically recognizes bacterial polysaccharides, which renders

it an effective antibacterial agent. Into what classification of enzymes does lysozyme fall?
(select one)
(a)
isomerase
(b)
protease
(c)
nuclease
(d)
hydrolase

25.

Some of the enzymes that oxidize sugars to yield usable cellular energy (for example, ATP)
are regulated by phosphorylation. For these enzymes, would you expect the inactive form to
be the phosphorylated form or the dephosphorylated form? Explain your answer.

26.

In a DNA double helix, indicate true or false.

(a) T F the two DNA strands are identical
(b) T F _purines pair with purines
(c) T F thymine pairs with cytosine
(d) T F the two DNA strands run antiparallel
(e) T F There are five different nucleotides that become incorporated into a DNA strand.
(f) T F Hydrogen bonds between each nucleotide hold individual DNA strands together

27.
one)

Which of the following chemical groups is not used to construct a DNA molecule? (select
(a)
(b)
(c)
(d)

28.

five-carbon sugar
phosphate
nitrogen-containing base
six-carbon sugar

Indicate whether the following statements are true or false. If a statement is false, explain why
it is false.
A. T F Each strand of DNA contains all the information needed to create a new doublestranded DNA molecule with the same sequence information.
B. T F All functional DNA sequences inside a cell code for protein products.

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29.

The complete set of information found in a given organisms DNA is called its (select one):
(a)
genetic code
(b)
coding sequence
(c)
gene
(d)
genome

30.

Given the sequence of one strand of a DNA helix as

5-GCATTCGTGGGTAG-3,

a) Write the sequence of the complementary strand and label the 5 and 3 ends.

b) Describe the difference between the 5 and 3 end of the DNA strand. Drawing a schematic
of the structure would be useful.

31.

The process of DNA replication requires that each of the parental DNA strands be used as a
___________________ to produce a duplicate of the opposing strand.
(a)
catalyst
(b)
competitor
(c)
template
(d)
copy

32.

If the genome of the bacterium E. coli requires about 20 minutes to replicate itself, how can
the genome of the fruit fly Drosophila be replicated in only 3 minutes? Select one
(a)
The Drosophila genome is smaller than the E. coli genome.
(b)
Eucaryotic DNA polymerase synthesizes DNA at a much faster rate than procaryotic
DNA polymerase.
(c)
The nuclear membrane keeps the Drosophila DNA concentrated in one place in the
cell, which increases the rate of polymerization.
(d)
Drosophila DNA contains more origins of replication than E. coli DNA.

33.

Indicate whether the following statements are true or false. If a statement is false, explain why
it is false.
a) T F When DNA is being replicated inside a cell, local heating occurs, allowing the two
strands to separate.
b) T F DNA replication is a bidirectional process that is initiated at multiple locations along
chromosomes in eucaryotic cells.
c) T F DNA replication is a unidirectional process in prokaryotic cells.

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34.

a) Name the enzyme that catalyzes the joining of a nucleotide to a growing DNA strand.
_________________
b) What prevents this enzyme from catalyzing the reverse reaction? (select all that apply)
(a)
hydrolysis of PPi to Pi + Pi
(b)
release of PPi from the nucleotide
(c)
hybridization of the new strand to the template
(d)
loss of ATP as an energy source

35.

The figure shows a replication bubble.

A.
C.
D.
E.
F.
36

On the figure, indicate where the origin of replication was located (use O).
Indicate by arrows the direction in which the newly made DNA strands (indicated by
dark lines) were synthesized.
Number the small (Okazaki) fragments on each strand 1, 2, and 3 in the order in which
they were synthesized.
Indicate the locations where the most recent DNA synthesis has occurred (use S).
Indicate the direction of movement of the replication forks with arrows.

You are examining the DNA sequences that code for the enzyme phosphofructokinase in
skinks and Komodo dragons. You notice that the coding sequence that actually directs the
sequence of amino acids in the enzyme is very similar in the two organisms but that the
surrounding sequences vary quite a bit. What is the most likely explanation for this? (select
one)
(a)
Coding sequences are repaired more efficiently.
(b)
Coding sequences are replicated more accurately.
(c)
Coding sequences are packaged more tightly in the chromosomes to protect them from
DNA damage.
(d)
Mutations in coding sequences are more likely to be deleterious to the organism than
mutations in noncoding sequences.

37. Briefly (in 1 sentence each) describe the function of each of the following organelles:
a. mitochondria
b. endoplasmic reticulum

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c. plasma membrane
d. Golgi apparatus
e. ribosomes
f. cytoskeleton
38.
Draw the chemical structures of two amino acids (using R1 and R2 for the two functional
groups). Then, draw the structure of the product, after the formation of the peptide bond. Circle the
peptide bond on this product molecule.

39. An enzyme behaves according Michaelis-Menten kinetics. The enzyme parameters are: Vmax=
10 mM/s; Km= 25 mM. Calculate the rate of reaction when the substrate concentration is 75 mM.

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40. Name the structures shown in the figure below. Select the names from the list below.
A._______________

B._________________

C._________________

D._______________

E._________________

F._________________

G._______________

H._________________

I._________________

deoxyribonucleotide
ribonucleotide
disaccharide

polypeptide
DNA
triglyceride

glucose
Fatty acid
phospholipid

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RNA
amino acid

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