Tutorial 3 Discussion Questions

1) How does chemistry & structure influence function in lipids? Use

phospholipids as an example.
The lipid end (fatty acid) of fatty acid is non polar (hydrophobic), and the phosphate
attached alcohol serves as a polar head. In the structure of cell membrane, the outer
and inner layers are exposed with these polar ends and the middle part contains lipid
layer. Thus, the hydrophobic lipid layer is sand witched between two hydrophilic
phosphate layers, so it is also called as “phospholipid bilayer (PLP, i.e. phosphate-
lipid-phosphate)”.

Thus, due to the amphipathic nature (both polar and nonpolar) of phospholipids, they

provide the nature of selectivity to the cell membrane.
B. Cholesterol:

Cholesterol is a sterol which is an essential structural component of animal cell it is the precursor
for the biosynthesis of steroid hormones. It belongs to the class of lipids and has a high melting
point of 1450C and so exists as solid at room temperature. Serum cholesterol levels
exceeding 200 mg/dL is considered elevated cholesterol levels.
Sterols are a type of lipids, which do not have any fatty acids in their structure. They are the
steroidal alcohols that contain four fused carbon rings in their backbone, and functional groups
are attached to the carbon skeleton at various positions.
Increased cholesterol will get deposited in the “intima” of blood vessels (inner walls), and forms
atheromatus plaques. These fatty plaques obstruct the passage of blood vessels, and causes
cardiac disorders such as “atherosclerosis.”
C). Sphingolipids: SGlycolipids are sugar containing lipids derived from sphingosine. They are
commonly present in all the cell membranes and are actively involved in cell to cell
communications.
D). Triacylglycerol:
Triacylglycerols are a type of lipids, and are the storage form of fatty acids. They are formed by
the attachment of three fatty acids to a single glycerol molecule.

2) True or False? A protein’s sequence determines its structure. Explain

 The chemistry of amino acid side chains is critical to protein structure
because these side chains can bond with one another to hold a length
of protein in a certain shape or conformation. Charged amino acid side
chains can form ionic bonds, and polar amino acids are capable of
forming hydrogen bonds. Hydrophobic side chains interact with each
other via weak van der Waals interactions. The vast majority of bonds
formed by these side chains are noncovalent. In fact, cysteines are the
only amino acids capable of forming covalent bonds, which they do
with their particular side chains. Because of side chain interactions, the
sequence and location of amino acids in a particular protein guides
where the bends and folds occur in that protein its amino acid sequence
— drives the folding and intramolecular bonding of the linear amino
acid chain, which ultimately determines the protein's unique three-
dimensional shape
 3) True or False? A protein’s tertiary structure includes the interactions between
separate polypeptide chains. Justify your answer.

Tertiary structure is the next level of complexity in protein folding. Tertiary

structure is the three-dimensional structure of a protein. While individual amino acids
in the primary sequence can interact with one another to form secondary structures
such as helices and sheets and individual amino acids from distant parts of the
primary sequence can intermingle via charge-charge, hydrophobic, disulfide, or other
interactions, the formation of these bonds and interactions will serve to change the
shape of the overall protein. The folding that we end up with for a given polypeptide
is the tertiary structure.

4) Distinguish between a simple protein and a conjugated protein. Give 2

examples of each.

A conjugated protein is a protein that functions in interaction with other

(non-polypeptide) chemical groups attached by covalent bonding or weak
interactions. Many proteins contain only amino acids and no other chemical
groups, and they are called simple proteins.

5) List three differences between the structure of DNA and RNA.

Quick Answer. DNA is double-stranded, while RNA is single-

stranded. RNA contains ribose as a sugar, while DNA contains deoxyribose.
Also, three of the nitrogenous bases are the same in the two types (adenine,
cytosine, and guanine), but DNA contains thymine while RNA contains uracil.

6) What is meant by the 5’ and 3’ extremities of nucleic acids

The 5' and 3' mean "five prime" and "three prime", which indicate the carbon numbers in
the DNA's sugar backbone. The 5' carbon has a phosphate group attached to it and the
3' carbon a hydroxyl (-OH) group. This asymmetry gives a DNA strand a "direction". For
example, DNA polymerase works in a 5' -> 3' direction, that is, it adds nucleotides to the
3' end of the molecule (the -OH group is not shown in diagram), thus advancing to that
direction (downwards).

7) What is the complementary sequence of nitrogenous bases for a

3′AGCCGTTAAC 5′ fragment of a DNA chain?
8) Nucleotide polymerization is a slightly endergonic reaction (ΔG = 8 kcal/mol),
yet this reaction proceeds spontaneously in the cell. How could this be
possible?

9) Which of the following deoxyoligonucleotides will hybridize with a DNA

containing the sequence (5')AGACTGGTC(3')?
A. (5')TCTGACCAG(3')
B. (5')GAGTCAACT(3')
C. (5')CTCATTGAG(3')
D. (5')GACCAGTCT(3')
E. (5')TCTGGATCT(3')

10) Mark clearly on the representation of a polypeptide, a peptide bond, the N-

 terminus, the C terminus and a hydrophobic sidechain.

11)If an enzyme is denatured, why does it no longer work?

12) Which of the following is correct regarding enzyme inhibition?

a) The inhibition can be reversible or irreversible
b) Reversible inhibition can competitive or non -competitive
c) Both a and b
d) It is always reversible

13) Explain your answer given the data in the table above.

14) Trypsin and chymotrypsin are members of the family of serine proteases.
They cleave peptide bonds at the C-terminal end of specific residues.
Chymotrypsin recognizes aromatic residues, while trypsin recognizes lysine
and arginine. The recognition of a particular side chain (side chain specificity)
is fully determined by the structure and properties of the binding pocket. In
the case of chymotrypsin the binding pocket is hydrophobic and is wide
enough to accommodate an aromatic ring. Given what you know about the
properties of Lysine/Arginine side chains, what can you say about the
size/shape and possible interactions that would provide the substrate
 specificity in the case of trypsin? I.e. what amino acid residues from the
trypsin molecule would you expect to find in the binding site?

*Look at your amino acid properties table given in your lecture notes. I would
provide the table to you in an exam situation.

WORKED EXAMPLE

Given ΔG for each of the following reactions,

1. ATP → ADP + Pi ΔG = –30.5 kJ/mol
2. glucose 6-phosphate → glucose + Pi ΔG = –13.8 kJ/mol
Show how you would calculate the standard free-energy change (ΔG) for the
reaction:
3. ATP + glucose → glucose 6-phosphate + ADP

Ans: Reaction 3 is the sum of reaction 1 and the reversal of reaction 2.

1. ATP → ADP + Pi ΔG1 = –30.5 kJ/mol
2. glucose + Pi → glucose 6-phosphate ΔG2= +13.8 kJ/mol
3. ATP + glucose → ADP + glucose 6-phosphate ΔG3'° = ΔG1 + ΔG2 = (–30.5 +
13.8) kJ/mol = –16.7 kJ/mol)

QUESTIONS
15) For the following reaction at 25°C, ΔH° = +115 kJ and ΔS° = +125 J/K.
Calculate
ΔG° for the reaction at 25
°C

(a) +152 kJ
(b) -56.7 kJ
(c) +77.8 kJ
(d) +37.1 kJ
(e) -86.2 kJ
Is this a spontaneous reaction? Why?

16)What is the standard entropy change of the reaction below at 298 K with each
compound at the standard pressure?

(a) -198.7 J/K

(b) 76.32 J/K
(c) 303.2 J/K
(d) -129.7 J/K
(e) 384.7 J/K

1.
The compound that consists of ribose linked by an N-glycosidic bond to N-
9 of adenine is:

A) a deoxyribonucleoside.
B) a purine nucleotide.
C) a pyrimidine nucleotide.
D) adenosine monophosphate.
E) adenosine.
E) adenosine.
2.
A major component of RNA but not of DNA is:

A) adenine.
B) cytosine.
C) guanine.
D) thymine.
E) uracil.
E) uracil.
3.
The difference between a ribonucleotide and a deoxyribonucleotide is:

A) a deoxyribonucleotide has an —H instead of an —OH at C-2.

B) a deoxyribonucleotide has alpha configuration; ribonucleotide has the
beta configuration at C-1.
C) a ribonucleotide has an extra —OH at C-4.
D) a ribonucleotide has more structural flexibility than deoxyribonucleotide.
E) a ribonucleotide is a pyranose, deoxyribonucleotide is a furanose.
A) a deoxyribonucleotide has an —H instead of an —OH at C-2.
4.
Which one of the following is true of the pentoses found in nucleic acids?

A) C-5 and C-1 of the pentose are joined to phosphate groups.

B) C-5 of the pentose is joined to a nitrogenous base, and C-1 to a
phosphate group.
C) The bond that joins nitrogenous bases to pentoses is an O-glycosidic
bond.
D) The pentoses are always in the -furanose forms.
E) The straight-chain and ring forms undergo constant interconversion.
D) The pentoses are always in the B-furanose forms.
5.
The phosphodiester bonds that link adjacent nucleotides in both RNA and
DNA:

A) always link A with T and G with C.

B) are susceptible to alkaline hydrolysis.
C) are uncharged at neutral pH.
D) form between the planar rings of adjacent bases.
E) join the 3' hydroxyl of one nucleotide to the 5' hydroxyl of the next.
E) join the 3' hydroxyl of one nucleotide to the 5' hydroxyl of the next.
6.
The phosphodiester bond that joins adjacent nucleotides in DNA:

A) associates ionically with metal ions, polyamines, and proteins.

B) is positively charged.
C) is susceptible to alkaline hydrolysis.
D) Links C-2 of one base to C-3 of the next.
E) links C-3 of deoxyribose to N-1 of thymine or cytosine.
A) associates ionically with metal ions, polyamines, and proteins.
7.
The alkaline hydrolysis of RNA does not produce:

A) 2'- AMP.
B) 2',3'-cGMP.
C) 2'-CMP.
D) 3',5'-cAMP.
E) 3'-UMP.
D) 3',5'-cAMP.
8.
The DNA oligonucleotide abbreviated pATCGAC:

A) has 7 phosphate groups.

B) has a hydroxyl at its 3' end.
C) has a phosphate on its 3' end.
D) has an A at its 3' end.
E) violates Chargaff's rules.
B) has a hydroxyl at its 3' end.
9.
For the oligoribonucleotide pACGUAC:

A) the nucleotide at the 3' end has a phosphate at its 3' hydroxyl.
B) the nucleotide at the 3' end is a purine.
C) the nucleotide at the 5' end has a 5' hydroxyl.
D) the nucleotide at the 5' end has a phosphate on its 5' hydroxyl.
E) the nucleotide at the 5' end is a pyrimidine.
D) the nucleotide at the 5' end has a phosphate on its 5' hydroxyl.
10.
The nucleic acid bases:

A) absorb ultraviolet light maximally at 280 nm.

B) are all about the same size.
C) are relatively hydrophilic.
D) are roughly planar.
E) can all stably base-pair with one another.
D) are roughly planar.
11.
Which of the following statements concerning the tautomeric forms of
bases such as uracil is correct?
A) The all-lactim form contains a ketone group.
B) The lactam form contains an alcohol group.
C) The lactam form predominates at neutral pH.
D) They are geometric isomers.
E) They are stereoisomers.
C) The lactam form predominates at neutral pH.
12.
In a double-stranded nucleic acid, cytosine typically base-pairs with:

A) adenosine.
B) guanine.
C) inosine.
D) thymine.
E) uracil.
B) guanine.
13.
In the Watson-Crick model for the DNA double helix (B form) the A-T and G-
C base pairs share which one of the following properties?

A) The distance between the two glycosidic (base-sugar) bonds is the same
in both base pairs, within a few tenths of an angstrom.
B) The molecular weights of the two base pairs are identical.
C) The number of hydrogen bonds formed between the two bases of the
base pair is the same.
D) The plane of neither base pair is perpendicular to the axis of the helix.
E) The proton-binding groups in both base pairs are in their charged or
ionized form.
A) The distance between the two glycosidic (base-sugar) bonds is the same in
both base pairs, within a few tenths of an angstrom.
14.
The experiment of Avery, MacLeod, and McCarty in which nonvirulent
bacteria were made virulent by transformation was significant because it
showed that:

A) bacteria can undergo transformation.

B) genes are composed of DNA only.
C) mice are more susceptible to pneumonia than are humans.
D) pneumonia can be cured by transformation.
E) virulence is determine genetically.
B) genes are composed of DNA only.
15.
Chargaff's rules state that in typical DNA:

A) A = G.
B) A = C.
C) A = U.
D) A + T = G + C.
E) A + G = T + C.
E) A + G = T + C.
16.
Based on Chargaff's rules, which of the following are possible base
compositions for double-stranded DNA?

%A %G %C %T %U
A) 5 45 45 5 0
B) 20 20 20 20 20
C) 35 15 35 15 0
D) all of the above
E) none of the above
A) 5 45 45 5 0
17.
In the Watson-Crick structure of DNA, the:

A) absence of 2'-hydroxyl groups allows bases to lie perpendicular to the

helical axis.
B) adenine content of one strand must equal the thymine content of the
same strand.
C) nucleotides are arranged in the A-form.
D) purine content (fraction of bases that are purines) must be the same in
both strands.
E) two strands are parallel.
A) absence of 2'-hydroxyl groups allows bases to lie perpendicular to the helical
axis.
18.
In the Watson-Crick model of DNA structure:

A) both strands run in the same direction, 3' to 5'; they are parallel.
B) phosphate groups project toward the middle of the helix, where they are
protected from interaction with water.
C) T can form three hydrogen bonds with either G or C in the opposite
strand.
D) the distance between the sugar backbone of the two strands is just large
enough to accommodate either two purines or two pyrimidines.
E) the distance between two adjacent bases in one strand is about 3.4 Å.
E) the distance between two adjacent bases in one strand is about 3.4 Å.
19.
Which of the following is not true of all naturally occurring DNA?

A) Deoxyribose units are connected by 3',5'-phosphodiester bonds.

B) The amount of A always equals the amount of T.
C) The ratio A+T/G+C is constant for all natural DNAs.
D) The two complementary strands are antiparallel.
E) Two hydrogen bonds form between A and T.
C) The ratio A+T/G+C is constant for all natural DNAs.
20.
In the Watson-Crick model of DNA structure (now called B-form DNA):

A) a purine in one strand always hydrogen bonds with a purine in the other
strand.
B) A-T pairs share three hydrogen bonds.
C) G-C pairs share two hydrogen bonds.
D) the 5' ends of both strands are at one end of the helix.
E) the bases occupy the interior of the helix.
E) the bases occupy the interior of the helix.
21.
The double helix of DNA in the B-form is stabilized by:

A) covalent bonds between the 3' end of one strand and the 5' end of the
other.
B) hydrogen bonding between the phosphate groups of two side-by-side
strands.
C) hydrogen bonds between the riboses of each strand.
D) nonspecific base-stacking interaction between two adjacent bases in the
same strand.
E) ribose interactions with the planar base pairs.
D) nonspecific base-stacking interaction between two adjacent bases in the same
strand.
22.
In nucleotides and nucleic acids, syn and anti conformations relate to:

A) base stereoisomers.
B) rotation around the phosphodiester bond.
C) rotation around the sugar-base bond.
D) sugar pucker.
E) sugar stereoisomers.
C) rotation around the sugar-base bond.
23.
B-form DNA in vivo is a ________-handed helix, _____ Å in diameter, with a
rise of ____ Å per base pair.

A) left; 20; 3.9

B) right; 18; 3.4
C) right; 18; 3.6
D) right; 20; 3.4
E) right; 23; 2.6
D) right; 20; 3.4
24.
In double-stranded DNA:

A) only a right-handed helix is possible.

B) sequences rich in A-T base pairs are denatured less readily than those
rich in G-C pairs.
C) the sequence of bases has no effect on the overall structure.
D) the two strands are parallel.
E) the two strands have complementary sequences.
E) the two strands have complementary sequences.
25.
Which of the following is a palindromic sequence?

A) AGGTCC
TCCAGG
B) CCTTCC
GCAAGG
C) GAATCC
CTTAGG
D) GGATCC
CCTAGG
E) GTATCC
CATAGG
D) GGATCC
CCTAGG
26.
Triple-helical DNA structures can result from Hoogsteen (non Watson-
Crick) interactions. These interactions are primarily:

A) covalent bonds involving deoxyribose.

B) covalent bonds involving the bases.
C) hydrogen bonds involving deoxyribose.
D) hydrogen bonds involving the bases.
E) hydrophobic interactions involving the bases.
D) hydrogen bonds involving the bases.
27.
Which of the following are possible base compositions for single-stranded
RNA?

%A %G %C %T %U
A) 5 45 45 0 5
B) 25 25 25 0 25
C) 35 10 30 0 25
D) all of the above
E) none of the above
D) all of the above
28.
Double-stranded regions of RNA:

A) are less stable than double-stranded regions of DNA.

B) can be observed in the laboratory, but probably have no biological
relevance.
C) can form between two self-complementary regions of the same single
strand of RNA.
D) do not occur.
E) have the two strands arranged in parallel (unlike those of DNA, which are
antiparallel).
C) can form between two self-complementary regions of the same single strand
of RNA.
29.
When double-stranded DNA is heated at neutral pH, which change does not
occur?

A) The absorption of ultraviolet (260 nm) light increases.

B) The covalent N-glycosidic bond between the base and the pentose
breaks.
C) The helical structure unwinds.
D) The hydrogen bonds between A and T break.
E) The viscosity of the solution decreases.
B) The covalent N-glycosidic bond between the base and the pentose breaks.
30.
Which of the following deoxyoligonucleotides will hybridize with a DNA
containing the sequence (5')AGACTGGTC(3')?

A) (5')CTCATTGAG(3')
B) (5')GACCAGTCT(3')
C) (5')GAGTCAACT(3')
D) (5')TCTGACCAG(3')
E) (5')TCTGGATCT(3')
B) (5')GACCAGTCT(3')
31.
The ribonucleotide polymer (5')GTGATCAAGC(3') could only form a double-
stranded structure with:

A) (5')CACTAGTTCG(3').
B) (5')CACUAGUUCG(3').
C) (5')CACUTTCGCCC(3').
D) (5')GCTTGATCAC(3').
E) (5')GCCTAGTTUG(3').
D) (5')GCTTGATCAC(3').
32.
In comparison with DNA-DNA double helices, the stability of DNA-RNA and
RNA-RNA helices is:

A) DNA-DNA > DNA-RNA > RNA-RNA.

B) DNA-DNA > RNA-RNA > DNA-RNA.
C) RNA-DNA > RNA-RNA > DNA-DNA.
D) RNA-RNA > DNA-DNA > DNA-RNA.
E) RNA-RNA > DNA-RNA > DNA-DNA.
E) RNA-RNA > DNA-RNA > DNA-DNA.
33.
In the laboratory, several factors are known to cause alteration of the
chemical structure of DNA. The factor(s) likely to be important in a living
cell is (are):

A) heat.
B) low pH.
C) oxygen.
D) UV light.
E) both C and D.
E) both C and D.
34.
Compounds that generate nitrous acid (such as nitrites, nitrates, and
nitrosamines) change DNA molecules by:

A) breakage of phosphodiester bonds.

B) deamination of bases.
C) depurination.
D) formation of thymine dimers.
E) transformation of A to T.
B) deamination of bases.
35.
In DNA sequencing by the Sanger (dideoxy) method:

A) radioactive dideoxy ATP is included in each of four reaction mixtures

before enzymatic synthesis of complementary strands.
B) specific enzymes are used to cut the newly synthesized DNA into small
pieces, which are then separated by electrophoresis.
C) the dideoxynucleotides must be present at high levels to obtain long
stretches of DNA sequence.
D) the role of the dideoxy CTP is to occasionally terminate enzymatic
synthesis of DNA where Gs occur in the template strands.
E) the template DNA strand is radioactive.
D) the role of the dideoxy CTP is to occasionally terminate enzymatic synthesis of
DNA where Gs occur in the template strands.
36.
In the chemical synthesis of DNA:

A) the dimethoxytrityl (DMT) group catalyzes formation of the

phosphodiester bond.
B) the direction of synthesis is 5' to 3'.
C) the maximum length of oligonucleotide that can be synthesized is 8-10
nucleotides.
D) the nucleotide initially attached to the silica gel support will become the
3' end of the finished product.
E) the protecting cyanoethyl groups are removed after each step.
D) the nucleotide initially attached to the silica gel support will become the 3' end
of the finished product.
37.
In living cells, nucleotides and their derivatives can serve as:

A) carriers of metabolic energy.

B) enzyme cofactors.
C) intracellular signals.
D) precursors for nucleic acid synthesis.
E) all of the above.
E) all of the above.
38.
The "energy carrier" ATP is an example of a(n):

A) deoxyribonucleoside triphosphate
B) di-nucleotide
C) peptide
D) ribonucleotide
E) ribonucleoside triphosphate
E) ribonucleoside triphosphate
39.
The carbon assimilation (Calvin Cycle) reactions of photosynthetic plants:

A) are driven ultimately by the energy of sunlight.

B) are important to plants, but ultimately of little significance for bacteria
and animals.
C) cannot occur in the light.
D) yield (reduced) NADH.
E) yield ATP, which is required for the light reactions.
A) are driven ultimately by the energy of sunlight.
40.
In photophosphorylation, absorption of light energy in chloroplast “light
reactions” leads to:

A) absorption of CO2 and release of O2

B) absorption of O2 and release of CO2.
C) hydrolysis of ATP and reduction of NADP+.
D) synthesis of ATP and oxidation of NADPH.
E) use of iron-sulfur proteins.
A) absorption of CO2 and release of O2
41.
All are true of photorespiration except:

A) It is driven by light.
B) It oxidizes substrates to CO2.
C) It produces O2.
D) It results from a lack of specificity of the enzyme rubisco.
E) It results in no fixation of carbon.
C) It produces O2.
42.
The compound that condenses with CO2 in the first reaction of carbon
dioxide assimilation is:

A) 3-phosphoglycerate.
B) ribose 1,5-bisphosphate.
C) ribulose 1,5-bisphosphate.
D) ribulose 5-phosphate.
E) rubisco
C) ribulose 1,5-bisphosphate.
43.
In what order do the following five steps occur in the photochemical
reaction centers?
1) Excitation of the chlorophyll a molecule at the reaction center
2) Replacement of the electron in the reaction center chlorophyll
3) Light excitation of antenna chlorophyll molecule
4) Passage of excited electron to electron-transfer chain5) Exiton transfer to
neighboring chlorophyll

A) 1-2-3-4-5
B) 3-2-5-4-1
C) 3-5-1-4-2
D) 4-2-3-5-1
E) 5-4-3-2-1
C) 3-5-1-4-2
44.
Which one of the following cellular organelles is not unique to plant cells, in
carrying out the indicated pathway or function of carbohydrate
metabolism?

A) Amyloplasts (starch synthesis)

B) Chloroplasts (Calvin cycle)
C) Glyoxysomes (glyoxlate cycle)
D) Mitochondria (citric acid cycle)
E) Vacuoles (organic acid storage)
D) Mitochondria (citric acid cycle)
45.
Water is the electron donor and NADP+ is the ultimate electron acceptor in
photophosphorylation.

A) True
B) False
A) True
46.
The light reactions in photosynthetic higher plants:

A) do not require chlorophyll.

B) produce ATP and consume NADH.
C) require the action of a single reaction center.
D) result in the splitting of H2O, yielding O2.
E) serve to produce light so that plants can see underground.
D) result in the splitting of H2O, yielding O2.
47.
The assimilation of CO2 into organic compounds (triose phosphates) in
green plants results in the production of ATP.

A) True
B) False
A) True
48.
Photosynthetic phosphorylation and oxidative phosphorylation appear to
be generally similar processes, both consisting of ATP synthesis coupled
to the transfer of electrons along an electron carrier chain. Which of the
following is not true of both processes?

A) Both contain cytochromes and flavins in their electron carrier chains.

B) Both processes are associated with membranous elements of the cell.
C) Both use oxygen as a terminal electron acceptor.
D) Each represents the major route of ATP synthesis in those cells in which
it is found.
E) Protons are pumped from the inside to the outside of both mitochondria
and chloroplast membranes.
C) Both use oxygen as a terminal electron acceptor.