DNA structure and function, RNA structure and function, DNA damage and repair, replication and case-based multiple-choice questions

1. Revision- Molecular Biology
part 1
Namrata Chhabra
MHPE, MD, MBBS, FAIMER FELLOW
Principal- in-charge, Professor & Head, Department of Biochemistry,
SSR Medical College, Mauritius

2. DNA STRUCTURE AND FUNCTIONS

3. DNA structure
DNA is composed of subunits called nucleotides
A nucleotide is made up of a sugar (deoxyribose), a phosphate group, and one
of four nitrogenous bases: adenine (A), thymine (T), guanine (G) or cytosine (C).
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4. Primary structure of DNA
● A linear sequence of
deoxyribonucleotides
linked together by 3'-5'
phosphodiester linkages
● The informational
content of DNA resides in
the sequence in which
monomers—purine and
pyrimidine
deoxyribonucleotides—
are ordered
4

5. 5
Secondary
structure
of DNA

6. Watson and Crick's model of DNA
● The structure of DNA, as represented in Watson and Crick's model, is a
double-stranded, antiparallel, right-handed helix.
● The sugar-phosphate backbones of the DNA strands make up the outside
of the helix, while the nitrogenous bases are found on the inside and
form hydrogen-bonded pairs that hold the DNA strands together.
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7. Secondary structure of DNA
DNA nucleotides are linked by
covalent bonds, formed between
the deoxyribose sugar of one
nucleotide and the phosphate
group of the subsequent.
This arrangement makes an
alternating chain of deoxyribose
sugar and phosphate groups in the
DNA polymer, a structure known
as the sugar-phosphate backbone
7

8. Chargaff’s rules
● The first rule was that in DNA the number of guanine units is equal to
the number of cytosine units, and the number of adenine units is equal
to the number of thymine units. This hinted at the base pair makeup of
DNA.
● The second rule was that the relative amounts of guanine, cytosine,
adenine and thymine bases vary from one species to another. This
hinted that DNA rather than protein could be the genetic material.
● These findings, called Chargaff's rules, turned out to be crucial to
Watson and Crick's model of the DNA double helix.
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9. Major and Minor grooves
● Major and minor grooves wind along
the DNA molecule parallel to the
phosphodiester backbones.
● In these grooves, proteins can
interact specifically with exposed
atoms of the nucleotides (via specific
hydrophobic and ionic interactions)
without disrupting the base pairing of
the double-helical DNA molecule.
9

10. Forms of DNA
Property A-DNA B-DNA Z-DNA
Helix Handedness Right Right Left
Base Pairs per turn 11 10.4 12
Rise per base pair along
axis
0.23nm 0.34nm 0.38nm
Pitch 2.46nm 3.40nm 4.56nm
Diameter 2.55nm 2.37nm 1.84nm
Conformation of
Glycosidic bond
anti anti Alternating anti and syn
Major Groove Present Present Absent
Minor Groove Present Present Deep cleft 10

11. Physiological form of DNA- B DNA
● The horizontal arrow indicates the
width of the double helix (20 Å).
● The vertical arrow indicates the
distance spanned by one complete
turn of the double helix (34 Å).
● The major and minor grooves are
depicted.
● Hydrogen bonds between A/T and
G/C bases indicated by short
horizontal lines.
11

12. Tertiary structure of DNA
In eukaryotic cells, DNA is folded into
chromatin.
Chromatin consists of very long double-
stranded DNA molecules and a nearly
equal mass of rather small basic proteins
termed histones as well as a smaller
amount of nonhistone proteins (most of
which are acidic and larger than histones)
and a small quantity of RNA.
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13. Tertiary
structure of
DNA

14. QUESTION-1
In DNA on a molar basis which of the following statements is correct ?
a) Adenine equals Thymine
b) Adenine equals Uracil
c) Guanine equals Adenine
d) Cytosine equals Thymine
e) Cytosine equals uracil

15. ANSWER
a) Adenine equals Thymine

16. QUESTION-2
A common mutagenic event is the deamination of cytosine in the DNA
to form Uracil. If the damaged strand is replicated, a CG base pair in
DNA will be converted to which of the following pairs ?
a) TA base pairs
b) GC base pairs
c) GG base pairs
d) UG base pairs

17. Answer
d) UG base pairs

18. RNA STRUCTURE, TYPES AND FUNCTIONS

19. Types of RNA
In all prokaryotic and eukaryotic organisms, three main classes of RNA molecules
exist-
1) Messenger RNA(m RNA)
2) Transfer RNA (t RNA)
3) Ribosomal RNA (r RNA)
The other are –
o small nuclear RNA (SnRNA),
o micro-RNA(mi RNA) and
o small interfering RNA(Si RNA) and
o heterogeneous nuclear RNA (hnRNA).
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20. Structural Characteristics of
m-RNA
5’ cap and 3’ tail impart stability to m RNA by protecting from
specific exonucleases.
20Biochemistry For Medics

21. Heterogeneous nuclear RNA (hnRNA)
Mature m –RNA is formed from primary transcript by capping, tailing, splicing and
base modification.
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22. Secondary and Tertiary structure of t- RNA
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23. Ribosomal RNA (rRNA)
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24. Small Nuclear RNAs (snRNAs).
SnRNA s are involved in the process of splicing (intron removal) of primary transcript to form
mature m RNA. The SnRNA s form complexes with proteins to form Ribonucleoprotein
particles called snRNPs
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25. Micro RNAs (miRNAs)
microRNAs, short non-coding RNAs present in all living organisms, have been shown to regulate
the expression of at least half of all human genes. These single-stranded RNAs exert their
regulatory action by binding messenger RNAs and preventing their translation into proteins.
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26. Small Interfering RNAs (siRNAs)
Small interfering RNA (siRNA) are 20-25 nucleotide-long double-stranded RNA molecules that have a variety
of roles in the cell. They are involved in the RNA interference (RNAi) pathway, where it interferes with the
expression of a specific gene by hybridizing to its corresponding RNA sequence in the target mRNA. This then
activates the degrading mRNA. Once the target mRNA is degraded, the mRNA cannot be translated into
protein.
26

27. QUESTION-3
Choose the incorrect statement about m RNA-
a) Poly (A) tail is added to the 3' end.
b) Cap is added to the 5’ end.
c) Methylation takes place at 2'-hydroxy and the N6 of adenylyl
residues.
d) Histone mRNAs lack 5’ cap
e) Introns are removed, and exons are spliced together

28. Answer
d) Histone mRNAs lack 5’ cap

29. QUESTION-4
The chemical structure of 5’ cap of eukaryotic m RNA cap is-
a) 5- methyl Adenosine triphosphate
b) 7- Hydroxy Guanosine triphosphate
c) 5- methyl guanosine triphosphate
d) 7- methyl guanosine triphosphate
e) 5,7 Dimethyl guanosine triphosphate

30. ANSWER
d) 7- methyl guanosine triphosphate

31. DNA damage and repair

32. Types of DNA damage
S.No. Type of Damage Examples
1) Single-base alteration A.Depurination
B.Deamination of cytosine to uracil
C.Deamination of adenine to hypoxanthine
D.Alkylation of base
E.Insertion or deletion of nucleotide
F.Base-analog incorporation
2) Two-base alterations
A. UV light–induced thymine-thymine (pyrimidine) dimer
B. Bifunctional Alkylating agent cross-linkage
3) Chain breaks A. Ionizing radiation
B. Radioactive disintegration of backbone element
C. Oxidative free radical formation
4) Cross-linkage A. Between bases in same or opposite strands
B. Between DNA and protein molecules (eg, histones)
32

33. DNA Repair
DNA repair can be grouped into two major functional
categories:
A) Direct Damage reversal
B) Excision of DNA damage
33

34. Direct Damage Reversal
ii) O6-methylguanine-DNA
methyltransferase I and II (MGMT), also
called DNA-alkyltransferases, remove
the modified bases like O6-alkylguanine
and O4-alkylthymine.
• The photolyase protein is not found in all
living cells. However, the DNA-
alkyltransferases are widespread in
nature.
34

35. i) Base Excision Repair (BER)
Base excision-repair of DNA
• The enzyme uracil DNA
glycosylase removes the
uracil created by
spontaneous deamination
of cytosine in the DNA.
• An endonuclease cuts the
backbone near the defect
• An endonuclease removes
a few bases
• The defect is filled in by the
action of a DNA
polymerase and
• The strand is rejoined by a
ligase.
35

36. ii) Nucleotide excision repair (NER)
• In eukaryotic cells the enzymes
cut between the third to fifth
phosphodiester bond 3' from
the lesion, and on the 5' side the
cut is somewhere between the
twenty-first and twenty-fifth
bonds.
• Thus, a fragment of DNA 27–29
nucleotides long is excised.
• After the strand is removed it is
replaced, again by exact base
pairing, through the action of
yet another polymeras e,and the
ends are joined to the existing
strands by DNA ligase.
36

37. iii) Mismatch repair (MMR)
• This mechanism corrects a
single mismatch base pair (eg, C
to A rather than T to A) or a
short region of unpaired DNA.
• The defective region is
recognized by an endonuclease
that makes a single-strand cut at
an adjacent methylated GATC
sequence.
• The DNA strand is removed
through the mutation, replaced,
and religated.
37

38. B) Repairing Strand Breaks
• Ionizing radiation and certain chemicals can produce both single-
strand breaks (SSBs) and double-strand breaks (DSBs) in the DNA
backbone.
i) Single-Strand Breaks (SSBs)
• Breaks in a single strand of the DNA molecule are repaired using the
same enzyme systems that are used in Base-Excision Repair (BER).
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39. B) Repairing Strand Breaks
39

40. Diseases associated with defective DNA repair
system
• Ataxia telangiectasia
• Bloom syndrome
• Cockayne's syndrome
• Progeria (Hutchinson-Gilford Progeria syndrome)
• Rothmund-Thomson syndrome
• Trichothiodystrophy
• Werner syndrome
• Xeroderma pigmentosum
• Hereditary nonpolyposis colon cancer.
40

41. QUESTION-5
The nucleotide excision repair is responsible for the excision of
approximately....... Bases
a) 10-20
b) 25-30
c) 200-300
d) 400-500

42. ANSWER
b) 25-30

43. Question-6
Hereditary nonpolyposis colon cancer is caused due to impaired activity
of :
a) Direct repair
b) Base excision repair
c) Mismatch repair
d) Nucleotide excision repair

44. ANSWER
c) Mismatch repair

45. Question-7
Which one of the following enzymes is responsible for direct DNA
repair?
a) UVR Endonuclease
b) Photolyase
c) GATC endonuclease
d) RNA polymerase

46. ANSWER
b) Photolyase

47. Question-8
GATC endonuclease is involved in which of the following repairs
mechanisms ?
a) Direct repair
b) Base excision repair
c) Mismatch repair
d) Nucleotide excision repair

48. ANSWER
c) Mismatch repair

49. DNA Replication

50. DNA Replication- Salient features
⦿ Semi conservative
⦿ Parental strands are not degraded
⚫ Base pairing allows each strand to
serve as a template for a new strand
⚫ New duplex has one parental and the
other one as newly synthesized
strand.

51. DNA Replication
⦿ Semi discontinuous
⦿ Leading & Lagging strands
Leading strand
◆ continuous synthesis
Lagging strand
◆ Okazaki fragments
◆ joined by ligases

52. DNA Replication
⦿ Energy of Replication
⦿ The nucleotides arrive as
⦿ Nucleoside triphosphates
⚫DNA base, sugar with PPP
○ P-P-P = energy for bonding
⚫DNA bases arrive with their own energy source for
bonding
⚫bonded by enzyme: DNA polymerase III

53. DNA Replication
⦿ Primer is needed
⚫DNA polymerase can only add nucleotides
to 3′ end of a growing DNA strand
○ need a “starter” nucleotide to make a
bond
⚫strand only grows 5′→3′.
⚫Template is read in the 3′-5′ direction while
polymerization takes place in the 5′→3′
direction

54. Replication Fork

55. Formation of super coils

56. Question-9
Which of the following eukaryotic DNA polymerases has intrinsic
primase activity?
A) DNA polymerase α
B) DNA polymerase β
C) DNA polymerase γ
D) DNA polymerase δ
E) DNA polymerase ϵ

57. ANSWER
A) DNA polymerase α

58. Question-10
In a newly synthesized prokaryotic DNA strand, the primers are
removed by-
A) DNA polymerase I
B) DNA polymerase II
C) DNA polymerase III
D) DNA Ligase
E) Topoisomerase II

59. ANSWER
A) DNA polymerase I

60. Question-11
Okazaki fragments are formed on the ----- strands and in the -----
direction.
a) Leading; 3’-5’
b) Lagging ; 3’-5’
c) Leading; 5’-3’
d) Lagging ; 5’-3’

61. ANSWER
d) Lagging ; 5’-3’

62. Question-12
The action of DNA Polymerase requires which of the following:
a) A 5’ hydroxyl group
b) Deoxy uridine triphosphate (dUTP)
c) NAD + as a cofactor
d) A 3’ hydroxyl group
e) Cytosine triphosphate (CTP)

63. ANSWER
d) A 3’ hydroxyl group

64. Question-13
Which statement best describes the ‘semi conservative replication’ of
DNA?
a) In each replication cycle, only one of the two DNA strands is
replicated
b) In each replication cycle one of the parental strands is conserved
c) In each replication cycle, the daughter cells acquire either the
parental stands or new stands
d) Only half of the DNA is replicated in each replication cycle
e) The genetic information is partly conserved in each of the replication
cycle.

65. ANSWER
b) In each replication cycle one of the parental strands is conserved

66. Question-14
Which of the following enzymes is not involved in DNA replication?
A) Helicase
B) Primase
C) Topo isomerase
D) DNA Polymerase
E)Restriction endonuclease

67. ANSWER
E) Restriction endonuclease

68. Question -15
The mobile complex between helicase and primase is called-
a) Prepriming complex
b) Origin replication element
c) DNA unwinding element
d) Primosome
e) Nucleosome

69. ANSWER
d) Primosome

70. Question 16
A 33-year-old, homosexual man is recently diagnosed with human
immunodeficiency virus (HIV) infection. His CD 4+ T-cell count is
dramatically reduced, and he has a high viral load. He is refereed to an
infectious disease clinic where they begin him on a nucleoside analog.
These drugs inhibit DNA synthesis because they lack which of the
following properties required for normal DNA polymerization ?
a) A 5’ phosphate
b) A 3’ hydroxyl
c) A – Methyl G cap
d) A poly A tail

71. ANSWER
b) A 3’ hydroxyl

72. Thank you