Biochemistry nucleic acid

1. 1
Nucleic Acids
Structures of Nucleic Acids
DNA Replication
RNA and Transcription
5/5/2023

2. Most human cells have 6 billion base pairs of
information.
All 6 billion base pairs would be 3.6 m in length if all of
the molecules were laid end to end.
Human beings are composed of approximately 10
trillion cells.
If all of this DNA were strung end to end, it would reach
to the sun and back about 65 times.
The total length of DNA in a eukaryotic cell is many orders of
magnitude longer than the diameter of the nucleus. For
example, human cells accommodate 2 meters of DNA in a
Did You Know?

3. 3
5/5/2023

4. 4
Nucleotides
Nucleic acids consist of nucleotides that
have a sugar, nitrogen base, and phosphate
nucleoside
Sugar
Base
PO4
5/5/2023

5. 5
Nitrogen-Containing Bases
N
N
N
N
H
NH2
N
N
O
CH3
O
H
H
N
N
N
N
O
H
NH2
H
N
N
NH2
CH3
O
H
N
N
O
CH3
O
H
H
adenine (A) thymine (T)
guanine (G) cytosine (C) uracil (U)
5/5/2023

6. 5/5/2023 6

7. 7
Sugars
O OH
CH2
OH
OH
HO HO O OH
CH2
OH
ribose deoxyribose
(no O)
5/5/2023

8. 8
Nucleosides in DNA
Base Sugar Nucleoside
Adenine (A) Deoxyribose Adenosine
Guanine (G) Deoxyribose Guanosine
Cytosine (C) Deoxyribose Cytidine
Thymine (T) Deoxyribose Thymidine
5/5/2023

9. 9
Nucleosides in RNA
Base Sugar Nucleoside
Adenine (A) ribose Adenosine
Guanine (G) ribose Guanosine
Cytosine (C) ribose Cytidine
Uracil (U) ribose Uridine
5/5/2023

10. 10
5/5/2023

11. 11
Example of a Nucleoside
O
OH
N
N
NH2
O
CH2
O
P
O
O-
O-
deoxyctyidine monophosphate (dCMP)
5/5/2023

12. 12
Nucleotides in DNA and RNA
DNA
dAMP Deoxyadenosine monophosphate
dGMP Deoxyguanosine monophosphate
dCMP Deoxycytidine monophosphate
dTMP Deoxythymidine monophosphate
RNA
AMP adenosine monophosphate
GMP guanosine monophosphate
CMP cytidine monophosphate
UMP uridine monophosphate
5/5/2023

13. 13
Nucleoside & Nucleotide Structures. Shown with Ribose as
the Sugar.
The corresponding deoxyribonucleotides are abbreviated dNMP, dNDP, &
dNTP. N-any base (A, G, C, U, or T).
5/5/2023

14. 14
Structure of Nucleic Acids
• Polymers of four nucleotides
• Linked by alternating sugar-phosphate bonds
• RNA: ribose and A, G, C, U
• DNA: deoxyribose and A,G,C,T
nucleotide nucleotide nucleotide nucleotide
P sugar
base
P sugar
base
P sugar
base
P sugar
base
5/5/2023

15. DNA RNA
15
5/5/2023

16. 16
Nucleic Acid Structure
3,5-phosphodiester bond
O
N
N
NH2
O
CH2
O
P
O
O
-
O
-
OH
O
N
N
NH2
CH2
O
P
O
O-
OH
O
N
N
AMP
CMP
3
5
5/5/2023

17. 17
Double Helix of DNA
• DNA contains two strands of nucleotides
• H bonds hold the two strands in a double-
helix structure
• A helix structure is like a spiral stair case
• Bases are always paired as A–T and G-C
• Thus the bases along one strand complement
the bases along the other
5/5/2023

18. 18
Complementary Base Pairs
•Two H bonds for A-T
•Three H bonds for G-C
5/5/2023

19. 19
Double Helix of DNA
5/5/2023

20. Characteristic DNA RNA
Length
DNA is significantly longer
than RNA, b/c it stores all
of the genetic information.
RNA is short because it carries
one gene at a time.
Number of strands Two One
Location in cell
Nucleus only - it is too big
to go through the nuclear
membrane.
Nucleus & cytoplasm; it can
travel everywhere b/c it's more
practical than hauling big ol'
DNA around whenever we want
to make a molecule.
Nitrogenous bases A, T, C, G A, U, C, G
Sugar used Deoxyribose Ribose
How it's made DNA replication Transcription 20
The Differences Between DNA & RNA
5/5/2023

21. DNA RNA
21
5/5/2023

22. Sugars
• Pentoses (5-C sugars)
• Numbering of sugars is “primed”
22
5/5/2023

23. Sugars
D-Ribose and 2’-Deoxyribose
*Lacks a 2’-OH group
23
5/5/2023

24. Nucleosides
24
5/5/2023

25. DNA RNA
25
5/5/2023

26. Phosphate Groups
• Mono-, di- or triphosphates
• Phosphates can be bonded to either C3 or
C5 atoms of the sugar
26
5/5/2023

27. Nucleotides
• Result from linking one or more phosphates
with a nucleoside onto the 5’ end of the
molecule through esterification
27
5/5/2023

28. Nucleotides
• RNA (ribonucleic acid) is a polymer of
ribonucleotides
• DNA (deoxyribonucleic acid) is a polymer
of deoxyribonucleotides
• Both deoxy- and ribonucleotides contain
Adenine, Guanine and Cytosine
– Ribonucleotides contain Uracil
– Deoxyribonucleotides contain Thymine 28
5/5/2023

29. Nucleotides
• Monomers for nucleic acid polymers
• Nucleoside Triphosphates are important
energy carriers (ATP, GTP)
• Important components of coenzymes
– FAD, NAD+ and Coenzyme A
29
5/5/2023

30. DNA Backbone Structure
• Alternate phosphate and sugar (deoxyribose), phosphate ester bonds
30
5/5/2023

31. DNA Backbone Structure
• Alternate phosphate and sugar (deoxyribose), phosphate ester bonds
31
5/5/2023

32. 32
Structure of a
Polynucleotide
32
5/5/2023

33. Nucleosides
• Result from linking one of the sugars with
a purine or pyrimidine base through an N-
glycosidic linkage
– Purines bond to the C1’ carbon of the sugar
at their N9 atoms
– Pyrimidines bond to the C1’ carbon of the
sugar at their N1 atoms
33
5/5/2023

34. Naming Conventions
• Nucleosides:
– Purine nucleosides end in “-sine”
• Adenosine, Guanosine
– Pyrimidine nucleosides end in “-dine”
• Thymidine, Cytidine, Uridine
• Nucleotides:
– Start with the nucleoside name from above
and add “mono-”, “di-”, or “triphosphate”
• Adenosine Monophosphate, Cytidine Triphosphate,
Deoxythymidine Diphosphate
34
5/5/2023

35. DNA Structure
 DNA consists of two molecules that are arranged into a
ladder-like structure called a Double Helix.
 A molecule of DNA is made up of millions of tiny subunits
called Nucleotides.
 Each nucleotide consists of:
1. Phosphate group
2. Pentose sugar
3. Nitrogenous base
35
5/5/2023

36. DNA STRUCTURE
• DNA = deoxyribonucleic acid
• Stores and transmits genetic information
needed for all cell functions
• Polymer consisting of 1000’s of nucleotides
• Nucleotide =
– 5 carbon sugar deoxyribose
– Phosphate group
– 1 of 4 nitrogen bases
36
5/5/2023

37. DNA STRUCTURE
• Structure of DNA is double strand of
covalently bonded nucleotides in twisted
ladder shape = double helix
• ‘Sides’ of ladder = sugar & phosphate groups
• ‘Rungs’ of ladder = nitrogen bases
37
5/5/2023

38. DNA STRUCTURE
• DNA displays anti-
parallelism = 2 chains of
nucleotides run
opposite to each other
in a head to tail
relationship
• 3’ to 5’ direction vs. 5’
to 3’ direction
38
5/5/2023

39. DNA STRUCTURE
39
5/5/2023

40. DNA – Some Info
DNA – Deoxyribonucleic Acid
• Named for Deoxyribose – the sugar
in DNA
• Located in the nucleus of a cell.
• "Blueprint of Life." - keeps codes for
proteins
40
5/5/2023

41. DNA Shape
• Double helix – twisted ladder
• Nucleotides are building blocks
– Group of a sugar (deoxyribose), a phosphate
group, and a nitrogenous base
– 4 types of nucleotides because 4 kinds of bases
41
5/5/2023

42. DNA STRUCTURE
• Bases are paired together in specific manner = ‘Base
pairing rule’
– Adenine only pairs with Thymine
– Guanine only pairs with Cytosine
• Bases held together in ‘rungs’ by weak hydrogen bonds
• 2 hydrogen bonds between A & T
• 3 hydrogen bonds between C & G
• The structure of DNA and sequence of bases
determines its function
42
5/5/2023

43. Nucleotides Bonded Together
1. What binds in the
middle?
2. What makes up the
outside of the
ladder?
3. What atoms cause
the bonds in the
middle? 43
5/5/2023

44. Where You Correct?
1. Bases bind in the middle
2. Phosphate and Sugar make up the outside of
the ladder
3. Hydrogen creates hydrogen bonds between
the bases in the middle.
44
5/5/2023

45. VOCABULARY
• Deoxyribonucleic acid – DNA – chain of
nucleotides
• Chromosomes – DNA wrapped around
proteins called histones
• Nucleosomes – DNA and histones wrapped in
bead-like structure
• Chromatin – active form of chromosomes
45
5/5/2023

46. Nucleosome Structure Nucleosomes are composed
of DNA wrapped around histone proteins.

50. Chargaff’s rules
Base composition of various DNAs
• Adenine and thymine, and guanine and cytosine, are always found in a 1;1 ratio and that the number of pyrimidine
residues always equals the number of purine residues.
These findings are known as Chargaff’s rules: [A] = [T]; [C] = [G]; [pyrimidines] = [purines].

51. DNA STABILITY
Melting is denaturation.
Annealing is renaturation.
Hydrophobic stacking provides stability.
Intercalating agents stack between bases.
The DNA double helix is stabilized by hydrophobic interactions
resulting from the individual base pairs’ stacking on top of each
other in the nonpolar interior of the double helix

52. The hydrogen bonds, like the hydrogen bonds of proteins,
contribute somewhat to the overall stability of the double
helix but contribute greatly to the specificity for forming the
correct base pairs.
An incorrect base pair would not be able to form as many
hydrogen bonds as a correct base pair and would be much less
stable.
The hydrogen bonds of the double helix ensure that the bases
are paired correctly

53. The double helix can be denatured by heating
(melting). Denatured DNA, like denatured protein,
loses its structure, and the two strands separate.
The melting temperature (Tm) is the temperature
at which the molecule is half denatured.
Melting of DNA is accompanied by an increase in
the absorbance of UV light with a wavelength of
260 nm. This is termed hyperchromicity and can be
used to observe DNA denaturation.
DNA denaturation is reversible. When cooled
under appropriate conditions, the two strands find
each other, pair correctly, and reform the double
helix. This is termed annealing.

56. STABILITY INCREASED BY
Decreased temperature
Increased GC content (three hydrogen bonds)
Increased salt (ionic strength)

57. The stability of the double helix is affected by the GC content.
A GC base pair has three hydrogen bonds, while an AT base pair
has only two. For this reason, sequences of DNA that are GC-
rich form more stable structures than AT-rich regions.
The phosphates of the backbone, having a negative charge, tend
to repel each other. This repulsion destabilizes the DNA double
helix. High ionic strength (high salt concentration) shields the
negatively charged phosphates from each other.
This decreases the repulsion and stabilizes the double helix.

58. Intercalating agents are hydrophobic, planar structures that can
fit between the DNA base pairs in the center of the DNA
double helix.
These compounds (ethidium bromide and actinomycin D are
often-used examples) take up space in the helix and cause the
helix to unwind a little bit by increasing the pitch.
The pitch is a measure of the distance between successive base
pairs.

59. STRUCTURE OF THE DOUBLE HELIX
• THREE MAJOR FORMS
– B-DNA
– A-DNA
– Z-DNA
• B-DNA IS BIOLOGICALLY THE MOST COMMON
– RIGHT-HANDED (20 ANGSTROM (A) DIAMETER)
– COMPLEMENTARY BASE-PAIRING (WATSON-CRICK)
• A-T
• G-C

60. GEOMETRY OF B-DNA
• IDEAL B-DNA HAS 10 BASE PAIRS PER TURN
• BASE THICKNESS
• PITCH = 10 X 3.4 = 34 A PER COMPLETE TURN
• MINOR GROOVE IS NARROW
• MAJOR GROOVE IS WIDE

61. A-DNA
• RIGHT-HANDED HELIX
• WIDER AND FLATTER THAN B-DNA
• 11.6 BP PER TURN
• PITCH OF 34 A
• OBSERVED UNDER DEHYDRATING CONDITIONS
• WHEN RELATIVE HUMIDITY IS ~ 75%
– B-DNA  A-DNA (REVERSIBLE)

62. Z-DNA
• A LEFT-HANDED HELIX
• SEEN IN CONDITIONS OF HIGH SALT CONCENTRATIONS
• IN COMPLEMENTARY POLYNUCLEOTIDES WITH ALTERNATING PURINES AND
PYRIMIDINES.
• REVERSIBLE CHANGE FROM B-DNA TO Z-DNA IN LOCALIZED REGIONS MAY
ACT AS A “SWITCH” TO REGULATE GENE EXPRESSION

63. Central Dogma of Molecular Biology
• The flow of information in the cell
starts at DNA, which replicates to
form more DNA. Information is
then ‘transcribed” into RNA, and
then it is “translated” into protein.
The proteins do most of the work in
the cell.
• Information does not flow in the
other direction. This is a molecular
version of the incorrectness of
“inheritance of acquired
characteristics”. Changes in
proteins do not affect the DNA in a
systematic manner (although they
can cause random changes in DNA.
63
5/5/2023

64. DNA Replication
64
5/5/2023
Transcription - DNA  RNA
Translation - RNA  protein

65. 65
. Extension of the central dogma to include RNA-dependent synthesis
of RNA & DNA.
5/5/2023