Download MBBS Biochemistry PPT 18 Nucleic Acid Lecture Notes

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Nucleotide chemistry

and Functions

1

Objectives

1. What are nucleotides

2. Why are bases named so

3. What are syn and anti conformers

4. What are different tautomers

5. Why mutation is common in genes

6. Biomedical Importance of nucleotides

7. Synthetic nucleotide

8. Clinical problem and MCQ

2
A 36 years old male patient is diagnosed

with Gout. Doctor has decided to

prescribe Allopurinol.

What modifications in the generic

purine ring would help a pharmacist

to prepare Allopurinol?

3

What are nucleotides

Why are bases named so

Circumstances of discovery

Guanine:

Isolated from Guano( bird manure)

Thymine: from thymus

4
Purine and pyrimidine. The atoms are

numbered according to the international

system.

5

Tautomerism of the oxo and amino

Functional groups of purines and

pyrimidines

6
Ribonucleosides: Syn and Anti conformers

7

Ribonucleosides: Syn conformer

8
Ribonucleotides

9

10
Modification of Polynucleotides

Can generate additional structure

11

uncommon naturally occurring

pyrimidines and purines.

12
Intermediates in the catabolism of

purine

13

Caffeine, a trimethylxanthine.

Theobromine:

3,7 dimethyl xanthine

Theophyline:

1,3 dimethyl xanthine

14
Why UV light causes

mutagenesis?

Conjugate double bond

How the concentration of nucleic

acid and nucleotides are

expressed and its implication

as research tool

Absorbance at 260 nm

Purity of nucleic acid

15

Biomedical importance

1.Serve as precursor of nucleic acid

2.Principal biologic transducer of free energy

e,g AT P, GTP

3.Second messanger

cAMP, cGMP

16
cAMP and cGMP

17

4. Methyl group donor and sulfate donor

Adenosine 3' phosphate-5'

phisphosulfonate

S-Adenosylmethionine

18
5. Allosteric regulator:

e,g ATP acts as allosteric inhibitor of phosphofructokinase

6. Sugar derivatives

a. UDP glucose and galactose: Biosynthesis of glycogen,

glucosyl disaccharide, oligosaccharides of glycoprotein

and proteoglycan

b. UDP glucuronic acid : Glucuronide conjugation of

bilirubin, drugs

7. Lipid derivatives

CDP acyglycerol: participates in biosynthesis of

phosphoglyceride, shingomyelin, sphingosine

19

8. Vitamin derivatives: Nucleotides

form a portion of Coenzymes

20
Many coenzymes and related

compounds are derivatives of

Adenosine monophosphate

21

Example of coenzymes : Derivative of

ribonucleoside

22
Clinical Application:

1. Chemotherapy of cancer and AIDS

2. As suppressor of immune response

During Organ transplantation

23

Synthetice Nucleotides and

their clinical implications

24
Synthetic purine analogs

25

Synthetic pyrimidine analogs

26
chemotherapy of cancer

organ transplantation to

suppress immunologic

rejection

27

Synthetic derivatives of nucleoside

triphosphates

Incapable of release of

Terminal phosphoryl group

Used as research

tool

28
What is DNA and RNA?

Polynucleotide

29

How to represent The primary structure

of a polynucleotide

30
Summary
1. Under physiologic conditions, the amino and

oxo tautomers predominate

2. Nucleic acids contain traces of 5-methylcytosine,

5-hydroxymethylcytosine, pseudouridine (),

and N-methylated heterocycles.

3. D-ribose or 2-deoxy-D-ribose linked to N-1 of a

pyrimidine or to N-9 of a purine by a -glycosidic bond

anti conformers predominate

4. A primed numeral indicates the hydroxyl to which the

phosphoryl group of the sugars of mononucleotides

(eg, 3-GMP,5-dCMP) is attached

31

5. Additional phosphoryl groups linked to the first

by acid anhydride bonds form nucleoside

diphosphates and triphosphates.

6. Nucleoside triphosphates have high group transfer

potential and participate in covalent bond syntheses

7. The cyclic phosphodiesters cAMP and cGMP function

as intracellular second messengers.

8. Mononucleotides linked by 3 5-phosphodiester

bonds

9. When represented as pTpGpT or TGCATCA, the

5-end is at the left, and all phosphodiester bonds

are 3 5.

32
Clinical Problems and

Multiple choice questions

33

1. Which of the following statements about

,-methylene and ,-imino derivatives of purine

and pyrimidine triphosphates Is CORRECT?

a. They are potential anticancer drugs

b. They are precursors of B vitamins.

C. They readily undergo hydrolytic removal of

the terminal phosphate.

d. They can be used to implicate involvement of

Nucleotide triphosphates by effects other than

phosphoryl transfer

Ans d

34
2. Which of the following statements about nucleotide

structures is NOT CORRECT?

a. Nucleotides are polyfunctional acids.

b. Caffeine and theobromine differ structurally solely with

respect to the number of methyl groups attached to their

ring nitrogens.

c. The atoms of the purine ring portion of pyrimidines are

numbered in the same direction as those of a pyrimidine.

d. NAD+, FMN, "active methionine" and coenzyme A all

Are derivatives of ribonucleosides

e. 3,5-Cyclic AMP and GMP (cAMP and cGMP) serve as

second messengers in human biochemistry.

Ans c.

35

A 36 years old male patient is diagnosed

with Gout. Doctor has decided to

prescribe Allopurinol.

What modifications in the generic

purine ring would help a pharmacist

to prepare Allopurinol

Ans: Exchange of C and N at 7 and 8 positions

36
37

VIDEO for DNA structure

38
Nucliec acid stucture and Function

Objectives

1. Functions of nucleic acid

2. What are the different forms of DNA

3. What are complementary pairs and why

4. Why there are specific number of hydrogen

bonds

5. Why DNA is more stable-

6. Chargaffs rule

7. Watson Crick model

8. Tm

Nucleoprotein

39

Functions of nucleic acid

The main functions is to store and transfer genetic information.

The deoxyribonucleic acid is the storage place for

genetic information in the cell.

The function of the nitrogenous base sequences in the

DNA backbone determines the proteins being synthesized

DNA controls the synthesis of RNA in the cell.

The genetic information is transmitted from DNA

to the protein synthesizers in the cell.

The function of the double helix of the DNA is that

no disorders occur in the genetic information if it is lost or damaged.

40
Functions of nucleic acid contd

RNA directs the production of new protein by

transmitting genetic information to the protein

building structures

m-RNA takes genetic message from RNA.

t-RNA transfers activated amino acid, to the site of

protein synthesis.

r-RNA are mostly present in the ribosomes, and

responsible for stability of m-RNA.

41

base pairing between complementary

deoxynucleotides: formation of hydrogen bonds

42
43

Why RNA is more susceptible to

degradation

Hydrolysis of RNA under alkaline

conditions

44
Hydrolysis of RNA

45

46
Based on data collected from DNAs of a great many different species,

Chargaff concluded:

1. The base composition of DNA generally varies

from one species to another.

2. DNA specimens isolated from different tissues of

the same species have the same base composition.

3. The base composition of DNA in a given species

does not change with an organism's age, nutritional

state, or changing environment.

4. In all cellular DNAs, regardless of the species,

the number of adenosine residues is equal to the

number of thymidine residues (that is, A T),and

the number of guanosine residues is equal to the

number of cytidine residues (G C).

47

The sum of the purine

residues equals the sum of

the pyrimidine

residues; that is, A+G=T+C

These quantitative

relationships, sometimes

called "Chargaff's rules,"

48
The Watson and Crick

model of the double-

helical structure of the B

form of DNA

49

Copyright to Harper

Structures of different forms of DNA

Different forms: A-E &Z

A form: DNA-RNA hybrids and

RNA-RNA double stranded regions

Z form: alternating purines and pyrimidi

Copyright to lippincott

50
Melting temperature of DNA molecules

with different nucleotide composition

Adopted from lippincott

51

For sequences less than 14 nucleotides the formula is:

Tm= (wA+xT) * 2 + (yG+zC) * 4

where w,x,y,z are the number of the bases A,T,G,C in the

sequence, respectively.

For sequences longer than 13 nucleotides, the equation used is

Tm= 64.9 +41*(yG+zC-16.4)/(wA+xT+yG+zC)

Both equations assume that the annealing occurs under

the standard conditions of 50 nM primer, 50 mM Na+, and pH 7.0.

52
Base composition

Salt concentration:

10 fold monovalent cation concentration

increase=Tm?

Organic solvent:

Fomamide addition= Tm ?

Factors influencing Tm

53

Importance of melting temperature
Video on PCR

54
Annealing temperature

55

RNA

56

Copyright to Harper
Secondary structure of RNA

57

Copyright to Harper

Cap structure attached to

eukaryotic mRNA

58

Copyright to Harper
Components of mammalian

ribosome

59

Copyright to Harper

A subset of small RNA (20-1000

nucleotides)

Involved in rRNA and mRNA processing

and gene regulation

U1,U2,U4,U5,U6---involved in intron

removal

U7 ---in production of correct 3' end of

histone mRNA

Small Nuclear RNA (snRNA)

60
tRNA secondary

structure

Copyright to lippincott

61

Tertiary structure of tRNA

Copyright to lippincott

62
DNA consists of four bases--A, G, C, and T--that are held in linear

array by phosphodiester bonds through the 3 and 5 positions of

adjacent deoxyribose moieties.

DNA is organized into two strands by the pairing of bases A to T

and G to C on complementary strands. These strands form

adouble helix around a central axis.

The 3 ? 109 bp of DNA in humans are organized into the haploid

complement of 23 chromosomes. The exact sequence of these 3

billion nucleotides defines the uniqueness of each individual

RNA exists in several different single-stranded structures, most of

which are directly or indirectly involved in protein synthesis or its

regulation. The linear array of nucleotides in RNA consists of A, G,

C, and U, and the sugar moiety is ribose.

The major forms of RNA include mRNA, rRNA, tRNA, and snRNAs

and regulatory ncRNAs.

Certain RNA molecules act as catalysts (ribozymes)--e.g,.the

large rRNA component performs the peptidyl transferase activity.

Summary

63

While studying the structure of a small gene that was

recently sequenced during the Human

GenomeProject, an investigator notices that one

strand of the DNA molecule contains 20 As, 25 Gs, 30

Cs, and 22 Ts . How many of each base is found in the

complete double-stranded molecule?

A. A = 40, G = 50, C = 60, T = 44.

B. A = 45, G = 45, C = 52, T = 52.

C. A = 50, G = 47, C = 50, T = 47.

D. A = 42, G = 55, C = 55, T = 42

E. A = 44, G = 60, C = 50, T = 40.

MCQ1

64
Any proteins that are structurally associated

with nucleic acids, either DNA or RNA

Nucleoproteins tend to be positively charged,

facilitating interaction with the negatively

charged nucleic acid chains.

A deoxyribonucleoprotein (DNP) is a

complex of DNA and protein.

examples are nucleosomes-DNA is wrapped around

clusters of eight histone proteins to form chromatin

Function : regulating DNA replication and

transcription.

involved in homologous recombination, a process

for repairing DNA

Nucleoprotein

65

Ribonucleoproteins: a complex

of ribonucleic acid and RNA-

binding protein

Examples: ribosome, the

enzyme telomerase, RNase P, hnRNP and

small nuclear RNPs

Functions: DNA replication, regulating

gene expression and regulating the

metabolism of RNA

66
structure of

nucleosomes.

Copyright to lippincott

67

Structural organization of euk

Copyri a

ght ry

to lippinc o

ott tic DNA

68
Compaction of DNA

in a eukaryotic chromosome

69

Copyright to Lehninger

70

Copyright to Lehninger
71

Video on DNA Packaging

72
Euchromatin: Transcriptional y

active chromatin, stains less

densely

Heterochromatin:

Transcriptional y inactive

chromatin, densely packed

during interphase

Euchromatin and Heterochromatin

73

Constitutive : Found near

centromere and telomere

Facultative : One X chromosome

in mammalian female

Hetero Chromatin:

74
Roles of modified histones

Modification

Effect

Acetylation of histones H3

gene transcription

and H4

Acetylation of core histones

Chromosomal assembly during

DNA replication.

Phosphorylation of histone H1 condensation of chromosomes

during the replication cycle

ADP-ribosylation of histones

DNA repair

Methylation of histones

activation and repression of gene

transcription.

Monoubiquitylation

gene activation, repression, and

heterochromatic gene silencing

Sumoylation of histones

transcription repression

(SUMO; small ubiquitin-related

75

modifier)

The relationship between chromosomal DNA and mRNA

76
Sequence classes of genome

Unique sequence DNA: single copy gene that code for protein

>50%

Repetitive sequence DNA: include sequences that vary in

copy number from 2 to 10^7

30%

Highly repetetive: 5-500 base pairs length repeated

1-10 million copies per haploid
Clustered

Transcriptionally inactive
Structural role

77

Moderately repetitive DNA sequences

< 1 million copies per haploid genome

Long/sh Interspersed repeats

Transcribed by RNA poymerase II

LINES (Long interspersed repeat sequences)

20,000-50,000 copies of 6-7 kbp

SINES (Short interspersed repeat sequences)

70-300 bp > 100,000 copies per genome

e,g Alu family

Both types appear to be Retroposons:

Disastrous consequence of transposition : Neurofibromatos7i8s
Microsatellite repeat sequences

2-6 bp sequences repeated upto 50 times

Most common dinucleotide repeats

AC repeat sequences occur at 50,000-100,000 locations

Useful in constructing genetic map

Useful to screen large number of family members rapidly

Trinucleotide repeat sequences

CGG---Fragile X syndrome

CAG---Huntington' Chorea

CTG--myotonic dystrophy

CAG--Spinobulbar muscular atrophy

Kennedy disease

79

Major Features of Human Mitochondrial

DNA

? Is circular, double-stranded,

? Contains 16,569 bp

? Encodes 13 protein subunits of the respiratory chain

Seven subunits of NADH dehydrogenase (complex I)

Cytochrome b of complex III

Three subunits of cytochrome oxidase (complex IV)

Two subunits of ATP synthase

? Encodes large (16S) and small (12S) mt ribosomal RNAs

? Encodes 22 mt tRNA molecules

? Genetic code differs slightly from the standard code

UGA (standard stop codon) is read as Trp

AGA and AGG (standard codons for Arg) are read as

stop codons

? Contains very few untranslated sequences

? High mutation rate (5-10 times that of nuclear DNA)

? Comparisons of mtDNA sequences provide evidence about

evolutionary origins of primates and other species

80
Transposon

Common in all types of organisms are short pieces of

DNA (usually less than 10Kb in length) that

can move from one position to another

in the chromosome of a cell.

Retroposon:

Eukaryotic genomes contain a special type of

Transposable elements, called retroposons,

which use reverse transcriptase

to transpose through an RNA intermediate.

81

DNA in eukaryotic cells is associated with a

variety of proteins, resulting in a structure called

chromatin.

Much of the DNA is associated with histone

proteins to form a structure called the

nucleosome. Nucleosomes are composed of an

octamer of histones around which about 150 bp

of DNA is wrapped.

Histones are subject to an extensive array of

dynamic covalent modifications that have

important regulatory consequences.

Nucleosomes and higher-order structures

formed from them serve to compact the DNA.

Summary

82
DNA in transcriptionally active regions is

relatively more sensitive to nuclease attack in

vitro; some regions, so-called hypersensitive

sites are exceptionally sensitive and are often

found to contain transcription control sites.

Highly transcriptionally active DNA (genes) is

often clustered in regions of each chromosome.

Within these regions, genes may be separated by

inactive DNA in nucleosomal structures.

After transcription, during RNA processing,

introns are removed and the exons are ligated

together to form the mature mRNA that appears

in the cytoplasm; this process is termed RNA

Sus pm

licinm

g.ary

83

Epigenetics

Information that is passed from one genetation to

the next ? to daughter cells at cell divisions or from

parent to offspring ?but is not encoded on

DNA sequences is referred to as epigenetic

information.

84
1. DNA Methylation

A covalent modification of nucleotide cytosine

at 5' position

By the enzyme DNA methytransferase 1

DNA methylation is the most useful epigenetic

marker for human diseases studies because it is

stable over a period of decades and is present in

archival specimen including paraffin blcks

Epigenetic information takes 3

forms

85

2. Post translational modifications of

nucleosomal histones

ATP independent process involving acetylation,

phosphorylation, ubiquitylation

Post translational modifications act through

recruitment of transcription factor, activation of

transcriptional enhancers, recruitment of

repressive proteins and interaction with DNA

methylation machinery

Second form of epigenetic

information

86
Higher order Chromatin structure

Example of which include loop organization

revealed by chromosome conformation capture

method

Large organized chromatin lysin modifications

Nuclear lamina associated domain

Third form of Epigenetic

information

87

Diet

Deprivation of methionine and folate lead to

liver and colon cancer

Folate deficieny--- impaired biosynthesis of active

precursor for DNA methylation, S adenosyl

methionine---Impairs synthesis of thymidylate

Exposure to nicotine causes substantial epigenetic

changes in smokers

Modulation of Epigenetic

information

88
Cancer

DNA methyltransferases, TET demethylase,

MBD ( methyl CpG binding domain) family of

methylation recognition gene are mutated in

lymphoma and colon cancer

Variability in DNA methylation was markedly

increased in the samples from women in whom

cancer developed years later

Aging

Genome wide hypomethylation in blood is

associated with breast cancer years later

89

The interconnecting bonds that connecting

the nucleotides of

RNA and DNA are termed:

A. N-glycosidic bonds

B. 3-5-phosphodiester linkages

C. Phosphomonoesters

D. -2-phosphodiester linkages

E. Peptide nucleic acid bonds

MCQ1

90
Which of the forces or interactions listed

below play the predominant role in driving

RNA secondary and tertiary structure

formation?

A. Hydrophilic repulsion

B. Formation of complementary base pair

regions

C. Hydrophobic interaction

D. van der Waals interactions

E. Salt bridge formation

MCQ2

91

Which entry below correctly describes the

approximate number of bp of DNA______,

which is separated into _____chromosomes

in atypical diploid human cell in a

nonreplicating state?

A. 64 billion, 23

B. 6.4 trillion, 46

C. 23 billion, 64

D. 64 billion, 46

E. 6.4 billion, 46

MCQ3

92
All but one of the following histones are

found located within the superhelix formed

between DNA and the histone octamer; this

histone is

A. Histone H2B

B. Histone H3

C. Histone H1

D. Histone H3

E. Hisone H4

MCQ4

93

Chromatin can be broadly defined as active

and repressed; a subclass of chromatin that

is specifically inactivated at certain times

within an organism's life and/or in particular

sets of differentiated cells is termed

A. Constitutive euchromatin

B. Facultative heterochromatin

C. Euchromatin

D. Constitutive heterochromatin

MCQ5

94

This post was last modified on 05 April 2022