Download MBBS (Bachelor of Medicine, Bachelor of Surgery) 1st year (First Year) Biochemistry ppt lectures Topic 18 Nucleic Acid Notes. - biochemistry notes pdf, biochemistry mbbs 1st year notes pdf, biochemistry mbbs notes pdf, biochemistry lecture notes, paramedical biochemistry notes, medical biochemistry pdf, biochemistry lecture notes 2022 ppt, biochemistry pdf.
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