Integrated Basic Medical Sciences

General Concepts
Biochemistry

Structure of Genetic Materials

2017

Dr. Jayendra Bajracharya

NAIHS-COM
 Sessions

Three sessions

Structures of nitrogenous bases,

nucleosides, nucleotides, and nucleic acids

Structure of DNA

Organization of DNA into chromosomes

 Session - 1

Structures of nitrogenous bases,

nucleosides, nucleotides, and nucleic acids
 Objectives
At the end of this session, I should be able to

List two nucleic acids present in living organisms

List three components of nucleic acids

Define nucleobase

List the nucleobases

Define nucleoside

Define nucleotide

Define nucleic acid

 Nucleic Acids

Two types in living organisms

Deoxyribonucleic acid or DNA

Ribonucleic acid or RNA

Components of Nucleic
Acids
Three components

Nucleobase

Pentose sugar

Ribose or deoxyribose

Phosphate
 Nucleobase

Nitrogen-containing heterocyclic compound

2 types

Pyrimidines

Purines
 Pyrimidines
Three pyrimidines

Cytosine

2-oxy 4-aminopyrimidine

Uracil

2,4-dixoypyrimidine

Thymine

2,4-dioxy 5-methylpyrimidine
Draw 2-oxy 4-aminopyrimidine (cytosine).
Draw 2-oxy 4-aminopyrimidine (cytosine).
Draw 2,4-dioxypyrimidine (uracil).
Draw 2,4-dioxypyrimidine (uracil).
Draw 2,4-dioxy 5-methylpyrimidine (thymine).
Draw 2,4-dioxy 5-methylpyrimidine (thymine).
 Purines

Two purines

Adenine

6-aminopurine

Guanine

2-amino 6-oxypurine
Draw 6-aminopurine (adenine).
Draw 6-aminopurine (adenine).
Draw 2-amino, 6-oxypurine (guanine).
Draw 2-amino, 6-oxypurine (guanine).
 Pentose Sugar
In RNA

β-D-ribose

In DNA

β-D-2-deoxyribose

Carbon atoms numbered from 1’ to 5’

Phosphate
 Nucleoside
Nucleobase + Sugar

N-glyosidic bond

C1' of the ribose or deoxyribose sugar

Nitrogen of nucleobase

N1 of pyrimidine

N9 of purine
 Nucleosides

Base Ribonucleoside Deoxyribonucleoside

Adenine Adenosine Deoxyadenosine

Guanine Guanosine Deoxyguanosine

Cytosine Cytidine Deoxycytidine

Uracil Uridine

Thymine Deoxythymidine or Thymidine

 Nucleotide
Nucleobase + Sugar + Phosphate

Phosphoester bond

C₅' of the ribose or deoxyribose sugar

Oxygen atom of phosphate group

 Monophosphate Nucleotides

Base Ribonucleotide Deoxyribonucleotide

Adenine Adenylate (AMP) Deoxyadenylate (dAMP)

Guanine Guanylate (GMP) Deoxyguanylate (dGMP)

Cytosine Cytidylate (CMP) Deoxycytidylate (dCMP)

Uracil Uridylate (UMP)

Deoxythymidylate
Thymine
or Thymidylate (dTMP or TMP)
 Diphosphate and Triphosphate
Nucleotides

Nucleotides with 2 or 3 phosphates

Substrates for monophosphate nucleotides of

DNA/RNA

Phosphoanhydride bond

Oxygen atom of one phosphate group

Oxygen atom of another phosphate group

 Diphosphate and Triphosphate Nucleotides

Base Ribonucleotide Deoxyribonucleotide

Adenine ADP ATP dADP dATP

Guanine GDP GTP dGDP dGTP

Cytosine CDP CTP dCDP dCTP

Uracil UDP UTP

dTTP or
Thymine dTDP or TDP
TTP
 Nucleic Acids
Polymeric strands of monophosphate nucleotides

3'-5' phosphodiester bond

A phosphoester bond formed between

OH group at 3' carbon of sugar of a preceding

nucleotide

Phosphate group at 5' carbon of sugar of next

nucleotide (phosphoester bond already present
in this nucleotide)
 Nucleic Acids
Polarity in a nucleic acid strand

Distinct 5' and 3' ends

Phosphate group at 5' end

Hydroxyl group at 3' end

 Nucleic Acids
Sequence of nucleobases in a nucleic acid strand

Always written in the 5' to 3' direction

5'-CAG-3' or simply, CAG

Position of phosphates shown as in pCpApG

DNA sequence represented as in dCdAdG

If written in 3' to 5' direction, directionality must

be specified as in 3'-CUG-5'
Sugar-phosphate
backbone
Session - 2

Structure of DNA
 Objectives
At the end of this session, I should be able
to

List six features of DNA double helix

Explain Chargaff's rules

List factors that stabilize DNA double

helix
Left-handed Double Helix Right-handed Double Helix
Left-handed Double Helix Right-handed Double Helix
 DNA Double Helix

Two polynucleotide strands

Right-handed or clockwise double helix

Sugar-phosphate backbone in exterior

and nucleobases in interior

Antiparallel
 DNA Double Helix
Two polynucleotide strands

Complementary base-pairing by
hydrogen bonds

2 hydrogen bonds between A and T

3 hydrogen bonds between G and C

 DNA Double Helix
Two polynucleotide strands

Complementary base pairing between

two strands by hydrogen bonds

2 hydrogen bonds between A and T

3 hydrogen bonds between G and C

 Chargaff's Rules
In double-stranded DNA

Amount of A = amount of T

Amount of G = amount of C

Total purines = total pyrimidines

 DNA Double Helix
Two polynucleotide strands

Strand-strand distance (helix diameter) - 2 nm

Base-base distance on a strand - 0.34 nm

One complete turn of helix - 3.4 nm

10 bases per turn

 DNA Double Helix

Two polynucleotide strands

Sugar -phosphate backbones not

equally spaced

Major groove - 2.2 nm

Minor groove - 1.2 nm

Stability of DNA Double Helix
Fine balance between three factors

Hydrogen bonds between bases

Hydrogen bonds between bases and surrounding

water molecules

Base-stacking interactions between adjacent

bases

Hydrophobic interactions

van der Waals interactions

 Session - 3

Organization of DNA into Chromosomes or

other Superhelical Structures
 Session - 3A

Organizations of Bacterial Chromosome

and Plasmid DNA
 Objectives

At the end of this session, I should be able

to

Explain the organization of bacterial

chromosome

Explain the organization of plasmid

DNA
 E. coli DNA

Length of E. coli DNA strand = 1 mm

Size of E. coli cell = 2 μm X 0.5 μm

Compaction of DNA required

Single circular chromosome with

supercoiled loops
Bacterial Chromosome
 Session - 3B

Organization of Eukaryotic Chromosomes

 Objectives
At the end of this session, I should be able to

Define chromatin

Define nucleosome

Define chromatosome

Define scaffold loop

Define chromatid

Define metaphasic chromosome

Human Chromosomes
 Chromatin
DNA + proteins associated with DNA = chromatin

Proteins associated with DNA

Histones

Positively charged

Rich in lysine and arginine

Non-histone proteins
 Nucleosome
Basic packaging unit of chromatin

Histone octamer

Aggregation of two copies each of

histones H2A, H2B, H3, and H4

146 bp of DNA double helix wound

around the outside of histone octamer
10nm Chromatin Fiber
Polynucleosomes

“Beads on a string”

Thickness of about 10 nm
 Chromatosome

Nucleosome + 20-90 bp linker DNA +

H1 histone
H1
30nm Chromatin Fiber

Chromatosomes packaged into a

solenoid-like structure

Thickness of 30 nm

6-7 chromatosomes per turn

 Scaffold Loop

30 nm chromatin fiber forms loops on

scaffold proteins

Thickness of 300 nm
 Chromatids
Further condensation of scaffold
loops

Thickness of 700 nm
 Metaphasic
Chromosome
A pair of chromatids

Thickness of 1400 nm
 Session - 3C

DNA Supercoiling and Topoisomerases

 Objectives
At the end of this session, I should be able to

Define DNA supercoiling.

List three topological states of DNA

Define topoisomerase

List the different types of topoisomerases

List the inhibitors of bacterial and eukaryotic

topoisomerases
 Supercoiling of DNA
Coiling of a coil

DNA supercoiling

DNA coil

DNA double helix

DNA supercoils

Further coiling of the axis of DNA double helix upon itself

Manifestation of structural strain

 Topological States
ofDNA
Three topological states of DNA

Relaxed DNA

No supercoils

Positively supercoiled DNA

Supercoiling that leads to overwound DNA

Negatively supercoiled DNA

Supercoiling that leads to underwound DNA

 Topoisomerases
Enzymes that change the amount of supercoiling in DNA molecules

Types

Type I

Breaks one of the two DNA strands, passes the unbroken strand through the
break, and ligates the broken ends

Examples - Topoisomerase I and III

Type II

Breaks both DNA strands, passes a supercoil through the break, and ligates
the broken ends

Examples - Topoisomerase II and IV

Different versions in bacteria and eukaryotes

Topoisomerases Type I

Topoisomerases I and III

Topoisomerases Type II

Topoisomerases II and IV
 Topoisomerase IV

Catenated chromosomes Decatenated chromosomes

 Bacterial Topoisomerases
Class Function

Topoisomerase I Type I Relaxes negative supercoils

Topoisomerase II Introduces negative

Type II
(DNA gyrase)* supercoils

Specialized functions in DNA

Topoisomerase III Type I
repair and replication

Decatenation of replicated
Topoisomerase IV* Type II
chromosomes

*Targeted by antibiotics such as ciprofloxacin

 Eukaryotic Topoisomerases
Class Function

Relaxes negative supercoils,

Topoisomerase I* Type I
especially during DNA replication

Topoisomerase IIα** Type II Relaxes positive or negative

supercoils; functions in chromatin
condensation, replication, and
Topoisomerase IIβ** Type II transcription

Specialized functions in DNA

Topoisomerase III Type I
repair and replication

*Targeted by anticancer drugs such as topotecan and irinotecan

**Targeted by anticancer drugs such as doxorubicin and etoposide
Thank you!