BIOC1600

DNA and Central Dogma

 Learning outcomes
• List the structural components of nucleic acids: nitrogenous base,
pentose, and phosphate
• Describe the features of the DNA double helix
• Outline the flow of genetic information during gene expression
• Define the term transcription and translation and relate these
processes to the flow of genetic information
• Use the codon table to predict the amino acid sequence encoded
by a template DNA or mRNA sequence
• Relate the effects of mutations on protein structures and functions
DNA and RNA as the hereditary material
• Griffith’s experiment (1928):
– a “transforming principle” from one strain of bacteria can
cause a heritable change in another strain of cells

• Avery, MacLeod, and McCarty’s experiment (1944):

– DNA is the transforming principle

• Hershey-Chase experiment (1952):

– Using bacteriophage, shown that DNA is the genetic
material
• Fraenkel-Conrat and Singer’s experiment on tobacco
mosaic virus (TMV) showed that RNA can serve as
the genetic material
 Both DNA and RNA can serve as
hereditary material
• DNA:
– Double-stranded (most organism)
– Single-stranded (in some viral genomes e.g. M13)
• RNA:
– In viruses
– Double-stranded (e.g. rotavirus)
– Single-stranded (e.g. SARS-CoV-2, influenza viruses)
 DNA as the hereditary material

Nuclear DNA
(inherited from both
parents)

(From mother only)

DNA present in both nucleus and mitochondria

www.nature.com
Maternal inheritance of mitochondrial DNA

male

female

Unaffected

Affected

• Offspring of affected
females are also
affected.
• Offspring of affected
males are not
affected.

Mitochondrial DNA is used in forensics

Nucleic acids are polymers of nucleotides
DNA RNA

Nucleotide (base + sugar +

phosphate) is the repeating unit
in nucleic acid

Nucleotides are joined together

by phosphodiester bonds

DNA = deoxyribonucleic acid

RNA = ribonucleic acid
Repeating structure and asymmetric
5′ and 3′ end in nucleic acid
Components of nucleotides

Nucleotide is the repeating

unit in nucleic acid
 Components of nucleotides
• Pentose sugars:

(in RNA) (in DNA)

• Phosphate:
 Components of nucleotides
• Nitrogenous bases:

N-9 of a purine and N-1 of

a pyrimidine are attached
to C-1 of sugar
5′ End

3′ End
 Primary structure of nucleic acid
• A DNA strand has directionality: 5′ end and 3′ end

= pApCpG = 5′ ACG 3′

Write nucleic acid

sequences in 5′ to 3′
direction
 Helical nature of DNA

X-ray diffraction data

suggested a helical structure of
DNA
For more interpretation:
https://physicsopenlab.org/2019/10/01/
double-helix-optical-diffraction-pattern/

Photo 51: X-ray diffraction pattern of a DNA fibre

(Rosalind Franklin and Ray Gosling, 1952)
 Structure of DNA: Chargaff’s rule
• 1950: Chargaff found that in DNA from many different
species:
% thymine = % adenine
% cytosine = % guanine

Erwin Chargaff
A/T = 1 (1905-2002)

G/C = 1
 Structure of DNA: double helix
• 1953 - Francis Crick and James Watson used model
building and combined all the knowledge of DNA to
determine its structure.

Watson and Crick, 1953

 Nucleic acids are polymers of nucleotides

DNA are double-

stranded

RNA are single-

stranded

Nucleotides are joined

together by
phosphodiester bonds

Repeating structure
and asymmetric 5′ and
3′ end in nucleic acid
 Base pairing in DNA

Purines pairs with pyrimidines via hydrogen bonds

Structure of DNA: double helix
Key features of DNA
• DNA is double-stranded
• Complementary base pairing:
adenine pairs with thymine;
cytosine pairs with guanine –
basis of DNA replication and
gene expression.
• Every base pair consists of one
purine and one pyrimidine.
• Antiparallel nature of the
strands: 5′ to 3′ for one strand
and 3′ to 5′ for the
complementary strand
 Key features of DNA
• right-handed double helix,
uniform diameter
• approximately 10 bases per
turn (B-DNA)
• complementary base pairing
and hydrophobic interaction
between adjacent bases
(base stacking) stabilize DNA
• bases are exposed in the
major and minor grooves
 Base pairs in DNA can interact with
other molecules
H-bond to Hydrophobic
other interaction with
molecules other molecules

H-bond acceptor
H-bond donor
Methyl group
Hydrogen atom

Pattern of potential H-bond donor and acceptors in major and minor groove of DNA
 Three forms of DNA

A form B form Z form

Nelson and Cox (2017) Lehninger Principles of Biochemistry

 Glycosidic bond conformation in DNA

4
6 5 3
7 5 1
8 6 2
4 2 1
9 3

Glycosidic
bond

anti conformation is generally favoured because of less steric hindrance

Sugar puckering in DNA

C2′-endo: C2′ lies above the

sugar ring, towards the base and
C5′.

https://x3dna.org/
Sugar puckering in DNA

C3′-endo: C3′ lies above the sugar

ring, towards the base and C5′.

C3′-endo pucker produces a shorter

phosphate-phosphate distance in
the backbone and a more compact
helix.
https://x3dna.org/
 Other functions of nucleic acids
• Energy currency e.g. ATP
• As messenger e.g. cAMP
• RNA can act as enzymes (ribozymes) – e.g. rRNA in protein
synthesis
• Single-stranded RNA/DNA can fold into distinct 3-D structures
(Aptamers) for molecular recognition

https://bonndoc.ulb.uni-bonn.de/
 Quadruplex DNA
• G-rich region
• 4 stranded structure, found in DNA (telomere and
promoter region) and RNA

G-quadruplex structure may

play important role in
maintaining telomere and play
regulatory roles in
transcriptional and
translational control
 DNA supercoiling
• Supercoiling: the coiling of the helical axis upon itself,
giving rise to the higher order structure.
• DNA in prokaryotes and eukaryotes is negatively
supercoiled
• Negative supercoiling allows packaging of DNA; favours
strand separation during replication and transcription

Brooker RJ (2012) Genetics: analysis & principles

Supercoiling of bacterial chromosome 36

Eukaryotic chromosome

• Linear DNA wraps

around histones to
form nucleosomes
• Nucleosomes further
packed into higher
order structures

37
Eukaryotic chromosome

DNA wraps around

histone core proteins in a
left-handed (counter
clockwise) direction to
form a nucleosome. DNA
is negatively supercoiled.

38
 DNA Supercoiling

↔ Negative

Toroidal (solenoidal) Interwound

supercoil supercoil

40
Linking number

Linking number is the number of

times the DNA strands wrap around
each other 41
 DNA topology
Lk = Tw + Wr
• Lk = linking number, the number of times one strand of
DNA wraps round the other
• Tw = twist, number of DNA turns
• Wr = writhe, number of supercoils

Linking number is unchanged for closed circular duplex DNA

or linear duplex DNA when the ends are not free to rotate

42
 DNA topology

Lk = Tw + Wr

Negatively supercoiled DNA:

• Can lead to localized strand separation
• Facilitates replication and transcription
• More compact 43
 Build up of positive superhelical turns
ahead of a moving replication fork

Negative Positive
Alberts B et al (2015) Molecular Biology of the Cell, 6th ed 44
 DNA topoisomerases
• Topoisomerases are enzymes that regulate DNA
supercoiling by catalysing winding and unwinding of
DNA strands.
– Remove DNA supercoils
– Unwind DNA for transcription and DNA replication
– Chromosome condensation
– Recombination, chromosome segregation
– etc.
• Class I topoisomerases
• Class II topoisomerases
45
 Central dogma

The central dogma of molecular biology: information flows from DNA to

RNA to protein.
 DNA replication
• Hydrogen bonds that hold the base pairs together are broken and
the helix is unwound
• Bases are added using the rules of complementary base pairing.
Each of the parental strand serves as a template for synthesis of a
new complementary strand
• DNA replication is highly accurate
 DNA replication

Primer strand

Template strand

DNA synthesis:
• A primer strand and a template strand are required.
• Complementary base pairing between primer and the template DNA.
• Incoming dNTPs are complementary to the template strand.
• DNA polymerase adds deoxyribonucleotides to the free 3′-OH end of the
primer strand. The newly synthesized strand grows in the 5′ to 3′
direction.
 Central dogma

The central dogma of molecular biology: information flows from DNA to

RNA to protein.
Transcription is the synthesis of RNA from
a DNA template
• RNA strand extends from
5′ to 3′ end.
• Template DNA is copied
from 3′ to 5′.
• RNA polymerase adds
ribonucleotides to 3′-OH
end, following Watson-
Crick base pairing.
• The RNA strand is
complementary and
antiparallel to the DNA
template.
• U instead of T is used.
 Gene expression in eukaryotes

RNA polymerase read the template

DNA strand and synthesizes an RNA
strand according to complementary
base pairing

In eukaryotes, introns are removed

and exons spliced together to produce
mRNA for protein synthesis.

In the cytoplasm, ribosome read the

mRNA sequence and direct the
synthesis of proteins

Gene expression: converting the genetic information of

DNA into the sequence of a protein
 Central dogma

The central dogma of molecular biology: information flows from DNA to

RNA to protein.
Translation
• Codon is made up of 3 bases
• Codons are non-overlapping
• Each codon specify one
amino acid
• Complementary base pairing
between codon on mRNA
and anticodon on tRNA

Ribosome reads the mRNA sequence

and translates it into a chain of amino
acids to make a protein.

Various antibiotics target protein

synthesis in bacteria.
Structure of tRNA
 Genetic code is nearly universal

• Universal genetic code Vertebrate mitochondrial genetic code

• Triplet of base sequences in mRNA
• AUG is also the start codon
Mutations: changes in DNA sequences
Deamination of nucleotide bases
HNO2
Which base will it pair with?

HNO2

HNO2
Deaminated bases could cause mutations
by mispairing
U
A
U
A
T
C U A
G G
C
G
C
G
C
G
Replication errors can cause insertion or
deletion of nucleotides
Phenotypic effects of point mutations
• Base substitutions:

Different Premature Same

amino acid termination amino acid
 Mutations – indels
• Insertion or deletion of one or more bases
• Result in frameshift mutations: change in amino acids
sequence after point of insertion or deletion

Amino acids codec from

sequences after the
mutation are different from
the original. Mutant protein
will be non-functional.
Frameshift mutations can alter protein
function

Frame-shift mutation
Phenylketonuria due to deficiency in PAH
Aspartame (E951) – a dipeptide of aspartic
acid and phenylalanine

Phenylalanine
hydroxylase (PAH)

Blocked in
phenylketonuria
Genetic variations - Pharmacogenetics

Genetic variations to differentiate between drug

responders and drug non-responders and those who
may have adverse drug reactions
 Genetic variations and differences in drug response

• Genetic polymorphisms in CYP2D6 contribute to differences in drug response

• Increased CYP2D6 function due to duplication of CYP2D6 genes
• Decreased CYP2D6 function due to mutations or gene deletion

• Poor efficacy with poor metabolizer phenotype

• Morphine toxicity risk with ultra-rapid metabolizer phenotype
Polymorphism in CYP2D6 and correlation between genotypes
and drug-metabolizing abilities.

May result in circulating drug levels that are either too high or
too low to achieve the normal therapeutic response.
 DNA fingerprinting

Colin Pitchfork, first person Professor Sir Alec Jeffreys developed

convicted for murder based on DNA fingerprinting in 1984
DNA fingerprinting in 1987
Classes of human genetic variants.

Nature Reviews Genetics

 DNA profiling uses many different
short tandem repeat (STR) markers

78
Application of STR polymorphism: paternity test
Chromosome no. of
STR locus location Repeat sequence repeats

D3S1358 3 [TCTG][TCTA] 9-20

VWA 12p12-pter [TCTG][TCTA] 10-24
FGA 4q28 CTTT 15-51.2
D8S1179 8 [TCTA][TCTG] 8-19
D21S11 21q21 [TCTA][TCTG] 24-38
D18S51 18q21.3 AGAA 7-27
D5S818 5q21-31 AGAT 7-16
D13S317 13q22-31 TATC 5-15
D7S820 7q11.21-22 GATA 6-15

Some short tandem repeat loci used in forensics

Polymerase chain reaction (PCR) to amply a DNA
fragment

Steps in a PCR cycle

https://www.thermofisher.com
 Polymerase chain reaction (PCR) to amply a DNA
fragment

Products of earlier cycle serve

as templates for later cycles
Molecular Biology of the Cell (© Garland Science 2008)
Animation
 PCR in forensic science
• PCR can amplify DNA from a very small amount
template DNA
• PCR can detect the presence of specific DNA
sequences
Genetic variation: DNA fingerprinting

PCR primers

Alleles with different

number of copies of the
repeat element

Separate PCR
products on gel
 Learning outcomes
• List the structural components of nucleic acids: nitrogenous base,
pentose, and phosphate
• Describe the features of the DNA double helix
• Outline the flow of genetic information during gene expression
• Define the term transcription and translation and relate these
processes to the flow of genetic information
• Use the codon table to predict the amino acid sequence encoded
by a template DNA or mRNA sequence
• Relate the effects of mutations on protein structures and functions
 Readings
• Berg JM et al (2012) Biochemistry 7th ed. WH
Freeman. Chapter 4
• Nelson DL, and Cox MM (2017) Lehninger
Principles of Biochemistry, 7th ed. WH Freeman.
Chapter 8
• Pierce BA (2020) Genetics: A Conceptual
Approach, 7th ed. Macmillan. Chapter 10