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MOLECULAR
GENETICS

BIO149

Prof. Ureah Thea A. Sevilla

DNA Deoxribonucleic Acid

DNA makes use of four of the five bases

Two

pyrimidines: thymine and cytosine

Two purines: adenine and guanine

The nucleotides are linked together by 35phosphodiester bonds

DNA consists of two polynucleotide strands

The

two strands interact through the base-pairing of

Adenine with Thymine bases and Guanine and Cytosine
bases.

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Deoxyadenosine triphosphate
Adenine (A)

Phosphate groups

2-deoxyribose
Fig. 13-4a, p. 206

Deoxyguanosine triphosphate
Guanine (G)

Phosphate groups

2-deoxyribose
Fig. 13-4a, p. 206

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Deoxythymidine triphosphate
Thymine (T)

Phosphate groups

2-deoxyribose
Fig. 13-4a, p. 206

Deoxycytidine triphosphate
Cytosine (C)

Phosphate groups

2-deoxyribose
Fig. 13-4a, p. 206

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Polynucleotides and Nucleic Acids

Nucleic acids are formed through linkage of one

nucleotide with another by forming a covalent bond
called 3-5-phosphodiester bond forming long
polynucleotide chain.

The Phosphodiester Bond

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Linkage of one nucleotide

with another forms a bond
specifically called
3-5 phosphodiester bond
The next nucleotide to be
attached to the growing
polynucleotide chain is
always added at the 3end.

5 3 Polynucleotide Chain

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Double strands of DNA

Anti-parallel strands of
the DNA

Major and Minor Groves of DNA

3.4-nanometer length of
each full twist of the double
helix (360 turn)

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DNA helix turn

Right-hand helix turn

10 base-pair per helix
turn (360 turn)

Chargaffs Rules (Erwin Chargaff)

The amounts of thymine and adenine in DNA are

the same, and the amounts of cytosine and guanine
are the same: A = T and G = C
percentage base pair equality:
%A = %T and %G = %C.
Proportion of adenine and guanine differs among
species

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The Human Genome

Genome is the complete set of genetic information

of an organism
The total length of the human genome is over 3
billion base pairs.
2001

Draft of Human Genome Sequence

2003 Finished Human Genome
(50 years after DNA structure solved)
Costed $3 billion

Importance of Knowing the Genome

To obtain a blueprint DNA directs all the

instructions needed for cell development and function
DNA underlies almost every aspect of human health,
both, in function and dysfunction
to study gene expression in a specific tissue, organ or
tumor
to study human variation
to study how humans relate to other organisms
to find correlations how genome information relates
to development of cancer, susceptibility to certain
diseases and drug metabolism

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Central Dogma of Molecular Genetics

OVERVIEW OF THE
BASIC MOLECULAR
PROCESSES

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DNA Replication

DNA replication is an essential aspect of cellular

and viral reproduction.
Replication of a double-stranded DNA results in two
double-stranded DNAs as products.

Semiconservative DNA Replication

Each strand of a DNA double helix is a template

for synthesis of a complementary strand of DNA
One template builds DNA continuously; the other
builds DNA discontinuously, in segments
Each new DNA molecule consist of one old strand
and one new strand

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Meselson-Stahl experiment

Semiconservative DNA Replication

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DNA REPLICATION PROCESS

INITIATION ELONGATION TERMINATION

Enzymes of DNA Replication

DNA helicase
Breaks

DNA polymerase
Joins

hydrogen bonds between DNA strands

free nucleotides into a new strand of DNA

DNA ligase
Joins

DNA segments on discontinuous strand

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Initiation Step

Duplex DNA is unwound at the origin

by DNA helicases
Helicases use energy from ATP
hydrolysis to separate the parental
(template) DNA strands.
DNA
HELICASE

Bidirectional Replication

The general consensus is that all prokaryotic and

eukaryotic cells employ a bidirectional mechanism
of DNA replication.

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INITIATION STEP

Initiation Step

Primases (specialized RNA polymerase) synthesize

RNA primers as starting oligonucleotide fragments
for attachment of incoming dNTP

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Synthesis of New DNA Strands

Each strand in a parental duplex DNA acts as a

template for synthesis of a daughter strand and
remains base-paired to the new strand, forming a
daughter duplex.
New strands are formed in the 5 to 3 direction.

ELONGATION STEP
Each DNA strand has two ends:
one with a 5 carbon, and one with
a 3 carbon.
DNA polymerase can add
nucleotides only at the 3 carbon.
In other words, DNA synthesis
proceeds only in the 5 to 3
direction.

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Elongation Step

At a replication fork, one daughter strand (the

leading strand) is elongated continuously. The other
daughter strand (the lagging strand) is formed as a
series of discontinuous.

Elongation Step

Okazaki fragments synthesized at the lagging

strand.

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Termination Step

RNA primers are removed

by5 to 3 exonuclease
activity of the DNA
polymerase
DNA ligases seal the nick
between Okazaki
fragments

TERMINATION STEP

DNA ligase
Joins

DNA segments on
discontinuous strand

Leading

strand
continuous synthesis

Lagging

strand
discontinuous synthesis

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Rate of DNA Replication

Problems

What is the complimentary sequence of the given

DNA strand?
5 ATG CCC GCG AAT GAG CGA GGC TAG 3

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Problems

What is the complimentary sequence of the given

DNA strand?
3 CCC ATA GCG CAA TTT ACG ATA GCA 5

Central Dogma of Molecular Genetics

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TRANSCRIPTION RNA Synthesis

process of RNA Synthesis

copying the 5 3 DNA in the form 5 3 RNA
RNA polymerase synthesize 5- 3 RNA strand using
DNA strand (antisense strand) as template
T in DNA is transcribed as A in RNA
G in DNA is transcribed as C in RNA
A in DNA is transcribed as U in RNA
C in DNA is transcribed as G in RNA

Transcription of
Protein-Coding Genes

Ribonucleoside triphosphates,
rNTPs: ATP, GTP, CTP and
UTP
A Template DNA Strand Is
Transcribed into a
Complementary RNA Chain
by RNA Polymerase

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Structures of RNA

Ribosomal RNA, rRNA

is

associated with a number of different proteins as

components of the ribosome (complex as site for
protein synthesis)
80% of the RNA in the cell

Transfer RNA, tRNA

smallest

RNA molecule (4S)

serves as adaptor molecule that carries its specific
amino acid to the site of protein synthesis
15% of the RNA in the cell

Structures of RNA

Messenger RNA, mRNA

carries

genetic information from the DNA to the

cytosol, where it is used as the template for protein
synthesis
5% of the RNA in the cell

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Structures of RNA

rRNA
tRNA

Transcription of Protein-Coding Genes

By convention, the site at which RNA polymerase begins transcription is

numbered 1.
Downstream denotes the direction in which a template DNA strand is
transcribed (toward the 3 end relative to the start site) while Upstream
denotes the opposite direction.
Nucleotide positions in the DNA sequence downstream from a start site are
indicated by a positive (+) sign; those upstream, by a negative (-) sign.

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TRANSCRIPTION: RNA SYNTHESIS

Basic
Transcription
process in
Prokaryotes

Basic Transcriptional Mechanism

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Promoter Regions

Basic Transcriptional Mechanism

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Termination of Transcription

Rho- independent Termination

Rho-dependent Termination

Rho factor acts as an ATP-dependent unwinding enzyme,

moving along the newly forming RNA molecule towards its 3
end and unwinding it from the DNA template as it proceeds.

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Post-Transcriptional Modifications

In eukaryotes, RNA is modified before it leaves the

nucleus as a mature mRNA
Introns
Noncoding

sequences that are removed from a new

RNA

Exons
Coding

sequences that stay in the RNA

Post-Transcriptional Modification

Addition of 7methylguanylate
at the 5 end
Addition of poly-A
at the 3 end
Removal of introns
and splicing of
exons

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Post-Transcriptional
Modification

Addition of 7methylguanylate at the 5 end

The distinguishing chemical

features are the 5-5 linkage
of 7-methylguanylate to the
initial nucleotide of the mRNA
molecule and the methyl group
on the 2 hydroxyl of the ribose
of the first nucleotide.

Problems

Given the DNA template, what is the sequence of

the RNA produced?
5 ATG CCC GCG AAT GAG CGA GGC TAG 3

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Problems

Given the DNA template, what is the sequence of

the RNA produced?
3 CCC ATA GCG CAA TTT ACG ATA GCA 5

Central Dogma of Molecular Genetics

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TRANSLATION: PROTEIN SYNTHESIS

INITIATION ELONGATION TERMINATION
POST-TRANSLATIONAL
MODIFICATION

THE GENETIC CODE

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THE STANDARD GENETIC CODE

Marshall Nirenberg and Philip Leder in 1964

In the genetic code, nucleotide triplets specify an
amino acid.
43 = 64 possible word codes
61 out of 64 possible word codes for
specific amino acids referred to as
codons

THE STANDARD GENETIC CODE

Characteristics of the genetic code:
Specificity specific codon always code for the
same amino acid
Redundancy an amino acid may have more than
one codon coding for it
Non-overlapping and commaless code is read
from a fixed starting point as a continuous
Contatins 3 codons that are stop signals

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Problems

Given the DNA template, what is the amino acid

sequence when it is translated?
5 ATG CCC GCG AAT GAG CGA GGC TAG 3

Problems

Given the DNA template, what is the amino acid

sequence when it is translated?
3 CCC ATA GCG CAA TTT ACG ATA GCA 5

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Elongation Step in Translation

Translation: Protein Synthesis

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Termination of Translation Process

Rate of Synthesis in Prokaryotes

E. coli contains about 15,000 ribosomes, each cell

can synthesize about 750 protein molecules of 300
residues in length per second, at full capacity.
At 37C, an E. coli ribosome can synthesize a 300-residue
polypeptide chain in about 20 seconds. This rate is almost
exactly the same as that calculated for prokaryotic transcription.

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References:

Voet and Voet, Biochemistry 2nd ed. Wiley Publication

(2004).
Starr and Taggart (2004). Biology. The Unity and
Diversity of Life, 10th edition, Wadsworth Group, Thomson
Learning, Inc., California
Lodish H, Berk A, Zipursky SL, et al. Molecular Cell
Biology, 5th edition. New York: W. H. Freeman; 2004.

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