For What ???

1962: Nobel Prize in Physiology and Medicine

Watson, J.D. and F.H. Crick, “Molecular Structure of Nucleic Acids: A

Structure for Deoxynucleic Acids”. Nature 171 (1953), p. 738.

James D. Francis H. Maurice H. F.

Watson Crick Wilkins

What about?
Rosalind Franklin
 The Structure of DNA
 DNA is composed of four nucleotides,
each containing: adenine, cytosine,
thymine, or guanine.

 The amounts of A = T, G = C, and

purines = pyrimidines [Chargaff’s
Rule].

 DNA is a double-stranded helix with

antiparallel strands [Watson and
Crick].

 Nucleotides in each strand are linked

by 5’-3’ phosphodiester bonds

 Bases on opposite strands are linked

by hydrogen bonding: A with T, and G
with C.
DNA Replication is “Semi-conservative”

 Each 2-stranded
daughter molecule is
only half new
 One original strand was
used as a template to
make the new strand
DNA Replication
 The copying of DNA is remarkable in its speed and
accuracy
 Involves unwinding the double helix and synthesizing two
new strands.
 More than a dozen enzymes and other proteins participate
in DNA replication
 The replication of a DNA molecule begins at special sites
called origins of replication, where the two strands are
separated
Mechanism of DNA Replication
 DNA replication is catalyzed by DNA polymerase which needs an RNA
primer
 RNA primase synthesizes primer on DNA strand
 DNA polymerase adds nucleotides to the 3’ end of the growing strand
The Mechanism of DNA Replication
 DNA synthesis on the leading strand is continuous
 The lagging strand grows the same general direction as the
leading strand (in the same direction as the Replication Fork).
However, DNA is made in the 5’-to-3’ direction
 Therefore, DNA synthesis on the lagging strand is discontinuous
 DNA is added as short fragments (Okasaki fragments) that are
subsequently ligated together

DNA polimerase

Ligase
DNA polymerase I degrades the
RNA primer and replaces it with
DNA
 The Mechanism of DNA Replication
 Many proteins assist in DNA replication

 DNA helicases unwind the double helix, the

template strands are stabilized by other
proteins

 Single-stranded DNA binding proteins make

the template available

 RNA primase catalyzes the synthesis of

short RNA primers, to which nucleotides are
added.

 DNA polymerase III extends the strand in the

5’-to-3’ direction

 DNA polymerase I degrades the RNA primer

and replaces it with DNA

 DNA ligase joins the DNA fragments into a

continuous daughter strand
 Enzymes in DNA replication

Helicase unwinds Binding proteins Primase adds

parental double helix stabilize separate short primer
strands to template strand

DNA polymerase III DNA polymerase I Ligase joins Okazaki

binds nucleotides (Exonuclease) removes fragments and seals
to form new strands RNA primer and inserts other nicks in sugar-
the correct bases phosphate backbone
 Replication
3’
3’ 5’
5’
3’

5’ 3’
5’

Helicase protein binds to DNA sequences called

origins and unwinds DNA strands.

Binding proteins prevent single strands from rewinding.

Primase protein makes a short segment of RNA
complementary to the DNA, a primer.
Replication
Overall direction 3’
of replication
3’ 5’
5’

3’

5’ 3’
5’

DNA polymerase enzyme adds DNA nucleotides

to the RNA primer.
Replication
Overall direction
3’
of replication
3’ 5’

5’
3’

5’ 3’
5’

DNA polymerase enzyme adds DNA nucleotides

to the RNA primer.

DNA polymerase proofreads bases added and

replaces incorrect nucleotides.
Replication
Overall direction
3’
of replication
3’ 5’

5’
3’

5’ 3’
5’

Leading strand synthesis continues in a

5’ to 3’ direction.
Replication
Overall direction
3’
of replication
3’ 5’

5’
Okazaki fragment
3’

5’ 3’ 5’ 3’
5’

Leading strand synthesis continues in a

5’ to 3’ direction.

Discontinuous synthesis produces 5’ to 3’ DNA

segments called Okazaki fragments.
Replication
Overall direction
3’
of replication
3’ 5’

5’
Okazaki fragment
3’

5’ 3’ 5’ 3’
5’

Leading strand synthesis continues in a

5’ to 3’ direction.

Discontinuous synthesis produces 5’ to 3’ DNA

segments called Okazaki fragments.
Replication

3’
3’ 5’

5’
3’
5’ 3’ 5’ 3’5’ 3’
5’

Leading strand synthesis continues in a

5’ to 3’ direction.

Discontinuous synthesis produces 5’ to 3’ DNA

segments called Okazaki fragments.
Replication

3’
3’ 5’

5’
3’
5’ 3’5’ 3’5’ 3’
5’

Leading strand synthesis continues in a

5’ to 3’ direction.

Discontinuous synthesis produces 5’ to 3’ DNA

segments called Okazaki fragments.
Replication

3’
3’ 5’

5’
3’
5’ 3’5’ 3’5’ 3’
5’

Exonuclease activity of DNA polymerase I removes RNA primers.

 Replication

3’
3’

5’
3’
5’ 3’5’ 3’
5’

Polymerase activity of DNA polymerase I fills the gaps.

Ligase forms bonds between sugar-phosphate backbone.
Transcription and Translation
 Cells are governed by a cellular chain of command
 DNA RNA protein
 Transcription
 Is the synthesis of RNA under the direction of DNA
 Produces messenger RNA (mRNA)
 Translation
 Is the actual synthesis of a polypeptide, which occurs under
the direction of mRNA
 Occurs on ribosomes
Transcription and Translation
 In a eukaryotic cell the nuclear envelope separates transcription
from translation
 Extensive RNA processing occurs in the nucleus

Nuclear
envelope

TRANSCRIPTION DNA

Pre-mRNA
RNA PROCESSING

mRNA

Ribosome

TRANSLATION
(b) Eukaryotic cell. The nucleus provides a separate
Polypeptide compartment for transcription. The original RNA
transcript, called pre-mRNA, is processed in various
ways before leaving the nucleus as mRNA.
Transcription
 Transcription is the DNA-
directed synthesis of RNA
 RNA synthesis
 Is catalyzed by RNA
polymerase, which pries the
DNA strands apart and hooks
together the RNA nucleotides
 Follows the same base-pairing
rules as DNA, except that in
RNA, uracil substitutes for
thymine
RNA
 RNA is single stranded, not double stranded like DNA
 RNA is short, only 1 gene long, where DNA is very long and contains
many genes
 RNA uses the sugar ribose instead of deoxyribose in DNA
 RNA uses the base uracil (U) instead of thymine (T) in DNA.

Table 17.1
 Synthesis of an RNA Transcript

 The stages of Promoter

Transcription unit

transcription are 5
3
DNA
3
5

Start point
 Initiation RNA polymerase 1
Initiation. After RNA polymerase binds to
 Elongation the promoter, the DNA strands unwind, and
the polymerase initiates RNA synthesis at the
start point on the template strand.
 Termination
5
3 3
5
Template strand of
Unwound RNA DNA
DNA transcript
2
Elongation. The polymerase moves downstream, unwinding the
DNA and elongating the RNA transcript 5  3 . In the wake of
transcription, the DNA strands re-form a double helix.
Rewound
RNA
5
3 3 3
5
5

RNA
transcript
3 Termination. Eventually, the RNA
transcript is released, and the
polymerase detaches from the DNA.

5
3 3
5

5 3
Completed RNA
transcript
Synthesis of an RNA Transcript - Initiation

TRANSCRIPTION DNA 1 Eukaryotic promoters

RNA PROCESSING Pre-mRNA
mRNA

 Promoters signal the initiation TRANSLATION Ribosome

Polypeptide
of RNA synthesis Promoter

5 T A T A A AA 3
 Transcription factors help 3 AT AT T T T

TATA box
5
Start point Template
eukaryotic RNA polymerase DNA strand

recognize promoter 2 Several transcription

factors
sequences Transcription
factors

5 3
3 5
3 Additional transcription
factors

RNA polymerase II
Transcription factors

5 3
3 5 5
RNA transcript
Transcription initiation complex
Synthesis of an RNA Transcript - Elongation
 RNA polymerase synthesizes a single strand of RNA against the DNA template strand
(anti-sense strand), adding nucleotides to the 3’ end of the RNA chain

 As RNA polymerase moves along the DNA it continues to untwist the double helix,
exposing about 10 to 20 DNA bases at a time for pairing with RNA nucleotides

Elongation Non-template
strand of DNA
RNA nucleotides

RNA
polymerase

T C C A A
A
3
3 end
U
A E G C A
5

T A G G T T

Direction of transcription
5 Template
(“downstream”)
strand of DNA

Newly made
RNA
Synthesis of an RNA Transcript - Termination
• Specific sequences in the DNA signal termination of transcription
• When one of these is encountered by the polymerase, the RNA
transcript is released from the DNA and the double helix can zip
up again.
 Translation
 Translation is the RNA-directed TRANSCRIPTION DNA

synthesis of a polypeptide mRNA

Ribosome
TRANSLATION
 Translation involves Polypeptide

 mRNA
Amino
 Ribosomes - Ribosomal RNA acids
Polypeptide
 Transfer RNA
 Genetic coding - codons tRNA with
amino acid
Ribosome attached

Gly

tRNA

Anticodon
A A A
U G G U U U G G C

5 Codons 3
mRNA
The Genetic Code
 Genetic information is encoded as a sequence of nonoverlapping base
triplets, or codons

DNA Gene 2
molecule
Gene 1
Gene 3

DNA strand 3 5
(template) A C C A A A C C G A G T

TRANSCRIPTION

U G G U U U G G C U C A
mRNA 5 3
Codon
TRANSLATION

Protein Trp Phe Gly Ser

Amino acid
The Genetic Code

 Codons: 3 base code for the production of a specific amino acid,

sequence of three of the four different nucleotides

 Since there are 4 bases and 3 positions in each codon, there are 4
x 4 x 4 = 64 possible codons

 64 codons but only 20 amino acids, therefore most have more than
1 codon

 3 of the 64 codons are used as STOP signals; they are found at the
end of every gene and mark the end of the protein

 One codon is used as a START signal: it is at the start of every

protein

 Universal: in all living organisms

The Genetic Code
 A codon in messenger RNA is either translated into an amino acid
or serves as a translational start/stop signal

Second mRNA base

U C A G
UUU UCU UAU UGU U
Phe Tyr Cys
UUC UCC UAC UGC C
U
UUA UCA Ser UAA Stop UGA Stop A
UUG Leu UCG UAG Stop

Third mRNA base (3 end)

UGG Trp G
First mRNA base (5 end)

CUU CCU CAU CGU U

His
CUC CCC CAC CGC C
C Leu CCA Pro Arg
CUA CAA CGA A
Gln
CUG CCG CAG CGG G
AUU ACU AAU AGU U
Asn
A
AUC lle ACC AAC AGC Ser C
Thr
AUA ACA AAA AGA A
Met or Lys Arg
AUG start ACG AAG AGG G
GUU GCU GAU GGU U
G GUC GCC GAC Asp GGC C
Val Ala Gly
GUA GCA GAA GGA A
GUG GCG GAG Glu GGG G
Thank’s 