Nucleic acids
Nucleic acids:
– Maintain genetic information
– Determine Protein Synthesis
DNA = deoxyribonucleic acid
– “Master Copy” for most cell information.
– Template for RNA
RNA = ribonucleic acid
– Transfers information from DNA
– Template for Proteins
1
Nucleic Acids
Chromosomes
(in nucleus)
Have genes
1 gene
1 enzyme or
protein
Enzymes determine
external & internal characteristics
2
NUCLEIC ACIDS
Long chains (polymers) of repeating nucleotides.
– Each nucleotide has 3 parts:
A heterocyclic
Amine Base
N
O
HO P OH
H
HO
O
O
OH
H
A phosphate unit
H
H
H
H
OH
A sugar
H
3
Nucleotide = phosphate + sugar + base
Phosphate
Base
O
O P
N
Sugar
O
O
O
H
-N-glycosidic
linkage
H
H
H
OH
H
Nucleoside = sugar + base
4
Nucleic Acids
Nucleic Acids = polymers of Nucleotides.
base
B
P
S
B
P
S
B
P
S
B
P
phosphate
S
B
B
P
S
P
S
sugar
5
THE SUGAR PART
• The major difference between RNA and DNA is
the different form of sugar used.
Ribose C5H10O5
in RNA
O
HOCH2
H
OH
H
H
OH
OH
H
DeoxyRibose C5H10O4
in DNA
O
HOCH2
H
OH
H
H
OH
H
H
The difference is at carbon #2.
6
The Nitrogenous Bases
5 bases used fall in two classes
Purines & Pyrimidines
N
N
N
N
N
N
H
A double ring
A single ring
(6 & 5 members)
(6 membered)
7
The Nitrogenous Bases
NH2
Purines:
N
N
Adenine (A)
O
N
H
N
H2N
H
N
H
Thiamine (T)
In DNA only
N
N
H
NH2
O
CH3
N
N
N
Guanine (G)
O
Pyrimidines:
H
O
H
O
H
N
N
H
Uracil (U)
In RNA only
O
N
N
H
Cytosine (C)
8
NH2
OH
O
P
O
N
N
O
Primary structure
N
N
5'
O
4' H
H
3'
OH
H
1'
H
O
2'
H
N
HN
OH
O
P
O
H2N
O
N
N
5'
O
4' H
H
3'
OH
H
1'
2'
H
P
O
N
O
O
CH3
N
OH
O
O
H
5'
O
4' H
H
3'
OH
H
1'
H
2'
H
9
Primary structure
NH2
5’
OH
O
P
O
N
O
5'
O
4' H
H
3'
O
O
Adenine (A)
Similar to proteins
N
with their peptide
bonds and side
H 1'
H
groups.
O
2'
H
N Guanine (G)
HN
N
N
P
O
Phosphate bonds
link DNA or RNA
nucleotides together
in a linear sequence.
H2N
O
N
N
5'
O
4'
H
H
3'
P
O
3’
O
H
2'
H
O
O
Thymine (T)
1'
H
O
O
CH3
N
N
5'
O
4'
H
H
3'
OH
H
1'
H
2'
H
10
Structure of DNA
11
In 1938 William Thomas
Astbury took the first fiber
diffraction pictures of
DNA, correctly predicting,
in an article in the journal
Nature, the overall
dimensions of the
molecule and that the
nucleotide bases were
stacked at intervals of 3.3Å
perpendicular to its long
axis. It was left, however,
to Watson and Crick after
the Second World War to
elucidate the detailed
double helical structure of
DNA.
12
Maurice Wilkins with one of
the cameras he developed
specially for X-ray diffraction
studies
13
Work on x-ray diffraction patterns by Maurice Wilkins and
Rosalind Franklin in 1953, revealed that the molecule had a
"helical shape“.
14
Rosalind Franklin is most associated with the discovery of
the structure of DNA. At 26, after she had her PhD, Franklin
began working in x-ray diffraction - using x-rays to create
images of crystallized solids. She pioneered the use of this
method in analyzing complex, unorganized matter such as large
biological molecules, and not just single crystals.
Franklin made marked advances in x-ray diffraction techniques
with DNA. She adjusted her equipment to produce an extremely
fine beam of x-rays. She extracted finer DNA fibers than ever
before and arranged them in parallel bundles. And she studied
the fibers' reactions to humid conditions. All of these allowed
her to discover crucial keys to DNA's structure. Maurice Wilkins,
her laboratory's second-in-command, shared her data, without
her knowledge, with James Watson and Francis Crick, at
Cambridge University, and they pulled ahead in the race,
ultimately publishing the proposed structure of DNA in March,
1953.
It is clear that without an unauthorized peek at Franklin's
unpublished data, Watson and Crick probably would neither
have published their famous paper on the structure of DNA in
1953, nor won their Nobel Prizes in 1962. Franklin did not share
the Nobel Prize; she died in 1958 at the age of 37.
15
Linus Pauling's incorrect triple helix model
of the structure of DNA, proposed in 1952,
http://www.youtube.com/watch?v=pR0zwrLSai4
16
1953, James
Watson & Francis
Crick and their
scale model for
DNA
17
DNA secondary and tertiary structure
Sugar-phosphate backbone
Causes each DNA chain to coil around the
outside of the attached bases like a spiral stair
case.
Base Pairing
Hydrogen bonding occurs between purines and
pyrimidines. This causes two DNA strands to
bond together.
adenine - thymine
guanine - cytosine
Always pair together!
Results in a double helix structure.
18
Base pairing and hydrogen bonding
H-N
N
N
N-H
guanine
N
cytosine
N
N
N-H
H 3C
H
thymine
N
H
|
N- H
N
N
adenine
N
N
N
19
Hydrogen bonding
Each base wants to
form either two or three
hydrogen bonds.
That’s why only certain
bases will form pairs.
C
G
T
A
G
C
C
G
A
T
20
Sugarphosphate
backbone
DNA coils
around
outside of
attached
bases like
a spiral
stair case.
Results in a
double helix
structure.
21
• Crick and Watson
(1962 Nobel Prize)
– Proposed the basic
structure of DNA
– 2 strands wrap
around each other
– Strands are
connected by Hbonds between the
amines.
• Like steps of a
spiral staircase
22
Role of RNA and DNA in Heredity
RNA and DNA are involved in three major processes in a
cell related to heredity as shown below:
1. Replication (DNA copies itself)
Replication is an important
process during mitosis
2. Transcription (The genetic code in DNA
is rewritten into RNA and carried to the
ribosomes by mRNA
3. Translation (tRNA carries amino acids
to the ribosomes as part of protein
synthesis
Transcription and
translation are two steps in
the biosynthesis of a
protein
23
DNA: Self - Replication
P
S
A
P
S
G
P
S
T
P
P
S
C
S
C
P
S
G
C
T
G
A
24
DNA: Self - Replication
P
S
A
T
P
S
G
C
P
S
P
S
T
C
A
G
P
S
C
G
P
S
G
C
25
Replication of DNA
Replication occurs on both halves
in opposite directions.
26
DNA Replication
27
RNA synthesis
In the first step,
RNA polymerase binds
to a promotor sequence
on the DNA chain.
This insures that
transcription occurs in
the correct direction.
The initial
reaction is to
separate the two
DNA strands.
28
RNA synthesis
initiation
sequence
termination
sequence
‘Special’ base
sequences in the
DNA indicate
where RNA
synthesis starts
and stops.
29
RNA synthesis
Once the
termination
sequence is
reached, the
new RNA molecule
and the
RNA synthase
are released.
The DNA recoils.
30
• The messenger RNA (mRNA) move
outside the nucleus to the cytoplasm
where Ribosomes are anxiously awaiting
their arrival.
rRNA
rRNA
31
• The messenger RNA (mRNA) move
outside the nucleus to the cytoplasm
where Ribosomes are anxiously awaiting
their arrival.
rRNA
rRNA
32
• The messenger RNA (mRNA) move
outside the nucleus to the cytoplasm
where Ribosomes are anxiously awaiting
their arrival.
rRNA
rRNA
33
• The messenger RNA (mRNA) move
outside the nucleus to the cytoplasm
where Ribosomes are anxiously awaiting
their arrival.
rRNA
rRNA
34
Ribosomal RNA – rRNA: Platform for protein
synthesis. Holds mRNA in place and helps
assemble proteins.
rRNA
rRNA
35
•The Ribosomes are like train stations
–The mRNA is the train slowly moving
through the station.
rRNA
Codons
AUG
5’
GCU
AUG
UUG
3’mRNA
rRNA
36
Transfer RNA - tRNA =
• relatively small compared to other RNA’s
(70-90 bases.)
• transports amino acids to site of protein
synthesis.
HO-
A
C
C
A
G
G
A U G
U
C
G
G U A
C G C G G
U
C
G
C
G
U
C
G
G
C
U
U
G
C A G G
C C
U C C
G G
C
C G
C
U
G
U
A
G
G C G C
U
U U
C
G A G
U
A
C
G
C
G
C
G
G
G
C G C
37
Anticodons on t-RNA
HO-
C
Site of amino
acid attachment
G
A
U
G
U
C
G
G U
Three base
anticodon site
A
C G
G
C
A
C
A
C
G
G
U
G
C
G
C
G
U
C
G
G
C
U
U
G
C
A
G
G
C
C
U
U
A
G
U
C
G C
C
C
G
G
C
G
C
U
G
C
G
U
A
C
G
C
G
C
G
A
U
G
U
G
C
G
C
G
Point of
attachment
to mRNA
38
The Genetic Code for Messenger RNA
First
Nucleotide
U
C
A
G
Second
Nucleotide
U
C
A
G
U
C
A
G
U
C
A
G
U
C
A
G
Third Nucleotide and amino acid coded
U
C
A
G
Phe
Phe
Leu
Leu
Ser
Ser
Ser
Ser
Tyr
Tyr
TC*
TC*
Cys
Cys
TC*
Trp
Leu
Leu
Leu
Leu
Pro
Pro
Pro
Pro
His
His
Gln
Gln
Arg
Arg
Arg
Arg
Ile
Ile
Ile
Met
Thr
Thr
Thr
Thr
Asn
Asn
Lys
Lys
Ser
Ser
Arg
Arg
Val
Val
Val
Val
Ala
Ala
Ala
Ala
Asp
Asp
Glu
Glu
Gly
Gly
Gly
Gly
*Termination codon
UUU or UUC is the codon for Phe. UUG is the codon
for Leu. AUG is the codon for Met.
39
39
Codons
There are two additional types of codons:
Initiation
AUG
(same as methionine)
Termination
UAG, UAA, UGA
A total of 64 condons are used for all amino
acids and for starting and stopping. All protein
synthesis starts with methionine. After the polypeptide has been made, an enzyme removes this
amino acid.
40
Protein Synthesis
1: Activation
Each AA is activated by reacting with an
ATP
The activated AA is then attached to
particular tRNA... (with the correct anticodon)
activated AA
anticodon
MET
C
G
A
41
The ribosome has three binding sites for tRNA
molecules that span the space between the two
ribosomal subunits: the
A (aminoacyl)
P (peptidyl)
E (exit) sites
42
Translation
MET
U A C
AUG
Initiation
factors
5’
GCU
AUG
UUG
mRNA
3’
Psite A site
ribosome unit
peptidyl
aminoacyl
43
Translation
Ala
MET
C G A
U A C
AUG
5’
GCU
AUG
UUG
mRNA
3’
Psite A site
ribosome unit
44
Translation
peptide bond
forms
MET
Ala
U A C
C G A
AUG
GCU
AUG
UUG
mRNA
3’
5’
ribosome unit
45
Translation
U A C
Phe
peptide bond
Met
Ala
A A G
U A C
UG
A
C G A
GCU
UUC
UUG
mRNA
3’
5’
ribosome unit
46
Translation
U A C
peptide bond
forms
Met
UG
A
Ala
Phe
C G A
A A G
GCU
UUC
UUG
mRNA
3’
5’
ribosome unit
47
https://www.youtube.com/watch?v=D3fOXt4MrOM
http://www.bing.com/videos/search?q=protein+synthesis+animation&view=detail&mid=511C5
DB5CF9714489C93511C5DB5CF9714489C93&first=0&FORM=NVPFVR
http://www.youtube.com/watch?v=TfYf_rPWUdY
48
Termination
After the last translocation (the last
codon is a STOP), no more AA are
added.
“Releasing factors” cleave the last
AA from the tRNA
The polypeptide is complete
49
Recombinant DNA
Circular DNA found in bacteria
E.Coli plasmid bodies
Restriction endonucleases cleave DNA at
specific genes
Result is a “sticky end”
Addition of a gene from a second
organism
Spliced DNA is replaced and organism
synthesizes the new protein
50
Recombinant DNA
Bacterium
Remove
gene segment
DNA
Plasmid
sticky ends
Cut gene
for insulin
Replace in
bacterium
51