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
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Nucleic Acids
Chromosomes
(in nucleus)
Have genes
1 gene
1 enzyme
Enzymes determine
external & internal characteristics
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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
OH
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H
A sugar
H
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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
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Nucleic Acids
Nucleic Acids = polymers of Nucleotides.
base
B
P
S
B
P
S
B
P
S
B
P
phosphate
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S
B
B
P
S
P
S
sugar
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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.
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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)
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The Nitrogenous Bases
NH2
Purines:
N
N
Adenine (A)
O
H
N
H2N
H
N
N
Thiamine (T)
In DNA only
N
N
N
N
Guanine (G)
H
NH2
O
CH3
H
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N
O
Pyrimidines:
H
O
H
O
H
N
N
H
Uracil (U)
In RNA only
O
N
N
H
Cytosine (C)
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Nucleotides Di- & Tri- Phosphates
NH2
Adenine
N
N
O
HO P OH
OH
O
HO P
O
N
N
O
5'
O
4' H
H
3'
ribose OH
1'
H
H
2'
OH
Adenosine 5’-monophosphate
(AMP)
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Nucleotides Di- & Tri- Phosphates
NH2
Adenine
N
N
O
HO P OH
OH
O
O
HO P O P
O
O
N
N
O
5'
O
4' H
H
ribose 3'
OH
1'
H
H
2'
OH
Adenosine 5’-monophosphate
(AMP)
Adenosine 5’-diphosphate (ADP)
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Nucleotides Di- & Tri- Phosphates
NH2
Adenine
N
N
O
O
O
HO P O P O P
O
O
Adenosine 5’-triphosphate (ATP)
O
N
N
O
5'
O
4' H
H
ribose 3'
OH
1'
H
H
2'
OH
Adenosine 5’-monophosphate
(AMP)
Adenosine 5’-diphosphate (ADP)
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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
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N
O
O
CH3
N
OH
O
O
H
5'
O
4' H
H
3'
OH
H
1'
H
2'
H
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Primary structure
NH2
5’
OH
O
P
O
N
O
5'
O
4' H
H
3'
O
O
P
O
Phosphate bonds
link DNA or RNA
nucleotides together
in a linear sequence.
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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
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
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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
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N
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DNA - Secondary Structure
Complementary Base Pairing
Position of H bonds and distance match with:
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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
G
A
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C
T
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Sugarphosphate
backbone
DNA coils
around
outside of
attached
bases like
a spiral
stair case.
Results in a double helix structure.
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The double helix
The combination of
the stairstep sugarphosphate backbone
and the bonding
between pairs results
in a double helix.
Distance between
bases = 0.34 nm
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One
complete
twist
is 3.4 nm
2 nm
between
strands
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DNA - Secondary Structure
Complementary Base Pairing
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• Crick and Watson
(1962 Nobel Prize)
– Proposed the basic
structure of DNA
– 2 strands wrap around
each other
– Strands are connected by
H-bonds between the
amines.
• Like steps of a spiral
staircase
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Chromosomes
Chromosomes consists of DNA strands coiled
around protein - histomes. The acidic DNA’s are
attracted to the basic histones.
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Chromosomes
The normal number of chromosome pairs varies
among the species.
Animal
Man
Cat
Mouse
Rabbit
Honeybee,
male
female
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Pairs
23
30
20
22
8
16
Plant
Onion
Rice
Rye
Tomato
White pine
Adder’s
tounge fern
Pairs
8
14
7
12
12
1262
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DNA: Self - Replication
P
S
P
A
S
G
P
S
T
P
P
S
C
S
C
P
S
G
C
T
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G
A
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DNA: Self - Replication
P
S
P
A
T
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S
G
C
P
S
P
S
T
C
A
G
P
S
C
G
P
S
G
C
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Replication of DNA
Replication occurs on both halves
in opposite directions.
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DNA Replication
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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.
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RNA synthesis
initiation
sequence
termination
sequence
‘Special’ base
sequences in the
DNA indicate
where RNA
synthesis starts
and stops.
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RNA synthesis
Once the
termination
sequence is
reached, the
new RNA molecule
and the
RNA synthase
are released.
The DNA recoils.
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• The messenger RNA (mRNA) move
outside the nucleus to the cytoplasm
where Ribosomes are anxiously awaiting
their arrival.
60 S
rRNA
rRNA
40 S
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• The messenger RNA (mRNA) move
outside the nucleus to the cytoplasm
where Ribosomes are anxiously awaiting
their arrival.
60 S
rRNA
rRNA
40 S
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• The messenger RNA (mRNA) move
outside the nucleus to the cytoplasm
where Ribosomes are anxiously awaiting
their arrival.
60 S
rRNA
rRNA
40 S
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• The messenger RNA (mRNA) move
outside the nucleus to the cytoplasm
where Ribosomes are anxiously awaiting
their arrival.
60 S
rRNA
rRNA
40 S
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Ribosomal RNA – rRNA: Platform for protein
synthesis. Holds mRNA in place and helps
assemble proteins.
60 S
rRNA
rRNA
40 S
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•The Ribosomes are like train stations
–The mRNA is the train slowly moving
through the station.
60 S
rRNA
Codons
AUG
GCU
AUG
5’
UUG
3’mRNA
rRNA
40 S
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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
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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
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
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A
G
C
G
Point of
attachment
to mRNA
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Amino acid codons
alanine
GCA, GCC, GCG
GCU, AGA, AGG
arginine
AGA, AGG, CGA
CGC, CGG, CGU
asparagine AAC, AAU
aspartate
GAC, GAU
cysteine
UGC, UGU
glutamate GAA, GAG
glutamine CAA, CAG
glycine
GAA, GCC, GGG
GGU
histidine
CAC, CAU
isoleucine AUA, AUC, AUU
leucine
CUA, CUC, CUG
CUU, UUA, UUG
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lysine
AAA, AAG
methionine
AUG
phenylalanine UUC, UUU
proline
CCA, CCC
CCG, CCU
serine
UCA, UCC
UCG, UCU
AGC, AGU
threonine
ACA, ACC
ACG, ACU
tryptophan
UGG
tyrosine
UCA, UCU
valine
GUA, GUC
GUG, GUU
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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
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fMET
C
G
A
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Translation
fMET
60S
U A C
AUG
Initiation
factors
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5’
GCU
AUG
UUG
mRNA
3’
Psite A site
40S ribosome unit
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Translation
Ala
fMET
60S
C G A
U A C
AUG
5’
GCU
AUG
UUG
mRNA
3’
Psite A site
40S ribosome unit
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Translation
peptide bond
forms
fMET
Ala
U A C
C G A
AUG
GCU
AUG
UUG
mRNA
3’
5’
ribosome unit
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Translation
U A C
Amino Acid
peptide bond
Met
Ala
Z Z Z
U A C
UG
A
C G A
GCU
UUC
UUG
mRNA
3’
5’
ribosome unit
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Translation
peptide bond
forms
U A C
Met
UG
A
Ala
???
C G A
? ?
?
GCU
UUC
UUG
mRNA
3’
5’
ribosome unit
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Recombinant DNA
Bacterium
Remove
gene segment
DNA
Plasmid
sticky ends
Cut gene
for insulin
Replace in
bacterium
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Learning Check
What is the sequence of bases in mRNA
produced
from a section of the template strand of DNA that
has
the sequence of bases: 3’–C–T–A–A–G–G–5’?
1. 5’–G–A–T–T–C–C–3’
2. 5’–G–A–U–U–C–C–3’
3. 5’–C–T–A–A–G–G–3’
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Solution
What is the sequence of bases in mRNA
produced
from a section of the template strand of DNA that
has
the sequence of bases: 3’–C–T–A–A–G–G–5’?
3’–C–T–A–A–G–G–5’?
2. 5’–G–A–U–U–C–C–5’
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Learning Check
The following section of DNA is used to
build a mRNA
for a protein.
3’—GAA—CCC—TTT—5’
A. What is the corresponding mRNA
sequence?
B. What are the anticodons on the tRNAs?
C. What is the amino acid order in the
peptide?
56
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Solution
3’—GAA—CCC—TTT—5’ DNA
A. What is the corresponding mRNA sequence?
5’—CUU—GGG—AAA—3’ mRNA
B. What are the anticodons for the tRNAs?
mRNA codons
CUU GGG AAA
tRNA anticodons
GAA CCC UUU
C. What is the amino acid order in the peptide?
mRNA 5’—CUU—GGG—AAA—3’
Leu — Gly — Lys
57
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