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Biophysics II
Nucleic Acids
Part 1d
Uli Nienhaus
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Nucleic Acids in Life’s Processes
DNA (107…1010 D)
Enzyme
DNA
Enzyme
mRNA
(100 − 4000 kD)
tRNA (25 kD)
+
free amino acids
rRNA
(40 − 1600 kD)
Ribosome
(E. coli: 2.7 MDa
20,000 ribonucl.
25 mass%)
Aminoacyl-tRNA
Enzyme
growing
polypeptide
chain
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Nucleic Acids: Primary Structure
U
U
C
A
U
G
A
C
Mononucleotide
P
5’
Base
Message
direction
P
5’
Phosphate
4’
3’
1’
Base
Base
2’
P
Base
Sugar
(Ribose)
A
3’
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Nucleic Acids: Primary Structure
5’
HO─CH2
HO
Base
5’
Base
OH
HO
OH
nucleoside
N
Uracil
5’-nucleotide
pN
HO─CH2
Base
3’
3’-nucleotide
Np
Sugars
in RNA
D-
D-
2
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Nucleic Acids: Nomenclature
Bases:
adenine, guanine, cytosine, thymine (uracil)
(Deoxy)ribonucleosides (base + sugar):
adenosine, guanosine, cytidine, thymidine (uridine)
Nucleoside-5‘/3‘-phosphate: nucleotide
(Deoxy)nucleotide units in RNA (DNA):
adenylate, guanylate, cytidylate, thymidylate (uridylate)
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Watson-Crick Base Pairing
T
A
10.85 Å
51.5°
C
G
10.85 Å
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Secondary Structure of DNA
22 Å
Double Helix
1 turn = 10 base pairs = 34 Å
base
Base pairing
- hydrogen bond formation
Base stacking
- hydrophobic interactions
- induced dipolar coupling
P
sugar
View along one strand of
a DNA double helix
(bases inside, sugar/phosphate
backbone outside)
Watson/Crick, 1953
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DNA Conformations
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DNA Conformations
major groove
groove
minor groove
A
B
Z
Structure of a DNA
oligonucleotide with
a drug (shown in pink)
bound in the minor
groove.
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Transfer-RNA (t-RNA): Tertiary Structure
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Transfer-RNA (t-RNA)
Acceptor
T stem stem
T loop
D loop
TΨC loop
variable loop
Anticodon stem
D stem
D loop
variable loop
Anticodon loop
Gm
A35 A
Anticodon
loop
Anticodon
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t-RNA: Base Pairing
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t-RNA Aminoacylation
At least 20 different aminoacyl-tRNA synthases exist which
link amino acids specifically to the t-RNAs
Class I: 2‘ esters
Class II: 3‘ esters
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Protein Synthesis
DNA
Transcription
mRNA
Translation
Protein
Transcription
- RNA polymerase synthesizes messenger RNA (mRNA) from DNA template.
- One subunit recognizes start signals on DNA.
- Binding of RNA polymerase locally unfolds DNA.
- There are also stop signals on the DNA.
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Translation at the Ribosome
E P A
1
mRNA
2
large ribosome subunit
3
Small ribosome subunit
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E site (exit site, binds free tRNA))
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P site (binds peptidyl-tRNA)
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A site (binds aminoacyl-tRNA)
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tRNA loaded with amino acid
(aminoacyl-tRNA synthases link
amino acids to tRNA, according to
antocodon. There are at least 20
different ones. Divided in two classes:
class I: 2’ ester
class II: 3’ ester)
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Amino acid
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Peptide chain
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unloaded tRNA
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Translation
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The Genetic Code
Relationship between base sequence of DNA and amino acid
sequence of proteins.
• The code is nearly universal.
• Three bases code for one amino acid
→ redundancy: 64 codes for 20 amino acids
• The code is sequential, non-overlapping.
Why is a degenerate code advantageous ?
• Minimizes effect of mutations.
• Permits alteration of base composition without
altering amino acid sequence.
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The Genetic Code
- XYC/XYU code for the same aa.
- XYG/XYA code for the same aa.
(except Trp, Met)
AUG also part of start sequence
Human mitochondria
use ‘special code’:
non-polar
non-polar
or
neutral polar
Charged
or
polar
Charged
or
polar
UGA: Trp
AUA: Met
AGA: Stop
AGG: Stop
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