From DNA

To RNA
To Protein
Timothy G. Standish, Ph. D.

©1998 Timothy G. Standish

 A Nucleotide
OH
Phosphate
NH2
HO P O Base
N N
O
N N
CH2
O
Sugar

OH H
OH
©1998 Timothy G. Standish
 Two Families of Bases
Purines Pyrimidines
NH2 O O
Adenine Thymine Uracil
CH3 (DNA) (RNA)
N
N NH NH
N N N O N O
O
Guanine NH2
N Cytosine
NH
N
N N NH2
N O
©1998 Timothy G. Standish
 Introduction
The Central Dogma
of Molecular Biology

Cell

Transcription DNA

mRNA
Translation Ribosome

Polypeptide
(protein)
 Transcription And Translation
In Prokaryotes
5’ 3’

3’ 5’
RNA
Pol.

Ribosome

mRNA
Ribosome
5’

©1998 Timothy G. Standish

 Eukaryotic Transcription

Nuclear
Cytoplasm
pores
DNA

Transcription
RNA
RNA
Processing
mRNA G AAAAAA G AAAAAA

Export
Nucleus

©1998 Timothy G. Standish

 Nucleotide Words
 Words in the nucleotide language
are all 3 letters or bases long.
 These three base “words” are
called codons
 This means that there can only be
43 = 64 unique words.

©1998 Timothy G. Standish

SUGAR-PHOS
OH
A Codon
NH2
HO P O
N
N Adenine

B A S E S
O
N N
CH2
O

O H
O

Guanine
HO P O
N
PH

O NH
N N NH2
CH2
ATE BACKBO

O H
NH2
Arginine
Adenine
HO P O
N
O N
N N
CH2
O
NE

OH H
©1998 Timothy G. Standish
 Redundancy in the Code
 Codons code for only 20 words, or amino acids.
 In addition to the amino acids, the start and stop
of a protein need to be coded for
 There are thus a total of 22 unique meanings for
the 64 codons, so many codons are synonyms.
 The fact that many amino acids are coded for
by several codons is called degeneracy

©1998 Timothy G. Standish

 Why Not Use Shorter
Codons?
 Ifeach codon was only 2 bases long,
there would be 42 = 16 possible unique
codons
 This would not provide enough unique
meanings to code for the 22 things (20
amino acids plus start and stop) that
have to be coded for.

©1998 Timothy G. Standish

 The Genetic Code
Neutral Non-polar
Polar SECOND BASE
Basic
Acidic U C A G
F UUU
UUC
Phe
UCU
UCC
UAU
UAC
Tyr
UGU
UGC
Cys U
C
T
I U UUA Leu UCA
Ser
UAA Stop UGA Stop A H
UUG UCG UAG UGG Trp G
R CUU CCU CAU CGU U
I
His
S C CUC
CUA
Leu CCC
CCA
Pro CAC
CAA
CGC
CGA
Arg C
A
R
Gln †
T CUG CCG CAG CGG G D
AUU ACU AAU AGU U
AUC Ile ACC AAC
Asn† AGC
Ser C
†Have amine B A AUA ACA
Thr
AAA Lys AGA Arg A B
AUGMet/start ACG AAG AGG G
groups
A GUU GCU GAU GGU U
A
Asp
*Listed as
S G GUC
GUA
Val GCC
GCA
Ala GAC
GAA
GGC
GGA
Gly* C
A
S
Glu
non-polar by E GUG GCG GAG GGG G E
some texts
©1998 Timothy G. Standish
 Initiation
 The small ribosome subunit binds to the 5’
untranslated region of mRNA
 The small ribosomal subunit slides along the mRNA
5’ to 3’ until it finds a start codon (AUG)
 The initiator tRNA with methionine binds to the start
codon
 The large ribosomal subunit binds with the initiator
tRNA in the P site

©1998 Timothy G. Standish

 How Codons Work:
tRNA the Translators
 tRNA - Transfer RNA
 Relatively small RNA molecules that fold in
a complex way to produce a 3 dimensional
shape with a specific amino acid on one end
and an anticodon on another part
 Associate a given amino acid with the codon
on the mRNA that codes for it

©1998 Timothy G. Standish

 Met-tRNA
Methionine
A
C
C
73
1 72
2 71
3 70
4 69
5 68
6 67
U* 7 66 Py 59A*
65 6463 62 C
1716 A
Pu
9 Pu
17:1
13 12 10
Py 49 5051 52 G T C
G* Py

G 22 23 Pu 25 47:16

2020:120:2A 26 47:15
27
1 4344
28 42 45
29 41 46
30 40 47
47:1
31 39
Py* 38
U Pu*
34
U 35
A 36
C
Anticodon ©1998 Timothy G. Standish
 Translation - Initiation

fMet

Large P A
subunit E
UAC
5’GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA 3’
Small mRNA
subunit

©1998 Timothy G. Standish

 Translation - Elongation
Polypeptide
Met Arg
Phe
Leu Ser
Gly
Aminoacyl tRNA

Ribosome P A UCU
E
CCA
5’GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA 3’
mRNA

©1998 Timothy G. Standish

 Translation - Elongation
Polypeptide
Met
Phe
Leu Ser
Gly Arg

Aminoacyl tRNA

Ribosome P A
E
CCA UCU
5’GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA 3’
mRNA

©1998 Timothy G. Standish

 Protein Synthesis
AMINE H O ACID
Alanine Serine
H N C OH H O H O
C
H N C OH H N C OH
ANYTHING R H
H C H C
Amino Acid C H C H
H H HO H

H2O H O H O
H N C N C OH
H C H C
C H C H
H H HO H ©1998 Timothy G. Standish
 Translation - Elongation
Polypeptide
Met
Phe
Leu Ser
Gly
Arg

Ribosome P A
E
CCA UCU
5’GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA 3’
mRNA

©1998 Timothy G. Standish

 Translation - Elongation
Polypeptide
Met
Phe Ala
Leu Ser
Gly
Arg Aminoacyl tRNA

Ribosome P A CGA
E
CCA
UCU
5’GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA 3’
mRNA

©1998 Timothy G. Standish

 Translation - Elongation
Polypeptide
Met
Phe
Leu Ser
Gly
Arg Ala

C CA
Ribosome P A
E
UCU CGA
5’GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA 3’
mRNA

©1998 Timothy G. Standish

©1998 Timothy G. Standish
 Problem 1
 Transcribe and translate the following DNA
sequence:
3’AATAGTACCGCAAATTTATCGCTT5’

5’UUAUCAUGGCGUUUAAAUAGCGAA3’

5’UUAUC,AUG,GCG,UUU,AAA,UAG,CGAA3’

Met--Ala--Phe--Lys--Stop

©1998 Timothy G. Standish

 The Genetic Code
Neutral Non-polar
Polar SECOND BASE
Basic
Acidic U C A G
F UUU
UUC
Phe
UCU
UCC
UAU
UAC
Tyr
UGU
UGC
Cys U
C
T
I U UUA Leu UCA
Ser
UAA Stop UGA Stop A H
UUG UCG UAG UGG Trp G
R CUU CCU CAU CGU U
I
His
S C CUC
CUA
Leu CCC
CCA
Pro CAC
CAA
CGC
CGA
Arg C
A
R
Gln †
T CUG CCG CAG CGG G D
AUU ACU AAU AGU U
AUC Ile ACC AAC
Asn† AGC
Ser C
†Have amine B A AUA ACA
Thr
AAA Lys AGA Arg A B
AUGMet/start ACG AAG AGG G
groups
A GUU GCU GAU GGU U
A
Asp
*Listed as
S G GUC
GUA
Val GCC
GCA
Ala GAC
GAA
GGC
GGA
Gly* C
A
S
Glu
non-polar by E GUG GCG GAG GGG G E
some texts
©1998 Timothy G. Standish