©1998 Timothy G. Standish

From DNAFrom DNATo RNATo RNA

To ProteinTo Protein

OH

OCH2

Sugar

HOH

A NucleotideA Nucleotide

NH2

N

N N

N

BaseP

O

OH

HO O

Phosphate

©1998 Timothy G. Standish

Pyrimidines

NH2

O

N

N NH

N

Guanine

N

N

Adenine

N

N

NH2

N O

NH2

N O

NH2

NCytosine

Uracil(RNA)CH3

N ON

O

NH

N ON

O

NH

Thymine(DNA)

Purines

©1998 Timothy G. Standish

Two Families of BasesTwo Families of Bases

DNA

mRNA

Transcription

IntroductionIntroduction

The Central Dogma The Central Dogma of Molecular Biologyof Molecular Biology

Cell

Polypeptide(protein)

TranslationRibosome

©1998 Timothy G. Standish

3’

5’

5’

3’

Transcription And Translation Transcription And Translation In ProkaryotesIn Prokaryotes

Ribosome

Ribosome5’

mRNA

RNAPol.

©1998 Timothy G. Standish

DNA

Cytoplasm

Nucleus

Eukaryotic TranscriptionEukaryotic Transcription

ExportG AAAAAA

RNA

Transcription

Nuclear pores

G AAAAAA

RNAProcessing

mRNA

©1998 Timothy G. Standish

Nucleotide WordsNucleotide 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

SU

GA

R-P

HO

SP

HA

TE

BA

CK

BO

NE

B A

S E

S

H

PO

O

HO

O

O

CH2NH2N

NH

N

N

HOH

P

O

O

HO

O

O

CH2

NH2

N

N

N

N

H

P

O

OH

HO

O

O

CH2

NH2

N

N

N

N

O

A CodonA Codon

GuanineGuanine

AdenineAdenine

AdenineAdenine

Arginine

©1998 Timothy G. Standish

Redundancy in the CodeRedundancy 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 Why Not Use Shorter Codons?Codons?

If each 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

S E C O N D B A S E

A

GGUGGCGGAGGG

Gly*

AGUAGCAGAAGG

Arg

G

CGUCGCCGACGG

Arg

GUGUUGCUGAUGG

C

GAUGACGAAGAG

AAUAACAAAAAG

Glu

CAUCACCAACAG

AUAUUACUAAUAG

Stop

Tyr

GUUGUCGUAGUG

Val

AUUAUCAUAAUG start

Ile

CUUCUCCUACUG

Leu

UUUUUUCUUAUUG

Leu

Phe

Met/

GCUGCCGCAGCG

Ala

ACUACCACAACG

Thr

CCUCCCCCACCG

Pro

CUCUUCCUCAUCG

Ser

UCAG

U

UCAG

UCAG

UCAG

Gln†

His

Trp

Cys THIRD

BASE

FIRST

BASE

The Genetic CodeThe Genetic Code

Asp

Lys

Asn†

Stop

Ser

Neutral Non-polarPolarBasicAcidic

†Have aminegroups

*Listed as non-polar bysome texts

©1998 Timothy G. Standish

InitiationInitiation 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:How Codons Work:tRNA the TranslatorstRNA the Translators

tRNA - Transfer RNARelatively 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

MethionineMet-tRNAMet-tRNA

U*

9

262223Pu

16

12Py 10

25

20:1

G*

17:1

Pu

A20:2

1713

20G

A5051

656463

G

62

52

CPu

59

A*

C

Py

T49

39

4142

31

2928

Pu*

43127

U35

38

36

Py*

34

403047:1

47:15

46

Py47:16

4544

47

73CCA

707172

66676869

321

7654

A CU

Anticodon

©1998 Timothy G. Standish

AE

Large subunit

P

Small subunit

Translation - InitiationTranslation - Initiation

fMet

UACGAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA5’mRNA

3’

©1998 Timothy G. Standish

AE

Ribosome P UCU

Arg

Aminoacyl tRNA

PheLeu

Met

SerGly

Polypeptide

CCA

Translation - ElongationTranslation - Elongation

GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA5’mRNA

3’

©1998 Timothy G. Standish

AE

Ribosome P

PheLeu

Met

SerGly

Polypeptide

Arg

Aminoacyl tRNA

UCUCCA

Translation - ElongationTranslation - Elongation

GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA5’mRNA

3’

©1998 Timothy G. Standish

ANYTHING

ACIDAMINE

Protein SynthesisProtein Synthesis

C

O

OHCN

H

HH

C

HO H

C

H

O

CN

H

HH

C

H H

C

H

O

OHCN

H

HH

C

HO H

Serine

C

H

O

OHCN

H

HH

C

H H

AlanineH

C

O

OHC

R

N

H

H

Amino Acid

H2O

©1998 Timothy G. Standish

AE

Ribosome P

CCA

Arg

UCU

PheLeu

Met

SerGly

Polypeptide

Translation - ElongationTranslation - Elongation

GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA5’mRNA

3’

©1998 Timothy G. Standish

AE

Ribosome P

Translation - ElongationTranslation - Elongation

Aminoacyl tRNA

CGA

Ala

CCA

Arg

UCU

PheLeu

Met

SerGly

Polypeptide

GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA5’mRNA

3’

©1998 Timothy G. Standish

AE

Ribosome P

Translation - ElongationTranslation - Elongation

CCA

Arg

UCU

PheLeu

Met

SerGly

Polypeptide

CGA

Ala

GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA5’mRNA

3’

©1998 Timothy G. Standish

Problem 1Problem 1Transcribe and translate the following

DNA sequence:3’AATAGTACCGCAAATTTATCGCTT5’

5’UUAUCAUGGCGUUUAAAUAGCGAA3’

5’UUAUC,AUG,GCG,UUU,AAA,UAG,CGAA3’

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