Chapter 17: From Gene to Protein

AP Biology 2013

Flow of Genetic InformationInformation content of DNA is in the form of specific sequences of nucleotides

DNA inherited by an organism leads to specific traits by dictating the synthesis of proteins

Proteins are the links between genotype and phenotype

Gene expression, the process by which DNA directs protein synthesis, includes transcription and translation

Fig. 17.1

DNA Directs Protein SynthesisTwo stages called transcription and translation

The ribosome is the site of translation

Each gene controls the production of one polypeptide (sometimes referred to as the “one gene, one protein” hypothesis)

Transcription

Synthesis of RNA under the direction of DNA (mRNA)

Translation

Synthesis of a polypeptide from mRNA (happens at ribosomes)

DNA RNA Protein

1

2

3

Prokaryotic vs. EukaryoticIn prokaryotes, translation of mRNA can begin before transcription has finished.

In eukaryotes, this is not possible.

DNA

mRNA Ribosome

Polypeptide

TRANSCRIPTION

TRANSLATION

TRANSCRIPTION

TRANSLATION

Polypeptide

Ribosome

DNA

mRNA

Pre-mRNA RNA PROCESSING

(a) Bacterial cell (b) Eukaryotic cell

Nuclear envelope Fig. 17.3

The CodonEach codon (3 nucleotide sequence) codes for an amino acid or a stop

The gene (DNA) determines the sequence of bases along the mRNA molecule

Codons are read from 5’ to 3’DNA template strand

TRANSCRIPTION

mRNA

TRANSLATION

Protein

Amino acid

Codon

Trp Phe Gly

5!

5!

Ser

U U U U U 3!

3!

5! 3!

G

G

G G C C

T

C

A

A

A A A A A

T T T T

T

G

G G G

C C C G G DNA molecule

Gene 1

Gene 2

Gene 3

C C

Fig. 17.4

Second mRNA base

Firs

t mR

NA

bas

e (5! e

nd o

f cod

on)

Third

mR

NA

bas

e (3! e

nd o

f cod

on)

UUU UUC UUA

CUU CUC CUA CUG

Phe

Leu

Leu

Ile

UCU UCC UCA UCG

Ser

CCU CCC CCA CCG

UAU UAC

Tyr

Pro

Thr

UAA Stop UAG Stop

UGA Stop

UGU UGC

Cys

UGG Trp

G C U

U

C

A

U

U

C

C

C A

U

A

A

A

G

G

His

Gln

Asn

Lys

Asp

CAU CGU CAC CAA CAG

CGC CGA CGG

G

AUU AUC AUA

ACU ACC ACA

AAU AAC AAA

AGU AGC AGA

Arg

Ser

Arg

Gly

ACG AUG AAG AGG

GUU GUC GUA GUG

GCU GCC GCA GCG

GAU GAC GAA GAG

Val Ala

GGU GGC GGA GGG

Glu Gly

G

U C A

Met or start

UUG

G

Fig. 17.5

UniversalityGenetic code is universal

Genes can be transcribed and translated after transplantation from one species to another (a) Tobacco plant expressing

a firefly gene gene (b) Pig expressing a jellyfish

Fig. 17.6

4

5

6

TranscriptionStarted with the binding of RNA polymerase at a promoter

Separates the DNA strand and adds the RNA nucleotides

Follows same base pairing rules except, uracil substitutes for thymine

Three stages:

Initiation

Elongation

Termination

Promoter

RNA polymerase Start point

DNA

5! 3!

Transcription unit

3! 5!

Elongation

5! 3!

3! 5!

Nontemplate strand of DNA

Template strand of DNA RNA transcript Unwound

DNA 2

3! 5! 3! 5!

3!

Rewound DNA

RNA transcript

5!

Termination 3

3! 5!

5! Completed RNA transcript

Direction of transcription (“downstream”)

5! 3!

3!

Initiation 1

Fig. 17.7

TranscriptionPromoter regions signal a binding site for the RNA polymerase

Transcription factors also help the RNA polymerase recognize the promoter sequence

RNA polymerase continues down the strand exposing 10-20 DNA bases at a time

Termination signals are different:

Prokaryotes: RNA polymerase stops at a termination sequence

Eukaryotes: RNA polymerase continues past a polyadenylation signal and will eventually fall off

Transcription initiation complex forms

3

DNA Promoter

Nontemplate strand

5! 3!

5! 3!

5! 3!

Transcription factors

RNA polymerase II Transcription factors

5! 3!

5! 3!

5! 3!

RNA transcript

Transcription initiation complex

5! 3!

TATA box

T

T T T T T

A A A A A

A A T

Several transcription factors bind to DNA

2

A eukaryotic promoter 1

Start point Template strand

Fig. 17.8

Nontemplate strand of DNA

RNA nucleotides

RNA polymerase

Template strand of DNA

3!

3! 5!

5!

5!

3!

Newly made RNA

Direction of transcription

A

A A A

A A

A

T

T T

T

T T T G

G G

C

C C

C C

G

C C C A A A

U

U

U

end

Fig. 17.9

Eukaryotic ModificationEnzymes in the nucleus modify pre-mRNA before it is released to the cytoplasm

The 5’ end receives a nucleotide cap

The 3’ end receives a poly-A tail

RNA splicing - removing introns and joins exons

Figs. 17.10 & 17.11

Protein-coding segment

Polyadenylation signal

5! 3!

3! 5! 5! Cap UTR Start codon

G P P P Stop codon UTR

AAUAAA

Poly-A tail

AAA AAA …

5! Exon Intron Exon 5! Cap Pre-mRNA

Codon numbers

1-30 31-104

mRNA 5! Cap

5!

Intron Exon

3! UTR

Introns cut out and exons spliced together

3!

105- 146

Poly-A tail

Coding segment

Poly-A tail

UTR 1-146

7

8

9

SpliceosomesRNA transcript (pre-mRNA)

5! Exon 1

Protein snRNA

snRNPs

Intron Exon 2

Other proteins

Spliceosome

5!

Spliceosome components

Cut-out intron mRNA

5! Exon 1 Exon 2

Fig. 17.12

Alternative RNA Splicing

Depending on which segments are treated as introns, different proteins can be formed.

Consists of regions called domains

Different exons code for different domains

Gene DNA

Exon 1 Exon 2 Exon 3 Intron Intron

Transcription

RNA processing

Translation

Domain 3

Domain 2

Domain 1

Polypeptide

TranslationTRANSCRIPTION

TRANSLATION

DNA

mRNA Ribosome

Polypeptide

Polypeptide Amino acids

tRNA with amino acid attached Ribosome

tRNA

Anticodon

mRNA

Trp

Phe Gly

A G C

A A A

C C G

U G G U U U G G C

Codons 5! 3!

10

11

12

tRNASingle RNA strand that is about 80 nucleotides long

Joining of amino acid to the correct tRNA is accomplished by aminoacyl-tRNA synthetase

Amino acid attachment site

3!

5!

Hydrogen bonds

Anticodon

(a) Two-dimensional structure (b) Three-dimensional structure (c) Symbol used

in this book

Anticodon Anticodon 3! 5!

Hydrogen bonds

Amino acid attachment site 5!

3!

A A G Fig. 17.15

Aminoacyl-tRNA synthetase (enzyme)

Amino acid

P P P Adenosine

ATP

P

P

P

P P i

i

i

Adenosine

tRNA

Adenosine P

tRNA

AMP

Computer model

Amino acid

Aminoacyl-tRNA synthetase

Aminoacyl tRNA (“charged tRNA”)

Fig. 17.16

RibosomesFacilitate the coupling of tRNA anticodons with mRNA codons

Made of proteins and RNA molecules (rRNA)tRNA molecules

Growing polypeptide Exit tunnel

E P A

Large subunit

Small subunit

mRNA 5!

3!

(a) Computer model of functioning ribosome

Exit tunnel Amino end

A site (Aminoacyl- tRNA binding site)

Small subunit

Large subunit

E P A mRNA

E

P site (Peptidyl-tRNA binding site)

mRNA binding site

(b) Schematic model showing binding sites

E site (Exit site)

(c) Schematic model with mRNA and tRNA

5! Codons

3!

tRNA

Growing polypeptide

Next amino acid to be added to polypeptide chain

Fig. 17.17

13

14

15

Translation Three stages:

INITIATION

Elongation

Termination

Initiator tRNA

mRNA

5!

5! 3! Start codon

Small ribosomal subunit

mRNA binding site

3!

Translation initiation complex

5! 3! 3! U

U A

A G C

P

P site

i +

GTP GDP

Met Met

Large ribosomal subunit

E A

5!

Fig. 17.18

Three stages:

Initiation

ELONGATION

Termination

TranslationAmino end of polypeptide

mRNA

5!

E

A site

3!

E

GTP

GDP + P i

P A

E

P A

GTP

GDP + P i

P A

E

Ribosome ready for next aminoacyl tRNA

P site

Fig. 17.19

Release factor

Stop codon (UAG, UAA, or UGA)

3!

5!

3!

5!

Free polypeptide

2 GTP

5!

3!

2 GDP + 2 i P

Three stages:

Initiation

ELONGATION

Termination

Translation

Fig. 17.20

16

17

18

PolyribosomesMany ribosomes can simultaneously tranlate a single mRNA molecule

This can result in signal amplification

Completed polypeptide

Incoming ribosomal subunits

Start of mRNA (5! end)

End of mRNA (3! end) (a)

Polyribosome

Ribosomes

mRNA

(b) 0.1 µm

Growing polypeptides

Fig. 17.21

Post-translational ModificationsMay be modified to impact the 3-D shape of the protein

Proteins destined for the endomembrane system or for secretion must be transported into the ER

Have signal peptides to which SRP (signal-recognition particle) binds, enabling the translation ribosome to bind to the ER

Ribosome

mRNA Signal peptide

SRP

1

SRP receptor protein

Translocation complex

ER LUMEN

2

3

4 5

6

Signal peptide removed

CYTOSOL

Protein

ER membrane

Fig. 17.22

TRANSCRIPTION DNA

RNA polymerase

Exon RNA transcript

RNA PROCESSING

NUCLEUS

Intron

RNA transcript (pre-mRNA)

Poly-A

Poly-A

Aminoacyl- tRNA synthetase

AMINO ACID ACTIVATION

Amino acid tRNA

5! Cap

Poly-A 3!

Growing polypeptide mRNA

Aminoacyl (charged) tRNA

Anticodon

Ribosomal subunits

A

A E TRANSLATION

5! Cap

CYTOPLASM

P E

Codon

Ribosome

5!

3!

Fig. 17.26

19

20

21

Point MutationsMutations - changes in genetic material

Point mutations - changes in one base pair

Substitutions - can cause missense or nonsense

Insertions and deletions - can cause frameshifts

Wild-type hemoglobin

Wild-type hemoglobin DNA 3!

3!

3! 5!

5! 3!

3! 5!

5! 5! 5! 3!

mRNA

A A G C T T

A A G mRNA

Normal hemoglobin Glu

Sickle-cell hemoglobin Val

A A

A U G

G T

T

Sickle-cell hemoglobin

Mutant hemoglobin DNA C

Fig. 17.23

Wild type

DNA template strand

mRNA5!

5!

3!

Protein

Amino end

A instead of G

(a) Nucleotide-pair substitution

3!

3!

5!

Met Lys Phe Gly Stop Carboxyl end

T T T T T T T T T T A A A A A A A A A C C

C

C A

A A A A A

G G G G G C C

G G G U U U U U G

(b) Nucleotide-pair insertion or deletion Extra A

3! 5!

5! 3!

Extra U 5! 3!

T T T T T T T T

A A A A

A A T G G G G

G A A A A C

C C C C A T 3! 5!

5! 3!

5! T T T T T A A A A C C A A C C T T T T T A A A A A T G G G G

U instead of C

Stop

U A A A A A G G G U U U U U G Met Lys Phe Gly

Silent (no effect on amino acid sequence)

T instead of C

T T T T T A A A A C C A G T C

T A T T T A A A A C C A G C C

A instead of G

C A A A A A G A G U U U U U G U A A A A G G G U U U G A C

A A U U A A U U G U G G C U A

G A U A U A A U G U G U U C G

Met Lys Phe Ser

Stop

Stop Met Lys

missing

missing

Frameshift causing immediate nonsense (1 nucleotide-pair insertion)

Frameshift causing extensive missense (1 nucleotide-pair deletion)

missing

T T T T T T C A A C C A A C G A G T T T A A A A A T G G G C

Leu Ala

Missense

A instead of T

T T T T T A A A A A C G G A G

A

C A U A A A G G G U U U U U G

T T T T T A T A A A C G G G G

Met

Nonsense

Stop

U instead of A

3! 5!

3! 5!

5! 3!

3! 5!

5! 3!

3! 5! 3! Met Phe Gly

No frameshift, but one amino acid missing (3 nucleotide-pair deletion)

missing

3! 5!

5! 3!

5! 3! U

T C A A A C A T T A C G T A G T T T G G A A T C

T T C

A A G

Met

3!

T

A

Stop

3! 5!

5! 3!

5! 3! Fig. 17.24

Proks vs. EuksIn prokaryotes, translation can begin while transcription is still in progress

In eukaryotes, RNA processing happens in the nucleus.

DNA

Polyribosome

mRNA

Direction of transcription

0.25 µm RNA polymerase

Polyribosome

Ribosome

DNA

mRNA (5! end)

RNA polymerase

Polypeptide (amino end)

22

23

24