CHAPTER 17

Gene Expression:
From Gene to Protein

What is a gene?
Beadle & Tatum
(has the precursor)

Bread mold
Requires arginine (an amino acid) to grow
Can make arginine from a precursor

Precursor ornithine citruline arginine

Enzyme A

Enzyme B

Enzyme C

What is a gene?
Beadle & Tatum
(has the precursor)

Bread mold
Mutated the mold (changed the DNA)
Can NO LONGER make arginine from a precursor

Precursor ornithine citruline arginine

Enzyme A

Enzyme B

Enzyme C

What is a gene?
Beadle & Tatum
(has the precursor)

Bread mold
Mutated the mold (changed the DNA)
Can NO LONGER make arginine from a precursor
One of the enzymes is no longer functional

Precursor ornithine citruline arginine

Enzyme A

Enzyme B

Enzyme C

 Different DNA mutations led to different growth

Therefore - DNA must specify the cells enzymes!
One gene-one enzyme
Since modified toone gene one polypeptide
Inactive enzyme:
A
B
C

Precursor ornithine citruline arginine

Enzyme A

Enzyme B

Enzyme C

Genes specify proteins via

transcription and translation

Central Dogma: the flow of

genetic information
Gene - Discrete
unit of hereditary
information

DNA
Transcription

mRNA
Translation

Protein

The Genetic Code

DNA codes for proteins
There are only 4 nucleotide bases (A T G
C) in DNA
But there are 20 different amino acids in
proteins

How can 4 DNA bases code for

20 amino acids?

The Genetic Code

If genetic code is one-nucleotide, then only 4 amino acids are
possible (41 = 4)
If genetic code is two-nucleotides, then only 16 amino acids are
possible (42 = 16)
If genetic code is three-nucleotides, then 64 amino acids are
possible (43 = 64)
So the genetic code is three-nucleotides

(a triplet code)

The Genetic Code Basics: Codons

DNA template strand (1 strand only)
Transcription to mRNA (Uracil replaces Thymine)
Translation to protein
Codons are read 5 to 3 (triplets of RNA bases)

The genetic code dictionary (this is

what the triplet codons spell)
Redundancy - several

codons code for the same

amino acid

Punctuation is needed
Start (AUG)
Stop (several)

Universal
Know how to use this
dictionary

Interpreting the Message Correctly

The codons need to be in the correct Reading Frame

This is why the
punctuation (Start and
Stop) is so important
What if the
reading frame
is shifted?

Frameshift

Transcription is the DNA-directed

synthesis of RNA:
a closer look
Eukaryotic cell
Occurs in the nucleus
Transcription yields:
Primary transcript
(Pre-mRNA)
RNA processing yields:
mRNA

Transcription
Overview
(1) Initiation

(2) Elongation
(3) Termination

(1) Initiation
Eukaryotic Promoter
TATA box
Start point
Transcription factors (proteins)
Bind to promotor
There are general and
specific transcription factors
(more in next Chap)
Allow attachment of
RNA polymerase II
Untwists DNA
RNA transcript synthesized
5 to 3 (Reads DNA 3 to 5)
No primer needed

(2) Elongation
RNA pol II synthesizes
~60 nucleotides per second
(dont need to know the
number, just kind of cool)
Multiple RNA polymerases
can bind to a gene (like a
convoy)

(3) Termination of transcription

Eukaryotes
RNA pol II reads DNA
sequence
through the STOP
codon
through a
polyadenylation signal
sequence
and just downstream
from that, proteins cut
the pre-mRNA free

Eukaryotic cells modify RNA after

transcription

RNA processing

RNA Processing
After transcription
(1) Alteration of mRNA ends
- 5 cap
- poly A tail

(2) RNA splicing

RNA Processing

(1) mRNA ends - 5 cap and poly A tail

Enzymatically added after transcription
Functions
Help mRNA out of the nucleus
Help protect mRNA from enzymatic
breakdown
Help ribosomes attach to 5 end (UTRs
help with this too)
(UTR = untranslated region)

RNA Processing
(2) RNA Splicing

The primary
transcript has
Introns and Exons
Introns are cut out
of primary
transcript
Now it is a mRNA

Introns and Exons

How are the introns cut out?

snRNPs

(small nuclear

ribonucleoproteins)

+ other
proteins =
Spliceosome

Why does out mRNA have introns

and exons?
Each exon codes for a
domain of the protein
Alternative splicing
different polypeptides
Important in evolution

Translation is the RNA-directed

synthesis of a polypeptide

Translation: making protein

Review

Made on ribosomes
Free ribosomes:
Cytoplasmic and nuclear proteins
Bound ribosomes (RER):
Export, membrane, lysosomal proteins
Translating genetic code to amino acid
sequence

A four base language A 20 amino acid language

Translation: the players

mRNA
tRNA
Ribosomes
Small subunit
Large subunit

Amino Acids

Transfer RNA (tRNA) is a key

player in translation
tRNA brings aa to a
growing protein
Anticodon
Amino acid
attachment site

Translation involves
2 specific recognition steps
(1) Correct match between a tRNA and
the amino acid that it carries
(2) Recognition of the mRNA codon by
the tRNA anticodon

(1) Correct match between a

tRNA and the amino acid that
it carries
Enzyme attaches correct aa
to each tRNA (matches aa to
anticodon)
Amino Acid + ATP + tRNA
Aminoacyl-tRNA
Synthetase

Aminoacyl tRNA
(Charged tRNA)

(Specific for
this aa and
tRNA)

(2) Recognition of the mRNA codon by

the tRNA anticodon
This happens on the
ribosome
There are 61 mRNA
codons (see the
dictionary)
But there are only 45
different tRNAs
Relaxed 3rd codon
pairing
This is called wobble

Ribosomes
Made in the nucleolus
Protein and RNA
(ribonucleoprotein)
Large and small subunit
Come together only with
mRNA
mRNA binding site
A site (incoming aa)
P site (growing protein)
E site (exit)

Building a Polypeptide

The Steps
(1) Initiation
(2) Elongation
(3) Termination

(1) Initiation
mRNA binds to small ribosome subunit
Initiator tRNA binds to START codon (methionine)
Sets reading frame (5 to 3)
Large subunit joins in (GTP is required)
Initiator tRNA is in the P site

(2) Elongation
Peptide bond
Dehydration
synthesis
Amino end
(N-terminus)
Carboxyl end
(C-terminus)

1) Codon
recognition
(req 2 GTP)

3) mRNA
Translocates
(req 1 GTP)

2) Peptide bond
formation

Other proteins (elongation factors) are also involved

(3) Termination
STOP codon in A site
Release factor binds instead of tRNA
Translation ends
Breaks bond between polypeptide and tRNA
Everyone goes home!

Polyribosomes (Polysomes) are like

convoys of ribosomes on an mRNA

What is the
function of these?

Getting Proteins to Specific Locations

(where they are needed)

Review
Free Ribosomes
Make proteins found in the cytoplasm and
nucleus
Bound Ribosomes
Make proteins for export, and those
found in the membrane or lysosomes

Getting Proteins to Specific Locations

All protein synthesis starts on free ribosomes
IF the polypeptide has a signal peptide (first 20 aa
of protein (zip code) RER
Helped there by a shuttle protein

After the polypeptide is synthesized, it needs

to be made into a functional protein
(1) Chaperonins create the right environment (hydrophilic)
for the protein to fold properly

Chapter 5

After the polypeptide is synthesized, it needs

to be made into a functional protein
(2) Other post-translational modifications

Examples (dont need to know these)

Attachment of sugars, lipids, etc.
Removal of aas from the amino end
Cleaving
Bringing 2 together

Summary
(Eukaryotes)

Gene expression
in prokaryotes is
different
No nucleus
Transcription and
translation are
coupled
No RNA processing
needed
No introns

Point mutations in DNA can

affect protein structure and
function

Point Mutations may affect protein

structure and function

What is a mutation?
What is a point mutation?
(1) Nucleotide-pair Substitutions
(2) Insertions and Deletions

(1) Nucleotide-pair Substitutions

Silent mutations

(1) Nucleotide-pair Substitutions

Missense mutations

(1) Nucleotide-pair Substitutions

Nonsense mutations

(2) Insertions and Deletions

Frameshift (causing nonsense mutation)

(2) Insertions and Deletions

Frameshift (causing extensive missense mutation)

(2) Insertions and Deletions

No Frameshift (missing or extra amino acid)

Seemingly simple mutations can

cause dramatic effects
(Sickle-cell disease)

Mutagens can increase the

likelihood of mutations
Mutagens include:
Radiation
X-ray
Ultraviolet

Chemicals that

act as base analogs

insert into DNA and cause
distortion

Viruses

HPV
Hepatitis b virus

Why is it important to
understand mutagens?
Mutations can cause
Cancer
Cell death
Inheritable mutations