Download WELCOME TO BIOLOGY 2002 - University of Indianapolis

Making Proteins
Central Dogma of Genetics
Nucleus
Information
storage
DNA
TRANSCRIPTION
mRNA
Information
carrier
Cytoplasm
mRNA
Active cell
machinery
TRANSLATION
Protein
The Genetic Code

The nucleotide sequence of DNA is a code; DNA is an
information-storage molecule without enzymatic capabilities
(F. Crick).

The information in DNA is copied into RNA, which is used to
make proteins (mRNA = messenger RNA).

Hypothesis: each of the 20 amino acids in proteins is specified
by one or more 3 base codons (Gamow).
How does the genetic code work?
There are 4 RNA bases (U, C, A, G) and they must specify 20 amino acids.
How many
bases
specify
G G
ACGC UG A U AA CC CG U C AG U UCC AACA U C G G UA AUCCGC C C AG AG C U mRNA
a single
amino acid? 1 Base?
3 Bases?
2 Bases?
4 Bases?...
A doublet code could
specify a maximum of
4 x 4 or 16 amino acids.
U C A G
1 2 3 4
4 < 20: Not enough
Since there are
only 4 bases, a
singlet code
could only
specify 4
amino acids.
U U UC U A U G
2
3
4
1
C U CC C A C G
6
5
7
8
AU AC AA AG
9
12
10 11
G U G C G A GG
13 14 15 16
16 < 20: Not enough
A triplet code could specify a
maximum of 4 x 4 x 4, or 64
amino acids.
UU U UU C U U A UUG
2
1
3
4
CC U C CC C C A CCG
6
5
7
8
A A U A A C A A A A AG
9
10
11
12
GG U G G C G GA etc...
14
15
13
64 > 20: More than enough
Figure 17.4 The dictionary of the genetic code
One gene-one
polypeptide hypothesis:
A gene is a length of a
DNA molecule that
contains the information to
produce one polypeptide
chain
Figure 17.2 Overview: the roles of transcription and translation in the flow of genetic information (Layer 1)
Figure 17.2 Overview: the roles of transcription and translation in the flow of genetic information (Layer 2)
Figure 17.2 Overview: the roles of transcription and translation in the flow of genetic information (Layer 3)
Figure 17.2 Overview: the roles of transcription and translation in the flow of genetic information (Layer 4)
Figure 17.2 Overview: the roles of transcription and translation in the flow of genetic information (Layer 5)
Transcription produces an RNA molecule complementary to a
DNA template
DNA
3’
RNA 3’
5’
3’
3’
5’
5’
P
RNA
Template
strand
5’
3’
P
P
P P P
3’
P
O
HO
OH
O
OH
C
U
G
A
T
C
O
O
O
O
P
P
P
5’
DNA
5’
P
RNA transcription is catalyzed by RNA polymerase
RNA
polymerase
DNA
Protein Synthesis Begins with the Process of
Gene Transcription

Steps of Transcription
• RNA polymerase binds to the promoter region of the DNA
• RNA polymerase unwinds the DNA.
• RNA polymerase reads DNA 3' to 5' and synthesizes
complementary RNA 5' to 3'.
Figure 17.6 The stages of transcription: initiation, elongation, and termination (Layer 1)
Figure 17.6 The stages of transcription: initiation, elongation, and termination (Layer 2)
Figure 17.6 The stages of transcription: initiation, elongation, and termination (Layer 3)
Figure 17.6 The stages of transcription: initiation, elongation, and termination (Layer 4)
Close up of transcription
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
In eukaryotes: proteins
called transcription
factors bind to the
promoter first, then RNA
polymerase binds to
start transcription
After Transcription

Transcription in Prokaryotes
• The RNA produced is ready to be translated = mRNA

Transcription in Eukaryotes
• The RNA produced must be modified before translation: 1°
transcript--> mRNA
• Eukaryotic mRNAs are processed in the nucleus by addition
of a 5' cap and 3' poly A tail
• Eukaryotic genes have introns: non-coding regions that
must be removed from the primary mRNA to make an intact
uninterrupted message.
RNA processing in Eukaryotes
Molecules called small
nuclear ribonucleoproteins
(snRNPs) combine to splice
introns from mRNA
Figure 17.11 Correspondence between exons and protein domains
After transcription, the next step is translation

Translation Converts the Nucleotide Sequence of mRNA into
the Amino Acid Sequence of a Protein

Translation occurs on ribosomes either in the cytoplasm or on
the endoplasmic reticulum
Structure of a ribosome
Large subunit
Small subunit
Proteins
E site
P site
A site
rRNAs =
ribosomal RNA
Active site
(contains
only rRNA)
The adaptor molecule between mRNA and protein is
tRNA (transfer RNA)
Stems are created
by hydrogen bonding
between complementary
base pairs
Loops consist
of unpaired
bases
Figure 17.13b The structure of transfer RNA (tRNA)
An aminoacyl-tRNA synthetase
joins a specific amino acid to a
tRNA
Early model of tRNA function
Amino
acid
Ser
3’
A
C
C
5’
Binding site for
amino acid
Binding site for
mRNA codon
Serine anticodon
A GU
5’
U CA
mRNA
Serine codon
3’
Figure 17.15 The anatomy of a functioning ribosome
Translation Converts the Nucleotide Sequence of
mRNA into the Amino Acid Sequence of a Protein

Translation occurs in three steps:
• Initiation: the ribosome 30S subunit binds mRNA and moves
to the AUG codon, which is the translation start site.
• The initiator methionine tRNA binds to the AUG start codon.
• The ribosome 50S subunit assembles so that the initiator tRNA and
the AUG codon are in the P site.
Figure 17.17 The initiation of translation
Translation Converts the Nucleotide Sequence of
mRNA into the Amino Acid Sequence of a Protein

Translation occurs in three steps:
• Elongation: amino acids are joined together and the ribosome
moves to the next codon.
• New tRNAs enters the A site of the ribosome
• A peptide bond forms between the polypeptide on the tRNA in
the P site and the amino acid in the A site, which transfers the
polypeptide to the A site tRNA.
• The ribosome moves along the mRNA in the 5' to 3' direction.
Figure 17.18 The elongation cycle of translation
Translation Converts the Nucleotide Sequence of
mRNA into the Amino Acid Sequence of a Protein

Translation occurs in three steps:
• Termination: when a stop codon on mRNA is encountered in the A
site, the completed polypeptide is released, and the ribosome
disengages.
• Release factors are required.
Figure 17.19 The termination of translation
Post-translational events affect the structure, activity,
and destination of the protein

Proteins must fold into their proper 3D structure.
Primary
structure
Tertiary
structure
Secondary
structure
Quaternary
structure

The Central Dogma: Information Flows from
DNA to RNA to Proteins (F.Crick)
Viruses that have RNA genomes contradict the central
dogma, but all cells conform to it.
Virus protein coat
Virus RNA
1. Start of infection.
2. Reverse transcriptase uses
Virus RNA enters host Virus RNA as template to
cells.
produce virus DNA
3. Virus DNA directs
4. End of infection.
the production of new New generation of
virus particles.
virus particles burst
from host cell.
Mutation and DNA Repair Mechanisms

Mutations are created by chemicals, radiation, errors
in meiosis and mistakes in DNA replication.
• Mutations can be deleterious, beneficial, or silent.
• Mutations in an individual are usually deleterious, may
cause disease and death.
• Mutations in a population are a source of genetic diversity
that allows evolution to occur.
Point mutations are a change in single base pair of DNA
A A C T G G C
A base-pair substitution:
Wild type
T T G A C C G
A A C T G G C
A A C T A G C
MUTANT
3'
5'
A A C T G G C
T T G A T C G
DNA replication
T T G A C C G
5'
3'
A A C T G G C
T T G A T C G
DNA replication
A A C T G G C
Wild type
Parental DNA
T T G A C C G
T T G A C C G
First generation
progeny
A A C T G G C
Wild type
T T G A C C G
Second generation
progeny
Figure 17.24 Categories of
Base-pair substitutions
DNA point mutations can lead to a different
amino acid sequence.
Phenotype
Start of coding sequence
CAC
DNA
sequence GTG
GTG
CAC
GAC
CTG
TGA
ACT
GGA
CCT
CTC
GAG
CTC
GAG
Normal
Amino
acid
sequence
Valine
CAC
DNA
sequence GTG
Histidine
GTG
CAC
Leucine
GAC
CTG
Threonine
Glutamic
Proline Glutamic
acid
acid
TGA
ACT
GGA
CCT
CAC
GTG
Normal red blood cells
CTC
GAG
Mutant
Amino
acid
sequence
Histidine
Valine
Threonine
Leucine
Proline
Valine
Glutamic
acid
Sickled red blood cells
Insertion or deletion of a
single base-pair causes
frameshift mutations
UV radiation can cause 2 thymines that are next to each other to
bind to each other instead of the adenines in the other strand
UV-induced thymine dimers caused DNA to kink
P
CH2
DNA strand
with adjacent
P
thymine
bases
CH
P
N
O
N Thymine
H
H
O
N Thymine
CH3
O
Kink
P
O
CH2 O
N
N
O
H
O
N
H
P
Thymine
dimer
H
O
UV light
N
2
CH2
O
CH3
O
H
P
H
O
CH3
H
N
O
CH3
Mutation and DNA Repair Mechanisms

DNA Repair Mechanisms
• DNA polymerase proofreads and corrects point mutations
during replication.
• Other excision repair systems scan newly formed DNA and
correct remaining mutations.
• Repair enzymes identify the correct template strand by its
methyl groups.
• Defects in repair system enzymes are implicated in a variety
of cancers.
DNA polymerase proofreads DNA during replication
3'
Mismatched
bases.
T
G
T
C
C
A
C
A
G
G
A
5'
T
C
G
C
G
5'
OH 3'
Polymerase
III can repair
mismatches.
5'
3'
5'
T
G
T
C
C
A
C
A
G
G
A
T
C
G
C
METHYLATION-DIRECTED MISMATCHED BASE REPAIR
Mismatch
1. Where a mismatch occurs, the
correct base is located on the
methylated strand: the incorrect base
occurs on the unmethylated strand.
2. Enzymes detect mismatch and nick
unmethylated strand.
3. DNA polymerase I excises
nucleotides on unmethylated strand.
4. DNA polymerase I fills in
gap in 5' 3' direction.
5. DNA ligase links new and
old nucleotides.
Repaired Mismatch
Some genetic diseases are associated with mutations
in DNA repair mechanisms
Xeroderma pigmentosum is a defect in
ultraviolet radiation induced DNA repair
mechanisms; characterized by severe
sensitivity to all sources of UV radiation
(especially sunlight). Symptoms include
blistering or freckling, premature aging of
skin,with increased cancers in these same
areas, blindness resulting from eye lesions
or surgery for skin lesions close to the eyes