Transcript Translation/Genetic Code

Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
13-13

Special codons:

AUG (which specifies methionine) = start codon



UAA, UAG and UGA = termination, or stop, codons
The code is degenerate

More than one codon can specify the same amino acid


For example: GGU, GGC, GGA and GGG all code for lysine
In most instances, the third base is the degenerate base


AUG specifies additional methionines within the coding sequence
It is sometime referred to as the wobble base
The code is nearly universal

Only a few rare exceptions have been noted

Refer to Table 13.3
Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
13-14

Figure 13.2 provides an overview of gene expression
Figure 13.2
13-16
Structure and Function of tRNA


In the 1950s, Francis Crick & Mahon Hoagland
proposed the adaptor hypothesis
tRNAs play a direct role in the recognition of
codons in the mRNA
Proline
anticodon
tRNA 2º Structure
Found in all tRNAs
D loop
TψC loop
D
D







loop
Figure 13.10 Structure of tRNA
The modified bases are:
I = inosine
mI = methylinosine
T = ribothymidine
D= dihydrouridine
m2G = dimethylguanosine
y = pseudouridine
3º Structure of tRNA
Charging of tRNAs

aminoacyl-tRNA synthetases


The enzymes that attach amino acids to tRNAs
There are >20 types



One for each amino acid
Ones for isoacceptor tRNAs put same a.a. on different tRNAs
Aminoacyl-tRNA synthetases catalyze a two-step
reaction


1- adenylation of amino acid
2- aminoacylation of tRNA
Aminoacyl tRNA
Synthetase Function
Figure 13.11
The amino acid is
attached to the 3’ OH
by an ester bond
tRNAs and the Wobble Rule




The genetic code is degenerate
There are >20 but < 64 tRNAs
How does the same tRNA bind to different codons?
Francis Crick proposed the wobble hypothesis in
1966 to explain the pattern of degeneracy,



1st two bases of the codon-anticodon pair strictly by
Watson-Crick rules
The 3rd position can wobble
This movement allows alternative H-bonding between
bases to form non-WC base paring
tRNAs charged with the same amino acid,
but that recognize multiple codons are
termed isoacceptor tRNAs
Figure 13.12 Wobble position and base pairing rules
Wobble Base-Pairing
between anticodon &
codon
Wobble pairing
Wobble pairing
W-C base pairing
Ribosome Structure and Assembly

Translation occurs on the surface of a large
macromolecular complex termed the ribosome

Prokaryotic cells


1 type of ribosome located in the cytoplasm
Eukaryotic cells



2 types of ribosomes
1 found in the cytoplasm
2nd found in organelles -Mitochondria; Chloroplasts

These are like prokaryotic ribosomes
Prokaryotic Ribosomes
(a) Bacterial cell
Figure 13.13
Eukaryotic Ribosomes
Figure 13.13
Functional Sites of Ribosomes

During bacterial translation, the mRNA lies on the
surface of the 30S subunit


Ribosomes contain three discrete sites




As a polypeptide is being synthesized, it exits through a
hole within the 50S subunit
Peptidyl site (P site)
Aminoacyl site (A site)
Exit site (E site)
Ribosomal structure is shown in Figure 13.14
Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
13-57
Figure 13.14
Stages of Translation



Initiation
Elongation
Termination
Stages of Translation
Initiator tRNA
Release
factors
Figure 13.15
Translation Initiation

Components





mRNA,
initiator tRNA,
Initiation factors
ribosomal subunits
The initiator tRNA

In prokaryotes, this tRNA is designated tRNAifmet


In eukaryotes, this tRNA is designated tRNAimet


It carries a methionine modified to N-formylmethionine
It carries an unmodified methionine
In both cases the initiator tRNA is different from a tRNAmet
that reads an internal AUG codon
Prokaryotic Ribosome-mRNA Recognition

16S rRNA binds to an mRNA at the ribosomal-binding site
or Shine-Dalgarno box
7 nt
Figure 13.17
16S rRNA
Prokaryotic Translation Initiation
(actually 9
nucleotides long)
Figure 13.16
Prokaryotic Translation Initiation
The tRNAiMet is
positioned in the P
site
All other tRNAs
enter the A site
Figure 13.16
Eukaryotic mRNA-Ribosoime
Recognition

In eukaryotes, the assembly of the initiation complex
is similar to that in bacteria

However, additional factors are required



Note that eukaryotic Initiation Factors are denoted eIF
Refer to Table 13.7
The initiator tRNA is designated tRNAmet

It carries a methionine rather than a formylmethionine
Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
13-65
Eukaryotic Ribosome Binding

The consensus sequence for optimal start codon
recognition is show here
Most important positions for codon selection


G C C (A/G)
-6 -5 -4
-3
Start codon
C C A U G G
-2 -1 +1 +2 +3 +4
This sequence is called Kozak’s consensus after
Marilyn Kozak who first determined it
Eukaryotic Translation Initiation





Initiation factors bind to the 5’ cap in mRNA
& to the pA tail
These recruit the 40S subunit, tRNAimet
The entire assembly scans along the mRNA
until reaching a Kozak’s consensus
Once right AUG found, the 60S subunit joins
Translation intitiates
Translation Elongation

During this stage, the amino acids are added to the
polypeptide chain, one at a time

The addition of each amino acid occurs via a series
of steps outlined in Figure 13.18

This process, though complex, can occur at a
remarkable rate


In bacteria  15-18 amino acids per second
In eukaryotes  6 amino acids per second
Translation Elongation – tRNA Entry


A charged tRNA
binds to the A site
EF-1 facilitates
tRNA entry
The 23S rRNA (a component of
the large subunit) is the actual
peptidyl transferase
Thus, the ribosome
is a ribozyme!
Figure 13.18


Peptidyl transferase catalyzes
peptide bond formation
The polypeptide is transferred to
the aminoacyl-tRNA in the A site
Translation
Elongation Translocation


The ribosome translocates one
codon to the right
promoted by EF-G


Figure 13.18
uncharged tRNA released
from E site
The process is repeated, again
and again, until a stop codon is
reached
Translation Termination


Occurs when a stop codon is reached in the mRNA
Three stop or nonsense codons




UAG
UAA
UGA
Recognized by proteins called release factors –
NOT tRNAs
Translation Termination

Bacteria have three release factors




RF1 - recognizes UAA and UAG
RF2 - recognizes UAA and UGA
RF3 - binds GTP and facilitates termination process
Eukaryotes only have one release factor

eRF1 - recognizes all three stop codons
Translation
Termination
Ribosomal subunits &
mRNA dissociate
Figure 13.19
Polypeptides Have Directionality

Translation begins at 5’ end of mRNA

5’3’

Peptide bonds are formed directionally

Peptide bond is formed between the COO- of the
previous amino acid in the chain and the NH2 of the
amino acid being added
Peptide Bond Formation
Carboxyl group
Figure 13.20
Amino group
Colinearity of DNA, mRNA, & Protein
Sequence
N terminal
Figure 13.20
C terminal

The amino acid
sequence of the
enzyme
lysozyme
Within the cell, the
protein will not be
found in this linear
state
 It will adapt a
compact 3-D
structure

129 amino acids
long
Figure 13.4

Indeed, this folding
can begin during
translation
The progression from
the primary to the 3-D
structure is dictated by
the amino acid
sequence within the
polypeptide
A protein
subunit
Figure 13.6
Molecular Basis of Phenotype