The document discusses the genetic basis for protein synthesis. It begins by explaining how genes encode proteins through transcription of DNA into mRNA and translation of mRNA codons into amino acid sequences. Early scientists like Garrod and Beadle and Tatum established through experiments that genes encode enzymes through a one gene-one polypeptide hypothesis. The genetic code is then explained, where mRNA codons specify 20 amino acids. Translation follows the codon sequences to produce a polypeptide with directionality from N-terminal to C-terminal end.

1. INTRODUCTION
 The translation of the mRNA codons into amino
acid sequences leads to the synthesis of proteins
 A variety of cellular components play important
roles in translation
 These include proteins, RNAs and small molecules
 In this chapter we will discuss the current state of
knowledge regarding the molecular features of
mRNA translation
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2.  Proteins are the active participants in cell
structure and function
 Genes that encode polypeptides are termed
structural genes
 These are transcribed into messenger RNA (mRNA)
 The main function of the genetic material is to
encode the production of cellular proteins
 In the correct cell, at the proper time, and in suitable
amounts
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13.1 THE GENETIC BASIS FOR
PROTEIN SYNTHESIS
2

3. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
 First to propose (at the beginning of the 20th
century) a relationship between genes and
protein production
 Garrod studied patients who had defects in their
ability to metabolize certain compounds
 Urine chemist
 He was particularly interested in alkaptonuria
 Patients bodies accumulate abnormal levels of
homogentisic acid (alkapton)
 Disease characterized by

Black urine and bluish black discoloration of cartilage and skin
Archibald Garrod
3

4. 4

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 He proposed that alkaptonuria was due to a
missing enzyme, namely homogentisic acid
oxidase
 Garrod also knew that alkaptonuria follows an
autosomal recessive pattern of inheritance
 He proposed that a relationship exists between the
inheritance of the trait and the inheritance of a
defective enzyme
Archibald Garrod
5

6. Metabolic pathway of phenylalanine metabolism and related
genetic diseases
Figure 13.1
Dietary
protein
CH2
NH2
Phenylalanine
Tyrosine
Phenylalanine
hydroxylase
Tyrosine
aminotransferase
Hydroxyphenylpyruvate
oxidase
Homogentisic
acid oxidase
p-hydroxyphenylpyruvic
acid
Homogentisic
acid
Maleylacetoacetic
acid
Phenylketonuria
Tyrosinosis
Alkaptonuria
COOHC
CH2HO COOHC
H
H
NH2
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6

7. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
 In the early 1940s, George Beadle and Edward
Tatum were also interested in the relationship
between genes, enzymes and traits
 Experiments supported Garrod’s idea that each gene
codes for one enzyme
 Their genetic model was Neurospora crassa (a
common bread mold)
 Their studies involved the analysis of simple nutritional
requirements
Beadle and Tatum’s Experiments
7

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 They analyzed more than 2,000 strains that had
been irradiated to produce mutations
 They analyzed enzyme pathways for synthesis of
vitamins and amino acids
 Figure 13.2 shows an example of their findings on
the synthesis of the amino acid methionine
Beadle and Tatum’s Experiments
8

9. Figure 13.2
Every mutant strain was blocked at one (and only one)
particular step in the synthesis pathway, showing that each
gene encoded one enzyme
1
3
4
1
3
1
3
1
3
1
2
3
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Neurospora
growth
WT WT WT WT WT
2
Minimal +O–acetylhomoserine +Cystathionine +Homocysteine +Methionine
(a) Growth of strains on minimal and supplemented growth media
(b) Simplified pathway for methionine biosynthesis
Homoserine O–acetylhomoserine Cystathionine Homocysteine Methionine
Enzyme 1 Enzyme 2 Enzyme 3 Enzyme 4
4 2 4 2 4 2 4
9

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 In the normal strains, methionine was synthesized
by cellular enzymes
 In the mutant strains, a genetic defect in one gene
prevented the synthesis of one protein required in one
step of the pathway to produce that amino acid
 Beadle and Tatum’s conclusion: A single gene
controlled the synthesis of a single enzyme
 This was referred to as the one gene–one enzyme
hypothesis
Beadle and Tatum’s Experiments
10

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 In later decades, this theory had to be modified
 1. Enzymes are only one category of proteins
 2. Some proteins are composed of two or more different
polypeptides

The term polypeptide denotes structure

The term protein denotes function

So it is more accurate to say a structural gene encodes a
polypeptide

In eukaryotes, alternative splicing means that a structural gene
can encode many different polypeptides
 3. Many genes have been identified that do not encode
polypeptides

For instance, functional RNA molecules (tRNA, rRNA, etc.)
Beadle and Tatum’s Experiments
11

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 Translation involves an interpretation of one
language into another
 In genetics, the nucleotide language of mRNA is
translated into the amino acid language of proteins
 Translation relies on the genetic code
 Refer to Table 13.1
 The genetic information is coded within mRNA in
groups of three nucleotides known as codons
The Genetic Code
12

13. Triplet codons correspond
to a specific amino acid
Multiple codons may encode
the same amino acid.
These are known as
synonymous codons
Three codons do not
encode an amino acid.
These are read as STOP
signals for translation
13

14. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
 Special codons:
 AUG (which specifies methionine) = start codon

This defines the reading frame for all following codons

AUG specifies additional methionines within the coding sequence
 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 glycine
 In most instances, the third base is the variable base

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 14

15. Figure 13.3
 Figure 13.3 provides an overview of gene expression
Note that the start codon sets the
reading frame for all remaining
codons
5′
Template strand
Coding strand
Transcription
3′
Translation
DNA
mRNA
tRNAPolypeptide
5 untranslated′ −
region
3 untranslated′ −
region
Start
codon
Codons Anticodons
3′
3′
5′
5′
A C T G C C C A T G G G G C TC G A CA G GC G G G A A T A A C C G T C G A G G
G G C A G C T C C
C C G U C G A G G
T T GC A C
T G A C G G G T A C C C C G AG C T GT C CG C C C T T A T TA A CG T G
5′ 3′
A C U G C C C A U G G G G C UC G A CA G GC G G G A A U A AU U GC A C
Met Gly LeuSer Asp Gly GluHis Leu
Stop
codon
UAC CCC GAGUCG CUG CCC CUUGUG A AC
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15

16. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
 Polypeptide synthesis has a directionality that
parallels the 5’ to 3’ orientation of mRNA
 During each cycle of elongation, a peptide bond is
formed between the carboxyl group of the last amino
acid in the polypeptide chain and the amino group in
the amino acid being added
 The first amino acid has an exposed amino group
 Said to be N-terminal or amino terminal end
 The last amino acid has an exposed carboxyl group
 Said to be C-terminal or carboxy terminal end
 Refer to Figure 13.6
A Polypeptide Chain Has Directionality
16

17. Figure 13.6 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
(a) Attachment of an amino acid to a peptide chain
(b) Directionality in a polypeptide and mRNA
H H H H H
H3N+
H3N+
H3N+
H3N+
C C C CN C C C+
+
N
R1 R2O O
O–
O–
R3 R4O
C
O
H H H H H H
Last peptide bond formed in the
growing chain of amino acids
H O–
O–
H2OC C C CN C CN C CN
R1 R2O O R3 R4O O
H HO
H3C
Amino
terminal
end
Carboxyl
terminal
end
Methionine Serine
Peptide bonds
Sequence in mRNA
Valine
CH2
CH3
CH3
CH2
CH2
OH
CH
S
C C CN
H
O
C CN C
H O H
Cysteine
CH2
SH
CN
H
O
C
Tyrosine
CH2
OH
H
CN C
H O
H
5′ 3′A U G A G C GU U U A C U G C
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H
17

18. Figure 13.7 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
 There are 20 amino acids that may be found in polypeptides
 Each contains a different side chain, or R group
 Each R group has its own particular chemical properties
 Nonpolar amino acids are
hydrophobic
 They are often buried
within the interior of a
folded protein
H
H
Glycine (Gly) G
(a) Nonpolar, aliphatic amino acids
H3N C COO–
CH3 CH3
CH
H
Alanine (Ala) A
H3N COO–
CH3 CH3
CH
CH2
H
Valine (Val) V
H3N C COO–
+
CH2CH2
CH2
H
Proline (Pro) P
H2N C COO–
+
CH2
CH3
CH3 CH
H
Leucine (Leu) L Methionine (Met) M
H3N C COO–
+
Cysteine (Cys) C
+
CH2
SH
H
H3N C COO–
CH2
CH2
CH3
S
H
H3N C COO–
+
H
Isoleucine (Ile) I
H3N C COO–
+
(b) Aromatic amino acids
Phenylalanine (Phe) F Tyrosine (Tyr) Y
H
H3N C COO–
+
CH2
H
H3N C COO–
+
CH2
OH
Tryptophan (Trp) W
H
H3N C COO–
+
CH2
N
H
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+
CH3
C
+
18

19. Figure 13.7 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
 Polar and charged amino acids are hydrophilic
 They are more likely to be on the surface of a protein
(c) Polar, neutral amino acids
Serine (Ser) S Threonine (Thr) T
H
H3N C COO–
+
CH2
OH
H
HCOH
H3N C
CH3
COO–
+
H
Glutamine (Gln) Q
H3N C COO–
+
CH2
C
O NH2
H
Asparagine (Asn) N
H3N C COO–
+
CH2
CH2
C
O NH2
H
Glutamic acid (Glu) E
H3N C COO–
+
CH2
C
O O–
H
Aspartic acid (Asp) D
H3N C COO–
+
CH2
CH2
C
O O–
(d) Polar, acidic amino acids (e) Polar, basic amino acids
Histidine (His) H
H
H3N C COO–
+
+
+ +
CH2
NH
HN
Lysine (Lys) K
H
H3N C COO–
+
CH2
CH2
CH2
CH2
NH3
Arginine (Arg) R
H
H3N C COO–
+
CH2
CH2
CH2
C
NH
NH2
NH2
(f) Nonstandard amino acids
Selenocysteine (Sec)
H
H3N C COO–
+
CH2
SeH
N
CH3
Pyrrolysine (Pyl)
H
H3N C COO–
+
CH2
CH2
CH2
CH2
NH
C O
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19

20. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
 There are four levels of structure in proteins
 1. Primary
 2. Secondary
 3. Tertiary
 4. Quaternary
 A protein’s primary structure is its amino acid
sequence
 Refer to Figure 13.8
Levels of Structure in Proteins
20

21. Lys
NH3
+
1
10
20
30
40
50
60
70
80
90
100
110
120
129
Val
Phe Gly Arg Cys Glu
Leu
Ala
Ala
Ala
Met
Lys
Arg
His
GlyLeuAspAsnTyrArgGlyTyr
Ser
Thr
Asp
Tyr Gly
Leu
Asn
SerGluPheLysAlaAlaCysValTrp
Asn
Leu
Gly
Phe
Asn
ThrGin
Ala
ThrAsnArgAsn
Thr
Asp
Gly
Ser
lle
Gln
lle
Asn
Ser
Arg Trp
Trp
Cys
Asn
Asp
Gly
ArgThrProGlySerArgAsnLeu
Cys
Asn
lle
Pro
Cys
Ser Ala Leu
Leu
Ser
Ser
Asp
lle
Thr
Arg Asn
Arg
Cys
Lys
Gly
Thr
Asp
AlaTrp ValAla
Asn
Met
Gly
Asp
Gly
Asp Ser Val lle Lys Lys Ala Cys
Asn
Val
Ser
Ala
Val
GlnAlaTrplleArgGlyCys
Arg
Leu
Trp
COO–
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Figure 13.8
The amino acid
sequence of the
enzyme lysozyme
129 amino acids
long
 Within the cell, the
protein will not be
found in this linear
state
 Rather, it will adopt
a compact 3-D
structure
 Indeed, this folding
can begin during
translation
 The progression from
the primary structure
to the 3-D structure is
dictated by the amino
acid sequence within
the polypeptide
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22. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
 The primary structure of a protein folds to form
regular, repeating shapes known as secondary
structures
 There are two types of secondary structures
 α helix
 β sheet
 Certain amino acids are good candidates for each structure
 These secondary structures are stabilized by the
formation of hydrogen bonds between atoms located in
the polypeptide backbone
 Refer to Figure 13.9
Levels of Structures in Proteins
22

23. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
 The short regions of secondary structure in a protein
fold into a three-dimensional tertiary structure
 Refer to Figure 13.9
 This is the final conformation of proteins that are
composed of a single polypeptide
 Structure determined by hydrophobic and ionic interactions as well as
hydrogen bonds and Van der Waals interactions
 Proteins made up of two or more polypeptides have
a quaternary structure
 This is formed when the various polypeptides associate
with one another to make a functional protein
 Refer to Figure 13.9
Levels of Structures in Proteins
23

24. Figure 13.9 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
α helix
β sheet
Primary
structure
Secondary
structure
Quaternary
structure
Tertiary
structure
Protein
subunit
Ala C
O
C
C
C
C
O
O
Val
Phe
Glu
Tyr
Leu
Iso
Ala
H
N
NH3
+
NH3
+
COO–
COO–
NH3
+
COO–
H
N
C
C
C
C O
O
HH
NN
H
N
C
C
C
C
C
C
O
O
C
O
H
H
N
NN
Depending on
the amino acid
sequence,
some regions
may fold into
an helix orα
sheet.β
Two or more
polypeptides
may associate
with each other.
Regions of
secondary
structure and
irregularly shaped
regions fold into a
three-dimensional
conformation.
C
C
C C
O
H
H
N
N
N
C
C
C
C C
C
O
O
H
H
N
C
C C
O
N
C
C C
O
NC
O
HC
C
C
O
O
H
H
NC
HC
C
O
H
N
O
C
C
HC
C
O
H
C
C
O
H
C
C
O
H
(a)
(b)
(c)
(d)
H
C
O
O C
H
H
H
O C
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24

25. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
 To a great extent, the characteristics of a cell depend on the
types of proteins its makes
 Proteins can perform a variety of functions
 Refer to Table 13.5
 A key category of proteins are enzymes
 Accelerate chemical reactions within a cell
 Can be divided into two main categories

Anabolic enzymes  Synthesize molecules and macromolecules

Catabolic enzymes  Break down large molecules into small ones
 Important in generating cellular energy
Functions of Proteins
13-38
25

26. 13-39
26

27.  In the 1950s, Francis Crick and Mahon Hoagland
proposed the adaptor hypothesis
 tRNAs play a direct role in the recognition of codons in
the mRNA
 In particular, the hypothesis proposed that tRNA
has two functions
 1. Recognizing a 3-base codon in mRNA
 2. Carrying an amino acid that is specific for that codon
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13.2 STRUCTURE AND
FUNCTION OF tRNA
27

28. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
 During mRNA-tRNA recognition, the anticodon in
tRNA binds to a complementary codon in mRNA
Recognition Between tRNA and mRNA
Figure 13.10
tRNAs are named
according to the
amino acid they bear
The anticodon is
anti-parallel to
the codon
Phenylalanine
tRNAPhe
tRNAPro
Phenylalanine
anticodon
Phenylalanine
codon
Proline
codon
A G
Proline
Proline
anticodon
U C
3 mRNA′5′
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G CA G
U C C G
28

29. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
 The secondary structure of tRNAs exhibits a
cloverleaf pattern
 It contains

Three stem-loop structures

A few variable sites

An acceptor stem with a 3’ single strand region
 The actual three-dimensional or tertiary structure
involves additional folding
 In addition to the normal A, U, G and C nucleotides,
tRNAs commonly contain modified nucleotides
 More than 80 of these can occur
tRNAs Share Common Structural
Features
29

30. Anticodon
U
G
G
C
G
A
A
UH2
UH2 UH2
30
10
19
40
60
70
Acceptor stem
50
U
I C
mI
P
G
PO4
OH
U
U
A
G
C
P
T
m2G
A
C
C
3′
5′
A
C
C
NH3
+
C R
C O
H
O Covalent
bond
between
tRNA
and an
amino
acid
U
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Stem–loop
Structure of tRNAFigure 13.12
Found in all tRNAs
Not found in all tRNAs
Other variable sites are
shown in blue as well
The modified bases are:
I = inosine
mI = methylinosine
T = ribothymidine
UH2 = dihydrouridine
m2G = dimethylguanosine
ψ = pseudouridine
30

31. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
 The enzymes that attach amino acids to tRNAs are
known as aminoacyl-tRNA synthetases
 There are 20 types

One for each amino acid
 Aminoacyl-tRNA synthetases catalyze a two-step
reaction involving three different molecules
 Amino acid, tRNA and ATP
 Refer to Figure 13.13
Charging of tRNAs
31

32. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
 The aminoacyl-tRNA synthetases are responsible
for the “second genetic code”
 The selection of the correct amino acid must be highly
accurate or the polypeptides may be nonfunctional
 Error rate is less than one in every 100,000
 Sequences throughout the tRNA including but not limited
to the anticodon are used as recognition sites
 Modified bases may affect
 translation rates
 recognition by aminoacyl-tRNA synthetases
 Codon-anticodon recognition
Charging of tRNAs
32

33. Figure 13.13
The amino acid is
attached to the 3’ end
of the tRNA by an
ester bond
P
P P
P P
Pyrophosphate
Specific
amino acid
Aminoacyl-tRNA
synthetase
A
P
A
P
A
3′
3′
5′
3′
5′
5′
AMP
ATP An amino acid and ATP bind to
the enzyme. AMP is covalently
bound to the amino acid, and
pyrophosphate is released.
The correct tRNA binds to the
enzyme. The amino acid
becomes covalently attached to
the 3 end of the tRNA. AMP is′
released.
The “charged” tRNA is
released.
tRNA
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33

34. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
 As mentioned earlier, the genetic code is degenerate
 With the exception of serine, arginine and leucine, this
degeneracy always occurs at the codon’s third position
 To explain this pattern of degeneracy, Francis Crick
proposed in 1966 the wobble hypothesis
 In the codon-anticodon recognition process, the first two
positions pair strictly according to the A – U /G – C rule
 However, the third position can actually “wobble” or move
a bit

Thus tolerating certain types of mismatches
tRNAs and the Wobble Rule
34

35. U
3′
5′
5′
Wobble
position
Nucleotide of
of tRNA anticodon
Third nucleotide
of mRNA codon
G
C
A
U
I
xm5
s2
U
xm5
Um
C, U
G
U, C, G, (A)
A, U, G, (C)
U, C, A
A, (G)
U, A, G
A
a) Location of wobble position
(b) Revised wobble rules
Phenylalanine
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3′
Um
xm5
U
xo5
U
k2
C
A A G
U U
Wobble position and base pairing rulesFigure 13.14
tRNAs that can recognize the same
codon are termed isoacceptor tRNAs
Recognized
very poorly by
the tRNA
 5-methyl-2-thiouridine
 inosine
 5-methyl-2’-O-methyluridine
 5-methyluridine
 lysidine
 2’-O-methyluridine
 5-hydroxyuridine
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You don’t need to
memorize these rules

36.  Translation occurs on the surface of a large
macromolecular complex termed the ribosome
 Bacterial cells have one type of ribosome
 Found in their cytoplasm
 Eukaryotic cells have two types of ribosomes
 One type is found in the cytoplasm
 The other is found in organelles

Mitochondria ; Chloroplasts
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13.3 RIBOSOME STRUCTURE
AND ASSEMBLY
36

37.  Unless otherwise noted the term eukaryotic
ribosome refers to the ribosomes in the cytosol
 A ribosome is composed of structures called the
large and small subunits
 Each subunit is formed from the assembly of

Proteins

rRNA
 Table 13.6 presents the composition of bacterial and
eukaryotic ribosomes
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13.3 RIBOSOME STRUCTURE
AND ASSEMBLY
37

38. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 38

39. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
 During bacterial translation, the mRNA lies on the
surface of the 30S subunit
 As a polypeptide is being synthesized, it exits through a
channel within the 50S subunit
 Ribosomes contain three discrete sites
 Peptidyl site (P site)
 Aminoacyl site (A site)
 Exit site (E site)
 Ribosomal structure is shown in Figure 13.15
Functional Sites of Ribosomes
39

40. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
Figure 13.15
(c) Model for ribosome structure
Polypeptide
30S
50S
3′5′
tRNA
mRNA
E P A
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40

41.  Translation can be viewed as occurring in three
stages
 Initiation
 Elongation
 Termination
 Refer to 13.16 for an overview of translation
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13.4 STAGES OF
TRANSLATION
41

42. mRNA
UAC
Anticodon
Initiator
tRNA – tRNA
with first
amino acid
AUG
Start codon
AUG
Start codon
UAG
Stop codon
UAG
Stop codon
Completed
polypeptide
Termination
Elongation
(This step
occurs many
times.)
Recycling of translational
components
Release
factor
Small
Large
Ribosomal
subunits
EE
A
E
AP
aa1
aa2
aa3
aa4
aa5
aa1
aa1
3′3′ 5′5′
3′5′
3′
5′
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P P A
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Figure 13.16
Initiator tRNA
Initiation
42

43. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
 The mRNA, initiator tRNA, and ribosomal subunits
associate to form an initiation complex
 This process requires three Initiation Factors
 The initiator tRNA recognizes the start codon in
mRNA
 In bacteria, this tRNA is designated tRNAfmet

It carries a methionine that has been covalently modified to
N-formylmethionine
 The start codon is AUG, but in some cases GUG or UUG

In all three cases, the first amino acid is N-formylmethionine
The Translation Initiation Stage
43

44. Shine-Dalgarno
sequence
mRNA
5′ 3′A U C U A G U A A G U U C A GG G U CG A GU C A C G C A GU G GG U A
3′
Start
codon
A U U C C C A C A G
C 16S rRNAU
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 The binding of mRNA to the 30S subunit is facilitated by a
ribosomal-binding site or Shine-Dalgarno sequence
 This is complementary to a sequence in the 16S rRNA
 Figure 13.17 outlines the steps that occur during
translational initiation in bacteria
Figure 13.18
Hydrogen bonding
Component of the
30S subunit
44

45. Figure 13.17 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
IF2, which uses GTP, promotes
the binding of the initiator tRNA
to the start codon in the P site.
Portion of
16S rRNA
The mRNA binds to the 30S subunit.
The Shine-Dalgarno sequence is
complementary to a portion of the
16S rRNA.
IF1 and IF3 bind to the 30S subunit.
3′
5′
30S subunit
Shine-
Dalgarno
sequence
(actually 9
nucleotides long)
Start
codon
IF3 IF1
IF1IF3
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45

46. Figure 13.17
70S initiation
complex
This marks the
end of the
initiation stage
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IF1 and IF3 are released.
IF2 hydrolyzes its GTP and is released.
The 50S subunit associates.
tRNAfMet
IF2
GTP
E AP
3′
5′
3′
5′
70S
initiation
complex
IF1IF3
Initiator tRNA
tRNAfMet
46

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 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
The Translation Initiation Stage
47

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 The start codon for eukaryotic translation is AUG
 Ribosome scans from the 5’ end of mRNA until it finds
the AUG start codon (not all AUGs can act as a start)
 The consensus sequence for optimal start codon
recognition is show here
Start codon
 G C C (A/G) C C A U G G
-6 -5 -4 -3 -2 -1 +1 +2 +3 +4
Most important positions for codon selection
 These rules are called Kozak’s rules

After Marilyn Kozak who first proposed them
 With that in mind, the start codon for eukaryotic
translation is usually the first AUG after the 5’ Cap!
48

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 Translational initiation in eukaryotes can be
summarized as such:
 An initiation factor protein complex (eIF4) binds to the 5’
cap in mRNA
 These are joined by a complex consisting of the 40S
subunit, tRNAmet
, and other initiation factors
 The entire assembly moves along the mRNA scanning
for the right start codon
 Once it finds this AUG, the 40S subunit binds to it
 The 60S subunit joins
 This forms the 80S initiation complex
49

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 During this stage, 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 13.19
 This process, though complex, can occur at a
remarkable rate
 In bacteria  15-20 amino acids per second
 In eukaryotes  2-6 amino acids per second
The Translation Elongation Stage
50

51. Figure 13.19
The 23S rRNA (a component of
the large subunit) is the actual
peptidyl transferase
Thus, the ribosome
is a ribozyme!
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3′
P site
Codon 3
Codon 4
mRNA
E site
A site
aa1
aa2
aa3
Ribosome
aa1
aa2
aa3
E
AP
aa4
A charged tRNA binds
to the A site. EF-Tu
facilitates tRNA binding
and hydrolyzes GTP.
Peptidyltransferase, which
is a component of the 50S
subunit, catalyzes peptide
bond formation between the
polypeptide and the amino
acid in the A site.The
polypeptide is transferred
to the A site.
5′
5′
3′
51

52. Figure 13.19
tRNAs at the P and A
sites move into the
E and P sites,
respectively
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Codon 4
Codon 5
Codon 3
3′5′
aa1
aa2
aa3
aa4
aa1aa2
aa3
E A
A
Codon 4
Codon 5
Codon 3
3′
5′
aa1
aa2aa3
aa4
E
A
P
P
aa4
This process is repeated, again and
again, until a stop codon is reached.
An uncharged
tRNA is released
from the E site.
The ribosome translocates
1 codon to the right. This
translocation is promoted
by EF-G, which hydrolyzes
GTP.
5′
3′
E
P
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52

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 The final stage occurs when a stop codon is
reached in the mRNA
 In most species there are three stop or nonsense codons

UAG

UAA

UGA
 These codons are not recognized by tRNAs, but by
proteins called release factors

Indeed, the 3-D structure of release factors mimics that of tRNAs
The Translation Termination Stage
53

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 Bacteria have three release factors
 RF1, which recognizes UAA and UAG
 RF2, which recognizes UAA and UGA
 RF3, which does not recognize any of the three codons

It binds GTP and helps facilitate the termination process
 Eukaryotes only have one release factor
 eRF, which recognizes all three stop codons
The Translation Termination Stage
54

55. Figure 13.20
3′
5′
Stop codon
in A site
tRNA in P
site carries
completed
polypeptide
E A
3′
5′
E A
mRNA
A release factor (RF) binds to the A site.
The polypeptide is cleaved from the tRNA
in the P site. The tRNA is then released.
The ribosomal subunits, mRNA, and
release factor dissociate.
Release
factor
3′
+
3′
5′
5′
50S subunit 30S subunit
mRNA
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P
P
55

56. 56

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 Bacteria lack a nucleus
 Therefore, both transcription and translation occur in the cytoplasm
 As soon an mRNA strand is long enough, a ribosome will
attach to its 5’ end
 So translation begins before transcription ends
 This phenomenon is termed coupling
 Refer to Figure 13.21
Bacterial Translation Can Begin
Before Transcription Is Completed
57

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Figure 13.21
Coupling between transcription and translation in bacteria
58

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