1. 13-13
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2. The code is nearly universal
Special codons:
AUG (which specifies methionine) = start codon
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 lysine
In most instances, the third base is the degenerate 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
13-14
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3. Figure 13.2 provides an overview of gene expression
13-16

4. 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

5. tRNA 2º Structure Figure 13.10 D loop TψC loop y = pseudouridine loop
Found in all tRNAs
D loop
TψC loop D D
The modified bases are:
I = inosine
mI = methylinosine
T = ribothymidine
D= dihydrouridine
m2G = dimethylguanosine
y = pseudouridine
loop
Structure of tRNA
Figure 13.10

6. 3º Structure of tRNA

7. 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

8. Aminoacyl tRNA Synthetase Function
Figure 13.11
The amino acid is attached to the 3’ OH by an ester bond

9. 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

10. Figure 13.12 Wobble position and base pairing rules
tRNAs charged with the same amino acid, but that recognize multiple codons are termed isoacceptor tRNAs
Wobble position and base pairing rules
Figure 13.12

11. Wobble Base-Pairing between anticodon & codon
W-C base pairing
Wobble pairing
Wobble pairing

12. 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

13. Prokaryotic Ribosomes
(a) Bacterial cell
Figure 13.13

14. Eukaryotic Ribosomes
Figure 13.13

15. Functional Sites of Ribosomes
During bacterial translation, the mRNA lies on the surface of the 30S subunit
As a polypeptide is being synthesized, it exits through a hole 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 13.14
13-57
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16. Figure 13.14

17. Stages of Translation
Initiation
Elongation
Termination

18. Stages of Translation
Initiator tRNA
Release factors
Figure 13.15

19. Translation Initiation
Components
mRNA,
initiator tRNA,
Initiation factors
ribosomal subunits
The initiator tRNA
In prokaryotes, this tRNA is designated tRNAifmet
It carries a methionine modified to N-formylmethionine
In eukaryotes, this tRNA is designated tRNAimet
It carries an unmodified methionine
In both cases the initiator tRNA is different from a tRNAmet that reads an internal AUG codon

20. Prokaryotic Ribosome-mRNA Recognition
16S rRNA binds to an mRNA at the ribosomal-binding site or Shine-Dalgarno box
7 nt
16S rRNA
Figure 13.17

21. Prokaryotic Translation Initiation
(actually 9
nucleotides long)
Figure 13.16

22. Prokaryotic Translation Initiation
The tRNAiMet is positioned in the P site
All other tRNAs enter the A site
Figure 13.16

23. 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
13-65
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24. Eukaryotic Ribosome Binding
The consensus sequence for optimal start codon recognition is show here
Start codon
G C C (A/G) C C A U G G
Most important positions for codon selection
This sequence is called Kozak’s consensus after Marilyn Kozak who first determined it

25. 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

26. 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  amino acids per second
In eukaryotes  6 amino acids per second

27. 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
Peptidyl transferase catalyzes peptide bond formation
The polypeptide is transferred to the aminoacyl-tRNA in the A site
Thus, the ribosome is a ribozyme!
Figure 13.18

28. Translation Elongation -Translocation
The ribosome translocates one codon to the right
promoted by EF-G
uncharged tRNA released from E site
The process is repeated, again and again, until a stop codon is reached
Figure 13.18

29. 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

30. 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

31. Translation Termination
Ribosomal subunits & mRNA dissociate
Figure 13.19

32. 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

33. Peptide Bond Formation
Carboxyl group
Amino group
Figure 13.20

34. Colinearity of DNA, mRNA, & Protein Sequence
N terminal
C terminal
Figure 13.20

35. 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
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
The amino acid sequence of the enzyme lysozyme
129 amino acids long
Figure 13.4

36. A protein subunit
Figure 13.6

37. Molecular Basis of Phenotype