1. Chapter 9 Proteins and Their Synthesis
Green Fluorescent Protein drawn in cartoon style with fluorophore highlighted as ball-and-stick; one wholly-reproduced protein, and cutaway version to show the fluorophore.

2. Review Central Dogma DNA RNA Protein aa - aa - aa - aa - aa - aa - aa
5’ ATG GAC CAG TCG GTT TAA GCT 3’
3’ TAC CTG GTC AGC CAA ATT CGT 5’
DNA
RNA
Protein
transcription
5’ AUG GAC CAG UCG GUU UAA GCU 3’
translation
aa - aa - aa - aa - aa - aa - aa

3. Protein Structure
via condensation

4. Protein Structure
Primary Structure

5. Protein folding is dependent on the amino acid R groups
H2N C COOH H
General Structure
There are 20 amino acids.
Their properties are determined by the R group.

6. There are 20 amino acids. Nonpolar or hydrophobic (9)
Polar (hydrophillic), but uncharged (6)
Polar (hydrophillic), but charged (5)

7. Nonpolar
(Hydrophobic)
ring

8. sulfur

11. Protein Structure
Primary Structure

12. Protein Structure Two major types of Secondary Structure α Helix
β Sheet

13. Protein Structure

14. How do we get from DNA to Primary protein structure ?
5’ ATG GAC CAG TCG GTT TAA GCT 3’
3’ TAC CTG GTC AGC CAA ATT CGT 5’
DNA
RNA
Protein
transcription
5’ AUG GAC CAG UCG GUU UAA GCU 3’
translation
aa - aa - aa - aa - aa - aa - aa

15. DNA (mRNA) is read in Triplets
-Codon – Group of 3 DNA bases codes for a specific amino acid
Ex. ATG = methionine
-This means the code is degenerate – more than one codon can specify one amino acid

16. The Genetic Code - Nonoverlapping

17. Key To The Genetic Code
Groups of 3 mRNA bases (codons) code for specific amino acids
5’ CCAACCGGG 3’
CCA-ACC-GGG
Pro-Thr-Gly

18. The Genetic Code – Stop Codons
UGA
UAA
UAG

19. Proteins and Genes are Colinear
Mutations in DNA show specific corresponding changes in the protein
Genes are converted to proteins in a linear fashion

20. Key To The Genetic Code CCG UGG AGA GAC UAA
Pro – Trp – Arg –Asp - Stop
CCG UCG AGA GAC UAA
Pro – Ser – Arg –Asp - Stop
CCG UGG CGA GAC UAA
Pro – Trp – Arg –Asp - Stop
CCG UGG AGA GAC UAA
Pro – Stop
CCG UGG AGA CGA CUA
Pro – Trp – Arg –Arg - Leu

21. The Genetic Code - Mutations
4 Types of Mutations
Silent mutations
Missense mutations
Nonsense mutations
Frameshift mutations

22. The Genetic Code mRNA has 3 potential “reading frames” Stop
5’ CUUACAGUUUAUUGAUACGGAGAAGG 3’
3’ GAAUGUCAAAUAACUAUGCCUCUUCC 5’
5’ CUU ACA GUU UAU UGA UAC GGA GAA GG 3’
3’ GAA UGU CAA AUA ACU AUG CCU CUU CC 5’
5’ C UUA CAG UUU AUU GAU ACG GAG AAG G 3’
3’ G AAU GUC AAA UAA CUA UGC CUC UUC C 5’
5’ CU UAC AGU UUA UUG AUA CGG AGA AGG 3’
3’ GA AUG UCA AAU AAC UAU GCC UCU UCC 5’
Stop
UAA
UGA
UAG

23. The Genetic Code mRNA has 3 potential reading frames Stop
5’ CUUACAGUUUAUUGAUACGGAGAAGG 3’
3’ GAAUGUCAAAUAACUAUGCCUCUUCC 5’
5’ CUU ACA GUU UAU UGA UAC GGA GAA GG 3’
3’ GAA UGU CAA AUA ACU AUG CCU CUU CC 5’
5’ C UUA CAG UUU AUU GAU ACG GAG AAG G 3’
3’ G AAU GUC AAA UAA CUA UGC CUC UUC C 5’
5’ CU UAC AGU UUA UUG AUA CGG AGA AGG 3’
3’ GA AUG UCA AAU AAC UAU GCC UCU UCC 5’
Stop
UAA
UGA
UAG

24. Review - RNA mRNA- messenger RNA tRNA- transfer RNA
rRNA- Ribosomal RNA

25. tRNA-The adapter

26. tRNA-The adapter
-tRNA functions as the adapter between amino acids and the RNA template
-tRNAs are structurally similar except in two regions
Amino acid attachment site
Anticodon

27. tRNA-The anticodon The tRNA anticodon 3 base sequence
Complementary to the codon
Base pairing between the mRNA and the tRNA
Oriented and written in the 3’ to 5’ direction
tRNA
mRNA
3’ CUG 5’
5’ GAC 3’
Aspartic Acid

28. Aminoacyl-tRNA synthetase
The enzyme responsible for joining an amino acid to its corresponding tRNA
20 tRNA synthetases – 1 for each amino acid

29. Wobble Allows one tRNA to recognize multiple codons
Occurs in the 3rd nucleotide of a codon

30. Wobble – A new set pairing of rules
I = Inosine: A rare base found in tRNA

31. Wobble – A new set pairing of rules
Isoaccepting tRNAs: tRNAs that accept the same amino acid but are transcribed from different genes

32. Wobble Problem
What anticodon would you predict for a tRNA species carrying isoleucine?

33. Ribosomes – General characteristics
Come together with tRNA and mRNA to create protein
Ribosome consist of one small and one large subunit
In prokaryotes, 30S and 50S subunits form a 70S particle
In Eukaryotes, 40S and 60S subunits form an 80S particle
Each subunit is composed of 1 to 3 types of rRNA and up to 49 proteins

34. Ribosomes – General characteristics

35. Ribosomes – General characteristics
rRNA folds up by intramolecular base pairing

36. Ribosomes – General characteristics

37. Translation
Synthesizing Protein

38. An overview

39. Translation Initiation - Prokaryotes
Translation begins at an AUG codon – Methionine
Requires a special “initiator” tRNA charged with Met – tRNAMeti
This involves the addition of a formyl group to methionine while it is attached to the initiator

40. Shine-Dalgarno Sequence
mRNA only associates with unbound 30S subunit

41. Translation Initiation – Prokaryotes Initiation Factors
3 initiation factor proteins are required for the start of translation in prokaryotes
IF1 – Binds to 30S subunit as part of the complete initiation complex. Could be involved in stability
IF2 – Binds to charged initiator tRNA and insures that other tRNAS do not enter initiation complex
IF3 – Keeps the 30S subunit disassociated from the 50S subunit and allows binding of mRNA

42. Figure
Figure

43. Figure
Figure

44. Figure
Figure

45. Translation Initiation – Eukaryotes
mRNA is produced in the nucleus and transported to the cytoplasm
5’ end of the mRNA is “capped” to prevent degradation
Eukaryotic Initiation Factors (eIF4A, eIF4B, and eIF4G) associate with the 5’ cap, the 40S subunit, and initiator tRNA
Complex moves 5’ to 3’ unwinding the mRNA until an initiation site (AUG) is discovered
Initiation factors are released and 60S subunit binds

46. mRNA is produced in the nucleus and transported to the cytoplasm
Figure
Figure
mRNA is produced in the nucleus and transported to the cytoplasm
mRNA is covered with proteins and often folds on itself
5’ end of the mRNA is “capped” to prevent degradation

47. Figure
Figure
4.Eukaryotic Initiation Factors (eIF4A, eIF4B, and eIF4G) associate with the 5’ cap, the 40S subunit, and initiator tRNA

48. Figure
5. Complex moves 5’ to 3’ unwinding the mRNA until an initiation site (AUG) is discovered

49. 6. Initiation factors are released and 60S subunit binds
Figure
6. Initiation factors are released and 60S subunit binds

50. Elongation Requires two protein Elongation Factors: EF-Tu and EF-G
Amino acids are added to the growing peptide chain at the rate of 2-15 amino acids per second

51. Elongation

52. Termination Release Factors – RF1, RF2 and RF3
RF1 recognizes UAA or UAG
RF2 recognizes UAA or UGA
RF3 assists both RF1 and RF2
Stop codon also called a nonsense codon
A water molecule in the peptidyltransferase center leads to the release of the peptide chain

53. Translation differences between Eukaryotes and Prokaryotes
Prokaryotes Eukaryotes
NO nuclear membrane
Translation coupled to transcription
Ribosomes bind the Shine Dalgarno sequence
mRNA can contain multiple genes
Formylmethionine bound to initiator tRNA
Presence of a nuclear membrane
mRNA exported from nucleus
Ribosome binds to the 5’ cap
mRNA has information for only one gene
Methionine bound to initiator tRNA

54. Posttranslational Folding
Proteins must fold correctly to be functional
Correct folding is not always energetically favorable in the cytoplasm
Chaperones (including GroE chaperonins) bind to nascent peptides and facilitate correct folding

55. Posttranslational modifications
Phosphorylation
Many proteins require some type of modification to become functional

56. Posttranslational modifications
Glycosylation – adding sugars
Signaling molecules
Cell wall proteins
Glycoproteins

57. Posttranslational modifications
Ubiquitination marks a protein for degradation
Short lived proteins
(functional in cell cycle)
- Damaged or mutated proteins

58. Summary Translation Post translational modifications Prokaryote
Eukaryote
Post translational modifications
Phosphorylation
Glycosylation
Ubiquitination