1. Translation, Part B
Chapter 9

2. The Proteome
Complete set of proteins in an organism, organ, tissue or cell.
Proteome is enriched by two cellular processes:
Alternative splicing of pre-mRNA
Posttranslational modification of proteins

3. Review Question
In bacteria, the Shine-Dalgarno sequence is found on the mRNA and is recognized by the ________________________ to reveal __________________________.
A) the 16S rRNA; the translation STOP codon
B) the 30S subunit; the translation START codon
C) initiator tRNA; the translation START codon
D) ribosome A site; the translation START codon

5. Posttranslational Events
Most newly synthesized proteins are unable to function.
Proteins need to be folded and some aa need to be modified for a protein to be functional
These events are categorized as posttranslational

6. Alternative splicing generates protein isoforms
Isoforms are proteins that are encoding by the same gene but have different combinations of functional domains.

7. Posttranslational Events
Protein folding inside the cell
Phosphorylation
Ubiquitination
Protein Targeting

10. Protein folding inside the cell (chaperones)

12. Phosphorylation and dephosphorylation of proteins
1000s of proteins are involved in (de)phosphorylation events in the cell
Many protein-protein interactions are regulated by phosphorylation

13. Ubiquitination targets a protein for degradation

19. Signal sequences target proteins for secretion

20. Application Question
The proteome for humans is about 70,000 proteins whereas only 21,000 protein-coding genes have been discovered. Which statement could explain this?
Splicing of eukaryotic mRNA can result in the production of more than one protein from a single gene.
Many of our proteins are actually produced by symbiotic organisms in our bodies.
Splicing of eukaryotic mRNA can result in the production of more than one protein from a single gene and many of our proteins are actually produced by symbiotic organisms in our bodies.
We do not know enough about the human genome to explain this fact.

21. Lets put it all togetherC A
Phe

23. More Practice
A gene makes a polypeptide 30 amino acids long containing an alternating sequence of phenylalanine and tyrosine. Assuming Phe = UUU and Tyr = UAU in mRNA, what are the sequences of nucleotides corresponding to this sequence in the following? a) the mRNA strand (sense) b) the non-template DNA strand (antisense or noncoding strand) c) the template DNA strand (sense or coding stand) d) the tRNA anticodon e) Do you think that the sequence is the only possible one for these amino acids? Assume that the wobble position for each of these codons can be changed to the base cytosine. Answer questions (a) through (d) again with this new information.

24. a) 5′-UUU UAU UUU UAU UUU …etc.
b) 5′-TTT TAT TTT TAT TTT TAT…etc.
c) 3′-AAA ATA AAA ATA AAA ATA …etc.
d) Phe anticodon-3′-AAA, Tyr anticodon-3′-AUA
e) Phe-also coded by UUC, Tyr-also coded by UAC
a-2) 5′-UUC UAC UUC UAC UUC UAC …etc.
b-2) 5′-TTC TAC TTC TAC TTC TAC…etc.
c-3) 3′-AAG ATG AAG ATG AAG…etc.
d-3) Phe anticodon-3′-AAG, Tyr anticodon-3′-AUG

25. Application Question
Many antibiotics target prokaryotic ribosomal function, blocking translation and causing rapid death in susceptible microbial populations. You have been assigned to a structure-based drug design project for a biotechnology company. In order for an antibiotic to be effective, it must be able to block an essential ribosomal function, and the drug must have access to the portion of the enzyme or enzyme complex being targeted. What processes/enzymes might you target in your drug design?
This is an open-ended question and there will be varied responses. Potential processes on the ribosome might be the entry site (A), where tRNAs enter the ribosome, the exit site (E), the peptidyl-transferase center, or even particular aminoacyl-transferase enzymes. Arrest of any of these processes would also arrest translation.

26. Concept check…
Two gametes, each carrying a mutant recessive allele for a different gene/enzyme in the adenine biosynthetic pathway, come together to form a diploid embryo. The individual derived from this embryo will display a: A) lethal phenotype in media lacking adenine supplementation. B) wild-type phenotype, capable of synthesizing adenine. C) a weak adenine requirement for survival (intermediate phenotype). D) a profound defect in adenine synthesis as two enzymes are missing.