Set 10

Question 1

What is the role of Shine-Dalgarno sequence?

Answer 1

Ribosome binding site/recruits ribosome to mRNA -prokaryotic.

Question 2

What is the role of Kozak sequence?

Answer 2

Consensus sequence that promotes ribosome binding in Eukaryotes bc it has an AUG embedded in it)
Houses the start codon

Question 3

What are the major differences in initiation of translation between eukaryotes and prokaryotes (remember: first AA and the way mRNA and tRNA bind to ribosomes)?

Answer 3

Prok: mRNA and small ribosomal subunit bind (interaction b/w shine dalgarno and 16s rRNA), then initiator tRNA and finally large ribosomal subunit. Translation starts.
Euk: small ribosomal subunit binds with initiator tRNA which then binds methyl cap on mRNA. Scans along looking for appropriate AUG (w/ proper sequence context of kozak sequence) and starts translation from there.

Question 4

Describe in detail events during initiation of the Eukaryotic (or Prokaryotic) translation.

Answer 4

Prokaryotic

• 16S rRNA subunit binds to SD sequence (part of 30S) on mRNA
• IF3 binds to free 30S subunit, blocking 50S (large) from binding small 30S
• IF1 binds to 16S to prevent tRNA from binding the A site
• IF2 complexes with GTP and initiator tRNA, then binds
• Initiator tRNA binds to P site
• 50 S subunit binds -> displaces IF1 and IF3; IF2 is released as well

● eukaryotic
40S ribosomal subunit binds initiator tRNA -> forms a complex
Complex binds mRNA & scans along until it reaches an appropriate AUG (Kozak consensus sequence)
Position initiator tRNA

Question 5

Briefly explain two cases of RNA having enzymatic capability (how many ribozymes did we mention in class)?

Answer 5

Splicing ribozymes for group 1 introns RNase P in bacteria - removes 5’ leader seq in tRNA.
Peptidyl transferase is a ribozyme.

Question 6

What is a peptidyl transferase? What is catalyzed by peptidyl transferase?

Answer 6

An enzymatic reaction performed by 23s rRNA (part of large ribosomal subunit); prokaryotic ribosomes are nucleoprotein ribozymes.

An aminoacyl-transferase; primary enzymatic function of the ribosome. It catalyzes the transfer of the growing peptide chain to the incoming activated amino acid and makes peptide bond

Question 7

How is gene expression controlled at the level of translation (mRNA is now in contact with ribosomes or their subunits/translation factors; three things mentioned in the class)?

Answer 7

Phosphorylation of translation factors, use of multiple AUG codons, and internal ribosome entry site (IRES).

Question 8

Which two factors greatly influence efficiency of protein synthesis?

Answer 8

● Simultaneous translation of a single mRNA by multiple ribosomes = polysomes
● Rapid recycling of ribosomal units

Question 9

What are the roles of PABI? What is the role of PABII?

Answer 9

PABPII in nucleus is responsible for rapidly adding the polyA tail

Question 10

Explain what happens with polypeptides after translation.

Answer 10

Nascent polypeptide chains fold and get outfitted with co-factors. They may also undergo cleaving. Additional covalent modifications may occur such as glycosylation, phosphorylation, acetylation and more. May also experience binding to other protein subunits.

Question 11

How are protein modifications related to the control of gene expression? List possible protein modifications.

Answer 11

Protein modifications are necessary for transport from cytoplasm. 
●	Proteolytic cleavage
●	Acylation
●	Glycosylation
●	Hydroxylation
●	Methylation
●	Phosphorylation
●	Prenylation
●	Sulfation
●	Ubiquitylation
●	Vit. C - dependent methylation
●	Vit. K - dependent methylation

Question 12

Explain endosymbiotic theory.

Answer 12

States that the genome of organelles resemble prokaryotic genomes more than nuclear genomes such that the genome is small, circular, and no histones associated.
Organelle’s protein-synthesizing machinery resembles prokaryotic machinery more than eukaryotic nuclear machinery:
● Prokaryotic-like rRNA and ribosomes
● fMET is first amino acid
● Different effects of antibiotics and protein synthesis inhibitors

Question 13

Which genome encodes for proteins found in mitochondria. Explain.

Answer 13

Proteins in mitochondria are made from a combination of mtDNA and (a majority from) nuclear DNA. Instead, mtDNA codes for most of the RNA components in protein synthesis and proteins for organelle function are imported from the cytoplasm.

Question 14

What are the characteristics of mitochondrial transcripts?

Answer 14

• double stranded circular DNA molecule; 17000 bp long

Question 15

How is normal tRNA : rRNA ratio maintained during the transcription of mitochondrial DNA?

Answer 15

H-strand transcription often stops at 3’ end of the 16S rRNA gene and starts again from pH.

Question 16

Define and explain the importance of heteroplasmy and homeoplasmy.

Answer 16

Heteroplasmy: a mixture of mutant and normal mtDNA molecules after mtDNA replication, imperfect transmission for how much is passed into each daughter cell.

Homeoplasmy: either pure mutant or pure normal mtDNA in the cell.

Question 17

Is mutation rate in mitochondrial DNA high or low? Explain why.

Answer 17

very high due to:
●	Exposure of mtDNA to oxygen free-radicals produced during respiration
●	Lack of protective histones
●	High rate of replication
●	Less efficient repair system