Lecture 8/31/18

Question 1

What is a fundamental part of tRNAs 3D structure?

Answer 1

Number of modified biochemical mods
A. Psi = Psuedouriodine
B. D = dihydrouridine

Remember AA is attached to CCA-3’ (acceptor stem)

Question 2

What happens at the 3rd position of the anticodon?

Answer 2

Wobble position (3rd nucleotide in an ANTICODON)

A messy (sloppy) binding site that goes along with the redundancy or degeneracy of the RNA

Generates variation

Question 3

Some tRNA genes contain intron. Why are these introns are spliced out by a specialized set of proteins but not the spliceosome?

Answer 3

Dependent on there 3D structures . They fold and introns are placed on the outside. The splice-some only works with linear structures and cant work with tRNA. They require specialized proteins to remove introns

Question 4

True or false: tRNA modifications are important for structure

Answer 4

True

Question 5

How are tRNAs charged w/ AA

Answer 5

Aminoacyl-tRNA synthase hydrolyzes ATP to fuel coupling of AA to tRNA

1. Aa linked to Carboxyl group (AMP)
2. Carboxyl transferee to 3’ end of RNA

Question 6

What are two things that ensure correct AA bonding in peptides

Answer 6

AA synthase (AA specific and tRNA specific) 
1. Built in proof reading mechanism 
tRNA is an adapter that couples the right AA

Question 7

What’s the proofreading mechanism in tRNA synthetases

Answer 7

Each amino acrylic t-Synthetases are AA specific
PrimaryBS - specific AA
SecondaryBS - allow similarly AA
Signals inactivation and AA gets kicked out

(Anticodon are recognized by tsynthetases too)

Question 8

How are AAs added to polypeptide chain

Answer 8

N-terminus to C-terminus

Formation of peptide bond is energetically favorable

Question 9

What cells types might need more ribosomes?

Answer 9

Rapidly replicating Cells

Question 10

What are characteristics of ribosomes?

Answer 10

A= amino acrylic tRNA bind, P=Peptidyl-tRNA site , E = GTFO
2 sites are always occupied
2/3s of it RNA;
It’s a riboenzyme; RNA itself that change conformations to enduce protein syn and proteins are there for structure support

Prokaryotes and Eukaryotic ribosomes share similar structure and function

Question 11

What are the steps of protein synthesis ? (4)

Answer 11

1. New tRNA binds to A site
2. C-term end of released from tRNA in P site (peptide bond formed)
3. Large subunit held by small unit moves across mRNA shifting to P and E sites on small subunits
4. Small subunits moves 3 nucleotides along the mRNA and ejects tRNA in the E site

Question 12

What are elongation factors?

Answer 12

EF-TU & EF-G in Prok

EF1 & EF2 in EUK
EF-TU AND EF1 increased accuracy

Question 13

How is protein synthesis initiated?

Answer 13

binding of specific proteins (elF4g) to poly A tail and (elF4E) to 5’ cap

Question 14

What is the consensus sequence around a start codon?

Answer 14

AUG - EUK
ATG in PROK

Must be flanked acc and g if not then ribosome will skip to the next AUG

Question 15

What binding to an A site terminates protein?

Answer 15

release factor binds to A site and a stop codon ex: UAG is read

Question 16

What did fungal biology lead to?

Answer 16

Fungi prevented bacterial attack using small molecules by targeting ribosomal function in bacteria

Lead to creation of ANTIBIOTICS

Question 17

What is nonsense mediated decay?

Answer 17

Prevents premature stop codons by eliminating the mRNA that contains it .

1. As mRNA leaves nucleopore it is tested by ribosome
2. Since EJC are bond at exon junctions it runs through a stop codon while EJC is present its premature
3. .mRNA is then rapidly removed

Question 18

When do proteins fold?

Answer 18

Immediality after synthesis

ENERGETICALLY FAVORABLE

Question 19

What are heatshock proteins?

Answer 19

Recognize proteins damaged by heat
Recognize wrongly placed hydrophobic regions on outside of proteins
Bind to them with hsp60

Question 20

What is hsp60

Answer 20

Barrel shaped protein that encloses a protein that misfolded proteins.

By unraveling them and then encourages correct protein formation

Question 21

What forms when incorrectly proteins are not eliminated?

Answer 21

Protein aggregates form and lead to proteopathies

Prison disease, Alzheimer’s, and Parkinson’s

Question 22

What is the last ditch effort to eliminate misfolded proteins

Answer 22

proteasome chop them up
When it is not fixed.
Mark them for death via ubiquitin

Question 23

How do proteasomes work?

Answer 23

Marked proteins enter proteosome
Special E3 proteins recognize misfolded proteins and add ubiquitin peptides linked lysine 4 (key identifier of proteodamage)
Use atp hydrolysis to unfold protein and degrade it

Question 24

What are chaperones?

Answer 24

Cells use additional chaperones to ensure that peptides fold onto the correct function or refold them if they got damaged