Lecture 6

Question 1

How many reading frames are in dsDNA and mRNA?

Answer 1

6 dsDNA

3 mRNA

Question 2

Open reading frame contains?

Answer 2

1) start codon
2) coding sequence
3) stop codon

Question 3

Eukaryotic tRNA molecules transcribed by?

Answer 3

RNA pol. III

Question 4

Eukaryotic tRNA molecules are processed….?

Answer 4

before leaving nucleus, trimed, and spliced (catalyzed by proteins)

Question 5

What % of tRNA are modified bases?

Answer 5

10

Question 6

Modified bases of tRNA molecules influence?

Answer 6

mol. conformation, base-pairing, amino acid coupling

Question 7

Degenerate genetic code (numbers only)

Answer 7

4^3= 64 codons code for 20 amino acids

Question 8

What are 2 possibilities that allows genetic code to be degenerate?

Answer 8

1) multiple tRNAs with multiple anticodons

2) 1 tRNA (with one anticodon) can regonize multiple codons

Question 9

aminoacyl-tRNA synthetase

Answer 9

is a dual check mechanism that couples correct amino acid to cognate tRNA, where tRNA acts like activated carrier to shuttle activated amino acid

Question 10

How does aminoacyl-tRNA synthetase assure correct amino acid pairing?

Answer 10

synthetase assesses nucleotide sequences of 1) anticodon, 2) amino acid acceptor arm, and 3) several other positions of tRNA

Question 11

Where does translation occur?

Answer 11

ribosomes in the cytosol (E, P, A site)

Question 12

Translation mechanism

Answer 12

1) small and large ribosomal subunits assembled at nucleolus
2) binding of mRNA joins subunits together to fomr a ribosome

Question 13

Large ribosome subunit contains what?

Answer 13

peptidyl transferase activity

Question 14

Peptidyl transferase activity mechanism

Answer 14

peptidyl-tRNA ttached to CTD of growing polypetide chaine

aminoacyl-tRNA frees tRNA molecules from peptidyl linkage

new peptidyl-tRNA molecule attached to CTD of growing polypetide chain

Question 15

3 tRNA binding sites are?

Answer 15

Aminoacyl-tRNA
peptidyl-tRNA
Exit

Question 16

How many tRNA binding sites are occupied at the same time?

Answer 16

2

Question 17

EF-Tu proofreading mechanisms for improving translation fidelity?

Answer 17

1) tight codon-anticodon pairing

2) delay of peptidyl-residue transfer

Question 18

Ef-Tu: tight codon-anticodon pairing

Answer 18

16S rRNA triggers conformational change in ribosome, EF-TU catalyzes GTP hydrolysis and dissociates from amino acyl group of tRNA

Question 19

eF-tu: peptidyl-residue transfer delay

Answer 19

weakly bound tRNA in A site, will cause tRNA to dissociate before peptidyl residue can be transferred

Question 20

EF-G

Answer 20

move ribosome forward

Question 21

How do biological processes overcome limitations to complementary base-pairing?

Answer 21

induced fit, kinetic proofreading and the sequential se of both mechanisms

Question 22

Why is translation initiation important?

Answer 22

determines reading frame and translation frequency

Question 23

Translation initiation mechanism

Answer 23

1) MtRNA + eIFs bind to small rSU in P site
2) Small rSU binds to 5’ cap with bound eIF4 E + G
3) Small rSU searches for first (5’ located) AUG eIFs drives this movement via ATP hydrolysis)
4) Encounter of start codon releases eIFs and
large rSU binds

Question 24

Bacterial translation initiation is mediated by?

Answer 24

Shine-Dalgarno sequence (AGGAGGU)

Question 25

Shine-dalgarno

Answer 25

initiates bacterial translation: functions as ribosome binding site through base pairing, replaces function of 5' cap of eukaryotic mRNA, enables polycistronic mRNAs

Question 26

translation termination mechanism

Answer 26

-Release factors bind to stop codon - peptidyl transferase add water to growing peptide chain to release peptide from a site -ribosome disassembles

Question 27

How is translation efficiency boosted?

Answer 27

polysomes (5'cap-poly A interaction allows efficient recycling of ribosomes)

Question 28

What triggers mRNA degradation?

Answer 28

abnormal splicing causes ribosome to stall at stop codon in the presence of EJC

Question 29

Co-translational protein folding

Answer 29

1) growing polypetide chain 2) folded N-terminal 3) folding CTD 4) folding of protein is complete after ribosomal release

Question 30

Two types of heat shock proteins

Answer 30

HSP70 | -HSP60 (chaperonin)

Question 31

HSP70 bind to?

Answer 31

- bind to nascent peptide chain from ribosome - hydrophobic patches - bind tightly after ATP hydrolysis and dissociate after ATP rebinding

Question 32

HSP60

Answer 32

form a barrel that acts like an isolation chamber, where the opening contains hydrophobic patches where misfolded proteins can be recognized

Question 33

E3 ligase

Answer 33

recognizes unfolded proteins and marks them for degradation

Question 34

proteosomes

Answer 34

degrade proteins into small peptides (nucleus and cytosol)

Question 35

Proteosomes recognize?

Answer 35

substrates fused to L48 linked ubiquitin chain

Question 36

Proteosome cap

Answer 36

unfoldase that unfolds proteins and threads them into proteasome

Question 37

unfoldase

Answer 37

hexameric AAA protein sharing structural homology to helicases and dynein

Question 38

Regulated destruction: What does it control and how can it be induced?

Answer 38

proteins - activation of ubiquitin ligase - activation of degradation signal

Question 39

activation of ubiquitin ligase

Answer 39

1- protein kinase phosphorylates protein 2- allosteric transition caused by ligand binding 3- allosteric transition caused by adding protein subunit

Question 40

activation of degradation signal

Answer 40

1-phosphorylation by protein kinase 2- unmasking by protein dissociation 3- destabilizing N-terminus

Question 41

Where are small and large ribosomal subunits made?

Answer 41

nucleolus