Lecture 9: DNA to protein

Question 1

Elongation factors

Answer 1

Drive translation forwards and improve its accuracy. Speed up synthesis by hydrolyzing GTP

Question 2

RNA related exosomes

Answer 2

Protein complex that cleans up damaged RNAs before they leave the nucleus
Contain RNAses to chop up RNA

Question 3

Other type of exosome

Answer 3

Cell derived vesicles present in most eukaryotic fluids
Contain molecular constituents of their cell of origin
Most contain an evolutionarily conserved common set of protein molecules

Question 4

miRNAs regulate expression of over ___% of all protein coding genes

Answer 4

Regulate expression of over 70% of all protein coding genes

Question 5

What causes termination of translation

Answer 5

Binding of release factor to the A site (stop codon)

Question 6

What protein helps mRNA out of nucleus

Answer 6

Nuclear export receptor protein

Question 7

Step four of translation

Answer 7

Small subunit moves 3 nucleotides along the mRNA and ejects the tRNA in the E site

Question 8

Fungi and antibiotics

Answer 8

Fungi produce many antibacterial compounds that exploit differences in ribosomal subunits. New abx have been created that target bacteria via their ribosomal structure

Question 9

How do alternative starting points arise in translation

Answer 9

Consensus sequences flank the start codon (AUG) and tell the ribosome to begin translation on that certain AUG

Question 10

Editing pocket

Answer 10

Second AA binding site in aminoacyl-tRNA synthetase that excludes correct AA but allows closely related AAs in. If it is occupied, the editing pocket with inactivate the tRNA

Question 11

Step one of translation

Answer 11

New tRNA binds to A site pairing with codon

Question 12

Why are tRNA introns not spliced by spliceosome

Answer 12

Splicing requires the tRNA to be folded properly and will not proceed if it is not. Therefore, this represents a quality control step in tRNA generation

Question 13

Wobble pase pairing

Answer 13

Nucleotides in the third “wobble” position can bind with multiple different nucleotides in anticodon

Question 14

Nucleolus

Answer 14

Ribosome producing factory. Site where rRNA is processed and assembled into ribosome subunits.

Question 15

Significance of nucleolus size

Answer 15

Size of the nucleolus reflects to cells need to generate proteins

Question 16

tRNA modifications

Answer 16

10% of nucleotides in tRNA are modified

Question 17

rRNA is responsible for (3)

Answer 17

Overall structure, the ability to position tRNAs and its catalytic activity

Question 18

Primary role of proteins in ribosome

Answer 18

Stabilize the RNA core

Question 19

MicroRNA definition, function

Answer 19

Small non-coding RNA molecule

Functions in RNA silencing and post-transcriptional regulation of gene expression via RNA degradation

Question 20

TATA box

Answer 20

Promotor region on DNA 25 nucleotides from the transcription initiation site

Question 21

Cajal bodies

Answer 21

Area where most snoRNAs are assembled into snRNP

Question 22

5’ Cap does what

Answer 22

Allows mRNA to be distinguished from non coding RNAs and is also important for establishing translation

Question 23

Step two of translation

Answer 23

Carboxyl end of growing peptide is released from tRNA in P-site. Peptide bond formation between previous AA added and the new one. tRNAs are in P site and A site

Question 24

Ribozyme

Answer 24

RNA capable of enzymatic function

Question 25

snoRNA - what are they and what do they do

Answer 25

Small nucleolar RNAs

Help implement biochemical modifications of noncoding RNAs with help of other proteins

Question 26

Nonsense mediated decay

Answer 26

Eliminates mRNAs that have premature stop codon as they try to exit the nuclear pore

Question 27

Protein folding begins

Answer 27

Before translation even finishes

Question 28

aminoacyl-tRNA synthetase

Answer 28

Helps ensure that the correct amino acid is coupled to the tRNA

Question 29

snRNP

Answer 29

snoRNA + specific proteins= snRNP

Question 30

Causes for concern for use of miRNA for therapeutic intervention

Answer 30

Precise delivery to tissue of significance

Off target interactions

Question 31

miRNA therapeutic potential

Answer 31

Can be used as knock-down tool to knockout gene and see what happens. Can target genes specifically. Tremendous potential for disease intervention in any case where stopping gene activity would be valuable

Question 32

Chaperone proteins

Answer 32

Ensure that peptides fold into the correct functional conformation or refold them if they get damaged

Question 33

Proteasome

Answer 33

Searches for misfolded proteins in nucleus and cytoplasm, ingests them and degrades them. Ubuiqulylation (at lysine 48) is the sign that the proteasome needs to degrade it.

Question 34

What are the steps involved in RNA processing before leaving the nucleus

Answer 34

5’ capping
Poly A tail
RNA splicing

Question 35

hsp60 family of heat shock proteins

Answer 35

This is a barrel shaped protein that fixes misfolded proteins. Captures proteins using hydrophobic interactions

Question 36

Step three of translation

Answer 36

Large subunit moves along mRNA held by small subunit, shifting tRNAs to P and E sites on small subunit

Question 37

What occurs in all living cells

Answer 37

The flow of information from DNA to RNA to protein

Transcription and translation

Question 38

What usually indicates protein is misfolded

Answer 38

Exposed section of hydrophobic amino acids

Question 39

miRNA processing

Answer 39

Transcription into Pri-miRNA
Processed by Drosha into Pre-miRNA
Exported from nucleus as DS-RNA
Processed by Dicer- loop is cut off, miRNA binds complementary strand of mRNA

Question 40

Most common modification of noncoding RNAs

Answer 40

Pseudouridylation and 2’O methylation