RNA and Genetic Code

Question 1

In what direction does the ribosome read the mRNA transcript, and in what direction does it synthesize the protein?

Answer 1

ribosome reads mRNA 5’ –> 3’

ribosome translates protein N terminal –> C terminal

Question 2

what is the function of aminoacyl-tRNA synthetase?

Answer 2

charges 3’ end of tRNAs with proper amino acid

Question 3

What is the CCA nucleotide sequence?

Answer 3

it is the terminal 3’ sequence on tRNA where amino acids bind (5’-CCA-3’)

Question 4

How many phosphoanhydride bonds from ATP is required for tRNA charging?

Answer 4

2 ATP bonds

aminoacyl-tRNA synthetase converts ATP to AMP+PPi

Question 5

What are the three stop codons?

Answer 5

UAG
UGA
UAA

Question 6

What is the RNAP II binding site in the DNA promoter region, in eukaryotes?

Answer 6

TATA box

contains high amount of T’s and A’s

Question 7

What are the difference functions of RNAP I, RNAP II, and RNAP III, in eukaryotes?

Answer 7

RNAP I - synthesizes rRNA in nucleolus
RNAP II - synthesizes hnRNA and snRNA
RNAP III - synthesizes tRNA and some rRNA

Question 8

what are snRNAs and snRNPs involved in?

Answer 8

splicing, forming the spliceosome

Question 9

what is a lariat?

Answer 9

the lasso-shaped structure that intron forms after it is spliced out

Question 10

what’s the size and components of the large ribosomal subunit in prokaryotes and eukaryotes?

Answer 10

large ribosomal subunit

prokaryotes: 50 - 5S + 23S
eukaryotes: 60 - 5S + 28S + 5.8S

Question 11

what’s the size and components of the small ribosomal subunit in prokaryotes and eukaryotes?

Answer 11

small ribosomal subunit

prokaryotes: 30 - 16S
eukaryotes: 40 - 18S

Question 12

what’s the size of the ribosome in eukaryotes and prokaryotes?

Answer 12

ribosome

prokaryotes: 70S
eukaryotes: 80S

Question 13

What is the rRNA that RNAP III synthesizes in eukaryotes?

Answer 13

5S, located in the large ribosomal subunit

Question 14

what is the shine-delgarno sequence?

Answer 14

in prokaryotes, it is the binding site for the small ribosomal subunit in the 5’ UTR of mRNA

Question 15

what on mRNA does the small ribosomal subunit bind to in eukaryotes?

Answer 15

5’ cap

Question 16

what is the function of peptidyl transferase?

Answer 16

an enzyme on large ribosomal subunit that uses GTP to form peptide bond

it transfers peptide chain to tRNA in P site to tRNA in A site.

Question 17

what’s the role of initiation factors?

Answer 17

help large ribosomal subunit bind to small ribosomal subunit

Question 18

what’s the role of elongation factors?

Answer 18

recruits aminoacyl-tRNAs and GTP, remove GDP

Question 19

Peptides that must be secreted from the cell contain a signal sequence that sends them where?

Answer 19

peptides for secretion contain a signal sequence that causes ribosome to attach to ER –> protein is trasnalted into lumen of rough ER –> protein goes to golgi apparatus –> protein is secreted through exocytosis

Question 20

How does termination of translation occur?

Answer 20

1. RF (release factor) binds to stop codon in A site.
2. water is added to peptide chain
3. peptide is hydrolyzed from tRNA by termination factors and peptidyl transferease

Question 21

what is prenylation?

Answer 21

addition of lipid groups to a protein, often to membrane-bound proteins

Question 22

According to the Jacob-Monod Model, what is the structure of an operon? (hint: prokaryotes)

Answer 22

From right to left (3’ –> 5’)

1. structural gene
2. operator site: binding site for repressor protein
3. promoter site: binding site for RNAP
4. regulate gene: codes for repressor protein

Question 23

what is an operon? (hint: prokaryotes)

Answer 23

a cluster of genes that are transcribed together as one mRNA (ex. trp operon - 5 enzymes involves in Trp synthesis)

Question 24

What’s the difference between an inducible system and a repressible system?

Answer 24

an inducible system is normally “off”. turned “on” by an inducer. repressor is active on operator.

a repressible system is normally “on”. turned “off” when repressor binds to a corepressor. unbound repressor is inactive on operator.

Question 25

What’s the difference between positive control and negative control, in prokaryotes?

Answer 25

positive control: protein binding to DNA increases transcription
negative control: protein binding to DNA decreases transcription

Question 26

the lac operon and trp operon are examples of what type of control and systems?

Answer 26

lac operon - negative inducible system

trp operon - negative represible system

Question 27

what is the function of the DNA-binding domain and activation domain of transcription factors?

Answer 27

DNA-binding domain: binds promoter or DNA response element

activation domain: recruits other TFs and regulatory proteins

Question 28

what are DNA response elements?

Answer 28

DNA sequences that only bind specific transcription factors

Question 29

Why does histone acetylation increase gene transcription?

Answer 29

Histones acetylases acetylate lysine residue on N-terminal of histone, decreasing positive charge of lysine. this decrease interaction between histone and DNA, causing more open DNA conformation.

Question 30

what two nucleotides undero DNA methylation?

Answer 30

adenine and cytosine

Question 31

does DNA methylation increase or decrease gene transcription?

Answer 31

decrease gene transcription