lecture 3 - gene expression

Question 1

process of transcription

Answer 1

-the double stranded DNA opens up
-the RNA polymerase which comes through and it needs to locate on the gene a specific region so that it can begin transcription
-the RNA polymerase moves along, you get your pre-mRNA transcript, that pre-mRNA transcript needs to be processed and in doing so it allows stability of that RNA transcript to remain within the nucleus so we can actually transcribe it
-once the pre-mRNA has been processed and your exons have been removed, this mature mRNA transcript has a 5’ GTP cap and a poly(A) tail is protecting that transcript and that’s important as it allows for the stability of the RNA so it can be transcribed
-RNA is very unstable it normally only is within the cell for anything from 5-20mins, it depends on the RNA transcript, so when we move that mRNA transcript out through the nuclear pores its targeted towards the ribosome, which is part of your RER
-it’s within the ribosome that we translate that mRNA to make the protein

Question 2

where does replication happen

Answer 2

nucleus

Question 3

where does transcription happen

Answer 3

nucleus

Question 4

where does translation happen

Answer 4

cytoplasm

Question 5

what is the basic building block of a protein

Answer 5

amino acids

Question 6

what is the structure of an amino acid

Answer 6

• a carbon with an amine group, carboxyl group, a hydrogen and a R group which varies depending on which amino acid we are looking at
  -has a simple structure

Question 7

what bonds join amino acids together

Answer 7

peptide bonds

Question 8

how do two amino acids join together

Answer 8

-condensation reaction, removes a water molecule
-the amine group of one amino acid and the carboxyl group of another amino acid join together

Question 9

what bases make a methionine (start codon)

Answer 9

AUG

Question 10

what are the stop codons?

Answer 10

UAA,UAG, UGA

Question 11

what are features of the genetic code?

Answer 11

-degenerate
-universal
-written in a triplet code
-non-overlapping
-non-ambiguity - while the same amino acid can be coded by more than one codon, the same codon shall not code for two or more different amino acids
-polarity - read in a 5’ to 3’ direction

Question 12

what are the amino acid groups depending on their biochemical properties?

Answer 12

-small
-nucleophilic
-aromatic
-amide
-hydrophobic
-basic
-acidic

Question 13

which amino acids are grouped as small?

Answer 13

-glycine
-alanine

Question 14

which amino acids are nucleophilic?

Answer 14

-serine
-Thr
-Cys

Question 15

aromatic amino acids?

Answer 15

-Phe
-Tyr
-Trp

Question 16

amide amino acids?

Answer 16

-Gln
-Asn

Question 17

basic amino acids?

Answer 17

-His
-Lys
-Arg

Question 18

acidic amino acids?

Answer 18

-Asp
-Glu

Question 19

hydrophobic amino acids?

Answer 19

-Val
-Leu
-Ile
-Met
-Pro

Question 20

does the body make essential or non-essential amino acids? which ones need to provided from our diet?

Answer 20

-the body makes the non-essential amino acids
-a group of essential amino acids, these are the ones we need in our diet

Question 21

how do we read the RNA and make a peptide?

Answer 21

-every region has 6 potential reading frames
-your coding region is where the transcript is coming from
-we read 3 bases at a time - a codon
-you have the RNA transcript which will end at the end of the gene
-if DNA is double stranded, you have antiparallel to that another strand which could be transcribed so there are more possible frames
-how the cell decides what happens depends on the orientation of the DNA
- you read from a 5’ to 3’ direction so on the other strand you would be reading in the other direction
-you need a methionine and also one of the stop codons for transcription to occur
-the one which is open will give the longest polypeptide

Question 22

process of splicing

Answer 22

The first step of splicing involves U1 and U2. U1 binds to the 5 splice site and U2 binds to the invariant site or the branch point. In the second step the remaining snRNPs bind to the earlier bound snRNPs. U5 and U4-U6 bind to the intron region and hence, now the spliceosome is assembled. Now, the spliceosome loops out the intron, and the two ends of the introns are brought close to each other. Further U1 and U4 are released and U6 is bound to both, the 5 splice site and U2.
In the next step the 5 end of the intron is cleaved and it attaches to the branch point of the intron, which is rich in A. Finally, the 3 end of the introns is also cleaved and the intron is released and further degraded by enzymes. The intron structure is called a Lariat (loop-like).
Lastly the two exons are joined together.
The snRNPs are used for splicing of other introns and the process of splicing continues for the remaining introns in the pre-mRNA.