Bentzen 8 - The Genetic Code

Question 1

Why is the nucleotide sequence in a triplet code (codons)?

Answer 1

There are 20 amino acids and 4 nucleic acid bases. So the number of possible codons:

4^n (N=# nucleotides per codon)

• 1 or 2 Bases is not enough
• 3 bases = 64 possible codons (enough!)

Question 2

What did Marshall Nirenberg and Philip Leder use to decipher the genetic code?

Answer 2

Ribosome bound tRNAs and many short mRNAs with known codons

They added the mRNAs one by one to a mix of ribosomes and amioacyl-tRNAs (tRNA + amino acid)

In each trial, 1 amino acids was radioactively labeled, so they could determine which of the aminoacyl-tRNA was bound to the short mRNA like sequence and ribosome

The mixture wa passed through a nitrocellulose filter, the tRNA paired with ribosome-bound mRNA stuck to the filter, unbound tRNAs passed through it

The filter was assayed to determine which amino acid with bound

Conclusion: When an mRNA with GUU was added the tRNAs on the filter were bound to valine, therefore the codon GUU specifies valine. Many other codons were determined by using this method

Question 3

How many codons are there?

Answer 3

64

Question 4

How many sense codons are there? (code for amino acids)

Answer 4

61, including AUG, the start codon for methionine

Question 5

What are the three nonsense codons?

Answer 5

UAA, UAG and UGA for stop, they terminate transcription and do not code for amino acids

Question 6

In what direction is a codon read for the codon table?

Answer 6

5’ to 3’ codons on the mRNA

Question 7

What does saying the code is ‘degenerate’ mean?

Answer 7

That several amino acids are specified by more than 1 codon (degeneracy)

The code is degenerate but not ambiguous! A codon never specifies more than one amino acid

Question 8

What are codons that specify the same amino acid called?

Answer 8

Synonymous

Question 9

How do most synonymous codons differ?

Answer 9

IN the third base, the 1st and 2nd are most important for distinguishing the amino acid. This way mutations in the third position rarely change amino acid specification

Question 10

What is partial degeneracy?

Answer 10

Changing the third base in a codon from a purine to purine (eg. G to A) or from a pyrimidine to a pyrimidine

Question 11

What is complete degeneracy?

Answer 11

Changing the third base in a codon to any of the four bases, but stil coding for the same amino acid.

Question 12

What are two ways that degeneracy of the genetic code is accommodated by?

Answer 12

1. Isoaccepting tRNAs, which bind the same amino acid, but recognize different codons
2. The wobble effect, which allows same aa-tRNA to pair with more than one codon

Question 13

How many different tRNAs are there?

Answer 13

30

Question 14

How many different amino acids are there?

Answer 14

20

Question 15

If there are 30 tRNAs and 20 amino acids, and all tRNAs are used, what is allowing this?

Answer 15

isoaccepting tRNAs which can recognize more than one codon for the same amino acid residue

Question 16

What is the wobble effect?

Answer 16

There are 61 sense codons but only 30 anticodons (tRNAs) so the same anticodon base pairs with different codons. This allows the same anticodon to base pair with more than one codon.

Wobble occurs between the 1st (5’) base of an anticodon of tRNA (the wobble position) and the 3rd base of a codon (3’). The wobble position base of an anticodon is allowed to move slightly form its normal position to form a non Watson-Crick base pair with the codon

Question 17

What is the wobble position on an anticodon?

Answer 17

The 1st base of anticodon of tRNA (5’)

Question 18

Which bases can pair with their non-Watson-Crick pairs when they’re in the wobble position?

Answer 18

G and U, also I (inosine) can pair with A, U or C

Question 19

What is inosine? What can it pair with when it’s in the wobble position on the anticodon?

Answer 19

Inosine (I) is a base pair that can pair with A, U, or C when in the wobble position

Question 20

In what orientation does the anticodon bind to the mRNA? (eg. 5’/3’)

Answer 20

They bind antiparallel to one another. Eg. the mRNA will be going 5’ to 3’ in one direction and the anticodon will be 3’ to 5’ in the same direction.

Question 21

Is the genetic code universal? Why or why not?

Answer 21

The genetic code is not universal across species, in some species what may code for Trp may code for Stop in another.

Question 22

What is the first codon of a reading frame (RF)? What amino acid does it code for?

Answer 22

AUG is always the first codon of a reading frame in mRNA. It codes for Met (methionine)

Question 23

What is a reading frame in RNA?

Answer 23

The protein coding region of the mRNA that begins with AUG (Met) and ends with the STOP codon.

Question 24

In what direction are codons of mRNA read?

Answer 24

5’ to 3’

Meaning if you’re looking AUG (Met) start codon, than look for 5’ - AUG - 3’

Question 25

How many reading frames are possible in DNA sequence?

Answer 25

Six, three for each strand

Question 26

What are point mutations? What are the three types?

Answer 26

They alter a single nucleotide

Silent mutation (no changes to amino acid sequence)

Missense mutation (an amino acid is changed)

Nonsense mutation (an early stop codon is made)

Question 27

What are frameshift mutations? The two types?

Answer 27

Mutations that effect the whole reading frame from one mutation. Includes:

Deletions
Insertion