The genetic code and transcription I

Question 1

The big picture:

Answer 1

• DNA is composed of a linear sequence of deoxyribonucleotides
  = dictates the structure of proteins [End products of most genes]

1. The info present on the template strand of the DNA is transcribed into a complementary RNA strand (mRNA).
2. The mRNA then carries this info out of the nucleus ( where DNA is stored in eukaryotic organisms) and into the cytoplasm
3. mRNA carries the message to the ribosomes ( in the cytoplasm)
   
   • where decoding takes place
4. Then conversion of nucleotide info into a sequence of amino acids
   = Translation

Question 2

Characteristics of the genetic code:

Answer 2

Linear, ribonucleotide bases
Three ribonucleotides (triplet) = codon
Unambiguous
Degenerate (18 out of 20)
Punctuation marks
Commas?
Non-overlapping
Colinear 
Universal

Question 3

Characteristics of the genetic code: explained

Answer 3

1. written in a Linear form
   - Using nucleotide bases as letters
   - The code is stored in the DNA and then transferred via complementary base pairing synthesis to RNA
   [ribonucleotide bases]
2. Three ribonucleotides (triplet) = codon
   [Triplet codon]
   - Each codon codes for a specific amino acid
   - There are three cases however, where the codon acts as punctuation - 3 stop codons
   - There is also one start codon
3. The code is degenerate, but unambiguous:
   > Degenerate (18 out of 20) amino acids:
   Each amino acid may be coded for by more than one codon
   
   • Only methionine and tryptophan which is encoded by a
     single codon each
     > Unambiguous:
     HOWEVER: each codon only ever specifies one amino acid
4. Punctuation marks
   - Start codon and stop codons
   Commas?
   - Comma-less, no internal punctuation.
   - Once translation starts, it continues until stop codon is reached
   ( without a break)
5. Non-overlapping
   - All nucleotides within a triplet code belong only to that codon
6. Colinear
   - The sequence is collinear with the sequence of amino acids which makes up the protein
   [The amino acid and nucleotide sequence lines up]
7. Universal
   - Used in viruses, prokaryotes, eukaryotes and archaea

Question 4

Start codon

Answer 4

AUG

Met- methionine

Question 5

Stop codons

Answer 5

UAA
UAG
UGA

Question 6

The code is also ordered

Answer 6

Example:
- Chemically similar amino acids often share similar metal bases

> Hydrophobic amino acids:
-Valine and alanine have a U or a C as their middle base

> Hydrophilic amino acids
- Such as serine and threonine often have a G or a C as their middle base

Question 7

What value does having an ordered code provide

Answer 7

Having an ordered code helps minimise the affects of mutation

Question 8

The pattern of degeneracy

Answer 8

• Often it is the first 2 letters of the codon that specifies for the same amino acid and it is only the 3rd nucleotide that changes
• Noticed by Francis Crick
  > wobble hypothesis:
  = During translation, It is the first 2 letters that are the most important
• Since hydrogen bonding at the 3rd nucleotide would be less specially constrained
  > Which means it doesn’t have to adhere so closely to base pairing rules

Question 9

Developing and Deciphering the Genetic code

Answer 9

1. DNA direct interaction with ribosomes?
   THOUGHT:
   - Info was copied from DNA to ribosomal RNA in nucleus
   -And then the rRNA served as the template for protein synthesis at the ribosome in cytoplasm.
   HOWEVER:
   There was accumulating evidence that suggested there was an unstable intermediate template.
   - And rRNA was shown to be extremely stable
   - mRNA discovered by Jacob & Monod
2. How 4 letters specify 20 words?
   Size of code words: 2, 3, or 4? (20 amino acids; Brenner)
   4^2=16 4^3=64 4^4=256
   4^3=64 - makes the most sense, 64 is more than the 20 Amino acids, but less than the 256, therefore triplet codon makes the most sense

Question 10

first proof for triplet nature of code

Answer 10

Came from Frameshift mutations
Crick et al.
- Were looking at infection of E. coli K12, by phage T4,
- and what happened when they induced mutation in the phage by a mutagen –> proflavine
Observed:
- When one or 2 nucleotides were inserted into a gene, this caused a frameshift mutation which resulted in the phage not being able to infect the E.coli
- However, the mutation of 3 nucleotides restored the reading frame and allowed the mutation to take place
- This is due to the non-overlapping nature of the genetic code
(each codon contains only its own 3 nucleotides)
> Hence, the reading frame must be set at the start of the first
codon
> The codons are then read in their 3 nucleotides
- Insertion of one nucleotide base into a codon will mutate one codon and will shift the reading frame one nucleotide to the right
- This now means that all future codons are out of the reading frame and are thus different to what they would’ve been originally
- The entire rest of the gene is out of frame = frameshift mutation
HOWEVER:
- If 3 nucleotides are inserted, this can affect one or two codons that are out of frame and mutated
- However, the remaining codons are returned to their reading frame and the function of the gene may therefore be saved
- this is only possible in a triplet code.

Gain/loss of 1 or 2 nts caused frameshift mutation (+/-; ++/–)
Mutations of 3 nts restored reading frame (+++/—)