L. 6 Protein Synthesis (Translation)

Question 1

L.O.

Answer 1

1. Explain the unique problems associated with converting the information as a nucleic
   acid sequence to an amino acid sequence.
2. Outline the unique problems associated with protein synthesis, with particular reference to the unfavourable thermodynamics of peptide bond formation and the requirement for order. Describe the strategies used by cells to overcome these problems.
3. Describe the general functions of proteins and RNA molecules that are required for Protein synthesis
4. Describe the differences between primary, secondary, tertiary and quarternary structure of proteins.
5. Appreciate that the protein sequence defines the protein fold and function, and that protein molecules are held together by the combination of many bonds.
6. Demonstrate how 3D protein structure is related to function using the example of the alpha helix in DNA binding proteins.

Question 2

Challenges of protein synthesis

Answer 2

• Need to convert a sequence of nucleotides into a sequence of amino acids
• Needs to have the correct order of animo acids
• A peptide bond is very thermodynamically unfavourable

Question 3

Peptide bonds

Answer 3

• 2 amino acids use condensation polymerisation to form a dipeptide
• Unfavourable due to lots of water around

Question 4

RNA based ‘tools’

Answer 4

mRNA - Messenger RNA:
- Contains templates for translation, which amoni acids are in which order

tRNA - Transfer RNA:
- Matches the correct amino acid to the template

rRNA - Ribosomal RNA:
- Combines with proteins to form ‘machiner’ for protein synthesis
- catalyses peptide bond formation

Question 5

aa-tRNA Synthetase

Answer 5

Lock and key situation
1. High energy from ATP is used to create a high energy bond in amino acid bond
2. AMP leaves and a high energy bond is transfered between tRNA and animo acid
3. Synthetase releases activated tRNA molecule
4. tRNA and amino acid are ready for protein synthesis

[heft]

• Attaches the amino acid to the corresponding tRNA
• Uses ATP hydrolysis to get the energy to make a high energy bond
• Catalyses the activation of amino acids

Question 6

Ribosome

Answer 6

• Enzyme (protein ‘machine’)

EPA sites

A = accept
P = peptide chain formation
E = Exit

Question 7

Protein Synthesis Initiation

Answer 7

1. Two parts of Ribosomes are seperate, small subunit binds to the mRNA and a methyanine tRNA (anticodon to the start codon)
2. The large subunit binds and creates the EPA sites, met-tRNA sits in the P-site.

Question 8

Protein Synthesis Elongation

Answer 8

1. Amino acid binds to the A site matching the correct codon with its anticodon
2. The Ribosome helps move the tRNA on the A-site to gain the P-site’s amino acid, and shifts along onto the P-site. The amino acids are bind together by peptide bonds.
3. The tRNA molecule on the P-site originally, then shifts to the E site.
4. Another tRNA with an amino acid then binds to the A site, shifting all the other tRNA’s along a site, A to P, P to E, and E-site tRNA leaves.
5. The Amino acid peptide chain stays on the tRNA which is currently on the P-site.
6. This repeats over and over, creating a long peptide chain at the P-site until termination occurs.

Question 9

Protein Synthesis Termination

Answer 9

1. Elongation has occured and an amino acid chain is built until a stop codon is reached.
2. When a stop codon is reached, there is no tRNA that matches the site.
3. A ‘Release Factor’ protein binds to the A-site on the ribosome
4. Water is added, breaking the bond from the peptide chain and the tRNA, causing the chain to be free.
5. All of the parts disassemble, ready to be used again on a new piece of mRNA.

Question 10

Protein structure

Answer 10

• After protein is made, it must be folded into correct shape and structure to have its function.
• The amino acid sequence codes for the proteins folding, hence shape and functions

Primary
Secondary
Tertiary
Quaternary

Do NOT have a 5’ and 3’ end
Rather a N and C end

Question 11

Primary Structure

Answer 11

Only the amino acid sequence

Question 12

Secondary structure

Answer 12

Local structure
- Eg. Alpha Helices and Beta sheet
-

Question 13

Tertiary structure

Answer 13

• Held together by bonds, driving forces = Hydrophobic (E.g.Polar, ionic, electrostatic interactions)
• Overall 3D arrangement of a polypeptide chain
• Secondary structures fold into tertiary structures
• Hydrophobic force drives the protein folding, middle inside is very hydrophobic

Question 14

Quaternary Structure

Answer 14

Organisation of many subunits
- Minimum of 2 tertiary structures

eg. Haemoglobin (4 tertiary)

Question 15

Secondary structure features

Answer 15

• Local features allow for formation and structure
• Backbone - Hydrogen bonding is very important to define the structure
• Sidechain interactions help hold the structure together and form the tertiary structure

Question 16

Secondary Structure: Alpha helices and Beta Sheets

Answer 16

Hydrogen bonding is very important:
In Apha Helices it holds together between the spirals
In Beta Sheets it holds together between Strands

Alpha helices:
- Side chains point out from helx, nothing inside

Beta Sheets:
- Side chains point away from structures

Question 17

Protein folding

Answer 17

• Info encoded in amino acid sequence
• Burial of hydrophobic surfaces and sidechains in an aqueous solvent
• Collapse of protein chain/ formation of secondary structure
• Parts of the protein interact with bonds to firm up the tertiary structure

Question 18

Biomolecules are…

Answer 18

• Dynamic
• Proteins and other structures are NOT rigid but ‘breathe’ as atoms move around

Question 19

Molecules, life and stability

Answer 19

Most life occurs in mild conditions on earth:
- 5-50ºC
- Atmospheric Psi
- ~7 pH neutral

Proteins can be Hydrolysed and broken down into parts in very acidic/ basic conditions with heat/ pressure
- Tertiary structure is easier to unfold. (eg. cooking an egg)

Question 20

Effects of mutations on protein structure and function

Answer 20

• effect on protein depends on the type of mutation
  Silent mutation
• no change

Frameshift mutation
- different protein sequence, unlikely to fold correctly. Likely to effect function

Point mutations
- Similar residue on active site may not have big effect, minor change in structure stability
- Different residue on active site may affect folding