BMP: Protein synthesis

Question 1

What is translation?

Answer 1

The production of a protein by tranalation of mRNA

Question 2

What relates the mRNA base sequence and the AA sequence in a protein

Answer 2

the genetic code

Question 3

What encodes for AAs

Answer 3

mRNA Codons - sets of 3 base pairs

The codons are degenerate which means each Codon codes for a specific AA. This means the genetic code is unambigous and not open for interpretation

Each AA may have more than one set of codons which codes for it

Question 4

How many codons sets are there?

Answer 4

4³ = 64

Question 5

What are stop and start codons?

Answer 5

UAA, UAG, UGA

Question 6

The genetic code is tolerant of point mutations. Give examples of these and why these might occur

Answer 6

• Insertion or deletion
• Spontaeous mutations arising during DNA replication or physical mutagen

Question 7

How is the genetic code read?

Answer 7

From 5’ to 3’

Question 8

What is the role of tRNA?

Answer 8

• Carries specific AA to the ribsome for incoperation into the protein structure
• Each tRNA molecule carries a specific AA

Question 9

Describe the binding of tRNA to AA

Answer 9

• The AA binds to tRNA via the 3’OH group on tRNA which is catalysed by aminoacyl tRNA synthase. The process requires ATP
• The later reaction of the binding of AAs together uses the energy liberated from cleavage of the ester bond

Question 10

Describe the binding between mRNA and tRNA

Answer 10

The codon in mRNA binds to the anticodon in TRNA. The base pairs are complementary

They aligin in an anti-parallel fashion

Question 11

Describe the wobble hypothesis

Answer 11

• Wobble hypothesis allows for broader specificity
• There is 61 possible codon sequences (64 but -3 stop codons)
• This means 61 species of tRNA molecule are required for complemntay base pairing. Most species have fewer than 45. The wobble hypothesis accounts for thi
• The 5’ base at the end of the anti codon which binds to the 3’ end of the codon on mRNA is not spatically confined -this means it allows binding to complementary bases and also unconentional bonding to non base pairs
• This allows the tRNA anticodon to code bind with several codons.
• Inosine can pair with A,U or G

Question 12

What is the structure of ribsosmes?

Answer 12

• Composed of rRNA and proteins
• Contains a small (40S) and large (60S) ribosomal subunit. The small is responsiable for monitoring the base pairing of the codon on mRNA to the anti codon on tRNA. The large is responsible for peptide bond formation
• Function is to translate the DNA sequence contained in mRNA to a protein

Question 13

What are the locations of ribsomes?

Answer 13

• When free they can move anywhere in the cytoplasm bar nucleus or oganelles
• When protein synthesis needs to occur, the ribosome will become membrane bound to the rough endoplasmic reticulum.
• The polypeptide chain ssynthesied will be inserted directly into the ER and carried to their targte destinations through the secretory pathway

Question 14

What are important sites on the tRNA and their functions?

Answer 14

• Peptidyl (P), amino acyl (A), Free tRNA ejection site (E)
• The amino acyl tRNA enetrs the ribosome through A. At site P the tRNA is held, which is linked to the growing polypeptide chain. AT site the free tRNA is ejected from the ribsome

Question 15

What does the ribsome catalyse?

Answer 15

• Interaction between mRNA and amino acyl tRNA
• Peptide bond formation between adjacent AAs

Question 16

Decribe the basic steps of translation

Answer 16

1. Activation
   
   • tRNA convarntly bond to correct AA
2. Initation
   
   • Small subunit of ribosome binds to 5’ end of mRNA
   • Starts at initation or start codon
     
     • Usually AUG
   • Aided by initation factors
3. Elongation
   
   • Ribsome moves along the mRNA molecule producing a polypeptide strand as tRNA adds AAs
4. Termination
   
   • Ribosome reaches a stop codon
     
     • UAG UAA UGA
   • Polypeptide released

Question 17

Describe initation

Answer 17

• •In eukaryotes initiation involves formation of the following complex;
  
  • mRNA, an 80S ribosome and methionyl-tRNAiMet.
• •This complex is built sequentially in a highly specific order.
• •Initially tRNAiMet picks up methionine from the bulk cytoplasm, followed by attachment to initiation factor 2-GTP (eIF2-GTP).
• •This assembly binds to a 40S ribosomal subunit linked to eIF3, attaching specifically at the peptidyl (P) site.
• •After passage through the nuclear pore, mature mRNA becomes attached to cap binding complex (eIF4F).
• •This subsequently joins the 40S assembly.
• •The mRNA is scanned to detect the initiation codon
  
  • AUG
  • This requires energy donated by ATP.
• •Once identified codon:anticodon base pairing occurs
  
  • all initiation factors dissociate along with GTP hydrolysis.
• •Finally the large 60S ribosomal subunit binds.

Question 18

Describe elongation

Answer 18

• •Elongation commences when the aminoacyl-tRNA (aa-tRNA), specified by the codon in the aminoacyl (A) site of the ribosome, binds.
• •The incoming aa-tRNA requires assistance from elongation factor 1A-GTP (EF1A-GTP).
• •Immediately upon aa-tRNA attachment to the A site GTP is hydrolysed and EF1A-GDP leaves.
• •Fresh EF1A-GTP must be regenerated to allow further aa-tRNA binding.
• •Released EF1A-GDP is bound by EF1B.
• •This stimulates replacement of GDP with GTP, and EF1B dissociates.
• •Reformed EF1A-GTP will then attach to fresh aa-tRNA.

Question 19

Desvribe peptide bond formation

Answer 19

• •The amino acids attached to the tRNA’s are then able to form a peptide bond.
• •A peptide bond forms between the a carboxyl group of one amino acid and the a amino group of the next e.g.
• •The reaction is catalysed by peptidyl transferase and synthesis proceed from the N to C terminus.
• •As a result, a dipeptidyl-tRNA is now present in the A site along with an uncharged tRNA in the P site.
• •Elongation continues with:
• –translocation of the ribosome along the mRNA a distance of one codon, involving EF2-GTP,
• –attachment of appropriate aa-tRNA at the now vacant A site (dipeptidyl-tRNA in P site),
• –loss of the uncharged tRNA from the E site.
• •A series of ribosomes bind forming a polysome

Allows multiple polypeptide synthesis

Question 20

Desribe termination

Answer 20

• •Upon entry of a stop codon (5’ UAA 3’, 5’ UAG 3’, or 5’ UGA 3’) into the A site termination occurs.
• •No aa-tRNA recognise these codons.
• •Release factors bind and stimulate
• –release of the completed polypeptide chain
• –detachment of mRNA
• –separation of the 80S ribosome into 40S and 60S subunits

Question 21

Describe protein processing

Answer 21

• •Released polypeptide may be post-translationally modified
  
  • e.g. glycosylation.
• Finally folds to produce a mature functional protein
• Post‐translational modifications can occur on the amino acid side chains or at the protein’s C‐ or N‐ termini. They can extend the chemical repertoire of the 20 standard amino acids by introducing new functional groups such as sugars, phosphate, acetate, amide groups, or methyl groups. Phosphorylation is a very common mechanism for regulating the activity of enzymes, and is the most common post‐translational modification.