lecture 9 concepts bchm

What is a codon?

A sequence of 3 nucleotides in mRNA that specifies an amino acid or stop signal.

Why are codons 3 bases long and not 2?

Two bases (4²=16) aren’t enough to encode 20 amino acids; three bases (4³=64) are sufficient.

Define "reading frame."

The division of nucleotides into codons, starting from a specific base. Each sequence has 3 possible reading frames.

tRNA acts as an ____ to translate the nucleotide message into a protein sequence. 

What is an ORF (open reading frame)?

A stretch of codons without a stop codon that usually encodes a protein.

Then Nirenberg and Matthew fed Poly (U) and radiolabeled amino acids to E coli, what did they find?

GGG did not generate any polypeptide, because it

forms tetraplexes that cannot be bound by ribosomes. It inhibits translation

What is the start codon and what amino acid does it encode?

AUG, encoding methionine (Met).

Name the three stop codons.

UAA, UGA, UAG.

Define missense mutation.

mutations in which a single new

base pair replaces another ie A for U

Define silent mutation

A base substitution that does not alter the amino acid.mutations in which the nucleotide is

different but the encoded amino acid stays the same

What is the function of the anticodon in tRNA?

The anticodon on tRNA base-pairs with the mRNA codon, helping to translate the genetic code during protein synthesis.

What is the "wobble base" in the context of codon-anticodon pairing?

The third base of the codon (first base of anticodon), which can form weak base pairs with the first base of the anticodon, allowing for mismatches and flexibility in codon recognition.

What did Francis Crick’s Wobble Hypothesis suggest about codon-anticodon pairing?

The first two nucleotides of the codon form strong base pairs, while the first base of the anticodon determines codon recognition flexibility, allowing a single tRNA to recognize multiple codons.

• If the wobble position is 

  • C or A, base pairing is specific

  • U or G, less speciggic, two codons may be read

  • I, all three codons read (because it can form wk H bonds with all )

Define transition mutation.

a type of missense mutation- replacement of a purine with another purine (A ↔ G) or pyrimidine with another pyrimidine (C ↔ U/T).

What usually happens when the first base of a codon mutates?

Conservative substitution (similar amino acid, similar properties ). Example: GUU (Val) → AUU (Ile).

Define translational frameshifting

Ribosome “hiccups” and shifts the reading frame, producing 2+ proteins from one mRNA.

Example of frameshifting in viruses?

Rous sarcoma virus: gag and pol proteins from one mRNA by a +1 shift.

Example of frameshifting in bacteria?

RF-2 synthesis: frameshift bypasses an early stop codon when RF-2 levels are low.

Protein synthesis can account for up to 90% of a cell’s chemical energy usage for biosynthetic reactions true or false?

True

What are the homologs between prokaryotic and eukaryotic initiation of protein syntheis

elF1A is a functional homolog of IF1

elF3 is a functional homolog of IF3

Explain the initiation for Protein synthesis in Eukaryotes

INITIATION

Step 1

• elF1A blocks tRNA binding to A site by binding there

• elF3 prevents premature joins of the 40+60s subunits—→conformational change

• elF1 binds to the E site 

Step 2

• a complex containing charged tRNA fMet, eIF2, and GTP binds to the 40S subunit, along with eIF5 and eIF5B

– creates a 43S, preinitiation complex

Step 3