Chapter 15 - The Genetic Code and Translation

Question 1

What are amino acids composed of?

Answer 1

Central carbon

Amine group

Carboxyl group

R group (radical group) - what differentiates amino acids in terms of unique chemical properties

Question 2

How are amino acids joined together?

Answer 2

Peptide bonds - formed by the loss of oxygen from carboxyl group and two hydrogens from amine group to form water and peptide bond

Question 3

What are the 2 ends of polypeptides?

Answer 3

C terminus - carboxyl terminus

N terminus - amine terminus

Question 4

What is the primary structure of a protein?

Answer 4

Sequence of amino acids

Question 5

What is the secondary structure of a protein?

Answer 5

Folds formed in the primary structure

Beta sheets or alpha helices

Formed through interactions of amino acids

Question 6

What is the tertiary structure of a protein?

Answer 6

Secondary structure folds further into 3D shape

Question 7

What is the quaternary structure of a protein?

Answer 7

Multiple polypeptide chains that associate into one larger protein

Question 8

What is the genetic code?

Answer 8

Triplet code (codon) gives enough combinations of nucleotides for all of the amino acids
- 64 total possibilities - 3 are stop codons (nonsense codons) and 61 are coding (sense codons)

Code is degenerate, or redundant, because it has more codes than there are amino acids

A single anticodon can pair with more than one codon

Genetic code is not overlapping
- There can be three ways to read triplets in a sequence - 3 reading frames
- Shifted down 1 nucleotide - amino acid chain changes
- Necessary for translation machinery to use correct reading frame - finds correct reading frame through start codon (Met/fMet), every triplet after is an amino acid, always end polypeptide with a stop codon

Question 9

What are synonymous codons?

Answer 9

Multiple encoding codons - different codons that code for the same amino acid

Question 10

How can a single anticodon pair with more than one codon?

Answer 10

A lot fo amino acids can be carried by more than one tRNA because of synonymous redundancy
- But there are still more codons than anticodons

Hydrogen bonds form between first two positions in the anticodon/codon pairing

In third position, there can be a weak pairing called the wobble position
- Allows for an anticodon that isn’t the perfect match to bond into codon

Question 11

What is translation?

Answer 11

How amino acid chains are assembled into a full protein

Both bacterial and eukaryotic translation are similar

Question 12

How is mRNA translated on a ribosome?

Direction and interactions

Answer 12

Ribosome attaches near 5’ end of mRNA
- Translated toward 3’ end

Polypeptide synthesis is from N terminus to C terminus direction
- N terminus sequence sticks out of ribosome

Protein synthesis occurs through RNA-RNA interactions:
- rRNA and mRNA - rRNA in small ribosomal subunit interacts with Shine-Dalgarno sequence
- mRNA and tRNA - interactions between codons and anticodons
- tRNA and rRNA interactions

Question 13

What are the 4 steps of translation?

Answer 13

tRNA charging

Initiation

Elongation

Termination

Question 14

What occurs during tRNA charging of translation?

Answer 14

tRNA is bound to appropriate amino acid
- Carboxyl group of amino acid attaches to CCA overhang of tRNA

Specificity is conferred between specific amino acids and tRNA through aminoacyl-tRNA transferases
- About 20 that help specify and recognize which amino acid and tRNA bind together

Requires ATP

2 steps:
- ATP is cleaved (-2 phosphates) and binds to carboxyl group to form aminoacyl-AMP
- Amino acid is transferred to the tRNA and AMP is released, resulting in aminoacyl-tRNA

tRNA charging has high accuracy because aminoacyl-tRNA transferases have proofreading capabilities

Question 15

What occurs during initiation of translation in prokaryotes?

Answer 15

Necessary molecules assemble - mRNA, small and large ribosomal subunits, initiation factors (3 proteins), initiator tRNA (fMet in bacteria), and GTP

3 steps:
mRNA binds to small ribosomal subunit
- Can only bind when subunits are separate
- Initiation factor 3 binds to small ribosomal subunit, preventing two subunits from coming togeher
- Specific sequences within mRNA are required for small subunit to bind into mRNA - Shine-Dalgarno sequence - helps ribosome position itself over start codon

Initiator tRNA binds to mRNA start codon
- Initiation factor 2 forms a complex with initiator tRNA and GTP - known as 30S initiation complex

Large ribosomal subunit joins initiation complex
- Occurs when initiation factor 3 dissociates from small subunit, allowing large subunit to come and join
- Whole initiation complex is now called 70S initiation complex

Question 16

What occurs during initiation of translation in eukaryotes?

Answer 16

5’ cap is bound by cap-binding proteins
- Helps shuttle mRNA from nucleus to cytoplasm
- Once in cytoplasm, begin to promote translation
- Eventually replaced by initiation factors

Initiation complex is formed by small ribosomal subunit, initiation factors, and initiator tRNA
- Recognizes where 5’ cap is and binds in there

Initiation complex scans mRNA, looking for start codon
- Stops scanning when start codon is found

Initiator tRNA pairs with codon

Initiation factors will release, and subunits of ribosome will bind

Proteins can also bind to poly(A) tail
- Can interact with cap-binding proteins to help binding of different ribosomal subunits
- Forms closed loop structures in mRNA

Question 17

What occurs during elongation in translation in prokaryotes and eukaryotes?

Answer 17

Requires 70S complex, charged tRNAs, several elongation factors, and GTP

3 steps:
Charged tRNA moves into A site
- Does this through elongation factor Tu and GTP to form 3 part complex
- tRNA binds with complex
- GTP is cleaved, releasing itself and elongation factor
- Elongation factor regenerates GTP

Peptide bond forms between amino acids attached to tRNAs attached to P and A sites
- With formation, there is a release of the amino acid from tRNA
- tRNA will be shifted to E site

Translocation occurs as ribosome moves down RNA
- Elongation factor G and hydrolysis of GTP to GDP help position ribosome over next codon
- tRNAs are not actually shifting site, but the ribosome is, which makes their sites shift
- Movement moves tRNA in P site to E site, and tRNA in A site to P site
- New tRNA moves into A site
- tRNA in E site gets released and gets recharged
- Translocation can pause itself if translation is delayed (since prokaryotes do both at same time)

Occurs within large ribosomal subunit

Continues until it hits a stop codon

Question 18

What are the 3 parts of ribosomes that are used during elongation by tRNAs?

Answer 18

A site

P site
- Initiator tRNA comes in at P site
- After that, all other tRNAs that come in will start at A site

E site (exit site)

Question 19

What occurs during termination in translation in prokaryotes and eukaryotes?

Answer 19

Translation ends when a stop codon is hit

When stop codon is hit, no tRNA enters into A site

Instead, a release factor enters A site and binds to ribosome in that position
- Promotes cleavage of polypeptide
- Cleavage occurs in tRNA at P site

Cleavage causes a conformational chage of ribosome that releases the release factor in the A site
- Causes tRNA to move to E site and release as well

Other factors release other components off of mRNA

Question 20

What occurs with polyribosomes?

Answer 20

In prokaryotes (and some eukaryotes), translation and transcription occur at the same time through multiple ribosomes (polyribosomes) successively attaching to transcribing mRNA and translating it

Question 21

What occurs with mRNA surveillance?

Answer 21

Mechanisms to detect errors in mRNA that could cause issues with translation

Trying to keep cell from wasting resrouces and producing truncated proteins