Ch. 17 The Genetic Code

Question 1

What does the genetic code refer to?

Answer 1

The Genetic Code refers to the coding of amino acids from nucleic acids (nucleic acid → aa).

Question 2

What are codons?

Answer 2

Three bases in mRNA that encode amino acids.

Question 3

What are anticodons?

Answer 3

Three bases on tRNAs that base pair with codons.

Question 4

What does an amino acid associate with for translation?

Answer 4

An amino acid has one or more specific tRNAs that they associate with.

Question 5

How are amino acids linked to their specific tRNA(s)?

Answer 5

Aminoacyl-tRNA transferase links amino acids to their specific tRNA(s).

Question 6

Why is the genetic code degenerate?

Answer 6

It is not perfect. There are more than 20 codons.

Question 7

How many total codons are their? Nonsense codons? The rest?

Answer 7

There are 64 possible codons. Three are nonsense (stop) codons and the remaining 61 encode for 20 different amino acids.

Question 8

What is typically true about the codons if an amino acid has more than one codon?

Answer 8

If an amino acids has more than one codon, the first two bases of the codon are often conserved, but the third can vary.

Question 9

Why can there be multiple codons for an amino acid? (3)

Answer 9

1. more than one tRNA may be used for one aa, with each tRNA having a different anticodon
2. the first position of an anticodon (which will base pair with the third “wobble” position of a codon) may form a non-standard base pair
3. some anticodons have inosine

Question 10

What is inosine?

Answer 10

A purine that can base pair with uracil and cytosine; kind of similar to adenosine.

Question 11

What does the wobble hypothesis describe?

Answer 11

It describes codon usage in cells.

Question 12

What are the four components of the wobble hypothesis?

Answer 12

1. The first two bases of a codon form standard pairs with tRNA
2. The first base of an anticodon pairs with the third base of a codon and determines the number of codons recognized by a specific tRNA
3. Different tRNAs are needed when either of the first two codon bases vary for an amino acid
4. A minimum of 32 tRNAs are required IF a cell’s genome were to use all 61 codons

Question 13

What is the tRNA property of an anticodon that has a C or A in the first position?

Answer 13

If C or A is the first base in the anticodon, only one codon is recognized by the tRNA.

Question 14

What is the tRNA property of an anticodon that has a U or G in the first position?

Answer 14

If U or G is the first base in the anticodon, more than one codon may be read by the tRNA (less specific).

Question 15

What is the tRNA property of an anticodon if I is in the first position?

Answer 15

If I is the first base in the anticodon, any of the three codons can be bound (A, C, or U).

Question 16

What does the flexibility of the codon/anticodon interaction allow for?

Answer 16

Flexibility of the codon/anticodon interaction allows for some mutations to occur WITHOUT consequence.

Question 17

What does a transition mutation in the third position of the codon do?

Answer 17

A transition mutation in the third position of the codon rarely affects amino acid coding or stop codons (wobble).

Question 18

What does a transition mutation in the first position of the codon do?

Answer 18

A transition mutation in the first position of the codon often leads to an amino acid change, but the amino acids has similar properties.

Question 19

What do hydrophobic amino acids typically have at position two? Polar?

Answer 19

Hydrophobic amino acids typically have a pyrimidine in position two. (C or U)

Polar amino acids typically have a purine in position two. (A or G)

Question 20

Comment on nonsense mutations vs missense mutations.

Answer 20

Nonsense mutations are more deleterious than missence, but can be amended.

Question 21

What are three ways nonsense mutations can be amended? (3)

Answer 21

1. Can have a mutation that reverts to the original codon or a missense codon
2. Can have a mutation in a tRNA that suppresses translational termination: suppressor tRNAs
3. Also possible to have suppressor tRNAs for missense mutations

Question 22

Why doesn’t a suppressor tRNA affect all expression of other genes using that stop codon? (3)

Answer 22

1. A cell can have more than one coding for that tRNA, and only one will be a suppressor tRNA
2. The standard tRNA can be expressed at a higher rate, whereas the suppressor tRNA is expressed at a lower rate
3. Cells may use that stop codon rarely or have multiple stops so that the expression of other proteins is not affected

Question 23

How can transcripts still be produced with a suppressor tRNA?

Answer 23

Insertion of an amino acid at a stop is inefficient, but enough to allow the cell to produce full length proteins.

Question 24

What are the rules of the Genetic Code? (4)

Answer 24

1. The code is non-overlapping (bases of a codon are only part of that codon)
2. There are NO gaps allowed in the code (indels will result in frameshifts)
3. The code is in triplets (one codon = three bases)
4. Protein synthesis is linear

Question 25

What does it mean that protein synthesis is linear?

Answer 25

The mRNA is read 5'→3' to produce an Nₜ→Cₜ polypeptide.

Question 26

What does the "universal" use of the Genetic Code suggest?

Answer 26

Suggests ancient evolution and presence of the genetic code in LUCA.

Question 27

Why does the Genetic Code resist change?

Answer 27

It resists change because a change in one codon for an amino acid requires that all codons in all genes be "updated" to accommodate the codon change.

Question 28

Why are the rules not fully universal?

Answer 28

With time, changes can accumulate in some taxa such that the rules are not fully universal.

Question 29

What are some exceptions to the code? (4)

Answer 29

- variant codon assignments - GUG (val) and UUG (leu) may initiate translation - UGA (stop) codons can code for selenocytesine - codon bias

Question 30

Where are variant codon assignments found?

Answer 30

Variant codon assignments are not common, but are present in mitochondria and some whole cells.

Question 31

What is selecocytesine?

Answer 31

The "21st" amino acid encoded by UGA and is required for many redox reactions.

Question 32

How is selenocytesine added to a polypeptide?

Answer 32

It is carried by a tRNA that recognizes UGA in a particular sequence context called selenocytesine insertion sequence (SCIS)

Question 33

What is codon bias?

Answer 33

When the occurrence of one codon for an amino acid is more frequently in mRNA than other codons for that same amino acid.

Question 34

What is a consequence of codon bias?

Answer 34

The tRNAs for more common codons have a higher expression level, thus some tRNAs are rarely used and can experience mutations that let them recognize non-standard codons.

Question 35

What is the example of codon bias in Candidia?

Answer 35

CUG in Candidia codes for serine instead of leucine. This is likely a result of rarely using CUG to code for serine.

Question 36

How many polypeptides are possible from one mRNA?

Answer 36

mRNA encodes one of three possible polypeptides depending on where translation begins.

Question 37

What are each possible grouping of codons called?

Answer 37

Each grouping is a reading frame.

Question 38

How do you decide which reading frame is used in translation?

Answer 38

Certain base patters in the mRNA dictate which reading frame is used in translation.

Question 39

What is the start codon?

Answer 39

AUG; where the coding region of mRNA begins

Question 40

What should follow the start codon?

Answer 40

There should be a long stretch of codons that follow the start codon without having a stop codon present.

Question 41

What is the stop codon?

Answer 41

UAG, UGA, UAA; where translation stops

Question 42

What is an open reading frame?

Answer 42

A start codon, a long stretch of codons, and a stop codon. (abbreviated to ORF)