Study Guide Lec 14

Question 1

Define a transition mutation

Answer 1

base substitutions in which one purine (A or G) is changed to the other purine, or a pyrimidine (T or C) is changed to the other pyrimidine.

Question 2

Define a transversion mutation

Answer 2

Transversions are base substitutions in which a purine is changed to a pyrimidine or vice versa.

Question 3

Which mutation is more common, transition or transversion?

Answer 3

Although transversions would seem to be statistically favored because there are eight possible transversions and only four possible transitions, about twice as many transition mutations are actually observed in the human genome.

Question 4

When and why do expanding nucleotide repeats occur?

Answer 4

occur when DNA insertion mutations result in an increase in the number of copies of a nucleotide repeat sequence. Such an increase in the number of copies of a nucleotide sequence may occur by errors in replication or unequal recombination.

Question 5

How do expanding nucleotide repeats relate to anticipation?

Answer 5

Within a given family, a particular type of nucleotide repeat may increase in number from generation to subsequent generation, increasing the severity of the mutation in a process called anticipation.

Question 6

A base substitution that changes the sequence and the meaning of a mRNA codon, resulting in a different amino acid being inserted into a protein, is called a ____ mutation.

Answer 6

missense

Question 7

____ mutations occur when a mutation replaces a sense codon with a stop (or nonsense) codon.

Answer 7

Nonsense

Question 8

A nucleotide substitution that changes the sequence of an mRNA codon, but not the meaning is called a ____ mutation.

Answer 8

silent

Question 9

In ____ mutations, the sequence and the meaning of an mRNA codon are changed. However, the amino acid substitution has little or no effect on protein function.

Answer 9

neutral

Question 10

____ ____ is the result of second mutations within an already mutated gene that restore a wild-type phenotype

Answer 10

intragenic suppression

Question 11

Briefly describe two different ways in which intragenic suppressors may reverse the effects of mutations.

Answer 11

The suppressor mutations are located at different sites within the gene from the original mutation. One type of suppressor mutation restores the original phenotype by reverting the meaning of a previously mutated codon to that of the original codon. The suppressor mutation occurs at a different position than the first mutation, which is still present within the codon. Intragenic suppression may also occur at two different locations within the same protein. If two regions of a protein interact, a mutation in one of these regions could disrupt that interaction. The suppressor mutation in the other region would restore the interaction. Finally, a frameshift mutation due to an insertion or deletion could be suppressed by a second insertion or deletion that restores the proper reading frame.

Question 12

Strand slippage that occurs during DNA replication and unequal crossover events due to misalignment at repetitive sequences have been shown to cause what?.

Answer 12

deletions and additions of nucleotides to DNA molecules

Question 13

Strand slippage results from the formation of small loops on either the template or the newly synthesized strand. If the loop forms on the template strand, then a ___ occurs. Loops formed on the newly synthesized strand result in _____.

Answer 13

deletion; insertions

Question 14

In regards to strand slippage, If, during crossing over, a misalignment of the two strands at repetitive sequence occurs, then the resolution of the crossover will result in what?

Answer 14

one DNA molecule containing an insertion and the other molecule containing a deletion.

Question 15

Base analogs have structures similar to the ____ and if present, may be incorporated into the DNA during replication.

Answer 15

nucleotides

Question 16

Many analogs have an increased tendency for ____, which can lead to mutations.

Answer 16

mispairing

Question 17

What is required for the base analog-induced mutations to be incorporated into the DNA?

Answer 17

DNA replication

Question 18

How do alkylating agents produce mutations? What type of mutations do they commonly cause?

Answer 18

Alkylating agents donate alkyl groups (either methyl or ethyl) to the nucleotide bases. The addition of the alkyl group results in mispairing of the alkylated base and typically leads to transition mutations.

Question 19

How does nitrous acid produce mutations?

Answer 19

Nitrous acid treatment results in the deamination of cytosine, producing uracil, which pairs with adenine. During the next round of replication, a CG to AT transition will occur. The deamination of guanine by nitrous acid produces xanthine. Xanthine can pair with either cytosine or thymine. If paired with thymine, then a CG to TA transition can occur.

Question 20

In regards to production of mutation, ____ works by adding a hydroxyl group to cytosine, producing hydroxylaminocytosine. The hydroxylaminocytosine has an increased tendency to undergo tautomeric shifts, which allow pairings with adenine, resulting in GC to AT transitions.

Answer 20

Hydroxylamine

Question 21

What is the purpose of the Ames test?

Answer 21

The Ames test allows for rapid and inexpensive detection of mutagenic and potentially carcinogenic compounds using bacteria

Question 22

In regards to the Ames test, the majority of carcinogenic compounds result in DNA damage and are mutagens. The increase in reversion rate of ___ bacteria to___ is used to detect the mutagenic potential of the compound being tested.

Answer 22

his–; his+

Question 23

Most transposable elements have terminal ____ repeats and are flanked by short ___ repeats that are generated at insertion sites during the transposition process.

Answer 23

inverted; direct

Question 24

Many transposable elements also contain a gene encoded one of the enzymes necessary for transposition. What are two common examples of these enzymes?

Answer 24

transposase or reverse transcriptase

Question 25

A retrotransposon relocates through an ___ intermediate.

Answer 25

RNA

Question 26

Describe the process in which a retrotransposon moves

Answer 26

First, it is transcribed into RNA. A reverse transcriptase encoded by the retrotransposon then reverse transcribes the RNA template into a DNA copy of the transposon, which then integrates into a new location in the host genome.

Question 27

Which class of transposable elements utilize replicative transposition and transpose through an RNA intermedicate?

Answer 27

Class I

Question 28

Which class of transposable elements utilize either replicative or conservative transposition and transpose through a DNA intermediate?

Answer 28

Class II

Question 29

Why are transposable elements often called genomic parasites?

Answer 29

Because they may not have an apparent benefit to a cell or organism and may be harmful to it.

Question 30

Transposable elements exist because they are efficient at ___ and ___

Answer 30

replicating and spreading

Question 31

True or false?

Transposable elements may serve an important role in genome plasticity and evolution

Answer 31

true

Question 32

Describe mismatch repair

Answer 32

Replication errors that are the result of base-pair mismatches are repaired. Mismatch-repair enzymes recognize distortions in the DNA structure due to mispairing and detect the newly synthesized strand by the lack of methylation on the new strand. The bulge is excised and DNA polymerase fills the gap and DNA ligase seals the repair.

Question 33

Describe direct repair

Answer 33

DNA damage is repaired by directly changing the damaged nucleotide back to its original structure. As for example the repair done by a photolyase or methyltransferase

Question 34

Name the following type of repair:
After the damaged base is removed by glycosylases, the phosphodiester bond is excised by AP endonucleases and other enzymes remove the deoxyribose sugar; then the entire nucleotide is replaced by DNA polymerase and the nick is sealed by DNA ligase.

Answer 34

base-excsion repair

Question 35

Name the following type of repair:
Repair enzymes recognize distortions of the DNA double-helix. Damaged regions are excised by enzymes (nucleases and helicases), which separate the strands of DNA and cut phosphodiester bonds on either side of the damaged region. The gap generated by the excision step is filled in by DNA polymerase and sealed by DNA ligase.

Answer 35

nucleotide-excision repair

Question 36

Homologous recombination and nonhomologous end joining are two major mechanisms for repair of what?

Answer 36

double-strand breaks

Question 37

How do homologous recombination and nonhomologous end joining differ?

Answer 37

Homologous recombination requires an identical DNA molecule (usually a sister chromatid) to repair a double-strand break. Nonhomologous end joining does not require a template.

Question 38

A codon that specifies the amino acid Gly undergoes a single-base substitution to become a nonsense mutation. In accord with the genetic code given in Figure 15.10, is this mutation a transition or a transversion? At which position of the codon does the mutation occur?

Answer 38

By examining the four codons that encode for Gly, GGU, GGC, GGA, and GGG, and the three nonsense codons, UGA, UAA, and UAG, we can determine that only one of the Gly codons, GGA, could be mutated to a nonsense codon by the single substitution of a U for a G at the first position:
GGA UGA
Because uracil is a pyrimidine and guanine is a purine, the mutation is a transversion.

Question 39

If a single transition occurs in a codon that specifies Phe, what amino acids can be specified by the mutated sequence?

Answer 39

Two codons can encode for Phe, UUU, and UUC. A single transition could occur at each of the positions of the codon resulting in different meanings.