Chapter 13: Gene Mutations, Transposable Elements, and DNA Repair Flashcards
What are the two basic categories of mutations in multicellular organisms?
- Somatic mutations
- Germline mutations
What are somatic mutations? What type of cells do they occur in?
- Occur in non-reproductive cells
- Passed to new cells through mitosis, creating clones of cells having the mutant gene
What are germline mutations? What type of cells do they occur in?
- Occur in cells that give rise to gametes
- Meiosis and sexual reproduction allow germline mutations to be passed to approximately half the members of the next generation, who will carry the mutation in all of their cells
Differentiate gene mutations and chromosome mutations.
- Both are germline mutations
- Gene mutations are relatively small DNA lesion that affects a single gene
- Chromosome mutations are a large-scale genetic alteration that affects chromosome structure or number
What are the three types of gene mutations?
- Base substitutions
- Base insertions
- Base deletions
What is base substitution?
The alteration of a single nucleotide within the DNA
What are insertions and deletions? What may they cause?
- Addition or removal of one or more nucleotide pairs
- May alter the reading frame (frame-shift) and change many codons
Why are insertions and deletions more detrimental than single base substitutions?
As they usually alter all amino acids encoded by nucleotides following the mutation
What is a transition?
Base substitution of a purine for a purine, or a pyrimidine for a pyrimidine
What is a transversion?
Base substitution of a purine for a pyrimidine, or a pyrimidine for a purine
How do transitions and transversions differ in their number of possibilities, and their frequency?
- Transversions have twice the number of possibilities
- Transitions arise more frequently
Which of the following changes is a transition base substitution?
A) Adenine is replaced by thymine
B) Cytosine is replaced by adenine
C) Guanine is replaced by adenine
D) Three nucleotide pairs are inserted into DNA
C) Guanine is replaced by adenine
What are expanding nucleotide repeats?
Mutations in which the number of copies of a set of nucleotides increases
What do the diseases caused by expanding trinucleotide repeats all possess in common?
- They all possess repeated sequences
- Example: The repeated sequence in Fragile-X syndrome is CGG, which is normally repeated 6 to 54 times, but increases to between 50 and 1500 times in an affected individual
What occurs to the chromosome in Fragile-X syndrome?
- A fragile site is present on the long-arm, due to an increased number of trinucleotide repeats
- The fragile site ends up breaking, and causes the phenotypes of Fragile-X syndrome
What is one of the possible models that explain for expanding nucleotide repeats?
- Formation of a hairpin (strand slippage)
- The formation of a hairpin causes part of the template strand to be replicated twice, increasing the number of repeats
- The strand with the extra repeat copies serve as a template for replication, resulting in a DNA molecule with additional copies
What is a forward mutation?
Alters the wild-type allele
What is a reverse mutation?
Changes a mutant allele back into the wild-type allele
What is a missense mutation?
Base substitution that results in a different amino acid in the protein
What is a nonsense mutation?
Changes a sense codon (one that specifies an amino acid) into a nonsense codon (one that terminates translation)
What occurs if a nonsense mutation occurs early in the mRNA sequence?
The protein will be truncated and usually non-functional
What is a silent mutation?
- Changes a codon to a synonymous codon that specifies the same amino acid
- Alters the DNA sequence without changing the amino acid sequence of the protein
Are silent mutations truly silent?
Not all of them, some may have phenotypic effects
What is a neutral mutation?
- Missense mutation that alters the amino acid sequence of a protein, but does not significantly change its function
- Neutral mutations occur when one amino acid is replaced by another that is chemically similar or when the affected amino acid has little influence on protein function
What is a loss-of-function mutation?
Causes the complete or partial absence of normal protein function
Which mutations are frequently recessive? Which are frequently dominant?
- Recessive: loss-of-function mutations
- Dominant: gain-of-function mutations
What is a gain-of-function mutation?
Causes the cell to produce a protein or gene produce whose function is not normally present
What is a conditional mutation?
- Expressed only under certain conditions
- Example: some conditional mutations affect the phenotype only at elevated temperatures
What is a lethal mutation?
One that causes premature death
Where do silent mutations normally occur?
On the third nucleotide of a codon
What is a suppressor mutation?
Genetic change that hides or suppresses the effect of another mutation at a DIFFERENT site
How does a suppressor mutation differ from a reverse mutation?
- A suppressor mutation occurs at a site that is distinct from the site of the original mutation, thus it is a double mutant
- A reverse mutation restores the original phenotype by changing the DNA sequence back to the wild-type
What are the two classes of suppressor mutations?
- Intragenic
- Intergenic
What is an intragenic suppressor mutation?
Suppresses the effect of an earlier mutation within the same gene
What is an intergenic suppressor mutation?
Suppresses the effect of an earlier mutation in another gene
What are the three ways intragenic suppressor mutations may function?
- If the original mutation is a one-base deletion, then the addition of a single base elsewhere in the gene will restore the former reading frame
- A mutation due to an insertion may be suppressed by a subsequent deletion in the same gene
- Making compensatory changes in the protein (ex: a missense mutation alters the folding of a protein, but a second missense mutation at a different site recreates the original folding pattern)
How may an intergenic suppressor mutation occur? Provide an example.
1) Base substitution produces a stop codon, which halts protein synthesis (non-functional protein)
2) At a different gene encoding for a tRNA, a mutation results in a codon capable of pairing with the stop codon produced by the first mutation
3) Translation continues past the stop codon, producing a full-length functional protein
Differentiate spontaneous and induced mutations.
- Spontaneous mutations occur under normal conditions
- Induced mutations result from changes caused by environmental chemicals or radiation
What was the primary cause of spontaneous replication error formerly thought to be?
Tautomeric shifts, in which the positions of protons in the DNA bases change
What mechanism was thought to be the primary cause of spontaneous replication errors?
- Tautomeric shifts, in which the positions of protons in the DNA bases change
- This is most likely NOT occurring during replication, as there is no evidence that we have tautomers in our DNA
How do non-standard base pairings arise?
Through wobble, in which normal, protonated, and other forms of the bases are able to pair because of the flexibility of the DNA helical structure
What is an incorporated error?
When a mispaired base has been incorporated into a newly synthesized nucleotide chain
What is a replicated error?
Creates a permanent mutation because all base pairings are correct and their is no mechanism for repair systems to detect the error
What are the three major causes of spontaneous replication error? What was used to be thought to be the primary reason?
- Mispairing due to wobble, strand slippage, and unequal crossing-over
- Tautomeric shifts
What spontaneous replication error arises in Huntington’s disease?
Strand slippage
How does strand slippage occur in a non-template strand?
A newly synthesized strand loops out, resulting in the addition of one nucleotide on the strand
How does strand slippage occur in
a template strand?
Strand slippage often occurs in a sequence of the same nucleotides, causing the template strand to loop out, resulting in the omission of one nucleotide on the strand
What is a cause of deletions and insertions that occurs during meiosis?
Unequal-crossing over results in one DNA molecule with an insertion and the other with a deletion
What are spontaneous chemical changes?
- Spontaneous alterations in DNA structure, such as depurination and deamination
- Can alter the pairing properties of the bases and cause errors in subsequent rounds of replication
What is depurination?
- As we age, depurination increases
- Depurination is the loss of a purine base from a nucleotide, producing an apurinic site
- Very common, and possesses repair mechanisms
What occurs at an apurinic site?
A nucleotide with the incorrect base (most often A) is incorporated into the newly synthesized strand
Does loss of pyrimidine also occur?
Yes, but at a much lower rate than depurination
What is deamination? Give example of deamination products.
The loss of an amino group (NH2) from a base
What cause chemically-induced mutations?
A number of environmental agents, including certain chemicals and radiation, damage DNA (mutagens)
What are base analogs?
- Chemicals with structures similar to those of any four standard bases of DNA
- DNA polymerases cannot differentiate between these analogs and standard bases, so they may be incorporated into newly synthesized DNA
What is 5-bromouracil?
- Base analog of thymine that is capable of pairing with adenine
- However, it occasionally mispairs with guanine when ionized, leading to a transition
What are alkylating agents? Give an example.
- Chemicals that donate alkyl groups, such as methyl, to nucleotide bases
- Example: EMS
What does the incorporation of bromouracil followed by mispairing lead to?
T-A –> C-G transition mutation
What are intercalating agents?
Chemicals that produce mutations by sandwiching themselves (intercalating) between adjacent bases in DNA
What are the effects of intercalating agents?
- Distort the 3D structure of the helix and cause single-nucleotide insertions and deletions in replication
- Often produce frameshift mutations, so the effects are often severe
What are intercalating agents used for primarily? Give examples.
- DNA imaging
- Ethidium bromide, proflavin, acridine
Base analogs are mutagenic because of which characteristic?
A) They produce changes in DNA polymerase that cause it to malfunction
B) They distort the structure of DNA
C) They are similar in structure to the normal bases
D) They chemically modify the normal bases
C) They are similar in structure to the normal bases
How does UV light cause mutations?
Primarily by producing pyrimidine dimers, resulting in the formation of strong covalent bonds between adjacent pyrimidine molecules on the same strand of DNA
How do pyrimidine dimers lead to skin cancer?
- Pyrimidine dimers distort the configuration of DNA and often block replication
- When unrepaired, this may lead to skin cancer
How are chemical mutagens, and carcinogens, identified?
The Ames test
How can chemicals be quickly screened for their ability to cause cancer through the Ames test?
1) Bacterial his- strains are mixed with liver enzymes, which have the ability to convert compounds into potential mutagens
2) Some of the bacterial strains are also mixed with the chemical to be tested
3) The bacteria are plated on a medium that lacks histidine
4) Bacterial colonies that appear on the plates have undergone a his- to his+ mutation
What are transposable elements?
- DNA sequences that can move about in the genome
- Often a cause of mutations
How abundant are transposable elements?
- Found in the genomes of all organisms, and are abundant for many
- 45% of human DNA
How do transposable elements cause mutations?
- Inserting into a gene and disrupting it
- Promoting DNA rearrangement, such as deletions, duplications, and inversions
Under what form are transposons in our body?
They are NOT active, as they are silenced through methylation
What are the two general characteristics of transposable elements?
- Flanking direct repeats
- Terminal inverted repeats
What are flanking direct repeats in transposons? Where are they found?
- Generated when a transposable element inserts into DNA
- Are NOT a part of the transposable element, and do not travel with it
How are flanking direct repeats created in transposition?
- In transposition, staggered cuts are made in DNA and the transposable element inserts into the cut
- Later, replication of the single-stranded pieces of DNA creates short repeats on either side of the inserted transposable element
What are terminal inverted repeats in transposons? Where are they found? What is their function?
- These repeats ARE a part of the transposable element
- Sequences within the transposon that are recognized by enzymes that catalyze transposition
What are the features that all types of transposition have in common?
1) Staggered-breaks are made in the DNA
2) The transposable element is joined to single-stranded ends of the DNA
3) DNA is replicated at the single-stranded gaps
Differentiate DNA transposons and retrotransposons.
- DNA transposons transpose as DNA
- Retrotransposons: elements that transpose through an RNA intermediate
What is replicative transposition?
- A new copy of the transposable element is introduced at a new site, while the old copy remains behind at the original site
- The number of copies of the transposable element increases
What is non-replicative transposition?
- The transposable element excises from the old site and inserts at a new site
- No increase in the number of copies
What genotype produces black grapes?
Gene regulates the synthesis of anthocyanin
What genotype produces white grapes?
Retrotransposon is inserted near the gene, disrupting the synthesis of anthocyanins
What genotype produces red grapes?
- A second mutation removes most of the retrotransposon, but a piece is left behind
- Anthocyanin production is partly restored
Why does transposition often lead to DNA rearrangement?
Because transposition entails the exchange of DNA sequences and recombination
What chromosomal rearrangement may transposition lead to?
- Deletion (transposable elements in the same direction)
- Inversion (transposable elements in opposite directions)
- Deletion and duplication (misalignment and unequal exchange)
What has significantly contributed to the large size of many eukaryotic genomes?
Increases in copy numbers of transposable elements
Who was Barbara McClintock? What did she work on?
- First to discover transposable elements, for which she won a Nobel prize
- She worked on multicolored kernels in corn
What do the transposable elements in maize, Ac and Ds, encode for?
- Ac: fully functional transposable element
- Ds: possesses a broken transcriptase, inhibiting it from jumping on its own
What is the cc genotype in corn? What colour kernels does it produce?
- No transposition
- Colourless (yellow or white) kernels
What is the Cc genotype in corn? What colour kernels does it produce?
- No transposition
- Produce pigment (purple kernel)
What is the Ctc genotype in corn? What colour kernels does it produce?
- Transposition
- Ac element produces transposase, which stimulates the transposition of a Ds element into the C allele, disrupting its pigment-producing function
- Colourless
What is the Ctc/Cc genotype in corn? What colour kernels does it produce?
- Transposition during development
- Further transposition of Ds element
- Cells in which Ds transposes out of the C allele produce pigment
- Other cells are colourless
What do variegated corn kernels result from?
The excision of Ds elements from genes controlling pigment production during development
What is the first line of defence for DNA repair mechanisms?
Proof-reading function of certain DNA polymerases
What type of damage is mismatch repair responsible for?
Replication errors, including mispaired bases and strand slippage
What type of damage is direct repair responsible for?
- Pyrimidine dimers
- Other specific types of alterations
What type of damage is base excision responsible for?
- Abnormal bases
- Modified bases
- Pyrimidine dimers
What type of damage is nucleotide excision responsible for?
DNA damage that distorts the double helix, including abnormal bases, modified bases, and pyrimidine dimers
What is mismatch repair?
Corrects incorrectly inserted nucleotides that escape proofreading by DNA polymerase during replication
What allows for old and newly synthesized nucleotide strands to be differentiated?
- Methylation
- Old strand (template) is methylated, but the new strand is not
What is direct repair?
- Restores the original (correct) structure of nucleotides
- Does NOT replace altered nucleotides
What is base-excision repair?
A modified base is first excised, and then the entire nucleotide is replaced
What are the functions of DNA glycosylases? What kind of repair mechanism is this?
- Base-excision repair
- Recognizes and removes a specific type of damaged base
- Produces an apurinic or apyrimidimic site
What is nucleotide-excision repair?
- Removes bulky DNA lesions (such as pyrimidine dimers) that distort the double helix
- The two strands are separated, and an enzyme cleaves the strand on both sides of the damage
- DNA polymerase fills the gap
Why do most DNA repair mechanisms require two nucleotide strands?
Because a template strand is needed to specify the correct base sequence
What does the deamination of cytosine produce?
Thymine
What does the deamination of adenine produce?
Guanine
How does an incorporated error differ from a replicated error?
- An incorporated error is due to a change that takes place in DNA. This change may be corrected by a DNA-repair pathway.
- However, if the error has been replicated, it is permanent and cannot be detected by repair pathways.
How do direct-repair mechanisms differ from mismatch repair and base-excision repair?
- Direct-repair mechanisms return an altered base to its correct structure without removing and replacing nucleotides.
- Mismatch repair and base-excision repair remove and replace nucleotides.
