Genetics - Chapter 13

Mutations Effecting DNA Structure

- Base Substitutions - Insertions or deletions - Expanding nucleotide repeats

Mutations Effecting Protein Sequence

- Frameshift mutation - Missense mutation - Nonsense mutation - Silent mutation

Mutation Causes

- Spontaneous Mutations - Chemically Induced - UV Light - Ionizing Radiation

DNA Repair

- most repair mechanisms require 2 strands of DNA - one strand where the mutated nucleotide will be replaced and the template strand that specifies the base sequence - there is more than one repair pathway that can be used; this redundancy ensures that all mistakes are almost always corrected

Examples of Base Substitutions

- silent mutations - missense mutations - nonsense mutations

What is a retrotransposon and how does it move?

-uses RNA intermediate to move -LTR, LINEs, SINEs, pseudogene

Types of Chemically Induced Mutations

1. Base Analogs 2. Modify DNA 3. Intercalating Agents

Special Class of Mutations

1. Conditional Mutation 2. Suppressor Mutation

2 Types of Suppressor Mutations

1. Intragenic 2. Intergenic

Types of DNA Repair

1. Mismatch repair 2. Direct repair 3. Base-excision repair 4. Nucleotide-excision repair

Mutations Effecting Function

1. Neutral Mutation 2. Loss-of-Function Mutation 3. Gain-of-Function Mutation 4. Lethal Mutation

Two Common Features of Transposons

1. Short Flanking Direct Repeats 2. Terminal Inverted Repeats

Categories of Mutations

1. Somatic mutations 2. Germ-line mutations

Types of Spontaneous Mutations

1. Spontaneous Replication Errors 2. Spontaneous Chemical Errors

What general characteristics are found in many transposable elements?

1. flanking direct repeats 2. terminal inverted repeats

What is the difference between a missense mutation and a nonsense mutation? A silent mutation and a neutral mutation?

A base substitution that changes the sequence and the meaning of an mRNA codon, resulting in a different amino acid being inserted into a protein, is called a missense mutation. Nonsense mutations occur when a mutation replaces a sense codon with a stop (or nonsense) codon.A nucleotide substitution that changes the sequence of an mRNA codon, but not the meaning, is called a silent mutation. In neutral 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.

What is the difference between a germline mutation and a somatic mutation?

A germline mutation occurs in the gametes (oocytes and/or sperm) and is passed onto the next generation and will be in every cell of the next generation. A somatic mutation occurs in cells in the body (but not in the gametes) and is not able to be passed onto the next generation.

Base-Excision Repair

A modified base is first removed and then the entire nucleotide is replaced

A mutagen is _____. A. an agent that causes a mutation B. a change in the nucleotide base sequence C. an unusual phenotype D. None of the above

A. an agent that causes a mutation

A ____ mutation occurs during the DNA replication that precedes meiosis, while a ____ mutation occurs during the DNA replication that precedes mitosis. A. germline; somatic B. germline; spontaneous C. somatic; germline D. spontaneous, point

A. germline; somatic

Mutations are biologically significant because A. they are the source of genetic variability for populations. B. they increase the number of reproductive cells. C. they neutralize the effect of ionizing radiation. D. they are found only in somatic cells E. None of the above.

A. they are the source of genetic variability for populations.

What is a mutation?

An inherited change in genetic information; mutations can affect the number or structure of chromosomes or they can affect a single gene and are called gene mutations

True or False. All mutations are harmful. A. True B. False C. Cannot be determined.

B. False

A point mutation that alters a codon so that the encoded amino acid is substituted with another is called a ____ mutation. A. silent B. missense C. nonsense D. transversion

B. missense

A point mutation that changes a codon specifying an amino acid into a stop codon is called a _____. A. missense mutation B. nonsense mutation C. frameshift mutation D. deletion mutation

B. nonsense mutation

During DNA repair nucleotdie excision repair can correct _____. A. mismatched bases B. pyrimidine dimers C. broken sugar-phosphate backbones D. conditional mutants

B. pyrimidine dimers

Transposable elements can induce mutations by all of the following mechanisms, EXCEPT: A. disrupting a gene when inserted into it. B. facilitating recombination between transposons, producing chromosomal mutations. C. causing a frameshift mutation. D. activating genes with their own promoter, dysregulating them. E. All of these are mechanisms used by transposons.

D. activating genes with their own promoter, dysregulating them.

Transposons (jumping genes)

DNA sequences that can change position within the genome

Transposable Elements

DNA sequences that can move about in the genome

Mutations can be caused by: A. replication errors. B. ionizing radiation. C. alkylating agents. D. base pairing errors. E. All of the above can cause mutations.

E. All of the above can cause mutations.

Mutations are characterized by all of the following criteria, EXCEPT: A. loss-of-function vs. gain-of-function. B. somatic vs. germ line. C. gene vs. chromosome. D. effect on DNA structure vs. effect on protein structure E. All of these are criteria used to characterize mutations.

E. All of these are criteria used to characterize mutations.

Briefly describe expanding nucleotide repeats.

Expanding nucleotide repeats 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.

Are mutations good or bad?

From an evolutionary perspective, mutations are the source of genetic variation, which is good. From a disease or disorder perspective, mutations are often the source of the problem and cause many detrimental effects, which is bad.

Briefly describe two different ways in which intragenic suppresors can reverse the effects of mutations.

Intragenic suppression is the result of second mutations within a gene that restore a wild type phenotype. 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 resent within a 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 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 y a second insertion or deletion that restores the proper reading frame.

In genetics, what is an Ames test used for?

It is a test which assays environmental chemicals for carcinogenic effects. It uses the bacterium Salmonella typhirmurium and tests the ability of the chemicals to revert mutant strains of the bacterium to the wild type (his- to his+).

What is the difference between a loss-of-function mutation and a gain-of-function mutation?

Loss-of-function mutations are often recessive requiring individuals be homozygous to have the problem. The mutation causes a complete or partial absence of normal protein function. Gain-of-function mutations are usually dominant requiring only one copy of the mutation to have the problem. This mutation causes the production of a protein whose function is not normally present.

Describe the difference between replicative and non-replicative transposition.

Replicative: Element is duplicated during reaction. One element stays put in original location. Copied element becomes transposed to new site. Non-Replicative: Element moves as physical entity from one site to another without to being duplicated.

What are some causes of mutations?

Spontaneous replication errors, spontaneous chemical errors, base analogs, mutagens, ionizing radiation, UV radiation, mistakes by DNA polymerase, mistakes in DNA repair enzymes.

What are the different ways in which mutations can be classified?

They can be based on their effect on DNA structure, function, protein sequence, and on what causes the mutation.

What is the difference between a transition and a transversion? Which type of base substitution is more common?

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

How can transposons alter gene function?

Transposons can disrupt the gene they jumped from, or the gene they jumped into and can cause frameshift mutations.

Expanding Nucleotide Repeats

a DNA insertion mutation that increases the number of copies of a set of nucleotides; the number of repeats increases with the passage of time; associated with many different genetic disorders, like Huntington disease and Fragile-X syndrome

Nucleotide-Excision Repair

a bulky DNA lesion (ex. pyrimidine dimer) is removed; the double strands are separated, the lesion removed, the gap filled in, and the new segment linked to the existing DNA

Base Substitutions (point mutation)

a change in a single nucleotide in the DNA; only a single codon is altered

Pyrimidine Dimers

a chemical bond can form between neighboring pyrimidines causing a distortion in the DNA; most of these dimers are repaired, but if they remain they can block replication and transcription

Loss-of-Function Mutation

a mutation causes a complete or partial absence of normal protein function; often recessive and require individuals to be homozygous to exhibit the problem; example: cystic fibrosis

Forward Mutation

a mutation that alters the wild-type allele

UV Light

can result in the formation of pyrimidine dimers

Induced Mutations

caused by environmental chemicals or radiation

Reverse Mutation

changes a mutant allele back to wild type

Gene Mutations

changes in a DNA sequence that are inherited or passed to the descendants of a cell or organism

Frameshift Mutation

changes the reading frame; caused by an insertion or deletion that disrupts the reading frame; has a drastic effect on phenotype, stopping protein synthesis or producing a truncated (shortened) protein that is often nonfunctional; the earlier in the sequence the deletion or insertion occurs, the more altered the protein produced is - drastic effects on phenotype

Examples of Transposons

hemophilia; color of grapes

How does transposition work?

movement of a transposable element from one location to another; can be transposed as a DNA molecule or through the production of an RNA intermediate (retrotransposon) that can be reverse transcribed into DNA can be replicative or nonreplicative

Conditional Mutation

mutations that are expressed only under certain conditions; for example, a temperature sensitive mutation can cause cell death at high temperatures, but might have no negative effect at a lower temperature

Suppressor Mutation

mutations that reverse the effect of mutation at a different site; phenotype = nonmutated; wild type; double mutant

Spontaneous Mutations

occur under normal conditions

Direct Repair

this does not replace nucleotides altered by a mutagen, but restores their original (correct) structures

Mismatch Repair

this replaces incorrect nucleotides that didn't get removed with DNA polymerase proofreading in replication; enzymes remove the incorrect nucleotides and DNA polymerase fills in the gap

Replicative Transposition

transposable element is copied; one copy remains in original site

Transition Substitution

when the change is a purine for a purine or a pyrimidine for a pyrimidine; more common since the chemical nature of the base is the same

In-Frame Insertions or Deletions

when the insertion/deletion is in a multiple of 3 nucleotides, the reading frame may stay in tact, although the protein will be affected by an addition/deletion of one or more amino acids

Transversion Substitution

when the purine is switched for a pyrimidine or vice versa; less common

2 Types of Base Substitutions

1. transition 2. transversion

What is the purpose of the Ames test? How are his- bacteria used in this test?

Test the mutagenic effects of chemicals. The Ames test detects whether a given chemical can cause a reversion mutation in his- bacteria.

Gain-of-Function Mutation

a mutation causing the production of a protein whose function is not normally present; often dominant, requiring only one copy of the mutation to exhibit the problem

Lethal Mutation

a mutation that causes premature death

Nonsense Mutation

a point mutation causing a change from an amino acid to a stop codon (nonsense codon); results in premature termination of translation so the protein is often truncated and nonfunctional

Missense Mutation

a point mutation causing a substitution of a different amino acid; may or may not affect protein function, depending on what the amino acid actually does; sickle cell disease

Intercalating Agents

chemicals that sandwich themselves between adjacent bases in DNA causing a change in the 3D structure of the helix; the insertions or deletions can result in a frameshift mutation having severe effects

Base Analogs

chemicals with structures similar to any of the four DNA bases; incorporation of an analog followed by mispairing leads to a permanent transition mutation

Ionizing Radiation

damages DNA by breaking phosphodiester bonds, breaking hydrogen bonds, and altering the structure of bases

Mutation Rates

the frequency or how often mutations occur over time; usually expressed as the number of mutations per biological unit (cell, gamete, or rounds of replication); generally low, but are strongly influenced by the genetics of the organism as well as the environment; differences in mutation rates can be a result of differing repair mechanisms, unequal exposure to mutagens, or biological differences in the rate of spontaneous mutations

Nonreplicative Transposition

the transposable element excises from the old site and inserts at a new site without any increase in the number of its copies

Short Flanking Direct Repeats

these are not part of the transposon itself; present on both sides of most; when the transposon is inserted, there are short, single-stranded pieces of DNA left from staggered cuts in the target DNA; when replication of these segments occurs, the flanking direct repeats are created

Terminal Inverted Repeats

these repeats are recognized by enzymes used in the process of transposition

How do transposons alter gene function?

they disrupt the gene they jumped from, or the gene they jumped into and can cause frameshift mutations

Define the following: point mutation, missense mutation, nonsense mutation, deletion mutation, insertion mutation, frameshift mutation

· Point mutation-a change in a single DNA base · Missense mutation-a point mutation that results in an amino acid change · Nonsense mutation-a point mutation that results in a premature stop codon resulting in a shortened or truncated protein · Deletion mutation-removal of any number of bases. May result in a frameshift (change in reading frame of mRNA) if not in multiples of three. · Insertion mutation-addition of any number of bases. May result in a frameshift if not in multiples of three. · Frameshift mutation- a mutation caused by an insertion or deletion that disrupts the reading frame.

List at least three different types of DNA repair and briefly explain how each is carried out.

- Mismatch Repair: This replaces incorrect nucleotides that didn't get removed with DNA polymerase proofreading in replication. Mismatch-repair enzymes remove the incorrect nucleotides and DNA polymerase fills in the gap. - Direct Repair: This does not replace nucleotides altered by a mutagen, but restores their original (correct) structures. - Base-excision repair: A modified base is first removed, then the entire nucleotide is replaced. - Nucleotide-excision repair: A bulky DNA lesion (ex. pyrimidine dimer) is removed. The double strands are separated, the lesion removed, the gap filled in, and the new segment linked to the existing DNA.

How do base analogs lead to mutations?

Base analogs have structures similar to the nucleotides and, if present, may be incorporated into the DNA during replication. Many analogs have an increased tendency for mispairing, which can lead to mutations. DNA replication is required for the base analog-induced mutations to be incorporated into the DNA.

Classifications of Mutations

Based on their effect on... - DNA structure - Function - Protein sequence - What causes the mutation

How do insertions and deletions arise?

Strand slippage that occurs during DNA replication and unequal crossover events due to misalignment at repetitive sequences have been shown to cause deletions and additions of nucleotides to DNA molecules. 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 deletion occurs. Loops formed on the newly synthesized strand result in insertions. If, during crossing over, a misalignment of the two strands at repetitive sequence occurs, then the resolution of the crossover will result in one DNA molecule containing an insertion and the other molecule containing a deletion.

Silent Mutation

a point mutation where one codon is changed to a synonymous codon; there is no change in amino acid sequence sometimes no effect, sometimes phenotypic effects; depends on where the affected codon is located

Neutral Mutation

a type of missense mutation that causes a change in amino acid, but has no change in function

Genetic Variation

allows organisms to adapt to environmental changes

SOS System in Bacteria

allows them to bypass the replication block; however, this system makes a lot of mistakes and is associated with an increase in the rate of mutation

Modify DNA (chemical mutagen)

alters their pairing properties and results in a transition mutation; chemical modifications can include alkylation, deamination, or hydroxylation

Insertions or Deletions (indels)

an addition or removal of a nucleotide pair; can cause frameshift mutations which can change many codons

Mutagen

any environmental agent that significantly increases the rate of mutation above the spontaneous rate

Ames Test

based on the fact that both cancers and mutations result from DNA damage; results from experiments have shown that 90% of carcinogens are also mutagens; the test uses his- bacteria to test chemicals for their baility to produce his- --> his+ mutations

Germ-Line Mutations

occur in cells that give rise to gametes; this type of mutation is passed on to future generations; offspring have the mutation in all of their cells, both somatic and germ-line

Somatic Mutations

occur in non-reproductive cells (somatic cells) creating isolated populations of mutant cells; reproduce by mitosis creating clones that have the mutation - often have no effect on phenotype; mutated cells die off and are replaced with normal cells - sometimes, the mutant cells persist and can create populations of cells that are the basis of many cancers - these mutations are passed on to the cell line, but not offspring

Chemically Induced Mutations

produced when a cell or organism is exposed to a mutagen

Intergenic Suppressor Mutation

suppress the effect of an earlier mutation in another gene

Intragenic Suppressor Mutation

suppressor mutations take place in the same gene that contains the mutation being suppressed; can be a point mutation that corrects the first mutation or may be an insertion/deletion to restore a mutated frameshift

Detecting Mutations

the Ames test: commonly used to identify mutagens and the potential for chemicals to cause cancer