Genetics Ch. 19 Gene Mutation, DNA Repair, and Recombination

Holiday Model

-2 homologous chromatids are aligned with each other and a break or nick occurs at identical sites in one strand of each of the two homologous chromatids. a model to explain the molecular mechanism of homologous recombination.

19.1 Effects of Mutations on Gene Structure and Function

19.1 Effects of Mutations on Gene Structure and Function

19.2 Random Nature of Mutations

19.2 Random Nature of Mutations

c. A mutation caused by UV light

19.3 COMPREHENSION QUESTIONS Which of the following is not an example of a spontaneous mutation? a. A mutation caused by an error in DNA replication b. A mutation caused by a tautomeric shift c. A mutation caused by UV light d. All of the above are spontaneous mutations.

19.4 Induced Mutations

19.4 Induced Mutations

19.5 DNA Repair

19.5 DNA Repair

19.6 Homologous Recombination

19.6 Homologous Recombination

replica plating

A method of identifying bacterial colonies that have certain mutations by transferring cells from each colony on a master plate to a second (replica) plate and observing their growth when exposed to different conditions.

b. nonsense mutation.

A mutation changes a codon that specifies tyrosine into a stop codon. This type of mutation is a a. missense mutation. b. nonsense mutation. c. frameshift mutation. d. neutral mutation.

nonsense mutation

A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein.

d. any of the above.

A point mutation could be caused by a. depurination. b. deamination. c. tautomeric shift. d. any of the above.

transversion mutation

A point mutation in which a pyrimidine is substitued for a purine, or vice versa.

b. over damaged DNA, have low fidelity

An advantage of translesion-replicating polymerases is that they can replicate _________________, but a disadvantage is that they _________________. a. very quickly, have low fidelity b. over damaged DNA, have low fidelity c. when resources are limited, are very slow d. over damaged DNA, are very slow

deleted from or added to the chromosomal DNA

Another way a gene mutation may occur is if a short sequence of base pairs is?

First, bacteria may have more than one copy of a chromosome per cell, though the copies are usually identical. These copies can exchange genetic material via homologous recombination. Second, during DNA replication, the replicated regions may also undergo homologous recombination. In bacteria, homologous recombination is particularly important in the repair of DNA segments that have been damaged.

Bacteria are usually haploid. They do not have pairs of homologous chromosomes. Even so, bacteria can undergo homologous recombination. How can the exchange of DNA segments occur in a haploid organism?

Purines

Bases with a double-ring structure. Adenine and Guanine

homologous recombination repair (HHR)

Book Deff: mechanism for repairing double-strand breaks that occurs when the DNA strands from a sister chromatid are used to repair a lesion in the other sister chromatid; also called homology-directed repair. See figure 19.21 for visual

Enzymes within the rat liver extract may convert nonautogenic molecules into mutagenic forms. Adding the extract allows researchers to identify molecules that may be mutagenic in people.

CONCEPT CHECK: What is the purpose of the rat liver extract in this procedure?

The deamination of 5-methylcytosine bc thymine is a base normally found in DNA. This makes it hard for DNA repair enzymes to distinguish between the correct and altered strand.

CONCEPT CHECK: Which of these two changes is more difficult for DNA repair enzymes to fix correctly? (a) The deamination of cytosine produces uracil. (b) The deamination of 5-methylcytosine produces thymine.

X-rays

Cause base deletions, single-stranded and double-stranded breaks in the DNA backbone, crosslinking, and oxidized bases

c. thymine dimers.

Concept check The function of photolyase is to repair a. double-strand breaks b. apurinic sites. c. thymine dimers. d. all of the above.

3' to 5' mismatch repair system.

DNA polymerase has a ___ to ___ proofreading ability that detects mismatches and removes them. However, if this proofreading ability fails, cells have additional DNA repair systems that detect base pair mismatches and fix them. An interesting DNA repair system that exists in all species is the ? The molecular mechanism of ....... has been studied extensively in E. coli. As shown in Figure 19.20, three proteins, designated MutS, MutL, and MutH, detect the mismatch and direct the removal of the mismatched base from the newly made strand. See figure 19.20 for an overview.

Nitrous acid

Deaminates bases

This test uses strains of a bacterium that cannot synthesize the amino acid histidine. These strains contain a point mutation within a gene that encodes an enzyme required for histidine biosynthesis. However, a second mutation-a reversion-may occur that restores the ability to synthesize histidine. The Ames test monitors the rate at which this second mutation occurs, thereby indicating whether an agent is mutagenic

Describe the Ames test

d. either a or b.

Double-strand breaks can be repaired by a. homologous recombination repair (HRR). b. nonhomologous end joining (NHEJ). c. nucleotide excision repair (NER). d. either a or b.

position effect

END of Subtopic: Changes in Chromosome Structure Can Affect the Expression of a Gene In other cases, a gene may be left intact, but its expression may be altered when it is moved to a new chromosomal location. a change in phenotype that occurs when the location of a gene changes from one chromosomal site to a different one.

conditional mutation

END of Subtopic: Gene Mutations Are Also Given Names That Describe How They Affect the Wild-Type Genotype and Phenotype A mutation that results in a characteristic phenotype only under certain environmental conditions.

Pyrimidines

END of Subtopic: Gene Mutations Are Molecular Changes in the DNA Sequence of a Gene cytosine, thymine, uracil

neutral mutation

END of Subtopic: Gene Mutations Can Alter the Coding Sequence Within a Gene a mutation that has no detectable effect on protein function or no detectable effect on the survival of the organism.

down promoter mutation

END of Subtopic: Gene Mutations Can Occur Outside of a Coding Sequence and Influence Gene Expression a mutation in a promoter that inhibits the rate of transcription

genetic mosaic

END of Subtopic: Mutations Can Occur in Germ-Line or Somatic Cells An individual with somatic regions that are genetically different from each other

in which a G-C base pair becomes a T-A base pair. This is a transversion mutation.

END of Subtopic: Oxidative Stress May Also Lead to DNA Damage and Mutation DNA bases are very susceptible to oxidation. Guanine bases are particularly vulnerable to oxidation, which can lead to several different oxidized products. The most thoroughly studied guanine oxidation product is commonly known as 8-oxoguanine (8- oxoG). Researchers often measure the amount of 8-oxoG in a sample of DNA to determine the extent of oxidative stress. Why are oxidized bases harmful? In the case of 8-oxoG, it base-pairs with adenine during DNA replication, causing mutations in which ???

intergenic mutation

END of subtopic: Suppressor Mutations Reverse the Phenotypic Effects of Another Mutation suppresses the effect of an earlier mutation in another gene

error-prone replication

End of Subtopic : Damaged DNA May Be Replicated by Translesion DNA Polymerases a form of DNA replication carried out by translesion-replicating polymerases that results in a high rate of mutation.

The Previous 3 enzymes work together. See figure 19.17 for visual

End of Subtopic: Base Excision Repair Removes a Damaged Base The Previous 3 enzymes work together. See figure 19.17 for visual

alkyltransferase

End of Subtopic: Damaged Bases Can Be Directly Repaired an enzyme that can remove methyl or ethyl groups from guanine bases. Surprisingly, this action permanently inactivates ________, which means it can be used only once!

MutH distinguished between the parental strand and the newly made daughter strand, which ensure that the daughter strand is repaired.

End of Subtopic: Mismatch Repair Systems Recognize and Correct a Base Pair Mismatch CONCEPT CHECK: Which of the three Mut proteins is responsible for ensuring that the mismatched base in the newly made daughter strand is the one that is removed? Need to review figure 19.20 before answering

tautomeric

End of Subtopic: Spontaneous Mutations Can Arise by Depurination, Deamination, or Tautomeric Shifts Shifts that result in base pairs being paired with the wrong base pair

In this experiment, Bacteria were grown into isolated colonies on plates. These colonies can be reproduced from an original plate to new plates by "stamping" the original plate with a cloth and then stamping empty plates with the same cloth. Bacteria from each colony are picked up on the cloth and then deposited on the new plates by the cloth. colonies are then stamped from the original plate onto a new plate that contains the antibiotic penicillin. some die, but not all. The Lederbergs set out to answer the question, "did the colonies on the new plate evolve antibiotic resistance because they were exposed to penicillin?" The answer is no: When the original plate is washed with penicillin, the same colonies (those in position X and Y) live — even though these colonies on the original plate have never encountered penicillin before.

Explain The Lederberg experiment

homologous recombination repair (HRR) and nonhomologous end joining (NHEJ).

How are DSBs repaired? The two main mechanisms are ?

The TNRE triplet repeat can form a hairpin, also called a stem-loop. See figure 19.11 for visual (In genetics file )

How does TNRE occur?

Enzymes ; vitamin C

If ROS accumulate, they can damage cellular molecules, including DNA, proteins, and lipids. To prevent this from happening, cells use a variety of _______, such as superoxide dismutase and catalase, to prevent the buildup of ROS. Small molecules, such as _______, may act as antioxidants. Also, certain foods contain other chemicals that act as antioxidants. Colorful fruits and vegetables, , are usually high in antioxidants.

a. significantly higher, is

In an Ames test, a ____________ number of colonies is observed if a substance ________ a mutagen, compared with the number of colonies for a control sample that is not exposed to the suspected mutagen. a. significantly higher, is b. significantly higher, is not c. significantly lower, is d. significantly lower, is not

mitochondria

In eukaryotes, ROS are naturally produced as unwanted by-products of energy production in ______. They may also be produced during certain types of immune responses and by a variety of detoxification reactions in the cell.

killing pathogens. In addition, some ROS are used in cell signaling.

In humans, the overaccumulation of ROS has been implicated in a wide variety of medical conditions, including cardiovascular disease, Alzheimer disease, chronic fatigue syndrome, and aging. However, the production of ROS is not always harmful. ROS are produced by the immune system as a means of??

a. detect DNA damage.

In nucleotide excision repair in E. coli, the function of the UvrA/UvrB complex is to a. detect DNA damage. b. make cuts on both sides of the damage. c. remove the damaged piece of DNA. d. replace the damaged DNA with undamaged DNA.

c. a hairpin, DNA replication

One way that TNRE may occur involves the formation of _________ that disrupts ____________. a. a double-strand break, chromosome segregation b. an apurinic site, DNA replication c. a hairpin, DNA replication d. a free radical, DNA structure

UV light

Promotes the formation of pyrimidine dimers, such as thymine dimers

Nucleotide Excision Repair (NER)

Start and END of subtopic: Nucleotide Excision Repair Systems Remove Segments of Damaged DNA a DNA repair system in which several nucleotides in the damaged strand are removed from the DNA and the undamaged strand is used as a template to resynthesize a normal strand. See figure 19.18 for visual (in genetics file)

Translesion synthesis

Start of Subtopic : Damaged DNA May Be Replicated by Translesion DNA Polymerases the synthesis of DNA over a template strand that harbors some type of DNA damage. This occurs via translesion-replicating polymerases.

Base Excision Repair (BER)

Start of Subtopic: Base Excision Repair Removes a Damaged Base a type of DNA repair in which a modified base is removed from a DNA strand. Following base removal, a short region of the DNA strand is removed and then resynthesized using the complementary strand as a template.

Breakpoint

Start of Subtopic: Changes in Chromosome Structure Can Affect the Expression of a Gene a region where two chromosome pieces break apart and rejoin with other chromosome pieces. here the gene is broken (next term refers to when the gene is conserved) can affect gene expression.

Photolyase

Start of Subtopic: Damaged Bases Can Be Directly Repaired an enzyme found in bacteria, fungi, most plants, and some animals that can recognize and split thymine dimers, which returns the DNA to its original condition.

reversion mutation

Start of Subtopic: Gene Mutations Are Also Given Names That Describe How They Affect the Wild-Type Genotype and Phenotype mutant phenotype to wild type phenotype

point mutation

Start of Subtopic: Gene Mutations Are Molecular Changes in the DNA Sequence of a Gene gene mutation in which a single base pair in DNA has been changed

silent mutation

Start of Subtopic: Gene Mutations Can Alter the Coding Sequence Within a Gene A mutation that changes a single nucleotide, but does not change the amino acid created.

up promoter mutation

Start of Subtopic: Gene Mutations Can Occur Outside of a Coding Sequence and Influence Gene Expression a mutation in a promoter that increases the rate of transcription

base pair mismatch

Start of Subtopic: Mismatch Repair Systems Recognize and Correct a Base Pair Mismatch a DNA abnormality in which two bases opposite each other in a double helix do not conform to the AT/GC rule. For example, if A were opposite C, that would be a base pair mismatch.

germ line

Start of Subtopic: Mutations Can Occur in Germ-Line or Somatic Cells cells that give rise to gametes such as egg and sperm cells

Reactive Oxygen Species (ROS)

Start of Subtopic: Oxidative Stress May Also Lead to DNA Damage and Mutation products of oxygen metabolism that are produced in all aerobic organisms and that can, if they accumulate, damage cellular molecules, including DNA, proteins, and lipids.

Ames test

Start of Subtopic: Testing Methods Can Determine If an Agent Is a Mutagen A procedure using bacteria to identify potential carcinogens Book Def: a test using strains of a bacterium, Salmonella typhimurium, to determine if a substance is a mutagen.

gene conversion

Start of Subtopic: The Holliday Model Describes a Molecular Mechanism for the Recombination Process the phenomenon in which one allele is converted to the allele on the homologous chromosome due to recombination or DNA repair.

An advantage is that I can occur at any stage of the cell cycle. A disadvantage is that It may be imprecise and result in a short deletion in the DNA.

Start of subtopic: Double-Strand Breaks Can Be Repaired by Homologous Recombination Repair or by Nonhomologous End Joining CONCEPT CHECK: What is an advantage and a disadvantage of the NHEJ repair system?

First, DSBs can result in chromosomal rearrangements such as inversions and translocations. In addition, DSBs can lead to terminal or interstitial deletions). Such genetic changes have the potential to result in detrimental phenotypic effects.

Start of subtopic: Double-Strand Breaks Can Be Repaired by Homologous Recombination Repair or by Nonhomologous End Joining Of the many types of DNA damage that can occur within living cells, the breakage of chromosomes—called a DNA double-strand break (DSB)—is perhaps the most dangerous. DSBs can be caused by ionizing radiation (X-rays or gamma rays), chemical mutagens, and certain drugs used for chemotherapy. In addition, reactive oxygen species that are the by-products of aerobic metabolism can cause double-strand breaks. Surprisingly, researchers estimate that naturally occurring double-strand breaks in a typical human cell occur at a rate of 10 to 100 breaks per cell per day! Such breaks are harmful in a variety of ways. List a couple of ways they can be harmful?

supressor mutation

Start of subtopic: Suppressor Mutations Reverse the Phenotypic Effects of Another Mutation suppresses the effect of an earlier mutation at a different site

The probability is 75% bc 3 of the 4 nucleotides that may be added to the newly made strand opposite the apurinic site are not the correct one.

Subtopic: Spontaneous Mutations Can Arise by Depurination, Deamination, or Tautomeric Shifts Conept CHECK: When DNA that has an apurinic site is replicated, what is the probability that a mutation will occur?

Because a complementary base is not present to specify the incoming base for the new strand, any of the four bases are added to the new strand in the region that is opposite the apurinic site. This may produce a new mutation.

Subtopic: Spontaneous Mutations Can Arise by Depurination, Deamination, or Tautomeric Shifts Fortunately, as discussed later in this chapter, apurinic sites are recognized by DNA repair enzymes, which can fix the problem. If the repair system fails, however, a mutation may result during subsequent rounds of DNA replication. What happens at an apurinic site during DNA replication?

involves the removal of a purine (adenine or guanine). The covalent bond between deoxyribose and a purine base is somewhat unstable and occasionally undergoes a spontaneous reaction with water that releases the base from the sugar, thereby creating an apurinic site

Subtopic: Spontaneous Mutations Can Arise by Depurination, Deamination, or Tautomeric Shifts The most common type of chemical change that may induce a spontaneous mutation that occurs naturally is depurination, which [....] from the DNA. Why is it so common?

Apurinc site

Subtopic: Spontaneous Mutations Can Arise by Depurination, Deamination, or Tautomeric Shifts a site in DNA that is missing a purine base.

Depurination

Subtopic: Spontaneous Mutations Can Arise by Depurination, Deamination, or Tautomeric Shifts the loss of a purine base from a nucleotide

d. All of the above

Which of the following DNA repair systems may involve the removal of a segment of a DNA strand? a. Base excision repair b. Nucleotide excision repair c. Mismatch repair d. All of the above

d. Both a and c are examples of somatic mutations.

Which of the following is an example of a somatic mutation? a. A mutation in an embryonic muscle cell b. A mutation in a sperm cell c. A mutation in an adult nerve cell d. Both a and c are examples of somatic mutations.

AP endonuclease

a DNA repair enzyme that recognizes a DNA region that is missing a base and makes a cut in the DNA backbone near that site.

mismatch repair system

a DNA repair system that recognizes base pair mismatches and repairs the newly made daughter strand that contains the incorrect base.

oxidative stress

a condition in which the production of oxidants and free radicals exceeds the body's ability to handle them and prevent damage

germ-line mutation

a mutation occurring in gametes; passed on to offspring.

framshift mutation

a mutation that involves the addition or deletion of a number of nucleotides not divisible by 3, which shifts the reading frame of the codons downstream from the mutation.

deleterious mutations

a mutation that is detrimental with regard to its effect on phenotype.

somatic mutation

a mutation that occurs in a body cell

base substitution

a point mutation in which one base is substituted for another.

heteroduplex

a region of double-stranded DNA that contains one or more base mismatches.

nonhomologous end joining (NHEJ).

a repair mechanism for double-strand breaks in which the ends of the DNA are pieced back together. This mechanism requires the participation of several proteins that play key roles in the process. Look at figure 19.22 for visual

tautomeric shift

a spontaneous mutation that involves a temporary change in a base structure to occur at the moment DNA polymerase is passing through this specific base. pyrimidines are usually in the keto form (and switch to enol), while purines are usually in amino form (and switch to imino). this creates AG and CT base pairings. This mismatch could be repaired via the proofreading function of DNA polymerase or via a mismatch repair system (discussed later in this chapter). However, if these repair mechanisms do not occur, the next round of DNA replication will produce a double helix with a mismatch base pair

Photoreactivation

a type of DNA repair mechanism of thymine dimers that involves photolyase and requires light.

trinucleotide repeat expansion (TNRE)

a type of mutation that involves an increase in the number of tandemly repeated trinucleotide sequences. The term refers to the phenomenon in which a repeated sequence of three nucleotides can readily increase in number from one generation to the next.

random mutation theory

according to this theory, mutations are a random process- they can occur in any gene and do not involve exposure of an organism to a particular condition that selects for specific types of mutations.

DNA N- glycosylase

an enzyme that can recognize an abnormal base and cleave the bond between it and the sugar in the DNA backbone.

missense point mutation

are base substitutions for which an amino acid change does result.

Holiday Junction

cross-shaped structure that forms during the process of genetic recombination.

transition mutation

purine to purine or pyrimidine to pyrimidine

hot spots

regions within a gene that are more likely to mutate than others.

intragenic suppressor mutation

suppresses the effect of an earlier mutation within the same gene

branch migration

the lateral movement of a Holliday junction

anticipation

the phenomenon in which the severity of an inherited disease tends to get worse in subsequent generations.

genetic recombination

the process in which alleles are assorted and passed to offspring in combinations that are different from those found in the parents.

Deamination uracil hydrogen bonds with adenine during DNA replication. Therefore, if a DNA template strand has uracil instead of cytosine, a newly made strand will incorporate adenine instead of guanine.

the removal of an amino group from a molecule. For example, the removal of an amino group from cytosine produces uracil. Cytosine is the primary base that will loose an amino group. DNA repair enzymes can recognize uracil as an inappropriate base within DNA and subsequently remove it. However, if such a repair does not take place, a mutation may result because ??

Deamination

the removal of an amino group from an amino acid

In some cases, the expansion is within the coding sequence of a gene. Typically, such an expansion involves CAG repeats. Because CAG encodes glutamine, these repeats cause the encoded proteins to contain long tracts of glutamine. The presence of glutamine tracts causes the proteins to aggregate. This aggregation of proteins or protein fragments carrying glutamine repeats is correlated with the progression of the disease.

what is responsible for the disease aspect of TNRE?