Genetics Exam 3 Review: Chapter 7

Spontaneous mutation information:

*all types of point mutations occur spontaneously Spontaneous mutations can occur during DNA replication, as well as during other stages of cell growth and division. Spontaneous mutations also can result from the movement of transposable genetic elements, *In humans, the spontaneous mutation rate for individual genes varies between 10-4 and 4x10-6 per gene per generation. *For eukaryotes in general, the spontaneous mutation rate is 10-4 to 10-6 per gene per generation, and for bacteria and phages the rate is 10-5 to 10-7 per gene per generation Most spontaneous errors are corrected by cellular repair systems; only some errors remain uncorrected as permanent changes.

methyl directed mismatch repair

*despite proofreading by DNA polymerase, a number of mismatched base pairs remain uncorrected after replication has been completed. in the next round of replication, these errors will become fixed as mutations if they are not repaired. Many mismatched base pairs left after DNA replication can be corrected by methyl directed mismatch repair. this system recognizes mismatched base pairs, excises the incorrect bases, and then carries out repair synthesis.

two common chemical events that produce spontaneous mutations

1. Depurination 2. Deamination *these events create lesions-damaged sites in the DNA

two terms are used to give a quantitative measure of the occurrence of mutations:

1. Mutation Rate 2. Mutation Frequency

Point mutations are divided into two classes bases on how they affect they phenotype:

1. a forward mutation-Changes a wild type gene to a mutant gene 2. a reverse mutation(reversion or back mutation)- changes a mutant gene at the same site so that it functions in a completely wild -type or nearly wild-type way. -For example, a reversion of a nonsense mutation occurs when a base pair change results in a change of the mRNA nonsense codon to a codon for an amino acid. if this reversion is back to the wild-type amino acid, the mutation is a true reversion. if the reversion is to some other amino acid, the mutation is partial reversion, and complete or partial function may be restored, depending on change. Reversion of missence mutations occurs in the same way.

Point mutations fall into two categories:

1. base pair substitutions 2. base pair insertions or deletions

mutations can be classified according to different criteria:

1. by their cause (spontaneous vs. induced) 2. effect on DNA ( point vs. chromosomal, substitution vs. insertion/deletion, transition vs. transversion) 3. their effect on an encoded protein (nonsense,missence,neutral,silent, and frameshift)

3 types of mutagens that work as base-modifying agents

1. deaminating agent 2. hydroxylating agent 3. alkylating agent

In E.coli there are two genes for controlling the SOS system:

1. lexA 2. recA

2 general types of base-pair substitution mutations:

1. transition mutation 2. transversion mutation

the SOS response works as follows:

1. when there is no DNA damage, the lexA- encoded protein, LexA, represses the transcription of about 17 genes whose protein products are involved in repairing and dealing with various kinds of DNA damage. 2. upon sufficient damage to DNA, the recA- encoded protein, RecA, is activated 3. activated RecA stimulates the LexA protein to cleave to itself, which in turn relieves the repression of the DNA repair genes. 4. As a result, the DNA repair genes are expressed, and DNA repair proceeds 5. after the DNA damage is dealt with, RecA is inactivated, and newly synthesized LexA protein again represses the DNA repair genes *The SOS response itself is a mutagenic system because mutations will be introduced into the DNA as a result of its activation. Such mutations are less harmful than the potentially lethal alternative caused by incompletely replicated DNA

the man-made sources of radiation is:

1. x-rays 2. cathode ray tube displays 3. watches and other devices that glow in the dark.

Chromosomal Changes

Changes involving whole chromosome or sections of them

There are 3 classes of nonsense suppressors, one for each of the stop codons, UAG, UAA, and UGA.

For example, if a gene for a tyrosine tRNA (which has the anticodon(3'-AUG-5') is mutated so that the tRNA has the anticodon 3'-AUC-5', the mutated suppressor tRNA (which still carries tyrosine) reads the nonsense codon 5'-UAG-3'. so, instead of chain termination occurring, tyrosine is inserted at that point in the polypeptide. *if the suppressor tRNA .Tyr gene has mutated so that the encoded tRNAs anticodon can read a nonsense codon, it can no longer read the original codon that specifies the amino acid it carries. This turns out not to be a problem, because nonsense suppressor tRNA genes typically are produced by mutations of tRNA genes that are present in two or more copies in the genome. If there is a mutation in one of the genes to produce a suppressor tRNA, then the other gene(s) produce(s) a tRNA molecule that reads the normal Tyr codon.

Radon

Is and invisible, inert radioactive gas with no smell or taste. the decay of radon produces ionizing radiation , which can induce mutations.

nucleotide excision repair

It involves four proteins: UvrA, UvrB, UvrC and UvrD encoded by the genes uvrA, uvrB, uvrC and uvrD. 1. a complex of two UvrA proteins and one UvrB protein slides along the DNA 2. When the complex recognizes a pyrimidine dimer or another serious distortion in the DNA, the UvrA subunits dissociate and a UvrC protein binds to the UvrB protein at the lesion. 3. the resulting UvrBC protein bound to the lesion makes one cute about four nucleotides to the 3' side in the damaged DNA strand (done by UvrB) and about seven nucleotides to the 5' side of the lesion (for by UvrC) 4. UvrB is then released, and UvrD binds to the 5' cut. UvrD is a helices that unwinds the region between the cuts, releasing the short single-stranded segment. 5. DNA polymerase 1 fills in the gap in the 5'-to-3' direction, and DNA ligase seals the final gap

base-Pair substitution mutations

Point mutations involving a change from one base pair to another- can occur if mismatched base pairs form during DNA replication.

Mutation Frequency

The number of occurrences of a particular kind of mutation,expressed as the proportion of cells or individuals in a population, such as the number of mutations per 100,000 organisms or the number per 1 million gametes.

repair of UV-induced pyrimidine dimers

Through photo reactivation, or light repair, UV light-induced thymine (or other pyrimidine) dimers are reverted directly to the original form by exposure to near-UV light in the wavelength range from 320 to 370 nm. - Photoreactivation occurs when an enzyme called photolyase (encoded by the phi gene) is activated by a photon of light and splits the dimers apart. Strains with mutations in the phr gene are defective in light repair. Photolyase has been found in bacteria and in simple eukaryotes, but not in humans.

intergenic(inter=between) suppressors

When suppressor mutations occur in a different gene where the original mutations occurred, but at a different site

Neutral mutation

a base -pair change in a gene that changes a codon in the mRNA such that the resulting amino acid substitution produces no deductible change in the function of the protein translated from that message. *a neutral mutation is a subset of missense mutations in which the new codon codes for a different amino acid that is chemically equivalent to the original or the amino acid is not functionally important and therefore does not affect the proteins function. consequently, the phenotype does not change.

base-pair substitution mutation

a change from one base pair to another in DNA

Point mutation

a change of one or a few base pairs. *A point mutation may change the phenotype of the organism if it occurs within the coding region of a gene or in the sequences regulating the gene.

nonsense mutation

a gene mutation in which a base-pair change alters an mRNA codon for an amino acid to a stop (nonsense) codon. (UAG,UAA,UGA) *a nonsense mutation causes premature termination of polypeptide chain synthesis, so shorter -than-normal polypeptide fragments (often nonfunctional) are released from the ribosomes

missence mutattion

a gene mutation in which a base-pair change causes a change in an mRNA codon so that a different amino acid is inserted into the polypeptide *a phenotypic change may or may not result, depending on the amino acid change involved

Suppressor mutation

a mutation at a different site from that of the original mutation. *a suppressor mutation masks or compensates for the effects of the initial mutation , but it does not reverse the original mutation.

Transversion mutation

a mutation from a pouring-pyrimidine base pair to a pyrimidine-purine base pair,such as G-C to C-G, or A-T to C-G. specifically, this means that the purine on one strand of the DNA (A in the second example) is changed to a pyrimidine (C in the example), while the pyrimidine on the complementary strand (T, the base paired to the A) is changed to the purine that base pairs with the altered pyrimidine (Gin this example)

Transition Mutation

a mutation from one purine-pyrimidine base pair to the other purine-pyrimidine base pair, such as A-T to G-C. This means that the purine on one strand of the DNA (A for example) us changed to the other purine, while the pyrimidine on the complementary strand (T, the base paired to the A) is changed to the other pyrimidine.

Germ-line mutation

a mutation in the germ line of sexually reproducing organisms. *May be transmitted by the gametes to the next generation, producing an individual with the mutation in both its somatic and its germ-line cells.

silent mutation(synonymous mutation)

a mutation that changes a base pair in a gene, but the altered codon in the mRNA specifies the same amino acid in the protein. in this case, the protein obviously has a wild-type function. *Silent mutations most often occur by changes such as this at the third- wobble-position of a codon. This makes sense from the degeneracy patterns of the genetic code.

Intergenic suppression is the result of

a second mutation in another gene.

Small additions and deletions can

also occur spontaneously during replication. They occur because of displacement -looping out- of bases from either the template or the growing DNA strand, generally in regions where a run of the same base or of a repetitive sequence is present. -If DNA loops out from the template strand, DNA polymerase skips the looped-out base or bases, producing a deletion mutation; if DNA polymerase synthesizes an untemplated base or bases, the new DNA loops out from the template, producing an addition.

Intragenic suppressors act by

altering a different nucleotide in the same codon where the original mutation occurred or by altering a nucleotide in a different codon.

frameshift mutation

an addition or delete of one base pair *this results in a nonfunctional protein. they may also generate new stop codons , resulting in a shortened poly[etide; they may result in longer-than-normal proteins because the normal stop codon is now in a different reading frame; or they may result in a significant alteration of the amino acid sequence of a polypeptide.

Base analogs

are bases that are similar to those normally found in DNA. like normal bases. base analogs exist in normal and rare tautomeric states. in each of the two states, the base analogs pairs with a different normal base in DNA *Because base analogs are so similar to the normal nitrogen bases, they may be incorporated into DNA in place of the normal bases. *One base analog mutagen is 5-bromouracil (5BU), which has a bromine residue instead of the methyl group of thymine. in its normal state, 5BU resembles thymine and pairs with guanine. 5BU induces mutation by switching between its two chemical states once the base analog has been incorporated into the DNA. if 5BU is incorporated in its normal state, it pairs with adenine, if it then changes into its rare state during replication, it pairs with guanine instead. in the next round of replication, the 5BU-G bas pair is resolved into a C-G base pair instead of the T-A base pair. by this process , a TA-to-CG transition mutation is produced. 5BU can also induce a CG-to-TA transition mutation if it is first incorporated into DNA in its rare state and then switches to the normal state during replication. *Not all base analogs are mutagens. for example, AZT is an analog of thymidine - but it is not a mutagen because it does not cause base-pair changes

Spontaneous mutation

are naturally occurring mutations

Depurination and deamination mutations may be repairable by...

base excision repair system

base-modifying agents

chemicals that act as mutagens by modifying the chemical structure and properties of bases.

base excision repair

damaged single bases or nucleotides are most commonly repaired by removing the base or the nucleotide involved and then inserting the correct base or nucleotide. *in base excision repair, a repair glycosylase enzyme removes the damaged base from the DNA by cleaving the bond between the base and the deoxyribose sugar. other enzymes then cleave the sugar-phosphate backbone before and after the now base-less sugar, releasing the sugar and leaving a gap in the DNA chain. the gap is filled with the correct nucleotide by a repair DNA polymerase and DNA ligase, with the opposite DNA strand used as the template. -Mutations caused by deprivation or deamination are examples of damage that may be repaired by base excision repair.

both inorganic and internecine suppressors operate to

decrease or eliminate the deleterious effects of the original mutation. however the mechanisms of the two suppressors are completely different

Tautomers

each base can exist in alternative states. when a base changes state, it has undergone a tautomeric shift.

mutations can be induced by...

exposing organisms to physical mutagens, such a radiation, or to chemical mutagens.

mis-match repair system

fixes errors that occur during DNA replication

suppressor genes

genes that cause the suppression of mutations in other genes -For example, in the case of nonsense suppressors, particular tRNA genes mutate so that their anticodons recognize a chain-terminating codon and put an amino acid into the chain. Thus, instead of polypeptide chain synthesis being stopped prematurely because of a nonsense mutation, the altered (suppressor) tRNA inserts an amino acid at that position, and full or partial function of the polypeptide is restored. This suppression process is not very efficient , but sufficient functional polypeptides are produced to reverse or partially reverse the phenotype.

Hydroxylamine (NH2OH) is a

hydroxylating mutagen that reacts specifically with cytosine, modifying it by adding a hydroxyl group (OH) so that it pairs with adenine instead of guanine. *mutations induced by hydroxyl amine can only be CG-to-TA transcriptions, so hydroxyl amine-induced mutations cannot be reverted by a second treatment with this chemical. however they can be reverted by treatment with other mutagens that cause TA-to-CG transition mutations

Chemical mutagens

include both naturally occurring chemicals and synthetic substances. These mutagens can be grouped into different classes based on their mechanism of action

Geneticists use mutagens to...

increase the frequency of mutation so that a significant number of organisms have mutations in the gene being studied.

base-modifying agents can

induce mutations at any point of the cell cycle

Nitrous acid, HNO2

is a deaminating agent that removes amino groups from the bases guanine, cytosine, and adenine. Nitrous acid modifies adenine to produce hypoxanthine, a base that pairs with cytosine rather then thymine, which results in an AT-to-GC transition mutation. Therefore, a nitrous acid-induced mutation can be reverted by a second treatment with nitrous acid.

In DNA, the keto form is

is the form usually found in each base and is responsible for the normal Watson-Crick base pairing of T with A and C with G. -However non-Watson-Crick base pairing can result if a base is in a rare tautomeric state, the enol form.

Translesion DNA synthesis and the SOS response

lesions that block the replication machinery from proceeding past that point can be lethal if unrepaired. fortunately, a last-resort process called translation DNA synthesis allows replication to continue past the lesions. *This process involves a special class of DNA polymerases that are synthesized only in response to DNA damage. in E.coli, such DNA damage activates a complex system called the SOS response( its called this because it is induced as a last resort, emergency response to mutational damage). the SOS response allows the cell to survive otherwise lethal events, although often at the expense of generating new mutations.

Depurination

loss of a purine from the DNA when the bond hydrolyzes between the base and the deoxyribose sugar, resulting in an apurinic site. *Depurination occurs because the covalent bond between the sugar and purine is much less stable than the bond between the sugar and pyrimidine and is very prone to breakage. *If such lesions are not repaired, there is no base to specify a complementary base during DNA replication, and the DNA polymerase may stall or dissociate from the DNA

what 3 genes are involved in the initial stages of mismatch repair

mutS, mutL, and mutH 1. MutS binds to the mismatch 2.then the repair system determines which base is the correct one (the base on the parental DNA strand) and which is the erroneous one (the base on the new DNA strand). 3. in E.coli, the two strands are distinguished by methylation of the A nucleotide in the sequence GATC. this sequence has an axis of symmetry; that is , the same sequence is present 5' to 3' on both DNA strands to give. 5'-GATC-3' and 3'-CTAG-5'. both A nucleotides in the sequence usually are methylated 4. after replication, the parental DNA strand has a methylated A in the GATC sequence, whereas the A in the GATC of the newly replicated DNA strand is not methylated until a short time after its synthesis. 5. therefore, the MutS protein bound to the mismatch and forms a complex with the mutL- and much-encoded proteins, MutL and MutH, to bring the unmethylated GATC sequence close to the mismatch 6. the MutH protein then nicks the unmethylated DNA strand at the GATC site, the mismatch is removed by an exonuclease, and the gap is repaired by DNA polymerase 3 and ligase. *this also takes place in eukaryotes but it is unclear how the new DNA strand is distinguished from the parental DNA strand (no methylation is involved).

UV light causes

mutations by increasing the chemical energy of certain molecules, such as pyrimidines, in DNA. one effect of UV radiation on DNA is the formation of abnormal chemical bonds between adjacent pyrimidine molecules in the same strand of the double helix. -this bonding is induced mostly between adjacent thymines,forming what are called thymine dimers, usually designated T^T. (C^C, C^T, and T^C pyrimidine dimers are also produced by UV radiation but in much lower amounts). *This unusual pairing produces a bulge in the DNA strand and disrupts the normal pairing of T bases with corresponding A bases on the opposite strand. Replication cannot proceed past the lesion, so the cell will die if enough pyrimidine dimers remain unrepaired

gene mutations (a point mutation)

mutations which affect the function of genes. *a gene mutation can alter the phenotype by changing the function of a protein

radiation occurs in...

non ionizing and ionizing forms

induced mutations typically

occur at a much higher frequency than do spontaneous mutations and hence have been useful in genetic studies

Induced mutations

occur when an organism is exposed either deliberately or accidentally to a physical or chemical agent., known as a mutagen, that interacts with DNA to cause a mutation

ionizing radiation

penetrates tissues,colliding with molecules and knocking electrons out of orbits, thereby creating ions. The ions can result in the breakage of covalent bonds, including those in the sugar-phosphate backbone of DNA. *ionizing radiation is the leading cause of gross chromosomal mutations in humans. high dosages of ionizing radiation kill cells-hence their use in treating some forms of cancer. at certain low levels of ionizing radiation, point mutations are commonly produced;at these levels there is a linear relationship between the rate of point mutations and the radiation dosage. *The effects of ionizing radiation doses are cumulative. that is, if a particular dose of radiation results in a certain number of point mutations, the same number of point mutations will be induced whether the radiation does is received over a short or over a long period of time.

Mutations induced by base analogs and intercalating agents depend on

replication

Intercalating agents

such as proflavin,acridine, and ethidium bromide(commonly used to stain DNA in gel electrophoresis experiments)-insert (intercalate) themselves between adjacent bases in one or both strands of the DNA double helix, causing the helix to relax. -if the intercalating agent inserts itself between adjacent base pairs of the DNA strand that is the template for new DNA synthesis, an extra base (chosen at random) is inserted into the new DNA strand opposite the intercalating agent *After one more round of replication, during which the intercalating agent is lost, the overall result is a base-pair addition mutation. - if the intercalating agent inserts itself into the new DNA strand in place of a base, then when that DNA double helix replicates after the intercalating agent is lost, the result is a base-pair deletion mutation. *since intercalating agents can cause either additions or deletions, frameshift mutations induced by intercalating agents can be reverted by a second treatment with those same agents

The effects of a mutation may be diminished or abolished by

suppressor mutation

Mutagenesis

the creation of mutations, can occur spontaneously or can be induced

adaptation

the environment induced and adaptive inheritable change *heritable adaptive traits result from the random mutation, rather than by adaptation as a result of induction by environmental influences.

Mutation Rate

the probability of a particular kind of mutation as a function of time, such as the number of mutations per nucleotide pair per generation, or the number per gene per generation

mutation

the process by which the sequence of base pairs in a DNA molecule is altered *a mutation may result in a change to either a DNA base pair or a chromosome. a cell with a mutation is a mutant cell

Deamination

the removal of an amino group from a base. For example, the deamination of cytosine produces uracil. -If uracil is not replaced, an adenine will be incorporated into the new DNA strand opposite it during replication,eventually resulting in a CG-toTA transition mutation. *DNA of both bacteria and eukaryotes contains small amounts of the modified base 5-methylcytosine in place of the normal base cytosine. Deamination of 5mC produces thymine, thereby changing the G-5mC base pair to the mismatched base pair, G-T. if the mismatch is not corrected, at the next replication cycle the G of the pair is in the template for C on the new DNA strand, while the T is a template for A on the new DNA strand. -The consequence is that one of the new DNA molecules has the normal G-C base pair,while the other is mutant, with an A-T base pair. In other words, deamination of 5mC can result in a GC-toAT transition mutation. *5mC deamination mutations are less likely to be corrected, locations of 5mC in the genome often appear as mutational hot spots-that is, nucleotides where a higher-than-average frequency of mutation occurs.

Base-pair substitutions in protein coding genes are defined by

their effects on amino acid sequences in proteins. *depending on how a base-pair substitution is translated via the genetic code, the mutations can result in no change to protein, an insignificant change, or a noticeable change

Treatment of cytosine with nitrous acid produces

uracil, which pairs with adenine to produce a CG-to-TA transition mutation during replication

somatic mutation

when a mutation happens to occur in a somatic cell (in multicellular organisms). *The mutant characteristics affects only the individual in which the mutation occurs and is not passed on the the succeeding generation.

3' to 5' exonuclease proofreading activity of the DNA polymerase

when an incorrect nucleotide is inserted, the polymerase often detects the mismatched base pair and corrects the area by "backspacing" to remove the wrong nucleotide and then resuming synthesis in the forward direction.

Transposable elements (transposition-Change in position)

when certain genetic elements in the chromosomes of prokaryotes and eukaryotes move from one location to another in the genome.

ionization occurs...

when energy is sufficient to knock an electron out of an atomic shell and hence break covalent bonds. -Except for ultraviolet light (UV),non ionizing radiation does not induce mutations; but all forms of ionizing radiation, such as X-rays, cosmic rays, and radon, can induce mutations.

Intragenic (intra=within) suppressors

when suppressor mutations occur within the same gene where the original mutations occurred, but at a different site.

treatment of guanine with nitrous acid produces

xanthine, but because this purine base has the same pairing properties as guanine, no mutation results