Chapter 18

Beneficial mutation

-enhances the survival or reproductive success of an organism

Replica plating

a technique in which a replica of bacterial colonies is transferred to a new petri plate.

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.

Mutagens

an agent that causes alterations in the structure of DNA.

Huntington disease

human disease that involves TNRE expansion -SBMA -table 18.5

In the case of the diseases listed in the terms, where is the repeat unit located in the gene:

(1) Huntington disease-HD-CAG-coding sequence (2)Fragile X syndrome-FRAXA-CGG-5'-UTR (3)Fragile X syndrome-FRAXE-GCC-5'-UTR (4)Dystrophia myotonica-DM-CTG-3'-UTR

chemical agents

-MUTAGENS -spontaneous mutations

DNA Sequences Known as ------- Are ------

-Trinucleotide Repeats -Hotspots for Mutation

Neutral mutation

-When a missense mutation has no detectable effect on protein function

Germ/Germ-line cells

-a lineage of cells that gives rise to gametes, sperm or egg cell.

Germ line mutation

-a mutation in a cell of the germ line. -can occur directly in a sperm or egg cell, or it can occur in a precursor cell that produces the gametes. -If a mutant gamete participates in fertilization, all cells of the resulting offspring will contain the mutation -when an individual with a germ-line mutation produces gametes, the mutation may be passed along to future generations of offspring.

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. None of the above

A mutation caused by UV light

Which of the following examples is likely to be caused by a somatic mutation? A. A purple flower has a small patch of white tissue. B. One child, in a family of seven, is an albino. C. One apple tree, in a very large orchard, produces its apples 2 weeks earlier than any of the other trees. D. A 60-year-old smoker develops lung cancer.

A. Yes. B. No, the albino trait affects the entire individual. C. No, the early apple-producing trait affects the entire tree. D. Yes.

Oxidative Stress May Also Lead to:

DNA Damage and Mutation

Spontaneous Mutations Can Arise by:

Depurination, Deamination, and Tautomeric Shifts

Explain what happens to the sequence of DNA during trinucleotide repeat expansion (TNRE). If someone was mildly affected with a TNRE disorder, what issues would be important when considering possible effects in future offspring?

During TNRE, a trinucleotide repeat sequence gets longer. If someone was mildly affected with a TNRE disorder, he or she might be concerned that an expansion of the repeat might occur during gamete formation, yielding offspring more severely affected with the disorder, a phenomenon called anticipation. This phenomenon may depend on the sex of the parent with the TNRE

*Mutations Can Occur in:*

Germ-Line or Somatic Cells

physical agents

MUTAGENS induced mutation

Mutation frequency

The mutation frequency for a gene is the number of mutant genes divided by the total number of copies of that gene within a population

Is the promoter involved with transcription or translation?

Transcription

Missense mutation

a base substitution that leads to a change in the amino acid sequence of the encoded polypeptide. -EX: Sickle cell disease

Point mutation

a change in a single base pair within the DNA

Base substitution

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

Induced mutations

caused by environmental agents

Spontaneous mutations

changes in DNA structure that result from natural random abnormalities in biological or chemical processes

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

d. Both a and c

A down promoter mutation causes the promoter of a gene to be _______ like the consensus sequence and _________ transcription:

less, inhibits

A mutation that changes a codon into a stop codon is a:

nonsense mutation

*Changes in Chromosome Structure Can Affect:*

the Expression of a Gene

*Suppressor Mutations Reverse:*

the Phenotypic Effects of Another Mutation

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

- a hairpin, DNA replication

Mutant allele

-A mutation may change a wild-type genotype by altering the DNA sequence of a gene. -such a mutation is rare in a population

Transition

-A point mutation involving a change of a pyrimidine to another pyrimidine, such as C to T, or a purine to another purine, such as A to G

Transversion

-a point mutation in which a purine is interchanged with a pyrimidine, or vice versa.

Intergenic suppressor

-a suppressor mutation that is in a different gene from the gene that contains the first mutation. -involve a change in the expression of one gene that compensates for a loss-of-function mutation affecting another gene

Lactose permease is encoded by the lacY gene of the lac operon. A mutation occurred at codon 64 that changed the normal glycine codon into a valine codon. The mutant lactose permease is unable to function. However, a second mutation, which changes codon 50 from an alanine codon to a threonine codon, is able to restore function. Are the following terms appropriate or inappropriate to describe this second mutation? A. Reversion B. Intragenic suppressor C. Intergenic suppressor D. Missense mutation

A: not appropriate bc the 2nd mutation is at a different codon B: appropriate C: Not appropriate bc the 2nd mutation is in the same gene as the first mutation D: appropriate

Are each of the following mutations silent, missense, nonsense, or frameshift mutations? The original DNA strand is 5ʹ-ATGGGACTAGATACC-3ʹ. (Note: Only the coding strand is shown; the first codon is methionine.) A. 5ʹ-ATGGGTCTAGATACC-3ʹ B. 5ʹ-ATGCGACTAGATACC-3ʹ C. 5ʹ-ATGGGACTAGTTACC-3ʹ D. 5ʹ-ATGGGACTAAGATACC-3ʹ

A: silent bc the same amino acid (glycine) is encoded by GGA compared to GGT B: missense bc a different amino acid is encoded by CGA compared to GGA C: missense bc a different amino acid is encoded by GTT compared to GAT D: frameshift bc an extra base is inserted into the sequence

With regard to TNRE, what is meant by the term anticipation?

Anticipation means that the TNRE expands even further in future generations. Anticipation may depend on the sex of the parent with the TNRE.

*Gene Mutations Are Also Given Names That Describe:*

How They Affect the Wild-Type Genotype and Phenotype

Wild type

In a natural population: -relatively prevalent genotype. Many or most genes exist as multiple alleles so that a population may have two or more wild-type alleles.

*Figure 18.3*

In part (b) the sequence of the eye color gene is not changed. The change in expression is due to a position effect

*Gene Mutations Are:*

Molecular Changes in the DNA Sequence of a Gene

Why aren't the terms "mutation" and "deleterious" synonyms?

Mutations are not always negative in regards to the survival of an organism and some mutations can be beneficial Deleterious mutations are always going to be detrimental with regard to its effect on phenotype.

*Figure 18.2*

Position effect means that the expression of a gene has been altered due to a change in its position along a chromosome

Suppressor mutation

-a mutation at a second site that suppresses the phenotypic effects of another mutation.

Down promoter mutation

-a mutation in a promoter that inhibits the rate of transcription -causes the promoter to become less like the consensus sequence, decreasing its affinity for transcription factors and decreasing the transcription rate.

What are two specific examples of mutations that can cause frameshift mutations?

-addition -deletion

What enzyme binds to the promoter?

RNA polymerase

*Gene Mutations Can Alter:*

The Coding Sequence Within a Gene

*Gene Mutations Can Occur Outside of:*

The Coding Sequence and Influence Gene Expression

Position effect

a change in phenotype that occurs when the position of a gene is changed from one chromosomal site to a different location

Up promoter mutation

-Promoter mutations that increase transcription

S1. Mutant tRNAs may act as nonsense and missense suppressors. At the molecular level, explain how you think these suppressors work.

*Answer*: A suppressor is a second-site mutation that suppresses the phenotypic effects of a first mutation. Intergenic suppressor mutations in tRNA genes can act as nonsense or missense suppressors. For example, let's suppose a first mutation puts a stop codon into a protein-encoding gene. A second mutation in a tRNA gene can alter the anticodon region of a tRNA so that the anticodon recognizes a stop codon but inserts an amino acid at this site. A missense suppressor is a mutation in a tRNA gene that changes the anticodon so that it puts in the wrong amino acid at a codon that is not a stop codon. These mutant tRNAs are termed missense tRNAs. For example, a tRNA that normally recognizes glutamic acid may incur a mutation that changes its anticodon sequence so it recognizes a glycine codon instead. Like nonsense suppressors, missense suppressors can be produced by mutations in the anticodon region of tRNAs so the tRNA recognizes an incorrect codon. Alternatively, missense suppressors can also be produced by mutations in aminoacyltRNA synthetases that cause them to attach the incorrect amino acid to a tRNA.

Discuss the consequences of a germ-line versus a somatic mutation.

-If a mutation within the germ line is passed to an offspring, all of the cells of the offspring's body will carry the mutation. A somatic mutation affects only the somatic cell in which it originated and all of the daughter cells that the somatic cell produces. -If a somatic mutation occurs early during embryonic development, it may affect a fairly large region of the organism. Because germ-line mutations affect the entire organism, they are potentially more harmful (or beneficial), but this is not always the case. Somatic mutations can cause quite harmful effects such as cancer.

Sickle cell anemia

-Missense mutation -involves a mutation in the β-globin gene, which alters the polypeptide sequence so the sixth amino acid is changed from a glutamic acid to valine. -This single amino acid substitution alters the structure and function of the hemoglobin protein. -One consequence of this alteration is that under conditions of low oxygen, the red blood cells assume a sickle shape (Figure 18.1). -In this case, a single amino acid substitution has a profound effect on the phenotype of cells and can even cause a serious disease.

Ames test

-To determine if an agent is mutagenic -monitor whether or not an agent increases the mutation rate. -This test uses strains of a bacterium, Salmonella typhimurium, that cannot synthesize the amino acid histidine. These strains contain a point mutation within a gene that encodes an enzyme required for histidine biosynthesis. The mutation renders the enzyme inactive. Therefore, the bacteria cannot grow on petri plates unless histidine has been added to the growth medium. However, a second mutation—a reversion—may occur that restores the ability to synthesize histidine. In other words, a second mutation can cause a reversion back to the wild-type condition. The Ames test monitors the rate at which this second mutation occurs, thereby indicating whether an agent increases the mutation rate above the spontaneous rate.

Deleterious mutation

-decreases the chances of survival and reproduction. -a mutation that is detrimental with regard to its effect on phenotype.

A mutation in one gene that reverses the phenotypic effects of a mutation in a different gene is:

an intergenic suppressor

Are mutations random events? Explain your answer:

-According to random mutation theory, spontaneous mutations can occur in any gene and do not involve exposure of the organism to a particular environment that selects for specific types of mutation. -However, the structure of chromatin may cause certain regions of the DNA to be more susceptible to random mutations. -For example, DNA in an open conformation may be more accessible to mutagens and more likely to incur mutations. -Similarly, hot spots—certain regions of a gene that are more likely to mutate than other regions -can occur within a single gene. -Also, another reason that some genes mutate at a higher rate is that some genes are larger than others, which provides a greater chance for mutation.

In the replica-plating experiments of the Lederbergs, bacterial colonies appeared at the same locations in each of two secondary plates because:

-the mutations occurred on the master plate prior to T1 exposure and prior to replica plating

TNRE

-trinucleotide repeat expansion -several human genetic diseases are caused -a repeated sequence of three nucleotides can readily increase in number from one generation to the next. -Typically CAG repeat

Distinguish between spontaneous and induced mutations. Which are more harmful? Which are avoidable?

A spontaneous mutation originates within a living cell. It may be due to spontaneous changes in nucleotide structure, errors in DNA replication, or products of normal metabolism that may alter the structure of DNA. The causes of induced mutations originate from outside the cell. They may be physical agents, such as UV light or X rays, or chemicals that act as mutagens. Both spontaneous and induced mutations may cause a harmful phenotype such as a cancer. In many cases, induced mutations are avoidable if the individual can prevent exposure to the environmental agent that acts as a mutagen.

What does a suppressor mutation suppress? What is the difference between an intragenic and an intergenic suppressor?

A suppressor mutation suppressed the phenotypic effects of some other mutation. Intragenic suppressors are within the same gene as the first mutation. Intergenic suppressors are in another gene

Hairpin/ stem loop structure

-How TNRE occurs -The formation of a hairpin during DNA replication can lead to an increase in the length of a DNA region if it occurs in the newly made daughter strand -After the hairpin forms, DNA polymerase may temporarily slip off the template strand.

Somatic mutations

-can happen at early or late stages of development -genetic alteration acquired by a cell that can be passed to the progeny of the mutated cell in the course of cell division

Mutagens

Agents known to alter the structure of DNA and thereby cause mutations

Mytonic Muscular Dystrophy

human disease that involves TNRE expansion -DM -table 18.5

Fragile X Syndromes

human disease that involves TNRE expansion -FRAXA -FRAXE -table 18.5

Somatic cells

-cells of the body excluding the germline cells. -Examples include muscle cells, nerve cells, and skin cells. -Mutations can also happen within somatic cells at early or late stages of development.

How does TNRE occur?

-key aspect of TNRE is that the triplet repeat can form a hairpin, also called a stemloop. -A consistent feature of the triplet sequences associated with TNRE is they contain at least one C and one G

Explain two ways that a chromosomal rearrangement can cause a position effect.

-One possibility is that a translocation may move a gene next to a heterochromatic region of another chromosome and thereby diminish its expression or it could be moved next to a euchromatic region and increase its expression. -Another possibility is that the translocation breakpoint may move the gene next to a new promoter or regulatory sequences that may now influence the gene's expression.

Anticipation

-Some TNRE disorders have the unusual feature of a progressively worsening severity in future generations -also called dynamic mutation -anticipation does not occur with all TNRE disorders and usually depends on whether the disease is inherited from the mother or father. -HD anticipation---inherited from father DM anticipation--inherited from mother

Mutation rate

-The likelihood that a gene will be altered by a new mutation -This rate is commonly expressed as the number of new mutations in a given gene per cell generation. -The spontaneous mutation rate for a particular gene is typically in the range of 1 in 100,000 to 1 in 1 billion, or 10 -5 -10 -9 per cell generation.

Outline how you would use the technique of replica plating to show that antibiotic resistance is due to random mutations:

-To show that antibiotic resistance is due to random mutation, one could follow the same basic strategy except the secondary plates would contain the antibiotic instead of T1 phage. -If the antibiotic resistance arose as a result of random mutation on the master plate, one would expect the antibiotic-resistant colonies to appear at the same locations on two different secondary plates.

Explain how the technique of replica plating supports the random mutation theory but conflicts with the physiological adaptation hypothesis:

-When cells from a master plate were replica plated onto two plates containing selective media with the T1 phage, T1-resistant colonies were observed at the same locations on both plates. -These results indicate that the mutations occurred randomly while on the master plate (in the absence of T1) rather than occurring as a result of exposure to T1. -In other words, mutations are random events and selective conditions may promote the survival of mutant strains that occur randomly.

Mutation

-a heritable change in the genetic material. -the structure of DNA has been changed permanently, and this alteration can be passed from mother to daughter cells during cell division. -If a mutation occurs in reproductive cells, it may also be passed from parent to offspring.

Nonsense mutation

-a mutation that involves a change from a sense codon to a stop codon. -This terminates the translation of the polypeptide earlier than expected, producing a truncated polypeptide -When a nonsense mutation occurs in a bacterial operon, it may also inhibit the expression of downstream genes.

Intragenic suppressor

-a suppressor mutation that is within the same gene as the first mutation that it suppresses. -often involves a change in protein structure that compensates for an abnormality in protein structure caused by the first mutation.

Lethal mutation

-extreme example of a deleterious mutation -results in death to a cell or organism -produces a lethal allele

Genetic variation

-genetic differences among members of the same species or among different species.

Frameshift

-involve the addition or deletion of a number of nucleotides that is not divisible by 3. -Because the codons are read in multiples of 3, this shifts the reading frame. -The translation of the mRNA then results in a completely different amino acid sequence downstream from the mutation.

Silent mutation

-mutation that do not alter the amino acid sequence of the encoded polypeptide even though the nucleotide sequence has changed. -Because the genetic code is degenerate, silent mutations can occur in certain bases within a codon, such as the third base, so the specific amino acid is not changed.

how do mutations within the coding sequence of a gene alter a polypeptide structure

-silent mutation -missense mutation -nonsense mutation -frameshift mutation

For each of the following mutations, is it a transition, transversion, addition, or deletion? The original DNA strand is 5ʹ-GGACTAGATAC-3ʹ (Note: Only the coding DNA strand is shown.) A. 5ʹ-GAACTAGATAC-3ʹ B. 5ʹ-GGACTAGAGAC-3ʹ C. 5ʹ-GGACTAGTAC-3ʹ D. 5ʹ-GGAGTAGATAC-3ʹ

A. G->A Transition B. T->G Transversion C. a single-nucleotide deletion D. C->G Transversion

How would each of the following types of mutations affect the amount of functional protein that is expressed from a gene? A. Nonsense B. Missense C. Up promoter mutation D. Mutation that affects splicing

A. It would probably inhibit protein function, particularly if it was not near the end pf the coding sequence. B. It may or may not affect protein function, depending on the nature of the amino acid substitution and whether the substitution is in a critical region of the protein C.It would increase the amount of functional protein D. It may affect protein function if the alteration in splicing changes an exon in the mRNA that results in a protein with a perturbed structure.

Trinucleotide repeat expansions (TNREs) are associated with several different human inherited diseases. Certain types of TNREs produce a long stretch of glutamines (an amino acid) within the encoded protein. This long stretch of glutamines somehow inhibits the function of the protein, thereby causing a disorder. When a TNRE exerts its detrimental effect by producing a glutamine stretch, are the following statements true or false? A. The TNRE is within the coding sequence of the gene. B. The TNRE prevents RNA polymerase from transcribing the gene properly. C. The trinucleotide sequence is CAG. D. The trinucleotide sequence is CCG.

A. True B. False; the TNRE is not within the promoter, it is within the coding sequence. C. True; CAG is a codon for glutamine. D. False; CCG is a codon for proline.