chapter 14 mutation and DNA repair

nonsense mutation^^^^

A mutation that creates a stop codon, terminating translation. - Polypeptides that are truncated are nearly always nonfunctional. -They are also unstable and are quickly destroyed. Eukaryotic cells have mechanisms to destroy mRNA molecules that contain premature stop codons. - change in a single base that results in a stop codon -AKA nonsense mutation

Which of the following enzymes is responsible for initiating the proofreading repair mechanism? DNA ligase DNA polymerase AP endonuclease DNA uracil glycosylase None of the answer options is correct.

DNA polymerase

A silent mutation is a mutation that only occurs in noncoding regions of DNA. true false

false

Any deviation in normal gene dosage is lethal. true false

false

DNA polymerase is responsible for the process called mismatch repair. true false

false

In base excision repair, a whole segment of DNA is removed and resynthesized. true false

false

Mutations will always decrease the activity of a gene. true false

false

People with xeroderma pigmentosum (XP) are sensitive to ultraviolet light because they lack the DNA proofreading function. true false

false

Spontaneous mutations that occur in somatic cells will be transmitted to offspring. true false

false

The use of antibiotics creates mutations in bacteria that make the bacteria resistant to these antibiotics. true false

false

Which of the following mutations would most likely have the most severe consequence? silent missense addition of a codon frameshift

frameshift

corn maze example

genetic changes that affect pigment formation can be observed directly in the kernels. The normal color of maize kernels is purple. Each kernel consists of many cells, and if no mutations affecting pigmentation occur in a kernel, it will be uniformly purple. The kernel pigments are synthesized by several different enzymes in a metabolic pathway, and any of these enzymes can be rendered nonfunctional by mutations in their genes, including the insertion of transposable elements. Since McClintock's work, we have learned that most transposable elements are segments of DNA a thousand or more base pairs long. When such a large piece of DNA inserts into a gene, it can interfere with transcription, cause errors in RNA processing, or disrupt the open reading frame. The result in the case of maize is that the cell is unable to produce pigment, and so the kernels will be yellow. -Among mutants affecting kernel pigmentation, McClintock observed certain mutants that resulted in kernels that were mostly yellow but speckled with purple. She suspected that these particular mutants might result from a transposable element jumping into and out of a gene. -McClintock realized that, just as the inability of the kernel cells to produce pigment was caused by a transposable element jumping into a gene, restoration of that ability could be caused by the transposable element jumping out again what causes sectoring in corn kernels experiement? BACKGROUND In the late 1940s, Barbara McClintock discovered what are now called transposable elements, DNA sequences that can move from one position to any other in the genome. She studied corn (Zea mays). Wild-type corn has purple kernels, resulting from expression of purple anthocyanin pigment (Fig. 14.11a). A mutant with yellow kernels results from lack of purple anthocyanin pigment. McClintock noticed that streaks of purple pigmentation could be seen in many yellow kernels (Fig. 14.11b). This observation indicated that the mutation causing yellow color was unstable and that the gene could revert to the normal purple color. HYPOTHESIS McClintock hypothesized that the yellow mutant color resulted from a transposable element, which she called Dissociator (Ds), jumping into a site near or in the anthocyanin gene and disrupting its function. She attributed the purple streaks to cell lineages in which the transposable element had jumped out again, restoring the anthocyanin gene. EXPERIMENT AND RESULTS By a series of genetic crosses, McClintock showed that the genetic instability of Ds was due to something on another chromosome that she called Activator (Ac). She set up crosses in which she could track the Ac-bearing chromosome. She observed that in the presence of Ac, cells in mutant yellow kernels reverted to normal purple, resulting in purple sectors in an otherwise yellow kernel. From this observation, she inferred that the Ds element had jumped out of the anthocyanin gene, restoring its function. She also demonstrated that restoration of the original purple color was associated with mutations elsewhere in the genome. From this observation, she inferred that the Ds element had integrated elsewhere in the genome, where it disrupted the function of another gene. CONCLUSION McClintock's conclusion is illustrated in Fig. 14.11c: Transposable elements can be excised from their original position in the genome and inserted into another position.

Which of the following would you expect to have the lowest rate of point mutations per replication? DNA viruses bacteria fruit flies RNA viruses humans

humans

Chronic myelogenous leukemia (CML) is caused when a segment of chromosome 9 and a segment of chromosome 22 both break off and switch places. How is this mutation classified? transposition deletion duplication reciprocal translocation inversion

reciprocal translocation

hotspots

sites in the genome that are especially mutable

most common mutation is the

substitution of one nucleotide pair for a different nucleotide pair. But are rare

transposition

the movement of transposable elements - it occurs by different mechanisms according to the type of transponson. -Removal of the transposon from its original position and repair of the cleavage leads to restoration of gene function. -Not all transposons undergo transposition by a cut-and-paste mechanism - retrotransposons undergo transposition by an RNA intermediate, and when these types of transposable elements move, the retrotransposon used as a template for transcription stays behind in its original location

DNA damage that affects the backbone and bases

- mutations can be induced by radiation or chemicals. -mutagen: An agent that increases the probability of mutation.he presence of a mutagen can increase the probability of mutation by a factor of 100 or more. - Some types of damage affect the structure of the DNA double helix. These include breaks in the sugar-phosphate backbone, one of the main mutagenic effects of X-rays. Breaks can occur in just one strand of the DNA or both. Ultraviolet light can cause cross-links between adjacent pyrimidine bases, especially thymine, resulting in the formation of thymine dimers. Covalent bonding between adjacent thymines in a DNA strand causes the double helix to become pinched, both the major groove and the minor groove become wider, and the T-A base pairing is weakened. - another type of structural damage is loss of a base from one of the deoxyribose sugars, resulting in a gap in one strand where no base is present. Spontaneous loss of a purine base is one of the most common types of DNA damage, occurring at the rate of about 13,000 purines lost per human cell per day. Most of these mutations result from the interaction between DNA and normal metabolic by-products. The rate increases with age, and it can also be increased by exposure to oxidizing agents such as household bleach or hydrogen peroxide. -Other types of damage affect the bases themselves. Bases that are chemically damaged tend to mispair. Some bases are damaged spontaneously when reaction with a water molecule replaces an amino group (-NH2) with an atom of oxygen (=O), which interferes with the base's ability to form hydrogen bonds with a complement. Some naturally occurring molecules mimic bases and can be incorporated into DNA and cause nucleotide substitutions. Caffeine mimics a purine base, for example (although to be mutagenic, the amount of caffeine required is far more than any normal person could possibly consume). -Chemicals that are highly reactive tend to be mutagenic, often because they add bulky side groups to the bases that hinder proper base pairing ^^^^ -x rays cause single stranded break in DNA backbone - missing bases can be caused by oxidtion agents. - bulking side groups can be caused by smoking

chromosomal mutations ^^^^

-Double-stranded breaks in DNA that are incorrectly repaired can lead to chromosomal mutations. The breaks may result from interactions between DNA and reactive molecules produced in metabolism or from reactive chemicals in the environment or by radiation (especially X-rays). - Chromosomal mutations can also arise from errors in DNA replication, particularly in sequences that are tandemly repeated along the DNA -Chromosomal mutations can delete or duplicate regions of a chromosome containing several or many genes, and the resulting change in gene copy number also changes the amount of the products of these genes in the cell. Chromosomal mutations can also alter the linear order of genes along a chromosome or interchange the arms of nonhomologous chromosomes - While these types of chromosomal mutations do not change gene copy number, they do affect chromosome pairing and segregation in meiosis. These effects distinguish chromosome abnormalities from nucleotide substitutions, small-scale deletions and duplications, transpositions, and other submicroscopic mutations. ^^^^ - mutations can be due to deletion or duplication - the extent of whether the mutation is has an effect or not depends on where it happens (in a non coding or coding region) - inversion: where the gene sequence has been flipped. This could be an issue in miosis particually in the matching up part (lineing up) - translocation- when a piece of a chromosome from another chromosome switch.

Small duplications play an important role in the origin of new genes in the course of evolution

-In most cases, when a gene is duplicated, one of the copies is free to change without causing harm to the organism because the other copy continues to carry out the normal function of the gene. -Occasionally, a mutation in the "extra" copy of the gene may result in a beneficial effect on survival or reproduction, and gradually a new gene is formed from the duplicate. These new genes usually have a function similar to that of the original gene.

small insertation/ deletion (another type of mutation) ^^^^^

-In noncoding DNA, such mutations have little or no effect. In protein-coding regions, their effects depend on their size - A small deletion or insertion that is an exact multiple of three nucleotides results in a polypeptide with as many fewer (in the case of a deletion) or more (in the case of an insertion) amino acids as there are codons deleted or inserted. Thus, a deletion of three nucleotides eliminates one amino acid, and an insertion of six adds two amino acids. -Small deletions or insertions that are not exact multiples of 3 can cause major changes in amino acid sequence because they do not insert or delete entire codons -Similarly, an insertion of a single nucleotide causes a one-nucleotide shift in the reading frame of the mRNA, and it changes all codons following the site of insertion. For this reason, such mutations are called frameshift mutations.When this mRNA is translated, the one-nucleotide shift in the reading frame results in an amino acid sequence that has no resemblance to the original protein. All amino acids downstream of the site of insertion are changed, resulting in loss of protein function. example: - The effects of a deletion of three nucleotides can be seen in cystic fibrosis. -The mutations responsible for cystic fibrosis are in the gene encoding the cystic fibrosis transmembrane conductance regulator -Malfunction of CFTR causes ion imbalances that result in abnormal secretions from the many cell types in which the CFTR gene is expressed. ^^^^^ - insertions or deletions can change the reading frame: - a reading frame of the mRNA contains the code to produce the correct protein, the phase of the groups of 3 bases in the mRNA determines the identity of the codons, this is the reading frame - DNA contains the sequence of bases that will be transcribed to mRNA which is translated to protein. So, the frame can be determined from the DNA sequence. - example: if given two strands and there is not an indication of which strand is the coding strand there will be six reading frames. three for each strand!!! - Start codon: AUG will be ATG when looking at DNA. When looking at a coding DNA sequence replace the T with a U!! - remeber that you start replicating at the 3' end and go to the 5' end. but they must be antiparallel so you would start writting the sequence with 5' and end 3' - the coding strand (non template)(5'-3') is the strand that will ressemble mRNA but the T will be replaced with a U. The templant strand (3'-5') is the strand that is used to figure out the corresponding bases. The coding strand is what is produced from the template strand.

Note that, while humans have the smallest rate of mutation per nucleotide per replication

-humans also have the largest rate of mutation per genome per generation -the number of newly arising mutations from the father increases with age.

correction of DNA damage ^^^^

-the simplest is the repair of breaks in the sugar-phosphate backbone, which are sealed by DNA ligase, an enzyme that can repair the break by using the energy in ATP to join the 3′ hydroxyl of one end to the 5′ phosphate of the other end. -One type of ligase seals single-stranded breaks in DNA, and a different type seals double-stranded breaks. Double-stranded breaks often result in chromosomal rearrangements because they are less likely to be repaired than single-stranded breaks. In addition to their importance in DNA replication and repair, ligases are an important tool in research in molecular biology because they allow DNA molecules from different sources to be joined to produce recombinant DNA ^^^^^^ - DNA ligase takes care of the breaks in the DNA backbone - requires a 5'PO and 3'OH group in order to make a phostiered bond in order to repair that break. -About 99% of the mispaired bases are corrected immediately by the proofreading function of DNA polymerase, in which the mispaired nucleotide is removed immediately after incorporation and replaced by the correct nucleotide. ^^^^^^ - proofreading is the function of the DNA polymerase. - when an incorrect nucleotide is placed the polymerase has a 3' to 5' editing function. it kind of takes a step back. (replication happens 5' to 3') -postreplication mismatch repair The correction of a mismatched base in a DNA strand by cleaving one of the strand backbones, degrading the sequence with the mismatch, and resynthesizing from the intact DNA strand. ^^^^ - MutS (enzyme) recognizes the mismatched bases - MutL identifies the strand that is carrying the incorrect base - MutH breaks the backbone to so that another enzyme that comes in next (exonuclease) can remove successive nucleotides, including the mismatched base. - DNA polymerase then fills in the gap and a ligase joins the backbone. - base excision repair: corrects abnormal or damaged bases In the first step of base excision repair, an abnormal or damaged base is cleaved from the sugar in the DNA backbone. Then, the baseless sugar is removed from the backbone, leaving a gap of one nucleotide. Finally, a repair polymerase inserts the correct nucleotide into the gap. ^^^^ - an enzyme (glycosylate) specifically comes and removes the base while leaving the backbone intact. - the gap that has been created is then repaired by other enzymes - nuceotide excision repair: mechanism used to repair short streched of DNA contaiining mismatched or damaged bases. -has a similar mechanism of action to mismatch repair but uses different enzymes -Instead of degrading a DNA strand nucleotide by nucleotide until the mismatch is removed, nucleotide excision repair removes an entire damaged section of a strand at once. Nucleotide excision repair is also used to remove nucleotides with bulky side groups, as well as thymine dimers resulting from ultraviolet light. -The importance of excision repair is illustrated by the disease xeroderma pigmentosum (XP), in which nucleotide excision repair is defective. People with XP are exquisitely sensitive to the UV radiation in sunlight. Because of the defect in nucleotide excision repair, damage to DNA resulting from UV light is not corrected, leading to the accumulation of mutations in skin cells. The result is high rates of skin cancer. People with XP must minimize their exposure to sunlight and in extreme cases stay out of the sun altogether. ^^^^^ -more than one base has been damaged (for example: a bulky group could be added) - an enzyme cleaves the DNA backbone at sites flanking the damage. - the damage is then removed - then the gap is repaired. ^^^^ TAQ question: mutations in mismatch repair genes will allow damaged DNA to be replicated. This is a post DNA replication process.

the most common chromosomal mutation

-those in which a segment of the chromosome is either present in two copies or is missing altogether - DUPLICATION: A region of a chromosome that is present twice instead of once.Although large duplications that include hundreds or thousands of genes are usually harmful and quickly eliminated from the population, small duplications including only one or a few genes can be maintained over many generations. Usually, duplication of a region of the genome is less harmful than deletion of the same region. DELETION: a region of the chromosome is missing. -A deletion can result from an error in replication or from the joining of breaks in a chromosome that occur on either side of the deleted region. Even though a deletion may eliminate a gene that is essential for survival, the deletion can persist in the population because chromosomes usually occur in homologous pairs. If one member of a homologous pair has a deletion of an essential gene but the gene is present in the other member of the pair, that one copy of the gene is often sufficient for survival and reproduction. In these cases, the deletion can be transmitted from generation to generation and persist harmlessly, as long as the chromosome is present along with a normal chromosome. -some deletions decrease the chance of survival or reproduction of an organism even when the homologous chromosome is normal. In general, the larger the deletion, the smaller the chance of survival. -It is usually not the total number of copies of each gene that matters, but rather the number of copies of each gene relative to other genes. -It is worth emphasizing that one rarely observes deletions or duplications that include the centromere. -The reason is that an abnormal chromosome without a centromere, or one with two centromeres, is usually lost within a few cell divisions because it cannot be directed properly into the daughter cells during cell division.

how mutations arise

1. mutations occur without regard to the needs of an organism. According to this hypothesis, the presence of the antibiotic in the experiment with bacterial cells does not direct or induce antibiotic resistance in the cells, but instead allows the small number of preexisting antibiotic-resistant mutants to flourish. 2. suggests that there is some sort of feedback between the needs of an organism and the process of mutation, and the environment directs specific mutations that are beneficial to the organism.

In the sickle-cell anemia mutation, the 5′-GAG-3′ codon for glutamic acid becomes the 5′-GUG-3′ codon for valine. Assuming a single nucleotide substitution accounts for this mutation, what is the change in the DNA? 3′-CTC-5′/5′-GAG-3′ to 3′-CAC-5′/5′-GTG-3′ 3′-CTC-5′/5′-GAG-3′ to 5′-CAC-3′/3′-GTG-5′ 5′-CTC-3′/3′-GAG-5′ to 5′-CAC-3′/3′-GTG-5′ 5′-CTC-3′/3′-GAG-5′ to 3′-CAC-5′/5′-GTG-3′

5′/5′-GTG-3′

transposable elements aka transposons

A DNA sequence that can replicate and move from one location to another in a DNA molecule - the genomes of virtually all organisms contain several types of transposable element, each present in multiple copies per genome.

Do mutations occur randomly, or are they directed by the environment?

BACKGROUND Researchers have long observed that beneficial mutations tend to persist in environments where they are useful—in the presence of antibiotic, bacterial populations become antibiotic resistant; in the presence of insecticides, insect populations become insecticide resistant. HYPOTHESIS These observations lead to two hypotheses about how a mutation, such as one that confers antibiotic resistance on bacteria, might arise. The first suggests that mutations occur randomly in bacterial populations and over time become more common in the population in the presence of antibiotic (which destroys those bacteria without the mutation). In other words, they occur randomly with respect to the needs of an organism. The second hypothesis suggests that the environment, in this case the application of antibiotic, induces or directs antibiotic resistance. METHOD To distinguish between these two hypotheses, Joshua and Esther Lederberg developed replica plating. In this technique, bacteria are grown on agar plates, where they form colonies (Fig. 14.5a). The cells in any one colony result from the division of a single original cell, and thus they constitute a group of cells that are genetically identical except for rare mutations that occur in the course of growth and division. Then a disk of sterilized velvet is pressed onto the plate. Cells from each colony stick to the velvet disk (in mirror image, but the relative positions of the colonies are preserved). The disk is then pressed onto the surface of a fresh plate, transferring to the new plate a few cells that originate from each colony on the first agar plate, in their initial positions. EXPERIMENT First, the Lederbergs grew bacterial colonies on medium without antibiotic, called a nonselective medium because all cells are able to grow and form colonies on it. Then, by replica plating, they transferred some cells from each colony to a plate containing antibiotic, so only antibiotic-resistant cells could multiply and form colonies. (Medium containing antibiotic is a selective medium because it "selects" for a particular attribute or element, in this case antibiotic-resistant cells.) Because replica plating preserves the arrangement of the colonies, the location of an antibiotic-resistant colony on the selective medium reveals the location of its parental colony on the nonselective plate (Fig. 14.5b). Finally, the Lederbergs were able to go back to the parental colony and demonstrate that it was a pure culture of antibiotic-resistant bacteria by plating cultures of this colony on selective medium (Fig. 14.5c). CONCLUSION The Lederbergs' replica-plating experiments demonstrated that antibiotic-resistant mutants can arise in the absence of antibiotic because at no time in the experiments did the cells on nonselective medium come into contact with the antibiotic. Only the successive generations of daughter cells carried over to selective medium by replica plating were exposed to the antibiotic. Nevertheless, by their procedure the Lederbergs were able to isolate pure colonies of antibiotic-resistant cells.

molecular clock

Estimates of the time when different taxa diverged, based on the amount of genetic divergence between them.

mutation for antibiotic resistance example:

If an antibiotic is added to a liquid culture of bacterial cells that are growing and dividing, most of the cells are killed, but a few survivors continue to grow and divide. These survivors are found to contain mutations that confer resistance to the antibiotic. -

What is the difference between mismatch repair and nucleotide excision repair? In mismatch repair, several nucleotides are replaced, whereas in nucleotide excision repair the sugar phosphate backbone is fixed. In mismatch repair, one nucleotide is replaced, whereas in nucleotide excision repair several nucleotides are replaced. In mismatch repair, several nucleotides are replaced, whereas in nucleotide excision repair it is just one. In mismatch repair, the sugar phosphate backbone is fixed, whereas in nucleotide excision repair, several nucleotides are replaced.

In mismatch repair, one nucleotide is replaced, whereas in nucleotide excision repair several nucleotides are replaced.

The fact that humans have a relatively large number of mutations per genome per generation when compared to other organisms can be explained by which of the following statements? Human cells don't divide as often as those of other organisms. Most of these mutations happen after reproduction, so they wouldn't be selected against. Most of a human's DNA is noncoding, so most of the mutations are neutral. Humans have multiple proteins doing the same job, and our cells don't divide as often as other those of other organisms. Humans are so complex we have multiple proteins doing the same job.

Most of a human's DNA is noncoding, so most of the mutations are neutral.

If mutations occur at random with respect to an organism's needs, how does a species become more adapted to its environment over time?

Mutant genes that are harmful or neutral are much less likely to persist in a population than ones that result in increased survival and reproduction because the latter mutations would lead to greater fitness.

RNA viruses and retroviruses have a relatively high rate of mutation because

RNA is a less stable molecule than DNA, but more importantly because the replication of these genomes lacks a proofreading function

The coding sequences of genes that specify proteins with the same function in related species sometimes differ from each other by an insertion or deletion of contiguous nucleotides. The number of nucleotides that are inserted or deleted is almost always an exact multiple of 3. Why is this expected?

The number of nucleotides that are inserted or deleted is almost always an exact multiple of 3 because each codon in the genetic code consists of three nucleotides. Any insertion or deletion that includes a number of nucleotides that is not an exact multiple of 3 shifts the reading frame, and the resulting sequencing will most likely code for a nonfunctional protein.

Which of the following statements concerning cancer and mutations is correct? Cancer can only occur with a mutation in a somatic cell. Cancer can only occur with a mutation in a germ cell. Usually multiple mutations are required in different genes to cause cancer. Usually a single mutation is all that is required to cause cancer. None of the answer options is correct.

Usually multiple mutations are required in different genes to cause cancer.

reciprocal translocation^^^^

^^^occurs when two different chromosomes undergo an exchange of parts. - In the formation of a reciprocal translocation, both chromosomes are broken and the terminal segments are exchanged before the breaks are repaired. In large genomes, the breaks are likely to occur in noncoding DNA, so the breaks themselves do not usually disrupt gene function. -Since reciprocal translocations change only the arrangement of genes and not their number, most reciprocal translocations do not affect the survival of organisms. -Problems can arise in meiosis because both chromosomes involved in the reciprocal translocation may not move together into the same daughter cells, resulting in gametes with only one part of the reciprocal translocation. This inequality does upset gene dosage, because these gametes have extra copies of genes in one of the chromosomes and are missing copies of genes in the other.

point mutation ^^^

a change in a single nucleotide. -The effect of a point mutation depends in part on where in the genome it occurs. In many multicellular eukaryotes, including humans, the vast majority of DNA in the genome does not code for protein or RNA -Most of the sequences in noncoding DNA have no known function, which may explain why many mutations in noncoding DNA have no detectable effects on the organism. -On the other hand, mutations in coding sequences do have predictable consequences in an organism. ^^^ can be silent, missesnse, or nonsense - change in a single base - do not change the reading frame unlike inserts/deletions.

^^^^^ what is a mutation

a change in the DNA sequence of an organism that can be passed onto daughter cells via cell division. These changes are often spontaneous. - must be permanent - will be replicated

most cancers result from the. example of p53 implication in cancer

accumulation of mutations in a single cell lineage of somatic cells, but the number of mutations, their sequence, and the genes involved differ from one type of cancer to the next -In most individuals with cancer, all the sequential mutations that cause the cancer are spontaneous mutations that take place in somatic cells. They are not transmitted through the germ line, and so there is little or no increased risk of cancer in the offspring -An example is the p53 gene, the nonmutant product of which detects DNA damage and slows the cell cycle to allow time for DNA repair - Mutations in p53 are one step in the mutational progression of many different types of cancer, including colon cancer and breast cancer. - In some families, however, there is a germ-line mutation in one of the genes implicated in cancer that is transmitted from parents to their children. In any child who inherits the mutation, all cells in the body contain the defective gene, and hence the cells already have taken one of the mutational steps that lead to cancer. The effect of such a germ-line mutation is therefore to reduce the number of additional mutations that would otherwise be necessary to produce cancer cells.

A transposable element can insert into any position in the genome except: regions near the telomere. regions near the centromere. regions near sequences coding for ribosomal RNA. inside another transposon. All of these choices are correct.

all

The procedure of replica plating demonstrated that mutations are random with respect to: point mutations or deletions. whether A or G is replaced with T or C the needs of the organism. All of these choices are correct.

all

magine that a researcher is studying a mouse that carries a mutation in Pax7 —a gene that is involved in muscle development. To his surprise, these Pax7 mutant mice appear relatively normal. What is a possible explanation for this? Other members of the Pax gene family have redundant functions in muscle development (and can compensate for the Pax7 mutation). The normal copy of Pax7 on the corresponding homologous chromosome is sufficient for mouse survival. These Pax7 mutant mice may have a synonymous mutation. All of these choices are correct.

all

A person has a mutation in the gene for DNA uracil glycosylase. What is the most likely result of this mutation? an increase in mutations the inability to produce mRNA that has uracil in it the inability to produce mRNA that has cytosine in it Nothing will happen. This enzyme is only involved in silent mutations. None of the other answer options is correct.

an increase in mutations

Replica plating showed that mutations for antibiotic resistance are not induced by the presence of the antibiotic because: antibiotic-sensitive cells are unable to form colonies in the presence of the antibiotic. antibiotic-resistant cells are able to form colonies in the absence of the antibiotic. antibiotic-resistant cells occur in colonies that never experienced the antibiotic. antibiotic-resistant cells are able to form colonies in the presence of the antibiotic.

antibiotic-resistant cells occur in colonies that never experienced the antibiotic.

The rates of evolutionary change in DNA: are constant among different gene families and thus are used to estimate the time of divergence. can only be determined in conserved genes. are constant in gene families with a diversity of members. are zero. are highly variable among different gene families.

are highly variable among different gene families.

Why do RNA viruses and retroviruses have such a high rate of mutation? because RNA polymerase is an unstable enzyme because RNA viruses and retroviruses initially cause host-cell mutations during replication because RNA is more fragile than DNA and therefore more likely to be damaged because viral polymerases lack a proofreading mechanism The third and fourth answers are true.

because viral polymerases lack a proofreading mechanism

DNA repair: always prevents errors. can fix chromosomal inversions and translocations. can involve excision of bases flanking a distortion in the helix. is only active during DNA replication. involves a set of proteins that are always active.

can involve excision of bases flanking a distortion in the helix

nonsynonymours mutations^^^^

change the amino acid sequence -the change in even a single amino acid can affect the three-dimensional structure of a protein, and therefore change its ability to function. - change in the second base of the nucelotide results a change of the amino acid - AKA missense mutation

A nonsense mutation: changes a codon for an amino acid into a codon for chain termination. changes the identity of one amino acid in a polypeptide chain. is usually due to a nucleotide substitution in the third position of a codon. shifts the reading frame of a messenger RNA.

changes a codon for an amino acid into a codon for chain termination.

How do most cancers arise? Question 1 choices Choice A., from a single mutations arising simultaneously in a cluster of cells Choice B., from a series of mutations that arise in the descendants of a single somatic cell Choice C., from multiple mutations arising simultaneously in a single cell Choice D., from mutations arising in a single cell that are then transmitted to other cells in the body

choice b

How do mutations arise? Question 2 choices Choice A., Mutations in cancer cells arise because they need to divide faster. Choice B., Mutations arise in a specific sequence where a mutation in one gene directly leads to a mutation in a specific second gene. Choice C., Mutations arise randomly and independent of other mutations in the cell. Choice D., Mutations arise simultaneously, where whole sets of mutations occur in a single event.

choice c

inversion

chromosomes in which the normal order of a block of genes is reversed. - typically produced when the region between two breaks in a chromosome is flipped in orientation before the breaks are repaired. Especially in large genomes, the breaks are likely to occur in noncoding DNA rather than within a gene. Whereas large inversions can cause problems in meiosis, small inversions are common in many populations and play an important role in chromosome evolution. - The accumulation of inversions over evolutionary time explains in part why the order of genes along a chromosome can differ even among closely related species.

synonymous mutation^^^

do not change the amino acid sequence of the resulting protein - wobble nucleotide - AKA silent mutation

A researcher has carried out Giesma staining on a set of human chromosomes, and has arranged these chromosomes into a karyotype. He notices that in a homologous pair, a band is missing from one of the chromosomes. This likely resulted from: a deletion. a duplication. an inversion. a reciprocal translocation. either a deletion or a reciprocal translocation.

either a deletion or a reciprocal translocation.

Mutations result from

may be caused by reactive molecules produced in the normal course of metabolism, by chemicals in the environment, or by radiation of various types, including X-rays and ultraviolet light. Most genomes also contain DNA sequences that can "jump" from one position to another in the genome, and their insertion into or near genes is a source of mutation. Yet another source of mutation is incorrectly repaired chromosome breaks caused by reactive chemicals or radiation. - most are spontaeneous (occuring by chance in the absence of any assignable cause), they occur randomly - mutations occur in greater numbers in men than women - mutations depend on the cell type - in humans the rate of mutation per nucleotide per replication is greater in somatic cells than in germ cells. ^^^^ what causes mutations: - errors during DNA replication - DNA segements moving within a genome - Environmental factors: chemical and radiation - Adverse cellular conditions: oxidative stress What are the overall/final effect of mutations? - diseases -genetic variation - evolution - no effect

Which of the following statements about mutations is true? A mutation: may leave the amino acid sequence of a protein unchanged. will result in a different phenotype. will be corrected. will be passed onto offspring. None of the answer options is correct.

may leave the amino acid sequence of a protein unchanged.

Imagine a gene in which the sequence that is transcribed into a GAG codon, which codes for glutamic acid, is mutated to GUG, which codes for valine. What type of mutation is this? missense frameshift silent nonsense base pair deletion

missense

Sickle-cell anemia results from what type of mutation? missense silent nonsense frameshift base pair deletion

missense

somatic mutations ^^^^

mutations in nonreproductive cells. they are not transmitted to future generations - the mutation rate that matters is the rate of mutation per nucleotide per replication. Although somatic mutations are not transmitted to future generations, they are transmitted to daughter cells in mitotic cell divisions. -Hence, a somatic mutation affects not only the cell in which it occurs, but also all the cells that descend from it. exmple: A mutation in a flower-color gene occurs in one cell, and as the cell replicates during development of the flower, all its descendants in the cell lineage—the generations of cells that originate from a single ancestral cell—carry that mutation, producing a sector with altered coloration. -Most cancers result from mutations in somatic cells -In some cases, the mutation increases the activity of a gene that promotes cell growth and division, while in other cases, it decreases the activity of a gene that restrains cell growth and division -To cause cancer, the mutations must occur sequentially in a single cell line ^^^^ somatic cells are any cels that aren't involved in meiosis Colon cancer example: - mutiple mutations needed in key genes (tumor supressors and pro octone for all cancers) - the key point is that mutations originate in one cell and then are being passed to daughter cells but only in that lineage. (so not every cell is affected) - in GERM LINE mutations: - every cell is going to have that mutation - the mutation is orignated in one of the gametes that was used to create a daughter cell. - every cell in the offspring will have that mutation. - a mutation that is inherited.

germ line mutations

mutations that occur in eggs and sperm and the cells. In contrast, germ-line mutations are transmitted to future generations because they occur in reproductive cells. -it is the rate of mutation per genome per generation that matters more. Germ-line mutations are important to the evolutionary process because, as they are passed from one generation of organism to the next, they may eventually come to be present in many individuals descended from the original carrier.

Which of the following statements is true regarding a chromosome deletion? Chromosome deletions do not affect gene dosage. If a deletion eliminates the centromere, the chromosome is still passed on during cell division. Small chromosomal deletions usually have serious and often fatal consequences for an organism. Small chromosomal deletions are easily detected by microscopy. None of the answer options is correct.

none

A point mutation that changes a UAC codon into a UAG codon is: silent mutation. missense mutation. nonsense mutation. frameshift mutation.

nonsense mutation.

duplication and divergence

process of creating new genes from duplicates of old ones -The term divergence refers to the slow accumulation of differences between duplicate copies of a gene that occurs on an evolutionary time scale. Multiple rounds of duplication and divergence can give rise to a group of genes with related functions known as a gene family. -

In the procedure of replica plating, the purpose of the sterilized velvet is: to protect the researchers from coming into contact with the bacteria. to protect the agar plates from bacteria in the air. to transfer bacterial cells from one agar plate to another. to induce new mutations that can grow on the selective plates.

to transfer bacterial cells from one agar plate to another.

A chromosomal segment that breaks off and attaches to another chromosome is what type of mutation? deletion duplication translocation inversion reciprocal translocation

translocation

A chromosomal mutation in which a segment is missing is called a deletion. true false

true

A nucleotide substitution typically has less severe consequences than a nucleotide addition or deletion. true false

true

A point mutation occurs when a single nucleotide gets replaced by a different one. true false

true

Even though the chance of a mutation for one given nucleotide is rare, mutations are rather common when looking at the whole genome. true false

true

Insertion of one nucleotide in a gene will lead to a frameshift mutation. true false

true

Only germline mutations are transmitted to the progeny. true false

true