BIOL 190: Chapter 13

What is the purpose of the Ames test?

Evaluation of the ability of a substance to cause mutation

The effects of ________mutagens on DNA structure is varied. Some can alkylate bases, others act as base analogues, and a few can insert between bases in the double helix and cause additions or deletions.

chemical

Mutagens can cause mutations by

chemically altering DNA nucleotides and disrupting DNA replication

A mutation may affect the amino acid sequence of a polypeptide only if it occurs within the

coding sequence of a structural gene.

Organisms possess different types of DNA repair systems. In a type called________ repair, an enzyme recognizes and removes an alkyl group, thus restoring the base to its original structure

direct

Induced mutations are caused by:

environmental agents.

Mutations that occur in noncoding sequences may affect gene .

expression

Consider the following four types of point mutations. Match each to its effect on the polypeptide sequence. silent mutation missense mutation nonsense mutation frameshift mutation

silent mutation- no effect missense mutation- one amino acid is changed to another nonsense mutation- an amino acid codon is changed to a stop codon frameshift mutation- the amino acid sequence is changed downstream of the mutation

Place the following types of mutations in order from the least effect on polypeptide sequence at the top to the most dramatic effect on polypeptide sequence at the bottom.

silent, missense, nonsense

Where must a mutation occur if it is to directly affect an amino acid sequence?

the coding region of a structural gene

Nonionizing radiation, such as ultraviolet light, can lead to:

the formation of a thymine dimer.

Somatic mutations are not transmitted to an individual's offspring because:

they do not occur in the gametes.

A site where two adjacent thymine bases become covalently cross-linked to one another is called a(n)

thymine dimer

This figure shows a DNA molecule that contains a(n)__________ , which is caused by ultraviolet light.

thymine dimer

Match the location of a mutation with its potential effect on gene expression. Promoter Splice junctions Translational regulatory element Intergenic region

- a possible increase or decrease in the rate of transcription - possible change in the ability of pre-mRNA to be properly produced - possible change in the ability of protein to be produced from mRNA - not as likely to have an effect on gene expression

Match each protein involved in nucleotide excision repair in E. coli with its function. UvrC UvrD DNA polymerase DNA ligase UvrA/UvrB complex

- cuts DNA on both sides of the damaged site - removed the damaged region - synthesizes new DNA to fill in the gap - seals newly synthesized DNA to the original strand- identifies a damaged site

Arrange the events that occur in nucleotide excision repair in E. coli in the correct order. Start with the earliest step on top.

- the UvrA-UvrB complex identifies a damaged site - UvrC makes cuts on both sides of the damaged site - UvrD binds and removed the damaged region - DNA polymerase synthesizes new DNA to fill the gap - DNA ligase seals the newly synthesized DNA to the original strand

Which of the following are ways that point mutations may alter a gene?

-A base pair is removed from a gene. -The base sequence within the gene is changed. -A nucleotide is added to a gene

What is a point mutation? What are the different types of point mutation? Give an example.

-A point mutation affects only a single base pair within the DNA -A base substitution involves a change where one base is replaced by another -Ex: T (in top strand) was replaced by G, and corresponding A (in bottom strand) was replaced with C -A single base pair can be added or deleted and cause a point mutation -Ex: A single base pair (A-T) has been added to the sequence

How can a point mutation within a coding region be classified?

-A point mutation within the coding region may be classified as a silent mutation, missense mutation, nonsense mutation, or frameshift mutation based on the impact on the polypeptide

How do living organisms repair DNA? List them.

-All living organisms require the ability to repair damage to DNA in order to minimize mutation -Cells contain several systems that detect and repair damage 1. Direct Repair: A repair enzyme recognizes and incorrect structure in the DNA and directly restores the correct structure 2. Base excision and nucleotide excision repair: An abnormal base or nucleotide is recognized and a portion of the strand containing the abnormality is removed. The complementary DNA strand is then used as a template for synthesizing a normal DNA strand. 3. Mismatch repair: Similar to excision repair, except that the DNA defect is base pair mismatch in the DNA, not an abnormal nucleotide. The mismatch is recognized, and a strand of DNA in this region is removed. The complementary strand is used to synthesize a normal strand of DNA

How do chemical mutagens alter DNA structure?

-Chemical mutagens can covalently modify the structure of nucleotides, act as base analogs, or cause distortion of the double helix

How do induced mutations occur?What are some common causes?

-Induced mutations are caused by environmental agents, called mutagens, that alter the structure of DNA -Mutagens can be classified as chemical or physical 1. Chemical agents: Chemical substances such as benzoapyrene, a chemical found in cigarette smoke, may cause changes in the structure of DNA 2. Physical agents: Physical agents such as UV light and X-rays can damage DNA

What is ionizing radiation? What can it do to DNA?

-Ionizing radiation (ex: X-rays) has high energy and penetrates deeply to create free radicals -Can cause deletions or breaks in one or both DNA strands

What is nonionizing radiation? What can it do to DNA?

-Nonionizing radiation (ex: UV light) has less energy and can only penetrate the surface -UV rays can cause thymine dimers to form; if not repaired, these dimers can cause gaps or incorporation of incorrect bases

What is the Nucleotide excision repair (NER)? What does it do? What does this process look like? List the steps.

-Nucleotide excision repair (NER) is the most common DNA repair system; it is found in all eukaryotes and prokaryotes -The region encompassing several nucleotides in the damaged strand is removed -The intact strand is used as a template for resynthesis of a normal complementary strand 1. The UvrA-UvrB complex tracks along the DNA in search of damaged DNA 2. After damage is detected, here a thymine dimer, the UvrAs are released, and UvrC binds to UvrB 3.UvrC makes cuts on both sides of the thymine dimer 4. UvrC is released, UvrD, a helicase, binds to UvrB and UvrB is released. UvrD removes the damaged region. UvrD is released. 5. DNA polymerase fills in the gap, and DNA ligase seals the new strand to the original strand

What can physical agents like x-rays and UV light do to DNA?

-Physical agents such as X-rays and UV light can damage DNA structure

How do spontaneous mutations occur? What are some common causes?

-Spontaneous mutations result from abnormalities in biological processes (ex: mistake during DNA replication) 1. Errors in DNA replication: An unpaired mistake by DNA polymerase may cause a point mutation 2. Toxic metabolic products: The products of normal metabolic processes may be reactive chemicals that alter the structure of DNA 3. Changes in nucleotide sequences: On rare occasions, the linkage between purines and deoxyribose can spontaneously break. Changes in base structure (isomerization) may cause mispairing during DNA replication 4. Transposons: DNA transposons are small segments of DNA that can insert at various sites in the genome. If they insert into a gene, they may inactivate the gene

What is the Ames test?

-The Ames test investigates whether a substance is a mutagen -The Ames test uses Salmonella typhimurium that cannot synthesize histidine due to a point mutation -The Ames test monitors the rate at which a second mutation (that restores capacity for histidine synthesis) occurs

How did of Joshua and Esther Lederberg use replica plating to show that mutations are random events? What did they conclude?

-The experiments of Joshua and Esther Lederberg addressed questions about the cause of mutations -They documented the presence of E. coli cells that were resistant to T1 bacteriophage (a virus that infects bacteria) -Data indicated that the mutations happened before exposure to the virus, consistent with these mutations occurring randomly -In addition to spontaneous mutations that occur at a background rate, various chemical and physical agents can induce mutations

What determines a mutation's severity and heritability?

-The time and location of a mutation determines its severity and heritability -Early in development versus adult cell -Germ-line cell versus somatic cell

Which of the following statements regarding nucleotide excision repair (NER) are true?

-The undamaged strand is used as a template to synthesize a normal strand. -a region of several nucleotides in the damaged strand is removed from the sequence.

What is a mutation? Why do we have mutations? Are new mutations harmful or beneficial? How do DNA repair systems fix mutations? What is an example of a mutation?

-is a heritable change in the genetic material -Mutations are essential to the continuity of life; they are the source of variation for natural selection -New mutations are more likely to be harmful than beneficial -DNA repair systems reverse most DNA damage before a permanent mutation can occur (Cancer is a disease caused by gene mutations; cigarette smoke contains chemicals that mutate DNA and may lead to lung cancer)

Consider a germ-line mutation that occurs in a sperm which fertilizes a normal egg to produce a zygote. In the individual that results from this zygote, ________% of the cells will contain the mutation, and ________% of the gametes produced by that individual will carry the mutation.

100, 50

The original sequence of a DNA molecule is 5'-AACCGGTT-3'. Match each mutated sequence with the correct description of the change that occurred. 5'-AACCCGTT-3' 5'-AACCCGGTT-3' 5'-AACGGTT-3'

5'-AACCCGTT-3'- base substitution 5'-AACCCGGTT-3'- single base addition 5'-AACGGTT-3'- single base deletion

Consider the following wild-type DNA sequence: 5'-CCAAGGTT-3'. Which of the following mutations is a base substitution?

5'-CCCAGGTT-3'

silent mutation

A mutation that changes a single nucleotide, but does not change the amino acid created.

What is a thymine dimer?

A site where two adjacent thymine bases become covalently cross-linked to each other

Which of the following are ways that chemical mutagens covalently modify the structure of nucleotides?

Alkylation of bases Deamination of bases

Which of the following organisms have the ability to repair DNA and thus minimize mutations? Multiple choice question.

All living things

How do the effects of germ-line mutations in a parent progress over the lifetime of an offspring receiving that mutation? Multiple choice question.

All of the cells of the individual's body, but only half of the gametes produced by that individual will carry the mutation.

The test, which was developed in the 1970s, to evaluate the ability of a substance to cause mutations is called the_____test

Ames

Which of the following are ways that ionizing radiation can alter DNA structure?

Base deletion Breaks in one or both DNA strands

How do point mutations affect DNA sequences?

By substituting one base for another By adding or subtracting a single base pair

In the Ames test, you expose S. typhimurium cells that cannot synthesize histidine to compound X, then plate them on a medium lacking histidine. The next day you observe a higher number of colonies on this plate versus the control plate, which has bacteria with no exposure. What reasonable conclusion can you draw?

Compound X is a mutagen.

A spontaneous point mutation may be caused during DNA replication when the enzyme___________ puts the wrong base in a newly-synthesized strand.

DNA polymerase

An alkylated base is recognized by an enzyme. The enzyme removes the alkyl group and restores the normal base structure. What type of DNA repair is this? Multiple choice question.

Direct repair

Which of the following exhibit nucleotide excision repair (NER)?

Humans Bacteria Plants Mice

Which of the following are chemical mutagens? Multiple select question.

Nitrous acid Benzo[a]pyrene Nitrogen mustard Ethyl methanesulfonate

Mutations outside a gene's coding sequence can affect gene expression. Which of the following sites, when mutated, would affect transcription?

Operator site Promoter

What is the process in which bacterial colonies are transferred from a master plate to secondary plates in the same configuration using a transferring agent such as a sterile velvet cloth?

Replica plating

The effects of what type of mutation are shown here?

Somatic cell mutation

In nucleotide excision repair, what serves as the template for synthesis of new DNA to replace the damaged strand?

The complementary strand of DNA

How do somatic mutations affect an individual's offspring?

The mutation does not occur in germ line cells and therefore does not affect offspring.

A compound is subjected to the Ames test to evaluate its ability to cause mutation. If the substance is a mutagen, what results are expected?

There will be more bacterial colonies on the plate exposed to the mutagen than on the control plate.

______ are small segments of DNA that can insert at various sites in the genome. If they insert into a gene, they may cause a spontaneous mutation.

Transposons

Which of the following are physical mutagens?

UV light X-rays

A mutation is best defined as:

a heritable change in the genetic material.

In NER, the function of UrvA, UrvB, UrvC, and UvrD is to

a)detect an irregularity in DNA structure b)remove a segment of the DNA strand containing the irregularity

Match each type of mutation to the image that shows its effects on polypeptide sequence. The original sequence of the DNA is 5'-ATGGCCGGCCCGAAAGAGACC-3'.

a. no mutation: A b. silent: B c. missense: C d. nonsense: D e. frameshift: E

Mutations can be categorized as

as spontaneous or induced

nonsense mutation

changes a normal codon to a stop codon and shortens the polypeptide

missense mutation

changes on amino acid in the polypeptide

Nitrous acid, nitrogen mustard, 5-bromouracil, and benzo(a)pyrene are examples of______mutagens

chemical

True or false: Nonsense and frameshift mutations generally result in less dramatic changes to a polypeptide sequence than missense mutations.

false

Mutations are essential for the long-term continuity of life because they supply the _______variation that is the foundation for evolutionary change.

genetic

This figure depicts a(n) _________- ___________mutation.

germ-line

Only mutations in ______ can be passed from parents to offspring

germ-line cells

What do germ-line cells and somatic cells give rise to?

germ-line cells give rise to gametes (sperm and egg cells) and somatic cells are all other body cells

Mutations can be divided into two main types. Spontaneous mutations result from abnormalities in biological processes, while_______ mutations are caused by environmental agents that enter the cell and alter the structure of DNA.

induced

A spontaneous mutation

is caused by an abnormality in a biological process

Mutations in noncoding sequences:

may affect gene expression.

A mutation changes an alanine codon into a valine codon. This is an example of a

missense mutation

A heritable change in genetic material is known as a(n)

mutation

frameshift mutation

mutation that shifts the "reading" frame of the genetic message by inserting or deleting a nucleotide. produces a different amino acid sequence

Mutations within______can affect gene expression. What are some common mutations within this that can affect gene expression?

noncoding sequences -Promoter: May increase or decrease transcription -Transcriptional regulatory element/operator site: May alter the regulation of transcription -Splice sites: May alter the ability of pre-mRNA to be properly spliced -Translational regulatory element: May alter the ability of mRNA to be translationally regulated -Intergenic region: Not as likely to affect gene expression

A key difference between germ-line and somatic mutations is that

only germ-line mutations can be passed to offspring

X-rays and ultraviolet light are examples of Blank______ mutagens.

physical

Nucleotide excision repair (NER) is found in:

prokaryotes and eukaryotes.

Bacterial colonies can be transferred from a master plate to secondary plates in the same configuration using a transferring agent such as a sterile velvet cloth. This technique is known as ____________

replica plating

New mutations are much more likely to be harmful than beneficial to the individual.

true

True or false: All living things possess mechanisms allowing them to minimize mutation. True false question.

true

The mutation shown in this figure is most likely the result of exposure to

ultraviolet light.