BIO Chapter 19 Learnsmart

Which processes are involved in homologous recombination according to the Holliday model?

- A junction is formed between invading DNA and existing DNA of the chromatid -A nick occurs at identical sites in one strand of each of the two homologous chromatids -Branch migration occurs as the junction between DNA of different helices moves laterally -single strands invade the opposite helix -heteroduplex regions form when homologous regions are not identical

Examples of mutagens

-5-bromouracil -nitrogen mustard -nitrous acid -2-aminopurine

Features consistent with the double-strand break model of recombination

-Formation of two Holliday junctions -Strand degradation following double-strand breaks -The use of DNA gap repair synthesis to restore regions removed by strand degradation -formation of a displacement (D) loop

Trinucleotide repeat expansion disorders

-Fragile X syndrome -Myotonic muscular dystrophy -Huntington disease

What things can cause double-strand breaks (DSB)

-Gamma rays -X-rays -ROS

Which recombination processes occur in bacterial cells?

-Homologous recombination of replicated regions during DNA replication -Exchange of segments between identical copies of bacterial chromosome within the same cell

Double strand breaks are typically repaired by

-Homologous recombination repair -Nonhomologous end joining

In base excision repair (BER) in e coli, DNA polymerase does what?

-Removes a segment containing abnormal DNA -Replaces the abnormal region with normal nucleotides

Mutations in the 5' UTR or 3' UTR of an mRNA molecule are most likely to affect what?

-Stability of mRNA -mRNA ability to be translated

Which things are used by cells to limit the harmful effects of ROS?

-Vitamin C -Catalase -Superoxide dismutase

Associated with ionizing energy

-high energy -short wavelength -gamma rays

Qualities of nonionizing radiation

-includes UV light -contains low energy -does not penetrate deep

Forms of tautomers

-keto -imino -amino -enol

Gene conversion occurs by the action of

-mismatch repair -DNA gap repair synthesis

The following are involved in crossing over

1. Breakage of non-sister chromatids at analogous regions 2. Exchange of corresponding chromosome segments 3. Alignment of a pair of homologous chromosomes

Steps of Base Excision Repair (BER)

1. N-glycosylase recognizes an abnormal base and cleaves the bond between the base and the sugar 2. AP endonuclease recognizes the missing base and cleaves the DNA backbone 3. DNA polymerase removes the damaged DNA and replaces it with normal DNA 4. DNA ligase makes a covalent connection in the DNA backbone

True statements about promoter mutations

1. Up promoter mutations cause the promoter sequence to be more like the consensus sequence 2. Down promoter mutations decrease the affinity of transcription factors to the promoter

What are the steps of the nucleotide excision repair (NER) system?

1. UvrA/UvrB complex tracks along the DNA in search of damaged DNA 2. UvrA is released and UvrC binds 3. UvrC makes cuts on both sides of the thymine dimer 4. UvrD removes the damaged region 5. UvrB and UvrC are released 6. DNA polymerase fills the gap and DNA ligase seals the region

Steps of homologous recombination

1.DSB is processed at the break site 2. Strand exchange 3. DNA synthesis 4. Resolution and ligation

Base analogs

2-aminopurine 5-bromouracil

The amino form is a common stable form of which bases?

A and C

An intergenic suppressor mutation may involve

A change in the expression of one gene that compensates for the loss-of-function mutation in another gene

Function of MutL in mismatch repair

Acts as a linker that helps loop DNA

The rare imino form of cytosine pairs with the common form of

Adenine

Which enzyme can remove methyl or ethyl groups from guanines that have been subjected to mutagens such as nitrogen mustard?

Alkyltransferase

Certain compounds have a structure similar to normal DNA bases and so can be incorporated into daughter strands during DNA replication. These compounds are called base ____

Analogues

In a neutral mutation, a negatively charged amino acid is substituted for

Another negatively-charged amino acid

Some trinucleotide repeat disorders get progressively more severe in future generations. This phenomenon is called

Anticipation

The Lederbergs' replica-plating experiment demonstrated that

Bacteria mutate randomly prior to exposure to viruses

Which changes can cause a frameshift mutation?

Base addition or deletion

Heteroduplex regions are created by the process of ____ ___, which occurs as a Holliday junction migrates

Branch migration

Nucleotide excision repair (NER) is the main system used in the repair of ______

Bulky, helix distorting lesions

The Ames test assays whether a chemical agent does what?

Causes mutations

Human diseases caused by mutations in genes involved in nucleotide excision repair

Cockayne syndrome and Xeroderma pigmentosum

Homologous recombination that produces a new combination of alleles occurs through

Crossover between homologous chromosomes during meiosis

In recombination, what is the process that synthesizes small stretches of DNA to replace those removed by strand degradation?

DNA gap repair synthesis

Function of MutS in mismatch repair

Detects the mismatch

Function of exonuclease in mismatch repair

Digests nonmethylated strand

Photoreactivation is a repair mechanism that can ____ a thymine dimer in the _____ of light

Directly split; presence

The breakage of chromosomes is referred to as a ___ ___ break

Double stranded

Which model recombination includes the formation of a D loop and the resolution of two Holliday junctions?

Double-strand break model

In the resolution phase of recombination, what kind of chromosomes will be produced?

Either recombinant or non-recombinant chromosomes will be produced, depending on which DNA strands are involved in the cutting and rejoining

How does ionizing radiation cause mutations

Forms free radicals that can introduce breaks into DNA molecule

A situation in which one allele is changed to the allele found on the homologous chromosome is called

Gene conversion

The number of mutant genes divided by the total number of genes within a population

Gene frequency

The mutation rate is commonly expressed at the number of new mutations in a given ____

Gene per cell generation

Cells that give rise to the gametes, such as eggs and sperm are ____ ____ cells

Germ line

Of the four bases normally found in DNA ____ is most vulnerable to oxidation

Guanine

Small sequence differences between homologous chromosomes may cause a recombinant chromosome to have a region with base mismatches, known as a

Heteroduplex

Which model for recombination involves the production of single-stranded breaks in each of the non-sister chromatids after which the strands invade the opposite helices

Holliday model

The process by which chromosomes exchange similar or identical DNA segments during meiosis

Homologous recombination

Areas within a single gene that are more likely to mutate than other regions are called

Hot spots

For a tautomeric shift to cause a mutation it must occur

Immediately prior to DNA replication

Acridine dyes induce mutations by

Inserting themselves between adjacent bases and distorting DNA structure

The restoration of protein function by a second mutation in a different gene is known as

Intergenic suppressor

Suppressor mutations that occur within the same gene as the first are called ____ suppressors

Intragenic

Function of MutH in mismatch repair

Makes a cut in nonmethylated strand

Alkylating agents covalently attach ___ or ___ groups to DNA bases, and thus disrupt their normal base pairing properties

Methyl or ethyl

The term ____ refers to an inherited change in the sequence of the genetic material.

Mutation

The probability that a gene will be altered by a new mutation is referred to as the

Mutation rate

Bacterial strains that lack one or more DNA repair systems have a very high mutation rate. These are called ____ strains

Mutator

A _____ mutation is a missense mutation that has no detectable effect on protein function

Neutral

Changes to DNA structure caused by ROS are called

Oxidative DNA damage

An imbalance between the production of reactive oxygen species and an organism's ability to break them down is known as

Oxidative stress

Which enzyme recognizes thymine dimers and corrects them?

Photolyase

The ______ _____ hypothesis states that the resistance of bacteria to T1 adaption should arise as a result of exposure to T1 phage but not before

Physiological adaption

The change of one base for another is described as a base ___ mutation

Point

The expression of an intact gene may be altered when it is moved to a new location. This is due to a

Position effect

This is when a gene's expression is changed due to its new location near regulatory sequences

Position effect

In addition to the DNA strands of the chromosomes involved in homologous recombination, the multiple steps in the pathway require the action of

Protein catalysts

A _____ mutation is one that converts a mutant allele back to the wild-type form

Reversion

Function of MutU in mismatch repair

Separates strands at the cleavage site

A main advantage of nonhomologous end joining is that it does not require a ___ ____ and it can take place throughout the cell cycle

Sister chromatid

Homologous recombination that does not produce a new combination of alleles is called ____ _____ exchange

Sister chromatid

A second mutation that occurs at a different site from the first mutation, and which returns the mutant back to the wild-type phenotype, is a(n) _____ mutation.

Suppressor

A tautomeric shift is a

Temporary change in base structure

In bacteria, the strand that is repaired in the mismatch repair system is

The nonmethylated strand

The synthesis of DNA over a template strand that harbors some type of DNA damage is called

Translesion synthesis

The oxidized form of guanine, 8-oxoguanine, can produce a ____ mutation

Transversion

The base cytosine is deaminated to produce the base

Uracil

The mutagen nitrous acid changes cytosine to _____ and adenine to ____

Uracil; hypoxanthine

A breakpoint refers to the region where

Where two chromosome pieces break and rejoin with other chromosome pieces

The covalent bond between deoxyribose and a purine base is rather unstable and can undergo a spontaneous reaction with water. The breaking of the bond releases the base and leaves an ____ site in the DNA

apurinic

Replica plating is a technique in which

bacterial colonies are transferred from one plate to another with a sterile piece of velvet cloth

Nitrous acid is a mutagen that acts via the process of

deamination

What is responsible for silent mutations

degeneracy of the genetic code

A trinucleotide repeat expansion commonly occurs via the formation of a

hairpin that interferes with DNA replication

The Ames test uses a strain of bacterium S. typhimurium that is unable to produce the amino acid

histidine

The protein alkyltransferase can only be used once because it

is inactivated by a methyl group

Translesion DNA polymerases are ____ accurate and ____ sensitive to geometric distortions than replicative DNA polymerases

less;less

An individual that has somatic regions with different genotypes is known as a genetic ____

mosaic

Alkylating agents include nitrogen ____ and ethyl _____

mustard; methanesulfonate

Breakage and rejoining of DNA strands to produce separate chromosomes at the end of recombination is called

resolution

A mutation that does not change the amino acid

silent mutation

The phenomenon in which a repeated sequence of three nucleotide bases increases in number generation after generation is called

trinucleotide repeat expansion