Genetics Ch. 18 HW

Select the examples of gain‑of‑function mutations.

D.a mutant gene expressed at a different time E.a mutant gene product with a new function -because, gain-of-function is a dominant charactereristics

Classify each definition or example as a somatic mutation, gametic (germ line) mutation, or both.

Somatic Mutation: -The mutation affects only the individual in which the mutation occurs and is not passed to the progeny. -A particular tobacco leaf becomes discolored due to a mutation halfway through the life of the plant. Gametic Mutation: -A man receives a pelvic X-ray. Nine months later, his child is born with a chromosomal abnormality. -The mutation arises in the gametes of the individual and is transmitted to the progeny. Both: -Mutation can be caused by an alteration in the DNA sequence. Explanation: Mutations are caused by an alteration in the DNA sequence. If these mutations pass on to the progeny, then they are termed as gametic mutation and if they don't pass on to next generation, rather die with the current generation, then they are termed as somatic mutation.

What is the defining characteristic of retrotransposons?

The answer is D (A retrotransposon is transposed through an RNA intermediate.)

Place each step of retrotransposition in the order in which it occurs.

-First step -retrotransposon is transcribed into RNA -sequence is reverse transcribed into double‑stranded DNA -integrase cuts the target DNA leaving 5′5′ overhangs -retrotransposon integrates into the host DNA -replication completes the sequence, adding flanking direct repeats -Last step

Select which examples are induced mutations.

-Nitrous acid causes the deamination of cytosine to uracil. -Ionizing radiation causes chromosomal fragmentation. Reason: Chemical mutagens and ionizing radiation /UV exposure causes induced mutations.

What is the Ames test?

-a test to screen for mutagenic chemicals a test to determine the mutagenic activity of chemicals by observing whether they cause mutations in sample bacteria.

Which mutagens incorporate into DNA and frequently pair with the wrong base?

Base analogs Reason : Base analogs have a very similar structure to one of the four nitrogenous bases which are used in DNA (adenine, guanine, cytosine or thymine). Base analog mutagens mimic bases to such an extent that they can be incorporated into DNA in place of one of the normal bases. This leads to an increase in the rate of mutation. To be mutagenic, a base analog must mispair frequently than the normal base it replaced.

Which of the sequences listed are possible flanking sequences that could be generated by a transposon insertion after the first six base pairs of the target sequence GATCCTGGCATA?

Flanking Seq are regions before and after transcribed region. At least one of the flanking sequences you selected is not correct. When a transposon recognizes a target sequence, the target sequence is cut to generate overhanging single strand ends. After the transposon inserts between this cut region, DNA polymerase fills in the single‑stranded regions and thus duplicates the original target sequence. Consider that because the insertion occurs in double‑stranded DNA, there is also a complementary strand.No other changes typically occur to the sequence during this process. ANSWERS: -CTAGGT -GATCCA

-After using a chemical mutagen to generate mutations in a DNA sequence, scientists noted a mutation from C to T at the 10th position within the coding region of a gene. This mutation led to a change of proline into serine at the fourth position in the resulting peptide.

Induced--> chemical mutagen used Missense-->. ccu->ucu b/c after it is same nucleotides for normal and mutant transition and point mutation c->t -A DNA mutation is a permanent change in a nucleotide sequence in the genome. Point mutations, also known as base substitutions, describe single nucleotide changes in a DNA sequence. There are two types of point mutations, transitions and transversions. Transitions occur when a purine nucleotide is changed to another purine, or when a pyrimidine is changed to another pyrimidine. Thus, in the example, the CC to TT in the 10th position (10C>T)(10C>T) mutation is a transition mutation because thymine and cytosine are both pyrimidines. Unlike transition mutations, transversions occur when a purine is changed to a pyrimidine, or a pyrimidine is changed to a purine. A point mutation in a protein‑coding DNA sequence results in a change in the mRNA sequence transcribed from that particular gene. A change in the mRNA codon sequence can then result in a change in the sequence of the protein or peptide which is translated from that particular mRNA. Missense mutations occur when a mutation changes the amino acid that a particular codon specifies. In the example, the 10C>T10C>T DNA mutation changes the fourth mRNA codon from CCUCCU to UCU.UCU. At the peptide level, this mutation led to the replacement of the proline residue with a serine residue in the 4th position (P4S or Pro4Ser). Whereas missense mutations result in changes in the peptide sequence, nonsense mutations are point mutations that results in a premature stop codon replacing the original amino acid. Induced mutations occur as a result of exposure to chemical mutagens or radiation. In this example, a chemical mutagen was used to induce mutations in a DNA sequence. Mutations can also occur spontaneously, which means that they arise naturally in organisms in the absence of mutagens. For example, a mutation that occurs during DNA replication that is not repaired can be considered a spontaneous mutation.

Match each term to a definition.

Loss-of-Function Mutation: A mutation that results in reduced or absent protein function. Conditional Mutation: A mutation that is only expressed in a certain situation. Intragenic Mutation: A mutation within the same gene that masks another mutation. Gain-of-Function Mutation: A mutation that results in a new or additional protein function. Intergenic Mutation: A mutation in a separate gene that masks another mutation.

The Ames test determines the frequency with which a chemical causes mutations in DNA. The results of the Ames test for the substances X, Y, and Z are provided. Label the carcinogenic potential of each of these substances based on the production of his+ revertants in the presence or absence of liver extract (± LE).

The Ames test is used to identify chemicals that can mutate DNA upon contact with the human body. Since accumulation of mutations can cause cancer, such chemicals are called mutagens or carcinogens. The Ames test determines the FREQUENCY with which a substance can induce mutations. One of the ways that the Ames test detects mutations is by measuring the rate at which the his− strains of the Salmonella bacterium are converted to his+ revertants. The his− strains carry mutations in the histidine operon that prevent histidine synthesis. So, his− cells cannot grow on plates without histidine. However, mutagens can mutate the histidine operon and reverse the his− mutations to produce his+ revertants. The his+ revertants synthesize histidine and therefore can grow in the absence of histidine. In this study, substances X, Y, and Z are mixed with his− strains and added to plates without histidine. Each substance is tested for its mutagenic potential in the presence and absence of liver extract (LE) from rats. LE is used in the Ames test to mimic the metabolic processes of mammalian livers, which may break down a non‑mutagenic substance into a potentially mutagenic form. Thus, addition of LE helps to determine if a chemical is potentially carcinogenic to humans if ingested and metabolized by the liver. For substance X, no his+ revertants are seen in the absence of LE. This suggests that substance X is not mutagenic in its natural form. But, substance X produces revertants in the presence of LE, suggesting that liver enzymes can convert substance X into a mutagenic form. So, substance X is likely carcinogenic upon ingestion. For substance Y, no his+ revertants are seen in the presence or absence of LE. This suggests that substance Y could be mutagenic, but not at rates detectable by the Ames test. So, substance Y is likely noncarcinogenic even upon ingestion. For substance Z, his+ revertants are observed in the absence of LE. This suggests that substance Z is mutagenic in its natural form and may be carcinogenic by inhalation or touching. However, no revertants are seen in the presence of LE, which is a rare instance. This suggests that substance Z is metabolized into a non‑mutagenic form by LE. So, substance Z may become noncarcinogenic when ingested. In this case, you cannot determine if substance Z will be carcinogenic. The Ames test is substantiated with further studies in rodent models that help to determine if substances are carcinogenic by inhalation, touch, or ingestion.

An insertion sequence contains a large deletion in its transposase gene. Under what circumstances would this insertion sequence be able to transpose?

There is another transposable element of the same type present in the cell and it expresses a functional transposase element

What generally causes thymine dimers to form in a strand of DNA, and why are thymine dimers a problem?

UV light can causes thymidine dimer potentially creating a mutation which lead to cancer. Explanation - Thymidine dimer are polymerized thymine bases. Thymidine dimer are formed by UV light exposure it leads to disorganization of bonds between two nucleotide. It is harmful and leads to cancer .

What is a nonreplicative (conservative) transposon? -a DNA sequence that moves throughout the genome by excision and insertion -a reversed transcribed DNA sequence with many inactive copies in the genome -a DNA sequence, less than 500 base pairs long, that is reverse transcribed into the genome -identical DNA sequences that repeat many times and are part of a transposable element

a DNA sequence that moves throughout the genome by excision and insertion -Transposons, also called transposable elements, are one of several types of DNA sequences that can move throughout the genome. Transposons can either remain fixed in number during transposition or replicate in order to transpose. Transposons that remain fixed in number are called nonreplicative, or conservative, transposons because they do not replicate during transposition. Nonreplicative transposons excise themselves and insert the excised region into a new position in the genome. Some other types of transposons, called retrotransposons, use reverse transcription through an RNA intermediate in order to insert into the genome. Short interspersed nuclear elements, SINEs, are a type of retrotransposon. SINEs are typically quite short, at about 500 base pairs or less. A SINE does not encode its own reverse transcriptase and is reliant upon other mobile elements for transposition. The most common SINEs in primates are the Alu sequences, that comprise about 11% of the human genome. Research suggests that SINEs played a role in novel evolution of some genes and can contribute to certain genetic diseases and cancer. Long interspersed nuclear elements (LINEs) are also a type of retrotransposon. Inactive LINEs are typically closer to 900 base pairs in length, whereas active LINEs are typically closer to 6,000 base pairs long. Approximately 20% of the human genome is composed of LINEs, most of which are inactive. Active LINEs have been associated with neurological disorders, such as schizophrenia, and other diseases, such as carcinoma. Long terminal repeats, LTRs, are highly repetitive DNA sequences found at the ends of some retrotransposons. A typical LTR contains repeated sequences that are identical and number in the hundreds or thousands. Viruses, such as the HIV virus, contain LTRs that function as promoters, enhancers, and for transcriptional control.

Which mutation is most likely to have a severe impact on the phenotype of an organism if it occurs within the first several bases of a gene coding region?

a frameshift mutation of one nucleotide -A frameshift mutation of one nucleotide likely to have a severe impact on the phenotype of an organism. Because frameshift mutation of one nucleotide cause change in more than one amino acids in a protein sequence. Frameshift mutation is a mutation in which addition or deletion of base pairs in a DNA resulting in the translation of the genetic code in an unnatural reading frame. A frameshift mutation of three nucleotides only change one amino acid in a protein sequence. Missense mutation and silent mutation is a point mutation that only affects one amino acid in a protein sequence.

What is an insertion sequence (IS) element?

a transposon between 700bp700bp and 2500 bp2500 bp long encoding only transposon activity proteins -An insertion sequence (IS) element is a small DNA sequence that is a basic type of transposable element. IS elements typically range in size from about 700 bp700 bp to 2500 bp.2500 bp. Whereas many other transposons encode additional nonessential proteins, an IS only encodes a transposase protein and a regulatory protein. Transposase is an enzyme that catalyzes the movement of the transposon, and the regulatory protein can either suppress or activate transposition. Although IS elements are a simple type of transposon, they can form a part of more complex transposons, called composite transposons. Composite transposons possess an IS element at each end that flanks additional genes. The region of DNA that is flanked by these IS elements is also carried along with the IS elements during transposition. The DNA site at which transposon insertion occurs is the target sequence. The general term transposon describes a DNA sequence that can move throughout the genome. One specific type of transposon is a retrotransposon. A retrotransposon moves within the genome by generating an RNA intermediate, rather than DNA. Viral elements are not a type of transposon, however, some viral elements integrate randomly into the host genome.

Retrotransposons are a type of transposable element, or transposon. These segments of DNA can duplicate and insert themselves into new locations in the genome. For example, the Alu sequence is about 300 bases long, and it is the most abundant retrotransposon in primate genomes. In fact, it makes up approximately 15% of the human genome. Choose the description that best explains how the Alu sequence can affect the size of the human genome.

can increase the size of the human genome because it adds 300 bases to the genome each time it is duplicated.

Which is not a characteristic of transposable elements? 1. only found in plants 2. short flanking direct repeats present on both side of a transposon 3. can take place through a DNA intermediate in some cases 4. able to insert at many different locations throughout a genome 5. staggered breaks made in the target DNA during insertion

only found in plants -They are also found in prokaryotes,and also yeast.