Gene Mutation, Transposition, and DNA Repair
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What would be the consequences of having no variation from changes in DNA sequences?
No adaptation to environmental changes, no phenotypic variability, and no evolution.
What allows geneticists to identify and study the genes responsible for the modified traits observed?
What are the seven different ways that mutations can be classified?
- Mutations can be classified by:
- 1. Their origin.
- 2. The type of cell in which they originate.
- 3. The circumstances under which they are expressed.
- 4. Their effect on gene function, in the sense of the effect on the protein produced.
- 5. Their effect on gene function, in the sense of the effect on the phenotype.
- 6. The type of molecular change in the DNA.
- 7. The effect they have on translation.
What are the types of mutations that are classified by their origin?
- Spontaneous- A mutation that is not induced by a mutagenic agent.
- Induced- An inducible enzyme system is an enzyme system under the control of an inducer, a regulatory molecule that acts to block a repressor and allow transcription.
What are the types of mutations that are classified by the type of cell in which they originate?
- Somatic- A nonheritale mutation occurring in a somatic cell.
- Germ-line- Mutations that occur in the gametes.
What are the types of mutations that are classified by the circumstances under which they are expressed?
- Conditional- A mutation that is expressed only under a certain condition; that is, a wild-type phenotype is expressed under certain (permissive) conditions and a mutant phenotype under other (restrictive) conditions.
What are the types of mutations that are classified by their effect on gene function, in the sense of the effet on the protein produced?
- Loss-of-function (knockout, null)- Mutations that produce alleles with reduced or no function.
- Hypomorphic (leaky)-
- Gain-of-function (extopic expression)- A mutation that produces a phenotype different from that of the normal allele and from any loss of function alleles.
What are the types of mutations that are classified by their effect on gene function, in the sense of the effect on the phenotype?
- Nutritional Mutant- A mutation that results in a loss of ability to synthesize an amino acid or vitamin.
- Behavioral Mutant- A mutation that effects the behavior of the organism.
- Regulatory Mutant- A mutation in a regulatory gene or a gene control region that can disrupt normal regulatory processes and inapporopriately activate or inactivate expression of a gene.
- Lethal- A mutation that interrupts a process that is essential to the survival of the organism.
What are the types of mutations that are classified by the type of molecular change in the DNA?
- Base Substitution (point mutation)- A single base change in a DNA molecule that produces a mutation.
- Transition- A type of base substitution in which a purine is substitued for a purine, or a pyrimidine for a pyrimidine.
- Transversion- A type of base substitution in which a purine is substituted for a pyrimidine or vice versa.
- Insertion- A mutation in which an extra base pair is inserted into the sequence.
- Deletion- A mutation in which a nucleotide is deleted from the sequence.
What are the types of mutations that are classified aby the effect they have on translation?
- Missense- A mutation that alters a codon to that of another amino acid and thus results in an alteration in the transation product.
- Silent- A mutation that alters a codon but does not result in a change in the amino acid at that position in the protein.
- Nonsense- A mutation that creates a nonsense codon that would result in a stop codon that would not make sense in the reading of the sequence.
- Frameshift- A mutational event leading to the insertion of one or more base pairs in a gene, shifting the codon reading frame in all codons that follow the mutational site.
What are tautomers and what consequences can they have on reading DNA?
Tautomers are alternate chemical forms that differ by only a single proton shift in the molecule of a purine or pyrimidine; they can increase the chance of mispairing during DNA replication.
How are insertions and deletions believed to occur?
These mutations can occur when one strand of the DNA template loops out and becomes displaced during replication, or when DNA polymerase slips or stutters during replication.
In what regions of DNA is replication slippage more common?
In regions containing repeated sequences and can contribute to hereditary diseases such as Fragile X syndrome and Huntington disease.
What causes tautomers to increase the chances of mispairing in DNA?
The shift of the proton change the bonding structure of the molecule, allowing hydrogen bonding with noncomplementary bases.
What are the most common causes of spontaneous mutations?
- Depurination- The loss of one of the nitrogenous bases in an intact double-helical DNA molecule.
- Deamination- An amino group in cytosine or adenine is converted to a keto-group in which a cytosine is converted to uracil and adenine is changed to hypoxanthine.
What are transposons?
Transposable genetic elements are DNA elements that can move within, or between geneomes.
What are mutagens?
Any agent that causes an increase in the spontaneous rate of mutation.
What are base analogs?
Compounds that can substitute for purines or pyrimidines during nucleic acid biosynthesis. They are similar to normal bases and can be incorporated into DNA, but can't be used for replication.
What are alkylating agents?
Agents that donate an alkyl group, such as CH3 or CH3CH2, to amino or keto groups in nucleotides. Ethylmethane sulfonate (EMS), AZT, and mustard gas.
What are acridine dyes and what do they cause?
They are chemical mutagens that cause frameshift mutations.
At what wavelength do purines and pyrimidines absorb UV radiation most intensely?
What is a major effect of UV radiation on DNA?
The creation of pyrimidine dimers which are chemical species consisting of two identical pyrimidines- particularly ones consisting of two thymine residues. The dimers distort the DNA conformation and inhibit normal replication.
What is the process of producing free radicals (chemical species containing one or more unpaired electrons) and what do they cause?
As x-rays penetrate cells, electrons are ejected from the atoms of molecules encountered by radiation. Free radicals can directly or indirectly affect the genetic material, altering purines and pyrimidines in DNA and resulting in point mutations.
What is ionizing radiation and what are its capabilities?
Radiation energetic enough to produce ions and other high-energy particles, is capable of breaking phosphodiester bonds, dirupting the integrity of chromosomes, and producing a variety of chromosomal aberations, such as deletions, translocations, and chromosomal fragmentation.
When do the most common types of mutations arise and how often does it occur?
Arise during DNA replication when an incorrect nucleotide is inserted by DNA polymerase. Enzymes make an error approximately once every 100,000 insertions, leading to an error rate of 10-5.
What enzyme proofreads the DNA and what percentage does it catch the errors?
DNA polymerase catches 99% of errors. If an incorrect nucleotide is inserted during polymerization, the enzyme can recognize the error and "reverse" its direction. It then behaves as a 3' to 5' exonuclease, cutting out the incorrect nucleotide and replacing it with the correct one.
What is the system that follows up after proofreading?
Mismatch repair in which the mismatches are detected, the incorrect nucleotide is removed, and the correct nucleotide is inserted in its place. It is a form of excision repair of DNA in which the repair mechanism is able to distinguish between the strand with the error and the strand that is correct.
Which nucleotide will base‑pair with the enol form of 5‑bromouracil?
What event could result in a frameshift mutation?
What enzyme is seen in bacteria that recognizes the sequence 5'-GATC-3', 3'-CTAG-5'?
Adenine methylase recognizes the sequence as a substrate and adds a methyl groupd to each of the adenine residues during DNA replication.
What is a thymine dimer?
In a polynucleotide strand, a lesion consisting of two adjacent tymine bases that become joined by a covalent bond. Usually caused by exposure to ultraviolet light, this lesion inhibits DNA replication.
What is an R factor (R plasmid)?
A bacterial plasmid that carries antibiotic resistance genes. Most R plasmids have two components: an r-determinant, which carries the antibiotic resistance genes, and the resistance transfer factor (RTF).
What is reverse genetics?
An experimental approach used to discover the function of a gene, after the gene has been identified, cloned, and sequenced. The cloned gene may be knocked out or have its expression altered and the resulting phenotype studied. An approach contrasted with forward genetics.
What is photoreactivation repair?
Light-induced repair of damage caused by exposure to ultraviolet light. Associated with an intracellular enzyme system.
What is forward genetics?
The approach used to identify a gene controlling a phenotypic trait in the absence of the gene's location in the genome or its DNA sequence.
What is postreplication repair?
A repair system that responds after damaged DNA has escaped repair and has failed to be completely replicated. Replication skips over lesion in backbone and continues, gap is filled by DNA pol. I then ligase. RecA protein directs a recombinational exchange with the corresponding region on the undamage parental strand.
What is SOS repair system?
A last resort effort to save the DNA. DNA synthesis becomes error-prone, inserting random and possibly incorrect nucleotides in places that owould normally stall DNA replication. Itself can become mutagenic.
What is photoreactivation repair?
UV-induced damage to DNA can be partially reversed if, following irradiation, the cells are exposed briefly to light in the blue range of the visible spectrum and is dependent upon PRE. The enzyme's mode of action is to cleave the bonds between thymine dimers, thus directly reversing the effect of UV radiation.
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