Lecture 12 Flashcards
What is a temperature-sensitive mutation?
A conditional mutation that produces the mutant phenotype in one (restrictive or non-permissive) temperature range and the wild-type phenotype in another (permissive) temperature range
What is a missense mutation?
A point mutation in which a single nucleotide change results in a codon that codes for a different amino acid
What is a nonsense mutation?
A point mutation in a sequence of DNA that results in a premature stop codon, or a nonsense codon in the transcribed mRNA, and in a truncated, incomplete, and usually nonfunctional protein product
What is a silent mutation?
DNA mutations that do not significantly alter the phenotype of the organism in which they occur. Silent mutations can occur in non-coding regions, or they may occur within exons
What are the four types of base substitution mutations?
Missense, nonsense, silent, and temperature-sensitive mutations
What are the types of small addition/deletion mutations?
Frameshift and in-frame mutations
What is a frameshift mutation?
An addition or deletion of a single or multiple nucleotides (not a multiple of 3) that causes a shift in the codons produced by genetic material
What is an in-frame mutation?
Addition or deletion mutations that result in no change in the codons produced by the genetic material, except for the affect area
What problems can arise from having a mutation in the promoter region of DNA?
1) If the region that binds transcription initiation factors is mutated, the factors (such as TFIIA, TFIID and IFIIB) will not bind and transcription will not take place
2) If the activator region upstream from the promoter region is mutated, the activating factors will not bind and transcription may take place at a slower rate or not at all
3) If the inhibitor region is mutated, the inhibitor factors will not bind and constitutive transcription will occur
What is constitutive transcription?
A gene that is transcribed continually compared to a facultative gene which is only transcribed as needed. Occurs when inhibitors are not present or a mutation disallows the inhibitors from acting during transcription
What is a splicing mutation?
A splice site mutation is a genetic mutation that inserts, deletes or changes a number of nucleotides in the specific site at which splicing of an intron takes place during the processing of precursor messenger RNA into mature messenger RNA. The abolishment of the splicing site results in one or more introns remaining in mature mRNA and may lead to the production of aberrant proteins. For example, mutations that cause the incorrect splicing of β-globin mRNA are responsible of some cases of β-thalassemia
What is genotypic reversion?
A point mutation can be reversed by another point mutation, in which the nucleotide is changed back to its original state (true reversion) or by second-site reversion (a complementary mutation elsewhere that results in regained gene functionality)
What is genotypic suppression?
A suppressor mutation is a second mutation that alleviates or reverts the phenotypic effects of an already existing mutation. Genetic suppression therefore restores the phenotype seen prior to the original background mutation
What is the difference between intragenic and intergenic suppression?
Intragenic occurs on the same gene as in the initial mutation did, while intergenic occurs on a different gene than the initial mutation did
What is polymerase fidelity?
The fidelity of a DNA polymerase is the result of accurate replication of a desired template. Specifically, this involves multiple steps, including the ability to read a template strand, select the appropriate nucleoside triphosphate and insert the correct nucleotide at the 3´ primer terminus, such that Watson-Crick base pairing is maintained. In addition to effective discrimination of correct versus incorrect nucleotide incorporation, some DNA polymerases possess a 3´→5´ exonuclease activity. This activity, known as “proofreading”, is used to excise incorrectly incorporated mononucleotides that are then replaced with the correct nucleotide. High-fidelity PCR utilizes DNA polymerases that couple low misincorporation rates with proofreading activity to give faithful replication of the target DNA of interest.
What is deamination and what is its function?
Deamination is the removal of an amine group from a molecule. Enzymes that catalyse this reaction are called deaminases. In the human body, deamination takes place primarily in the liver, however glutamate is also deaminated in the kidneys. Deamination is the process by which amino acids are broken down if there is an excess of protein intake. The amino group is removed from the amino acid and converted to ammonia.
What is depurination?
Depurination is a chemical reaction of purine deoxyribonucleosides, deoxyadenosine and deoxyguanosine, and ribonucleosides, adenosine or guanosine, in which the β-N-glycosidic bond is hydrolytically cleaved releasing a nucleic base, adenine or guanine, respectively. The second product of depurination of deoxyribonucleosides and ribonucleosides is sugar, 2’-deoxyribose and ribose, respectively. When depurination occurs with DNA, it leads to the formation of apurinic site and results in an alteration of the structure. Depurination is known to play a major role in cancer initiation.
What is Strand-slippage?
Slipped strand mispairing (SSM) is a mutation process which occurs during DNA replication. It involves denaturation and displacement of the DNA strands, resulting in mispairing of the complementary bases.
How do you calculate mutation rate?
Mutation rate (mu) is calculated for rare autosomal dominant traits in human populations as mu = n/2N where N = number of births, and n is the number of affected patients with unaffected parents (2N because there are two alleles)
What is mutagenesis?
Mutagenesis is a process by which the genetic information of an organism is changed in a stable manner, resulting in a (heritable) mutation. It may occur spontaneously in nature, or as a result of exposure to mutagens.
When is a mutation considered to be a polymorphism?
Mutations occurring at a frequency greater than 1% are called polymorphisms
What is mutation rate?
Mutation rate is defined as the number of new mutations per generation
What is the ultimate source for all genetic variability, which is required for evolution?
Mutagenesis
What are examples of macromutations?
Translocations, inversions, large deletion, large insertions, and amplification
What is a chromosomal translocation?
A chromosome abnormality caused by rearrangement of parts between nonhomologous chromosomes. A gene fusion may be created when the translocation joins two otherwise-separated genes, the occurrence of which is common in cancer. Translocations can be balanced (in an even exchange of material with no genetic information extra or missing, and ideally full functionality) or unbalanced (where the exchange of chromosome material is unequal resulting in extra or missing genes).
What is a chromosomal inversion?
An inversion is a chromosome rearrangement in which a segment of a chromosome is reversed end to end. An inversion occurs when a single chromosome undergoes breakage and rearrangement within itself. Inversions are of two types: paracentric and pericentric. Paracentric inversions do not include the centromere and both breaks occur in one arm of the chromosome. Pericentric inversions include the centromere and there is a break point in each arm.
What is gene amplification?
Gene duplication (or chromosomal duplication or gene amplification) is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene. Gene duplications can arise as products of several types of errors in DNA replication and repair machinery as well as through fortuitous capture by selfish genetic elements
Which type of point mutation contribute to genetic disease the most?
Missense (50%, Nonsense 12%, small addition/deletion 25%, & RNA splicing/promoter 10%)
What is the difference between reversion and suppression?
Reversion occurs on the same codon while suppression occurs elsewhere along the gene or on another gene
Most phenotypic reversion are caused by _____
Genetic suppression, not genetic reversion
What are the three major (four total) fidelity checks in DNA replication?
1) Polymerase “Selectivity” - special characteristics of enzyme-template-dNTP complex (“ternary complex”)
2) Polymerase proofreading
3) Post-replication mismatch repair
4) A collection of repair and error-avoidance mechanisms
What are two critical problems associated with mismatch repair?
1) How to recognize newly synthesized DNA strand vs. template strand (“hemi-methylation” used as a transient marker for new strand)
2) How to ensure mismatch is “patched” (cut at unmethylated GATC, and expand gap towards mismatch)
What is the cause of familial non-polypopsis colon cancer?
Patients are defective in mismatch repair genes and suffer from early colorectal and extracolonic cancers
What are three major examples of spontaneous DNA damage?
Deamination, Oxidation, & Depurination
What is the most important DNA lesion produced by oxygen radicals?
8-Oxoguanine because it is the most mutagenic
What is the difference between DNA damage (lesion) and a DNA mutation?
DNA damages and mutation are fundamentally different. Damages are physical abnormalities in the DNA and can be recognized by enzymes, and, thus, they can be correctly repaired if redundant information, such as the undamaged sequence in the complementary DNA strand or in a homologous chromosome, is available for copying. In contrast to DNA damage, a mutation is a change in the base sequence of the DNA. A mutation cannot be recognized by enzymes once the base change is present in both DNA strands, and, thus, a mutation cannot be repaired
What percentage of genetic disorders are due to point mutations?
50%
Can a nucleotide base reversion that results in a different amino acid be considered an equivalent genetic reversion?
Yes. Glutamate –> Aspartate. Both are acidic amino acids with very similar functions and would be considered to be an equivalent genetic reversion
What is an example of somatic mosaicism caused by reversion?
Some patients with Junctional Epidermolysis Bullosa due to a homozygous defect in the LAMB3 gene can nevertheless show healthy skin patches in which LAMB3 has reverted to wild type function by intragenic 2nd site suppressor mutations
When must DNA proofreading be done?
Directly after a DNA polymerase inserts a mismatched base pair. If the proofreading (exonuclease activity) is not done directly after mismatching the base pair, the DNA polymerase will continue adding base pairs along the strand and will no longer be close enough to the affected site in order to fix it
When can strand slippage occur?
Only during DNA replication
Deamination mostly affects which type of base?
Cytosine
Why does 8-oxoguanine mispair with adenine instead of cytosine?
Base pairs are normally always in anti formation. 8-oxoguanine flips into syn formation, allowing only 2 hydrogen bonds to form from 8-oxoguanine (perfect match to adenine; this occurs 80% of the time; other 20% it binds to cytosine)
