Mutations, Repair and Recombination Flashcards
What is an allele?
one of several alternative forms of a gene. In a diploid cell, each gene will typically have two alleles, occupying the corresponding position (locus) on homologous chromosomes
What are AP endonucleases?
an enzyme that is involved in theDNA base excision repair pathway (BER). Its main role in the repair of damaged or mismatched nucleotides inDNAis to create a nick in the phosphodiester backbone of theAPsite created whenDNAglycosylase removes the damaged base
What is an ATM protein?
protein kinase activated by double-strand DNA breaks. If breaks are not repaired, ATM initiates a signal cascade that cumulates in cell cycle arrest
What is base excision repair?
DNA repair pathway in which single faulty bases are removed from the DNA helix and replaced
What is base substitution?
A type of mutation involving replacement orsubstitutionof a single nucleotidebasewith another in DNA or RNA molecule
What is branch migration?
the process by which base pairs on homologousDNAstrands are consecutively exchanged at a Holliday junction, moving thebranchpoint up or down theDNA sequence
What is deamination?
the removal of anaminogroup from amolecule
What is a deletion mutation?
A type ofmutationwherein one or fewnucleotidebase pairs are deleted or lost from achromosomeespecially during thereplicationof genetic material
What is depurination?
The removal, by hydrolysis, of a purine base fromDNA.
What is DNA glycosylase?
An enzyme involved in base excision repair that catalyze the first step of this process. They remove the damaged nitrogenous base while leaving the sugar-phosphate backbone intact, creating an apurinic/apyrimidinic site, commonly referred to as anAP site
What is a duplication mutation?
A particular kind ofmutationinvolving the production of one or more copies of any piece ofDNA, including sometimes ageneor even an entire chromosome
What is a frameshift?
agenetic mutationcaused by indels (insertions or deletions) of a number of nucleotides in a DNA sequence that is not divisible by three
What is gene conversion?
process by which DNA sequence information can be transferred from one DNA helix (which remains unchanged) to another DNA helix whose sequence is altered. It often accompanies general recombination events
What is a germline mutation?
Agenechange in a body’s reproductive cell (egg or sperm) that becomes incorporated into theDNAof every cell in the body of the offspring.Germline mutationsare passed on from parents to offspring
What is a heteroduplex?
a double-stranded (duplex) molecule of nucleic acid originated through thegeneticrecombination of single complementary strands derived from different sources, such as from different homologous chromosomes or even from different organisms
What is a heterozygote advantage?
the case in which theheterozygousgenotype has a higher relative fitness than either the homozygous dominant or homozygous recessive genotype
What is a Holliday junction?
X-shaped structure observed in DNA undergoing recombination, in which the two DNA molecules are held together at the site of crossing-over, also called a cross-strand exchange
What are homologous chromosomes?
the maternal and paternal copies of a particular chromosome in a diploid cell
What is a homozygote?
an individual having two copies of the same allele at a locus
What is an insertion mutation?
A type of mutation characterized by the insertion of one or few nucleotide base pairs to a chromosome
What is an inversion mutation?
A defect in thechromosomein which a segment of thechromosomebreaks off and reinserted in the same place but in thereversedirection relative to the rest of thechromosome
What is a Ku protein?
a dimeric protein complex that binds toDNAdouble-strand breakendsand is required for thenon-homologous end joining(NHEJ) pathway ofDNA repair
What is meiosis I?
the first of two rounds of chromosome segregation following meiotic chromosome duplication; segregated the homologs, each composed of a tightly linked pair of sister chromatids
What is meiosis II?
the second of two rounds of chromosome segregation following meiotic chromosome duplication; segregated the sister chromatids of each homolog
What is a missense mutation?
A form of pointmutationresulting in a codon that codes for a different amino acid, and thus, causes the synthesis of a protein with an altered amino acid sequence during translation
What is mitosis?
the process where a single cell divides resulting in generally two identical cells, each containing the same number of chromosomes andgeneticcontent as that of the original cell
What is a mutagen?
a physical or chemical agent that changes thegeneticmaterial, usuallyDNA, of an organism and thus increases the frequency of mutations above the natural background level
What is a mutation?
heritable change in the nucleotide sequence of a chromosome
What is natural selection?
A process fundamental to evolution as described by Charles Darwin. Bynatural selection, any characteristic of an individual that allows it to survive to produce more offspring will eventually appear in every individual of the species, simply because those members will have more offspring
What is nonhomologous end joining?
a DNA repair mechanism for double-strand breaks in which the broken ends of DNA are brought together and rejoined by DNA ligation, generally with the loss of one or more nucleotides at the site of joining
What is a nonsense mutation?
a pointmutation in a sequence ofDNAthat results in a premature stop codon, or anonsensecodon in the transcribed mRNA, and in a truncated, incomplete, and usually non-functional protein product.
What is nucleotide excision repair?
types of DNA repair that corrects damage of the DNA double helix, such as that caused by chemicals or UV light, by cutting out the damaged region on one template strand and resynthesising it using the undamaged strand as template
What is a point mutation?
agenetic mutationin the form of insertion/deletion (indels) or substitution to a single nucleotide base in a sequence ofDNAor RNA
What is a polymorphism?
describes genome sequences that coexist as two or more sequence variants at high frequency in a population
What is a Rad 51 protein?
eukaryotic protein that catalyses synapsis of DNA strands during genetic recombination
What is a RecA protein?
Prototype for a class of DNA-binding proteins that catalyse synapsis of DNA strands during genetic recombination in prokaryotes
What is recombination?
the production of offspring with combinations of traits that differ from those found in either parent. In eukaryotes,genetic recombinationduring meiosis can lead to a novel set ofgeneticinformation that can be passed on from the parents to the offspring
What is RFLP analysis?
a technique that exploits variations in homologousDNAsequences. RFLP analysiswas an important tool in genome mapping, localization ofgenesforgeneticdisorders, determination of risk for disease, and paternity testing
What is a silent mutation?
mutation sin DNA that do not significantly alter the phenotype of the organism in which they occur.Silent mutations can occur in non-coding regions (outside of genes or within introns), or they may occur within exons
What are sister chromatids?
tightly linked pair of chromosomes that arise from chromosome duplication during S phase. They separate during M phase and segregate into different daughter cells
What is a somatic mutation?
geneticalteration acquired by a cell that can be passed to the progeny of themutatedcell in the course of cell division
What is a spo11 protein?
aproteinused in a complex during meiotic recombination. OneSpo11 proteinis involved per strand ofDNA, thus twoSpo11 proteinsare involved in each double stranded break event.
What are sporadic cases?
a disease that is not inherited from parents, but arises via a mutation
What is strand invasion?
The process in which the nucleoprotein complex (composed of the broken single-strand DNAand the recombinase) searches and identifies a region of homology in intact duplexDNA
What are tautomers?
a separate type isomer by an organic compound that has the property that it can quickly change their isomeric form by chemical reaction called tautomerization.
What is a translocation mutation?
a chromosome abnormality caused by rearrangement of parts between nonhomologous chromosomes. A gene fusion may be created when thetranslocationjoins two otherwise-separatedgenes, it is detected on cytogenetics or a karyotype of affected cells
True or False: somatic mutations are passed onto offspring
False - only mutations in germ cells can be passed onto offspring
What are the major classes of mutation?
Point mutations
Large scale mutations
Trinucleotide repeat expansion (dynamic)
What are the types of point mutation?
Base substitution
Single base deletion/insertion
What are the types of base substitution?
Missense
Nonsense
Silent
Is a base substitution or a deletion/insertion more damaging?
Base deletion/insertion because this causes a frameshift which can result in a completely different protein, a nonfunctioning protein or a very short protein
What are the types of large scale mutations?
Deletion/insertion
Inversion
Duplication
Translocation
Why is Duschene Muscular Dystrophy more severe than Becker Muscular Dystrophy?
Both DMD and BMD occur due to a large deletion mutation. The DMD deletion is one nucleotide less than the BMD deletion. This one less deletion causes a complete frameshift resulting in a more severe case. The deletion in BMD is a multiple of 3 so it does not cause a frameshift
What are the causes mutations?
Retroviruses and transposons
Spontaneous
Induced
What causes an induced mutation?
A mutagen, such as a chemical (base analogues, intercalating agents, base modifiers) or radiation (UV light, electromagnetic ionising agents)
What does UV light do to DNA?
UV light causes covalent linkage between two adjacent pyrimidine bases creating lesions in the DNA
What are the two most common DNA repair pathways?
Base excision repair
Nucleotide excision repair
What does base excision repair do?
Removes small non-helix distorting lesions
How does base excision repair work?
DNA glycosylases recognise specific type of altered base and catalyses its hydrolytic removal by breaking the bonds. The altered base is detected by flipping out of the helix. AP endonucleases recognise the missing tooth in the DNA which cuts the phosphodiester backbone, removing the nucleotide. DNA polymerase then adds a new nucleotide and DNA ligase seals the nicks
What does nucleotide excision repair do?
Repairs damage caused by large changes to the DNA helix such as UV damage
How does nucleotide excision repair work?
A large multienzyme complex scans DNA for distortions in the double helix. Once found, it cleaves the phosphodiester backbone of the abnormal strand on both sides of the distortion. DNA helicase peels away the single-strand oligonucleotide containing the lesion. The large gap is then repaired by DNA polymerase and sealed by DNA ligase
What is Xeroderma pigmentosum?
An autosomal recessive genetic defect where nucleotide excision repair enzymes are mutated. This means that patients have a high risk of developing skin cancer from UV damage
How does emergency repair of heavily damaged DNA work?
In emergencies, less accurate back-up polymerases are employed to replicate through the DNA damage-translesion polymerases but they lack exonucleolytic proofreading activity. Because of their inaccuracy they only add a few nucleotides before falling off where the normal polyerase continues on.
How are double-stranded breaks caused?
They can occur from environmental damage such as radiation or reactive chemicals but most of the time they occur during DNA replication when replication forks become stalled
What two mechanisms of repair can be used to repair a double-stranded break?
Non-homologous end joining
Homolgous end joining
How does non-homologous end joining work?
Broken ends are simply brought together by Ku proteins and rejoined by DNA ligation generally with the loss of one or more nucleotides.
What is an overview of how homologous end joining works?
The sister chromatid is used as a template to restore the sequence. This can result in rearranged sequences crucial for meiosis. It can only occur after a DNA strand is freed from pairing with its complementary strand. Exonuclease degrades the 5’ end making a 3’ overhang. The 3’ overhang invades the sister chromatid and DNA synthesis occurs. Once the repair has occurred replication can continue
How does strand invasion work in prokaryotes?
RecA protein intertwines the DNA single strand and DNA duplex in sequence independent manner. The DNA single strand searches the duplex for homologous sequences in triplets (transient base pairs). Once an extended sequence is located, the single strand displaces one strand of the duplex and forms base pairs with the other strand resulting in a heteroduplex
How does branch migration occur?
Once strand invasion has occurred, the point of strand exchange (called the branch point) can move through branch migration. An unpaired region of one of the single strands displaces a paired region of the other single strand, moving the branch point
Through which mechanism is genetic variation created in germ cells?
Homologous recombination
What structure is created during homologous recombination?
Holliday junction
How are Holliday junctions resolved?
In bacteria, a specialised endonuclease, RuvC, cleaves the Holliday junction, leaving nicks in the DNA which DNA ligase can seal (process more complex in eukaryotes)
True or False: In homologous recombination, the heteroduplex region must have completely complementary sequences
False - The heteroduplex regions can tolerate a small percentage of mismatched base pairs
Does meiosis always follow the law of genetics?
No - ocassionally meiosis yields 3 copies of maternal version and only on copy of the paternal allele. This occurs because if the two strands that make up the heterodulex region do not have identical nucleotide sequences, one of the strands will be repaired by the cell’s mismatch repair system. It will randomly choose which strand to repair. This causes a loss of one of the alleles
What is an example of mutation detection technology?
RFLP analysis
