MOD 5: DNA Mutation, Repair, and Transposons Flashcards
What are the four characteristics of a genetic material?
- Replication
- Storage of information
- Expression of information
- Variation by mutation
This refers to any change in an organism’s genome nucleotide
Mutation
This refers to the source of genetic variation and provides the raw material for natural selection
Mutation
Mutation leads to genetic damage and contributes to ____________, ____________, and ____________
Cell death; genetic diseases; cancer
Mutation affects organisms depending on the type. What are the three known effects?
- Base-pair alteration
- Location of mutation
- Function of the affected gene product
TRUE OR FALSE: Mutation can occur spontaneously
TRUE
Natural biological mutation = ____________
Chemical processes = ____________
Happen naturally; external environment
TRUE OR FALSE: Mutation can be induced by external factors
TRUE; By chemicals or radiation
This type of mutation may cause a wide variety of human diseases
Single-gene mutations
Mutations are counteracted by a number of ____________
DNA repair mechanisms
This can cause chromosome breaks and induce mutations within coding and gene-regulatory regions
Transposable elements
This reads the nucleotides in codons
tRNA
What are the classifications of gene mutations?
- Point mutation
- Substitution
- Frameshift mutation
- Deletion
- Insertion
This characteristic of the DNA allows the DNA to yield the same code even with changes on the last nucleotide
DNA wobble
What are the three effects of function?
- Loss of function
- Gain of function
- Suppressor mutation
This effect of gene mutation reduces or eliminates gene function — the gene is dead.
Loss of function
This effect of gene mutation codes for gene products with enhances, negative, or new functions
Gain of function
This effect of gene mutation is a second mutation that either reverts or relieves the effect of the previous mutation
Suppressor mutation
What are the three types of mutation under the loss of function?
- Null mutation
- Recessive mutation
- Dominant mutation
This refers to the complete loss of gene function in which two genes are affected
Null mutation
This type of mutation shows wild-type phenotype — only one allele has the mutation; the other is still working.
Recessive mutation
This type of mutation shows mutant phenotype.
Dominant mutation
Dominant negative mutation may result from a disease in which one allele is inactivated.
Even though the other gene is still working, it won’t be expressed due to the small amount of gene products produced.
What do you call this disease?
Haploinsufficiency
Mutation by Phenotypic Effects:
This classification of mutation shows visible morphological trait.
Example: Mendel’s pea characteristics
Visible
Mutation by Phenotypic Effects:
This classification of mutation alters nutritional characteristics.
Example: Loss of ability to synthesize an essential amino acid in bacteria
Nutritional
Mutation by Phenotypic Effects:
This classification of mutation yields changes in protein function.
Example: Defective hemoglobin leading to sickle-cell anemia in humans
Biochemical
Mutation by Phenotypic Effects:
This classification of mutation leads to behavior pattern changes.
Example: Brain mutations affecting Drosophila mating behaviors.
Behavioral
Mutation by Phenotypic Effects:
This classification of mutation yields altered gene expression.
Example: Regulatory gene mutations affecting expression of the lac operon in E. coli
Regulatory
Mutation by Phenotypic Effects:
This classification of mutation alters the organism’s survival.
Example: Tay-sachs and Huntington diseases in humans
Lethal
Mutation by Phenotypic Effects:
This classification of mutation occurs in which the phenotype expressed only certain environmental conditions.
Example: Temperature-sensitive mutations affecting coat color in Siamese cats
Conditional
What are the two types of location mutation?
- Somatic mutation
- Autosomal mutation
This type of location mutation occurs in any cell in the body except germ cells.
Somatic mutation
TRUE OR FALSE: Somatic mutation can be passed on across generations and affect offsprings.
FALSE; Gene remains with the person only.
This type of location mutation involves germ cells; x-linked and y-linked
Autosomal mutation
This type of location mutation involves germ cells; x-linked and y-linked
Autosomal mutation
TRUE OR FALSE: Autosomal mutation can be passed on to offspring
TRUE
This type of mutation can occur spontaneously through natural biological and/or chemical processes.
Spontaneous mutations
What is the difference between germ line cells and not germ line cells?
In germ line cells, the whole body gets the mutation
In not germ line cells, only patches in the tissue of the mutation are affected
This type of mutation can be induced by external factors such as chemicals and/or radiation.
Induced mutations
This refers to the likelihood that a gene will undergo mutation in a single generation
Mutation rate
TRUE OR FALSE: Mutation rate varies between organisms but is the same within the species.
FALSE; Mutation rate also varies within the species, from gene to gene.
This refers to the part of the gene that is usually mutated
Mutation hot spots
In slippage, when looping occurs on the newly synthesized strand, what happens to the nucleotides?
The result is the addition of nucleotides
In slippage, when looping occurs on the template strand, what happens to the nucleotides?
The result is the omission of nucleotides
This refers to the transfer of double bonds
Tautomeric shifts
Tautomeric shifts are caused by the movement of __________
Protons
This refers to the loss of one of the nitrogenous bases in an intact double-helical DNA molecule
Depurination
What are the two usual nitrogenous bases involved in depurination?
Guanine and adenine
What two nitrogenous bases are involved in deamination?
Cytosine and adenine
In deamination, an amino group in cytosine or adenine is converted into a __________ group
Keto
In these bases, cytosine is converted to __________, and adenine is changed to __________ — resembling the compound, __________
Uracil; guanine; hypoxanthine
An oxygen that becomes more negative becomes a __________
Superoxide
TRUE OR FALSE: Superoxides are not really reactive
FALSE; They are highly reactive
Oxidative damage may cause 5 breaks. What are they?
- Base mismatch
- Single-strand breaks
- Double-strand breaks
- Crosslink inter-strand breaks
- Crosslink intra-strand breaks
What are the four effects of oxidative damage?
- Mitochondrial dysfunction
- Synaptic deficit
- Necrosis
- Cognitive impairment
What are the causes of Reactive Oxygen Species (ROS)?
- UV
- Radiations
- Chemical pollutants
What are the four chemical reactions under induced mutation?
- Base analogs
- Intercalating, alkylating, and adduct-forming agents
- Ultraviolet light
- Ionizing radiation
Base analogs show the similarity of the chemical structure of __________ and __________
5-bromouracil (5-BU) and thymine
In the common keto form, 5-BU base-pairs normally with __________
Adenine
In the rare enol form, 5-BU pairs anonymously with _________
Guanine
This refers to molecules that go in between DNA strands
Intercalating agents
What are the two dyes used as intercalating agents?
- Acridine orange
- Ethidium bromide
This refers to the dye that causes frameshift mutation by creating unusual spacing between nucleotides
Acridine orange
This refers to the dye that causes frameshift mutation by creating unusual spacing between nucleotides
Acridine orange
This refers to the dye that fluoresces when viewed under AGE
Ethidium bromide
Alkylating agents convert __________ to __________
Guanine to 6-ethylguanine
What alkylating agent converts guanine to 6-ethylguanine?
Ethylmethane sulfonate (EMS)
What nitrogenous base does 6-ethylguanine base-pair with?
Thymine
This mutating agent is effective, common, and does not always cause bad mutations.
Ethyl Methanesulfonate (EMS)
This is a segment of DNA bound to a cancer-causing chemical
DNA adduct
These are used as biomarkers of exposure in scientific experiments, binding to DNA and leading to cancer
DNA adduct
DNA adduct is usually a product of a reaction between __________ and __________
Chemicals and one’s DNA
This is a significant constituent of tobacco smoke
Acetaldehyde
This binds to DNA, causes crosslinking, and leads to cell death
Cisplatin
This is a naturally-occurring produce of lipid peroxidation
Malondialdehyde
What are the 14 chemicals that form DNA adducts?
- Acetaldehyde
- Cisplatin
- DMBA
- Malondialdehyde
- Polycyclic Aromatic Hydrocarbons (PAHs)
- Nitro-PAHs
- Aflatoxins
- Mustards
- Aromatic Amines
- Heterocyclic Aromatic Amines (HAAs)
- Methylating Agents
- Other alkylating agents
- Haloalkanes
- Nitrosamines
This refers to electromagentic spectrum and their associated wavelengths
Ultraviolet light and ionizing radiation
Mutations can be induced by many types of __________ and __________
Chemicals and radiation
What are the different types of mutation that causes disease?
- Missense
- Nonsense
- Insertion
- Deletion
- Trinucleotide repeat expansions
This type of mutation causes the disorder achondroplasia.
Molecular change:
Glycine to arginine at position 380 of FGFR3 gene
Missense
This type of mutation causes the disorder Marfan syndrome.
Molecular change:
Tyrosine to STOP codon at position 2113 of fibrillin-1 gene
Nonsense
This type of mutation causes the disorder Familial hypercholesterolemia.
Molecular change:
Various short insertions through the LDLR gene
Insertion
This type of mutation causes the disorder cystic fibrosis.
Molecular change:
Three-base-pair deletion of phenylalanine codon at position 508 of CFTR gene
Deletion
This type of mutation causes the disorder Huntington disease
Molecular change:
>40 repeats of (CAG) sequence in coding region of Huntingtin gene
Trinucleotide repeat expansions
This is a hereditary condition in which the growth of long bones is restricted by the ossification of cartilage
Achondroplasia
This results in very short limbs and sometimes a face that is small in relation to the skull
Achondroplasia
The Marfan syndrome affects what tissue that provides support for the body and organs?
Connective tissue
This syndrome damages the blood vessels, heart, eyes, skin, lungs, and the bones of the hips, spine, feet, and rib cage
Marfan syndrome
Familial hypercholesterolemia is caused by a defect on what chromosome?
Chromosome 19
This disease makes the body unable to remove low density lipoprotein cholesterol from the blood
Familial hypercholesterolemia
What is damaged by cystic fibrosis?
The lungs, digestive tract, and other organs
This disease may be inherited and affect cells that produce mucus, sweat, and digestive juices
Cystic fibrosis
This consists of a group of human diseases that are a result of an abnormal expansion of repetitive sequences
Trinucleotide repeat disorders
What organ system is affected by the trinucleotide repeat disorders?
Nervous system
This DNA repair system detects incorrect bases and reverses them
Proofreading
This is activated when proofreading still has errors, replacing incorrect nucleotides with correct ones
Mismatch repair (MMR)
This repair system is the last resort type or repair, allowing cells to continue to survive even with a lot of damages/mutations
SOS Repair system
TRUE OR FALSE: The SOS repair system allows cells to survive without mutations
FALSE; Cells are enabled to survive, but are mutated
The SOS repair system is always repressed by what protein?
LexA protein
This revers to the reversal of UV damage, requiring UV-induced damage forming pyrimidine dimers
Photoreactivation repair
Photoreactivation repair is dependent on proteins called __________
Photoreactivation Enzyme (PRE) or phytolyase
TRUE OR FALSE: Photoreactivation repairs are present in humans but not in bacteria, fungi, plants, and some vertebrates
FALSE; Present in bacteria, fungi, plants and some vertebrates; Absent in humans
This is referred to as excision repair or cut-and-paste mechanisms
Base excision repair (BER)
What are the three steps in base excision repair (BER)?
- Recognition of damage and enzymatically cliipping it out by an endonuclease
- DNA polymerase fills in the gap
- DNA ligase seals the final nick
What are the two types of base excision repairs (BER)?
Class 1 - Copy & Paste
Class 2 - Cut & Paste
This class of BER is the longer method, requiring the transposon to get transcribed, undergoing reverse transcription
Class 1 - Copy & Paste
This class of BER cuts the region and pastes it to another part. It is the shorter method
Class 2 - Cut & Paste
What are the two transposable elements in humans?
- Long Interspersed Elements (LINEs)
- Short Interspersed Elements ( SINEs)