Chapter 15 Flashcards
Define mutation
Alteration to the nucleotide sequence of DNA
What can mutations impact
mRNA sequence and protein sequence, resulting in disruptions of protein function and cell health.
Define mutation rate
Describes the frequency of mutations, usually measured as the frequency of nucleotide changes at each nucleotide in the genome.
What is the human mutation rate?
~1.1 x 10^-8 mutations per nucleotide per generation.
What is the chance of a nucleotide in the human genome mutating?
Each nucleotide has a 1 in 100million chance - this is sensitive to the person’s age and environment/lifestyle
What can cause mutation rates to vary within an organism?
Cell type, lifestyle/environment, and gene region.
How much higher are somatic cell mutations than germ cells?
4 - 25x higher than in germ cells
Define mutation hotspots
Some DNA regions have much higher mutation rates than normal
Define point mutation
One base pair is exchanged for another
What are the 5 types of point mutations
Missense
Nonsense
Silent
Transversion
Transition
Define missense mutation
Changes codon such that a different amino acid results.
Define nonsense mutation
Changes codon into a stop codon - results in a shortened protein
Define silent mutation
Changes codon but NOT amino acid - due to redundancy of genetic code.
Still can have an affect on DNA - think changes to promoter sequence and introns.
Define transversion
When pyrimidine is exchanged for a purine or vice versa
What are the purines?
Adenine and Guanine
What are the pyrimidines?
Cytosine and Thymine
Define transition
A pyrimidine is exchanged for a pyrimidine OR a purine for a purine
Define insertion mutation
New nucleotides are added to the sequence
Define deletion mutation
Nucleotide(s) are removed from the sequence
Define frameshift mutation
An insertion or deletion mutation. A mutation that shifts the reading frame and all subsequent codons.
Define loss-of-function mutation
Mutation results in reduction of function of gene. Typically recessive
Define null mutation
Complete loss of function of gene due to mutation
Define dominant negative mutation
Exception to LOF being recessive. A dominant negative mutation is dominant, due to the mutated protein inactivating the wild type protein.
Define dimer
A pair of proteins. If a WT protein forms a dimer with a broken protein, then the dimer won’t work correctly.
Define gain of function mutation
Mutation increases the function of the gene. Typically a dominant mutation.
What are 2 examples of neutral mutations?
- Silent mutation
- special cases of missense mutations -> neutral if the new amino acid is similar to the old.
Define neutral mutation
Nucleotide change occurs, but doesn’t harm the organism. Mutations in noncoding DNA regions are sometimes neutral.
Define suppressor mutation
Second mutation that removes the effect of the first mutation - restores conditions to normal
Define intragenic suppressor
Suppressor in the SAME gene as the first mutation
Example of intragenic suppressor
Mutation 1 is an insertion in gene 1, causing a frameshift and ruining the protein. Mutation 2 is a deletion in gene 1, near the first mutation, restoring the proper reading frame and mostly fixing the protein.
Define intergenic suppressor
Suppressor in a different gene from the first mutation
Give an example of intergenic suppressor
Mutation 1 in gene 1 changes protein 1 so that it can’t bind with protein 2. Mutation 2 in gene 2 then mutates protein 2 such that it is once again able to bind with protein 1
Define spontaneous mutation
Mutation occurs naturally, independent of external factors.
Define induced mutation
Environmental factor causes a mutation
Can a mutation be both induced and spontaneous?
Yes - the environment can influence DNA polymerase/repair.
Define base mismatch
Incorporation of the wrong base, causing mutations
Define tautomerization
Process where a hydrogen atom temporarily changes position in a molecule.
What does tautomerization do to a base?
Alters the base-pairing interface, causing the wrong base pair to form due to H-bond alignment.
What do tautomer bases pair as?
Tautomer T -> Guanine
Tautomer C -> Adenine
(typically happens to pyrimidines)
How does a tautomerization affect the first generation and second generation?
First gen - base mismatch
Second gen - inherits mutation due to DNA polymerase interpreting daughter stand wrong.
Define replication slippage
DNA polymerase accidentally slides forwards or backwards on parent DNA, either skipping a nucleotide or copying a nucleotide twice.
What does replication slippage result in?
Insertions or deletions. Caused by small bulges forming on parent or daughter DNA in repetitive DNA sequences.
Define depurination
When a nucleotide within a DNA strand loses its base. Caused by the breakage of the covalent bond between the base and 1C sugar.
What is the most common bases depurination occurs with?
Adenine and Guanine (pyrimidines).
What happens after depurination?
DNA polymerase comes across the missing base and puts a random base opposite to it, causing a mutation.
Define deamination
When an amino group (NH2) in a cytosine or adenine is lost.
What are the new base pairs after deamination?
Cytosine turns into Uracil, pairing with adenine.
Adenine turns into hypoxanthine, pairing with cytosine.
Define oxidative damage
ROS/RNS damage proteins, lipids, and DNA in the cell
Define ROS
Reactive oxygen species
Define RNS
Reactive nitrogen species
Define mutagens
Chemicals or agents that induce mutations. There are natural and artificial mutagens
Define base analog mutagens
Chemicals with similar structure to a nucleotide base. Can be accidentally incorporated into DNA
Example of base analog
BrdU (bromodeoxyuridine). Similar in structure to thymine but can pair with adenine or guanine, frequently causing mutations upon replication.
Example of a structure-changing chemical (changes base structure)
EMS (ethylmethane sulfonate). Alters guanine to make it pair with thymine. Causes a C->T transition in the daughter strand.
Define intercalating agents
Chemicals that bind inside of DNA strands, causing replication issues and mutations
Define radiation
Energy associated with waves that can cause DNA damage.
Shorter wavelengths = XXX energy?
Higher energy.
Higher energy waves are more likely to cause damage.
Define pyrimidine dimers
Neighboring pyrimidines on the same DNA strand form covalent bonds, caused by radiation.
Define nucleotide-excision repair
Removes nucleotides near a site of damage.
How does nucleotide-excision repair work?
Endonuclease cuts the DNA around the damage, and the DNA polymerase adds nucleotides to replace them, then ligase seals the gap in the new DNA.
Define homologous recombination
AKA homology-directed repair. The repairing of double strand breaks, using homologous chromosomes as a repair template.
What are the steps to homologous recombination? (4)
- Exonuclease generates an overhang of DNA near the strand break
- Overhanging DNA is inserted into the homologous chromosome
- DNA polymerase extends the innervated pieces, using the homologous chromosome as a template
- Overhanging portion is now released, and it is resealed with the other end of the break
Define nonhomologous end joining
Repairing of double strand breaks. Protein recognizes the break and seals the gap back together
What is the issue with nonhomologous end joining?
It can accidentally seal the wrong ends back together
Define transposable elements
Nucleotide sequence that can jump genes / move locations in the genome.
~50% of genome derives from TEs.
AKA transposons.
What are the ways transposons can alter the genome function (4):
- Can enter an exon and disrupt protein
- Can enter near a promoter and increase transcription
- Can enter the intron and alter splicing patterns
-Can bring regulatory sequences
When are transposons activated?
In response to stress.
Cells re-organize their DNA when stresses, attempting to undergo adaptations to become healthier. - High risk, high reward
Define transposase
Enzyme that cuts each side of TE, allowing it to be taken to a new region.
It also cuts the new DNA and inputs the TE
Define inverted terminal repeats
ITRs. Short, identical, inverted sequences that transposase recognizes on DNA transposons.
Usually have an ORF with instructions to make transposase.
How does Transposase and ITR work together?
Transposase cuts each ITR, carries it around, then cuts the target DNA, creating a staggered cut. This generates overhanging pieces of DNA, and a transposon is inserted in the target.
The gaps on the staggered ends are then filled in.
Define direct repeats
(DRs) are the filled in gaps on the sides of the TE
Define nonautonomous transposon
Lacks a functional transposase ORF and cannot move on its own.
Needs transposase from an autonomous transposon
Define autonomous transposon
Has a functional transposase ORF
Define retrotransposon
TEs that move through the genome using an RNA intermediate.
retroTEs are transcribed to make RNA, then reverse trancribed to make DNA which is then pasted in other sites of the genome.
Define reverse transcriptase
An enzyme that uses RNA to make DNA
Define integrase
Enzyme that helps the new DNA integrate into the genome
What do retrotransposons contain to help them integrate?
The genetic code to produce reverse transcriptase and integrase.
What are the steps to a retroTE jump?
- Transposon is transcribed by RNA polymerase
- mRNA is translated by the ribosome
- Reverse transcriptase makes DNA using mRNA
- Integrase cuts destination DNA, then puts the transposon DNA in the target site.
Define autonomous retroTE
Capable of independent movement - have both reverse transcriptase and integrase
Define nonautonomous retroTE
Lack eihter functional integrase or reverse transcriptase. Depends on autonomous retroTEs to help it move.
How are transposons kept inactive? (3ways)
- Transcriptional repressors
- DNA methylation of TE genes
- PIWI RNAs
What do transcriptional repressors do to inactivate TEs?
Repressors bind to the TE, preventing transcription
What does DNA methylation do to inactivate TEs?
Adds methyl groups to cytosine bases, preventing RNA polymerase from binding. Typically, transposon promoters are methylated.
What do PIWI RNAs do to inactivate TEs?
SMall RNAs (24-32nts) bind to PIWI proteins, and guide these proteins to transposons.
These PIWI proteins have an endonuclease function and cleave the transposon RNA.
What is a transposon’s significance during neurogenesis?
Newly developing neurons in the hippocampus express transposons, creating genetic differences between different somatic cells of the same organism (making each neuron functionally different - necessary for learning!)
Define somatic mosaicism
Genetic differences between somatic cells of the same organism.
