Chapter 9 Flashcards
What is a genetic polymorphism?
When there are multiple allele versions at a genetic locus.
Do humans have a wild type sequence?
No - humans do not have a DNA sequence that is considered wild type.
What is a pan genome?
These are a collection of all genetic diversity present in a particular species.
What is the difference between polymorphism and mutations?
DNA sequence variations are common in the population for polymorphism, however, mutations are rare in the population. However, since the lines are similar we use them interchangably.
What are SNPs?
These are single nucleotide polymorphism these are the most common type of genetic variation among humans. Between the DNA sequencethere is a single base pair difference.
What are the 3 causes of polymorphisms?
1.) Spontaneous DNA replication error
2.) Tautomerization/Ionization
3.) Spontaneous or induced chemical changes to a nucleotide
What are the types of tautomerization/ionization?
SNPs -> Transtions
-> Transversions
What is a transition?
This is a mutation where a single nucleotide changes where a pryimidine is replaced with a different pyrimidine OR a purine is replaced with a different purine.
What are the 2 consequences of DNA replication?
1.) When DNA polymerase adds an incorrect base this leads to a mismatched base pair.
2.) Mismatching caused by tautomerization/ionization is the chemical change in the base tricks DNA polymerase into adding the wrong base.
How is DNA mismatch repair?
The DNA polymerase I and III acts as a proofreader that uses 3’ to 5’ exonuclease activity.
What is exonuclease?
These are cuts that are made to the DNA in the ends.
What is endonuclease?
These are cuts that are made into the DNA in the middle of the strands.
How are transitions/transversions communicated?
They are conveyed by a notation where the base pair is used.
What is tautomerization?
Each base exists in different chemical isoforms known as tautomers with different stabilities - the keto DNA form is the most stable.
How does tautomerization occur?
Changes in the position of the base’s atoms and bonds between the atoms which leads to different forms in equilbirium.
What is ionization?
Proton exchange between water and hydrogen bonds.
Why does exonuclease travel 3’ to 5’?
This occurs because the original DNA synthesis occurs in the 5’ to 3’ direction so when you are repairing and backtracking you are going backwards so 3’ to 5’.
What can the cellular environment cause?
Spontaneous or chemically induced modification of a nucleotide that affects its base pairing.
What is depurination?
The hydrolysis or breaking of the glyscosidic bond between the sugar and the base however the phosphodiester bond remains intact. This specifically acts to the purine A and G.
What is the glyscosidic bond?
This bond is between the sugar and the nitrogenous base.
What are the different options for mutations occurring relative to the base?
During replication either there is no complementary base being added, or the apurinic site pairs with another base thus causing a mutation.
What is deamination?
This is hydrolytic removal of an amino group and Cytosine, Adenine, and Guanine contain an amino group and can undergo deamination.
What is oxidative stress?
This is the reactive oxygen species in our cells that are normal results of aerobic metabolism.
What are chemically induced changes?
These are changes that can be made to the form or the structure of the molecule.
What happens if the transition is change from C->U what is in the strand? Is it uracil?
No - because the focus is DNA synthesis and moving forward it will be thymine instead of uracil continuing the synthesis.
What are the chemicals called that can cause mutations?
Mutagens which can result in SNPs
Are there more types of transitions or transversions?
Transversions which have 8 possibilities and transitions have 4 possibilities.
In humans which type transition or tansversions is more common?
In human cells the more common type is the transition because it is trading one purine or pyrimidine for another so it is easier to occur because the same ring is being substituted and tend to be less deterimental on the amino acids.
What are Indels?
These are the deletion and insertion mutations.
What are point mutations?
Single base pair is added, deleted, or changed -> this is an umberella term that involves a change in a single base pair includes a SNP or indel.
What are the 3 types of indels?
1.) Nonrepetitive indels include the point mutations
2.) STRs are the short tandem repeats of 2-9 nucleotides
3.) VNTRs these are the variable number tandem repeats of 10-100 nucleotides
What are STR alleles?
The number of repetitive regions.
Where can STR occur?
These can occur in exon, introns, regulatory regions, and nonfunctional DNA.
Why is a SNP preferred over the STR locus as a method to differentiate individuals?
For a SNP locus there are usually 2 different alleles with a maximum of 4. However, for a STR or microsatellite locus can have multiple different alleles so, it is a more confident way of determining the difference between 2 people.
Which has a higher mutation rate SNPs or STR?
STR - due to snippage
What is replication slippage?
When a region of the newly synthesized strand loops out and forms a hairpin and binds to itself - and then when the daughter strand acts as a template for more DNA synthesis that hairpin will be removed.
Due to replication slippage will the new daughter strand include more or less repeated regions?
There will be more because if there is a region that is removed the repeated regions move up a little in the template strand and more repeated regions will be made.
How does the replication slippage occur for the deletion mutation?
The hairpin structure forms in the template strand so the daughter strand that is synthesized is shorter .
What are the differences between the replication slippage in deletion and insertion?
1.) The hairpin forms in the template for deletion and the hairpin forms in the daughter strand for insertion.
2.) The insertion results in more repeats and a deletion results in fewer repeats.
Why does the CAG form the hairpin structure?
This is because in the loop the C-G bond together and when a molecule is CG rich there are more hydrogen bonds and is more stable.
What are the different types of the R group in the amino group?
- Nonpolar
- Polar
- Positively charged
- Negatively charged
What is a peptide bond?
This is the bond that forms between the amino group of one acid and the carboxyl group of another acid.
Does the amino acid have directionality?
Yes - the order is based off of the N and C terminal ends
the N comes first and then the C comes second.
What are codons?
These are 3 mRNA nucleotides that are put together and are used to generate the amino acids.
What does it mean when we say the code is degenerate?
There are many codons that encode the same amino acid.
What is the START codon?
AUG - which initiates translation.
What is the STOP codon?
There are a few of them and these stop translation.
What does the start codon determine for the strand?
The open reading frame and where the mRNA is read from 5’ to 3’ and translation occurs in the same direction as well.
How do the mRNA codons bind together?
The molecule tRNA has an anticodon loop which is oriented in the 3’ to 5’ direction because it is the complementary to the mRNA codon.
At what end does the amino acid attatch to?
The amino acids attatch to the 3’ end of the tRNA molecule.
Is the tRNA charged?
Yes once the aminoacyl-tRNA synthetase
What makeup the ribosome?
The ribosomes consist of 1/3 proteins and 2/3 rRNA and there are 2 subunits a large and a small subunit.
In what direction does the mRNA move?
The 5’ to 3’ direction
What are the 3 sites of the tRNA molecules?
E, A, P
What is the order of the 3 sites of the tRNA?
E, P, A
At which site does the peptide bond form?
At site P
How does the mRNA know where to bind in prokaryotes?
There is an mRNA sequence known as the Shine-Dalgarno sequence that is recognized by the rRNA in the ribosomal subunit.
How does the mRNA know where to bind in eukaryotes?
This is the Kozak sequence which fulfils a similar function of positioning the ribosome.
How does the tRNA know when to stop?
There are release factors in site A which recognize the stop codon, then the polypeptide chain is released from the tRNA, then the ribosome subunit breaks aparat and then reforms on another mRNA.
What type of mutations can SNP’s prevent? In what position of the codon?
The 3rd position of the codon and it can be used to prevent transitions and lead to silent mutations.
What are the 4 outcomes that can occur when there is a SNP in mutations?
1.) No mutation
2.) Silent mutation (nonsynonomous)
3.) Missense mutation (synonymous)
4.) Nonsense mutation (early termination)
When will a silent mutation not be silent?
The mRNA sequence has changed if the silent mutation is near the end of an exon it can interfere with splicing. The mRNA sequence has changed and altering the mRNA structure and the ability.
What type of Indel will not impact all of the amino acids?
When there are 3 added or 3 removed.
What are the regulatory elements?
These are the enhancer and promoter region.
What are the coding elements?
These are the introns and exons.
What is a mature mRNA?
This is the spliced mRNA that does not have the introns in it.
How does splicing occur?
The machinary splicosome finds the nucleotides between the exon and intron junction and cuts it there.
What are the 3 outcomes of the mutations in the regulatory elements?
1.) No mRNA - No proteins
2.) More mRNA - More proteins
3.) Less mRNA - Less proteins
How can mutations be detected in DNA?
Through PCR -> Sequencing
How can the effect of mutations on mRNA be detected?
qPCR of mRNA -> cDNA
How can the impact of mutation be detected on the protein?
A Western Blot can be used which is used to detect a particular protein in a mixture of proteins which can determine the size and the level of the protein expression.
How are Western Blots conducted?
1.) Gel electrophoresis
2.) Add SDS to make a linearized protein due to the negative charge of the SDS (denatures the protein)
3.) To determine the size of a protein use a protein ladder
4.) To visualize the protein use a probe which is an antibody that has high affinity to bind to the protein of interest but it is still colourless at this point
5.) Then a secondary antibody has a fluorescent tag and it binds to the primary antibody and allows for the visualization of the gene
