BIOL 311 Topic 7

What does SNPs stand for?

Single nucleotide polymorphisms

What are the two types of mutations?

1. SNPs (single nucleotide polymorphisms)

2. Indels (insertions - deletions)

What are he two types of SNPs?

• transitions

• transversions

What are the two types of indels?

• non-repetitive

• short tandem repeats (STRs)

What is a point mutation?

A type of SNP - a base substituion

What is the difference between transitions and transversions?

Transition: a base is replaced by another base of the same type

Purine ↔ Purine (A ↔ G)

Pyrimidine ↔ Pyrimidine (C ↔ T)

Transversion: a base is replaced by a base of a different type

Purine ↔ Pyrimidine (A or G ↔ C or T)

Which are more common: transitions or transversions?

Transitions are more common than transversions.

Why do transitions happen more often than transversions?

Transitions involve replacing a base with another of the same type (purine ↔ purine or pyrimidine ↔ pyrimidine), causing less distortion to the DNA structure.

Transversions switch between purines and pyrimidines, which is a bigger structural change and occurs less frequently.

What causes SNPS?

1. spontaneous mutations

2. induced mutations

What are the types of spontaneous mutations?

• DNA replication error (mismatching)

• chemical changes to nucleotides

→ depurination

→ deamination

What are induced mutations?

exposure to external mutagens

What is depurination?

the hydrolysis of the N-glycosidic bond between purine bases and the sugar-phosphate backbone resulting in an apurinic/abasic site

What is an abasic site?

a location in DNA where the base is missing, but the sugar-phosphate backbone remains intact.

What is the result of an abasic site?

During replication, its either paired with no complementary base OR a specific random base leading to mutations

Why does depurination specifically happens to purines?

because the bond between the purine base and the sugar is chemically more unstable and breaks spontaneously, forming an abasic site. Pyrimidines (C and T) are much less likely to be lost this way.

Are purines or pyrimidines more stable in DNA?

Pyrimidines are generally more stable in DNA than purines because they are smaller single-ring structures, making their bond to the sugar less prone to spontaneous breakage (like depurination, which mainly affects purines).

What is deaminiation?

the hydrolytic removal of an amino group from a nitrogenous base by adding a water to remove NH₃ (the NH₂ in the bases)

What bases does deamination occur in?

A, G and C - not T because it doesn’t have an amino group (NH₂)

What does deamination often result in?

SNPs (specifically transitions)

What is a non repetitive mutation?

a unique genetic change that occurs spontaneously in a single individual or lineage rather than at a genetic "hotspot".

What is an indel?

an insertion or deletion of bases

How are coding regions of DNA read?

DNA can be read in three different ways, depending on where you start reading the bases in groups of three. Each starting point gives a different set of codons and can produce a different protein.

What types of mutations cause a frameshift?

Indel mutations

Why do STRs (microsatellites) differ significantly from one person to another between individuals?

Because DNA polymerase often slips during replication in repetitive DNA, causing insertions or deletions of repeat units, leading to differences in the number of repeats between individuals.

What are Short Tandem Repeats (microsatellites)?

short DNA sequences that are repeated back-to-back in a row in the genome.

Why do STRs cause problems for DNA polymerase? Why do they have a high mutation rate?

DNA polymerase can slip or lose its place when copying STRs because the repeated sequences are very similar, which can lead to insertions or deletions (errors in the number of repeats).

Where are STRs found?

there are many STR regions found in the human genome – in exons, introns, regulatory regions, and nonfunctional DNA

What is an allele?

A different version of a DNA sequence at a specific genetic locus.

How many alleles do SNPs usually have?

Typically 2 alleles, sometimes up to 4.

Why is the number of SNP alleles limited?

Because only four nucleotides (A, T, C, G) can occur at the variable position.

In an STR, what changes between alleles?

The number of repeats, not the repeat sequence itself.

How many alleles can STR loci often have?

More than 20 alleles.

Why do STRs have many more alleles than SNPs?

Because repeat numbers can vary widely among individuals while there is only 4 bases to switch between

Which marker type is more polymorphic: SNPs or STRs?

STRs.

Why are STRs useful in forensic DNA profiling?

They have many alleles, making individuals easier to distinguish since each individual is unique to one another

Compare SNPs and STRs.

SNP:

• Single-base change; usually 2–4 alleles.

• Common in genetic studies

STR:

• Variable repeat number; often >20 alleles.

• Common in forensic identification.

What is the relationship between gel electrophoresis and CODIS?

Gel electrophoresis = makes the DNA “barcode”

CODIS = compares that barcode to a database

Gel electrophoresis produces the data, CODIS uses the data for matching.

How does DNA fingerprinting work?

DNA fingerprinting involves collecting samples, amplifying specific DNA regions using PCR, and visualizing the results through gel electrophoresis or sequencing to determine identity or biological relationships.

How does gel electrophoresis work?

Gel electrophoresis separates DNA fragments by size using an electric field on agrose gels. DNA is negatively charged, so it moves through a gel toward the positive end. Smaller fragments move faster and farther, while larger fragments move more slowly and stay closer to the starting point.

How is DNAs seperated by weight?

molecular weight - base pairs (bp) or kilobases (Kb)