Theme 5 Module 1: Genetic Variation - Comprehensive Notes

Theme 5: The Principles of Inheritance - Module 1: Genetic Variation

Introduction

Theme 5 focuses on the principles of inheritance.
Module 1 investigates genetic variation.

Module Objectives

Examine different types of DNA sequences that lead to genetic variation.
Identify how genetic variation can be detected.
Compare harmless and harmful changes in DNA sequences.
Understand the prevalence of different DNA sequences and variations within and across various populations.

The Human Genome

The human genome contains the complete set of instructions for life.
Exons and regulatory elements coding for proteins make up a small portion of eukaryotic genomes.
Noncoding and repeated sequences serve their own functions.
Types of repeated nucleotide sequences:
- Tandem repeats: Up to several thousand nucleotides long, present next to each other in multiple identical or near-identical copies.
- Simple-sequence repeats: As short as 2 nucleotides, repeated many times throughout a DNA sequence stretch.
All these sequences result in genetic variation within and across organisms.
Not all variations in DNA sequence have an observed effect, especially in non-protein coding regions.
Some genetic variations have less serious effects, while others can be beneficial.
The overall outcome depends on the nature and location of the change.
Consider the effects of changes in noncoding vs. coding or regulatory regions.

Genome Sequence Projects

Primary goal: Map each chromosome with high resolution.
Determine the underlying DNA sequences.
Identify nucleotide sequences of coding and non-coding DNA regions.
Provide insight into mechanisms of inherited diseases and genetic variability.
DNA polymorphisms: Two or more alternative forms (alleles) at a chromosomal region (or locus).
- Differ in a single nucleotide base or have variable numbers of tandem nucleotide repeats.
DNA sequencing projects have revealed many DNA polymorphisms across genomes, mostly in non-coding regions.
Polymorphisms allow for the assembly of high-density genetic maps and are referred to as DNA markers.
DNA markers are detectable using microarray analysis, PCR, Southern blot, or DNA sequencing.
Used to identify individuals and show relatedness (DNA fingerprinting).

Single Nucleotide Polymorphisms (SNPs)

99.9% of human DNA sequences are the same; genetic variations account for differences between individuals.
SNPs are common types of genetic variation caused by single nucleotide base changes or substitutions in a DNA sequence.
Occur in a significant portion of a population.
SNPs are scattered throughout the genome in both noncoding and coding regions.
High frequency: approximately 1 in every 350 bp, resulting in millions of SNPs per human genome.
SNPs near a gene can be used as DNA markers for that gene.
If an SNP is linked to a gene of interest, it is passed on together from parent to child.
DNA microarray analysis is commonly used to detect SNP genotypes.

DNA Microarray Analysis for SNPs

Oligonucleotides matching the common allele and all possible variant SNP alleles are attached to a microarray chip.
Millions of short, single-stranded oligonucleotides of known sequence, containing a nucleotide base complementary to the SNP allele, are attached to the chip.
Single-stranded fluorescently labeled DNA fragments from individuals being tested are hybridized to the chip.
The position of oligonucleotide probes allows matching of the emergent fluorescent pattern to specific SNPs.
Information can be obtained on whether an individual is homozygous or heterozygous for each SNP.
Example: Detecting two possible SNP alleles (C-G and A-T).
Each SNP genotype reveals a distinct fluorescence pattern.
The fluorescence pattern indicates if an individual is homozygous for C-G, heterozygous for C-G/A-T, or homozygous for T-A.
Probing for different SNPs reveals variations in a population, resulting in a unique SNP profile for each individual.
These variations may not affect gene function or cause disease but serve as markers to identify aspects of an individual’s genome.

Variable Number of Tandem Repeats (VNTRs)

While all mammals have essentially the same set of genes, variations in short, repeated DNA sequences (VNTRs) can account for differences between species.
Tandem repeats: Patterns of one or more nucleotides repeated directly adjacent to each other.
VNTRs vary in length between individuals across populations.
VNTRs are identified using PCR and gel electrophoresis analysis.
Sequence-specific primers target and amplify flanking regions of the variable repeats.
Amplified DNA fragments are separated and detected using gel electrophoresis.

DNA Fingerprinting

Detection of VNTRs with variable lengths is used to identify individuals based on their DNA profiles.
VNTR locations (loci) are similar between closely related individuals but variable enough that unrelated individuals are unlikely to have the same VNTRs.
Detection of VNTRs and other polymorphisms can determine genetic family relationships and be used in forensic investigations.
The combination of various markers makes up a person’s unique genetic profile, which can be compared across individuals.

Silent Variations

Most variations in the human genome have no known effect because they occur in noncoding regions of the DNA.
These are detectable using molecular techniques and are often referred to as silent variations.

Harmful Variations

Variations in protein coding or regulatory regions of DNA can be harmful.
These variations result in an altered gene product, which can lead to detrimental effects.
Sickle cell anemia is an example of an inherited genetic disease with characteristic variations in gene sequence (alleles) passed down from parent to child.
Genotype: Representation of the pair of alleles carried by a person.
Phenotype: The cell or body's interpretation of the genotype.
Red blood cells containing a variation of the oxygen-binding hemoglobin protein assume a sickled shape, which is the cellular phenotype of sickle cell disease.
Physiological phenotype: Oxygen is not carried efficiently, and sickled red blood cells can block capillaries, leading to anemia and acute pain.

Beta-Globin Gene and Sickle Cell Anemia

The gene for the Beta-globin protein lies on chromosome 11 (an autosome).
Every person carries two alleles for the gene: one from the mother and one from the father.
Most people have two HbA alleles, coding for the functional Beta-globin protein.
These individuals are homozygous for the HbA allele and have smooth, biconcave red blood cells.

HbS Genotype

The HbS (sickle cell) genotype is caused by a single nucleotide polymorphism in the protein coding sequence of the beta-hemoglobin gene.
A person with two HbS alleles is homozygous and cannot make functional beta-globin proteins.
The SNP leads to an amino acid substitution of glutamine to valine, altering the tertiary structure of the hemoglobin protein.
This is a harmful variation since in addition to a decreased efficiency of hemoglobin to bind to a transport oxygen, this mutation will also lead to a biochemical change at the protein level which will result in the aggregation of the abnormal beta- hemoglobin protein.
This causes long rod-like structures within red blood cells, leading to the sickle shape.
This can cause blockage of capillaries, anemia, and acute pain throughout the body due to damage to vital organs and tissues.

Heterozygous Individuals and Sickle Cell Trait

Individuals inheriting an HbA allele from one parent and an HbS allele from the other are heterozygous and develop a sickle-cell trait.
Some hemoglobin in the heterozygote's body will be sickle-cell beta hemoglobin under certain conditions, but the rest will be normal.
The person will exhibit no symptoms of sickle cell anemia.
Heterozygotes for the beta hemoglobin HbA/HbS alleles produce enough normal hemoglobin to overcome the effect of the abnormal hemoglobin.

Variation in Populations

Due to DNA polymorphisms, no two human individuals have the exact same genome.
DNA fingerprinting allows for large-scale population genetic analyses to establish variability across populations and between ethnic groups.
The sickle cell anemia mutant gene may confer a selective advantage and resistance to malaria in regions with endemic malaria.
The sickle cell mutation is advantageous in regions prone to malaria outbreaks, even though it is harmful at the cellular level.
The sickle-cell mutation is found in many populations with different alleles or haplotypes emerging independently across various populations.
There are a possible 5 distinct beta-globin haplotypes found across different patients that correlates with regional distribution of each distinct sickle cell anemia single nucleotide polymorphism.
Heterozygotes for the sickle cell allele are resistant to malaria infection in these regions.

Copy Number Variations (CNVs)

SNPs and VNTRs are examples of genetic polymorphisms contributing to genetic variation.
Variations in gene copy number can also contribute to genetic differences between individuals.
Some CNVs occur in noncoding DNA regions; others are present as tandem copies of a coding region along a chromosome.
A region normally present in one copy per chromosome may be duplicated or deleted.
CNVs can be identified based on relative fluorescence intensities detected during DNA microarray analysis.
Greater numbers of copies of the chromosome sequence are indicated by higher fluorescence outputs on the microarray chip.

Gene Duplications and the AMY1 Gene

Gene duplications are usually found adjacent to each other along chromosomes.
The human AMY1 gene, coding for the starch-digesting enzyme amylase, has detectable copy number differences along chromosome 1.
Comparisons across different groups of individuals with varying ancestral diets show differences.
Societies with historic low-starch diets have fewer copies of the AMY1 gene compared to those with long histories of high-starch diets.
The hypothesis is that these gene copy variations reflect selective pressures, with extra copies conferring an advantage in digesting starch in high-starch diets.
DNA polymorphisms contribute to harmful and beneficial effects and contribute to genetic variation between individuals and across populations.

Module Summary

Single nucleotide polymorphisms, variable tandem repeats, and copy number variations in DNA sequences all contribute to DNA polymorphisms detected during DNA sequencing.
Techniques for detecting these genetic variations include microarray analysis, PCR, gel electrophoresis, and DNA sequencing.
Some DNA polymorphisms are harmless, while others can lead to detrimental effects or selective advantages.
DNA polymorphisms drive genetic diversity across populations and species.