Theme 5 – The Principles of Inheritence

Module 1: Genetic Variation

Unit 1: Genetic Variation
Different sequences lead to genetic variation
- There are noncoding & repeated sequences that serve their own function
- We also have a variety of diff. repeated nucleotide sequences such as tandem repeats
o tandem repeats: can be up to several thousand nucleotides in length & be present next
to each other in multiple identical or near identical copies)
o simple-sequence repeats: repeats as short as 2 nucleotides that are repeated over &
over throughout a DNA sequence stretch
- these diff. possible sequences are spread throughout the genome and can result in genetic variation within & across
organisms
o BUT not all variations in the sequence of DNA in our genomes will have an observed effect (especially if the
variations are in non-protein coding regions of genome)
o Also, some effects are less serious than others, and some can even be beneficial
- Overall outcome of distribution of diff. sequences depends on the exact nature of the change & where in the genome
the change occurs

DNA polymorphisms & genetic variations

- Genome sequence projects: underlying DNA sequences can be determined & is possible to identify the nucleotide
sequences of coding & non-coding DNA regions
o Provides insight into mechanisms of inherited diseases & genetic variability
- DNA polymorphisms: one of two or more alternative forms (alleles) at a chromosomal region (or locus) that differs in
either a single nucleotide base or have variable numbers of tandem nucleotide repeats in a given population of
individuals
o DNA sequencing showed that there are a large # of DNA polymorphisms across the genomes of many organisms
 reside mostly in non-coding regions of DNA
o Polymorphisms allow for assembly of high-density genetic maps & are so are often referred to as DNA markers
 DNA markers are detectable using various techniques (incl. microarray analysis, PCR & Southern blot, DNA
sequencing) and can be used to identify individuals & show relatedness like in DNA fingerprinting

Unit 2: Detecting Variation

- 99.9% of human DNA sequences are the same, genetic variations accounts for the difference we observe in people
- Single nucleotide polymorphisms (SNPs): one of the most common types of genetic variation
o Single nucleotide base change or substitution in a DNA sequence that can occur in a significant portion of a
population
o Often found scattered throughout the genome & can be found in coding & noncoding regions
o Frequency: 1 in every 350 base pairs. There could be millions of SNP’s spread throughout each human genome
o Most are at noncoding regions but if SNPs are found close to a gene, they can be used as DNA markers for that
specific gene
o If close enough or linked to a gene of interest, then every time that gene is passed on from parent to child, then the
SNP is also passed on
- DNA microarray analysis used to detect SNP genotypes
o When analyzing SNPs using DNA microarray analysis, oligonucleotides that match the common allele & all
possible variant SNP alleles are attached to the glass on the microarray chip
o Millions of short, single-stranded oligonucleotides of known sequence (and that contain a nucleotide base in the
middle that is complementary to the SNP allele) are attached to the chip
o Fragments of the single-stranded fluorescently-labelled DNA of individual being tested are hybridized to the chip
o Because you know the position of all oligonucleotide probes on the chip, you can match the emergent fluorescent
pattern based on which SNP each individual has
  Can obtain info on whether the individual is homozygous or heterozygous for each SNP
- In diagram, detecting for 2 possible SNP alleles: C-G & A-T:
o Each SNP genotype will reveal a distinct pattern of fluorescence so the fluorescence pattern on the microarray
will indicate where an individual is homozygous for C-G allele, heterozygous for C-G/A-T allele, or homozygous
for the T-A single nucleotide polymorphism allele
- Each individual in population will have their own SNP profile
- These variations don’t affect gene function or cause disease  they are markers to identify aspects of an individual’s
genome

Variable Number Tandem Repeats (VNTRs)

- Variations in short sequences of DNA that are repeated in tandem
- Tandem repeats: patterns of one or more nucleotides that are repeated
o Repetitions are directly adjacent to each other and can be found in various lengths b/w diff. individuals across
populations
- Can be identified using PCR & gel electrophoresis analysis
o Tandem repeat sites are targeted and amplified with sequence-specific primers that target flanking regions of the
variable repeats
o Resulting amplified DNA fragments are then separated & detected w/ gel electrophoresis

Detecting VNTRs with PCR – can be used by researchers to assist in identification of individuals based on respective
DNA profiles (DNA fingerprinting)
- DNA fingerprinting uses variable number of tandem repeats b/c VNTR locations (or loci) are very similar b/w closely
related individuals but they are also variable enough that it is extremely unlikely that any unrelated individuals would
have the same VNTRs
- Detection of VNTRs & other polymorphisms can be applied to determine genetic family relationships or during crime
scene forensic investigations

Unit 3: Variation & Disease

Variations: from genotype to phenotype
- Most variations in human genome have no known effect (mostly occur in noncoding regions)
o Detectable using many molecular techniques & often referred to as silent variations
- Some variations that occur in protein coding or regulatory regions can be harmful b/c will result in production of an
altered gene product & can lead to detrimental effects
- E.g. sickle cell anemia: inherited genetic disease (characteristic variations in gene sequence or alleles are passed down
from parent to child)
o Genotype: representation of the pair of alleles passed down from parent to child
o Phenotype: the cell or bodies’ interpretation of the genotype
- The red blood cells have a variation of the oxygen binding haemoglobin protein & so they assume a sickled shape that
is diff. from the normal biconcave round shape (cellular phenotype)
- Physiological phenotype: diff. levels in the organism; oxygen is not carried as efficiently around the body & the odd
sickled RBCs can block the fine capillaries of the circulatory system leading to anemia & acute pain throughout the
body
- Gene for beta-globin protein lies on an autosome (chromosome 11)  means every person carries 2 alleles for the
gene  one inherited from mother, one from father
o Most people, these two alleles are both HbA alleles with sequences that code for the functional beta-globin
protein  considered homozygous for the HbA allele
 Will have cellular phenotypes that are the smooth & biconcave red blood cells
- HbS (sickle cell genotype) brought about by a mutation (a single nucleotide polymorphism that occurs in the protein
coding sequence of the beta-hemoglobin gene
o 2 HbS alleles will be homozygous, but will not be able to make the functional beta-globin proteins
o This single nucleotide polymorphism is a simple mutation that leads to an amino acid substitution of a glutamine
to a valine, and leads to an altered 3D shape (tertiary structure) of the final protein
  Harmful variation b/c will lead to a biochemical change at the protein level which will result in aggregation of
the abnormal beta-hemoglobin protein
- - If inherits one HbA allele and one HbS allele  heterozygous  will develop a sickle-cell trait
o Some of hemoglobin will be sickle-cell beta hemoglobin
o Rest of beta-hemoglobin will largely be normal & person will exhibit no symptoms
o Heterozygotes for the beta hemoglobin alleles will produce enough of the normal hemoglobin to overcome the
effect of the abnormal hemoglobin

Unit 4: Variation in Populations

Beta globin variations
- Due to various DNA polymorphisms, no 2 human individuals will have the exact same genome, base pair for base
pair
- Using DNA fingerprinting, it is possible to conduct large scale population genetic analyses to establish the variability
across populations & between ethnic groups
- Through global analyses of epidemiology, the sickle cell anemia mutant gene may confer heterozygous individuals in
a population with a selective advantage & resistance to malaria in regions with endemic & continuous malaria threats
o Provides evidence that this mutation may be advantageous in regions that are prone to malaria outbreaks
- Found that sickle-cell mutation is found in many populations with diff. alleles or haplotypes emerging independently
across various populations
- Among nations with the highest prevalence of sickle-cell anemia, found that there are a possible 5 distinct beta-globin
haplotypes found across diff. patients that correlated w/ regional distribution if each distinct sickle cell anemia single
nucleotide polymorphism
o These haplotypes found to be broadly distributed with one haplotype found to be distributed across various
nations or even multiple haplotypes found within a single nation
o Heterozygotes for the sickle cell allele are resistant to malaria infection

Variation in gene copy number

- Variations in gene copy number can also contribute to genetic differences
- Some of these copy number variations (CNVs) occur in noncoding regions, but other copy number variations can be
present as many tandem copies of a coding region along a chromosome
- A region of the genome that is normally present in only one copy per chromosome may be duplicated or deleted
- Copy number variations can be identified based on relative fluorescence intensities that are detected during DNA
microarray analysis  the greater the number of copied of chromosome sequence, the higher the fluorescence on the
microarray chip

Effect of gene copy number on phenotype

- Gene duplications usually found to be adjacent to each other along the chromosomes
- The human AMY1 gene (codes for amylase) has a detectable number of copy number differences along chromosome
1 when comparing across people with varying histories in the diets of their ancestors
o Historic low-starch diets = fewer copies of AMY1 gene
o Historic high starch diets = more copies
- These gene copy variations are a direct reflection of selective pressures (more copies in high-starch diets b/c
advantage when digesting starch)