Theme 5 Flashcards
DNA polymorphisms
1 or 2 alternate forms (alleles) at a chromosomal region that differs in either a single nucleotide base or have variable numbers of tandem repeats (VNTRs) in a given population of individuals
DNA markers
on a genetic map, are DNA polymorphisms that occur in non-coding DNA
- detectable by microarray analysis, PCR, southern blot techniques or DNA sequencing
SNPs
Single Nucleotide Polymorphisms
- variations brought on by single nucleotide base pair substitutions in DNA that occur in a significant portion of a population
- one of the most common types of genetic variation, scattered throughout the genome
- when found close to a gene, used as markers for finding a particular gene
detecting SNPs
genotyping microarray is used
- loading wells with:
C, G, A, T - they will match one strand of one allele of the SNP
and X, Y - deliberate mismatches adjacent to SNP
- 2 possible alleles are tested for and whichever wells they base pair in will fluoresce (the well will)
note: electrophoresis is not an option because a change in SNP won’t change bp length
tandem repeats
patterns of 1 or more nucleotides that are repeated directly adjacent to another, found in various lengths in individuals across a population
- results in the variations observed between species
detecting VNTRs
using PCR and gel electrophoresis
- tandem repeats are targeted and amplified with primers specific to flanking regions
- bands that migrate the least distance are larger and therefore contain a greater number of VNTR copies
- used in DNA profiling (DNA fingerprinting) but is extremely unlikely that any unrelated individuals would have the same VNTRs
genotype
a representation of the pair of alleles carried by a person
phenotype
the cell or body’s interpretation of the genotype
sickle cell anemia phenotype
- sickle shaped cells that don’t carry oxygen properly and lead to anemia
- sickle cells can also block capillaries and cause acute pain
HbA / HbA genotype results for beta-globin
phenotype: regular RBC are produced
- no symptoms of sickle cell anemia
homozygous genotype for HbA alleles
- codes for AA glutamine
HbS / HbS genotype results for beta-globin
phenotype: symptoms of sickle cell anemia
- no functional beta-globin proteins
homozygous genotype for HbS alleles
- amino acid produced is valine instead of glutamine, causing altered tertiary 3D structure that has decreased oxygen binding ability and aggregation causes RBC to have sickle shape
HbA / HbS genotype results for beta-globin
heterozygous genotype, 2 alleles are different (1 from each parent)
phenotype: no symptoms of sickle cell anemia, though cells exhibit both protein variants (both glutamine and valine)
- enough of the normal beta-globin to give us normal enough Hb to carry oxygen properly
beta-globin variations in populations around the world
- across nations with the highest prevalence of sickle cell anemia, it’s been found that there are 5 possible distinct B-globin haplotypes found across patients that correlate to each region with sickle cell anemia SNPs
individuals heterozygous for sickle cell allele
have a protective effect against malaria, a selective advantage
variation in gene copy number (CNV)
- a region of a chromosome that may be duplicated or deleted compared to the normal amount of copies present
- can occur in coding and non-coding regions
CNV detection
copy number variations detected based on fluorescence intensities during DNA microarray analysis where more fluorescence means there are more copy numbers
the effect of gene copy number on phenotype
- variations are thought to be a direct result of selective pressures such as an advantage to digesting more starch if you have a greater copy number
ex. AMY1 copy number is higher in individuals with a historically high starch diet
sequence polymorphism vs. length polymorphism
sequence: changes the message with one nucleotide
length: ex. tandem repeats - useful in paternity testing
linked SNPs
don’t necessarily cause a change but are close enough to a coding region that it gets copied with the genome
causative SNPs
affect the way a protein functions, correlating with a disease
ex. in an intron (indirectly) or an exon (directly) because exons code for genetic material
using PCR to detect VNTR differences in paternity testing
- need to look at many VNTRs to be sure
- when neither fragment matches the father, the child is likely someone else’s
meiosis
replication of gametes which are haploid rather than diploid
- has 2 rounds
- allows production of offspring that are not genetically identical
prophase 1
- homologous chromosomes condense and undergo synapsis
- final product is recombinant chromatids
recombination
a process that occurs in prophase 1
- involves the crossing over of homologous chromosomes and results in genetic variation
synapsis
pairing and physical connection of homologous chromosomes during prophase 1 via synaptromeal complex which holds the homologous chromosomes together during synapsis
sister chromatids vs. homologous chromosomes
sister chromatids: a pair of chromosomes that have been duplicated
homologous chromosomes: are individual chromosomes inherited from each parent and could be different
crossing over
exchange of corresponding segments of DNA b/w homologous chromosome pairs
- occurs at x-shaped regions called chiasmata
- increases genetic diversity
chiasmata
where 2 homologous chromosomes physically cross over to exchange DNA segments during prophase 1
reductional division
refers to meiosis 1
- called reductional division because of the reduction in chromosome number (each chromosome has 23 chromosomes by the end)
equational division
refers to meiosis 2
- called equational because parent cells start off with the same number of chromosomes as the gametes produced at the end of meiosis 2
- possible because duplicated sister chromatids gets separated
- more similar to mitosis
dominant trait
the ones that appear in offspring of. cross b/w true breeding or homozygous parents
anaphase 1
homologous chromosomes separate but sister chromatids do not separate
- synaptonemal complex breaks down to allow this
telophase 1
daughter cells are ready to move into prophase 2 when each half has a complete haploid cell of duplicated chromosomes (with each chromosome consisting of a pair of recombinant chromatids)
- at the end of telophase 1, nuclear envelope reforms, chromosomes slightly uncoil and cytokinesis follows to produce 2 separate cells
prophase 2
nuclear envelope breaks down and chromosomes condense
- spindle apparatus reforms
anaphase 2
sister chromatids separate (they are NOT genetically identical because of crossing over)
- proteins holding sister chromatids together break down to allow separation
non-disjunction
results in some gametes having extra chromosomes and other gametes having less chromosomes
- leads to detrimental effects in generated offspring
- can also occur in mitosis and be observed in cancer cells
homozygous organisms
carried 2 identical alleles for a specific trait
Gregor Mendel
characterized traits as dominant or recessive
- developed 2 laws: law of segregation and the law of independent assortment
why is the blended model of inheritance not valid
because F1 offspring would be a blend of the 2 colours but instead they were reflective of the ratio of dominant to recessive
Mendel’s 1st law of segregation
states that 2 alleles of a gene separate from each other into different gametes during gamete formation in both parents
- based on the assumption that alternate versions of genes account for variations in inherited traits
- if 2 alleles at a locus differ, then the dominant allele determines the organism’s final trait
- attributed to separation of chromosomes during anaphase 1
Punnett square
illustrates prediction of offspring b/w individuals of known traits
- must consider possible gametes produced
- practice one
Mendel’s 2nd law of independent assortment
only applies to non homologous chromosomes, and genes/allele pairs found on different chromosomes
- states that the segregation of one set of alleles of a gene pair is independent of the segregation of another set of alleles in a different gene pair
- depends on alignment of homologous chromosomes at metaphase plate during metaphase 1
monohybrids
organisms that are heterozygous for the trait produced by the cross
nondisjunction in meiosis vs. mitosis
in meiosis - it affects the embryo which will affect the whole organism
- when homologous chromosomes do not separate during meiosis 1
- when sister chromatids do not separate during meiosis 2
in mitosis - it affects only a certain cell types but can result in a tumour
meiosis in males vs females
it is less energetically costly for males and so they can reproduce throughout their lifetime
the result of nondisjunction in meiosis
- one gamete gets an extra copy of a chromosome while the other receives no copy
- other chromosomes are distributed properly
- mostly happens because of spindle checkpoint malfunctions
aneuploid cells
have an abnormal number of chromosomes
chromosomal abnormalities result in
40-50% of spontaneous abortions
monosomy
having one less chromosome in a gamete that combines with a normal gamete (the gamete therefore contains 1 copy of that particular gene)
trisomy
has 3 copies of a chromosome
- therefore 2 of the same kind will be present in a gamete
mitotic arrested males
can also produce sperm cells with abnormal chromosome numbers (aneupoloidy)
down syndrome
3 copies of chromosomes 21
- affects 1/700 children
- usually parents are older, from oocytes that have undergone nondisjunction
- dev’tal challenges
- usually live to be 50-60, and die from immune disorders or heart disease
bioinformatic analysis
allows scientists to analyze proteins present in amniotic fluid that are characteristic of down syndrome development
Dr. Brian Golding
looks at biology and math - computational biology
- looks at trisomy of chromosome 21 and has seen abnormal interactions b/w proteins
Klinefelter syndrome
males with an extra X chromosome (genotype XXY)
- most common aneuploidy in humans (1/500-1000 men)
- can come from males or females,
- men have more feminized structure, breast dev’t
- autosomes are find but males generally produce less viable gametes
Turner syndrome
monosomy of the X chromosome (most result in spontaneous abortions)
genotype XO
- less development and sterile, webbed neck
- 1/5000 births
Caster Semenya
- a female track star who had a hypersensitivity to androgen (hyperandrogenism) which lead to an uproar about gender testing in south african track and field association which probably ruined her career
- this sucks because other platforms (NBA) look for performance enhancing polymorphisms (ex. being very tall)
causal relationship b/w aneuploidy and tumourigenesis
- mitotic chromosome instability is a feature of most cancer cells and it can lead to aneuploidy
ex. males w breast cancer - have multiple copies of many chromosomes with lots of mismatching compared to healthy cells – this variation makes it hard to treat cancer cells
weakened mitotic checkpoint
results in chromosome instability
ex. delay in splitting of chromosomes or one gets pulled away super quickly affecting many genes and causes aneuploidy
- Taxol is the drug that targets this and can stabilize microtubules against depolymerization so the cell remains in metaphase-anaphase and leads to apoptosis of cancer cells
symbols on pedigree charts: what do they mean
- single horizontal line - mating b/w individuals
- vertical line - offspring from these people arranged horizontally L to R in order of birth
- double line = mating b/w relatives
- circles: female
- squares: male
- open symbol: not affected
- filled in symbol: affected
- lines running at a 45 degree angle to 2 people: twins
sex chromosomes
- the tips of the arms on the X and Y chromosomes shares a small region of homology and that’s where recombination can occur
- almost none of the genes in the X chromosome have the same counterparts on the Y chromosome
- X is much larger than Y
explain how default is female
fathers can pass on an X or Y chromosome
- in humans, the presence of the Y chromosome sets off a cascade of events leading the development of the male phenotype
Ishihara colour test
R/G colour blind test
- composed of dots with an internal pattern forming a number in red and green
red-green colour blindness
an X-linked trait
- women who are heterozygous are carriers and can pass the trait to offspring
- any male receiving the recessive colour blind allele will be colourblind because they have only 1 locus for this
- only women heterozygous for the colour blind allele will be colour blind
carrier
heterozygous individuals that do not show the phenotype but can pass the affected allele to their offspring
haemophilia
an X-linked recessive blood clotting disorder
- queen victoria was the first member of the royal fam to have it
linked genes on the X-chromosome
there are about 1100 genes on it
P arm: short arm
Q arm: long arm
- the genes for colour blindness and haemophilia are linked (both on the end of the Q arm)
linked genes
genes positioned close enough together on a chromosome (autosomes or X chromosomes) and tend to be inherited together and do not segregate independently
are linked genes always inherited together?
no. linkage can be broken in prophase 1 of meiosis 1 when crossing over occurs, as a result, offspring may inherit only one of the genes due to the recombination effects that occur b/w linked genes
recombination of alleles
- the position of the genes does not change but the relative association of the alleles would change: this is caused by crossing over
- alternately, if linked genes were immediately adjacent to one another, there would be no crossing over b/w the 2 genes: thus recombination of genes depends on the distance b/w them
recombination frequency
is less when genes are close together
- can help us determine the distance between genes if we know the recombination frequency
linkage map
shows the relative distance b/w genes on a chromosome
ex. genes for haemophilia and colour blindness are 12 map units apart (12million bp) - this distance is large enough for crossing over to occur b/w the 2 genes
- these are somewhat impractical for human applications so we use SNPs and markers to create high density linkage maps
high density linkage maps
identify genetic loci that are only a few bp apart and they can map human genes that determine various characteristics
- still looks at the frequency of recombination
genome wide association studies (GWAS)
looks across SNP linkage maps for an association b/w a phenotype and a SNP
- human SNP linkage maps: quicker and allow us to look at hundreds of thousands of people
HMGA2 gene
an example of a GWAS
- found to contribute to less than 1 cm variation in height in humans
cellular proteomes
can interact with one another based on the presence of membrane bound surface proteins
ABO gene
the alleles we carry determine our blood type
- the ABO locus has 3 main alleles: A, B, and O
- an example of a variation that does not alter function
A, B and O alleles on the ABO gene
- A and B alleles code for a specific glycotransferase enzyme that catalyzes formation of A or B agglutinogens that are expressed on the cell surface
- O alleles code for an inactive glycosyltransferase enzyme
- the AB blood type has several SNPs that lead to formation of slightly different transferases
HIV
human immunodeficiency virus
- invades T cells by interacting with 2 surface proteins: T cell surface CD4 receptor protein and CCR5 co-receptor protein
- once attached, the virus is engulfed by the cell and the infection begins, leading to the death of the T-cell and a compromised immune system
CCR5 allele alteration
a mutation that allows T-cells to be immune to HIV infection
- after mutation, a stop codon results from a frameshift mutation that produces an inactive CCR5 protein
- this mutation in 14th century Europe prevented people from getting bubonic plague and so this mutation has been selected for by natural selection
where do SNPs occur most often?
more are in non-coding regins than in coding regions
Dr. David Meyre
Austin Solek is working under him
- Dr. Meyre has a population genomics program and was part of the team that published the 1st GWAS in complex diseases (2007)
- studies the genetic basis of obesity and T2D - found that there was a region of linkage on chromosome 6q and identified 7 loci contributing to adult obesity
- discovered SIM1 gene responsible for a form of childhood obesity
- identified that OGTT is a good indicator of T2D
Dr. Ghulam Mufti
hopes to provide more into upon diagnosis of cancer
- uses microarray analysis to identify all the genes that a person has and when cancer cells are added to the chip, the squares that light up should reveal a type of gene expression happening
- this might be the start to customized medicine in terms of predicting how a patient’s cancer will behave
DNA sequences variations in humans many determine how humans:
develop diseases
respond to drugs, pathogens, chemicals and vaccines
