genetics bio 2
Gregor Mendel
monk in Austria who used garden pea plants to explain the inheritance of characteristics considered the father of modern genetics, planted 1000s of seeds per trial and did many trials to make sure
artificial pollination
can be accomplished by taking a paintbrush and transferring pollen (male gamete) on the anther of one plant to the stigma of another, this pollen travels down the the style and fertilizes an egg (anthers removed and kept in a paper bag to prevent self fertilization or outside factors)
results of artificial pollination
two different purebred varities together did not create a blend, only one feature would be expressed, self-fertilizing the offspring resulted in progeny expressing two different traits in a 3:1 ratio. Conclusions were that organisms have genes, they possess two versions of each (alleles), each gamete contains only one version of each gene, parents contribute equally to inheritence of offspring, for each gene one is dominant
mendel's law of segregation
when gametes form, alleles are separated so that each gamete carries only one allele for each gene
mendel's law of independent assortment
the segregation of alleles for one gene occurs independently to that of any other gene. This does not hold true for genes located on the same chromosome (e.g linked genes)
Mendel's principle of dominance
recessive alleles will be masked by dominant alleles. Not all genes show a complete dominance hierarchy, some genes show co-dominance or incomplete dominance
Genotype
the symbolic representation of a pair of alleles possessed by an organism
Phenotype
the characteristics or traits of an organism. E.g type O blood, five fingers on each hand
dominant allele
An allele that has the same effect on the phenotype whether it is paired with the same allele (homozygous) or a different one (heterozygous). Dominant alleles are always expressed in the phenotype. E.g the genotype Aa gives the dominant trait A
recessive allele
an allele that only has an effect on the phenotype only when present in the homozygous state. E.g the genotype aa gives rise to the recessive trait because there is no dominant allele to mask it
homozygous
when the maternal and paternal alleles are the same. E.g AA (homozygous dominant) or aa (homozygous recessive)
heterozygous
the maternal and paternal alleles are different. e.g Aa
carrier
an individual that has a recessive allele of a gene that does not have an effect on their phenotype. They may not express this gene but can carry it on to their offspring who might
pure-breeding
individuals of the same phenotype that, when crossed with each other, produce offspring which also all have the same phenotype. they are homozygous
codominant alleles
pairs of alleles that both affect the phenotype when present in a heterozygote. E.g a parent with curly hair and one with straight hair can have children with different degrees of hair curliness
causes of phenotypes
most phenotypes are caused by interactions between genotypes and the environment, however some determined solely by genotype and some by environmental factors
test cross
testing a suspected heterozygote plant or animal by crossing it with a known homozygous recessive (aa). since the recessive allele can be masked it is often impossible to tell if an organism is AA or Aa until they produce an offspring with a recessive trait
locus
the particular position on homologous chromosomes of a gene. each gene is found at a specific place on a specific pair of chromsomes
environmental factors that affect phenotypes
height (affected by diet), skin colours, cancer
how to make a punnet grid
Determine the parents' genotypes. Determine the gametes which the parents could produce (an individual with AA can only make A, carriers (Aa) can make a or A, (aa) can only make a)
draw, then deduce the chance and ratio
p generation
the parental generation
f1 generation
offspring of parental generation
f2 generation
the offspring of a cross between f1 individuals
Phenotypic plasticity
the ability to express a phenotype in response to an environmental change. Can generate changes in physiology (birds produce more maltase when less insects to eat), morphology (plants activate genes with growth hormones to make thicker leaves when there's more light), behaviour (bird migration), phenology (flowering of plants in response to seasons)
genetic diseases
genetic diseases are very rare, the number of genes present in the human genome along with the fact that most conditions are autosomal recessive, it is unlikely that one parent will have a mutation on a disease related gene, and the probability that both parents have it on the same gene is extremely small
phenylketonuria (PKU)
a rare metabolic disorder that can be destructive to the nervous system, causing intellectual disability. About 1 of every 15,000 babies are born with it. This is caused by a recessive allele of the PAH gene on chromosome 12. Low level of phenylalanine hydroxolase which converts amino acids and this can impair brain development. if both parents are carriers there is a 25% chance of having a child with it.
genetic diseases (recessive alleles)
most genetic diseases are caused by the recessive allele of a gene, individuals with the disease must have two copies of the recessive allele. If a person has one recessive and one dominant they are carriers.
Huntington's disease
an autosomal dominant disorder caused by a mutation to the HTT gene on chromosome 4. The HTT gene possesses a repeating trinucleotide sequence that is usually present in low amounts
pedigree charts
used to trace family histories and deduce genotypes and risk iin the case of inherited gene-related disorders
incomplete dominance
when neither allele for a gene completely conceals the presence of the other. Both alleles are equally dominant, producing a new phenotype (intermediate expression of a trait, looks like a blend)
blood typing
the blood type is controlled by the ABO gene. This gene has three different alleles. The O allele produces no antigen, the A allele produces the type A antigen, and the B allele produces the B antigen.
blood typing test
a lab technician mixes blood with antibodies that attack types A and B and see how the blood reacts. If the blood cells clump together (agglutinate) when mixed with B antibodies you have type B. Then it will be mixed into the anti-Rh serum, if the blood cells clump together you have Rh-positive blood
sex chromosomes
the first 22 pairs of chromosomes in a human are homologous chromosomes and are referred to as autosomes. The 23rd pair are sex chromosomes and non homologous. the X chromosome contains more genes as it is longer, some alleles of the X chromosome cannot pair up with anything on the Y chromosome as it is too small
sex determination
If present the SRY gene encodes for a protein known as testis determining factor (TDF). This is a DNA binding protein which acts as a transcription factor promoting the expression of other genes. The testis produces a hormone called MIF which causes degeneration of female organs. Testis also produces testosterone. Without TDF the gonads become ovaries
sex linkeage
sex linked traits are those which are carried on the X-chromosome in the non-homologous region. X-linked traits are exhibited more often in males. Examples of sex linked genetic disorders are hemophilia and colour blindness
colour blindness
the red-green gene is carried at locus Xq28. This locus is in the non-homologous region, so there is no corresponding gene (or allele) on the Y chromosome. Normal vision is dominant over colour blindness. Genes found in the locus are responsible for producing photoreceptive pigments in cone cells in the eye. If one of them is mutant pigments will not be produced properly and the eye cannot distinguish visbile wavelengths on the spectrum
because Xq28 is in a non-homologous region compared to the Y chromosome it is known as a sex-linked disorder
Hemophilia
blod clotting is a metabloic pathway and requires globular proteins called clotting factors. A recessive X-linked mutation in hemophiliacs results in one of these factors not being produced. Heterozygous females are carriers
autosomal dominant
if both parents are affected and an offspring is unaffected, the trait must be dominant. All affected individuals must have at least one affected parent. If both parents are unaffected, all offspring must be unaffected
autosomal recessive
if both parents are unaffected and an offspring is affected, the trait must be recessive (parents are carriers), if both parents show a trait, all offspring must also exhibit the trait
determining x-linked inheritance
it is not possible ot confirm sex linkeage from pedigree charts, as autosomal traits could potentially generate the same results, however certain trends can be used to confirm that a trait is not x-linked dominant or recessive
x-linked dominant
if a male shows a trait, so too must all daughters as well as his mother. An unaffected mother cannot have affected sons or an affected father. X-linked dominant traits tend to be more common in females
X-linked recessive
if a female shows a trait, so too must all sons as well as her father. An unaffected mother an have affected sons if she is a carrier. X-linked recessive traits tend to be more common in males
discrete variation
when individuals fall into a number of distinct categories such as blood types.
continuous variation
when phenotypes vary gradually from one extreme to another. Polygenic inheritence involves two or more genes influencing the expression of one trait - with two or more allelic pairs found at different loci, and the number of genotypes is gradually increased.
dihybrid crosses
Mendel wanted to know if the inheritance of one characteristic influenced the inheritance of a different characteristic. First he produced plants that were purebred for pea's texture and colour. Consider two traits, each carried on separate chromosomes (unlinked). In homozygous recessive and dominant crossed it will always produce one with both dominant traits
Test crosses - dihybrid genes
if we do not know the genotype of one parent, we can use test crosses to estimate. E.g if there are the genotypes ssyy, and the phenotypes Ry, rg, and X, and some green peas are found the unknown genotype must be ssYy, if there are no green the unknown parent must be ssYY
locus
the particular position on homologous chromosomes of a gene. Each gene is found at a specific place on a specific pair of chromosomes.
Human chromosome nomenclature
chromosomes have major landmarks (e.g centromere, primary constriction). The centromere divides the chromosomes into the short or p and long or q arms. Each arm is divided into 1-4 regions, each band within a region is numbered centromere to telomere (ap at ends of chromosomes). Bands can be divided into sub bands, the larger the number the further. E.g 7(chromosomal number) q (arm) 2(region number) 2(band number) 1(sub-band number)
linked genes
pairs or groups of genes that are on the same chromosome and that tend to be inherited together. linkeage groups are all of the genes on any one chromosome. there are two types of linkage, autosomal (genes found on the same autosome) and sex linkage (genes are found on the sex chromosome and shows a pattern in frequency between males and females)
Chi-squared test
they are a statistical measure that are used to determine whether the difference between an observed and expected frequency distribution is statistically significant. If observed frequencies do not conform to those expected for an unlinked dihybrid cross, this suggests that either genes are linked and hence not independently assorted, the inheritance of traits are not random, and may be affected by natural selection
method of chi-square test
1. identify hypothesis (null versus alternative)
2. construct a table of frequencies (observed vs expected)
3. apply the chi-squared formula to determine the chi-square value
4. determine the degree of freedom (df)
5. identify the p value (should be <0.05)
6. ompare the value of the chi-squared with the critical value, if it is greater then the null hypothesis is rejected and vice versa
null hypothesis
there is no significant difference between observed and expected frequencies (i.e genes are unlinked), H0
alternative hypothesis
there is a significant difference between observed and expected frequencies (i.e genes are linked)
chi-squared test formula
x^2 = sigma (0-E)^2/ E
determining degrees of freedom
the mathematical restriction that designates what range of values fall within each significance level. The degree of freedom is calculated from the table of frequencies according to the following formula. df = (m-1)(n-1), m = number of rows, n = number of columns. For all dihybrid crosses, the degree of freedom should be number of phenotypes - 1
gene silencing
refers to the ability of a cell to prevent the expression of a particular gene. While this occurs naturally, it can also be induced by scientists to study the function of genes, gene interactions and potentially treat inherited diseases
gene knockout
a genetic technique whereby a specific gene is rendered inoperative within an organism. The organism is called a knockout organism
knockout mice
used as models in order to test the effectiveness of drugs, conditions that have been studied using them are obesity, diabetes, anxiety, longevity, propensity to developing cancer, substance abuse, and cardiovascular disease
cre-loxP system
using this, gene knockout can be targeted to specific tissues within the organism. The system uses the enzyme Cre recombinase to remove genetic sequences located between two lox sites. Using technology, LoxP sequences are inserted on either side of a gene, the Cre gene is inserted next to a tissue specific promoter in another test animal. When the two animals are bred the offspring will possess both, and the gene located between the lox sites will be removed
RNA interference
short interfering RNA is a double-stranded RNA molecule that is roughly 20-25 base pairs in length. siRNA interferes with the expression of genes by causing the mRNA transcripts to be broken prior to translation. With the siRNA unwinds, the passenger strand is degraded and the guide strand remains, which will hybridize to its complementary mRNA sequence and get a protein complex (RISC) which will destroy the targeted mRNA, preventing the translation of the gene
Gene transfer - Cas9 and CIRSPR
can be used in gene therapy, a virus vector is used to insert the recombinant plasmid into the genes of affected cells. The virus is chosen or designed to target only those specific cells
CIRSPR-Cas9
a type of immune system discovered in bacteria which has been adapted by scientists to be a biotechnology tool for editing DNA. It is made up of a DNA-cutting enzyme and a programmable RNA molecule so it can precisely target any gene.
guide RNA
a sequence of rna that is synthesized to match a target sequence of interest, such as a sequence within a particular gene
target RNA
a sequence of dna that matches a sequence of about 20 nulceotides in the guide RNA and will be targeted by the Cas9 nuclease
PAM
a three-nucleotide sequence consisting of 5'-NGG-3' in which the N represents any nucleotide followed by two guanines and allows for the guide rna to bind to the target rna. In humans, PAM occurs approximately every 50 bases or less which explains why you can use the Cas9 guide RNA complex to target any human gene
targeting process
the cas9-guide rna complex is a molecular scissor with a gps. It recognizes and binds to a three nucleotide sequence motif called PAM. When guide RNa is added to cas9, it will guide cas9 to this target sequence.
binding process
cas9 recognizes and binds to PAM in the cell's dna, after it unwinds and pulls apart the double helix upstream of PAM. If the sequence of the unpaired DNA strand is not an exact match to the sequence within the guide RNA, cas9 disengages and zips the dna back up, but it they match the rna base pairs with the dna to form a new helix
cleaving process
when the guide rna perfectly aligns with the target dna, they will join to form a DNA-RNA helix. This activates Cas9's nuclease which makes specific cuts in the DNA. Two active sites on the nuclease domain of cas9 generate the cuts and cleave both dna strands and results in a double stranded dna break
NHEJ Dna repair
more frequently used, faster repairing because the cell does not use a template to join broken DNA ends together. It is prone to errors that can introduce mutations into the target sequence. Errors are rare, and when correct cas9 will recognize the target sequence and cleave it over and over again which results in a mutation.
Homology Directed repair
uses homologous DNA template to repair breaks. Scientits can add an RNA copy of the desired replacement base sequence for the gene called the RT template to the guide RNA. A RT enzyme is attached ot the cas9 so that it can assemble a strand of DNA nucleotides complementary to the RT template. Part of cas9 is inactivated so that it only makes one cut in one of the dna strands. RT adds dna nucleotides to extend the dna strands.
benefits of CIRSPR cas9
treats disorders caused by single gene mutations (sickle cell anemia), can delete entire chromosomes (get rid of down syndrome) Can introduce traits to crops and livestock (GMO), modifying mosquitoes to get rid of their ability to carry viruses, modifying plants to make renewable fuels to replace fossil fuels
risks of CIRSPR Cas9
potential off target mutations in the genome, cost of technology is very high, potential misuse of technology (e.g editing embryos, eugenics).
conserved and highly conserved sequences
genes evolve and mutate at different rates. Conserved show minimal mutations over time, and highly conserved show almost no change. Commonly conserved genes are typically genes that are needed for all cells (ones involved in DNA replication, sequences for cellular respiration). To visualize sequences, they combine the science of genomics and bioinformatics (e.g ECR Browser)
functional requirements
substances vital to a cell's survival tend to be more conserved. Natural selection conserves these sequences by necessity and does not let any mutations pass down to the next generation (callled purifying or negative selection)
slower mutation rates
some zones of a sequence are less prone to mutation leading to a slower mutation rate (refers to how many changes there are in a genetic sequence over time). Higher mutation rates in non-coding DNA regions because it does not undergo purifying selection. Proofreading functions are more active in areas where error could have more negative consequences and vice versa.