NOTE: CRISPR will not be on the exam
innate immunity vs adaptive immunity
innate immunity is non specific defences that act the same way against all foreign agents.
Adaptive immunity is a specific response for each individual pathogen.
Bacteriophage
a virus that infects bacteria
CRISPR purpose
bacteria's adaptive immunity defense system against bacteriophages
CRISPR gene region consists of
repeats & spacers
CRISPR repeats
Repeated sequences of nucleotides that are distributed throughout a CRISPR region - genetic signature
CRISPR spacers
in between repeated sequences, unique DNA sequences that are derived from past encounters with viruses or other foreign genetic elements
CRISPR adaptation phase
occurs when bacteria are exposed to bacteriophage virus for the first time, cas1 and cas 2 genes are expressed as a cas1cas2 complex and break up bacteriophage DNA strand, some pieces of it are then inserted into CRISPR system
nucleases
degrade nucleic acids (DNA & RNA)
nucleases in CRISPR response
Cas1 and Cas2 expressed genes together
what is transcribed in CRISPR expression phase
transcription of entire CRISPR gene (Repeats and spacers)
What occurs during CRISPR expression phase?
precrRNA and tracrRNA are transcribed and bind together due to complimentary base pairing. Cas9 proteins are also expressed, and these bind to the complex just formed.
CRNA guides cas protein to bind to complimentary pairs of DNA or RNA of foreign material, then they break up and degrade these foreign sequences.
The chromosomal theory of inheritance states that
chromosomes are carriers of genetic information
sytenic genes
genes located on the same chromosome
Bateson and Punnett dihybrid cross results
Crossed purple/red and long/round pollen genes true breeding for each, and allowed F1 generation to self fertilize. Found that parental phenotypes were most numerous.
Why did Bateson and Punnett still see differing phenotypes from the parents despite linked assortment occurring?
Crossing over events could have occurred between the parental chromosomes that were dominant or recessive linked.
What did Bateson and Punnett results tell us?
Crossing over can occur, but it is more likely that it does not occur in the offspring production
synaptonemal complex
a zipper-like structure composed of proteins, which connects two homologous chromosomes tightly along their lengths in prophase 1
Chiasma
The microscopically visible site where crossing over has occurred between chromatids of homologous chromosomes during prophase I of meiosis.
recombinant chromosomes
A chromosome created when crossing over combines the DNA from two parents into a single chromosome.
More space between genes on a chromosome means
more space for crossing over to occur - higher chance of a random cross over event to happen
More recombinants in a cross is due to
more distance between two genes on homologs
test cross
the crossing of an individual of unknown genotype with a homozygous recessive individual to determine the unknown genotype
Distance of genes formula
= (total # recombinants/total# of all offspring ) * 100
units used to describe distance
map units (m.u.) or CentiMorgans
1 map unit = __% recombination in a test cross
1%
Karyotype
A display of the chromosome pairs of a cell arranged by size and shape in an organized manner.
Autosomes
non-sex chromosomes (1-22)
sex chromosomes
XY, determine sex of an individual
metaphase spread
Analysis of chromosomes arrested during metaphase. The chromosomes are highly condensed at this stage of cell division and are visible under a light microscope.
Classification of chromosomes for a karyotype
size (first is largest), location of centromere, G-banding
metaphase chromosome centromere locations
metacentric, submetacentric, Afrocentric, telocentric
metacentric
centromere approximately in middle of chromosome
submetacentric
centromere slightly off center
acrocentric
centromere close to end
telocentric
centromere at end
G-banding of chromosomes
Giemsa stain binds to naked DNA. Stains phosphate groups, darker in regions rich of A-T base pairs. Allows for identification of chromosomes in karyotype
p chromosome
short arm of chromosome
q chromosome
long arm of chromosome
does a metacentric chromosome still have a long arm and short arm?
Yes
types of changes in chromosomal structure
deletion, duplication, inversion, simple translocation, reciprocal translocation
chromosomal structure deletion
region of chromosome is deleted
chromosomal structure duplication
region of chromosome is duplicated
chromosomal structure inversion
region of chromosome is inverted (flipped)
simple translocation chromosomal structure
one region moves and attaches to another region
reciprocal translocation chromosomal structure
one region from each chromosome switch places
types of chromosomal deletions
terminal deletion & interstitial deletion
terminal deletion
deletion at end of chromosome
interstitial deletion
chromosome breaks at two locations, the central fragment is lost, and the outer pieces rejoin
clastogens
any substances that can break the backbone of DNA
Non-allelic homologous recombination (NAHR)
a form of homologous recombination that occurs between two lengths of DNA that have high sequence similarity, but are not alleles (not at the same spot on each chromosomes - misaligned)
two ways you can get deletions
clastogens or NAHR
Cri du chat syndrome
A deletion of the short arm of chromosome 5, many issues caused by a small deletion
when is deletion most important?
when a part or an essential gene is deleted
essential gene
a gene that is essential for survival
replication slippage
occurs during DNA replication, DNA polymerase can be unstable and fall off replicating strand, and return at a spot it has already replicated because the region looks similar, thus, some of the region after replication has been duplicated
Processitivity
how stable enzyme is on DNA backbone
Homologues
chromosomes that are given the same number, but are of opposite parental origin
How do homologues form
gene duplication occurs, over generations, the two genes can become very different due to gradual accumulation of DNA mutations
Paralogs
homologous genes in the same species
pericentric inversion
inversion that includes the centromere
peracentric inversion
inversion that does not include the centromere
Most inversions
do not result in an abnormality
Detrimental inversion cases
position effect, chromosomal break happens in middle of an essential gene
position effect
change in expression of a gene associated with a change in the gene's location within the genome
Euchromatin
loosely packed chromatin
Heterochromatin
tightly packed chromatin
tightly packed chromatin usually results in gene...
silencing
facultative heterochromatin
Regions that can interconvert between euchromatin and heterochromatin
facultative heterochromatin is useful because
it helps control gene expression with its versatility
Chromatin
Clusters of DNA, RNA, and proteins in the nucleus of a cell
constitutive heterochromatin
Regions that are always heterochromatic, telomeres & centromeres
variegation in drosophila example
position effect, genes on euchromatin are inverted and are then closer to centromere (heterochromatin region), and now the gene is less likely to be expressed
hemophilia example
essential gene is disrupted by chromosomal break, sequence is inverted, and gene is unable to be finished because exons are out of order
The middle gene of a three gene mapping experiment can be determined by examining the genotypes of which of the following?
Offspring that exhibit double crossover events.
A crossover in meiosis is an exchange of genetic material between __________.
non-sister chromatids of homologous chromosomes
define the principle of linkage?
Both two or more genes that are physically connected on a chromosome and genes that are transmitted to the next generation as a group
The production of gene families, such as the globin genes is the result of ________.
gene duplications
When does crossing over occur?
Prophase 1
Gene duplications may be caused by __________.
crossing over of misaligned chromosomes
A tall (T) tomato plant with mottled (m) leaves is crossed with a short (t) plant with normal (M) leaves. You get all tall, normal leafed F1 plants.You cross the F1 plants with a short, mottled leafed plant. What would be the expected values from this hypothesis?
Tall mottled 250, Short normal leaves 250, Tall normal leaves 250, Short mottled leaves 250 - explain: TtMm x ttmm gives TtMm, ttMm, Ttmm, and ttmm possibilities. 4 options mean divide total pop. /4 = 1000/4 = 250 expected for each phenotype
two mechanisms that result in translocation events
non homologous crossover/recombination, chromosomal breakage incorrectly repaired
incorrect chromosomal repair from environmental breakage - how does it happen?
environmental agent causes 2 chromosomes to break, DNA repair recognize reactive ends and incorrectly correct them, causing reciprocal translocation.
Homologous Recombination vs nonhomologous recombination vs non allelic homologous recombination
homologous: crossing over between homologous chromosomes (we want this to happen, exact same spot). nonhomologous: crossover between non homologous chromosomes that results in reciprocal translocation. Non-allelic: occurs between high similar sequences that are not alleles, not at the exact same place (misaligned)
non homologous recombination
cross over between nonohomologous chromosomes results in reciprocal translocation
balanced translocation
a translocation, such as a reciprocal translocation, in which the total amount of genetic material is normal or nearly normal
Why translocation is usually detrimental
position effect, if break occurs in middle of important gene
Philadelphia chromosome & CML
chromosomal break between chromosome 9 and 22, ABL on chromosome 9 encourage cell cycle division, common break BCR region on chromosome 22, both sites break, and the ABL and BCR genes come together on chromosome 22 (changed Philadelphia chromosome), this new chromosome cannot be silenced - continuous cell division, results in CML type of cancer.
Familial Down Syndrome
Robertsonian translocation between chromosomes 14 and 21
Robertsonian translocation - how does it happen (criteria for it)
two ACROCENTRIC chromosomes, fusion of both long arms
How does robertsonian translocation lead to familial Down syndrome?
A parent who has undergone robertsonion translocation in reproduction makes some gametes with only one chromosome copy, when a normal sperm interacts with a long arm mutant chromosome, the long arm counts as a trisomy and leads to familial Down syndrome
Euploidy
total number of chromosomes divides into perfect sets
Types of Euploidy
diploid (2n), triploid (3n), tetraploid (4n)
Aneuploidy
total # of chromosomes do not divide into perfect sets
types of aneuploidy
trisomy (2n+1), monosomy (2n-1)
imbalance of gene products in trisomy and monosomy
normal individuals make 100% expression, trisomy makes the one 3 chromosome set have 150%, monosomy has the one one chromosome set have 50%
Trisomy where an organism can still live
13, 18, 21 (note: these are generally smaller chromosomes, fewer genes changed in expression means lesser drastic effects)
why don't trisomies happen in chromosome 1?
it is so detrimental that a spontaneous abortion would happen before the mother even knew
Nondisjunction can occur when
anaphase of meiosis 1 and 2