WK 2 Flashcards
The law of segregation
Traits are controlled by alleles (forms of a gene at a specific locus), which segregate during meiosis (gamete formation; each gamete carries only one allele of each gene) and re-form randomly in a fertilized zygote.
The law of independent assortment
Alleles controlling traits segregate independently during meiosis.
Does not hold true for linked genes.
Chromosomes are composed of
chromatin which are histones (proteins) and DNA
Core histones
8 proteins.
2 copies of each type of histone.
Chromatin packing: interphase vs. mitosis
Interphase:
- ‘uncondensed’ chromatin
- cooked spaghetti all tangled
Mitosis:
- extremely highly condensed chromatin
- especially in metaphase
Cycle of condensation and decondensation as a chromosome proceeds through the cell cycle.
Relaxed in interphase
Starts compacting in prophase
Condensed in metaphase
Each chromosome occupies a specific spot called
a chromosome territory.
Chromosomes dense with genes seem to be closer to the center of the nucleus.
Bigger chromosomes with lower gene density are around the periphery.
Nucleosome
DNA wrapped around eight core histone proteins: two each of histones H2A, H2B, H3, and H4. Histone H1 is bound to linker DNAimmediately outside the nucleosome and keeps in place the DNA wrapped round the nucleosome. Core histones have an extensive α-helical structure and a protruding N-terminal tail.
‘The Histone Code’ Hypothesis
A hypothesis which states that DNA transcription is largely regulated by post-translational modifications to histones proteins.
Most of gene expression is modified by histone tails.
N terminal tail has post translational modifications that determine what happens to the structure and function of this DNA.
- These changes can result in phenotypic changes without changing the genotype.
Epi genetic regulation
change the phenotype without changing the genotype
histone proteins
1 of H1, and 2 of the rest: H2A, H2B, H3, and H4
H2A – have diff types of H2A histones
- X
- Z
- Etc
These diff members have diff AA sequences
H2AX
involved in DNA damage repair
Some areas that are more prone to DNA damage have more
When there is DNA damage, it (H2AX) gets phosphorylated and that signals DNA repair machinery to come to the area and do repair
Acetylation
acetyl group added (- charge) which causes the DNA to open up in that region
Methylation
methyl group added
Could signal down regulation or up regulation of gene expression
Ubiquitination
a signal for degradation
Interphase chromatin types
euchromatin and heterochromatin
Euchromatin
“open chromatin”; lightly packed; often under active transcription; weak binding of H1; in humans, 90% of chromatin in interphase cells is euchromatin
Accessible and active – gene expression happening
Heterochromatin
“condensed chromatin”; tightly packed; less accessible for transcription; tight binding of H1
No gene expression happening
Transmission electron microscopy
Electrons go through the sample
How many electrons = how dense the sample is
Less dense = more electrons go through = lighter image
Less dense = euchromatin
Two types of heterochromatin
constitutive and facultative
Constitutive heterochromatin
most of the heterochromatin in cells; permanently, irreversibly condensed; associated with gene-poor DNA and highly-repetitive DNA sequences (centromeres, telomeres, much of the Y chromosome); genetically inactive in somatic cells; if through some chromosome rearrangement an actively expressed gene is transposed from a euchromatic region to a heterochromatic region, it is silenced.
Dna Not expressed
Packed and tucked away
Has roles but no gene expression
Facultative heterochromatin
condensed structure that can be reversed(decondensed) and can be rich in genes; in female somatic cells one of the two X chromosomes is highly condensed – X-inactivation.
X-inactivation
Random process that happens early in female development.
Within the first week of embryogenesis, one or the other X is chosen at random to become the future inactive X.
That X then becomes the inactive X (Xi) in that cell and its progeny and forms the Barr body in interphase nuclei. The resulting female embryo is a clonal mosaic of two epigenetically determined cell types: one expresses alleles from the maternal X, whereas the other expresses alleles from the paternal X.
Can have skewed X inactivation.
- Instead of 50-50, have extreme numbers
An example of epigenetics regulation
Long non functional RNA that is non coding which starts coating the chromosome and signals and creates compaction and silencing of the chromosome
Some genes can escape this and complicate things
Epigenetics modifications can silence chunks or whole chromosome
Cytogenetics
The study of the architecture of chromosomes in cells and their role in heredity.
Involves testing samples of tissue, blood, or bone marrow in a laboratory to look for changes in chromosomes, including broken, missing,rearranged, or extra chromosomes. In cytogenetics, we are mostly dealing with condensed chromosomes (it is hard to analyze decondensed chromosomes)
Used a lot in clinical labs, used to determine a diagnosis.
Karyotype
(chromosome chart): major clinical tool that describes the chromosome count of an organism, what chromosomes look like under a light microscope, according to their length, the position of the centromeres, banding pattern, differences between the sex chromosomes, and any other physical characteristics.
Conventional cytogenetics
karyotyping/chromosome banding - Preparing samples and looking at them under a microscope
Molecular cytogenetics
Molecular cytogenetics uses probes:
Fluorescence in situ hybridization (FISH)
Comparative genomic hybridization (CGH)
Centromere
Where the spindles attach and pull apart in anaphase
Telomeres
at each end
They get degraded over time to prevent the actual DNA from being degraded
They protect the chromosome
They are repetitive sequences
short arm
p arm
long arm
q arm
Metacentric
Short and long arm are same length
Submetacentric
Short arm is short and long arm is long
Acrocentric
Short arm is very short and long arm is very long
Telocentric
No short arm
Telomere at the top, then centromere, then long arm and telomere
Not found in humans unless there’s a structural mutation that happens
Found in some animals
How to obtain a chromosome spread / karyotype
Grow cells in culture
Add colchicine/colcemid
Swell and fix cells
Spread cells on slide
Stain and image
Karyogram
Chromosomes arranged by size (largest to smallest) in pairs, and then sex chromosomes last
Giemsa or G-banding
most common banding method
Giemsa binds preferentially binds to A and T (AT rich residues)
A and T are gene poor, non coding regions
Dark stain on A and T
Light bands in euchromatic regions (C and G)
Used to see if you’re missing parts of chromosomes
Reverse or R-banding
shows the reverse banding pattern of Giemsa (i.e., reversal of light and dark G-bands). The numbering of the bands is identical with both binding methods. Heat denaturation followed by Giemsa staining.
The opposite staining pattern of G banding
C-banding
centromeric and pericentromeric DNA are composed of repetitive satellite DNA, which are easily visualized using constitutive heterochromatin (C-banding) methods.
Used to find where the centromere is
To see if something is wrong with centromeres
silver-based NOR staining
short arms of the acrocentric chromosomes house the ribosomal RNA gene clusters in the nucleolar organizing regions (NORs), which form the nucleolus of the cell.
Used to find NOR regions
Silver staining – detect proteins that are relating to the NOR regions
These regions form the nucleolus
T-banding
telomeres are composed of (TTAGGG)n mini-satellite repeats that staindarkly with T-banding.
Used to find where the telomere is
To see if something wrong with telomeres
Q-banding
Same as G but instead you use something fluorescent
Can detect smaller regions and amount and get better staining and results than G banding
Most used technique
DAPI – blue fluorescent stain that binds to dna and used to detect dna in micrographs
NOR
nucleolar organizing region
leads to formation of nucleolus
Idiogram
Schematic diagram that provides a pictorial reference point that is useful for locating the positions of individual genes on chromosomes, and for identifying various abnormalities associated with a range of chromosomal disorders.
- Turn a karyogram into an ideogram
- Centromere is shown in dark lines
- Grey is repetitive dna
How many bp or genes in one band?
Bands can contain millions of basepairs, and many genes (up to hundreds of genes).
- (one band ≠ one gene) - simply an area of genes
- Each band is numbers starting at the centromere and becomes larger as it go towards the telomere
CFTR gene = 7q31.2 (what does the location tell you?)
CFTR - Cystic Fibrosis Transmembrane Conductance Regulator
- Chromosome 7
- Arm q (long arm) Region 3
- Band 1
- Sub-band 2
- = 7q31.2
