WK 2

Question 1

The law of segregation

Answer 1

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.

Question 2

The law of independent assortment

Answer 2

Alleles controlling traits segregate independently during meiosis.
Does not hold true for linked genes.

Question 3

Chromosomes are composed of

Answer 3

chromatin which are histones (proteins) and DNA

Question 4

Core histones

Answer 4

8 proteins.
2 copies of each type of histone.

Question 5

Chromatin packing: interphase vs. mitosis

Answer 5

Interphase:
- ‘uncondensed’ chromatin
- cooked spaghetti all tangled

Mitosis:
- extremely highly condensed chromatin
- especially in metaphase

Question 6

Cycle of condensation and decondensation as a chromosome proceeds through the cell cycle.

Answer 6

Relaxed in interphase
Starts compacting in prophase
Condensed in metaphase

Question 7

Each chromosome occupies a specific spot called

Answer 7

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.

Question 8

Nucleosome

Answer 8

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.

Question 9

‘The Histone Code’ Hypothesis

Answer 9

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.

Question 10

Epi genetic regulation

Answer 10

change the phenotype without changing the genotype

Question 11

histone proteins

Answer 11

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

Question 12

H2AX

Answer 12

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

Question 13

Acetylation

Answer 13

acetyl group added (- charge) which causes the DNA to open up in that region

Question 14

Methylation

Answer 14

methyl group added

Could signal down regulation or up regulation of gene expression

Question 15

Ubiquitination

Answer 15

a signal for degradation

Question 16

Interphase chromatin types

Answer 16

euchromatin and heterochromatin

Question 17

Euchromatin

Answer 17

“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

Question 18

Heterochromatin

Answer 18

“condensed chromatin”; tightly packed; less accessible for transcription; tight binding of H1

No gene expression happening

Question 19

Transmission electron microscopy

Answer 19

Electrons go through the sample

How many electrons = how dense the sample is

Less dense = more electrons go through = lighter image

Less dense = euchromatin

Question 20

Two types of heterochromatin

Answer 20

constitutive and facultative

Question 21

Constitutive heterochromatin

Answer 21

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

Question 22

Facultative heterochromatin

Answer 22

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.

Question 23

X-inactivation

Answer 23

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

Question 24

Cytogenetics

Answer 24

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.

Question 25

Karyotype

Answer 25

(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.

Question 26

Conventional cytogenetics

Answer 26

karyotyping/chromosome banding - Preparing samples and looking at them under a microscope

Question 27

Molecular cytogenetics

Answer 27

Molecular cytogenetics uses probes:
Fluorescence in situ hybridization (FISH)
Comparative genomic hybridization (CGH)

Question 28

Centromere

Answer 28

Where the spindles attach and pull apart in anaphase

Question 29

Telomeres

Answer 29

at each end

They get degraded over time to prevent the actual DNA from being degraded

They protect the chromosome

They are repetitive sequences

Question 30

short arm

Answer 30

p arm

Question 31

long arm

Answer 31

q arm

Question 32

Metacentric

Answer 32

Short and long arm are same length

Question 33

Submetacentric

Answer 33

Short arm is short and long arm is long

Question 34

Acrocentric

Answer 34

Short arm is very short and long arm is very long

Question 35

Telocentric

Answer 35

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

Question 36

How to obtain a chromosome spread / karyotype

Answer 36

Grow cells in culture
Add colchicine/colcemid
Swell and fix cells
Spread cells on slide
Stain and image

Question 37

Karyogram

Answer 37

Chromosomes arranged by size (largest to smallest) in pairs, and then sex chromosomes last

Question 38

Giemsa or G-banding

Answer 38

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

Question 39

Reverse or R-banding

Answer 39

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

Question 40

C-banding

Answer 40

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

Question 41

silver-based NOR staining

Answer 41

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

Question 42

T-banding

Answer 42

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

Question 43

Q-banding

Answer 43

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

Question 44

NOR

Answer 44

nucleolar organizing region

leads to formation of nucleolus

Question 45

Idiogram

Answer 45

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

Question 46

How many bp or genes in one band?

Answer 46

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

Question 47

CFTR gene = 7q31.2 (what does the location tell you?)

Answer 47

CFTR - Cystic Fibrosis Transmembrane Conductance Regulator
- Chromosome 7
- Arm q (long arm) Region 3
- Band 1
- Sub-band 2
- = 7q31.2