Chp 3 Lec 1 + 2

Question 1

1. What do maps reveal in genomics?
2. Different types of map describe different types of observation:
3. Mapping also revealed that the organization of hereditary info is?
4. What is it that the genome sequence don’t reveal?

Answer 1

1. Organization of the hereditary material.
2. 1. Linkage maps of Gene’s
3. 2. Chromosome banding patterns
4. 3. Restriction maps
5. 4. DNA sequences
6. Linear and one-dimensional and co-linear and static form
7. 1. How info is implemented in space and time
8. 2. How gene expression is choreographed by orderly development programmes.
9. 3. The influence of environment, experience as well as epigenetics on the structure and activities o the organism, beyond the genome itself.

Question 2

1. In some cases, genes for different traits do not show independent assortment but are linked, their alleles are said to be?
2. Linked traits are governed by?
3. What is crossing over(recombination)?

Answer 2

1. Co-inherited
2. Genes on the same chromosome, however in many cases linkage is incomplete.
3. Exchange of genetic material between homologous chromosomes, can separate or bring together alleles of different chromosomes.

Question 3

1. Thomas Hunt Morgan observed varying degrees of linkage in___pairs of genes and suggested that ________could be a measure of distance between genes on a chromosome.
2. What observation did Alfred Sturtevant make? He made it possible to determine_____and plot them along chromosome at____.
3. Unit of length in gene map is____, defined by___.
4. How much is 1cM in humans and mention what it varies with ?
5. Crossing over is reduced in which regions? What are ‘hot spots’ regarded as?
6. It is estimated that ____ takes place in no more than ___ of our genome.

Answer 3

1. Different, the extent of recombination
2. He found that genetic distance, as measured by crossing-over frequency is additive.
   The order of genes along each chromosome, positions consistent with distance between them.
3. Morgan, the relation that 1cM corresponds to a 1% recombination frequency.
4. ~10⁶ bp and it varies with the (1) location in the genome, (2) the distance between genes, and (3) the gender - M= 1cM is 1.05Mb; F= ~0.88Mb
5. Pericentromic regions and telomeric regions. They are regarded as other regions for crossing over.
6. ~80% of genetic recombination, ~25%

Question 4

Why is it that linkage guides the search for genes?

Then is the target gene is( likely/ unlikely) to be on the same chromosome, at a position near to the marker.

Answer 4

• to find the marker of known location that tends to be co-inherited with disease phenotype.
• Likely

Question 5

Linkage disequilibrium is the non random association between ___or ___.

Linkage and linkage disequilibrium(LD) are closely related, but distinct concepts, state what each entails.

Answer 5

• Two genetic markers or loci
• linkage entails the distribution of locus among chromosomes. LD entails the distribution of allelic patterns in populations.

Question 6

Close linkage of two locus on a chromosome is a common source of?

Why wouldn’t two genes at opposite ends of the same chromosome show significant LD, although they are linked?

Conversely it is possible, although rare to? Name the two ways this can happen.

Answer 6

• Long-term persistence of LD
• because crossing over is frequent.

Observe LD between two genes on different chromosomes.
(1) immigrants introduce SNPs into a larger population, followed by preferential intermarry for many generations. (2) by interactions between gene products that allow only certain combinations of alleles to be viable- epistatic interactions

Question 7

1. Why is it that LD is considered a much finer tool for localizing genes than linkage?
2. Features for LD: M, A and B, x and y?
3. Therefore why is it a high probability that x and y will be co-inherited with M and A and B will be separated?

Answer 7

1. Because LD is detectable between loci ~0.01 - 0.02cM apart (~10 - 20kb), whereas linkage applies to markers that are no less than 1cM apart.
2. M= mutations(occured 50 human generations ago)
   A and B = phenotypic traits (1 cM away from M)
   x and y = closely spaced markers (0.1 away from M)
3. Probability of recombination is very small (0.1cM = 0.001) ; P( recomb. 50 generations)= 0.001 × 50 = 0.05
   Because probability of recomb. is 0.01; P(recomb. 50 generations)= 0.5

Question 8

1.During chromosome banding pattern maps, what is the most common used pattern?

2. State what each of these contain or reflect:
   (2. 1) Bands
   (2. 2) Darker regions
   (2. 3) Karyotype? also it is largely constant for all individuals ____, but varies____; due to ____during evolution.
3. What is the one barrier to fertility that contributes to species separation(divergence)?

Answer 8

1. G-banding, produced by Giemsa stain

2.1. Reflect base composition and chromosome loop structure
2.2. Contain highly condensed heterochromatin( thus it’s tightly packed DNA) of relatively low GC/AT ratio + sparse in gene content (genes occur on lighter regions)
2.3. Comprises the structure of individual chromosomes.
Within a species, between species, chromosome rearrangement.

3. Is the inability of cells with incongruent karyotypes to pair properly.

Question 9

Although most individuals of a species have the same Karyotype, occasionally aberrant(abnormal) chromosomes appear, some of them are?

Answer 9

Lethal and others correlate with disease

Question 10

Nomenclature of chromosome bands features:

Answer 10

Numbered 1, 2,3 etc

Arms: p and a separated by the centromere

Bands from centromere outwards numbered q1,q2, q3 etc and p1,p2,p3 etc

Additional subdivisions: p1.1, p1.2 etc and q1.1, q1.2 etc

Question 11

1. Deletion loop in salivary gland chromosomes leading to psuedodominance in Drosophila demonstrates ___between the two maps. This study showed that chromosomes carry __.
2. The modern technique for mapping gene’s onto chromosomes is?
3. Simultaneous FISH with two probes can detect?

Answer 11

1. Collinearity, hereditary info.
2. Fluorescent in situ hybridization (FISH), fluorescently- labelled probe(DNA seq), with a resolution of ~10⁵bp, and can go as low as 10³bp.
3. (1) linkage and even estimate genetic distance
   (2) chromosomal abnormalities

Question 12

When comparing human and chimpanzees chromosomes we see what?

What are syntenic blocks?

Relationships suggested by comparisons of banding patterns reflect?

Answer 12

Large-scale rearrangements that took place, e.g human chr 2 is split into two separate chromosomes in the chimpanzee.

Regions in the corresponding chr regions of the two species showing conversation of banding patterns.

Conservation at the level of DNA seq( macro vs microsynteny)