1. Higher Eukaryotic Chromosomes

Question 1

Explain chromosome anatomy

Answer 1

• telomeres
• centromere
• sister chromatids
• short (p) / long (q) arm

Question 2

Explain terms sister chromatids, centromere, telomeres

Answer 2

• Sister chromatids: indentical copies of a chromosome - formed by replication - joined by centromere
• Centromere: constricted region on a replicated chromosome - kinetochores assembles - spindle fibers attach
• Telomeres: chromosome end regions - contain repetitve DNA seq. - stable + don’t fuse with other telomeres

Question 3

Explain human karyotype

Answer 3

Human karyotype:
- 23 pairs of homologous = 46 chromosomes
- 44 autosomes + 2 sex chromosomes
- Assebled largest -> smallest (1- largest, 21 - smallest) + sex chromosomes

Question 4

Explain what is a karyotype

Answer 4

Karyotype: a set of chromosomes unique to an organism’s cells

Question 5

Why is the chromosome number uninformative in comparing organisms?

Answer 5

Chromosome number /gene number doesn’t relate to organism complexity:
- burds 39
- human 46

• kidney bean 5.2x10^9 genes
• human 3.2x10^9

Question 6

Does chromosome number remain similar in similar organisms?

Answer 6

Not necessarily - Muntjac genus
23 vs 4

Question 7

What are the possible chromosome classifications based on centromere position?

Answer 7

• Metacentric
• Submetacentric
• Acrocentric

Question 8

What is secondary constriction chromosome?

Answer 8

Secondary constriction: narrower region on chromosome arms - centromere is primary constriction

Satellite chromosomes (SATs) - in humans associated with chrom. 13, 14, 15, 21, 22

Secondary constrictions can act as NORs

Question 9

What are nucleolar organization regions (NORs)?

Answer 9

NORs: chromosomes segments - contain the genes for rRNA - give rise to the interphase nucleoli

NORs - secondary constrictions

Question 10

How can similar size chromosomes be distinguished?

Answer 10

By staining - banding pattern - distinct for each chromosome
- Giemsa
- FISH mapping

Question 11

Explain G-banding

Answer 11

Chromosome staining method
- Giemsa stain
- light (GC rich - gene rich)
- dark bands (AT rich, gene poor)

Question 12

Explain FISH gene mapping

Answer 12

For mapping genes on chromosomes:
- specific sequence complimentary hybridization with fluorescent probe

Question 13

Can chromosomes be labelled not at metaphase?

Answer 13

Yes, interphase chromosome territories labelled by FISH

Question 14

What is digital karyotyping?

Answer 14

Digital karyotyping: for quantifying gene copies in genome

Question 15

What are the types of chromosome abnormalities?

Answer 15

• Numerical abnormalities (polyploidy, aneuploidt, monosomy, trisomy)
• Structural abnormalities (gene rearrangements)

Question 16

Explain polyploidy, aneuploidy, monosomy, trisomy

Answer 16

-Polyploidy: 1+ additional chromosomes in each pair -> 3n humans not viable but common in fish, plants
- Aneuploidy: loss/gain of genetic material in single chromosome
- Monosomy: loss of one chromosome in karyotype (2n-1)
- Trisomy: gain of one chromosome in karyotype (2n+1)

Question 17

What is the most common cause of most enuploidy?

Answer 17

Non-disjunction during gamete meiosis

Question 18

What are the possible causes of aneuploidy in humans?

Answer 18

• Tolerated in sex chromosomes - gene dosage
• Not tolerated in autosomes - unbalanced genomes => spontaneous miscarriage (aborts itself if chromosome abnormality)

Question 19

What are the possible chromosome rearrangements causing structural chromosome abnormalities?

Answer 19

Chromosome rearrangements:
- duplication
- deletion
- inversion
- translocation

Question 20

Which chromosome rearrangements are balanced and unbalanced?

Answer 20

• Unbalanced: duplication / deletion - too little / many genes
• Balanced: translocation - gene dosage stays the same - location changed (ex inversion)

=> inversion better tolerated than duplications/deletions
(duplication not the same as insertion - here DUPLICATION)

Question 21

Explain non-homologous end joining (NHEJ)

Answer 21

NHEJ: repairs ds DNA breaks- break ends are directly ligated without homologous template

In contrast: homology directed repair (HDR) - requires a homologous sequence to guide repair

Question 22

Explain how gene duplication / deletion occurs

Answer 22

Duplication / deletion occurs between LCRs - double stranded chromosome break - exchange -> recombined duplication / recombined deletion => unbalanced gene dosage

=> duplications / deletions cause disease - protein overexpression / underexpression due to changed gene repeat # - unbalanced gene dosage

Question 23

What are low copy repeats (LCRs)?

Answer 23

Low copy repeats (LCRs): regions of duplicated DNA - more than 1 kb in size - share a sequence similarity >90%

On chromosomes - LCR hotspots - majority of duplications / deletions occur

Question 24

Explain how gene translocation occurs

Answer 24

Translocation: chromosome breaks - fragmented pieces re-attach to different chromosomes

Most common chromosome rearrangement - carriers healthy and fertile

Question 25

What are the types of chromosome translocations?

Answer 25

- **Reciprocal** translocations (adjacent / alternate segregation) - **Robertsonian** translocations

Question 26

What are reciprocal chromosome translocations?

Answer 26

**Reciprocal**: genetic **exchange between non-homologous** - parts of chromosome arms **exchange genes** (not whole arms exchanged)

Question 27

What are the different outcomes of different chromosome translocations?

Answer 27

**Depends how** chromosomes **segregate** and which separation axis form in meiosis 1. **Adjacent** segregation - **horizontal**=> unbalanced - **could be viable** 2. **Adjacent** segregation - **vertical** => unbalanced - **unviable** 3. **Alternate** segregation => balanced / normal - **viable**

Question 28

Explain Robertsonian translocation

Answer 28

**Robertsonian**: genetic exchange between **non-homologous acrocentric** chromosomes - **centric fusion** => **two chromosomes form one** large fused chromosome -> depending on gamete which is used for fertilization - effect size (diff final gametes) Because p arm so small - main genes in q - if p lost => still **balanced translocation**

Question 29

How can Down syndrome be caused by Robertsonian translocation?

Answer 29

Because **q arm** has all the **important genes** in **acrocentric** chromosomes - Robertsonian translocated chromosome -> **third repeat of same genes** -> trisomy However - only 3.5% of Down syndrome caused by Robertsonian translocation - majority caused by nondisjunction

Question 30

Explain what is Philadelphia chromosome

Answer 30

**Philadelphia** chromosome (22q-): made in chromosome t**ranslocation between 9q and 22q** - BCR+ABL gene fusion -> **BCR+ABL fusion protein** => chronic myeloid leukemia (**CML**) Philadelphia chromosome can be diagnosed by karyotyping - **FISH BCR and ABL** genes - **if together on one chromosome** => CML

Question 31

Example: chromosome abnormalities visible in karyotyping

Answer 31

Used FISH

Question 32

What are copy number variations (CNVs)?

Answer 32

Copy number variations (CNVs): **general term** used to describe **repeated genome sequences** - the number of repeats **varies between individuals** of same species - associated with many phenotypes - **duplications in tandem** - CNVs often rely on fixed segmental duplications

Question 33

What are the types of CNVs?

Answer 33

- **Short** repeats - **Long** repeats (if one repeat mutates - the correct protein still produced)

Question 34

What is segmental duplication?

Answer 34

**Segmental duplication**: chromosome rearrangement in which a whole **gene segment** is **duplicated** rather than only one gene - Fixed segmental duplications generate **non-essential genes** - can evolve + generate further de novo rearrangements - Example: in Asia starch very common in culture diet - asians have more **AMY1 amylase enzyme repeats** - advantage -> low repeat # releates to obesity

Question 35

What is de novo in biology?

Answer 35

Question 36

What are fixed meiotic rearrangements?

Answer 36

**Fixed meiotic rearrangement**: chromosome rearrangement **passed** to the next generation - **Karyotypes evolve** via fixed meiotic rearrangements

Question 37

What is synteny and syntenic genes?

Answer 37

**Synteny**: **conserved order of similar gene** **blocks** in different species Syntenic genes: genes arranged in same blocks in different species - Species that share synteny - common ancestor

Question 38

How can syntenic chromosomes be identified experimentally?

Answer 38

Cross species chromosome painting - **ZOO FISH**: detects **conserved synteny** - shared ancestry for chromocomal blocks - one **species' sequences** used as **probes** for the **other spiecies sequence** -> if diff colour on chromosome -> syntenic chromosomes - same common ancestor

Question 39

What is the ancestral eutherian karyotype?

Answer 39

**Ancestral eutherian karyotype**: n = 22 + X; the **MRCA** to the human karyotype and cattle lineages - Karyotype analysis between species can help determine evolutionary relationships Human chromosome blocks in ancestral karyotype

Question 40

Lecture summary + keys terms

Answer 40

Question 41

Explain pericentric vs paracentric inversion

Answer 41

**Paracentric**: inversion **doesn't involve** the **centromere** - inverted segment **exclusive to p / q arm** -> no change in length of arms **Pericentric**: inversion **involves both p + q arms and centromere** -> change in length of arms

Question 42

Detailed prokaryotic vs eukaryotic gene structure

Answer 42

https://microbenotes.com/gene-a-comprehensive-guide/

Question 43

What is non-allelic homologous recombination?

Answer 43

**NAHR**: **HR** that occurs **between two** lengths of DNA that have **high sequence similarity**, but are **not alleles**