DNA & Chromosome Organization

Question 1

Three components of the DNA

Answer 1

Nitrogen base
deoxy-D-ribose (deoxyribose)
Phosphate Group

Question 2

Bond/Linkage between the nitrogenous base and the sugar component

Answer 2

N-glycosidic bond

Question 3

Bond/Linkage between the pentose sugar and the phosphate group

Answer 3

phosphodiester bond/phosphodiester linkage

Question 4

1 complete turn of DNA Double Helix

Answer 4

10 bp (3.4 nm or 34 Å)

Question 5

distance between 2 bases

Answer 5

0.34 nm or 3.4 Å

Question 6

Do all proteins have quaternary structures? Why or why not?

Answer 6

Not all proteins have quaternary structures because there are functional proteins that are monomeric, which means they only contain a single subunit of polypeptide.

Question 7

Practical Applications of Molecular Biology

Answer 7

1. DNA fingerprinting
2. Estimation of genetic variation
3. Determination of evolutionary relationships
4. Development of molecular markers for agriculture and food
5. Development of molecular diagnostic tools

Question 8

What is biotechnology?

Answer 8

Biotechnology is a technology (or a combination of agricultural, molecular, and medical technologies) that utilizes biological processes, organisms, or parts of living organisms to provide new services and/or products.

Question 9

Applications of Biotechnology

Answer 9

1. wine and cheese making (using microorganisms, fermentation)
2. antibiotics
3. vaccines and monoclonal antibodies
4. insulin and other hormones
5. addition of nutrients

Question 10

How is a prokaryotic chromosome packaged?

Answer 10

The DNA molecules are associated with basic proteins (H and HU) to form about 100 independent domains, each domain negatively supercoiled, and therefore highly folded, forming a single chromosome.

Question 11

How is a eukaryotic chromosome packaged?

Answer 11

Four types of histone proteins—H3₂-H4₂ tetramer associated with two H2A-H2B dimers—form the nucleosome octamer core. The DNA double helix (which is 2 nm wide) is wound around this core one and 2/3 times. This DNA-core nucleosome bead is linked to another bead via a linker DNA, which is associated with another type of histone, H1. Linked beads form the beads-on-a-string formation which is 11 nm wide. The beads-on-a-string further coils to form the 30-nm chromatin fiber, which is condensed further to form the 300-nm looped domains. This is packaged further to form the condensed section of a chromosome 700 nm wide, which is then highly folded, forming the 1400-nm chromosome.

Question 12

Post-translational modifications of the histone tails

Answer 12

1. Acetylation
2. Methylation
3. Phosphorylation
4. Ubiquitination
5. Sumoylation

Question 13

PTM of histone tails: What happens during acetylation?

Answer 13

Addition of an acetyl group (Ac) to a lysine (K) residue via HAT relaxes the chromatin, making it less positively charged, which makes it conducive for transcription and replication. Removal of Ac via HDAC maintains the positive charge, closing the chromatin, which makes it inaccessible to transcription or replication.

Question 14

PTM of histone tails: What happens during methylation?

Answer 14

Addition of a methyl group (Me) to a lysine (K) residue (of H3 and H4 tails) or an arginine (R) residue via HMT prevents acetylation, which maintains the positive charge of the chromatin, making it inaccessible and therefore inactivating the genes.

Question 15

PTM of histone tails: What happens during phosphorylation?

Answer 15

Addition of a phosphate group (P) to the serine (S) and threonine (T) side chains can result in the modification of different cellular processes.
Phosphorylation at…
H3 is involved in regulating transcription,
H2AX is involved in mitotic chromatin condensation, and
H2B is involved in DNA damage response and apoptosis.

Question 16

Phosphorylation at…
(1) is involved in regulating transcription,
(2) is involved in mitotic chromatin condensation, and
(3) is involved in DNA damage response and apoptosis.

Answer 16

1. H3
2. H2AX
3. H2B

Question 17

PTM of histone tails: What happens during Ubiquitination?

Answer 17

Addition of a single ubiquitin (Ub) to or monoubiquitination of the lysine (residue) of H2A and H2B tails alters the chromatin structure and allows access to transcription. It also further induces other PTMs of proteins. Enzymes involved are ubiquitin ligases and deubiquitinating enzymes.

Question 18

PTM of histone tails: What happens during sumoylation?

Answer 18

Addition of a ubiquitin-like protein called SUMO (small ubiquitin-like modifier) or sentrin allows protein localization and protects the tail from ubiquitination. It can recruit HDACs that can mediate gene silencing, and can be reversed by proteases.

Question 19

SARs
MARs

Answer 19

scaffold-associated regions
matrix-attachment regions

Question 20

What makes up the complete chromatin complex?

Answer 20

DNA
histone octamers
non-histone chromatin-associated proteins

Question 21

Define a gene.

Answer 21

A gene is a set of bases or a nucleotide sequence that codes for an RNA sequence that can be translated to a polypeptide chain, and eventually, a functional protein (protein-coding or structural genes), or that regulates the expression of other genes (regulatory genes). Regulatory genes control the expression of structural genes, and together they constitute an individual’s genotype, which then determines its observable traits (phenotype).