[W2] Key Concepts

Question 1

Why is genome size not a good indicator of genetic complexity?

Answer 1

There’s no clear correlation; some simple organisms have large genomes due to repetitive elements.

Question 2

What type of DNA typically encodes polypeptides?

Answer 2

Nonrepetitive DNA.

Question 3

What makes up a large part of moderately repetitive DNA?

Answer 3

Transposons.

Question 4

What percentage of the human genome is made of exons?

Answer 4

Only 1%.

Question 5

How many genes are in the human genome?

Answer 5

About 20,000.

Question 6

How many protein variants (proteome) does the human genome produce?

Answer 6

50,000 to 60,000 due to alternative splicing.

Question 7

What is the function of telomeres?

Answer 7

They stabilize chromosome ends and protect them.

Question 8

What is the repeating sequence found in human telomeres?

Answer 8

(T/A)1–4 G>2 or 5′-TTAGGG-3′.

Question 9

What enzyme synthesizes telomeres?

Answer 9

Telomerase.

Question 10

What type of enzyme is telomerase?

Answer 10

A ribonucleoprotein with reverse transcriptase activity.

Question 11

When is telomerase active?

Answer 11

In actively dividing cells.

Question 12

What happens when telomeres are lost?

Answer 12

Cells undergo senescence.

Question 13

What are G-bands on chromosomes?

Answer 13

Striations with lower G-C content.

Question 14

Where are genes mostly concentrated in chromosomes?

Answer 14

G-C–rich interbands.

Question 15

What is DNA supercoiling?

Answer 15

Winding of the DNA double helix around itself to change topology.

Question 16

Where does supercoiling occur?

Answer 16

In closed DNA (circular or anchored linear DNA).

Question 17

How is DNA packaged in spherical DNA viruses?

Answer 17

Inserted into a preassembled protein shell.

Question 18

What organizes bacterial chromosomes?

Answer 18

Nucleoid-associated proteins (e.g., HNS, HU).

Question 19

What are bacterial macrodomains?

Answer 19

Ori, right, ter, and left regions with distinct spatial patterns.

Question 20

What is the average supercoiling density in bacteria?

Answer 20

~1 turn per 100 base pairs.

Question 21

How is interphase chromatin organized in eukaryotes?

Answer 21

Into loops and domains attached to a nuclear matrix.

Question 22

What are matrix attachment regions rich in?

Answer 22

A-T base pairs.

Question 23

What is euchromatin?

Answer 23

Less tightly packed chromatin visible in interphase.

Question 24

What is heterochromatin?

Answer 24

Densely packed chromatin that remains so throughout interphase.

Question 25

What histone variant characterizes centromeres?

Answer 25

A centromere-specific H3 variant.

Question 26

What kind of DNA is commonly found at centromeres?

Answer 26

Repetitive satellite DNA.

Question 27

What enzyme is used to study nucleosomes?

Answer 27

MNase (Micrococcal Nuclease).

Question 28

What is the basic unit of chromatin?

Answer 28

The nucleosome.

Question 29

How much DNA does a nucleosome contain?

Answer 29

About 200 base pairs.

Question 30

What are the core histones?

Answer 30

H2A, H2B, H3, and H4.

Question 31

What does histone H1 do?

Answer 31

Binds linker DNA, helping compact chromatin.

Question 32

What is the histone code hypothesis?

Answer 32

Combinations of histone modifications define chromatin function.

Question 33

What domain recognizes acetylated histones?

Answer 33

Bromodomain.

Question 34

What recognizes methylated lysines on histones?

Answer 34

Chromodomain, PHD domain, Tudor domain.

Question 35

Which core histone has no known variants?

Answer 35

H4.

Question 36

What is the 10-nm fiber in chromatin?

Answer 36

A string of nucleosomes (primary structure).

Question 37

What is the 30-nm fiber?

Answer 37

A secondary structure formed by nucleosome interactions.

Question 38

What proteins help assemble nucleosomes during replication?

Answer 38

CAF-1 and ASF1.

Question 39

What helps in replication-independent assembly?

Answer 39

HIRA and histone variant H3.3.

Question 40

What does DNase sensitivity reveal?

Answer 40

Open, accessible chromatin regions.

Question 41

What are DNase hypersensitive sites?

Answer 41

Sites exposed due to the absence of nucleosomes, often regulatory.

Question 42

What are TADs?

Answer 42

Stable chromatin domains (~1 Mb) where internal interactions are more frequent.

Question 43

What are insulators?

Answer 43

Elements that block the effects of enhancers/silencers and prevent heterochromatin spread.

Question 44

What defines TAD boundaries?

Answer 44

Insulator elements.

Question 45

What are the types of DNA sequences in eukaryotic genomes?

Answer 45

Eukaryotic genomes have nonrepetitive sequences (coding for proteins) and repetitive sequences, often consisting of transposons.

Question 46

How are repeated sequences distributed in the genome?

Answer 46

Over 50% of the human genome consists of repeated, mostly nonfunctional transposon sequences.

Question 47

How much of the human genome is protein-coding?

Answer 47

Only ~1% is exonic; genes (exons + introns) make up ~25% of the genome.

Question 48

What is the structure and function of telomeres?

Answer 48

Telomeres are simple repeats like (T/A)1–4 G>2 at the chromosome ends that maintain stability and participate in meiosis via the cytoskeleton.

Question 49

What enzyme synthesizes telomeres and how?

Answer 49

Telomerase extends 3' ends using its own RNA template to add TTAGGG repeats in humans.

Question 50

Where is telomerase active?

Answer 50

Actively dividing cells. Inactive in quiescent cells; loss leads to senescence.

Question 51

What causes G-banding patterns in chromosomes?

Answer 51

Certain stains create G-bands (AT-rich) and interbands (GC-rich); genes are concentrated in interbands.

Question 52

What is a nucleoid?

Answer 52

The bacterial genome organized into loops by proteins like HNS and HU.

Question 53

How is the bacterial genome organized?

Answer 53

~400 negatively supercoiled domains with 4 macrodomains (ori, right, ter, left).

Question 54

How is eukaryotic DNA structured during interphase and mitosis?

Answer 54

Interphase: Euchromatin (less packed), Heterochromatin (densely packed). Mitosis: condensed chromosomes.

Question 55

What is the role of the nuclear matrix and scaffold?

Answer 55

DNA loops attach to A-T rich matrix regions during interphase; metaphase chromosomes have protein scaffolds.

Question 56

What defines a functional centromere?

Answer 56

A centromeric histone H3 variant and repetitive satellite DNA; specified epigenetically.

Question 57

What is linker DNA?

Answer 57

DNA between nucleosomes, 7–115 bp long, susceptible to early MNase cleavage.

Question 58

How are histones arranged in nucleosomes?

Answer 58

H3-H4 tetramer + two H2A-H2B dimers; H1 binds linker DNA.

Question 59

How are histones modified?

Answer 59

By methylation, acetylation, phosphorylation, etc., forming a 'histone code' that affects gene regulation.

Question 60

What are histone variants?

Answer 60

Alternative forms of core histones (except H4), with distinct functions.

Question 61

What are the primary and secondary chromatin structures?

Answer 61

Primary: 10-nm 'beads on a string'. Secondary: 30-nm fibers with 6 nucleosomes/turn, forming solenoids or zigzags.

Question 62

What stabilizes 30-nm fibers?

Answer 62

Histone H1, histone tails, and ionic strength.

Question 63

Are nucleosomes randomly positioned?

Answer 63

No; positions depend on DNA sequence and DNA-binding proteins that define boundaries.

Question 64

What are DNase I hypersensitive sites?

Answer 64

DNA regions more exposed due to absence of nucleosomes, often found at promoters and origins of replication.

Question 65

What does DNase sensitivity indicate?

Answer 65

Regions of open chromatin, often involved in gene expression regulation.