DNA

Question 1

It is the DNAs Packaging Material

Found in the Nucleus of Eukaryotic Cells

Answer 1

Chromatin

Question 2

The Chromatin Consists of the Following:

Answer 2

Double Stranded DNA
Histone Proteins
non Histone Proteins
Small amount of RNA

Question 3

It condenses DNA

Answer 3

Chromatin Molecules, Especially Histones

Question 4

It is a Family of Basic Positively Charged Proteins

Answer 4

Histones

Question 5

Types of Histones

Answer 5

H1, H2A, H2B, H3, H4

Question 6

This histone are loosely bound to chromatin and easily removed with salt

Answer 6

H1

Question 7

These are Nucleosome Core Histones

Answer 7

H2A, H2B, H3, H4

Question 8

These histones form a tetramer

Answer 8

H3, H4

Question 9

These Histone form Dimers

Answer 9

H2A and H2B

Question 10

1/3 are rich in basic Amino Acids
Has High content of Lysine and Arginine
Makes Histones positively charged at Physiologic PH

Answer 10

N-Terminal

Question 11

Linked to turning genes On or Off

Answer 11

Acetylation and Methylation

Question 12

Involved in assembling chromosomes during DNA copying

Answer 12

Core Histone Acetylation

Question 13

Associated with DNA Repair

Answer 13

ADP ribosylation

Question 14

Associated with turning genes ON, OFF, and silencing specific regions (heterochromatin).

Answer 14

Monoubiquitylation

Question 15

Associated with turning genes OFF.

Answer 15

Sumoylation

Question 16

Linked to turning genes ON.

Answer 16

H2Az

Question 17

● Organizational/basic unit of chromatin

● Composed of DNA wound around an octameric complex of histone molecules (including H2A to H4)

Answer 17

Nucleosome

Question 18

They form ionic bonds with negatively charged DNA

Answer 18

Positively Charged Histones

Question 19

They are not needed to form the basic nucleosome core

Answer 19

H1

Question 20

Interacts with the DNA where it enters and exit the nucleosome

Answer 20

H1

Question 21

○ Primary particle upon which the DNA coils around
○ Central to nucleosome formation

Answer 21

H3 and H4

Question 22

○ Stabilize the primary particle
○ Firmly binds two additional half-turns of DNA previously bound only loosely to the (H3-H4)2

Answer 22

● H2A and H2B

Question 23

○ Facilitates assembly of nucleosomes
○ Exhibit high affinity for binding histones

Answer 23

Histone chaperones

Question 24

This are active regions with very short segments senstive to DNase I

They are mark locations where nucleosome structure is disrupted

Answer 24

Hypersensitive Areas

Question 25

Two types of heterochromatin

Answer 25

Constitutive heterochromatin Facultative heterochromatin

Question 26

Type of Heterochromatin that are always condensed and inactive Found near centromeres and chromosomal ends (telomeres)

Answer 26

Constitutive Heterochromatin

Question 27

● Can switch between condensed (inactive) and decondensed (active) states

Answer 27

Facultative heterochromatin

Question 28

Actively transcribed regions appear as

Answer 28

decondensed puffs ■ Transcription enzymes ■ Sites of RNA synthesis

Question 29

● Connects the sister chromatids (central point) ● It often correlates with: ● Its position is characteristic for each chromosome type ○ Lower levels of methylated cytosine (5-methyldeoxycytidine or meC) in the DNA ○ Specific histone variants or modifications (PTMs like phosphorylation, acetylation) ● Hypersensitive Areas ○ Within active regions, very short segments (100-300 nucleotides) are even more sensitive (10x) to DNase I ○ Likely have an layered structure allowing easy enzyme access ○ Often found just upstream (before the start) of active genes ○ Mark locations where nucleosome structure is disrupted ■ Often by bound regulatory proteins (transcription factors) ○ Gene capable of being transcribed ● Rich in adenine-thymine (A-T) base pairs

Answer 29

Centromere

Question 30

● Anchor for mitotic spindle on which chromosomal segregation occurs during mitosis ● Formed by the complex of centromeres

Answer 30

Kinetochore

Question 31

● Structures at the ends of each chromosome ● Consist of short thymine-guanine rich repeats

Answer 31

Telomeres

Question 32

● Maintains telomere length ● Attractive target for cancer chemotherapy and drug development

Answer 32

Telomerase

Question 33

● Anchor for mitotic spindle on which chromosomal segregation occurs during mitosis ● Formed by the complex of centromeres

Answer 33

Kinetochore

Question 34

○ Includes most single-copy protein-coding genes ○ More than half the DNA in eukaryotic organisms

Answer 34

Unique-sequence DNA (nonrepetitive)

Question 35

○ Present in multiple copies ○ Atleast 30% of the genome which can be classified as: ● 54/67 mitochondrial polypeptides ○ Encoded by nuclear genes ● The rest are coded by mitochondrial DNA ○ Human mitochondria contain 2-10 copies of a small circular dsDNA molecule ■ 1% of total cellular DNA ● mtDNA codes for: ■ Moderately repetitive ■ Highly repetitive

Answer 35

Repetitive-sequence DNA

Question 36

● Exist as both dispersed and grouped tandem arrays ● Consist of 2 to 6 bp repeated up to 50 times ● Most common: AC repeat on one strand, TG on the other

Answer 36

Microsatellite Repeat Sequences

Question 37

Unstable expansion of (CGG)n repeats

Answer 37

Fragile X syndrome

Question 38

Huntington chorea

Answer 38

CAG

Question 39

Myotonic dystrophy

Answer 39

CTG

Question 40

Spinobulbar muscular dystrophy

Answer 40

CAG

Question 41

Kennedy Disease

Answer 41

CAG

Question 42

○ Animal viruses that can contribute to the development of cancer by altering the host cell’s DNA ■ Direct integration of DNA into the chromosomes

Answer 42

Oncogenic Diseases

Question 43

○ Synthesizes double stranded DNA copies generated by the action of the viral RNA-dependent DNA polymerase or reverse transcriptase

Answer 43

Retroviruses

Question 44

Capable of recombining with the DNA of a bacterial host

Answer 44

Bacterial Viruses

Question 45

Small, non-viral DNA that are capable of transposing themselves in and out of the host genome

Answer 45

Jumping DNA

Question 46

● Other term for processed genes ● Can be transcribed but not translated ○ Because it contains nonsense codons ● Step 1: Origin of Replication In the E. coli ● dnaA (ORI-binding protein) ○ Identifies the oriC region in the dsDNA and binds to the latter ○ Binding event leads to the local denaturation and unwinding of an adjacent AT-rich regions of DNA ■ AT-rich regions: forms a complex consisting of 150 to 250 bp of DNA and multimers of the single-stranded DNA-binding (SSB) protein In the yeast ● Autonomously replicating sequences (ARS) ○ Replicators ○ Contains origin replication element (ORE) ■ Degenerate 11-bp sequence ○ Proteins which are analogous to the dnaA protein of E. ■ Cannot encode a functional protein

Answer 46

Pseudogenes

Question 47

*pair up and eliminate any mismatched sequences between them ○ Sequences become perfectly or nearly identical

Answer 47

Homologous Chromosomes

Question 48

○ Occurs when the cell’s repair machinery mistakenly treat them as homologous regions then pair up to due to: coli bind to the ORE ORE-binding proteins + ORE = origin recognition complex (ORC) ● DNA unwinding element (DUE) ○ Adjacent to the ORE ○ Approx. 80 bp AT-rich sequence ○ Origin of replication in yeast ○ Minichromosome maintenance (MCM) protein complex binds to the DUE ■ Duplicated genes ■ Repetitive sequences ■ Transposable elements

Answer 48

Non Homolgous Chromosomes

Question 49

Gene Conversion Brings About

Answer 49

Repair of DNA Homogenization of the sequences of the members of repetitive DNA families

Question 50

Steps Involved in DNA replication in Eukaryotes

Answer 50

1. Identification of the Origins of replication 2. ATP HYDROLYSIS DRIVEN REMOVAL OF nucleosomes and unwinding of dsDNA to provide dsDNA template 3. Formation of replication fork 4. Initiation of DNA Synthesis 5. Formation of replication bubbles 6. Reconstitution of chromatin structure