Lecture 3

Question 1

What is unique about viral and bacterial chromosomes?

Answer 1

• single nucleic acid molecule
• largely devoid of associated proteins
• much smaller than eukaryotic chromosomes
• contains less genetic information

Question 2

What is unique specifically about viral chromosomes?

Answer 2

• nucleic acid, either DNA or RNA, single or double stranded
• circular or linear molecules
• viral genetic material is inert until released into host cell
• able to package long DNA into a small volume just like bacteria and eukaryotic cells
• viruses are not considered to be alive

Question 3

Bacterial chromosomes

Answer 3

• circukar, double-stranded DNA compacted into nucleoid
• their DNA is associated with HU and histone-like nucleoid structuring
• unlike viral chromosomes, bacterial chromosomes are readily replicated and transcribed

Question 4

What is supercoiling?

Answer 4

• supercoiling is the compaction of DNA
• closed circular molecules
• more compact and sediment more rapidly than linear forms

Question 5

What changes in a super coiled piece of DNA?

Answer 5

2 turns of the helix are removed to hinder the stability of the strand, this promotes the formation of DNA super coils that are very stable again
ex) if the strand started with 20 turns it would end up with 18

Question 6

Topoisomerases

Answer 6

• enzyme that cut one or both strands of DNA
• winds or unwinds helix before resealing ends

Question 7

In what type of cells is supercoiled DNA and topoisomerases found?

Answer 7

Eukaryotic

Question 8

What is common between Prokaryote and eukaryote DNA when it comes to supercoiling?

Answer 8

Replication and transcription create supercoils downstream as double helix unwinds

Question 9

Chromatin

Answer 9

• not visible during cell cycle
• at interphase, eukaryotic chromosomes uncoil and decondense into a form called chromatin
• during interphase, chromatin is dispersed throughout the nucleus
• during cell division, chromatin coils and condenses back into visible chromosomes

Question 10

Histones

Answer 10

• positively charge proteins associated with chromosomal DNA in eukaryotes
• contain large amounts of lysine and arginine
• makes electrostatic bonding to negatively charged phosphate possible

Question 11

What are the five main types of histones

Answer 11

H1, H2A, H2B, H3, H3
- when two combine they form an octomer histone complex

Question 12

nucelosomes

Answer 12

• electron microscopic observations of chromatin revealed fibers composed of linear array of these spherical particles
• resemble bead on a string
• are condensed several times to form intact chromatids
• resemble beads on a string
• are condensed several times to form intact chromatids

Question 13

Chromatin remodeling

Answer 13

• to accommodate DNA-protein interactions, chromatin structure must change

Question 14

What happens to chromatins to facilitate replication and gene expression?

Answer 14

• relax compact structure
• expose regions of DNA to regulatory proteins
• have a reversal mechanism for inactivity

Question 15

Superhelix

Answer 15

• twists and turns of DNA superhelix encircle histones
• principal packaging unit of DNA in eukaryotic nucleus

Question 16

Histone tails

Answer 16

unstructured histone tails are not packed into folded histone domains within nucleosome
- tails that hare devoid of secondary structure protrude through minor groove

Question 17

Chemical modifications

Answer 17

are important to genetic function

Question 18

Acetylation

Answer 18

• enzyme histone acetyltransferase
• addition of acetyl group to positively charged amino group on side chain (lysine)
• changes net charge of protein by neutralizing positive charge

Question 19

How are targets for chemical modification made along chromatin

Answer 19

By histone tails

Question 20

Methylation

Answer 20

• enzyme methyltransferase
• adds methyl groups to arginine and lysine residues in histones
• positive correlation with gene activity

Question 21

Phosphorylation

Answer 21

• enzyme kinase
• adds phosphate groups to hydroxyl groups of amino acids serine and histidine

Question 22

Methylation of the nitrogenous base cytosine within polynucleotide chains of DNA

Answer 22

• forms 5-methyl cytosine
• usually negatively correlated with gene activity

Question 23

CpG island

Answer 23

• long repeats of cytosine and guanine
• region of DNA where many cytosine guanine dinucleotides are present

Question 24

Euchromatin

Answer 24

• uncoiled and active
• appears unstained during interphase

Question 25

Heterochromatin

Answer 25

- condensed areas are mostly inactive appears stained during interphase - genetically inactive: lacks genes or contains repressed genes - replicated later in S phase than euchromatin - telomere maintains chromosome integrity - centromere involved in chromosome movement

Question 26

Chromosome-banding techniques

Answer 26

- differential staining along longitudinal axis of mitotic chromosome - staining patterns resemble polytene chromosome

Question 27

C-banding

Answer 27

- mitotic chromosomes have a characteristic banding pattern - only centromeres (heterochromatin) take up stain

Question 28

G-banding

Answer 28

- differential staining along length of each chromosome - digestion of mitotic chromosome by enzyme - introduce trypsin to DNA

Question 29

Nomenclature for human chromosome banding

Answer 29

- based on G-banding - nomenclature applied to X chromosome - regions of X chromosome are distinguished but its banding pattern

Question 30

Repetitive DNA sequences

Answer 30

- are repeated many times within eukaryotic chromosomes - several categories of repetitive DNA

Question 31

Satellite DNA

Answer 31

- highly repetitive and consists of short repeated sequences - makes up variable proportion of total DNA - found in heterochromatic centromeric regions of chromosomes - not found in prokaryotes

Question 32

Centromeres

Answer 32

- separation of homologs during mitosis and meiosis depends on centromeres - are the primary constrictions along eukaryotic chromosomes

Question 33

Kinetochore proteins

Answer 33

region that binds to spindle fiber microtubules during cell division

Question 34

Moderately repetitive DNA includes...

Answer 34

- variable number tandem repeats (VNTRs) - minisatellites - microsatellites (short tandem repeats, STRs)

Question 35

VNTRs

Answer 35

Variable number tandem repeats - repeating DNA sequences 15-100 bp long - found within and between genes

Question 36

Microsatellites or STRs

Answer 36

short tandem repeats - tandemly repeated sequences - dispersed throughout genome - consist of di-, tri-, tetra-, and pentanucleotides

Question 37

SINES and LINES

Answer 37

Short interspersed elements and long interspersed elements - 850k LINES in human genome - transposable sequences that are mobile and can relocate within genome - dispersed throughout genome rather than tandemly repeated - constitute 1/3 of human genome

Question 38

Retrotransposons

Answer 38

- transposable elements generated bia RNA intermediate (LINEs)

Question 39

What portion of eukaryotic genome constitutes protein-encoding genes

Answer 39

2-10%

Question 40

Pseudogenes

Answer 40

- large number of single-copy noncoding regions DNA sequences representing evolutionary vestiges - have undergone significant mutational alterations (insertions and deletions) - are not transcribed