Chapter 4: DNA and Chromosomes

Question 1

what nitrogenous bases are purines?

Answer 1

A & G

Question 2

What nitrogenous bases are pyrimidines?

Answer 2

T & C

Question 3

This is the coding region of a gene within the DNA

Answer 3

an exon

Question 4

This is the non-coding region of a gene that is usually removed after transcription

Answer 4

intron

Question 5

about what length of DNA is packed into what amount of space when its in the mitotic chromosome form?

Answer 5

2 meters in 6 um

Question 6

about how much DNA is actually coding for protein?

Answer 6

~2%

Question 7

From where are the “leftover/unused/junk” portions of the DNA sourced? (2)

Answer 7

1. retroviral remnants
2. transposon activity

Question 8

About how large are histones wound with DNA

Answer 8

11 nm

Question 9

What is the mass ratio of chromosomes?

Answer 9

1:1:1 ; DNA: histone: non-histone

Question 10

About how many base pairs long are nucleosomes>

Answer 10

~200 bp

Question 11

What are the 4 different types of protein structures within the histone?

Answer 11

1. H2A
2. H2B
3. H3
4. H4

Question 12

What is the purpose of the N-terminus tails present in histone proteins?

Answer 12

aids in DNA interactions (release/coiling) and folding/packaging of DNA

Question 13

About how many times a second does a histone protein wrap/unwrap from DNA?

Answer 13

4x a second

Question 14

What is the size of tightly bound “zig-zag” chromatin? how much larger than the beads-on-a-string model is this?

Answer 14

30 nm; 3x larger

Question 15

what is heterochromatin?

Answer 15

very dense regions of chromatin; expression is highly restrictive/repressed

Question 16

What is euchromatin?

Answer 16

more unwound regions of chromatin; easier access for transcription/replication

Question 17

what happens when the white eye gene in Drosophila is translocated closer to heterochromatin?

Answer 17

patchy or all-white eyes

Question 18

Methylation of K9 on a histone’s N-terminal tail does what?

Answer 18

heterochromatin formation (gene supression)

Question 19

Methylation fo K4 and acetylation of K9 on an N-terminal tail does what?

Answer 19

euchromatin formation (gene expression)

Question 20

Methylation of K27 on an N-terminal tail does what?

Answer 20

heterochromatin formation (gene silencing)

Question 21

Where can giant chromosomes occur?

Answer 21

the salivary glands of fruit flies

Question 22

What are giant chromosomes?

Answer 22

tremendous DNA replication without splitting; easily reveals chromosome patterns

Question 23

What is CRISPR/Cas9 technology sourced from?

Answer 23

Bacterial immune systems

Question 24

A section of bacterial DNA that is modified after phage/plasmid exposure

Answer 24

CRISPR

Question 25

How long are the proto-spacer DNA sequences identified by canonical Cas9?

Answer 25

~20 base pairs

Question 26

What is PAM?

Answer 26

protospacer adjacent motif; (NGG) flanks protospacer in the invading nucleic acid

Question 27

What is the function of PAM?

Answer 27

used by other CRISPR machinery to identify/recognize target regions of invading nucleic acid

Question 28

This is a CRISPR associated protein responsible for identifying "non-self" or invading sequences; attaches to protospacers wiht PAM sequences

Answer 28

Cas1

Question 29

These are identical, palindromic sequences that separate various protospacers and form hairpin loops of guide RNA

Answer 29

CRISPR repeat sequences

Question 30

What are the two snipping regions of Cas9

Answer 30

HNH and RuVC

Question 31

this is the biotechnical version of casRNA that is used in lab scenarios; very different from canonical/wt Cas9

Answer 31

sgRNA (single-guide RNA)

Question 32

What RNA molecules are important for canonical Cas9 targetting?

Answer 32

crRNA (crispr RNA) & tracrRNA (trans-activating crispr RNA)

Question 33

What RNA molecules are important for Cas9 targeting in the LAB?

Answer 33

sgRNA

Question 34

What does the HNH region of canonical Cas9 do?

Answer 34

snips DNA at the target strand

Question 35

What does the RuVC region of canonical Cas9 do?

Answer 35

snips non-target strand

Question 36

a "panic process" method of DNA repair after a Cas9 break; DNA is messily stuck together-->produces indels

Answer 36

NHEJ (non-homologous end joining) repair

Question 37

What can NHEJ repair be used for when utilizing CRISPR/Cas9 tech?

Answer 37

knockout gene creation via indels

Question 38

This is a less panicky method of DNA repair after Cas9-mediated dsDNA breaks; inserts complementary DNA

Answer 38

HDR (homology-directed repair)

Question 39

What is a good reason to encourage HDR when working with CRISPR/Cas9?

Answer 39

can create knockouts/remove dmg genes; sticky-ends can allow for gene insertion

Question 40

This CRISPR protein has no nuclease activity in its complex; however, it can still identify and bond with target g-DNA

Answer 40

dCas9 (dead/null)

Question 41

what are two modifications that can be made to dCas9?

Answer 41

1. adding transcription modifiers 2. use different PAM sequences

Question 42

Histone acetylation results in gene ___

Answer 42

activation

Question 43

Histone demethylation results in gene ___

Answer 43

repression

Question 44

DNA demethylation results in ____

Answer 44

activation

Question 45

DNA acetylation results in gene _____

Answer 45

repression