Chapter 4: DNA and Chromosomes Flashcards
what nitrogenous bases are purines?
A & G
What nitrogenous bases are pyrimidines?
T & C
This is the coding region of a gene within the DNA
an exon
This is the non-coding region of a gene that is usually removed after transcription
intron
about what length of DNA is packed into what amount of space when its in the mitotic chromosome form?
2 meters in 6 um
about how much DNA is actually coding for protein?
~2%
From where are the “leftover/unused/junk” portions of the DNA sourced? (2)
- retroviral remnants
- transposon activity
About how large are histones wound with DNA
11 nm
What is the mass ratio of chromosomes?
1:1:1 ; DNA: histone: non-histone
About how many base pairs long are nucleosomes>
~200 bp
What are the 4 different types of protein structures within the histone?
- H2A
- H2B
- H3
- H4
What is the purpose of the N-terminus tails present in histone proteins?
aids in DNA interactions (release/coiling) and folding/packaging of DNA
About how many times a second does a histone protein wrap/unwrap from DNA?
4x a second
What is the size of tightly bound “zig-zag” chromatin? how much larger than the beads-on-a-string model is this?
30 nm; 3x larger
what is heterochromatin?
very dense regions of chromatin; expression is highly restrictive/repressed
What is euchromatin?
more unwound regions of chromatin; easier access for transcription/replication
what happens when the white eye gene in Drosophila is translocated closer to heterochromatin?
patchy or all-white eyes
Methylation of K9 on a histone’s N-terminal tail does what?
heterochromatin formation (gene supression)
Methylation fo K4 and acetylation of K9 on an N-terminal tail does what?
euchromatin formation (gene expression)
Methylation of K27 on an N-terminal tail does what?
heterochromatin formation (gene silencing)
Where can giant chromosomes occur?
the salivary glands of fruit flies
What are giant chromosomes?
tremendous DNA replication without splitting; easily reveals chromosome patterns
What is CRISPR/Cas9 technology sourced from?
Bacterial immune systems
A section of bacterial DNA that is modified after phage/plasmid exposure
CRISPR
How long are the proto-spacer DNA sequences identified by canonical Cas9?
~20 base pairs
What is PAM?
protospacer adjacent motif; (NGG) flanks protospacer in the invading nucleic acid
What is the function of PAM?
used by other CRISPR machinery to identify/recognize target regions of invading nucleic acid
This is a CRISPR associated protein responsible for identifying “non-self” or invading sequences; attaches to protospacers wiht PAM sequences
Cas1
These are identical, palindromic sequences that separate various protospacers and form hairpin loops of guide RNA
CRISPR repeat sequences
What are the two snipping regions of Cas9
HNH and RuVC
this is the biotechnical version of casRNA that is used in lab scenarios; very different from canonical/wt Cas9
sgRNA (single-guide RNA)
What RNA molecules are important for canonical Cas9 targetting?
crRNA (crispr RNA) & tracrRNA (trans-activating crispr RNA)
What RNA molecules are important for Cas9 targeting in the LAB?
sgRNA
What does the HNH region of canonical Cas9 do?
snips DNA at the target strand
What does the RuVC region of canonical Cas9 do?
snips non-target strand
a “panic process” method of DNA repair after a Cas9 break; DNA is messily stuck together–>produces indels
NHEJ (non-homologous end joining) repair
What can NHEJ repair be used for when utilizing CRISPR/Cas9 tech?
knockout gene creation via indels
This is a less panicky method of DNA repair after Cas9-mediated dsDNA breaks; inserts complementary DNA
HDR (homology-directed repair)
What is a good reason to encourage HDR when working with CRISPR/Cas9?
can create knockouts/remove dmg genes; sticky-ends can allow for gene insertion
This CRISPR protein has no nuclease activity in its complex; however, it can still identify and bond with target g-DNA
dCas9 (dead/null)
what are two modifications that can be made to dCas9?
- adding transcription modifiers
- use different PAM sequences
Histone acetylation results in gene ___
activation
Histone demethylation results in gene ___
repression
DNA demethylation results in ____
activation
DNA acetylation results in gene _____
repression
