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MCBG > E1, L5 > Flashcards

E1, L5 Flashcards

(49 cards)

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1
Q

Is DNA during interphase organized?

A

Yes! To allow for appropriate cellular machinery to access

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2
Q

What 3 DNA sequences are required?

A

origin of replication (where DNA replication begins), centromere (region where mitotic spindle attaches, assisting in lining up chromosomes and pulling to opposite poles), telomere (at the ends of linear chromosomes protecting them, made of telomeric DNA + proteins)

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3
Q

What do centromeres and telomeres contain in terms of DNA sequence?

A

Specific DNA sequences that bind specific proteins, highly compacted

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4
Q

What are genes?

A

DNA sequences that produce a functional RNA molecule (encodes a protein or forms a structural or regulatory RNA). They are comprised of exons, usually introns, and regulatory regions

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5
Q

What percentage of human DNA is unique sequences?

A

50%

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6
Q

heterochromatin

A

doesn’t contain expressed genes, tightly wound up

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7
Q

euchromatin

A

contains expressed genes, more open

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8
Q

exon

A

coding region of DNA, 1.5% of DNA

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9
Q

What are non-repetitive sequences usually? (ones that are not introns or exons)

A

regulatory sequences, promoters, enhancers, non-coding RNA

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10
Q

What do for repetitive sequences usually code for?

A

telomeres, centromeres, LINES, SINES, retroviral RNA elements

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11
Q

What are LINES or SINES

A

long/short intervening sequences

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12
Q

nucleosome

A

protein-DNA complex

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13
Q

Desribe the components of the nucleosome core protein

A

consists of 8 subunits, 2 H2A, 2 H2B, 2 H3, 2 H4

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14
Q

Describe the core proteins in terms of dimers that form, tetramer, and the overall structure?

A

H2A/H2B form a dimer, H3/H4 form a dimer. The H3/H4 dimers form a tetramer since H3 molecules interact with each other

The tetramer forms the center, and DNA wraps around this portion. The H2A/H2B dimers are on the outside on opp ends

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15
Q

Core protein structure illustration

A
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16
Q

How many DNA basepairs does the nucleosome contain?

A

~200

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17
Q

How many DNA basepairs wrap around the core protein? How many H-bonds?

A

147 DNA basepairs, 142 H-Bonds

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18
Q

What is the dimension of the beads on the string?

A

11 nm

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19
Q

How many times does DNA wrap around the core protein?

A

1.67 times

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20
Q

Where are the N-terminals of the histone subunits?

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A

On the outside

21
Q

Describe the core histone proteins?

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A

they all (H2A, H2B, HC, HD) histone folds (3 a-helicle structures), as well a N-terminal tail and a very short C-terminal

22
Q

Compare features of highly condenses and less condensed chromatin

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A

Highly condenses is not as active, not used as much. Heterochromatin. Less condenses is more metabolically active, used more often. Euchromatin

23
Q

How long does the wrapped nucleosome exist for? How long does the unwrapped exist for?

Study These Flashcards
A

250 miliseconds, 10-15 miliseconds

24
Q

What helps in unwrapping DNA and allows chromain to be dynamic?

Study These Flashcards
A

ATP Dependent Chromatin Remodeling Complexes

25
How does ATP Dependent Chromain Remodeling Complexes work?
Harnesses energy from ATP to faciliate the movement of DNA on core protein, making DNA less tightly wound
26
What are the 2 mechanisms that ATP Dependent Chromatin Remodeling complexes use?
(1) slides DNA to make DNA availabel to proteins in the cell (2) with assistance of histone chaperones, they either exchange H2A-H2B histones, or completely remove octameric core of DNA
27
What are histone chaperones?
Help out with Chromatin remodeling. They are temporary storage facilities for H2A-H2B or the core protein when they are being switched out or removed by ATP Dependent Chromatin Remodeling Complexes
28
What is histone H1?
does not have histone fold structure. attaches to the histone core protein at the point where DNA enters and exits, makes wound DNA more tight
29
What are inter-nucleosome tail interactions?
Helps DNA condense into chromatin structure, N-terminals interact with adjacent nucleosme core proteins
30
condensins
takes 300 nm looped fiber and further condenses it. made of 2 antiparallel coiled proteins that take the looped structures and condense.
31
How is the 30 nm chromatin fiber formed?
Nucleosomes fold up. There are three models: 1) zig-zag model, 2) solenoid model also N-termianl interactions
32
scaffold proteins
loop the 30 nm fibers, high level expressed genes are not looped as tightly
33
What does the acetylation of lysine do?
Changes lysine charge from +1 --\> 0 This makes the lysine no longer attracted to the - charged DNA, opening up the structure
34
What does the methylation of lysine do?
Charge remains the same, but proteins will interact with methylated lysine differently. Also depends on hwo many methyl substituteions are performed
35
What does serine phosphorylation do?
Makes serine go from a charge of 0 --\> -1 This makes the serine repel from the negatively charged DNA, creating an opening
36
How do covalent modifications lead to consequences in terms of DNA metabolism?
combination of modifications can have differnet meanings, and can either silence or express genes
37
What covalent modification leads to heterochromain formation? (gene silencing)
methylation of lysine 9 on H3
38
What covalent modifications lead to gene expression?
Lysine 4 methylation, lysine 4 acetylation
39
What modification leads to gene expression
serine 10 phosphorylation, lysine 14 acetylation
40
What modifications lead to X chromosome inactivation
lysine 27 methylation
41
histone writer
once the gene regulatory protein binds, this "histone modifying enzyme" is recruited and places post-translational mark on histone tail
42
histone reader
reads this mark and binds, recruting the same catlyting enzyme to mark the next tail or to silence/express the gene. binds to the 3D structure of the histone tails (methylation, phosphorylation, etc.)
43
describe the histone 3 variant for centromere
facilitates binding of kinetochore. the nucleosomes alternate in regions of normal H3 that is dimethylated at lysine 4, and with centromere-specific H3 variant -H3 variant AKA CENP-A
44
What does the H2AX variant do?
aids with DNA repair process
45
What is the difference between genetics and epigenetics?
Genetic changes are caused by mutation and are passed on to both somatic and germ cells Epigenetic changes are caused by change in chromatin, and are passed down only to somatic cells but not germ cells (ex: change in histones, changing DNA from euchromatin to heterochromatin)
46
What are the 3 types of barriers that separate euchromatin and heterochromatin
1) protein that physically blocks the spread of heterochromatin 2) protein that proteins euchromatin 3) proteins with enzymatic activity that act on heterochromatin to prevent spreading
47
What does heterochromatin usually contain?
no genes (centromeres + telomeres) or is resistant to DNA expression
48
Mechanism for heterochromatin formation and spread
49
How do drugs target components of epigenetic machinery for treatment of disease?
Will ty to reverse these changes in epigenetic machinery. Modifcations in histone modifications, chromatin remodeling, DNA modifications

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