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Biochem Weeks 1-2 > nucleic acid and chromatin structure > Flashcards

nucleic acid and chromatin structure Flashcards

1
Q

central dogma of molecular biology is the flow …

A

of genetic information from
DNA to DNA (replication)
DNA to RNA (transcription)
RNA to DNA (reverse transcription)
RNA directly to protein (translation)

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2
Q
A

nucleoside is without phosphate group

nucleotide is with phosphate group

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3
Q

the primary structure of DNA refers to …

A

nucleotide (dNTP) chain linked by 3’-5’ phosphodiester bonds

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4
Q

phosphodiester bonds create …; form between …; have … polarity; … project inwards from the backbone

A

the backbone of DNA

between 3’-hydroxyl group of nucleotide // 5’-hydroxyl group of deoxyribose on incoming nucleotide through phosphoryl group

5’-3’ polarity (free 5’ phosphate, free 3’-OH group)

nitrogenous bases

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5
Q

methylation of histone H3 at lysine 4 …

A

activates transcription

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6
Q

dNTPs (deoxyribonucleotides) form … of DNA and are composed of …

A

basic building blocks / the monomeric unit

nitrogenous base, deoxyribose, & phosphate

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7
Q

purines

A

Adenine

Guanine

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8
Q

pyrimidines

A

Cytosine

Thymine

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9
Q

pharmacological importance of major/minor grooves in DNA:

A

provide access for binding regulatory proteins to their specific recognition sequences

ex. antibiotic Actinomycin D (deactinomycin) has been used to treat cancer by:

-binding to minor groove

-causes cytotoxic effects in cancer

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10
Q

dATP

A

adenosine triphosphate

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11
Q

dTTP

A

thymine triphosphate

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12
Q

dGTP

A

guanine triphosphate

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13
Q

dCTP

A

cytosine triphosphate

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14
Q

the DNA double helix is stabilized by …

A

H bonds between the bases

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15
Q

Adenine (A) pairs with Thymine (T) with …

A

2 hydrogen bonds

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16
Q

Guanine (G) pairs with Cytosine (C) with …

A

3 hydrogen bonds

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17
Q

Chargaff rule states that …

A

in any sample of dsDNA:

A = T
amount of A equals the amount of T

G = C
amount of G equals the amount of C

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18
Q

when does DNA strand separation occur? how does this occur?

A

when hydrogen bonds are disrupted (called denaturation / annealing)

occurs when it reaches melting temperature (Tm) [the temp at which one half of helical structure is lost]

*the primary structure is not affected by denaturation

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19
Q

how do DNA strands reform the double helix?

A

through a process called renaturation / reannealing

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20
Q

diameter of helix

A

2 nm

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21
Q

distance between nucleotides

A

0.34 nm

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22
Q

number of base pairs per turn for each form of DNA (there are three)

A

alpha form: 11 bp/turn

beta form: 10 bp/turn

z form: 12 bp/turn

23
Q

length of one turn (360 degrees in total)

24
Q

chromosomal DNA primarily exists in what form of DNA?

25
transitions between beta and z forms of DNA play a role in regulating ...
gene expression
26
circular dsDNA is present in ...
mitochondria chloroplasts prokaryotic organisms plasmids
27
major and minor grooves are binding sites for ...
regulatory proteins and transcription factors
28
DNA is organized in the nucleus as ...
chromatin
29
human somatic cell contains # chromosomes, and total DNA is # long
46 chromosomes 2 m long
30
chromatin is ... that forms ... within ...
a complex of DNA and proteins forms chromosomes within nucleus of eukaryotic cells
31
nucleosomes are composed of ...
DNA and histones
32
list the histone proteins:
H1 H2A H2B H3 H4
33
the nucleosome core is made up of ...
core histone octamer (H2A, H2B, H3, H4) x2
34
the linker histone is ...
H1
35
the dsDNA wound nearly twice around the nucleosome core is # bp long
146
36
the linker DNA bound by the linker histone (H1) separating each nucleosome is # bp long
50 - 70 bp
37
nucleosomes are tightly packed to form ... shaped in a ...
a nucleofilament coil, a 30-nm fiber
38
a nucleofilament is organized into ..., that are anchored by ...
loops a nuclear scaffold containing several proteins
39
euchromatin is ...
transcriptionally active less dense/compact regions of chromatin
40
heterochromatin is ...
inactive and tightly packed regions of chromatin prevents the access of transcription machinery
41
converting between heterochromatin and euchromatin is called ...
chromatin remodeling
42
chromatin remodeling occurs mostly by ...
the covalent modification of histones such as: -acetylation -methylation
43
chromatin remodeling is essential for ...
DNA replication and transcription
44
histone acetylation is catalyzed by ...
HATs (histone acetyltransferases)
45
histone deacetylation is catalyzed by ...
HDAC histone deacetylase
46
acetylation of lysine residues (addition of acetyl groups to Lys residues) in the histone ...
weakens/decreases the DNA-histone interactions by eliminating the positive charge in the histone which makes it accessible to transcription machinery
47
HDAC is associated with gene silencing because ...
it catalyzes removing acetyl groups from histones, causing DNA-histone interactions to strengthen, making it less accessible to transcription machinery
48
methylation (attachment of 1-3 methyl groups) to H3 and H4 histones occurs at ...
specific lysine or arginine residues
49
trimethylation of histone H3 at lysine 27 ...
marks repression
50
histone methylation is mediated by ...
HMTs (histone methyltransferases) [two types depending on site of methylation: histone arginine N-methyltransferase histone lysine N-methyltransferase] diagram in notion
51
histone demethylation is carried out by ...
HDMs (histone demethylases) diagram in notion
52
methylation occurs because ... acts as the methyl group donor and is converted into ...
SAM (S-adenosyl methionine) SAH (S-adenosyl homocysteine) diagram in notion
53
the length of one turn of DNA is …
3.4 nm
54
the length between each nucleic acid is …
0.34 nm

Biochem Weeks 1-2 (8 decks)

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