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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)

A

34 nm

24
Q

chromosomal DNA primarily exists in what form of DNA?

A

beta DNA

25
Q

transitions between beta and z forms of DNA play a role in regulating …

A

gene expression

26
Q

circular dsDNA is present in …

A

mitochondria
chloroplasts
prokaryotic organisms
plasmids

27
Q

major and minor grooves are binding sites for …

A

regulatory proteins and transcription factors

28
Q

DNA is organized in the nucleus as …

A

chromatin

29
Q

human somatic cell contains # chromosomes, and total DNA is # long

A

46 chromosomes

2 m long

30
Q

chromatin is … that forms … within …

A

a complex of DNA and proteins

forms chromosomes

within nucleus of eukaryotic cells

31
Q

nucleosomes are composed of …

A

DNA and histones

32
Q

list the histone proteins:

A

H1
H2A
H2B
H3
H4

33
Q

the nucleosome core is made up of …

A

core histone octamer
(H2A, H2B, H3, H4) x2

34
Q

the linker histone is …

A

H1

35
Q

the dsDNA wound nearly twice around the nucleosome core is # bp long

A

146

36
Q

the linker DNA bound by the linker histone (H1) separating each nucleosome is # bp long

A

50 - 70 bp

37
Q

nucleosomes are tightly packed to form … shaped in a …

A

a nucleofilament

coil, a 30-nm fiber

38
Q

a nucleofilament is organized into …, that are anchored by …

A

loops

a nuclear scaffold containing several proteins

39
Q

euchromatin is …

A

transcriptionally active

less dense/compact regions of chromatin

40
Q

heterochromatin is …

A

inactive and tightly packed regions of chromatin

prevents the access of transcription machinery

41
Q

converting between heterochromatin and euchromatin is called …

A

chromatin remodeling

42
Q

chromatin remodeling occurs mostly by …

A

the covalent modification of histones such as:

-acetylation
-methylation

43
Q

chromatin remodeling is essential for …

A

DNA replication and transcription

44
Q

histone acetylation is catalyzed by …

A

HATs (histone acetyltransferases)

45
Q

histone deacetylation is catalyzed by …

A

HDAC histone deacetylase

46
Q

acetylation of lysine residues (addition of acetyl groups to Lys residues) in the histone …

A

weakens/decreases the DNA-histone interactions

by eliminating the positive charge in the histone

which makes it accessible to transcription machinery

47
Q

HDAC is associated with gene silencing because …

A

it catalyzes removing acetyl groups from histones, causing DNA-histone interactions to strengthen, making it less accessible to transcription machinery

48
Q

methylation (attachment of 1-3 methyl groups) to H3 and H4 histones occurs at …

A

specific lysine or arginine residues

49
Q

trimethylation of histone H3 at lysine 27 …

A

marks repression

50
Q

histone methylation is mediated by …

A

HMTs (histone methyltransferases)

[two types depending on site of methylation:
histone arginine N-methyltransferase
histone lysine N-methyltransferase]

diagram in notion

51
Q

histone demethylation is carried out by …

A

HDMs (histone demethylases)

diagram in notion

52
Q

methylation occurs because … acts as the methyl group donor and is converted into …

A

SAM (S-adenosyl methionine)

SAH (S-adenosyl homocysteine)

diagram in notion

53
Q

the length of one turn of DNA is …

A

3.4 nm

54
Q

the length between each nucleic acid is …

A

0.34 nm

Biochem Weeks 1-2 (8 decks)

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