Chap 2 Flashcards

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1
Q

Nucleoside

A

Base, sugar, but no phosphate

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2
Q

RNA 2’ carbon

A

OH

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3
Q

Length of RNA is measured by

A

Nucleotide number

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4
Q

two strands/secondary structure is stabilized by

A

Base pairs h bonding (of backbone) and base stacking

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5
Q

Base stacking

A

Bases stack like stairs to keep together, keeps water out (hydrophobic)

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6
Q

Major groves

A

Wide grove- where proteins can interact with DNA the most

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7
Q

Minor grove

A

Narrower grove, interacted with less

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8
Q

B form/ watson crick form

A

Standard, right handed, 10.5 bp/turn, high humidity, low salt, 5’ to 3’, major groove is deep and minor grove is shallow and broad

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9
Q

A form

A

Right handed, 11bp/turn, low humidity, high salt, associated with RNA, major and minor grove is moderate,

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10
Q

Z DNA

A

Left handed, “single grove”, 12 bp/turn, high MgCl or ethanol and methylated cytosine, linked to certain diseases, can occur in vivo

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11
Q

Nucleic acid

A

polymers made up of nucleotides

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12
Q

Nucleotide

A

Nucleic acid subunits made of a sugar, phosphate, and nitrogenous base

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13
Q

Deoxyribose

A

H on 2’ C

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14
Q

Chargaffs rules

A

GC content varies across species, but within the species, it is the same

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15
Q

DNA is held together by

A

Covalent bonds (phosphodiester bonds) and h bonds (bases bonds)

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16
Q

Hyperchromicity

A

As dna melts, its absorption of UV increases

17
Q

Melting temperature

A

The temp at which half the bases in the dsDNA sample has melted

18
Q

Hybridization

A

Complementary base pairs from two different sources

19
Q

Denaturation temp effected by

A

GC content, salt concentration (higher salt, higher temp), ph,

20
Q

Reanneling rate effected by

A

Concentration of DNA, repeativity,

21
Q

Cop curve ?

A

Show how long dna will reanneal

22
Q

Slipped structure

A

(DNA 2nd) in short tandem repeats, can result in deletions and insertions

23
Q

Cruciforms

A

At palindromes or inverted repeats, a loop is forms, leads to genetic instability,

24
Q

Triple helices

A

(DNA 2nd) Happens in mirror repeats, extra strand pops up in major grove, leaves one DNA single stranded,

25
Q

Hoogsteen base pairs

A

3 base pairs bonding, associated with friedreich ataxia (loss of muscular coordination and heart enlargement), alt ways to Watson crick bond

26
Q

G quadruplex

A

(DNA2) 4 stranded in a stretch of tandem guanine, for gene regulation, found in telomeres and promoters

27
Q

Super coiling is done to

A

Conserve space, put energy into DNA molecule (negative), unwinds DNA for replication, transcription and recombination (negative)

28
Q

Linking number

A

Number of times two hydrogen bonded strands cross each other

29
Q

Writhes

A

Number of time DNA helix is coiled about itself

30
Q

Linking number formula

A

Twist plus writhes

31
Q

Partial denaturation

A

Done to relieve strained supercoiling

32
Q

Why does positive supercoiling occur

A

DNA replication and transcription (ahead of fork),

33
Q

Topoisomerases

A

Release supercoiling

34
Q

primary structure of DNA

A

nucleic acid and nucleotides, held by phosodiester bonds

35
Q

fidelity of DNA replication

A

proofreading DNA repair mechanisms and correct mistakes

36
Q

dsDNA has a - core

A

hydrophobic

37
Q

negative supercoiling

A

saves space, energy into DNA molecule, almost all DNA in pro and euk is negatively supercoiled, under wound

38
Q

DNA tertiary structure

A

supercoiling

39
Q

RNP

A

Catalyze replication, transcription,
ribosome, the enzyme telomerase, vault ribonucleoproteins, RNase