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BIOC 302 Part 2 > Nuclei Acid Structure and Chromosomes > Flashcards

Nuclei Acid Structure and Chromosomes Flashcards

1
Q

how are nucleic acids formed?

A

5’-P is esterified by 3’-OH of another nucleotide to form a phosphodiester bond

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2
Q

what results from the nature of phosphodiester bonds?

A
  • DNA and RNA have polarity/non-symmetrical bond
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3
Q

what direction is DNA written in?

A

5’ to 3’ direction

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4
Q

how are nucleic acids named?

A
  • name bases using one letter code in 5’ to 3’ direction
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5
Q

what observations helped solve the structure of DNA? (4)

A
  1. Franklin: X-ray image suggested double helix structure
  2. Chargott rules: A = T =/= G = C
  3. Donohue: A-T (2-H bonds) and G-C (3-H bonds) can form H-bonds
  4. Furberg: bases are at right angles to sugars
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6
Q

what is the orientation and composition of the DNA helix? (2)

A
  • DNA is a right handed double helix

- composed of polynucleotide chains

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7
Q

define how the DNA strands are complementary (2)

A
  • A pairs with T; G pairs with C

- the sequence of one strand determines the sequence of the other

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8
Q

define how the DNA strands are anti-parallel

A
  • the DNA strands run in opposite directions

- one is 5’ -> 3’ and the second is 3’ -> 5’

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9
Q

what are the two ways that describe how DNA strands are oriented with each other? (2)

A
  • the 2 DNA strands are complementary

- the 2 stands are anti-parallel

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10
Q

what components of DNA are on the outside/inside?

A
  • sugar phosphate backbone is on the outside - - the bases are on the inside of the helix
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11
Q

how are bases oriented to the DNA helix axis?

A
  • bases are almost perpendicular to the helix axis
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12
Q

how much are DNA bases separated by?

A
  • separated by 3.4 A
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13
Q

how long is the repeating DNA helix section and how many bases are in each turn of these repeating DNA helixes? (2)

A
  • repeats itself every 34 A

- 10.5 bases per turn of helix

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14
Q

what is the diameter of the DNA helix?

A
  • 20 A
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15
Q

what are the three known forms of DNA?

A
  1. B-DNA
  2. A-DNA
  3. Z-DNA
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16
Q

what is the form of carbon in the sugars of B-DNA?

A
  • C-2’ form of sugar
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17
Q

how is B-DNA generally characterized? (3)

A
  • hydrated DNA
  • most abundant form of DNA
  • geometry describes “relaxed state” of DNA
18
Q

how is A-DNA generally characterized?

A
  • dehydrated DNA that is essentially a squished version of B-DNA
19
Q

how is Z-DNA generally characterized?

A
  • unstable and transient, making it hard to isolate or study
20
Q

what forces hold DNA together? (4)

A
  1. H-bonds between bases (A-T, C-G)
  2. stacking of bases
  3. hydrophobic interactions
  4. electrostatic repulsion of phosphates
21
Q

how do proteins access DNA bases? (2)

A
  • major groove

- minor groove

22
Q

what groove do proteins interact with more often and why?

A
  • major groove because more functional groups are exposed here
23
Q

how do proteins interacts with DNA?

A
  • via H-bonds between size chains of amino acids and bases
24
Q

what are the characteristics of RNA? (2)

A
  • usually single stranded, but some parts can be double stranded
  • can have very complex structure
25
Q

DNA denaturation

A
  • separation of DNA strands
26
Q

how can DNA be denatured? (2)

A
  • increasing temperature (easiest)

- changing pH

27
Q

what determines the melting temperature of DNA?

A
  • the temperature where half of the DNA molecule is single stranded
28
Q

DNA renaturation

A
  • previously denatured strands will reanneal to form original DNA molecule if conditions are reverted back to normal
29
Q

linking number (2)

A
  • how many times strands are wrapped around each other

- changing the linking number in DNA will create supercoils

30
Q

overwinding DNA (2)

A
  • positive supercoils

- increase in the linking number

31
Q

underwinding DNA (2)

A
  • negative supercoils

- decreases linking number

32
Q

topoisomerase

A
  • enzymes that change topology/linking number of DNA
33
Q

whats are some of topoisomerases’ functions (2)

A
  • primary way of packing DNA for bacteria’s circular genomes
  • implication in DNA replication and transcription where separation of strands creates supercoils that need to be resolved
34
Q

type I topoisomerases (2)

A
  • change linking number by +/- 1

- does not require ATP

35
Q

how do type I topoisomerases function? (3)

A
  1. make a ss break in DNA using tyrosine as a catalyst
  2. pass second strand through ss break
  3. reseal ss break
36
Q

type II topoisomerases (2)

A
  • change linking number by +/- 2

- require 2 molecules of ATP

37
Q

how do type II topoisomerases function? (3)

A
  • making ds break
  • pass dsDNA fragment through dsDNA break
  • broken DNA is re-ligated and 2nd DNA segment is released
38
Q

bacterial DNA gyrase

A
  • type of type II topoisomerase that decreases linkage number by 2
39
Q

how is DNA packaged in bacteria? (2)

A
  • circular genome with supercoils created by topoisomerases

- histone-like proteins help DNA supercoiling

40
Q

how is DNA packaged in eukaryotes? (2)

A
  • DNA forms complex with proteins to form chromatin

- chromatin is further packaged into chromosomes

41
Q

nucleosomes (2)

A
  • basic unit of chromatin

- made up of DNA “wrapped” around histones

42
Q

histones (2)

  • composition
  • function of composition
A
  • contain high percentage of basic amino acids, lysine and arginine
  • lys and arg allow electrostatic interactions to form between histones and negatively charge DNA

BIOC 302 Part 2 (7 decks)

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