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BMS1. Replication and Repair (GELINAS) > Nucleic Acids (Gelinas) > Flashcards

Nucleic Acids (Gelinas) Flashcards

1
Q

Function of nucleic acids (DNA and RNA):

A
  • store and express genetic information
  • transmit genetic info from generation to generation
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2
Q

What class of viruses carry genetic information in the form of RNA?

A
  • retroviruses
    • i.e. HIV
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3
Q

DNA Replication:

A
  • copies genetic information
  • transmits genetic information to daughter cells
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4
Q

DNA Transcription:

A
  • expresses genetic information contained in DNA through RNA synthesis
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5
Q

DNA repair:

A
  • corrects damage resulting from replication errors or environmental insults
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6
Q

DNA Recombination:

A
  • joins two parental DNA segments to form a hybrid molecule
    • chromosome crossing over during meiosis
    • generation of antibody diversity
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7
Q

Process of DNA → RNA:

A

Transcription

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8
Q

Process of RNA → Protein:

A

Translation

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9
Q

Flow of genetic information in cells:

A
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10
Q

Flow of genetic information in certain viruses (retroviruses):

A
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11
Q

The three elements that compose a nucleic acid:

A
  1. base (purine or pyrimidine)
  2. 5-carbon sugar
  3. phosphate group
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12
Q

The four bases in DNA:

A

deoxyribonucleotides

  1. A (Purine)
  2. C (Pyrimidine)
  3. G (Purine)
  4. T (Pyrimidine)
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13
Q

The four bases of RNA:

A

ribonucleotides

  1. A (Purine)
  2. C (Pyrimidine)
  3. G (Purine)
  4. U (Pyrimidine)
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14
Q

Base methylation allows:

A

DNA recognition by proteins that control gene expression

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15
Q

Purine bases:

A

A and G

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16
Q

Pyrimidine bases:

A

C, T, U

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17
Q

Nucleoside:

A
  • base linked to a 5-carbon sugar
    • N-glcosydic bond
  • base + ribose = RNA
  • base + 2-deoxyribose = DNA
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18
Q

Nucleoside + phosphate =

A

nucleotide

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19
Q

Nucleoside analogs are useful for:

A
  • anti-viral and anti-cancer therapy
  • incorporated into growing DNA strands during viral or cellular DNA replication and block further DNA synthesis
    • minimal side effects
  • used in herpes and HIV
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20
Q

Primary structure of DNA:

A

polynucleotide chain

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21
Q

Secondary structure of DNA:

A

alpha-helices

(DNA double helix)

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22
Q

Tertiary structure of DNA:

A

supercoiled DNA helices

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23
Q

How are nucleotides bonded to one another?

A
  • A 3ʼ, 5ʼ- phosphodiester bond is formed between the 3ʼ-hydroxyl group on the sugar of one nucleotide and the 5ʼ-phosphate group of the next nucleotide, releasing a pyrophosphate group.
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24
Q

Nucleases:

A
  • enzymes that cleave polynucleotide chains by hydrolyzing phosphodiester bonds.
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25
Q

Exonucleases:

A
  • remove nucleotides from either or both the 5ʼ and 3ʼ ends, depending on specificity.
26
Q

Endonucleases:

A
  • only cleave internal phosphodiester bonds
27
Q

Restriction enzymes:

A
  • endonucleases
  • cleave DNA in a sequence-specific manner
  • useful in molecular biology
28
Q

Most common DNA secondary structure found in cells:

A
  • B-form double helix
29
Q

Characteristics of the B-form double helix in DNA:

A
  1. right handed
  2. two anti-parallel polynucleotide strands
  3. outer sugar-phosphate backbone
  4. base pairs stacked on the inside, perpendicular to the axis
  5. held together by hydrogen bonds
  6. major and minor grooves
30
Q

Per helical turn in DNA, how many base pairs are there? How many angstroms per helical turn?

A

10 base pairs per helical turn

34 angstroms per helical turn

31
Q

Proteins that regulate gene expression bind to what groove of DNA double helix?

A

major

32
Q

Histone proteins found in chromatin bind to what groove in DNA double helix?

A

minor

33
Q

Number of hydrogen bonds between A and T:

A

2

34
Q

Number of hydrogen bonds between G and C:

A

3

35
Q

Chargaff’s Rule:

A
  • always an equal amount of purines and pyrimidines in double-stranded DNA.
  • due to base-pairing
36
Q

Relaxed form of DNA:

A

B-form double-helix

37
Q

Supercoiled form of DNA:

A

when the double-helix coils upon itself

38
Q

Negative supercoils:

A
  • left-hand twist (untwist helix)
  • fewer helical turns than relaxed DNA
  • energetically favored
  • facilitate DNA strand separation during replication, repair, recombination and transcription.
39
Q

The binding of eukaryotic histone proteins forces the DNA double-helix to:

A

wrap around them, generating a negative supercoil

40
Q

How are negative super coils formed?

A
  1. partially unwind double-helix
  2. DNA underwound; bubble forms
  3. negative supercoil forms to compensate for increased tension in double helix that is not unwound
41
Q

DNA topoisomerases are:

A
  • enzymes that introduce “swivel points” in the DNA helix to change its tertiary structure.
  • used in the setting of supercoiling
42
Q

How do DNA topoisomerases work?

A
  • transiently break one or both DNA strands, pass the strand(s) through the break, and rejoin them.
43
Q

Positive supercoiling:

A
  • right-handed twist (helix twisted tighter)
  • more helical turns than relaxed (B-form) DNA double helix
  • helix distorts and “knots” in response to increased tension
44
Q

Eukaryotic topo I and topo II can remove what kind of supercoils?

A
  • both negative and positive supercoils.
45
Q

Topoisomerase I (Topo I) function and energy requirement:

A
  • cuts a single strand of the double-helix to relieve tension of supercoiling
  • NO ATP
46
Q

Topoisomerase II (Topo II) function and energy requirement:

A
  • cuts both DNA strands in helix to relieve tension of supercoiling
  • REQUIRES ATP
47
Q

Bacterial DNA gyrase:

A
  • unusual topo II
  • can remove positive and negative supercoils
  • can introduce negative supercoils into relaxed DNA
  • requires ATP
48
Q

By inhibiting specific steps in the action of topoisomerases, certain drugs can:

A
  • convert topoisomerases into DNA breaking agents and lead to cell death.
    • topoisomerases can cut DNA
    • can alter cutting ability
    • can alter DNA rejoining ability
49
Q

In prokaryotes, DNA is associated with non-histone proteins that can condense the DNA to form a:

A

nucleoid (a non-membrane-bound region of the cell).

50
Q

Histones:

A
  • small basic proteins rich in arginine and lysine
  • associated with DNA;
    • when associated = CHROMATIN
51
Q

Chromatin:

A
  • DNA associated with histone proteins
  • histone proteins induce negative supercoiling
52
Q

5 classes of histones:

A
  • H1
  • H2A
  • H2B
  • H3
  • H4
53
Q

Nucleosome cores:

A
  • roughly 140 bp of DNA (1 and 3/4 negative supercoil) wound around a histone octamer comprised of two molecules each of histones H2A, H2B, H3 and H4.
54
Q

In chromatin, nucleosome cores are separated by:

A
  • a DNA spacer of roughly 20-80 bp in length (resembling beads on a string).
  • binds histone H1
55
Q

Euchromatin:

A
  • extended, active DNA (being expressed as protein)
56
Q

Heterochromatin:

A
  • condensed, mostly inactive DNA
57
Q

Histone modifications (such as by acetylation or methylation) affect:

A
  • regional compaction of chromatin
  • regulation of gene expression
58
Q

Histone H1 role:

A
  • one unit of histone H1 binds the spacer DNA
    • promotes tight packing of nucleosomes
  • chromatin then winds into solenoid
59
Q

General process of chromosome formation from DNA synthesis:

A
  1. DNA replicated, forms double helix
  2. histones bind to DNA in octamers, nucleosomes form “beads on string”
  3. histone H1 binds to spacer DNA in between nucleosomes
  4. solenoid forms
  5. solenoid loops around protein scaffold
  6. chromosome formed
60
Q

A condensed metaphase chromosome contains:

A
  • two chromatids joined by a centromere
  • ends of linear chromosomes form telomeres

BMS1. Replication and Repair (GELINAS) (6 decks)

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