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1) Biochemistry I > Nucleic Acids > Flashcards

Nucleic Acids Flashcards

1
Q

What are nucleic acids composed of?

A
  • Phosphate
  • Pentose
  • Purine or pyrimidine base
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2
Q

How are nucleic acids formed?

A

Two condensation reactions

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3
Q

What is the first condensation reaction of nucleic acids?

A

Phosphate is linked to carbon 5’ through a phospho-ester bond

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4
Q

What is the second condensation reaction of nucleic acids?

A

Purine or pyrimide (nucleic acid bases) is linked to carbon 1’ through a beta N-glycosidic bond

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5
Q

What is the difference between deoxyribose and ribose?

A

Deoxyribose: no O, just H at carbon 2’ (DNA)
Oxyribose: OH at carbon 2’ (RNA)

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6
Q

How many phosphate groups does a nucleotide contain?

A

One/nucleotide

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7
Q

Why are the numbers primed?

A

To distinguish them from the atoms in nitrogen bases

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8
Q

What are the 2 classes of nucleobases?

A

Derivatives of pyrimidine and purine

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9
Q

What are nucleobases chemically?

A

Nitrogen-containing heteroaromatic molecules

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10
Q

Name 2 characteristics of nucleobases.

A
  • Planar or almost planar structures

- Absorb UV light around 250-270 nm

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11
Q

What # membered ring is purine? Pyrimidine?

A

Purine: 9 membered ring
Pyrimidine: 6

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12
Q

Name the 2 purines.

A

Adenine and Guanine

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13
Q

Name the 3 pyramidines.

A

Cytosine, Thymine, Uracil

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14
Q

Where is Thymine found? Where is Uracil found?

A

Thymine: DNA
Uracil: RNA

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15
Q

What does a nucleobase contain?

A

Nitrogenous base

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16
Q

What does a nucleoside contain?

A

Nitrogenous base and a pentose

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17
Q

What does a nucleotide contain?

A

Nitrogenous base, pentose and phosphate

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18
Q

How does polynucleotide polymerization occur?

A

3’ hydroxyl attacks the alpha-phosphate of another nucleotide (attached to carbon 5’) and releases a pyrophosphate

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19
Q

What kind of linkage do you form between 2 nucleotides? Between what?

A

Phosphodiester linkage

- 3’ and 5’

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20
Q

What is the convention for writing DNA/RNA polymers?

A
  • Top to bottom, left to write

- 5’ end to 3’ end

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21
Q

What is the backbone of DNA/RNA polymer made of?

A

Alternating phosphate and sugar groups

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22
Q

Which end of DNA/RNA polymers are phosphorylated? Which aren’t?

A

Phosphorylated: 5’ end

NOT phosphorylated: 3’ end

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23
Q

What are oligonucleotides? Polynucleotides?

A

Oligonucleotides: less than 50 nucleotides
Polynucleotides: > 50

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24
Q

What are DNA/RNA polymers sensitive to? Which is more sensitive? Why?

A
  • Sensitive to alkaline (base) hydrolysis

- RNA is more sensitive due to 2’ OH

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25
Q

What is the shorthand representation of phosphodiester linkage?

A

3’-5’

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26
Q

In the early 1900s, scientists believed that proteins were responsible for the storage and transport of nucleic acids. Name the 3 discoveries that proved them wrong.

A
  • Griffit: I don’t know if proteins are responsible created a doubt, maybe it is nucleic acids
  • Avery: proved it was DNA, could not rule out proteins
  • Hershey: ruled out proteins completely
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27
Q

What was Griffith? What year did he conduct his experiment in? What was his discovery? Why is it only doubt?

A
  • Bacteriologist
  • 1928
  • Transforming Principle
  • Some proteins are heat resistant, only creates doubt
28
Q

What is the transforming principle by Griffith?

A

transforming material (unlikely proteins)
crossed from the heat killed virulent S strain to the
non-virulent R live strain
- Mixture of heat-killed virulent and live nonvirulent bacteria
- dead bacteria of a virulent type and live bacteria of a non-virulent type were both injected in mice –> dead mice + virulent bacteria could be extracted from the dead mouse

29
Q

What did Avery do? What was his conclusion?

A

Mixing of purified fractions from virulent with live non-virulent bacteria
and isolation of S-virulent strain on petri dish
- DNase-treated but NOT protease-treated
- Transforming factor is DNA

30
Q

What was Hershey’s conclusion? How is protein ruled out?

A

Injected material from the Bacteriophage was P32 labeled and nucleic acids are the ones that contain phosphorus! DNA is responsible for the storage and transfer of genetic material
- Amino acids (cysteine and methionine) both have S groups, but radioactive S were not transferred, so protein is not responsible for the storage and transfer of genetic material

31
Q

What was Crick and what was Watson? What did they want to discover? What did they discover?

A

Crick: physicist
Watson: molecular biologist
- Wanted to determine the structure of nucleic acids
- Evidence that nucleic acids can store genetic material in the sequence of their bases

32
Q

What information helped Crick and Watson in their discoveries? (3)

A

1) Nucleic acids are helical in structure (2 helices) - Rosalind Franklin
2) The two strands are separated by 3 A (Rosalind Franklin)
3) Chargaff’s Rule: A+C = T+G, nucleotides have a constant ratio

33
Q

What did Crick and Watson state in their publication that explained the secret of life?

A

Not only storing, but possible copying mechanism for the genetic material

34
Q

How many hydrogen bonds do AT have? How many hydrogen bonds do GC?

A

AT: 2 hydrogen bonds
GC: 3 hydrogen bonds

35
Q

Do you need more energy to break GC or AT bonds?

A

GC, since 3 hydrogen bonds

36
Q

What is the distance between nucleobases?

A

3 A

37
Q

Is the double helix right or left handed?

A

Right

38
Q

What grooves does the helix contain? What is the pitch from one groove to the next? What is the width of the double helix? How many nucleotides per helix turn?

A
  • Major and minor
  • 36 A
  • 20 A
  • 10.4 nucleotides/helix turn
39
Q

Where do the phosphates and sugar groups point? Where do the nucleic acids point?

A

Phosphate and sugar: outside

Nucleic acid: inside

40
Q

How are the bases held together? (2)

A
  • Hydrogen bonds

- Van der Waals interaction

41
Q

The bases are separated to each other along the helix axis by what?

A

3.4 A

42
Q

Describe the strands of the helix.

A
  • 2 anti-parallel

- complimentary (5’—3’ & 3’—5’)

43
Q

How does DNA get converted to protein?

A
  • Replication of DNA
  • Transcription -> RNA
  • RNA -> Protein through translation
44
Q

Name the 3 postulated methods of DNA replication.

A

1) Semi-Conservative
2) Conservative
3) Dispersive

45
Q

What is the major disadvantage of conservative DNA replication?

A

No genetic variation, not a good evolutionary concept

46
Q

What would happen if DNA replication were to occur by a conservative mechanism?

A

two original template strands would stay together, and would instead produce an entirely new double-stranded copy.

47
Q

Is DNA replication unidirectional or bidirectional? Explain how we found this out.

A
  • Bidirectional
  • Take bacteria and grow in small amount of THYMIDINE (since DNA), spread on slide, put it on a film, the more you expose it, the darker the signal once you develop the film
  • Dark lines on both sides = bidirectional
48
Q

Name the 4 components needed for DNA replication.

A

1) DNA template
2) Primer strand
3) dNTPs (deoxyribonucleoside triphosphate)
4) Various bacterial fractions

49
Q

What is the importance of the primer strand?

A

Provides you with a 3’ hydroxyl end, the end that does the nucleophilic attack on dNTPs, which is required for DNA replication

50
Q

What do DNA polymerases catalyze? In what direction?

A

The stepwise addition of deoxyribonucleotides (5’-3’)

51
Q

What characteristics of DNA polymerase I and DNA polymerase III share?

A

1) It has 5’ — 3’ polymerase activity
2) It has 3’ — 5’ exonuclease activity (proof reading)
3) Requires a DNA template

52
Q

What is an exonuclease?

A

Removes nucleotides from the end of a polynucleotide molecule

53
Q

What does DNA polymerase I have that DNA polymerase III doesn’t? What does it do?

A
  • 5’—3’ exonuclease activity (removes added primers)
54
Q

How do DNA polymerase I and DNA polymerase III compare in terms of processing?

A

1: moderately processive (dissociates after adding 20 dNTPs)
3: synthesizes 1000 dNTPs/second

55
Q

The three activities of DNA polymerase I occur where? How many subunits make up DNA polymerase III?

A
  • On a single polypeptide (I)

- 10 subunits (III)

56
Q

What does Helicase do? Does it require energy?

A

Unwinding of the DNA double Helix

Requires energy

57
Q

What do single strand binding proteins do?

A

To keep DNA strands separate, to not form back the helix

58
Q

What does topoisomerase do?

A

Releases the stress of DNA unwinding through transient DNA cut and ligation

59
Q

What does primase not require to add complimentary base pairs? It is a must for what? What is it made of? What is the extension of DNA done by?

A
  • Does not require free 3’OH group to add complimentary base pairs
  • Must for Leading and Lagging Strand
  • RNA primer, extension of DNA done by DNA polymerase
60
Q

How many primers do you need for the leading strand?

A

One

61
Q

The lagging strand synthesis is unique. How does it occur? What are these called?

A
  • Occurs in a fragmented fraction

- Okazaki fragments

62
Q

How many primers do you need for the lagging strand? How does DNA synthesis occur?

A
  • You need a primer for EVERY fraction

- Then DNA copies, then primer, then DNA

63
Q

What removes the RNA primer? What does it put instead?

A

5’-3’ exonuclease activity of DNA polymerase I

- Fills the gap with DNA

64
Q

What joins the DNA fragments on the lagging strand?

A

DNA ligase

65
Q

What enzymes act as the rate limiting step for DNA replication?

A

Helicase and primase

1) Biochemistry I (12 decks)

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