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BIOCH 200 > Nucleotides and Nucleic Acids > Flashcards

Nucleotides and Nucleic Acids Flashcards

Readings: Chapter 19 pp 573-586

1
Q

What are four processes in which mono and dinucleotides are involved in?

A
  1. oxidation-reduction reactions
  2. Energy transfer
  3. intracellular signalling (cAMP)
  4. Biosynthetic reactions (ATP - energy transfer | NADPH - redox reactions)
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2
Q

How are polynucleotides used (2)

A
  1. storing and decoding genetic information (DNA/RNA)
  2. enzymes - ribozymes (eg ribosomes)
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3
Q

What are nucleotides composed of?

A
  • Phosphate(s)
  • Sugar
  • Nitrogen-containing aromatic base (Heterocyclic rings)
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4
Q

How does the number of phosphates differ between nucleotide polymers and mononucleotides

A

Nucleotide polymers often have 1 phosphate for each sugar and base

BUT

Mononucleotides may contain multiple phosphates

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5
Q

What determines the structure of the nucleic acids?

A

The structure of nucleotides incorporated into nucleic acids determines the structure of the nucleic acids.

ie structure of monomers influences polymers

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6
Q

What is the image?

How do you know?

A

A basic pyrimidine

  • 6-member ring
  • N at positions 1 and 3
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7
Q

What is the image?

How do you know?

A

Basic Purine

  • 6-member ring with 5-member ring
  • N at positions 1, 3, 7, 9
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8
Q

What is the molecule in the image?

How do you know?

How many hydrogen bonds can it form?

A

Uracil:

  • pyrimidine
  • 6-membered ring with N at 1 and 3
  • Substituents at positions 2, and 4 (in this case 2 carbonyl groups)
  • Can form 6 H-bonds
    • 2 as donor
    • 4 as acceptor
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9
Q

What is the molecule in the image?

How do you know?

How many hydrogen bonds can it form?

A

Thymine

  • Pyrimidine: 6-member ring with N at 1,3
  • Substituents at 2,4 (in this image, carbonyl groups)
  • methyl group at 5
  • Can form 6 H bonds
    • 2 donor
    • 4 as acceptor
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10
Q

What is the molecule in the image?

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How many hydrogen bonds can it form?

A

Cytosine

  • Pyrimidine: 6 member ring with N at 1 and 3
  • Carbonyl at C2
  • NH2 at C4
  • Can form 6 H-Bonds
    • 3 donor
    • 3 acceptor
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11
Q

What is the molecule in the image?

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How many H-Bonds can it form?

A

Adenine

  • Purine: 6 member ring + 5 member ring
    • N at 1, 3, 7, 9
  • NH2 at C6
  • 6 H-bonds
    • 3 acceptor
    • 3 donor
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12
Q

What is the molecule in the image?
How do you know?

How many H-bonds can it form?

A

Guanine:

  • Purine
    • 6C ring + 5C ring
    • N at 1, 3, 7, 9
  • Carbonyl at C4
  • NH2 at C2
  • 7 H-bonds
    • 3 acceptor
    • 4 donor
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13
Q

How do Uracil and thymine differ in the pattern of H-bond potential?

A

They don’t.

Uracil and thymine have the same pattern of H-Bond potential

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14
Q

Why can the N at C3 in Cytosine be a H-bond acceptor?

A

The N at C3 has no H associated therefore it is sp2 hybridized with a lone pair

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15
Q

Hydrogen attached to nitrogen can always act as a __________

A

Hydrogen attached to nitrogen can always act as a Hydrogen bond donor

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16
Q

Can a nitrogen within a ring be a hydrogen bond acceptor?

A

Not unless it has a lone pair within sp2 hybridized orbital such as the case with N1,3,7 in adenine, N7 in guanine and N3 in cytosine

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17
Q

All H-bond potential for Purines and pyrimidines is localized to the _______

A

All H-bond potential for Purines and pyrimidines is localized to the equatorial region of the bases

  • ie around the edge of a planar structure of either purine based ring or pyrimidine based ring
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18
Q

What is the difference between thymine and uracil?

A

Thymine has a methyl group at C5

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19
Q

What is a nucleoside?

A

Base + Sugar

-Purine or Pyrimidine base linked to a 5C sugar (pentose)

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20
Q

Purine and pyrimidine bases are linked to a five-carbon sugar to form _______

A

Purine and pyrimidine bases are linked to a five-carbon sugar to form nucleosides

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21
Q

How are pyrimidines attached to pentose?

A

N1 in pyrimidines attaches to the 1’ C of the sugar (loses h-attachment)

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22
Q

How do purines attach to the 5C sugar to form nucleosides?

A

Through N9 to 1’C in the sugar

  • N9 will no longer be able to form an H-bond when attached to sugar
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23
Q

How are ribose and deoxyribose different?

A

In ribose there is 2’ OH and a 3’ OH

In deoxyribose there is a 3’ OH but NO 2’OH

  • therefore, in DNA, the sugar is 2’ deoxyribose
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24
Q

How do you name nucleosides?

Purines:

Pyrimidines:

A

How do you name nucleosides?

  • Purines:
    • Adenine+ribose = adenosine (ribonucleoside)
    • Adenine+deoxyribose = deoxyadenosine
    • Guanine + ribose = guanosine
    • Guanine+deoxyribose = deoxyguanosine
  • Pyrimidines:
    • Cytosine
      • +ribose = cytidine
    • Thymine
      • +deoxyribose = deoxythmidine
      • +ribose (RARE) = thymidine or ribothymidine
    • Uracil
      • +ribose + uridine
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25
Q

What is a nucleotide?

A

Nucleoside (nitrogenous base + pentose) + phosphate

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26
Q

In nucleotides, phosphates are typically found attached to _______ (especially in NTP’s) - default

A

In nucleotides, phosphates are typically found attached to C-5’ (especially in NTP’s)

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27
Q

What other regions of the pentose sugar can attach bond to phosphates?

A

C-2’ or C-3’

C-5’ is the default, so unless otherwise specified, assume C-5’

(eg deoxyadenosine 5’ triphosphate (dATP))

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28
Q

__________ are polymers of nucleotides linked by 3’-5’ phosphodiester bonds

A

Nucleic acids are polymers of nucleotides (monomers) linked by 3’-5’ phosphodiester bonds (covalent)

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29
Q

What type of bond is indicated in the image?

A

Phosphoester bond

O

||

R1-O-P-OX

|

O-

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30
Q

__________ link carbons to phosphate groups

A

phosphoesters link carbons to phosphate groups

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31
Q

_________ link two different carbons to one phosphate group

A

Phosphodiesters link two different carbons to one phosphate group

32
Q

What type of bond links two phosphates together?

A

Phosphoanhydrides

33
Q

Phosphodiester bonds in nucleic acids create _________ structures with a “___________”

A

Phosphodiester bonds in nucleic acids create asymmetric structures with a “sense of direction”

34
Q

Nucleotide sequences are written from _____ to ____

A

Nucleotide sequences are written from 5’ to 3’

35
Q

What is the primary structure for a nucleic acid?

A

The order of nucleotide residues (AGTC)

36
Q

What is the NET charge of DNA and RNA?

A

Net charge is NEG- from the phosphate group

37
Q

How do the backbones of RNA and DNA differ?

A

RNA is more polar because it has 2’OH with H-bonding potential

DNA is less polar

38
Q

Both DNA and RNA will have a 5’ _______ group and a 3’ ____ group

A

Both DNA and RNA will have a 5’ phosphate group and a 3’ -OH group

39
Q

Given the sequence:

5’ - ATGCAATG - 3’

Is the structure DNA or RNA?

A

Most likely DNA because contains T

Could be written as ATGCAATG or dAdTdGdCdAdAdTdG

40
Q

Given the sequence 5’ - ACGCAAGG - 3’ is the structure most likely RNA or DNA?

A

Cannot be determined, could be either RNA or DNA. No U or T = requires more info

41
Q

Given the primary structure, 5’ - UCGUUCA - 3’ , what is the polymer?

A

Likely RNA because contains U

42
Q

What would the products be for the following reaction?

A

Hydrolysis of phosphodiester bone with phosphodiesterase (hydrolase) 5’ phosphate and 3’Oh are products

43
Q

Spontaneous, alkaline hydrolysis of phosphodiester bonds will occur in RNA, DNA or both?

A

RNA only - DNA is more stable because no OH at 2’ position

44
Q

why is DNA more stable than RNA under alkaline conditions?

A

Because it lacks the 2’OH found in RNA preventing hydrolysis by OH-

45
Q

Cytosine deaminates to form _______

A

Cytosine deaminates to form uracil

46
Q

What is incorporated at the 3’ end of the nucleic acid and represents the end of the chain?

A

dideoxynucleotide (ddNTP)

No OH in the sugar = incapable of forming anymore phosphodiester bonds

47
Q

What are 7 common properties because Pyrimidine bases and Purine bases?

A
  1. Heterocyclic
  2. Aromatic (electron delocalization - relatively non-polar)
  3. Basically planar
  4. Poorly soluble in water (relatively hydrophobic)
  5. Largely hydrophobic with some polar groups (ability for form H-bonds)
  6. Tend to absorb UV light
  7. Sugar-phosphate backbone is polar
48
Q

What effect on the A260nm/A280nm ratio would you expect with Protein contamination?

A

Decrease ratio

1.95 for pure DNA

<1.95 = protein contamination

49
Q

What effect would you expect on the A260nm/A280nm ratio from RNA contamination

A

Increase ratio (single-stranded absorbs more)

1.95 for pure DNA

>1.95 = RNA contamination

50
Q

What is the Beer-lambert Law?

What does it suggest about the relationship between concentration and Absorbance?

A

A=(El)c

A= absorbance

E = extinction coefficient

l = length path

c = concentration

  • Absorbance varies directly with concentration
51
Q

Primary structure of nucleic acids is the _________

A

Primary structure of nucleic acids is the sequence of nucleotide residues

52
Q

Each chain of the DNA double helix is connected to the other through _____ between the bases (covalent or non-covalent)?

A

Each chain of the DNA double helix is connected to the other through hydrogen bonds between the bases (covalent or non-covalent)?

53
Q

What are Chargaff’s Rules?

A

In DNA,

A=T

C=G

  • helped watson and crick deduce the double-helical structure of DNA
54
Q

What is a hydrogen bond?

How do they compare to covalent bonds

A

Polar interaction in which a H-atom is shared by two electronegative atoms

MUCH WEAKER than covalent bonds, but in large numbers, help stabalize

55
Q

What is required in order for H-bonds to form between or within biochemical macromolecules?

A

They must be shielded from water (water is very good at acting as donor and acceptor and will replace DNA as the donor/acceptor)

56
Q

The _____ and _____ functional groups on the four bases found in DNA allow for specific hydrogen bonding interactions between the bases?

A

The amino and carbonyl functional groups on the four bases found in DNA allow for specific hydrogen bonding interactions between the bases?

=complementary

57
Q

A-T vs C-G

Which are stronger?

A

C-G (3 H-bonds)

58
Q

What is B-form DNA?

  • Stabilised by _______ and ______
    • _______ is the primary stabilising force
  • Strands are _______ with an overall ______-handed twist
A

What is B-form DNA?

The expected form of DNA in an aqueous environment

  • Stabilised by base stacking interactions and Hydrogen bonds
    • Base-stacking is the primary stabilising force
  • Strands are anti-parallel with an overall right-handed twist
59
Q

What are the base-stacking forces that stabilize B-form DNA?

A
  • Primarily van der Walls - favourable interactions
  • Also hydrophobic forces (faces of bases are hydrophobic)
    • from exclusion of water
60
Q

What is important about the Major groove?

A

It is open enough to provide space for proteins to bind and interact

61
Q

General features of B-form DNA

  • _____ core containing _______ and exterior is ______
  • Bases largely excluded from _____
    • Stabilizes ________
  • ________ exposed to h2O
  • H-bonds in _______ interactions
  • ~___bp per turn
A

General features of B-form DNA

  • Hydrophobic core containing base pairs and exterior is polar (sugar/phosphate (-))
  • Bases largely excluded from H2O
    • Stabilizes H-bonds - not important for structure but lack of H-bonds will disrupt
  • Ribose/deoxyribose (sugar) exposed to h2O
  • H-bonds in pairing interactions (base pairs)
  • ~10bp per turn
62
Q

In a space-filling model of DNA if we see a methyl group, what does that indicate?

A

Methyl group indicates an AT pair

No methyl group = CG pair

63
Q

What feature gives nucleic acids a sense of direction?

What is the direction?

A

Asymmetry in bonds that connect individual nucleotides together.

5’ - 3’

64
Q

What is DNA denaturation (melting)?

A
  • Separation of the two paired strands
    • double-stranded DNA (dsDNA) to single-stranded DNA (ssDNA)
  • Disruption of non-covalent forces
    • Base-stacking and hydrogen bonding
  • Essential for some cellular processes
    • Energy dependent
    • Replication and transcription require strand separation
65
Q

How does absorption change with DNA denaturation?

A

Increase in absorption at 260nm as strands separate

UV absorbance increases as DNA goes from ds to ss

66
Q

What is Tm?

A

midpoint of melting

  • transition halfway between ds and ss
67
Q

What is hyperchromicity?

A

High absorbance

Observed with SS DNA

68
Q

What is Hypochromicity?

A

Low absorbance

Seen with ddDNA

69
Q

Is DNA denaturation reversible?

A

Yes, rate depends on the complexity of the nucleic acid (nucleation)

70
Q

Renaturation requires proper ________

A

Renaturation requires proper base pairing *(nucleation)* - Slow phase

and Zippering - fast face

71
Q

How does a high GC content affect Tm?

A

High GC = elevated Tm (more energy required to break)

NOT BECAUSE OF H-BONDING but because of BASE STACKING

GC pairs have stronger base-stacking interactions than AT pairs

72
Q

How does changing pH affect Tm?

A

Increasing or decreasing pH destabilizes

  • affects protonation state
73
Q

How does changing salt concentrations affect Tm?

A
  • Ions shield the negative charges on phosphate backbone
    • Mg2+ dissolves DNA(neg)
    • Positively charged proteins (histones)
  • Low salt decreases Tm
    • destabilizes double helix
  • Increased salt elevates Tm
    • stabilizes the double helix
74
Q

What characteristic of nucleic acids enables hybridization?

A

The denaturation and renaturation behaviour of nucleic acids enables hybridization

75
Q

RNA secondary structures are stabilised by ______ and ________

A

RNA secondary structures are stabilised by base stacking interactions and Hydrogen bonds

  • Hydrogen bonds
    • base pairs
      • watson-crick: A/U; G/C
      • non-watson-crick: eg G/U
    • 2’OH (not in DNA)
      • form H-bond as donors/acceptors
  • Base stacking
    • Helical; right handed structures
    • Hydrophobic/van der Waals interactions
76
Q

What is the approx A260/A280 ratio for RNA?

A

~2.1

BIOCH 200 (9 decks)

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