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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?

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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?

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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?
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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
What is a nucleotide?
Nucleoside (nitrogenous base + pentose) + phosphate
26
In nucleotides, phosphates are typically found attached to _______ (especially in NTP's) - default
In nucleotides, phosphates are typically found attached to _C-5'_ (especially in NTP's)
27
What other regions of the pentose sugar can attach bond to phosphates?
C-2' or C-3' C-5' is the default, so unless otherwise specified, assume C-5' (eg deoxyadenosine 5' triphosphate (dATP))
28
\_\_\_\_\_\_\_\_\_\_ are polymers of nucleotides linked by 3'-5' phosphodiester bonds
_Nucleic acids_ are polymers of nucleotides (monomers) linked by 3'-5' phosphodiester bonds (covalent)
29
What type of bond is indicated in the image?
Phosphoester bond O || R1-O-P-OX | O-
30
\_\_\_\_\_\_\_\_\_\_ link carbons to phosphate groups
_phosphoesters_ link carbons to phosphate groups
31
\_\_\_\_\_\_\_\_\_ link two different carbons to one phosphate group
_Phosphodiesters_ link two different carbons to one phosphate group
32
What type of bond links two phosphates together?
Phosphoanhydrides
33
Phosphodiester bonds in nucleic acids create _________ structures with a "\_\_\_\_\_\_\_\_\_\_\_"
Phosphodiester bonds in nucleic acids create _asymmetric_ structures with a "_sense of direction_"
34
Nucleotide sequences are written from _____ to \_\_\_\_
Nucleotide sequences are written from _5'_ to _3'_
35
What is the primary structure for a nucleic acid?
The order of nucleotide residues (AGTC)
36
What is the NET charge of DNA and RNA?
Net charge is NEG- from the phosphate group
37
How do the backbones of RNA and DNA differ?
RNA is more polar because it has 2'OH with H-bonding potential DNA is less polar
38
Both DNA and RNA will have a 5' _______ group and a 3' ____ group
Both DNA and RNA will have a 5' _phosphate_ group and a 3' -_OH_ group
39
Given the sequence: 5' - ATGCAATG - 3' Is the structure DNA or RNA?
Most likely DNA because contains **T** Could be written as ATGCAATG or dAdTdGdCdAdAdTdG
40
Given the sequence 5' - ACGCAAGG - 3' is the structure most likely RNA or DNA?
Cannot be determined, could be either RNA or DNA. No U or T = requires more info
41
Given the primary structure, 5' - UCGUUCA - 3' , what is the polymer?
Likely RNA because contains U
42
What would the products be for the following reaction?
Hydrolysis of phosphodiester bone with phosphodiesterase (hydrolase) 5' phosphate and 3'Oh are products
43
Spontaneous, alkaline hydrolysis of phosphodiester bonds will occur in RNA, DNA or both?
RNA only - DNA is more stable because no OH at 2' position
44
why is DNA more stable than RNA under alkaline conditions?
Because it lacks the 2'OH found in RNA preventing hydrolysis by OH-
45
Cytosine deaminates to form \_\_\_\_\_\_\_
Cytosine deaminates to form _uracil_
46
What is incorporated at the 3' end of the nucleic acid and represents the end of the chain?
dideoxynucleotide (ddNTP) No OH in the sugar = incapable of forming anymore phosphodiester bonds
47
What are 7 common properties because Pyrimidine bases and Purine bases?
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
What effect on the A260nm/A280nm ratio would you expect with Protein contamination?
Decrease ratio 1.95 for pure DNA \<1.95 = protein contamination
49
What effect would you expect on the A260nm/A280nm ratio from RNA contamination
Increase ratio (single-stranded absorbs more) 1.95 for pure DNA \>1.95 = RNA contamination
50
What is the Beer-lambert Law? What does it suggest about the relationship between concentration and Absorbance?
A=(El)c A= absorbance E = extinction coefficient l = length path c = concentration * Absorbance varies directly with concentration
51
Primary structure of nucleic acids is the \_\_\_\_\_\_\_\_\_
Primary structure of nucleic acids is the _sequence of nucleotide residues_
52
Each chain of the DNA double helix is connected to the other through _____ between the bases (covalent or non-covalent)?
Each chain of the DNA double helix is connected to the other through _hydrogen bonds_ between the bases (covalent or **non-covalent**)?
53
What are Chargaff's Rules?
In DNA, A=T C=G - helped watson and crick deduce the double-helical structure of DNA
54
What is a hydrogen bond? How do they compare to covalent bonds
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
What is required in order for H-bonds to form between or within biochemical macromolecules?
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
The _____ and _____ functional groups on the four bases found in DNA allow for specific hydrogen bonding interactions between the bases?
The _amino_ and _carbonyl_ functional groups on the four bases found in DNA allow for specific hydrogen bonding interactions between the bases? =**complementary**
57
A-T vs C-G Which are stronger?
C-G (3 H-bonds)
58
What is B-form DNA? * Stabilised by _______ and \_\_\_\_\_\_ * _______ is the primary stabilising force * Strands are _______ with an overall \_\_\_\_\_\_-handed twist
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
What are the base-stacking forces that stabilize B-form DNA?
* Primarily van der Walls - favourable interactions * Also hydrophobic forces (faces of bases are hydrophobic) * from exclusion of water
60
What is important about the Major groove?
It is open enough to provide space for proteins to bind and interact
61
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
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) * ~**_10_**bp per turn
62
In a space-filling model of DNA if we see a methyl group, what does that indicate?
Methyl group indicates an AT pair No methyl group = CG pair
63
What feature gives nucleic acids a sense of direction? What is the direction?
Asymmetry in bonds that connect individual nucleotides together. 5' - 3'
64
What is DNA denaturation (melting)?
* 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
How does absorption change with DNA denaturation?
Increase in absorption at 260nm as strands separate UV absorbance increases as DNA goes from ds to ss
66
What is Tm?
midpoint of melting - transition halfway between ds and ss
67
What is hyperchromicity?
High absorbance Observed with SS DNA
68
What is Hypochromicity?
Low absorbance Seen with ddDNA
69
Is DNA denaturation reversible?
Yes, rate depends on the complexity of the nucleic acid (nucleation)
70
Renaturation requires proper \_\_\_\_\_\_\_\_
Renaturation requires proper _base pairing ***(nucleation)***_ - Slow phase and Zippering - fast face
71
How does a high GC content affect Tm?
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
How does changing pH affect Tm?
Increasing or decreasing pH destabilizes - affects protonation state
73
How does changing salt concentrations affect Tm?
* 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
What characteristic of nucleic acids enables hybridization?
The denaturation and renaturation behaviour of nucleic acids enables hybridization
75
RNA secondary structures are stabilised by ______ and \_\_\_\_\_\_\_\_
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
What is the approx A260/A280 ratio for RNA?
~2.1

BIOCH 200 (9 decks)

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