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BIOCH 200 > 2. Nucleic Acids > Flashcards

2. Nucleic Acids Flashcards

1
Q

what are the types of nucleic acids, what are they composed of

A

Types of nucleic acids: DNA, RNA

composed of nucleotides:
- contains a base - Adenine, cytosine, guanine, thymine, uracil
- a sugar - deoxyribose and ribose
- a phosphate

the structure of nucleotides incorporated into the polymer determines the structure of the nucleic acid

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2
Q

DNA

A

A polymer of deoxynucleotides whose sequence of bases encodes genetic information in all living cells

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3
Q

RNA

A

A polymer of ribonucleotides, such as messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA)

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4
Q

nucleotide

A
  • compound consisting of a nucleoside esterified to one or more phosphate groups
  • monomeric units of nucleic acids
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5
Q

nucleoside

A

compound consisting of a nitrogenous base linked to a 5-carbon sugar (ribose or deoxyribose)

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6
Q

deoxynucleotide

A

nucleotide in which the pentose is 2’-deoxyribose

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7
Q

2 common sugars

A

deoxyribose and ribose

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8
Q

bp and kb

A

bp - base pairs
kb - kilo base pairs (1000 base pairs)

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9
Q

oligonucleotide

A

A polynucleotide consisting of a few nucleotide residues

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10
Q

B-DNA

A

The standard conformation of double-helical DNA

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11
Q

stacking interactions

A

The stabilizing van der Waals interactions between successive (stacked) bases in a polynucleotide

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12
Q

melting temperature (Tm)

A

The midpoint temperature of the melting curve for the thermal denaturation of a macromolecule.
For a lipid, the temperature of transition from an ordered crystalline state to a more fluid state

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13
Q

denaturation and renaturation

A

denaturation: the loss of ordered structure in a polymer
i.e disruption of native conformation (unfolded polypeptide), unstacking of bases, separation of strands in a nucleic acid

renaturation: the refolding of a denatured macromolecule so as to regain its native conformation

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14
Q

anneal

A

to allow base pairing between complementary single polynucleotide strands so that double-stranded segments form

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15
Q

Distinguish between properties of purine and pyrimidine bases.

A

Purines: Adenine (A), Guanine (G)

  • double ring structure, basically planar, slight pucker in purine base
  • poorly soluble in water
  • largely hydrophobic with some polar groups (ability to form H-bonds)

Pyrimidines: Cytosine (C), Thymine (T), Uracil (U)

  • heterocyclic
  • aromatic, electron delocalization
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16
Q

What are the 5 common bases? Which are classified as pyrimidines and which are purines?

A

Purines: Adenine (A), Guanine (G)

Pyrimidines: Cytosine (C), Thymine (T), Uracil (U)

T - DNA
U - RNA

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17
Q

Is the sugar phosphate backbone polar or non polar?

A

polar

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18
Q

Name and distinguish between the two sugars that are incorporated into nucleotides

A

Ribose: found in ribose, has a -OH attatched to the 2’ carbon of the sugar ring in replace for a H present in deoxyribose

Deoxyribose: found in DNA, lacks -OH on the 2’ carbon (deoxy)

  • both are furanose rings (5 membered with an oxygen)
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19
Q

naming of nucleosides and nucleotides

A

Nucleosides:

  • -osine in purines replaces -ines
    (eg. adenine + ribose = adenosine)
  • pyrimidines → end in -idine
    (eg. cytosine + ribose = cytidine)
  • deoxy- is added as a prefix for nucleosides with deoxyribose sugar
    (eg. thymine + deoxyribose = deoxythymidine

Nucleotides:
* nucleoside name + “5’ ____ - phosphate”
* ____ is the prefix for amount of phosphate’s in the phosphate group (mono-/di-/tri-/tetra-)
* phosphates attatched to multiple carbon/OH groups are described using bis-/tris- prefixes along with including the atom number that the phosphate is attatched to
(eg. adenosine 2’, 5’ bisphosphate)

5’ refers to carbon in the sugar ring, most of the time attatched to 5’ carbon but can be C2 or C3 as well

20
Q

compare the structure of nucleosides with the structure of nucleotides

A
  • nucleosides: sugar + base, no phosphodiester bond
  • nucleotide: sugar + base + phosphate group, contains phosphodiester bond
21
Q

Define the term nucleic acid

A
  • also known as a polynucleotide
  • polymer of nucleic acids
  • major nucleic acids: deoxyribonucleic acid (DNA), ribonucleic acid (RNA)
22
Q

explain why nucleic acids are said to have a “sense of direction”

A
  • phosphodiester bonds in nucleic acids create asymmetric structures with a “sense of direction” →
  • phosphodiester bonds link the 3’ carbon of one sugar and the 5’ carbon of the next sugar → creates a repeating sugar-phosphate backbone.

5’ end → 3’ end

23
Q

What are the 5’ and 3’ ends of nucleic acid base sequences?

A
  • The 5’ end of the nucleic acid chain has a free phosphate group attached to the 5’ carbon of the sugar.
  • The 3’ end has a free hydroxyl (-OH) group attached to the 3’ carbon of the sugar
  • nucleotides joined by phosphodiesters are described as residues
24
Q

What is the primary (1°) structure for a nucleic acid?

A

the sequence of nucleotide residues; the order of monomers in a polymer

25
Q

abbreviations for primary structures of nucleic acids

A

based on the first letter of each nucleotide written in sequence from 5’ → 3’ by convention

e.g: 5’ - ATGCAATG - 3’
can also be written as:
ATGCAATG, 5’-dAdTdGdCdCdCdTdG-3’, dAdTdGdCdCdCdTdG (DNA)

  • T indicates the nucleic acid is likely DNA
  • U indicated the nucleic acid is likely RNA
26
Q

phosphoesters, phosphodiesters, phosphoanhydrides

A
  1. phosphoesters: (phosphate esters), link carbons to phosphate groups
  2. phosphodiesters: link two different carbons to one phosphate group
  3. phosphoanhydrides: link two phosphates to each other (within a phosphate group)
27
Q

describe and compare the primary structure of RNA and DNA

A

Both: have a net (-) charge, a polar backbone, a phosphodiester linkage following from the 5’ end of the nucleotide to the 3’ end, and a free 3’ -OH group at the 3’ end

RNA: contains uracil instead of thymine and is a little more polar due to the extra -OH on the 2’ carbon of the nucleotide sugars (ribose)

DNA: contains thymine instead of uracil, slightly less polar than RNA due to H+ on 2’ carbon

28
Q

explain why RNA is susceptible to alkaline hydrolysis whereas DNA is resistant

A

phosphodiester bond spontaneously hydrolyze (phosphodiesterase) at pH>10

In DNA, the absence of a 2’ OH prevents the reaction. This makes DNA more stable than RBA under alkaline conditions

29
Q

Nomenclature for polynucleotides

A
  • mononucleotide - 1 nucleotide (ATP, ADP, FMN)
  • dinucleotide - 2 nucleotides (FAD, NAD+, dCdG)
  • Tri-/Tetra-, etc
  • oligonucleotide (more than 20 <50 nucleotides)
  • polynucleotides (large number)
30
Q

Explain why the bases in a nucleic acid “stack: and identify the forces that favour stacking

A
31
Q

State Chargaff’s rules and explain what they tell you about a nucleic acid

A
  • nucleotides in DNA were not all
    present in equal numbers and base composition varies from organism to organism
  • Chargaff noted that the amount of A is equal to the amount of T, the amount of C is equal to the amount of G, and the total amount of A/G is equal to the total amount of C/T.
  • Chargaff’s “rules” could be satisfied by a molecule with two polynucleotide strands in which A and C in one strand pair with T and G in the other
32
Q

describe the double helical structure of B-DNA (6)

B-form is the most common form of DNA

A
  1. double helix: 2 chains connected to the other through H-bonds between bases (non-covalent), the strands are anti-parallel, with an overall right-handed twist
  2. hydrophobic core/polar exterior - base pairs largely excluded from water (stabilizes H-bonds) and stack on top of each other - base pair edges are exposed in the major/minor grooves
  3. The twisting of the DNA “ladder” into a helix creates two grooves of unequal width, the major and minor grooves.
  4. ribose/deoxyribose and phosphates (very polar) exposed to water
  5. H-bonds in pairing interactions
  6. ~10 base pairs/turn

antiparallel: complenatary strands should run in opposite directions of 5’-3’

33
Q

State how strands of DNA align with one another specifically rather than randomly

A

hydrogen bonding between the four bases: amino and carbonyl functional groups found in DNA (along with the right nitrogen atoms) allow for specific hydrogen bonding interactions between the bases.

  • 2 hydrogen bonds link A/T, T/A
  • 3 hydrogen bonds link G/C, C/G

formation of base pairs requires the correct hydrogen bonding interactions between bases in the two strands

34
Q

Describe how the structure of double-stranded DNA is stabilized

A
  1. Hydrogen bonds - between base pairs
  2. Base stacking (primary stabilising force) - primarily van der Waals forces, hydrophobic forces
35
Q

State why it is important that the structure of DNA is stabilized by non-covalent forces only

A

The polar sugar/phosphate backbone is found on the outside while the more hydrophobic bases stack in the core of the structure

36
Q

State the role for the grooves in the structure of double-stranded DNA

A
  • Other hydrogen bonding sites on the bases are open to the major and minor grooves where they can interact with solvent
37
Q

List the major differences between RNA and DNA 3-D structures

A

DNA - double stranded (helical), base pairs A/T, G/C, interstrand base pairing

RNA - single stranded, base pairs A/U, G/C, intrastrand base pairing, partially SS and partially duplex - much more dependant on nucleotide sequence than dsDNA

38
Q

State why the denaturation of a double helix is feasible and identify the chemical conditions that can cause denaturation

A
  • denaturation must happen for replication or transcription
  • Increasing temperature
39
Q

Define “melting” of a double stranded molecule of DNA

page 28

A
  • separation of the two paired strands (dd→ss)
  • disruption of non-covalent forces (base-stacking/hydrogen bonding)
  • cooperative process: SLOW & hard to start, easy to continue (FAST zippering)
  • changes in absorption properties occur (increase in absorption at 260nm as strands separate
  • essential for some cellular processes (replication/transcription)
40
Q

Define the terms hyperchromicity and hypochromicity with respect to double-stranded nucleic acids

A

hyperchromicity - a relatively high absorbance, DS→SS DNA

hypochromicity - low absorbance, SS→DS DNA

41
Q

Explain the term renaturation

A
  • Reformation of DS DNA so it regains its native conformation
  • occurs in slow cooling (20-25℃ below Tₘ) - rapid coolin can result in improper base pairing
    1. proper base pairing
    2. cooperative: nucleation (slow), zippering (fast)
42
Q

what is Tₘ?

A

Tₘ - the midpoint of melting
affected by sequence of nucleotides, composition, and solvent

43
Q

Describe and explain the relationship between the Tm of a double-stranded nucleic acid and its relative content of C and G

A

Tₘ is higher for for nucleic acids containing more C/G pairs
* base stacking is stronger in G/C pairs: makes 3 hydrogen bonds → G donates 2 and accepts 1, C accepts 2 and donates 1
* A/G pairs only have 2 hydrogen bonds between them (regions of A/T pairs in DNA tend to denature first)

44
Q

State how and why the Tm of a nucleic acid is affected by pH and ionic strength

slide 31

A

pH: increasing/decreasing pH will decrease Tm by affecting protonation state

  • Tm is highest at pH 7

salt concentrations: ions shield negative charges on phosphate backbone (Mg2+, positively charged proteins)

  • low salt → decreases Tm (destabilizes dbl helix)
  • high salt → increases Tm (stabilizes dbl helix)
45
Q

State whether or not RNA can “melt” and justify your answer

A

RNA can melt but it’s ,=melting curve is less steep and starts at a higher absorbance due to having a mix of SS and DS RNA

  • A260nm of free nucleotides > SS > DS
  • Abs increases as disorder of structure increases

BIOCH 200 (7 decks)

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