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Biochemistry 301 > Chapter 3 > Flashcards

Chapter 3 Flashcards

1
Q

Properties of Nitrogenous Bases

A
  • heterocyclic
  • aromatic
  • planar rings
  • hydrophobic with varying polar groups
  • synthesized in cells from amino acids
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2
Q

Base to Sugar

Reaction

Linkage

A

C1’ linked to base

Pyr - N1

Pur - N9

Condensation Reaction

N-glycosidic bond

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3
Q

Purpose of Nucleotides in cell

A
  • energy currency
  • nucleic acid building blocks
  • coenzymes (NAD - nicotinamide adenine dinucleotide)
  • ADP - glucose
  • cAMP
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4
Q

Phosphodiester bond

A

links phosphate to sugar

3’ OH linked to phosphate of next nucleotide

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5
Q

Phosphoanhydride

A

links phosphate to phosphate

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6
Q

ADP and ATP

A

best known nucleotides

adenosine diphospate and adenosine triphosphate

large, negative delta G of hydration

high phosphoryl transfer potential

ATP = 5mM in cell (fairly high)

Nucleotide Derivative: ADP - glucose

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7
Q

Ends of DNA

A

5’ End - phosphate off of 5’ C of sugar

3’ End - OH off of 3’C of sugar

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8
Q

RNA Polynucleotide

A

because of angles (from extra -OH group), RNA has a little twist, so the bases kinda stack on top of each other.

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9
Q

Thymine and Guanine

A

have keto and enol form

keto form preferred

makes an H-bond acceptor instead of donor

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10
Q

Chargaff’s Rules

A

A=T

G=C

(purine-pyrimidine pairs)

each pair takes up exactly the same amount of space (keeps backbone regular distance along chain)

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11
Q

B-Form DNA

Handedness

Diameter

Base pairs per helicle turn

Helix pitch (rise per turn)

A

Right

~20Ang.

10

36 degrees

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12
Q

B-Form DNA

Interior Base pairs

Helix rise per base pair

A

Interior base pairs are stacked - this causes the exclusion of water and makes it very stable. Sugars are slightly tilted, but the helix axis is near parallel. Base stacking is the primary stabilizing force of helix structure.

3.4 Ang. (Van der Waals distance)

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13
Q

B-Form DNA

Polar Exterior

A

Sugar-phosphate backbone

Associated with Mg2+ ion because phosphate groups are ionized at physiological conditions.

Exposed to solven

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14
Q

H-Bonding allows

A

dynamic structural changes induced by proteins/cellular conditions

-> replication and repair

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15
Q

B-DNA

Base tilt normal to helix axis

Major groove

Minor groove

Sugar Pucker

Glycosidic bond conformation

A

6 degrees

wide&deep

narrow&deep

C2’ ends

anti

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16
Q

DNA-RNA Helix

A

Hybrid helices exist primarily for shorter periods to complete task inolved

->replication and repair

protein expression

17
Q

RNA Structure

A
  • mostly single-stranded and variable
  • Ribose sugar 2’ OH alters nucleotide conformation due to sugar pucker
  • often highly folded with some base-pairing, but less stacking
  • bases “tilt” more stacking
  • more base-pairing variation
  • dynamic structure built for function and carrying info
  • contains modified and varied base derivatives other than A, U, C, and G.
18
Q

Alkaline Hydrolysis of RNA

A

basis of limit RNA half-life

catlytic RNA’s hydrolize phosphodiester bonds

19
Q

DNA Denaturation and Renaturation

Hydrogen bonds

Stacking interactions

Ionic Interactions

A

related to helix stability

stacking provides majority of helix stability

PCR; spectroscopy

Hydrogen bonds: necessary for specificity, but interchangeable between bases and water - no real contribution to DNA helix stability

Stacking interactions: from hydrophobic forces (not like amino acids) van der waals -> nonpolar solvent destabilized DNA

Ionic interactions: cations shield negative phosphates; monovalent - nonspecific binding - specific binding to phosphates

20
Q

Hyperchromic effect

A

double-stranded DNA (pH 7.0), max abs @ 260nm

absorbance increases 12-40% with denaturation

because of stacking energies (GC greatest)

21
Q

Tm

A

Melting temperature

sequence-dependent

cooperative (all or nothing)

solution: ions present, solvent, pH - affects (lower pH destabilizes h-bodning, causes Tm to go down)

G-C DNA has higher Tm than AT DNA due to increased stacking, 3 vs. 2 h-bonds

22
Q

Renaturation

A

single-strands reanneal when temp decreased slowly

heat or chaotropic agents (like urea, act to dehydrate DNA) can denature DNA

23
Q

DNA Replication

Central Dogma of Molecular Biology

A

DNA -> transcription mRNA ->RNA -> translation tRNA -> protein

Biochemistry 301 (10 decks)

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