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NB CH 2 Flashcards

(52 cards)

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1
Q

Peptide bonds

A

-Covalent bonds between amino acids to form polypeptides and proteins (planar)
-Sharing electrons between O, C, N (C-O and C-N)
-Partial double bond character: shorter than single bond, larger than double bond length
-Formed via condensation reaction between carboxyl and amino acid

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2
Q

Polar vs nonpolar

A

Polar: (hydrophilic) covalent bonds with dipole
Non-polar: (hydrophobic) equal share of electrons

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3
Q

Two important properties of water

A
  1. Form hydrogen bonds
  2. Be ionized (OH-) and (H3O+)
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4
Q

Non-covalent interactions

A
  1. Salt bridge: ionic interactions between charged atoms
  2. Hydrogen bonds: interactions between polar atoms with partial charges (dipoles)
  3. van der Waals: weak attractions between atoms at a certain distance

= electrostatic interactions

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5
Q

Hydrogen donor vs acceptor

A

Donor: shorter bondlength
Acceptor: longer bondlength

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5
Q

Aqueous enviroment affects?

A
  1. Strength of interactions b/w molecules
  2. Types of interactions that occur
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5
Q

AMP
CMP
GMP
TMP

A

AMP - adenylate
CMP - cytidylate
GMP - guanylate
TMP - thymidylate

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6
Q

Nucleotides vs Nucleoside

A

Nucleotide: sugar + base + phosphate
Nucleoside: sugar + base

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6
Q

What determines strength of interaction?

A
  1. Shape
  2. Chemical nature of surface
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6
Q

Deoxyribose vs Ribose

A

Deoxyribose: DNA (2’ just H)
Ribose: RNA (2’ OH)
1’ connected to base
5’ connected to phosphate

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6
Q

Purines vs pyrimidines

A

Purine: (double ring) adenine + guanine [N9]
Pyrimidines: (single ring) cytosine + thymine + uracil [N1]

Connected to 1’ of sugar via GLYCOSIDIC bond

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6
Q

Bond between bases and sugars?

A

Glycosidic bond

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7
Q

Nucleotides are joined together by?

A

Phosphodiester bonds

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8
Q

Tautomers

A

Two molecules with same molecular formula but different connectivity

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9
Q

Important roles of nucleotides & their derivatives

A
  1. Catalyze chemical reactions:
    NAD+/NADH, FAD/FADH2, NADP+/NADPH
  2. Energy storage and carrier:
    ATP (phosphate)
  3. Carriers of chemical group:
    ATP (phosphate), CoA (acyl), SAM (methyl)

! All contain adenosine !

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10
Q

NAD+ and FAD?

A

NAD+ - Nicotinamide Adenine Dinucleotide
FAD: Flavin Adenine Dinucleotide

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11
Q

Double stranded DNA via?

A

Non-covalent Hydrogen Bonds

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12
Q

Complementary base pairs

A

A and T - 2 hydrogen bonds
C and G - 3 hydrogen bonds

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13
Q

Antiparellel

A

5’ end of one strand pairs with 3’ end of other

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14
Q

Most energetically favorable formation of DNA?

A

Right-handed double helix (clockwise rotation)

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15
Q

Base-stacking in DNA

Study These Flashcards
A

Energetically favourable & stable (via van der waals interactions)
Hydrophobic bases in center
Hydrophilic sugar-phosphate backbone outside

16
Q

B-DNA

Study These Flashcards
A

10.5 base pairs/turn
Right-handed
Protein interaction

17
Q

A-DNA

Study These Flashcards
A

11 base pairs/turn
Right-handed
RNA structure

18
Q

Z-DNA

Study These Flashcards
A

12 base pairs/turn
Left-handed
Not clear roles

19
Supercoiled DNA
Naturally occurring form of DNA where the double helix is further twisted or coiled on itself, creating a compact and strained structure, which is important for DNA organization, replication, and transcription
20
Induce supercoiling?
Cut & twist - 10.5 bp/turn to fewer = DNA twists back to preferred number bases per turn
21
Preferred supercoiling?
Negative (unwind DNA -> rejoin) Clockwise twisting
22
Positive supercoiling?
Twist DNA -> rejoin Counterclockwise twisting
23
Linking number
Nr of times one strand wraps around another (B-DNA: Lk=20)
24
Twist
Nr of turns in DNA helix (B-DNA: Tw=20) Right-handed: + Left handed: -
25
Writhe
Number of supercoiling (relaxed: Wr=0) Negative supercoiling: - Positive supercoiling: +
26
Topoisomerase
Introduce or remove supercoils from DNA with energy (ATP hydrolysis) by temporarily breaking DNA and twisting it
27
RNA Structure
1. Primary structure: RNA sequence 5' to 3' 2. Secondary structure: short double-helical regions 3. Tertiary structure: arrangement of double-helices and single stranded regions of RNA
27
Importance of 2'OH in RNA
1) STRUCTURE favours A-type helix more extensive hydrogen bonds = more interactions 2) FUNCTION facilitates reaction that cleave phosphodiester bonds (much lower stability, short term functions)
28
Non-canonical Base Pairs
Di-methylated guanine-adenine Wobble base pair (guanine-uridine)
29
Covariations
Differences that occur among species, yet cnserve interactions
30
Amphipathic
Both hydrophilic and hydrophobic characteristics
31
Cysteine (Amino acid side chain)
(Hydrophilic) Sulfhydryl (-SH) groups form covalent bonds with one another to make disulfide salt bridges (-S-S-) for stabilization of protein
32
pKa
pH at which half the population are charged
33
Acidic vs Basic vs Neutral side chains
Acidic: + charged (D, E) Basic: - charged (K, R, H) Neutral: Histidine (H+ donor or acceptor)
34
Polypeptide
Polymer of amino acids N-terminus = exposed amino acid C-terminus = exposed carboxyl Synthesized from N- to C-terminus
35
Ramachandran plot
Indicates restricted conformation
36
Four levels of protein structure
1. Primary: amino acid sequence 2. Secondary: short regions of repeated structures 3. Tertiary: final folded shape 4. Quaternary: complex proteins (more than one polypeptide)
37
Secondary structure 1: Alpha helix
Right-handed Hydrogen bonds between carbonyl oxygen and amide nitrogen (4 residues away) Amphipathic - philic outside, phobic inside [L, M, Q and E]
38
Secondary structure 2: Beta Sheet
Peptide backbones form hydrogen bond to one another Sheet-like, slightly twisted Amphipathic [V, I and F]
39
Protein folding driven by?
Hydrophobic interactions Energetically favorable - entropy increases Polar residues remain on outside Internal protein tightly packed inside
40
Types of Protein Folds
Globular: roughly spherical & low ratio of surface area to volume Coiled-coil: highly elongated & 2 alpha helices
41
Divergent vs Convergent evolution
Divergent: (protein variants) Convergent: (diff structure, similar function)
42
Protein domains
Compact region that can fold on its own = each diff functions
43
Major vs Minor groove
Minor: less variability Major: regulatory proteins interact primarily here via non-covalent interactions
44
Carbohydrate + protein
Glycoprotein
45
Carbohydrate + lipid
Glycolipid

Molecular Biology (8 decks)

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