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Pre-Clinical Science > Protein basics > Flashcards

Protein basics Flashcards

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1
Q

Nonpolar AAs

A

GAVLIMP TP
“GAVin LIMPs out of the restroom with TP on his shoe”

  • Glycine
  • Alanine
  • Valine
  • Leucine
  • Isoleucine
  • Methionine
  • Proline
  • Tryptophan
  • Phenylalanine
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2
Q

Polar (+) AAs

A

HAL

“HAL is alway positive”

  • Histadine
  • Arginine
  • Lysine
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3
Q

Polar (-) AAs

A

AG

“Polls AGrregate negative answers”

  • Aspartate
  • Glutamate
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4
Q

Polar (neutral) AAs

A

“Those Girls Think About Shopping Constantly”

  • Tyrosine
  • Glutamine
  • Threonine
  • Asparagine
  • Serine
  • Cysteine
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5
Q

Essential AAs

A

PVT TIM HALL

  • Phenylalanine
  • Valine
  • Threonine
  • Tryptophan
  • Isoleucine
  • Methionine
  • Histidine
  • Arginine*
  • Leucine
  • Lysine

Arg during growth/dev.

T ≠ Tyrosine (derived from Phe via Phe Hydroxylase)

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6
Q

Alanine

A

Ala (A) = Nonpolar

Side Chain: -CH3 (methyl)

Codons: GCX (4)

1 of 2 highly glucogenic AAs (also glutamine)

Non-Ess: Glc→Pyr→Ala

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7
Q

Arginine

A

Arg (R) = Polar (+), Basic

Side Chain: -(CH2)3-Guanidine

Codons: CGX + AGA, AGG (6)

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8
Q

Aspartate (Aspartic acid)

A

Asp (D) = Polar (-)

Side Chain: -CH2COOH

Codons: GAU & GAC (2)

Non-Ess: OAA→Asp

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9
Q

Asparagine

A

Asn (D) = Polar (neutral)

Side Chain: -CH2(CO)NH2

Codons: AAU & AAC (2)

Non-Ess: OAA→Asp→Asn

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10
Q

Cysteine

A

Cys (C) = Polar (neutral)

Side Chain: -CH2SH

Codons: UGU & UGC (2)

**Form disulfide bonds**

Non-Ess: Glc→3PG→Ser→Cys

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11
Q

Glutamine

A

Gln (Q) = Polar (neutral)

Side Chain: -(CH2)2(CO)NH2

Codons: CAA & CAG (2)

1 of 2 highly glucogenic AAs (also alanine)

Non-Ess: TCA→a-KG→Glu→Gln

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12
Q

Glutamate

(glutamic acid)

A

Glu (E) = Polar (-)

Side Chain: -(CH2)2COOH

Codons: GAA & GAG (2)

Non-Ess: TCA→a-KG→Glu

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13
Q

Glycine

A

Gly (G) = Nonpolar

Side Chain: -H

Codons: GGX (4)

Non-Ess: Glc→3PG→Ser→Gly

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14
Q

Histidine

A

His (H) = Polar (+)

Side Chain: -CH2-imidazole

Codons: CAU & CAC (2)

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15
Q

Isoleucine

A

Ile (I) = Nonpolar

Side Chain: -CH(CH3)CH2CH3

Codons: AUU, AUC & AUA (3)

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16
Q

Leucine

A

Leu (L) = Nonpolar

Side Chain: -CH2CH(CH3)2

Codons: CUX, UUA, UUG (6)

1 of 2 ketogenic AA (also lysine)

17
Q

Lysine

A

Lys (K) = Polar (+)

Side Chain: -(CH2)4NH2

Codons: AAA & AAG (2)

1 of 2 ketogenic AA (also leucine)

18
Q

Methionine

A

Met (M) = Nonpolar

Side Chain: -CH2CH2SCH3

Codons: AUG (1)

19
Q

Proline

A

Pro (P) = Nonpolar

Side Chain: pyrrolidine

Codons: CCX

Non-Ess: TCA→a-KG→Pro

20
Q

Serine

A

Ser (S) = Polar (neutral)

Side Chain: -CH2OH (methanol)

Codons: UCX, AGU, AGC (6)

Non-Ess: Glc→3PG→Ser

21
Q

Threonine

A

Thr (T) = Polar (neutral)

Side Chain: -CH(OH)CH3

Codons: ACX (4)

22
Q

Tryptophan

A

Trp (W) = Nonpolar

Codon: UGG (1)

23
Q

Tyrosine

A

Tyr (Y) = Polar (neutral)

Side Chain: -CH2-Phenol

Codons: UAC & UAU (2)

Non-Ess: Phe→Tyr

24
Q

Valine

A

Val (V) = Nonpolar

Side Chain: -CH(CH3)2

Codons: GUX (4)

25
Q

Key Features of Peptide Bonds

A
  1. Very stable in trans configuration
  2. Partial double bond character = flat
  3. No rotation around C-N bond

Protein structure is defined by Φ (phi) & Ψ (psi):

  • Φ = angle of roation around Ca-N
  • Ψ = angle or rotation around Ca-C
  • Angles due to character of R groups
26
Q

α-helix characteristics

A
  • 2º structure
  • 3.6 residues per helical turn
  • Stabilized by h-bonding (C=O: ⇔ HN)
  • Proline = helix breaker (no rotation of N-C bond)
  • L-amino aa form R-hand helix
    • more stable than L-hand helix
27
Q

ß-pleated sheets

A
  • 2º structure
  • Parallel or Anti-Parallel
  • Parallel have aa R groups on both sides
  • CC: parallel form Amyloid plaques
    • E.g. Alzheimer’s and Prion diseases
28
Q

ß-turns

A
  • 2º structure
  • a.k.a “tight bends” or “ß-bends”
  • Small R-groups required
29
Q

3° structure

A
  • Folded structure
  • Often divided into domains for large proteins
  • Stabilized by:
    • Covalent disulfide bonds
    • Hydrophobic interations
    • Ionic interations
    • H-bonds
    • Dipole-dipole interations
30
Q

Types of denaturants

A
  • Heat
  • pH changes
  • Detergents
    • Triton (mild)
    • Sodium duodecyl sulfate - SDS (harsh)
  • Organic solvent (e.g. EtOH, DMSO)
  • Mechanical stress
  • Urea and Guanidine HCl
    • disrupt 3° & 4° structures
31
Q

aromatic AAs

A

Phe, Tyr, Trp

32
Q

branch chain AAs (BCAA)

A

Largely metabolized in skeletal muscle

  • Ile → Ketogenic & Glucogenic
  • Leu → Ketogenic
  • Val → Glucogenic

Transaminationed, then ox-decarboxylation

33
Q

AA transamination

A

Transamination possibe for 17 AAs

NOT: Proline, Lysine, & Thrionine

AA group transfered to a-Keto acid

34
Q

Non-Essential AAs synthesized from Essential AAs

A

Thionine —> Cysteine**

Phenylalanin → Tyrosine

**Cys also made from Ser

Pre-Clinical Science (2 decks)

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