GAVLIMP TP "_GAV_in _LIMP_s out of the restroom with _TP_ on his shoe" Glycine Alanine Valine Leucine Isoleucine Methionine Proline Tryptophan Phenylalanine

HAL "_HAL_ is alway positive" Histadine Arginine Lysine

AG " Pol ls _AG_rregate negative answers" Aspartate Glutamate

"_T_hose _G_irls _T_hink _A_bout _S_hopping _C_onstantly" Tyrosine Glutamine Threonine Asparagine Serine Cysteine

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_)

Protein basics Flashcards by Tim Merino

Nonpolar AAs

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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Polar (+) AAs

HAL

“HAL is alway positive”

Histadine
Arginine
Lysine

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Polar (-) AAs

“Polls AGrregate negative answers”

Aspartate
Glutamate

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Polar (neutral) AAs

“Those Girls Think About Shopping Constantly”

Tyrosine
Glutamine
Threonine
Asparagine
Serine
Cysteine

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Essential AAs

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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Alanine

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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Arginine

Arg (R) = Polar (+), Basic

Side Chain: -(CH₂)₃-Guanidine

Codons: CGX + AGA, AGG (6)

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Aspartate (Aspartic acid)

Asp (D) = Polar (-)

Side Chain: -CH₂COOH

Codons: GAU & GAC (2)

Non-Ess: OAA→Asp

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Asparagine

Asn (D) = Polar (neutral)

Side Chain: -CH₂(CO)NH₂

Codons: AAU & AAC (2)

Non-Ess: OAA→Asp→Asn

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Cysteine

Cys (C) = Polar (neutral)

Side Chain: -CH₂SH

Codons: UGU & UGC (2)

**Form disulfide bonds**

Non-Ess: Glc→3PG→Ser→Cys

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Glutamine

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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Glutamate

(glutamic acid)

Glu (E) = Polar (-)

Side Chain: -(CH₂)₂COOH

Codons: GAA & GAG (2)

Non-Ess: TCA→a-KG→Glu

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Glycine

Gly (G) = Nonpolar

Side Chain: -H

Codons: GGX (4)

Non-Ess: Glc→3PG→Ser→Gly

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Histidine

His (H) = Polar (+)

Side Chain: -CH2-imidazole

Codons: CAU & CAC (2)

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Isoleucine

Ile (I) = Nonpolar

Side Chain: -CH(CH₃)CH₂CH₃

Codons: AUU, AUC & AUA (3)

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Leucine

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Leu (L) = Nonpolar

Side Chain: -CH₂CH(CH₃)₂

Codons: CUX, UUA, UUG (6)

1 of 2 ketogenic AA (also lysine)

Lysine

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Lys (K) = Polar (+)

Side Chain: -(CH₂)₄NH₂

Codons: AAA & AAG (2)

1 of 2 ketogenic AA (also leucine)

Methionine

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Met (M) = Nonpolar

Side Chain: -CH₂CH₂SCH₃

Codons: AUG (1)

Proline

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Pro (P) = Nonpolar

Side Chain: pyrrolidine

Codons: CCX

Non-Ess: TCA→a-KG→Pro

Serine

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Ser (S) = Polar (neutral)

Side Chain: -CH2OH (methanol)

Codons: UCX, AGU, AGC (6)

Non-Ess: Glc→3PG→Ser

Threonine

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Thr (T) = Polar (neutral)

Side Chain: -CH(OH)CH₃

Codons: ACX (4)

Tryptophan

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Trp (W) = Nonpolar

Codon: UGG (1)

Tyrosine

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Tyr (Y) = Polar (neutral)

Side Chain: -CH₂-Phenol

Codons: UAC & UAU (2)

Non-Ess: Phe→Tyr

Valine

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Val (V) = Nonpolar

Side Chain: -CH(CH₃)₂

Codons: GUX (4)

Key Features of Peptide Bonds

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 C_a-N * Ψ = angle or rotation around C_a-C * Angles due to character of R groups

α-helix characteristics

* **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

ß-pleated sheets

* **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

ß-turns

* 2º structure * a.k.a "tight bends" or "ß-bends" * Small R-groups required

3° structure

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

Types of denaturants

* 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

aromatic AAs

Phe, Tyr, Trp

branch chain AAs (BCAA)

Largely metabolized in skeletal muscle * Ile → Ketogenic & Glucogenic * Leu → Ketogenic * Val → Glucogenic Transaminationed, then ox-decarboxylation

AA transamination

Transamination **possibe for 17 AAs** NOT: Proline, Lysine, & Thrionine _AA group_ transfered to _a-Keto acid_

Non-Essential AAs synthesized from Essential AAs

Thionine ---\> Cysteine\*\* Phenylalanin → Tyrosine \*\*Cys also made from Ser

Protein basics Flashcards

(34 cards)