BIOCHEM - All 20 Amino Acids, Protease, Types of Globins and Proteins

A Ala Alanine

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G Gly Glycine

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I Ile Isoleucine

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L Leu Leucine

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M Met Methionine

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P Pro Proline

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V Val Valine

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Valine, Alanine, Methionine, Proline, Leucine, Isoleucine, Glycine

List the amino acids in the Nonpolar, aliphatic R group

Nonpolar, aliphatic R group

Hydrophobic amino acids often grouped in the middle of a folded protein. Name the Group

F Phe Phenylalanine

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Y Tyr Tyrosine pKa: 10.07

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W Trp Tryptophan

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Phenylalanine, Tyrosine, Tryptophan

List the amino acids in the Aromatic R Group

Relatively nonpolar (hydrophobic)

Aromatic R group amino acids are ____

S Ser Serine

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T Thr Threonine

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C Cys Cysteine , pKa: 8.18

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N Asn Asparagine

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Q Gln Glutamine

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Serine Threonine Cysteine Asparagine Glutamine

List the amino acids in the Polar, Uncharged R Group

K Lys Lysine : 10.53

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R Arg Arginine pKa: 12.48

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H His Histidine

Give the symbol, abbreviation, Name of this amino acid, identify pka : 6.00

Lysine, Arginine, Histidine

List the amino acids in the Positively Charged R Group

D Asp Aspartate, pKa: 3.65

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E Glu Glutamate pKa:4.25

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Trypsin

Cleaves at C-side of Lys, Arg (except when followed by Pro)

Chymotrypsin

Cleaves at C-side of aromatic amino acids (Phe, Trp, Tyr).

Pepsin

Cleaves at N-side of aromatic amino acids (Tyr, Trp, Phe) and Leu.

Carboxyl peptidase

Cleaves amino acid at the C-terminus.

Cyanogen bromide

Cleaves at C-terminal side of methionine residues.

Oligomer/Multimer:

Multisubunit protein, with repeating structural units called protomers.

Globular

Folded into spherical/globular shape

Intrinsically disordered proteins

Lack stable tertiary structures, often lack a hydrophobic core, high in charged residues and Pro. Facilitate interaction with multiple partners.

Fibrous proteins

Long strands or sheets, structural function

Edman Degradation

creates phenylthiohydantion PTH dervatives

Dansyl Chloride

Creates Dansyl derivates of the amino aid at the n-terminus

Lithium Borohydride

Followed by acid hydroloysis create alchol derivates at c-terminus. classical used to identify c-terminal amino acids

FDNB, dansyl chloride, dabsyl chloride

label amino-terminal a-amino group and e-amino group of lysine residues

Aromatic amino acids

Phenylalanine (Phe, F) → nonpolar, hydrophobic

Structure at pH 7: +H₃N–CH(CH₂–C₆H₅)–COO⁻

Tyrosine (Tyr, Y) → polar (hydrophilic, can H-bond)

Structure: +H₃N–CH(CH₂–C₆H₄–OH)–COO⁻

Tryptophan (Trp, W) → relatively nonpolar but has N in indole ring, amphipathic

Structure: +H₃N–CH(CH₂–indole)–COO⁻

Sulfur-containing amino acids

Cys, C — +H₃N–CH(CH₂–SH)–COO⁻ — polar (forms disulfides)

Met, M — +H₃N–CH(CH₂–CH₂–S–CH₃)–COO⁻ — hydrophobic

Acidic amino acids

Aspartic acid (Asp, D) → acidic, hydrophilic (side chain COO⁻ at pH 7)

Structure: +H₃N–CH(CH₂–COO⁻)–COO⁻

Glutamic acid (Glu, E) → acidic, hydrophilic (side chain COO⁻ at pH 7)

Structure: +H₃N–CH(CH₂–CH₂–COO⁻)–COO⁻

Basic amino acids

Lysine (Lys, K) → basic, hydrophilic (side chain NH₃⁺ at pH 7)

Structure: +H₃N–CH(CH₂)₄–NH₃⁺ –COO⁻

Arginine (Arg, R) → basic, hydrophilic (guanidinium group)

Structure: +H₃N–CH(CH₂)₃–NH–C(=NH₂⁺)–NH₂ –COO⁻

Histidine (His, H) → polar, weakly basic (imidazole ~ partially protonated near pH 7)

Structure: +H₃N–CH(CH₂–imidazole)–COO⁻

Amide amino acids

Asparagine (Asn, N) → polar, hydrophilic

Structure: +H₃N–CH(CH₂–CONH₂)–COO⁻

Glutamine (Gln, Q) → polar, hydrophilic

Structure: +H₃N–CH(CH₂–CH₂–CONH₂)–COO⁻

Branched-chain amino acids (BCAAs)

Valine (Val, V) → nonpolar, hydrophobic

Structure: +H₃N–CH(CH(CH₃)₂)–COO⁻

Leucine (Leu, L) → nonpolar, hydrophobic

Structure: +H₃N–CH(CH₂–CH(CH₃)₂)–COO⁻

Isoleucine (Ile, I) → nonpolar, hydrophobic

Structure: +H₃N–CH(CH(CH₃)–CH₂–CH₃)–COO⁻

Cyclic saturated secondary amino acid

Pro, P — +H₂N⁺ (in pyrrolidine ring) –CH–COO⁻ — hydrophobic

Paper Electrophoresis

Separation of amino acids/peptides on paper based on charge; molecules migrate in an electric field according to net charge at a given pH.

Dialysis

Separates small molecules from macromolecules using a semipermeable membrane; diffusion allows salts/small solutes to pass while proteins/DNA stay inside

Ion-Exchange Chromatography

Elution achieved by increasing salt concentration or changing pH.

Gel Filtration Chromatography (Size-Exclusion)

Separates proteins based on size; larger molecules elute first because they bypass pores, while smaller molecules are delayed.

Affinity Chromatography

Separates proteins by specific binding interactions (e.g., antibody–antigen, substrate–enzyme). Protein of interest binds to a ligand immobilized on the matrix.

Immobilized Metal Affinity Chromatography (IMAC/His-tag purification)

Uses Ni²⁺, Co²⁺, or Zn²⁺ to bind histidine-tagged proteins. Bound proteins are eluted by lowering pH or adding imidazole.

SDS-PAGE (SDS–Polyacrylamide Gel Electrophoresis)

Denatures proteins with SDS, giving uniform negative charge; separates by molecular weight. Smaller proteins move faster through the gel.

Isoelectric Focusing

Separates proteins based on isoelectric point (pI). Proteins migrate in a pH gradient until they reach their pI (net charge = 0).

2D Gel Electrophoresis

Combines IEF (first dimension) and SDS-PAGE (second dimension) to separate proteins by both pI and size.

X-ray Diffraction / Protein Crystallography

Determines 3D structure of crystallized proteins. X-rays diffract off electron clouds; Fourier transform gives electron density map.

NMR Spectroscopy

Studies proteins in solution. Uses nuclear spin (¹H, ¹³C, ¹⁵N, etc.) to give structural and dynamic information, including conformational changes.

Cryo-Electron Microscopy (Cryo-EM)

Visualizes biomolecules frozen in vitreous ice. Useful for large complexes and membrane proteins without need for crystallization.

Electrospray Ionization Mass Spectrometry (ESI-MS)

Produces charged protein/peptide ions in gas phase; measures mass-to-charge ratio (m/z) for molecular weight determination.

MALDI-MS (Matrix-Assisted Laser Desorption Ionization)

Soft ionization technique for peptides/proteins. Sample co-crystallized with matrix, hit with laser, ions measured by time-of-flight MS.

LC-MS/MS Peptide Sequencing

Uses liquid chromatography coupled with tandem MS. First MS separates peptides, second MS fragments them to determine amino acid sequence.

MS/MS Cleavage

Fragmentation pattern in tandem MS used to deduce peptide sequence.