Proteins, peptides & Amino Acids - Vocabulary Flashcards

Vocabulary flashcards covering key terms and definitions from the Proteins, Peptides, and Amino Acids lecture notes.

Proteins

Macromolecules that form the basis of structure and function of life; composed of 20 amino acids; arranged into primary, secondary, tertiary, and quaternary structures; constitute a large portion of cellular dry weight.

Amino acid

Building block of proteins; contains a carboxyl group, an amino group, and a variable side chain (R); can exist as L- or D- isomers and form zwitterions at physiological pH.

Amino acid structure (amino, carboxyl, R group)

Amino acids have a carboxyl group and an amino group attached to the same central carbon, with a side chain (R) that determines identity and properties.

Zwitterion

A dipolar ion where the molecule carries both positive and negative charges; amino acids in neutral solution exist predominantly as zwitterions.

Isoelectric point (pI)

The pH at which an amino acid carries no net charge (exists as a zwitterion); calculated as an average of ionizable group pKa values.

Essential amino acids

Amino acids that cannot be synthesized by the body in adequate amounts and must be obtained from the diet (e.g., Ile, Leu, Lys, Met, Phe, Thr, Trp, Val, His in infants); Arginine and Histidine are often semi-essential in adults.

Semi-essential amino acids

Amino acids that must be obtained from diet under certain conditions; Arginine and Histidine are commonly cited as semi-essential for adults.

Nonessential amino acids

Amino acids that can be synthesized by the body and are not required in the diet (e.g., Gly, Ala, Gln, Glu, Ser, Tyr).

Aliphatic amino acids

Amino acids with nonaromatic, nonpolar side chains (e.g., Gly, Ala, Val, Leu, Ile); tend to be hydrophobic.

Branched-chain amino acids

Valine, Leucine, and Isoleucine; have branched aliphatic side chains and play key roles in protein structure.

Aromatic amino acids

Amino acids with aromatic rings: Phenylalanine, Tyrosine, Tryptophan (Tyrosine may be considered aromatic; Proline is an imino acid).

Sulfur-containing amino acids

Amino acids containing sulfur: Cysteine (sulfhydryl group) and Methionine (thioether); Cys can form disulfide bonds.

Polar, uncharged amino acids

Amino acids with polar side chains but no net charge at physiological pH (e.g., Ser, Thr, Asn, Gln, Cys, Tyr).

Positively charged (basic) amino acids

Amino acids with basic, positively charged side chains at physiological pH: Lysine, Arginine, Histidine.

Negatively charged (acidic) amino acids

Amino acids with acidic, negatively charged side chains at physiological pH: Aspartate (Asp), Glutamate (Glu); their amides are Asparagine (Asn) and Glutamine (Gln).

D- and L- forms of amino acids

Enantiomers of amino acids; proteins predominantly use L-amino acids; D-forms occur in some antibiotics and bacterial cell walls.

Peptide bond

Covalent bond formed by condensation between the amino group of one amino acid and the carboxyl group of another; rigid, planar, and usually trans.

Primary structure

The linear sequence of amino acids in a protein; determined by genes and largely dictates function.

Secondary structure

Localized folding patterns of the polypeptide, including the alpha-helix and beta-pleated sheet, stabilized by hydrogen bonds.

Alpha-helix

Right- or left-handed helical structure common in proteins; stabilized by hydrogen bonds along the backbone.

Beta-pleated sheet

Sheet-like secondary structure formed by H-bonds between extended polypeptide strands; can be parallel or antiparallel.

Tertiary structure

Three-dimensional shape of a single polypeptide, stabilized by hydrogen bonds, disulfide bonds, ionic interactions, and hydrophobic effects.

Quaternary structure

Assembly of two or more polypeptide subunits into a multimeric protein; interactions include H-bonds, hydrophobic forces, and ionic bonds.

Denaturation

Loss of protein structure and function due to heat, acids/bases, salts, mechanical force, X-rays, UV light, or solvents; primary structure remains intact.

Proteolysis/Digestion of protein

Breakdown of proteins into peptides and amino acids during digestion, beginning in the mouth/stomach and continuing in the small intestine.

Edman degradation

A method for determining the amino-terminal sequence of a peptide using Edman’s reagent.

Sanger sequencing (reagent)

A method for determining amino acid sequence of peptides using Sanger’s reagent.

Biuret reaction

Colorimetric test for proteins using copper sulfate in alkaline conditions; yields a purple color with peptide bonds.

Ninhydrin reaction

A colorimetric test for amino acids; yields Ruhemann’s purple with most amino acids (yellow with proline/hydroxyproline).

Glutathione

A tripeptide (Glu-Cys-Gly) that acts as a cellular antioxidant and cofactor for glutathione-dependent enzymes.

Monosodium glutamate (MSG)

Sodium salt of glutamic acid used as a flavor enhancer; excessive intake linked to Chinese restaurant syndrome in sensitive individuals.

pK1 and pK2

Dissociation constants for the carboxyl (pK1) and amino (pK2) groups of amino acids; determine the isoelectric point.

Amino acids as amino acids in metabolism (decarboxylation)

Removal of carboxyl group from amino acids to form amines (e.g., histamine from histidine, GABA from glutamate). Enzymes called decarboxylases catalyze these reactions.

Derived amino acids

Amino acids modified after protein synthesis (e.g., hydroxyproline in collagen; gamma-carboxyglutamate in clotting factors; ornithine, citrulline in metabolism).

Nonstandard amino acids

Amino acids not incorporated into proteins (e.g., β-alanine, taurine, thyroid hormones thyroxine, DOPA, GABA in some contexts).

Nutritional classification of amino acids

Essential vs nonessential amino acids based on dietary need and body's ability to synthesize them; some listed as conditionally essential.

Mighty Twenty mnemonic (PVT TIM HALL)

Mnemonic used to remember essential amino acids: Phenylalanine, Valine, Tryptophan, Threonine, Isoleucine, Methionine, Histidine, Arginine (semi-essential), Leucine, Lysine.

Covalent bonds in proteins

Peptide bonds link amino acids; other covalent interactions include disulfide bonds (between cysteines) contributing to structure.

Protein purification (lab)

Chromatographic techniques exploit size, charge, and binding properties to isolate proteins; structural info via X-ray, NMR, or electron microscopy.

Proteins

Macromolecules that form the basis of structure and function of life; composed of 20 amino acids; arranged into primary, secondary, tertiary, and quaternary structures; constitute a large portion of cellular dry weight.

Amino acid

Building block of proteins; contains a carboxyl group, an amino group, and a variable side chain (R); can exist as L- or D- isomers and form zwitterions at physiological pH.

Amino acid structure (amino, carboxyl, R group)

Amino acids have a carboxyl group and an amino group attached to the same central carbon, with a side chain (R) that determines identity and properties.

Zwitterion

A dipolar ion where the molecule carries both positive and negative charges; amino acids in neutral solution exist predominantly as zwitterions.

Isoelectric point (pI)

The pH at which an amino acid carries no net charge (exists as a zwitterion); calculated as an average of ionizable group pKa values.

Essential amino acids

Amino acids that cannot be synthesized by the body in adequate amounts and must be obtained from the diet (e.g., Ile, Leu, Lys, Met, Phe, Thr, Trp, Val, His in infants); Arginine and Histidine are often semi-essential in adults.

Semi-essential amino acids

Amino acids that must be obtained from diet under certain conditions; Arginine and Histidine are commonly cited as semi-essential for adults.

Nonessential amino acids

Amino acids that can be synthesized by the body and are not required in the diet (e.g., Gly, Ala, Gln, Glu, Ser, Tyr).

Aliphatic amino acids

Amino acids with nonaromatic, nonpolar side chains (e.g., Gly, Ala, Val, Leu, Ile); tend to be hydrophobic.

Branched-chain amino acids

Valine, Leucine, and Isoleucine; have branched aliphatic side chains and play key roles in protein structure.

Aromatic amino acids

Amino acids with aromatic rings: Phenylalanine, Tyrosine, Tryptophan (Tyrosine may be considered aromatic; Proline is an imino acid).

Sulfur-containing amino acids

Amino acids containing sulfur: Cysteine (sulfhydryl group) and Methionine (thioether); Cys can form disulfide bonds.

Polar, uncharged amino acids

Amino acids with polar side chains but no net charge at physiological pH (e.g., Ser, Thr, Asn, Gln, Cys, Tyr).

Positively charged (basic) amino acids

Amino acids with basic, positively charged side chains at physiological pH: Lysine, Arginine, Histidine.

Negatively charged (acidic) amino acids

Amino acids with acidic, negatively charged side chains at physiological pH: Aspartate (Asp), Glutamate (Glu); their amides are Asparagine (Asn) and Glutamine (Gln).

D- and L- forms of amino acids

Enantiomers of amino acids; proteins predominantly use L-amino acids; D-forms occur in some antibiotics and bacterial cell walls.

Peptide bond

Covalent bond formed by condensation between the amino group of one amino acid and the carboxyl group of another; rigid, planar, and usually trans.

Primary structure

The linear sequence of amino acids in a protein; determined by genes and largely dictates function.

Secondary structure

Localized folding patterns of the polypeptide, including the alpha-helix and beta-pleated sheet, stabilized by hydrogen bonds.

Alpha-helix

Right- or left-handed helical structure common in proteins; stabilized by hydrogen bonds along the backbone.

Beta-pleated sheet

Sheet-like secondary structure formed by H-bonds between extended polypeptide strands; can be parallel or antiparallel.

Tertiary structure

Three-dimensional shape of a single polypeptide, stabilized by hydrogen bonds, disulfide bonds, ionic interactions, and hydrophobic effects.

Quaternary structure

Assembly of two or more polypeptide subunits into a multimeric protein; interactions include H-bonds, hydrophobic forces, and ionic bonds.

Denaturation

Loss of protein structure and function due to heat, acids/bases, salts, mechanical force, X-rays, UV light, or solvents; primary structure remains intact.

Proteolysis/Digestion of protein

Breakdown of proteins into peptides and amino acids during digestion, beginning in the mouth/stomach and continuing in the small intestine.

Edman degradation

A method for determining the amino-terminal sequence of a peptide using Edman’s reagent.

Sanger sequencing (reagent)

A method for determining amino acid sequence of peptides using Sanger’s reagent.

Biuret reaction

Colorimetric test for proteins using copper sulfate in alkaline conditions; yields a purple color with peptide bonds.

Ninhydrin reaction

A colorimetric test for amino acids; yields Ruhemann’s purple with most amino acids (yellow with proline/hydroxyproline).

Glutathione

A tripeptide (Glu-Cys-Gly) that acts as a cellular antioxidant and cofactor for glutathione-dependent enzymes.

Monosodium glutamate (MSG)

Sodium salt of glutamic acid used as a flavor enhancer; excessive intake linked to Chinese restaurant syndrome in sensitive individuals.

pK1 and pK2

Dissociation constants for the carboxyl (pK1) and amino (pK2) groups of amino acids; determine the isoelectric point.

Amino acids as amino acids in metabolism (decarboxylation)

Removal of carboxyl group from amino acids to form amines (e.g., histamine from histidine, GABA from glutamate). Enzymes called decarboxylases catalyze these reactions.

Derived amino acids

Amino acids modified after protein synthesis (e.g., hydroxyproline in collagen; gamma-carboxyglutamate in clotting factors; ornithine, citrulline in metabolism).

Nonstandard amino acids

Amino acids not incorporated into proteins (e.g., β-alanine, taurine, thyroid hormones thyroxine, DOPA, GABA in some contexts).

Nutritional classification of amino acids

Essential vs nonessential amino acids based on dietary need and body's ability to synthesize them; some listed as conditionally essential.

Mighty Twenty mnemonic (PVT TIM HALL)

Mnemonic used to remember essential amino acids: Phenylalanine, Valine, Tryptophan, Threonine, Isoleucine, Methionine, Histidine, Arginine (semi-essential), Leucine, Lysine.

Covalent bonds in proteins

Peptide bonds link amino acids; other covalent interactions include disulfide bonds (between cysteines) contributing to structure.

Protein purification (lab)

Chromatographic techniques exploit size, charge, and binding properties to isolate proteins; structural info via X-ray, NMR, or electron microscopy.

Forces stabilizing protein tertiary and quaternary structures

Non-covalent interactions like hydrogen bonds, ionic interactions (salt bridges), hydrophobic interactions, and covalent disulfide bonds (primarily in tertiary structure) stabilize the 3D shape of proteins.

Protein purification methods (general)

Laboratory techniques used to isolate specific proteins from complex mixtures, often leveraging differences in protein size, charge, solubility, or binding affinity. Common methods include various types of chromatography and electrophoresis.

Size Exclusion Chromatography (SEC) / Gel Filtration Chromatography

A chromatographic method that separates proteins based on their size; larger proteins elute faster as they cannot enter the pores of the stationary phase beads, while smaller proteins are delayed by entering the pores.

A chromatographic method that separates proteins based on their net charge; proteins bind to charged resin beads and are then eluted by changing the pH or salt concentration.