Amino Acids, Peptides, and Proteins Overview

Amino Acid

Molecule with amino and carboxyl functional groups.

Alpha Carbon

Central carbon in amino acids with four groups.

R Group

Side chain that defines amino acid properties.

Proteinogenic Amino Acids

20 amino acids encoded by human genetic code.

Chiral Center

Carbon atom with four different substituents.

Optically Active

Substance that rotates plane-polarized light.

Glycine

Smallest amino acid, achiral with hydrogen side chain.

L-Amino Acids

Amino acids with amino group on left in Fischer projection.

D-Amino Acids

Amino acids with amino group on right in Fischer projection.

Cysteine

L-amino acid with (R) absolute configuration.

Methionine

Amino acid containing a sulfur atom.

Proline

Cyclic amino acid with unique structure.

Nonpolar Amino Acids

Amino acids with hydrophobic side chains.

Hydrogen Atom

One of the four groups attached to alpha carbon.

Carboxyl Group

Functional group (-COOH) in amino acids.

Amino Group

Functional group (-NH2) in amino acids.

Neurotransmitter

Chemical messenger in the nervous system.

Ornithine

Amino acid involved in urea cycle.

Valine

Branched-chain amino acid with hydrophobic properties.

Leucine

Essential branched-chain amino acid.

Isoleucine

Branched-chain amino acid with two stereoisomers.

Alanine

Nonpolar amino acid with a methyl side chain.

Amino Acid Classification

Grouping based on side chain structures.

Flexibility

Proline's structure limits protein flexibility.

Amino Nitrogen

Nitrogen in amino acids that bonds to carbon.

Imine

Molecule with a carbon-nitrogen double bond.

Tryptophan

Largest amino acid with a double-ring system.

Phenylalanine

Smallest amino acid with a benzyl side chain.

Tyrosine

Phenylalanine with an added hydroxyl group.

Serine

Amino acid with a polar hydroxyl side chain.

Threonine

Similar to serine, with an additional methyl group.

Asparagine

Amino acid with an amide side chain.

Glutamine

Similar to asparagine, with an additional carbon.

Negatively Charged Side Chains

Amino acids with charges at physiological pH.

Aspartic Acid

Deprotonated form is aspartate, an acidic amino acid.

Glutamic Acid

Deprotonated form is glutamate, an acidic amino acid.

Charged Side Chains

Amino acids with positively or negatively charged groups.

Lysine

Amino acid with a terminal primary amino group.

Arginine

Contains three nitrogen atoms in its side chain.

Histidine

Amino acid with a proton-gaining side chain.

Hydrogen Bonding

Interaction between polar side chains in proteins.

Sulfur vs. Oxygen

Sulfur's bonds in cysteine are longer and weaker.

Aromatic Side Chains

Amino acids with uncharged aromatic side chains.

Imidazole

A ring structure containing two nitrogen atoms.

pKa

pH at which half of molecules are deprotonated.

Protonation

Addition of a proton to a molecule.

Deprotonation

Removal of a proton from a molecule.

Physiologic pH

Normal body pH, approximately 7.4.

Hydrophobic Amino Acids

Amino acids that repel water, e.g., alanine.

Hydrophilic Amino Acids

Amino acids that attract water, e.g., lysine.

Alkyl Side Chains

Long carbon chains in hydrophobic amino acids.

Titration Curve

Graph of pH versus the amount of titrant.

Amphoteric Species

Substances that can act as acids or bases.

Ionizable Groups

Functional groups that can gain or lose protons.

Acidic Group

Carboxylic acid group in amino acids.

Basic Group

Amino group in amino acids.

Protonated Form

Form of a molecule with an added proton.

Deprotonated Form

Form of a molecule without a proton.

pKa1

pKa for the carboxyl group, around 2.

pKa2

pKa for the amino group, between 9 and 10.

Physiological Conditions

Normal biological environment affecting amino acid behavior.

Nucleophilic Attack

Reaction where a nucleophile attacks a substrate.

Zwitterion

A molecule with both positive and negative charges, neutral overall.

Acidic pH

pH below 7, where amino acids are positively charged.

Neutral pH

pH around 7, where zwitterions exist.

Basic pH

pH above 7, where amino acids are negatively charged.

Carboxylate group

Deprotonated form of the carboxylic acid group (-COO-).

Titration

Process of adding a base to an acid to determine pKa.

Buffer solution

Solution that resists changes in pH near its pKa.

Equivalents

Amount of acid or base in titration relative to solute.

Fully protonated

State where all acidic groups are protonated.

Half-deprotonated

State where half of the acidic groups are deprotonated.

Conjugate base

The species that remains after an acid donates a proton.

Conjugate acid

The species formed when a base accepts a proton.

Internal salts

Salts formed within a molecule, like zwitterions.

Protonated amino group

Amino group in its +1 charged form at low pH.

Deprotonated carboxyl group

Carboxyl group in its -1 charged form at high pH.

pH of human blood

Normal physiological pH, approximately 7.4.

Milk of magnesia

Antacid with a pH around 10.5, affecting amino acids.

Isoelectric Point (pI)

pH where molecule is electrically neutral.

Buffering Phase

pH remains constant during titration.

Acidic Amino Acids

Have lower isoelectric points.

Basic Amino Acids

Have higher isoelectric points.

Peptide Bond

Covalent bond linking amino acids.

Dipeptide

Peptide consisting of two amino acid residues.

Tripeptide

Peptide consisting of three amino acid residues.

Hydrolysis

Chemical breakdown of a compound due to water.

Trypsin

Enzyme that cleaves peptide bonds.

Chymotrypsin

Enzyme that hydrolyzes peptide bonds.

pKa Values

Used to calculate isoelectric points.

Equivalents of Base

Amount of base added in titration.

Protonated State

State where a molecule has gained protons.

Oligopeptide

Peptide with up to 20 amino acid residues.

Polypeptide

Long chain of amino acids, over 20 residues.

Amino Terminus

Free amino end of a peptide chain.

Carboxy Terminus

Free carboxyl end of a peptide chain.

Condensation Reaction

Reaction forming peptide bonds, releasing water.

Amide Bond

Bond formed between carbonyl and nitrogen groups.

Electrophilic Carbonyl

Carbonyl carbon that attracts nucleophiles during bond formation.

Nucleophilic Amino Group

Amino group that attacks carbonyl in peptide formation.