Amino Acids and Protein Structure: Key Concepts for Biology

Protein digestion

Breaking proteins into amino acids by enzymes like pepsin and trypsin.

Amino acid pool

The free amino acids in the body used for making proteins or other molecules.

Protein turnover

Continuous breakdown and synthesis of proteins in the body.

Amino acids

Made of carbon, hydrogen, oxygen, nitrogen, sometimes sulfur.

Zwitterion

An amino acid with both a positive (NH₃⁺) and negative (COO⁻) charge.

Ionizable groups

Aspartate, glutamate, lysine, arginine, histidine, cysteine, tyrosine.

Stereochemistry of amino acids

Amino acids are chiral (except glycine), can be D- or L-form.

D- vs L-amino acids

L-amino acids are used in proteins; D-amino acids are rare in humans.

Standard vs nonstandard amino acids

Standard = used in proteins; nonstandard = modified or rare amino acids.

Amino acids with more than 1 carboxyl group

Aspartate and glutamate.

Amino acid with a γ-carboxyl group

Glutamate.

Amino acid with an ε-amino group

Lysine.

Amino acid with an imidazole side chain

Histidine.

Amino acid with an indole group

Tryptophan.

Amino acid with a guanidinium group

Arginine.

Amino acids with hydroxylic (alcohol) side chains

Serine, threonine.

Amino acid with phenolic hydroxyl group

Tyrosine.

Amino acids containing sulfur

Cysteine, methionine.

Amino acid that can form disulfide bonds

Cysteine.

Amino acids with aliphatic side chains

Glycine, alanine, valine, leucine, isoleucine.

Amino acids with aromatic side chains

Phenylalanine, tyrosine, tryptophan.

Acidic amino acids

Aspartate, glutamate.

Basic amino acids

Lysine, arginine, histidine.

Amino acids as acids or bases

They can donate H⁺ (acid) or accept H⁺ (base) via ionizable groups.

Electrophoretic mobility of amino acids

Movement of amino acids in an electric field depends on their charge.

pI of an amino acid

The pH at which it has no net charge.

Essential vs nonessential amino acids

Essential = must get from diet; nonessential = body can make them.

Glucogenic vs ketogenic amino acids

Glucogenic → glucose; ketogenic → ketone bodies; some do both.

Amino acids converted to histamine

Histidine → histamine.

Amino acid precursor of GABA

Glutamate.

Amino acid precursor of serotonin

Tryptophan.

Catecholamines

Dopamine, norepinephrine, epinephrine (from tyrosine).

Peptide bond

Bond between the carboxyl of one amino acid and amino of another.

Physiologically active peptides examples

Insulin, glucagon, oxytocin, vasopressin.

Simple vs conjugated proteins

Simple = only amino acids; Conjugated = amino acids + non-protein part.

Examples of conjugated proteins

Glycoproteins, lipoproteins, metalloproteins.

Protein functions examples

Transport (hemoglobin), contractile (actin, myosin), enzymes, defense (antibodies).

Bonds responsible for protein structure

Hydrogen, disulfide, ionic, hydrophobic interactions, peptide bonds.

Levels of protein structure

Primary → sequence; Secondary → α-helix/β-sheet; Tertiary → 3D folding; Quaternary → multiple chains.

Fibrous vs globular proteins

Fibrous → structural, elongated (collagen); Globular → functional, compact (hemoglobin).

Hemoglobin vs myoglobin

Hemoglobin → transports O₂ in blood, 4 subunits; Myoglobin → stores O₂ in muscle, 1 subunit.

Sickle cell anemia protein defect

Mutation in hemoglobin → abnormal shape.

Structure of antibody

Y-shaped protein with variable region (binds antigen) and constant region.

Diseases from abnormal protein structure

Alzheimer's, Parkinson's, prion diseases.

Proteomics

Study of all proteins in a cell or organism.

Chromatography vs electrophoresis

Chromatography separates by solubility/affinity; Electrophoresis separates by size/charge.

Western blot vs ELISA

Western blot → detects proteins; ELISA → detects proteins or antibodies.

What is the definition of a peptide

A compound consisting of short chains (2 or more amino acids linked together in a chain by polypeptide bonds)

Give example of 4 peptide hormones

Insulin, glucagon, Angiotensin, oxytocin

Insulin

Produced by B cells in pancreas; promotes absorption of glucose from blood into secret tissues.

Glucagon

produced by a cells in pancreas; raises blood glucose during hypoglycemia.

Glucagon o

Like peptide 1 (GLP-1) regulates blood sugar levels promote weight loss

Angiotensin

Regulates blood pressure

Oxytocin

Stimulates contraction of smooth muscle (labor contractions)

Host defense peptides

The body's first line of defense, that helps protect against bacteria

What are antimicrobial peptides?

Short proteins produced by the body

Antimicrobial peptides

Inhibit the growth of microbes

Examples of AMPs

Bacitracin, polymxyins, vancomycin, Daptomycin

inflammatory mediators

Substance release by cells during injury or infection for example bradykinin

What are the enkephalins and their primary function?

Pentapeptide and neuropeptides that regulate pain and act as neurotransmitters in the brain and spinal cord.

Name the two main types of enkephalins and their amino acid sequences?

Met-enkep Tyr-Gly-Gly-Phe-Met

Leu-enkep Tyr-Gly-Gly-Phe-leu

Why must people with PKU avoid aspartame?

Because it contains phenylalanine,one which they cannot metabolize properly