Week 2: Amino Acids, Peptides, Protein Structure, & Collagen

What are the functional classes of proteins?

Enzymes (catalysis), transport, structure, movement, signaling, defense

What do all amino acids have?

Central alpha-carbon, amino group (-NH3+), carboxyl group (-COO^-), R group

What are the key properties of amino acids?

Chirality: the alpha-carbon is a chiral center for 19/20 amino acids (except for Glycine)

Stereochemistry: built exclusively from L-isomers of amino acids

Zwitterions: at physiological pH 7.4, they have both positive and negative charges

What are the nonpolar, aliphatic R groups?

Glycine, Alanine, Valine, Leucine, Isoleucine, Proline

Property: hydrophobic (oily)

Function: cluster in the protein interior, away from water; a major driver of protein folding

Glycine

Nonpolar, aliphatic; Gly [G]

Alanine

Nonpolar, aliphatic; Ala [A]

Valine

Nonpolar, aliphatic; Val [V]

Leucine

Nonpolar, aliphatic; Leu [L]

Isoleucine

Nonpolar, aliphatic; Ile (T)

What are the aromatic R groups?

Phenylalanine, Tyrosine, Tryptophan

Property: generally hydrophobic; absorbs UV light

Tyrosine and tryptophan have partial polarity, making them less hydrophobic than phenylalanine

Phenylalanine

Aromatic; Phe [F]

Tyrosine

Aromatic; Try [Y]; anti-cancer drugs inhibit tyrosine binding

Tryptophan

Aromatic; Trp [W]; essential amino acid to take in food

What are the polar, uncharged R groups?

Serine, Threonine, Cysteine, Asparagine, Glutamine

Property: hydrophilic; can form hydrogen bonds

Location: found on protein surface

Serine

Polar, uncharged; Ser [S]

Threonine

Polar, uncharged; Thr [T]

Proline

Pro [P]; rigid, ring structure; creates kinks or bends and is known as a "helix breaker"

Cysteine

Cys [C]; contains a sulfhydryl (-SH) group that can form a covalent disulfide bond

Histidine

His [H]; pKa near physiologic pH, allowing it to act as a proton donor/acceptor in enzyme catalysis

What are negatively charged (acidic) groups?

Aspartate, Glutamate

Property: very hydrophilic; deprotonated (negative) at pH 7.4

Aspartic Acid (Aspartate)

Negatively charged; Asp [D]

Glutamic Acid (Glutamate)

Negatively charged; Glu [E]

What are the positively charged (basic) groups?

Lysine, Arginine, Histidine

Property: very hydrophilic; protonated (positive) at pH 7.4 (except Histidine can be neutral)

Lysine

Positively charged; Lys [K]

Argine

Positively charged; Arg [R]

Isoelectric point (pl)

The specific pH at which an amino acid has a net charge of zero; low pH -> positive charge; high pH -> negative charge

Peptide bond

Links amino acids together with the amide bond being formed via a dehydration reaction; rigid and planar due to partial double-bond character (no rotation); forms a repeating backbone sequence; R groups project outwards from the backbone; ALWAYS FORMED B/T AMINO GROUP AND CARBOXYLIC GROUP

N-Terminus

At the end where the amino group is (left side)

C-Terminus

At the end where the carboxylic group is (right side)

What is Glutathione (GSH)?

Tripeptide composed of glutamate, cysteine, and glycine (Glu-Cys-Gly); a major antioxidant in cells, protecting them from oxidative damage

Insulin and glucagon

Regulate blood glucose

Vasopressin and oxytocin

Small peptide hormones with critical physiological roles

What is the hierarchy of protein structure?

Primary, secondary, tertiary, quaternary

Primary structure

A linear sequence of amino acids determined by DNA and stabilized by covalent peptide bonds

Function: the "blueprint" that dictates all higher levels of folding

Ex: Sickle Cell

Secondary structure

Regular, repeating patterns of the polypeptide backbones and is stabilized by hydrogen bonds between backbone C=O and N-H groups; R groups aren't involved in stabilization

Alpha-helix

A rigid, right-handed spiral

H-bonds: between C=O of residue n and N-H residue n+4

R groups: project outwards from helix

Found in hair and myoglobin

Disrupted by: Proline, Glycine, bulky or charged R groups

Beta-sheet

Formed from two or more polypeptide segments lined up side-by-side and backbone is in an extended, zig-zag conformation

H-bonds: form b/t adjacent strands

Types: antiparallel and parallel

R groups: project alternatively above and below the sheet

Tertiary structure

Overall 3D shape of a single polypeptide chain and describes how secondary structures are packed together; stabilized by interactions b/t R groups

What are the interactions that stabilize the tertiary structures?

Hydrophobic (primary driving force): nonpolar R groups buried in protein core

Hydrogen: b/t polar R groups

Ionic bonds (salt bridges): b/t oppositely charged R groups

Disulfide: covalent bond b/t two Cysteine residues; acts as a "molecular staple"

Quaternary structure

Applies only to proteins w/ more than one polypeptide subunit and describes the arrangement and interaction of subunits; held together by the same forces as tertiary

What is protein folding?

A polypeptide chain acquires its native 3D structure and is driven by the hydrophobic effect and assisted by chaperone proteins (prevent misfolding and aggregation)

What is misfolding?

Can lead to loss of function or creation of a toxin protein causing disease

What is denaturation?

Loss of a protein's secondary, tertiary, and quaternary structures resulting in loss of biological function

What are denaturing agents?

Heat (disrupts weak interactions), extreme pH (alters charge on R groups, disrupts ionic bonds), detergents & urea (disrupts hydrophobic interactions)

What is collagen?

Most abundant protein in the body (25%); fibrous structural protein; provides tensile strength to connective tissues; found in skin, bones, tendons, cartilage, blood vessels

What is collagen's structure?

Gly-X-Y (X= Proline, Y= Hydroxyproline); triple helix; Glycine's small size allows tight packing of chains

What is the post-translational modification of collagen?

Hydroxyproline and hydroxylysine are created after translation. Prolyl hydroxylase and lysyl hydroxylase add -OH groups and they are essential for hydrogen bonds that stablize the triple helix

Vitamin C (Ascorbic Aids)

Required cofactor for prolyl and lysyl hydroxylase; keeps iron in the enzyme's active site in reduced (Fe2+) state which is necessary for functioning; deficiency directly impairs synthesis of stable collagen

Scurvy

Cause: dietary deficiency of Vitamin C

Biochemical defect: inactive prolyl and lysyl hydroxylases

Pathophysiology: collagen chains are synthesized but not hydroxylated; a stable triple helix can’t be formed; connective tissue becomes weak and fragile

Symptoms: easy brusiing, bleeding gums, poor wound healing

Osteogenesis Imperfecta (OI)

“Brittle Bone Disease”

Cause: genetic mutation in Type I collagen genes

Biochemcial defect: often, a substitution of a bulky amino acid for a critical Glycine

Pathophysiology: the bulky R group distrupts the tight packing of the triple helix, creating weak collagen

Symptoms: brittle bones, fractures, blue sclerae

Ehlers-Danlos Syndrome

Cause: group of genetic disorders

Defect: often involves defective corss-linking of collagen fibrils

Symptoms: hypermobile joints, fragile skin