Proteins

Protein

Peptides with >100aa residues

Peptide Bond

Dehydration reaction between the N and C terminus of aa

Primary Structure

Sequence of aa

Secondary Structure

Arrangements of backbone atoms

Tertiary Structure

3D structure of all atoms and prosthetic groups

Quaternary Structure

Spatial arrangement of multiple subunits

Subunit

Polypeptides that can chain together to form proteins

Prosthetic Group

Not made of aa or ribosomes

Part of function

Disulfide Bond

Covalent bond formed between two Cystine atoms

Salt Bridge

Electrostatic attraction between two oppositely charged groups
Positive → lysine, arginine, histidine
Negative → aspartate, glutamate

Fibrous Protein

Structural proteins that contain stiff, elongated, fibrous regions

Globular Protein

Compact, highly-folded, globular structure

Sections of a-helix and B-sheet

Hydrophobic effect

a-helix

Right-handed helical coil

H-bond between carbonyl oxygen of one residue and N-H hydrogen 4 residues later

Core atoms in vdW

Peptides with oppositely charged R groups

B-sheet

H-bonded chains

Pleated appearance to maximize H-bonds
Peptides with bulky R groups

Antiparallel B-sheet

Strands run in opposite directions

More stable H-bonds

Parallel B-sheet

Strands run in same direction

Diagonal H-bonds

B-bend

Abrupt change in direction of backbone

Strong H-bond between carbonyl oxygen of one residue and N-H hydrogen 3 residues later, residue 2 is normally Proline

Coiled-Coil

Two or more a-helices coil around each other in leftward, counter clockwise direction

Native Structure

Tertiary structure naturally formed

Random Coil Structure

Non-specific arrangement of polymer chain

No fixed stucture

Cis-conformation

R-groups on same side

Sometimes proline

Trans-conformation

R-groups on opposite sides

More common

Denaturation

Heat, pH, detergents, chaotropic agents (increase hydrophobic)

Protein loses tertiary structure and function

Protein Conformation

Primary sequence determines interactions that form other sturtcures

Unimolecular Micelle

Hydrophobic tails face inwards while hydrophilic heads face outwards to maximize favorable interactions

Protein Stability

Hydrophobic effect, electrostatic interactions. disulfide bonds, metal ions

Hydrophobic Effect

The tendency of nonpolar substances to aggregate in aqueous solutions, minimizing their exposure to water and stabilizing protein structures

a-keratin

Tough, insoluble protein

Right-handed a-helical structure form left-handed coiled coil

Rich in cys → disulfide bonds to cross-link

Collagen

Strong, insoluble, fibrous protein

Left-handed collagen helix structure, 3 residues per turn form right-handed super helical structure

Scurvy

Deficiency of vitamin C in diet → failure of prolyl hydroxylase to make Hyp

Skin lesions Fragile blood vessels Poor wound healing

Lathyrism

Presence of ODAP in diet → failure of lysyl oxidase to covalently cross-link collagens

Abnormal bones, joints, and large blood vessels

Osteogenesis Imperfecta

Genetic mutations that change primary sequence of Type I collagen → structural distortions in collagen triple helix structure

Varies with nature and position of mutation

Ehlers-Danlos Syndromes

Collagen deficiencies or abnormal activity of collagen-processing enzymes

Hyperextensible joints and skin etc.

Motif

Short, conserved sequence or pattern within protein

Domain

Independent unit of protein that can fold and function on it’s own