BMS527-Lecture 2: Protein Function

Vocabulary-style flashcards covering key protein concepts, structures, and protein analysis techniques from BMS527 Lecture 2.

1° structure

Linear sequence of covalently bonded amino acids in a protein (the primary sequence).

2° structure

Local organization of the polypeptide backbone, stabilized mainly by hydrogen bonds (alpha helices and beta sheets).

3° structure

Overall three-dimensional fold of a single polypeptide chain (global 3D shape).

4° structure

Arrangement of multiple polypeptide chains into a functional protein complex.

Globular proteins

Compact, water-soluble proteins with functional roles (e.g., hemoglobin, enzymes, immunoglobulins).

Fibrous proteins

Elongated structural proteins forming fibers (e.g., collagen, keratin, elastin).

Immunoglobulins (antibodies)

Glycoproteins made by B cells that recognize antigens; composed of heavy and light chains with constant and variable regions.

IgG structure

Two identical heavy chains and two identical light chains; Fab regions (variable) and Fc region (constant).

Immunoglobulin fold

Beta-sandwich fold consisting of two antiparallel beta sheets common in antibodies.

CDR loops

Complementarity-determining regions; hypervariable loops at ends of antibody variable regions that determine antigen binding.

G-actin

Globular actin monomer; polymerizes to form F-actin.

F-actin

Filamentous actin; two helical strands formed from G-actin; forms cytoskeletal networks.

Actin roles

Involves muscle contraction, cell motility, division, vesicle transport, and maintenance of cell shape.

Myoglobin

Oxygen-binding protein in muscle; stores and facilitates O2 delivery; high affinity for O2.

Hemoglobin (Hb)

65-kD α2β2 tetramer with four heme groups; exhibits cooperative O2 binding and allosteric regulation.

Heme

Iron-containing porphyrin prosthetic group in Hb/Mb; Fe2+ coordinated by nitrogens and a histidine; binds O2.

Oxygen binding curves

Hb shows a sigmoidal (cooperative) binding curve; Mb shows a hyperbolic curve due to lack of cooperativity.

2,3-BPG

Allosteric metabolite that binds deoxy Hb and lowers O2 affinity, promoting oxygen release in tissues.

CO2 binding to Hb

CO2 binds at the N-terminus and stabilizes the T state, reducing O2 affinity (negative allosteric effect).

Fetal hemoglobin (HbF)

Hb with α2γ2; higher O2 affinity than adult Hb, aiding transfer from mother to fetus.

Sickle cell anemia

Single E6V mutation in the beta chain of Hb causing polymerization and rigid, misshapen RBCs; treated by expressing fetal Hb.

2,3-bisphosphoglycerate (2,3-BPG) site

Allosteric site on Hb where 2,3-BPG binds, decreasing O2 affinity.

Desmosine

Crosslinking residue in elastin formed from four lysine residues; enables an elastic network.

Elastin

Fibrous connective tissue protein with rubber-like elasticity; little hydroxyproline/lysine; desmosine crosslinks provide extensibility.

Keratin (α-keratin)

Fibrous, alpha-helical protein; forms coiled-coil structures; hydrophobic residues promote interactions; cysteine crosslinks increase strength.

Keratin (β-keratin)

Keratin in birds/reptiles rich in beta-sheet structure; a distinct fibrous class from α-keratin.

Collagen

Most abundant protein; extracellular; forms a triple-helix; Gly-X-Y repeats; rich in proline/hydroxyproline; essential for tensile strength.

Gly-X-Y motif

Repeating collagen sequence where X is often Pro and Y is often hydroxyproline; stabilizes the triple helix.

Hydroxyproline (Hyp)

Proline hydroxylation in collagen; enables strong hydrogen bonding and helix stability.

Hydroxylysine (Hyl)

Lysine hydroxylation in collagen; sites for glycosylation and crosslinking.

Prolyl hydroxylase

Enzyme that hydroxylates proline in collagen precursors; requires ascorbate, Fe2+, and α-ketoglutarate (produces hydroxyproline).

Vitamin C role

Ascorbate acts as a cofactor for prolyl hydroxylase; deficiency impairs collagen synthesis (scurvy).

PTMs in collagen

Post-translational modifications (hyp, hyl) that stabilize collagen and promote crosslinking.

Protein analysis tools - SDS-PAGE

Denaturing gel electrophoresis that separates proteins by size using SDS to impart uniform negative charge.

Non-denaturing PAGE (Native PAGE)

Gel electrophoresis performed without denaturation to study proteins in their native state.

Isoelectric focusing (IEF)

Separates proteins by isoelectric point on a pH gradient.

Size-exclusion chromatography

Column chromatography separating proteins by size; larger proteins elute earlier.

Ion-exchange chromatography

Separation by charge; proteins interact with charged resin; eluted by salt or pH gradient.

Affinity chromatography

Separation by specific binding to a ligand on the column; elution by competition or gradient.

Bradford assay

Colorimetric method to determine protein concentration using Coomassie dye; dye binding shifts absorbance.

X-ray crystallography

Technique to determine protein structure by diffraction from protein crystals.

NMR spectroscopy

Determines protein structure in solution using isotopic labeling; provides dynamic information; size limitations.