Ch. 3 - Nonenzymatic Protein Function and Protein Analysis

4% of MCAT Biochemistry content

What do structural proteins compose?

The cytoskeleton, anchoring proteins, and much of the extracellular matrix.

What are the most common structural proteins?

Collagen, elastin, keratin, actin, and tubulin.

What is the nature of structural proteins?

They are generally fibrous in nature.

What are motor proteins responsible for?

Generating force through conformational changes

ex. muscle contraction, vesicle movement, and cell motility.

Name examples of motor proteins.

Myosin, kinesin, and dynein.

What is the function of binding proteins?

To bind specific substrates to sequester them in the body or maintain their steady-state concentration.

What do cell adhesion molecules (CAM) do?

They allow cells to bind to other cells or surfaces.

What are cadherins?

Calcium-dependent glycoproteins that hold similar cells together.

What are integrins?

Membrane-spanning proteins that allow cells to adhere to proteins in the extracellular matrix and may also have signaling capabilities.

What is the function of selectins?

They allow cells to adhere to carbohydrates on the surfaces of other cells, mainly in the immune system.

What do antibodies (immunoglobulins) target?

A specific antigen, which may be a protein on a pathogen or a toxin.

What are the components of an antibody?

Two identical heavy chains and two identical light chains held together by disulfide linkages and noncovalent interactions.

What is the role of ion channels in biosignaling?

They regulate ion flow into or out of a cell.

What are the three main types of ion channels?

Ungated channels, voltage-gated channels, and ligand-gated channels.

What is the function of enzyme-linked receptors?

They participate in cell signaling by binding extracellular ligands and initiating second messenger cascades.

What is the mechanism of G protein-coupled receptors?

They associate with a trimeric G protein, which initiates second messenger systems upon ligand binding.

What happens when a ligand binds to a G protein-coupled receptor?

GDP is replaced with GTP

• the α subunit dissociates from the β and γ subunits to alter adenylate cyclase or phospholipase C activity.

What happens after the G protein α subunit is activated?

GTP is dephosphorylated to GDP

• the α subunit rebinds to the β and γ subunits.

What does electrophoresis use to observe protein migration?

A gel matrix in response to an electric field.

What does native PAGE do?

It maintains the protein’s shape but makes comparisons difficult due to differing mass-to-charge ratios.

What does SDS-PAGE do?

It denatures proteins and masks native charge, allowing size comparisons but preventing functional protein recapture.

How does isoelectric focusing work?

It separates proteins by their isoelectric point (pI), where the protein migrates until pH = pI.

What is the principle behind chromatography?

Separation of protein mixtures based on their affinity for a stationary phase or a mobile phase.

What is column chromatography?

A technique using polar beads (stationary phase) and a nonpolar solvent (mobile phase) to separate proteins.

How does ion-exchange chromatography work?

It uses a charged column and a variably saline eluent to separate proteins.

What is size-exclusion chromatography?

A method where larger molecules elute first because they are not trapped in small pores of porous beads.

.What does affinity chromatography use to separate proteins?

A bound receptor or ligand and an eluent with free ligand or receptor for the protein of interest.

How is protein structure primarily determined?

Through X-ray crystallography, though NMR can also be used.

How is amino acid composition determined?

By simple hydrolysis, while amino acid sequencing requires sequential degradation, like Edman degradation.

How is enzyme activity typically determined?

By following a known reaction process, often with a color change.

What are common methods to determine protein concentration?

UV spectroscopy or colorimetric reactions

ex. BCA assay, Lowry reagent assay, and Bradford protein assay.

What is the most common protein assay?

The Bradford protein assay, which changes color from brown-green to blue.