biochemistry chapter 3

What do structural proteins compose?

Cytoskeleton, Anchoring proteins, Extracellular matrix

Name two common structural proteins.

Collagen, Elastin, Keratin, Actin, Tubulin

How are motor proteins characterized?

By having one or more heads capable of generating force through conformational change.

List one application of motor proteins.

Muscle contraction, Vesicle movement within cells, Cell motility

Give examples of motor proteins.

Myosin, Kinesin, Dynein

What is the role of binding proteins?

To bind a specific substrate, sequestering it or holding its concentration steady.

What do cell adhesion molecules (CAM) do?

Allow cells to bind to other cells or surfaces.

What are cadherins?

Calcium-dependent glycoproteins that hold similar cells together.

Describe integrins.

They have two membrane-spanning chains and allow cells to adhere to proteins in the extracellular matrix.

What role do selectins play in the body?

Allow cells to adhere to carbohydrates on the surfaces of other cells, notably in the immune system.

What are antibodies (immunoglobulins) used for?

To target a specific antigen, such as a protein on a pathogen or a toxin.

Describe the structure of an antibody.

Made of two identical heavy chains and two light chains, held by disulfide linkages.

What are the three types of ion channels?

Ungated, Voltage-gated, Ligand-gated

How do ungated channels function?

They are always open.

What triggers voltage-gated channels to open?

Changes in membrane potential.

What is the function of ligand-gated channels?

Open in the presence of a specific binding substance, such as a hormone or neurotransmitter.

What role do enzyme-linked receptors play in cell signaling?

They bind extracellular ligands and initiate second messenger cascades.

What are G protein-coupled receptors associated with?

A trimeric G protein that initiates second messenger systems.

What happens to GDP when a ligand binds to a G protein?

GDP is replaced with GTP, activating the G protein.

What does the activated α subunit do?

It alters the activity of adenylate cyclase or phospholipase C.

What occurs when GTP is dephosphorylated?

The α subunit rebinds to the β and γ subunits.

What technique does electrophoresis use?

A gel matrix to observe the migration of proteins in an electric field.

What is the purpose of native PAGE?

It maintains protein shape but results are hard to compare due to varying mass-to-charge ratios.

What does SDS-PAGE do to proteins?

Denatures them and masks the native charge for accurate size comparison.

How does isoelectric focusing work?

It separates proteins by pI; proteins migrate until pH = pI.

What is the function of chromatography in protein analysis?

Separates protein mixtures based on affinity to stationary or mobile phases.

What is used in column chromatography?

Beads of a polar compound with a nonpolar solvent.

What characterizes ion-exchange chromatography?

A charged column and a variably saline eluent.

What does size-exclusion chromatography rely on?

Porous beads; larger molecules elute first.

What is utilized in affinity chromatography?

A bound receptor or ligand and an eluent with free ligand or receptor.

How can amino acid composition be determined?

By simple hydrolysis.

What process is used for amino acid sequencing?

Sequential degradation like Edman degradation.

How is enzyme activity determined?

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

How can protein concentration be measured?

Colorimetrically, using either UV spectroscopy or color change reactions.

What color change occurs in the Bradford protein assay?

From brown-green to blue.

What method primarily determines protein structure?

X-ray crystallography

Which technique can also be used alongside X-ray crystallography?

NMR (Nuclear Magnetic Resonance)

How is amino acid composition determined?

By simple hydrolysis

What process is required for amino acid sequencing?

Sequential degradation (e.g., Edman degradation)

How are activity levels of enzymatic samples determined?

By following a known reaction which often shows a color change

What are the methods to determine protein concentration?

Colorimetrically, using UV spectroscopy or color change reactions

What is the common method for protein concentration analysis?

The Bradford protein assay