Kaplan Biochemistry: Chapter 3 - Nonenzymatic Protein Function and Protein Analysis

What is the primary function of structural proteins?

They support cellular shape and organization and form part of the extracellular matrix.

Name the five most common structural proteins in the human body.

Collagen, elastin, keratin, actin, tubulin.

True or False: Structural proteins are usually globular in nature.

False; they are generally fibrous.

What disorder is associated with defective collagen formation?

Osteogenesis imperfecta (brittle bone disease)

Collagen is composed of three left-handed helices woven into what type of helix?

A secondary right-handed helix

What is the main function of elastin?

To stretch and recoil, restoring tissue shape.

Keratins are primarily found in which type of cells?

Epithelial cells

Actin filaments are also known as?

Microfilaments

True or False: Actin filaments have polarity allowing motor proteins to travel unidirectionally.

True

What protein makes up microtubules?

Tubulin

Which motor protein moves along actin filaments?

Myosin

What are the two motor proteins that move along microtubules?

Kinesin and dynein

Kinesins move cargo toward which end of microtubules?

The positive end (usually toward the cell periphery)

Dyneins move cargo toward which end of microtubules?

The negative end (usually toward the nucleus)

Motor proteins generate force through what type of activity?

ATPase activity (hydrolyzing ATP)

What is the difference between a binding protein for sequestration vs transport?

Sequestration proteins have high affinity across all concentrations; transport proteins vary affinity to allow binding/unbinding.

Name the three main types of cell adhesion molecules (CAMs).

Cadherins, integrins, selectins

Cadherins are dependent on which ion to function?

Calcium

True or False: Integrins are only structural proteins.

False; they also have signaling capabilities.

Which CAM binds to carbohydrates on other cells?

Selectins

What is the primary function of immunoglobulins?

To recognize and neutralize antigens (toxins, pathogens)

List the three possible outcomes when an antibody binds its antigen.

Neutralization, opsonization, agglutination

Which type of ion channel is always open?

Ungated channels

Voltage-gated channels open in response to what?

Changes in membrane potential

Ligand-gated channels open in response to what?

Binding of a specific ligand (e.g., neurotransmitter)

True or False: Km and Vmax apply only to enzymes, not transporters.

False; transporters follow similar kinetics.

Name the three domains of enzyme-linked receptors.

Membrane-spanning domain, ligand-binding domain, catalytic domain

Which G protein stimulates adenylate cyclase?

Gs

Which G protein inhibits adenylate cyclase?

Gi

Which G protein activates phospholipase C?

Gq

True or False: The alpha subunit of a G protein is active when bound to GDP.

False; it is active when bound to GTP.

What is the stationary phase in chromatography?

The solid medium through which the sample passes and interacts.

In column chromatography, what effect does polarity have on retention time?

The more similar a compound is to the stationary phase, the longer it is retained.

True or False: In size-exclusion chromatography, the smallest molecules elute first.

False; largest molecules elute first.

What is the main principle behind affinity chromatography?

Proteins are retained based on high affinity for a specific ligand attached to the column.

What does SDS do in SDS-PAGE?

Denatures proteins and imparts a uniform negative charge.

Native PAGE preserves what aspect of proteins?

Their functional, folded state

True or False: Isoelectric focusing separates proteins based on size.

False; separates based on isoelectric point (pI)

What does the Edman degradation sequence?

The N-terminal amino acids of a protein (up to ~50-70 residues)

True or False: Edman degradation proceeds from the C-terminal end.

False; it proceeds from the N-terminal end

Which protein assay uses Coomassie Brilliant Blue dye?

Bradford assay

What color change occurs in the Bradford assay when protein binds dye?

Green-brown (acidic) to blue (basic, protein-bound)

Name one drawback of the Bradford assay.

Variable dye binding with different amino acids; less accurate for mixed protein solutions.

What is the main advantage of X-ray crystallography?

High-resolution determination of protein structure

Name an alternative method for determining protein structure besides X-ray crystallography.

NMR spectroscopy

What is the primary function of structural proteins in cells?

Support cellular shape and organization; provide strength and mechanical support

Name the five major structural proteins discussed in MCAT Biochemistry.

Collagen, elastin, keratin, actin, tubulin

True or False: Motor proteins do not have enzymatic activity.

False; motor proteins act as ATPases

Which structural protein is the most abundant in eukaryotic cells?

Actin

Which motor protein interacts primarily with actin?

Myosin

Which motor proteins are associated with microtubules?

Kinesin and dynein

What is the function of kinesins in cells?

Move vesicles toward the positive end of microtubules

What is the function of dyneins in cells?

Move vesicles toward the negative end of microtubules

Fill in the blank: Collagen is characterized by a fiber structure.

Trihelical

Which structural protein allows tissues to stretch and recoil like a spring?

Elastin

Keratins are primarily found in which type of cells?

Epithelial cells

True or False: Cadherins mediate calcium-independent cell adhesion.

False; cadherins are calcium-dependent

Which CAM allows cells to adhere to carbohydrates on other cell surfaces?

Selectins

Integrins have membrane-spanning chains and can signal to the cell interior.

Two (α and β)

List three outcomes when an antibody binds to its antigen.

Neutralization, opsonization, agglutination

What is the Y-shaped protein in the immune system that binds antigens?

Antibody or immunoglobulin (Ig)

Multiple Choice: Which of the following proteins is fibrous?;A) Actin; B) Collagen; C) Kinesin; D) Enzyme-linked receptor

B) Collagen

True or False: Actin filaments are polar structures with a positive and negative end.

True

Which ion channel type is always open and unregulated?

Ungated channels

Voltage-gated channels open in response to what stimulus?

Change in membrane potential

Ligand-gated channels open in response to what?

Binding of a specific ligand or substance

Fill in the blank: G protein-coupled receptors have membrane-spanning α-helices.

Seven

Gs, Gi, and Gq are types of .

G proteins

What does Gs protein do to adenylate cyclase?

Stimulates it, increasing cAMP

What does Gi protein do to adenylate cyclase?

Inhibits it, decreasing cAMP

What does Gq protein activate?

Phospholipase C

True or False: Enzyme-linked receptors have a catalytic domain.

True

Name three domains of an enzyme-linked receptor.

Membrane-spanning, ligand-binding, catalytic

What type of chromatography separates proteins based on net charge?

Ion-exchange chromatography

Which chromatography method separates proteins based on size?

Size-exclusion chromatography

Which chromatography method uses a ligand or antibody to capture a specific protein?

Affinity chromatography

True or False: In size-exclusion chromatography, smaller molecules elute first.

False; larger molecules elute first

What does SDS do in SDS-PAGE?

Denatures proteins and gives them a uniform negative charge

Native PAGE differs from SDS-PAGE because it preserves what?

Protein’s native structure and function

Fill in the blank: Isoelectric focusing separates proteins based on .

Isoelectric point (pI)

True or False: A protein stops moving in isoelectric focusing when pH

pI.

Which protein sequencing method removes the N-terminal amino acid sequentially?

Edman degradation

Name two enzymes used for sequential digestion of larger proteins.

Trypsin and chymotrypsin

What is the main principle behind the Bradford protein assay?

Protein binds Coomassie dye, causing a color change proportional to concentration

True or False: The Edman degradation proceeds from the C-terminal.

False; it proceeds from the N-terminal

Fill in the blank: X-ray crystallography determines protein structure by measuring density.

Electron

Name a limitation of protein activity assays.

Affected by purification method, assay conditions, or presence of contaminants

Which protein binds calcium or DNA for transport or regulation?

Binding proteins

What is the role of integrin αIIbβ3 in platelets?

Allows platelets to stick to fibrinogen and stabilize clots

True or False: Structural proteins generally have highly repetitive secondary structures.

True

Which motor protein is responsible for the power stroke in sarcomere contraction?

Myosin

What is the main difference between binding proteins involved in sequestration vs. transport?

Sequestration proteins have high affinity at all concentrations; transport proteins have variable affinity

Multiple Choice: Which CAM family mediates calcium-dependent adhesion?;A) Integrins; B) Cadherins; C) Selectins; D) Antibodies

B) Cadherins

What is opsonization?

Marking a pathogen for destruction by other immune cells

What is agglutination in immunology?

Clumping together of antigens and antibodies for phagocytosis

Which protein is used by white blood cells to migrate during inflammation?

Selectins

True or False: Kinesin and dynein move vesicles in the same direction on microtubules.

False

What is the net charge of a protein at its isoelectric point?

Neutral

Which chromatography method allows immediate identification and quantification of proteins?

All forms, especially column and affinity chromatography

What type of ion channels are commonly targeted by calcium channel blockers?

Voltage-gated channels