Chapter 4: Protein Structure and Function

A comprehensive set of practice flashcards covering major concepts from the lecture notes on protein structure and function, including types of proteins, levels of structure, folding, interactions, enzyme mechanisms, regulation, and common experimental techniques.

What is the general function of enzymes?

Catalyze covalent bond breakage or formation.

What is the function of structural proteins?

Provide mechanical support to cells and tissues.

Name a blood protein that transports oxygen.

Hemoglobin.

Name a blood protein that transports lipids.

Serum albumin.

Name a blood protein that transports iron.

Transferrin.

Give an example of a motor protein and its role.

Myosin generates movement in muscle; kinesin/dynein move organelles or power cilia beating.

What is the function of storage proteins?

Store amino acids or ions (e.g., ferritin stores iron; ovalbumin and casein provide amino acids).

Give an example of a signal protein and its role.

Insulin regulates glucose levels; NGF and EGF are growth factors that coordinate physiological functions.

What is the function of receptor proteins?

Detect signals and transmit them to the cell’s response machinery.

What do transcription regulators do?

Bind to DNA to switch genes on or off (e.g., Lac repressor).

What are special-purpose proteins?

Proteins with highly variable properties; examples include antifreeze proteins, GFP, monellin, and mussel glue proteins.

What is primary structure?

The unique amino acid sequence of a protein, determined by DNA.

What is a peptide bond?

Bond linking amino acids in a polypeptide chain.

What are the four levels of protein structure?

Primary, secondary, tertiary, and quaternary structures.

What determines a protein’s primary structure?

The sequence of amino acids encoded by DNA.

What is an alpha helix?

A secondary structure stabilized by hydrogen bonds; right- or left-handed; ~0.54 nm per turn; can form coiled-coils.

What is a beta sheet?

A beta pleated sheet, can be antiparallel or parallel; contributes to protein stability (e.g., silk).

What is a coiled-coil?

Intertwined alpha helices forming a rod-like structure.

What is amyloid formation and misfolding?

Misfolded beta-sheet rich structures that can aggregate into amyloid fibrils; prions can propagate misfolded forms.

What is tertiary structure?

The full 3D conformation of a single polypeptide, including interactions among R groups.

What bonds stabilize tertiary structure?

Disulfide bridges, ionic bonds, hydrogen bonds, hydrophobic interactions, and van der Waals attractions.

Where are disulfide bonds commonly found and what do they do?

Common in secreted proteins and extracellular matrix; covalently reinforce a protein’s conformation outside the cell.

What is quaternary structure?

Assembly of more than one polypeptide chain into a functional protein.

What is an example of a protein with quaternary structure?

Hemoglobin, which has two alpha and two beta subunits.

What is a protein family?

A group of proteins sharing similar amino acid sequences and 3D structures; members resemble each other (e.g., serine proteases).

Why are 3D structure and function linked in proteins?

Because binding to specific molecules depends on a compatible 3D shape and surface properties.

What is a binding site?

A region on a protein’s surface that interacts with another molecule via noncovalent bonds, often a cavity formed by specific amino acids.

What is a ligand?

A substance that binds to a protein with specificity and affinity through noncovalent interactions.

Are interior amino acids part of binding sites?

Not typically; they help maintain the proper 3D shape necessary for binding.

How do enzymes catalyze reactions?

Form an enzyme–substrate complex, orient substrates, lower activation energy, form product, and release it; the active site can template the reaction.

Give an enzyme example and its substrate-action from the notes.

Lysozyme cuts polysaccharide chains in bacterial cell walls.

What is feedback inhibition?

Allosteric regulation where binding at an allosteric site inhibits enzyme activity, controlling biosynthetic pathways.

What is allosteric regulation?

Regulation where a molecule binds at a site other than the active site to alter activity; can be positive or negative.

What is phosphorylation in protein regulation?

Covalent modification by adding phosphate groups via kinases (and removed by phosphatases), a common regulatory mechanism.

What is a molecular switch in proteins?

GTP binding/hydrolysis acts as a switch to turn proteins on or off.

What is the starting step in protein purification?

Breaking open cells/tissues via homogenization to release contents.

What is centrifugation used for?

To separate a homogenate into fractions based on size and density.

What is differential centrifugation?

Repeated centrifugation at increasing speeds to fractionate cell components into pellets and supernatants.

What is velocity sedimentation?

Separation of components in a dilute sucrose gradient according to sedimentation rate.

What is equilibrium (density gradient) sedimentation?

Separation by buoyant density in a density gradient (e.g., sucrose or CsCl) until components settle at their density.

What is column chromatography used for?

Purify proteins by passing a mixture through a matrix; separation by charge, size, hydrophobicity, or affinity.

Name the three kinds of chromatography described.

Ion-exchange, gel-filtration (size-exclusion), and affinity chromatography.

What does gel electrophoresis (SDS-PAGE) accomplish?

Separates polypeptide chains by molecular weight after binding SDS and reducing agents.

What is isoelectric focusing?

Separation by isoelectric point in a pH gradient; proteins migrate to the pH where their net charge is zero.

What is two-dimensional gel electrophoresis?

First separate by charge (isoelectric focusing), then by size (SDS-PAGE) to resolve many proteins as spots.

What does X-ray crystallography determine?

Atomic-level 3D structure by analyzing diffraction patterns from protein crystals.

What does NMR spectroscopy determine?

3D structure of smaller proteins (typically <= ~50 kDa) in solution by nuclear magnetic resonance.

What is cryo-electron microscopy (cryo-EM) best for?

Determining structures of large macromolecular machines and membrane proteins without crystallization by imaging frozen specimens and computationally reconstructing a 3D map.

What is Rubisco?

Ribulose-1,5-bisphosphate carboxylase/oxygenase, an enzyme central to CO2 fixation in photosynthesis.

How long are typical protein primary structures?

30 to 10,000 amino acids, with an average of about 50–2000.

How are proteins grouped into domains or families in practice?

By sequence similarity and 3D structure; members of a family resemble each other.

Why are disulfide bonds important and where are they usually found?

Covalent bonds that reinforce structure, commonly found in secreted proteins and extracellular matrix; form outside the cell.

What is the role of hydrophobic and hydrophilic amino acids in folding?

Hydrophobic residues cluster in the interior; hydrophilic residues tend to be on the outside, stabilizing folded structures.

What does a binding site typically look like on a protein?

Often a cavity formed by a specific arrangement of amino acids that binds a ligand via noncovalent interactions.

What is the form of the light-activated pump mentioned in the notes?

Bacteriorhodopsin, a light-activated proton pump in archaeal membranes.

What is the term for proteins that can form a green fluorescent protein signal?

Green fluorescent protein (GFP) as an example of a special-purpose protein.

What is the function of ferritin?

Stores iron in the liver as a storage protein.

What is the effect of hydrogen bonds on secondary structure?

Stabilize α helices and β sheets within the polypeptide backbone and between side chains.”

What is a typical outcome of protein misfolding in cells?

Misfolded proteins can aggregate and form amyloid structures; prions can propagate the misfolded form.

What is the relationship between protein shape and binding specificity?

Binding is highly specific; only certain ligands fit the binding site based on shape and chemistry.

What role do chaperone proteins play in folding?

Assist newly synthesized polypeptides to fold correctly, sometimes sequestering them in a chamber until properly folded.

What is the basic principle behind velocity vs. equilibrium sedimentation in centrifugation?

Velocity separates by sedimentation rate; equilibrium separates by buoyant density in a gradient.