Protein Structure & Function

Proteins

These are the most functionally diverse macromolecules.

Structural Biology

The main goal of this field is to be able to predict the structure, function, & behavior of the machines from their chemical formulas through chemistry & physics.

covalent

Amino acids are held together by ______________ bonds.

Microprotein

This is a protein that is only a few amino acids long.

Proteinogenic Amino Acids

These are amino acids that are incorporated into proteins during translation.

side-chain

Amino acids differ from each other only by their ________________.

Chiral Amino Acid

This is an amino acid with four different groups attached to the a-carbon.

L-stereoisomers

All proteinogenic amino acids are ____________________.

peptide bonds

Amino acids are joined by __________________.

Amino Acid Residue

This is an amino acid after it has been incorporated into a protein.

Secondary Structure

This is the regular, recurring arrangement in space of adjacent amino acid residues in a polypeptide chain; maintained by hydrogen bonds between amide hydrogens & carbonyl oxygens of the peptide backbone.

trans

The ___________ isomer is preferred.

a-helix

This is the most common secondary structural element.

far apart

In the B-sheet, interacting amino acids are often ______________ in the primary sequence.

Beta Barrel

This is a tertiary structure that is comprised of circular Beta Sheets (cytoplasmic & transmembrane proteins).

Porin

This is when a Beta Barrel forms a hole (pore).

short

Turns are ____________.

long

Loops are ___________.

Pi Helix

This is a wider helix, usually a single-turn helix embedded with an a-helix.

3.10 Helix

This is the 2nd most common; tight elongated helix.

Tertiary Structure

This refers to the overall 3-D arrangement of the polypeptide chain in space; generally stabilized by side chain, polar hydrophilic hydrogen, & ionic bond interactions, internal & hydrophobic.

Globular Proteins

These proteins are compact & spherical in shape; usually water-soluble.

Fibrous Proteins

These form long, extended filaments; tend to stick together & become structural fibers; water-insoluble

Integral (Intrinsic) Membrane Proteins

These are fully/partially embedded in the membrane; insoluble- lose structure outside of membrane.

Peripheral (Extrinsic) Membrane Proteins

These are bound to the membrane indirectly via interactions with the integral proteins or directly via interactions with the lipid polar head groups.

Intrinsically Disordered Protein

This kind of protein lacks a fixed/ordered 3-D structure, but adopts structure in response to stress/cell signaling.

Quaternary Structure

This is the 3-D organization of multi-subunit proteins and how those subunits stick together.

Glycocalyx

This is the protective layer of the cell.

Disulfide Bond

This is the bond between two cysteine residues (covalent); maintains protein structure.

Sequence Motif

This is a readily recognizable sequence of amino acids that often have a common function (identified by analysis of primary structure).

Structural Motif

These are secondary structural elements that have a specific function (identified by secondary & tertiary structural analysis)

Protein Domains

These are distinct functional and/or structural units in a protein, basically show what protein does/is.

Topological Domains

These parts of a protein have a specific fold.

Structural Domain

These perform a specific structural role.

Functional Domain

These have a specific functional role.

Protein Family

This is a group of proteins that share a common evolutionary origin.

Folding

This is when a protein assumes its functional (native) structure.

Denaturation

This is the inverse process in which a protein loses its structure & activity.

Renaturaiton

This is when a protein resumes its native state after denaturation.

Uniqueness of 3 structure

This is part of the thermodynamic hypothesis that represents free energy minimum & there are no folds with comparable free energy minimum.

Stability

This is part of the thermodynamic hypothesis where small changes in the surrounding environment cannot give rise to changes in the minimum configuration.

Kinetical Accessibility

This is part of the thermodynamic hypothesis where the path in the free energy surface from the unfolded state to the folded state is smooth; folding path avoids complex changes in shape.

Levinthal’s Paradox

This ultimately states that folding is not random, and it must proceed through some kind of pathway. There are folding intermediates, which accelerate protein folding.

Local structure nucleation- formation of a-helices and B-strands.

This is the 1st step of protein folding.

Hydrophobic collapse- driven by hydrophobic interactions.

This is the 2nd step in protein folding.

Molten-Globule Formation- a compact, partially folded conformation that has substantial 2 structure. It has increased solvent-exposed hydrophobic surface area relative to native state.

This is the 3rd (longest) step in protein folding.

Native-state formation

This is the 4th step in protein folding.

core

In the folded protein, hydrophobic residues will form a hydrophobic __________ at the center.