Chapter 3: Protein Structure and Function

A chain composed of fewer than 50 amino acid residues linked together by peptide bonds.

Peptide

The location in an enzyme molecule where substrates (reactant molecules) bind and react.

Active site

Hydrolysis is the reverse reaction. - Breaks polymers apart by _______ a water molecule

Adding

A secondary structure in proteins formed when the polypeptide backbone coils into a spiral shape stabilized by hydrogen bonding.

Alpha-helix

A small organic molecule with a central carbon atom bonded to an amino group (-NH3), a carboxyl group (-COOH3), a hydrogen atom, and a side chain. When amino acids are linked together to form proteins, they are referred to as residues.

Amino acid

A secondary structure in proteins., formed when polypeptide backbone folds into a sheetlike shape stabilized by hydrogen bonding.

Beta-pleated sheet

Acceleration of the rate of a chemical reaction due to a decrease in the free energy of the transition state, called the activation energy.

Catalysis

___________ and _______ side chains are hydrophilic: they interact readily with water. - side chain with a negative charge - side chain with a positive charge - side chain that have an oxygen atom

Charged, polar

For a macromolecule, loss of its three-dimensional structure due to breakage of covalent and/or noncovalent chemical bonds, usually caused by exposure to heat, certain chemicals, or extreme pH conditions.

Denaturation

A ______ (unfolded) protein is unable to function normally.

Denatured

A covalent bond between two sulfur atoms, typically in the side chains of certain amino acids (e.g., cysteine). Often contributes to tertiary and quaternary levels of protein structure.

Disulfide bond

A protein catalyst used by living organisms to increase the rate of biological reactions.

Enzyme

5 important types of R-group interactions:

Hydrogen bonds, hydrophobic interactions, van der Waals interactions, covalent disulfide bonds, ionic bonds

Interacting readily with water. Hydrophilic compounds are typically polar compounds containing partially or fully charged atoms.

Hydrophilic

Not interacting readily with water. Hydrophobic compounds are typically nonpolar molecules.

Hydrophobic

Nonpolar side chains are ___________

Hydrophobic, they do not interact with water

In water, the amino and carboxyl groups ________. The resulting charges: (1) Help the amino acids ________ in solution (2) Make the amino acids more ________

Ionize Stay Reactive

Monomers polymerize through condensation (dehydration) reactions. -Results in the ______ of a water molecule

Loss

A group of proteins, and possibly other nonprotein macromolecules, that assemble to carry out a particular function.

Macromolecular machine

Proteins are _________________.

Macromolecules

A protein that facilitates the folding or refolding of a protein into its correct three-dimensional shape.

Molecular chaperone

Proteins called ________ ________ help proteins fold correctly in cells.

Molecular chaperones

What charge do acidic electrically charged side chains have?

Negative (-)

A chain composed of fewer than 50 amino acid residues linked together by peptide bonds. Often referred to simply as peptide.

Oligopeptide

The covalent bond formed by a condensation reaction between two amino acids.

Peptide bond

A chain typically consisting of 50 or more amino acids linked together by peptide bonds.

Polypeptide

What charge do basic electrically charged side chains have?

Positive (+)

Protein ________ ________ is its unique sequence of amino acids.

Primary structure

The sequence of amino acid residues in a protein polymer; also the sequence of nucleotides in a single nucleic acid strand.

Primary structure

_______ ________ is fundamental to the higher levels of protein structure.

Primary structure

All proteins have four basic structures:

Primary, secondary, tertiary, quaternary

An infectious particle that consists entirely of protein. Prion proteins adopt two differently folded shapes; a normally folded shape and infectious, often disease causing shape. The infectious version can bind normally folded prion proteins and cause them to adopt the infectious shape. Also called proteinaceous infectious particles.

Prion

A macromolecule consisting of one or more polypeptide chains. Each polypeptide has a unique sequence of amino acids and each protein generally possesses a characteristic three-dimensional shape.

Protein

Normal ________ _______ is crucial and often _______. - Result of chemical bonds and interactions - Folded molecule more energetically stable than unfolded molecule- less potential energy.

Protein folding, spontaneous

Amino acids are the building blocks of _________.

Proteins

-Many proteins contain several distinct polypeptide subunits that interact to form a single structure. -The bonding of two or more distinct polypeptide subunits produces ________ ________.

Quaternary structure

In proteins, the overall three-dimensional shape formed from the combination of two or more polypeptide chains (subunits); determined by the number, relative positions, and interactions of the subunits. In nucleic acids, two or more distinct single strands will form this level of structure through hydrogen bonding between complementary bases and hydrophobic interactions with the aqueous environment.

Quaternary structure

Part of an amnio acid's core structure that varies from a single hydrogen atom to large structures containing carbon rings. R-group variability is responsible for the variability in amino acid structure and function. Also called side chains.

R-group

Can occur only when a polypeptide bends do that C=O and N-H groups are close together.

Secondary structure

In proteins, localized folding of a polypeptide chain into regular structures (i.e., alpha-helices and beta-pleated sheets) stabilized by hydrogen bonding between atoms of the peptide backbone. In nucleic acids, elements of structure (e.g., helices and hairpins) stabilized by hydrogen bonding between complementary bases and hydrophobic interactions with the aqueous environment.

Secondary structure

Protein _______ _________ is formed by hydrogen bonds between groups forming the peptide bonds. -The carbonyl group of one amino acid -The amino group of another amino acid

Secondary structure

Part of an amino acid's core structure that varies from a single hydrogen atom to large structures containing carbon rings. R-group variability is responsible for the variability in amino acid structure and function.

Side chain

(1) A reactant that interacts with a catalyst, such as an enzyme or ribozyme, in a chemical reaction. (2) A surface on which a cell or organism sits.

Substrate

A distinctive three-dimensional shape of the polypeptide that results from the interactions between R-groups or between R-groups and the peptide backbone.

Tertiary structure

The overall three dimensional shape of a single polypeptide chain, resulting from multiple interactions among the amino acid side chains and the peptide backbone. In nucleic acids, three-dimensional shape is formed by hydrogen bonding between complementary bases and other interactions.

Tertiary structure

Amino acids polymerize when a bond forms between the _______ ____ of one amino acid and an _______ _____ of another. (C-N bond, peptide bond)

carboxyl group, amino group