Exam 1 Review:  Chapter 2 - Proteins and Enzymes

protein - Any of a group of complex organic macromolecules which contain carbon, hydrogen, oxygen, nitrogen, and usually sulfur; they are polymers composed of one or more chains of amino acids linked covalently by peptide bonds; their three dimensional structure is complex and categorized into four structural levels, primary, secondary, tertiary, and quaternary; they are fundamental components of all living cells and include many functional types, such as structural fibers, membrane transporters, enzymes, hormones and other signal compounds, and antibodies and other immune compounds, which are necessary for the proper functioning of an organism; they are essential in the diet for the growth and repair of tissue and can be obtained from foods such as meat, fish, eggs, milk, and legumes.

amino acids - Any organic compound containing an amino group (NH₂), a carboxylic acid group (COOH), and any of various side groups ("R groups"); especially any of the 20 compounds that have the basic formula NH₂CHRCOOH, and that link together by peptide bonds to form proteins or that function as chemical messengers and as intermediates in metabolism.

peptide bonds - The characteristic covalent chemical bonds formed by dehydration synthesis between the carboxyl groups and amino groups of neighboring amino acids, establishing the initial linear linkages of the polypeptide chain, and representing the primary level of structural arrangement in the hierarchy of all protein structures.

primary structure - In the hierarchy of protein structure, the first level - determined by the covalent peptide bonds between adjacent amino acids which produces the linear polypeptide chain.

secondary structure - In the hierarchy of protein structure, the second level, which is determined by the (usually hydrogen) bonds between adjacent or nearby amino acids; examples are the α-helix, β-pleated sheet, and random coil.

tertiary structure - The bonding relationships between distant amino acids which determine the larger three-dimensional bending and folding of the protein into its complex functional shape; the third level in the hierarchy of protein structure.

quaternary structure - In the hierarchy of protein structure, the fourth level - determined by the bonds, either covalent or non-covalent, between amino acids on different polypeptide chains; only those proteins whose functional whole is composed of two or more polypeptide chains exhibit quaternary structure.

enzyme - Complex proteins which are produced by cells and act as organic catalysts in specific biochemical/metabolic reactions.

catalyst - Any substance, usually used in small amounts relative to the reactants, which modifies and usually increases the rate of a reaction without being consumed in the process and, ads a result, enables a chemical reaction to proceed under different conditions (as at a lower temperature) than otherwise possible.

substrate (enzyme) - The general term for a molecule which acts as a reactant in an enzyme catalyzed reaction; it is attracted to the enzyme active site and positioned to have an ideal orientation to undergo the chemical reaction being catalyzed.

active site (enzyme) - The portion of an enzyme, usually a depression or groove at one small part on the surface of the enzyme molecule, at which substrate(s) bind and where catalysis of the substrate(s) occurs; binding of the substrate(s) is determined by the specific three-dimensional fit between the substrate molecules(s) and the dimensions of the site as well as by compatible attractive forces such as opportunities for hydrogen or ionic bonding between substrate(s) and the site; such sites are typically very substrate specific, i.e., they accept only one or a very limited number of very similar substrate molecules; its binding and catalytic properties are determined by the specific sequence of amino acids at the site and their three-dimensional arrangement.

enzyme-substrate complex - The name given to the brief and reversible multi-molecular aggregate structure composed of the protein catalyst bound with its substrate(s); the bonding may consist of a variety of different types of bonds from the weakest hydrophobic attractions up to the temporary formation of new covalent bonds.

enzyme + substrate(s) Û enzyme-substrate(s) complex Û enzyme + product(s)

product (enzyme) - The general term for a  molecule which is formed as an output in an enzyme catalyzed reaction; it is created and released from the enzyme active site.

denaturation - (1) To cause the structure of (a protein) to unfold or be rearranged, usually at the secondary, tertiary or quaternary levels, by a change in temperature, the addition of an organic solvent or a detergent, or by a change in the pH or electrolyte/salt mix in the medium, so that some of its original properties, especially its biological activity, are diminished or eliminated; the process may be reversible or irreversible.  (2)  To cause the paired strands of (double-stranded DNA) to separate into individual single strands, usually by the gentle application of heat; the process is usually reversible.

List:

 8. four examples of major functions for protein molecules.

          (1) structural components of cytoplasm, cellular membranes and intercellular materials
          (2) oxygen storage/transport compounds
          (3) regulatory molecules = signal compounds
          (4) catalysts for biochemical reactions
          (5) immune defensive compounds
          (6) membrane and plasma transport compounds

 9. 4 levels of protein structure.

          primary - secondary - tertiary - quaternary

Describe:

2. the important differences between fibrous and globular proteins, and examples of each.

 

	Fibrous Proteins	Globular Proteins
important differences	shape:  long and thin less soluble in water	shape:  compact and relatively spherical more soluble in water
examples	collagen, elastin, actin, myosin, fibrin, etc.	hemoglobin, myoglobin, enzymes, most membrane proteins, albumin and most plasma proteins, etc.

Sketch and Label:

2. an enzyme-catalyzed reaction sequence.

 

A + B + enzyme Û intermediate A-B-enzyme complex Û C + D + enzyme (unchanged)