Concept 5.4: Proteins have many structures, resulting in a wide range of functions Proteins account for more than 50% of the dry mass of most cells Proteins have more chemical and physical versatility than any other type of macromolecule Protein functions include structural support, storage, transport, cellular communications, movement, and defense against foreign substances

These are examples of protein function Proteins can do so many different things because they are chemically and physically versatile Table 5-1

Enzymes are probably the most important type of protein Enzymes are probably the most important type of protein. They act as catalysts to speed up chemical reactions Enzymes can perform their functions repeatedly, functioning as workhorses that carry out the processes of life

Proteins are polypeptides Polypeptides are polymers built from a set of 20 amino acid monomers All cells use the same set of 20 amino acids to construct their proteins A protein consists of one or more polypeptides

Amino Acid Monomers Amino acids are small organic molecules with both carboxyl and amino functional groups They also have side chains called R groups Amino acids differ based on R group properties

Some R groups are nonpolar or hydrophobic Glycine (Gly or G) Alanine (Ala or A) Valine (Val or V) Leucine (Leu or L) Isoleucine (Ile or I) Figure 5.17 The 20 amino acids of proteins Methionine (Met or M) Phenylalanine (Phe or F) Tryptophan (Trp or W) Proline (Pro or P)

Some R groups are polar Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) Tyrosine (Tyr or Y) Asparagine (Asn or N) Glutamine (Gln or Q) Figure 5.17 The 20 amino acids of proteins

Some R groups are so polar that they have an electric charge under cellular conditions Acidic Basic Figure 5.17 The 20 amino acids of proteins Aspartic acid (Asp or D) Glutamic acid (Glu or E) Lysine (Lys or K) Arginine (Arg or R) Histidine (His or H)

Amino Acids in Polymers A polypeptide is a polymer of amino acids that are linked by peptide bonds Polypeptides range in length from a few to more than a thousand monomers Each type of polypeptide has a unique linear sequence of amino acids

Peptide Bond Formation Condensation reaction Peptide bond (a) Side chains or R groups Peptide bond Figure 5.18 Making a polypeptide chain Backbone Amino end (N-terminus) Carboxyl end (C-terminus) (b)

Properties of Amino Acid Polymers Two distinct ends or termini: carboxy and amino Backbone of peptide bonds, strong covalent bond Chemical properties influenced by sum total of R groups Exact order or sequence of amino acids influences shape and biological properties

A ribbon model of lysozyme A space-filling model of lysozyme Lysozyme is the name of one important protein Groove Groove Figure 5.19 Structure of a protein, the enzyme lysozyme A ribbon model of lysozyme A space-filling model of lysozyme Ribbon diagram shows position of backbone Space filling shows all atoms

A protein’s structure determines its function The sequence of amino acids determines a protein’s three-dimensional structure A protein’s structure determines its function Antibody protein Protein from flu virus Figure 5.20 An antibody binding to a protein from a flu virus

A Hierarchy of Four Levels of Protein Structure The primary structure of a protein is its unique sequence of amino acids (1o) Secondary structure, found in most proteins, consists of coils and folds in the polypeptide chain (2o) Tertiary structure is determined by interactions among various side chains (R groups) (3o) Quaternary structure results when a protein consists of multiple polypeptide chains (4o)

Primary structure, the sequence of amino acids in a protein, is like the order of letters in a long word Primary structure is determined by inherited genetic information

+H3N Primary Structure Amino end Amino acid subunits 1 5 10 15 20 25 Figure 5.21 Levels of protein structure—primary structure 20 25

The coils and folds of secondary structure result from hydrogen bonds between repeating constituents of the polypeptide backbone Usually the interactions are among amino acids that are close to one another in the primary structure Typical secondary structures are a coil called an  helix and a folded structure called a  pleated sheet For the Cell Biology Video An Idealized Alpha Helix: No Sidechains, go to Animation and Video Files. For the Cell Biology Video An Idealized Alpha Helix, go to Animation and Video Files. For the Cell Biology Video An Idealized Beta Pleated Sheet Cartoon, go to Animation and Video Files. For the Cell Biology Video An Idealized Beta Pleated Sheet, go to Animation and Video Files.

Also possible for a part of a protein to have no particular secondary Secondary structure Beta pleated sheet Examples of amino acid subunits Figure 5.21 Levels of protein structure—secondary structure Alpha helix Also possible for a part of a protein to have no particular secondary structure

Tertiary structure is determined by interactions between R groups, not between backbone constituents (aka conformation or configuration) Refers to overall shape in space These interactions between R groups include hydrogen bonds, ”ionic bonds”, hydrophobic interactions, and van der Waals interactions May be interactions between R groups on widely-separated amino acids Covalent bonds called disulfide bridges may reinforce the protein’s structure

Hydrophobic interactions and van der Waals interactions Polypeptide backbone Hydrogen bond Disulfide bridge Figure 5.21 Levels of protein structure—tertiary and quaternary structures Ionic bond

Quaternary structure results when two or more polypeptide chains form one macromolecule Collagen is a fibrous protein consisting of three polypeptides coiled like a rope Hemoglobin is a globular protein consisting of four polypeptides: two alpha and two beta chains (the chains also associate with a non-amino acid chemical-iron) Some polypeptides do not have any quaternary structure. Some have it only part of the time and not the rest

Polypeptide Beta Chains chain Iron Heme Alpha Chains Hemoglobin Figure 5.21 Levels of protein structure—tertiary and quaternary structures Heme Alpha Chains Hemoglobin Collagen

Some images of Quaternary structure

What Determines Protein Structure? In addition to primary structure, physical and chemical conditions can affect structure Alterations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel This loss of a protein’s native structure is called denaturation A denatured protein loses its ability to function properly

Denaturation Normal protein Denatured protein Renaturation Figure 5.23 Denaturation and renaturation of a protein Normal protein Denatured protein Renaturation

Cells have to devote significant attention to protein folding Chaperonins or chaperone proteins are used to help correct folding occur

An unfolded polypeptide enters the cylinder from one end. Cap attachment causes the cylinder to change shape, creating a hydrophilic environment for polypeptide folding. The cap comes off, and the properly folded protein is released. Chaperonin (fully assembled)