Concept.4: Proteins have many structures, resulting in a wide range of functions Proteins account for more than 0% of the dry mass of most cells Protein functions include structural support, storage, transport, cellular communications, movement, and defense against foreign substances Table 1 hydrolytic enzymes Enzymes are a type of protein that acts as a catalyst to speed up chemical reactions Enzymes can perform their functions repeatedly, functioning as workhorses that carry out the processes of life Animation: Enzymes Protiens Chapter 1
Fig. 16 Substrate (sucrose) Glucose OH Fructose H O Enzyme (sucrase) H 2 O Enzyme Substrate Complex Induced fit model of enzyme activity Polypeptides Polypeptides are polymers built from the same set of 20 amino acids A protein consists of one or more polypeptides ADH = l chain Hemoglobin = 4 chains polypeptide chain is a string of amino acids An active protein might be one chain or many chains Amino Acid Monomers Amino acids are organic molecules with carboxyl and amino groups Amino acids differ in their properties due to differing side chains, called R groups Protiens Chapter 2
Fig. UN1 carbon Amino group Carboxyl group Fig. 17 Nonpola r Glycine (Gly or G) Alanine (Ala or A) Valine (Val or V) Leucine (Leu or L) Isoleucin e (Ile or I) Methionin e (Met or M) Phenylalanin Trypotphan e (Trp or W) (Phe or F) Pola r Proline (Pro or P) Serine Threonine Cysteine Tyrosine Asparagin Glutamin (Ser or (Thr or T) (Cys or C) (Tyr or Y) e e S) (Asn or N) (Gln or Q) Electricall y Acidi charged Basi c c Aspartic acid (Asp or D) Glutamic acid (Glu or E) Lysine Arginine Histidine (Lys or K) (Arg or R) (His or H) Aug 13 8:47 AM Protiens Chapter 3
Fig. 17a Nonpolar Glycine (Gly or G) Alanine (Ala or A) Valine (Val or V) Leucine (Leu or L) Isoleucine (Ile or I) Methionine (Met or M) Phenylalanine (Phe or F) Tryptophan (Trp or W) Proline (Pro or P) Fig. 17c Acidic Electrically charged Basic Aspartic acidglutamic acid (Asp or D) (Glu or E) Lysine (Lys or K) Arginine (Arg or R) Histidine (His or H) Amino Acid Polymers Amino acids are linked by peptide bonds A polypeptide is a polymer of amino acids Polypeptides range in length from a few to more than a thousand monomers Each polypeptide has a unique linear sequence of amino acids Protiens Chapter 4
Fig. 18 Peptide bond (a) Peptide bond Side chains Backbone (b) Amino end (N terminus) Carboxyl end (C terminus) Protein Structure and Function A functional protein consists of one or more polypeptides twisted, folded, and coiled into a unique shape Fig. 19 Groove Groove (a) A ribbon model of lysozyme (b) A space filling model of lysozyme Protiens Chapter
Fig. 19a Groove (a) A ribbon model of lysozyme Fig. 19b Groove (b) A space filling model of lysozyme The sequence of amino acids determines a protein s three dimensional structure A protein s structure determines its function Protiens Chapter 6
Fig. 20 Antibody protein Protein from flu virus Four Levels of Protein Structure The primary structure of a protein is its unique sequence of amino acids Secondary structure, found in most proteins, consists of coils and folds in the polypeptide chain Tertiary structure is determined by interactions among various side chains (R groups) Quaternary structure results when a protein consists of multiple polypeptide chains Animation: Protein Structure Introduction 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 Animation: Primary Protein Structure Protiens Chapter 7
1 8 10 0 12 0 1 9 2 0 8 0 11 1 0 7 12 10 9 0 11 0 2 AP Bio Fig. 21 Primary Structure Secondary Structure Tertiary Structure Quaternary Structure pleated sheet + H3N Amino end Examples of amino acid subunits helix Fig. 21a Primary Structure 1 + H3 N Amino end 10 1 Amino acid subunits 20 2 Fig. 21b + H3N Amino end Amino acid subunits Carboxyl end Protiens Chapter 8
The coils and folds of secondary structure result from hydrogen bonds between repeating constituents of the polypeptide backbone Typical secondary structures are a coil called an helix and a folded structure called a pleated sheet Animation: Secondary Protein Structure Fig. 21c pleated sheet Secondary Structure Examples of amino acid subunits helix Fig. 21d Abdominal glands of the spider secrete silk fibers made of a structural protein containing b pleated sheets. The radiating strands, made of dry silk fibers, maintain the shape of the web. The spiral strands (capture strands) are elastic, stretching in response to wind, rain, and the touch of insects. Protiens Chapter 9
Tertiary structure is determined by interactions between R groups, rather than interactions between backbone constituents These interactions between R groups include hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions Strong covalent bonds called disulfide bridges may reinforce the protein s structure Animation: Tertiary Protein Structure Fig. 21e Tertiary Structure Quaternary Structure Fig. 21f Hydrogen bond Hydrophobic interactions and van der Waals interactions Polypeptide backbone Disulfide bridge Ionic bond Protiens Chapter 10
Fig. 21g Polypeptide chain Chains Iron Heme Collagen Chains Hemoglobin 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 Animation: Quaternary Protein Structure Sickle Cell Disease: A Change in Primary Structure A slight change in primary structure can affect a protein s structure and ability to function Sickle cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin Protiens Chapter 11
Fig. 22 Primary structur e Secondary and tertiary structures Normal Valhemoglobin His LeuThr Pro Glu Glu 1 2 3 4 6 7 subuni t Primary structur e Secondary and tertiary structures Sickle cell hemoglobin Val His Leu Thr Pro Val Glu 1 2 3 4 6 7 Exposed hydrophobi c subuni region t Quaternar y structure Normal hemoglobi n (top view) Quaternar y structure Sickle cell hemoglobi n Functio n Red blood cell shape Molecules do not associate with one another; each carries oxygen. Normal red blood cells are full of individual hemoglobin moledules, each carrying oxygen. 10 µm Functio n Red blood cell shape Molecules interact with one another and crystallize into a fiber; capacity to carry oxygen is greatly reduced. Fibers of abnormal hemoglobin deform red blood cell into sickle shape. 10 µm Fig. 22a Primary structur e Secondary and tertiary structures Normal hemoglobin Va His Le Th Pr Glu Glu l1 2 u3 r4 o 6 7 subuni t Quaternary structure Normal hemoglobin (top view) Function Molecules do not associate with one another; each carries oxygen. Fig. 22b Primary structur e Secondary and tertiary structures Exposed hydrophobic region Sickle cell hemoglobin Va His Le Th Pr Va Glu l1 2 u3 r4 o l6 7 subuni t Quaternary structure Sickle cell hemoglobin Function Molecules interact with one another and crystallize into a fiber; capacity to carry oxygen is greatly reduced. Protiens Chapter 12
Fig. 22c 10 µm 10 µm Normal red blood cells are full of individual hemoglobin molecules, each carrying oxygen. Fibers of abnormal hemoglobin deform red blood cell into sickle shape. 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 is biologically inactive Fig. 23 Denaturation Normal protein Renaturation Denatured protein Protiens Chapter 13
Protein Folding in the Cell It is hard to predict a protein s structure from its primary structure Most proteins probably go through several states on their way to a stable structure Chaperonins are protein molecules that assist the proper folding of other proteins Protiens Chapter 14