Proteins PDF

Chapter 5 The Structure and Function of Large Biological Molecules PowerPoint® Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions from Joan Sharp Copyright © 2008 Pearson Education, In...

Chapter 5 The Structure and Function of Large Biological Molecules PowerPoint® Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions from Joan Sharp Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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 Protein functions include structural support, storage, transport, cellular communications, movement, and defense against foreign substances Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Table 5-1  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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 5-16 Substrate (sucrose) Glucose Enzyme (sucrase) OH H2O Fructose HO Polypeptides Polypeptides are polymers built from the same set of 20 amino acids A protein consists of one or more polypeptides Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 5-UN1 carbon Amino Carboxyl group group Fig. 5-17 Nonpolar Glycine Alanine Valine Leucine Isoleucine (Gly or G) (Ala or A) (Val or V) (Leu or L) (Ile or I) Methionine Phenylalanine Trypotphan Proline (Met or M) (Phe or F) (Trp or W) (Pro or P) Polar Serine Threonine Cysteine Tyrosine Asparagine Glutamine (Ser or S) (Thr or T) (Cys or C) (Tyr or Y) (Asn or N) (Gln or Q) Electrically charged Acidic Basic Aspartic acid Glutamic acid Lysine Arginine Histidine (Asp or D) (Glu or E) (Lys or K) (Arg or R) (His or H) Fig. 5-17a Nonpolar Glycine Alanine Valine Leucine Isoleucine (Gly or G) (Ala or A) (Val or V) (Leu or L) (Ile or I) Methionine Phenylalanine Tryptophan Proline (Met or M) (Phe or F) (Trp or W) (Pro or P) Fig. 5-17b Polar Serine Threonine Cysteine Tyrosine Asparagine Glutamine (Ser or S) (Thr or T) (Cys or C) (Tyr or Y) (Asn or N) (Gln or Q) Fig. 5-17c Electrically charged Acidic Basic Aspartic acid Glutamic acid Lysine Arginine Histidine (Asp or D) (Glu or E) (Lys or K) (Arg or R) (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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 5-18 Peptide bond (a) Side chains Peptide bond Backbone Amino end Carboxyl end (b) (N-terminus) (C-terminus) Protein Structure and Function A functional protein consists of one or more polypeptides twisted, folded, and coiled into a unique shape Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 5-19 Groove Groove (a) A ribbon model of lysozyme (b) A space-filling model of lysozyme Fig. 5-19a Groove (a) A ribbon model of lysozyme Fig. 5-19b 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 5-20 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings  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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 5-21 Primary Secondary Tertiary Quaternary Structure Structure Structure Structure pleated sheet +H 3N Amino end Examples of amino acid subunits helix Fig. 5-21a Primary Structure 1 +H N 5 3 Amino end 10 15 Amino acid subunits 20 25 Fig. 5-21b 1 +H 5 3N Amino end 10 15 Amino acid subunits 20 25 75 80 85 90 95 105 100 110 115 120 125 Carboxyl end  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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 5-21c Secondary Structure pleated sheet Examples of amino acid subunits helix Fig. 5-21d Abdominal glands of the spider secrete silk fibers made of a structural protein containing 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.  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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 5-21e Tertiary Structure Quaternary Structure Fig. 5-21f Hydrophobic interactions and van der Waals interactions Polypeptide backbone Hydrogen bond Disulfide bridge Ionic bond Fig. 5-21g Polypeptide Chains chain Iron Heme Chains Hemoglobin Collagen  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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 5-22 Normal hemoglobin Sickle-cell hemoglobin Val His Leu Thr Pro Glu Glu Primary Primary Val His Leu Thr Pro Val Glu structure structure 1 2 3 4 5 6 7 1 2 3 4 5 6 7 Exposed Secondary Secondary hydrophobic and tertiary subunit and tertiary region subunit structures structures Quaternary Normal Quaternary Sickle-cell structure hemoglobin structure hemoglobin (top view) Function Molecules do Function Molecules not associate interact with with one one another and another; each crystallize into carries oxygen. a fiber; capacity to carry oxygen is greatly reduced. 10 µm 10 µm Red blood Normal red blood Red blood Fibers of abnormal cell shape cells are full of cell shape hemoglobin deform individual red blood cell into hemoglobin sickle shape. moledules, each carrying oxygen. Fig. 5-22a Normal hemoglobin Primary Val His Leu Thr Pro Glu Glu structure 1 2 3 4 5 6 7 Secondary and tertiary subunit structures Quaternary Normal structure hemoglobin (top view) Function Molecules do not associate with one another; each carries oxygen. Fig. 5-22b Sickle-cell hemoglobin Primary Val His Leu Thr Pro Val Glu structure 1 2 3 4 5 6 7 Exposed Secondary hydrophobic and tertiary region subunit structures Quaternary Sickle-cell structure hemoglobin Function Molecules interact with one another and crystallize into a fiber; capacity to carry oxygen is greatly reduced. Fig. 5-22c 10 µm 10 µm Normal red blood Fibers of abnormal cells are full of hemoglobin deform individual red blood cell into hemoglobin sickle shape. molecules, each carrying oxygen. 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 5-23 Denaturation Normal protein Renaturation Denatured protein 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 5-24 Correctly folded protein Polypeptide Cap Hollow cylinder Chaperonin Steps of Chaperonin 2 The cap attaches, causing the 3 The cap comes (fully assembled) Action: cylinder to change shape in off, and the properly 1 An unfolded poly- such a way that it creates a folded protein is peptide enters the hydrophilic environment for released. cylinder from one end. the folding of the polypeptide. Fig. 5-24a Cap Hollow cylinder Chaperonin (fully assembled) Fig. 5-24b Correctly folded protein Polypeptide Steps of Chaperonin 2 The cap attaches, causing the 3 The cap comes Action: cylinder to change shape in off, and the properly 1 An unfolded poly- such a way that it creates a folded protein is peptide enters the hydrophilic environment for released. cylinder from one end. the folding of the polypeptide.  Scientists use X-ray crystallography to determine a protein’s structure Another method is nuclear magnetic resonance (NMR) spectroscopy, which does not require protein crystallization Bioinformatics uses computer programs to predict protein structure from amino acid sequences Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 5-25 EXPERIMENT Diffracted X-rays X-ray source X-ray beam Crystal Digital detector X-ray diffraction pattern RESULTS RNA polymerase II DNA RNA Fig. 5-25a EXPERIMENT Diffracted X-rays X-ray source X-ray beam Crystal Digital detector X-ray diffraction pattern Fig. 5-25b RESULTS RNA polymerase II DNA RNA