Proteins

Copyright © 2005 Pearson Education, Inc. publishing as 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 [Animations are listed on slides that follow the figure]

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Animation: Structural Proteins Animation: Structural Proteins Animation: Storage Proteins Animation: Storage Proteins Animation: Transport Proteins Animation: Transport Proteins Animation: Receptor Proteins Animation: Receptor Proteins Animation: Contractile Proteins Animation: Contractile Proteins Animation: Defensive Proteins Animation: Defensive Proteins Animation: Enzymes Animation: Enzymes

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Animation: Hormonal Proteins Animation: Hormonal Proteins Animation: Sensory Proteins Animation: Sensory Proteins Animation: Gene Regulatory Proteins Animation: Gene Regulatory Proteins

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Enzymes are a type of protein that acts as a catalyst, speeding up chemical reactions Enzymes can perform their functions repeatedly, functioning as workhorses that carry out the processes of life

LE 5-16 Substrate (sucrose) Enzyme (sucrose) Fructose Glucose

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Polypeptides Polypeptides are polymers of amino acids A protein consists of one or more polypeptides

Copyright © 2005 Pearson Education, Inc. publishing as 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 Cells use 20 amino acids to make thousands of proteins

LE 5-UN78 Amino group Carboxyl group  carbon

LE 5-17a Isoleucine (Ile) Methionine (Met) Phenylalanine (Phe) Tryptophan (Trp) Proline (Pro) Leucine (Leu) Valine (Val) Alanine (Ala) Nonpolar Glycine (Gly)

LE 5-17b Asparagine (Asn) Glutamine (Gln)Threonine (Thr) Polar Serine (Ser) Cysteine (Cys) Tyrosine (Tyr)

LE 5-17c Electrically charged Aspartic acid (Asp) Acidic Basic Glutamic acid (Glu) Lysine (Lys)Arginine (Arg) Histidine (His)

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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 monomers to more than a thousand Each polypeptide has a unique linear sequence of amino acids

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Determining the Amino Acid Sequence of a Polypeptide The amino acid sequences of polypeptides were first determined by chemical methods Most of the steps involved in sequencing a polypeptide are now automated

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Protein Conformation and Function A functional protein consists of one or more polypeptides twisted, folded, and coiled into a unique shape The sequence of amino acids determines a protein’s three-dimensional conformation A protein’s conformation determines its function Ribbon models and space-filling models can depict a protein’s conformation

LE 5-19 A ribbon model Groove A space-filling model

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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 Animation: Protein Structure Introduction

LE 5-20 Amino acid subunits  pleated sheet + H 3 N Amino end  helix

Copyright © 2005 Pearson Education, Inc. publishing as 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 Animation: Primary Protein Structure

LE 5-20a Amino acid subunits Carboxyl end Amino end

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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 alpha helix and a folded structure called a beta pleated sheet Animation: Secondary Protein Structure Animation: Secondary Protein Structure

LE 5-20b Amino acid subunits  pleated sheet  helix

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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 conformation Animation: Tertiary Protein Structure Animation: Tertiary Protein Structure

LE 5-20d Hydrophobic interactions and van der Waals interactions Polypeptide backbone Disulfide bridge Ionic bond Hydrogen bond

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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 Animation: Quaternary Protein Structure

LE 5-20e  Chains  Chains Hemoglobin Iron Heme Collagen Polypeptide chain Polypeptide chain

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Sickle-Cell Disease: A Simple Change in Primary Structure A slight change in primary structure can affect a protein’s conformation and ability to function Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin

LE 5-21a Red blood cell shape Normal cells are full of individual hemoglobin molecules, each carrying oxygen. 10 µm Red blood cell shape Fibers of abnormal hemoglobin deform cell into sickle shape.

LE 5-21b Primary structure Secondary and tertiary structures Normal hemoglobin Val His Leu 4 Thr 5 Pro 6 Glu 7 Primary structure Secondary and tertiary structures Sickle-cell hemoglobin Val His Leu 4 Thr 5 Pro 6 ValGlu 7 Quaternary structure Normal hemoglobin (top view)         Function Molecules do not associate with one another; each carries oxygen. Quaternary structure Sickle-cell hemoglobin Function Molecules interact with one another to crystallize into a fiber; capacity to carry oxygen is greatly reduced. Exposed hydrophobic region  subunit

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings What Determines Protein Conformation? In addition to primary structure, physical and chemical conditions can affect conformation Alternations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel This loss of a protein’s native conformation is called denaturation A denatured protein is biologically inactive

LE 5-22 Denaturation Renaturation Denatured proteinNormal protein

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The Protein-Folding Problem It is hard to predict a protein’s conformation from its primary structure Most proteins probably go through several states on their way to a stable conformation Chaperonins are protein molecules that assist the proper folding of other proteins

LE 5-23a Chaperonin (fully assembled) Hollow cylinder Cap

LE 5-23b Polypeptide Correctly folded protein An unfolded poly- peptide enters the cylinder from one end. Steps of Chaperonin Action: The cap comes off, and the properly folded protein is released. The cap attaches, causing the cylinder to change shape in such a way that it creates a hydrophilic environment for the folding of the polypeptide.

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Scientists use X-ray crystallography to determine a protein’s conformation Another method is nuclear magnetic resonance (NMR) spectroscopy, which does not require protein crystallization

LE 5-24a Photographic film Diffracted X-rays X-ray source X-ray beam X-ray diffraction pattern Crystal

LE 5-24b Nucleic acid 3D computer model X-ray diffraction pattern Protein