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Macromolecules of Life Proteins and Nucleic Acids Chapter 5 You already know a lot about proteins! You’ve been working with them in lab for the past 2-3 weeks! • Biuret – [protein] • Gel Electrophoresis • Enzymes Protein Definition • Consists of one or more polypeptides folded, coiled, and twisted into a specific 3D shape • Proteios – “first place” • There are many different shapes of proteins depending on its FUNCTION – – – – – – Enzymes Cell signaling Defense Structural support Transport Receptors Two similar terms • Protein – already defined • Polypeptide – polymer made of repeating subunits of amino acids (monomer) – usually refers to a long linear strand of amino acids that will then get folded into a 3D shape (protein) Fig. 5-2a HO 1 2 3 H Short polymer HO Unlinked monomer Dehydration removes a water molecule, forming a new bond HO 1 H 2 3 H2O 4 H Longer polymer (a) Dehydration reaction in the synthesis of a polymer Fig. 5-2b HO 1 2 3 4 Hydrolysis adds a water molecule, breaking a bond HO (b) 1 2 Hydrolysis of a polymer 3 H H2O H HO H Fig. 5-UN1 carbon Amino group Carboxyl group Fig. 5-17 Nonpolar Glycine (Gly or G) Valine (Val or V) Alanine (Ala or A) Methionine (Met or M) Leucine (Leu or L) Trypotphan (Trp or W) Phenylalanine (Phe or F) Isoleucine (Ile or I) Proline (Pro or P) Polar Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) Tyrosine (Tyr or Y) Asparagine Glutamine (Asn or N) (Gln or Q) Electrically charged Acidic Aspartic acid Glutamic acid (Glu or E) (Asp or D) Basic Lysine (Lys or K) Arginine (Arg or R) Histidine (His or H) Fig. 5-17a Nonpolar Glycine (Gly or G) Methionine (Met or M) Alanine (Ala or A) Valine (Val or V) Phenylalanine (Phe or F) Leucine (Leu or L) Tryptophan (Trp or W) Isoleucine (Ile or I) Proline (Pro or P) Fig. 5-17b Polar Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) Tyrosine (Tyr or Y) Asparagine Glutamine (Asn or N) (Gln or Q) Fig. 5-17c Electrically charged Acidic Aspartic acid Glutamic acid (Glu or E) (Asp or D) Basic Lysine (Lys or K) Arginine (Arg or R) Histidine (His or H) Fig. 5-18 Peptide bond (a) Side chains Peptide bond Backbone (b) Amino end (N-terminus) Carboxyl end (C-terminus) Fig. 5-UN5 Fig. 5-21 Primary Structure Secondary Structure pleated sheet +H N 3 Amino end Examples of amino acid subunits helix Tertiary Structure Quaternary Structure Fig. 5-21a Primary Structure 1 5 H3N Amino end + 10 Amino acid subunits 15 20 25 Fig. 5-21b 1 5 +H 3N Amino end 10 Amino acid subunits 15 20 25 75 80 90 85 95 105 100 110 115 120 125 Carboxyl end Fig. 5-21c Secondary Structure pleated sheet Examples of amino acid subunits helix Fig. 5-21f Hydrophobic interactions and van der Waals interactions Polypeptide backbone Hydrogen bond Disulfide bridge Ionic bond Fig. 5-21e Tertiary Structure Quaternary Structure Fig. 5-21g Polypeptide chain Chains Iron Heme Chains Hemoglobin Collagen Fig. 5-22a Normal hemoglobin Primary structure Val His Leu Thr Pro Glu Glu 1 2 3 4 5 7 6 Secondary and tertiary structures subunit Quaternary structure Normal hemoglobin (top view) Function Molecules do not associate with one another; each carries oxygen. Fig. 5-22b Sickle-cell hemoglobin Primary structure Secondary and tertiary structures Val His Leu Thr Pro Val Glu 1 2 3 4 5 6 7 Exposed hydrophobic region subunit Quaternary structure Sickle-cell hemoglobin Function Molecules interact with one another and crystallize into a fiber; capacity to carry oxygen is greatly reduced. Fig. 5-22c 10 µm Normal red blood cells are full of individual hemoglobin molecules, each carrying oxygen. 10 µm 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 5-23 Denaturation Normal protein Renaturation Denatured protein The Roles of Nucleic Acids • There are two types of nucleic acids: – Deoxyribonucleic acid (DNA) – Ribonucleic acid (RNA) • DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis • Protein synthesis occurs in ribosomes Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 5-26-3 DNA 1 Synthesis of mRNA in the nucleus mRNA NUCLEUS CYTOPLASM mRNA 2 Movement of mRNA into cytoplasm via nuclear pore Ribosome 3 Synthesis of protein Polypeptide Amino acids Fig. 5-27ab 5' end 5'C 3'C Nucleoside Nitrogenous base 5'C Phosphate group 5'C 3'C (b) Nucleotide 3' end (a) Polynucleotide, or nucleic acid 3'C Sugar (pentose) Fig. 5-27c-1 Nitrogenous bases Pyrimidines Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA) Purines Adenine (A) Guanine (G) (c) Nucleoside components: nitrogenous bases Fig. 5-27c-2 Sugars Deoxyribose (in DNA) Ribose (in RNA) (c) Nucleoside components: sugars Nucleotide Polymers • Adjacent nucleotides are joined by covalent bonds (phosphodiester linkage) • The nitrogenous bases in DNA pair up and form hydrogen bonds: – adenine (A) always with thymine (T) – guanine (G) always with cytosine (C) • Forms a double helix Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 5-28 5' end 3' end Sugar-phosphate backbones Base pair (joined by hydrogen bonding) Old strands Nucleotide about to be added to a new strand 3' end 5' end New strands 5' end 3' end 5' end 3' end