The Structure and Function of Macromolecules Chapter Proteins

2 Macromolecules: The Molecules of Life Carbohydrates Carbohydrates Nucleic Acids Nucleic Acids Proteins Proteins Lipids Lipids

3 Proteins Polypeptides -- polymers of amino acids Polypeptides -- polymers of amino acids Protein -- one or more polypeptides Protein -- one or more polypeptides Proteins -- many structures with wide range of functions Proteins -- many structures with wide range of functions Proteins -- more than 50% of the dry mass of most cells Proteins -- more than 50% of the dry mass of most cells Proteins -- include structural support, storage, transport, cellular communications, movement, and defense against foreign substances Proteins -- include structural support, storage, transport, cellular communications, movement, and defense against foreign substances

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5 Amino Acid Monomers Organic molecules with carboxyl and amino groups Organic molecules with carboxyl and amino groups Different properties due to differing side chains, called R groups Different properties due to differing side chains, called R groups 20 amino acids to make thousands of proteins 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)

10 Amino Acid Polymers Amino acids -- linked by peptide bonds Amino acids -- linked by peptide bonds A polypeptide -- polymer of amino acids A polypeptide -- polymer of amino acids Polypeptide length -- few monomers to more than a thousand Polypeptide length -- few monomers to more than a thousand Each polypeptide has a unique linear sequence of amino acids Each polypeptide has a unique linear sequence of amino acids

11 Determining the Amino Acid Sequence of a Polypeptide First determined by chemical methods First determined by chemical methods Now? Mostly automated – DNA sequencer Now? Mostly automated – DNA sequencer

LE 5-20a Amino acid subunits Carboxyl end Amino end Primary structure unique sequence of amino acids unique sequence of amino acids

13 LE 5-20b Secondary structure Interactions between backbone components Interactions between backbone components  Hydrogen bonds  Typical secondary structures are coils (alpha helix) and a folded structure (beta pleated sheet) Amino acid subunits  pleated sheet  helix

14 LE 5-20d Hydrophobic interactions and van der Waals interactions Polypeptide backbone Disulfide bridge Ionic bond Hydrogen bond Tertiary Structure Interactions between R groups Interactions between R groups  Include hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions  Disulfide bridges may reinforce the protein’s conformation

15 Four Levels of Protein Structure Primary structure -- unique sequence of amino acids Primary structure -- unique sequence of amino acids Secondary structure – interactions between backbone components Secondary structure – interactions between backbone components Tertiary structure -- interactions between various side chains (R groups) Tertiary structure -- interactions between various side chains (R groups) Quaternary structure – proteins consisting of multiple polypeptide chains Quaternary structure – proteins consisting of multiple polypeptide chains

16 Collagen is a fibrous protein consisting of three polypeptides coiled like a rope 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 Hemoglobin is a globular protein consisting of four polypeptides: two alpha and two beta chains Proteins with Quaternary Structure

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18 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 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 Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin 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

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

21 Conformation and Function Conformation – 3-D shape Conformation – 3-D shape Functional protein -- one or more polypeptides twisted, folded, and coiled into a unique shape Functional protein -- one or more polypeptides twisted, folded, and coiled into a unique shape Sequence -- determines a protein’s three- dimensional conformation Sequence -- determines a protein’s three- dimensional conformation Conformation -- determines its function Conformation -- determines its function Ribbon models and space-filling models can depict a protein’s conformation Ribbon models and space-filling models can depict a protein’s conformation

22 What Determines Protein Conformation? In addition to primary structure, physical and chemical conditions can affect 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 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 This loss of a protein’s native conformation is called denaturation A denatured protein is biologically inactive A denatured protein is biologically inactive

LE 5-22 Denaturation Renaturation Denatured proteinNormal protein

24 The Protein-Folding Problem Prediction of conformation is non-trivial Prediction of conformation is non-trivial  Thousands of possible conformations! Most proteins probably go through several states on their way to a stable conformation Most proteins probably go through several states on their way to a stable conformation Chaperonins assist the proper folding of other proteins Chaperonins 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.

27 Scientists use X-ray crystallography to determine a protein’s conformation 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 Another method is nuclear magnetic resonance (NMR) spectroscopy, which does not require protein crystallization

3D computer model X-ray diffraction pattern

29 The Flow of Genetic Information The information content -- DNA sequence The information content -- DNA sequence DNA – directs synthesis of proteins DNA – directs synthesis of proteins Gene manufacture Gene manufacture  Transcription  Translation Ribosome -- where translation happens Ribosome -- where translation happens

30 LE 17-4 DNA molecule Gene 1 Gene 2 Gene 3 DNA strand (template) 3 TRANSCRIPTION Codon mRNA TRANSLATION Protein Amino acid 3 5 5

31 Nutritional Mutants in Neurospora Beadle and Tatum – irradiated mold resulting in inability to synthesize certain molecules Beadle and Tatum – irradiated mold resulting in inability to synthesize certain molecules  Three classes of arginine-deficient mutants  3 different enzymes necessary for synthesizing arginine “One gene–one enzyme” hypothesis “One gene–one enzyme” hypothesis

32 The Products of Gene Expression: A Developing Story Not all proteins are enzymes! Not all proteins are enzymes! One gene–one protein One gene–one protein Quaternary structure -- each component needs its own gene Quaternary structure -- each component needs its own gene  ATP synthase has 16 subunits! Now -- Beadle and Tatum’s hypothesis “one gene–one polypeptide” Now -- Beadle and Tatum’s hypothesis “one gene–one polypeptide”

33 Basic Principles of Transcription and Translation Transcription -- synthesis of RNA under the direction of DNA Transcription -- synthesis of RNA under the direction of DNA  produces messenger RNA (mRNA)  “language” of DNA to “language” of RNA Translation -- synthesis of a polypeptide under the direction of mRNA Translation -- synthesis of a polypeptide under the direction of mRNA  Ribosomes are the sites of translation  “language” of Nucleic Acids to “language” of Amino Acids

34 LE 17-4 DNA molecule Gene 1 Gene 2 Gene 3 DNA strand (template) 3 TRANSCRIPTION Codon mRNA TRANSLATION Protein Amino acid 3 5 5

35 DNA to RNA DNA in eukaryotes is in the nucleus DNA in eukaryotes is in the nucleus Protein synthesis occurs at ribosomes in the cytoplasm Protein synthesis occurs at ribosomes in the cytoplasm DNA information -- from nucleus to cytoplasm DNA information -- from nucleus to cytoplasm  intermediary (RNA)

36 RNA Intermediaries

37 A ribosome has three binding sites for tRNA: A ribosome has three binding sites for tRNA:  P site -- holds the tRNA  The A site -- holds the tRNA with next amino acid  The E site -- exit site, where discharged tRNAs leave the ribosome