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Proteins Chapter 3 A. P. Biology Mr. Knowles Liberty Senior High School Proteins are Most Common Functions of Proteins 1. Enzymes- Metabolism 2. Structural- Collagen and Keratin 3. Cell Recognition- proteins on cellular surface. 4. Regulation of Gene ExpressionGene Repressors or Enhancers. 5. Defense- Antibodies. • An overview of protein functions Table 5.1 Two Types of Proteins 1. Fibrous Proteins- rope-like, structural proteins; form shape of cells and tissues. Ex. Collagen-the most abundant protein of vertebrates. 2. Globular Proteins- have specific shapes for their functions. Ex. Enzymes and antibodies. 1. Proteins can be Structural 2. Proteins can be Globular X-ray crystallography: Is used to determine a protein’s threedimensional structure. X-ray diffraction pattern Photographic film Diffracted X-rays X-ray X-ray beam source Crystal Nucleic acid Figure 5.24 (a) X-ray diffraction pattern (b) 3D computer model Protein Papain Proteins • Most diverse organic compound. • Composed of amino acids- each with an amino group (NH2) and a carboxylic acid group (COOH). • Different chemical group(s) attached to central C- R group . Amino Acid Polymers • Amino acids – Are linked by peptide bonds Peptide OH bond OH SH CH2 CH2 H N H CH2 H C C H O N H C C H O OH H (a) N C C H O OH DESMOSOMES H2O OH DESMOSOMES DESMOSOMES CH2 CH2 H H H Figure 5.18 (b) N C C H O Amino end (N-terminus) N Side chains SH Peptide bond CH2 OH H C C H O N C C H O Carboxyl end (C-terminus) OH Backbone CH3 CH3 H H3N+ C CH3 O H3N+ C C H3N+ C CH CH3 CH3 O C CH3 CH3 CH2 CH2 O H3N+ C C O H3C H3N+ C • 20 different amino acids make up proteins O– O– O– CH O C C O– O– H H H H H Glycine (Gly) Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine (Ile) Nonpolar CH3 CH2 S NH CH2 CH2 H3N+ C CH2 O H3N+ C C Methionine (Met) Figure 5.17 H3 C O– O– H C N+ H Phenylalanine (Phe) CH2 H2N C O C O– CH2 O H2C O H C O– H Tryptophan (Trp) Proline (Pro) OH NH2 O C NH2 O OH Polar CH2 H3N+ C CH O H3N+ C O– H C CH2 O H3N+ C C CH2 O C H3N+ C Threonine (Thr) H3N+ C H Cysteine (Cys) Tyrosine (Tyr) O– O CH2 H3N+ C O H C C C O C O– O– H H Asparagine (Asn) H3N+ NH3+ O Glutamine (Gln) CH2 C CH2 CH2 CH2 CH2 CH2 CH2 CH2 C O C O– H H3N+ C O C NH2+ H3N+ C NH CH2 H3N+ C O C O– H CH2 O– H NH+ NH2 C CH2 C O– H3N+ Basic C Electrically charged CH2 O O– H Acidic –O CH2 CH2 O O– O– H Serine (Ser) C SH CH3 OH O C O– H Aspartic acid (Asp) Glutamic acid (Glu) Lysine (Lys) Arginine (Arg) Histidine (His) Amino Acids • Are the monomers of proteins. • Only 20 naturally occurring amino acids. • The R group gives each of the amino acids its unique property. • All 20 amino acids can be grouped into 5 basic groups. 5 Groups of Amino Acids (Fig. 3.15) 1. Nonpolar- have R groups that contain CH2 and CH3. 2. Polar Uncharged- R groups that have O or only H. 3. Ionizable- have R groups that are acids and bases. 4. Aromatic- R groups that have organic rings. 5 Groups of Amino Acids (Fig. 3.15) 5. Special-function- amino acids that are only used for very specific functions; methionine begins protein synthesis, proline causes kinks in the protein polymer, cysteine links chains together. The 20 Common Amino Acids (Fig. 3.15) Click below for another view! Proteins • Are polymers of amino acids. • Joined by peptide bonds. • Di- Tri- and Polypeptides. Globular Proteins • Are long amino acids chains folded into complex shapes. • All of the internal amino acids are nonpolar. • Water excludes nonpolar amino acids – hydrophobic interactions. Globular Proteins Have Four Levels of Structure 1. Primary- the specific sequence of amino acids in the polypeptide chain. • R groups have no role in the backbone, so any sequence of amino acids is possible. • Therefore, 100 amino acids may be rearranged in 20100 different possible sequences. Primary Structure: Is the unique sequence of amino acids in a polypeptide. Pro Gly Thr Gly Thr +H N 3 Gly Amino acid subunits Glu Amino end Pro Leu Seu Lys Cys Met Val Lys Val Leu Asp Ala Arg Val Gly Ser Pro Ala Glu Lle Asp Thr Lys Ser Trp Lys Ala Leu Gly Tyr lle Ser Pro Phe His Glu His Ala Glu Ala Asn Thr Phe Asp Val Arg Ser Gly Pro Val Tyr lle Thr Ala Ala Arg Leu Leu Thr Ser Tyr Ser Tyr Pro Ser Thr Ala o Val Val Figure 5.20 Thr Asn Pro Lys Glu c Carboxyl end o– Globular Protein Structure 2. Secondary- folding or coiling of the chain into a pattern due to weak H bonds between amino acids. • H bonds form between the main chain of amino acids. • Two Kinds of Secondary Structure Secondary Structures • Alpha Helix- H bonds between one amino acid and another further down the chain. Pulls the chain into a coil. • Beta Sheet- H bonds occur across two separate chains. If chains are parallel, they may form a sheet-like structure. Secondary Structure: – Is the folding or coiling of the polypeptide into a repeating configuration. – Includes the helix and the pleated sheet. pleated sheet H O O H H R C C N Amino acid subunits N C C C N C C N R O H H C H C H O H N O C H N O C N C N H O C H C R H C H O C H C R H C R R N O C N H O H N C C R Figure 5.20 O C C H R H O C H H C N R H C H H C helix H C C N H O C C R O H H O R C N HC N R R R H R C C N O H H H O HC N O H H C C N R C N R C C N R R O O H H O H C C R R C N H H H C N O O H C C R C N H H H C N O C Alpha Helix- The First Type of Secondary Protein Structure Beta Sheet- Another Type of Protein Secondary Structure Show me the levels of protein structure. Secondary Structures • Some patterns of alpha helices and/or beta sheets are very common in protein structures. • When secondary structures are organized into specific structures within proteins-motifs. Ex. ΒBarrel or α-turn-α motifs Β-barrel Motif in a Cell Membrane Protein Globular Protein Structure 3. Tertiary Structure- folding and positioning of nonpolar R groups into the interior of the protein (hydrophobic interactions). • Held together by weak van der Waal’s forces. • Precise fitting of R groups within the interior. A change may destabilize a protein’s shape. Tertiary Structure: – Is the overall three-dimensional shape of a polypeptide. – Results from interactions between amino acids and R groups. Hydrophobic CH2 CH 2 Hydrogen bond O H O interactions and van der Waals interactions CH H3C CH3 H3C CH3 CH HO C CH2 CH2 S S CH2 Disulfide bridge O CH2 NH3+ -O C CH2 Ionic bond Polypeptide backbone Globular Protein Structure 4. Quaternary Structure- two or more polypepetide chains associate to form a protein. • Each chain is called a subunit. • Subunits are not necessarily the same. • Ex. Hemoglobin = 2 α-chain subunits + 2 β-chain subunits. Quaternary Structure: – Is the overall protein structure that results from the aggregation of two or more polypeptide subunits. Polypeptide chain Collagen Chains Iron Heme Chains Hemoglobin The four levels of protein structure +H N 3 Amino end Amino acid subunits helix Quaternary Structure of Hemoglobin Hemoglobin structure and sickle-cell disease Primary structure Normal hemoglobin Sickle-cell hemoglobin Primary Val His Leu Thr Pro Glul Glu . . . Val His Leu Thr Pro Val Glu . . . structure 1 2 3 4 5 6 7 1 2 3 4 5 6 7 Secondary and tertiary structures Secondary subunit and tertiary structures Quaternary Hemoglobin A structure Function Red blood cell shape Figure 5.21 Molecules do not associate with one another, each carries oxygen. Normal cells are full of individual hemoglobin molecules, each carrying oxygen Quaternary structure subunit Function 10 m 10 m Red blood cell shape Exposed hydrophobic region Hemoglobin S Molecules interact with one another to crystallize into a fiber, capacity to carry oxygen is greatly reduced. Fibers of abnormal hemoglobin deform cell into sickle shape. Is Protein Folding Important? Normal Prion Scrapie Prion Reverse Transcriptase of HIV Cobra Toxin Shape of the Protein • Tertiary and Quaternary structures provide shape. • These structures are maintained by H bonds and other weak forces between R groups of amino acids. Protein Folding Conditions that Affect Protein Shape Can disrupt H bonds by: • High Temperature • pH Changes (Acidic or Basic) • Ion Concentration (Salt) Disrupting the 2°, 3°, 4° structure is called denaturation. Denaturation: Is when a protein unravels and loses its native conformation. Denaturation Normal protein Figure 5.22 Denatured protein Renaturation Enzymes: – Are a type of protein that acts as a catalyst, speeding up chemical reactions. 1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts. 2 Substrate binds to enzyme. Substrate (sucrose) Glucose OH Enzyme (sucrase) H2O Fructose H O 4 Products are released. Figure 5.16 3 Substrate is converted to products. Enzymes are Proteins • Organic catalysts - increase the rate of chemical reactions in cells. • Hold reactant molecules close together for reaction to occur- uses an active site. • The active site is used to bind the reactant molecules-substrate. Lock-and-Key Model Show me the model, Luke! Write your predictions! Gelatin = Substrate Pineapple = Papain (Enzyme)