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Chapter 11. Protein Structure and Function • These are biopolymers that are constructed from a limited set of amino acids. • They are the most plentiful organic substances in the cell. • About half of the dry mass of a cell is composed of proteins. • They serve a wide range of functions. • Enzymes Protein function biological catalysts. • Immunoglobulins antibodies of immune system. • Transport move materials around hemoglobin for O2. • Regulatory hormones, control of metabolism. • Structural • • Movement coverings and support skin, tendons, hair, bone. muscle, cilia, flagella. Amino acids • All proteins are composed of amino acids. • Twenty common amino acids. • All are -amino acids. • Except for proline, primary amino- group is attached to the carbon - the carbon just after the acid group. carbon General Structure H | R-C-COOH | NH2 Amino acids • Because both acid and base groups are present, an amino acid can form a +/- ion. H | R-C-COOH | NH2 H | R-C-COO | NH3+ • The position of the equilibrium is based on pH and the type of amino acid. Called a zwitterion. Some amino acid examples alanine H | CH3-C-COO| +NH 3 H | CH3 -S-CH2-CH2-C-COO| +NH 3 methionine valine N H tryptophan H3 C H \ | HC-C-COO/ | H3C +NH3 H | CH2-C-COO| +NH 3 Some amino acid examples glycine O H | H-C-COO| +NH 3 H || | -O-C-CH -CH -C-COO2 2 | +NH 3 glutamic acid H | HO-CH2-C-COO| +NH 3 serine O H || | H2N-C-CH2-C-COO| +NH 3 asparagine Abbreviations • • • • • • • • glycine alanine valine leucine isoleucine methionine phenylalanine tryptophan Gly Ala Val Leu Ile Met Phe Trp G A V L I M F W Groups of Amino Acids • Hydrophobic • Polar, neutral • Negatively charged • positively charged Primary protein structure • Proteins are polymers made up of amino acids. • Peptide bond are • H • H | H2NCCOOH + | R | H2NCCOOH | R’ how the amino acids linked together to make a protein. H O H | || | H2N - C - C - N - C - COOH | | | R H R’ + H2O Four levels of protein structure • Primary structure The sequence of amino acids in a protein. • Secondary structure Way that chains of amino acids are coiled or folded (-helix, -sheet, random coil). • Tertiary structure Way -helix, -sheet, random coils fold and coil. • Quaternary structure Way that two or more peptide chains pack together. Primary structure • All proteins have the same covalent backbone. H O H O H O H | || | || | || | H2N - C - C - NH - C - C - NH - C - C - NH - C - COOH | | | | R R’ R’’ R’’’ • Part of a protein. Secondary structure • Long chains of amino acids commonly fold or curl into a regular repeating structure. • Structure is a result of hydrogen bonding between amino acids within the protein. • Common secondary structures are: - helix - pleated sheet • Secondary structure adds new properties to a protein like strength, flexibility, ... -helix One common type of secondary structure. Properties of an -helix include strength and low solubility in water. Originally proposed by Pauling and Corey in 1951. -helix QuickTime™ and a Graphics decompressor are needed to see this picture. -helix C || O H | N C || OH | HN | N H | N C H || | O N H | N C || O C || O H | C H || H N C | O | || N C O N || C O || O Every amide hydrogen and carbonyl oxygen is involved in a hydrogen bond. Collagen • Family of related proteins. • About one third of all protein in humans. • Structural protein • Provides strength to bones, tendon, skin, blood vessels. • Forms triple helix - tropocollagen. Tropocollagen -Pleated sheets • Another secondary structure for protein. • Held together by hydrogen bonding between adjacent sheets of protein. R R C | R C | R H | N C || O | C C || O N | H R H | | C N O || C O || C H | N C | R N | C H | R | C C || O H | N C || O N | H R | O C || C O || C C | R N | C H | R -Pleated sheets • Silk fibroin - main protein of silk is an example of a pleated sheet structure. Composed primarily of glycine and alanine. Stack like corrugated cardboard for extra strength. Beta sheet Tertiary structure of proteins • Fibrous proteins • insoluble in water • form used by connective tissues • silk, collagen, -keratins • Globular proteins • soluble in water • form used by cell proteins • 3-D structure - tertiary Tertiary structure of proteins • Results from interaction of side chains. • The protein folds into a tertiary structure. • Possible side chain interactions: • Similar solubilities • Ionic attractions • Electrostatic attraction between + and sidechains • Covalent bonding Sulfide crosslink Tertiary structure of proteins Hydrophobic interaction -S-S- -COO- H3N+- Salt bridge Hydrogen bonding Quaternary structure of proteins • Many proteins are not single peptide strands. • They are combinations of several proteins • - aggregate of smaller globular proteins. • Conjugated protein - incorporate another type of group that performs a specific function. • prosthetic group Quaternary structure of proteins Aggregate structure This example shows four different proteins and two prosthetic groups. Hemoglobin and myoglobin • Hemoglobin • oxygen transport protein of red blood cells. • Myoglobin • oxygen storage protein of skeletal muscles. • As with the cytochrome example, both proteins use heme groups. It acts as the binding site for molecular oxygen. Heme • myoglobin • 1 heme group • hemoglobin • 4 heme groups Myoglobin Heme Hemoglobin 2 chains 4 heme 2 chains Oxygen Transport Example - cytochrome C 550 Heme structure Contains Fe2+ Used in metabolism. Aggregate of proteins and other structures. Sickle cell anemia • Defective gene results in production of mutant hemoglobin. • Still transports oxygen but results in deformed blood cells - elongated, sickle shaped. • Difficult to pass through capillaries. Causes organ damage, reduced circulation. • Affects 0.4 % of African-American. Comparison of normal and sickle cell hemoglobin Normal Sickle Summary of protein structure primary secondary H O H O H | || | || | H2N - C - C- NH - C - C - N - C - COOH | | | | R R’ H R’’ tertiary quaternary Denaturation of Proteins The loss of secondary, tertiary, and quaternary structures • 1) pH extremes. • 2). Heat • 3). Mechanical Agitation (foaming) • 4). Detergents • 5). Organic Solvents • 6). Inorganic Salts -