Chp Chemistry 121 Winter 2009 LA Tech Chapter 20. Protiens Sections… → The protein made by spiders to produce a web is a form of silk that can be exceptionally strong.

Chp Chemistry 121 Winter 2009 LA Tech Chapter 20. Proteins 20.1 Characteristics of Proteins 20.2 Amino Acids: The Building Blocks for Proteins 20.3 Chirality and Amino Acids 20.4 Acid-Base Properties of Amino Acids 20.5 Cysteine: A Chemically Unique Amino Acid 20.6 Peptide Formation 20.7 Biochemically Important Small Peptides 20.8 General Structural Characteristics of Proteins 20.9 Primary Structure of Proteins Secondary Structure of Proteins Tertiary Structure of Proteins Quaternary Structure of Proteins Fibrous and Globular Proteins Protein Hydrolysis Protein Denaturation Glycoproteins Lipoproteins

Chp Chemistry 121 Winter 2009 LA Tech Chapter 21. Protein and the Amino Acids 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.

Chp Chemistry 121 Winter 2009 LA Tech Protein function Enzymesbiological catalysts. Immuno- antibodies of immune system. globulins globulins Transportmove materials around -hemoglobin for O 2. Regulatoryhormones, control of metabolism. Structuralcoverings and support - skin, tendons, hair, bone. Movementmuscle, cilia, flagella.

Chp Chemistry 121 Winter 2009 LA Tech Types of Proteins

Chp Chemistry 121 Winter 2009 LA Tech 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. General Structure

Chp Chemistry 121 Winter 2009 LA Tech Handedness/Chirality of Amino Acids

Chp Chemistry 121 Winter 2009 LA Tech Amino acids Because both acid and base groups are present, an amino acid can form a +/- ion. H H H H | | | | R-C-COOH R-C-COO - R-C-COOH R-C-COO - | | | | NH 2 NH 3 + NH 2 NH 3 + The position of the equilibrium is based on pH and the type of amino acid. Called a zwitterion.

Chp Chemistry 121 Winter 2009 LA Tech Some amino acid examples H 3 C H 3 C H \ \ | HC HC-C-COO - / / | H 3 C H 3 C + NH 3 valine H | CH 3 - CH 3 -C-COO - | + NH 3 alanine H | CH 3 -S-CH 2 -CH 2 CH 3 -S-CH 2 -CH 2 -C-COO - | + NH 3 methionine NH H | CH 2 CH 2 -C-COO - | + NH 3 tryptophan

Chp Chemistry 121 Winter 2009 LA Tech Some amino acid examples H | HO-CH 2 HO-CH 2 -C-COO - | + NH 3 serine H | H H-C-COO - | + NH 3 glycine O O H | | | | | H 2 N-C-CH 2 H 2 N-C-CH 2 -C-COO - | + NH 3 asparagine O O H | | | | | O-C-CH 2 -CH 2 - O-C-CH 2 -CH 2 -C-COO - | + NH 3 glutamic acid

Chp Chemistry 121 Winter 2009 LA Tech Groups of Amino Acids Hydrophobic Polar, neutral Negatively charged-Acidic positively charged-Basic

Chp Chemistry 121 Winter 2009 LA Tech Non-polar Amino Acids

Chp Chemistry 121 Winter 2009 LA Tech Ploar/Neutral Amino Acids

Chp Chemistry 121 Winter 2009 LA Tech Ploar Acidic/Basic Amino Acids

Chp Chemistry 121 Winter 2009 LA Tech Abbreviations glycine Gly G alanine Ala A valine Val V leucine Leu L isoleucine Ile I methionine Met M phenylalanine Phe F tryptophan Trp W Proline Pro P

Chp Chemistry 121 Winter 2009 LA Tech Primary protein structure Proteins are polymers made up of amino acids. Peptide bond - how the amino acids are linked together to make a protein. H | H 2 NCCOOH | | R R + H H | | H 2 NCCOOH | | R’ R’ H O H O | || | || H 2 N - C - C - | | R R H H | | N - C - COOH | | | | H R’ + H 2 O

Chp Chemistry 121 Winter 2009 LA Tech 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.

Chp Chemistry 121 Winter 2009 LA Tech Three levels of structure: telephone cord

Chp Chemistry 121 Winter 2009 LA Tech Summary of protein structure primarysecondary tertiary quaternary H O H O | || | || H 2 N - C - C | | R R H H | | N - C - COOH | | | | H R’’ H O H O | || | || - NH - C - C - | | R’ R’

Chp Chemistry 121 Winter 2009 LA Tech All proteins have the same covalent backbone. Part of a protein. Primary structure H O H O | || | || H 2 N - C - C | | R R H H | | NH - C - COOH | | R’’’ R’’’ H O H O | || | || - NH - C - C - | | R’ R’ H O H O | || | || - NH - C - C - | | R’’ R’’

Chp Chemistry 121 Winter 2009 LA Tech Separation of three amino acids Separation of Lys, Phe, and Glu using electrophoresis after hydrolysis of protein

Chp Chemistry 121 Winter 2009 LA Tech 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,...

Chp Chemistry 121 Winter 2009 LA Tech  -helix Every amide hydrogen and carbonyl oxygen is involved in a hydrogen bond.

Chp Chemistry 121 Winter 2009 LA Tech Representations of the helix secondary structure

Chp Chemistry 121 Winter 2009 LA Tech  -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.

Chp Chemistry 121 Winter 2009 LA Tech The coiled-coil structures The coiled-coil structure of the fibrous protein beta kerotin.

Chp Chemistry 121 Winter 2009 LA TechCollagen 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.

Chp Chemistry 121 Winter 2009 LA Tech Collagen

Chp Chemistry 121 Winter 2009 LA Tech  -Pleated sheets Another secondary structure for protein. Held together by hydrogen bonding between adjacent sheets of protein. C|RC|R R|CR|C R|CR|C R|CR|C R|CR|C C|RC|R C|RC|R C|RC|R C|RC|R C|RC|R N|HN|H N|HN|H N|HN|H O || C O || C O || C O || C || O C || O C || O C || O H|NH|N H|NH|N H|NH|N H|NH|N N|HN|H The hydrogen bonding between the carbonyl oxygen atom of one peptide linkage and the amide hydrogen atom of another peptide linkage.

Chp Chemistry 121 Winter 2009 LA Tech  -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.

Chp Chemistry 121 Winter 2009 LA Tech  -Pleated sheets

Chp Chemistry 121 Winter 2009 LA Tech 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

Chp Chemistry 121 Winter 2009 LA Tech 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

Chp Chemistry 121 Winter 2009 LA Tech Tertiary Structure

Chp Chemistry 121 Winter 2009 LA Tech Tertiary Structure of Proteins - S - S - Salt bridge Sulfide crosslink Hydrogen bonding Hydrophobic interaction -COO - H 3 N + - -O \ H - O \ H

Chp Chemistry 121 Winter 2009 LA Tech Four types of interactions between amino acid R groups

Chp Chemistry 121 Winter 2009 LA Tech 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

Chp Chemistry 121 Winter 2009 LA Tech Quaternary structure of proteins Aggregate structure This example shows four different proteins and two prosthetic groups.

Chp Chemistry 121 Winter 2009 LA Tech 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.

Chp Chemistry 121 Winter 2009 LA Tech Heme myoglobin 1 heme group hemoglobin 4 heme groups

Chp Chemistry 121 Winter 2009 LA TechMyoglobin Heme

Chp Chemistry 121 Winter 2009 LA TechHemoglobin 4 heme 2  chains 2  chains

Chp Chemistry 121 Winter 2009 LA Tech Oxygen Transport

Chp Chemistry 121 Winter 2009 LA Tech Example - cytochrome C 550 Aggregate of proteins and other structures. Heme structure Contains Fe 2+ Used in metabolism.

Chp Chemistry 121 Winter 2009 LA Tech 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.

Chp Chemistry 121 Winter 2009 LA Tech Comparison of normal and sickle cell hemoglobin NormalSickle

Chp Chemistry 121 Winter 2009 LA Tech 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 -

Chp Chemistry 121 Winter 2009 LA Tech Heat-Denaturation of Proteins

Chp Chemistry 121 Winter 2009 LA Tech Permanent for Hair