Chapter Twenty Proteins

Ch 20 | 2 of 59 TypeExamples Structuraltendons, cartilage, hair, nails Contractile muscles Transporthemoglobin Storagemilk Hormonalinsulin, growth hormone Enzymecatalyzes reactions in cells Protection immune response Roles of Proteins

Ch 20 | 3 of 59 Roles of Proteins

Ch 20 | 4 of 59 Proteins are polymers of amino acids Contain a carboxylic acid group and an amino group on the alpha carbon Side group R gives unique characteristics Rside chain I H 2 N— C — COOH I H Amino Acids

Ch 20 | 5 of 59 Nonpolar –An amino acid that contains a nonpolar side chain –R = H, CH 3, alkyl groups, aromatic Polar –An amino acid with a side chain that is polar but neutral – O ll R = –CH 2 OH, –CH 2 SH, –CH 2 C–NH 2, (polar groups with –O-, -SH, -N-) Classifying Amino Acids

Ch 20 | 6 of 59 The 20 Standard Amino Acids, Grouped According to Side-Chain Polarity.

Ch 20 | 7 of 59 The 20 Standard Amino Acids, Grouped According to Side- Chain Polarity. (cont’d)

Ch 20 | 8 of 59 Polar/Acidic –An amino acid that contains a second carboxyl group in its side chain –R = –CH 2 COOH, or -COOH Polar/ Basic –An amino acid that contains a second amino group in its side chain –R = –CH 2 CH 2 NH 2 Classifying Amino Acids

Ch 20 | 9 of 59 The 20 Standard Amino Acids, Grouped According to Side-Chain Polarity. (cont’d)

Ch 20 | 10 of amino acids not synthesized by the body Arg, His, Ile, Leu, Lys, Met, Phe, Thr, Trp, Val Must obtain from the diet All in diary products 1 or more missing in grains and vegetables Essential Amino Acids

Ch 20 | 11 of 59 Fischer Projections of Amino Acids All amino acids except glycine are chiral. Amino acids have stereoisomers In biological systems, only L amino acids are used in proteins D-Alanine L-AlanineL-CysteineD-Cysteine

Ch 20 | 12 of 59 Designation of handedness in standard amino acid structures involves aligning the carbon chain vertically and looking at the position of the horizontally aligned NH 2 group.

Ch 20 | 13 of 59 Ionization of the –NH 2 and the –COOH group –-COOH loses a proton (acid) –-NH 2 gains a proton (base) Zwitterion has both a + and – charge Zwitterion is neutral overall NH 2 –CH 2 –COOH H 3 N–CH 2 –COO – glycine Zwitterion of glycine Zwitterions +

Ch 20 | 14 of 59 H + OH – + + H 3 N–CH 2 –COOH H 3 N–CH 2 –COO – H 2 N–CH 2 –COO – Positive ion zwitterion Negative ion Low pH neutral pH High pH pH and Ionization In solution, at least three different forms of amino acids can exist: positive ion, zwitterion, and negative ion

Ch 20 | 15 of 59 pH and Ionization Acidic amino acids such as aspartic acid have a second carboxyl group that can donate and accept protons –Amino acids with ionizable side chains have 4 forms in solution -Cys, Tyr, Lys, Arg, His, Asp, Glu Whether a group is ionized or not depends on its pKa –If pH > pKa, the group has been deprotonated –If pH < pKa, the group is protonated

16 Amino Acid  -carboxylic acid  -amino Side chain Alanine Arginine Asparagine Aspartic Acid Cysteine Glutamic Acid Glutamine Glycine Histidine Isoleucine Leucine Lysine Methionine Phenylalanine Proline Serine Threonine Tryptophan Tyrosine Valine

Ch 20 | 17 of 59 Step-wise Ionization of Amino Acids 1. Draw the amino acid in the fully protonated form –Low pH –All acid groups are protonated (-COOH) –All amino groups are protonated (-NH 3 + ) 2. Identify the protons that will come off (and the order in which they will come off) 3. Take the protons off 1 by 1 Example: Glutamic Acid

Ch 20 | 18 of 59 Ionization of Glutamic Acid Draw the step-wise ionization of glutamic acid to result in this form.

Ch 20 | 19 of 59 HomeWork Assignment What overall charge will the following amino acids have at pH 5.5? Glutamic Acid Lysine Phenylalanine

Ch 20 | 20 of 59 Electrophoresis Electrophoresis separates amino acids according to their charges –Positively charged amino acids move towards the negative electrode –Negatively charged amino acids move toward the positive electrode –Neutral amino acids will not move in either direction Amino acids are visualized as separate bands on filter paper or thin layer plate

Ch 20 | 21 of 59 Electrophoresis

Ch 20 | 22 of 59 Amide bond formed by the carboxylate group of an amino acid and the –amino group of the next amino acid O CH 3 + | | + | NH 3 –CH 2 –COH + H 3 N–CH–COO – O CH 3 + | | | NH 3 –CH 2 –C – N–CH–COO – | peptide bond H Peptide Bonds

Ch 20 | 23 of 59 Peptides Peptide –A sequence of amino acids in which the amino acids are joined together through amide (peptide) bonds Dipeptide –A peptide consisting of 2 amino acids Tripeptide –A peptide consisting of 3 amino acids Polypeptide –A peptide consisting of many amino acids

Ch 20 | 24 of 59 Amino acids linked by amide (peptide) bonds Gly Lys Phe Arg Ser H 2 N- -COOH endPeptide bonds end Name: Glycyllysylphenylarginylserine Peptides N- terminus C- terminus

Ch 20 | 25 of 59 Protein Structure A polypeptide containing 50 or more amino acids is called a protein There are different ways to describe the structure of a protein: –Primary Structure –Secondary Structure –Tertiary Structure –Quaternary Structure

Ch 20 | 26 of 59 Three-dimensional arrangement of amino acids with the polypeptide chain in a corkscrew shape Held by H bonds between the H of –N-H group and the – O of C=O of the fourth amino acid along the chain Looks like a coiled “telephone cord” Secondary Structure: Alpha Helices

Ch 20 | 27 of 59 Specific overall shape of a protein Results from cross-links between R groups of amino acids in chain disulfide –S–S– + ionic –COO – H 3 N– H bonds C=O HO– hydrophobic –CH 3 H 3 C– Tertiary Structure

Ch 20 | 28 of 59 Levels of Protein Structure

Ch 20 | 29 of 59 A telephone cord has three levels of structure. Levels of Protein Structure

Ch 20 | 30 of 59 Primary Structure Human Myoglobin

Ch 20 | 31 of 59 Secondary Structure Geometrical orientation of polypeptide chains Two main kinds of secondary structure: –Alpha helices –Beta pleated sheets

Ch 20 | 32 of 59 The hydrogen bonding between the carbonyl oxygen atom of one peptide linkage and the amide hydrogen atom of another peptide linkage. Secondary Structure

Ch 20 | 33 of 59 Two pleated sheet protein structure. Secondary Structure

Ch 20 | 34 of 59 Four representations of the helix secondary structure. Secondary Structure

Ch 20 | 35 of 59 The secondary structure of a single protein. Secondary Structure

Ch 20 | 36 of 59 Four types of interactions between amino acid R groups produce the tertiary structure of a protein. Tertiary Structure

Ch 20 | 37 of 59 The tertiary structure of the single-chain protein myoglobin. Tertiary Structure

Ch 20 | 38 of 59 Disulfide bonds involving cysteine residues can form in two different ways. Disulfide Bonding

Ch 20 | 39 of 59 Human insulin, a small two-chain protein, has both intrachain and interchain disulfide linkages as part of its tertiary structure. Human Insulin

Ch 20 | 40 of 59 Substitutions in Insulin

Ch 20 | 41 of 59 Disulfides and Hair

Ch 20 | 42 of 59 A schematic diagram showing the tertiary structure of the single-chain protein myoglobin.

Ch 20 | 43 of 59 Proteins with two or more chains –Quaternary structure is the relative organization of multiple chains to each other Example is hemoglobin Carries oxygen in blood Four polypeptide chains Each chain has a heme group to bind oxygen A conjugated protein (has a prosthetic group) Quaternary Structure

Ch 20 | 44 of 59 Tertiary and quaternary structure of the oxygen- carrying protein hemoglobin. Quaternary Structure

Ch 20 | 45 of 59 Globular proteins Fibrous proteins “spherical” shapelong, thin fibers Water solubleNot water soluble Multiple Types of 2 o structure1 Type of 2 o Structure Transport, Metabolism, etc.Strength, Protection More numerousFew in the body InsulinHair HemoglobinWool Enzymes Skin AntibodiesNails Globular and Fibrous Proteins

Ch 20 | 46 of 59 The tail feathers of a peacock. Fibrous Protein is α-keratin Fibrous Proteins PhotoDisc

Ch 20 | 47 of 59 The coiled-coil structure of the fibrous protein alpha keratin. Fibrous Proteins

Ch 20 | 48 of 59 Fibrous Proteins

Ch 20 | 49 of 59 Three helical peptide chains. Collagen

Ch 20 | 50 of 59 →Electron Micrograph Collagen fibers Collagen Prof. P.M. Motta & E. Vizza / Photo Researchers

Ch 20 | 51 of 59 Protein denaturation process. Protein Denaturation

Ch 20 | 52 of 59 Heat denatures the protein in egg white. Heat Denaturation E.R. Degginger

Ch 20 | 53 of 59 Hard boiling an egg Wiping the skin with alcohol swab for injection Cooking food to destroy E. coli. Heat used to cauterize blood vessels Autoclave sterilizes instruments Milk is heated to make yogurt Applications of Denaturation

Ch 20 | 54 of 59 Denaturation

Ch 20 | 55 of 59 Disulfides and Hair

Ch 20 | 56 of 59 Structure of immunoglobulin. Immunoglobulins

Ch 20 | 57 of 59 Immunoglobulin- antigen complex Immunoglobulins

Ch 20 | 58 of 59 Break down of peptide bonds Requires acid or base, water and heat Gives smaller peptides and amino acids Similar to digestion of proteins using enzymes Occurs in cells to provide amino acids to synthesize other proteins and tissues Protein Hydrolysis

Ch 20 | 59 of 59 Hydrolysis of a Dipeptide