Amino Acids, Proteins, and Enzymes Chemistry 203 Chapter 21 Amino Acids, Proteins, and Enzymes

Fibrinogen helps blood clotting Function of proteins Fibrinogen helps blood clotting

Function of proteins

Proteins - Proteins account for 50% of the dry weight of the human body. - Unlike lipids and carbohydrates, proteins are not stored, so they must be consumed daily. - Current recommended daily intake for adults is 0.8 grams of protein per kg of body weight (more is needed for children). - Dietary protein comes from eating meat and milk.

Proteins Fibrous proteins: Globular proteins: 100,000 different proteins in human body Fibrous proteins: Insoluble in water – used for structural purposes (Keratin & Collagen). Globular proteins: More or less soluble in water – used for nonstructural purposes.

Amino acids Are the building blocks of proteins. Contain carboxylic acid and amino groups. Are ionized in solution (soluble in water). They are ionic compounds (solids-high melting points). Contain a different side group (R) for each. side chain H2N— C —COOH H3N— C —COO− R R Zwitterion + H H α-carbon Ionized form (Salt) This form never exist in nature.

H Amino acids │ H3N—C —COO− + H glycine CH3 H alanine Only difference: containing a different side chain (R) for each. H │ H3N—C —COO− H glycine CH3 H alanine +

Amino acids Amino acids are classified as: Nonpolar (Neutral) amino acids (hydrophobic) with hydrocarbon (alkyl or aromatic) sides chains. Polar (Neutral) amino acids (hydrophilic) with polar or ionic side chains. Acidic amino acids (hydrophilic) with acidic side chains (-COOH). Basic amino acids (hydrophilic) with –NH2 side chains.

Amino acids There are many amino acids. There are only 20 different amino acids in the proteins in humans. They are called α amino acids. - Humans cannot synthesize 10 of these 20 amino acids. (Essential Amino Acids) - They must be obtained from the diet (almost daily basis).

Nonpolar (Neutral) amino acids

Polar (Neutral) amino acids

Acidic and basic amino acids

All of the α-amino acids are chiral (except glycine) Fischer projections All of the α-amino acids are chiral (except glycine) Four different groups are attached to central carbon (α-carbon). CH2SH D-cysteine L-cysteine L isomers is found in the body proteins and in nature.

Ionization and pH - pH: 6 to 7 Isoelectric point (pI) Positive charges = Negative charges No net charge (Neutral) - Zwitterion pH: 3 or less -COO- acts as a base and accepts an H+ pH: 10 or higher -NH3+ acts as an acid and loses an H+ -

Ionization and pH The net charge on an amino acid depends on the pH of the solution in which it is dissolved.

Ionization and pH Each amino acid has a fixed and constant pI.

When an amide links two amino acids (Peptide bond). A dipeptide forms: When an amide links two amino acids (Peptide bond). Between the COO− of one amino acid and the NH3 + of the next amino acid. (amide bond)

Peptide Dipeptide: A molecule containing two amino acids joined by a peptide bond. Tripeptide: A molecule containing three amino acids joined by peptide bonds. Polypeptide: A macromolecule containing many amino acids joined by peptide bonds. Protein: A biological macromolecule containing at least 40 amino acids joined by peptide bonds.

Naming of peptides C-terminal amino acid: the amino acid at the end of the chain having the free -COO- group (always written at the left). N-terminal amino acid: the amino acid at the end of the chain having the free -NH3+ group (always written at the right).

- Begin from the N terminal. Naming of peptides - Begin from the N terminal. Drop “-ine” or “-ic acid” and it is replaced by “-yl”. Give the full name of amino acid at the C terminal. H3N-CH-C-NH-CH2-C-NH-CH-C-O CH3 CH2OH O + - From alanine alanyl From glycine glycyl From serine serine Alanylglycylserine (Ala-Gly-Ser)

Biologically Active Peptides - Enkephalins, pentapeptides made in the brain, act as pain killers and sedatives by binding to pain receptors. - Addictive drugs morphine and heroin bind to these same pain receptors, thus producing a similar physiological response, though longer lasting. - Enkephalins belong to the family of polypeptides called endorphins (16-31 amino acids), which are known for their pain reducing and mood enhancing effects.

Biologically Active Peptides Enkephalins: Met-enkephalin: It contains a C-terminal methionine. Leu-enkephalin: It contains a C-terminal leucine.

Biologically Active Peptides Oxytocin and vasopressin are cyclic nonapeptide hormones, which have identical sequences except for two amino acids.

Biologically Active Peptides Oxytocin stimulates the contraction of uterine muscles, and signals for milk production; it is often used to induce labor. Vasopressin, antidiuretic hormone (ADH) targets the kidneys and helps to limit urine production to keep body fluids up during dehydration.

Structure of proteins 1. Primary structure 2. Secondary structure 3. Tertiary structure 4. Quaternary structure

Primary Structure of proteins The order of amino acids held together by peptide bonds. Each protein in our body has a unique sequence of amino acids. The backbone of a protein. - All bond angles are 120o, giving the protein a zigzag arrangement. C H 3 C H S 3 C H C H S H C H 3 2 C H O C H O C H O C H O + 3 + 2 2 H N C H C N C H C N C H C N C H C O - 3 H H H Ala─Leu─Cys─Met

Cysteine The -SH (sulfhydryl) group of cysteine is easily oxidized to an -S-S- (disulfide).

Primary Structure of proteins NH3+ NH3+ Primary Structure of proteins The primary structure of insulin: - Is a hormone that regulates the glucose level in the blood. - Was the first amino acid order determined. - Contains of two polypeptide chains linked by disulfide bonds (formed by side chains (R)). - Chain A has 21 amino acids and chain B has 30 amino acids. - Genetic engineers can produce it for treatment of diabetes. O C O- O C O- Chain A Chain B

Secondary Structure of proteins Describes the way the amino acids next to or near to each other along the polypeptide are arranged in space. 1. Alpha helix (α helix) 2. Beta-pleated sheet (-pleated sheet) 3. Triple helix (found in Collagen) 4. Some regions are random arrangements.

Secondary Structure - α-helix A section of polypeptide chain coils into a rigid spiral. Held by H bonds between the H of N-H group and the O of C=O of the fourth amino acid down the chain (next turn). looks like a coiled “telephone cord.” All R- groups point outward from the helix. Myosin in muscle and α-Keratin in hair have this arrangement. H-bond

Secondary Structure - -pleated sheet Consists of polypeptide chains (strands) arranged side by side. Has hydrogen bonds between the peptide chains. Has R groups above and below the sheet (vertical). Is typical of fibrous proteins such as silk. O H

Secondary Structure – Triple helix (Superhelix) - Collagen is the most abundant protein. - Three polypeptide chains (three α-helix) woven together. - It is found in connective tissues: bone, teeth, blood vessels, tendons, and cartilage. - Consists of glycine (33%), proline (22%), alanine (12%), and smaller amount of hydroxyproline and hydroxylysine. - High % of glycine allows the chains to lie close to each other. - We need vitamin C to form H-bonding (a special enzyme).

Tertiary Structure The tertiary structure is determined by attractions and repulsions between the side chains (R) of the amino acids in a polypeptide chain. Interactions between side chains of the amino acids fold a protein into a specific three-dimensional shape. -S-S-

Tertiary Structure Disulfide (-S-S-) (2) salt bridge (acid-base) (3) Hydrophilic (polar) (4) hydrophobic (nonpolar) (5) Hydrogen bond

Tertiary Structure Shorthand symbols on a protein Ribbon diagram: Lysozyme (an enzyme)

Globular proteins Myoglobin Have compact, spherical shape. Almost soluble in water. - Carry out the work of the cells: Synthesis, transport, and metabolism Myoglobin Stores oxygen in muscles. 153 amino acids in a single polypeptide chain (mostly α-helix).

Have long, thin shape and insoluble in water. Fibrous proteins Have long, thin shape and insoluble in water. - Involve in the structure of cells and tissues. α-keratin: skin, nail, hair, and bone Superhelix: Collagen -keratin: feathers of birds Large amount of -pleated sheet

α-keratin: hair, wool, skin, and nails Fibrous proteins α-keratin: hair, wool, skin, and nails - They are made of two mainly a-helix chains coiled around each other in a superhelix (supercoil). - These coils wind around other coils making larger and stronger structures (like hair). - α-helix chains bond together by disulfide bond (-S-S-) - More disulfide bonds, more rigid materials (horns & nails). Collagen

Quaternary Structure Hemoglobin Occurs when two or more protein units (polypeptide subunits) combine. Is stabilized by the same interactions found in tertiary structures (between side chains). Hemoglobin consists of four polypeptide chains as subunits. Is a globular protein and transports oxygen in blood (four molecules of O2). CO is poisonous because it binds 200 times more strongly to the Fe2+ than does O2 (Cells can die from lack of O2). α chain  chain  chain α chain Hemoglobin

Conjugated Proteins They are composed of a protein unit and a nonprotein molecule. Myoglobin & Hemoglobin Heme: a complex organic compound containing the Fe2+.

Sickle Cell Hemoglobin Sickle cell anemia is a disease where a single amino acid of both β subunits is changed from glutamic acid to valine. - A genetic mutation in the DNA sequence that is responsible for synthesis of hemoglobin. - Red blood cells containing these mutated hemoglobin units become elongated and crescent (sickle) shaped (more fragile). - These red blood cells will rupture capillaries, causing pain and inflammation, leading to organ damage, and eventually a painful death.

Summary of protein Structure

Summary of protein Structure

Denaturation - Is a process of destroying a protein Active protein Denatured protein - Is a process of destroying a protein by chemical and physical means. We can destroy secondary, tertiary, or quaternary structure but the primary structure is not affected. - Denaturing agents: heat, acids and bases, organic compounds, heavy metal ions, and mechanical agitation. Some denaturations are reversible, while others permanently damage the protein. Ovalbumin

Denaturation Heat: H bonds, Hydrophobic interactions Detergents: H bonds Acids and bases: Salt bridges, H bonds. Reducing agents: Disulfide bonds Heavy metal ions (transition metal ions Pb2+, Hg2+): Disulfide bonds Alcohols: H bonds, Hydrophilic interactions Agitation: H bonds, Hydrophobic interactions

Enzymes

Enzyme H…H H2 + I2   2HI … I … I - Like a catalyst, they increase the rate of biological reactions (106 to 1012 times faster). - But, they are not changed at the end of the reaction. Eact - They are made of proteins. - Lower the activation energy for the reaction.  2HI H2 + I2  H…H I … I … - Less energy is required to convert reactants to products.

Most of enzymes are globular proteins (water soluble). Proteins are not the only biological catalysts. Most of enzymes are specific. (Trypsin: cleaves the peptide bonds of proteins) Some enzymes are localized according to need. (digestive enzymes: stomach)

Names of Enzymes with the suffix « -ase ». By replacing the end of the name of reaction or reacting compound with the suffix « -ase ». Oxidoreductases: oxidation-reduction reactions (oxidase-reductase). Transferases: transfer a group between two compounds. Hydrolases: hydrolysis reactions. Lyases: add or remove groups involving a double bond without hydrolysis. Isomerases: rearrange atoms in a molecule to form a isomer. Ligases: form bonds between molecules.

Enzyme - Substrate: the compound or compounds whose reaction an enzyme catalyzes. - Active site: the specific portion of the enzyme to which a substrate binds during reaction.

Enzyme catalyzed reaction An enzyme catalyzes a reaction by, Attaching to a substrate at the active site (by side chain (R) attractions). Forming an Enzyme-Substrate Complex (ES). Forming and releasing products. E + S ES E + P Enzyme: globular protein

1. Lock-and-Key model Enzyme has a rigid, nonflexible shape. An enzyme binds only substrates that exactly fit the active site. The enzyme is analogous to a lock. - The substrate is the key that fits into the lock

2. Induced-Fit model - Enzyme structure is flexible, not rigid. - Enzyme and substrate adjust the shape of the active site to bind substrate. - The range of substrate specificity increases. - A different substrate could not induce these structural changes and no catalysis would occur.

Factors affecting enzyme activity Activity of enzyme: how fast an enzyme catalyzes the reaction. 1. Temperature 2. pH 3. Substrate concentration 4. enzyme concentration 5. Enzyme inhibition

Temperature Enzymes are very sensitive to temperature. At low T, enzyme shows little activity (not an enough amount of energy for the catalyzed reaction). - At very high T, enzyme is destroyed (tertiary structure is denatured). - Optimum temperature: 37°C or body temperature.

pH Optimum pH: is 7.4 in our body. Lower or higher pH can change the shape of enzyme. (active site change and substrate cannot fit in it) But optimum pH in stomach is 2. Stomach enzyme (Pepsin) needs an acidic pH to digest the food. - Some damages of enzyme are reversible.

Substrate and enzyme concentration Rate of reaction ↑ Substrate concentration ↑ First: Rate of reaction ↑ End: Rate of reaction reaches to its maximum: all of the enzymes are combined with substrates. Maximum activity

Enzyme inhibition Inhibitors cause enzymes to lose catalytic activity. Competitive inhibitor Noncompetitive inhibitor

Competitive Inhibitor Inhibitor has a structure that is so similar to the substrate. It competes for the active site on the enzyme. Solution: increasing the substrate concentration.

Noncompetitive Inhibitor Inhibitor is not similar to the substrate. It does not compete for the active site. When it is bonded to enzyme, change the shape of enzyme (active site) and substrate cannot fit in the active site (change tertiary structure). Like heavy metal ions (Pb2+, Ag+, or Hg2+) that bond with –COO-, or –OH groups of amino acid in an enzyme. Penicillin inhibits an enzyme needed for formation of cell walls in bacteria: infection is stopped. Solution: some chemical reagent can remove the inhibitors. Inhibitor Site

Competitive and Noncompetitive Inhibitor

Enzyme cofactors Metal ions: bond to side chains. (coenzyme) protein Metal ion Organic molecules (coenzyme) Simple enzyme (apoenzyme) Enzyme + Cofactor Enzyme + Cofactor (coenzyme) Metal ions: bond to side chains. obtain from foods. Fe2+ and Cu2+ are gain or loss electrons in redox reactions. Zn2+ stabilize amino acid side chain during reactions.

Enzyme cofactors Enzyme and cofactors work together. Catalyze reactions properly.

Vitamins and Coenzymes Vitamins are organic molecules that must be obtained from the diet. (our body cannot make them) Water-soluble vitamins: have a polar group (-OH, -COOH, or …) - They are not stored in the body (must be taken). - They can be easily destroyed by heat, oxygen, and ultraviolet light (need care). Fat-soluble vitamins: have a nonpolar group (alkyl, aromatic, or …) - They are stored in the body (taking too much = toxic). A, D, E, and K are not coenzymes, but they are important: vision, formation of bone, proper blood clotting.

Zymogens (Proenzymes) Zymogen (Proenzyme): an inactive enzyme that becomes an active enzyme after a chemical change (remove or change some polypeptides). Trypsinogen (inactive enzyme) Trypsin (active enzyme) Pancreas Small intestine Digestive enzyme (hydrolyzes the peptide bonds of proteins)

- Most of enzymes are in cells. Enzymes in medicine - Most of enzymes are in cells. Small amounts of them are in body fluids (blood, urine,…). Level of enzyme activity can be monitored. Find some diseases

Enzymes in medicine Certain enzymes are present in higher amounts in particular cells. If these cells are damaged or die, the enzymes are released into the bloodstream and can be detected. Enzyme Condition Creatine phosphokinase Heart attack Alkaline phosphatase Liver or bone disease Acid phosphatase Prostate cancer

Enzymes in medicine Inhibitors can be useful drugs. Penicillin inhibits the enzyme that forms cell walls of bacteria, destroying the bacterium. ACE (angiotensin-converting enzyme) causes blood vessels to narrow, increasing blood pressure. ACE inhibitors are given to those with high blood pressure to prevent ACE’s synthesis from it’s zymogen. HIV protease is an essential enzyme that allows the virus to make copies of itself. HIV protease inhibitors interfere with this copying, decreasing the virus population in the patient.