Proteins PDF

Proteins  Protein - naturally occuring unbranched polymer in which the monomer units are amino acids From the Greek proteios – “ of first importance” - Proteins account for 15% of a cell’s overall mass. - Unlike lipids and carbohydrates, proteins are not stored, so they must b...

Proteins  Protein - naturally occuring unbranched polymer in which the monomer units are amino acids From the Greek proteios – “ of first importance” - Proteins account for 15% of a cell’s overall mass. - 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).  Classification based on function 1. Catalytic proteins - enzymes 2. Defense proteins - immunoglobins or antibodies 3. Transport proteins – hemoglobin, lipoproteins 4. Messenger proteins – insulin, glucagon 5. Contractile proteins – actin, myosin 6. Structural proteins - collagen, α-keratin 7. Transmembrane proteins – protein channels 8. Storage proteins - myoglobin 9. Regulatory proteins – proteolytic enzymes, zymogens 10. Nutrient proteins – casein, ovalbumin 11. Buffer proteins - hemoglobin 12. Fluid balance proteins – albumin, globulin Function of proteins  Protein Classification by Shape 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 R R Zwitterion H2N— C —COOH H+3N— C —COO− H H α-carbon Ionized form (Salt) This form never exist in nature.  Amino acids Only difference: containing a different side chain (R) for each. H │ + H3N—C —COO− │ H glycine CH3 │ + H3N—C —COO− │ 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. Polar Acidic amino acids (hydrophilic) with acidic side chains (-COOH). Polar 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  Fischer projections All of the α-amino acids are chiral (except glycine) Four different groups are attached to central carbon (α- carbon). CH2SH 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.  Peptide 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 right). N-terminal amino acid: the amino acid at the end of the chain having the free -NH3+ group (always written at the left).  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. O O O + - H3N-CH-C-NH-CH2-C-NH-CH-C- O CH CH OH 3 2 From alanine From glycine From serine alanyl glycyl 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.  Conantokins are a small family of helical peptides that are derived from the venom of predatory marine snails of the genus Conus. Conantokins are linear conopeptides 17–27 residues in length that contain multiple γ-carboxyglutamate residues in their sequence. Because of the lack of disulfide bonds in the sequence of conantokins, the presence of Gla is important for the formation of a helical structure. The binding of calcium ions to these peptides leads to a conformational change in their structure thought to be important for their bioactivity. 104 The therapeutic potential of clinically available NMDA receptor antagonists is currently limited because of the prevalence of undesirable side effects, thought to be a result of a lack of specificity. Contulakin-G was discovered over 15 years ago as a member of the neurotensin (NT) family from the venom of predatory marine snail, Conus geographus Contulakin-G is a 16 amino acid peptide Dr. Lourdes J. Cruz is the National Scientist whose research has contributed to the discovery of these peptides  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. CH3 CH3 S CH CH3 SH CH2 + CH3 O + CH O CH2 O CH2 O H3N CH C N CH C N CH C N CH C O- H H H Ala─Leu─Cys─M et  Cysteine The -SH (sulfhydryl) group of cysteine is easily oxidized to an -S-S- (disulfide).  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)). O C - Chain A has 21 amino acids and O- chain B has 30 amino acids. - Genetic engineers can produce it for treatment of diabetes. 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 (β-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 H-bond have this arrangement.  Secondary Structure - β-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 (1) 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 - 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).  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 β-keratin: feathers of birds Large amount of β-pleated sheet  Fibrous proteins α-keratin: hair, wool, skin, and nails - They are made of two mainly α-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 Occurs when two or more protein units (polypeptide subunits) combine. α chain β Is stabilized by the same interactions chain 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). β α chain chain CO is poisonous because it binds 200 times more strongly to the Fe2+ than does Hemoglobin O2 (Cells can die from lack of O2).  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  Denaturatio n Active protein - Is a process of destroying a protein by chemical and physical means. Ovalbumin - 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 Denatured protein mechanical agitation. - Some denaturations are reversible, while others permanently damage the protein.  Denaturatio n 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 - 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. - They are made of proteins. Eact - Lower the activation energy for the reaction. Eact H H … H2 + I2 → → … … I …I 2HI - Less energy is required to convert reactants to products.  Enzyme - 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. - They are made of proteins. Eact - Lower the activation energy for the reaction. Eact H H … H2 + I2 → → … … I 2HI … I - Less energy is required to convert reactants to products.  Enzyme - 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 - 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  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 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. Inhibitor - 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 Site inhibitors. Competitive and Noncompetitive Inhibitor  Enzyme cofactors protein Simple enzyme (apoenzyme) protein Metal ion Enzyme + Cofactor Organic protein molecules Enzyme + Cofactor (coenzyme) (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) Pancreas Trypsin (active enzyme) Small intestine Digestive enzyme (hydrolyzes the peptide bonds of proteins)  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 its 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.