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Transcript
Protein Function Zinc-finger nuclease cleaves nucleotides in DNA ATP Synthase adds phosphate to ADP Carbonic Anhydrase • CO2 is a byproduct of cell metabolism and is carried back to the lungs through the bloodstream for disposal. • The majority is converted to soluble carbonic acid (bicarbonate) and carried out by the lungs. K = 1.7×10-3 (Not product favored) • The unassisted reaction is too slow to sufficiently remove CO2. • The protein Carbonic anhydrase speeds up reaction rate by 106 x • The same protein re-establishes equilibrium in lungs to convert back to CO2, which we breathe out. • It’s why carbonated beverages taste fizzy once they hit our tongue and CA converts it to CO2(g). Enzyme: catalyst that facilitates a biochemical reaction • Active site: region of the protein where the reaction occurs • Binding site: region that binds the substrate • High specificity for a single type of substrate Cleaves (breaks) peptide bonds at: Aromatics Basic (+) Small, neutral (Tyr, Phe, Trp) (Arg, Lys) (Ala, Gly, Val) Catalytic triad of a protease: Frequently observed active site in hydrolases (with Asp, His, Ser) Enzymes may need cofactors (coenzymes e.g. vitamins/ peptides or metal ions) to assist in catalysis. ATP is found in kinases: enzymes that add phosphate groups to other proteins. Vitamin A: Undergoes cis/trans isomerization when hit with light. (Opsin proteins found in eye tissue). Carbonic anhydrase active site: 3 Histidines coordinated to a Zn+2 +2 TedEd: How do Vitamins work; www.youtube.com/watch?v=ISZLTJH5lYg SciShow: How the Vitamins Got Their Names; www.youtube.com/watch?v=NnmgM_Lz3o0 Carbonic Anhydrase Mechanism • Every enzyme has a unique mechanism (pathway) in its function. • Upon finishing, enzymes regenerate their original state to repeat. 1. Zn+2 bound H2O is polarized enough to dissociate as an ionic compound (OH-/H+). Loses H+ 2. CO2 substrate binds in active site 3. OH- attacks CO2 and converts it into bicarbonate ion. 4. Release of HCO3- and addition of another H2O regenerate native site. Some Mechanisms are very complex with many steps Catalytic mechanism of chymotrypsin (cleaving amide bonds at aromatic residues) Trypsin & chymotrypsin structure similarity Despite binding different substrates, their pathways are nearly identical The enzyme-substrate binding complex Lock-and-key model devised by Emil Fischer in 1894. Substrate fits into corresponding rigid binding site on enzyme. Induced fit model: substrate fits into flexible pocket and imparts a conformational change in the enzyme. It is now observed that the conformational change is necessary in many proteins for their function. Conformational changes can occur upon binding the substrate. Myoglobin upon binding O2 ATP Synthase www.youtube.com/watch?v=PjdPTY1wHdQ Inhibitors slow or prevent enzyme catalysis A large fraction of medicines act as enzyme inhibitors. • NSAIDs (aspirin & ibuprofen) inhibit cyclooxgenase which make prostaglandin, causing inflammation. • Opioids inhibit the neural cell receptors that communicate pain. Natural metabolites are involved in regulatory processes as inhibitors (feedback inhibition) High norepinephrine conc. inhibits Tyrosine hydroxylase to prevent further production. DNews: What Happens When You’re Hooked?; https://www.youtube.com/watch?v=GKpAZgrMTC8 SciShow: Why We Have Pain, & How We Kill It; www.youtube.com/watch?v=GmHGUTNoL-I Inhibitors function in different ways Competitive Inhibitors seek the same binding site as the substrate and compete for binding. Noncompetitive (allosteric) Inhibitors bind elsewhere on the enzyme and alter the protein conformation making it less efficient. Suicide Inhibitors irreversibly bind to active site. Nerve gases are acetylcholinesterase inhibitors which prevent the muscles from retracting. Cyanide inhibition of ATP synthesis www.youtube.com/watch?v=fBXSJGxfnbU Article link: http://www.compoundchem.com/2014/10/07/nerveagentspart1/ Enzyme Classification Reaction Catalyzing Redox reaction: electron transfer Functional group transfer Hydrolysis (breaking) of various covalent bonds using water Cleavage or formation of double bonds without water Rearrange groups within a molecule to form a similar isomer Joining of two molecules, forming single bonds E.C. 1: Oxidoreductase: change the oxidation state of the substrate. Some reduce O2 to H2O in the process. coenzyme Tyrosinase is a Cu-enzyme that catalyzes the production of melanin and other pigments from tyrosine by oxidation, as in the blackening of a peeled or sliced potato exposed to air. E.C. 2: Transferase: transfer functional groups to a protein. (e.g. Kinases add phosphate, very important in cell signaling) Choline acetyl-transferase produces acetylcholine, the neurotransmitter responsible for triggering muscle contraction, by transferring an acetyl group to a choline. + acetyl group from Acetyl-CoA coenzyme choline acetylcholine E.C. 3: Hydrolase: Cleave molecules by adding H2O across the bond. (e.g. proteases cleave peptides, lipases break fats) Elastase cleaves proteins at small non-polar residues Maltose Starch: glucose polymer (polysaccaharide) Most common carbohydrate Amylase E.C. 4: Lyase: breaks bonds without water; often forming or breaking double bonds. Both neurotransmitters AsapScience: Your Brain on Drugs: Alcohol https://www.youtube.com/watch?v=vkpz7xFTWJo End product of Glycolysis Ethanol production via yeast by fermentation. E.C. 5: Isomerase: interconverts isomers by rearranging molecule (no net addition or subtraction). Found in pathway to use glycerol as energy source once removed from Fatty compounds Phosphoglucose Isomerase Glucose-6-phosphate Fructose-6-phosphate Glycolysis step # 2 to utilize glucose to produce ATP in this anaerobic process E.C. 6: Ligase: connect two molecules together; commonly use ATP energy to drive reaction. DNA Ligases connect complementary DNA strands in repair of breaks by forming phosphodiester bonds. Mechanism of Recombination: https://www.youtube.com/watch?v=8rXizmLjegI Motor Proteins: promote cellular motion by ATP hydrolysis. Myosin enables muscle contraction in muscle fibers enabling all (in)voluntary motions from lifting to blinking. Trillions of Myosin proteins use ATP energy to contract to generate muscle movement. SciShow: What is Sarin Gas? www.youtube.com/watch?v=w3sJEbcT7IE Motor Proteins: Kinesin and Dynein • Move along microtubules that act like cell scaffolding • Intracellular transport (when diffusion isn’t good enough) • Separation of the chromosomes during mitosis & meiosis. • Used in cilia and flagella (cell motility) SciShow: Motor Proteins; www.youtube.com/watch?v=SgR4ojtPw5Q Lipid Vesicle with “cargo”: • New proteins • Enzymes • Antibodies • Molecules • Cell Waste The Kinesin Linear Motor www.youtube.com/watch?v =kOeJwQ0OXc4 Fibrous Microtubules (tubulin: structural protein polymer) Structural proteins are fibrous, insoluble, and give cells and organelles stability and rigidness. • Collagen is the most abundant protein in mammals, making up more than a third of the body’s protein. • Composed of 3 chains in a helix. The sequence normally follows the pattern “Gly-Pro-X” and can span over 1,400 residues per chain. • It is the major structural protein of connective tissues (e.g. cartilage) • It forms a network of fibers and provides tensile strength to the tissue. • Gram for gram, collagen is stronger than steel. TedEd: How do scars form?; https://www.youtube.com/watch?v=ucRMDdw82yw Antibodies: the Immune response • In response to foreign molecules, white blood cells produce Y-shaped proteins called antibodies (or immunoglobins). • Each antibody binds tightly to a specific antigen. • Binding inactivates the antigen or marks it for degradation via other enzymes. The Immune System Explained www.youtube.com/watch?v=zQGOcOUBi6s SciShow: All About Allergies www.youtube.com/watch?v=hmb066Vzdek Antibodies: Vaccination • Vaccines are dead/weakened organisms (or their product) that can be introduced to yield antibodies for the pathogen. • The immune system generates and keeps available antibodies for future protection. • The body can more effectively destroy disease causing pathogens when it has already made antibodies to target them. Measles Explained — Vaccinate or Not? www.youtube.com/watch?v=y0opgc1WoS4 SciShow: Anti-vaccination www.youtube.com/watch?v=Rzxr9FeZf1g http://www.compoundchem.com/2015/02/10/vaccines/ Transport proteins facilitate the movement of molecules/particles across the body, cell, or membrane. Storage proteins keep a reserve of metal ions, amino acids, nucleic acids or other chemical species needed quickly. Hemoglobin: O2 transport from lungs Dopamine Transporter: removes dopamine from between synaptic clefts of nerve cells to end the signal. ~4,500 Fe atoms • Stores and releases Iron in a controlled fashion • Free Iron can be toxic to the cell Asap Science: What is Gluten?; www.youtube.com/watch?v=DXjpb7SFi3s Membrane Channels: Carrier proteins • Many lipophilic molecules can pass through a membrane by simple diffusion. • Polar molecules can not passively transport themselves through a membrane and require a channel Membrane Transport Channels • Highly selective for a particular ion. • Can exist in open and closed states and are heavily regulated • Needed to create cell electric potentials for nervous system Benzocaine (commonly found in cough drops and topical creams) is used as a local anesthetic and functions by inhibiting sodium ion membrane channel. Crash Course: Membranes & Transport; www.youtube.com/watch?v=dPKvHrD1eS4 Cell Receptors bind ligands to pass along a signal into a cell. • Embedded in cell’s plasma membrane • Each protein is very specific to ligand • Ligands: peptide, toxin, hormone, neurotransmitter, etc • Over 50% of pharmaceuticals bind to cell receptors TedEd: The Science of Spiciness www.youtube.com/watch?v=qD0_yWgifDM Capsaicin coord.info/GC446DJ http://www.compoundchem.com/2014/02/27/chemical-structures-of-neurotransmitters/ Regulatory Proteins The addition of ubiquitin can affect proteins in many ways: It can signal for their degradation via the proteasome, alter their cellular location, affect their activity, and promote or prevent protein interactions Lysosome Organelle Contain more than 50 different enzymes, which are all optimally active at an acidic environment of about pH 4.5 (about the pH of black coffee). Thus lysosomes act as the waste disposal system of the cell by digesting unwanted materials in the cytoplasm, both from outside of the cell and obsolete components inside the cell. Proteasome Denaturation: the loss of protein folded conformation • Loss of structure results in a loss of protein function. • Not normally reversible (need chaperones) • Can lead to protein aggregation: non-specific folding (gathering) of proteins. • Coagulation: precipitation of unfolded protein SciShow- Prions: The Real Zombie Maker www.youtube.com/watch?v=Cubu-k7kSvw Ways to Denature a Protein Temperature: increases molecular movement and breaking of stabilizing bonding forces. pH: Alter protonation state of ionizable residues, disrupt electrostatic interactions. (Buffers are often used to regulate pH) Organic solvents: disrupt exterior H-bonds between residues & H2O Detergents: disrupt hydrophobic interactions Chaotropic reagents: small chemicals that can be added to disrupt H-bonds (e.g. urea, Arg-side chain) TedEd: How to unboil an egg; www.youtube.com/watch?v=CHMY4G9gTPA