1. Protein Function ATP Synthase adds phosphate to ADP Zinc-finger nuclease cleaves nucleotides in DNA

3. Carbonic Anhydrase CO 2 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 CO 2. The protein Carbonic anhydrase speeds up reaction rate by 10 6 x The same protein re-establishes equilibrium in lungs to convert back to CO 2, which we breathe out. It’s why carbonated beverages taste fizzy once they hit our tongue and CA converts it to CO 2(g).

4. 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 Catalytic triad of a protease: Frequently observed active site in hydrolases (with Asp, His, Ser) Cleaves (breaks) peptide bonds at: Aromatics (Tyr, Phe, Trp) Basic (+) (Arg, Lys) Small, neutral (Ala, Gly, Val)

5. Enzymes may need cofactors (coenzymes e.g. vitamins/ peptides or metal ions) to assist in catalysis. +2 Carbonic anhydrase active site: 3 Histidines coordinated to a Zn +2 Vitamin A: Undergoes cis/trans isomerization when hit with light. (Opsin proteins found in eye tissue). ATP is found in kinases: enzymes that add phosphate groups to other proteins.

6. 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

7. Carbonic Anhydrase Mechanism 1. Zn +2 bound H 2 O is polarized enough to dissociate as an ionic compound (OH - /H + ). Loses H + Every enzyme has a unique mechanism (pathway) in its function. Upon finishing, enzymes regenerate their original state to repeat. 2. CO 2 substrate binds in active site 3. OH - attacks CO 2 and converts it into bicarbonate ion. 4. Release of HCO 3 - and addition of another H 2 O regenerate native site.

8. Some Mechanisms are very complex with many steps Trypsin & chymotrypsin structure similarity Catalytic mechanism of chymotrypsin (cleaving amide bonds at aromatic residues) Despite binding different substrates, their pathways are nearly identical

9. 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.

10. Conformational changes can occur upon binding the substrate. ATP Synthase www.youtube.com/watch?v=PjdPTY1wHdQ Myoglobin upon binding O 2

11. 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. High norepinephrine conc. inhibits Tyrosine hydroxylase to prevent further production. Natural metabolites are involved in regulatory processes as inhibitors (feedback inhibition) DNews: What Happens When You’re Hooked?; https://www.youtube.com/watch?v=GKpAZgrMTC8

12. SciShow: Why We Have Pain, & How We Kill It; www.youtube.com/watch?v=GmHGUTNoL-I

13. 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. Cyanide inhibition of ATP synthesis www.youtube.com/watch?v=fBXSJGxfnbU Nerve gases are acetylcholinesterase inhibitors which prevent the muscles from retracting. Suicide Inhibitors irreversibly bind to active site.

14. Article link: http://www.compoundchem.com/2014/10/07/nerveagentspart1/

15. Enzyme Classification Redox reaction: electron transfer Reaction Catalyzing Functional group transfer Hydrolysis (breaking) of various covalent bonds using water Rearrange groups within a molecule to form a similar isomer Joining of two molecules, forming single bonds Cleavage or formation of double bonds without water

16. E.C. 1: Oxidoreductase: change the oxidation state of the substrate. Some reduce O 2 to H 2 O 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.

17. 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 cholineacetylcholine

18. E.C. 3: Hydrolase: Cleave molecules by adding H 2 O across the bond. (e.g. proteases cleave peptides, lipases break fats) Elastase cleaves proteins at small non-polar residues Starch: glucose polymer (polysaccaharide) Most common carbohydrate Amylase Maltose

19. E.C. 4: Lyase: breaks bonds without water; often forming or breaking double bonds. AsapScience: Your Brain on Drugs: Alcohol https://www.youtube.com/watch?v=vkpz7xFTWJo Both neurotransmitters End product of Glycolysis Ethanol production via yeast by fermentation.

20. 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 Glycolysis step # 2 to utilize glucose to produce ATP in this anaerobic process Glucose-6-phosphateFructose-6-phosphate Phosphoglucose Isomerase

21. E.C. 6: Ligase: connect two molecules together; commonly use ATP energy to drive reaction. Mechanism of Recombination: https://www.youtube.com/watch?v=8rXizmLjegI DNA Ligases connect complementary DNA strands in repair of breaks by forming phosphodiester bonds.

22. 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

23. 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) The Kinesin Linear Motor www.youtube.com/watch?v =kOeJwQ0OXc4 Lipid Vesicle with “cargo”: New proteins Enzymes Antibodies Molecules Cell Waste Fibrous Microtubules (tubulin: structural protein polymer) SciShow: Motor Proteins; www.youtube.com/watch?v=SgR4ojtPw5Q

24. 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

25. 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

26. 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

27. http://www.compoundchem.com/2015/02/10/vaccines/

28. Stores and releases Iron in a controlled fashion Free Iron can be toxic to the cell Storage proteins keep a reserve of metal ions, amino acids, nucleic acids or other chemical species needed quickly. Transport proteins facilitate the movement of molecules/particles across the body, cell, or membrane. ~4,500 Fe atoms Hemoglobin: O 2 transport from lungs Dopamine Transporter: removes dopamine from between synaptic clefts of nerve cells to end the signal. Asap Science: What is Gluten?; www.youtube.com/watch?v=DXjpb7SFi3s

29. 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

30. 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 Crash Course: Membranes & Transport; www.youtube.com/watch?v=dPKvHrD1eS4 Benzocaine (commonly found in cough drops and topical creams) is used as a local anesthetic and functions by inhibiting sodium ion membrane channel.

31. 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

32. http://www.compoundchem.com/2014/02/27/chemical-structures-of-neurotransmitters/

33. 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 Proteasome 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. Lysosome Organelle

34. 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

35. 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 & H 2 O 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