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Crash Course in Biochemistry …4 years in 40 min! Nick Lyle Proteins – What are they? • Not just a dietary concern ! • Numerous activities in all organisms: – – – – Structural & Transport Enzymatic (Like Machines -> real nano-tech) Signaling & Regulatory Generalization: Responsible for all rXns. in your body (ask aud. examples) Structural Examples • Keratin – Makes up hair and nails – Disulfide bond hold coilcoil together – Perm: Break disulfides and reform them Structural Examples • Cell Adhesion: – Helps cells stick to other cells. Immunological cells find their target • Cytoskeleton: – Protein scaffold to which cellular components hitch a ride on Enzymatic Examples • Enzymes run chemical reactions • Substrate Product • Usually 1 unique protein for EVERY unique reaction Enzymatic Examples • Glycolysis: – Get energy from breaking down sugar – Universal • The Process: – See: http://www.rcsb.org/pdb/molecules/pdb50_1.html So Many Reactions! Enzymatic Examples • Notice: Specific protein at every step • This just a tiny fraction of what we know • Like a circuit: Where our knowledge of CS is useful • Drugs: are ways to ‘hack’ the circuit by changing protein behavior – Caffeine – Statins and Cholesterol Caffeine Example • Epinepherine stimulates production of cAMP • cAMP increases rate of many rXn’s, including glycolysis (PFK) • Phosphodiesterase eliminates cAMP • Caffeine is a phosphodiesterase Inhibitor Enzymatic + structural example • Muscles: Use ATP to move Carrier Example • Hemoglobin: Carries Oxygen Transport Example • Sodium-potassium pump – Net Effect: push positive charge outside – Electrical field made used for nerve conduction What are proteins? • Like magnetic beads on a string • 20 different beads possible (amino acids) - The sidechain (R-group) is the difference between the 20 AA’s. - Hook together like Legos, 1 way to connect - Backbone repeats 20 Possible Amino Acids • Common to all life What are proteins? • Regular protein 100-400 AA’s Protein Folding: Sidechains attract and repel each other, surround water pushes and pulls (hydrophobic, hydrophilic). This force mashes the protein into a particular shape. Simulated folding animation: http://intro.bio.umb.edu/111-112/111F98Lect/folding.html Protein Structure • Folding results in only 1 conformation (structure or fold) • Sequence determines structure • Structure determines function • Structure VERY important – Gives insights to how protein works – Cant drive with square wheels – Heat denatures proteins – Digestive Zymogens • Sequence structure computationally impossible Structure and Active site • Part of protein where reaction occurs What if shape different? RuBP won’t bind, No reaction. Some mutations change critical active site residues. Genetic Mutations and Disease: sickle cell, PKU Protein-Protein Docking • Some proteins bind (stick) to each other in a highly specific way – See hemoglobin • The final complex is functional • Individual pieces are not – Toxic truncated peptides • RNA polymerase How are Proteins Made? • DNA is set of instructions (Opcode) – Bases like sidechains – A-T G-C – Like many programs concatenated together Genes… • 1 gene makes 1 protein • Genes separated by control regions • Tells where genes start and stop • This still not well understood Genes read by RNA polymerase • Regulatory regions attract TF’s, which attracts RNA poly. • RNA (single strand) is a copy of a gene Ribosome: RNA Protein