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Crash Course in Biochemistry       …4 years in 40 min!
Proteins – What are they?• Not just a dietary concern !• Numerous activities in all organisms:  –   Structural & Transport...
Structural Examples• Keratin  – Makes up hair and nails  – Disulfide bond hold coil-   coil together  – Perm: Break disulf...
Structural Examples• Cell Adhesion:  – Helps cells stick  to other cells.  Immunological cells  find their target• Cytoske...
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.r...
So Many Reactions!
Enzymatic Examples• Notice: Specific protein at every step• This just a tiny fraction of what we  know• Like a circuit: Wh...
Caffeine Example• Epinepherine stimulates production  of cAMP• cAMP increases rate of many rXn’s,  including glycolysis (P...
Enzymatic + structuralexample• 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 ner...
What are proteins?• Like magnetic beads on a string• 20 different beads possible (amino  acids)               - The sidech...
20 Possible Amino Acids• Common to all life
What are proteins?• Regular protein 100-400 AA’sProtein Folding:Sidechains attract and repel each other, surround water pu...
Protein Structure• Folding results in only 1  conformation (structure or fold)• Sequence determines structure• Structure d...
Structure and Active site• Part of protein where reaction occurs What if shape different? RuBP won’t bind, No reaction. So...
Protein-Protein Docking• Some proteins bind (stick) to each  other in a highly specific way    – See hemoglobin•   The fin...
How are Proteins Made?• DNA is set of instructions (Opcode)  – Bases like    sidechains  – A-T G-C  – Like many  programs ...
Genes…• 1 gene makes 1  protein• Genes separated  by control regions• Tells where genes  start and stop• This still not we...
Genes read by RNApolymerase• Regulatory regions attract TF’s,  which attracts RNA poly.• RNA (single strand) is a  copy of...
Ribosome: RNA Protein
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Crash course of biochemistry

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Crash course of biochemistry

  1. 1. Crash Course in Biochemistry …4 years in 40 min!
  2. 2. 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)
  3. 3. Structural Examples• Keratin – Makes up hair and nails – Disulfide bond hold coil- coil together – Perm: Break disulfides and reform them
  4. 4. 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
  5. 5. Enzymatic Examples• Enzymes run chemical reactions• Substrate  Product• Usually 1 unique protein for EVERY unique reaction
  6. 6. Enzymatic Examples• Glycolysis: – Get energy from breaking down sugar – Universal• The Process: – See: http://www.rcsb.org/pdb/molecules/pdb50_1.html
  7. 7. So Many Reactions!
  8. 8. 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
  9. 9. 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
  10. 10. Enzymatic + structuralexample• Muscles: Use ATP to move
  11. 11. Carrier Example• Hemoglobin: Carries Oxygen
  12. 12. Transport Example• Sodium-potassium pump – Net Effect: push positive charge outside – Electrical field made used for nerve conduction
  13. 13. 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
  14. 14. 20 Possible Amino Acids• Common to all life
  15. 15. What are proteins?• Regular protein 100-400 AA’sProtein Folding:Sidechains attract and repel each other, surround water pushesand pulls (hydrophobic, hydrophilic). This force mashes the proteininto a particular shape.Simulated folding animation: http://intro.bio.umb.edu/111-112/111F98Lect/folding.html
  16. 16. 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
  17. 17. 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
  18. 18. 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
  19. 19. How are Proteins Made?• DNA is set of instructions (Opcode) – Bases like sidechains – A-T G-C – Like many programs concatenated together
  20. 20. Genes…• 1 gene makes 1 protein• Genes separated by control regions• Tells where genes start and stop• This still not well understood
  21. 21. Genes read by RNApolymerase• Regulatory regions attract TF’s, which attracts RNA poly.• RNA (single strand) is a copy of a gene
  22. 22. Ribosome: RNA Protein

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