Crash Course in Biochemistry

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Crash Course in Biochemistry

• 4 years in 40 min!

Nick Lyle
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Proteins What are they?

• Not just a dietary concern !
• Numerous activities in all organisms
• Structural Transport
• Enzymatic (Like Machines -gt real nano-tech)
• Signaling Regulatory
• Generalization Responsible for all rXns. in your
  body (ask aud. examples)

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Structural Examples

• Keratin
• Makes up hair and nails
• Disulfide bond hold coil-
• coil together
• Perm Break disulfides and
• reform them

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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

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Enzymatic Examples

• Enzymes run chemical reactions
• Substrate ? Product
• Usually 1 unique protein for EVERY unique reaction

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Enzymatic Examples

• Glycolysis
• Get energy from
• breaking down
• sugar
• Universal
• The Process
• See http//www.rcsb.org/pdb/molecules/pdb50_1.htm
  l

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So Many Reactions!
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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

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Caffeine Example

• Epinepherine stimulates production of cAMP
• cAMP increases rate of many rXns, including
  glycolysis (PFK)
• Phosphodiesterase eliminates cAMP
• Caffeine is a phosphodiesterase Inhibitor

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Enzymatic structural example

• Muscles Use ATP to move

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Carrier Example

• Hemoglobin Carries Oxygen

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Transport Example

• Sodium-potassium pump
• Net Effect push positive charge outside
• Electrical field made used for nerve conduction

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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 AAs.
• Hook together like Legos, 1 way to connect
• Backbone repeats

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20 Possible Amino Acids

• Common to all life

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What are proteins?

• Regular protein 100-400 AAs

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/111-1
12/111F98Lect/folding.html
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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

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Structure and Active site

• Part of protein where reaction occurs

What if shape different? RuBP wont bind, No
reaction. Some mutations change critical active
site residues. Genetic Mutations and Disease
sickle cell, PKU
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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

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How are Proteins Made?

• DNA is set of instructions (Opcode)
• Bases like
• sidechains
• A-T G-C
• Like many
• programs
• concatenated
• together

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Genes

• 1 gene makes 1
• protein
• Genes separated
• by control regions
• Tells where genes
• start and stop
• This still not well
• understood

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Genes read by RNA polymerase

• Regulatory regions attract TFs, which attracts
  RNA poly.
• RNA (single strand) is a
• copy of a gene

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Ribosome RNA? Protein