crash course of biochemistry
TRANSCRIPT
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Crash Course in Biochemistry…4 years in 40 min!
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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)
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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.html
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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 rXn’s,
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 AA’s.
- 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 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
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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 won’t 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 TF’s,
which attracts RNA poly.
• RNA (single strand) is a
copy of a gene
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Ribosome: RNA Protein