Title: Crash Course in Biochemistry
1Crash Course in Biochemistry
Nick Lyle
2Proteins 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)
3Structural Examples
- Keratin
- Makes up hair and nails
- Disulfide bond hold coil-
- coil together
- Perm Break disulfides and
- reform them
4Structural 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
5Enzymatic Examples
- Enzymes run chemical reactions
- Substrate ? Product
- Usually 1 unique protein for EVERY unique reaction
6Enzymatic Examples
- Glycolysis
- Get energy from
- breaking down
- sugar
- Universal
- The Process
- See http//www.rcsb.org/pdb/molecules/pdb50_1.htm
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8So Many Reactions!
9Enzymatic 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
10Caffeine Example
- Epinepherine stimulates production of cAMP
- cAMP increases rate of many rXns, including
glycolysis (PFK) - Phosphodiesterase eliminates cAMP
- Caffeine is a phosphodiesterase Inhibitor
11Enzymatic structural example
12Carrier Example
- Hemoglobin Carries Oxygen
13Transport Example
- Sodium-potassium pump
- Net Effect push positive charge outside
- Electrical field made used for nerve conduction
14What 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
1520 Possible Amino Acids
16What 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
17Protein 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
18Structure 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
19Protein-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
20How are Proteins Made?
- DNA is set of instructions (Opcode)
- Bases like
- sidechains
- A-T G-C
- Like many
- programs
- concatenated
- together
21Genes
- 1 gene makes 1
- protein
- Genes separated
- by control regions
- Tells where genes
- start and stop
- This still not well
- understood
22Genes read by RNA polymerase
- Regulatory regions attract TFs, which attracts
RNA poly. - RNA (single strand) is a
- copy of a gene
23Ribosome RNA? Protein