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

– 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 coil-

coil 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