What you should know from today’s lecture

• Examples and chemical basis of the diversity of proteins and their functions.

• Levels of protein structure and the chemical bonds that stabilize each level.

• 3-D structure determines biological function.

• Denaturation.

• Enzymes and catalysis.

• Enzyme cofactors, vitamins, and minerals.

• Biochemical pathways.

Function Example

Structural Muscle fiber (myosin)

Rhino horn (keratin)

Hormonal Insulin, leptin, hGH

Binding Antibodies (-globulin), receptors, snake venom

Transport Na+/K+ pump, hemoglobin, HDL

N storage Gluten, zein, albumin

Enzymes/catalytic

Sucrase, amylase, protease, nuclease

Misc. Antifreeze

Infectious Mad cow disease (prion)

The diverse functions of proteins

Fig. 3.16, p. 43

Levels of protein structure

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Why is it so hard to predict protein folding?

• Even a small protein made of just 100 amino acids has 3200 possible backbone configurations.

• The fastest supercomputers can do 1015 calculations per second.

• Even at that speed, it would take 1080 seconds to calculate the 3-dimensional shape of the small protein.

• The universe is only 1020 seconds old.

• A real protein folds in a microsecond (10-6 seconds).

Protein denaturation• Hydrogen bonds are broken,

destroying 3-D structure, and, therefore, protein function

• Denatured proteins are less soluble in water

• Covalent peptide bonds are NOT broken

• Common protein denaturants are gentle heat (100oC or less), solvents such as ethanol, even violent mechanical action such as beating an egg white

• Sometimes reversible, sometimes not

Biochemical reactionsA-P-P-PATP

A-P-P + P + energyADP

substrates(reactants)

products

Rules of thumb:•Chemical reactions proceed spontaneously from few complex molecules to a greater number of less complex molecules; from higher bond energy to lower energy•Making a more complex molecule from simpler substrates requires energy input

Catalysts• Increase the rate of a

chemical reaction

• Do not affect the equilibrium of the reaction

• Participate in the reaction but are not ‘used up’

• Are neither a substrate nor a product of the reaction

• Protein catalysts (enzymes) are exquisitely specific for their substrates and products

• Enzymes typically accelerate reaction rates by thousands or millions of times

The effect of enzymes on chemical reactions

O

OHO

OH

HO

OH

P

OO

HO

OH

HO OH

P1:19

G1P : G6P

How do enzymes work?

Lock-and-keyInduced fit

Sucrose Glucose + FructoseSucrase

Enzyme cofactors (coenzymes)

• Provide a wider range of chemically active ‘functional’ groups than are available in the 20 amino acid ‘R’ groups

• Vitamins

Example: nicotinic acid (niacin) in NADH and NADPH

• MineralsIron (Fe++) in hemoglobin

Magnesium (Mg++) in chlorophyll

Biochemical pathways