In biochemistry we are primarily concerned with the chemistry of the three main atoms of the biosphere, H, C and O (accounting for ~90-95% of the mass of most plants) plus N, P and S and several ions such as Fe^+2/+3, Cu^+1/+2, Na⁺, K⁺, Ca⁺² and Cl^-. Other very minor but necessary elemental constituents of plants include Zn⁺², B⁺³, Mn^+3/+4, Mo^+4/+6.

The abundance (relative to 1000 atoms of C) of major elements in plants and animals is illustrated in the following table:

Element	Zea mays (corn)	Homo sapiens (humans)
Hydrogen	1705	2038
Carbon	1000	1000
Oxygen	765	252
Nitrogen	29	143
Potassium	6.5	6
Calcium	1.6	25
Phosphorus	1.8	22
Magnesium	2.0	1.4
Sulfur	1.5	5.2
Chlorine	1.1	2.8
Iron	0.4	0.05

It is important to note that atoms such as C, H, O and N need electrons to fill their outer shells and can share electrons to form covalent bonds.

H - 1 bond
C - 4 bonds
O - 2 bonds
N - 3 bonds

Carbon atoms can bond to each other and form long chains.  The lower the atomic weight, the stronger the covalent bonds will be.  Why?  Can you name any very strong carbon polymers?

Of central importance in biochemistry is the principal solvent molecule water.  The form and function of most biological molecules includes their interaction with water.  As you learned in previous biochemistry courses water has unique chemical propertie. Some of these will be briefly reviewed here.  Based on its molecular weight, water would be expected to be a gas at temperatures>-100° C.  In fact the temperature at which water is in the liquid state sets the limits on most biological processes.  By comparison H₂S is a gas at temperatures>-59° C.

Water

		2 unshared pairs of electrons of oxygen excess electrons around oxygen (S-)
	Electronegativity	attraction of an atom or molecule for electrons Oxygen is the most electronegative atom in the biological world.
	H-bonding	attraction of H to electronegative group (e.g. O, N, S)

H₂O exists as a "polymer"

• should be viscous, but bonds are very weak (4.5 cal/mol to break)
• turnover of H-bonding 10^-11 seconds

Low ionization

1 liter of H2O

=

Heat of Vaporization - calories necessary to raise 1 g of liquid at boiling point to 1 g of vapor.

H2O	540 cal.
CH2CH2OH	262 cal.

H₂O has a large cooling effect when it evaporates.  When sunlight hits a leaf, H₂O evaporates and the leaf doesn't get hot.

Many biological molecules exist as isomers.

Geometric isomers:

Stereoisomers:

Most natural sugars are the D-isomers.  Only L-isomers of amino acids are present in proteins, although some D amino acids can be bound in antibiotics and small peptides.

Enzyme catalyzed reactions normally give one or the other stereoisomer.  Racemic mixtures have equal proportions of the possible isomers.  Most chemical syntheses give racemic mixtures.  Engineered plants therefore have tremendous potential in the future for production of specific isomers needed in medicine or industry.

Classification of life based on nutritive requirements:

Autotrophs	Heterotrophs
Use inorganic carbon (CO2, HCO3-, CO32-) Use inorganic nitrogen (NO3, NH4+) Use inorganic sulfur (SO42-) synthesize all necessary growth factors	Require reduced carbon Require reduced nitrogen Require reduced sulfur require essential amino acids, fatty acids, vitamins, etc.

Are all plants autotrophs?

Autotrophs can be further divided into photosynthetic and chemosynthetic organisms.

As you might guess, chemosynthetic organisms use chemical energy, e.g.:

Nearly all life on earth (with the possible exception of some deep sea vents) and essentially all reduced carbon including fossil fuels are the result of photosynthesis.

The earth is thought to be ~4.9 billion years old and plants are thought to have first evolved ~3 billion years ago.  In present times it is estimated that ~2 x 10¹¹ tons of CO₂ are fixed annually from photosynthesis.  ~½ of CO₂ in perennials ends up as cellulose or other wall components.  In certain environments hydrocarbons made by plants are not consumed by heterotrophs and accumulate.

In what sort of environments and in what forms does fixed carbon usually accumulate?

Heterotrophs can be classified as:

• Saprophytes:  live off dead organic matter
• Parasites:  live and grow on living cells
1. obligate:  only grow on living organisms
2. facultative:  function on living or dead matter
• Symbionts:  benefit to host greater than any harm, e.g.:
1. lichen:  blue green alga + fungus
2. mycorrhizae:  grow on roots of plants and supply nutrients (especially P) for the plant

Bioenergetics

Energy is the capacity to do work and overcome resistance.  Molecules tend to seek the least organized, least energetic state or highest enthalpy, H.

Equilibrium in a biological system is death - i.e. organisms require a regular input of energy.  Energy in biological systems is supplied by certain forms of chemical energy (see review) such as highly reduced molecules or high-energy structures.  Chemical energy has traditionally been measured in calories, abbreviated cal, but the SI unit, the joule, is now recommended.

Gibbs free energy, G, (named for J. Willard Gibbs, one of the founders of thermodynamics) = H - TS where T is the temperature (°K) and S is the entropy.

• DG is that portion of total energy that is available to do work and can be transferred to another system.
• energy is liberated as a reaction proceeds toward equilibrium under constant conditions of temperature and pressure.
• at equilibrium DG = 0.

R = the gas constant 1.987 cal/mol.
T = temperature in degrees Kelvin, 273.15 + °C

Standard free energy is designated DG°

• compares reaction with a standard
• reactants and products are kept at 1 M, T=25°C & pressure = 1 atmosphere

DG° = -RTlnK_eq

with a strongly -DG° at equilibrium there will be a higher molar concentration of C + D than A + B.

For the following reaction series the change in free energy is given for each step

The reaction can be coupled to an exergonic reaction

Kinase has two substrates glucose and ATP and binds to both.  The Gibbs Free Energy for the overall reaction is DG° = -4 (+3.3 - 7.3).  Therefore this reaction would tend to go toward G-6-P and ADP.

Another example:

DG° = 7.7 - 7.6 - 8.0 = ^-7.9

There are 4 major classes or groups of molecules in cells.

Three of them can be used as sources of energy although only two of them are used except under adverse conditions.

Why is so much more energy present in oils than carbohydrates?

Enzymes catalyze most biochemical reactions.

• Most enzymes are proteins; some are ribonucleic acids.
• Like other catalysts enzymes increase the rate of reactions
• They do this by decreasing the energy of activation of reactions
• This allows biochemical reactions to occur at physiological temperatures (e.g. 4-40°C in plants)
• Increase reaction rates at physiological temperatures as much as 10¹⁷_, but do not affect the equilibrium of the reaction or K_eq
• Usually highly stereospecific for both substrates and products
Enzymes bind substrates forming an intermediate structure which reduces the energy need for activation and imposes conditions on substrate molecules that favors reactions.

Q₁₀ = _________________

Q₁₀ for chemical reactions ~= _________________

Q₁₀ for physical reactions (e.g. light reactions of photosynthesis) ~= _________________

High Energy Structures

1. Phosphoric Acid Anhydrides

2. Mixed Anhydrides

Oxidation is ______________________________________________

Reduction is ______________________________________________

A reductant (easily oxidized) reduces something
An oxidant (easily reduced) oxidizes something

Redox Potential - capacity to gain or lose electrons

• The more negative the redox potential, the more easily it will lose e^-, so it will be more readily oxidized.
• The less negative the redox potential, the less easily it will lose e^-, so it will be more readily reduced.
• Electrons are transferred from molecules with more negative to ones with less negative redox potentials.

DG° = -nFDE´o

n = # of electrons transferred F = Faraday's constant (23,063 cal/volt equivalent) DE´o  = redox potential -- E´o  reduced - DE´o oxidized

In respiration, NADH + H⁺ + ½O₂ + H₂O

DG°	= -nFDE´o = -(2)*(23,063)*[0.817 -(-0.32)] = -52.5 kcal form 3 ATPs for each NADH oxidized

Form 3 ATPs for each NADH = 21.9/52.5 * 100 = 42% energy trapped in ATP; other 58% lost as heat -- remarkably high efficiency compared to industrial processes!

Respiratory Quotient, RQ = CO₂ produced ÷ O₂ consumed
-- gives an idea of what the principal substrates that are being respirated

Substrate	RQ
Carbohydrate	1
Protein	0.8-0.9
Fat or Oil	0.7

• need a lot of O₂ to oxidize protein or fat and oil compared to CO₂ produced