Primary Photosynthetic carbon assimilation mechanisms
1)C3 carbon metabolism
2)C2 carbon metabolism a.k.a. photorespiration
Secondary Photosynthetic pathways as evolutionary pathways to accelerate carbon assimilation and reduce oxygenase activity
1)C4 carbon metabolism
4)Thermodynamic limitationsGeneral Introduction to Plant Biochemistry Chemistry fundamentally is the making and breaking of bonds between atoms and/or molecules. Biochemistry (or biological chemistry) is the making and breaking of bonds between molecules in biological systems. Plant biochemistry encompasses most of biochemistry since plants are capable of synthesizing most molecules known in nature. Because you all have taken general biochemistry courses, this course will focus on formation of essential molecules that are mostly ultimately derived from plants and the synthesis of molecules unique to plants but important to the natural world or human kind.
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:
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.
H2O exists as a "polymer"
|1 liter of H2O||=|
Many biological molecules exist as isomers.
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.Metabolism
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 can be further divided into photosynthetic and chemosynthetic organisms.
As you might guess, chemosynthetic organisms use chemical energy,
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:
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.
Standard free energy is designated DG°
DG° = -RTlnKeq
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
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.
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.
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
|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 +
= -(2)*(23,063)*[0.817 -(-0.32)]
= -52.5 kcal
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
-- gives an idea of what the principal substrates that are being respirated
|Fat or Oil||0.7|
|Aerobic C6H12O6 + 6O2||6CO2 + 6H2O||DG° = -686 kcal|
|Anaerobic C6H12O6||2CH3CHOHCOOH||DG° = -47 kcal|
|All materials © 2001 Dr. David Hildebrand or Dr. Bob Houtz, unless otherwise noted.|
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