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The four major classes of biological molecules
polymers monomers
carbohydrates (starch, cellulose) sugars (glucose)
proteins amino acids (20 to choose from)
lipids (fats or oils = triglycerides) fatty acids (+ glycerol)
nucleic acids (DNA, RNA) nucleotides (sugar, phosphate, N-base)

monomer vs. polymer
mer = unit
mono = one
poly = many
polymers are made many identical (starch) or similar (proteins) monomers

The monomers are joined by covalent bonds to make the polymers. Water is released as the covalent bonds form = condensation reaction.
(When the polymers are broken down - or digested - to release the monomers, water is added to break the covalent bond = hydrolysis reaction.)

Mainly made of C, H, O. 1 C : 2 H : 1 O [CH2O]
monosaccharides: glucose, fructose (two examples of hexoses)
disaccharides: sucrose
polysaccharides: starch, cellulose

Functions of carbohydrates:
1. Structural
        Cell Wall: cellulose (40-60% of plant cell walls)
2. Storage of food (calories) in seeds, roots, stems, wood, bark, leaves
        Starch: amylose and amylopectin
3. Transport of calories and carbon skeletons

contain C, H, O, N, and some S (two of the 20 amino acids have S)
Polymers of amino acids
The covalent bond between amino acids is called a peptide bond. Therefore, proteins are sometimes called polypeptides.
The 20 amino acids have the same basic format, differing only in what is known as the R group.
H-bonds and covalent bonds between S atoms of the R groups give proteins their shapes and functional properties.

Functions of proteins
1. Structural
        The plant cell wall is 2-10% protein.
        Cellular membranes are 40-75% protein.
2. Storage
        Seeds, roots, stems (wood and bark of woody plants): storage of calories and N
3. Enzymes
        catalysts: speed up chemical reactions but are not consumed or changed by the reaction
        As enzymes, proteins are responsible for all metabolic reactions and the synthesis of all of the other molecules found in organisms (pigments, hormones, etc.)

Hydrocarbons, nonpolar. Contain H, C, and just a hint of O.

Functions of lipids
1. Storage
        triglycerides (triacylglycerides, TAGs):  glycerol (3 C sugar alcohol) + 3 fatty acids
                the fatty acids can be saturated or unsaturated
                fats = solid at RT; oils = liquid at RT
                for calorie storage, are usually found just in seeds. Exceptions: fruit of avocado, olive
2. Structural
        phospholipids in cell membranes
                glycerol + 2 fatty acids + phosphate
                phosphate end is polar = hydrophilic
                fatty acid end is non-polar = hydrophobic
                spontaneously form a bilayer in water: two hydrophilic surfaces with a hydrophobic interior
                fatty acids + long chain alcohols
                cutin: in cuticle, which covers above ground plant parts
                suberin: in cell walls of the endodermis (roots, pine needles) and cork cells (bark)

Nucleic Acids
contain C, H, O, N, P
Basic building block: nucleotide
            5 C sugar (pentose): ribose or deoxyribose
            N-base: cytosine, guanine, adenine, thymine/uracil
important monomers (ATP) and dinucleotides (NAD+)
polymers: DNA (two nucleotide polymer strands held together by H-bonds) and RNA (one nucleotide polymer strand)

Gene expression: DNA --> RNA --> protein

Organic Acids
intermediates in many reaction pathways and cycles; more oxidized than sugars but more reduced than CO2; acidity of plant vacuoles  

second most common organic molecule after cellulose; reinforces cell wall, most notably in tracheary elements and sclerenchyma cells; decay resistant
Porphyrins (tetrapyrroles)
    Chlorophylls:  complexed with Mg (magnesium)
    Hemes (cytochromes, other heme-containing proteins):  complexed with Fe (iron)
In cytochromes, the Fe undergoes oxidation/reduction  (Fe3+/Fe2+) during electron transfer processes of the mitochondrial electron transport chain and chloroplast Z-scheme.


Secondary Metabolites

primary metabolites
found in all plants
perform essential roles in development and metabolism
examples: protein amino acids, cell wall sugars, hormones, photosynthetic pigments

secondary metabolites
generally distributed among limited groups of plants (Family, Order, etc.)
functions are often unknown
chemical structures and synthetic pathways are often complex
three main groups of molecules:  phenolics, terpenes, alkaloids

Molecule classes are not confined to secondary metabolites
terpene primary metabolites: β-carotene, lutein, zeaxanthin, abscisic acid, gibberellins, brassinosteroids
terpene secondary metabolites: essential oils, saponins, rubber

roles of secondary metabolites in plants:
anti-herbivory agents
anti-microbial agents
attractants for pollinators and seed/fruit dispersers

Oxidation and Reduction
Metabolism is the exchange of matter and energy between an organism and its environment.  Chemically, metabolism will involve oxidation and reduction reactions of organic molecules.  The carbon atoms in organic compounds are oxidized or reduced as metabolism takes place.  In a strict chemical definition, oxidation is the loss of electrons and reduction is the gain of electrons. This is fairly obvious when we look at ions like Fe in heme because of the changes to the Fe ion's charge.   In practical terms, when looking at carbon compounds during metabolism, watch the number of oxygen and hydrogen atoms per carbon atom.  For example, let's compare carbon dioxide and a carbohydrate.  Carbon dioxide (CO2) is a low energy form of carbon, and the carbon atom in carbon dioxide is said to be in a highly oxidized state.  Carbohydrates, such as the simple sugar glucose (C6H12O6), are high energy forms of carbon.  The carbon atoms in glucose are said to be reduced.  Compare the number of oxygen atoms to carbon atoms in carbon dioxide and glucose.  In carbon dioxide, there are two oxygen atoms for the one carbon atom.  In glucose, there is one oxygen atom per carbon.  This indicates that the carbon in carbon dioxide is more oxidized than the carbon in glucose.  Also, because glucose has less oxygen per carbon than carbon dioxide, the carbons in glucose are more reduced than the carbon in carbon dioxide.  Now look at the number of hydrogen atoms per carbon.  Carbon dioxide has no hydrogen atoms, while glucose has two hydrogens for each carbon.  Reduced carbon atoms have more hydrogen associated with them than oxidized carbons do.  How reduced are the carbon atoms in a typical fat, like palmitic acid?  The chemical formula is C16 H32O2.  There are two hydrogens per carbon, just like in glucose, but there is only one oxygen atom for every eight carbon atoms.  Fats contain very reduced carbon.  The more reduced a carbon atom is, the more energy (calories) it contains.  This is why fats contain more calories per C than carbohydrates do; the carbon in fats is more reduced than the carbon in carbohydrates.  So when we look at matter and energy conversions during metabolism, we are looking at oxidation and reduction of carbon atoms, with reduction putting energy into carbon atoms (as happens during photosynthesis) and oxidation releasing that energy (as happens during respiration).


Condensation vs. Hydrolysis
    Relate to the synthesis and breakdown of polymers in living organisms

    examples of monomers and polymers
    What distinguishes carbohydrates structurally from other groups of molecules?
    What functions do carbohydrates and soluble sugars have in cells?

    What distinguishes lipids structurally from other groups of molecules?
    What functions do lipids have in cells?

    monomers; peptide bond
    primary, secondary, tertiary, and quaternary structure
    What distinguishes proteins and amino acids structurally from other groups of molecules?
    What functions do proteins have in cells?

Nucleic Acids
    examples of monomers, dimers, and polymers
    What distinguishes nucleic acids  structurally from other groups of molecules?
    What functions do nucleic acids and nucleotides have in cells?

    basic structure; complexes with a metal ion
    function of chlorophylls (Mg = magnesium)
    function of cytochromes (Fe = iron)

Oxidation vs. Reduction
    Relate to carbon atoms in organic molecules and CO2
    With regard to calories, what is the consequence of reduction of C?  Of oxidation?

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25 August 2003; links checked 25 August 2003