The Chemistry of Life

Why Carbon?

Source of vast chemical diversity in living things is a function of the chemical bonding capacity of carbon.

• Carbon forms bonds with C,H,O,N
• Hydrocarbons: carbon bonded to C and H
  • Straight chain; Branched and Ring
  • Derivative hydrocarbons: substitution of other elements or groups
• Isomers: same atomic content and molecular formula but different atomic arrangement
• Functional groups: chemical reactivity

Four Major Groups of Organic Compounds Found in Living Systems

• Carbohydrate
  • Sugars: simple and complex
• Lipids
  • Fats and Oils
• Proteins
  • Structural and Catalytic
• Nucleic Acids
  • RNA and DNA

The Role of Carbohydrates (CH2O)n

• Ready energy:
  • Monosaccharides: simple sugars (e.g. glucose)
    • rapidly hydrolyzable for energy release
    • contain functional groups that allow higher orders of organization
  • Disaccharide: two simple sugars linked by a covalent bond (e.g.. sucrose, lactose, maltose)
    • transport form of carbohydrates
    • formed by dehydration synthesis
• Storage and Structure:
  • Polysaccharides: complex sugar formed from multiple simple sugars
    • Starches: principle storage in plants
    • Glycogen: principle storage in animals
    • Cellulose: structure in plants
    • Chitin: structure in animals

Lipids

• Lipids are derivative hydrocarbon
  • In simplest form contain a carboxyl group at one end (-COOH) (Fatty acid)
  • Primarily nonpolar (nonsoluble in water)
  • Some are complex with the addition of ionic groups (Changes solubility)
• Fatty acids are esterified to the glycerol molecule by dehydration synthesis

Role of Lipids

• Storage of energy and insulation
  • Neutral lipids: Fats and Oil
    • Saturated hydrocarbons
    • Unsaturated hydrocarbons
  • Energy content of fats is 2.5 times that of simple sugars on a per gram basis
    • If all the energy stored as fats in our bodies were converted into sugar, our weight would increase by about 70 to 80 pounds

Role of lipids

• Structural components of biological membranes
  • Phospholipids and glycolipids
    • Form sheet based on their amphipathic nature
    • Bilayer structure formed by hydrophobic interactions
• Chemical Messengers
  • Steroids: some vitamins and hormones

Proteins

• More complex structurally than carbohydrates and lipids
• Polymers of amino acids
• Fundamental to both the structure and function of living organisms

Roles of Proteins

• Structural: All types of tissues
• Catalytic activities: Enzymes
• Storage: Amino acids and energy
• Chemical Messengers: Hormones
• Transport: Contractile proteins and Membrane carriers
• Defense: Immunoglobulins

Protein Structure

• Primary structure: polymer of amino acids
  • 20 amino acids found in biological proteins
    • Amino acids all share same basic structural backbone
    • Classified by "R" group
      • Provide different chemical behavior
  • Linkage between amino acids is a peptide bond.
    • Linked amino acids form a polypeptide
    • For a 100 amino polypeptide there are 20 100 possible combinations
• Secondary structure: higher order spatial conformations
  • Alfa (a) helix is a coiling into a regular cylinder
    • Results from intramolecular weak bond (H bonds)
    • Moderately ridged in nature
      • Keratin (fibrous): Skin, nails, hooves and horns (hard)
      • Keratin: Hair and wool (soft)
      • Beta (b) pleated sheet: side by side polypeptides are cross-linked by H bonds
        • Results are flexible and strong but resist stretching
          • Silk, spider webs, feathers, scales and beaks of reptiles and birds
• Tertiary Structure: Three dimensional folding superimposed on the secondary structures.
  • Arises due to nature of the "R" groups and interactions between the secondary structures
  • Contains regions of a helices and b-pleated sheets which give differing characteristics to proteins
  • Stabilized by covalent disulfide bonds
• Quaternary Structure: Proteins composed of two or more independently folded polypeptides
  • Held together usually by weak bonds

Roles of Nucleic Acids

• Information Storage and Transmission
  • Material that genes, the units of heredity
  • Nucleic acids are polymers of nucleotides
    • Nucleotides have a common basic composition
    • Nitrogenous base
    • Phosphate group
    • sugar molecule (ribose or deoxyribose)

Deoxyribonucleic Acid (DNA)

• Information storage
• Nucleotides:
  • Adenine , Guanine (Purines)
  • Cytosine, Thymine (Pyrimidines)
• Nucleic acids are bonded together such that the phosphate of one nucleotide is attached to the sugar of the next.
  • Creating long polymers

DNA Structure

• DNA molecules carry the hereditary information in the sequence of the four nucleotides within the structure.
• DNA molecules do not exist as single strands.
  • Two DNA chains arranged in opposite directions are held together by hydrogen bonds between their nucleotide nitrogenous bases
• Association of two strands of DNA results in a regular helical coiling with the important constraint
  • Each pair of nucleotides adjacent to one and other must be a specific purine-pyrimidine pairing
  • A with T
  • G with C

Ribonucleic Acid (RNA)

• Ribonucleic acid is constructed similar to DNA except that the nitrogenous base uracil is substituted for thymine.
• RNA's have diverse functions with the cell
  • Messengers (mRNA)
  • Structures (rRNA)
  • Transport (tRNA)
  • Catalysis (Ribozymes)

How Chemical Reactions Work

• All energy in the biosphere is in directly derived from the capture energy from the sun.
  • Excitation of electrons to higher energy orbitals
  • This energy is harvested to fuel the processes of life
• Study of energy transfer processes is known as Thermodynamics

Free Energy

• Free energy (G) is energy in a system that is available to do work
• First Law of Thermodynamics: The total energy of universe remains constant.
  • Energy can neither be created or distroyed, it can only change form
• Second Law of Thermodynamics: The total order of the universe tends toward the highest degree of randomness (entropy)
• The change in free energy (DG) that accompanies any chemical reaction determines if the reaction will proceed spontaneously.

In other words, the direction of a chemical reaction will depend upon whether the products have more or less energy than the reactants.

• -DG determines a spontaneous reaction
• +DG is a nonspontaneous process

Free Energy of a Reaction

• The total change in G is determined by the initial and final states

DG = G_f - G_i

• Exergonic reactions release energy during reaction process (- DG)
• Endergonic reaction require the input of energy to drive the reaction (+ DG)

Reaction Direction and Equilibrium Constants

• Forward and Backward Reaction

A + B C + D

• If the forward reaction is exergonic then the reverse reaction must be endergonic
  • Endergonic reaction can proceed in nature, slowly, due the distribution of kinetic energy in any population of molecules
• Equilibrium Constants (Keq) is the stable ratio between the forward and backward reaction

Energy of Activation

• In order for any two chemicals to react they must come very close to together in the proper orientation .
  • Combination of these reactants into a product often requires the breakage of covalent bond
  • The energy required to initiate this process is referred to as Energy of Activation (Ea)
    • Once the activation barrier is overcome the energy released in the reaction may drive subsequent reactions

Catalysts

• Chemical reactions can be accelerated by the addition of other compounds.
  • a substance that speeds up a reaction but is unchanged during the course of the reaction is referred to as a catalyst.
  • Catalysts only affect the rate of a reaction, not direction or the final equilibrium.
  • Catalysts function by reducing the Ea

Biological Catalysts

• Enzymes: How they function as catalysts
  • Enzymes are specific they react with only a small number of compounds referred to as the substrate(s).
  • Enzymes can be regulated by the presences or absence of critical compounds
  • The key enzyme specificityis it's shape (particularily the shape of the active site)

Enzymes function as catalysts by:

1. Forming complexes with the reacting molecules.

2. Changing their shape slightly to improve the fit between enzyme and substrate.

3. Increasing the local concentration of the molecules.

4. Orienting the molecules correctly so that the reaction can occur efficiently.

5. Changing shape of the substrate molecule, allowing them to reach the transition state.

Regulation of enzyme activity

• Effects of temperature
• Effects of pH
• Effects of concentration
• Effect of regulatory compounds
  • Competitive inhibition
  • Noncompetitive inhibition
    • Allosteric regulation

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• This page is maintained by James C. Pushnik: jpushnik@ecst.csuchico.edu
• Last modified 11/8/96