the essence of life...

1. the essence of life... biology 1

2. outline • Water: the most important molecule in the equation of life? • Inorganics • Organics

3. H2O • Earth is misnamed - in fact, the earth’s surface is covered by 70% water • Living cells are 70–95% water • Life evolved in water • Search for life on other planets can be simplified as a search for other planets containing water • The vitally important fluid nature of water is due to hydrogen bonds, as a result of the covalent bonding between H and O2

4. The polar nature of the covalent bond between hydrogen and oxygen is critical in forming the known properties of water • Solvency - H2O is the universal solvent • Cohesiveness - leads to adhesion, capillary action and surface tension • Buffer - H2O can mediate processes by acting as a buffer • Heat capacity - H2O can absorb heat, resisting temperature changes

5. Solvency of H2O • Polarity of water causes it to be an efficient solvent of ionic compounds, termed hydrophylic compounds • Most biochemical reactions involve solutes dissolved in water • Water is an essential medium for transport of reactants and products for biochemical reactions • Non-polar molecules tend not to dissolve in H2O—termed hydrophobic

6. Cohesion of H2O molecules • Transient hydrogen bonding causes water molecules to ‘stick’ together • Allows water to ‘stick’ to a substrate (adhesion)—e.g., a plant vessel wall • Cohesion results in capillary action • Cohesion causes a surface tension at air/water interface, causes water to bead

7. H2O as a buffer • Water can protect cells from environments of dangerously high chemical concentrations • By acting as a buffer (e.g., acid/base environments), water minimizes fluctuations in pH

8. The high heat capacity of H2O • Hydrogen bonds require extra energy to break—thus, H2O has an unusually high heat capacity • A large body of H2O can act as a heat sink (reducing greenhouse effect?) • Evaporative cooling is a major mechanism in keeping organisms from overheating • The marine environment has a relatively stable temperature

9. Other inorganics • Life requires other inorganic molecules and elements to mediate biochemical processes • In some cases they are reactants • In other cases they are an defining part of an organic molecule • For example, Na+Cl-, K+, Mg+, HCO3-

10. Organics • Involve carbon, which has an outer shell of 4 electrons, leaving 4 free spaces • Organic molecules are thus generally based on a unit shape of a triangular based pyramid • Organic molecules are generally defined by the elements other than carbon in them, and by the types of bonds they form with carbon

11. Organic molecules are often formed of monomers (small, basic units) which may join together to form polymers (long chains of monomers). • One typical method of polymerization is by the condensation reaction (removal of an OH- group and an H+ group from two respective monomers to form water, leaving a bond between the two monomers • Condensation reactions can be reversed via hydrolysis (the addition of water to a bond within a polymer • Condensation and hydrolysis reaction are common mechanisms in metabolism

12. Biologically important organic molecules • Carbohydrates (for short term energy) • Lipids (for long-term energy and membrane structure) • Proteins (for membrane and other organelle structure • Nucleic acids (for the construction of DNA and RNA—the cell “management”)

13. Carbohydrates • Monomer form is the monosaccharide (in the ratio of CH2O). For example, • 6-carbon sugar (hexose): e.g., Glucose (C6H12O6) • 5-carbon sugar (pentose): e.g., Ribose • Two monosaccharides can join together to become a disaccharide via a condensation reaction that creates a glycosidic linkage. For example • Sucrose (Glucose + Fructose) • Maltose (Glucose + Glucose)

14. Many monomers joined together form the polymer polysaccharide • Polysaccharides are a good source of medium term energy. For example, • Starch (a helical glucose polymer with a 1-4 linkages, either unbranched (amylose) or branched (amylopectin) • Glycogen (highly branched form of amylopectin) • Polysaccharides are also structurally important. For example, • Cellulose (D-glucose unbranched chain using b 1-4 linkages) • Chitin (in fact an amino sugar)

15. Lipids • Typically hydrophobic compounds • Fats are important for long term energy stores, and consist of 3 fatty acid chains joined at one end by a molecule of glycerol via an ester link • Fatty acid chains vary in length, and may have double bonds (unsaturated) or not (saturated) • Saturated fats are usually solid at room temp., and are found in animals • Unsaturated fats are usually liquid at room temp., and are found in plants

16. Phospholipids have one of the fatty acids in a triglyceride replaced by a phosphate group • The fatty acid hydrocarbon tails are hydrophobic • The phosphate group (ionic) is hydrophillic • Phospholipids thus show ambivalent behavior to water • Phospholipids are a major component in the structure of a biological membrane • Biological membranes can be argued to play perhaps the most important role in cellular metabolism

17. A third group of lipids are the Steroids • Steroids play an important role in the regulation of metabolism. For example, • Cholestrol • All fats have high energy bonds. Hydrolysis reactions thus yield high energy. Fats are typically broken down for their high energy content

18. Proteins • Proteins are made of monomers termed Amino Acids which: • have both an amine (NH2) and a carboxyl acid (COOH) group • A third group (given the symbol ‘R’) defines the amino acid • Amino acids join together via condensation to form polypeptide chains (linked by peptide bonds). Components of these chains then interact to give a unique 3-dimensional structure, vital for the macromolecule’s reactivity • Such a 3-dimensionally shaped polypeptide is termed a protein

19. There are only 20 common amino acids • Proteins are defined by 4 types of structure • Primary structure refers to the sequence and the types of amino acids linked together. Polypeptide chains are typically very long) • Secondary structure refers to linkages between carbons within the polypeptide backbone (b pleating, a helix coiling) by hydrogen bonds

20. Tertiary structure refers to linkages between R-groups, including • Hydrogen bonds • Sulphur bridges • Others • Quarternary structure refers to incorporation of other polypeptide chains. For example, • Hemoglobin consists of 4 polypeptide chains around Fe

21. Nucleic Acid • Nucleic acids store and transmit hereditary information • This information ultimately is expressed through the production of goal-specific proteins, including enzymes and structural molecules • There are two types of nucleic acid: • DNA (deoxyribonucleic acid) • RNA (ribonucleic acid)

22. Nucleic acids are polymers, the individual unit (monomer) of which is the nucleotide • Nucleotides have: • A “backbone” • A pentose sugar • Ribose • Deoxyribose • A Phosphate group • A nitrogenous base

23. DNA • Is a double stranded helix (model first proposed by Watson and Crick). Deoxyribose lacks an OH group on the 2nd carbon • Nitrogenous bases always pair purine to pyrimidine. Specifically, • Adenine-Thymine (A-T) • Guanine-Cytosine (G-C) • Contains coded information to program all cell activity • Makes up genes, which in turn group into chromosones • Is responsible for the manufacture of mRNA

24. RNA • Is a single stranded nucleic acid that is the intermediate agent in production of proteins • Components of RNA are similar to that of DNA, except uracil (U) is substituted for thymine (T) • There are several kinds of RNA, including • Messenger mRNA • Transfer tRNA • Ribosomal rRNA • Other uses for nucleotides include chemical transfer agents (ATP) and electron transfer agents (NAD)