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Organic chemistry – the chemistry of life • • • • Based on carbon Takes place in water (aqueous solution) In a narrow range of temperatures (on earth) Is complex, vastly more complex than any other chemical system known • Dominated by large polymeric molecules • Matter is made of combinations of elements • Elements are substances that cannot be broken down or converted into other substances by chemical means, like carbon • An atom is the smallest particle of an element that still retains it’s chemical properties • Groups of atoms linked together form molecules including the molecules of life • Atoms have a nucleus which is positively charged due to the protons (neutrons have no charge) which is surrounded by a cloud of electrons, which have a negative charge. • Atomic number = number of protons, and determines the chemical behavior of the element • Number of neutrons can vary and have no charge. (12C, carbon has 6 protons and 6 neutrons.) They contribute to the stability of the nucleus – too many or too few and it may disintegrate by radioactive decay. These are isotopes. – Ex. 14C has 6 protons and 8 neutrons and is unstable. • Atomic weight = number of protons plus neutrons – Ex. 14C has an atomic weight of 14 Figure 2.2 • The mass of an atom is specified in daltons, one dalton = mass of one hydrogen atom. • One gram of hydrogen = 6 X 1023 atoms • 6 X 1023 = Avogadro’s number = the number of molecules in a mole of the any substance • molecular weight of any substance is the mass of 6 X 1023 atoms = a mole of that substance. – 1 mole of carbon weighs 12 grams Figure 2.3 Figure 2.4 • Electrons move continuously around the nucleus. They move in discrete orbits or electron shells. • The electrons in the closest shell are very strongly attracted to the positive nucleus. This shell holds only 2 electrons. • The next or second shell can hold up to eight electrons. This shell is farther away from the positive nucleus and the electrons are less tightly bound. • The third shell holds up to eight electrons but the fourth and fifth shells hold up to 18 electrons. • An atom with the outermost shell full is stable and not inclined to react with other atoms. • Atoms with unfilled electron shells are less stable and have a strong tendency to react with other atoms. Figure 2.5 • Atoms with unfilled outer shells tend to interact by exchanging or sharing electrons in order to fill their outer shells. • The number of electrons an atom needs to complete its outer shell is its valence. • When atoms gain or lose electrons, the bond is ionic. • When atoms share electrons, the bond is covalent. • Covalent bonds can be polar, when the electrons are shared unequally. Become ions cation anion Packed together in a precise 3-D array. Salts are usually soluble in water due to interaction of polar water molecules and charged ions. The molecules of the cell are held together by covalent bonds. These bonds do not break in water. They are stronger than ionic bonds Shared electrons form a cloud around both nuclei which is densest in between them and holds them together. The repulsion of the 2 positive nuclei and the attraction of the positive nuclei and the negative electron cloud balance out at a specific bond length. Table 2-2 • Bond strength is measured in kilocalories per mole (6 X 1023), the energy required to break the bond. • Kilocalorie = the energy needed to raise the temperature of one liter of water by one degree centigrade. • Covalent bonds are very strong. Breaking and making these bonds requires specific catalysts (enzymes) and is carefully controlled by the cell. • Covalent bonds result in specific bond angles, length, and bond energies. This precise geometry is the basis for the 3-D shape of organic molecules. Figure 2-9 • Noncovalent bonds are usually weaker on a one to one basis. Panel 2-7 and Figure 2-12 6 electrons, needs 2 A single bond allows rotation, is longer and not a strong as a double bond A double bond is stronger, shorter, and more rigid. Bonds help to determine the 3-D shape of a molecule. Non-covalent bonds are weak but lots of weak bonds together can be relatively strong. Life hinges on the properties of water • Properties of water are due to hydrogen bonds (non-covalent) • The two bonds between oxygen and hydrogen are highly polar because the oxygen is larger and more positive it attracts the electrons more strongly. Therefore the oxygen side of water is more negative and the hydrogen sides are more positively charged. • The slightly positive hydrogen attracts negative ions or negative areas on polar molecules. These are hydrogen bonds. • Hydrogen bonds are much weaker than covalent bonds and are easily broken by random thermal motions. The hydrogen bonds of water are continually made and broken. • Hydrogen bonds give water it’s life giving properties - stays liquid at room temp, has a high boiling point, and high surface tension. • Many hydrogen bonds together can be very strong and are important for the folding of large molecules into their unique shape and for interactions between molecules. * • Molecules that are polar and ions are called hydrophilic because they form hydrogen bonds with water. – Sugars, DNA, RNA, many proteins • Molecules that are not polar do not dissolve in water and are called hydrophobic. – Hydrocarbons in cell membranes • When a molecule with a hydrogen in a highly polar covalent bond dissolves in water, the hydrogen virtually give up its electron and becomes a proton (H+). • This proton can leave it’s electron behind and become attracted to the oxygen atom in another water molecule, forming a hydronium ion (H30+). • These protons are constantly jumping form here to there. • Substances that release protons when they dissolve in water are acids. • Substances that raise the concentration of the hydroxyl ion (OH-) are bases (alkaline). • The concentration of protons is expressed by the pH scale. The pH inside the cell must be closely regulated close to pH of 7. • Water is neutral, pH = 7 A cell is formed from carbon compounds organic molecules • Carbon-carbon bonds are highly stable and can form chains, branched chains, and rings. • Carbon can also combine with other molecules to add chemical groups with specific chemical behavior and physical properties. Glycerol plus fatty acids = triacylglycerol (pg 58) Amino acids Peptide bonds Nucleic acids phospholipids 2 phosphoric acids minus water Cells contain four major families of small organic molecules small organic molecules: *monomers for macromolecules *energy sources *formed and broken down into a distinct set of simple compounds Simple sugars, monosaccharides, carbohydrates (CH2O)n Glucose Sugar polymers can be branched, contain different types of bonds and different derivatives. The result is tremendous variety and complexity, making the sequence and arrangement of a particular carbohyrate very difficult to determine compared to the sequence of proteins and DNA. •cell membranes (recognition etc.) •glycolipids and glycoproteins (ABO blood types) •mechanical support •cellulose in plants (cell wall) chitin in insects (exoskeleton) •energy (glucose) storage •Glycogen (animals) and starch (plants) Most fatty acids are linked to other molecules by their carboxylic acid group. Different fatty acids differ only in the length of their hydrocarbon chains and the number and position of the carbon-carbon double bonds. Serve as concentrated energy reserve in cells. Can be broken down to produce 6Xs the usable energy weight for weight as glucose. Are stored in the cytoplasm of many cells as droplets of triacylglycerol. Animal fats found in meat, butter, and cream are usually saturated, and solid at room temperature. Plant oils like corn oil contain more unsaturated fatty acids. Peanut and olive oil contain monounsaturated fatty acids. Molecules with both hydrophobic and hydrophilic regions are termed amphipathic Amino acids have a carboxylic acid group and an amino group linked to the alpha carbon. The chemical variety results from the side chain attached to the alpha carbon. These can be charged (5 ) or uncharged and polar (hydrophilic) or non polar (hydrophobic). Notice that the hydrogen atoms nearest to nitrogen are smaller since their electrons are pulled in by the large nitrogen nucleus, creating a smaller electron cloud around them. Nucleotides can act as short-term carriers of chemical energy ATP adenosine triphosphate Formed by oxidation of food. The phosphates are linked by phosphoanhydride bonds which release large amounts of useful energy when broken. The terminal phosphate is frequently split off by hydrolysis, releasing energy which drived energy-requiring reactions in the cell Ribonucleic acid (RNA) contains bases A, G, C, and U. Usually occurs as single stranded molecules. Deoxyribonucleic acid (DNA) contains bases A, G, C, and T and is always doublestranded. The two polynucleotide strands are held together by hydrogen bonds between bases. Macromolecules are abundant in cells Each polymer is built by enzymes which covalently bond monomers by condensation reactions Macromolecules contain a specific sequence of monomers covalently linked. The diversity that results is demonstrated by proteins. 20 amino acids allow for 20200 possible 200 aa polypeptides. Macromolecules are extremely diverse and versatile proteins serve as enzymes to catalyze reactions subunits to build structural components of cells molecular motors to produce force and movement Single covalent bonds allow rotation and therefore unlimited conformations (shapes). However, macromolecules normally have one stable conformation due to many non-covalant bonds forming between different areas of the molecule. ionic bonds hydrogen bonds van der Waals attractions hydrophobic forces When two molecules fit closely and are attracted by many non-covalent interactions, their binding affinity can be strong. This is the basis for the specificity of binding of macromolecules to other molecules, as in enzyme specificity for their substrates, DNA double helix, multimolecular structures like ribosomes.