Review of Atoms, Bonds, and Molecules

I. Atoms

A. Matter

1. conventional matter - defined as a substance that has mass and occupies space - consists of atoms.
2. there are 94 different types of naturally occurring atoms - defined by differences in the number of protons in the nucleus. These are the naturally occurring elements. Atoms are also defined as the smallest unit of a pure substance (one element) that retains the properties of that substance and cannot be subdivided further by chemical means.
3. compounds are substances composed of two or more types of elements in a fixed ratio, with a particular structure/spatial arrangement maintained by chemical bonds (ionic or covalent). So, NaCl (table salt) is an ionic compound. H2O (water) is a covalent compound.
4. molecules are substances of two or more atoms bound together by covalent bonds. So, it is inappropriate to refer to a 'molecule' of NaCl (which is ionic). Two atoms of hydrogen bound together by a covalent bond is a molecule of hydrogen. It is not a compound, as it only contains one type of element. For compounds consisting of covalently bound atoms, a molecule is the smallest unit of the compound that maintains the properties of that compound. So, we can have one molecule of water, which is also a compound.

B. Properties of Atoms

We will use a very simplistic 'Bohr' model of atomic structure, emphasizing the particulate nature of matter (rather than the wave nature) and excluding a consideration of quarks. For a more detailed account, feel free to see this link from the University of Oregon and Wikipedia.

1. atoms have a nucleus containing protons (mass ~ 1 atomic mass unit; elementary charge = +1 ) and neutrons (mass ~ 1 atomic mass unit; elementary charge = 0). The number of protons defines the type of atom - the element - and it's atomic number. The mass of an atom is largely determined by the mass of protons and neutrons. Although all atoms of an element have the same number of protons, the number of neutrons can vary. These atoms with variable numbers of neutrons are called isotopes. Those with an excess number of neutrons are less stable and will loose them over time. These are radioisotopes, and they emit energy when they loose a neutron. They loose them at a constant rate, so you can date how old they are by how many have changed to the more stable state. Atoms with unequal numbers of protons and electrons have a net charge and are called ions.
2. the nucleus is surrounded by a cloud of electrons (mass ~ 0; elementary charge = -1), represented as shells and orbitals: Shells 1, 2, 3 have 1, 4, 9 orbitals, 'containing' a maximum of 2, 8, 18 electrons, respectively. The orbitals are 1000's of times the width of the nucleus, so an atom (and hence, all matter) is mostly space. For comparison, if you envision the nucleus of a carbon atom as a basketball (about 12 inches in diameter), the outermost electrons would be orbiting 5 miles away.
3. the distance between the orbital and the nucleus correlates with the energy of the electron (in terms of a wave function).
4. as electrons gain energy, they 'orbit' farther from nucleus. Without an input of energy, an atom will lose energy and approach it's lowest energy state, occupying the closest 'unoccupied' orbital available.
5. changing orbitals - and energy states - is a discrete process. Electrons must gain or lose discrete amounts of energy (quanta) to change position to another orbital.
6. Binding properties are largely governed by the number of electrons in the outermost orbital/shell. They achieve greater stability when the outermost orbitals/shells are full. They achieve this stability by losing, gaining, or sharing electrons with other atoms.

II. Bonds

A. Covalent Bonds

Atoms share electons in pairs: H2, H2O, etc. These are the primary bonds in biologically important molecules - they can be non-polar (shared evenly) like H2 - or polar (shared unevenly...creating a charge difference across the molecule - as in water, where the shared electrons are held more tightly by the larger oxygen nucleus, pulling the electron cloud off the hydrogen nucleu, revealing some of its positive charge).

B. Ions and Ionic Bonds

If the attraction between nuclei is very unequal, the shared electrons can be stripped from one of the atoms and taken by the other. This creates charged particles (ions) which may then be attracted to one another based on their opposite charge. (NaCl)

C. Hydrogen Bonds

These are weak ionic bonds, weak forces of attraction between a partially charged Hydrogen Atom (+ charge) and a negatively charged molecule or the negative portion of a molecule.

III. Molecules

A. Water

       1. Structure

            - H2O is a polar molecule with partially positive hydrogen ends and a partially negative oxygen end
            - thus, water forms hydrogen bonds with other water molecules, and other charged substances (polar or ionic).

       2. Properties and Their Importance

        a. often called a 'universal' solvent because polar and ionic compounds dissolve in water; once dissolved, they can interact with other solutes. By 'dissolving', we mean the separation of molecules or ions from one another. This happens because the water molecules can get between the molecules/ions and bind to them, separating these molecules/ions in solution.

        b. water has a 'high specific heat' - meaning that it takes lots of energy to change its temperature and state. So, aqueous solutions (cells and aqueous environments) are thermally stable.

        c. water dissociates into H+ and OH- ions, at a concentration of 1 x 10-7 molecules in pure water = pH of 7.

        d. water is 'cohesive', in that it 'sticks' to iself; and it is'adhesive', in that it sticks to charged surfaces. Capillary action in vascular plants and small blood vessels is a function of these properties.

B. Carbohydrates

        1. Structure:
                - monomer - monosaccharide (simple sugar) - CnH2nOn  (glucose, galactose, fructose are 6 carbon sugars; ribose, ribulose, deoxyribose are 5 carbon sugars)

               - disaccharides: sucrose (glucose + fructose); maltose - (2 glucose)

                - polymer - polysaccharide - chain of sugars
                        starch, glycogen, chitin, cellulose

                - monomers are linked together into polymers using dehydration synthesis - a removal of a water molecule (dehydration) and the synthesis of a bond. This requires energy and is catalyzed by enzymes in living systems.

        2. Function:
                a. energy storage:
                         - all large biomolecules have lots of bonds and thus store lots of energy.  But, the larger the molecule, the more time it takes to harvest all the energy by metabolic breakdown (catabolism).  So, polysaccarides serve better as 'longer-term' energy storage than monosaccharides, whereas monosaccarides, because they can be metabolized more quickly, serve better as a short term energy supply. (starch in plants andglycogen in the liver of animals are longer term storage molecules; glucose is the short-term energy molecule in all of life)

                b. Structural:
                         - cellulose is just a long chain of glucose.  And decomposers break down wood to create the sugars they will use for metabolic energy.
                         - chitin is the primary component of exoskeletons in arthropods.

    C. Proteins - (we will cover this in more detil during the lecture on protein synthesis)

        1. Structure:
                monomer - amino acid - amine (NH2) group at one end and carboxyl group (COOH) at other
                        there are 20 different amino acids that are found in living systems.

                polymer - polypeptide - 100 to 300 amino acids long.  The AA's are linked by dehydration synthesis reactions into a long linear chain.  Because there are 20 Amino Acids ("letters") that can be used in their construction, proteins can have a limitless number of different combinations (like letters in different combinations make differnt "words").  This variety in form means variety in function.

**Higher levels of structure:

1. the primary structure of a polypeptide/protein is the linear sequence of amino acids

2. this linear sequence can take a helical or "pleated" sheet shape, depending on bond angles and soforth. These are secondary levels structure

3. some proteins then fold upon themselves, taking a globular shape. This globular shape is maintained by bonds between different functional groups of differnt amino acids. Enzymes and cell membrane proteins are common globular proteins.this is called tertiary structure.

4. Sometimes, single proteins are not functional on their own - they must be combined with other proteins to forma a protein with a quaternary structure. Hemoglobin, with 2 alpha and 2 beta globular polypeptides, is one example. collagen is another, composed of several helical polypeptides.

        2. Function:
                a. Energy Storage: (all biomolecules can be broken down for energy harvest.  Typically, since proteins are doing something else, too, they are broken down last so that the organism can maintain this function that the protein performs for as long as possible).
                b. Structural:
                        after water, animals are largely proteinaceous
                        collagen, elastin, muscle proteins, etc.
                c. Metabolic:
                        all biological reactions are catalyzed.  Most biological catalysts are proteinaceous ENZYMES
                d. transport:
                        cell membrane - there are proteins that assist transport across the membrane
                        organism - hemoglobin, for instance, transport oxygen
                e. Immunity:
                        antibodies are proteins.

D. Fats and Lipids:

        1. Structure:
            monomer - fatty acid - long carbon chain with a carboxyl group (COOH)
                 - can be saturated (with H - no double bonds between C's) or unsaturated (a double bond)

                 - animal fats are usually saturated, and are solid at room temp. Plant and fish fats are usually unsaturated, and are liquid at room temp and are called 'oils'. By saturating a plant fat, it can be made solid - hydrogenated fat or oil. (changing peanut oil into peanut butter, or vegetable oil into "crisco"). During this process, trans-fats are also created. These are unsaturated fats with a trans (not cis) conformation. Trans-fats have been associated with atherosclerosis
 
            polymer - fat (triglyceride)
                    - three fatty acids attached by dehydration synthesis to a glycerol molecule
 
                     - phospholipid:  glycerol with 2 fatty acids and a phosphate (PO4) group.  The PO4 is negatively charged (thus, polar), while the fatty acids are non-polar.  This accounts for how these molecules orient in aqueous solutions, forming membranes. A "choline" groups is typically attached to the phosphate.

        2. Function:
                a. Energy storage: saturated fats are very dense - the fatty acids fit together, in parallel, very snugly.  So, to store the most energy in the smallest space, fats are the preferred medium.

                b. Cell membranes - barrier to water soluble materials. The non-polar lipid "bilayer" is a barrier to water soluble materials (that are ionic or polar). So, ionic and polar compounds can't just flow into the cell; the cell can regulate how much of what gets in and out.

                c. Insulation
 
                d. Hormones - derived from fats, lipid soluble, slip right theough cell membranes into cells, so they can function at very low concentrations.

E. Nucleic Acids (DNA/RNA) - we will cover this in more detail later

Study Questions:

1) What is the basic structure of an atom (mass, charge, and location of its components)?

2) What is the relationship between electrons, orbital distance, and energy?

3) What are isotopes and ions?

4) What are covalent, ionic, and hydrogen bonds?

5) Draw the structure of water, including all electrons in their shells. Also identify the covalent bonds, and the position of the partial charges on the molecule.

6) What two large classes of compounds dissolve in water? Why?

7) What is the basic structure of a monosaccharide?

8) What type of molecule are chitin and cellulose?

9) Show how two monosaccharides are linked together. What is the name of this reaction?

10) What is the structure of a fatty acid? A triglyceride?

11) What is the monomeric unit of proteins? Draw one, without specifying the variable group.

12) Show how two amino acids are linked together. What is the name of the reaction?