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, 4orbitals, "containing" a maximum of 2, 8, 8 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.
A. Covalent BondsAtoms 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.
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
2. this linear sequence can take a helical or "pleated" sheet shape, depending on bond angles and soforth. These are secondary levels 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
E. Nucleic Acids (DNA/RNA)
DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are nucleic acids - polymers consisting of a linear sequence of linked nucleotide monomers. We will describe the structure of the monomers first, and then describe how they are linked into linear polymers. Finally, we will describe the double-stranded structure of ds-DNA.
1. The monomers are "nucleotides"
- Nitrogenous Base: each nucleotide has a single nitrogenous base attached to the 1" carbon of the sugar. This nitrogenous base may be a double-ringed structure (purine) or a single ringed (pyrimidine) structure. The purines are adenine (A) and guanine (G). The pyrimidines are thymine (T), cytosine (C), and uracil (U). DNA nucleotides may carry A, G, C, or T. RNA nucleotides carry either A, G, C, or U.
2. Polymerization is by "dehydration synthesis"
As with all other classes of biologically important polymers, monomers are linked into polymers by dehydration synthesis. In nucleic acid formation, this involves binding the phosphate group of one nucleotide to the -OH group on the 3" carbon of the existing chain. For the purposes of seeing how this reaction works, we can envision an H+ on one of the negatively charged oxygens of the phosphate group. Then, a molceule of water can be removed from these two -OH groups, leaving an oxygen binding the sugar of one nucleotide to the phosphate of the next.
This creates a "dinucleotide". It has a polarity/directionality; it is different at its ends. At one end, the reactive group is the phosophate on the 5" carbon. This is called the 5" end of the chain. At the other end, the reactive group is the free -OH on the 3" carbon; this is the 3" end of the chain. So, a nucleic acid strand has a 5" - 3" polarity.
a. the nitrogenous bases on the two strands are "complementary" to each other, and form weak hydrogen bonds between them. A always pairs with T, and C always pairs with G. As such, there is always a double-ringed purine pairing with a single-ringed pyrimidine, and the width of the double-helix is constant over its entire length.
b. the two strands (helices) are anti-parallel: they are arranged with opposite polarity. One strands points 5" - 3", while the other points 3" - 5". The direction of the pentose sugars and the type of reactive group at the ends of the chains show this relationship.
4. RNA performs a wide variety of functions in living cells:
a. m-RNA (for "messenger") is the copy of a gene. It is the sequence of nitrogenous bases in m-RNA that is actually read by the ribosome to determine the structure of a protein.
b. r-RNA (for "ribosomal") is made the same way, as a copy of DNA. However, it is not carrying the recipe for a protein; rather, it is functional as RNA. It is placed IN the Ribosome, and it helps to ‘read’ the m-RNA.
c. t-RNA (for "transfer") is also made as a copy of DNA, but it is also functional as an RNA molecule. Its function is to bind to a specific amino acid and incorporate it into the amino acid sequence as instructed by the m-RNA and ribosome.
d. mi-RNA (micro-RNA) and si-RNA (small interfering RNA) bind to m-RNA and splice it; inhibiting the synthesis of its protein. This is a regulatory function.
e. sn-RNA (small nuclear RNA) are short sequences that process initial m-RNA products, and also regulate the production of r-RNA, maintain telomeres, and regulate the action of transcription factors. Regulatory functions.