A basic understanding of chemistry is extremely important to understanding biology and biological systems -- organisms, their tissues and their cells are ultimately composed of atoms and molecules and many important biological processes are chemical reactions -- e.g. metabolism, photosynthesis, growth.
I am going to assume that you have had no chemistry -- we will begin at the beginning and just cover some very basic chemistry.
The atom is the basic chemical unit.
1. nucleus -- contains subatomic protons (+ charge) and neutrons (no charge).
2. electrons (- charge) -- rotate around the nucleus -- generally, the number electrons = the number of protons in the nucleus.
Figure 2.3 from the text shows simplified models of the atoms called hydrogen (H) and helium (He).
There are 92 naturally occurring kinds of atoms or elements -- differ from one another by having different number of protons and neutrons in the nucleus and different numbers of electrons revolving around the nucleus.
95% of living material is made of only 4 different atoms:
1. 20% carbon (C)
2. 62% oxygen (0)
3. 10% hydrogen (H)
4. 3% nitrogen (N)
Remaining 5% made up of 30 different elements.
Atoms are not usually found by themselves &emdash;&emdash; they combine with other atoms to form molecules -- e.g. O atoms combine with one another to form O2-- this is the form that oxygen generally is found -- when different atoms combine a compound is formed -- e.g. H2O, NH3, CO2, NaCl.
The ability of particular atoms to combine or react with other atoms is determined by the atom’s electron configuration -- electrons move around nucleus in levels called shells representing different energy levels.
Atoms that have outer electron shells that are filled are inert = nonreactive
Other atoms, including H, C, O, and N, do not have filled outer shells and they are reactive -- they readily combine with other atoms.
Atoms combine and are held together by chemical bonds -- there are three types of chemical bonds:
1. ionic bond.
2. covalent bond
3. hydrogen bond
Ionic bonding: One way that atoms may achieve electron stability in their outer shell is by losing or gaining electrons and becoming ions.
Example: sodium (Na) and chlorine (Cl) often form ions (Na+, Cl-) -- sodium losses an electron and chlorine picks up an electron -- since they are ions with opposite charges, they are attracted to one another and an ionic bond is formed -- the resulting molecule is a compound called sodium chloride (NaCl) (table salt).
Ionic bonds are strong when the compound exists as a dry solid -- in water, these compounds dissolve readily back into ions.
Covalent bonding: rather than gaining or losing electrons, atoms may share electrons with other atoms to fill both their outer shells and give them stability.
Two types of covalent bonds: nonpolar and polar covalent bonds.
Nonpolar covalent bonds: equal sharing of electrons -- e.g. H2, O2, N2
Polar covalent bonds: unequal sharing of electrons -- often occurs when atoms are of different sizes -- e.g. NH3, CO2, H2O
Figure 2.12:
Hydrogen bonds -- differ from ionic and covalent bonds.
Ionic and covalent bonds are bond between atoms to form molecules -- but, hydrogen bonds form between molecules.
Hydrogen bonds are produced when polar molecules are present -- e.g. a water molecule, because of covalent bonding between oxygen and hydrogen, has a positive and negative pole -- the negative pole on one water molecule will be attracted to and will form a hydrogen bond with another water molecule.
Hydrogen bonding gives water many of its biologically important characteristics -- e.g. high specific heat, surface tension, cohesiveness.
Let's now consider the concepts of acids and bases.
Some compounds release large numbers of H+ ions when they are in water -- these are called acids -- e.g. HCl, H2SO4 are acids.
On the other hand, some compounds release OH- ions when they are in water -- these compounds are called bases -- e.g. NaOH, KOH are bases.
Strengths of acids and bases are measured by the pH scale --ranges from 0 to 14 -- measures relative concentrations of H+ and OH- ions -- pure water is neutral and has pH = 7.0 -- anything with a pH less than 7 is an acid; pH greater than 7 is a base.
Figure 2.12 in the text gives some pH values for common substances -- important biologically because chemical reactions in cells are pH specific -- disruptions in pH will adversely affect organisms -- may effect entire groups of organisms -- e.g. acid rain and effect on lakes.
Organisms must maintain relatively constant internal pH (homeostasis) to live.
pH of blood = 7.4 -- slightly basic --serious illness or death may result if this pH isn't maintained within narrow limits -- -- yet H+ and OH- may be added to blood through various metabolic processes -- how is "pH" balance maintained?
Blood also contains special chemical compounds called "buffers" -- buffers pick up excess H+ or OH- ions or release them if they are in short supply -- by doing this, they act to keep pH in blood (and cells) from changing.
Let’s now turn our attention to some of the molecules that are important to cells and other living systems.
As previously mentioned, 4 atoms (C, O, H, and N) make up 95% of living tissue. Water is one very important compound found in living material -- other important compounds consist of carbon -- organic compounds.
There are four major groups of biologically important molecules:
1. Carbohydrates
2. Lipids
3. Proteins.
4. Nucleic acids.
I. Carbohydrates -- group of compounds composed of carbon, hydrogen and oxygen -- this category includes several subgroups of molecules,
Monosaccharides (simple sugars): consist of 3-6 carbon atoms, 6-12 hydrogen atoms and 3-6 oxygen atoms (1 C : 2 H : 1 O).
e.g. glucose is a 6-carbon sugar that is of central importance to biological systems because it is the primary "food molecule" used by cells as a source of energy.
Figure 3.5:
Polysaccharides: large molecules (macromolecules) consisting of several hundred to several thousand monosaccharides linked together.
Notice that polysaccharides are made up of many smaller subunits (monosaccharides) -- macromolecules made up of small subunits are called polymers and the small subunits called monomers -- this pattern is seen in several types of biologically important molecules.
Polysaccharides have several functions, but one of the most important is that they are the storage form for monosaccharides -- e.g. when plant cells contain excess monosaccharides, they convert them to molecules of starch for storage; in animals a polysaccharide called glycogen serves the same function -- starch and glycogen are easily broken down back into their monosaccharide subunits when energy is needed.
II. Lipids.
Fats -- type of lipid consisting of a 3-carbon molecule called glycerol and 3 fatty acids -- fats are a storage form of energy.
Fatty acid = chain of 16-18 carbon atoms with hydrogens attached -- a fatty acid is bonded to each carbon on a glycerol to make a fat -- here’s what one looks like (don’t write this down).
Two other important kinds of lipids:
1. phospholipids -- fats that contain phosphorus -- major component of cell membranes.
2. steroids -- hormones important to growth, reproduction, etc.
III. Proteins -- most diverse group of biological molecules -- many different functions -- proteins act as enzymes and control the rate of chemical reactions in cells; others are structural materials (e.g. hair, claws, nails, feathers); others used for transport (e.g. hemoglobin); proteins can also be used as an energy source.
Proteins are macromolecules -- polymers of smaller monomer subunits called amino acids -- may consist of dozens or even hundreds of amino acids.
Amino acids -- contain C, H, O like carbohydrates, but they also contain nitrogen -- some may also contain sulfur -- amino acids consist of the following:
(Figure 3.13)
1. amino group: -NH3
2. carboxyl group: -COOH (group may release H+ ion and is thus acid)
3. remainder of molecule: -R may be short or long chain of carbons, may be ring structure.
This particular amino acid is called valine.
There are 20 different amino acids in living material -- different a.a's have different R groups -- e.g. valine and cysteine.
Two amino acids can be linked together to form a dipeptide -- bond formed between amino group of one a.a. and carboxyl of another -- this bond is called a peptide bond.
Many amino acids linked together by peptide bonds form chains (polymers) called polypeptides -- a protein may be a single polypeptide or it may consist of several different polypeptide chains.
Organisms possess many different proteins -- e.g. 700 different proteins in a simple bacteria -- probably around 10,000 in your own body.
Protein function determined by protein structure -- structure determined by the numbers and kinds of amino acids that make up the protein.
Proteins lose their ability to function if their structure changes.
Denaturation: changing of protein structure -- can be cause by changes in pH, temperature (e.g. heat), radiation, chemical agents -- a familiar example of denaturation to an extreme is the hard-boiled egg -- organisms must guard against changes in pH, temp, etc. that may denature their proteins.
IV. Nucleic acids -- long polymers of smaller subunits called nucleotides -- macromolecules that control structure and function of a cell -- important nucleic acids:
1. deoxyribonucleic acid (DNA) -- the genetic material that is passed from parent to offspring -- contains information that give organisms there characteristics.
2. ribonucleic acid (RNA) -- works with DNA to control the construction of proteins (protein synthesis).
Nucleotide -- consists of 1) a 5-carbon sugar (e.g. ribose); 2) a phosphate group; and 3) a nitrogenous base (single or double ring).
Nucleotides form chains (nucleic acids) that have a phosphate-sugar-phosphate backbone -- single chain = RNA; double chain = DNA
DNA -- hydrogen bonds between nitrogenous bases links sugar-phosphate backbones together.
NEXT TIME: Cell Structure and Function