Sonoma State University 2002
Department of Biology - Hanes
Animal Physiology
Chapter 3: Molecules, Energy, & Biosynthesis
Lecture
Application
Discussion
Reflection
This chapter should be easy review and we will not spend a lot of time on it. I will emphasize those portions with which students traditionally have trouble or which are basic to the following studies. Review chemical bonding and molecular structures.
Biochemicals
There are a number of theories and experiments which show that biochemicals essential to life can be synthesized under conditions that probably occurred during the formation of the earth. Experiments have produced amino acids, peptides, and nucleic acids. Accumulations of some organic chemicals form structures that are synonymous with those found in living systems. For example, phospholipids will form water enclosed membranes much like cells.
Water
Water is a very small molecule. It is asymmetrical making it dipolar which gives it many of its very special properties.Molecules of water hydrogen bond for an average time of 10-10 to 10-11 sec depending upon temperature. The hydrogen bond energy is 4.5 kcal/mol whereas the covalent bond energy is 110 kcal/mol.
Liquid water has increased cohesiveness (attraction between water molecules) and adhesiveness (attraction to other polar molecules like glass) over other similar molecules that are not as polar as NH3, H2S. This accounts for high surface tension, high boiling point, and low freezing point.
Liquid water also will insert itself between other molecules that are polar and create separated ions. For this reason it is an excellent solvent of polar molecules. Ions become hydrated by water (surrounded by oriented water molecules) making them act much larger in diameter than they are.
Water will hydrogen bond with polar groups on an amphipathic molecule as soaps and detergents. "Amphipathic" molecules often make micelles or membranes in water (Figs 3-9, 4-2).
Colligative Properties of Water
Colligative refers to those properties distorted by the fraction of molecules dissolved in the water. We must count molecules - so molal solutions are mentioned. There are 6.023X1023 molecules in a mole (in 18 g water, 342 g sucrose, 32 g O2). A one Molal solution is a molecular weight of solute in 1000 g water. This is inconvenient, so we use molar solutions that are close to the same concentrations. These are a molecular weight of solute in 1000 ml of solution. So 342 g sucrose dissolved in 1000 g water is one molal. If the same amount of sugar is dissolved in water and the total volume made up to 1000 ml, it is a 1 molar solution. If we want to express a concentration of a mixture of molecules, we can speak of osmoles and we can measure the osmolarity by colligative properties. An osmole is a mole of dissolved particles (6.023X1023 particles) in a liter of water, even if the particles are a mixture of different kinds of molecules. So we can measure the osmolarity of blood, cell fluid, oceans, freshwater, etc. even if we don't know the proportions of molecules in these. The colligative properties of water are its:
Of course some ionizing molecules only partially ionize at different temperatures and the colligative properties are dependent on the proportion of individual particles whether ions or molecules - so one can determine the "activity coefficients" of chemicals by using these relationships of the colligative properties. Commonly physiologists tend to ignore chemical activities as dilute solutions as are mostly the case in physiology are nearly 100% active.
Acids & Bases
Water ionizes slightly (10-7 of a mole is in the form of H3O+ and -OH). The protons (H+) can be passed from molecule to molecule. Other molecules also ionize releasing H+ (ex. HNO3 to H+ and -NO3) that associate with water to make H3O. We call these "acids". Other molecules will attract protons and combine with them, taking them away from water (ex. NH3 and H+ to NH4+). We call these "bases". The addition or removal of H+ from water solutions affects the proportions of "hydronium" and "hydroxyl" ions in water in accordance with the law of mass action. This involves the dissociation constant of water and states that the concentration of hydronium ion times the concentration of hydroxyl ion must be equal to 10-14 moles/l. So if acid is added to water and makes a hydronium ion concentration of 10-3, then the concentration of hydroxyl ion must be 10-11 moles/l. If a base absorbs protons from water and makes a concentration of hydronium ion of 10-9 moles/l, then the concentration of hydroxyl ion must be 10-5 moles/l. The pH of a solution is a shorthand way to represent these numbers. pH is the negative of the exponent of the hydronium ion concentration. So a neutral water solution would have a pH of 7 and in the above two examples would be a pH of 3 and 9 respectively. Any value for a solution above 7 would be considered basic and any solution with a pH below 7 would be considered acid. The pH of neutrality (pN) rises as temperature falls and most animals regulate at a pH above neutral rather than a set pH (the set point would be a higher pH at lower temperatures).
The Biological Importance of pH
Protons (H+) can be passed from molecule to molecule and this fact is important in photosynthesis and the production of ATP with the electron transport chain in mitochondria.Ionized molecules do not pass through cell membranes well, but small unionized molecules may pass quite easily. As NH3 and CO2 pass easily while NH4+ and -HCO3 do not.
Some molecules as amino acids are called "zwitterions" because they can be negatively or positively charged depending upon the pH of the solutions they are in. They can also act as pH "buffers".
pH Buffer Systems
A buffer is a partially ionized molecule in solution so the solution must contain an acid (potential proton donor) and a base (potential proton acceptor). We will designate these as HA and -A respectively. The "Henderson-Hasselbach" equation states the following:
K' = [H+] [-A] Where [] = molar concentration of
[HA] K' = dissociation constant
pK' = -log10 K'
The pK' is convenient and analogous to pH
A pK' that is large means that the molecule is slightly ionized and
is a weak acid; and a pK' that is small is a strong acid or highly
ionized.
pH = pK' + log [-A]
[HA]
So one can calculate the pH of a buffer if the pK' and the proportion of hydrogen donor and acceptors is known. The greatest buffering capacity of a solution is when [HA] and [-A] are large and equal. This happens when pH = pK' (since log10 1 = 0). This is a condition in which the concentrations of an acid and its salts are equal. See Fig 3-13 which illustrates what happens to pH as H+ is removed from a solution that contains a buffer.
Electrical Terminology
Read the small section on p 49 and become familiar with electrical terms emphasized. Be able to define them and understand what they mean.
BIOLOGICAL MOLECULES
There are many important biological molecules including water, elements, salts, etc. We will concentrate, for now, on the large, organic, calorically important, common molecules.
Lipids
"Lipids" are defined as molecules that dissolve well in organic solvents (gasoline) and not so well in water. "Fats" are lipid molecules that contain "fatty acids". Fatty acids are chains of carbon and hydrogen atoms that have a "carboxyl group" on their business ends. Saturated fatty acids are those that have no double bonds, they are saturated with hydrogen. Unsaturated fatty acids have one or more double bonds. All biological fatty acids have double bonds that are "cis", that is the hydrogens on either side of the double bond are on the same side of the molecule. When biological fats are partially "hydrogenated", some of the double bonds will be converted to "trans". Cis double bonds bend the molecule at the double bond, trans double bonds do not. Trans double bonds are not considered healthy in a diet. The number of double bonds in a molecule decreases the melting point of the fat. This has significance in the behavior of a fatty membrane under different temperature conditions."Triglycerides" ("neutral fats") are three fatty acids covalently bonded to the three OH groups of a glycerol molecule forming a multiple ester. "Diglycerides" have two fatty acids attached to glycerol, etc. "Phospholipids" have two fatty acids attached to glycerol and the third OH group covalently bound to a phosphate group or a phosphate group that has other organic molecules attached to it. Cell membranes are composed of a mixture of phospholipids, one of which is lecithin. Neutral fats are the main component of stored fat in fat cells. Neutral fats and phospholipids are both amphipathic. The long hydrocarbon chain of fats is hydrophobic (dissolves easily in organic solvents and other long hydrocarbon chains). The glycerol end and especially the phosphate group on phospholipids is hydrophilic (associates well with water and shuns the fatty side). For this reason, phospholipids especially are perfect for forming membranes. When water is present, they do not form large blobs easily as the phosphate-glycerol end seeks water and it is most readily found at the interface of water and lipid. Think about why membranes form naturally from phospholipids that are arranged in a double layer with the phosphate-glycerol ends facing toward water. There are some fatty acids that are "essential", that is they are required in the diet since animals need them and can not synthesize them. These are the omega 3 and omega 6 fatty acids that is the first double bond is between the 3-4 carbon and the 6-7 carbon from the end away from the carboxyl group. These are called the linolenic and linoleic acid series respectively. The double bonds in biological fatty acids are always separated by one saturated carbon. One of the linoleic acid series, arachadonic acid (20C omega 6, 4 double bonds) , is the source of prostaglandins, thromboxane, and other autocoids. Fats contain 9.5 Kcal/g, a very high caloric value per weight. Since they do not dissolve in water, they have no water of hydration.
Carbohydrates
"Carbohydrates" have the general formula (CH2O)x and are composed of sugars which are polyhydroxyl aldehydes and ketones. "Monosaccharides" are simple sugars as glucose, fructose and galactose. "Disaccharides" are two simple sugars covalently bonded as sucrose (glucose + fructose), lactose (glucose + galactose), and maltose (glucose + glucose). "polysaccharides" are many simple sugars covalently bonded as cellulose (glucose beta-linked), dextrins (glucose a-linked), and starches (mostly glucose alpha-linked and sometimes branched-chained). Glycogen is a branched, glucose animal starch. Simple sugars are excellent cellular caloric sources. Nerve cells can only utilize glucose as an energy source. Sugars may also be attached to proteins as glycoproteins and may act as receptors on cell membranes. Carbohydrates may also act as "quick" energy sources for cells as they are reduced to simple sugars. They supply about 5 Kcal/g of pure carbohydrate except that starches require an amount of water, their water of hydration - so they are not a great energy source per weight as they occur in the body.
Proteins
"Proteins" are long, linear chains of amino acids. The sequence of amino acids is determined by the genetic code. The genetic code codes for only 20 different amino acids. There are a few proteins that animals use that contain amino acids other than the 20 that are coded for. This means that these amino acids must be converted from one of the twenty while they are on the protein. Other non-coded amino acids are synthesized and used for neurotransmitters etc., not in proteins. Most proteins are enzymes (speed up chemical reactions), but many are non-enzyme, structural chemicals. Proteins can also have moieties of fats (lipoproteins) or carbohydrates (glycoproteins) or non-protein organic compounds as the vitamins. Some proteins or parts of proteins form an alpha helix, other parts may be arranged in pleated sheets. Some parts of the protein may be fat soluble, other parts water soluble. Some proteins are globular in overall shape (only short segments of a-helix), while others are more linear. All of these characteristics of the tertiary structure are determined by the side-chains on the amino acids. The amino acid cysteine has a sulfhydryl group on the end of its side chain which can covalently bond with another sulfhydryl group to link two parts of a chain or two different chains of amino acids. Different side-chains will also impart different electrical charges to the molecule and these can buffer or change with pH. Proteins, when oxidized for energy, release 4.5 Kcal/g in the pure state; but proteins also require some water of hydration and the nitrogen released in the process must be converted to less toxic compounds than nitrogen oxides so there is energy lost in the conversion to ammonia, urea or uric acid. Therefore proteins are not an efficient caloric storage molecule.
Proteins can be "tangled" chains of amino acids with particular configurations or a beta configuration that consists of a pleated sheet. Pleated sheets may also cause damage as they accumulate in cells as the "amyloids" in some cells or "tangles in Alzheimer's disease.
Nucleic Acids
While these are important, they are covered so thoroughly in other courses that we will not discuss them much. When they are broken down in digestion, they may be converted to uric acid, a nitrogenous waste product.
Work the pH practice problems and make up your own questions until you understand the quantitative manipulation of buffer solutions.
Note the electrical nomenclature and symbols on pp 50-52. We will be using these at a later date. Can you draw a diagram for a household circuit?
Draw graphs of Vo vs [substrate] that illustrate the difference between competitive inhibition and non-competitive inhibition.
What are the ramifications of water being a polar molecule?What are the effects of pH changes on biochemicals? Of what value, is producing a strong acid at the beginning of digestion?
What are the special characteristics of proteins, carbohydrates, and lipids?
Can you make an argument that life evolved from inorganically produced biochemicals?What examples can you give of chemical characteristics that contribute to characteristics of living organisms (polarity, amphipathic, hydrogen bonding)? What about energy relationships between molecules?