Bios 208 1st EditionExam # 2 Study Guide o Water Molecule>o pH o The pH scale measures howacidic or basic a substance is. Itranges from 0 to 14. A pH of 7 isneutral. A pH less than 7 isacidic, and a pH greater than 7is basic. >o Organic Compoundso A number of characteristic groups can replace the hydrogensattached to skeletons of organic moleculeso Functional groups are the components of organic moleculesthat are most commonly involved in chemical reactionso Hydrocarbonso Some hydrocarbons make straight chain molecules ofincreasing length, but they can also branch to form isomers.o Isomers have the same formula but different structures…e.g. butane and isobutane are both C4H10.o Some hydrocarbons can have isomers based upon where their double bond is located.o E.g. 1-butene, 2-butene.o Certain hydrocarbons also form cyclic structures which form rings.o E.g. cyclohexane (single bonds) and benzene (alternating single and double bonds).o Functional groupso Distinctive properties of organic molecules depend on the carbon skeleton and on the molecular components attached to it.o A number of characteristic groups can replace the hydrogens attached to skeletons of organic molecules.o Functional groups are the components of organic molecules that are most commonly involved in chemical reactions.o The number and arrangement of functional groups give each molecule its unique properties.o Some function groups include:o Hydroxyl- Alcohols = usually end in -ol. - Polar as a result of the electrons spending more time near the electronegative oxygen atom.- Can form hydrogen bonds with water molecules, helping dissolve organic compounds such as sugars.o Carbonyl- Ketones if the carbonyl group is within a carbon skeleton.- A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal.- Ketone and aldehyde groups are also found in sugars, giving rise to two major groupsof sugars: ketoses (containing ketone groups) and aldoses (containing aldehyde groups).o Carboxyl- Carboxylic acids or organic acids.- Acts as an acid; can donate an H+ because the covalent bond between oxygen and hydrogen is polar.- Found in cells in the ionized form with a charge of 1– and called a carboxylate ion.o Amino- Amines.- Acts as a base; can pick up an H+ from the surrounding solution (water, in living organisms).- Found in cells in the ionized form with a charge of 1+.o Sulfhydryl- Thiols.- Two sulfhydryl groups can react, forming a covalent bond. This “cross-linking” helps stabilize protein structure.- Cross-linking of cysteines in hair proteins maintains the curliness or straightness of hair. Straight hair can be “permanently” curled by shaping it around curlers and then breaking and re-forming the cross-linking bonds.o Phosphate- Organic phosphates.- Contributes negative charge to the molecule of which it is a part (2– when at the end of a molecule, as at left; 1– when located internally in a chain of phosphates).- Molecules containing phosphate groups have the potential to react with water, releasing energy.- Phosphate group significance- ATP is an important source of energy for cellular processes. One phosphate containing molecule, adenosine triphosphate (ATP), is the primary energy transferring molecule in the cell.- ATP consists of an organic molecule called adenosine attached to a string of three phosphate groups.o Methyl- Methylated compounds.- Addition of a methyl group to DNA, or to molecules bound to DNA, affects the expression of genes.- Arrangement of methyl groups in male and female sex hormones affects their shape and function.o Isomerso Structural isomers have the same empirical formula, but a different arrangement of bonds.- C5H12.o Geometric isomers must have: - A C=C double bond (no rotation around this bond).- Different substituents are on the carbons: can be on the same side, or across from each other.- C2H2Cl2.o Stereo Isomers- Also called Enantiomers are related to each other by mirror symmetry - Like left and right hands. - An asymmetric carbon must be present (i.e., a carbon with 4 different substituents)- L-alanine and D-alanine are amino acids. - Only the L-form is used to make proteins.- They are mirror image molecules.o Lipids and Fatso Lipids- Contain many C-C and C-H bonds.- Hydrophobic.- Store lots of energy in these bonds.- Large molecules, but NOT polymers.- There are many types. Triglycerides: fats and oils (energy storage). Phospholipids: bilayer membranes. Steroids: membranes; hormones.o Fats and Oils- Fat synthesis involves a dehydration reaction. A fatty acid (chain of 16-20 C’s) is joined by its carboxyl group to glycerol.- The bond formed is an ester linkage.- Fat molecule (triacylglycerol, triglyceride, or TG). Three fatty acids are attached to one glycerol by ester linkages.- Hard fats from animals (butter, lard, bacon grease) are solid at room temperature (~25ºC) due to tight packing of saturated fatty acids.- Oils from plants (olive oil, corn oil) are liquid at RT due to cis.- Double bonds in unsaturated fatty acids, such bonds cause bends or kinks, which prevents solidification.o General Polymer Structureo Biological Polymers- Large and complex: carbohydrates, proteins and nucleic acids (lipids are large but arenot polymers).- Assembled from small and simple monomers called subunits. They exhibit emergent properties.- There are about 50 common biological monomers, some of which have functions of their own.o General functions:- Storage.- Structure, e.g. a spider’s web is made of proteins.- Information.o Monomers are joined to form polymers by a process called dehydration synthesis or condensation.o One H2O is released for each bond formed.o Energy is required.o Polymers are broken down by hydrolysis. One H2O is consumed for each bond broken.o Energy is released.o Polysaccharideso Starch- Contains only glucose- Joined by 1, 4 linkages.- Branched or unbranched.- Coiled and hydrated in aqueous solution.o Carbohydrateso General functions and properties.o Monosaccharides have the formula (CH2O).- n = 3 triose C3H6O3.- n = 5 pentose C5H10O5.- n = 6 hexose C6H12O6.o Functions: energy storage (starch).- Structure (cellulose, chitin).- Information (cell surface receptors).o Monosaccharides.- Aldoses have a terminal carbonyl group (-C=O) and ketoses have an internal carbonyl group.- Hydroxyl groups (-OH) are on the other carbons.- Glucose and fructose are structural isomers.- Glucose and