2. Macromolecule - molecules composed of repeating molecular units (biopolymers).

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1 Biochemistry I Biological Principles I. FUNDAMENTAL PRINCIPLES UPON WHICH BIOCHEMISTRY IS BASED A. Prerequisite Requirements Technically, you must have completed or earned credit for Organic Chemistry II to be enrolled in this class unless you have special permission from the Chemistry Department. If you are enrolled in this class, you must also be enrolled in the corresponding lab for this class; unless you have departmental approval otherwise. This means that the student understands and can apply concepts related to molecules and their interactions, identify basic organic molecules and their functional groups, conduct quantitative analysis associated with fundamental reactions, solve any single variable, linear equality, and that they can read, comprehend, and/or apply concepts and/or instructions related to such systems as well as rudimentary science. If you are not fluent in these principles (and fluent means able to complete almost any exercise involving these principles, not that you have heard of them), you should not enroll in this class until you are. It is not required, but advisable that you have completed Analytical Chemistry. B. Purpose The purpose of this instructional unit is to outline the fundamental principles associated with beginning the study of biochemistry. This is not and all inclusive module, you must use your textbook! C. Definitions (only what s presumed new) 1. Biomolecule - molecules typically associated with organisms. 2. Macromolecule - molecules composed of repeating molecular units (biopolymers). 3. Supramolecular Complexes - two or more molecules (including one or more macromolecules) joined by noncovalent bonding. 4. Hydrophobic Interaction - nonpolar substances in aqueous solution aggregate and bond in response to their repulsion from water and water s stronger attraction to polar components of the solution (including other water molecules). 5. Ligand - when two entities interact, the smaller and/or more mobile is usually designated the ligand. 6. Complementarity - entities match (note, not entities are the same or alike, but that they match). Substances interact best when they compliment each other with respect to structure, polarity, and charge. Structural complementarity means the surfaces of the entities match; a protrusion on one entity matches an indentation on another. When polarity is complementarity, the polar groups of one entity align with the polar groups of another and likewise for nonpolar groups. If two entities are complementarity as far as charge, the charges on one entity align with the opposite charges of the other entity. The maximum interaction is achieved if all three properties are complementarity. The text only discusses structural complementarity. 7. Denaturation - the loss of an entity s structural order that does not involve breaking covalent bonds. 8. Hydrolysis - a chemical reaction in which water molecules cause the breaking of covalent bonds in a substance (not to be confused with denaturation). 9. Virus - a mobile, supramolecular complex of nucleic acids, proteins, and other organic molecules capable of reproducing itself in other life forms by using the life form s replication tools. 10. Lysogeny - a stage of a virus cycle where it is dormant in a host; almost all viral substances are inactive (note, the virus is not incapacitated, just inactive). 11. Lysis - a stage of a virus cycle where all of the viral machinery as well as required host replication tools become active, and new viral particles are made (in droves).

2 D. Lessons 1. Life on Earth A quick synopsis of life on earth is: certain life forms (plants, algae, and some prokaryotic organisms) assimilate CO 2 to trap energy from sunlight. They subsequently produce larger molecules from the CO 2 (biomolecules), stripping the CO 2 of the O 2, and returning the O 2 to the environment. Life forms incapable of doing the same assimilate the biomolecular byproducts (usually by ingesting the organisms) and break them down, trapping the released energy, and using O 2 from the environment to trap freed electrons, releasing CO 2 into the environment as a consequence. For most organisms on earth, energy sequestered or produced is stored in molecules like ATP and NADPH. 2. Biological Entities The entities associated with living organisms are as follows: 1) inorganic precursors - small molecules with molar masses under 100g/mol including CO 2, O 2, H 2 O, N 2, etc 2) metabolites - intermediate sized molecules produced or used in basic metabolic reactions including small carbohydrates, large anions and cations, Molecules like pyruvate and citrate, etc 3) subunits (or building blocks) - large molecules used to make macromolecules including amino acids, nucleotides, carbohydrates, glycerol and fatty acids, etc 4) macromolecules - very large molecules composed of repeating molecular units called subunits including DNA, RNA, lipids, proteins, etc 5) supramolecular complexes - two or more types of molecules (including one or more macromolecules) joined by noncovalent bonding including virus, membranes, ribosomes, cytoskeletons, etc 6) organelles - regions of a cell that are segregated from the rest of the cell by a membrane and that serve a specific function including nuclei, mitochondria, chloroplast, endoplasmic reticulum, etc. Organelles are made of all the other entity types. 7) cells - a structure surrounded by a membrane and a molecular mesh capable of replication, growth, metabolism, and stimulus response. Cells are made of all the other entity types. Cell types include prokaryote and eukaryote. 3. Properties a. Information - molecules associated with life are typically asymmetric, they have distinct ends; they are structurally polar - like a zipper. The consequence of this is that large molecules like macromolecules may contain information. This property is next to impossible for symmetric molecules. ABCDEFGFEDCBA The set of characters on the left contains ABCDEFGHIJKLM less information than the set on the right even though they contain the same amount of characters. b. Stickiness - molecules associated with life are capable of reversibly sticking to other molecules; they stick, then come undone with little input of energy. Molecules can come together and complete tasks, then separate until the task needs to be repeated. Without the stickiness, the interactions between molecules would be to short for almost any biological reaction. This stickiness is called non-covalent bonding; bonding without the sharing of electrons (so it is much weaker, hence reversible under typical conditions).

3 The forces that cause the stickiness are always electrostatic in nature. They include: * ionic interactions * dipole interactions * van der Waals interactions * hydrophobic interactions Functional groups like amine groups and oxide groups have full electromagnetic charges (units of + or - one) because some atom has gained or lost electrons. These functional groups make ionic regions of molecules. Ionic groups are attracted to their opposite charge. Polar molecules, like water, have partial charges because the electronegativity of one atom in the molecule is greater than the electronegativity of the other, and the atom with the greater electronegativity will attract negative charge (electrons) more. These partial charges are always present and always on the same atoms so the molecules are permanent dipoles. Dipoles are attracted to their opposite charge. Nonpolar substances have partial charges either because of induction and/or because of the movement of electrons in the molecule. These partial charges come and go very quickly and they can be anywhere in the molecule, hence the molecule can only be a temporary dipole. Temporary dipoles are attracted to their opposite charge. c. Complementarity - Entities may be complementary as far as any combination of structure, polarity, or charge. If either are incompatible, the strength of the interaction between the entities is reduced. Maximum interaction is attained if all three levels of complementarity are at work. The entities in A are complementary with respect to structure. The entities in B are complementary with respect to structure, polarity and, in one case, charge. The entities in C are complementary with respect to structure and charge. d. Structure - The atoms that make up a unit of substance are held together (bound to each other) by covalent, ionic, or metallic bonds. Substances containing mostly covalent bonds are called molecules. Substances composed of aggregations of anions and cations held together by ionic bonds are called ionic compounds. Substances composed of metal atoms bound together are called, well, metals. The 3-dimensional shape of one unit of a molecule, or a sample of ionic compound or metal is the 3-dimensional structure of that substance. Molecules may interact with other molecules or within themselves by much weaker interactions called molecular interactions. If these interactions are all internal to

4 one unit of a molecule, the shape is called the molecule s conformation. If two or more molecules interact to make a complex (a group of molecules held together by molecular interactions), the shape of the complex is the 3-dimensional structure of the complex. The shape of the complex is also called the conformation of the complex. Now, bonds can be formed, but they can also be broken. The covalent bonds that hold molecules together are much stronger so breaking them is much harder. Hence, breaking covalent bonds requires way more energy than breaking molecular interactions. Hydrolysis (B) is the breaking of covalent bonds using water. Hydrolysis results in the production of new substances and loss of original ones. Hydrolysis is virtually impossible to reverse under standard conditions. Denaturation (A) is the breaking of noncovalent interactions; loss of conformation. Denaturation does not change the identity of a substance and is usually easily reversible under standard conditions. Digesting proteins occurs by hydrolysis; proteins are hydrolyzed. Straightening hair is denaturation; the strands of protein are denatured (although, if you leave the denaturant in long enough, the hair will be hydrolyzed; and you, bald). e. Cells - There are two types of cells on earth; prokaryote and eukaryote. Prokaryotic organisms do not have organelles, eukaryotic organisms do. Virus are neither technically (virus are supramolecular complexes, not cells); they are classified by the type of cells that they invade (infect). Virus that infect prokaryotic organisms, only infect prokaryotic organisms, and are called, prokaryotic virus or bacteriophage. Likewise, virus that only infect eukaryotic organisms are called eukaryotic virus. T4 is a well studied prokaryotic virus. HIV is a well studied eukaryotic virus. E. Application 1. What is the most common gas in the atmosphere? a. N 2 b. O 2 c. CO 2 d. H 2 O 2. Which substance is ionic? a. MnO 4 - b. NH 4 + c. NaNO 3 d. Al(s) 3. Which substance is polar? a. CH 3 CH 2 CH 2 CH 2 CH 3 b. CO 2 c. NaCl d. NH 3 4. Which inorganic precursor is produced by plants? a. monosaccharide b. CO 2 c. O 2 d. RNA 5. The sulfhydryl group of one entity interacts with a carbon radical of another. If the

5 region surrounding the sulfhydryl group is mostly nonpolar, which type of region surrounding the radical will produce the longest interaction between the groups? a. Nonpolar b. Polar c. Cationic d. Anionic 6. What is the best analogy for denaturation and hydrolysis? a. Physical and chemical change b. Applying and removing tape c. Extinguishing fire with water d. Mitosis of cells 7. Report two cell components (that are larger than macromolecules) that all organisms have in common? ANSWERS: 8. All prokaryotic organisms are unicellular. TRUE or FALSE 9. All eukaryotic organisms are multicellular. TRUE or FALSE 10. Compare the volume of HIV to that of T4 and report the quantitative results.

The Logic of Biological Phenomena

The Logic of Biological Phenomena molecules are lifeless yet, in appropriate complexity and number, molecules compose living things What makes living things distinct? they can grow they can move they can