CHAPTER 2 INTRODUCTORY CHEMISTRY & BIOCHEMISTRY
Why is it necessary to study chemistry? Living things are made of matter (anything that occupies space & has mass) & matter follows the laws of chemistry. Even the characteristics we consider to be unique to living things are the result of chemical reactions (ex. movement as a result of muscle contractions).
I. THE ATOM
A. Atom - smallest unit of matter unique to a particular element.
B. Element - A substance made up of only one kind of atom - ex. carbon contains only carbon atoms. Elements can't be broken down into other substances by ordinary chemical means. Each element displays unique properties (ex. some are gases, some are solids, some are metals, etc.). About 92 elements occur naturally (there are also some man-made elements). Some of the elements important to our study of living systems are carbon, oxygen, hydrogen, nitrogen, sodium, chlorine, phosphorus, and potassium. You may also be familiar with the elements lead, iron, iodine, gold, silver, and copper, nickel, and platinum.
C. Some Important Things to Know about Atoms & Elements:
1. An atom consists of 2 basic parts:
a. nucleus - the nucleus contains protons & neutrons:
1.) protons - positively charged; all atoms have protons; protons give the nucleus a positive charge.
2.) neutrons - neutral in charge; fxn.: "stabilizers"; all atoms except hydrogen have one or more neutrons.
b. electrons negatively charged; occupy orbit energy levels or shells around the nucleus; attracted to the positive charge of the nucleus; in an atom, the number of electrons always equals the number of protons, so the atom, as a whole, has no charge; electrons determine the chemical properties of elements (ex. whether they are a liquid, solid, or gas, etc.).
2. atomic number = number of protons (or number of electrons); in an atom, the number of protons always equals the number of electrons; this number differs for each element.
3. atomic mass number = number of protons + number of neutrons; the number of electrons is not included in the mass number due to their insignificant mass.
4. The 6 elements important for building organic molecules like carbohydrates, lipids, proteins, and nucleotides are: carbon, hydrogen, oxygen, sulfur, nitrogen, & phosphorus.
Note: Be able to determine the number of electrons, protons, & neutrons in an atom, given the atomic number & atomic mass. Ex. Sodium (Na) has an atomic number of 11 & an atomic mass of 23. A Sodium atom has 11 protons, 11 electrons, & 12 neutrons.
II. CHEMICAL REACTIONS
A. More about Electrons
1. Electrons orbit around the nucleus at different energy levels or shells the 1st shell (k shell) can hold no more than 2 electrons; the next shell (l shell) can hold 8 electrons, 2 electrons in each of 4 orbitals; the next shell (m shell) also holds 8 electrons. These will be the only shells that we will deal with in this class.
2. An atom is the most stable when all of its shells are completely filled (the k shell fills first, then the l shell, then the m shell, & so on).
3. The atoms of many elements have partially filled outer shells, therefore they are not very stable; these atoms tend to react with other atoms to completely fill their outer shells &, in doing so, they form chemical bonds; it is important to remember that it's the electrons of an atom that participate in the chemical bonds that form between atoms. Molecules are formed when 2 or more atoms are joined together by interactions between the electrons of their outer electron shells.
B. Chemical Bonds
1. Ionic bonds
a. definition - in ionic bonds electrons are transferred to other atoms to completely fill
outer shells; atoms are electrically neutral, but when they gain or lose electrons in
combining with other atoms, they are called ions (charged
atoms) & they take on a positive or negative charge; in other words, the transfer of
electrons upsets the balance of protons & electrons in an atom; atoms that lose
electrons are positively charged, atoms that gain electrons are negatively charged; ionic bonds involve the attractions between these
oppositely charged ions. So, before you can
have an ionic bond, you have got to have oppositely charged ions, & to create ions you
have got to transfer electrons.
b. example: NaCl (sodium chloride- table salt); Na (at. # 11) has one electron in its outer m shell - it needs 7 electrons to fill this shell - it is easier for Na just to give this electron away, & eliminate the m shell entirely. Cl (at. # 17) has 7 electrons in its outer m shell - it only needs 1 electron to fill its outer shell. Therefore, when Na & Cl atoms react, Na gives up its outer electron to Cl. Because Na gives up an electron, it now has 11 protons & 10 electrons, resulting in a positively charged atom. Cl now has 17 protons & 18 electrons, resulting in a negatively charged atom. Na+ & Cl- ions are attracted to each other because of their opposite charges & an ionic bond is formed. The attraction is the ionic bond! Only the electron # changes when ions are formed!
2. Covalent bonds - more common in the human body & are more stable.
a. definition - Electrons are not transferred, but are shared. The shared electrons spend part of their time around the nucleus of one atom & part of their time around the other. Each pair of electrons shared equals one covalent bond (if 2 pair of electrons are shared between 2 atoms, a double covalent bond is formed, a triple covalent bond occurs when 3 pr. of electrons are shared). We only discuss single covalent bonds.
b. example: methane (CH4); a carbon atom can form four covalent bonds - it has 4 electrons in its outer shell, therefore it needs 4 more electrons to fill its outer shell; hydrogen has one electron in its outer shell, therefore it needs one electron to fill its outer shell. Rather than give 4 electrons away or accept 4 electrons, carbon shares its 4 electrons in its outer shell with 4 Hydrogen atoms.
c. polar vs. nonpolar - covalent bonds can be polar or nonpolar; if both atoms exert the same pull on the shared electrons (equal sharing), the bond is nonpolar (example: methane); if there is unequal sharing of electrons, the bond is polar; in molecules with polar covalent bonds, there is an atom that has a much larger nucleus (more protons) than the other atoms in the molecule; the atom with the most protons is more attractive to the shared electrons, so the electrons spend most of their time around this atom's nucleus; all of these electrons spending most of their time around a particular nucleus gives this part of the molecule a partial negative charge; the other atom(s) in the molecule acquire a partial positive charge, because the shared electrons are not spending much time around them. Shared electrons in polar covalent bonds are not spending all of their time around a particular nucleus - if this were the case then we would be talking about electrons being transferred (as in ionic bonds).
4. Hydrogen bonds - These bonds result from polar covalent bonds; they form between molecules & occur between the slightly negative atom of one molecule & the slightly positive atom of another molecule. These bonds can occur between hydrogen & oxygen & between hydrogen & nitrogen. Hydrogen bonds are weaker than ionic & covalent bonds, because the charges on the molecules are "partial" or weak charges.
C. Chemical Reactions - A chemical reaction when atoms or molecules (called reactants) collide and are transformed into different combinations of the same atoms or molecules (called products). In this process, chemical bonds break and new ones form. In living systems special proteins called enzymes catalyze these chemical reactions (they make them go). We'll talk more about enzymes later.
1. A single water molecule is made up of one oxygen atom & two hydrogen atoms (H2O).
2. Oxygen has 8 protons, while each hydrogen has only one proton. Oxygen forms a covalent bond with each hydrogen so that the outer shells of each atom are complete.
3. Because the oxygen atom has more protons (positives) than the hydrogen nuclei, the shared electrons have a greater attraction to the oxygen nucleus & spend more time around it than they do around the hydrogen nuclei (unequal sharing of electrons). The oxygen atom therefore has 10 electrons (8 of its own & 1 from each hydrogen) spending most of their time around its nucleus of 8 protons - this gives the oxygen end of the water molecule a partially negative charge. Since the hydrogen electrons are spending most of their time around the oxygen atom, the hydrogen atoms, which have one proton each, take on a partially positive charge. This results in a polar molecule (a molecule that has partially positive & negative regions). Their polarity allows water molecules to interact with one another, forming hydrogen bonds. The same type of interaction is possible between water & many other polar substances. Polar substances are hydrophilic (water-loving) & nonpolar substances are hydrophobic (water-fearing).
B. PROPERTIES OF WATER - Hydrophilic & hydrophobic interactions underlie several properties of water that are biologically important.
1. Temperature-Stabilizing Effects:
Note: The temperature of a substance is a measure of how fast its molecules are moving; the higher the temperature of a substance, the faster its molecules are moving.
a.) heating water - It takes considerable heat to raise the temperature of water because the hydrogen bonds between the water molecules restrict the movement of the molecules; in order for the temperature of water to rise, a number of H bonds must be broken - this takes a lot of energy. This resistance to temperature change helps living cells to maintain a relatively constant temperature; this is important because biochemical reactions take place within a narrow temperature range (this has to do with the action of enzymes). This resistance to temperature change also helps organisms that live in aquatic or marine environments.
2. Water As a Solvent - the polarity of water is also responsible for water's capacity as a solvent (something that dissolves something else); water is an excellent solvent for ions & other polar molecules (solutes) in cells.
C. ACIDS AND BASES
When molecules of inorganic acids, bases, or salts dissolve in water of body cells, they undergo ionization or dissociation (they break apart into their individual ions).
1. Acids & Bases Generally Defined
Acid - Defined as a solute that releases H+ ions in a solution
[ex. HCl - hydrochloric acid dissociates into H+ ions & Cl- ions]
Base - Defined as a solute that removes H+ ions from a solution; many release OH- ions in this process.
[ex. Mg(OH)2 - magnesium hydroxide dissociates into OH- ions & Mg++ ions].
2. pH Scale - Fluids are assigned a pH value (0 -14), which refers to the hydrogen ion concentration present in the fluid. The hydrogen ion concentration is abbreviated as [H+].
a. acid - pH below 7.0; base - pH above 7.0; neutral - pH = 7.0
b. pH = - log [ H+ ] (formula for calculating pH)
c. It is a common misconception to think that as the [H+] increases, the pH also increases! The rule is: As [H+] increases, pH decreases! This can be seen from the following example:
solution A: [H +] = 1 x 10-2 or 0.01 pH = -log[1 x 10-3] = 2
solution B: [H+ ] = 1 x 10-8 or 0.00000001 pH = -log[1 x 10-4] = 8
(A quick way to find the pH of these solutions is to look at the exponent or count the number of decimal places in the [H+])
Solution A is more acidic than Solution B - Solution has a higher [H+] than Solution B (0.001 > 0.0001); therefore, Solution A has a lower pH than B.
When you think about a pH value, think that this number is really the number of decimal places in the hydrogen ion concentration. The larger the number, the more decimal places there are, indicating a smaller hydrogen ion concentration.
3. Buffers - help maintain a constant pH by removing or adding H+ ions; the pH inside living systems is generally between 7.35-7.45 (exception: the hydrochloric acid in the digestive system makes the pH here 2-3); this pH range is important, as many biochemical reactions take place only within this range; buffers can combine with hydrogen ions &/or release them, & so help stabilize the pH.
4 Groups of Organic Compounds Important in Living Organisms:
Carbohydrates Lipids Proteins Nucleotides
Organic compound defined A compound containing carbon (with exception of carbon dioxide); found in all living things.
THE CENTRAL ROLE OF CARBON
A. The Carbon Backbone - The processes of life are primarily the result of the chemistry compounds of carbon. Because of carbon's tendency to form four covalent bonds in four different directions, carbon can form an unbelievably large number of different compounds of high complexity; organic compounds derive their basic shapes from the carbon atoms; this shape helps determine the compound's function in living systems.
B. Functional groups - The structure & behavior of organic compounds also depends on the properties of their functional groups; functional groups are groups of atoms (ex. hydrogen, oxygen, nitrogen, phosphorus, sulfur) attached to the carbon backbone.
A. Structure: generally made up of only three elements: carbon, hydrogen, & oxygen
B. Three Principle Classes of Carbohydrates:
a. Structure - composed of single sugar molecule; the atoms in a sugar molecule can form a straight chain or a ring (rings are more common in the body).
b. Examples - Glucose, Ribose, Fructose, Galactose
d. Functions - monosaccharides are important energy molecules in living things; glucose is the primary energy source for humans & many other animals; also important as building blocks of larger sugars.
2. Oligosaccharides - composed of short chains of monosaccharides; Examples:
a. Sucrose (table sugar) is a disaccharide composed of glucose & fructose; sucrose is the form in which sugars are transported in plants.
b. Lactose (milk sugar) is a disaccharide composed of glucose & galactose.
Sucrose = Glucose + Fructose
2. Polysaccharides - straight or branched chains of many monosaccharide units
a. Storage Polysaccharides
1.) Starch - sugar storage in plants.
2.) Glycogen animal starch; principle storage form for glucose in higher animals; this energy storage is short term; lipids are used for long term energy storage.
b. Structural Polysaccharides
1.) Cellulose Principal component of the plant cell wall; also found in the cell walls of algae and fungi. Monosaccharides are bonded together in such a way that the molecule resists breakdown by multicellular organisms. We dont have the digestive enzymes to break the bonds; however, some microorganisms do have these enzymes; this is why microbes are so important in the gut of a termite, cow, etc.)
2.) Chitin contains nitrogen; forms the cell wall of some fungi (its the same stuff insect exoskeletons are made of!)
A. Protein Structure:
1. Proteins are composed of subunits called amino acids (there are 20 different amino acids that make up proteins). Amino acids contain carbon, hydrogen, oxygen, and nitrogen. Some also contain sulfur. Amino acids have a structure similar to the one below. The R stands for some other atom or group of atoms bonded to the central carbon atom in the molecule. The sequence of amino acids in a chain helps determine the structure & shape of the protein & therefore the function of the protein; there are many possible combinations of amino acids that produce the many different kinds of proteins.
H H O
H R OH
2. Peptide bonds - linkage formed between one amino acid & another amino acid; the name of these bonds is why chains of amino acids are called polypeptides.
3. Producing the three dimensional structure
of a protein: We have been discussing proteins as
"chains of amino acids." However,
the final structure of proteins is not a straight chain of amino acids. Proteins are very complex, three-dimensional
molecules, with numerous twists & folds. The
amino acid chain of every kind of protein is folded in a very specific way [the chain will
twist & fold itself based on the linkage of amino acids in a specific sequence &
the environmental conditions (i.e., temperature & pH)].
There are several bonds & forces which give a protein its specific 3-D
structure (i.e., hydrogen bonds, ionic bonds, etc.); these bonds link distant parts of the
molecule, forming loops, twists, etc. Destruction
of a protein's 3-D structure by extreme heat or pH is called denaturation (see
"enzymes" on the next page for how this occurs).
Analogy for protein structure: Think of a phone cord. Pull it straight (like a straight chain of a.a.),
then let it twist, then roll the twisted cord into a ball.
(Every type of protein folds and twists in a very specific way.)
B. Some Specific Functions of Proteins:
1. Structural Proteins: collagen in connective tissue, keratin in the skin, cytoskeleton in cells
2. Functional Proteins:
a. membrane transport proteins transport substances across the cell membrane
b. cell movement ex. flagellum
c. enzymes as catalysts (enzymes speed up the rate of chemical reactions); all life processes are primarily the result of chemical reactions; molecules in living things require enzymes in order to react; without enzymes, chemical reactions in living things cant occur; see below for more information on enzymes.
d. antibodies in the immune response
C. Enzymes a large, globular protein molecule that accelerates a specific chemical reaction. Virtually all chemical reactions that take place in cells involve enzymes!!! Most of a cells proteins are enzymes.
1. Why are enzymes needed? In order for particular molecules to react with one another, they must be in close proximity & must collide with sufficient force to overcome the mutual repulsion of their negatively charged electron clouds & to break existing chemical bonds within the molecules. The force with which they collide depends on their kinetic energy (energy of motion). Most chemical reactions require an initial input of energy to get started, which increases the kinetic energy of the molecules, enabling a greater number of them to collide with sufficient force. In the chemistry lab, we can supply this energy with heat. In a cell, many different reactions are going on at the same time, therefore heat cannot be used as it would be nondiscriminatory (it would affect many reactions at the same time). Cells get around this problem by using enzymes, which serve as catalysts (they get the chemical reactions going). The enzymes form a temporary association with the molecules that are to react, bringing them close to one another & weakening the existing chemical bonds, making it easier for new ones to form.
2. Enzyme Structure & Function - Enzymes are large, complex, globular proteins consisting of one or more polypeptide chains. The molecules that enzymes acts on are known as the substrates. Enzymes are folded to form a groove or pocket (called an active site) on their surface into which the substrate fits & where the chemical reactions take place. See diagram below:
3. Effects of Temperature & pH on Enzyme Function
1. Temperature: As the temperature increases, so does the rate of enzyme catalyzed reactions, but only up to a certain point. At high temperatures, the enzymes are denatured (due to the vibration of molecules at high temperatures, the bonds that maintain the enzyme's structure are broken & the protein unfolds). If denaturation is severe, the damage to the enzyme is irreversible.
2. pH: The shape of the enzyme depends partly on attraction between positively & negatively charged amino acids. As the pH changes (acidic - more H+, basic - fewer H+), these charges change, changing the shape of the enzyme & its function. Remember: the optimum pH for most enzymes is 6-8. (exception: the stomach which has a pH of 2)
Note: All proteins can be denatured by heat and extreme pH.
This molecule has both protein and polysaccharide components and it forms the cell wall of eubacteria. It may be one or several layers thick. It is an extremely strong protective covering. Glycan strands in all eubacteria are made of alternating units of 2 modified sugars, N-acetylglucosamine (NAGA) and N-acetylmuramic acid (NAMA). (Its structure is similar to a chain link fence!) More later!
A. General Structure - all lipids are mostly nonpolar (hydrophobic) & are insoluble in polar solvents such as water; lipid structure varies greatly & is discussed below for each type.
B. Some General Functions:
1. long term energy storage (example: glycerides); energy is stored in the chemical bonds; excess carbohydrates, proteins or fats are converted to triglycerides & are stored in adipose (fat) tissue.
2. structural (example: phospholipids make up the cell membrane of cells)
C. Types of Lipids:
1. Lipids with Fatty Acids Glycerides & Phospholipids:
1.) Structure: classified as mono-, di-, & triglycerides, depending on the number of fatty acids attached a single glycerol molecule; glycerol has 3 carbon atoms & 3 hydroxyl (OH) groups; fatty acids are long, nonpolar chains composed of hydrogen & 4 to 24 carbon atoms, with a carboxyl (COOH) group at one end.
a.) Saturated fatty acids - all carbons in the fatty acid tails are joined together by single carbon to carbon bonds & as many hydrogen atoms as possible are linked to the carbons (the carbons are said to be "saturated" with hydrogens); triglycerides with many saturated fatty acids are solid at room temperature; occur mostly in animal tissues, but also in a few plant products; examples: butter, lard, cocoa butter, palm oil, coconut oil; the liver produces cholesterol from some breakdown products of saturated fats.
b.) Unsaturated fatty acids - one or more double bonds occur between carbon atoms in the fatty acid tails; this cuts down on the number of hydrogen atoms that can bond to the carbons; liquids at room temperature; the double bonds create a kink in the shape of the molecule prevent the fatty acids from packing close together & becoming solidified; unsaturated fatty acids are more common in plants; monounsaturated fatty acids are better for you that the polyunsaturated ones; the polys can produce compounds called trans fatty acids, which increase the risk of heart disease.
A triglyceride molecule:
H--C---O---C--CC--C--C--CCCCC--CH saturated f.a.
O H H H H H H H H H H
H H H H H H H H H H
H--C---O---C--CC--C--C--C--CCCCC--H saturated f.a.
O H H H H H H H H H H
H H H H H H H H H H
HC---O---CCCC==CCCCCCC---H unsaturated f.a.
H O H H H H H H H H
2.) Functions of Glycerides
a.) Energy - For most organisms and cellular microorganisms, sugars in excess of what can be stored as glycogen are converted into fats for more permanent storage; this is not the case in bacteria!
1.) Structure - 2 fatty acids & 1 phosphate group are linked to a glycerol molecule; a small polar group is linked to the phosphate group; this results in a molecule with a dual nature - the molecule has a nonpolar, hydrophobic end & a polar, hydrophilic end.
2.) Function: Structural. The phosphate end of the molecule & its polar group are called the "head" of the molecule; the two fatty acids are called the "tails" of the molecule; the head is hydrophilic ("water-loving"), while the 2 fatty acid "tails" are hydrophobic ("water-fearing"). This arrangement forms the structural basis of cellular membranes & is called the phospholipid bilayer.
2 Fatty AcidTails (nonpolar)
2. Lipids without Fatty Acids: Steroids
a. Structure - different from other lipids; they consist of 4 interlocking carbon rings with numerous hydrogens attached; while they have no fatty acids, they are still nonpolar & hydrophobic, so they are classified as lipids.
b. Some Examples:
1.) cholesterol - important component in eukaryotic cell membranes & serves as the starting material for the synthesis of other steroids. Not found in the cell membranes of bacteria with the exception of the Mycoplasms.
A. Structure: nucleotide = phosphate(s) + monosaccharide + a nitrogen-containing compound (called a base); its the bases that spell out the genetic message in DNA & RNA).
1. Nucleotides are the basic subunits of nucleic acids such as
a. DNA (deoxyribonucleic nucleic acid) - carrier of the genetic message - makes up chromosomes in the nucleus of the cell.
b. RNA (ribonucleic acid) - transcribes genetic message present in DNA & produces proteins from it.
2. Nucleotides also make up the adenosine phosphates (ex. ATP - adenosine triphosphate used for energy molecule in the cell).
3. Nucleotides make up some coenzymes (ex. NAD & FAD); these molecules function as electron carriers in some biochemical reactions; they are called the cells reducing power. Well talk about this more in the metabolism chapter.