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Chemistry for Bio 11 Chemistry is relevant to Biological Concepts • All Living things are made of matter • The interactions of matter are described by chemical principles • Biolgists are interested in: – Biochemical reactions – Complex biological molecules – Chemical energy – The chemical environment Biochemical reactions • All living things are collections of a vast number of chemical reactions • Even the simplest living things contain impossibly complex pathways Complex biological molecules • All living things are made of complex macromolecules • Chemical principles rule their assembly Chemical energy Photosynthesis creates molecules rich in energy: • 6CO2(g)+ 6H2O(l) + hν C6H12O6(s) + 6O2(g) The Chemical Environment • The physical properties of water determine the fate of life on earth • pH, salinity and other chemical factors influence Basic principles of chemistry Atoms Atoms are the smallest individual unit of matter • Atoms are comprised of protons, neutrons and electrons Proton: Charge= +1, Mass= 1 Neutron: Chg= 0, mass= 1 Electron: Chg = -1, mass= ~0 Mass= p + n Charge = p - e LE 2-4a Electron cloud 6e– 2e– Nucleus 2 Protons 2 Neutrons 2 Electrons Helium atom Mass number = 4 6 Protons 6 Neutrons 6 Electrons Carbon atom Mass number = 12 Elements are defined by the number of their protons • There are 92 naturally occurring elements • Many others have been synthesized Atomic number: # protons Atomic mass: protons Isotopes- different atoms of same element, with different # neutrons Atomic weight: Naturally occurring average of isotopes of a substance 96% of human tissue is comprised of 6 elements • Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorous, Sulfur (CHNOPS) • 25 elements serve known functions in the body, incl. Ca, K, Na, Cl, Mg, Fe Atomic structure • Protons and electrons in the nucleus • Electrons orbit around • Bohr atom- classic model featuring electrons in “planetary” orbitals • Each orbit holds a determined number of electrons (first holds two, 2nd and 3rd hold eight The number of neutrons in atoms is variable • Isotopes • Some isotopes are stable, others are radioactive Isotopes of carbon have important applications in biology and archaeology Other radioactive isotopes are also important Electron cloud model • Currently accepted model of atomic structure • 90% probability cloud • Mostly empty space • Unfilled orbitals found in unstable, reactive elements • Therefore, orbitals influence bonding Molecules, compounds, chemical reactions, and bonding Elements combine in chemical reactions to form compounds • Molecules- 2 or more atoms combined in a specific way • Compounds- different elements in a molecule, in exact, whole-number ratios, joined by a chemical bond • 2 major means of intramolecular chemical bonding: Covalent (incl. polar and nonpolar) and Ionic Atoms are stable when their outer shells are filled with electrons • • • • Shell 1: Holds 2 electrons Shell 2: Holds 8 Shell 3: Holds 8 Hydrogen- 1p, 1e, seeks a second electron in its outermost shell • Carbon seeks 4 • The electrons in the outermost shell are called valence electrons Noble gases have a stable electron structure • Their outer orbitals have a full complement of electrons • Noble gases are very unreactive LE 2-7 In ionic bonding, an atom takes an electron from another atom, forming 2 ions Transfer of electron Na+ Sodium ion Na Sodium atom Cl Chlorine atom ClChloride ion Sodium chloride (NaCl) 5. Ions • Ions- Charged atoms or molecules • Anion- negative ion • Cation- positive ion • Ionization- reaction producing ions • Salt- a neutral compound comprised of ions LE 2-7a-2 Na+ Sodium ion ClChloride ion Sodium chloride (NaCl) LE 2-7b Na+ Cl- Water dissolves many ionic compounds (“like dissolves like”) Individual soluble ions are not physically bound to each other In covalent bonding, pairs of valence electrons are shared, and molecules are formed LE 2-17a + 2 H2 + O2 2 H2O LE 2-6b Nitrogen (N) Atomic number = 7 Oxygen (O) Atomic number = 8 In neutral molecules, carbon always forms 4 bonds Structural formula Ball-and-stick model Space-filling model Methane The 4 single bonds of carbon point to the corners of a tetrahedron. LE 3-1b Ethane Propane Carbon skeletons vary in length. LE 3-1c Butane Isobutane Skeletons may be unbranched or branched. LE 3-1d 1-Butene 2-Butene Skeletons may have double bonds, which can vary in location. LE 3-1e Cyclohexane Benzene Skeletons may be arranged in rings. Organic Chemistry • The chemistry of carbon • Hydrocarbons are the most basic example – Combustible – Can form rings The variety of carbon compounds is limitless All terrestrial life is based on carbon Biological Chemistry II: pH, Intermolecular forces and biomolecules Bio 11 Covalent bonds hold together the macromolecules of life • Living things create macromolecular products for structure: • 6CO2(g)+ 6H2O(l) + hν C6H12O6(s) + 6O2(g) • Macromolecules as reactants are broken down for energy: C6H12O6(s) + 6O2(g) 6CO2(g)+ 6H2O(l) All the reactions of a living thing are called its metabolism Electronegativity determines properties of covalently bonded molecules Electronegativity = “electron greediness” • Atoms in covalently bonded molecules do not always share electrons equally • This creates polar molecules • Polar regions of water molecules interact to form hydrogen bonds • Hydrogen bonds: weak/temporary intermolecular forces Some electronegativity values • • • • • Hydrogen: 2.20 Oxygen: 3.44 Carbon: 2.55 Chlorine: 3.16 Sodium: 0.93 • Difference between: • H and O: 1.22 • H and C: 0.35 Hydrogen bonding in water determine many of water’s unique properties • H-bonds can form a lattice (ice) • H-bonds require much energy to break • H-bonds give water surface tension Hydrogen bond Water dissolves many ionic compounds (“like dissolves like”) Intermolecular Hydrogen bonds give water its surface tension Intermolecular Hydrogen bonds require much heat in order to be broken Hydrogen bonds don’t only happen between water molecules • Ethanol contains –OH group and can form Hbonds • H-bonds can form between nitrogen and hydrogen Water also forms ions sometimes H2O ↔ H+ + OH• Spontaneously happens to water molecules • 1/ 107 water molecules are ionized in distilled water • In dH2O, [H+ ]= [OH-] salt - neutral molecule releases ions acid releases hydrogen H+, burns base releases hydroxide OH–, slimy pH is a measure of acidity/basicity • • • • • • • • pH = -log [H+] (logarithmic scale) pH 1 6.9: acid pH 7.114: base pH 7 neutral buffers - absorb excess H+ or OH– - stomach 2, urine 5-7.8, blood 7.4 Acids donate [H+] to water Bases remove [H+] from water (or donate [OH-] to water) • Proteins are very sensitive to small changes in pH pH is a measure of acidity/basicity • • • • • • pH = -log [H+] (logarithmic scale) pH 1 6.9: acid pH 7.114: base pH 7 neutral Acids donate [H+] to water Bases remove [H+] from water (or donate [OH-] to water) • Proteins are very sensitive to small changes in pH Ionization reactions can increase or decrease pH • NaCl Na+ + Cl• HCl H+ + Cl• NaOH Na+ + OHH+ + OH- H2O LE 2-15 pH scale H+ H+ H+ H+ OH + OH- H H+ H+ Lemon juice, gastric juice H+ Grapefruit juice, soft drink Acidic solution Tomato juice Human urine OH- OH- - H+ H+ OH OH OHH+ H+ H+ Neutral solution NEUTRAL [H+[ - Pure water Human blood Seawater Milk of magnesia Household ammonia OHOHOH- OHH+ H+ OH- Household bleach OH- Basic solution Oven cleaner Figure 2.16b Figure 2.16a 7. FUNCTIONAL GROUPS hydroxide group – OH amino group – NH2 carboxyl group – COOH phosphate group – PO4 methyl group – CH3 The physical/ chemical properties of carbon skeletons can be modified by functional groups figure 02-20b.jpg 2.20 – Part 2 Figure 2.20 – Part 2 Functional groups can radically change the function of a molecule Estradiol Female lion Testosterone Male lion • The six functional groups that are most important in the chemistry of life: – Hydroxyl group (alcohols)* – Carbonyl group – Carboxyl group (carboxylic acids)* – Amino group* – Sulfhydryl group – Phosphate group* – Methyl group* LE 4-10aa STRUCTURE (may be written HO—) Ethanol, the alcohol present in alcoholic beverages NAME OF COMPOUNDS Alcohols (their specific names usually end in -ol) FUNCTIONAL PROPERTIES Is polar as a result of the electronegative oxygen atom drawing electrons toward itself. Attracts water molecules, helping dissolve organic compounds such as sugars (see Figure 5.3). LE 4-10ab Acetone, the simplest ketone STRUCTURE EXAMPLE Acetone, the simplest ketone NAME OF COMPOUNDS Propanal, an aldehyde Ketones if the carbonyl group is within a carbon skeleton FUNCTIONAL PROPERTIES Aldehydes if the carbonyl group is at the end of the carbon skeleton A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. LE 4-10ac STRUCTURE EXAMPLE Acetic acid, which gives vinegar its sour taste NAME OF COMPOUNDS Carboxylic acids, or organic acids FUNCTIONAL PROPERTIES Has acidic properties because it is a source of hydrogen ions. The covalent bond between oxygen and hydrogen is so polar that hydrogen ions (H+) tend to dissociate reversibly; for example, Acetic acid Acetate ion In cells, found in the ionic form, which is called a carboxylate group. LE 4-10ba STRUCTURE EXAMPLE Glycine Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. NAME OF COMPOUNDS Amine FUNCTIONAL PROPERTIES Acts as a base; can pick up a proton from the surrounding solution: (nonionized) (ionized) Ionized, with a charge of 1+, under cellular conditions LE 4-10bb STRUCTURE EXAMPLE (may be written HS—) Ethanethiol NAME OF COMPOUNDS Thiols FUNCTIONAL PROPERTIES Two sulfhydryl groups can interact to help stabilize protein structure (see Figure 5.20). LE 4-10bc STRUCTURE EXAMPLE Glycerol phosphate NAME OF COMPOUNDS Organic phosphates FUNCTIONAL PROPERTIES Makes the molecule of which it is a part an anion (negatively charged ion). Can transfer energy between organic molecules. Organic molecules are good energy sources Energy is required to form covalent bonds; energy is released when bonds are broken Most molecules in living things fall into four categories • • • • Carbohydrates Lipids Proteins Nucleic acids These all exhibit modular construction Modular housing Made of interchangeable parts Freight trains have modular assembly Modular assembly allows a wide variety of products from a few pieces Most biopolymers of life are formed by dehydration synthesis Hydrolysis is the reverse reaction (Catabolic) Carbohydrates • “Carbon” + “Hydro” • Formula (CH2O)n • Different from hydrocarbons • Soluble in water • Includes: table sugar, honey, starch, glycogen, cellulose, high fructose corn syrup • Glucose is the monomer Glucose can cyclize to form a ring structure Atoms in bonds are free to rotate around the bonds Glucose + Glucose = Maltose Sugar dimer) (A Sugars are not limited to 6 carbons • Sugars can be from 3 to 8 sugars • 6 and 5-carbon varieties are the most common (pentoses and hexoses) Two common sugar dimers Raffinose, a sugar trimer, can be found in legumes Chain can be extended to thousands 9. Carbohydrates • functions - principle source of energy (4 kcal/g) - structure & energy storage in plants atoms - C H O structure - ring or chain of 56 C’s monosaccharide - single sugars (example: glucose) disaccharide - double sugars (example: sucrose) polysaccharide - polymer or chain of 100’s sugars - starch & cellulose (mostly plants) - glycogen (animals, esp. liver) Proteins are made of amino acids Proteins are polymers made of 20 different kinds of amino acid monomers table 03-02bc.jpg Table 3.2 – Part 2 Table 3.2 – Part 2 table 03-02d.jpg Table 3.2 – Part 3 Table 3.2 – Part 3 figure 03-04.jpg Modular assembly of amino acids through dehydration synthesis Formation of a peptide bond 3.4 Proteins have an incredible variety of structures Proteins have an incredible variety of functions Hair, skin, fingernails, muscles, eye pigments, are all made of protein Enzymes are critical protein machines • Enzymes speed up chemical reactions in the body • Their shape is necessary to their function • Shape is dependent on protein structure Proteins have four levels of structure • • • • • Primary Secondary Tertiary Quaternary Protein structure depends on all these levels of interaction Primary structure • • • • • Determined by the sequence of amino acids Amino acids linked by peptide bonds Chain is called polypeptide Sequence proceeds from “N-terminus” to “C-terminus” Amino acid sequence determined by DNA code Secondary structure • Hydrogen bonding between amino acid side chains • Amino group hydrogens bind with Oxygens from carboxyl end Alpha-helix and Beta-sheet are two important 2o structural motifs Tertiary structure • The folding interactions from amino acid side chains of a polypeptide • The folding of 2o domains upon each other • Interactions can be ionic, Hbonds, hydrophobic, or covalent • Proper 3o structure depends on pH, temperature A lightbulb filament has multiple levels of structure Quaternary structure • The interactions of multiple polypeptides to form a functional protein London dispersion/induced dipole intermolecular interactions occur between hydrophobic molecules • Between hydrophobic/ non-polar/ lipophilic molecules • Effects are cumulative over large hydrocarbon chains Lipids • • • • • • Non-polar High-energy molecules For energy storage Forms cell membranes Hormones Members of family include oils, fats, waxes, and cholesterol (steroids) Hydrocarbons are nonpolar • So are lipids • Nonpolar substances are usually insoluble in water • Interact through London dispersion/ induced dipole interactions Lipids are non-polar • Therefore, they are hydrophobic • C and H are similarly electronegative • Do not mix easily with water • C-H bond is high in energy • Lipids make good energy storage molecules Triglycerides are a primary lipid structure Dehydration synthesis links fatty acids to glycerol Fatty acids can be saturated and unsaturated (“cis” and “trans”) Cis- and Trans- fatty acids are isomers • Melting point is very different because of shape • Health effects are very different Triglycerides can be modified to form phospholipids • Phospholipids are amphipathic- having a polar and nonpolar region • Hyrophilic head, hydrophobic tails • Primary constituent of cell membranes Steroids and cholesterol are also lipids Estradiol Female lion Cholesterol Testosterone Male lion Isoprenoids constitute another important subcategory of lipids • The 5-carbon isoprene subunit can be used to form many important compounds • Artemisinin is an important antimalarial isoprenoid Nucleic acids • Informational molecules in cells • Include DNA, RNA, and ATP/ADP • DNA is the code to make a protein • Living things are made up of protein • Have other functions Nulceotides are the subunits of nucleic acids • Consist of a sugar, a phosphate, and a nitrogen-containing base • Sugar can be deoxygenated • Bases contain the genetic information Hydrogen bonds hold the two sides of the DNA ladder together • DNA bases have –OH and –NH2 groups • Sides of ladder are covalently bonded • Rungs held together with H-bonds Review • • • • • • • • • Atomic structure- protons, neutrons electrons Valence electrons Carbon pH Functional groups Carbohydrate structure Protein structure Lipid structure Nucleic acid structure