BASIC CHEMISTRY AND BIOCHEMISTRY BASIC CHEMISTRY MEET THE ELEMENTS ATOMIC THEORY OF MATTER (vocabulary) 1.Atoms = building blocks of matter that cannot be divided any further by ordinary chemical means 2.Molecule = two or more atoms combined that act as a single particle, the smallest particle that retains the properties 3.Elements = substances made of only one kind of atom ATOMIC THEORY OF MATTER (vocabulary) 4.Compounds = two or more kinds of atoms in a substance in definite proportions 5.Isotopes = varieties in the normal number of neutrons on the nucleus (The atomic number stays the same, the mass number changes) 6.Radioactivity = a nuclear process in which an atom is undergoing changes by emitting charged particles STRUCTURE OF THE ATOM particle charge mass location proton (+) 1 amu in nucleus electron (-) 0 in orbitals neutron ( ) 1 amu in nucleus A Happy Atom has all its orbital places filled. 7.Atomic number = # of protons (also the number of electrons in a neutral atom) 8.Atomic mass or mass number = number of protons plus the number of neutrons in the nucleus. ATOMIC ORBITALS (energy levels) nucleus Level 1 2 electrons orbit Level 2 8 electrons orbit Level 3 8 electrons orbit Remember: A Happy Atom has all its orbital places filled. CHEMICAL BONDING Chemical bond = force of attraction that holds atoms together There are two kinds of bonds between atoms 1. Covalent Bonds = chemical bond that is formed by the sharing of electrons 2.Ionic Bonds = chemical bond that is formed by transfer of electrons COVALENT BOND Covalent Bond = chemical bond that is formed by the sharing of electrons (covalent bonds form molecules) HYDROGEN ATOM OXYGEN ATOM Remember: A Happy Atom has all its orbital places filled. IONIC BOND Ionic bond = chemical bond that is formed by transfer of electrons Remember: A Happy Atom has all its orbital places filled Sodium (Na) has 1 electron in its outer energy level is it happy? Chlorine (Cl) has 7 electron in its outer energy level is it happy? IONIC BOND Sodium and Chlorine ions are formed What is an ion? Ion = atom with an excess charge by the loss or gain of electrons Sodium has lost one electron (one less () charge) so it now has a net charge of +1 Chlorine has gained one electron (one more () charge) so it now has a net charge of -1 The (+) charge of Na is attracted to the (-) of the Cl and this attraction forms an ionic bond! NaCl Na Cl CHEMICAL FORMULAS Each element (symbol) and its proportions (subscripts) are represented information All elements are listed in the periodic table 6 atoms of Carbon (C) 12 atoms of hydrogen (H) 6 atoms of oxygen (O) For example C 6 H 12 O 6 means: CHEMICAL FORMULAS Examples are: H2OH2O CO 2 C 6 H 12 O 6 CH 4 STRUCTURAL FORMULAS A Structural formula shows the kinds and number of atoms as well as the chemical bonds H H O HHCC benzene water glucose acetylene CHEMICAL EQUATIONS Reactants = the original substances before a chemical reaction (left of the arrow) Products = new substances formed after a chemical reaction (right of the arrow) Law of Conservation of Mass = mass can neither be created or destroyed (chemical reaction formulas must balance) + 2 molecules of hydrogen (2H 2 ) + 1 molecule of oxygen (O 2 ) 2 molecules of water (2H 2 O) Complete pages 6 and 7 in your packet BIOCHEMISTRY The Chemical Compounds of Life BIOLOGICALLY IMPORTANT COMPOUNDS ORGANIC COMPOUNDS: Species that naturally contain carbon and hydrogen (living organisms and their products) Most also contain O (oxygen) and N (nitrogen) Only a few elements are found in organic compounds May also have P (phosphorous), S (sulfur), Fe (iron), Ca (calcium), Na (sodium), Cl (chlorine), Mg (magnesium), K (potassium) BIOLOGICALLY IMPORTANT COMPOUNDS INORGANIC COMPOUNDS: DO NOT CONTAIN CARBON (with hydrogen) May have carbonate compounds (CO2, CaCO, etc.) but not carbon with hydrogen. Living organisms do contain inorganic compounds IMPORTANT INORGANIC COMPOUNDS 1.WATER The most important inorganic compound in living organisms 65% of the body Many biological processes require water 2.SALTS Help maintain water balance in the cells Provide ions for many biological processes 3)ACIDS and BASES Help maintain homeostasis The Structure of Organic Compounds Organic compounds are large and complex because of the carbon atom Four vacancies for electrons allow 4 covalent bonds Carbon has an atomic # of 6 which means it has 6 protons and 6 electrons It has 4 vacancies in the outer energy level CHEMICAL COMPOUNDS OF LIFE Living organisms depend upon a variety of molecules for their survival. Some are used to build complex parts of an organism; some supply energy; while others provide instructions for the operation of the organism. There are many organic compounds found in organisms, but they can be classified into 4 main types: I.CARBOHYDRATES II.LIPIDS III.NUCLEIC ACIDS IV.PROTEINS CARBOHYDRATES Carbohydrates are compounds of C (carbon), H (hydrogen), and O (oxygen) They have the same ratio H:O as in water (H 2 O) = 2:1 (twice as many H as O) *Monosaccharides = simple sugars = C 6 H 12 O 6 ALWAYS END IN OSE EX: MALTOSE, FRUCTOSE, GLUCOSE RELEASE ENERGY WHEN BREAKING DOWN GLUCOSE INTO CO 2 AND H 2 O C 6 H 12 O 2 CO 2 + H 2 O MOST ORGANISMS USE GLUCOSE AS A SOURCE OF ENERGY CARBOHYDRATES THIS IS A MONOSACCHARIDE MOLECULE! THIS IS A SIMPLE SUGAR! THIS IS GLUCOSE! THIS IS C 6 H 12 O 6 ! CARBOHYDRATES DISACCHARIDE = two simple sugars joined POLYSACCHARIDE = several simple sugars joined POLYMERS = long chains of repeating molecules (many) (molecules) CARBOHYDRATES Sugars stored in plants are called STARCH Sugars stored in the liver of animals are called GLYCOGEN Glycogen will be changed into glucose when the body needs it for energy! CARBOHYDRATES BUILDING BLOCKS OF CARBOHYDRATES ARE SIMPLE SUGARS OR MONOSACCHARIDES LIPIDS (fats, oils, and waxes) Made of carbon, oxygen, and hydrogen (there less oxygen in lipids than in carbohydrates) Reserve energy supply in an organism 2 times as much energy as carbohydrates Plants store oils in seeds Mammals store fats under the skin Waxes are formed from fatty acids and substances similar to glycerol Fats and oils are formed from fatty acids and glycerol LIPIDS (fats, oils, and waxes) BUILDING BLOCKS of LIPIDS (fats and oils) ARE 1 GLYCEROL + 3 FATTY ACIDS The Structure of a Fatty Acid Lipid molecule The Fatty Acid has 2 parts: 1.Chain of carbon atoms with hydrogen atoms bonded (hydrocarbon chain) 2.Carboxyl group SATURATED vs UNSATURATED FATTY ACIDS SATURATED FATTY ACIDS: Fats that have all single carbon-to-carbon bonds Tend to be solids at room temperature (ie. butter) Tend to increase the amount of cholesterol in the body Cause deposits that lead to hardening and narrowing of arteries SATURATED vs UNSATURATED FATTY ACIDS UNSATURATED FATS Fats that have a double or triple carbon-to-carbon bond Tend to be oils at room temperature Tend to decrease blood cholesterol Polyunsaturated fats = a chain that has more than one double or triple bond Complete the crossword puzzle on page 11 in your packet NUCLEIC ACIDS Compounds that contain phosphorus (P) and nitrogen (N) Also carbon, hydrogen, and oxygen Two types of Nucleic Acids: 1.DNA 2.RNA NUCLEIC ACIDS (DNA) DNA = deoxyribonucleic acid Found in the nucleus of the cell Directs and controls heredity information and the development and activities of the cell THE STRUCTURE OF DNA DNA is made of: Repeated chains of nucleotides Nucleotides are made of: 5 carbon sugar (deoxyribose) Phosphate group (PO 4 ) Nitrogenous base (A,T,C,G) THE STRUCTURE OF DNA DNA The DNA molecule is made of repeating chains of nucleotides The sugar and phosphate groups are the sides of the ladder Nitrogenous base pairs are the rungs of the ladder The bases are adenine (A), thymine (T), cytosine (C), and guanine (G) adenine (A) always pairs with thymine (T) cytosine (C) always pairs with Guanine (G) RNA RNA = ribonucleic acid RNA structure: A single strand or chain of bases The sugar is ribose The base thymine is replaced with uracil RNA is involved with protein synthesis PROTEINS Compounds that contain nitrogen, carbon, hydrogen, and oxygen Many contain sulfur and phosphorus Great range of properties that give live complexity 20 different amino acids found in proteins AMINO ACIDS ARE THE BUILDING BLOCKS OF PROTEINS STRUCTURE OF AN AMINO ACID 1.One central carbon atom (C) 2.One carboxyl group (COOH) 3.One amino group (NH 3 ) 4.One hydrogen atom (H) 5.One side chain (R) GLYCINE is the simplest amino acid the side chain is only one H atom Examples of the different amino acids PROTEIN VOCABULARY Dipeptide = two amino acids bonded together The peptide bond = the bond between amino acids Polypeptide = a long chain of amino acids ORGANIC COMPOUND ATOMS BUILDING BLOCKS EXAMPLESUSES CARBOHYDRATES C H O H:O is 2:1 ex: C 6 H 12 O 6 glucose Monosaccharides (simple sugars) Disaccharides (2 sugars) Polysaccharides (many sugars) glucose, fructose, galactose maltose, sucrose, lactose starch, cellulose, glycogen, chitin Quick energy ose ending carbon ring shape ORGANIC COMPOUND ATOMS BUILDING BLOCKS EXAMPLESUSES CARBOHYDRATES C H O H:O is 2:1 ex: C 6 H 12 O 6 glucose Monosaccharides (simple sugars) Disaccharides (2 sugars) Polysaccharides (many sugars) glucose, fructose, galactose maltose, sucrose, lactose starch, cellulose, glycogen, chitin Quick energy ose ending carbon ring shape LIPIDS C H O H:O is 2:1 ex: C 20 H 24 O 3 1 glycerol 3 fatty acids (hydrocarbon chain) fats, oils, waxes Stored energy makes up cell membrane ORGANIC COMPOUND ATOMS BUILDING BLOCKS EXAMPLESUSES CARBOHYDRATES C H O H:O is 2:1 ex: C 6 H 12 O 6 glucose Monosaccharides (simple sugars) Disaccharides (2 sugars) Polysaccharides (many sugars) glucose, fructose, galactose maltose, sucrose, lactose starch, cellulose, glycogen, chitin Quick energy ose ending carbon ring shape LIPIDS C H O H:O is 2:1 ex: C 20 H 24 O 3 1 glycerol 3 fatty acids (hydrocarbon chain) fats, oils, waxes Stored energy makes up cell membrane PROTEINS C H O N 20 amino acids dipeptide (2) polypeptide (many) glycine, alanine insulin, hemoglobin Build and repair ie: muscles hormones enzymes ORGANIC COMPOUND ATOMS BUILDING BLOCKS EXAMPLESUSES CARBOHYDRATES C H O H:O is 2:1 ex: C 6 H 12 O 6 glucose Monosaccharides (simple sugars) Disaccharides (2 sugars) Polysaccharides (many sugars) glucose, fructose, galactose maltose, sucrose, lactose starch, cellulose, glycogen, chitin Quick energy ose ending carbon ring shape LIPIDS C H O H:O is 2:1 ex: C 20 H 24 O 3 1 glycerol 3 fatty acids (hydrocarbon chain) fats, oils, waxes Stored energy makes up cell membrane PROTEINS C H O N 20 amino acids dipeptide (2) polypeptide (many) glycine, alanine insulin, hemoglobin Build and repair ie: muscles hormones enzymes NUCLEIC ACIDS C H O P N Nucleotides (sugar, phosphate nitrogenous base) DNA = deoxyribonucleic acid RNA = ribonucleic acid hereditary material protein synthesis Complete page 15 in your packet DEHYDRATION SYNTHESIS DEHYDRATION = to remove water SYNTHESIS = to make more complex H and OH are removed from the glucose molecules (to make water), this is the dehydration part Then the two glucose molecules have open bonding sites so they can join together to make more complex, this is the synthesis part. Dehydration synthesis = to make more complex by removing water HYDROLYSIS To break down by adding water Turn to page 17 in your packet Dehydration Synthesis of a Carbohydrate In carbohydrates, two monosaccharides form a bond to create a disaccharide Dehydration Synthesis of a Protein In proteins, two amino acids form a peptide bond to create a dipeptide molecule Dehydration Synthesis of a Fatty Acid In lipids, we remove 3 molecules of water! Then the glycerol molecule bonds with the 3 fatty acids Vocabulary Review 1.monomer = 2.polymer = 3.dehydration synthesis = 4.hydrolysis = A small molecule that will combine with other small molecules to form a chain A large molecule (chain) formed from combined repeated smaller units (monomers) Combining molecules by the removal of water Breaking down molecules by the addition of water Complete pages 18, 19, and 20 in your packet ENZYMES The importance of enzymes: Enzymes are proteins Enzymes enter the chemical reaction temporarily and are not changed Enzymes are used over and over again Enzymes are organic catalysts ENZYMES A catalyst is a substance that brings about a chemical reaction without being changed itself The substrate is the substance the enzyme acts upon HOW ENZYMES WORK The active site matches up with the substrate Forms enzyme-substrate complex Enzyme will either break down or bond molecules Enzymes are very specific one specific enzyme matches one specific substrate ENZYME SPECIFICITY How do enzymes work? substrate: molecules upon which an enzyme acts. The enzyme is shaped so that it can only lock up with a specific substrate molecule. Each enzyme is specific for one and ONLY one substrate (one lock - one key) active site: part of the enzyme that fits with the substrate Note that the active site has a specific fit for this particular substrate and no other. (enzyme) substrate > product REMEMBER: Each enzyme is specific for one and ONLY one substrate If the substrate and enzyme are not a match the reaction will not proceed TWO ENZYME THEORIES 1.LOCK AND KEY THEORY 2.INDUCED FIT THEORY Naming the Enzyme The prefix comes from the substrate (the material acted upon) Enzymes end in ase (the suffix) For example: Maltase (malt/ase) = an enzyme that breaks down ________ Lipases (lip/ases) = enzymes that break down ______ Proteases (prote/ases) = enzymes that break down ________ lipids proteins maltose FACTORS AFFECTING ENZYME FUNCTION: REMEMBER Enzymes are powerful one enzyme molecule can catalyze thousands of substrate reactions each second enzymes speed up the reaction without raising the temperature of the environment BUT ENZYME REACTION vs TEMPERATURE Enzymes work the best at certain temperatures, usually the temperature of the natural environment Enzymes become denatured at high temperatures (the high temp will change the shape of the active site so the enzyme no longer fits) ENZYME REACTION vs pH Enzymes work the best at a certain pH, usually the pH of the natural environment ENZYME REACTION vs CONCENTRATIONS The rate of an enzyme controlled reaction depends upon the concentrations of enzymes and substrates COENZYMES SOME ENZYMES NEED SUBSTANCES CALLED COENZYMES IN ORDER TO FUNCTION Coenzymes are organic substances Coenzymes are not proteins Most coenzymes are vitamins A COENZYME ALLOWS AN ENZYME TO PERFORM ITS CATALYTIC FUNCTION Acids, Bases, and Salts TERMS Acids = any compound that produces hydrogen ions (H + ) in solution HCl = H + + Cl - Base = any compound that produces hydroxide ion (OH - ) in solution NaOH = Na + + OH - TERMS Neutralization = when quantities of acids and bases are mixed together and no extra H + or OH - remain HCl + NaOH NaCl + H 2 O (acid) + (base) (salt) + (water) TERMS Salts = the ionic compound obtained from the neutralization reaction between and acid and a base HCl + NaOH --- Na + + Cl - + H 2 O Solid NaCl (salt) found if water is evaporated The pH scale H 2 O --- H + + OH - Neutral pure water, no excess of H + or OH - (not an acid or a base) If the H + concentration increases, it becomes acidic If the OH - concentration increases, it becomes basic The pH scale pH measures the concentration of H + Scale runs if the [H + ] > [H 2 O] = acid if the [H + ] < [H 2 O] = base The Scale high [H + ] = acids = low pH values = neutral = 7 low [H + ] = bases = high pH values = 8 14 Indicators Indicator: substance that changes color when pH goes above or below a certain value Litmus: Red = acid / Blue = base Methyl orange: red to yellow indicates base Phenolphthalein: colorless to red indicates base (compare to indicator paper to read actual pH)