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Biochemistry The Chemistry of Life Basic Chemistry • Atom – Simplest unit of matter – Made up of three different “subatomic” particles Subatomic Particles • Protons – Have a positive charge (+) – Have mass – Located in nucleus • Neutrons – Are neutral, have no charge (0) – Have mass – Located in nucleus • Electrons – Have a negative charge (-) – Almost no mass – Located in “energy levels” outside of nucleus • Atomic Number: – Tells you the number of protons an atom has, and also the # of electrons Atoms are neutral # Protons (+) = # Electrons (-) • Atomic Mass: – Add together the number of protons and neutrons in nucleus of atom – Electrons hardly contribute any mass • Isotopes: – Atoms of one type of element with different atomic masses – Same # of protons – Different # neutrons – Changes the mass only, the properties are the same • Radioactive Isotopes: – The nucleus of some isotopes is unstable – The atom with emit radiation – Radiation can be measured with tools • ex. Geiger counter – These isotopes can be used as useful tools in science – Ex: • Carbon-14 dating • Radiation treatment for cancer • Elements – Substance made of only one type of atom – Each element has a unique atomic # – Elements most commonly found in living things • • • • Carbon (C) Hydrogen (H) Oxygen (O) Nitrogen (N) • Compounds – Two or more elements chemically combined – Atoms held together by bonds. – Once bonds form, compounds will have new, and different properties – Organic Compounds • Contains carbon and hydrogen (and often O, N) • Ex: Glucose (C6H12O6), carbohydrate, lipids, proteins – Inorganic Compounds • Doesn’t contain carbon and hydrogen together • Ex: H2O, CO2, NH3, NaCl • Why do atoms form compounds? – Bonds that form between atoms give atoms a stable outer electron level. – Called a “stable octet” of valence electrons (8) Types of Chemical Bonds • Ionic Bonds: – One or more electrons are transferred from one atom to another. – Neutral atoms become positive & negative ions – Forms salts • (Ex: NaCl) Ionic bond = attraction between (+) and (-) ions • Covalent Bonds: – Electrons are shared between atoms – Each bond represents a shared pair of electrons – Can form single, double or even triple bonds Covalent bonds form molecules – Subscripts in the formula tell # of each atom • Ex: H2O, NH3, CO2, CH4 Ionic Bonds: Transfer electrons Covalent Bonds: Share Electrons Properties of Water • Water is necessary for life • Contains covalent bonds Water Molecules: H2O (look like Mickey Mouse) • Water is a “Polar” molecule (like a magnet) • The bonds are “polar” – Oxygen attracts the electrons more than Hydrogen • Hydrogen Bonding: bonding between the (+) H of one molecule and the (-) end of another molecule. – Makes water good at sticking to itself and other substances – Makes water good dissolver • Cohesion: water sticks to itself – Ex: • Water forms “beads” on smooth surface • Surface Tension allows insect to “skate” • Adhesion: water sticks to other substances – Ex: Capillary action: water molecules rise up small tubes • Heat Capacity: – Water has a relatively high heat capacity – Ex: • Lakes and oceans can absorb a lot of heat from sun without a drastic temperature change • Water as a Solvent: – Dissolves most ionic and covalent substances – “Universal Solvent” = many things can dissolve in it. – Solute: substance being dissolved – Solvent: substance in which solute dissolves – Solution: evenly disbursed mixture – Suspensions: material in the water but just suspended not dissolved (ex: blood cells in blood) pH of Solutions • pH Scale: way to measure concentration of H+ ions in solution – Ranges from 0 to 14 – Pure water is neutral pH = 7 • Litmus Paper: – Used to test pH of a solution • Red = acidic • Blue = basic • Acids: Form H+ ions – pH is <7 – Ex: HCl (stomach acid), lemon juice • Bases: Produces OH- (hydroxide ions) – Also called “alkaline” – pH >7 – Ex: Lye (NaOH) used as drain cleaner • Buffers: – Maintain pH at a certain level – Usually between 6.5 – 7.5 (close to neutral) – Helps to maintain homeostasis in organism Major Types of Chemical Reactions • Dehydration Synthesis: (Condensation) – Chemically combine two smaller molecules – Water is removed – “Dehydrate” = remove water – “Synthesis” = to make • Hydrolysis: – Break apart large molecule into smaller pieces – Water is added – “Hydro” = water “Lysis” = to break • Polymerization: – Create a large molecule (polymer) – Join up smaller “monomer” units – Often a dehydration synthesis reaction Ex: Join amino acids (monomer) to make protein (polymer) Join glucose (monosaccharide) to make starch (polysaccharide) Organic Compounds Carbohydrates • Sugars and starches • FUNCTION: – Used as an energy source – Energy released during cellular respiration • Made of carbon, hydrogen and oxygen Ex: C6H12O6, C12H22O11 • Ratio of H of O is always 2:1 • Basic Structure: – “Ring” made of 5 carbons and 1 oxygen – Rings can join up by dehydration synthesis 3 Types of Carbohydrates • Monosaccharide's: 1 sugar ring • Disaccharides: 2 sugar rings • Polysaccharides: many sugar rings • Monosaccharide's: (Simple sugars) – All have formula C6H12O6 – Single ring structure – End in “-ose” – Ex: glucose, fructose, galactose • Disaccharides: double sugars – All have formula C12H22O11 – End in “-ose” – Ex: sucrose, lactose, maltose • Polysaccharides: 3 or more sugar units • Ex: – Starch (energy storage in plants) – Glycogen (how animals store sugar in liver) – Cellulose (plant cell walls) – Chitin (insect exoskeletons) • Simple sugars form into complex sugars by dehydration synthesis (condensation). • Combining molecules by removing water Monosac. + Monosac. Disac. + Water C6H12O6 + C6H12O6 C12H22O11 + H2O and H2O • Complex sugars are broken down into simple sugars by hydrolysis. • Breaking down molecules by adding water • Also called chemical digestion Disac.+ Water Monosac. + Monosac. C12H22O11 + H2O C6H12O6 + C6H12O6 Dehydration Synthesis and Hydrolysis are OPPOSITE Reactions **Chemical reactions are often enzyme mediated. Lipids • Fats, oils and waxes • FUNCTION: – Long term energy storage – Insulation – Protective coating around cells – Cell membranes • Made of carbon, hydrogen, and oxygen • Ratio of H to O is not 2:1 – Ex: C15H26O6 (fewer oxygens) • Animals store energy mostly as fats • Plants store energy mostly as oils Lipids • Made up of: – 1 glycerol molecule – 3 long fatty acid chains – Looks like a giant letter “E” – Also called a “triglyceride” GLYCEROL Note: 3 “OH” groups FATTY ACID CHAIN Note: CARBOXYL GROUP: “COOH” group at end of molecule Basic Lipid Structure • Lipids are: – formed by dehydration synthesis – broken down by hydrolysis Saturated vs. Unsaturated Fats – Saturated: • all single bonds between carbon atoms – Unsaturated: • One or more double bonds between carbon atoms • Makes fatty acid more bent Proteins • Protein Structure: – Made of carbon, hydrogen, oxygen and NITROGEN – Large complex polymer molecules that can have a large range of sizes, shapes and properties Proteins • FUNCTIONS: – Enzymes: speed up chemical reactions – Hormones: chemical messengers – Antibodies: defend against disease – Hemoglobin: binds oxygen to red blood cells – Cell growth and repair – Cell Membrane Channels • Amino Acid: basic building block of proteins Parts of an Amino Acid • Carboxylic Acid Group • Amino Group • “R”-Group (varies depending on amino acid) Examples of Different Amino Acids • There are 20 different amino acids • All have different “R” groups Peptide Bond: bond between amino acids Dipeptide: two amino acids joined. Polypeptide: many amino acids joined – Proteins are polypeptides Forming a Peptide Bond and H2O + H2O • Amino acids join up to form proteins at ribosome • The function of the protein comes from it’s specific sequence of amino acids and the shape the protein forms • The “code” for the specific sequence of amino acids comes from DNA Nucleic Acids • Large complex macromolecule • Stores information in “code” • Composed of carbon, hydrogen, oxygen, nitrogen and phosphorus Structure of Nucleic Acids: • Made of chains of nucleotides Nucleotide: (made of 3 components) – Phosphate Group – Sugar – Nitrogenous Base Two Types of Nucleic Acids • DNA: (Deoxyribonucleic Acid) – Contain genetic information – Found in nucleus – Divides when cell divides • RNA: (Ribonucleic Acid) – Copies code from DNA – Takes code to ribosomes for protein synthesis – Found in nucleus and cytoplasm Differences Between DNA & RNA – DNA: • Double strand of nucleotides • Sugar is deoxyribose • Nitrogenous Bases – Adenine, Thymine, Cytosine, Guanine – RNA: • Single strand of nucleotides • Sugar is ribose • Nitrogenous bases – Adenine, Uracil, Cytosine, Guanine •