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Biochemistry Elements • Pure substances that cannot be chemically broken down • Over 100 identified • Less than 30 are biologically important • 90% of living things are made up of just 4 elements Atoms • Atom- basic unit of all matter 4 Biologically important atoms: Carbon (C) Hydrogen (H) Oxygen (O) Nitrogen (N) Atomic Structure 2 Main Parts of an atom: 1. The nucleus- made of protons and neutrons 2. Energy levels- where electrons can be found Energy levels • The 1st energy level can hold 2 electrons • The 2nd energy level can hold 8 electrons • Electrons in outer energy levels have more energy than electrons in inner energy levels Valence Shells • Noble gases- group 8, have full outer energy shell (valence shell)– and so are not reactive • What are valence electrons? • Octet rule- when atoms combine to form molecules through bonding, the valence shell needs to be filled Drawing of an Atom Periodic Table • Mass # - number of protons and neutrons in nucleus • Atomic # -number of protons (and subsequently electrons) in an atom 2 Types of Bonding 1. Ionic bonding- a transfer of e- occurs and results in an ion 2. Covalent bonding- bond that results in a sharing of ePolar-unequal sharing of e- (ex: NaCl) Nonpolar-equal sharing of e- (O2) Common Structural Formulas Molecules Water Carbon Dioxide Energy Law of conservation of energy- amt. of energy in universe is fixed, energy can be converted from one form to another but can not be created or destroyed What is energy? States of matter 1. Solid- fixed shape and volume, particles tightly packed 2. Liquid-fixed volume, no fixed shape (take shape of container) flow freely in container States of Matter 3. Gas- no fixed shape or volume (particles have little attraction to eachother- can fill volume of container Chemical Reactions • Organisms undergo thousands of chemical rxns as part of their life processes • Generally speaking: Reactants Products Chemical Reactions Ex: CO2 + H20 H2CO3 This reaction is reversible Energy Transfer • During chemical rxns, energy is released or absorbed • Exergonic rxns- involve net release of energy • Endergonic rxns- involve net absorbtion of energy Activation Energy • Most chemical rxns require addition of energy to reactants to get started • What is activation energy? Catalysts- substances that reduce the amount of activation energy needed for rxn to occur Activation Energy • In living things, enzymes are important catalysts • Enzymes are usually proteins • Enzymes usually end in suffix –”ase” • Enzymes are specific for different chemical rxns Redox Reactions • Involve a transfer of electrons between atoms • Oxidation rxn- reactant loses electrons • Reduction rxn- reactant gains electrons Solutions • Made of 2 parts: solute and solvent • Could be a mixture of solids, liquids, or gases • Solute- substance dissolved in solution • Solvent- substance in which solute is dissolved • Ex: Kool aid? What is the solute? Solvent? Solutions • All solutions have a concentration Ex: 2g of salt per 100 ml solution 50g of salt per 100 ml solution Saturated solutions are ones in which no more solute can dissolve Most solutions in biology are aqueous Ex: cells, marine organisms, nutrients plants get from moist soils Dissociation of Water • OH- is the hydroxide ion • H3O+ is the hydronium ion Acids and Bases • Neutral solutions have the same #s of hydronium and hydroxide ions • Ex: Water Acids • Acids have more H3O+ ions than OH- ions • Ex: HCl • Acids tend to have a sour taste and in concentrated forms are very corrosive Bases • Bases have more OH- ions than H3O+ ions • Ex: NaOH • Bases tend to have a bitter taste and feel slippery when they react with oils of your skin to form soap pH • pH scale compares relative concentrations of H+ and OH- ions in a solution • • • • pH scale ranges from 0 to 14 pH of 7 is neutral Below 7 is acidic Above 7 is basic pH • Change in one unit of pH scale represents a tenfold change in acidity or alkalinity • Ex: pH of 3 is 10x more acidic than pH of 4 • pH of 12 is 100x more basic than pH of 10 Buffers • Chemical substances that neutralize small amounts of acid or base added to a solution • Buffering systems in your body maintain pH values of body fluids at normal and safe levels Water • Important to all living things • Makes up 70-95% of most organisms • Known as the “universal solvent” Polarity of Water • Water is a polar molecule- this means that there are charges in different regions of a water molecule • It is because of the polar nature that water is good at dissolving other substances Hydrogen Bonding • Water molecules are also attracted to each other because of it’s polar nature • A hydrogen bond is formed when the + region of one water molecule is attracted to the – region of another water molecule Hydrogen Bonding • H bonds are weak bonds that can be easily broken, but there is a significant attractive force that causes water to attract to itself and other substances: Hydrogen Bonding • Cohesion- when water molecules attract themselves • Adhesion- when water molecules attract another substance • These two properties are the reason water can move up stems of plants against gravity Water Properties • Water has a high specific heat This means it takes a lot of energy added as heat to raise the temp. of 1g of water by 1 degree Celsius Water is also less dense in solid form– this allows life to survive in water in the winter Organic Molecules • What is the difference b/t monomers and polymers? • Polymers form when monomers join together through condensation reactions in these reactions, a molecule of water is released Organic Molecules • The opposite of a condensation rxn is hydrolysis –this is the breaking down of polymers by adding water Energy Currency • All living things require energy to carry out processes that keep them alive • This energy is often found in the compound ATP (Adenosine Triphosphate) Organic Molecules • Primarily made of C, H, O, N • Carbon bonds in many ways to form: Straight chains Rings Branched chains 4 Biologically Important Molecules 1. 2. 3. 4. Carbohydrates Lipids Proteins Nucleic Acids Carbohydrates Why Important: Cellular structural building blocks #1 Energy Source (cellATP) Carbohydrates Ex: simple sugars (monosaccharides) double sugars (disaccharides) Carbohydrates Polysaccharides (complex or stored carbs) Lipids Why Important: Cellular structural building blocks #2 Energy Source Examples: Fats Oils Waxes- found on leaves (cuticle) Proteins Why Important: Cellular structural building blocks #3 Energy Source -Made of amino acid sub-units -there are 20 different amino acids -amino acids are arranged in various order and # to make proteins Proteins -Proteins are very complex -Not random Examples Hemoglobin Insulin Enzymes Antibodies Proteins Surplus carbohydrates, lipids, and proteins can be stored as fat Nucleic Acids Examples 1. DNA 2. RNA Why Important: -Genetic info -Instructions to build & run cells -Instructions to make proteins Nucleic Acids 3. ATP -Usable form of cellular energy made from carbs, lipids, & proteins *All nucleic acids are made of nucleotide sub-units Nucleic Acids • 1. 2. 3. Each nucleotide sub-unit has 3 parts: Phosphate group Pentose sugar Nitrogenous Base Nucleic Acids • There are 5 Nitrogenous Bases: Adenine (A) Guanine ( G) Uracil (U) Thymine (T) Cytosine (C) Nucleic Acids In DNA the bases pair up: A—T G—C Same pairings in RNA except there is no Thymine, it is replaced with Uracil Organization from Atoms to Organisms