Chemistry in Biology

Chemistry in BiologyChapter 6Honors BiologyEQ: How is chemistry related to the growth and survival of living organisms?6.1: Atoms, Elements, and CompoundsChemistry is the study of matter. Matter is anything that has mass and takes up space.Atoms are the building blocks of matter.THE STRUCTURE OF ATOMS:Billions of atoms could fit on the head of a pin!Atoms are made up of even smaller particles NeutronsProtonsElectronsThe Structure of Atoms:Nucleus the center of an atomWithin this nucleus are protons and neutrons.Neutrons particles that have no chargeProtons particles with a positive chargeElectrons negatively charged particles located outside the nucleus.Constantly move around the nucleus in energy levels.Are attracted to the protonsAtoms contain an equal number of protons and neutrons so the overall charge of an atom is neutral.An Atom:

Elements:

Horizontal rows called periods.Vertical columns called groups similar chemical and physical properties.5Elements:An element is a pure substance that cannot be broken down into other substances by chemical or physical means.Are made of only one type of atom.Information collected about each element has been organized into a chart called the periodic table of elements. Organized into horizontal rows called periods,And vertical columns called groups.

Isotopes:Isotopes atoms of the same element that have different numbers of neutrons.Mass (A) = # of protons + # of neutronsAtomic number (Z)= number ofprotons How many neutrons in Carbon 14?14 (mass#) 6 (atomic #) = 8 neutrons

Carbon 14 is a radioactive isotope.

Radioactive Isotopes:A change in the number of neutrons CAN change the stability of the nucleus causing it to decay (or break apart).When a nucleus decays, it gives off radiation that can be detected and used for many applications.Isotopes that give off radiation are called radioactive isotopes.Carbon 14 is a radioactive isotope found in all living things.Half life the amount of time it takes for half of the carbon 14 to decay.Scientists can determine the age of an object by calculating how much carbon 14 remains in the sample.Radioactive isotopes can be used for medical purposes (radiation therapy to treat cancer, radioactive labeling to track certain subsatnces).8CompoundsElements can combine to form more complex substances.Compounds are pure substances formed when two or more different elements combine.NaClCaClH2OCO2Chemical Bonds:A chemical bond is the force that holds substances together.Electrons are directly involved in forming chemical bonds.Each energy level has a specific number of electrons that it can hold at any time.The first energy level (the one closest to the nucleus) can hold up to two electrons.The second energy level can hold up to eight electrons.Chemical Bonds (continued)A partially filled energy level is not as stable as an energy level that is empty or completely filled.Atoms become more stable by losing electrons or attracting electrons from other atoms.THIS RESULTS IN THE FORMATION OF CHEMICAL BONDS BETWEEN ATOMS.It is the forming of chemical bonds that stores energy and the breaking of chemical bonds that provides energy for growth, development, adaptation, and reproduction in living things.The Two Main Types of Chemical Bonds Are:1. Covalent Bonds2. Ionic Bonds

Covalent bond the chemical bond that forms when electrons are shared. Most compounds in living organisms have covalent bonds holding them together.

Ionic bond an electrical attraction between two oppositely charged atoms or groups of atoms called ions. Substances formed by ionic bonds are called ionic compounds.

Ion = an atom that has lost or gained one or more electrons; carries an electric charge.Ions in living things include sodium, potassium, calcium, chloride, and carbonate ions. They help maintain homeostasis as they travel in and out of cells. In addition, ions help transmit signals among cells that allow you to see, taste, hear, feel, and smell.12Types of Compounds:1. Molecule - a compound in which the atoms are held together by covalent bonds.2. Ionic compound a substance formed by ionic bonds.

Van Der Waals Forces:Attractive forces between molecules due to the random movement of electrons which can cause an unequal distribution of electrons around the molecule.Not as strong as a covalent bond or an ionic bond but they play a key role in biological processes.

Activity:Turn to page 155 in the text and answer questions 1-6.

6.2: Chemical ReactionsChemical reactions allow living things to grow, develop, reproduce, and adapt.The human body is a 24 hour reaction factory!A chemical reaction is the process by which atoms or groups of atoms in substances are reorganized into different substances. Chemical bonds are broken and/or formed during chemical reactions.Two Examples of Chemical Reactions are:The formation of rust on metal.

Glow sticksRust forms when oxygen in the air reacts with iron:

The rust on these gear components is a compound called iron oxide and it was formed when oxygen in the air reacted with the iron components.18

A light stick consists of a glass vial, containing one chemical solution, housed inside a larger plastic vial, containing another solution. When you bend the plastic vial, the glass vial breaks, the two solutions flow together, and the resulting chemical reaction causes a fluorescent dye to emit light.

Physical ChangesIts important to know that substances can undergo changes that do not involve chemical reactions.Water, for example, can undergo physical changes:

Water > Water Vapor > WaterWater > Ice > WaterThe water is undergoing a physical change but its composition is not changed.20Reactants and ProductsA chemical equation shows the reactants on the right side of an arrow, and the products on the left.Reactants the starting substances of a chemical reaction.Products The substances formed during the reaction.Reactants ProductsC6H12O6 + O2 6CO2 + 6H2OBalanced Equations:C6H12O6 + O2 6CO2 + 6H2OThe number of atoms of each element on the reactant side must equal the number of atoms of the same element on the product side.1. Use coefficients to make the number of atoms on each side of the equation equal.2. Multiply the coefficient by the subscript for each element.Is the above equation balanced?

No, the above equation is not balanced. To balance this equation you must put the coefficient 6 in front of the oxygen reactant.22Energy of ReactionsThe key to starting a chemical reaction is energy.Activation energy is the minimum amount of energy needed for reactants to form products in a chemical reaction.

+=

The flame above provides the activation energy for the reaction of the substances in the candle wick with oxygen. Once the reaction begins, no further input of energy is required the candle will continue to burn on its own. 23Activation Energy Video Cliphttp://www.youtube.com/watch?v=VbIaK6PLrRM Exothermic Reaction

EnergyProgress of ReactionHeat is given offAn exothermic reaction = the energy of the product is lower than the energy of the reactants and energy was released.The peak in the graph represents the amount of energy that must be added to the system to make the reaction go. Some reactions never take place because they have a very high activation energy.25Endothermic Reaction

An endothermic reaction the energy of the products is higher than the energy of the reactants.This type of reaction takes in heat so the reaction will feel cold.When we added vinegar to baking soda, we created an endothermic reaction. Did you notice the reaction felt cold?26EnzymesSometimes, the activation energy required for a reaction to take place is too high. The reaction cant take place unless additional substances are present to reduce the activation energy.A catalyst is a substrate that lowers the activation energy needed to start a chemical reaction.Does not increase how much product is madeDoesnt get used up in a reactionEnzymes special proteins that act as biological catalysts to speed up the rate of reactions.Enzymes are not used up by a chemical reaction. Once it has participated in a chemical reaction, it can be used again. Most enzymes are specific to one reaction.Example: Amylase is an enzyme found in saliva. It breaks down amylose, one of two components of starch.27Enzymes

Without Enzyme

With Enzyme

Free energy released by the reaction

Compare the activation energy of the reaction without enzyme to the activation energy of the reaction with enzyme.28How Enzymes Work:

Active SitesThe reactants that bind to the enzyme are called substrates.Active site the specific location where a substrate binds to an enzyme. Active site and substrate have complimentary shapes. They are specific for each other.The enzyme-substrate complex helps chemical bonds in the reactants to be broken and new bonds to form. The substrates react to form products. The enzyme then releases the products.29Factors that affect enzyme function:Temperature if.Too high enzyme will denatureToo cold enzyme activity will slow

pH enzymes will denature if pH isToo acidic (H+ ions)Too basic (OH- ions)30Section 6.3: Water and SolutionsProperties of water (H2O):Water is a polar molecule it has an unequal distribution of charges.Hydrogen bonds a weak attraction involving a hydrogen atom and an oxygen atom. Van der Waals forces are responsible for keeping water molecules together.Water has surface tension due to Van der Waals forces.Water striders can stand on water.Water droplets can form.

Water is a Polar Molecule

MixturesA mixture is a combination of two or more substances in which each substance retains its individual characteristics and properties.Homogenous mixture uniform composition throughoutHeterogenous mixture components remain distinct, do not dissolveA solution is a homogenous mixture. Two components of a solution are:Solvent substance in which another substance is dissolvedSolute the substance that is dissolved in the solvent.

Acids and Bases:Acids are substances that release hydrogen ions when dissolved in water.The more hydrogen ions a substance releases, the more acidic the solution becomes.Substances that release hydroxide ions (OH-) when dissolved in water are called bases.NaOH is a common base that breaks apart in water to release Na+ and OH- ions. The more OH- ions present, the more basic a solution is.pH:

The amount of hydrogen ionsor hydroxide ions in a solution determines the strength of an acid or a base.We can easily measure the pH of a solution using a pH meter or pH paper. See the pH scale to the right.Water is neutral (pH 7)Acids have a pH lower than that of water.Bases have a pH higher than that of water.Whats a buffer?The majority of biological processes carried out by cells occur between pH 6.5 and 7.5. In order to maintain homeostasis, its important to control H+ levels.

Buffers are mixtures that can react with acids or bases to keep the pH in a cell within the 6.5 to 7.5 pH range.356.4: The Building Blocks of LifeOrganisms are made up of carbon-based molecules.Carbon is a component of almost all biological molecules.Organic chemistry the study of organic compounds (compounds containing carbon).

Carbon:Has 4 electrons in its outer energy level. This energy level can hold 8 electrons so one carbon atomCan form 4 covalent bonds with other atoms.Carbon atoms can bond to each other in different ways:Straight chain molecules:

Branched molecules:

Ring molecules:

Macromolecules - Are large molecules that are formed by joining smaller organic molecules together.Monomer a single molecule that can bindto several others just like it to form a polymer.Polymer many monomers linked together by covalent bonds.

There are 4 major categories of macromolecules:Carbohydrates

Lipids

Proteins

Nucleic Acids

CarbohydratesCompounds composed of carbon, hydrogen, and oxygen (CH2O)n.This glucose monosaccharide playsa central role as an energy source fororganisms.Monosaccharides can be linked toform disaccharides (sucrose) orPolysaccharides.

Glucose(Monosaccharide)CHOs: monosaccharide = glucose disaccharides = sucrose (table sugar) lactose (milk sugar) polysaccharide glycogen is an energy storage form of glucose found in the liver and muscles.When the body needs energy and no glucose is available, the body will break glycogen down into glucose.Plants cellulose is a carbohydrate which provides structural support for the plants cell walls.40LipidsFats, oils, waxesLipid molecules are made up of carbon and hydrogen.Store energyBasic structure of a lipid includes fatty acid chains (tails):Tails are chains of carbon bonded together by either single or double bonds. Hydrogen atoms are bonded to the carbon atoms.Saturated single bonds between carbon atoms so no more hydrogens can bond.Unsaturated one double bond between C atoms, so at least one hydrogen can bond.Polyunsaturated fats are fats with more than one double bond in the tail.41

Phospholipids and SteroidsPhospholipid bilayerSteroids CholesterolHormones

ProteinsCompounds made of small carbon compounds called amino acids.Amino acids are small compounds made of carbon, nitrogen, oxygen, hydrogen and sometimes sulfur.All amino acids share the same general structure:

Peptide bondsCentral carbon atomAmino groupCarboxyl groupVariable side chain there are 20 different ones Several covalent bonds called peptide bonds join aas together to form protein chains.

44Proteins (cont.)Can have up to 4 levels of structure:PrimarySecondaryHelixpleatTertiary a globular arrangement (hemoglobin)Quaternary proteins bound to other proteinsStructure depends on the number of amino acids in a chain and how they are arranged.

Proteins (cont.)Muscle, skin, hair are made up of proteinsAre involved in almost every function of your bodyCells contain 10,000 different proteins that provideStructural supportTransport substancesCommunicate signals between cellsCatalysts for enzymatic reactionsControl cell growthNucleic Acids:Nucleic acids are complex macromolecules that store and transmit genetic information. Two types:DNA (deoxyribonucleic acid)RNA (ribonucleic acid)Made of smaller repeating subunits called nucleotides which are composed ofCarbonNitrogenOxygenPhosphorusHydrogenNucleotide: