2 Fundamental unit of matter Nucleus Protons: Positive charge; mass of 1 The AtomFundamental unit of matterNucleusProtons: Positive charge; mass of 1Neutrons: No charge; mass of 1ElectronsSpin around the nucleus in orbitals (shells)Negative charge; No massElectrically negative: # of protons = # electrons
4 Electrons Electrons carry energy. How?? Electrons are negatively charged as such, they are attracted to the positive charge in the nucleus. Meanwhile, electrons repel other electrons.REMEMBER… OPPOSITES ATTRACT and SAME REPELSElectrons spin around the nucleus at various levels. They are attracted to the nucleus but repel each other, therefore it takes work to keep them in orbit.Example is an apple in your hand.
5 Volumes of space that surround the nucleus Electrons move in orbitals Electron OrbitalsVolumes of space that surround thenucleusElectrons move in orbitals
6 Electron shells and electron orbitals Constants:The 1st shell in any atom can hold 2 electronsThe 2nd shell in any atom can hold 8 electronsThe 3rd shell in any atom can hold 8 electronsShell # of electrons each shell can holdFirst shellSecond shell 8Third shellP + N
7 Electron Movement Electron shells = energy levels Electron orbital = Volume of space around a nucleus where an electron is most likely to be foundUseful Analogy:planets (electrons) ORBITING around the sun (nucleus)
8 Why is it necessary to understand how electron orbitals work Why is it necessary to understand how electron orbitals work? This isn’t a Chemistry class, right??Electrons and the energy they posses (their energy state) determine the chemical behavior of atoms thus, the losing, gaining or sharing of electrons is the BASIS FOR CHEMICAL REACTIONS IN WHICH CHEMICAL BONDS FORM (chemical bonds include hydrogen bonding, ionic bonding and covalent bonding).
9 If electrons couldn’t lose or gain other electrons, or share with other electrons, chemical bonds would NOT form!Example, H2O
13 How to Read the Periodic Table Elements are arranged: LEFT to RIGHT and TOP to BOTTOM in order of increasing atomic mass.Rows are arranged in periods Ex. H and He are in period C and O are in period 2The period number of an element = highest energy level an electron in that element occupies in an unexcited stateTherefore,H and He have 1 electron shellC and O have 2 electron shells
14 C 12 Columns represent groups and families. Each element symbol has 2 numbers listed: atomic number and atomic mass.Atomic NumberNumber of protons in the nucleus6C12Atomic MassNumber of protons and neutrons in the nucleus
16 Carbon Carbon Facts: 6 protons (Atomic # is 6) 6 neutrons (Atomic mass is 12…so, how do you get 6?)N = Atomic Mass - P6 electrons (Atomic # is 6)Is the first electron shell full (inactive)?Is the second electron shell full?How many unpaired orbitals does C have?YesNo4
17 Can an element ever have a variable number of neutrons? CarbonCarbon Facts:How many chemical bonds can Carbon form with other atoms?4Can an element ever have a variable number of neutrons?
18 IsotopesSame atom but with a different # of neutrons, thus a different atomic massAtomic number = # protons in the nucleusAtomic mass = # protons + # neutronsHaving a different number of neutrons in the nucleus DOES NOT change the chemical properties of an element BUT it DOES change the stability of the element!!
19 Isotope Atomic # # protons # protons # protons 6 6 6 Atomic Mass # P + # N #P + # N # P + # N6 + 6 = 126 + 7 = 136 + 8 = 14
20 Medical Uses of Radioactive Isotopes Short-lived isotopes are used clinically to diagnose pathological abnormalities/diseaseEx. Use of 99Tc for renal scan99 Tc (tracer) is introduced through your bloodstreamKidney cells take up the radioactive tracer (isotope of Tc = 99Tc)A camera detects emissions from the tracer and records them.What makes 99Tc specific for kidney cells?
21 The isotope is specific for a protein unique to kidney cells. Remember, electrons are the basis for chemical reactions!!So… if 99Tc has a different number of neutrons in its nucleus, the stability of the electrons in the other shell of that 99Tc atom are changed.There are 43 isotopes of Technitium!It just so happens that the particular stability of 99Tc seeks to form a chemical bond with this unique kidney protein.
22 Matter Any substance in the universe that has mass and occupies space Matter is transformed through chemical bondingConservation of Matter = Matter cannot be created or destroyed but… it can be transformedUse of an equation to show how matter is transformed:Reactants ProductsSodium + Chloride Sodium chloride Na Cl NaCl
23 Important Bonds in Biological Membranes Way in which atoms link to one another to form moleculesLinks are formed through the exchange of electronsAtoms are driven to react to become more stableAtomic stability is achieved by filling an outer electron shellNon-reactive elements have full outer shells = INACTIVETypes of chemical bondingIonic bondingCovalent bondingHydrogen bonding
24 Ionic BondingCreates ions (charged atoms): one atom loses electrons and becomes a (+) charged ion while another gains electrons and becomes (-) chargedNote: in charged atoms, the # of protons DOES NOT equal the # of electrons!!!! # Protons = # ElectronsFormed when atoms are attracted to each other by opposite electrical charges (i.e. magnet)Two key properties of ionic bonding:They are strong bond (although NOT the strongest)They are non-directional
25 Ionic BondingExample: Table saltReactants:Sodium atom has 1 lone electron in its outer orbital (Ax)+Chloride atom has 7 electrons in its outer orbital (Ax)Products:Sodium ION that has given up an electron from its outer shellChloride ION that has accepted an electron from Sodium and has included it in its outer shell
27 Both the sodium ion and the chloride ion are electrically attracted because of the opposite charges incurred by the altered electron orbitals.This electrical attraction results in the formation of an elaborate matrix resulting in a crystal of table salt.
28 Covalent Bonds Electrons are shared between atoms Two key properties of covalent bonding:VERY STONG!!! (strongest type of bond)DirectionalCarbon ALWAYS forms a covalent bond!!!!!2 types:Non-polar Covalent: electrons are equally sharedGenerates hydrophobic molecules (“water hating”)Polar Covalent: electrons are unequally sharedGenerated hydrophilic bonds (”water loving”)
34 Solutions A homogenous mixture of 2 or more substances Solute = ingredient being dissolvedSolvent = substance that does the dissolvingExample. You make a solution of water and salt. Which is the solute and which is the solvent?Solute = SaltSolvent = WaterComponents of solutions Acids Bases Salts pH
35 Components of Solutions, continued AcidsA substance that puts hydrogen ions (H+ )into a solutionExample: Hydrochloric Acid placed in waterHCl + H2O Cl- + H+Water HCl dissolved in waterHHHHHHHH
36 Components of Solutions, continued BasesA substance that puts hydroxide ions (OH-) into solutionExample: Sodium Hydroxide dissolved in waterNaOH + H2O Na+ + OH-Water NaOH dissolved in waterOHOHOHOHOHOHOHOH
37 Components of Solutions, continued SaltsA substance that puts other ions into solution (ions other than H+ and OH-)Example: Sodium chloride dissolved in waterNaCl + H2O Na+ + Cl- + H2OClNaNaNaClClClNaNaClNaNaClClNaCl
38 Salts are formed when acids and bases are added to each other; this results in neutralization of the acid and base.HCl + NaOH NaCl + H2O(Acid) (Base) (Salt) (Water)
39 Components of Solutions, continued pHA logarithmic scale that measures the acidity of alkalinity (basicity) of a solutionNote: the difference between 2 units on the pH scale is 10, therefore, the difference between 3 pH units is…100pH scaleNeutral : pH = 7Acidic : pH < 7Basic : pH > 7Buffers keep pH within normal limits
41 The Importance of Water to Life Three quarters of the Earth’s surface is waterTwo thirds of the human body is composed of waterAll organisms require waterSince water is an essential part of life, it’s surprising that the bond that 2 atoms of H make with 1 atom of O is so weak. Actually, the bond that forms a single H20 molecule (which is what type of bond??) lasts only 1 / 100,000,000,000 of a second!However, water molecules form extensive lattices with other water molecules. This occurrence leads to the important physical properties of water!
42 WaterWater is a polar covalently bonded molecule that forms hydrogen bonds with other polar covalently bonded water molecules.Universal solventIce (solid water) is less dense than liquid ice.Ex. Ice floats in liquid water4. Water has a high capacity to store heat. Water stabilizes Earth’s temperature (Remember, water comprises ¾ Earth’s surface.5. Adhesion and cohesion
43 Properties of WaterBonds to hydrophilic substances and repels hydrophobic onesStabilizes temperatureExpands when it freezesCohesiveDissolves substances
45 Cohesion Surface Tension Since water is polar, it is attracted to other polar molecules. Cohesion occurs when the other polar molecule is water.Surface TensionCreated by cohesion and due to the strong hydrogen bonding between the polar water molecules.
47 Forming Macromolecules Organic moleculeFormed by living organismsCarbon-based core with functional groups attachedFunctional groupGroups of atoms with special chemical propertiesConfer specific chemical properties on the molecules that posses themEx.MacromoleculesPotentially large molecules (Macro-) that are the building materials of cells. They are the material that makes up the body of cells and the machinery that runs within cellsThousands of different types in an organism BUT the body is made of 4 types (protein, nucleic acid, carbohydrates, lipids)
49 More on Macromolecules Polymer: a molecule made of MANY chains of a similar subunitMonomer: a single molecule that is the BASIC building block of a macromoleculeMonomers can combine to form a polymerView animation on Polymer formation
50 Dehydration Synthesis The process of FORMING a macromoleculeForms a COVALENT bond between two subunits:A hydroxyl (OH) group is removed from one subunitA hydrogen (H) is removed from the other subunitSmall molecule + small molecule large molecule + H20View animation
51 Hydrolysis Reactions The BREAKING up of a polymer Adds a water molecule (H20)H20 comes in and…A hydrogen becomes attached to one subunitA hydroxyl (OH) becomes attached to the other subunitResults in the BREAKING of the covalent bond that previously held the macromolecule (polymer) togetherLarge molecule + H small moleculesView animation
52 Carbohydrates Contain C, H, O atoms (1:2:1 ratio) # Carbon atoms = # Oxygen atomsHydrophilicExcellent for energy storageWhy?? The C-H bonds store energy. When an organism requires an energy source, C-H bonds are the ones most often broken. This results in the release of stored energy.Comprise 1-2% of a cells mass2 types: simple carbohydratescomplex carbohydrates
53 Simple Carbohydrates Monosaccharide Simple sugar Consists of one subunit; smallest carbsEx. Glucose (C6H12O6)Also, fructose, ribose, deoxyriboseSee Figure 3.29DisaccharideResult of linkage of two monosaccharidesEx. Sucrose, lactose, maltoseSee Figure 3.30
54 Complex Carbohydrates PolysaccharidesLong chain polymers of sugarsThe body converts soluble sugars into insoluble forms (polysaccharides). These polysaccharides are then deposited throughout the body in specific storage areas.Preferred form of energy storagePlants: starch = glucose polysaccharide that plants use to store energyAnimals: glycogen = highly insoluble macromolecule formed of glucose and polysaccharides that serves as stored energyCelluose = indigestible b/c we lack enzymes to break it down = fiber; synthesized by plants for cell wall constructionUtilized by plants and animals as structural polysaccharides (chitin and cellulose); linkage is unique such that the chains are not recognized by enzymes that normally break polysaccharide bonds.
55 LipidsContain C, H, and OHydrophobic (held together by non-polar covalent bonds)Used as long term storageContains MORE energy-rich C-H bonds than carbs
56 Lipids I. Triglycerides (Fat) Fats are synthesized from 2 components:1. Fatty acid: long chain C and H atoms ending in a COOH group2. Glycerol: a three C molecule; note, glycerol is an alcoholGlycerol forms a backbone to which 3 fatty acids are attached via a dehydration reaction fat moleculeProvides long term energy storage, insulation
57 Lipids, continued Triglycerides SaturatedFatty acids with ALL internal carbon atoms forming covalent bonds with two hydrogen atomsAnimal sourceSolid at room temperature and body temp (37C)UnsaturatedFats with fatty acids that have double bonds between 1 or more pairs of carbon atomsPlant sourceKink imparts a 30° bend:Liquid at room temperature Low melting pointWhen we eat fat, lipase digests the fat and breaks it down to the 3 individual fatty acidsThe longer the fatty acid chain, the HIGHER the melting tempI.E. Butter – is a saturated triglyceride (composed of different saturated triglycerides). That is why it melts slowly, not all at once! Different triglycerides melt at different temps.Unsaturated fats melt at lower temps than saturated (> irregular the shape of unsat = lower melting point); as unsat increases, MP reducesSolid at RT b/c they pack very well – they are straight like sticks, whereas unsaturated is liquid at RT b/c the kinks imparted by the double bonds make them pack less efficiently
58 Why are unsaturated fats good while saturated fats are bad for your health? The C C bond in unsaturated fats creates a negative charge that causes the fat molecules to repel each other rather than stick together (as they do in long chain saturated fats).
59 Hydrogenation Example: Margarine Margarine is formed from heating oil (unsaturated triglycerides) in the presence of a metal catalyst (aluminum) and hydrogen. That environment breaks the C C and replaces it with two hydrogen atoms producing very hard, saturated fats. Chemists vary the degree of time that hydrogenation occurs resulting in a product that is soft and spreadable (partially hydrogenated).N.B. Margarine is 10-50% trans fatty acids = BADMargarine has been found to be contaminated with aluminum. Al is a causative agent in ADCatalyst = something that facilitates a chemical reaction without itself being used upAD = Alzheimer’s Disease
60 What is a trans-fatty acid? Trans fatty acids have hydrogen atoms on opposite sides of the double bonded carbonsCis fatty acids have hydrogen atoms that on the same side with each otherThe enzymes that metabolize fat can only metabolize cis fatty acids
61 Butter is a saturated triglyceride Butter is a saturated triglyceride. Why does butter soften as it melts, why doesn’t it instantly melt?Because the fatty acid chains that come off the glycerol backbone differ. Each different fatty acid has a different melting point.
62 Common fats Saturated Unsaturated Palmitic acid Omega-3 Palmitic acod Myristic acid = id’d from nutmeg; found in N-terminus of plasma mem associated cytoplasmic proteins
63 Types of Lipids II. Phospholipid III. Steroid Glycerol + 2 fatty acids + phosphate groupPolar group at one end (glycerol and phosphate) and highly nonpolar group at other end (fatty acid tails)Ex. Cell membraneIII. Steroid4-interlocking ringsFound in cell membranesEx. Cholesterol, hormonesPer gram, Fat has twice the energy as carbs
64 Basic structure of a triglyceride Basic structure of a phospholipid
66 Protein Comprises 10-30% cell mass Functional roles (enzymes) and structural roles (collagen, keratin)All proteins are a long polymer chain of amino acid subunitssmall molecules, 20 totalall 20 have a basic structure of a central carbon atom to which the 4 following are attached: hydrogen atomamino group (-NH2)carboxyl group (-COOH)an “R” groupCollagen = cartilage, bones, tendonsKeratin = feathers of birds
68 How to make a proteinLink specific amino acids together in a particular orderPeptide bond = covalent bond that links 2 amino acids togetherPolypeptides = long chains of amino acids liked by peptide bonds
69 Protein Structure Structure determines function What determines protein structure?Amino acid sequence of the proteinFour levels of protein structure:PrimarySecondaryTertiaryQuaternaryAll levels of protein structure are ultimately determined by amino acid sequence!!
70 Primary Structure of Protein The sequence of amino acids of a polypeptide chain
71 Secondary Structure of a Protein Initial folding of the polypeptide chain caused by formation of hydrogen bondsCan result in sheets (Beta sheets) or coils (alpha helices) of polypeptidesBecause some AAs are polar and some are nonpolar, a polypeptide folds in solution: nonpolar regions are forced together (forced by the polar groups and their attraction to water resulting in the polar groups repulsion of nonpolar amino acids)
72 Tertiary Structure of a Protein A folded and twisted moleculeRepulsion by water forces nonpolar amino acids towards the interior leaving polar amino acids exposed to the exterior
73 Quaternary Structure of a Protein Spatial arrangement of several component polypeptide chains
74 Denaturation What influences how a polypeptide folds in solution? The polar nature of the environmentWhen the polar nature of the environment changes (↑ temp or ↓ pH), hydrogen bonding may be altered which may then cause unfolding of the protein, or denaturation.Ex. Frying an egg
75 Nucleic AcidsLong polymers of nucleotides that serve as information storage devices of cellsNucleotides have 3 components:A five carbon sugarA phosphate group (PO4)An organic nitrogen-containing basePolynucleotide chains- Chain of nucleic acids in which sugars are linked in a line by the phosphate groups…SUGAR – P – SUGAR – P - SUGAR – P …
76 Nucleic Acids DNA and RNA DNA (deoxyribonucleic acid) Possible nucleotides: Adenine, Guanine, Cytosine, THYMINEStructure: 2 nucleotide strands = double helixRNA (ribonucleic acid)Possible nucleotides: Adenine, Guanine, Cytosine, URACILLong, single strandHow do nucleic acids function as information storage devices?Each nucleotide serves as a letter and each nucleic acid has different nucleotides (letters)
78 Everyday ScienceLactose Intolerance – the inability to digest foods containing milk due to a lack of the lactase enzyme (enzyme, a protein that disrupts chemical bonds in other molecules allowing reactions to occur or preventing their occurrence).Normally, milk sugar (lactose) is digested by the lactase enzyme. Lactase binds to lactose in milk and breaks the chemical bonds that are responsible for holding the sugar together. This allows the broken down sugars to pass through the bloodstream and be utilized by the body.LI people lack the lactase enzyme, thus they cannot digest milk protein. This leads to a buildup of leading to nausea, cramps and bloaing.
80 Questions What is the strongest type of single bonded molecule? Covalent bond (both polar and non-polar types)2. Isotopes have a different measure of stability when compared to their ‘parent’ element on the periodic table. True or FalseTrue3. You can determine the number of neutrons present in an atom by subtracting the number of protons from the ____.Atomic mass4. When preparing a solution, you accidentally add too much of an acidic component. This creates an excess of _____. The desired pH is 8; the pH you measure is 6. You decide that it shouldn’t make too much of a difference, you’re only 2 units off. What is wrong with this logic?H+, or Hydrogen ions
81 A difference of 2 units on the pH scale correlates to a 100 fold more acidic solution. Therefore, your solution has 100 times more Hydrogen ions then the desired solution concentration.
82 Websites for additional info from today’s lecture: Interactive periodic table