BSC 215 Week 3 Notes
BSC 215 Week 3 Notes BSC 215
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This 10 page Class Notes was uploaded by Jordana Baraad on Thursday September 1, 2016. The Class Notes belongs to BSC 215 at University of Alabama - Tuscaloosa taught by Dr. Jason Pienaar in Fall 2016. Since its upload, it has received 15 views. For similar materials see Human Anatomy & Physiology I in Biological Sciences at University of Alabama - Tuscaloosa.
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Date Created: 09/01/16
8/30/16 CQ: Atom w/ atomic #8, and mass number 17? 8 protons, 9 neutrns, 8 electrons (if neutral) LO7: Compare and contrast ionic, nonpolar covalent, polar covalent and hydrogen bonds using biological examples • Types of chemical bonds depend on ways valence electrons are distributed when forming molecules • Ionic bonds transfer of electrons between atoms • Nonpolar covalent bonds equal sharing of electrons strongest type! • Polar covalent bonds unequal sharing of electrons one side more neg; one side more pos • Hydrogen bonds attractions between polar molecules regardless of what the polar molecules are on the way to ionic bonding (partial charge in Hbonds; full charge in ionic) • Van de Waal’s forces brief attractions between temporarily polar molecules sim to Hbonds and ionic bonds, but TEMPORARY Ionic bonds Starts with transfer of electrons from one atom to another, then opposites attract Na wants to get rid of electron; can’t give up to blank space That’s where Cl comes in; needs donor Important biologically by NaCl = electrolyte Conducts electricity in cells/ nerves Nonpolar covalent bonds Sharing of electrons in order to satisfy octet (or duet rule) o Ex. CH 4satisfies octet rule for C; duet rule for H Equidistant spacing of H’s No side of molec diff charged from other sides (no neg/pos) Double & triple covalent bondsVery strong! o Ex. O2: double; N2 : triple Determine which by seeing hm bonds needed to fulfill octet rule STRONGEST chem bonds Strength: triple covalent >> double >> single >> other types of bonds Polar covalent bonds Sharing of electrons in order to satisfy octet (or duet rule) BUT, one atom has a greater affinity for the electrons o creating a slight charge difference (poles) Best ex. = water (H2O) o 1 O shares electrons w/ 2 H’s o O has bigger nucleus (more protons) stronger attraction for electrons On avg. electrons spend most time on Oside O gets partial neg charge H gets partial pos charge Less charge difference than in ionic Hydrogen bonds Weak electrostatic interactions btwn slightly polar molecs “weak form of ionic bond” Hydrogen bonds give water the properties of: Solvency: Water as “universal solvent” Can’t dissolve everything; just polar things Counterexample: fats—allow membranes to exist Most molecs that matter in cell biology are polar Allow for dissolution in water; hydrophilic Chemical reactivity: phys participates in rxns Hydrolysis reactions: add water (hydrolyze) to break bond Dehydration synthesis: take away water to make bond Cohesion: water molecs sticking to self Ex. puddling on floor Thermal stability: need to overcome electrostatic attractions to change phase Requires more energy to boil water (polar) than ethanol (nonpolar) Adhesion: sticking to self Ex. water sticking to wall (via Hbonds) Try to prevent this in blood—don’t want blood (majority water) to stick to veins/ arteries Weak attractions between polar molecules (e.g. water) CQ2: Which of following contains polar covalent bonds? H2O H2 and CH4: polar covalent; NaCl: ionic Van de Waals forces Brief attractions between non polar molecules due to temporary polarization (electron cloud disturbances) Enzymes, water, acids & bases Learning outcomes 1. Understand the notation and basic energetics of chemical bond formation 2. Describe the factors that influence reaction rates 3. Explain the properties, actions and importance of enzymes 4. Discuss the physiologically important properties of water 5. Define and describe the properties of acids and bases with respect to hydrogen ions 6. Explain what the pH scale measures be able to calculate w/ pH ( log) 7. Explain how a pH buffer works acts as both acid and base; depending on environmental pH soaks up excess H or releases H Reactants Products Decomposition Chemical reaction: chemical bonds are broken, formed or rearranged or electrons are transferred between atoms (standard notation) Reactants Products Decomposition: AB A + B o Reactants more complex/ larger than products o Nature of bonds doesn’t matter Synthesis: A + B AB o Opposite of decomp o Products larger/ more complex than reactants Exchange: AB + CD AC + BD o NO change in size/ complexity o AB/ CD have “swapped” partners Reversible: AB ⇌ A + B o ALL the above rxns are reversible o Typ faster rate in one direction LO1: Understand the notation and basic energetics of chemical bond formation Reversible synthesis / decomposition reaction CO 2+ H 2 ⇌ H CO2 3 left right: synthesis rxn o H2CO 3can release a H; holds onto electrons o H leaves as proton o Acts as weak acid o Reverse: acts as weak base Fate depends on pH of solution it’s in Exchange reaction HCl + NaOH ⇌ H2O + NaCl LO1: Understand the notation and energetics of chemical bond formation Chemical energy: Potential energy stored in chemical bonds (covalent bonds) When break those bonds, energy released that can do work Ex. glucose has lots potential chem energy—molecule of choice for biorxns Electrical energy: Flow of ions Discussed more with respect to nerves Mechanical energy: Energy directly transferred from one object to another Endergonic reactions: Products have higher energy than reactants Need to put energy into system Anabolic rxns—building biomolecules requires energy Exergonic reactions: Reactants have higher energy than products Get energy out of rxn Catabolic rxns—digestion/ breakdown to release energy so orgs can use it For now, focus on chemical energy, endergonic/ exergonic LO2: Describe the factors that influence reaction rates ***For a chemical reaction to occur 2 things must happen: 1. reactants must come into physical contact with one another a. dep on phys proximity at same time b. cell mechanisms work to bring molecs in concentration @ same place/ time 2. reactants must overcome the repulsive forces of their electrons get electrons over barrier to be attracted to other nuclei How do we make 1 & 2 happen? LO2: Describe the factors that influence reaction rates Concentration: higher concentration = more molecules in given space more likely to collide if more particles Temperature: more kinetic energy higher speed more collision likelihood Reactant properties: ex. state/ phase of matter increased molecular motion increased collision likelihood Ex. liquid Catalysts: “master builders/ breakers” literally bring molecules together or put tension on bonds (only a little excess energy req to break) active site where desired reactant molecules fit together so they can interact CQ 3 Chem energy stored in bonds is: potential energy CQ 4 Digestion exergonic bc chemical bonds are broken and energy is released? T/F True LO3: Explain the properties, actions and importance of enzymes Bio ex. enzymesubstrate complex Sucrose (enzyme) works on molecule sucrose Sucrose = glucose + fructose; disaccharide (2 subunits of sugar) Covalently bonded by glycosidic bond Don’t need to be able to recognize partic sugars DO need to recognize that dealing w/ sugars/ saccharides Goal: break glycosidic bond—turn sucrose glucose (glycolysis/ Krebs cycle) 2 hydroxyl groups (OH) formed components come from surrounding water—hydrolysis Sucrose puts tension on glycosidic bond; requires only a little more energy to break Forms enzymesubstrate complex Lowers activation energy KNOW free energy diagram Red line: energy req w/o catalyst Blue line: energy req w/ catalyst Still some req to overcome activation energy Cellular rxns can happen with less energy input due to catalysts present Increasing rxn rate Biasing rxn direction LO3: Explain the properties, actions and importance of enzymes Biological catalysts: Lower activation energy required to make or break covalent bonds Highly specific: Unique, active site regions bind specific molecules (substrates) Reusable: Enzymes structure reverts to original form after catalyzing reactions CQ 5: Enzymes bind w/ substrates at active sites and are permanently altered by binding process. T/F? False—enzymes are reusable; once product formed and release; enzymes move on unchanged LO4: Discuss the physiologically important properties of water going back to water as “universal solvent” Solvent Hydrophobic V. hydrophilic? o Hydrophilic = polar; hydrophobic = nonpolar o Ex. NaCl Hydration Spheres: Keep ions dissociated o Allow movement and interaction with other ions o H atoms surround anions (ex. Cl ) + Insulates Cl from Na ; NaCl binding prevented o Electrostatic interaction btwn water and solute Concentration gradient + electrostatic interactions osmosis How to burst bacteria? Make holes in cell wall Water rushes in burst 9/1/16 KNOW HOW TO CALCULATE –logs FOR pH and [ ] FOR TEST LO5: Define and describe the properties of acids and bases with respect to hydrogen ions All acids are electrolytes o Ionize & dissociate in water one is cation (pos); one is anion (neg) o Proton donors o Concentration of H in solution determines acidity HW: why does lower conc higher pH; higher conc lower pH? Release Hydrogen ions into solution (H+) Concentration [H+] in solution determines acidity HCL H + CL LO5: Define and describe the properties of acids and bases with respect to hydrogen ions All bases are electrolytes Ionize & dissociate in water o Proton acceptors o Release hydroxyl ions into solution [OH ] Thereby taking H ions out of solution Concentration [OH ] determines alkalinity o Indirectly measuring [H ] + NaOH > Na + OH OH + H > H O2 LO6: Explain what the pH scale measures Negative logarithm (log base 10) of hydrogen ion concentration in solution o HIGHER [H+] = LOWER pH More acidic o LOWER [H+] = HIGHER pH More alkaline / basic Calculator exercise: Enter: 10 ^ (2) = ??? = .01 Using “log 10 convert .01 to 2 Different process on diff calcs For me, enter: log (Ans) + Also, use inverse logs to convert pH vals to [H ] pH scale ex. lemon juice (citric acid) and gastric acid have low pH, high [H ] ex. oven cleaner: strong base high pH strong bases even more destructive than strong acids, remove H from blood inventor: Danish biochemist brewing beer; wanted it not too acidic/ basic LO7: Explain how a pH buffer works Buffers: molecules that prevent rapid shifts in pH • Weak acids and bases that maintain equilibrium • Release H+ into solution when pH rises • Bind H+ out of solution when pH falls LO7: Explain how a pH buffer works Buffers: prevent rapid shifts in pH Weak Acids (Was) and Weak Bases (WB)s that maintain equilib Release H+ into solution when pH rises ([H+] falling) Bind H+ out of solution when pH falls ( [H+] rising) e.g. Carbonic acid in blood 6 7 8 9 death normal death acidosis alkalosis Why breathe into brown paper bag when hyperventilating? Get more CO2 into bloodstream reduces blood pH to norm Overcomes the alkalosis that has started + H 2O ⇌3HCO + H 3 If rxn proceeds to right? (pH increases/ decreases) pH decreases (addition of strong acid more H in reactants) If rxn proceeds to left? pH rises (addition of strong base more H bound) buffers: ***Reversible chemical reactions! Law of mass action: the rate of a chemical reaction is directly proportional to the concentration of reacting substances Organic macromolecules Learning outcomes 1. What do we mean by organic compounds? 2. Explain the relationship between monomers and polymers 3. Define and give examples of dehydration synthesis and hydrolysis reactions 4. Compare and contrast the general molecular structures of 4 major biomolecules carbohydrates, lipids, proteins and nucleic acids and identify their monomers 5. Discuss some physiological and structural roles of carbohydrates, lipids, proteins and nucleic acids in the human body largest: nucleic acids (DNA—millions of base pairs (monomers)) 6. Describe the four levels of protein structure and discuss how protein shape is required for function LO1: What do we mean by organic compounds? “chemistry of life” Molecules made up of carbon backbones & Functional groups Molecule in slide = glucose Ex. of carbohydrate; Carbon backbone 2 representations dashed (going out) and solid (projecting out) triangles (squiggly = high energy, moving) all dashed lines (no 3d rep) Functional Groups We Need to Know Made from C, O, P, N< H Hydroxyl (OH) Found in Carbohydrates Methyl (CH3) Lipids, amino acids Carboxyl/ carboxylic acid (COOH) Lipids, Amino acids Phosphate (H P2 ) 4 Nucleic acids Amino (NH ) 2 Amino acids (but “amino” part is basic) “acid” of amino acid comes from COOH LO2: Explain the relationship between monomers and polymers Polymer: Macromolecule made up of repeating identical or similar subunits (monomers) Poly (many) + mer (unit) • e.g. DNA, RNA, Proteins, Carbohydrates, Lipids ex. dehydration synthesis monomer containing (OH) + monomer containing (OH) dimer (in ether form) H2O lost (dehydration) “synthesis” bc 1 molec made from 2 LO3: Define and give examples of dehydration synthesis and hydrolysis reactions Dehydration synthesis: anabolic reaction in which two monomers are linked by a covalent bond and a water molecules is formed Endergonic Ex. glucose + fructose sucrose Hydrolysis: catabolic reaction in which the covalent bond linking the monomers is broken by the addition of water molecule atoms Ex. sucrose glucose + fructose + energy exergonic LO4: Compare and contrast the general molecular structures of carbohydrates, lipids, proteins and nucleic acids and identify their monomers •Carbohydrates Contain Carbon, Hydrogen & Oxygen • Monomers: 1C:2H:1O = (CH2O) (Monosaccharides) Polymers: (CH2O)n (polysaccharides) linked by glycositic bonds ***KNOW THE 1:2:1 C:H:O RATIO (if given 1, predict other 2) Lipids • Contain Carbon, Hydrogen & Oxygen • Monomers: ~(1C:2H)n:2O = eg (C15H31COOH) (fatty acids) • Polymers: e.g. triglycerides (3 fatty acids + glycerol) 2 best energy molecule after glucose stored in adiposites come in all shapes/ sizes steroids (4 carbon rings) (ex. cholesterol—stiffens cell membrane) triglyceride (precursor to phospholipid) held together by ester bonds Proteins Contain C, H, O, N (unique set of atoms—don’t need to know formulas) • Monomers: Amino acids (20) gen structure—need to know!! central carbon amino group carboxylic acid R group (radical) group = placeholder for 1 of 20 side chains —don’t need to know all 20 Side chains versatility of proteins • Polymers: polypeptides / proteins held together by peptide bond (formed by dehydration synthesis) ex. myoglobin: carries oxygen mitochondria in muscle cells ex. hemoglobin: carries oxygen thru blood myoglobin presence of N distinguishes from carbohydrate/ lipid absence of P distinguishes from nucleic acid Nucleic Acids Contain C, H, O, N, P (sim to proteins) • Monomers: Nucleotides (mononucleotides) • Polymers: DNA (deoxyribonucleic acids) & RNA (ribonucleic acids) DNA missing –OH on 2’ Carbon RNA has high energy bond on 2’ carbon—can act as enzyme Held together by peptide bonds LO5: Discuss some physiological and structural roles of carbohydrates, lipids, proteins and nucleic acids in the human body Glycogen synthesized & stored in: Liver (blood glucose) Muscles Brain Uterus & Vagina Examlike Q Amt ATP, GTP, UTP, CTP—which expect to see most of? ATP: dual function—energy molec and RNA LO5 (cont): Lipids Fatty acid: Energy molecules (2 best) & building blocks for polymers Potential energy stored in covalent bonds Steroid Storage: Cholesterol, testosterone, estrogen Help muscle growth Promote membrane rigidity Triglyceride: Storage of fatty acid, building block of phospholipids Equivalent of glycogen for lipids Phospholipid: Major cell membrane component Take one fatty acid (FA) away from glycerol Amphiphilic Phosphate: hydrophic; charged—outsidefacing heads Lipid: hydrophobic; uncharged—inward facing tails Protiens Globular proteins: Enzymes, transport etc Ex. hemoglobin carries oxygen throughout bloodstream Via 4 iron atoms that interact w/ oxygen Rust of interaction red blood Fibrous proteins: structural / mechanical “ropey” ex. collagen = most abundant protein (skin, hair, bones, muscles) DNA: heredity material ATP: Energy currency (AND nucleotide, if remove phosphate —dual function) **High energy bond = phosphate anhydride bond – 2 are present removing one P: ATP ADP high energy remove another: ADP AMP high energy removing another—not high energy LO6: Describe the four levels of protein structure and discuss how protein shape is required for function Primary: Sequence of amino acids Secondary: Amino acid chains arranged in (alpha) helices or (beta) sheets (hydrogen bonds) Tertiary: Folding into fibrous or globular shapes (Hydrophobic interactions, disulfide bridges & Van der Waals forces) Quaternary: 2 or more polypeptide chains (Hydrophobic interactions & ionic bonds) Each level dictates higher order structure