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Tuesday January 3rd, 2017 Class 1 Learning Goals Biochemistry: Elements in water • After this class, you should be able to: – Decide if a molecule is primarily polar or primarily non-polar – Determine if a molecule is likely to dissolve in water – Predict likely hydrogen bonds – Explain Bio200 course logistics to a classmate – Assess life as mixture primarily of a few elements and judge any particular element as a potential primary building block for life Chemical compositions: The planet: The crust: The atmosphere: The ocean: A bacteria: A squid: You: Fe O N O O O O O other elements… other elements… O other elements… other elements… C H N other elements… C H N other elements… C H N other elements… H Peer Instruction Elemental biology C N O 1) Does life on Earth have very large elements? Why or why not? 2) What can C, N, and O do that He and Rb can’t? O > N > C ≅ H ‘Pauling Scale’ of electronegativity: 3.44 3.04 2.55 2.20 (reference) 3) What is electronegativity? 4) What does this mean for bonds in living creatures? Peer Instruction Is this molecule hydrophobic or hydrophilic? In aqueous solution, which scenario is more likely? Why? Scenario #1 Scenario #2 4 common ways to organize H, C, N and O: Carbohydrates (CH2O)n Proteins (C2H4O2N+[X])n Nucleic Acids ~(C5H5N2O2)n Lipids ~C44H72O8NP Concept Questions • The element Argon does not make up a large portion of living organisms. Is this something that you would expect? Why or why not? • • • Can benzene hydrogen bond with water? Can formaldehyde hydrogen bond with water? Can formaldehyde hydrogen bond with benzene? • Imagine two massive proteins composed of 10,000 atoms. At the end of one protein is a hydroxyl group, while the other protein has a phosphate group in the same place. How are these massive molecules similar or different? Does it matter? • • • How well do you expect octane to dissolve in a pure solution of liquid ethanol? How well do you expect nitrate to dissolve in a pure solution of liquid methane? Butane does not dissolve well in water. Why? Explain your answer in terms of water molecules and their weak binding to each other. • What Bio200 assignments should you complete each week? You: O C H N other elements… • • • • • • • • • • • Logistics Course Coordinators: Liz Warfield and Christine Savolainen Your TAs (who you’ll meet in lab) Getting a spot in the lab – You MUST show up to your first lab (or you may be dropped from the entire course) – Looking for a spot? Communicate with Course Coordinator Liz Warfield Class discussion board: Engagement and proper academic conduct is expected (10 points) Points breakdown – 5 exams (The first four are worth 80, and the final is worth 120) – Clickers (80 points) – Daily Reading Quizzes (2 pts per day, lowest 3 quizzes dropped) – 9 Labs (Each worth 10 points, including the 2 point online pre-lab) – Seminar (30 points) Polling points – Using PollEverywhere, so get registered as per the website – A variety of grading schemes depending on question Reading Quizzes – Why we use them – How best to read for this class Homework this week: – Chemistry skills quiz (as many chances as you’d like for a high score – Pre-Lab #1 – 3 more Reading Quizzes Seminar: finding more later this week. Exams: finding out more later this week Most importantly, you. Wednesday January 4th, 2017 Class 2 Learning Goals Entropy and Carbohydrates • After this class, you should be able to: – Determine if entropy is increasing or decreasing for a given scenario – Use entropy to determine if a system is becoming more stable (lower energy) or less stable (higher energy) – Identify a carbohydrate molecule by name, composition or structure – Describe multiple carbohydrate compounds comprised of the same elemental components – Predict biological roles (structural, energy storage, identification) for carbohydrate polymers based on structural characteristics Entropy: Energy spreading out Peer Instruction 1) In which situation is energy more spread out? Situation 1 Situation 2 2) Do these situations give you any information about bond enthalpy? For #3, assume total bond enthalpy is the same in both situations. 3) In which situation is the overall energy higher? Overall entropy in the universe is increasing. 4) What does the universe look like in the far distant future? 5) Is this reaction possible? If so, how? + + ! Creating polymers: A general process • Many biological macromolecules are made by: – linking individual molecular units • (___________, like a monosaccharide or a nucleotide) – into a chain-form macromolecules • (a _________, like a polysaccharide or DNA) • The two reaction directions have special names: – Condensation reactions (adding monomers together) – Hydrolysis reactions (taking polymers apart) Peer Instruction Is this a carbohydrate? (CH2O)3 Glucose Are these two molecules the same? Galactose (CH2O)_ Are glucose and galactose different molecules? Notice the suffix: Carbohydrates: Ring configurations Peer Instruction Linear form of glucose Ring forms of glucose α-Glucose β-Glucose Do alpha-glucose and beta-glucose differ: In molecular formula? In general shape? In # of carbons? In precise shapes and charges? C-H and C-C bonds can be harvested for redox energy to be used in other chemical reactions C-H and C-C can be harvested for energy. Memorize this. Why these bonds? It’s complicated. How it this energy harvested? Week 6! What Do Carbohydrates Polymers Do? • Carbohydrates are important building blocks in the synthesis of other molecules. • Carbohydrates can: – Store chemical energy. – Provide cells with fibrous structural materials. – Help create cell identity. Carbohydrates: Energy Storage Peer Instruction What is the monomer in the polymers shown? What is similar/different about the polymers shown? Carbohydrates: Protective Barriers Which polymer forms a tougher layer? Which polymer is more expensive to build? Peer Instruction Peer Instruction How can carbohydrates help cells tell each other apart? Outside of cell Inside of cell Concept Questions • Is entropy increasing or decreasing as a game of chess is played? – What about while wood is burned to give CO2 and water? – What about during a hydrolysis reaction for a carbohydrate polymer? • Is acetic acid a carbohydrate? How do you know? – • • A harder one: Is chitin a carbohydrate? Why or why not? Find a molecular formula of the form (CH2O)N from which you can make three different molecular structures. Find a structure for the carbohydrate polymer inulin. Predict whether or not this polymer: – – – – Can pack tightly for storage of lots energy? Where in the molecule is most of the energy stored? Can allow rapid energy usage? What glucose polymer is most similar to inulin? Would inulin be a useful molecule for cellular identification? Why or why not? Bio200 has 14+ office hours per week. In Hck 302 (unless otherwise noted): • Mondays: 9:20am • Tuesdays: 9:30am, 1:30pm, 2:30pm • Wednesdays: 9:20am, 12:40pm, 1:30pm, 3:30pm, • Thursdays: 12:40pm, 1:30pm, 3:30pm, 4:30pm • Fridays: 10:30-12:30 (in Kane 120 on non-exam weeks) • Also: – By appointment with Liz Warfield or Ben Wiggins – Help on Piazza from students and staff – During labs or immediately after if the TA has time Thursday January 5th, 2017 Class 3 Learning Goals Proteins, especially Enzymes • After this class, you should be able to: – Relate the diversity of protein function in cells to the special flexibility of polymers of amino acids. – Compare and contrast amino acids by R-group components – Classify changes into categories by differences in level of structure (primary, secondary, tertiary, quarternary) – Predict reaction consequences of structural changes in enzymes – Rationalize the special value of molecular catalysts for living cells Big list: What do organisms need to do? Peer Instruction Peer Instruction Explain which parts of the amino acid are the: • Tetrahedral Carbon R H O • Carboxyl Group • Amino Group N C C • Singular Hydrogen H H O • Side-Chain H Because life on Earth is primarily found in water, proteins typically reside in a different form. What is the difference? H H H + N R C H O C O This is called the ‘zwitterion’ form Peer Instruction When amino acids are polymerized: 1) What are the reactive parts? 2) What are the by-products? 3) Is entropy of the amino acids increasing or decreasing? 4) Describe the ‘peptide bond’. H H + N H H O C C H R1 + H N H R2 R1 O + H H + N H - O O C H H C O - R2 O + C C N C H H C - + O This new bond is a special covalent bond known as the ‘peptide bond’ H O H Nonpolar side chains Polar side chains Glycine (G) Gly Alanine (A) Ala Methionine (M) Met Serine (S) Ser Valine (V) Val Phenylalanine (F) Phe Threonine (T) Thr Cysteine (C) Cys Leucine (L) Leu Tryptophan (W) Trp Tyrosine (Y) Tyr Acidic Asparagine (N) Asn Isoleucine (I) Ile Proline (P) Pro Glutamine (Q) Gln Basic Electrically charged side chains Aspartate (D) Asp Glutamate (E) Glu Lysine (K) Lys Arginine (R) Arg Histidine (H) His Structure levels in proteins The grey molecule is a protein. It is shown here interacting with a red/blue DNA molecule. What is: Primary structure: Secondary structure: Tertiary structure: 25 Peer Instruction 1) Describe the differences and similarities between alpha-helix and beta-sheet configurations. α-helix 2) Find a region in this protein of: Alpha-helix Beta-Sheet Unstructured ‘loop’ β-pleated sheet α-helix Protein Tertiary Structure Peer Instruction Label the 4-5 intramolecular bonds shown here. Why are these bonds important? Peer Instruction Enzymes: A Three-Step Model Substrates Transition state Enzyme Shape changes 1. Initiation: What rolesite ofinthe Reactants bindis to the the active a specific orientation, forming an enzyme-substrate complex. Products enzyme? Could the reaction occur without the enzyme? Does the 2. Transition state facilitation: Interactions between enzyme and substrate enzyme contribute lower the activation energyenergy? required. 3. Termination: Products have lower affinity for active site and are released. Enzyme is unchanged after the reaction. Enzymes: Catalysis of Biological Chemistry Peer Instruction Task: Define all terms shown. Transition state Reactants Activation Energy Products Concept Questions • • Why are proteins not completely flexible? Why are proteins not completely stiff? • Discuss the properties of a protein that was a simple chain of threonines. • Define the protein structure level of change for: – A lost hydrogen bond – An extra disulfide interaction – Three reordered peptide bonds • Predict two consequences for an enzyme that loses four important hydrophobic side chains. • Most living organisms make their own molecular catalysts. These sometimes-huge molecules can be very expensive in terms of molecular energy to build. Why is this worthwhile for the organism? Exam format for Bio200 • Step 1: The ‘Public Version’ – 60% or more of test released one week prior to exam-time – This is the basis for an extra RQ question (due Monday) • Step 2: Understand & Edit – Help to produce a readable and correct final version – Public Version with Edits will be released on the pre-exam Tuesday • Step 3: Study – A lot. – In ways that maximize your time. • Step 4: Perform – Friday exam – Overcome the stress and do the best you can. • Step 5: Grade – And re-grade – Points: 5 pts for submitting a regrade (or a null) on one of the first four exams • Step 6: Understand your performance and adjust for success Peer Instruction Why is this enzyme sensitive to changes in pH? Why might this enzyme be sensitive to change in temperature? If you could change the amino-acids in this enzyme, how would you change them to make the enzyme functional at higher temperatures? 32 You will be analyzing β-galactosidase activity in lab next week. β-galactosidase is an enzyme that can break down lactose. Why would enzyme supplements be more useful for lactose-intolerant individuals than glucose supplements? 33 Peer Instruction Competitive inhibition directly blocks the active site. Competitive inhibitor Substrate Enzyme When a regulatory molecule binds the active site, the substrate cannot bind. When the concentration of competitive inhibitors goes up, the reaction rate tends to go (up?/down?). Increasing the binding strength of the substrate for the enzyme would (increase?/decrease?) the competitive inhibition. Peer Instruction Allosteric regulation occurs when a regulatory molecule binds somewhere other than the active site. Substrate Enzyme or Regulatory molecule 1) When the regulatory molecule binds to a different site on the enzyme, it induces a shape change that makes the active site either: Left) more available to substrate, or Right) less available to substrate Which allosteric regulator (right or left) increases the reaction rate? Friday, January 6th, 2017 Class 4 Learning Goals Nucleic Acids • After this class, you should be able to: – Identify the structural features of nucleic acid monomers that: – Form the bonds in polymers – Form the bonds in base pairs – Contain charge distribution energy – Give the monomer a specific identity (A, G, U, etc) – Give the nickname for a nucleic acid from a simplified structure – Analyze the mechanism through which ATP provides energy to biochemical reactions – Describe the double-helix structure of DNA and RNA in terms of phosphodiester bonds, base pair bonds and polarity – Predict nucleotide abundances of A, T, G and C given the abundance of any one of them. Peer Instruction Identify the: phosphate group sugar nitrogenous base Is this from a ribonucleotide or a deoxyribonucleotide? How do you know? In life on Earth, nucleic acid monomers are named A, T, G, C and U. Which bonds with which? The Nucleotide: Energy Storage Molecule ATP The addition of phosphate groups raises the potential energy of the monomer Naming: __P= tri-phosphate (could be mono- or di-phosphate A=adenosine base N=____ base ______=any triphosphate deoxynucleotide base Why ATP is Useful The problem with endothermic biological reactions + Free Energy Reaction Progress Why ATP is Useful Phosphate hydrolysis is massively exothermic + Free Energy Reaction Progress Why ATP is Useful: Enzymes combine reactions to become exothermic (aka exergonic) + + + + Free Energy Reaction Progress Building DNA: The Double Helix Cartoon of base pairing Cartoon of double helix Double-stranded DNA: Base Pair Bonding Only purine-pyrimidine pairs fit inside the double helix. Hydrogen bonds form: between G-C pairs and A-T pairs. Purine-pyrimidine pair JUST RIGHT Purine-purine pair NOT ENOUGH SPACE Pyrimidine-pyrimidine pair TOO MUCH SPACE Space inside sugarphosphate backbones Sugar-phosphate backbone 5ʹ 3ʹ Guanine Cytosine Adenine Thymine 3ʹ 5ʹ DNA contains thymine, whereas RNA contains uracil Note: Base pairs form with antiparallel backbone structure Building a Nucleic Acid: The Phosphodiester Backbone Electrons attack the phosphate core at the ___ carbon This creates a phosphodiester linkage __________ Reaction Building a nucleic acid: Double Helix Measurements Distance between bases: 0.34 nm Length of one complete turn of helix: 3.4 nm (__ rungs per turn) Width of the helix: 2.0 nm Peer Instruction RNA: Structure and Function The primary structure of RNA differs from DNA in two ways: - - Loop Stem Single stranded Double stranded The presence of the 2’–OH group on ribose makes RNA much (more/less) reactive and (more/less) stable than DNA. Building DNA: Making a Copy “It has not escaped our attention that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.” -Watson and Crick, 1953 Concept Questions • Find the structure of a nucleotide, and point out the nitrogenous base, the phosphate group(s), the ribose ring, whether it is DNA or RNA, what base it is, and whether this is a relatively high-energy or lowenergy molecule compared to other nucleotides. • What is the nickname for this nucleotide? (for example: ‘dGMP’) • Explain, without skipping over any parts, why adding ATP hydrolysis to a reaction can allow an organism to drive an otherwise impossible reaction. • Imagine that the genome of a new bacteria found on Mars is 35% Guanine. What percentage of the new genome is likely to be Cytosine? What assumptions are you making in your calculation? • Why is RNA more like protein than DNA? • Why is it more like DNA than protein? • What extra work must you do to complete a Bio200 exam? • Is this a good or bad exam system? Why?