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Download Class4 1-6 Win16 Enzymes and Nucleic Acids Notes
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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 REACTION MECHANISM 1. 2. 3. 6. 5. 4. Respond at PollEv.com/biology200 (or text BIOLOGY200 to 22333 once to join) Clicker Question #1 The His119 side chain: 1. 2. 3. 4. 5. 6. Is part of a single amino acid Can lose a proton Can perform a condensation reaction Is part of a tertiary structure Cannot gain a proton Has a completely useless C=N portion Clicker Question #2 The water molecule shown in Panel 5: 1. 2. 3. 4. 5. 6. Is necessary to regenerate the enzyme Is the most important substrate Is rarely found near the enzyme Slows the reaction rate Is more polar than a normal water molecule Is in the active site of the enzyme Clicker Question #3 How many times can an enzyme catalyze a particular reaction? You can assume there are infinite substrate molecules present. Choose the best answer. 1. 1 2. 3-5 3. An infinite number of reactions 4. Many, but not infinite 5. It depends on the enzyme 6. Only 1 per type of substrate, but it can catalyze many different kinds of chemical reactions 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? 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? 7 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? Clicker Question #4 Can a single protein have more than one allosteric site? Why or why not? 1. 2. 3. 4. No, more than one would be too complicated. No, multiple sites would interfere with each other. Yes, every amino acid is always an allosteric site. Yes, any region that could bind another molecule is a potential allosteric site. 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 Clicker Question #3 Chargaff’s Rule: We know that in DNA there are A-T and G-C base-pairs. If I tell you that a DNA molecule is 30% guanine, what is the % of thymine in that molecule? 1. 2. 3. 4. 5. 6. 0% 10% 20% 30% 40% 50% 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?