MCAT Biology Biochemistry I PDF

MCAT Biology and Biochemistry Biochemistry I Class 1 Macromolecules Enzymes  MCAT Biology Introduction MCAT Biology Introduction Me! MCAT Bio Basics MCAT Student Guide Course Support Videos Specifics of Interacting in the Online Course...

MCAT Biology and Biochemistry Biochemistry I Class 1 Macromolecules Enzymes  MCAT Biology Introduction MCAT Biology Introduction Me! MCAT Bio Basics MCAT Student Guide Course Support Videos Specifics of Interacting in the Online Course Let’s get started!  MCAT Biology Lecture 1 Outline Biochemistry I Biologically Relevant Macromolecules -proteins -carbohydrates -lipids Thermodynamics Reaction Coupling Kinetics Reaction Coordinate Graph Enzymes – Structure, Function, Regulation V vs. [S] Graph Enzyme Inhibition Lineweaver-Burk Plots General Passage Info and Techniques ICC Passage 1 and Solutions  MCAT Biology 4 Biologically Relevant Macromolecules They are: 1. Proteins 2. carbs & 3. lipids 4. Nucleic acids All these macromolecules are ___________________ (made from monomers). Polymer - enzymes that make them are called _______________________. Polymerase polymerization reactions. - reactions are called _____________________ * Often run via DEHYDRATION SYNTHESIS 1) sometimes called CONDENSATION 2 separate compounds 2) the opposite would be HYDROLYSIS combing them by taking water out.  MCAT Biology Proteins 1) Monomer = ____________________ amino acids 2) ______________ 20 ad different kinds in the human body a aa very high yield AMINO ACIDS : know for all 20 : H Know: O amino carboxyl Structure of R group Classification (polar, non-polar, H2N C C acidic, basic, neutral) G R OH Charge at physiological pH flash cards 1- and 3-letter abbreviations backbone - important “mutation notation”, e.g.,00 R322K (NCC) = important um zndary structure I letter abbrev MCAT Biology Proteins – Peptide Bond Formation H O leaves H2N C C HeO R OH H H O N C C H R OH  MCAT Biology Protein Structure 1 Ni want add add at C term C' new ad. PP N + Synth : - Primary structure: amino acid sequence - Secondary structure: between hydrogen bonding a mino acids The backbones of (NCC) -helix created by β-pleated sheet < bonding  MCAT Biology Protein Structure 2 R-group - Tertiary Structure (folding) is due to ____________ interactions with in a polypeptide. Two main types of interaction: Broadly speaking ( middle 1. nonpolar / nonpolar : to Non-covalent 2. polar neutral / polar neutral surface 3. acid / base (electrostatic) -closer to surface aqu. enviro. Covalent 1. disulfide bridges cystine (R) involve actual chem ones only - need to be broken bond - Quaternary Structure due to ____________ R-group interactions between different polypeptides (between different polypeptide) only structureswr multiple has go sub. have to not every  MCAT Biology Protein Functions Protein jobs : enzymes hormone transporter structural antibodies receptors Channels structure cytokines adhesion molecules  MCAT Biology Carbohydrates – Monosaccharides * monomer = MONOSACCHARIDES Monosaccharides - Formula: CNHzNON 1: 2 : # Of carbon 3 common: Chexose Sugars : 6 carbons)N = 1) Glucose 2 H , 20c 2) Fructose 6 carbon sugars 3) Galactose 2 others: 1) Ribose 5 carbon sugars 2) Deoxyribose  MCAT Biology Carbohydrates – Disaccharides Monosaccharide + Monosaccharide = DISACCHARIDE DISACCHARIDES 3 common: (all of the following are a glucose attached to something else) syth through dehydration occur 1) Maltose = glucose + glucose frutose 2) Sucrose = glucose + 3) Lactose = glucose + galactose Formula: ON CNHz ciz * Haz Oi  MCAT Biology Carbohydrates – Polysaccharides Multiple monosaccharides = polysaccharide storage for glucose POLYSACCHARIDES 3 common: 1) Glycogen: energy storage in animals 2) Starch: glucose storage in plants 3) Cellulose: Plant structure Functions: of P P.. in body : - cell surface markers -energy storage  MCAT Biology Lipids – Saturated Fats * monomer = HYDROCARBON HYDROCARBON Structure: Polymer : … O 11 OH - C (SATURATED) Fatty Acid can't add anymore Hydrogens u M 2 SOLID @ room temperature -lard , baking grease  MCAT Biology Lipids – Unsaturated Fats bod a HYDROCARBON Structure: pulled off hydrogens : Double - - … HO less It than could (UNSATURATED) Fatty Acid - fats w/ or more double bonds A ~ LIQUID @ room temperature m at RT. - can't line up : Liquid bond A cis double seen in nature  MCAT Biology Lipids – 4 Forms acid giyero + fatty 1) Triglyceride. - HO HO 4 HO GLYCEROL ↳ ↳ HzV FATTY ACIDS lost ester bonds esterification : joined by formed  MCAT Biology Lipids – Triglycerides Functions: Triglyceride energy storage insulation Protection of organs  MCAT Biology Lipids – Phospholipids 2) Phospholipids. both hydrophobic ? ampathic - hydrophilic & Glob Functions: membrane formation : lipid bilayer  MCAT Biology Lipids – Terpenes Intro 3) Terpenes : Built from multiple ____________________ isoprene units C5Hio 5 + + + … = Terpene 2 4 I 3 isoprene isoprene isoprene 2 Need at least __________ isoprenes to make a terpene.  MCAT Biology I Lipids – Terpenes, cont’ 2 Squalene = 6 isoprenes named on how many isoprene units double Classification: _____terpene +ri 3 2 iso mano : di : iso Functions: earwax precursor Cholesterol , terpenoids Vitamin A - derrived from isoprene  MCAT Biology Lipids – Steroids 4) Cholesterol and derivatives (3 six-carbon rings + 1 five-carbon ring) 3 I 7 2 Functions: steroid precursor bile salts membrane fluidity  MCAT Biology Thermodynamics Gibbs free enthalpy temperature energy entropy ∆G = ∆H - T∆S potential kinetic energy energy - - stored energy of movement energy ∆G < 0 reaction · Kinetic is greater ASLAH () : spontaneous than potential ∆G > 0 non spontaneous c+ ∆G = 0 equilibrium  MCAT Biology Reaction Coupling “exergonic” : give off energy A + B C + D DG = - 7 DGC0 : ( - ( “endergonic” : need energy W + X Y + Z XG = 2 AG) O combine A + B + W + X C + D + Y + Z -G = 5 - overcomes unfavor. reactions. unfavorable react atphydrolysis : reaction coupling drives. ATP ADP + Pi very exergonic ΔG of ATP hydrolysis in the body = -12 kCal/mol (or ~ -57 kJ/mol) ex1 Protein Surth. Ion against con gradient  MCAT Biology Kinetics A + B ABCD C + D transition state - High energy - Transient transition Energy of Activation: Energy needed to produce ___________________ state for reaction to proceed barrier needed ↑ Sa = R  MCAT Biology Reaction Coordinate Graph TS Ea crivation Energy R G = release free energy P Reaction Coordinate What can we do to make the “hill-riding” reaction faster? the hill hid riding up Yes! Make the hill smaller reduce Ea  MCAT Biology Catalysts Catalysts - increase rate of reaction by: Stabilize TS 1. 2. reduce Ea TS & lower Ea *with catalyst TS* Ea Ea* Energy R * no change in DG G P Reaction Coordinate  MCAT Biology Enzymes Enzymes: Physiological Catalyst 3 defining characteristics: 1. must increase the rate of the reaction 2. must not be used up in the reaction 3. specific for a particular reaction  MCAT Biology Enzyme Structure and Regulation Protein Control : Phosphorigation allosteric site - P Primary Conti enzymes & Phosphorolyation enzyme A on - turns enzyme or of active site S ubstrate and most common * S allosteric regulationS - blocks non conformational S S change. S Fits Win active site -where substrate binds -where the reaction occurs Ott/tense enzyme fir sub at on/relaxed Unable active Site  MCAT Biology More Enzyme Regulation negative feedback E ↳ a b C' A B C D ⑦ S M back goes to Stop positive feedback must have external regulator to stop cycle - child birth ext reg baby =  MCAT Biology V vs. [S] Graph Vmax is a constant, depends on: 1. enzyme concentration 2. specific enzyme you are using V ~.... · - - - - Comp - - Rxn non comp rate 1 - uncomp 112 v ↑ ov -. Of Rate I product. ! form hm hm wi comp [S]Substrate in con. ASSUME CONSTANT [E] nzyme 3 different conditions: /2 Vmax Km = [S] required to reach _______________. 1. SCE& -like an affinity the E has for S an for enzyme 2. S-E sub waiting ↑ ______ affinity = ______ E Km 3. E  MCAT Biology Enzyme Inhibition 1. Competitive Inhibition 2. Non-Competitive Inhibition binds at: active site binds at: allosteric site (E alone), does - substrate Unable bind not change shape of active site effect on Vmax: no change ↓ amount of funct. enzume effect on Vmax: decrease Vmax effect on Km: increase effect on Km: unchanged - 3. Uncompetitive Inhibition 4. Mixed Inhibition binds at: allosteric site of ES binds at: allosteric site of E alone (and complex DOES change shape of active site) OR to ES complex allosteric inhabi. ↓ Ezyme effect on Vmax: zon. decrease effect on Vmax: decrease effect on Km: decrease effect on Km: increase/decrease ALWAYS ASSUME REVERSIBILITY. come. off - enzymes  MCAT Biology Lineweaver-Burk Plots "I Inverse plot: ________ S vs. ________ y-intercept represents: Vmax As you move towards the origin, the denominator gets bigger. x-intercept represents: - /hm ⑳ comp. ⑧ comp - uncomp. O 1/V Yumax - - ⑨ -- ⑨ - "I hm 1/[S]  MCAT Biology General Passage Info/Techniques The Passage - Not to be mastered, just another source of info - Skim or skip - Read for location of information - Figures and experiments: no heavy analysis Skip really long experiment - Graphs: axes, trends, outliers, statistics Passage Tools 1. Highlighting: BE SELECTIVE Main theme Definitions Reversals to the theme Relationships Italics Stuff that seems unexpected 2. Noteboard (scratch paper): KEEP IT ORGANIZED, CREATE A “MAP” Passage number, Q range, topic, maybe time P1, P2, P3 with notes Q1, Q2, Q3 with notes (if needed) SKIP next to passage or Q (if needed)  MCAT Biology Question Types Question Types: 1. Memory: know it. 25% 2. Explicit: find it. 30-45% 3. Implicit: figure it out. 30-45% Tools and Techniques: 1. Strikeout /POE: Draw a line through an answer choice you have eliminated Draw a line through false Roman numeral items 2. Highlighting: LEAST, EXCEPT, NOT True Roman numeral items 3. Skipping around Do the test in YOUR order, easiest to hardest Skip long questions, skip questions that require analysis DON’T skip 2x2s MCAT Biology ICC Passage 1 Text Umax 35 : - umax : uncomp · dosent reach 1 · competitive - Vmax : lower km lower - : control  MCAT Biology ICC Passage 1 Noteboard 1 Q1-G enzymes Psg P ,: m mod ? m P2 : [S] - = Umax - = linear · equation varible Ex 1 : control Ex7 : inhib a Ex 3 : inhib b  MCAT Biology ICC Passage 1, Question 1 Question type: EXPLICIT SKIP? Y / N o  MCAT Biology ↓ ICC Passage 1, Question 2 Question type: IMPLICIT SKIP? Y / N umax unchang COMP : hm : B X O X X  MCAT Biology ICC Passage 1, Question 3 Question type: IMPLICIT SKIP? Y / N ↑ um for substrate ↓ affinity = = no change - - umax - - 6  MCAT Biology ICC Passage 1, Question 4 Question type: EXPLICIT SKIP? Y / N O uncomp.  MCAT Biology ICC Passage 1, Question 5 Question type: MEMORY SKIP? Y / N true false F : comp. inhibit  MCAT Biology ICC Passage 1, Question 6 Question type: IMPLICIT SKIP? Y / N umax would change for sub attinty same  MCAT Biology REMEMBER! Remember to Use Strategies When Doing Homework Passages!! Passage Strategies: 1. Skimming/Highlighting (remember the six types of things to highlight) 2. What to look for on graphs: a. axes, trends, outliers, statistics (no heavy analysis) 3. Noteboard notes: a. passage heading b. paragraph notes c. SKIP if you skip a question Question Strategies: 1. Skipping: long questions, question that require analysis 2. Roman numeral strategy: a. start with the item that appears in exactly two answer choices b. if there are two such items, start with the shorter one c. eliminate answer choices as you go