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Ib Hl Biochemistry Lab Manual

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Ib Hl Biochemistry Lab Manual IB HL BIOCHEMISTRY PROBLEM SETS AND LAB MANUAL FAIRVIEW HIGH SCHOOL 2019-20 IB BIOLOGY Exam Please do not write in this book Written/ edited/ compiled by Brian Cox Table of Contents Section 1: Problem Sets Unit 1: Macromolecules Chemistry Review Notes 1 Optional Chemistry Review Problem Set 5 Required Chapter 5 Problem Set 9 Unit 2: Introduction to Metabolism Optional Chemistry Review Problem Set 18 Required Unit 2 Problem Set 21 Unit 3: Cellular Respiration Required Unit 3 Problem Set 36 Unit 4: Replication, Transcription, Translation, Regulation of Gene Expression Watson and Crick’s Structure of DNA (from the journal Nature, April 1953) 41 Required Unit 4 Problem Set 47 Unit 5: Biotechnology Required Unit 5 Problem Set 64 Section 2: Labs Expt # Experiment Page 1 Hydrophobic/Hydrophilic 72 2 Levels of Protein Structure and 75 Principles of Protein Folding 3 Purification of Green and Blue Fluorescent 91 Proteins and Protein Denaturation (Adapted from Edvotek Lab #255) 4 Experimental Design: Factor that affects rate of enzyme catalyzed 94 reaction 5 Investigating effect of pH on activity of perioxidase enzyme 95 6 Measuring the Rate of Cellular Respiration of 101 Peas (Adapted from AP lab #5: Cell Respiration) 7 Molecular Details of Cellular Respiration 106 Computer Simulation Lab 8 DNA Replication Simulation 108 9 Tryp And Lac Operon Simulation Activities 111 10 Eukaryotic Gene Expression Simulation 115 11 Transformation experiment – insertion of plasmid 117 containing pGlo gene. BioRad kit lab 12 Bacterial ID Lab (NIH interactive computer simulation) 121 SAFETY CONTRACT FOR IB BIOCHEMISTRY 1) Read over safety concerns described in lab manual before each experiment; listen to discussion of safety issues in class. Concentrate during the lab period. 2) Safety glasses must be worn in the lab during any experiments involving chemicals or biological samples. Gloves should be worn during some experiments. 3) Immediately inform instructor of any accidents. 4) If chemicals or bacterial sample contact your skin, you should immediately wash the affected area thoroughly with soap and water. If chemicals contact eyes, flush the eyes for 15 minutes with water from eyewash. 5) Handling organic chemicals: - Volatile organic chemicals should be handled in a fume hood. - Organic fumes are very flammable – kept away from open flames. - Organic waste must be disposed off in the appropriate waste container. It cannot be disposed of in the sink. 5) Handling Bacterial Samples: - Although the bacteria samples we work with in this course are believed to be completely harmless to humans, always minimize your exposure. Avoid contact with bacterial colonies. - All materials that contact bacteria directly should be disposed of in a sterilizing bleach bath and not placed directly in the trash. 6) Wash hands with soap and water at the end of each laboratory period. I have read and understand the safety rules for IB Biochemistry. I understand that actions that endanger yourself or others in the lab may result in dismissal from the lab. Signed, CHEMISTRY REVIEW NOTES LEWIS DOT STRUCTURES # of electrons (e-) needed to fill valence level = # of bonds (each bond is the equivalent of gaining 1 e-) Most common 4 elements in organic/biological molecules: C – makes 4 covalent bonds; N makes 3 covalent bonds (N+ will make 4) ; O makes 2 covalent bonds (O- makes 1 covalent bond); H makes 1 covalent bond Other common elements: P makes 5 bonds, S makes 2 bonds, Ca and Mg form +2 ions and makes ionic bond; K and Na form +1 ions and makes ionic bonds ORGANIC CHEMISTRY FUNCTIONAL GROUPS- structural components of hydrocarbon molecules which are most commonly involved in chemical reactions. Memorize functional groups below: See pp. 64 & 65 in Campbell’s. Note: R represents a hydrocarbon chain. FUNCTIONAL GROUP FORMULA NAME EXAMPLE Hydroxyl R -OH Alcohol Ethanol Notes: OH is polar; can form H-bonds and act as nucleophile Carbonyl R - C – H Aldehyde Formaldehyde R - C – R’ Ketones Acetone Notes: CO group is polar, can act as H-bond acceptor and act as electrophile Carboxyl R - C-OH R - C –O- Carboxylic Acid Acetic Acid (neutral) (ionized) Notes: - COOH is polar, can act as an acid (H+ donor), - COO- is resonance stabilized + Amino - NH2 - NH3 amines Glycine (amino acid) (neutral) (ionized) + + Notes: -NH2 is polar, can act as base (H ) acceptor, nonbonding pair on N attract H Sulfhydryl -SH Thiols ethanethiol Notes: S-H moderately polar, S is good nucleophile, S-H and S-H can form S-S bond Methyl CH3 5 – methyl cytidine 1 Notes: Nonpolar, addition of methyl to DNA or molecules bound to DNA can affect gene expression Phosphate - O – P – O Organic phosphates Glycerol phosphate Notes: Ionized at neutral pH; phosphate groups are good “leaving groups” ; often involved in energy transfer reactions VSEPR – PREDICTING 3-DIMENSIONAL SHAPES • Biological Activity of molecule is determined by both chemical behavior and 3-D shape of molecule • VSEPR (Valence Shell Electron Pair Repulsion Theory) – predict 3-D shape by predicting how bonding and nonbonding electron pairs will arrange themselves around central atom to minimize electrostatic repulsion • Double and Triple bonds count as single bonding region • Important Geometries for common important biochemical molecules Bonding Nonbonding Geometry Pairs Pairs 2 0 linear 3 0 Trigonal planar 4 0 tetrahedral 3 1 Trigonal pyramidal 2 2 bent ISOMERS- Compounds with the same molecular formula, but different structures and therefore different properties. 3 types of isomers: ➢ Structural isomers – different covalent arrangements (different connection pattern) Example: n- butane isobutane ➢ Geometric isomers – variation in arrangement in space about a double bond Example: Cis – dichloroethene Trans-dichloroethen 2 Key point: Rotation is impossible around a double bond. (Would require breaking pi bond) ➢ Enantiomers (chiral molecules) – variation in arrangment in space around an asymmetric carbon (C is bonded to 4 different groups). - molecules are not identical (cannot be superimposed on each other) ; mirror images. Example: CHBrClOH has 2 forms: DIPOLE MOMENTS Dipole – a molecule in which one side of the molecule is partially positive and the other end is partially negative; (caused by asymmetric distribution of electron density) Steps for determining a dipole moment: 1) Determine 3-D structure 2) Look for polar bonds (electronegativity difference between bonded atoms) 3) Sum up polar bonds to determine net dipole (if symmetric = polar bonds cancel) 4) Use to indicate overall dipole. Arrow always points to towards ∂- INTERMOLECULAR FORCES ▪ Weak forces of attraction between molecules (much weaker than covalent or ionic bonds Important Note: Macromolecules like proteins, DNA, and carbohydrate polymers are so long that different parts of the chains can interact with itself via “intermolecular” forces (i.e. these forces can be intramolecular for large molecules) ▪ 3 Intermolecular forces – Hydrogen bonding, dipole-dipole, London Dispersion Forces (also known as Van Der Waals) forces Dipole-dipole attraction – weak electrostatic attraction between two molecules which have net dipole moments. The molecules line up with the partial positive end of one molecules next to the partial negative end of the second molecule. Example: 3 Hydrogen Bonds- an especially strong dipole-dipole attraction involving a hydrogen bridging two very electronegative atoms. Requirements for H-bonding:. 1) H-bond donor- H covalently bonded to F,O,N ( H-F, H-O, H-N) AND 2) H-bond acceptor F,O,N with nonbonding pair of e- available Strength of attraction between + and – charges depends on: 1) Size of + and – charge: H-X, where X = F,O,N ; X is very electronegative => very polar bond => large partial + (∂+) and – (∂-) 2) Distance between charges: (H, F, O, N are all small atoms => allows for close approach) H-bonds are very important in biological interactions which two molecules to specifically recognize each other. Specificity – requirement that partial + surface aligns with partial – surface requires specific alignment of molecules Examples: Connection between DNA strands (base pairing), Enzyme-substrate interactions, Receptor/ligand interactions Bond strength- H-bonds are strong enough to hold molecules near each other but don’t require large amounts of energy to break when molecules need to separate London Dispersion Forces – “ instantaneous” dipole attraction that occurs between 2 nonpolar molecules - Generally weakest of intermolecular attractions- strength is very dependent on size of electron cloud. Other Intermolecular/ Intramolecular bonding important in biochemistry: Salt Bridge - ionic bond between parts of molecule with full + and – charges Ion-dipole – electrostatic attraction between a full + or – and a partially charged (dipole) region Hydrophobic interaction – term used to describe the observation that nonpolar molecules tend to aggregate together in water Important Properties of Water 1) polarity and ability to form Hydrogen bonds 2) excellent solvent for polar substances; poor solvent for nonpolar 3) cohesion and adhesion 4) Relatively high specific heat capacity 5) Transparent to light 4 CHEMISTRY REVIEW PROBLEMS (Optional) (Optional problems = not turned in for credit:) This material is foundation knowledge you need to be successful in Unit 1. Strongly recommended for careful completion for all students who have not completed 2 years of IB Chemistry. (Use a separate sheet of paper for written answers) Reading: Quick Skim of Chapter 2, read carefully
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