BSC 450/ 500 Exam 1 Study Guide (re-uploaded)
BSC 450/ 500 Exam 1 Study Guide (re-uploaded) BSC 450
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This 7 page Study Guide was uploaded by Jordana Baraad on Sunday September 13, 2015. The Study Guide belongs to BSC 450 at University of Alabama - Tuscaloosa taught by Dr. Ramonell in Summer 2015. Since its upload, it has received 97 views. For similar materials see Fundamentals of Biochemistry in Biological Sciences at University of Alabama - Tuscaloosa.
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Date Created: 09/13/15
BSC 450550 Exam 1 Study Guide Chapters 14 Chapter 1 o What are the three domains of life and what characterizes each one Archaea single membrane w peptidoglycanlike layer andor porous protein shell More closely related to Eucharia than bacteria Inhabit extreme environment plasmid DNA Bacteria peptidoglycan double membrane Gram positive or negative plasmid DNA Nucleoid region Eucharia plasma membrane phospholipid bilayer nucleus membrane bound organelles ie ER Golgi bodies lysosomes What are the common structural elements of cells and what is their function Membrane cytosol genetic material nucleoid region or nucleus Know the basic functional groups of biological molecules and essential elements for life Basic functional groups thioester amide hydroxyl phosphoanhydride phosphoryl imidazolelike amino Essential elements Phosphorus Oxygen Nitrogen Carbon Hydrogen Understand that the structure of biomolecules often gives them speci c functions chirality role of carbon etc Chirality 4 different substituents on stereocenter Stereoisomers different conformation gives different physical properties Geometric isomers ie cis v trans different phys and chem properties Enantiomers stereoisomers that are nonsuperposable mirror images Identical phys properties except w polarized light React identically w achiral reagents Usually only 1 enantiomer biologically active Diastereomers nonenantiomeric stereoisomers different phys and chem properties Know the basic principles of bioenergetics and thermodynamics free energy and chemical equilibrium and how they relate to one another Bioenergetics keq products reactants Ka H CBWA Thermodynamics Gibb s free energy AG AH T AS Relationship AG RT In K Chapter 2 Know in detail the four types of weak interactions that occur between biological molecules and how they work Hydrogen bonds bonding of hydrogen with electronegative atom main ex electronegative oxygen binds with electropositive hydrogen to create intermolecular bonding between water bonding strongest weak force imp in DNARNA proteins polysaccharides and binding mechanisms Electrostatic ionic interactions attraction between fully charged electronegative and electropositive atoms force generated by them calculated by Coulomb s law Van der Waal s lnteractions London Forces distortion of electrons in cloud at any given time give partial positive and negative charges induced dipoles which attract one another possible between any 2 atoms distance is limiting factor often come into play in enzyme active sites Hydrophobic interactions loose association grouping in order to minimize contact with water or polar solvents inside of micelle clathrate or membrane bilayers seen when amphipathic molecules in polar solvents Know the special properties of water and why water is a good medium for life Unique properties given by hydrogen bonds Universal solvent Polarity dissolves polar quothydrophilicquot substances Electrostatic dissolves salts by hydrating and stabilizing cations and anions Interaction w itself above all other molecules Cohesion and adhesion Atypically high melting point boiling point heat of vaponzann Lots thermal energy necessary to break enough bonds to Disrupt crystal lattice High speci c heat water acts as quotheat bufferquot in keeping organisms temperature fairly constant Low density in solid form allows underwater ecosystems to survive beneath icedover surface Use the HendersonHaselbalch equation to solve problems 39 PF EH 110 1 39 139 3quot E1 mm Be able to draw ionization equilibria for amino acids and know which species will predominate at a speci c pH Understand pKa and pH and how they interact pH concentration of hydrogen ions in solution pKa relative strength of a weak acid or base stronger acid has lower pka pH at center of titration curve Be able to predict how weak acids and bases will behave in water Weak acids partially ionize hydrogen ion released pH lowered Weak bases accept hydrogen ion pH increased Extent of process described by ka acid dissociation constant Be able to interpret titration curves of weak acids and bases Reveals pka at center Understand how buffers work and what buffering capacity means Buffers added to solution to reduce the increase of acicidity or basicity as acid or base is added ie change in pH Buffering capacity pH range at which buffer is able to resist minimize pH change Flatter portion near middle of titration curve Works best wn 2 pH units of pH of original solution 1 unit Ex for blood pH 74 the range would be 6484 Max buffering capacity pH pka Be able to work through problems similar to worked examples 23 2 4 26 and examples worked in class Other example problems are available at the end of chapter 2 Equations that will be included on the exam KW 10 x 103914 M2 ion product of water R 831st Jmol K gas constant Chapter 3 Know the structure threeletter code and single letter code for the amino acids Aliphatic Ala A Val V Leu L lie I Met M Pro P Gly G Nonpolar aromatic Phe F Tyr Y Trp W Polar uncharged Cys C Ser S Thr T Asn N Gln Q Polar positively charged His H Arg R Lys K Polar negatively charged Asp D Glu E OR Hydrophobic aliphatic Ala A Val A Leu L lie I Hydroxylcontaining Ser S Thr T Aromatic Tryptophan W Tyrosine Y Phenylalanine F SulfurContaining Cys C Met M Outlier Pro P His H Acidic Asp D Glu E Amidecontaining Asn N Gln Q Basic Lys K Arg R Understand what weak interactions are possible with each amino acid side chain Hydrogen bonding polar hydroxylcontaining sulfurcontaining acidic basic amide containing less so Ser S Thr T Tyr Y Cys C weak Met M Asn N Gln Q Lys K Arg R His H Hydrophobic interaction nonpolar hydrophobic aliphatic aromatic basic less so but included bc of long chains Ala A Val V Leu L lie I Phe F Tyr Y Trp W Met M Pro P Gly G but chain too small to contribute much Lys K Arg R Cys C Electrostatic interactions positively charged negatively charged acidic basic Asp D Glu E Lys K Arg R His H Van der Waal s forces all Disul de bonds sulfurcontaining NOTE disul de bridges are nonpolar hydrophobic Cys C gtgt His H Understand the ionization behavior of amino acids and peptides Acidic pH cationic form protonated carboxyl and amino groups Neutral pH neutral form deprotonated carboxyl protonated amino group zwitterion Alkaline pH anionic form deprotonated carboxyl and amino groups Be able to interpret titration curves of amino acids and calculate pl pl average of pk s on either side of zwitterionic state of aa zwitterion net charge 0 sum of charges on carboxyl group amino group and side chain Understand the basic concepts behind the methods used to characterize peptides and proteins that we discussed in class Peptide polymer of amino acids v protein polypeptide w conformation small compared to prot cofactors coenzymes prosthetic grps etc mw lt 10 kDa mw Z 10 kDa Chapter 4 0 Understand the structure and properties of the peptide bond 0 Amino N terminus w partial charge 0 Carboxyl C terminus w partial charge 0 Resonance prevents rotation about CN bond 0 CD rotation about dCN p rotation about about dCC Understand the four levels of protein structure in detail including the intermolecular forces that are working at each level 0 1 amino acid sequence covalent bonding on polypeptide backbone resonance 0 2 local spatial arrangement of polypeptide backbone Hbonding l alpha helix and beta conformation o 3 3D spatial arrangement mostly hydrophobic 0 major contributors in stabilizing globular proteins nonpolar molecules or groups cluster together when protein is in water increasing water s entropy electrostatic and polar interactions 0 maximized in most thermodynamically stable structures hydrogen bonding also prevalent in motifs folds some Van der Waal s forces and disul de bonds 0 4 association of multiple 3D subunits l superstructure any andor all weak forces 0 Be able to interpret a Ramachandran plot you should know which regions of the plot correspond to which type of secondary structure 0 Upper region beta 0 Lower region alpha 0 Upper right region righthanded alpha not seen in nature 0 Understand the structure of the brous proteins keratin collagen and silk and how this differs from globular proteins 0 Keratin helix of alphahelixes 2 chain coiled cois proto bril o Collagen triple lefthanded helix l bril 0 Silk lots of beta pleats sheets lots packed together 0 Understand how proteins fold and what might cause them to denature break apart 0 Info necessary for folding contained in polypeptide sequence Anfinsen s Ribonuclease Refolding Experiment 0 quotcomplete collapsequot rapidly assume lowest energy fold native fold lowest energy most thermodynamically favorable nonrandom Levinthal s paradox o aided by chaperones or chaperonins O 0 several causes of denaturation extreme temperature or pH organic solvents denaturing agents urea and guanidinium hydrochloride
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