biochem test 1
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| chemistry that deals with the chemical compounds and processes occurring in organisms; and the chemical characteristics and reactions of a particular living organism or biological substance. | show 🗑
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| show | living matter
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| basic principles of biochemistry can be applied towards all living organisms. T or F | show 🗑
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| Glycolysis, an almost________ central pathway of glucose metabolism. | show 🗑
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| show | conserved
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| biochemistry is _______ in our daily life | show 🗑
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| show | human biology and medicine, agriculture, industrial applications, and the environment (and more)
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| 5 important characteristics of living matter? | show 🗑
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| living matter - High degree of________ at molecular and organismal levels. | show 🗑
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| show | energy
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| energy _______ and _______ keep organisms alive | show 🗑
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| show | 1) from sunlight - plants, green bacteria, cyanobacteria 2) from nutrients/fuels- animals and most bactiera
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| living matter must be able to ________ between self and non self and ______ and _______ to change in the surrounding; immune system recognizes a bacteria, virus, etc. and mounts an immune response | show 🗑
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| living matter - regulated interactions between individual components that are ______ and ________ ex: cell signaling map and brain signaling for movment | show 🗑
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| living matter - fairly _______ self replication (DNA) while allowing enough _____ for evolution. biological reproduction with near-perfect fidelity | show 🗑
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| show | prokaryotes: bacteria and archaea
eukaryotes: eukarya
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| structural heirarchy of living matter? | show 🗑
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| simple organic compounds | show 🗑
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| macromolecules | show 🗑
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| show | C, H, O, N, P, S
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| less abundant essential elements (homeostasis) | show 🗑
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| trace amounts of these essential elements (metabolism, enzymatic cofactors) | show 🗑
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| what simple organic compound? components: nitrogenous base, five carbon sugars, phosphate | show 🗑
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| what simple organic compound? long chains of hydrophobic, insoluble | show 🗑
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| what simple organic compound? parent sugar is glucose | show 🗑
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| show | functional groups
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| GO OVER COMMON FUNCTIONAL GROUP FLASH CARDS HOE | show 🗑
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| show | specific.
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| 1. Macromolecules have______ binding domains. 2. Only certain molecules can bind – ______ and ______. 3. Binding of chiral biomolecules is________. | show 🗑
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| Biological Molecules’ Function Depends on ______ ______ Structure | show 🗑
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| show | 1) geometric isomers (cis vs trans) 2) stereoisomers (four, 2 asymmetric carbon) 3) enantiomers (mirror images, 2 pairs) 4) diastereomers (all non-mirror image pairs)
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| major macromolecules? (4) | show 🗑
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| show | monomeric units (nucleotides, amino acids, sugars) --> marcomolecules (DNA, protein, cellulose) --> supramolecular complexes (chromatin, plasma membrane, cell wall) --> cell/organelles
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| • All living organisms are made of______. • Cells are NOT all the same. • The simplest living organisms are_______-celled. • Larger organisms consist of many cells that are different in _____, _____, and _______ | show 🗑
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| what do eukaryotes have that prokaryotes don't? | show 🗑
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| show |
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| show | chemical
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| show | catabolism and anabolism
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| show | catabolism
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| part of metabolism that is reductive, constructive, and stores energy; goes from simple molecules to complex molecule; low energy --> high energy molecules and requires in put of ATP and reduced electron carrire | show 🗑
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| show | exergonic; endergonic
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| show | simultaneously
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| show | oxidation of glucose (C6H12O6 + 6O2 --> 6CO2 AND 6H20
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| catabolism is oxidative and degradative; it generates _______ and reduces ________ | show 🗑
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| show | exergonic
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| why is ATP the chemical currency of energy? | show 🗑
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| . For any physical or chemical change, the total amount of energy in the universe remains constant; 2. Energy may change form or it may be transported from one region to another, but it can not be created or destroyed. | show 🗑
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| Cells are efficient_______ of energy (convert energy from one form to another) , capable of interconverting _____, ________, _______, and _______ energy with great efficiency. | show 🗑
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| show | ; convert
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| organisms perform energy ______ to accomplish work and stay alive | show 🗑
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| Anabolic pathways________ cellular components from simple precursor molecules; _______ chemical energy (ATP and NADH or NADPH); they are ______ when compared to oxidative catabolic pathways | show 🗑
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| show | gluconeogenesis
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| in gluconeogenesis, Essentially same reactions in all tissues and all species. The_______ context and the________ of gluconeogenesis differ between species and tissues. | show 🗑
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| important gluconeogenesis precursors in animals? | show 🗑
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| show | endergonic
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| show | second law of thermodynamics
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| (the amount of energy capable of doing work during a reaction at constant temperature and pressure). | show 🗑
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| the heat content of the reaction system). | show 🗑
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| show | entropy (S)
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| show | negative (exergonic)
+∆S - increasing disorder; products more disordered than reaactants
-∆H - release heat
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| relationship between ∆G, ∆H, and ∆S in biological systems for constant temp and pressure | show 🗑
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| show | Positive; Negative
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| ü Endergonic ü ΔG > 0 ü Reactants are stable ü Reaction is not spontaneous | show 🗑
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| show | favorable - ex: breakdown
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| show | coupling; ATP
∆G3 = ∆G1 + ∆G2
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| show | common intermediate; LECTURE 2 EQUATION!!
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| show | transition state - lecture 2 page 5
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| show | activation energy
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| show | slower
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| At the equilibrium concentrations of substrates and products, the forward rate_____ the reverse rate and there is no further______ in the system. | show 🗑
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| When a reaction is not at equilibrium, the driving force that moves the reaction towards equilibrium is expressed quantitatively as the free energy change for the reaction, _____. | show 🗑
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| Keq =? | show 🗑
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| For chemical reactions, ΔG'o is dependent on the ______ | show 🗑
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| with a larger Keq, that means the concentrations of products are increased, and standard free energy change (∆G) is more negative, which means its more ________ | show 🗑
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| when Keq is greater than 1, ∆G is negative, and starting with all components at 1M, the reaction proceeds _______ | show 🗑
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| show | at equlibirum
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| show | in reverse
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| show | constant
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| Living cells are different from test tubes!_______ free energy change (ΔG) (not standard) determines the spontaneity of a reaction. ∆G (actual) = ∆G (standard) + RT lnKeq | show 🗑
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| how to speed up reactions, that would work in test tube but not suitable for living organisms | show 🗑
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| how to speed up reactions, that would work in living organisms? | show 🗑
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| Enzymes Lower the _____ ______ to Increase the Reaction Rate | show 🗑
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| LECTURE 2 NOTES - CHANGE REACTION BY COUPLING WITH A FAST ONE NOTES ! | show 🗑
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| who did this experiment? Abiotic formation of organic compounds under primitive atmospheric conditions; “Primordial Soup” Simple Organic Compounds (Biomolecules) | show 🗑
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| evolutionary benchmarks - Modern Humans ________y ears ago First land vertebrates _______ years ago | show 🗑
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| show | water; aqueous; water
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| show | charged; polar
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| water is a poor solvent for ________ substances (nonpolar gases, N2, O2, lipids, others) | show 🗑
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| required for degradation for high energy chemicals (oxidation), so because our blood is aqueous, water is poor solvent for oxygen so need proteins to carr it | show 🗑
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| show | amphipathic
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| what has a higher solubility in water? oxygen or CO2? why? | show 🗑
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| show | Electronegativity
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| water molecule's shape is a distorted _______ | show 🗑
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| show | 4; 2; energy to break H-bond vs energy to break the covalent O-H bond: 1:20
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| In ice, each water molecule can form hydrogen bonds with four neighboring water molecules. A crystal lattice structure makes ice less_____ than liquid water, and thus ice floats on liquid water. | show 🗑
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| Melting of ice and evaporation of water occur_______ at room temperature. ΔG = ΔH − TΔS; melting and evaporation at room temp have +∆H --> release heat and ∆S - increase entropy | show 🗑
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| show | hydrogen, ionic, van der waals, hydrophobic
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| show | acceptors and donors;
hydrogen acceptors differ as long as its partial negative/ has LP, but donor has to have a hydrogen that has a partial positive
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| a hydrogen bond in a biomolecule is stronger when it is ________ rather than when it is ________ | show 🗑
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| ionic interactions are Electrostatic interactions between permanently_______ species • Electrostatic interactions between the_____ and a permanent______ | show 🗑
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| show | anions; cations; water and NaCl
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| Van der Waals interactions are: • Weak interatomic attractions (reversible, easily broken) • Universal: occur between two _______ atoms that come next to each other | show 🗑
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| show | van der waals
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| 2 components of van der waals? | show 🗑
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| show | attractive
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| van der waals (Steric repulsion) that dominates at short distance. | show 🗑
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| compounds that have hydrophilic group and hydrophobic group | show 🗑
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| hydrophobic interactions - lipid in water, water will try to form cage and they are highly ordered --> entropy decreased. so the lipid ______ and hydrophobic groups condense and releases trapped water and allows entropy to increase bc random h20 released | show 🗑
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| • amphipathic • nonpolar group in the middle • polar group facing out, interacting with water • energy wise – more favorable ; minimize ordered shell of water molecules; increase entropy of water | show 🗑
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| _____Interactions are Crucial to Macromolecular Structure and Function | show 🗑
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| show | colligative properties
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| show | non-colligative properties
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| show | concentrated; osmotic
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| show | osmolarity
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| show | Isotonic; Hypertonic; Hypotonic
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| it is very rare that 2 water molecules connected by a hydrogen bond disassociate into hydronium ion (H3O+) and hydroxyl ion; most water remains _______ in the pure water form | show 🗑
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| what is wrong with this commonly seen formula? H2O --> H+ + OH- | show 🗑
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| ionization of water - ______ ______:rapid net movement of a proton, because the covalent and H- bonds are interchangeable. very rapid | show 🗑
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| show | opposite
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| constant that is a Fixed value that is characteristic for each specific reaction. concentration of products over reactants ; determined by electrical conductivity measurements | show 🗑
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| show | 1.8 x 10^-16 M
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| Kw, ion product of water is equal to what? | show 🗑
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| at pH=7, the concentration of[H+] and [OH] are what? Kw = [H+][OH-]= 1 x 10^-14 M^2 | show 🗑
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| a mathematical term that means the negative log of. | show 🗑
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| pH = what mathematically? | show 🗑
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| pH + pOH = ? | show 🗑
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| show | pH > 7
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| neutral condition water, [H+] = [OH-] | show 🗑
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| acidic conditions [H+] greater; [OH-] smaller | show 🗑
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| show |
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| show | true
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| Strong Acid + Strong Base = ??? HCl + NaOH | show 🗑
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| acids that only dissociate to a limited degree in water | show 🗑
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| for weak acids, the extent of dissociation is ___-dependent | show 🗑
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| for weak acids: ow pH, high [H+] push the reaction to the______ very little of the weak acid will be dissociated into ions. | show 🗑
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| for weak acids, high pH, low [H+] push the reaction to the_____ most of the weak acid will be dissociated into ions. | show 🗑
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| acid dissociation constant | show 🗑
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| show |
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| weak acids - When the pH = pKa, ____ _____ of the weak acid will be dissociated into ions. | show 🗑
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| when [A-] =[HA], then pH=? | show 🗑
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| LECTURE 5 PAGE 6 TITRATION | show 🗑
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| show | 50%
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| show | Acetic acid is the strongest acid (pKa = 4.76). - lowest pKa
Dihydrogen phosphate is in the middle (pKa = 6.86).
Ammonium ion is the weakest acid (pKa = 9.25).
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| the smaller the pKa, the ________ the acidity | show 🗑
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| show | acetic acid and acetate are conjugate acid/base pair; acetic acid is proton donor and acetate is proton acceptor
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| acid that gives up only one proton - CH3COOH(equilibrium arrows) H+ + CH3COO- | show 🗑
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| show | diprotic acid
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| acid that gives up three protons (H3PO4) | show 🗑
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| for diprotic and triprotic, which is the stronger weaker acid? | show 🗑
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| Almost every biological process is_____- dependent. A small change in pH produces a______ change in the rate of the process. | show 🗑
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| show | cytosolic; buffers; constancy
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| aqueous systems that resist changes in pH when small amounts of acid (H+) or base (OH-) are added. | show 🗑
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| Buffer is composed of a______ acid (proton donor) and its ______ _____(proton acceptor). Each conjugate acid-base pair has a characteristic pH zone to function as an effective buffer. | show 🗑
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| a flat zone on the titration curve – addition of given amounts of acid (H+) or base (OH-) has less effect on pH that outside the zone. EX: acetic acid, pH=pKa @4.76, this region is between 3.76 and 5.76 for acetic acid/acetate | show 🗑
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| show | phosphate and bicarbonate
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| show | phosphate buffer system - pH 5.9 to 7.9
H2PO4 --> H+ + HPO4 -
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| which important physiological buffer? good for blood plasma buffer; effective buffer near pH 7.4, the pH depends on concentrations of CO2 gas, dissolved CO2 converted into H2CO3 and HCO3- | show 🗑
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| show | acidosis - pathological condition or exercise
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| the most abundant biological macromolecules, found in all cells and all parts of cells. | show 🗑
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| show | diverse
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| building blocks of proteins | show 🗑
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| show | 20;
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| Cells produce structurally and functionally diverse proteins by covalently linking the same 20 amino acids in different ________ and ________ | show 🗑
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| general structure of alpha amino acids - a carboxyl group and an amino group bond to the same alpha carbon - applies to 19 of the AAs but not ________ why? | show 🗑
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| show | organic nomenclature and biochemical designation
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| show | Organic; Biochemical
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| the alpha carbon is ________ in 19 common amino acids, but not glycerine; which means there are two possible stereosiomers that are nonsuperimposable mirror images or what? | show 🗑
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| for most amino acids, if the amino group is on the left and R group below, it is "___" conformation but if amino group is on the right and R group below it is "____" conformation | show 🗑
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| L and D only refer to the absolute configuration of the four substituents around the chiral α-carbon in amino acids. Virtually all amino acid residues in proteins are____ stereoisomers. | show 🗑
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| Cells use enzymes with_________ active sites to select L amino acids! | show 🗑
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| Depending on the R substituents, the 20 common amino acids can be placed into______ groups. R groups vary in structure, size, charge, and solubility in water | show 🗑
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| show |
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| show | uncommon amino acids
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| show |
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| show | broken
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| show | carboxyl
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| ionization of amino acids - At neutral pH, the carboxyl group is______ but the amino group is______. The net charge is zero; such ions are called______. | show 🗑
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| show | neutral
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| show | zwitterions - lectrue 6 page 6
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| show |
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| α-carboxyl group is much_____ acidic than in carboxylic acids • α-amino group is slightly_____ basic than in amines | show 🗑
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| show | predominate
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| For amino acids without ionizable side chains, the Isoelectric Point (equivalence point, pI) is = ??? | show 🗑
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| show | zero; least; migrate
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| Ionizable side chains can be________. • Titration curves are more complex. • pKa values are discernable if two pKa values are more than two pH units apart. | show 🗑
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| show | 1) identify zwitterion (net charge = 0) 2) identify pKa that defines ACID strength 3) identify pKa value that defines base strength 4) average those 2 pKa values - lecture 6 page 8
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| show | negatively; positively; Histidine
MAKE SURE LECTURE 6 PAGE 8 MEMORIZE CHART IS IN THERE
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| biochem lecture 6 notebook notes | show 🗑
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| show | peptide bond.
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| peptide bonds are formed from a __________ reaction | show 🗑
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| the peptide bond: is less_______ (more stable) ² exhibits_______ moment in the trans configuration (favored) ² is______ and nearly________ (this one has to do with structure) | show 🗑
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| show | double; chem 471 09_06 lecture page 1
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| in a peptide, which bonds can rotate? | show 🗑
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| show | N-terminal to C-terminal
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| show | answer in notes biochem lecture 6 and on laptop highlight
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| No generalization can be made to relate the size of peptides and proteins to their functions. True or False? | show 🗑
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| show | oligopeptides
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| show | polypeptide
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| show | 10,000; GENERALLY - EACH AMINO ACID THE AVERAGE WEIGHT IS 110 G
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| show | true
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| show | noncovalent; covalent
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| show | Cofactors; Coenzymes; Prosthetic
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| proteins that contain permanently associated chemical groups, in addition to amino acids. | show 🗑
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| show | Prosthetic; 09/06 lecture page 5 table 3-4
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| Protein function depends on its _____ _______sequence. classical methods sequence one amino acid at a time | show 🗑
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| The amino acid sequences of millions of proteins have been determined indirectly by_______ sequencing. • Automation and_______ spectrometry provide faster alternative methods to determine amino acid sequences. | show 🗑
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| show | purify the target protein and reducing the level of complexity by cleaving it into smaller peptides by proteases or chemicals and then sequence each peptide
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| in protein methods, for proteolysis, Some proteases cleave proteins into smaller polypeptides, by catalyzing the hydrolytic cleavage of the peptide bond adjacent to particular _____ _______residues. | show 🗑
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| show | oxidizing and reducing agents
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| show | chemical sequencing - edman degradation
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| what molecules are to be analyzed in mass spectroscopy? | show 🗑
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| show | mass spectroscopy
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| show | each AA has a specific mass to charge ratio (m/z) and then you assemble the peptide sequence based on m/z values
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| when membrane has this lipid, it allows the membrane to curve which allows machinery for ETC in mitochondria; required for mitochondrial structure and function | show 🗑
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| show | bioactivity
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| show | homogenation; centrifugation
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| in research example with CLS, to separate CLS protein from other components is done by _________, analyzing the CLS protein is done by _______, and resolving the structure of the CLS protein is done by ________ | show 🗑
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| show | bioassay-guided isolation - "quality control" that just makes sure sample is active before initiating isolation effort
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| show | centrifugation
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| on low speed for centrifugation of homogenized tissue, there are what 2 main densities/ | show 🗑
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| on high speed for centrifugation of homogenized tissue, there are what 2 main densities/ | show 🗑
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| show | sucrose density centfigugation -- prepare series of sucrose solutions and different layers of sucrose with different densities then poke hole and collect fraction
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| how do you acquire soluble proteins in protein methods? lecture 09/08 page 3 | show 🗑
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| chromotagraphy is used in protein _________ | show 🗑
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| 3 phases of chromotagraphy | show 🗑
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| solid porous matrix inside the column. what chromotagraphy phase? | show 🗑
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| show | mobile
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| show | effluent
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| show | ion exchange, size exclusion, affinity
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| 2 types of ion exchange chromatography | show 🗑
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| show | + (positively) ; negative; acidic - bc column is positive, protein are negative, want to pull protein from positive matrix, the acidic solution gives more protons and helps protein fall off the matrix
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| show | negative; positive; basic - negatively charged basic eludes and pulls positive proteins from negative matrix
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| show | negative
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| ch 3 problem 17 | show 🗑
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| show | first; last ; smaller can get stuck in matrix and larger cannot
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| show | affinity chromatography
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| show | immobilized ligand is linked to the matrix. protein of interest binds to the ligand. unwanted proteins washed through the column protein of interest is eluted with ligand solution
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| show | dialysis
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| in electrophoresis, Gel matrix_______ the mobility of proteins according to their size and shape. and Running buffer_________ electricity. | show 🗑
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| in electrophoresis, what electrode to they migrate to? | show 🗑
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| After electrophoresis: the proteins can be visualized by staining the gel (i.e., Coomassie blue).Each band corresponds to a ________. small migrate faster compared to larger proteins | show 🗑
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| what does SDS page do to a protein? | show 🗑
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| show | distance traveled on gel/total gel length
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| show |
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| show | first - isolectric focusing on pI point and charge
second: SDS-PAGE - molecular/weight and size
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| show | ok
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| show | isoelectric points.; zero
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| Protein molecules adopt a specific 3-dimensional conformation (called the _____ _______). this conformation is mainly held together by favorable_________ interactions. | show 🗑
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| show | energy
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| protein structure: AA sequence that determines function | show 🗑
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| show | secondary
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| show | tertiary
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| show | quaternary
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| show | no - bc it doesn't have multiple subunits
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| show | covalently
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| show | hydrogen
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| show | alpha helix
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| show | compact
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| show | α helix ; dipole between N+ and O-...
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| _________Affects α-Helix Stability | show 🗑
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| show | small hydrophobic
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| alpha Helix breakers: _____ (cyclic R-group, can’t rotate). _____ (tiny R-group (H) supports other conformations) | show 🗑
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| why can't proline rotate well? | show 🗑
|
||||
| beta strand: Extended peptide chains naturally make a pleated geometry. • α-Carbons are the_______. • R-groups________ (up, down, up, down....) • Planar peptide bonds are in the_______. | show 🗑
|
||||
| what secondary structure for protein? -Peptide chains align side-by-side. -Interstrand H-bond-Parallel and Antiparallel | show 🗑
|
||||
| same direction of beta sheet vs opposite direction beta sheet | show 🗑
|
||||
| show | beta turn
🗑
|
||||
| show | Proline or glycine
🗑
|
||||
| show | • Proline in 2nd position.
• Proline: conformationally
restricted with fixed φ angle, keeps turn rigid.
🗑
|
||||
| show | Glycine in 3rd position
• Glycine: small and flexible,
allows for tight corners.
🗑
|
||||
| show | 2
🗑
|
||||
| show | becaust there is a H-bond between carbonyl oxygen in AA1 and amino group hydrogen in AA 2
🗑
|
||||
| Peptide bond configuration: • Nearly all peptide bonds not involving proline are in the_______ configuration (>99.95%). | show 🗑
|
||||
| Peptide conformation is defined by dihedral angles (or torsion angles). Dihedral angles: o Φ (phi): what angle? ψ (psi): ? | show 🗑
|
||||
| show |
🗑
|
||||
| show | ok
🗑
|
||||
| show | circular dichroism (CD) analysis for secondary structure
🗑
|
||||
| show | tertiary structure
🗑
|
||||
| 2 major classes of tertiary structure:________ proteins: long strands or sheets_________ proteins": spherical or global shape | show 🗑
|
||||
| show | tertiary structrure: fibrous proteins
🗑
|
||||
| show | tertiary structure: globular proteins
🗑
|
||||
| The arrangement of two or more polypeptide chains (subunits) in 3-D complexes. | show 🗑
|
||||
| show | x-ray crystallography and NMR spectroscopy
🗑
|
||||
| show | x-ray crystallography
🗑
|
||||
| pros and cons of x ray crystallography? | show 🗑
|
||||
| 1)Dissolve the protein 2) Collect NMR data 3) Assign NMR signals 4) Calculate the structure | show 🗑
|
||||
| show | Pros: No need to crystallize the protein; motional dynamics of whole molecule.
Cons: only suitable for small proteins
🗑
|
||||
| show | IN NOTES LECTURE 9 BIOCHEM
🗑
|
||||
| for beta turns, _______ is preferred as the turn because it is easier to turn as cis rather than trans | show 🗑
|
||||
| show | negative
🗑
|
||||
| show | proteostasis; like homeostasis but for proteins
🗑
|
||||
| misfolded proteins _______ | show 🗑
|
||||
| show | synthesis --> folding --> unfolding --> misfolded, aggregates --> remodling --> degradation
🗑
|
||||
| show | thermodynamically
🗑
|
||||
| Protein folding is a fast process. Sometimes protein folding happens spontaneously. More often it occurs with the assistance of specialized enzymes and complexes called________ . | show 🗑
|
||||
| proteins that Interact with partially folded or misfolded polypeptides and facilitate correct folding. | show 🗑
|
||||
| chaperone proteins are present in organisms franging from bacteria to humans. they require energy in the form of _______ to function because thermodynamic prefers randomness, and going from misfolded to a more organized correct fold requires energy | show 🗑
|
||||
| show | Hsp70 and Chaperonins
🗑
|
||||
| loss of a protein's 3D structure | show 🗑
|
||||
| when a protein loses its 3D structure it doesnt carry out the biological function T or F | show 🗑
|
||||
| show | cooperative; Melting temperature
🗑
|
||||
| show | CD • Has the alpha helix, beta conformation, and random coil
• Change structure (no longer alpha, beta, or something) change in Beta conformation is different (or whatever your secondary structure is)
🗑
|
||||
| show | heat, extremes of pH, miscible organic solvents, solutes, detergents
🗑
|
||||
| -Heat disrupts____-bonds. - Extremes of pH disrupt______ interactions and ______-bonds. Miscible organic solvents (i.e. alcohol or acetone) disrupt________ interactions. | show 🗑
|
||||
| _______(i.e., urea) disrupt hydrophobic interactions and H-bonds. § _______ disrupt hydrophobic interactions. | show 🗑
|
||||
| show |
🗑
|
||||
| show | native
🗑
|
||||
| show | mitochondria
🗑
|
||||
| o to go through ETC,_______ is the final electron acceptor o ATP mainly produced through ETC and mitochondria and oxygen helps create_______ gradient | show 🗑
|
||||
| show | turbine - lecture 9/13 page 4
🗑
|
||||
| WHY WE NEED OXYGEN, MITOCHONDRIA, ETC, FOR COMPLEX___ IN ETC – COMPLEX USES OXYGEN HAS ELECTRON ACCEPTOR, NEED PROTON GRADIENT TO PRODUCE ATP Enzyme for complex is cytochrome c oxidase - forms water | show 🗑
|
||||
| show | poor
🗑
|
||||
| show | poor water solubility - can't ge carried to tissues in sufficient quantitiy and ineffective diffusion over long distance in larger multicellular animals
🗑
|
||||
| what oxygen binding proteins? A) transports oxygen; tetramer B) stores oxygen; monomer | show 🗑
|
||||
| show | globins
🗑
|
||||
| globin that is a monomer, protect neurons from hypoxia and ischemia | show 🗑
|
||||
| show | cytoglobin
🗑
|
||||
| hemoglobin and myoglobin are the most-studied/best-understood proteins. they are first ones with 3D structures determined. they are ______ proteins, so their tertiary structure contains several types of secondary structure; important enzymes/regulatory | show 🗑
|
||||
| hemoglobin and myoglobin - examples ofr how other proteins work: a. ________ interactions with other molecules. b. ______ – conformational changes essential for function. c. ________ binding – specific and reversible. | show 🗑
|
||||
| Hemoglobin and myoglobin are________ proteins (conjugated proteins with the bound prosthetic group heme). | show 🗑
|
||||
| show | heme
🗑
|
||||
| Heme:________ oxygen binding. key function | show 🗑
|
||||
| true or false: None of the amino acid side chains can bind oxygen. | show 🗑
|
||||
| Transition metals such as____ and ______r have a strong tendency to bind oxygen. Free iron is highly reactive& generates ____ _____ ______(ROS) that damage macromolecules. | show 🗑
|
||||
| show | ROS - reactive oxygen species (damage macromolecules)
🗑
|
||||
| show | ‘open’ coordination
🗑
|
||||
| show | oxidation
🗑
|
||||
| protein that Stores O2 in muscles for metabolism. | show 🗑
|
||||
| myoglobin structure is Eight __--______segments connected by β–turns. there is______ heme per molecule | show 🗑
|
||||
| _______ is a ligand for myoglobin. • Myoglobin binds oxygen at the specific binding site. • Same applies to hemoglobin, except that the binding is more complex. | show 🗑
|
||||
| show | ligand
🗑
|
||||
| a region in the protein where the ligand binds. | show 🗑
|
||||
| show | non-covalent
🗑
|
||||
| show | Equilibrium; P + L ⇌ PL
🗑
|
||||
| chapter 5 problem 1 | show 🗑
|
||||
| show | Ka = [PL]/[P][L]
Kd = 1/Ka
🗑
|
||||
| show | θ(theta)
🗑
|
||||
| Kd = _____when θ= 0.5; θ depends on the free [ligand] and Kd; | show 🗑
|
||||
| The fraction of bound sites θ depends on: 1) the____ ______ concentration, and 2) ________ | show 🗑
|
||||
| if one protein has a higher association constant for a ligand, (Ka) , than another protein, what does that mean? | show 🗑
|
||||
| for ligand analysis, the smaller the disassociation constant, the ________ the affinity | show 🗑
|
||||
| practice problems lecture 09/15 from galina's notes page 4 and page 6 with myoglobin | show 🗑
|
||||
| show | strong
🗑
|
||||
| show | weak
🗑
|
||||
| show | Molecular
🗑
|
||||
| show | p artial pressure
🗑
|
||||
| show | θ = pO2/pO2+Kd
🗑
|
||||
| show | its good for O2 storage but not O2 transport because its theta is still about 1 fro 4 kPa and will not release the oxygen
🗑
|
||||
| show | pO2
🗑
|
||||
| show | Sigmoid
🗑
|
||||
| show | 4
🗑
|
||||
| hemoglobin is a tetramer of two subunits (α2β2). α and β______ form a dimer.Tetramer is a dimer of αβ dimers. | show 🗑
|
||||
| Hemoglobin in________ (red blood cells) binds and carries nearly all the O2 in the whole blood. these cells transport O2 | show 🗑
|
||||
| show | erythrocytes
🗑
|
||||
| myoglobin is a monomers, so can it have quaternary structure? | show 🗑
|
||||
| show | similar
🗑
|
||||
| there is a low identical sequence between alpha and beta subunits in hemoglobin, and there is no D-helix in alpha subunit, but in the Heme binding pocket: ___ and _____ helices in both subunits. | show 🗑
|
||||
| what are the subunit interactions in hemoglobin for the 4 subunits (alpha 1, alpha 2, beta 1, beta 2 = tetramer) | show 🗑
|
||||
| show | tense state and relaxed state
🗑
|
||||
| predominant conformation of deoxyhemoglobin. | show 🗑
|
||||
| hemoglobin conformation that has a higher affinity for O2 than the T state. central cavity is collapsed and binds oxygen | show 🗑
|
||||
| show | apo state
🗑
|
||||
| • R state conformation • Collapsed central cavity • High affinity for O2 what state of hemoglobin? | show 🗑
|
||||
| show | oxygen
🗑
|
||||
| show | low; high; allosteric
🗑
|
||||
| o Upon binding of first oxygen and the rest of the hemoglobin affinity of oxygen is_______ | show 🗑
|
||||
| cooperative ligand binding - hill equation in lecture 11 notebooks | show 🗑
|
||||
| (slope of Hill plot, degree of interaction): nH | show 🗑
|
||||
| Hill coefficient values and ligand binding co- operativity: nH = 1: ______ nH>1:_______ nH<1: _______ | show 🗑
|
||||
| show | multiple; interact; conformational
🗑
|
||||
| first binding event increases affinity at remaining sites. | show 🗑
|
||||
| show | negative cooperativity - nH< 1
🗑
|
||||
| show | sigmoidal
🗑
|
||||
| show | DECREASES
🗑
|
||||
| show | dissociation
🗑
|
||||
| the effect of pH and [CO2]/pCO2 on the binding and release of O2 by Hb. high oxygen, Hb binds O2 and releases H+. low oxygen (tissue), hemoglobin binds H+ and releases O2 | show 🗑
|
||||
| o When pH is_____, the hemoglobin has lower affinity for oxygen releases oxygen o pH is_____, binds more oxygen | show 🗑
|
||||
| when pH jumps from 7.4 to 7.2 what is the impact on affinity of hemoglobin for oxygen? | show 🗑
|
||||
| chapter 5 problems 3a and 3B in lecture 11 notes | show 🗑
|
||||
| intermediate in glycolysis, Polyanion, high in erythrocytes. LECTURE 09/18 PAGE 5 | show 🗑
|
||||
| show | reduces
🗑
|
||||
| chapter 5 problem 3a,3b,3c lecture 11 | show 🗑
|
||||
| show | CO poisioning
🗑
|
||||
| show | true
🗑
|
||||
| • Life-threatening. • Individuals homozygous for the sickle-cell allele of the gene encoding Hb β subunit. • Normal Hb (Hb A) remains soluble upon deoxygenation. Mutated deoxygenated Hb (Hb S) forms insoluble fiber. | show 🗑
|
||||
| show | hydrophobic
🗑
|
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