58 Cards in this Set
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Conformation
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3D spatial arrangement of atoms within any given molecule arising from the freedom of rotation about a single covalent bond
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Dihedral Angle
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Aka-torsion angle
the angle between 2 intersecting planes
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Configuration
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differing 3D spatial arrangements of atoms within molecules that have the same chemical makeup or molecular formula
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Geometric Isomers
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Isomers resulting from the different spatial arrangements of atoms across a double bond
-creates cis and trans
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Stereoisomers
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isomers resulting from the different spatial arrangements of atoms about a chiral center
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Chiral Center
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A molecule with 4 different chemical groups bound to a central C atom
-creates non-superimposable mirror images
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Enantiomers
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non-superimposable mirror images
-ex: hands
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First Law of Thermodynamics
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energy cannot be created or destroyed; only conserved from one form to another
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Enthalpy
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-H
-A measure of the heat content of a system
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Exothermic Rxn
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- Neg. Delta H
-Releases heat/ energy into surrounding
-feels hot
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Endothermic Rxn
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-pos. delta H
-absorbs heat from surroundings
-feels cold
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Bond Enthalpy
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the energy required to break a chemical bond
-Positive energy
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Entropy
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-s
-measure of disorder
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Degrees of Freedom
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W
if the order of the sys. inc. (dec. DoF)- neg delta S
if the order of the sys dec. (inc. DoF), pos. delta S entropically favorable
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Gibbs Free Energy
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the portion of the total energy of the system that can do work at constant temp and pressure
-Delta G the amount of energy absorbed or released in a rxn
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Delta G
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Exergonic- run with neg. delta G (release of free energy and SPONTANEOUS)
Endergonic- run with pos. Delta G (absorbs free energy and NON-SPONTANEOUS)
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Equilibrium
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run whose forward and reverse rates are equal. (free energy has been minimized)
-not necessarily equal concentrations
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Two ways free energy will be used
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1. Measure of Stability
2. Measure of work capacity
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Hydrogen Bond
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The electrostatic interaction between a lone pair on one electronegative atom and the H+ covalently bonded to a separate electronegative atom
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Electronegative
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Measure of the ability of an atom to attract electrons to itself in a covalent bond
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Dipole
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asymmetric distribution of electrons within a covalent bond
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Hydrophobic Effect
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the tendency of a non polar solutes to come together when placed in a polar solvent
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Amphipathic
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molecule with domains of 2 different natures such as polar and non polar
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Cathrate Cage
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Molecular interaction water molecules will adopt when surrounding a molecule resulting in an ice-like structure of water
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Ionic Bond
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-aka salt bridge
-electrostatic interaction between 2 atoms/molecules with formal charges
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Formal Charges
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arise when an atom has less (pos) or more (neg.) valence shell e- in the lewis structure compared to bare atom
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Dielectric Constant
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a measure of the polarizability of the solvent
-low for non polar
-high for polar solvents
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Equilibrium Constant (Keq)
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ratio of concentration of product and concentration of reactant for any run once equilibrium has been achieved
=[Products]/[reactants]
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Acids
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Proton donor
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Base
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Proton acceptors
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Conjugate Base
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the base formed when an acid loses its proton
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Ka (dissociation constant)
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-equilibrium constant for an ionization run
- Represents the affinity of a conjugate base for a proton
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Le Chatelier's Principle
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Stress is applied to a system at equilibrium, the eq. will adjust to minimize the effects of the stress
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Buffer
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solution consisting of a conjugate acid/base pair that resists large changes in pH.
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Buffering Region
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region in which a buffer is able to resist changes in pH. (centered around Pk)
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Non Polar Amino Acids
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GAPVILM
Glycine G
Alanine A
Proline P
Valine V
Isoleucine I
Leucine L
Methionine M
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Polar Amino Acids
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SCQYTNW
Serine S
Threonine T
Tyrosine Y
Asparagine N
GlutamineQ
Cysteine C
Tryptophan W
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Basic Amino Acids
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KRH
Lysine K
Argenine R
Histidine H
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Acidic Amino Acids
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DE
Asparatate D
Glutamate E
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Peptide Bond
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substituted amide linkage between an Alpha amino group and the alpha carboxyl resulting in the elimination of water
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number of peptide bonds
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n-1
n is the amino acids in the protein
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the N terminus
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1st AA in the protein with free amino group
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C terminus
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last AA in the protein with a free carboxyl group
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peptide backbone
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all atoms in the protein excluding those found in the side chains
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Phi angle
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circle with a line
angle between alpha carbon and amino group
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Psi Angle
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pitch fork
angle between alpha carbon and carboxyl group
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Ramachandran Plot
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plot of allowed conformations for most amino acid neighbors. Shows the psi & phi angles providing stable conformations. (limited space occupied because of psi and phi steric clash and planar peptide bond)
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Rotamers
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set of preferred dihedral angles each AA side chain will adopt
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Primary Structure
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description of all covalent bonds linking AA together in a protein. Typically thought of as the sequence of AA in a peptide chain
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Secondary Structure
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Describes the reoccurring backbone structural patterns found in a protein structure
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Structural features of an alpha helix
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1) Right or left handed
2) 5.4 A ptich
3) 3.6 residues/turn
4) R groups point away from axis
5) R groups off set from one another
6) Backbone Hydrogen bonding
7) Idealized backbone torsion angles (-57 and -47)
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Beta Sheet
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Structural pattern in which the peptide backbone forms pleated strands that interact with one another to form a sheet
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Beta Strands
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fully extended peptide chain that has a pleated appearance
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Structural Features of a beta sheet
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1. pleated appearance
2. Side chain alteration
3. Hydrogen Bonding
4. Antiparallel vs parallel sheets
5. Idealized Backbone torsion angles
6. Connections between strands
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Hydrophobic Core
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interior of a globular protein that consists primarily of hydrophobia side chains
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Prosthetic group
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non-protein (organic or metallic) molecule that has permanent association with a protein and its essential for its function
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Motif
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3D spatial arrangement of structural patterns within a protein that consists of 2 or more secondary structural elements and their interconnecting loops (IE alpha beta alpha)
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Domain
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Portion of polypeptide chain that is structurally and functionally independent of the rest of the protein
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BC 351: THE FOUNDATIONS OF BIOCHEMISTRY