BICH 410: EXAM 1
96 Cards in this Set
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A peptide bond is a
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covalent bond
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Non-Polar Amino Acids
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Alanine
Valine
Leucine
Isoleucine
Proline
Phenylalanine
Methionine
Tryptophan
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Polar, Uncharged Amino Acids
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Asparagine
Glutamine
Tyrosine
Threonine
Serine
Cysteine
Glycine (except doesn't form H-bond with water)
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Acidic Amino Acids
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Aspartic Acid
Glutamic Acid
Both have a net negative charge at neutral pH.
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Basic Amino Acids
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Histidine
Arginine
Lysine
Net positive charge at neutral pH
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Hydrophobic Amino Acids
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GAVLIPF
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Hydrophilic Amino Acids
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RNDCEQHST
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Amphiphatic
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LMYW
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Order of Deprotonation
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Carboxyl Group
Side Chain Carboxyl group
Amine Group
Side Chain amine group
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At low pH, all ionizable groups are
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protonated (H+ on), cationic form
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At mid pH what form dominates?
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Zwitterion (no net charge)
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At high pH, ionizable groups are
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deprotonated (H+off), anionic form
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When pH<pKa
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H+ on
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When pH>pKa
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H+ off
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Isoelectric point
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pH at which molecule carries no net charge
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C,H,O,N constitute __% of atoms in the human body
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99%
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Organic molecules contain
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carbon
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Thermodynamics
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Study of heat and energy and its effect on matter
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1st Law of Thermodynamics
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Energy is neither created nor destroyed
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2nd Law of Thermodynamics
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Total entropy of the universe is always increasing
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Enthalpy
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(H) - Reflects the number and kinds of chemical bonds or non-covalent interactions made or broken
Energy of system and its surrounding are constant E=q+w
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Entropy
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(S) - Randomness or disorder.
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Endothermic
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ΔH>0
Heat is absorbed, new bonds formed are less stable, non-favorable
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Exothermic
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ΔH<0
Heat is evolved by system, new bonds are more stable, favorable
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Living organisms are _______ systems
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open
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Open systems take up nutrients and release waste products are never at _______
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Equilibrium
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Steady State
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Existing with a constant flow so that the system does not change with time. Formation and degradation of individual components are balanced.
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Enzymes
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Molecules that catalyze or promote certain chemical processes by physically interacting with substrates to provide a more favorable pathway
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Endergonic
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ΔG>0
non-spontaneous
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Exergonic
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ΔG<0
Spontaneous
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Entropy (S)
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...
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When ΔS<0 the final state is ____ ordered than initial state
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More. Products are more complex and ordered.
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When ΔS>0, the final state is ____ ordered than the initial state
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Less. Products are less complex and more disordered.
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Isolated System
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No exchange of matter or energy
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Isolated System
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No exchange of matter or energy
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Close System
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Energy change may occur
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Open System
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Energy and/or matter exchange can occur
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Keq>>1
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Favors product formation so ΔGº is large and negative
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Keq<<1
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Favors reactant formation so ΔGº is large and positive
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When ΔGº=0 ________ occurs
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equilibrium
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The relationship between Keq and ΔGº is ______ dependent
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Temperature
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How to drive unfavorable reaction forward
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Compartmentation: increased concentrations of reactants
Coupling of reactions: favorable + unfavorable
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Hydrophilic
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Polar, ionic
interact (dissolve) in water
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Hydrophobic
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non-polar
do no interact with water
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Polar
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Unequal sharing of electrons
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Polarity is determined by the ________ of the atom
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Electronegativity. Atoms within polar molecules can carry a partial negative charge or partial positive charge.
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Electrostatic interactions between the ______ of the water molecules allow for formation of _______ bonds.
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Dipoles;hydrogen
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Hydrogen Bond
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electrostatic interaction between a weakly acidic donor group (O-H or N-H) and a weakly basic acceptor group (O or N). Strongest H-bonds have the donor atom and the acceptor atom 180º apart. Non-linear h-bonds are weaker.
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Entropy ______ as salt dissolves in water.
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Increases. Spontaneous reaction that is entropically driven.
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Aggregation
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Dispersion of lipids in water: entropy is decreased
Clusters of lipid molecules: entropy is increased.
Aggregation of non-polar molecules allows for greater disorder of the water molecules.
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Hydrophobic Effect
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Tendency of water to minimize its contacts with hydrophobic molecules
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Hydrophobic interactions
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Apparent affinity of non-polar substances for each other in the presence of water. Entropically driven process. Weakly temperature dependent.
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At low temperatures, mobility of water molecules are ________
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lessened, Change in entropy is less favorable at low temp. change in free energy increases, becoming more unfavorable.
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Amphiphatic
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Contain both polar and non-polar groups.
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Aggregates are stabilized by _________ effects
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Hydrophobic
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Non-covalent interactions
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Weaker than covalent in bond strength but numerous non-covalent interactions occur making them important in overall structure and thus function.
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___________ Bonds determine the complexity of molecular interactions within and between biomolecules.
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Non-covalent
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Non-Covalent bonds are ______ and ______
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Reversible;specific.
Size, shape, and type of interaction all must be correct for binding and/or proper folding.
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Proton Jumping
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Accounts for increased mobilities of H+ and OH-
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Keq is the ratio of
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Products to reactants
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Ionization Constant of Water (Kw)
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Water only weakly ionizes. Kw=[H+][OH-]= 1 x 10-14 M
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pH = -log[H+]
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Concentrations of [H+] over 14 orders of magnitude, though this change is small because [H+] is very low relative to [H2O]
Soren Sorenson
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Acid is proton ______
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donor
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Base is proton _______
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Acceptor
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The strength of an acid is based on its _______ ______ or its ability to transfer a _____ to water
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dissociation constant; proton
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In a biological system, we classify molecules on the basis of their _______, their interaction with water
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Polarity
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At physiological pH, amino groups are _______.
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Protonated
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At physiological pH, carboxylic acid groups are in their conjugate base form or _________.
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Deprotonated.
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Charge of free carboxyl and free amino group
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pka = 3.5 (carboxyl)
pka = 8.5 (amino)
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Two amino acids condense to form a dipeptide through a __________ reaction.
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Condensation.
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Avg. Weight of an amino acid is _____ Da
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110 Da/
1 residue
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Beer-Lambert Law
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A=∈lc
absorb = extinction coeff x path length x concentration
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Protein Purification
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1) Isolate protein
2) Detection of protein
3) Assay protein activity
4) Separation Techniques
5) Quantitation
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Salting Out
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Different proteins precipitate at different salt concentrations. Use low concentration to precipitate unwanted proteins (removes protein with lower solubility). Use higher salt concentration to precipitate target protein.
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Ion exchange Chromatography
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charge
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Hydrophobic Interaction Chromatography
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Purifies non-polar molecules. Based on interactions between non-polar protein and phenyl group. As salt concentration is decreased, hydrophobic proteins elute.
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Gel Filtration Chromatography
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Separate by size or molecular weight
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Affinity Chromatography
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binding affinity
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UV Detection
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Aromatic amino acids
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Purification Assessment
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Desired protein/amount of protein = purity. If desired protein is an enzyme then amount is quantitated as "activity" and purity is know as "specific activity"
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Gel Electrophoresis
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estimate weight and polarity. SDS - detergent used to denature protein and disrupt subunit interactions.
All proteins coated with SDS have negative charge thus separate by size rather than charge.
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Isoelectric focusing
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Determine pH.
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Protease
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An enzyme that hydrolyzes peptide bonds
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Endopeptidases
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hydrolyze internal peptide bond
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Exopeptidases
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hydrolyze N-Term or C-Term
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Edman Degradation
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1) Subunit interactions depend on weak force
2) Cleavage of disulfide bonds
3) Determine AA sequence
4) End group determination
- N-Term: Dansyl Chloride, FDNB
- C-Term: Corboxypeptidases A/B
5) Cleave each chain into smaller fragments
6) Repeat Step 5
7) Sequence all pept…
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Trypsin
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Cleaves c-term side of Arg,Lys
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Chymotrypsin
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Cleaves c-term side of Phe, Trp, Tyr
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CNBr
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Cleaves c-term side of Met
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Mass Spectrometry
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Measure mass-to-charge (m/z) ratio for ions in the gas phase. <25 residues.
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Electrospray Ionization (ESI)
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used to regenerate gas-phased macromolecular ions
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Primary Structure determined by ________ bonds
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covalent
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Secondary structure determined predominately by backbone ______
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H-bonds
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Tertiary Structure determined by ________ interactions, __ bonds, ionic interactions, van der waals, hydrophobic interactions
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side-chain; H-bonds
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Peptide Bond
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40% double bond character. Two resonance structures. uncharged, but polar. Planar because of peptide bond.
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α-helix
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3.6 residues/turn
5.4 A/ 1 turn
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Signal Transduction - Flashcards