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179 Cards in this Set
- Front
- Back
What is the "Progenote"?
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A breakthrough organism which gave rise to everything; LUCA - last universal common ancestor
|
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What were the prebiotic energy sources?
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- Radiation from sun
- Electric discharge (lightning) - Radioactivity - Volcanoes |
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What were the initial raw materials on Earth?
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CO2, CH4, N2, H2, H2O, NH3
|
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What molecule is abundant in many structures which are necessary for life? Why?
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Adenine - When concentrated HCN is refluxed, the major product is adenine; therefore abundant prebiotically
|
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How do new enzymes/proteins begin?
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Gene duplication yields an extra copy that can evolve with a new function
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What is phosphotriesterase?
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A molecule which is found in bacteria that hydrolyzes pesticides and nerve toxins; evidence of the quick evolution of enzymes
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Evo-Devo stands for what?
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Evolutionary development
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What percent of the typical cell is water?
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70%
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What leads to Hydrogen Bonding in water?
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Electrical asymmetry; partial positive on hydrogens, partial negative on oxygen
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How does hydrogen bonding affect melting points?
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More hydrogen bonds, higher melting point
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Which is the H-bond donor?
H-bond acceptor? |
Donor = Hydrogen involved
Acceptor = Atom bonded to Hydrogen |
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The hydrophobic effect causes what change in entropy?
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ΔS = Positive, because H bond potential is disrupted by hydrophobic molecules
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What are Van der Waals interactions?
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Weak interactions which operate at close range between transient dipoles induced in each atom by the other
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The stronger the acid, the ______ the pKa; why?
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Stronger acids = lower pKa = lower pH --- higher likelihood to ionize
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What is the Henderson Hasselbalch Equation?
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pH = pKa + log [A-]/[HA]
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How does the Greek lettering system work for R groups?
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αC = carbon attached to amino and carboxyl group
β, γ, δ, ε, etc carbons go consecutively downwards |
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What is the difference between configuration and conformation?
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- Configurations - can be interconverted only by breaking and reforming one or more covalent bonds
- Conformation - Interconverted by rotation about a bond without breaking a covalent bond |
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What are stereoisomers which are nonsuperimposable?
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Enantiomers
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Which enantiomer of amino acids is found in proteins?
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L-amino acids
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Which amino acids absorb UV light?
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Tryptophan**
Tyrosine* Phenylalanine |
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The isoelectric point is the pH when the amino acid is?
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at a neutral charge
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Which amino acids were found in the prebiotic atmosphere?
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Glycine, Alanine, valine, leucine, isoleucine, proline, serine, threonine, aspartate, glutamate
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Which amino acid kinks protein structure?
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Proline
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Which amino acid has a neutral pKa and is involved in H+ transfers?
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Histidine
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Which nonstandard amino acid is involved in blood clotting?
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γ-Carboxyglutamate
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Which nonstandard amino acid is a pre-cursor for arginine?
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Ornithine
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What is the average pKa of COOH on amino acids?
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~2
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What is the average pKa of NH2 on amino acids?
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~9-10
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How are peptide bonds formed in vitro (test tube)?
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1) Attachment to resin
2) Removal of protecting group (Fmoc) 3) Activation of next amino acid 4) Peptide bond formation 5) Removal of polypeptide from resin |
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What is the purpose of Fmoc?
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It is a protecting group which prevents unwanted reactions at the α-amino group of the residue
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How does chemical synthesis (in vitro) of proteins differ from that done naturally (in vivo)?
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In vitro - synthesis proceeds from the C-terminus to the N-terminus; reverse of the In vivo method (N-->C)
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When naming peptides, start at which end?
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N-terminus
|
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If the molecular weight of a peptide is <10,000 it is designated as?
>10,000 is what? |
<10,000 = Polypeptide
>10,000 = Protein |
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What is the average weight of an amino acid (adjusted for the percentage at which the amino acid occurs in proteins)
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MW = 110
|
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What are some functions of proteins?
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- Catalysis
- Transport - Nutrient / Storage - Motion - Structure - Defense - Regulation - Many other miscellaneous |
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99.9% of reactions have what?
|
An enzyme catalyst
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What are two examples of transport proteins?
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Ex: O2 doesn't diffuse very quickly; hemoglobin provides transport
Ex: Lipoproteins |
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What are the main components for motion in muscle?
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Action / Myosin
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What is the main protein involved in structure?
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Collagen
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What are examples of kinds of proteins involved in defense?
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Immunoglobins
Venoms/Toxins |
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What kind of proteins are involved in regulation?
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Hormones with extracellular signals
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Why do some proteins have carbohydrates attached? Name?
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Glycoproteins - used to identify cells
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Why do some proteins contain metal cofactors? Name?
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Metallo-enzymes - 1/3 of enzymes have metal cofactors
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Why are lipids sometimes on proteins?
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Helpful to embed in membrane
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What are two ways to detect proteins?
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1) UV Absorption (tryptophan especially)
2) Colorimetric Assays - Lowry Blue Complex - Bradford Blue Dye (Coomassie) (Color intensity proportional to amount of protein) |
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Why is the Bradford Blue Dye (Coomassie) better than Lowry Blue Complex?
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Coomassie doesn't destroy the proteins in the process?
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What is the reaction rate proportional to?
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The amount of enzyme present
|
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What is the "international enzyme unit"?
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The amount of enzyme that will convert one μmol of substrate to product in one minute at 30˚C
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What are the units of activity?
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Units (of desired protein) per mL of solution
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What are the units of specific activity?
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Units (of desired protein) per mg of protein total
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What is the measure of purity of a protein?
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The specific activity
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How can proteins be precipitated?
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1) Salt (NH4SO4) - best, most gentle
2) pH Extremes - can kill proteins 3) Heat - can kill proteins |
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How does Ion-Exchange Chromatography work?
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- Beads in column have charged particles, either all positive or all negative
- Liquids w/ proteins going through will go through at different rates depending on charge or proteins - Fractions will contain different proteins w/ different charges |
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How does Size-Exclusion Chromatography work? What is its other name?
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Gel Filtration
- Bigger proteins go through column faster than small because small proteins get stuck in the porous polymer beads |
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How does Affinity Chromatography work?
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- Polymer bound ligand (with affinity for protein of interest) is placed in column
- Protein mixture is poured through - Unwanted proteins wash through column - Protein of interest is eluted by ligand solution |
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How do you determine when the protein is pure?
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- When further fractionation does not increase the specific activity
- Electrophoresis |
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What does electrophoresis take place in?
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Polyacrylamide which allows the proteins to go through based on their molecular weights
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What is the function of Sodium Dodecyl Sulfate (SDS)?
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SDS binds to proteins in amounts proportional to their length, partially denatures the structures, as well as gives them all an overwhelming negative charge; this allows the proteins to move through proportional to their MW
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How do proteins get visualized after they have gone through electrophoresis?
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Coomassie blue dye which binds to the proteins but not to the gel
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What trends should be seen in a Purification Table?
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- Decrease in total protein (mg)
- Total enzyme (units) stays as high as possible - Specific Activity (units/mg) increases |
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What kind of bonds make up the primary structure of proteins?
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Covalent bonds: peptide bonds and disulfide bonds
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How can the N-terminus be determined?
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Using Sanger's method for direct protein sequencing;
- FDNB attacks the N-terminus and adds to end - Strong Acid is added which removes the N-terminal A.A. with the FDNB leaving the remaining peptide chain |
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What are proteases? What are 4 we learned about?
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Enzymes that catalyze the hydrolysis of peptide bonds
1) Trypsin** 2) Chymotrypsin** 3) Pepsin 4) Elastae |
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What does Trypsin do?
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Protease which cleaves on the carboxyl side of Lysine or Arginine
|
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What does Chymotrypsin do?
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Protease which cleaves on the carboxyl side of Tyrosine, Tryptophan, and Phenylalanine
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How does CNBr cleave peptides?
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It hydrolyzes peptide bonds at the C-terminus of methionine residues
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How are Disulfide Bonds cleaved?
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1) Oxidation by Performic Acid
OR 1) Reduction by Dithiothreitol 2) Carboxymethylation by Iodoacetate (important or the previous step will revert to a sulfide bond |
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What reactant is used in sequencing by the Edman Degradation?
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1) Phenylisothiocyanate w/ OH-
(Benz-N=C=S) 2) H+ => Phenylthiohydantoin Derivative (determine A.A. from this compound) and then continue on remaining peptide chain |
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How can large polypeptides be sequenced?
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Breaking them down into smaller fragments and piecing it together
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Specifically, what is the process for sequencing large polypeptides?
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1) Hydrolyze to separate amino acids
2) Determine # of each A.A. 3) Conclude which protease(s) would be useful based on # of A.A. / # of breaks 4) Determine N-Terminus of Polypeptide (w/ Sanger Method: FDNB + HCl) 5) Reduce Disulfide Bonds 6) Cleave w/ proteases, establish sequence via overlaps |
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Why can't large polypeptides be sequenced solely by the Edman Degradation?
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The longer the polypeptide chain the lower the overall accuracy of the sequencing; thus they must be broken down into smaller fractions.
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How are Disulfide Bonds located (specifically which Cysteine residues are linked together)?
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- Two samples, one cleave disulfide bonds, one leave them
- Cleave with protease - Electrophoresis - Compare fragments on a gel - The run w/o disulfide bond cleavage should have larger bands; that w/ disulfide bond cleavage will have 2+ bands missing which is replaced by larger band |
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What is a Consensus Sequence?
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A DNA or amino acid sequence consisting of the residues that most commonly occur at each position in a set of similar sequences
- use cool letter graph - use symbols, [ ] = these A.A. could be present, x(#) = a lot of options could be here, { } = any AA except for these |
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The C-O bond is _____ than expected in peptide linkages.
The C-N bond is _____ than expected in peptide linkages. |
C-O is longer than expected (not always "double" bond)
C-N is shorter than expected (not always "single" bond) |
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Because the peptide bond is not solely composed of a C=O and C-N bond... what effect does this have on the rotation of the peptide backbone?
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There is not free rotation in the backbone of the peptide bond
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Around which bonds is there free rotation in the peptide backbone?
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N-C(alpha) and C(alpha)-C bonds have free rotation
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Which rotation angle is referred to by ϕ (phi)?
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C - Cα - N - C dihedral / torsion bond angle
(180° means N trans; 0° is cis) |
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Which rotation angle is referred to by ψ (psi)?
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N - Cα - C - N dihedral / torsion bond angle
(180° means N trans; 0° is cis) |
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In an α-helix, are the R groups on the inside of the helix or outside?
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Outside of helix
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How far is one turn of the α-helix? How many amino acid residues is that?
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0.54 nm
3.6 residues |
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In which direction do α-helices rotate?
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Right-handed
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Why are α-helices such stable conformations?
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It makes optimal use of internal hydrogen bonds; the N-H is lined up with the C=O of the 4th A.A. on the N-terminal side
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Why is Proline very rarely found in α-helices?
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Its nitrogen atom is part of a rigid ring, making N-Cα bond rotation impossible, resulting in destabilizing kinks
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What's the difference between Parallel and Anti-Parallel β sheets?
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- Parallel - same amino-to-carboxyl orientations
- Anti-Parallel - opposite amino-to-carboxyl orientations |
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Are Parallel or Anti-Parallel β sheets more stable/common?
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Anti-Parallel is more stable and more common (more direct H-bond alignment between N-H and C=O)
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Why is silk so slippery?
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Anti-parallel β sheets with small R groups (glycine and alanine)
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How are the ends of anti-parallel β-sheets linked?
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β Turns: 180 deg turn involving 4 A.A. residues w/ a H-bond between the 1st and 4th A.A. involved
|
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How are the two types of β turns different?
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- Type 1 - often includes Proline due to readily assumed cis configuration which is amenable to a tight turn
- Type 2 - includes glycine which is small and flexible (less steric hindrance) |
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What does a Ramachandran Plot show?
|
The possible and likelihood of different combinations of dihedral / torsion angles in proteins (ψ vs ϕ
- dark blue = most favored - non blue = doesn't happen |
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Which type of dihedral band angle combination is suspected to be possible, but no one has ever found a long enough chain of it?
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Left-handed α-helix
|
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Which amino acid residue can fall outside of the Ramachandran Plot expected values?
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Glycine due to its small H side-chain which allows it to take part in many conformations that are sterically forbidden for other a.a.
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What is distinct about Fibrous proteins compared to Globular proteins?
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- Fibrous usually have just one type of secondary structure with a simple tertiary structure
- Globular usually have multiple types of secondary structure |
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What are the typical functions of Fibrous proteins?
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Provide support, shape, and external protection
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What are the typical functions of Globular proteins?
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Enzymes and regulatory functions
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When two α-helices are twisted together what is it called? What is known about the handedness?
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Superhelix
- Handedness is opposite that of the individual helices |
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In perms, what are the main steps?
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1) Break disulfide bonds in hair with Thioglycolate
2) Curl hair 3) Oxidize sulfide bonds again; different linkages occur causing hair to curl |
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α-Keratin is an example of what kind of protein?
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Fibrous protein - hair - made up of many superhelices - protofilaments - protofibril
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What is the most abundant protein in the body?
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Collagen
|
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What is the structure of collagen?
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Single L-handed helix (not an α-helix) w/ 3 A.A. residues per turn; 3 α chains (separate polypeptides) are supertwisted about each other (right-handed)
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Collagen is constructed of a repeating tripeptide made of what?
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Gly-X-Y where X and Y = Proline or 4-Hydroxyproline
- Proline prefers C-endo conformation - Y prefers to be in C-exo conformation which is less stable, but it is reinforced by the hydroxylation |
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How is Proline hydrolyzed to 4-hydroxyproline (the preferred conformation for c-exo in the Y position of the collagen tripeptide)?
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Prolyl Hydroxylase hydrolyzes Proline; requires vitamin C (ascorbic acid)
|
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What is it called when there are Vitamin C deficiencies? What happens?
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Scurvy - collagen defects - gums bleed, sore joints, nose bleeds, die
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How are collagen α chains cross-linked?
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With unusual amino acid residues - dehydrohydroxylysinonorleucine - lysine residues covalently bonded to hylysine residues
|
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What are two genetic defects involving collagen?
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- Osteogenesis Imperfecta: affects bone formation in babies - Gly to Cis mutation (doesn't fit tightly)
- Ehlers-Danlos Syndrome: loose joints, soft skin, eye problems and bone deformations - Gly to Ser mutation |
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Why is gelatin (a protein) not a good source of protein?
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Lacks many essential amino acids; primarily consists of glycine (35%), alanine (11%), and proline/hydroxyproline (21%)
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What stabilizes the 3-D structure of globular proteins?
|
- Electrostatic Forces (ionic interactions / salt bridges)
- Hydrogen Bonds (small contribution, however unpaired donor or acceptor is detrimental to stability) - Hydrophobic Forces (most important, increases entropy) - Disulfide bonds |
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What are two pictorial ways to represent protein 3-D structure?
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- Surface contour conformation (shows reaction sites)
- Ribbon representation (shows secondary structures) |
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What was the protein on which the preliminary understanding of tertiary structure was discovered? How?
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Myoglobin by John Kendrew (1950s) with x-ray diffraction
|
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What are the functions of myoglobin?
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- Stores oxygen
- Facilitates oxygen diffusion in rapidly contracting muscle tissues - Underwater mammals have a lot of this so they can stay under a long time |
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How does X-Ray diffraction give the structure of a protein?
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- Protein is crystallized
- X-Ray beams diffracted through - Pattern of spots is used to reconstruct the image of protein (e- density) - Model structure into e- density map - Answer of where atoms in protein are |
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How can scientists determine the structure of a protein?
|
- NMR (only for smaller molecules)
- X-Ray Diffraction |
|
What did scientists learn about protein structure from myoglobin?
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- Predicted secondary structure exists
- Very compact - Hydrophobic residues buried - Proline often found at bends - All species similar; 3-D structure conserved over evolution |
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Are β sheets typically planar?
|
No, they tend to twist slightly in a right-handed fashion
|
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How are two antiparallel β sheets connected?
|
β bends
|
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What types of connections are more common between β strands?
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Right-handed connections
|
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What is a motif in protein structure?
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A recognizable folding pattern involving two or more elements of secondary structure and the connections between them; may or may not be independently stable
|
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What are some examples of motifs in protein structure?
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- β barrel
- β-α-β loop --> α/β barrel (made up of many loops, much more stable than individual loop) |
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What is a domain in protein structure?
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Part of a polypeptide chain that is independently stable; usually each domain has a specific, discrete function
|
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How many domains are in a protein?
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Depends on individual protein; some have multiple domains, some have just one
|
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What are the 4 classes of motifs/folds?
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1) All α
2) All β 3) α / β (interspersed) 4) α + β (segregated) |
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Serum albumin is in all α protein, what is it's function?
|
Carries many things, regulates osmotic pressure, found in bloodstream
|
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Bacterioferritin (cytochorome b1) is an all α protein, what is its function?
|
E- carrier which binds Fe atom or cofactor
|
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How is UDP N-acetylglucosamine acyltransferase's structure critical to its function?
|
It is an all β structure (parallel) which forms long deep pockets to synthesize long lipids in.
|
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What is the purpose of Collagenase-3?
|
All β structure which looks like it has four bladed β propellers; used to get rid of collagen in places it does not belong
|
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Alcohol dehydrogenase has which kind of fold structure?
|
α/β
|
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The green fluorescent protein found in jellyfish for glowing has what kind of fold structure?
|
α +β
(β barrel w/ α parts) |
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What stabilizes quaternary structure?
|
The same factors which stabilized individual subunits (hydrophobic effects, hydrogen bonding, van der waals...)
|
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How does a protein know which way to fold?
|
** it does not randomly sample all possible conformations **
- Formation of short stretches of secondary structure - Formations of stable subdomains and domains - Some proteins have loose "molten globule" intermediate - Enzymes catalyze some steps (disulfide bond formation and proline isomerization) ** Chaperones ** |
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What are chaperones and why are they useful?
|
Large protein complexes with huge chambers which allow proteins to fold up to proper structure
|
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What ways can proteins be denatured?
|
- Heat (disrupts H-bonds and others)
- Urea (disrupts hydrophobic interactions) - pH Extremes (disrupts ionic interactions) - High [Salt] (disrupts ionic interactions) - Detergents (disrupts hydrophobic interactions) - HS-CH2-CH2-OH (mercaptoethanol, reduces disulfide bonds) |
|
What does the term "denaturation" mean?
|
Loss of activity, not loss of ALL structure; just enough loss of structure so that protein loses its function
|
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What lesson was learned from Anfinsen's experiment? How?
|
** Primary structure determines tertiary structure
- EXP: ribonuclease treated with urea and mercaptoethanol = denatured; when removed, the protein refolded precisely and regained activity = renaturation |
|
What are Ligands?
|
Molecules that are bound reversibly to a protein; transient in nature
|
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Where do ligands bind to proteins?
|
Binding sites which are complementary to the specific protein-ligand interaction
|
|
How flexible are proteins?
|
- Not rigid
- Undergo conformational changes (big or small) - Breathing - molecular vibrations |
|
What usually happens when a ligand binds to the specific binding site on a protein?
|
- Coupled with conformation change, causing an induced fit which is more complementary to the ligand
|
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How are myoglobin and hemoglobin related/similar/different?
|
Myoglobin (Mb)
- 1 subunit, MW = 16,700 - Found in muscle for oxygen storage Hemoglobin - 4 subunits (α2β2), MW = 64,500 (4x myoglobin) - Found in blood for oxygen transport |
|
What does Oxygen bind to?
|
- Transition metals: Fe2+ is suitable for reversible binding
- Found in heme |
|
Why do globins need heme / Fe2+ to bind oxygen?
|
No amino acid is suitable for reversible binding of Oxygen
|
|
Why must free iron in organisms be controlled / bound? How is this taken care of?
|
It can be very damaging to DNA and other macromolecules; It is sequestered, to make it less reactive, within a protein-bound prosthetic group called heme
|
|
When iron is sequestered in heme, what is the structure that directly surrounds the iron?
|
Porphyrin ring which prevents Fe2+ from changing to Fe3+ (does not bind oxygen)
|
|
Where is the heme located in heme-containing proteins?
|
Deep within the protein structure
|
|
The Fe2+ within the porphyrin ring has two open coordination bonds; what is attached to them?
|
1) Histidine residue - attached at N
2) Binding site for O2 |
|
Why is CO highly toxic to aerobic organisms?
|
It is coordinated to heme iron with greater affinity than O2; therefore O2 would be excluded and organism would die
|
|
What is the structure of myoglobin?
|
Single polypeptide with a heme molecule; made up of eight α-helical segments connected by bends
|
|
What is the equilibrium expression, which describes the reversible binding of a protein (P) to a ligand (L)?
|
P + L <-- --> PL
Ka = [PL] / [P][L] = 1/Kd Ka = association constant [M^-1] Kd = dissociation constant [M] |
|
What does Ka (the association constant) measure?
|
The affinity of the ligand, L, for the protein, P.
|
|
What is the Binding Equilibrium equations?
|
Θ = Binding sites occupied / Total binding sites = [PL] / [PL]+[P]
Rearranged: Θ=Ka[L] / Ka[L]+1 = [L] / [L] + Kd |
|
How does Kd related to binding?
|
Increase Kd= weaker binding
Decrease Kd= stronger binding |
|
What is the relationship when half of the binding sites are occupied, Θ=1/2?
|
Dissociation constant Kd = concentration of the ligand
|
|
What is the specific equation for ligand/protein when Oxygen is the ligand?
|
Θ = [O2] / [O2]+[O2]_0.5
[O2]_0.5 = concentration at 1/2 saturated |
|
What are the strong interactions holding hemoglobin together?
|
Strong interactions between "unlike" subunits (α to β, β to α); also hydrophobic interactions, H-bonds, and ionic pairs
|
|
Oxygen induces conformational changes in hemoglobin; what are the two states?
|
- T = "tense" - low oxygen affinity; predominates in absence of oxygen
- R = "relaxed" - high oxygen affinity - oxygen binding triggers T to R transition |
|
Why is a hyperbolic binding curve inappropriate for the binding of oxygen with myoglobin/protein that binds oxygen?
|
- If it was high-affinity, the protein would pick up oxygen well in the lungs (high pressure) but not release it in the tissues (low pressure)
- If it was low-affinity, it would be able to release the oxygen in the tissues, but wouldn't pick up much from the lungs |
|
What is the appropriate binding curve for oxygen binding to proteins (myoglobin)? Why?
|
- A sigmoid cooperative binding curve
- Lower affinity for oxygen in lower pressures (tissues) allows it to release oxygen to tissues - Higher affinity for oxygen in higher pressures (lungs) allows it to pick up oxygen in lungs |
|
What does allosteric binding refer to?
|
The binding of one ligand affects the binding of others
|
|
What is the Hill equation?
|
log (Θ / 1-Θ) = n log [L] - log (Kd)
|
|
What is plotted on the coordinates of the Hill Plot?
|
y = log (Θ / 1-Θ)
x = log [L] ((log pO2)) b = - log (Kd) m = n (Hill coefficient) |
|
What does the slope of the Hill plot represent (n)?
|
When n = 1, ligand binding is not cooperative
When n>1, positive cooperation in ligand binding |
|
There are two models of cooperative binding, what are they?
|
1) Symmetry model - subunits of a cooperatively binding protein are functionally identical; two conformations possible, all subunits undergo transition simultaneously
2) Sequential model - ligand binding can induce a change of conformation in individual subunits which increases the likelihood of nearby subunits transitioning |
|
What can hemoglobin transport besides O2?
|
H+ and CO2 (inverse of O2 binding)
|
|
What state do H+ and CO2 prefer for hemoglobin?
|
T state = tense = low oxygen affinity
|
|
What is the Bohr effect?
|
- At low pH (high H+), high CO2, affinity of hemoglobin for oxygen is low and O2 is released in tissues
- At high pH (low H+), low CO2, affinity of hemoglobin for oxygen increases and more O2 is bound for transport |
|
How does BPG affect oxygen binding?
|
Binding of BPG stabilizes the T (tense) state which decreases Oxygen binding... causing more oxygen to be released into the tissues
|
|
When does Sickle Cell Anemia occur?
|
Caused by mutation in hemoglobin (Glu to Val at pos. 6)
- Leads to fewer erythrocytes, unusual shape, weakness and pain |
|
What are three principles of enzymatic catalysis?
|
1) Enzymes effect rates, not equilibria
2) Enzyme-transition state complementarity 3) Many parts of a substrate contribute |
|
What are Ribozymes involved in?
|
- Mainly in RNA metabolism
- Exception: synthesis of proteins on ribosomes |
|
What is a prosthetic group?
|
A coenzyme or metal ion that is very tightly or even covalently bound to the enzyme protein.
|
|
Where do enzyme-catalyzed reactions take place?
|
Active Site
- analogous to ligand binding site (except that a reaction is facilitated) - usually a cleft or pocket on the enzyme, lined w/ amino acid residues and cofactors positioned to optimally facilitate reaction |
|
How is the standard free-energy change in biochemistry regulated?
|
pH = 7
|
|
What is binding energy used for?
|
- Entropy reduction - hold substrates in proper orientation to react
- Desolvation - replace H-bonds to H2O - Strain - facilitates any geometric or electrostatic distortion required - Induced Fit - bring reactive groups on enzyme into proper orientation for catalysis |
|
What is heterolytic cleavage? Homolytic?
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E- pair ends up entirely on one atom (most often)
E- pair split between two atoms to produce radicals (very reactive) |
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What is the most common reaction?
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Proton transfer
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What are cofactors?
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Groups or molecules (other than AA residues) which are important to catalysis
i.e., metals (metalloenzymes), coenzymes (from vitamins) |
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What is an enzyme without a prosthetic group? With?
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W/O: Apoenzyme
W/: Holenzyme - active |
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What are metals used for in enzymes?
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Metals bind to substrate to orient them; mediate redox rxns; electrostatic shielding or stabilization of neg. charge
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What does Mg2+ do for ATP?
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Shields the negative charges; very highly charged is not ideal biologically, hard to go through membranes...
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How do covalent catalysts occur?
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- Formation of covalent complex w/ nucleophilic attack
- Catalyst must be linked to substrate transiently |
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What are some requirements of covalent catalysts?
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- Catalyst (imidazole) must be better nucleophile than acyl acceptor (H2O)
- Intermediate must be more reactive than substrate - Intermediate must be less stable than product |