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Biochem Exam 2
| Question | Answer | Reasoning |
|---|---|---|
| Alanine single letter notation | A | |
| Arganine single letter notation | R | |
| Asparagine single letter notation | N | |
| Aspartate/Aspartic Acid single letter notation | D | |
| Cysteine single letter notation | C | |
| Glutamate/Glutamic acid single letter notation | E | |
| Glutamine single letter notation | Q | |
| Glycine single letter notation | G | |
| Histidine single letter notation | H | |
| Hydroxyproline single letter notation | O | |
| Isoleucine single letter notation | I | |
| Leucine single letter notation | L | |
| Lysine single letter notation | K | |
| Methionine single letter notation | M | |
| Phenylalanine single letter notation | F | |
| Proline single letter notation | P | |
| Pyroglutamatic single letter notation | U | |
| Serine single letter notation | S | |
| Theronine single letter notation | T | |
| Tryptophan single letter notation | W | |
| Tyrosine single letter notation | Y | |
| Valine single letter notation | V | |
| AAs with large molecular weight | Glycine, Alanine, Serine | |
| AAs with small molecular weight | Arganine, Phenylalanine, Tryptophan | |
| Hydrophobic AAs | Alanine Isoleucine Leucine Phenylalanine Proline Valine | |
| Hydrophillic AAs | Glycine (kinda, but not really) Arginine Asparagine Aspartic acid Cysteine Glutamic acid Glutamine Histidine Serine Threonine | |
| Amphipathic AAs | Lysine Methionine Tryptophan Tyrosine | |
| What "drives" protein folding? | Hydrophobicity | Because the hydrophobic wants to band together to keep dry within middle of protein |
| Which AAs are negative at pH 7 | Acids, Aspartic and Glutamic-Acid | COO- within side chains |
| Which AAs are positive at pH 7 | Histidine (partially), Lysine, Arginine | NH+/NH2/NH3+ wihtin side chains |
| Which AAs are important for metal coordination? | Aspartate & Glutamate | |
| Which AAs are aromatic? | Phenylalanine, Tyrosine, Tryptophan | |
| What isomer of AAs occur naturally? | L/S | |
| Which AAs have 2 chiral centers? | Isoleucine and Theronine | |
| Which AA is the only R? | Cysteine | |
| Which AA has an Sulfahydro group in its side chain? | Cysteine | |
| Which AA has a Sulfide group in its side chain? | Methionine | |
| What are the AAs human synthesize (non essential AAs)? | Alanine Aspartate Glutamate Asparagine Glutamine Serine Glycine Proline Cysteine Tyrosine | |
| Which AAs are essential? | Theronine Valine Isoleucine Leucine Lysine Methionine Arginine histidine Phenylalanine Tryptophan | |
| What is the avg pKa of AA carboxyl groups? | 2 | |
| What is the avg pKa of AA amine groups? | 9 | |
| Isoelectric point | pH where molecule has a net charge of 0 | |
| pH>pI | (-) charge | |
| pH<pI | (+) charge | |
| How can pI be calculated? | (pK1 + pK2)/2 | |
| what is the pKa of an AA with a β-carboxyl group in its side chain? (Aspartic Acid) | 3.9 | |
| What is the pKa of an AA with a 𝛾-carboxyl group in its side chain? (like Glutamic Acid) | 4.3 | |
| What is the pKa of the side chain in an AA with an imidazole group in its side chain? | 6 | |
| If pH<pKa which dominates, conj base or conj acid? | conj acid | |
| If pH>pKa which dominates, conj acid or conj base? | conj base | |
| What are imidazole groups good for in AAs? | stacking and distributing charges | |
| What is the pKa of the side chain in an AA with a Sulfhydryl like Cysteine? | 8.3 | |
| What is the pKa of the side chain in an AA with a phenolic OH group like Tyrosine? | 10.1 | |
| What is the pKa of the side chain in an AA with a ε-amine, like Lysine? | 10.5 | |
| What is the pKa of the side chain in an AA with a guanidino group, like Arginine? | 12.5 | |
| What is the pKa of the side chain in an AA with a hydroxy group, like Serine or Theronine? | ~13 | |
| Waht is the formula for calculating pI of an AA with an Acidic side chain? | (pK1 + pK2)/2 | |
| What is the formula for calculating pI of an AA with a Basic side chain? | (pK2 + pK3)/2 | |
| What influences pKa values of side chains in AAs? | environment | residues, groups, solvent accessibility, etc |
| What AAs are rarely seen in proteins or organisms? | Selecocysteine and Pyrrolysine | |
| What AAs are not found in proteins but act as NTs? | GABA, Epinephrine, Histamine, Serotonin | |
| What rare modified AAs are found in connective tissue proteins? | Hydroxylysine and Hydroxyproline | |
| What rare modified AAs are found in blood-clotting proteins? | Carboxyl-glutamate | |
| What rare modified AAs are found in bacteriorhodopsin? | Pyroglutamate | |
| How many residues make up a Dipeptide? | 2 | |
| how many residues make up a Tripeptide? | 3 | |
| How many resudes make up a Oligopeptide? | 10/12-20 | |
| How many resides make up a Polypeptide? | <50 but >20 | |
| How residues make up a Protein? | 50+ | |
| Proteins with a single polypeptide chain are... | Monomeric | |
| Proteins with more than one polypeptide chains... | Multimeric | |
| Proteins with one kind of polypeptide chain are... | Homomultimers | |
| Proteins with 2+ kinds of polypeptide chains are... | Heteromultimers | |
| What are the protein classifications based on general shape? | Fibrous and Globular | |
| Proteins with a Fibrous shape are usually | Strucutral proteins, ex: collagen, elastin, and keratin | |
| Proteins with a Globular shape are usually | Cytosolic enzymes | |
| What are the protein classifications based on general solubility? | Soluble and Insoluble | |
| Where are hydrophobic AAs located in soluble proteins? | (usually) inside | |
| Where are hydrophobic AAs located in insoluble proteins, like membrane proteins? | outside | |
| What are hydrophobic AAs in insoluble proteins soluble in? | detergents | |
| What defines a proteins primary structre? | AA sequence | |
| What definnes a proteins secondary structure? | local structues (α-helices and β-sheets) | |
| What is a proteins tertiary structure? | overall 3D shape | |
| What defines a proteins quaternary structure? | subunit or chain interactions into oligomers | |
| In solution, are proteins dynamic or static? | dynamic | |
| What factors influence a proteins solubility? | pH and ionic strength | |
| When are proteins least soluble? | at pI | b/c net charge is 0 and salt in salting in or out is ionic (charged) |
| What is salting in? | protein purification process where low [salt] increase solubility of charged proteins | due to reduction in charge-charge interactions |
| What is salting out? | protein purification process where high [salt] decrease solubility | salt competes for water which is needed to solvate the protein |
| How can salting in or salting out help purify a protein? | adding right concetration of ammonium sulfate can cause contaminants or molecule of interest to precip out of soln | |
| What is S100 fraction/ S100 proteins? | solubility in 100% ammonium sulfate at neutral pH | 226 |
| SKIPPED TO LAST PART OF CHAPTER 5 | GO BACK LATER | OR DONT... |
| What are homologous proteins? | proteins with similar sequences | |
| What are orthologous proteins? | proteins with similar sequences and from different species | ancesteral gene |
| What are paralogous proteins? | proteins with similar sequences from the same species? | gene duplication |
| What is BLAST? | Basic Local Alignemnt Serach Tool | aka national database of protein sequences |
| After sequencing a protein how can it be aligned in the right order? | BLAST | |
| What does sequence similarity of proteins imply? | evolutionary relation | |
| What are conserved residues in a BLAST report? | blue, same sequences | |
| What are similar residues in a BLAST report? | yellow, similar sequences | |
| T/F: all proteins with similar strucutral features carry out the same/similar function | F | proteins with similar structures can carry out different OR similar functions Proteins with different srtuctures can also carry out same or different funcitons |
| What angle is Cα-N called? | Phi, φ | |
| What angle is Cα-C called? | Psi, ψ | |
| How many DoF do peptide backbones have? | 2, Psi and Phi | |
| How are rotations viewed from Cα in peptide backbones? | starting at 0, positive values are clockwise | |
| What DoF angels arent possible? | φ = 0°, ψ = 180° φ = 180°, ψ = 0° φ = 0°, ψ = 0° | due to steric hinderence |
| What AA has a fixed Phi angle of -60? | Proline | |
| What type of interactions provide dynamic stability? | weak interactions | if proteins had covalent bonds they wouldnt be able to move in soln and would be mostly static |
| Where do ionic bonds occur in proteins? | surface | |
| Were do H-bonds form in proteins? | whereever possible | strognest "weak force", add more stabilty without hindering dynamic abillity of proteins |
| What happens to H-bonding groups located within the hydrophobic core of a protein? | secondary structure neutralizes charge/polarity | |
| What are the types of secondary structures? | Helices, β-sheets, β-turns, and random coil | |
| What are the types of supersecondary structures? | Coiled coils, β-hairpins, β-α-β, Helix-turn-Helix, Greek keys, α-α hairpin, EF hand, etc | |
| α-Helices have how many residues per turn? | 3.6 | |
| What are the DoF in an α-helix? | φ = −60° ψ = −45 to -50° | |
| What is the diameter of an α-helix? | 6 Å | |
| What is the pitch/rise of an α-helix? | 5.4 Å or 1.5 Å /residue | |
| What is the average # of residues per α-helix? | 10 | |
| α-helix are almost always ____ handed? | right-handed | due to sterics, close approach of side chains in L-AAs |
| Why are left-handed α-helix shorter? | contain Glycine | close approach of Carbonyl oxygen and β-carbon |
| H-bonds in an α-helix point in what direction? | same | gives δ+ charge at Amino end, and δ- carboxyl end |
| Which AAs can break α-helices? | Glycine and Proline | Proline is kinky, Glycine breaks helix in secondary structure interactions |
| Helical Wheel | reveals polar/non-polar characteristics of helices | |
| Where are amphipathic helices often found? | proteins surface | |
| Where are non-polar residues (of helices) often found? | core | |
| What are the other types of "non-α-helices"? | pi and 3_10 helices | |
| Where do H-bonds form on β-sheets? | between C=O and N-H residues on differetn strands | |
| What do β-sheet/strands form on polypeptides? | different regions | |
| What type of β-sheet have bent H-bonds? | Parallel | |
| What type of β-sheet have straight H-bonds? | Anti-parallel | |
| Which β-sheet is more favorable anti-parallel or parallel? | Anti | distance of H-bonds play role in (stability?) straight line< diagonal line |
| What gives β-sheets their zig-zag structure? | Cα are slightly above or below plane, and sidecahins projecting upward or downward | |
| What are the DoF in Parallel β-sheets? | φ = −120° ψ = 105° | |
| How many strands do Parallel β-sheets have? | 5+ | |
| Where are hydrophobic sidechains located in Parallel β-sheets? | both sides of plane, non alternating | |
| What are the DoF in Anti-parallel β-sheets? | φ = −135° ψ = 140° | |
| How many strands do Anti-parallel β-sheets have? | <5 | |
| Where are hydrophobic sidechains located in Anti-parallel β-sheets? | one side, alternating | |
| What is the rise/pitch of Anti-parallel strands of β-sheets? | 3.47 Å or 0.695 Å/2 residue | |
| What is the rise/pitch of Parallel strands of β-sheets? | 3.25 Å or 0.65 Å/2 residue | |
| How long are each strand of β-sheets? | 5-10 residues | |
| T/F: β-sheets can be mixed parallel and anti-parallel | T | |
| β-sheets often have a _____-handed twist | right | |
| What are Topology diagrams useful for? | comparing structures | |
| What do β-turn allow proteins to do? | reverse direction | |
| What is a β-turn? | Carbonyl Carbon of residue 1 is H-bonded to Amide proton of residue 4 (3 away from start) | |
| What are the types of β-turns? | Type 1 and Type 2 | |
| What directions do Type 1 and 2 β-turns correlate with? | Type 1=left Type 2=right | |
| Which type of β-turns is more common? | Type 1 | |
| What AAs are prevalent in β-turns? | Proline and Glycine | |
| What do β-turns promote? | formation of anti-parallel β-sheets | |
| What can be thought of as a "3 residue, 0 pitch helix" | β-turns | |
| What are the DoF for Type 1 β-turns? | φ+1=-60, ψ+1=-30 or φ+2=-90, ψ+2=0 | |
| What are the DoF for Type 2 β-turns? | φ+1=-60, ψ+1=120 or φ+2=80, ψ+2=0 | |
| What are helices and strands conencted by? | Random coils | |
| What is a Random coil? | loops conneting secondary structures that are not random nor coiled | |
| Why are random coils called random? | no recurring bonding patterns | |
| Where are random coils usually located? | protein surface | to connect things, participate in bind events |
| What are random coils abundant in? | charged and polar residues | C=O and N-H form H-bonds with water |
| T/F: Random coils are flexible | T | |
| What are super-secondary protein structures ? | β-hairpins, β-α-β motif, Coiled coil | |
| What is a β-hairpin? | 2 adjacent anti-parallel strans joined by a 2-5 reside loop | |
| What is a β-α-β motif? | 2 adjacent parallel strands connected by an α-helix that is usually above the β-plane | |
| What is a Coiled coil? | 2 helices wound around each other in a supercoil or super-helix | ex: DNA |
| Define α-Keratin | fiberous protein found in hair, fingernails, claws, horns, and beaks | 303 |
| What combine and make protein domains? | Secondary and supersecondary structures, | |
| What is a protein domain? | (full or part ) polypeptide chain that folds into stable tertiary structures in aq soln | hydrophobicity drives folding, weak forces like VDW and h-bonds allows dymanic ability |
| How long is a domain AA sequence? | less than 250 | |
| Unlike supersecondary structures, what do domains have? | associated function(s) | a single domain can have multiple functions w/one protein and/or other domains |
| What combine to make multi-domain proteins? | domains | |
| T/F: larger proteins (usually) have larger domains | F | Larger proteins usually have more domains rather than larger |
| What % of domains re-occur in different proteins? | 90 | |
| What does SCOP stand for? | Structural Classification of Protiens | |
| What is SCOP based on? | manually curated evolutionary and structural relationships among known proteins | |
| What is CATH? | Class, Architecture, Topology, Homologous superfamily | |
| How do CATH and SCOP differ? | combines manual analysis with quantative algorithmic analysis | |
| What is the SCOP hierarchy (descending) | Class Fold Superfamily Family Domains | |
| What is the CATH hierarchy (desceding) | Class Architecture Topology Homologous Superfamily Sequence Family Domain | |
| What arre the four major classes of protein structure? | α, β, α/β, and α+β | |
| What are created with/in quarternary protein structures? | catalytic and regulatory sites | |
| Where are catalytic and regulatory sites created within quaternary protein strucutres? | subunit interfaces | |
| What is Cooperativity between protein quaternary structures? | conformational changes of one catalytic site affects another? | idk the definition |
| What is Anfinsen's Classic experiment? | used a protein to refold itself | |
| What genreal understanding about proteins did Anfinsen's experiment give rise to? | All of the information necessary for folding the peptide hain into its native structure is conteained within the primary AA strucutre of the peptide | |
| What treatment can unfold Ribonuclease? | urea and β-Mercaptoethanol (MCE) | |
| What does stable folding maximize in proteins? | max # of weak interactions | |
| When proteins what is exposed and what is burried? | Polar residues are exposed and hydrophobic residues are burried | |
| What do exposed polar residues interact with? | solvent waters | |
| What is the Protein Folding Energy Landscape? | Funnel theory for folding process of proteins | many unfolded states at the top/rim that fold into fewer possibilites of lower energy |
| Why do proteins fold? (besides hydrophobicity) | to have favorable free energy (Enthalpy driven) | |
| What is the range of ΔG for protein folding? | (-)20- (-40) kJ/mol (SMALL) | |
| What does microcalorimetry of protein unfolding suggest? | favorable Enthalpy change is the principle contributor to folding | |
| T/F: Proteins are marginally stable and dynamic | T | |
| What protein is affected by Alzheimers Disease? | β-Amyloid peptide | |
| What protein is affected by Familial amyloidotic polyneuropathy Cancer? | p53 | |
| What protein is affected by Creutzfeldt-Jakob disease? | Prion | |
| What protein is affected by Hereditary empthysema? | α1-Antitrypsin | |
| What protein is affected by Cystic fibrosis? | CFTR (CF transmembrane condunctance regulator) | |
| What is protein denaturation? | loss of proteins structure and function | |
| What is the Tm at which a protein is unfolded? | temperature at which 50% is unfolded | |
| What are molecular chaperones? | help proteins fold by preventing extracellular inappropriate liaisons | |
| Where are chaperones found? | all cells | |
| How do chaperones work? | prevent intermolecular nonproduictive interactions between hydrophobic sequences until productive folding interactions can occur | |
| What do chaperones recogonize? | Hydrophibic residues | |
| What drives folding through the hydroplysis of ATP? | chaperones | |
| What is another name for chaperones? | Heat-shoch proteins (HSPs) | |
| When are HSPs upregulated? | when cells are exposed to heat | |
| What are the Chaperonins? | Hsp70 and Hsp60 | |
| What are the principle chaperones? | Hsp-60,70 and 90 | |
| What are Nascent proteins and how do they interact with ribosome-associated chaperones? | newly made undolfed proteins that are passed to Hsp70 | |
| What are the protein folding pathways? | 1) Chaperone-independant 2)Hsp70 assisted 3) Hsp70 and Chaperonin complex assisted | |
| What is Hsp70 called in bacteria? | Dnak | |
| What are the domains of Hsp70? | ATPase and Peptide binding | |
| What is the Anfinsen cage? | partially enclosed space where Hsp60/Chaperonins/GroES-GroEL keep partially folded proteins | |
| What is GroES-GroEL? | Chaperonin complexes that force unfodling and then folding to bury hydrophobic residues, driven by ATP | |
| What does ΔG tell us about a reaction? | favorability/ thermodynamic potentiality | |
| What do the kinetics of a reactions tell us? | speed at which a favorable reaction occurs | |
| Why are enzymes important to kinetics? | accelerate reaction rates | |
| What are usually proteins but can also be ribozymes, and speed up rxn rates? | Enzymes | |
| How do enzymes work? | bind substrate through weak interactions to active site | |
| At the active site, what influences enazyme mechanism? | protonation of key AAs | |
| To what degree to enzymes accelerate reacations compared to no catalyzation? | 10^21 | |
| What is the normal rate of rxns? | 10^9 to 10^20 | |
| What is ezyme specificity? | enzymes bind specific substrates and catalyze specific rxns | |
| Where does enzyme specificity come from? | structural determinants at the active site | |
| What are the characteristics of enzymes? | 1) Catalyze thermodynamically favorable rxns causing them to accelerate 2) Specificity 3) Regulated agents of metabolism | |
| What is the catalytic power of Urease? | 1x10^14 | 3x10^(-)10 to 3x10^4 |
| What are the 6 classes of Enzymes? | Oxidoreductases Transferases Hydrolases Lysases/Synthases Isomerases Ligases/Sinthetases | |
| What are the important subclasses of Oxidoreductases? | Dehydrogenases, Oxidases, Peroxidases, Reductases, Monooxygenases, Dioxygenases | |
| What are the important subclasses of Transferases? | C-Transferases, Glycosyltransferases, Aminotransferases, Phosphotransferases | |
| What are the important subclasses of Hydrolases? | Esterases, Glycosidases, Peptidases, Amidases | |
| What are the important subclasses of synthases? | C-C, C-O, C-N, C-S Lyases | |
| What are the important subclasses of isomersases? | Epimerases, cis-trans isomerases, Intramolecular transferases | |
| What are the important subclasses of Ligases? | C-C, C-O, C-N, C-S Ligases | |
| How do Synthases and Synthetases differ? | Synthetases are ATP coupled reactions | |
| What is an Apoenzyme? | protein part of enzyme | |
| What is a Holoenzyme? | protein part of enzyme + cofactors | |
| What is a Cofactor? | non-protein part of enzyme that is essential for catalytic f(x) | |
| What is a Coenzyme? | non-protein molecule | |
| What is a Substrate? | compound(s) whose rxn are catalyzed by enzymes | |
| What are active sites? | specific portion of enxyme where the substrate bind during a rxn | |
| What enzymes require Fe2+ or Fe3+? | Cytochrome oxidase, Catalase, Peroxidase | |
| What enzyme requires Cu2+? | Cytochrome oxidase | |
| What enzyme requires Zn2+? | DNA polymerase, Carbonic anhydrase, Alcohol dehydrogenase | |
| What enzymes require Mg2+? | Hexokinase, G6P, Pyruvate kinase | |
| What enzyme requires Mn2+? | Arginase | |
| What enzyme requrie K+? | Pyruvate Kinase | |
| What enzyme requires Ni2+? | Urease | |
| What enzyme requires Mo? | Nitrate reducatase | |
| What enzyme requires Se? | Glutathionse peroxidase | |
| What are Ribozymes? | segments of RNA that display enzyme activity in absense of a protein | |
| What are the kinects of a rxn with no enzyme? | A -> P, v=k[A] | |
| What are the kinetics of a rxn with an enzyme? | A+B->P, v=k[A][B] | |
| What is the the Michaelis-Menten eqn for an enzyme catalyzed rxn? | S + E <--> ES -> E + P | |
| What step of the Michaelis-Menton eqn is reversible? | K1/K-1, K2 is irreversible | |
| What step of the Michaelis-Menton eqn is faster? | K1/K-1 | |
| In reagrds to the Michaelis-Menton eqn, what is the rapid equilibrium assumption | K1 & K-1 >> K2 | |
| What are the assumptions for the Michaelis-Menton eqn? | So>>E, Po=0, and K2 is the rate limiting step | |
| Michaelis-Menton eqns/model | v = k2[ES] 2. [E]total = [E] + [ES] (No EP) 3. Keq = [E][S]/[ES] = k-1/k1 = KS = 1 /Ka (Describes relative amounts of E, S and ES) | |
| What are the exception to the Michaelis-Menton model? | allosteric enzymes | |
| What is the 1/2 point of Vmax? | Km, Michaelis-Menton constant | |
| What generalization/assumption was made in the Briggs & Haldane? | ES quickly reaches a constant value | [S][E]K1=[ES](k2+k-1) |
| What is Km? | [S][E]/[ES]=(k2+k-1)/k1, substrate concentration at half Vmax | |
| Briggs and Haldane eqns/model | 1. v = k2[ES] 2. [E]total = [E] + [ES] 3. [S][E]/[ES] = (k2 + k-1)/k1 = Km | |
| In the Briggs and Haldone model, what is Km when k-1>>k2? | Ks | |
| What is Vmax? | When E is completey bound to S ([S] is at saturation), Vmax=k2[Et] | |
| Memorize | v=(Vmax[S])/(Km + [S]) Vmax=k2[Et] Km=(k-1+k2)/k1 | |
| What is Kcat? | turnover number, # of substrate molecules converted to product per enzyme molecule per unit of time (WHEN E IS SATURATED WITH SUBSTRATE) | |
| What is the Kcat of a "perfect enzyme"? | diffusion rate/limit | |
| What is Kcat when the Michaelis-Menton model applies? | k2 | |
| Waht is the catalytic efficiency? | Kcat/Km, estimate of how perfect an enzyme is | |
| What does the catalytic efficiency measure? | how well an enzyme perfroms when S is low | |
| What would the catalytic efficiency need to be for an enzyme to be considered a perfect ensyme? | 10^8 to 10^9 M-1sec-1 (upper limit) | |
| What does v approach when [S]>>Km? | Vmax | |
| what order kinetics would a rxn follow when [S]<<Km? | 1st order | |
| What is the Lineweaver-Burk plot? | 1/v=(Km/Vmax)/(1/[S])+ (1/Vmax) | |
| What are the types of Enzyme inhibition? | Reversible and Irreversible | |
| What is an inhibitor? | any natural or synthetic ligand that decreases the speed of an enzyme-catalyzed rxn | |
| How do reversible inhibitors inhibit? | recersible binding to one or more of the enzyme forms present during the rxn | |
| What is a competitive inhibitor? | inhibitor that competes with the substrate for the same site on enzyme | |
| What do competitive inhibitors reduce? | [ES]... v b/c v=k2[ES] | |
| How can competitive inhibitors be overcome? | high [S] | |
| How do competitive inhibitors affect Vmax and Km? | increases Km (shifts to right), and doesnt affect Vmax | Km=x-intercept |
| What do sulfonamides competitively inhibit? | DHPS (Dihydroteroate synthase) | |
| What is DHPS substrate? | PABA | |
| What does DHPS synthesize? | THF (Tetrahydrofolate) | |
| How does Methanol interact with the liver? | converted into formaldehyde by alcohol dehydrogenase | |
| How is methanol poisoning treated? | Ethanol | ethanol competes with methanol for binding to alcohol dehydrogenase, slows prod of formaldehyde |
| How is antifreeze poisoning treated? | Ethanol | |
| What are the types of non-competitive inhibitors? | pure and mixed | |
| What is Pure non-comp inhibition? | EI and IES have equal affinity, binding of Inhibitor does not influence binding of Substrate | KI=K'I |
| How does pure non-comp inhibition affect Vmax and Km? | Reduces Vmax (shifts upwards), doesnt affect Km | as if [E] was reduced |
| What is Mixed non-comp inhibition? | Inhibitor binding influences substrate binding | KI≠ K'I |
| How does mixed non-comp inhibition affect Vmax and Km? | reduced Vmax, increases OR decreases Km | Km increase= left shift Km decrease= right shift |
| What is uncompetitive inhibition? | Inhibitor combines with ES complex, reduces k2 | |
| How does uncomp-inhibition affect Vmax and Km? | decreases Vmax and Km at same rate, slope is unaffected | |
| What is the net effect of Irrebersible inhibition? | loss of [E] | |
| What are suicide subdtrates? | irreversible inhibitors that bind to enzyme unitil death | |
| What type of inhibitor is Penicillin an example of? | irreversible | |
| What do Organophoshates, Parathion insecticides, and Sarin nerve gas all have in common? | ACHEs | |
| What are bisubstrate reactions? | reactions involving 2+ substrates | |
| What are the 2 types of bisubstrate reactions? | single displacement and double displacement | |
| What are the types of single displacement reactions? | random and ordered | |
| What % of biochemical reactions are bisubstrate reactions? | >60% | |
| What is a single displacement rxn? | both substrates bind to the enzyme before products are formed | |
| What is the rate limiting step in single displacement rxns? | AEB (substrate 1&2 + Enzyme) -> PEQ (products+ Enzyme+ excess substrate?) | what does Q stand for? |
| Creatine Kinase, and most kinases, have a mechanism that is an example of... | random single displacement | |
| In an ordered single displacement rxn, when does substrate B bind? | AFTER substrate A has bound to E | In random single displacement B or A can bind first or at same time. |
| What does a single displacement bisubstrate curve resemble? | noncomp inhibitors | |
| In a single displacement bisubstrate curve, what does increased [B] casue? | decrase Vmax and Km at same rate? | |
| What is a double displacement rxn? | two substrates bind and react seperately in ping-pong manner, aka Burst kinetics | Substrate 1 is released prior to substrate 2 binding, puts enzyme in a primed state |
| What is an Enzyme when primed in a double displacement rxn? | covalently modified enzyme intermediate | |
| What does a double displacement bisubstrate curve resemble? | uncomp inhibiton | |
| What is the Glutamate-> Aspartate with aminotransferase rxn an example of? | double displacement bisubstrate mechanism | |
| What does a Lineweaver-Burk plot distinguish about bisubstrate rxns? | if rxn mech is single or double displacement | |
| What does a substrate binding assay determine about bisubstrate rxn? | ordered or random | |
| How could Exchange rxns distinguish a bisubstrate rxn? | attempting reverse rxn in absence of one substrate can distinguish if double or single | double displacement allows rxn, single woudlnt |
| What is an example of Exchnage reactions? | Sucrose phosphorylase and Maltose phosphorylase both cleave disaccharides to add Pi to one product | surcose rxn=double maltose rxn= single |
| What is a tranition state? | high energy, short lived and unstable configuration of reactants, somewhere along the rxn timeline | |
| Are transition states intermediates? | no | |
| T/F: transition states have high ΔG and 1+ partial bond | T | |
| How is the rxn rate related to [X‡]? | proportional to the reactant molecules that transition | |
| What do enzymes do to the ΔG of transition states? | lowers | |
| How do enzymes lower free energy? | binding to transition state more tightly than substrate | Induced fit model>>lock & key |
| What is catalysis? | enzyme catalyzation process | |
| Why does X‡ need to be more stable than substrate? | decreased ΔS due to formation of ES complex increases the natural binding energy of ES | |
| How is ES destabilized? | strucutral strain, desolvation, or electrostatic effects | |
| Why does structural strain of ES occur? | induced fit binding favoring the formation of X‡ | lock and key model explains specificity but induced fit is more accurate |
| How does desolvation destabilize ES? | charged gourps on substrate are desolvates (moved/displaced) to make substrate and enzyme rxn more reactive and likely to occur | |
| Hoe do electrostatic effects destabilize ES? | Unfavorable interaction between like charges on substrate and enzyme | both have same charge and become unstable after binding |
| How are Keq and ΔGrxn affected by enzymes? | not changed, only activation energy (ΔG‡) is lowered. the speed of which Keq is obtained is increased | |
| To what degree do enzymes increase the speed of which Keq is obtained? | 10^7 to 10^14 | |
| What is the enzemyatic effeciency of Fructose-1,6-biphosphate? | 10.5x10^21 | |
| What is the enzemyatic effeciency of β-amylase? | 7.2x10^17 | |
| What is the enzemyatic effeciency of Staphylococal nuclease? | 1.4x10^17 | |
| What is the enzemyatic effeciency of Alkaline phophatase? | 1.4x10^16 | |
| What is the enzemyatic effeciency of Urease? | 1.0x10^14 | |
| What is the enzemyatic effeciency of Chymptrypsin? | 1.0x10^12 | |
| What is the enzemyatic effeciency of Hexokinase? | >1.3x10^10 | |
| What is the enzemyatic effeciency of Alcohol dehydrogenase? | >4.5x10^6 | |
| What is the enzemyatic effeciency of Carbonic anhydrase? | 1.0x10^7 | |
| What is the enzemyatic effeciency of Creatine Kinase? | >1.33x10^4 | |
| What are TSAs? | Transition State Analogs, stable molecules that are chemically and structurally similar to X‡ | |
| What do TSAs act similar to? | comp inhibitors | thus making good drugs |
| Why would TSAs bind better than comp inhibitors? | because structurally similar to X‡ and X‡ are bound more tighly than substrate | |
| What do Pyrrole-2-carboxylate and Δ-1-Pyrroline-2-carbocylate mimic? | Planar X‡ of Proline racemase rxn | |
| In the yeast adolase rxn, what molecule mimics the enediolate transition state? | Phosphoglycolohydroxamate | |
| What TSA drugs lower blood pressure? | Enalapril and Aliskiren | |
| What are Statins TSA inhibitors of? | HMG-CoA reductase | |
| What do Statins do? | lower serum choslesterol | |
| What are Protease inhibitors drugs for? | AIDS | |
| What TSA is a pesticide target? | Juvenile hormone esterase | |
| What TSA is a viral neuraminidase inhibitor? | Tamiflu | |
| What is Neuraminidase? | major glycoprotein on influenze virus membrane envelope | |
| What are glycoproteins essential for? | help virus stuck to cells to aid infection and replication | |
| What is influenza? | endemic illness taht affects 5-15% of earths population, resulting in ~500,000 death anually | |
| What are the mechanisisms of Catalysis? | 1) proximity/ near-attack complexes 2) covalent 3) General acid-base 4)metal ion 5) low barrier H-bonds ? | |
| What is catalysis by proximity? | Enzymes bring/become close enough to substrates and at the right angle/orientation so that collision between the two occur at higher frequency | |
| What is NAC? | near-attack complexes, pre-orginization of bonds into simmilar/same angle fromed in X‡ | |
| How are NACs characterized? | reacting atoms within 3.2 Å and angle of ±15° | angle is within 30° of that formed in X‡ |
| T/F: Alcohol dehydrogenase is a NAC? | T | |
| Why is protein motion/movement essential to enzyme catalysis? | active site Δconformation can; assist substrate binding, position catalytic groups, Induce NACs, assist bond break/make, assist subtrate conversion to product | |
| What is covalent catalysis? | active site residues or prosthetic groups temporariliy from covalent bond with substrate | |
| What are prosthetic groups? | organic molecules assisting w/f(x) | |
| What does covalent catalysis facilitate? | e- transfer | |
| When does covalent catalysis occur? | often due to nucleophilic attk by AA-R chain on electrophilic substrate groups | |
| What kind of rxn is Trysin+papain? | Nucelophilic attk | |
| What do Trypsin and Chymotrypsin react with to from the covalent intermediate Acyl-Ser? | Serine | |
| What does Glyceraldehyde-3-P dehydrogenase react with to from the covalent intermediate Acyl-Cys? | Cysteine | |
| What does Phosphoglucomutase react with to from the covalent intermediate Phospho-Ser? | Serine | |
| What do Phosphoglycerate mutase and Succinyl-CoA synthetase react with to from the covalent intermediate Phospho-His? | Histidine | |
| What do Aldolase and Pyridoxal phosphate enzymes react with to from the covalent intermediate Schiff base? | Lysine (and other amino groups) | |
| What is general acid-base catalysis? | transfer of a proton in the X‡ | |
| What are the AAs that can interact in a general acid base catalysis rxn? | Glu, Asp, or His | positively charged AAs |
| What does general acid-base catalysis facilitate? | proton transfer | |
| What can proton transfer in X‡ casue? | 1)Nucleophile activation 2)Stabilization of charged groups 3)Stabilization of TS thorugh improved electrostatic interactions | |
| T/F: H20 can act as an acid or base in acid-base catalysis? | T | |
| What AAs within active sites create catalytic agents when pKa is shifted? | Histidine Cysteine Asparagine Arginine Glutamate Lysine Tyrosine Serine Theronine Apartate Glutamine | |
| How can other residues wihtin the active site function in secondary roles (those that dont act in acid-base catalysis)? | 1) Raising or lowering pKa 2) Orient catalytic residues 3) Change charge stabilization 4) Proton transfer vis H tunneling | |
| What is metal ion catalysis? | metal ions lose charge easliy and exist as cations | |
| What orientation does Zn like? | planar geometry | |
| How does metal ions existing as cations assist catalysis? | 1) stabilize transient and intermediate structures 2) assist forming strong nucleophilic species 3) hold substrate inside active site 4) stabilize charge | |
| What are LBHBs? | Low-Barrier H-Bonds, Oxygens are equally distanced from H allowing H-bonds to be stronger | |
| How do LBHBs assist catalysis? | When formed energy is released and can be recycled | |
| What are Trypsin, chymotrypsin, elastase, Thrombin, Subtilisin, Plasmin, Tissue plasminogen activator examples of? | Serine Proteases | |
| What are Trypsin, Chymotrypsin, and Elasetase? | digestive enzymes secreted as proenzymes/zygogens | |
| What is Thrombin? | serine proteases in blood clotting cascade | |
| What is Subtilisin? | bacterial serine protease (enzyme) | |
| What is Plasmin? | serine protease taht cleaves fibrin polymers of blood clots | |
| What is Tissue plasminogen activator? | serine protease that cleaves plasmin proenzyme pasminogen | |
| What is Tissue plasminogen activator prescribed for? | prevent heart attacks | |
| What is ACHE? | enzyme that breaks down ACh, mechaninstically similar to pretease | |
| What AAs does Trysin cleave? | Carbonyl of Arg or Lys | |
| What AAs does Chymotrypsin cleave? | carbonyl of aromatics, Phe or Tyr | |
| What AAs does Elastase cleave? | carbonyl of small neutral residues | |
| When wouldnt Trypsin cleave an Arg or Lys? | if followed by Proline | |
| What is the catalytic traid? | Ser195, Asp102, and His57 | |
| T/F: Trypsin, Chymotrypsin, and Elastase are structually different but mechanicistically similar | F | similar structure and mech |
| How does the nature of a substrate binding pocket determine specificity? | Trypsin= negatively charged pocket Chymotrypsin= hydrophobic pocket Elastin=shallow pocket | |
| What is useful about nitrophenlate in Chymotrypsin kinetics? | absorbs at 400nm | |
| When chymotrypsin is assayed, what is observed? | burst kinetics | suggest fast 1st step and 2nd slow step |
| What region of serine proteases display burst kinetics? | C-terminal | |
| What is Acyl-enzyme intermediate an intermediate of? | Serine proteases kinetics | |
| What is the slow step of serine proteases kinetics? | hydrophilic attack on Acyl-enzyme intermediate | |
| What is P2 in Serine protease kinetics? | N-terminal | |
| What types of catalysis is serine protease mech a mix of? | covalent and acid-base | |
| What AAs acts as acid-base in serine protease mech? | His57 | |
| What AAs forms a covalent bond with the peptide in serine protease mech? | Ser195 | |
| In the serine protease mech, how does the covalent bond formation change the geometry? | Trigonal C into Tetrahedral C | |
| In the serine protease mech, how is the tetrahedral oxyanion intermediate stabilized? | back bone N-H groups of Gly193 and of Ser195 | |
| What serine protease mechinvolves 2 tetrahedral oxyanion X‡s? | Chymotrypsin | |
| How are the X‡s of Chymotrypsin mech stabilized? | pair of amide groups, aka Oxyanion hole | |
| In the oxyanion hole, how is the O- stabilized? | by interaction with backbone NH (amide) groups of Ser195 and Gly193 | |
| What general catalytic traids are acids that orient and stabilize bases? | Asp, Glu, His | |
| What general catalytic traids are bases that polarize bucleophiles? | His (and sometimes Lys, rare) | |
| What general catalytic traids are nucleophiles that attack the substrate? | Ser, Cys and sometimes Thr | |
| How do Aspartic proteases differ from Serine proteases? | Different structure and mech | |
| What is different about Aspartic protease and Serine protease mehcs? | 1) no covalent catalysis 2) active site has two Asp (pepsin 32 & 215) 3) peptide bind is cleaved between two hydrophobic AAs | |
| What is the strucutre of HIV-1 protease? | homodimer | |
| What is the structure of pepsin? | monomer | |
| How does pepsin interact with HIV-1 protease? | one catalytic Asp from each terminal, C-term and N-term, are contrib to active site | |
| How does pH affect Asp protease mech? | one Asp needs to be protonated and other deprotonated when substrate binds | |
| What is pepsins observed pKa in Asp protease rxn? | 1.5 | |
| What is pepsins normal pKa in Asp protease rxn? | 3.9-4.0 | |
| What does HIV-1 protease do to the HIV genome? | cleaves polyprotein | |
| What does HIV-1 protease imitate? | Asp protease | |
| What do we use as drugs for AIDS patients? | protease inhibitors, Invirase and Crixivan | |
| 𝛾αβεφψΔX‡ΔG‡° |
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trejonathan93
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