Science Quiz / Biochem Test 1

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Can you name these terms for Biochemistry Test 1?

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Mechanism of catalysis. Charged intermediates are stabilized by proton transfers, general without H20, specific in the presence of H20
Created in first step of urea cycle in mitochondrial matrix, from ornithine and carbamoyl phosphate
Y intercept of Lineweaver Burk plot
Digestive enzyme from pancreas, hydrolyzes peptides, prefers lysine and arginine peptides, used in amino acid sequencing
Class of enzymes that catalyze redox reactions, often have metal cofactors to transfer electrons
Mechanism of catalysis. Redox reactions, transfer of electrons
Amino Acid. R group is a propyl group with methyl on first carbon. Aliphatic, nonpolar and hydrophobic
Folding Factor. Covalent linkages between Cysteine residues to form Cystine. Each cysteine is oxidized to form the bond, reduction breaks the bond.
Class of enzymes that perform group transfer reactions, includes kinases
Michaelis-Menten constant, concentration of [S] when Vo=1/2Vmax, low means tight binding, high means weaker affinity
A full polypeptide chain, non-covalently bound to others to form a quaternary structure
Mechanism of catalysis. Changes reaction pathway, transient bonds between enzyme and substrate are created, requires nucleophiles (Y,T,S)
Class of enzymes that add or remove functional groups, break and create double bonds
Losing protein structure. Can occur at 2, 3, 4 levels. Caused by solvents, temperature, change in pH & disruption of ionic interactions
X intercept of Lineweaver Burk Plot
Formed in fourth step of urea cycle, from arginine, H20 is added and urea is left, goes into beginning of cycle
Level of protein structure. The chain of amino acids. Determines the properties of the higher levels of folding
Model of protein binding. A substrate binds an enzyme and the enzyme conformationally changes to create a better site for binding. creates favorable environment for reactions
Class of enzymes that perform hydrolysis reactions, breaking bonds with H20
Level of protein structure. The total 3D structure of protein. Guided by folding interactions (5 Major Interactions)
Involved in first step of urea cycle, reacts with ornithine to form citrulline, amide group with phosphate attached, phosphate lost in reaction with ornithine
Conformational changes in one subunit of a quaternary structure after binding substrate causes conformational changes in other subunits
Amino Acid. R group is isopropyl group. Aliphatic, hydrophobic, and nonpolar
Enzymes that catalyze the attachment of phosphoryl groups
Organic compounds that assist an enzyme, includes vitamins
Enzymes lower activation energy by stabilizing these structures, preferentially bind over substrate or product
Initial rate of reaction, how much substrate concentration changes over time
Type of Reversible Inhibition where an inhibitor binds to the active site of the enzyme & competes with substrate
Type of Reversible Inhibition where an inhibitor binds to the ES complex at a site away from the active site after substrate binds
Inhibition where Km is unchanged and Vmax decreases
Protein technique. Diffracts radiation around crystal. Angles define structure/location of every atom. No dynamic info., difficult to perform
Protein Technique. Polymer beads in a column with porous surface. Smaller molecules trapped in pores. Larger molecules elute faster
Formed in third step of urea cycle, from argininosuccinate, loss of fumarate, cleaved by argininosuccinate
Type of Irreversible Inhibition where a substrate partially undergoes reaction before covalenty binding to enzyme and disrupting enzymatic function
The energy released from noncovalent interactions between an enzyme and its substrate
Number of substrates converted to product in a unit of time by a single enzyme when enzyme is saturated with substrate, units of reciprocal seconds
Structure on same polypeptide that folds and functions independently of the rest of the protein
Slope of Lineweaver Burk plot
Substrate binding at one site of a protein affects binding of substrates at other sites of a protein
Digestive enzyme from stomach, hydrolyzes peptide bonds, prefers aromatic residues
Type of Reversible Inhibition where an inhibitor binds to either the ES complex or the enzyme alone away from active site. Causes conformational changes to prevent substrate
Level of protein structure. Composed of multiple complete peptide chains. Each is a subunit. Can participate in cooperativity
Formed in second step of urea cycle, from citrullyl-AMP intermediate and Aspartate (or other amino acid)
Folding Factor. Interactions due to polarity. Certain residues create an inner core to avoid interacting with aqueous environment on outside of protein. Important for globular fold
Level of protein structure. Regular structures created through Hydrogen bonding. A-Helices & B-sheets.
Specific, repeated arrangement of secondary structures
An active enzyme with a cofactor or coenzyme bound
Class of enzymes that transfer functional groups within the same molecule
Type of Irreversible Inhibition where a substrate mimics a transition state and thus preferentially binds with the enzyme over substrate itself
Graph of enzyme kinetics based on the double reciprocal of the Michaelis Menten equation, in slope intercept form, 1/Vo=Km/Vmax[S]+1/Vmax
Inhibition where Km increases and Vmax does not change
Inactive enzymes, modified to become active by proteolytic cleavage, includes digestive enzymes such as trypsinogen, chymotrypsinogen, pepsinogen
Amino Acid. R group is a methyl group. Involved in urea cycle metabolism for transferring amines, aliphatic, nonpolar, hydrophobic
Digestive enzyme from pancreas, hydrolyzes peptides, cleaves peptides preferentially at aromatic amino acids
Class of enzymes that ligate substrates together, usually by cleavage of ATP
Amino Acid. R group is a single H. Able to rotate freely, highly present in B-Turns, aliphatic & nonpolar, hydrophobic
Amino Acid. R group is isobutyl group. Aliphatic, nonpolar and hydrophobic
Folding Factor. Interactions between positively and negatively charged species. Includes interactions with metal ions and charged residues
Type of Inhibition by Noncovalent interactions, enzyme retains function
Byproduct of third step of urea cycle, goes into citric acid cycle, separated from argininosuccinate by argininosuccinase
Inhibition where Km decreases and Vmax decreases
Max velocity, rate when enzyme is saturated with substrate. Theoretical maximum capacity of enzyme
Amino Acid. R group is cyclic 5 member ring with amine. No terminal amino group. Protonated and charged N in ring. Present in B-Turns due to sharp angles. Has cis and trans forms.
An enzyme without its cofactor or coenzyme
Inorganic compounds that assist an enzyme, includes metal ions
Folding Factor. Interactions between atoms due to the momentary movement of electrons. Can cause attractions. Ubiquitous in protein, stabilizing effect.
Compound created as byproduct of amino acid metabolism, less toxic than ammonia, very soluble, excreted through urine
Folding Factor. Noncovalent bonds between an electronegative atom and a hydrogen atom. Defines A-helices and B-sheets
Protein structure with no discernable structure. Likely to have more charged residues to interact with water
Intermediate formed in the second step of the urea cycle, from the addition of ATP to citrulline with loss of two phosphates from ATP, forms argininosuccinate after loss of AMP
Type of Inhibition involving covalent interactions, enyme function or structure is destroyed, functional groups disrupted

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