Biochemistry Flashcards
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| 7224480619 | Glycine (G) (Gly) | Nonpolar (hydrophobic) Only Non-Chiral Neurotransmitter invovled in synthesis of numerous molecules and has a low pKa due to positive amine group precursor of betaine, creatine, and porphyrins such as heme, and nucleotide |  | 0 |
| 7224490285 | Proline (P) (Pro) | Nonpolar/hydrophobic Very stable and found in turns due to kinked structure Not aromatic |  | 1 |
| 7224496094 | Valine (V) (Val) | Hydrophobic/nonpolar metabolism |  | 2 |
| 7224503747 | Leucine (L) (Leu) | Hydrophobic/nonpolar |  | 3 |
| 7224504849 | Isoleucine (I) (Ile) | nonpolar/hydrophobic has TWO chiral centers |  | 4 |
| 7224506816 | Alanine (A) (Ala) | nonpolar/hydrophobic chiral small side chain generic AA that can be substituted for other AA |  | 5 |
| 7224508665 | Tryptophan (W) (Trp) | Some polarity least abundant in protein can hydrogen bond precursor of serotonin, melatonin, and niacin (vit B3) |  | 6 |
| 7224511367 | Methionine (M) (Met) | Hydrophobic/nonpolar One of two amino acids that has a sulfur bond (does not hydrogen bond) rare |  | 7 |
| 7224515790 | Phenylalanine (F) (Phe) | hydrophobic aromatic |  | 8 |
| 7224517965 | Serine (S) (Ser) | Uncharged, polar Alcohol (hydroxyl group) H bonds and dehydration rxn important in metabolism |  | 9 |
| 7224519788 | Threonine (T) (Thr) | Uncharged, polar Alcohol (hydroxyl group) dual chirality H-bonds |  | 10 |
| 7224521704 | Tyrosine (Y) (Tyr) | Polar, uncharged precursor of dopamine, norepinephrine, and epinephrine usually protonated |  | 11 |
| 7224524111 | Asparagine (N) (Asn) | amide polar, uncharged was first AA discovered (in asparagus) H bonds |  | 12 |
| 7224528217 | Glutamine (Q) (Gln) | polar, uncharged amide groups H bonds precursor of nucleotide |  | 13 |
| 7224529805 | Cysteine (C) (Cys) | Nucleophilic polar, uncharged only AA with thiol group can be ionized |  | 14 |
| 7224533065 | Histidine (H) (His) | basic pka 6 important for acid/base rxn and enzymes precursor of histamine |  | 15 |
| 7224536659 | Lysine (K) (Lys) | basic usually protonated b/c it has higher pka (10) precursor of carnitine |  | 16 |
| 7224538091 | Arginine (R) (Arg) | basic precursor of nitric oxide and creatine |  | 17 |
| 7224540848 | Aspartate (D) (Asp) | acid precursor of nucleotide |  | 18 |
| 7224544087 | Glutamate (E) (Glu) | acid |  | 19 |
| 7226361634 | Enantiomers | Have mirror images. Body only allows for the L isomer | 20 | |
| 7226475507 | Acetylation | NH2 of lysine, terminus. Most common modification, Important in histones (postive charge on histone binds DNA and acetylation loosens it--transcription regulation) | 21 | |
| 7226498645 | Phosphorylation | OH of ser, thr, tyr common modification | 22 | |
| 7226500087 | cysteine vs. cystine | cysteine is reduced (double SH) and cystine is oxidated (double S bonded) Clinically important in cystinuria bc cystine can reach solubility limit much more quickly than a free AA | 23 | |
| 7226511552 | beta-alanine | natural (and synthetic) amino acid found in vitamin B5 (pantothenic acid) not found in proteins | 24 | |
| 7226518658 | gamma-amino butyric acid (GABA) | chief inhibitory neurotransmitter in the mammalian CNS. Naturally occuring amino acid but not found in proteins | 25 | |
| 7226555600 | isoelectric point | is between 2 lowest buffering regions in an acidic AA and between 2 highest buffering regions in a basic AA | 26 | |
| 7226562810 | Hydropathy index | the bigger the number the more nonpolar (hydrophobic) | 27 | |
| 7226568308 | histamine | decarboxylation of histidine | 28 | |
| 7226583508 | creatine | Formation takes place in liver and kidney then are transferred to muscle. Arginine & glycine combine to forn guanidinoacetate. that is then methylated with methionine to for creatine. Creatine is used to make creatine phosphate but neither form are completely stable and therefore they spontaneously cycle to make creatinine. Creatinine is used to measure kidney function bc it isn't reabsorbed. | 29 | |
| 7226610968 | pyroglutamic acid | found in GnRH and TRH looks similar to proline but has additional double bonded O |  | 30 |
| 7226615616 | TRH | pyroGlu-His-Pro-NH2 biologically active peptide both termini are blocked and therefore has no charge (other than possible small charge on histidine) unique even though only three AAs long | 31 | |
| 7226620419 | GnRH | pyroGlu-His-Trp-Ser-Tyr-Gly-Leu-Arg-Pro-NH2 biologically active peptide | 32 | |
| 7226625501 | What is the relationship between molecular weight and number of amino acids? | weight of AA is ~114 on average therefore weight of molecule is around 100x number of AA Shorter chains are preferred bc less chance of error | 33 | |
| 7226637531 | Metal in proteins | 1/3 of proteins have metal inside their structure. there for electron transport or other functionality. | 34 | |
| 7226639485 | Insulin | Hexamer (6 identical subunits) is inactive form. Monomer is active form when it dissociates. Its side chain is produced as a single chain then post-translationally is processed (clipped) into A and B chains. On B chain there are Proline (B28) and Lysine (B29). Two rapid forms of recombinant insulin are: 1. Humalog("lispro") switches B28 & B29 2. Novolog(aspart) substitutes asp for pro at B28 position THIS POSITION IS IMPORTANT FOR STABILIZING HEXAMER. Mess with it and it dissociates quickly to monomer (fast acting). | 35 | |
| 7226672402 | Gap in same sequence from two different organisms | gap may indicate that region is interacting with solvent or at the surface. Corresponding sequence has charged AAs where the gap is indicating possible water interaction | 36 | |
| 7226762806 | primary structure | consists of AAs linked together by peptide and disulfide bonds | 37 | |
| 7226763981 | secondary structure | helix; polypeptide structure arranged into units ex: alpha-helix; involves AAs that are bonded 4 residues ahead; b-sheets | 38 | |
| 7226765340 | tertiary structure | folded peptide | 39 | |
| 7226770901 | quaternary structure | multi-subunit proteins | 40 | |
| 7226773993 | cis and trans configuration | almost all AAs are in trans confirmation but proline can be either | 41 | |
| 7226776194 | L or R | most are R handed in nature | 42 | |
| 7226777844 | peptide bond | rotation around alpha carbon (lower the degree of freedom less entropy to use folded up) peptide bond is rigid which is important for folding N donates H and O accepts it | 43 | |
| 7226781028 | Anti-parallel beta sheet | goes in the direction of the carboxyl group form a surface with stretched out H bonds between strands sheets aren't flat, they're twisted B sheets are found in interior of globular proteins | 44 | |
| 7226787967 | non-repetitive regions | turns (i.e. hairpin) or coils/loops that link regions of secondary structure. Occur between anti-parallel sheets. Proline, glycine, and polar AA are used at turns bc they turn to surface and interact with solvent/water | 45 | |
| 7226793930 | Protein types | Globular Membrane Structural (fibrous) Disordered/unstructured protein protein fibrils | 46 | |
| 7226807571 | globular proteins | water soluble, not very stable, will unfold easily. compact, tightly packed together advantageous because they can be broken down easily and faster turn over | 47 | |
| 7226813049 | membrane proteins | partially lipid soluble, hydrophobic | 48 | |
| 7226813627 | structural proteins | fibrous i.e. collagen and keratin | 49 | |
| 7226816863 | intrinsically disordered/unstructured proteins | lack of stable tertiary structure when the protein exists as an isolated polypeptide chain in vitro. have amorphous shape until they bind something and becomes rigid/ordered | 50 | |
| 7226823269 | protein fibrils | abnormal aggregates forming thin fibers (fibrils), usually through beta sheet stacking. (involved in neurodegenerative diseases) | 51 | |
| 7226840625 | motif or fold | motif is recognizable folding pattern involving two or more elements of secondary structure and the connection(s) between them; may or may not have a specific role fold is same as motif just a larger functional unit | 52 | |
| 7226842985 | domain | folds that have independent function. will fold by itself. ex: troponin C. single chain but folded into two distinct conformations with different functions (important in muscle phys) | 53 | |
| 7226859759 | C2 vs. C3 cyclic symmetry | C2: 2 subunits (dimer) that has rotational symmetry and only needs two turns to get back to original position (180 degrees) C3: has three-fold axis b/c of three identical subunits. | 54 | |
| 7226864805 | Where do you find beta sheets? | interior of globular proteins | 55 | |
| 7226865795 | Entropy favors ______ proteins | unfolded. That is because polar water wants to hydrogen bond | 56 | |
| 7226866806 | metal inside of proteins | increase stability of proteins due to locking down parts of protein and acting as a cross link. | 57 | |
| 7226870955 | Sickle cell hemoglobin | Valine substituted in for Gal on beta 6 causes self-association and polymerization surface polar-to-hydrophobic mutation that lowers solubility. mutation leads to hydrophobic interaction b/w heme tetramers fibril formation at high concentration | 58 | |
| 7226877861 | enzyme vs. chemical catalysts | enzymes have higher reaction rate, milder reaction conditions, greater reaction specificity, and capacity for regulation | 59 | |
| 7226880385 | cofactor | broad term meaning any nonprotein component of an enzyme required for catalytic activity typically metals | 60 | |
| 7226881044 | coenzyme | complex organic or organometallic cofactors required for catalytic activity. typically organic and can be reversible. coenzyme is a cofactor but not all cofactors are coenzymes. | 61 | |
| 7226883449 | prosthetic group | a cofactor that is very tightly or even covalently bound to the enzyme protein (not reversible) | 62 | |
| 7226883777 | holoenzyme | a complete, catalytically active enzyme together with its prosthetic group (fully functional unit) | 63 | |
| 7226884468 | apoenzyme | protein part of an enzyme which normally also contains prosthetic group | 64 | |
| 7226886471 | protein isoforms | different forms of the SAME protein produced by related genes or alternate splicing of a gene different structural forms of same enzyme (same sequence) usually come from same gene | 65 | |
| 7226889963 | isozymes | multiple forms of an enzyme that catalyze same reaction but differ in amino acid sequence, substrate affinity, vmax, and/or regulatory properties. May occur in same species, in same tissue, or even same cell. different enzyme that catalyzes the same reaction | 66 | |
| 7226907217 | six types of enzymes | oxidoreductase transferases hydrolases lyases isomerases ligases | 67 | |
| 7226908371 | oxidoreductase | electron transfer. catalyze oxidation-reduction reactions such as lactate to pyruvate ex: alcohol dehydrogenase | 68 | |
| 7226908985 | transferases | chemical transfer. catalyze transfer of C-, N-, or P- containing groups like serine to glycine | 69 | |
| 7226909776 | Hydrolases | use water to cleave bonds at carbonyl group like ester or amide. ex: urea to ammonia ex: trypsin | 70 | |
| 7226911753 | lyases | cleavage of carbon containing bonds (C-C, C-s, and certain C-N bonds) | 71 | |
| 7226916682 | isomerases | catalyze racemization of optical or geometric isomers. | 72 | |
| 7226917181 | ligases | catalyze formation of bonds between carbon and O, S, and N coupled to hydrolysis of high-energy phosphates. (requires ATP) | 73 | |
| 7226923404 | initial rate | rate of first 10% . more substrate added, the quicker the reaction until saturation or equilibrium is reached. | 74 | |
| 7226924757 | km | Michaelis constant; an approximation of the binding affinity of a substrate increased km = lower affinity (takes more substrate to saturate active site) low km doesn't neccesarily mean that it is a good substrate because it has to turn over to product and not just bind | 75 | |
| 7226925533 | vmax | maximum velocity of the enzyme under specific conditions used -measure of how well the enzyme works and binds to substrate | 76 | |
| 7226926376 | kcat | turnover number of the enzyme, a first order rate constant derived from vmax and the enzyme concentration | 77 | |
| 7226928664 | kcat/km | catalytic efficiency. best measure of how good a substrate is BEST way to compare enzymes | 78 |