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BC 351- Unit 2
| Question | Answer |
|---|---|
| protein motifs | not stable on their own-> larger structures made up of secondary structures |
| protein motif examples | beta hairpin, alpha turn alpha |
| protein domains | stable on their own; a single polypeptide can have multiple domains |
| 5 protein folding "rules" | hydrophobic forces drive folding, alpha helices and beta sheets are separate, amino acids near each other in protein tend to be near each other in primary structure, beta sheets don't become interdigitated, beta sheets tend to twist |
| the structural classification of proteins is based primarily on | secondary structure content and arrangement |
| tetramer | 4 subunits, 2 sets of the same one |
| protomer | two identical heterodimers |
| Leventhal's paradox | protein folding would take forever to happen randomly, so it's not random |
| two theories of protein folding | hierarchical, molten globule |
| hierarchical model of protein folding | primary -> quaternary structures |
| molten globule model of protein folding | hydrophobic collapse, massages into correct shape |
| sock model for protein folding | saves time if you pair socks when you pull them out rather than just waiting for matches |
| experiments on denaturation and renaturation after the reduction and deoxidation of SS bonds in RNase have shown that | primary sequence is sufficient to determine secondary and tertiary structure |
| ligands | small molecules that bind reversibly through non-covalent interactions |
| binding sites | pocket/cleft where ligand binds; should conform well with several interactions |
| conformation | ligands can change the shape of proteins |
| induced fit/allostery | the changes that proteins undergo when ligand binds |
| how does hemoglobin prevent CO from binding? | distal histidine (helps somewhat but still has a high affinity) |
| when oxygen binds to a heme-containing protein, the two open coordination bonds of Fe2+ are occupied by | one O2 molecule and one amino acid atom |
| the strength and specificity of binding between two molecules is dependent on (4) | temperature, pH, binding site, number of non covalent interactions |
| Kd | dissociation contstant; lower= higher affinity; measured in M; 1/Ka |
| when [L]= Kd... | then 1/2 of the sites are bound |
| Two molecules, A and B, have a KA = 10^6 M-1 for AB complex formation. When both molecules are at 10-5 M (10 μM) the proportion of A and B in an AB complex will be | >90% because 10^-5 is 10x larger than 10^-6 (which is Kd) |
| theta= (for oxygen binding to hemoglobin) | pO2/(pO2+Kd) |
| T state of hemoglobin | binds BPG and CO2 more tightly |
| R state of hemoglobin | binds O2 more tightly |
| pH and hemoglobin | tissues have a lower pH than the lungs so O2 is released here (lower pH stabilizes T state) |
| difference between fetal and adult hemoglobin | fetal has a gamma subunit instead of beta, so gower BPG affinity |
| sickle cell anemia | when goes to T state, it associates into large strands/fibers |
| four types of catalysis | acid-base, covalent intermediate, reaction intermediate stabilization, orientation/proximity |
| ΔΔG‡cat | difference between catalyzed and uncatalyzed |
| ΔG‡ | transition state-substrate |
| acid and base catalysis (2) | 1) involves making reactants better electrophiles and nucleophiles 2) works through transition state stabilization |
| transition state stabilization | puts strain on S, pulling towards transition state |
| A mutation in an enzyme | reduce the rate of the catalyzed reaction |
| two signals leading to apoptosis | extracellular death receptor, intracellular (DNA damage and oncogene expression) |
| what is Km? | [S] at 1/2 Vmax |
| Enzymes exhibit saturation behavior (become insensitive to more substrate, have a VMax) because | enzymes have a fixed number of active sites where substrate binds |
| kcat | Vmax/[Et] (reactions per second) |
| Lineweaver-Burk plot | -1/Km (x-intercept); 1/Vmax= y intercept |
| two enzyme preparations have the same Km, but the bacterially expressed enzyme has a 10x lower Vmax... why? | 90% of the enzyme expressed is inactive |
| competitive inhibition | affects Km only |
| uncompetitive inhibition | affects Km and Vmax |
| PGP | binds hydrophobic, neutral, + charged drugs; normal functions to excrete toxins from the body |
| PGP inhibitors | have a higher affinity for PGP binding pocket than the broad range of things that bind to it |
| domains | stable, independently folding components of proteins |
| motifs | not stable on their own; subset of exons that are used repeatedly |
| why multiple copies of a polypeptide subunit? | fewer genes |
| two types of symmetry on oligomeric proteins | helical and rotational |
| homoallostery | change in shape leading in response to substrate binding |
| heteroallostery | a change in shape in response to non-substrate ligand binding |
| four types of catalytic mechanisms | acid base, covalent catalysis, transition state stabilization, proximity/orientation |
| covalent catalysis | covalent bond is formed between a functional group on the enzyme and a substrate transition state intermediate |
| histidine-57 functions (2) | 1) makes oxygen a better nucleophile 2) binds w/ N of peptide bond to make it a better LG |
| serine-195 function (1) | replaces water in the hydrolysis of a peptide bond (covalent catalysis) |
| binding of glucose to hexokinase | induces a conformational change that continues the reaction |
| demonstrate that at high [S], V0 approaches Vmax | Km is really small, so V0= Vmax[S]/[S], so V0=Vmax |
| V0= | Vmax [S] / Km + [S] |
| key conditions for M&M | Km is approximately Kd |
| units of mcat/Km ratio | s-1 M-1 |
| proteins have regions that show specific, evolutionarily conserved patterns of folding called | motifs or folds |
| do all protein subunits have to be identical? | no |
| rotational symmetry (4) | seen in oligomeric proteins; seen in viruses; rotation about 1 or more axis; results in closed, packed structures |
| will changing salt concentration result in protein denaturation? | no |
| the average protein will not be denatured by what acid? | iodoacetic acid |
| Leventhal's paradox | is solved by proteins folding in a step-by-step, non random fashion |
| interactions of ligands w/ proteins | are usually transient |
| highly specific intermolecular interactions | involve as many as 15-20 hydrogen bonds |
| a prosthetic group is | permanently associated w/ the protein |
| oxygen binding to myoglobin is | hyperbolic |
| transition from T state to R state is triggered by | oxygen binding |
| BPG is a(n) _____ | allosteric modulator |
| BPG is found in hemoglobin where? | in red blood cells |
| in catalyzing reactions, enzymes change what? | ΔG‡ (activation energy) |
| transition state analogs | exhibit a greater affinity for the enzyme |
| the serine-195 hydroxyl group does what? | participates in covalent catalysis |
| the greater affinity of the active site for binding the substrate relative to the affinity for binding the transition state intermediate causes what? | not good enzyme catalysis (hard to convert to product) |
| irreversible inhibition | covalent linkages |
| Km is greater for enzymes... | with lower affinities for a substrate |
| kcat is a function of | Vmax and total E |
| reasons cancer patients don't respond to chemotherapy (5) | increased cellular export, increased DNA repair, decreased tumor blood supply, activation of P450 detoxifying system, decreased programmed cell death signaling |
| ABC transporters (3) | keep toxins from affecting a developing fetus, protect genomes of stem cells, keep toxins from passing blood-brain barrier |
| multi drug resistance proteins | can interfere w/ treating brain disorders by keeping drugs from entering the brain |
| P-glycoprotein inhibitors also | inhibit cytochrome p450 detoxification |
Created by:
melaniebeale
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