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BioChem Exam 2
BioChem
| Question | Answer |
|---|---|
| What is the biological catalyst? | Enzymes |
| What is the study of enzymes? | Enzymology |
| Enzymes are essential to life since they catalyze chemical reactions with what specification? | Efficiently, selectively |
| The reaction conditions with an enzyme are what, when compared to that with a chemically catalyzed reaction? | Milder |
| What is increased, with an enzyme, when compared to uncatalyzed and chemically catalyzed reactions? | Reaction rates |
| What allows for a greater reaction specificity with respect to substrates and products? | Enzymes |
| True/False: Enzymes do not have any capacity for regulation. | False |
| What kind of reaction has half times in milliseconds? | Catalyzed |
| Enzymes catalyze reactions 10^? to 10^? times faster than the uncatalyzed reaction. | 6, 12 |
| What are the three catalysts for Nitrogen fixation? | Lightning, Haber process, Symbiotic bacteria (nitrogenase enzyme) |
| In the treatment of methanol poisoning they will give ethanol (alcohol). This is an example of an enzyme's what? | Geometric Specificity |
| Enzymes bind to a specific orientation of substrates, what is this referred to? | Stereospecificity |
| The regulation of the activity of an enzyme by the binding of an inhibitor or activator at a site on the protein separate from the substrate-binding site | Allostery |
| What are types of covalent modifications done by enzymes? | Phosphorylation, acetylation, and removal of inhibitory peptides |
| What is responsible for assembly into macromolecular complexes? | Enzymes |
| The regulation of a metabolic pathway by the inhibition of an enzyme that catalyzes a reaction early in the pathway by the product of the pathway? | Feedback inhibition |
| What is another term for active site? | Catalytic site |
| What makes a holoenzyme? | Cofactor binds to apoenzyme to allow substrate binding |
| In enzyme nomenclature, what is the common ending? | ase |
| In enzyme nomenclature, formal names describe the precise what? | Reaction catalyzed |
| What are small molecules/metal ions (Cu, Fe, K, Mg, Mn, Ni, Zn) that are required by some enzymes to catalyze reactions, the site at which the chemistry occurs? | Cofactor |
| What are organic cofactors often derived from vitamins, may associate transiently or be tightly linked (prosthetic groups), required as carriers of specific atoms or functional groups? | Coenzymes |
| Pellagra is a disease caused by a deficiency in what coenzyme, that leads to lesions on the arms and skin? | Niacin |
| In a reaction, enzymes can only alter what in a reaction? | Kinetics |
| What are used to modify or destroy a catalytic functional group? | Irreversible inhibitors |
| What kinds of inhibitors binds like a substrate and is acted upon by an enzyme, is converted into a irreversible inhibitor during catalysis, and are not very common? | Suicide inhibitors |
| Suicide inhibitor is different from an irreversible inhibitor because it changes what? | Enzyme conformation or active site |
| An amino acid residue that may directly participate in the reaction catalyzed by pepsin is A. Serine B. Glu C. Ile D. Lys | B |
| When the lines are parallel on a graph, what kind of inhibition takes place? | Uncompetitive inhibition |
| What does the Michaelis-Menten model assume? | Enzyme, substrate, and enzyme-substrate product are all in equilibrium |
| What catalyzes the hydrolytic cleavage of peptide bonds? | Serine proteases |
| What are the three important serine proteases found in the pancreas that function in the digestion of proteins? | Trypsin, Chymotrypsin, Elastase |
| What level of organization will Chymotrypsin be able to achieve? | Quantenary |
| Which serine protease catalyzes peptide hydrolysis, but not via direct addition of water to the peptide bond? | Chymotrypsin |
| What are the two steps of the MECHANISM Chymotrypsin utilizes? | Acylation, deacylation |
| What kind of residue (amino acids) does Chymotrypsin bind to at the active site? | Aromatic |
| During which part of the mechanism, of Chymotrypsin, does enzyme acylation and release of p-NP occur? | Fast step |
| During which part of the mechanism, of Chymotrypsin, does the hydrolysis of acyl-enzyme intermediate occur? | Slow step |
| What are the three amino acids present in the catalytic triad of the Chymotrypsin? | His57, Ser195, Asp102 |
| Where will the Chymotrypsin cleave? | C-terminal of Aromatic residue |
| In the Chymotrypsin mechanism, what acts as a general base to abstract a proton from Ser195? | His57 |
| In the Chymotrypsin mechanism, after His57 abstracts a proton from Ser195, what works to stabilize His57+? | Asp102 carboxylate |
| In the Chymotrypsin mechanism, after His57+ is stabilized, what acts as a nucleophile to attack C=O? | Ser195-O(-) |
| In the Chymotrypsin mechanism, a H-bonded chain makes Ser195 a better what? | Nucleophile |
| In the Chymotrypsin mechanism, the nucleophilic attack of alkoxide ion on peptide carbonyl carbon leads to what? | Tetrahedral intermediate (acyl-enzyme) |
| In the Chymotrypsin mechanism, the negatively-charged O is stabilized by what, via H-bonds to backbone amide protons of Ser and Gly? | Oxyanion hole |
| What prefers to cleave between Phe and Pro amino acid pairs? | HIV protease |
| What is helps to cleave peptide bonds in HIV protease? | Aspartyl protease |
| What is "pro" (prefix) or "gen" (suffix) used for in nomenclature? | Inactive form of enzymes |
| What does HIV protease reaction mechanism lack that is found in Serine proteases? | Oxyanion hole, covalently attached intermediate, acyl-enzyme complex |
| What kind of analogs are anti-HIV protease inhibitors? | Transition-state analogs |
| What utilizes divalent cations in peptide bond cleavage? | Enolase |
| What stabilizes the enolate intermediate? | 2 Mg2+ ions |
| What is required in cell wall synthesis? | Cross-linkage of peptidoglycan |
| What links peptidoglycan chains (made of polysaccharide chains)? | D-Ala-containing peptide |
| What carries out cross-linking in the peptidoglycan chains (made of polysaccharide chains)? | Transpeptidase |
| What, in peptidoglycan synthesis, works to replace one peptide bond with another? | Transpeptidase |
| What is inhibited by B-lactam antibiotics/penicillin? | Transpeptidase |
| What can make bacteria antibiotic resistant? | B-lactamases |
| In the mechanism of penicillin inactivation, B-lactamases inactivate B-lactams by promoting what? | Cleavage of B-lactam ring |
| What is the suicide inhibitor of B-lactamases? | Clavulanic acid |
| What is used to pull the aromatic ring (which is where it enters) for His57 to abstract a proton from Ser195? | Hydrophobic pocket |
| What occurs to cause a tetrahedral intermediate due to this occurring from the alkoxide ion on the peptide carbonyl? | Nucleophilic attack |
| In the mechanism of penicillin inactivation, B-lactamases inactivate B-lactams by promoting cleavage of B-lactam ring thus doing what? | B-lactam not substrate/inhibitor of transpeptidase |
| What are the steps of Chymotrypsin mechanism | acid catalysis, base catalysis, covalent catalysis and , acid catalysis, product release and reset |
| What is controlled by the response of certain enzymes to certain signals? | Metabolism |
| What does the regulation of enzymes via allostery involve? | Reversible non-covalent binding of homotropic or heterotropic modulator, bind separate regulatory subunits |
| What does the regulation of enzymes via covalent modification involve? | Phosphorylation |
| What does the regulation of enzymes via cleavage involve? | Activation of zymogens by proteolytic cleavage |
| What are the subunits of allosteric enzymes? | Catalytic, regulatory |
| In allosteric regulation, why is aspartate (from aspartate transcarbamoylase) positively regulated by heterotropic ATP but negatively regulated by heterotropic CTP? | CTP goes through negative feedback, ATP positively ... |
| Allosteric control of ATCase by CTP is an example of what? | Feedback inhibition |
| What does covalent modification affect? | Protein structure, function |
| What does covalent modification result in? | Enzyme turned on/off, degradation, change in localization, substrate preference, binding partners |
| Glycogen phosphorylase is regulated by what, existing in a form (active) and b form (less active), this of 2 Ser converts b to a, phosphorylase kinase (converts b to a) activates, protein phosphorylase 1 (converts a to b) inhibits? | Phosphorylation |
| A proenzyme is also known as what? | Zymogen |
| When enzymes and proteins (especially secreted enzymes) are produced in inactive (pro) form, inactive precursors are converted to active enzymes by what? | Enzymatic (specific) or autolytic cleavage |
| If you are starving, what will be active? kinase or phosphorylase | Phosphorylase |
| Chymotrypsin and trypsin are activated by what? | Proteolytic cleavage of zymogen forms |
| The role of an enzyme in an enzyme-catalyzed reaction is to: | Increase rate at which substrate is converted into product, lower activation energy |
| The role of the metal ion (Mg2+) in catalysis by enolase is to: | Stabilize transition state intermediate |
| Penicillin and related drugs inhibit the enzyme ----, which is produced by ----. | Transpeptidase, bacteria |
| What is the formula for carbohydrates? | Cn(H2O)n |
| What produces carbohydrates? | CO2 and H2O via photosynthesis in plants |
| What is the most unique thing about carbohydrate? | Only energy source for the brain |
| What are structural things made of carbohydrates? | Cell walls, exoskeleton |
| What is a monosaccharide? | Simple sugars, single unit, aldehydes or ketones, 3 carbons and up |
| What is true of all carbohydrates? | Made of aldehydes or ketones |
| What is a oligosaccharide and what form is most common? | Short chains of monosaccharides, disaccharides |
| In carbohydrate nomenclature, what will always end in "ose"? | Mono- and disaccharides |
| Which carbon will always carry the oxygen in aldose? | First carbon |
| In nomenclature, for every n chiral centers, there are how many stereoisomers? | 2^n |
| What are the most biologically relevantly sugars (configuraton)? | D |
| What are enatiomers? | Non super-imposable mirror images |
| Enatiomers have different configuration where? | Every chiral center |
| In which process will you find D-glyceraldehyde? | Glycolysis |
| What are diastereomers? | Not mirror images of each other, differ in configuration in at least one chiral center (but not all) |
| What are epimers? | Not mirror images of each other, have ONLY ONE difference in chiral centers |
| Some ketoses that did not get a unique name are named by inserting what immediately prior to the "ose" in the name of the corresponding aldose? | "ul" |
| Where are most sugars found to be cyclic? | In vivo |
| What are 5-membered cyclic sugars? | Furanoses |
| What are 6-membered cyclic sugars? | Pyranoses |
| Which carbon is drawn on the right by convention? | Anomeric |
| What kind of sugars are referred to as "reducing"? | Anomeric carbon has free hydroxyl group |
| What is an example of a reducing sugar? | Aldose |
| What happens when a linear sugar cyclizes? | Alcohol added to aldehyde or ketone |
| What kind of carbon is produced in cyclization of sugar? | Anomeric |
| When looking at a linear sugar, where is the bottom found? | Right |
| When looking at a linear sugar, where is the top found? | Left |
| What are anomers? | Cyclic epimers |
| What happens when you add an alcohol to a hemiacetyl or hemiketal? | Two monosaccharides join to form disaccharide, have glycosidic bond with acetyal |
| Why will acetal not be hydrolyzed by base or open up into chain form? | Stable |
| What are some common names for disaccharides? | Maltose, lactose, sucrose |
| What is the ending of an anomer-stereoisomer-ringed form of monosaccharide 1? | "yl" |
| What is the ending of an anomer-stereoisomer-ringed form of monosaccharide 2? | "side" |
| What determines the length of polysaccharides? | Enzymatic activity |
| What are the types of homopolysaccharides? | Unbranched, branched |
| What are the types of heteropolysaccharides? | Two monomer types, unbranched; multiple monomer types, branched |
| What is the branched homopolysaccharide of glucose? | Glycogen |
| Glycogen is made of what kind of linkages? | a1->4 |
| What is the main storage polysaccharide in animals? | Glycogen |
| What is the main storage homopolysaccharide in plants? | Starch |
| What helps us to digest starch? | Amylase |
| What are the linkages of glycose polymers of cellulose? | B1->4 |
| What has ideal dimension to accommodate iodide ions? | Amylose helix |
| Other than using "ase" in the ending or having formal names the describe the precise reaction catalyzed, what is another way to name enzymes? | Enzyme commission classification (EC number) |
| What is the class name when the type of reaction catalyzed is the following: transfer of elections (hydride ions or H atoms)? | Oxidoreductases |
| What is the class name when the type of reaction catalyzed is the following: group transfer reactions? | Transferases |
| What is the class name when the type of reaction catalyzed is the following: hydrolysis reactions (transfer of functional groups to water)? | Hydrolases |
| What is the class name when the type of reaction catalyzed is the following: cleavage of C-C, C-O, C-N, or other bonds by elimination, leaving double bonds or rings, or addition of groups to double bonds? | Lysases |
| What is the class name when the type of reaction catalyzed is the following: transfer of groups within molecules to yield isomeric forms? | Isomerases |
| What is the class name when the type of reaction catalyzed is the following: formation of C-C, C-S, C-O, and C-N bonds by condensation reactions coupled to cleavage of ATP or similar cofactor? | Ligases |
| Enzymes are classified based on what? | Reaction type catalyzed |
| Deficiency in coenzyme dietary precursors can cause what? | Disease |
| What are the standard conditions for a reaction? | 298K, [solute] = 1M, pGAS = 1 atm (101.3 kPa) |
| Reaction intermediates in a catalytic reaction are detectable/nondetectable? | Detectable |
| What is the rate-limiting step? | Highest energy barrier (smallest k) |
| True/False: Enzymes catalyze both forward and reverse reactions. | True |
| Enzymes don't set equilibrium, but they do what? | Get you there faster |
| In a reaction with an enzyme complementary to the transition state, what is lowered by DG(M)? | Energy required |
| Where is the catalytic power of enzymes through binding optimized? | Transition states |
| Where do enzymes preferentially bind? | Transition states |
| Is the following conversion entropically favorable or unfavorable: uncatalyzed bimolecular reactions (2 free reactants into single restricted transition state)? | Unfavorable |
| Is the following conversion entropically favorable or unfavorable: uncatalyzed unimolecular reactions (flexible reactant to rigid transition state)? | Unfavorable for flexible reactants |
| In entropy reduction through catalyzed reactions, when is the entropy cost paid? | During binding |
| Is the following conversion entropically favorable or unfavorable: catalyzed reactions (enzyme uses binding energy of substrates to organize reactants to fairly rigid ES complex) (rigid reactant complex to rigid transition state)? | Favorable |
| How do enzymes induce (reaction types) entropy reduction? | Uncatalyzed bimolecular reactions, uncatalyzed unimolecular reactions, catalyzed reactions |
| In entropy reduction, via enzymes, is uncatalyzed bimolecular reactions or uncatalyzed unimolecular reactions (flexible reactant to rigid transition state) more favorable (though still unfavorable) and why? | Uncatalyzed unimolecular reactions, reacting groups closer to each other |
| In entropy reduction, via enzymes, is uncatalyzed bimolecular reactions or uncatalyzed unimolecular reactions (constrained reactant to rigid transition state) more favorable (though still unfavorable) and why? | Uncatalyzed unimolecular reactions, reacting groups closer to each other and unable to rotate |
| What is the desolvation of substrates, via enzymes? | Interactions between S and water are replaced by interactions between S and E |
| What is the distortion of substrates, via enzymes? | Some weak interactions with E occur only in transition state, compensates for energy required to distort bonds |
| What is meant by the catalytic functional groups on E must be properly aligned? | Induced fit, as important to catalysis as it was to binding |
| What are the methods for enzymes catalyzing a reaction? | General acid-base catalysis, covalent catalysis, metal ion catalysis |
| True/False: A single enzyme can make use of more than one method to catalyze a reaction. | True |
| In acid-base catalysis, what is not stable and can decay to reactants? | Charged intermediates |
| What is specific acid-base catalysis? | When donation/abstraction is carried out by water itself |
| In acid-base catalysis, acids-bases seek to do what by donating (acids) or abstracting (bases) protons? | Neutralize charges |
| What acts as general acids/bases in enzyme active sites? | Amino acid side chains |
| What occurs frequently in conjunction with general acid-base catalysis? | Covalent catalysis |
| What is formed by covalent catalysis? | Covalent ES complex |
| What results from covalent catalysis? | New reaction pathway than un |
| In covalent catalysis, as long as the steps involved in forming and breaking the covalent bonds are FASTER than the uncatalyzed reaction, what will occur? | Catalysis |
| In metal ion catalysis, metal can do what to substrates? | Orient them |
| What can metals do in metal ion catalysis? | Orient substrates, contribute binding energy, change redox state |
| How do metals, in metal ion catalysis, how do metals contribute to binding energy? | Stabilize charged transition states |
| How do metals, in metal ion catalysis, how can metals change the redox state? | Pick up and/or donate electrons |
| What are the assumptions for a catalyzed reaction? | Enzyme not used up, steady-state assumption |
| True/False: Km is an affinity constant but does not give an idea of an enzyme's affinity. | False |
| The actual meaning of Km depends on the complexity of what? | Complexity of enzymatic mechanism |
| What is Km? | Concentration of substrate [S] leading to initial velocity (Vo) that's half maximal velocity (Vmax) |
| In regard to the definition, what leads to a more complicated definition of Km? | More complex mechanism (more steps) |
| As a dissociation constant for ES, as Km gets smaller, what happens to the affinity of the enzyme for its substrate? | Increases |
| What tells you how efficiently an enzyme catalyzes the reaction in each encounter between E and S, is a second-order constant? | Specificity constant |
| What is achieved when a reaction rate is diffusion-controlled? | Catalytic perfection |
| In enzymes that have two or more substrates, and are bound in different modes, what are the modes for an enzyme reaction involving a ternary complex? | Random order, ordered |
| In enzymes that have two or more substrates, and are bound in different modes, what are the modes for an enzyme reaction in which there is no ternary complex? | Ping-pong mechanism |
| What can help to distinguish between the ping-pong mechanism and mechanism forming a ternary complex? | Enzyme kinetics |
| Some allosteric enzymes have separate catalytic and regulatory subunits, which is especially true of what? | Heterotropic allosteric enzymes |
| Many biochemical processes are organized into what? | Pathways |
| In many biochemical processes, the first enzyme is what by the final product of the pathway (i.e. feedback inhibition)? | Allosterically regulated |
| What is the advantage of inhibiting the first enzyme in a pathway? | Prevents waste of products or toxicity from too much end product |
| What is the graphical representation of enzyme kinetics? | Lineweaver Burk |
| What is another name for a proenzyme? | Zymogen |
| Inactive precursors are converted to what by enzymatic (specific) cleavage (could be autolytic)? | Active enzyme |
| What does covalent modification of an enzyme do? | Affect structure, change charge (ion pairing, H-bonding), alter binding surface, block active sites |
| What is the result of covalent bonding of an enzyme? | Enzyme on/off (tuned up/down), change localization, change substrate preference, change binding partners, degradation |
| Phosphorylation carried out by kinases is specific/nonspecific? | Specific |
| What enzymatic process involves the covalent attachment of phosphate? | Phosphorylation |
| How do kinases carry out phosphorylation? | Recognize sequence motifs |
| In the reversal of phosphorylation, what removes the phosphate group and is it specific or less specific? | Phosphatases, less specific |
| What are the two forms of glycogen phosphorylase? | a, b |
| Which form of glycogen phosphorylase is more active? | a |
| What converts form b of glycogen phosphorylase into form a? | Phosphorylation of 2 Ser |
| What plays a role in converting form b of glycogen phosphorylase into form a to play a role in activation? | Phosphorylase kinase |
| What plays a role in converting form a of glycogen phosphorylase into form b to play a role in inhibition? | Protein phosphatase 1 |
| What are molecules interfering with catalysis, reversible or irreversible, are frequently potent toxins (also medically useful), important regulators of metabolic processes (feedback inhibition)? | Enzyme inhibitors |
| What are the reversible enzyme inhibitors? | Competitive, uncompetitive, mixed, noncompetitive |
| What happens in competitive inhibition? | Substance competes directly with substrate for enzyme binding site |
| What happens in uncompetitive inhibition? | Substance binding directly to ES complex but not to free enzyme |
| What happens in mixed inhibition? | Binding to E and ES at site distinct from substrate |
| What kind of enzymatic inhibitor can modify or destroy a catalytic functional group? | Irreversible inhibitors |
| Irreversible inhibitors are useful in identifying what? | Active site residues |
| What kind of enzymatic inhibitors are extremely potent poisons? | Irreversible inhibitors |
| What kind of enzymatic inhibitors undergo covalent or extremely tight non-covalent modification? | Irreversible inhibitors |
| What happens with a suicide inhibitor? | Binds like substrate and acted upon by enzyme |
| At some point during catalysis, suicide inhibitors are converted into what? | Irreversible inhibitors |
| What kind of enzymatic inhibitor is medically important because it becomes activated only when bound to the enzyme (lowers side effects)? | Suicide inhibitor |
| The pH optimum of an enzyme is found where, in regard to body or outside? | Near pH of enzyme's environment |
| pH, of an enzyme, affects what of R groups of catalytic residues? | Ionization |
| Which serine protease cleaves after large hydrophobic/aromatic side chains (Trp, Phe, Tyr)? | Chymotrypsin |
| What makes up Chymotrypsin? | 3 polypeptides linked with disulfide bonds |
| What do proteases cleave, in addition to cleaving esters slowly? | Peptide bonds |
| What is the fast step of the mechanism utilized by chymotrypsin? | Enzyme acylation and release of p-NP |
| What is the slow step of the mechanism utilized by chymotrypsin? | Hydrolysis of acyl-enzyme intermediate |
| The chymotrypsin active site residue, Ser195, was identified with what residue-specific reagent (chemically labeled with this)? | DIFP |
| In the chymotrypsin active site, what makes up the electron sink? | H-bonded chain from Ser195 to His57 to Asp102 |
| What specifically arises from specificity pockets? | Chymotrypsin, trypsin, elastase |
| What kind of specificity pocket does chymotrypsin come from? | Hydrophobic pocket |
| In the chymotrypsin reaction mechanism, water directly attacks what in the acylation and deacylation steps? | Acyl bond |
| True/False: In the chymotrypsin reaction mechanism, water does not directly attack the peptide bond of the substrate. | True |
| In the chymotrypsin mechanism, the H-bond to Gly only occurs in the short-lived intermediate and is known as what? | TS stabilization |
| In the chymotrypsin mechanism, when the tetrahedral intermediate collapses, what happens? | Reforms C=O, breaks C-N bond |
| In the chymotrypsin mechanism, after tetrahedral intermediate collapse, what acts as a general acid to protonate an amino group making it a better leaving group? | His57 |
| In the chymotrypsin mechanism, after tetrahedral intermediate collapse and the amino group leaves, what remains? | Acyl-enzyme intermediate |
| In the chymotrypsin mechanism, after the amino group leaves and the acyl-enzyme intermediate remains, what is covalently bound to Ser195? | N-terminal peptide |
| In the chymotrypsin mechanism, after the amino group leaves and the acyl-enzyme intermediate remains and the N-terminal peptide is bound to Ser195, acts as a general base again to abstract proton from water? | His57 |
| In the chymotrypsin mechanism, after the amino group leaves and the acyl-enzyme intermediate remains and His57 takes proton from water, what does the remaining OH(-) do? | Acts as nucleophile to attack C=O |
| The HIV protease has what at its active site? | Aspartate |
| What is the HIV protease that is used for peptide bond cleavage? | Aspartyl protease |
| True/False: Water does directly attack the peptide bond in HIV protease. | True |
| Which protease has no covalent enzyme-substrate complex? | HIV protease |
| What prefers to cleave between Phe and Pro amino acid pairs? | HIV protease |
| True/False: The HIV Protease does undergo general acid-base catalysis, but the negatively charged tetrahedral intermediate has no oxyanion hole. No covalently attached intermediate, no acyl-enzyme complex. | True |
| What, on the anti-HIV protease inhibitors, mimics the negatively charged oxygen of a tetrahedral intermediate? | OH |
| What, on the anti-HIV protease inhibitors, fits into the hydrophobic pocket? | Benzyl group |
| Enolase uses divalent cations to convert 2-Phosphoglycerate into what? | Phosphoenolpyruvate |
| In the enolase reaction mechanism, (step 1) what acts as a general base (abstracts proton by general base catalysis)? | Lys345 |
| In the enolase reaction mechanism, (step 1) what is made more acidic by an adjacent carboxyl group, in which electron-withdrawing properties are enhance by interactions with Mg2+ ions? | C2 proton |
| In the enolase reaction mechanism, (step 2) what acts as a general acid and makes -OH a better leaving group (H2O)? | Glu211 |
| What do antibiotics target in bacteria? | Peptidoglycan synthesis |
| In the synthesis of peptidoglycan, what attacks carbonyl of peptide bonds to form a covalent linkage between the substrate peptidoglycan and transpeptidase? | Active site Ser |
| What, being formed, crosslinks the two peptidoglycan chains? | Peptide bonds |
| In the synthesis of peptidoglycan, what (rather than water) carries out the second nucleophilic attack releasing the enzyme? | Peptidoglycan chain #2 |
| In the enolase reaction mechanism, what allows for one peptide bond to be replaced with another? | Transpeptidase |
| What is the structure of all B-lactams antibiotics? | 5-membered thiazolidine ring fused with 4-membered strained B-lactam ring |
| In the mechanism of B-lactam antibiotics, the nucleophilic attack by transpeptidase active site Ser on the B-lactam amide group produces what? | Inactive acyl-enzyme intermediate |
| What can make bacteria antibiotic resistant? | B-lactamases |
| In antibiotic resistance, B-lactamases inactivate B-lactams by promoting what? | Cleavage of B-lactam ring |
| In antibiotic resistance, the cleavage of the B-lactam ring makes B-lactam no longer a substrate/inhibitor of what? | Transpeptidase |
| What is a suicide inhibitor of B-lactamases? | Clavulanic acid |
| In counter move against B-lactamases, B-lactamase's active site Ser nucleophilically attacks clavulanic acid resulting in a reactive group that is attacked by a nucleophile in the active site to result in what? | Irreversibly acylated enzyme |
| What are the three type of regulation of enzymes? | Allostery, covalent modification, cleavage |
| A benefit of biochemical processes being organized into pathways is that the product of one enzyme becomes what? | Substrate of next |
| What is often the final product of a biosynthetic pathway, due to it catalyzing an early step in the pathway? | Heterotropic allosteric inhibitor |
| What is CTP an example of, as CTP is this of ATCase and controls the level of CTP in the cell? | Feedback inhibitor |
| The effects caused by covalent modifications are permanent until what? | Removed by another enzyme |
| Chymotrypsin and trypsin are activated by what? | Proteolytic cleavage of zymogen forms |
| What is responsible for the proteolytic cleavage of the zymogen form of chymotrypsin, resulting in its activation? | Trypsin |
| What is responsible for the proteolytic cleavage of the zymogen form of trypsinogen, resulting in its activation? | Enteropeptidase |
| Glycogen phosphorylase is regulated in response to what? | Phosphorylation |
| Molecules with low complexity will have low or high entropy? | High entropy |
| Molecules with high complexity will have low or high entropy? | Low entropy |
| What is metabolism? | Sum of all chemical reactions in a cell |
| Building complex structures that are low in entropy is only possible when what occurs in the process? | Energy is spent |
| What are the metabolic reactions that build complexity in a cell? | Anabolic, biosynthetic |
| What are the metabolic reactions that generate energy in a cell? | Catabolic |
| What is the ultimate source of energy on Earth? | Sun |
| What is the 1st law of thermodynamics? | Cannot create or destroy energy, can transform energy from one form to another |
| What is the 2nd law of thermodynamics? | In transformation of energy, entropy must increase |
| How do living organisms increase the entropy of the universe in the process of transforming energy? | Extract usable energy, release useless energy (heat) |
| At equilibrium, the scale (between the reactants and the products) will tip in what direction? | Lowest energy, more thermodynamically stable |
| True/False: Equilibrium means that the concentration of products must equal the concentration of reactants. | False |
| True/False: Not all reactions in a cell are exergonic. | True |
| On key concept of metabolism is that unfavorable reactions are what to allow them to proceed? | Coupled with favorable reactions |
| Why is hydrolysis of ATP favorable under standard conditions? | Better charge separation and solvation in products, more favorable resonance stabilization of products |
| What is meant by better charge separation of products in the reason hydrolysis of ATP is favorable under standard conditions? | Less repulsion between negative phosphates |
| What is meant by better solvation of products in the reason hydrolysis of ATP is favorable under standard conditions? | ADP ionizes right away |
| What is meant by more favorable resonance stabilization of products in the reason hydrolysis of ATP is favorable under standard conditions? | Free phosphate |
| What becomes even more favorable (even more negative) if the actual concentration of reactants (ATP) exceeds its equilibrium concentration? | Free energy change |
| Although the actual concentrations of ATP depend on the tissue type, you can see that in general Cellular ATP concentration is usually far below/equal/far above the equilibrium concentration, making ATP a very potent source of chemical energy? | Far above |
| True/False: ATP is not the only phosphorylated compound whose hydrolysis is favorable. | True |
| Hydrolysis of thioesters, such as acetyl-CoA, is favorable or unfavorable? | Strongly favorable |
| True/False: You can also hydrolyze molecules other than phosphates for energy. | True |
| Why do thioesters have a strongly favorable reaction (for hydrolysis) even though they do not undergo resonance like oxyesters? | Start at higher free energy level |
| Thioesters are donor of what? | Acyl groups |
| When a reaction uses the energy of ATP to proceed forward (coupled reaction), what is actually occurring? | Group transfer |
| What happens to the free energy change for the transformation, when looking at the different pathways from reactants to products? | Stays the same |
| True/False: ATP is non-versatile, means no group transfer reactions are possible. | False |
| What is the point of group transfer? | Put on good leaving group |
| Electromotive force (emf) is proportional to what? | Difference in affinity |
| Electromotive force (emf) can be harnessed to do what? | Work |
| In biological systems, oxidation is frequently synonymous with what? | Dehydrogenation |
| How can electrons be transferred in biological redox reactions? | Directly as electrons, as hydrogen atoms, as hydride ions, when something combines directly with oxygen |
| Oxidation reactions always occur with what? | Reduction reactions |
| Oxidizing agents always do what in regard to a reducing agent? | Accepts electrons from |
| To determine which way a reaction proceeds (in an oxidation-reduction reaction), you need to determine what for each half-reaction? | Reduction potential |
| What are the molecules of life? | Proteins, nucleic acids, carbohydrates, lipids |
| What can be made of >20 monosaccharides, can be linear or branched, and differ in their linkages? | Polysaccharides |
| For monosaccharides, how many carbons are in triose? | 3 |
| For monosaccharides, how many carbons are in tetrose? | 4 |
| For monosaccharides, how many carbons are in pentose? | 5 |
| For monosaccharides, how many carbons are in hexose? | 6 |
| For carbohydrates, what is aldose? | Carbohydrate that is an aldehyde |
| For carbohydrates, what is ketose? | Carbohydrate that is a ketone |
| What are non super-imposable mirror images, example is two stereoisomers of glyceraldehyde? | Enantiomers |
| Enantiomers have a different configuration where? | Every chiral center |
| Enantiomers have identical chemical and physical properties with the exception of what? | Rotation of polarized light |
| Stereoisomers of carbohydrates are designated D or L based on the configuration of the chiral center found where? | Furthest from the C=O |
| Will the stereoisomers of carbohydrates be designated as D or L based on the configuration of the chiral center found where the -OH is on the right? | D |
| Will the stereoisomers of carbohydrates be designated as D or L based on the configuration of the chiral center found where the -OH is on the left? | L |
| The D-Aldose, D-glyceraldehyde, is found in what pathway or cycle? | Glycolysis |
| The D-Aldose, D-Erythrose, is found in what pathway or cycle? | Pentose phosphate pathway |
| The D-Aldose, D-ribose, is found in what? | Nucleic acids |
| What are sugars that differ in configuration in at least one chiral center but not all? | Diastereomers |
| What are sugars that differ in configuration in exactly one chiral center? | Epimers |
| True/False: Diastereomers have the same chemical and physical properties. | False |
| What is the relationship between the following carbohydrates: D-galactose, D-glucose? | Epimers |
| What is the relationship between the following carbohydrates: D-galactose, D-mannose? | Diastereomers |
| What is the relationship between the following carbohydrates: D-glucose, D-mannose? | Epimers |
| The D-Ketose, Dihydroxyacetone, is found in what pathway or cycle? | Glycolysis |
| Ketoses that did not get a unique name are named by inserting what immediately prior to the “ose” in the name of the corresponding aldose? | "ul" |
| The D-Ketoses, D-ribulose and D-xylulose, are found in what pathway or cycle? | Pentose phosphate pathway |
| Where are most sugars cyclic? | In vivo |
| What are the 5-membered cyclic sugars called? | Furanoses |
| What are the 6-membered cyclic sugars called? | Pyranoses |
| What are the reducing sugars? | Aldoses |
| What happens when a linear sugar cyclizes? | Alcohol added to aldehyde or ketone |
| A new chiral center formed by the cyclization of sugar is called what? | Anomeric carbon |
| A new chiral center formed by the cyclization of sugar, leading to anomeric carbon, means that there are two new what possible? | Stereoisomers |
| What are cyclic epimers? | Anomers |
| What is the anomeric -OH group that is found below the plane? | Alpha |
| What are the anomeric -OH found above the plane? | Beta |
| When two monosaccharides join to form a disaccharide, an alcohol is added to what? | Hemiacetal or hemiketal |
| What kind of bond results from the combination of anomeric carbon and an -OH of another sugar? | O-glycosidic bond |
| What is the result of an O-glycosidic bond? | Acetal or ketal |
| An acetal is fairly stable, and thus will be hydrolyzed by what? | Acid and heat |
| What is much more stable than hemiacetal, and thus will not open up into chain form? | Acetal |
| O-glycosidic bonds can form a variety of linkages due to what? | Use of different OH groups or epimers |
| What is produced if the OH in the second sugar is on the anomeric carbon (glycosidic bond joins two anomeric carbons)? | Nonreducing sugar |
| What kind of sugars have no free anomeric carbon, two acetals, and no hemiacetal to open up into the linear form? | Nonreducing sugar |
| What is the common disaccharide that is a malt sugar (think brewing) that can be cleaved by maltase? | Maltose |
| What is the common disaccharide that is a milk sugar that can be cleaved by lactase? | Lactose |
| What is the common disaccharide that is table sugar (made by plants) that can be cleaved by sucrase? | Sucrose |
| In the naming of disaccharides, what is the parent of sucrose? | Glucose (aldose) |
| In the naming of disaccharides, the short name of a nonreducing sugar will always contain what? | Double-headed arrow |
| What are stereoisomers that differ at only the anomeric carbon? | Anomers |
| Why do polysaccharides not have a defined molecular weight? | No template, no start-stop, length determined by enzymatic activity |
| What are the two types of homopolysaccharides? | Unbranched, branched |
| What are the two types of heteropolysaccharides? | Two monomer types (unbranched), multiple monomer types (branched) |
| What is glycogen? | Branched homopolysaccharide of glucose |
| Where are the linked chains in glycogen? | a1 to 4; a1 to 6 (every 8-12 residues) |
| What is the main storage polysaccharide in animals? | Glycogen |
| What is starch? | Mixture of 2 homopolysaccharides of glucose |
| What is the unbranched starch polymer of (a1 to 4) linked residues? | Amylose |
| What is the branched (like glycogen) starch polymer with branch-points with (a1 to 6) linkers occurring every 24-30 residues? | Amylopectin |
| What is the main storage homopolysaccharide in plants? | Starch |
| Glycogen and starch are found in what? | Granules |
| What contain enzymes to make and break the polymers, also have glycogen and starch in them? | Granules |
| Which forms of glycogen and/or starch have one reducing end but many nonreducing ends? | Glycogen, amylopectin |
| When does enzymatic processing occur in glycogen and starch, on the many nonreducing ends? | Simultaneously |
| We are evolutionarily programmed to crave starch, but what helps us to digest it? | Amylase |
| What are the glucose polymers linked via B1 to 4 linked chains? | Cellulose |
| What forms between adjacent monomers in cellulose? | Hydrogen bonds |
| Additional hydrogen-bonds between chains forming an extensive network that gives cellulose what? | Tensile strength |
| What are some of the main characteristics of cellulose that make it undigestible to humans? | Tough, fibrous, insoluble in water |
| What is the enzyme made in fungi that helps to digest cellulose and what is cleaved in this process? | Cellulase, B1 to 4 linkages |
| Why can cows eat grass and termites eat your porch? | Live symbiotically with microorganisms in gut that produce cellulase |
| What conformation is amylose (in starch) found in and why? | Helical, lowest energy |
| What conformation is cellulose found in and why? | Extended conformation, maximize hydrogen bonds, lowest energy |
| Amylose helix has an ideal dimension to accommodate what? | Iodide ions |
| The binding of ions inside amylose alters their what, leading to intense blue-black color? | Electrochemical properties |
| What is similar to cellulose because it forms extended fibers, is tough/insoluble, can't be digested by vertebrates? | Chitin |
| What is the component that is different from chitin to cellulose (this instead of glucose)? | N-acetylglucosamine |
| What is the structure of chitin? | Linear, unbranched B1 to 4 linked chains |
| Where is chitin found? | Cell walls of mushrooms, exoskeletons |
| What is agar? | Complex mixture of hetereopolysaccharides containing modified galactose |
| Where is agar found? | Cell wall of some seaweeds |
| For what is agar used for in labs? | Provide growth surface for bacteria |
| Agarose is a component of agar used as a matrix for what? | Separate DNA by electrophoresis |
| What is a combination of uronic acid and amino sugar? | Glycosaminoglycans |
| What makes up glycosaminoglycans? | Anionic polysaccharide chains, repeating disaccharides |
| Glycosaminoglycans can be what to give them additional negative charge? | Extensively sulfated |
| Why is a negative charge on glycosaminoglycans a good thing? | Extended conformation (minimize repulsion), highly hydrated (excellent for connective tissue/joint lubrication) |
| In what conformation will you find Heparin in, and at what weight? | Linear polymer, 3-40 kDa |
| What kind of glycosaminoglycans have the highest negative charge density among biomolecules? | Heparin |
| What are the benefits of the negative charge of heparin? | Makes it sticky to positive charges, prevent blood clotting, decrease virulence of bacteria/viruses, growth factor for blood vessels |
| How does heparin prevent blood clotting? | Activating protease inhibitor antithrombin |
| How does heparin decrease virulence of bacteria/viruses? | Sticks to them |
| What are sulfated glycosaminoglycans (like heparan sulfate) and a large rod-shaped core protein? | Proteoglycans |
| Proteoglycans are mostly what by mass (>80-90%)? | Carbohydrate |
| What is the role of proteoglycans? | Interact with variety of receptors from neighboring cells and regulate cell growth (help cells talk to each other) |
| Syndecans (proteoglycans) bind to what? | Integrins |
| What are integrins? | Receptor for proteoglycans |
| Where are integrins found? | Linked to cytoskeleton, other proteins |
| What allows for transmission of signal from cell 1 to cell 2 to regulate processes such as cell growth, motility, apoptosis, wound healing, etc.? | Proteoglycans |
| What are glycoproteins? | Proteins with covalently attached carbohydrates |
| Glycoproteins are made up more by what, rather than sugar (~1-10% carbohydrate by mass)? | Protein |
| What kind of bonds are found, in a glycoprotein, between anomeric carbon of sugar and OH of Ser or Thr? | O-glycosidic bonds |
| The O-glycosidic bonds found in glycoproteins occur where? | Golgi only |
| What kind of bonds are found, in a glycoprotein, between anomeric carbon of sugar and NH2 group of Asn? | N-glycosyl bonds |
| The N-glycosyl bonds found in glycoproteins occur where? | ER and Golgi |
| Most of what kind of proteins are glycosylated? | Secreted, plasma membrane |
| In glycoproteins, the following is very important for what aspect: folding, trafficking of proteins in secretory pathway, protein stability, mediate protein-protein interactions, cell-cell communication, cell-cell adhesion, and more? | Glycosylation |
| What are glycolipids? | Lipids with covalently bound oligosaccharides |
| For glycolipids, in vertebrates, what composition determines blood groups? | Ganglioside carbohydrate |
| In terms of glycolipids, in gram-negative bacteria, what component covers the peptidoglycan layer? | Lipopolysaccharides |
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