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NWHSU biochem exam 2
| Question | Answer |
|---|---|
| What do enzymes do? | Increase reaction rate by lowering the activation energy (Biocatalyst) |
| Are enzymes used up in reactions? | Nope, nope! |
| How much of an enzyme is needed to effect a reaction? | Just a small amount is necessary and can have a big effect |
| Enzymes vs. inorganic catalysts | Very specific!, Substrate (reactant) & Reaction, Mild conditions (pH, Temp, P) |
| Vast majority of enzymes are.. | proteins |
| Enzymes end with.. | "-ase" |
| Many enzymes require what component to perform proper functioning? | a non-amino acid component |
| Can enzymes function as polypeptides | Oh, you bet! |
| Name for a functional enzyme | Holoenzyme |
| Polypeptide component of an enzyme | Apoenzyme |
| Organic substance | Coenzyme |
| Inorganic substance | Cofactor |
| Reaction formula without an enzyme | S ---------> P |
| Reaction formula WITH an enzyme | E + S <---> E + P OR E + S <---> ES <---> EP <---> E + P |
| Importance of enzyme kinetics? | To help us understand and predict enzymatic reactions & factors affecting them To study the reaction rate vs [S] relationship |
| The independent variable.. (X) | [S] |
| The dependent variable.. (Y) | V-naught (Vo) |
| Non-reversible enzyme regulation includes.. (3 subtypes) | Proteolytic Cleavage Hormones: insulin glucagon Proteases in digestive tract: trypsin, chymotrypsin Blood clotting cascade |
| Types of proteolytic cleavage | hormones- insulin, glucagon proteases in digestive tract- trypsin, chymotrypsin blood clotting cascade |
| Glutamate Carboxylase, involved in the formation of blood clots is dependent on.. | Vitamin K |
| cofactors required for the proper functioning of the coagulation cascade.. (blood clotting) | Ca2+, phospholipid & Vitamin K |
| Vitamin K antagonists, competing for Vit. K binding site | 1.) Dicoumarol 2.) Warfarin-> Coumadin (blood thinner) |
| What are glycolipids? | membrane lipids carrying oligosaccharides |
| Example of a glycolipid | blood types- determined by variations of small oligosaccharides |
| glycolipids are ___________ in the membrane | hydrophobic |
| glycolipids are ___________ on the surface of RBC's | hydrophilic |
| Lipopolysaccharides are found.. | in the outer membrane of gram-negative bacteria |
| Lipopolysaccharides- immune system reacts to.. | Lipid A (the endotoxin) of the lysed cells |
| Is there variation in the polysaccharide formation of lipopolysaccharides? | Slight variations occur- "serotypes" |
| where do polysaccharides of pathogens bind? | to host surface structures |
| The Sugar Code leads to formation of.. | many unique polymers that have specific (non-covalent) interactions with binding proteins (like a lock & key!) |
| Reasons for multitude of oligosaccharides: | 1.) large # of building block types (~20-30 monosaccharides) 2.) # of building blocks not restricted a.] alpha or beta configuration b.] 1->1, 1->2, 1->3, 1->4, 1->6 c.] # of branches, types of branches |
| Lectins are often.. | Receptors |
| Lectins are proteins with.. | specific binding sites for specific oligosaccharides |
| Lectins are specific for.. | cell to cell recognition, transfer of hormone signals, adhesion between cells |
| Oligosaccharides (comonents of a variety of glycoproteins/glycolipids on the outer surface of plasma membranes, interact with lectins in the.. | extracellular milieu |
| viruses that infect animal cells (think influenza, etc) bind to.. | cell surface glyoproteins as the 1st step in infection |
| bacterial toxins (think cholera & pertussis) bind to.. | surface glycolipids before entering a cell |
| some bacteria, like H. pylori, adhere to.. | animal cells where they colonize or infect the cells |
| Selectins (lectins) in the plasma membrane of certain cells mediate.. | cell-cell interactions like those of neutrophils with endothelial cells at an infection site |
| Mannose 6-phosphate receptor/lectin of the trans Golgi complex binds.. | the oligosaccharide of lysosomal enzymes, targeting them for transfer into lysosomes |
| Functions of carbohydrates: | source of energy (glucose), storage of energy, protection/shape (cell wall) & for adhesion, signaling (glycocalyx) |
| Carbohydrates structure: | polyhydroxy-aldehydes or ketones (carbonyl groups) --> (CH2O)n, may contain P, S, N ; oligosaccharides (small polymers- aka: disaccharides, trisaccharides, etc --> nutrients) or polysaccharides (aka- very large polymers) |
| Ketose | Any of a class of simple sugars (monosaccharides) containing a ketone group. |
| Aldose | Any of a class of simple sugars (monosaccharides) containing a aldehyde group. |
| Simple sugars end in.. | "ose" (for carbohydrates) |
| name for 3 carbon atoms.. | triose |
| name for 4 carbon atoms.. | tetrose |
| name for 5 carbon atoms.. | pentose(one of 2 most important groups) |
| name for 6 carbon atoms.. | hexose (one of 2 most important groups) |
| name for 7 carbon atoms.. | heptose |
| D-sugar | H O \ // C | H-C-OH <-- "OH" ON THE RIGHT | CH2OH aldo-triose, chiral center, D-Glyceraldehyde D-carbohydrates occur in nature |
| L-sugar | H O \ // C | HO-C-H <-- "OH" ON THE LEFT | CH2OH L-Glyceraldehyde |
| Mirror images = | enantiomers |
| Draw glucose structure.. | H O \ // C | H-C-OH | HO-C-H | H-C-OH | H-C-OH <--For L-Glucose, switch H w/ OH | CH2OH D-glucose, other config combos @C2-C5 = diastereomers, total possibilies with 4 chiral C's: 2^4=16 |
| Draw D-glyceraldehyde structure.. | H O \ // C | H-C-OH {D-Aldose} | CH2OH |
| Draw D-Mannose structure.. | H O \ // C | HO-C-H | HO-C-H | H-C-OH | H-C-OH | CH2OH {Aldose} |
| Draw D-Galactose structure.. | H O \ // C | H-C-OH | HO-C-H | HO-C-H | H-C-OH | CH2OH {Aldose} |
| Draw D-Ribose (RNA) strucure.. | H O \ // C | H-C-OH | H-C-OH | H-C-OH | CH2OH {Aldose} |
| Which structures are epimers of D-glucose? | D-mannose & D-galactose (differ in configuration at the 1st carbon) |
| Draw Dihydroxyacetone structure.. | CH2OH | C=O | CH2OH {ketose} |
| Draw D-fructose structure.. | CH2OH | C=O | HO-C-H | H-C-OH | H-C-OH | CH2OH {ketose} |
| Monosaccharides with non-chiral C1 can undergo.. | spontaneous cyclization where C1 becomes chiral with 2 options of configuration |
| Alpha cyclic structure of monosaccharide = | (First carbon) C-OH in opposite direction as CH2OH (Carbon 6) |
| Beta cyclic structure of monosaccharide = | (First carbon) C-OH in same direction as CH2OH (carbon 6) |
| When a linear monosaccharide becomes cyclic it is called a.. | hemiacetal (aldose) or hemiketal (ketose) |
| Hemiacetal's & Hemiketal's are.. | compounds that are derived from aldehydes and ketones, respectively |
| what are alpha & beta anomers? | either of a pair of cyclic stereoisomers (designated α or β) of a sugar or glycoside, differing only in configuration at the reducing carbon atom |
| Haworth Perspective Formula.. | OH & H on far right can switch places, when OH is down = alpha, when it is up = beta |
| what do conformational formulas do? | provide possible chair forms of a molecular structure. |
| Disaccharides are formed when.. | two monosaccharides undergo a condensation reaction which involves the elimination of a small molecule, such as water, from the functional groups only. |
| What happens when disaccharides undergo hydrolysis? | they cleave to fro two monosaccharides |
| Are hydrolysis & condensation reactions enzyme catalyzed? | You betcha. |
| Common disaccharides.. | Lactose & Sucrose |
| Pseudonym for sucrose.. | table sugar |
| Why are peeps lactose intolerant? | due to lack of hydrolytic enzyme lactase which can break the Beta 1->4 bond |
| 3 disaccharides? | Maltose, lactose, sucrose |
| Maltose building blocks? | glucose, alpha-configuration, 1->4 connection |
| Lactose building blocks? | galactose & glucose, beta-configuration, 1->4 connection |
| Sucrose building blocks? | Glucose & fructose, alpha1 & beta2 configuration, alpha1<->2Beta connection |
| Hemiacetal (hemiketal) formation | spontaneous equilibrium, 2 possible outcomes (alpha or beta) |
| acetal (ketal) formation | enzyme-catalyzed goes to completion, 1 outcome, (alpha, beta, 1, 2, 3...) |
| hemiacetal (hemiketal) rxn partners | -OH + C=O (aldehyde, ketone) |
| Acetal (ketal) rxn partners | hemiacetal (ketal) + -OH |
| hemiacetal (hemiketal) outcome | NO H2O formation |
| acetal (ketal) outcome | H2O formation |
| hemiacetal (hemiketal) breaking | spontaneous |
| Acetal (ketal) breaking | enzyme-catalyzed |
| Commonly used for regulatory purposes.. | feedback inhibition |
| mechanism for feedback inhibition | allosteric regulation |
| what type of response is typical for a multi subunit protein | a sigmoid response |
| allosteric enzymes are.. | enzymes that change their conformational ensemble upon binding of an effector, which results in an apparent change in binding affinity at a different ligand binding site. |
| allosteric enzymes consist of.. | catalytic unit, regulatory unit, substrate & positive modulator |
| Where is reversible covalent modification (regulation) common? | quite common in higher organisms |
| ATP = | adenosine tri-phosphate |
| ADP = | adenosine di-phosphateP |
| phosphorylation reaction.. | Enz--(Protein Kinase)--> {{need to fix}} **In the reverse reaction use Protein Phosphates instead of Kinase. |
| Example of enzyme phosphorylation: (reversible covalent modification) | Glycogen-Phosphorylase |
| Function of Glycogen-Phosphorylase? (reversible covalent modification) | release of glucose from glycogen (glucose polymer), gets activated when the blood glucose is low |
| Phosphorylase Phosphatase associated with.. | Insulin (blood glucose increase) |
| Phosphorylase kinase associated with.. | (fight/flight, exercise) epinephrine, glucagon (low blood glucose) |
| Reversible covalent modification (regulation) typical for bacteria? | Methylation |
| Are monosaccharides reducing agents? Are they sweet? | They sure are! & Yes. |
| Why do we use Benedict's reagent/Fehling's reaction? | it is a chemical compound that can detect glucose or fructose. (used to test for simple sugars) Only occurs when the ring opens |
| Reducing Sugars "rule" | Sweet tasting carb's (sugars) -mono, di, trisaccharides- are reducing carbohydrates, meanwhile, polysaccharides are non-reducing |
| Exception to the reducing sugars "rule" | Neither ring can open--> non-reducing (but tastes sweet) |
| Are disaccharides reducing sugars? Are they sweet? | mostly yes & yes |
| Are trisaccharides (molasses) reducing sugars? sweet? | yes & yeees |
| Are polysaccharides reducing? Sweet? | nope & nooope |
| Used in clinistix? | glucose oxidase, tests for presence of glucose |
| Glycoproteins are greater than or equal to.. | oligosaccharide attached to a protein |
| Glycoproteins are found.. | in cytoplasmic membranes & soluble proteins |
| Glycoprotein functioning.. | functions in support, adhesion (communication & cell-cell adherence), movement and regulation. |
| Glycoprotein examples | Blood types & Antibodies, hormones, milk proteins (secreted proteins) |
| Oligosaccharide linkages.. | glycosidic bonds |
| Types of glycoconjugates | proteoglycans, glycoproteins |
| Proteoglycan structure | polysaccharide connected to 1 or more proteins |
| where are proteoglycans located | in the extra cellular matrix |
| what do proteoglycans interact (non-covalently) with? | glycocalyx on cell surfaces |
| 3 types of reversible inhibition: | Mixed, competitive, & noncompetitive inhibition |
| LB-Plot for mixed inhibition | Lines intersect in the 2nd quadrant, Vmax decrease, Km increase |
| Noncompetitive inhibition LB-Plot | Lines intersect on the x-axis, Vmax decreases, Km stays the same |
| Effect of pH on enzyme activity | As pH increases, enzyme activity increases until it reaches an optimal point in which enzymes denatures and as pH increases, the enzyme loses its effectiveness |
| Effect of temperature on enzyme activity | As the temperature increases, enzyme activity increases until it reaches an optimal point in which the enzyme denatures and loses its effectiveness |
| How do enzymes work in cells? | in groups, as part of pathways or cycles |
| Name for product of one enzyme RXN that became the substrate of another RXN | metabolites |
| Are all enzymes regulated in cells? | Nope, only key enzymes. |
| Types of enzyme regulation (modulation) | inhibition & activation |
| Enzyme regulation overview: | {{Look up in notes, helpful!}} |
| Michaelis-Menten Equation: | Vo = Vmax [S]/Km + [S] |
| Independent variable in MM Equation | [S], ("X" variable) |
| Dependent variable in MM Equation | Vo, ("Y" variable), the rate of rxn/velocity of rxn |
| Constant in the MM Equation | Vmax, (theoretical maximal velocity) |
| In MM Equation Km is.. | @ 1/2Vmax |
| 1/2Vmax in MM Equation | Km |
| Lineweaver Burke Equation | 1/Vo = Km/Vmax * 1/[S] + 1/Vmax |
| Line equation | Equal to the Lineweaver Burke Equation: y = mx + b y = 1/Vo m = Km/ Vmax x = 1/[S] b = 1/Vmax |
| Competitive inhibition LB-Plot | Lines intersect @ the Y-intercept |
| Competitive inhibition Vmax & Km | Vmax = unchanged & Km = increase |
| Competitive inhibition equation | E + S <---> ES ---> E + P I= inhibitor, S= substrate, E= enzyme, P= product |
| Where does I bind in Competitive inhibition? | @ the active site, thus preventing binding of S |
| Structure of the inhibitor in Competitive inhibition | Inhibitor has a similar structure to Substrate |
| Uncompetitive inhibition equation | E + S <---> ES <---> E + P |
| Uncompetitive inhibition LB-Plot | Lines don't intersect |
| Uncompetitive inhibition Vmax & Km | Both decrease |
| What kind of bond is commonly used in biochemistry? | glycosidic bond = acetal or ketal, involving one or more carbohydrates EXAMPLES.. monosaccharide-monosaccharide monoxaccharide-lipid monosaccharide-amino acid |
| Types of polysaccharides: | 1.) HOMOPOLYSACCHARIDES (1 type of building block- monosaccharide), can be branched or unbranched. 2.) HETEROPOLYSACCARIDES, can be branched or unbranched |
| Building block of a homopolysaccharide | Glucose! |
| Detail of the reducing & nonreducing ends of a homopolysaccharide | Rings & cannot be opened |
| How does Amylopectin react in starch? | refuses to branches in starch (glycogen) |
| Cellulase details? | 1.) Cellulase is the enzyme that breaks the B1-->4 bond in cellulose., 2.) Not found in any higher organisms, 3.) Used by ruminating animals, originates from bacteria in (rumen?) |
| Lactase details? | breaks down a B1-->4 bond |
| 2 heteropolysaccharides are found in the cell walls of bacteria? | Muramic acid & N-acetylmuramic acid |
| Where is peptidoglycan found? | It is a polysaccharide in bacterial cell walls, unbranched and hetero |
| How does peptidoglycan "kind of branch"? | through cross-linking with oligopeptides |
| How is peptidoglycan inhibited? | biosynthesis of peptidoglycan is inhibited by certain antibiotics (e.g. penicillin) |
| So, what's that Chitin stuff all about? | Funny you asked, it is a tough, protective, semitransparent substance, primarily a nitrogen-containing polysaccharide, forming the principal component of arthropod exoskeletons and the cell walls of certain fungi. |
| What are glycosaminoglycans? | long unbranched polysaccharides consisting of a repeating disaccharide unit. |
| Glycosaminoglycans: Hyaluronate details? | Extracellular- a) joint lubrication b) jelly like consistency c) associated with lots of H2O |
| Glycosaminoglycans: Heparin details? | -regulation of blood clotting (blood thinner) |
| Polysaccharide breakdown- Starch: (homo) | monosaccharide | linkage | function ------------------------------------------- glucose | alpha 1->4 | store energy in alpha 1->6 plants |
| Polysaccharide breakdown- Glycogen: (homo) | monosaccharide | linkage | function ------------------------------------------- glucose | alpha 1->4 | store energy in alpha 1->6 animals |
| Polysaccharide breakdown- Cellulose: (homo) | monosaccharide | linkage | function ------------------------------------------- glucose | beta 1->4 | plant cell walls |
| Polysaccharide breakdown- Dextran: (homo) | monosaccharide | linkage | function ------------------------------------------- glucose | beta 1->3 |biofilm formation of bacteria |
| Polysaccharide breakdown- Peptidoglycan: (hetero (unbranched)) | monosaccharide |linkage| function ------------------------------------------- n-acetylglucosamine|B1->4 |bacteria cell walls n-acetylmuramic acid |
| Polysaccharide breakdown- Hyaluronate: (hetero (unbranched)) | monosaccharide | linkage | function ------------------------------------------- Glucosamine | beta 1->3 |xtracellular matrix n-acetyl- | beta 1->4 |->joint lubrication glucosamine | (alt.) | |
| Polysaccharide breakdown- Heparin: (hetero (unbranched)) | monosaccharide | linkage | function ------------------------------------------- sulfated iduronic|alpha 1->4| prevent blood acid & sulfated | | clotting glucuronic acid |
| Glutamate carboxylase involved in blood clotting is... | Vitamin K dependent |
| feedback inhibition is an example of _______ inhibition. | reversible, non covalent |
| which of the following describes the typical feedback inhibition the best? | allosteric |
| proteases in the small intestine get activated by | proteolytic cleavage of C- and/or N-termini |
| carbohydrates are poly ___________ compounds | -hydroxy carbonyl |
| A heptose consists of _____ carbons | 7 |
| Mannose is a _______ of glucose | epimer |
| The carbonyl group depicted is located on carbon #... CH2OH | C=O | H-C-OH | H-C-OH | CH2OH | 2 |
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