Biochem Final
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| Cofactors= ? | Things like Metal ions
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| Coenzymes = ? | Small organic groups that are only transiently associated with the enzyme
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| Prosthetic groups= ? | organic groups that are permanently associated with the enzyme
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| What reactions occur in the mitochondria? | TCA cycle, FA oxidation, and oxidation of pyruvate
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| What reactions occur in the cytosol? | Glycolysis, Pentose phosphate pathway and FA biosynthesis
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| What reactions occur in the Nucleus? | DNA and RNA synthesis
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| What reactions occur in the Lysosome? | Degardation of complex macromolecules
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| What reactions occur in the peroxisomes? | additional FA oxidation and detoxification of peroxides occur
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| Sum up what an enzyme does: | The enzyme lowers the energy barrier. It does NOT change the equilibrium constant of a reaction, but it does speed the reaction towards equilibrium (slide #6)
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| what is Velocity of an enzyme? | The rate of product formation per unit of time
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| According to The Rate Law/Effect of Concentration on reaction rate, if N = 0, then what? | Then the reaction proceeds at a rate independent of the concentration of the reactant.
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| According to The Rate Law/Effect of concentration on reaction rate, if N=1, then what? | Then the reaction proceeds at a rate directly proportional to the concentration of the reactant
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| According to the rate law/Effect of concentration on reaction rate, If N=2, then what? | Then the reaction proceeds at a rate proportional to the SQUARE of the concentration of the reactant.
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| What effects enzymes? | Substrate concentration, PH, and Temp
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| What enzymes exhibit Michaelis-Menton Kinetics? | Enzymes that show a hyperbolic curve in response to substrate concentration
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| What enzymes are said to be allosteric enzymes? | Enzymes that show a sigmoid curve in response to substrate concentration
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| What is the optimal temp range for enzymes in humans? | 37C
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| where can you find Thermophilic bacteria? | hot springs (their proteins do not denature until they are very hot
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| At substrate concentrations well below the Km of an enzyme, describe the rate of reaction = | The reaction is 1st order and therefore proceeds at a rate DIRECTLY DEPENDENT of the substrate concentration
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| At substrate concentrations well above the Km of an enzyme, describe the rate of reaction = | The reaction is 0 order and therefore proceeds at a rate related to the square of the substrate concentration
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| How does Temperature affect most enzymes? | Increasing temp speeds up enzyme reactions to a certain point, but too much increase will denature the enzyme. basically
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| At what PH would you find Pepsin? | (in stomach = Acidic)
1.5
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| At what PH would you find Trypsin? | Around 5.5
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| At what PH would you find Alkaline Phosphatase? | Basic - around PH 9
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| What are the 4 modes of enzyme inhibition? | Mixed, Competitive, uncompetitive, and noncompetitive
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| A competitive inhibitor will have what effect on a target enzyme? | Increases Km, does not affect Vmax
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| What are the 3 assumptions with M-M kinetics model? | (1) [S] >>> than the total [ENZYME] (2) The reaction is at steady state (3) The Initial velocities are used to analyze the enzyme
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| The catalytic efficiency of an enzyme is reflected how? | In the kcat value which is equal to the Vmax divided by the total enzyme concentration
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| In M-M kinetics, Km is equal to what? | Equal to the substrate concentration at which the enzyme is at 1/2 Vmax
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| At a low Km, the enzyme has ______ affinity for the substrate | High
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| At High Km, the enzyme has _____ affinity for the substrate | Low
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| On a Lineweaver-Burke plot of enzyme kinetics date, which value provides the Km? | The negative inverse of the X-intercept
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| On a Lineweaver-Burke plot of enzyme kinetics date, which value provides the Vmax? | The y-intercept
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| Competitive Inhibition occurs how? | Occurs when the inhibitor binds at the active site in place of the endogenous substrate
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| What happens to Vmax and Km in Competitive Inhibition? | Vmax remains the same, Km goes up
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| Non competitive Inhibition occurs how? | This type of inhibitor doesn't bind at the active site, but instead binds at an allosteric site away from the active site. It binds to the enzyme in the presence and absence of the native substrate
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| What happens to Vmax and Km in Noncompetitive Inhibition? | Vmax of the enzyme decreases, Km is not affected (because the noncompetitive inhibitor does not interfere with the binding of the substrate)
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| Enzyme Regulation includes what? | Positive regulation, activation, as well as inhibition
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| Allosteric Mechanisms are what? | Mechanisms where the site of the effector binding is away from the active site of the enzyme. The allosteric site is distincy from the active site.
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| Allosteric can be Positive/negative/both? | Both. They can also modify an enzymes Km/Vmax
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| Allosteric enzymes show what kind of curve? | Sigmoidal kinetics/curve
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| Homotropic effectors are what? | Are the substrate of the enzyme acting as the regulatory molecule. These effectors are most often positive effectors so binding is cooperative. (O2 and Hb)
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| Heterotropic effectors are what? | Are effectors that are different than the substrate. The best example of this is a sceme known as feedback inhibition, where the product of an enzyme (metabolic) pathway feeds back to inhibit an earlier step in the pathway.
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| What is FEEDBACK INHIBITION? | It is where the product of an metabolic pathway feeds back to inhibit an earlier step in the pathway
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| Phosphorylation/De-phosphorylation occurs predominantly at what 3 AA? | Ser, Thr and Tyr residues
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| A noncompetitive inhibitor will bind where on a protein? | At an allosteric site
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| Proteins can be activated by phosphorylation, such as what? | Glycogen Phosphorylase
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| Proteins can be inactivated by phosphorylation, such as what? | Glycogen Synthesise
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| Vitamin B3 is used to Synthesize which cofactor? | Nicotinamide Adenine Dinucleotide (NADH/NAD+)
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| Vitamin B2 is used to synthesize which cofactor? | Flavin Mononucleotide (FAD/FADH2/FMN/FMNH2)
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| Vitamin B1 is used to synthesize which cofactor? | Thiamine Pyrophosphate (TPP)
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| Vitamin B5 is used to synthesize which cofactor? | CoASH (coenzyme A)
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| Vitamin B6 is used to synthesize which cofactor? | Pyridoxal Phosphate
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| Vitamin B9 is used to synthesize which cofactor? | Tetrahydrofolate (THF)
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| Vitamin B12 is used to synthesize which cofactor? | Cobalamin
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| Vitamin H is used to synthesize which cofactor? | Biotin
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| Vitamin C is used to synthesize which cofactor? | Ascorbic Acid
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| Another Name for Vit B1 | Thiamine
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| Another Name for Vit B2 | Riboflavin
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| Another Name for Vit B3 | Niacin
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| Another Name for Vit B5 | CoASH
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| Another Name for Vit B6 | Pyridoxine
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| Another name for Vit B9 | Folic Acid
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| Another name for Vit B12 | Cobalamin
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| Deficiency in Vit B3 = | Pellagra (diarrhea, dermatitis, dementia)
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| Deficiency in Vit B2 = | Cheilosis (cracking at the corner of the lips, scaling of the lips)
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| Deficiency in Vit B1 = | Beri Beri and Spina Bifida
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| Deficiency in Vit B5 = | Unknown?
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| Deficiency in Vit B6 = | Peripheral Neuropathy
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| Deficiency in Vit B9 = | Magaloblastic Anemia and neural tube defects
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| Deficiency in Vit B12 = | Pernicious Anemia and Folate Trap
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| Deficiency in Vit H = | Only happens when eating too many raw eggs
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| Deficiency in Vit C = | Scurvy
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| GLUT-1 = | abundant in erythrocytes and at the blood/brain barrier. GLUCOSE UPTAKE
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| GLUT-2 = | In liver, kidney, and beta cells of the pancreas. GLUCOSE IN OR OUT OF CELLS
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| GLUT-3 = | Is the primary transporter in neurons. GLUCOSE UPTAKE
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| GLUT-4 = | Is abundant in MUSCLE and ADIPOSE TISSUE. GLUCOSE UPTAKE.
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| Which GLUT's are primarily involved in glucose UPTAKE? | GLUT 1/3/4
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| Which GLUT's are primarily involved in transporting glucose either into/out of cells depending on need of the organism? | GLUT-2 (ONLY)
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| Why are the enzymes in the plasma often used as diagnostics? | The can signal tissue damage, they can mark a change in metabolism, they can serve as a marker of a congenital defect.
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| THE GLUT transporters are examples of what kind of transporter? | Uniport
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| In glycolysis, where is ATP consumed? | Steps 1 and 3
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| In glycolysis, where is ATP regenerated? | Steps 7 and 10
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| Net total of ATP per Glucose in Glycolysis? | 2
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| Glucokinase vs Hexokinases for Km? | Glucokinase has a much higher Km than other hexokinases with a high Vmax
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| Glucokinase vs Hexokinases for M-M kinetics? | Hexokinasess DO follow M-M, but Glucokinases DO NOT!! Glucokinases follow sigmoidal kinetics
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| Glucokinases vs Hexokinases G6P? | Glucokinases are NOT inhibited by physiological concentrations of G6P, but Hexokinases ARE inhibited by it.
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| What enzymes are potential control points (non-reversible) for glycolysis? | Hexokinase, Phosphofructokinase-1 (PFK-1), and Pyruvate Kinase -- they have large negative Delta G's
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| Which small molecule as the GREATEST effect on the direction of flux through PFK-1 and therefore, glycolysis? | Fruc, 2-6-BP (activates PFK-1 and deactivates FBP, thus Fru-6Phos can only continue onto Fru-1,6-BP)
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| Which hormone is responsible for increasing the production of Fructose 2,6 BP? | Insulin
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| Which 2 molecules are interchangable? and which one continues on to furthe Glycolysis? | DHAP and Glyceraldehyde-3-Phosphate (GAP). GAP continues on to become interchangable with (2) 1,3-BPG
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| What are the products of AEROBIC glycolysis of 1 glucose molecule? | 2 NADH, 2 ATP, 2 Pyruvate
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| How are glucokinase and hexokinases the same? | They both have specificity for hexose sugars
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| In the presence of a low concentration of glucose and a high concentration of fructose-6-phsophate, where does glucokinase reside in the cell? | Nucleus
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| What converts ATP to cAMP? | Adenylyl Cyclase
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| GLucose to G6P is catalyzed by what? | Hexokinase and MG2++
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| G6P to F6P is catalyzed by what? | Phosphoglucose isomerase (PGI)
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| F6P to FBP (fructose 1,6-bisphosphate) is catalyzed by what? | Phosphofructokinase (PFK) and MG2++
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| FBP to DHAP/GAP is catalyzed by what? | Aldolase
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| GAP to DHAP (and vis versa) is catalyzed by what? | Enediol intermediate (triose phsophate isomerase)
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| GAP to 1,3-BPG is catalyzed by what? | Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)
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| 1,3-BPG to 3PG is catalyzed by what? | Phosphoglycerate Kinase (PGK) and MG2++
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| 3PG to 2PG is catalyzed by what? | Phosphoglycerate mutase (PGM)
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| 2PG to PEP is catalyzed by what? | Enolase
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| PEP to Pyruvate is catalyzed by what? | Pyruvate Kinase (PK)
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| Muscle uses: Hexokinase/Glucokinase/both/neither? | Hexokinase
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| Liver uses: Hexokinase/glucokinase/both/neither? | Glucokinase (which is specific for glucose and doesn't phosphorylate fructose)
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| What are the 5 coenzymes for pyruvate dehydrogenase complex? | CoA, NAD+, FAD+, Lipoic Acid (lipoamide), and TPP
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| What are the 3 fates of Pyruvate in humans? | Lactate, CO2 + H20, and Alanine + Glucose
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| Which molecules regulate Citrate Synthase? | Citrate, NADH/NADH+, Succunyl-CoA
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| 1 complete round of Krebs Cycle yields what? | 2 CO2, 3 NADH, 1 FADH2, 1 GTP/ATP
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| Which ones are HIGH energy molecules? | ATP, Acetyl-CoA, NADH, Glucose
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| Which ones are LOW energy molecules? | ADP, AMP, Pyruvate, NAD+, CA+
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| The total net synthesis of ATP from 1 molecule of glucose is? | ~38 under aerobic conditions.
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| NADH = _____ ATP | 3 ATP
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| FADH = ____ ATP | 2 ATP
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| Which 3 enzymes are likely to function far from equilibrium under physiological conditions? | Citrate Synthase, Isocitrate dehydrogenase, Alpha-ketaglutarate dehydrogenase
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| The C4 epimer of Alph-D-glucopyronose is ___? | Alpha-D Mannose
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| Which AA are hydrophobic? | GLY, ALA, VAL, LEU, ILE, MET, PRO, PHE, TYP
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| Which AA are ESSENTIAL? | VAL, ILE, LEU, MET, PHE, TYP, THR, LYS, HIS
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| List the FA in order from HIGHEST MP to LOWEST MP: | HIGHEST (long single bonded chain): Arachadonic>Steric>Palmic Acid >> (double bonds) Oleic > Linolecic > Alpha-linoleic > Arachidonic (4 double bonds)
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| Proline net charge at pH7? | 0
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| Glutamate net charge at PH 1 and pH 10? | pH 1 = +1 // pH 10 = -2
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| Lysine net charge at pH 1 and pH 10? | pH 1 = +2 // pH 10 = -1
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| Alanine net charge at pH 1 and pH 10? | ph 1 = +1 // pH 10 = -1
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| What are some characteristics of DNA? | Right handed, 5'->3', Double stranded, structurally flexible
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| Which of the following reactions is NOT anaplerotic with respect to the Citric Acid Cycle? | FA biosynthesis
(ones that ARE anaplerotic = AA catabolism, Pyruvate carbaxylase, and pyruvate dehydrogenase)
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| What is the net yield of ATP from electron transport/oxidative phosphorylation of NADH? | 3
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| What is the terminal electron acceptor of electron transport? | Oxygen
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| Which of the following bonds has the highest and lowest potential energy? | covalent bonds(highest) and London dispersion (weakest)
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| According to Henderson-Hasselbalch equation, when the pH of a solution of a weak acid is greater than the pKa,.... | The Concentration of the conjucant BASE is greater than the ACID
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| The Anomeric carbon of Alpha-D-Fructofuranose is________? | C2 (fructofuranOSE = Ketose = C2 has main branch)
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| In 0-order reaction, the rate of product formation is = ? | Independent of the concentration of the reactant
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| A reaction with __ delta H and ___ delta S will be NONspontaeous at all temps | + and -
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| A reaction with ___ delta H and _____ delta S will be SPONTANEOUS at all temps | - and +
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| A reaction with ___ delta H and _____ delta S will be SPONTANEOUS at temps ABOVE T= DeltaH/DeltaS | + and+
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| Which combinations of AA will for a salt bridge? | ARG and ASP
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| Function of Co Q? | Energy transduction
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| Function of Retinol? | (Vit A) = Antioxidant and Vision
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| Function of Vit K? | Blood clotting
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| Function of Vit E? | Antioxidant
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| 2,3-Bisphosphoglycerate does which of the following? | Stabalizes T-state of Hb
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| What describes how O2 binds to Hb? | Cooperatively
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| An enzyme prosthetic group is defined as: | An organic group that permanently associated with an enzyme
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| Lyases = ? | Catalyze cleavage of C-C, C-S and C-N bonds
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| Oxidoreductases = ? | Catalyzes oxidation-reduction reactions
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| Transferases = ? | Catalyze transfer of C/N/or P containing groups
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| Hydrolases = ? | Catalyze cleavage of bonds by adding water
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| Isomerases = ? | Catalyze racemization of optical or geometric isomers
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| Ligases = ? | Catalyze formation of bonds between C and O/S/ and N coupled to hydrolysis of High energy phosphates
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| What are the 5 ALDOSE'S we need to know? | Glyceraldehyde, Ribose, Glucose, Mannose, Galatose
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| What are the 2(3?) Ketoses we need to know? | Dihydroxyacetone (Ribulose), and Fructose
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| HemiACETAL = ? | Alcohol +Aldehyde
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| HemiKETAL = ? | Alcohol + Ketone
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| Sucrose is made up from what? | alpha D Glu + Beta D Fructose
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| Maltose is made up from what? | Alpha-(1-4) Glu + Alpha-(1-4) Glu
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| IsoMaltose is made up from what? | Alpha (1-6) Glu + Alpha (1-6) Glu
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| Lactose is made up from what? | Beta (1-4) Gal, Glu
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| Cellibiose is made up from what? | Beta (1-4) Glu
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| How are Amylopectin and Glycogen related? | Due to branching
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| Amylopectin branching at what point? | 28th point
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| Glycogen branching at what point? | 14th point
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| Hyluronate is found where? | in eyes, synovial fluid, viterous humor
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| Chondroitin is found where? | In Cartilage
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| Dermatin Sulfate is found where? | in wound healing
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| Keratin Sulfate is found where? | Found throughout the body
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| Heparin is found where? | In blood clotting
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| Oxidation of what carbon in Alpha-D=GLucopyranose yeilds Glucuronic Acid? | C6
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| Reduction of what carbon in D-Ribose yeilds D-Ribitol? | C1
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| What are the 9 essencial AA? | HIS, MET, VAL, LEU, ISO, PHE, TYR, THR, LYS
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| Base skeleton for all sphingolipids? | Sphingosine
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| What are the 5 main hormones we need to know? | Cortisol, Aldesterone, Testosterone, Beta Estradiol, Progesteron
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| Cortisol is in charge of what? | Regulating Metabolism
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| Aldesterone is in charge of what? | Regulating salt/water excretion from kidneys
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| Progesteron is in charge of what? | Pregnancy
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| What is at C1 position in a glycerolphospholipid? | C-16 SATURATED FA (Saturated = no double bonds)
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| What is at C2 position in a glycerolphospholipid? | C-20 UNSATURATED FA (unsaturated = Double bonds)
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| What is at C3 position in a glycerolphospholipid? | Phosphate group
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