Fundamentals Of Biochemical Reactions Flashcards by Sarah Gillen

Biological reactions within the body are thermodynamically regulated by what biochemical property?

Free energy (dG)

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What is the relative value of dG in an exergonic reaction?

An endergonic reaction?

Exergonic: dG < 0 (spontaneous)

Endergonic: dG > 0 (non-spontaneous)

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When dG = 0, reaction is said to be in equilibrium. What is the value of Keq in this scenario?

Keq = 1 at equilibrium

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True or false: A reaction with a value of -4.23 for dG is spontaneous under standard conditions; it will occur more quickly than a similar reaction with a value of -1.22 for dG.

False; both reactions will occur spontaneously, but the value of dG is not indicative of reaction rate. Even spontaneous reactions may occur slowly if a catalyzing enzyme is not present. It is the presence of enzyme that dictates reaction rate, NOT free energy.

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Le Chatelier’s principle (of mass action) indicates that the sign of dG is dependent on _______

Keq

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In order for a reaction to be driven forward by coupling:

The coupled reactions must share a common ___________

Free energy parameters are ___________

Intermediate

Additive

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ADH requires oxidized NAD+ for catalytic activity. In the reaction catalyzed by ADH, an alcohol is oxidized to an aldehyde as NAD+ is reduced to NADH and dissociates from the enzyme. The NAD is functioning as a(n):

A. Apoenzyme
B. Coenzyme
C. Cofactor
D. Heterotropic effector

B. Coenzyme

[note that cofactors are typically metal ions, while coenzymes are small organic molecules]

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What is the simplest beta-keto acid? (Basic form in physiological conditions)

Acetoacetate

[this is an intermediate of fatty acid metabolism; beta oxidation of AOA converts it to Acetyl CoA]

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What is the result of b-hydroxybutyrate dehydrogenase acting on acetoacetate, and what is the significance of this molecule?

B-hydroxybutyric acid

-This is the first ketone to be produced in the fasting state; it is able to cross the blood-brain barrier. Epileptic patients can control seizures with ketogenic diet, which controls blood-brain beta-hydroxybutyrate levels

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What is the body’s buffering system and what is the range of ideal physiological pH?

Bicarbonate buffer system (H2CO3/HCO3), maintains a pH of 7.37-7.43

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Kidneys regulate blood pH by removing protons in the form of _______ and reabsorbing ________.

Low blood pH increases removal of ______ and reabsorption of ________.

High pH results in fewer ______ removed and less ______ reabsorption.

NH4+ ; HCO3

H+ ; bicarb

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The 2 varieties of acid-base imbalances include a metabolic component and a respiratory component:

__________ is the metabolic component.

__________ is the respiratory component.

Bicarbonate

CO2

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Describe acidosis (respiratory and metabolic) in terms of equilibrium shift

Equilibrium shifts to the left due to excess CO2

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Describe alkalosis (respiratory and metabolic) in terms of equilibrium shift

Equilibrium shifts to the right due to insufficient CO2

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Describe metabolic acidosis in terms of pH, pCO2, [HCO3-], and compensatory response

pH decrease

pCO2 decrease

[HCO3-] decrease

Compensatory response: hyperventilation

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Describe respiratory acidosis in terms of pH, pCO2, [HCO3-], and compensatory response

pH decrease

pCO2 increase

[HCO3-] increase

Compensatory response: increase in renal bicarb reabsorption

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Describe metabolic alkalosis in terms of pH, pCO2, [HCO3-], and compensatory response

pH increase

pCO2 increase

[HCO3-] increase

Compensatory response: hypoventilation

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Describe respiratory alkalosis in terms of pH, pCO2, [HCO3-], and compensatory response

pH increase

pCO2 decrease

[HCO3-] decrease

Compensatory response: decreased renal bicarb reabsorption

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Which of the following might result from diarrhea, weakened kidney function, or the addition of lactate to the blood?

A. Metabolic acidosis
B. Respiratory acidosis
C. Metabolic alkalosis
D. Respiratory alkalosis

A. Metabolic acidosis

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Which of the following might result from excessive vomiting or following a dose of antacid?

A. Metabolic acidosis
B. Respiratory acidosis
C. Metabolic alkalosis
D. Respiratory alkalosis

C. Metabolic alkalosis

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What effect do enzymes have on the free energy of a reaction?

NONE!

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What enzyme class cleaves bonds via the addition of water and what are some examples?

Hydrolases

[Esterases, Glycosidases, Peptidases, Amidases]

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What enzyme class forms C-O, C-S, C-N, or C-C bonds with the hydrolysis of ATP and what are some examples?

Ligases (synthetases)

[C-C ligases, C-O ligases, C-N ligases, C-S ligases]

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What enzyme class adds or removes atoms (e.g., elements of water, ammonia, or CO2) to or from a double bond; and what are some examples?

Lyases (synthases)

[C-C lyases, C-O lyases, C-N lyases, C-S lyases]

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What enzyme class rearranges molecules and what are some examples?

Isomerases [epimerases, cis/trans isomerases, intramolecular transferases]

What enzyme class transfers a functional group (e.g., amino, phosphate, etc.) between molecules; and what are some examples?

Transferases [C1 transferases, glycosyltransferases, aminotransferases, phosphotransferases]

What enzyme class transfers electrons from a donor to an acceptor; and what are some examples?

Oxidoreductases [dehydrogenases, oxidases, peroxidases, reductases, monooxygenases, dioxygenases]

An enzyme that is not bound to its cofactor is known as an _______________, while an enzyme that is bound to its cofactor is called a _____________

Apoenzyme Holoenzyme

The substrate binding site of an enzyme is called the active site, where residues directly interact with the substrate. What are the 2 primary hypotheses for how this takes place, and which one is more widely accepted?

Lock and key hypothesis (perfect fit hypothesis) Induced fit hypothesis (binding induces conformational changes in active site *** this one is more widely accepted)

The catalytic site of the enzyme is the site responsible for reducing the activation energy of a reaction, thus facilitating its progression. It is often thought of as the "catalytic triad" which is made up of what 3 components?

Acid - Base - Nucleophile [for example: aspartate (acid), histidine (base), and serine (nucleophile)]

One subtype of coenzyme called a __________ facilitates a temporary association, meaning it binds the enzyme and detaches in an altered state

Cosubstrate [example: NAD+ becomes loosely associated with enzyme and leaves in its reduced form NADH]

One subtype of coenzyme called a __________ __________ becomes permanently associated with the enzyme

Prosthetic group [example: FAD becomes tightly bound to enzyme but remains in its original form]

Coenzymes adenosylcobalamin and methylcobalamin are derived from what vitamin source?

B12 (cobalamin)

Coenzyme Ascorbate is derived from what vitamin source?

C (ascorbic acid)

Coenzyme biotin is derived from vitamin source biotin (not a typo) and is associated with what type of enzyme?

Carboxylases (like pyruvate carboxylase and acetyl CoA carboxylase)

Flavin nucleotides like FMN and FAD are derived from what vitamin source?

B2 (riboflavin)

Heme is a coenzyme that is involved in what types of enzymes/proteins/functions?

Hemoglobin and myoglobin, cytochromes, catalases and peroxidases

Lipoic acid is a coenzyme involved in what types of enzyme interactions/proteins/functions?

Alpha-ketoglutarate dehydrogenase complex, branched chain alpha keto acid dehydrogenase, PDH complex

NAD+ and NADP+ are coenzymes derived from what vitamin source?

B3 (niacin)

Pantothenic acid and coenzyme A are coenzymes derived from what vitamin source?

B5 (pantothenic acid)

Pyridoxal phosphate is a coenzyme derived from what vitamin source?

B6 (pyridoxine)

Tetrahydrofolate (THF) is a coenzyme derived from what vitamin source?

Folate

Thiamine pyrophosphate (TPP) is a coenzyme derived from what vitamin source?

B1 (thiamine)

Which metal ions (trace elements) are considered essential in terms of nutrition?

``` Cu Fe Mg Se Zn ```

__________ and __________ are essential metal ions, but are not considered co-factors because they do not associate with an enzyme

Chromium; iodine

__________ is not an essential ion, but rather an allosteric regulator in that it binds to other enzymes in a calmodulin complex

Calcium

A _____________ deficiency is associated with impaired glucose tolerance, although there is no identified associated enzyme

Chromium

___________ is involved in T3 and T4 structure, so it is involved in thyroid issues

Iodine

Which of the essential metal ion cofactors is required by the following enzymes: ``` Cytochrome C oxidase Ferroxidase Superoxide dismutase Lysyl oxidase Tyrosinase ```

Which of the essential metal ion cofactors is required by glutathione peroxidase?

Selenium

Which of the essential metal ion cofactors is required by the following enzymes: ATPases Adenylate cyclase Kinases

Which of the essential metal ion cofactors is required by the following enzymes: Heme proteins Cytochromes Catalases and peroxidases

Which of the essential metal ion cofactors is required by the following enzymes: ``` Superoxide dismutase Collagenase Alcohol dehydrogenase Alkaline phosphatase Transcription factors Carbonic anhydrase ```

What are the 2 primary factors affecting enzymatic activity and what are the optimal physiological values?

Temperature = 37 C (reaction rate doubles for each 10 degree rise in temp) pH = 4-8 (with exception of gastric enzymes like pepsin in stomach)

What is indicated by the Km value in enzyme kinetics?

Enzyme-substrate affinity So a high Km means weak binding because more substrate is necessary to bind enzyme and push reaction forward

If a mutation to a gene that codes for an enzyme results in a 10-fold increase in the Km for its biological substrate, what effect does the mutation have on the affinity of the enzyme for the substrate? A. An increase in Km indicates an increased affinity for the enzyme of the substrate B. An increase in Km indicates a decreased affinity of the enzyme for the substrate C. Km has no direct relationship with enzyme-substrate affinity D. A 10-fold increase in Km corresponds to a 10-fold increase in substrate affinity E. A 10-fold increase in Km corresponds to a 10-fold decrease in substrate affinity

B. An increase in Km indicates a decreased affinity of the enzyme for the substrate

What type of enzyme inhibition can be overcome by the addition of substrate?

Competitive inhibitors

Malonate, sulfanilamide, and methotrexate are examples of what type of inhibitors?

Competitive inhibitors

What type of inhibitors bind to the enzyme and ES complex at a site other than the substrate binding site?

Noncompetitive inhibitors

What type of inhibitors only bind the ES complex at a site other than the substrate binding site and what is an example of this?

Uncompetitive; example: lithium

Describe the effect that a competitive inhibitor has on the Km and Vmax of a reaction

Km increased Vmax unaffected

Describe the effect that an uncompetitive inhibitor has on the Km and Vmax of a reaction

Km reduced Vmax reduced

Describe the effect that a noncompetitive inhibitor has on the Km and Vmax of a reaction

Km unaffected Vmax reduced

Gastric proton pump inhibitors commonly known as Prilosec, Prevacid, and Nexium act on ______ ATPases that are found in the parietal cells that line the gastric lumen to pump H+ into the lumen where it combines with Cl to form HCl. ____________ is transported out in exchange for the chloride

H+/K+ Bicarb

Conditions like ulcers, indigestion, and heartburn require a decrease in gastric acid, thus proton pump inhibitors are prescribed. What are some potential side effects of the reduced HCl production caused by taking these medications?

Reduced HCl production causes hypochlorhydria, which can reduce absorption of nutrients, increase sensitivity to food poisoning, reduce gastric enzyme efficiency (particularly pepsin, gastric amylase, and gastric lipase)

How are Metalloenzymes, which are enzymes requiring a metallic cofactor, inhibited?

Metalloenzymes are inhibited by chelating factors that bind metal ions [example: EDTA as a treatment for lead poisoning, with potential side effect of nephrotoxicity because of Pb-EDTA excreted in urine]

A patient presents with abdominal pain, sideroblastic anemia, irritability, headaches, impaired nervous system developement, and encephalopathy. You suspect lead poisoning, which is confirmed by lab testing. Lead inhibits ______________ and ________________, which causes the above symptoms. What treatment do you administer and how does it work?

ALA dehydratase; ferrochelatase You administer Ca-EDTA because Pb has a higher affinity for EDTA than Ca, and the Pb-EDTA can then be excreted in the urine

Enzyme inactivation is associated with what effects on Vmax and Km of the reaction?

Decrease in Vmax Unchanged Km (no affect on affinity) [this is only overcome by synthesis of new enzymes]

What are some examples of heavy metals that may destroy or covalently modify key amino acids functional groups resulting in enzyme inactivation?

Lead, organophosphates, cyanide, sulfide, aspirin

Why are surgical patients withdrawn from aspirin for a week prior to a procedure?

Because the irreversible inactivation of cyclooxygenases in platelets can impair clotting function necessary to prevent severe bleeding in surgery

An _____________ effector is one that noncovalently binds to a site other than the catalytic site of an enzyme and affects substrate binding by inducing conformational changes

Allosteric [can have positive or negative effect]

___________ are enzymes that share some catalytic function but differ in their primary sequence

Isozymes

What are the 2 primary enzymes utilized as cardiac markers in MI's, and what 2 are no longer used?

Still used: CK-MB (immediate), troponin (serial readings/time lapse) No longer used: LDH-1, AST

____________ are inactive precursors responsible for enzymatic regulation and are typically proteolytic, meaning that cleavage of a specific peptide bond generates the active form

Proenzymes (zymogens)

Define troponin in the context of its use as a marker during myocardial infarction

Troponin is a protein complex pertinent to muscle contraction (elevated IC Ca) and relaxation (depressed IC Ca) It is at maximum sensitivity at 10-24 hours following onset of acute MI

Enzymes can be very useful in medical diagnosis. They are typically always present, but elevated above normal in pathological conditions. What enzyme is elevated in someone with bone disease?

Alkaline phosphatase

Enzymes can be very useful in medical diagnosis. They are typically always present, but elevated above normal in pathological conditions. What enzymes are elevated in someone with obstructive liver disease?

Sorbitol dehydrogenase Lactate dehydrogenase (LDH-5)

Enzymes can be very useful in medical diagnosis. They are typically always present, but elevated above normal in pathological conditions. What enzyme is elevated in someone with prostate cancer?

Acid phosphatase

Enzymes can be very useful in medical diagnosis. They are typically always present, but elevated above normal in pathological conditions. What enzyme is elevated in someone with acute pancreatitis?

Amylase

Enzymes can be very useful in medical diagnosis. They are typically always present, but elevated above normal in pathological conditions. What enzymes are elevated in someone with muscular dystrophy?

Aldolase and ASH

Enzymes can be very useful in medical diagnosis. They are typically always present, but elevated above normal in pathological conditions. What enzyme is elevated in someone with a general liver disorder?

CK-MM