Lect 1 Fundamentals Biochemical Reactions Flashcards Preview

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Flashcards in Lect 1 Fundamentals Biochemical Reactions Deck (47):
1

Metabolism is a _ 

  • Series of Biochemical reactions

2

Metabolism's purpose is to _

  • capture/harness energy from nutrients to sustain life

3

Metabolism's goals are _

Produce energy (catabolism)

Synthesize biomolecules (anabolism)

4

Exergonic/Endergonic Definitions

Exergonic releases energy (deltaG < 0)

Endergonic consumes energy (deltaG > 0)

5

Free Energy Change (delta G) = _ 

What is the Free Energy Equation?

delta G = Dynamics of biochemical reaction

deltaG = deltaGo' + RT ln [C][D]/[A][B]

6

Keq is equal to the ratio of the _ 

Products over Reactants

[C][D] / [A][B]

7

Equilibrium Constant (Keq) & Standard Free Energy (deltaGo') relationships

delta G is directly related to Keq

Keq = 1 --> deltaGo' = 0

Keq > 1 --> deltaGo' < 0

Keq < 1 --> deltaGo' > 0

8

 

What are the kcal/mol values of:

ATP --> ADP + Pi

ATP --> AMP + PPi

PPi --> Pi + Pi

 

ATP --> ADP + Pi = -7.3 kcal/mol

ATP --> AMP + PPi = -10.9 kcal/mol

PPi --> Pi + Pi = -4.0 kcal/mol

9

Mass Action (Le Chatelier)

  • Keq dependent on [R] and [P]
  • Altering [R] or [P] alters reaction kinetics

10

Input of Energy (Couple Reactions)

Endergonic + Exergonic

Must share a common intermediate

Final deltaGo' determines reaction fate

11

Addition/Elimination Rxn

Transfer atom to multiple bond or elimination of atom to form double bond

12

Substitution Rxn

Replace functional group with another

13

Rearrangements (Isomerizations)

Shifting functional group within a molecule

14

Oxidation-Reduction Rxn

Transfer of e- from one molecule to another

15

Acid Base Rxn

Donating protons (acids) and accepting protons (bases)

Most important to preserve life

16

Physiological pH Range

7.37-7.43

17

What is the dissociation constant (K)

What is pKa an indicator of

Equilibrium constant indicating tendency of acid to dissociate

Acid strength (low pKa = strong acid)

18

How does the Kidney regulate blood pH

Remove H+ in form of NH4+ and reabsorb HCO3-

Low pH: increased H+ removal and HCO3- reabsorption

High pH --> less H+ removal and HCO3- reabsorption

19

Name the Disorders Associated with Acid-Base Imbalances

Respiratory Acidosis (Hypoventilation)

Respiratory Alkalosis (Hyperventilation

Metabolic Acidosis

Metabolic Alkalosis

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20

Enzymes are biological _ that _ reaction rates

They bind to _ and convert them to _

Catalysts

Increase 

Substrates to Products

21

Enzymes increase reaction rate by _

  • Lowering activation energy (EA)
    • Minimum amount of energy to convert S to intermediate 
  • Stabilizing transition state intermediate
  • Provide more energetically favorable reaction pathway

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22

Name the Enzyme Classes

Oxidoreductases

Transferases

Isomerases

Lyases (Synthases) - add/remove atoms to form double bond

Ligases (Synthetases) - form bonds with ATP hydrolysis

Hydrolases - cleave bonds via addition of water

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23

Enzymes made up of _ and folded into _ and _ structure

  • Polypeptides
  • Folded into tertiary and quaternary structure

24

What is the purpose of the Active Site

  • Substrate binding location

25

Lock and Key Hypothesis

Substrate is perfect fit for active site

26

Induced Fit Hypothesis

Binding induces conformation changes in active site

27

What are Cofactors?

How do they interact with enzyme?

Metal ions, Essential trace elements

Interact with enzyme via noncovalent interaction and stabilize active site

28

Common Cofactor Examples and their Enzymes

Cu: Cytochrome C Oxidase

Fe: Heme proteins

Mg: ATPases

Se: Glutathione peroxidase (antioxidant) - detoxify H2O2

Zn: Carbonic Anhydrase

29

What are Coenzymes?

Small organic molecules dervied from vitamins

30

Difference between Co-Substrate and Prosthetic Groups

  • Co-Substrate: Temporary Association (bind then detach in altered state)
  • Prosthetic: Permanent Association (FAD, FMN, Heme)

31

What Factors Affect Enzyme Activity?

  • Temperature: 37o
    • ​Rate doubles every 10oC until optimal temperature
    • Heat induced denaturation
  • pH: between 4-8
    • Exception: gastric enzymes (Pepsin)
  • Covalent Modification
    • Phosphorylation/Dephosphorylation

32

What is the proton pump and where is it located?

Why would PPIs be prescribed?

  • Proton Pump = H+/K+ ATPase
    • Parietal cells lining gastric lumen
  • Pumps H+ into lumen --> Combines with Cl- to form HC
  • Indigestion, heartburn, ulcers require decrease gastric acid
    • PPIs prescribed (Omeprazole, lansoprazole)
      • Reduce HCl production

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33

What is Hypochlorhydria?

  • Lower HCl production --> Reduce nutrient absorption, increase food poison sensitivity, reduce gastric enzyme efficiency (pepsin, gastric amylase, gastric lipase)

34

Enzyme Kinetics describes what?

What 3 things is it dependent on?

  • Rate of enzyme-catalyzed reaction
  • Dependent on:
    • Initial Substrate [S]
    • Enzyme-Substrate affinity (Km)
    • Reaction velocity (v, Vmax)

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35

What are the Michaelis Menten and Lineweaver Burk Equations?

Know the MM equation

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36

Describe the Michaelis-Menten and Lineweaver Burk Plots

What do the x and y intercepts and slope mean on LB Plots?

x-int = -1 / Km

y-int = 1 / Vmax

slope = Km / Vmax

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37

How does Competitive Inhibition work?

Effects on Vmax and Km?

Can it be overcome?

Describe the inhibition on the graphs

  • Compete with substrate binding
  • No effect on Vmax
  • Km increased
  • If [I] is fixed, then increasing [S] allows substrate to outcompete inhibitor

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38

How does Noncompetitive Inhibition work?

Effects on Vmax and Km?

Can it be overcome?

Describe inhibition on graphs

  • Binds to E and to ES complex
  • Decrease in Vmax
  • Km unaffected
  • Inhibitor effects cannot be overcome by increasing substrate concentration

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39

How does Uncompetitive Inhibition work?

Effects on Vmax and Km?

Describe inhibition on graphs

  • Only binds to ES complex
  • Decrease in Vmax and Km by same factor

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40

What are Metalloenzymes?

How does chelation affect the enzymes?

  • Enzymes requiring metal ions as cofactors (Mg, Zn)
  • Chelating of cofactors will inhibit enzyme activity
    • Chelating agent: Ethylene Diamine Tetraacetic Acid (EDTA)

41

Why is Lead (Pb) toxic?

Heme is a coenzyme of _

Pb poisoning Sx include _ 

Tx with _ and why does it work?

 

  • Inhibits 2 enzymes in heme biosynthesis
  • Heme is coenzyme of hemoglobin
  • Sx: abdominal pain, sideroblastic anemia, irritability, HA, signs of impaired nervous system development and encephalopathy
  • Tx: Ca-EDTA with dimercoprol
    • Pb (higher affinity for EDTA) displaces Ca to form Pb-EDTA (excreted)

42

Irreversible Inhibition caused by _ and what are examples of inhibitors? 

Effects on Vmax and Km?

Can it be overcome?

  • Destruction/Covalent Modification of functional groups of AAs in enzyme
    • Ex: Pb, Hg, organophosphates, cyanide, sulfide, aspirin
  • Decrease Vmax and Km unchanged
  • Only overcome by new E synthesis

 

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43

How do Allosteric Enzymes work?

  • Activity modulated by noncovalent binding of metabolite to site other than the catalytic site
  • Affects S binding by inducing conformational changes
  • Effectors: positive (activators, lower Km) or negative (inhibitors, raise Km)
    • Feedback Inhibition

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44

What are Isozymes?

  • Enzymes with the same catalytic function, different primary sequence
    • Different biophysical properties

45

Isozymes that are Markers of MI and how are they detected?

Creatine Kinase (CK-MB)

Aspartate Aminotransferase (AST)

LDH-1

Blood serum levels increase after MI

46

Troponin in MI

  • Troponin is Trimeric
  • Troponin cTn-I (cardiac muscle) used as biomarker for detection of MI

47

What are Proenzymes (Zymogen)?

How do they become active?

Inactive precursor of enzyme

Need proteolytic breakdown to be active via cleavage of specific peptide bond