Lect 1 Fundamentals Biochemical Reactions Flashcards
Metabolism is a _
- Series of Biochemical reactions
Metabolism’s purpose is to _
- capture/harness energy from nutrients to sustain life
Metabolism’s goals are _
Produce energy (catabolism)
Synthesize biomolecules (anabolism)
Exergonic/Endergonic Definitions
Exergonic releases energy (deltaG < 0)
Endergonic consumes energy (deltaG > 0)
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]
Keq is equal to the ratio of the _
Products over Reactants
[C][D] / [A][B]
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
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
Mass Action (Le Chatelier)
- Keq dependent on [R] and [P]
- Altering [R] or [P] alters reaction kinetics
Input of Energy (Couple Reactions)
Endergonic + Exergonic
Must share a common intermediate
Final deltaGo’ determines reaction fate
Addition/Elimination Rxn
Transfer atom to multiple bond or elimination of atom to form double bond
Substitution Rxn
Replace functional group with another
Rearrangements (Isomerizations)
Shifting functional group within a molecule
Oxidation-Reduction Rxn
Transfer of e- from one molecule to another
Acid Base Rxn
Donating protons (acids) and accepting protons (bases)
Most important to preserve life
Physiological pH Range
7.37-7.43
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)
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
Name the Disorders Associated with Acid-Base Imbalances
Respiratory Acidosis (Hypoventilation)
Respiratory Alkalosis (Hyperventilation
Metabolic Acidosis
Metabolic Alkalosis
Enzymes are biological _ that _ reaction rates
They bind to _ and convert them to _
Catalysts
Increase
Substrates to Products
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
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
Enzymes made up of _ and folded into _ and _ structure
- Polypeptides
- Folded into tertiary and quaternary structure
What is the purpose of the Active Site
- Substrate binding location
Lock and Key Hypothesis
Substrate is perfect fit for active site
Induced Fit Hypothesis
Binding induces conformation changes in active site
What are Cofactors?
How do they interact with enzyme?
Metal ions, Essential trace elements
Interact with enzyme via noncovalent interaction and stabilize active site
Common Cofactor Examples and their Enzymes
Cu: Cytochrome C Oxidase
Fe: Heme proteins
Mg: ATPases
Se: Glutathione peroxidase (antioxidant) - detoxify H2O2
Zn: Carbonic Anhydrase
What are Coenzymes?
Small organic molecules dervied from vitamins
Difference between Co-Substrate and Prosthetic Groups
- Co-Substrate: Temporary Association (bind then detach in altered state)
- Prosthetic: Permanent Association (FAD, FMN, Heme)
What Factors Affect Enzyme Activity?
-
Temperature: 37oC
- Rate doubles every 10oC until optimal temperature
- Heat induced denaturation
-
pH: between 4-8
- Exception: gastric enzymes (Pepsin)
-
Covalent Modification
- Phosphorylation/Dephosphorylation
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
-
PPIs prescribed (Omeprazole, lansoprazole)
What is Hypochlorhydria?
- Lower HCl production –> Reduce nutrient absorption, increase food poison sensitivity, reduce gastric enzyme efficiency (pepsin, gastric amylase, gastric lipase)
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)
What are the Michaelis Menten and Lineweaver Burk Equations?
Know the MM equation
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
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
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
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
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)
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)
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
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
What are Isozymes?
- Enzymes with the same catalytic function, different primary sequence
- Different biophysical properties
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
Troponin in MI
- Troponin is Trimeric
- Troponin cTn-I (cardiac muscle) used as biomarker for detection of MI
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
