Fundamentals of Biochemical Reactions Flashcards
1
Q
- ΔG = 0, ________
- ΔG < 0, ________ (______, energy producing, favors _____)
- ΔG > 0, ________ (______, energy consuming, favors _____)
A
- equilibrium
- spontaneous, exergonic, products
- non-spontaneous, endergonic, reactants
2
Q
- free energy is the available energy to do work
- change in free energy is the energy difference between the products and the reactants
- reaction rate is not dependent on the magnitude of the free energy change, but rather the enzyme catalyzing the reaction
A
Gibbs free energy
3
Q
When Keq = 1 (at equilibrium), ΔG* is = ___.
( ΔG* = -RT(lnKeq) )
A
0
4
Q
What does the value of ΔG dictate? (2)
A
- sponteneity: which way a reaction will progress, whether products or reactants are favored
- whether a reaction will need help to prgoress, either from a couple reaction that provides energy or an enzyme
5
Q
- when Keq = 1, ΔG* ____
- when Keq > 1, ΔG* ____
- when Keq < 1, ΔG* ____
A
- = 0, equlibrium
- < 0, spontaenous and proceed to the right
- > 0, non-spontaneous and will proceed to the left
6
Q
How can an unfavorable reaction be driven against it’s equilibrium? (2)
A
- mass action (Le Chatelier’s principle): increase the concentration of reactants or decrease the concentration of products
- input of energy (coupled reactions): ATP is often the coupled reaction as it is extremely exergonic, example used is the condesation of ammonia (NH3) and glutamate to glutamine
7
Q
What are the 5 types of reactions?
A
- addition/elimination
- substitution
- rearrangements
- oxidation-reduction
- acid-base
8
Q
- biochemical reaction class
- involves the transfer of one or more atoms to a multiple bond, OR the removal of one or more atoms that results in a multiple bond
A
additions/eliminations
9
Q
- biochemical reaction class
- replacement of one functional group with another
- example: hydroxyl groups of sugars can be replaced by amino groups
A
substitution
10
Q
- biochemical reaction class
- shifting of functional groups within the same molecule to produce isomers
- two main types of isomers:
1. structural: have same atoms but different bonds
2. spatial: have the same atoms and bonds but different spatial arrangements and are nonsuperimposible
A
rearrangements (isomerizations)
11
Q
- biochemical reaction class
- involve the transfer of electrons from one molecule (reducing agent) to another (oxidizing agent)
- oxidation: addition of oxygen or removal of hydrogen
A
oxidation-reduction
12
Q
Acid-Base reactions
- these reactions involve ____ (donate protons) and ____ (accept protons)
A
- acids, bases
13
Q
What is the normal pH range for blood?
A
7.37-7.43
14
Q
What is the body’s buffering system?
A
carbonic acid/bicarbonate (H2CO3/HCO3-)
15
Q
- acetoacetate: simplest β-keto acid
- intermediate of fatty acid metabolism: β-oxidation of AOA converts it to acetyl-CoA
- β-hydroxybutryric acid is produced from acetoacetate
- first ketone produced in fasting state, able to cross BBB
- how is this relevant to epileptic patients?
A
they are able to control seizures with ketogenic diet, blood β-hydroxybutyrate levels correlate best with seizure control
16
Q
How do the kidneys regulate blood pH?
A
They remove protons in the form of NH4+ and reabsorb HCO3-. Low blood pH triggers and increase in both the removal of protons and the reabsorption of bicarbonate. When the pH of blood is too high, fewer protons are removed and less bicarbonate is reabsorbed
17
Q
- acid-base imbalance
- low pH, low CO2, low HCO3-
- caused by: addition of strong acid (e.g. lactate, ketone bodies) or loss of HCO3- (e.g. diarrhea, weakened kidney function)
- compensatory repsponse: hyperventilation
A
metabolic acidosis
18
Q
- acid-base imbalance
- low pH, high pCO2, high HCO3-
- causued by: hypoventilation that leads to an increase in the concentration of CO2 in blood, as a result, the reaction is shifted to the left which causes elevated H+ and low pH
- compensatory response: increase renal HCO3- absorption
A
respiratory acidosis
19
Q
- acid-base imbalance
- high pH, high pCO2, high HCO3-
- caused by addition of a strong base (e.g. ingestion of antacid) or loss of acid (e.g. vomiting)
- compensatory response: hypoventilation
A
metabolic alkalosis
20
Q
- acid-base imbalance
- high pH, low pCO2, low HCO3-
- caused by hyperventilation that leads to a decrease in the concentration of CO2 in the blood, as a result, the reaction shifts to the right which causes low H+ and high pH
- compensatory response: lowered renal HCO3 absorption
A
respiratory alkalosis
21
Q
- made connection between disease and errors in biochemical pathways
- mutations in enzymes can cause disease in by affecting biochemical pathways (Inborn Errors of Metabolism, glycogen storage diseases)
A
Sir Archibald Garrod
22
Q
How do enzymes catalyze reactions?
A
- lower activation energy (Ea)
- increase reaction rate
*enzymes have no effect on delta(G)
23
Q
How do enzymes increase reaction rate?
A
Provide a more energetically favorable pathway and a stabilized transition state
24
Q
- class of enzyme
- transfer electrons from a donor (reducing agent) to an acceptor (oxidizing agent)
- dehydrogenases, oxidases, peroxidases, reductases, monooxygenases, dioxygenases
A
oxidoreductases
25
- class of enzyme
- transfer a functional group (e.g. amino, phosphate) between molecules
- phosphorylation: on/off switch, almost half of all enzymes are phosphorylated, 2/3 of all eukaryotic proteins are temporarily phosphorylated
- C1-transferases, glycosyltransferases, aminotransferases, phosphotransferases
transferases
26
- class of enzyme
- rearrange/isomerize molecules
- epimerases, cis trans isomerases, intramolecular transferases
isomerases
27
- class of enzyme
- add or remove atoms (e.g. elements of water, ammonia, or CO2) to or from a double bond
- C-C-lyases, C-O-lyases, C-N-lyases, C-S-lyases
lyases ("synthases")
28
- class of enzyme
- form (C-O, C-S, C-N, or C-C) bonds with the hydrolysis of ATP
- C-C ligases, C-O ligases, C-N ligases, C-S ligases
ligases ('synthetases")
29
- class of enzyme
- cleave bonds via the addition of water
- esterases, glycosidases, peptidases, amidases
hydrolases
30
- substrate binding location
- lock and key hypothesis (substrate is a prefect fit) and induced fit hypothesis (binding induces conformational changes)
- binding sensitive to pH, temperature, etc.
- catalytic triad: acid, base, neutrophile
active site
31
- non-protein
- organic or inorganic
- metal cofactors: metal ions, noncovalent interaction
- coenzymes: small organic molecules, derived from vitamins
cofactors
32
- a type of cofactor
- small organic molecules usually obtained from vitamins
- can either be prosthetic groups (tightly bound) or cosubstrates (loosely bound)
- pyridoxal phosphate is critical in transaminase reactions (amino acid metabolism and urea cycle function)
coenzymes
33
What are the two types of coenzymes and what differentiates them?
- **cosubstrate**: temporary association, bind and detach in altered state (examples: NAD+ loosely associated, leaves in a changed form (reduced)
- **prosthetic**: permanent association (examples: FAD tightly bound, remains in original form; heme)
34
- a type of cofactor
- essential trace elements in food
- chromium and iodine are essential ions, however they are not cofactors as there is no associated enzyme
- the associated enzymes cannot function without _____ \_\_\_\_
- Cu is important for energy production
- Fe is critical for oxygen delivery
- Zn is important for function of many metabolic enzymes (body's buffering system)
metal ions
35
- B1 = thiamine (TPP): carbohydrate and AA metabolism
- B2 = riboflavin (FAD/FMN): Kreb's cycle and electron transport chain
- B3 = niacin (NAD/NADP): catabolic reactions
- B6 = pyridozine (PLP): AA metabolism
- B7 = biotin: carboxylation reactions, acts as the carrier of CO2
- B9 = folate: trasnfer of one-carbon fragments, synthesis of thymine and purines, methylation of DNA
- B12 = cobalamins: folate metabolism, methionine synthesis, intra-molecular transfer of carboxyl groups)
important coenzymes
36
- also known as H+/K+ ATPase
- found in the parietal cells that line the gastric lumen
- pump H+ into the lumen where it combine swith Cl- to form HCL
- conditions like ulcers, indigestion, heartburn, require decrease in gastric acid, thus these are prescribed (Omperazole, Lansoprazole, Esomeprazole)
- reduced HCL production causes hypochlorhydria which can reduce absorption of nutrients, increase sensitivty to food poisoning, reduce gastric enzyme efficiency (particularly pepsin, gastric amylase, and gastric lipase)
proton pump inhibitors
37
- noncovalently binds to a site other than the catalytic site
- affects substrate binding by inducing conformational changes
- positive (activators) and negative (inhibitors)
allosteric effector
38
- inactive precursor form of an enzyme
- cleavage of a peptide bond within the _____ generates the active mature enzyme
- pepsinogen/pepsin, trypsinogen/trypsin, prothrombin/thrombin, chymotrypsinogen/chymotrypsin
proenzymes (zymogens)
39
- enzymes that catalyze the same chemical reaction, but differ in amino acid sequence
- different biophysical properties (pH, temp, kinetics)
- different binding sites
- markers of MI: ______ of lactate dehydrogenase (LDH-1), creatine kinase (CK-MB), and aspartate aminotransferase (AST)
isozymes
## Footnote
**\*LDH and AST not used anymore, can be used as a distractor on board exams**
40
- protein complex pertinent to muscle contraction (elevated intracellular Ca2-) and relaxation (depressed intracellular Ca2+)
- trimer: Tn-C, Tn-T, Tn-I
- Ca2+ binding causes conformational change, transitted to tropomyosin, allowing myosin to bind to actin filaments \> muscle contraction
- Tn-I has 3 subunits: cTn-I in cardiac muscle, sTn-I in skeletal muscle
- troponins have overtaken traditional cardiac enzymes (AST, LDH) for detection of MI
- maxium sensitivity 10-24 hours following onset of acute MI
troponin in MI
41
Enzymes used for medical diagnoses:
alkaline phosphatase:
sorbitol dehydrogenase, lactate dehydrogenase (LDH-5)
acid phosphatase
amylase
aldolase and ASH
CK-MM
- bone disease
- obstructive liver disease
- prostatic cancer
- acute pancreatitis
- muscular dystrophy
- liver disorder
