Term
| Explain the basic principles of acid / base balance |
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Definition
- Changes in pH occur due to changes in H+ or HCO3-
- Governed by the Henderson-Hasselbalch Equation:
pH = 6.1 + log (HCO3- / PaCO2 x 0.0301)
Acidemia: Increase in H+ or loss of HCO3-
Alkalemia: Loss of H+ or increase in HCO3- |
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Term
| List the physiological consequences of acid / base disorders |
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Definition
4 disturbances: respiratory acidosis, respiratory alkalosis, metabolic alkalosis, and metabolic acidosis (increased anion gap and normal anion gap)
-Proteins denature & change confirmation (shape) at extremes of pH
- Lose enzymatic function
- Lose receptor binding & electrical conduction
- Hypotension
- Bradycardia
- Seizure |
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Term
| Common causes of respiratory acidosis |
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Definition
A. Hypoventilation
- Opiate overdose
- Benzodiazepine overdose
- Extreme Kyphoscoliosis
- Extreme Obesity (pickwickian syndrome)
B. Airway Obstruction:
- COPD – chronic bronchitis
- Foreign body / mass airway obstruction |
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Term
| Common causes of respiratory alkalosis |
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Definition
Hyperventilation:
- Acute salicylism
- Fever and sepsis
- Pneumonia
- Acute asthma
- Pulmonary Embolism
- Congestive Heart Failure |
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Term
| Common causes of metabolic acidosis |
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Definition
Production of Excess Metabolic acids:
- Uremia (renal failure)
- Diabetic ketoacidosis
- Lactic acidosis
- Hypoxia / ischemia
- Sepsis / severe infection
- Ingestion of assorted toxic substances
Loss of Metabolic base (Bicarbonate):
- Diarrhea
- Renal causes |
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Term
| Common causes of metabolic alkalosis |
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Definition
Excess of Metabolic base:
- Ingestion of HCO3- (milk-alkali syndrome)
Loss of Metabolic acid:
- Vomiting
- Diuretic use
- Volume contraction |
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Term
|
Definition
dissociate or ionize to > 90%
pKa or pKb < 2.0 (far from physiological pH) |
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Term
|
Definition
pKa (pKeq for an acid) of weak acid < 7
pKa of weak base (protonated) > 7
pKa or pKb > 2.0 |
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Term
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Definition
| dissociates more than once; have multiple acidic groups |
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Term
| Define conjugate acid/base |
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Definition
| base or acid created once acid/base dissociates |
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Term
|
Definition
the same osmolarity
for example
- isotonic saline solution is a solution of salt whose osmolarity is the same as blood plasma |
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Term
|
Definition
molecules having both acidic & basic groups (e.g.,amino acids, proteins).
- At physiological pH, neutral or simple amino acids exist as zwitterions with no net charge (isoelectric) near pH 7.0. |
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Term
|
Definition
pKa = -log Ka
pKb = –log Kb
tells the strength of the weak acid or base; the higher the weaker |
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Term
| Define buffering capacity |
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Definition
| measure of the resistance of a buffer solution to pH change on addition of H+ or OH- |
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Term
|
Definition
| measure of solute concentration measured as osmoles of solute per liter |
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Term
| What hormones and plasma constituents control plasma osmolarity? |
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Definition
Plasma constituents: Na+, Cl-, and HCO3-
Plasma Osmotic activity == 0.308 M sucrose and 0.154 M NaCl or 0.9% isotonic saline
Hormones: ADH/vasopressin (renal water retention) and Aldosterone (renal Na+ retention)
Blood plasma and isotonic saline solution = 286 mOsmolar
Other 2 metabolites that effect it: glucose and urea |
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Term
| Describe the 2 types of Diabetes Insipidus |
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Definition
1. NDI (arises in the kidneys) - Nephrogenic Diabetes insipidus is characterized by an inability to concentrate urine despite normal or elevated plasma concentrations of vasopressin
- Polyuria (large urine volume) with hyposthenuria (low urinary osmolarity), and polydipsia (excessive thirst) are the cardinal clinical manifestations of the disease
- Problem with AQP2 (aquaporin 2) stimulation by ADH leading to non-reabsorption of the normal 10% of water at the end of the renal glomeruli
- Hyperosmolar hyperglycemic nonketotic coma (HHNC) is a serious condition in which the blood sugar level rises very high. The sugar exceeds the kidney’s threshold for retention the excess blood sugar is excreted in the urine. HHNC increases the amount of urine (diuresis or polyuria) due to sugar osmolarity and often leads to dehydration. Severe dehydration can cause seizures, coma, even death. Typically occurs in people with type 2 diabetes who are not controlling their blood sugar levels or have become dehydrated.
2. Neurohypophyseal type - due to low AVP (Arginine vasopressin |
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Term
| How to calculate blood plasma osmolarity |
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Definition
| mOsm/L = 2 X [Na+] + [glucose] (mg/dL) / 18 + BUN (mg/dL) / 2.8 |
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Term
| Identify by structural formula, compounds and functional groups that act as weak acids |
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Definition
NH4+, H2CO3, and H3PO4
Main functional groups that acts as a weak acid –COOH (terminal carboxyl group on amino acids) |
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Term
| Identify by structural formula, compounds and functional groups that act as weak bases |
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Definition
NH3 and HCO3-
Main functional group that acts as a weak base is –NH3+ (terminal amino group on amino acid) |
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Term
| Identify by structural formula, compounds and functional groups that constitute polyprotic acids or ampholyte |
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Definition
Alanine [ CH3CH(NH2)COOH ] is a polyprotic acid and so is phosphoric acid [H3PO4] (acts as an ampholyte)
- Equivalence points occur equidistant between the two pKa's on either side of the equivalence point, and the pH at this point can be estimated by calculating the mean of these two pKa's.
- Aspartic acid [HOOCCH(NH2)CH2COOH] another example |
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Term
| Define isoelectric point (pI) |
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Definition
- the pH at which an ampholyte (amino acids or proteins that have undergone (de)ionization) has no net electrical charge and thus will not migrate in an electrical field.
- Proteins containing more acidic side chain groups (Glu and Asp) than basic groups (Lys and Arg) have pI's below 7.0 (basic proteins have pI above 7.0).
- By titrating an amino acid or protein to its isoelectric point, a balance between these opposite charges can be obtained; at pI, they are zwitterions (no net charge)
pI = (pKa1 + pKa2)/2 |
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Term
| Define the normal blood pH range and describe how biological fluid loss can lead to acid-base imbalance. |
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Definition
- Physiological pH is narrow range of 7.35 - 7.45 primarily ; concentration of 40 nM of H+
- Controlled by blood buffer (CO2/HCO3-), lungs (ventilation) and kidney (net excretion of H+ or HCO3- ). - - The physiological limits of blood pH represent only a 2 to 4 fold change in H+ concentration. If pH falls below 7.2, vital functions (cardiovascular system) are compromised requiring that HCO3- be administered to correct the base deficit.
Serum osmolarity can be affected by both ketoacidosis (high - blood ketoacids such as ketone bodies) and hyperglycemia (high blood glucose) and compounded by water loss or dehydration that accompanies the urinary loss of ketoacids (ketouria) and glucose (glucosuria).
- Excessive loss of an acidic body fluid leads to excess base and loss of an alkaline fluid to excess acid |
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Term
| Knowing pKa and molecular mass, how would you calculate the approximate quantities of weak acid and salt or weak base and salt required to prepare a buffer of a given pH and concentration? |
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Definition
Depending on where you are in the titration, 3 different solutions are applied:
1. All acid: Ka = {(HA)(A-)}/HA = x2/ (HA – x)
If it’s a weak acid then x in the denominator is negligible
2. 10 to 90% titrated: Henderson-Hasselbach Equation
3. All Base: Kb = Kw/Ka = [(OH)(HA)]/A-
Another useful equation: M = V1M1 = V2M2 |
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Term
| Define the optimum buffer capacity based on concentration and pKa |
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Definition
| Maximum buffer capacity is where pH = pKa. Buffer should be within + 1 pH unit of pKa. Capacity Also increases with buffer concentration. |
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Term
Identify the pKa (midpoint), the equivalence point and the major ionic species present on the titration curve |
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Definition
Titration curve for Polyprotic Acid
[image]For Monoprotic Acids: At the midpoint, 50 % of the acid or base has been titrated and pKa = pH so the ratio of the acid or base to its salt is 1:1At the equivalence point, 100% of the acid or base has been titrated (0 acid/base and 100% salt) |
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Term
| Titration curve of amino acid (pI) |
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Definition
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Term
| Describe how diet affects acid-base balance and the types of nutrients that lead to the production of "fixed acids" or the production of excess base during metabolism. |
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Definition
- Metabolism of body fuels produces the volatile acid, CO2 (readily removed by lungs; can only have 15 -23 moles CO2/day) and “fixed acids” (sulfate, phosphate, metabolizable cations; high in meat and eggs; can have 70 to 100 mmoles/day) that can only be eliminated by kidney
Fixed acids – (nonvolatile) produced from sources other than CO2; not excreted by lungs
Major - sulfur containing amino acids: Met and Cys yield SO42- + 2 H+
Phospho-amino acids + phospholipids yield HPO42- + 2 H+
Metabolizable cations (arginine-HCl) yield acid.
Fruits and vegetables are lower in fixed acids and yield net alkali due to metabolizable anions (i.e., K+ citrate, Na+ lactate, Na+glutamate) |
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Term
| Causes of Metabolic Acidosis due to diet |
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Definition
1. renal failure (primary cause) = Inability to excrete daily fixed acid
2. Ingestion of methanol produces formic acid -> CNS depression. (There is also damage to the retinal cells of the eyes by oxidation products)
3. Ethylene glycol (antifreeze) converts to oxalic acid -> CNS depression and severe kidney damage
Treatment = bases, NaHCO3 or sodium lactate, in combination with other therapeutic measures
**Chronic metabolic acidosis leads to bone dissolution as bone serves as a large base reserve |
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Term
| Describe the function of bicarbonate and CO2 in physiological regulation of pH and its regulation by lung and kidney |
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Definition
- H2CO3 / HCO3- = most important buffer in the blood and interstitial fluid and major chemical species for CO2 transport to lungs
- 1st line of defense against addition of acid or base to blood
addition of acid to the blood consumes the base, HCO3-
addition of base consumes the acid, H2CO3
- 2nd line of defense is dynamic and involves ventilation of CO2 by the lung and the control of H+ excretion by the kidney |
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Term
| Describe lung regulation of pH |
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Definition
- Lung is really good buffering system because it’s an open system (Venous blood is more acidic than arterial blood due to metabolism of CO2); keeps pH within physiological range; acid component, CO2, can be regulated rapidly
- Regulates blood pH by adjusting PCO2 (acidic component of blood buffer)
- ↑ ventilation → ↓PCO2
- Salicylate (aspirin) intoxication results in respiratory alkalosis due to hyperventilation (loss of CO2); later stage is metabolic acidosis due to aspirin’s effect on oxidative metab. |
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Term
| Describe Kidney regulation of pH |
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Definition
- HCO3- (base component of blood buffer) can be excreted to diminish base excess or new bicarbonate can be formed by net renal excretion of H+ in the form of an acid salt (NH4+ or H2PO4- salts).
- Proximal convoluted tubule = Na+ and HCO3- recovered (essential for blood pH buffering); does not result in excretion of acid
- Distal Convoluted Tubule = Glutaminase is an enzyme that absorbs NH3+ to absorb H+; results in excretion of acid
Total Urine Acidity = ( Titratable acid + NH4+ - HCO3- ) |
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Term
| What is the role of Carbonic Anhydrase in RBCs and Kidney |
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Definition
- A zinc-containing enzyme essential for H2CO3/CO2 and HCO3- transfer; facilitates equilibration of CO2 gas with aqueous phase of blood; each complete pass of blood requires 1 minute.
- In RBC, it facilitates the transport of CO2 by fixing it in the form of carbonic acid (dissociates to HCO3-) so it can be carried until delivered to the lung
- In Kidney (specifically the epithelium of proximal convoluted tubule), it facilitates renal recovery of HCO3- by uptaking CO2 which it converts to carbonic acid which dissociates to HCO3- |
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Term
| renal tubular acidosis (RTA) |
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Definition
- accumulation of acid in the body due to failure of the kidneys to acidify the urine
- two possible causes:
1. Proximal tubule failure to recover bicarbonate (RTA Type 2)
- Some drugs inhibit carbonic anhydrase, causing loss of bicarbonate and accompanying loss of water in urine (alkaline diuresis) -> met. acidosis
2. Distal tubule failure to uptake NH4+ and H+ (RTA Type 1)
Renal failure – retention of fixed acids |
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Term
|
Definition
high concentrations of ketone bodies formed by breakdown of fatty acids and the deamination of amino acids
Metabolic disorder |
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Term
|
Definition
| combination of lack of oxygen leading to lower pH levels and anaerobic glucose metabolism leading to lactic acid build up (tissue hypoxia) |
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Term
|
Definition
- defined as [Na+] - ([HCO3-] + [Cl-]) and equals 138 - (24 + 102) or 12 for normal serum
- Not a clinical electrolyte value nor real deficit of anions
Helps distinguish between different types of metabolic acidosis
In Ketoacidosis, the “gap” increases b/c there is an overproduction of unmeasured anions (ketone bodies, mainly acetoacetate and hydroxybutyrate); coupled with decrease in HCO3- concentration increases the gap significantly
In other types, loss of HCO3- accompanied by balanced increase in CL- (hyperchloremic acidosis)
Seen with diarrhea and RTA |
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Term
| Describe the mechanism and physiological reason for renal production of ammonia and how its excretion compensates in maintaining acid-base balance. Define the role of glutamine and glutaminase in this process. What other acid or basic salts could be excreted to maintain acid/base balance. |
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Definition
| Acidification of the urine (active H+ pumping) results in an increase in ammonia excretion as the NH4+ ion due to free diffusion of NH3 across tubular epithelium. The ammonia is released by the action of the enzyme glutaminase on glutamine and diffuses into the lumen fluid and is trapped as the NH4+ ion in the more acid lumen. Approximately 25% of acidity in urine is titratable (to pH 7.0); the remainder (75%) occurs as buffered ammonium salts and is termed buffered acidity. Excretion of NH4+ in the urine permits (1) the removal of large amounts of protons or acidity within a relatively limited pH range and also (2) spares Na+ and K+ since the acid salts can be excreted as ammonium salts. Impairment of this ability to excrete ammonia leads to another type of renal tubular acidosis I. |
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Term
| Identify the thermodynamic terms that determine if a reaction is spontaneous in a living system. |
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Definition
- Entropy (S) – measure of randomness/disorder; any spontaneous change results in an increase in entropy of the universe (system and surroundings; this is the 2nd law of therm). ∆S is hard to measure.
- 1st law of therm: energy is neither created nor destroyed, although it can be converted from one form to another
- Free Energy (G) - describes max amount of work a system can do as it approaches equilibrium
- Enthalpy (H) - ∆H is the change in enthalpy or heat content
∆H = Hproducts – Hreactants (can measure)
Determined by changes in chem structure/energy (bond energy, resonance, steric effects solvation) in going from reactant to product
- When products have less chem energy (more stable) than reactants, excess energy is liberated heat: ∆H = -
(Some spontaneous reactions do absorb heat) |
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Term
| Define and distinguish (equation) ΔG and ΔGo |
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Definition
ΔG – change in free energy – describes max amount of work a system can do as it approaches equilibrium
∆G = Gproducts – Greactants
Determines the direction of a reaction but not the rate nor pathway
∆G = ∆H - T∆S where T is the absolute temp
A variable which depends on the steady state (ss) or in vivo concentrations of reactants and products and describes distance from equilibrium
In living cells, many rxns are not at equi; -∆G determines if rxn is spontaneous
∆G°- the change in free energy under standard conditions (25°C, 1 atm pressure, 1M concentration of reactants and products
∆G = ∆G° + 2.3 RT log([products]ss/[reactants]ss)
∆G° is a constant, which depends on the structures of the reactants and products and entropy changes |
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Term
| Define exergonic reaction and endergonic reaction |
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Definition
Exergonic Reaction - ∆G is negative (<0), reaction occurs spontaneously
Endergonic Reaction - ∆G is positive, reaction needs energy to proceed |
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Term
| Define a reaction at equilibrium |
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Definition
| No net change in concentration of reactants or products, ∆G = 0 |
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Term
| Define the relationship (equation) between the equilibrium constant, ΔGo, relative concentrations of reactants and products |
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Definition
if [B]eq > [A]eq then Keq is >1 and ∆G0 is negative
if [B]eq < [A]eq then Keq is <1 and ∆G0 is positive
if [B]eq = [A]eq then Keq = 1 and ∆G0 is 0 |
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Term
|
Definition
At equilibrium, ∆G = 0 so ∆G0 = - 2.3RT log([products]eq/[reactants]eq)
∆G0 = - 2.3 RT log Keq 2.3 RT = 1.36 kcal/mol
Keq = kf / kr = [B]eq/[A]eq, where k is equal to rate of reaction respectively |
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Term
| Define the term that governs the rate of a reaction |
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Definition
| Activation Energy – determines rate; difference between a and the transition state of the reaction; energy needed to drive reaction toward completion |
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Term
| Define when a thermodynamic value should be used with a change of sign |
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Definition
| When you reverse the rxn then you flip the value to the opposite sign |
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Term
| Identify the properties of high energy compounds |
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Definition
Large negative ∆G° on hydrolysis
High energy compounds have ∆G° values between -5 to -15 kcal/mole (Keq = 104- 1010)
The products of hydrolysis are more stable than the reactants |
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Term
| Identify the chemical Types of High Energy Compounds |
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Definition
Phosphoric acid anhydrides
Thioesters (R-S-CO-R’)
Enol Phosphates (R-C=C-OPO32-)
Phospho-carboxylic anhydrides (R-CO-OPO32-) |
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Term
| Why are the products of the hydrolysis of high energy compounds? |
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Definition
Greater resonance stability
Less bond strain due to electrostatic repulsion of oxygen atoms
Phosphate ionization occurs with large negative ∆G°’ (standard free energy change at pH 7)
Tautomerization to more stable keto structures |
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Term
| Specific High Energy Compounds |
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Definition
| ATP, ADP, Phosphoenolpyruvate, Creatine phosphate, Acetyl CoA |
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Term
| Describe a metabolic pathway including coupled reactions, and the relationship between exergonic reactions and endergonic reactions. |
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Definition
- Metabolic pathways are sets of Coupled Reactions (share a common intermediate and thus ∆G values are additive)
- Not at equilibrium in living organisms; in a dynamic steady state
- Nutrients/substrates flow thru pathway due to irreversible and coupled rxns, and removal of the products by other pathways or exit from cell
- Favorable exergonic rxn can drive an endergonic rxn thru common intermediate by coupling
- Catabolic (energy producing) pathways are NEVER the reverse of anabolic (energy requiring) pathways; each has diff set of chem rxns so ∆G is negative overall
- Irreversible rxns commit a metabolite to a pathway; determine the flow thru the pathway and are thus the regulated steps in the pathway |
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Term
| Distinguish the reactions and overall ΔG in catabolic pathways and their opposing anabolic pathways. |
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Definition
Catabolic = -change of G; produces ATP
Anabolic = + change of G; uses ATP |
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Term
| Distinguish ΔG for irreversible steps and reversible steps in a metabolic pathway. |
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Definition
- Irreversible rxns occur with large negative ∆G, not near equilibrium
- Reversible rxns occur with ∆G near zero (recall that ∆G = 0 means at equi so rate of Forward rxn = rate of reverse rxn) |
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Term
| Describe the relationship between the steady state ratio of [products]ss/[reactants]ss compared to the equilibrium ratio of [products]eq/[reactants]eq for an irreversible step and for a reversible step in a metabolic pathway. |
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Definition
For reversible: [products]ss/[reactants]ss ≈ [products]eq/[reactants]eq
For irreversible: [products]ss/[reactants]ss << [products]eq/[reactants]eq
∆G = -2.3 RT log([products]eq/[reactants]eq) + 2.3 RT log([products]ss/[reactants]ss) |
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Term
| Evaluate the importance of regulating irreversible reactions in a metabolic pathway. |
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Definition
- Irreversible rxns determine the rate of reaction
- Through partial and complete inhibition irreversible rxns are regulated
- inhibition of the enzyme that catalyzes the irreversible rxn helps to sustain certain [product] or diminish it totally |
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Term
| Explain the central role of ATP in catabolic and anabolic pathways. |
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Definition
- Plays central role in metabolism b/c its ∆G° of hydrolysis is intermediate between phosphate donors and phosphate acceptors
- ADP is a phosphate acceptor and ATP is a phosphate donor; work together to facilitate catabolic and anabolic pathways (basically, the hydrolysis reaction is coupled with anabolic and catabolic rxns) |
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Term
| List the types of weak, noncovalent interactions important for protein structure. |
|
Definition
1. Ionic Interactions
2. H Bonding
3. The Hydrophobic Effect
4. Van Der Waals Forces |
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Term
|
Definition
- Force of attraction b/n ions = E = [kq1q2]/[D(rAB)2 , where r is distance of separation, q represents magnitude of charges, k is a constant, and D is a measure of how environment influences rxn between the charges
- Allows charged residues to be present within proteins; opposite charges form “salt bridge” and thus cancel out each other’s charges
- Stabilizes structure of proteins; protects from high temps
Central to PCR (this is how tag polymerase works) |
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Term
|
Definition
- Attraction between H atom attached to a N, O, of F atom and a N, O, or F atom on another molecule (or part of the same molecule)
- Due to high polarity of X-H bond; H atom ends up being “shared” between the 2 electronegative atoms
Weaker and longer than covalent bond
- Strongest when donor and acceptor atoms are in line with H
- Critically important for structure and function of macromolecules such as proteins, and in DNA where it’s responsible for base-pairing that underlies inheritance |
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Term
|
Definition
- Water is less ordered (higher entropy) when hydrophobic molecules clustered together; thermodynamic effect
Drives folding of globular proteins and other macromolecs
Promotes intermolecular interactions (i.e. enzyme-substrate) |
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Term
|
Definition
- Between uncharged but polarizable groups; both attractive and repulsive terms
- EVDW = A/r^6AB + B/r^12AB
- Balance between 2 opposing forces (attractive and repulsive) determines optimal VdW contact distance (rAB ≈ 2.8 to 4.1 Ǻ)
- 1st term is attractive term and 2nd term is repulsive term
As you get closer Separation of charge occurs in one group, creating a dipole where the other group has a separation of charge as well creating a dipole and thus dipole-dipole attraction but once gets too close then it goes back to repulsion; hence there is an optimal distance where the dipole-dipole attraction is maximized
The reason attraction decreases once too close is that physically too close so the electron clouds overlap |
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Term
| Describe the structure and identify the parts of a “standard” amino acid |
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Definition
- Each has an α-amino group (except for proline which has an imino group)
- Each has an α-carboxyl group
- All are amphoteric; can exist as zwitterions
- All have at least one asymmetric carbon (except Glycine b/c has 2 of same group)
- Have two different enantiomers; non-superimposable mirror images
- In proteins it is the L-configuration that is always present, because the enzyme that is responsible for synthesis for amino acids do it in a stereospecific way where amino acid is only added in specific way to carbon (L-config below with middle axis coming out of the page) |
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Term
| Amino Acids: Nonpolar, Aliphatic R group |
|
Definition
(Aliphatic = acyclic or cyclic with no aromaticity (conjugated ring of unsaturated bonds))
Glycine, Gly, G
Alanine, Ala, A
Leucine, Leu, L
Isoleucine, Ile, I
Methionine, Met, M
Proline, Pro, P |
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|
Term
| Amino Acids: Aromatic Side Chain |
|
Definition
Phenylalanine, Phe, F
Tyrosine, Tyr, Y
Tryptophan, Trp, W |
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|
Term
| Amino Acids: Polar, Uncharged side chain |
|
Definition
Serine, Ser, S
Threonine, Thr, T
Asparganine, Asn, N
Glutamine, Gln, Q
Cysteine, Cys, C |
|
|
Term
| Amino Acids: Positively charged side chains |
|
Definition
Lysine, Lys, K
Arginine, Arg, R
Histidine, His, H |
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|
Term
| Amino Acids: Negatively charged side chains |
|
Definition
Aspartate, Asp, D
Glutamate, Glu, E |
|
|
Term
|
Definition
Alanine
ALA
A
Neutral, Nonpolar |
|
|
Term
|
Definition
Arginine
Arg
R
Basic, Polar |
|
|
Term
|
Definition
Asparganine
Asn
N
Neutral, Polar |
|
|
Term
|
Definition
Aspartic Acid
Asp
D
Acidic, Polar |
|
|
Term
|
Definition
Cysteine
Cys
C
Neutral, Slightly Polar |
|
|
Term
|
Definition
Glutamic Acid
Glu
E
Acidic, Polar
|
|
|
Term
|
Definition
Glutamine
Gln
Q
Neutral, Polar |
|
|
Term
|
Definition
Glycine
Gly
G
Neutral, Nonpolar |
|
|
Term
|
Definition
Histidine
His
H
Basic, Polar |
|
|
Term
|
Definition
Isoleucine
Ile
I
Neutral, Nonpolar |
|
|
Term
|
Definition
Leucine
Leu
L
Neutral, Nonpolar |
|
|
Term
|
Definition
Lysine
Lys
K
Basic, Polar |
|
|
Term
|
Definition
Methionine
Met
M
Neutral, Nonpolar |
|
|
Term
|
Definition
Phenylalanine
Phe
F
Neutral, Nonpolar |
|
|
Term
|
Definition
Proline
Pro
P
Neutral, Nonpolar |
|
|
Term
|
Definition
Serine
Ser
S
Neutral, Polar
|
|
|
Term
|
Definition
Threonine
Thr
T
Neutral, Polar |
|
|
Term
|
Definition
Tryptophan
Trp
W
Neutral, Slightly Polar
|
|
|
Term
|
Definition
Tyrosine
Tyr
Y
Neutral, Polar |
|
|
Term
|
Definition
Valine
Val
V
Neutral, Nonpolar |
|
|
Term
| Define the terms “zwitterion” and “pI,” calculate the pI for an amino acid given the pKs of its ionizable groups, and predict its charge given the pH. |
|
Definition
Zwitterion – dipolar ions that have no net charge
pI = isoelectric point = pH at which no net charge for a molecule
pI = average of pKas on a given amino acid
when pI < pH, then will be negative
when pI > pH, then will be positive |
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Term
| Describe the special properties of each of the following amino acids: Proline, cysteine, tyrosine and tryptophan, and histidine. |
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Definition
Proline is a helix breaker; creates kinks in helices
Cysteine forms disulfide bonds
Tyrosine and Tryptophan absorb light at 280 nm; can use absorbance to determine how much protein is present
Histidine can deprotonate allowing hemoglobin to act as a buffer |
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Term
Define and describe (by drawing a diagram) the peptide bond |
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Definition
[image]
- Pep bond is formed between carboxyl and amino groups of diff AAs with the elimination of one water molecule
- Pep bonds are very strong; only cleaved by proteases
- Pep bonds are formed in the ribosome where proteins are formed
- Flexible but conformationally restricted by partial double bond character; bond is short and allows no rotation about it; six atoms lie in the same plane
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Term
| Partial Double Bond Character of Peptide Bond |
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Definition
[image]
Shorter, no rotation about it, flat |
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Term
the peptide psi and phi dihedral angles |
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Definition
[image]
- psi and phi dihedral angles determine the path of the polypep chain in 3D space
- can rotate from -180 to 180
- along with rigidity of pep bond, this allows polypep.s to fold into unique 3D shapes
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Term
| The peptide's tendency to be in a trans- versus a cis- configuration |
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Definition
Most AAs adopt trans-config because the cis-config is unfavorable
Only proline adopts cis-config b/c in cis there are no large groups in the same plane like there are in the trans config; opposite for other AAs |
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Term
| pKa of terminal alpha-carboxyl group |
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Definition
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Term
| pKa of apspartic acid and glutamic acid |
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Definition
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Term
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Definition
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Term
| pKa of terminal alpha-amino group |
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Definition
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Definition
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Definition
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Term
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Definition
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Term
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Definition
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Term
| Explain the sentence: “Polypeptides are flexible yet conformationally restricted.” |
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Definition
| The partial double bond character of the peptide bond restricts the number of conformations because it does not allow rotation about it but the phi and psi angles on the alpha carbon have a large degree of rotation making polypeptides still flexible. |
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Term
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Definition
-carbonyl of residue i is H bonded to NH of i+3 residue (so bonds to every fourth residue); this bond holds alpha helix together
- Rise/residue (length of each residue) = 1.5 Angstroms, n = # residues/turn = 3.6, p (pitch) = 5.4 Angstroms
- side chains of an alpha helix radiate outward from the helix axis (minimize steric hindrance b/n side chains and provides functional groups for protein-protein and protein-ligand interactions)
-amphipathic = when one side of helix has hydrophobic side chains & other has hydrophilic |
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Term
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Definition
- basic unit is the beta strand; two or more strands must align to form sheet (individual strands are not stable by themselves)
- beta strand is more extended structure then an alpha helix; like a stretched out helix with n = 2 residues/ turn and p = 6.8 Angstroms
-can align either parallel or antiparallel (ex is silk); mixed sheets contain both
- side chains project above and below plane of sheet which minimizes steric clash and allows sheets to stack
- often connected to alpha helices in protein |
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Term
| Describe the Reverse Turn |
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Definition
- The reverse turn allows a long polypep chain to fold back on itself (nearly 1/3 of residues in globular proteins are in reverse turns)
- Most common is Beta turn (named this b/c connect to successive strands of antiparallel beta sheets)
- 4 residues required to complete a turn (residues i to i+3); - - 1st residue hydrogen bonds to 4th
- Gly and Pro common in beta turns but tend to disrupt the alpha helix
- 2 types: I and II differ in orientation of pep unit liking residues 2 and 3 |
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Term
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Definition
- more elaborate than turns; located on surface of protein; - - participate in interactions with other molecules
- don’t have regular, periodic structure
- often well defined structurally |
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Term
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Definition
| the linear sequence of amino acids in a polypep chain written from N-terminus to C-terminus going left to right |
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Term
| Define Secondary Structure |
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Definition
- forms when all the psi and phi dihedral angles of a contiguous stretch of polypeptide adopt the same set of values
- Regular local folding of short stretch of polypeptide into one of several specific structural forms
- Various helices, various pleated sheets, reverse turns, and loops (no regular, repeating structure) |
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Term
| Define Tertiary Structure |
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Definition
- the folding of a continuous sequence of 2° elements into a specific and unique 3-D architecture
- Simple classification scheme: alpha-domain proteins (mostly alpha helices), beta domain proteins (mostly beta sheet), the alpha/beta domain proteins (both)
- Determine structure thru x-ray crystallography and NMR(better for smaller) |
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Term
| Define Quaternary Structure |
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Definition
- arrangement of two or more polypeptides in association
- Each component polypeptide is called a subunit of the oligomer (quaternary)
- Two subunits = dimer; three subunits = trimer
- Each polypep has its own tertiary fold (specific arrangement that functions as a single unit)
- Oligomers may consist of identical subunits or combo of different subunits
- Stabilized by non-covalent forces only
- Globin, alpha/beta barrel, and beta barrel |
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Term
| Identify whether a particular amino acid replacement is conservative or not |
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Definition
Conservative mutation: AA (#1) changed to similar AA (#2)
Ex: change from Leu to Ile is not large effect b/c same hydrophobic properties
Non-conservative mutation: AA (#1) changed to dissimilar AA
Ex: change from Glu to Val, leads to sickle cell anemia |
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Term
| List which amino acids tend to be found in which secondary structural elements, i.e., their propensities for a given type of structure, and explain why. |
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Definition
Glycine and Proline are common in beta turns; glycine because it’s has the smallest R group
Proline disrupts an alpha helix b/c its secondary amino group is not geometrically compatible with the right-handed spiral of the alpha helix; inserts a kink in the chain which interferes with the smooth, helical structure |
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Term
| Explain the motif helix-loop-helix |
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Definition
| feature of some transcription factor proteins that bind DNA and direct transcription; contains helix having side chains that form base-specific, non-covalent contacts with target DNA |
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Term
| Explain the motif zinc finger |
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Definition
- (DNA binding motif) binds into major groove of B-DNA double helix; particular side chains make base-specific contacts with DNA double helix
- occurs via H-bonds, salt bridges, and hydrophobic interactions
- 30 residues long (n), use side chains of 2 His and 2 Cys residues to coordinate Zinc ion (stabilizes finger structure; motif won’t form without zinc)
- Structure solved using multi-dimensional NMR spectroscopy
- Leucine zipper DNA binding motif also commonly found in transcription factors |
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Term
| Explain the motif 4-helix bundle |
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Definition
- Common “tertiary” fold in both water soluble and membrane bound proteins
- Four globular bundles: core side chains =hydrophobic and surface side chains = hydrophilic; so its comprised of amphipathic helices
- Hydrophobic packing stabilizes structure
Ex: electron transport chain protein cytochrome b-562 folds as a 4 helix bundle; but hydrophobic side chains project outward while polar/charged groups on inside; membrane protein |
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Term
| Describe the quaternary structure globin |
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Definition
heme containing proteins involved in binding and transporting oxygen
Contains 8 alpha (alpha domain protein)
Ex. Hemoglobin (transports oxygen in blood) – 7 alpha helices for alpha subunit and 8 for beta subunit |
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Term
| Describe quaternary structure time barrel fold |
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Definition
laborate closed barrel structure that contains alternating segments of alpha helices and beta strands
Ex. Triosephosphate Isomerase (TIM) and other glycolytic enzymes (adolase, enolase, pyruvate kinase) have domains that fold into this structure |
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Term
| Describe the quaternary structure beta barrel |
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Definition
retinol binding protein is a good example; topology of 8 antiparallel beta strands linked by beta turns; barrel interior lined with Hydrophobic sidechains; hydrophilic hydroxyl tail of retinol exposed to solvent at open end of barrel
RBP is the plasma carrier for retinol; metabolite binding unit of RBP has an elaborate cage-like structure, an Up and Down Beta Barrel |
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Term
| Describe the structure of myoglobin, mentioning its helical content, its overall tertiary structure, its prosthetic group, and its hydrophobic core. |
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Definition
- Myoglobin is a single polypeptide structurally similar to individual subunit polypeptide chains of hemoglobin
- Folded into 8 alpha helices (alpha domain – tertiary structure)
- Prosthetic group: noncovalently attached heme is imbedded in a hydrophobic pocket
- Nonpolar amino acids packed closely together in interior and stabilized by hydrophobic interactions while charged amino acids located on surface of molecule where they form H-bonds with each other and water |
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Term
| Outline the steps by which X-ray crystallography can be used to determine the three-dimensional structure of a protein via x-ray diffraction of crystallized form |
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Definition
1. Crystallization of Protein
2. X-rays are generated and directed toward the Crystallized Protein (4 ways)
(a) Bombarding a metal source with a beam of high-energy electrons
(b) Exposing a substance to a primary beam of x-rays to create a secondary beam of x-ray fluorescence
(c) Radioactive decay process that generates s-rays
(d) Synchrotron radiation source
3. Creation of an electron density map based on the measured intensities of the diffraction pattern on the film |
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Term
| Describe the overall structure of hemoglobin |
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Definition
Tetramer with 2 types of subunits; α2β2
Each subunit adopts globin fold and has one heme prosthetic group
2 alpha subunits, two beta subunits (all helices); similar but not identical |
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Term
| Describe the overall structure of phosphofructokinase |
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Definition
(PFK-1) tetramer of 4 identical subunits
4 catalytic sites and 4 regulatory sites
Allosterically inhibited by ATP, citrate; actvated by AMP, Fru-2-6-BP
Key control point for glycolysis |
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Term
| Describe the overall structure of Aspartate Transcarbamylase |
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Definition
12 subunits and 2 types of subunit; α6β6
Catalyzes 1st commtted step in pyrimidine nucleotide biosynthesis, formation of N-carbamoylaspartate and Pi from carbamoyl phosphate and aspartate
2 catalytic trimmers (C3) and 3 regulatory dimers (r2) come together to form C6r6 complex; Dodecamer (12 subunits)
Inhibited (feedback) by CTP; activated by ATP
Example of an allosteric enzyme |
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Term
| State some of the functional attributes that oligomeric proteins have that monomeric ones do not have. |
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Definition
- Regulation thru cooperative effects
- Channeling of substrates between diff functional sites (multienzyme complexes) Helps speed up pathways b/c it makes substrates readily available for the following active sites |
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Term
| Define “isoform” and give some examples of protein isoforms. Explain how a clinical test (for myocardial infarction, for example) can be based on the detection of higher levels of a particular isoform of a protein. |
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Definition
isoform – any of several different forms of the same protein
different forms of CKMB ( or CKMM) … if you have a myocardial infarcation you will have alot of CKMM and CKMB
examples: 5 isoforms of LDH (LDH-1, LDH -2, and so on
also hemoglobin (HbF, HbA, and so on) |
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Term
| Define “chaperone,” and list some types of chaperones. |
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Definition
Chaperones – class of intracellular protein machines that assist other cellular proteins in adopting folded structures; bind to unfolded and partially folded proteins and prevent improper association
Ex: GroEL/GroES
Hsp47 (heat shock protein) – collagen chaperone |
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Term
| Name some common protein denaturants |
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Definition
Chemical Denaturants – urea, guanidine hcl, and sodium dodecyl sulfate (SDS)
Other Denaturing agents – heat (thermal unfolding), sometimes low temp (cold denaturation), pH extremes
Neither of the above denature disulfide bonds; break w/ beta mercaptoethanol or DTT |
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Term
| Indicate how a protein’s function is intimately tied to its structure |
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Definition
Biologically inactive when unfolded; if you destroy fold, destroy function
Irreversible in vivo accumulation of unfolded/misfolded proteins is cause of class of degenerative diseases called amyloidosis that cause plaque in tissue (ex. Mad cow) |
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Term
| Evaluate the statement “Amino acid sequence determines tertiary structure.” |
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Definition
AA side chains guide the folding of the polypep to form a compact structure
Final functional protein is NOT FULLY DEFINED by its AA sequence
Post-translational modifications are used to fine tune properties of proteins (covalently modified)
Introduce local charges, hydrophobic groups, hydrophilic groups, antigenic properties
Nearly all modifications due to specific enzymatic activities
except the nonezymatic glycation of Hb to form HbA1c (this is spontaneous) |
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Term
| Briefly describe the protein folding process. |
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Definition
1. As a peptide folds, its AA side chains are attracted and repulsed according to chem prop.s (charges, H-bonds, hydrophobic interactions, and disulfide bonds)
2. Protein folds with low energy state
3. Chaperones interact with polypep. at various stages during folding process to guide proper synthesis of folding |
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Term
| Describe the structure of the prion protein in its noninfective (PrPc) and infective (PrPsc) forms. How are the two structures different, and alike? |
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Definition
PrPc – benign noninfectious form; mostly alpha helical
PrPsc – infectious form (beta sheet forms) |
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Term
| Explain why it was revolutionary for Stanley Prusiner to propose that an infectious agent could be made entirely of protein. |
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Definition
| Heretical idea – goes against accepted dogma which says that nucleic acid must be involved |
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Term
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Definition
- Prion disease
- caused from infection in genetically susceptible sheep
- neurodegenerative, caused sheep to scrape off their wool |
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Term
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Definition
- Prion DIsease
- caused by ritualistic canabalism (infected brain tissue)
- effects the Fore people |
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Term
| Creutzfeldt-Jacob disease |
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Definition
- Prion Disease
- a form of brain damage that leads to a rapid decrease of mental function and movement.
- from Prion-contaminated HGH, grafts, etc.
- can be familial (rare) |
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Term
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Definition
- Prion Disease
- bovine prions (?); transfer from eating cow meat from cow w/ Mad Cow disease |
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Term
| List and describe some “amyloid diseases” related to the misfolding of proteins |
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Definition
Alzheimer’s disease – dementia
Mad cow Disease (BSE) – fatal neurodegenerative disease in cattle
CJD – degenerative neurological disorder that’s incurable and invariably fatal (like mad cow for humans) |
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