# Biochem

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Acidic dissociation

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1. General expression: HA is the acid (proton donor) and
A- is the conjugate base (proton acceptor):
k1 HA --> H+ + Ak-1

2. An acid dissociates in water to yield a hydrogen ion (H+) and
its conjugate base
Acid (acetic acid) CH3COOH --> Conjugate base (acetate) H+ + CH3COO-

3. A base combines with H+ in water to form its conjugate acid
Ammonia (base) Ammonium ion (conjugate acid) NH3 + H+ --> NH4+

k1[HA] = forward rate, k-1[H+][A-] = reverse rate

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Measures of acidity

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1. pKa • When forward & reverse rates are equal, acidic dissociation
• constant, Ka, is defined by: o k1/k-1 = [H+][A-] / [HA] = Ka Expresses the STRENGTH OF AN ACID pKa = -log[Ka]

• • Strong acid has pKa of Ω (H+ binds loosely to conjugate base) 2 • Weak acid has a pKa of ∆10 (H+ binds tightly to conjugate base) 2. pH • Henderson-Hasselbalch equation: pH = pKa + log [A-]/[HA]
• • A measure of the ACIDITY OF A SOLUTION pH = -log[H+]
Neutral solution has a [H+] of 10-7  pH = 7

Biochem 5 • • Acidic solution has a [H+] > 10  pH < 7 Alkaline solution has a [H+] < 10-7  pH > 7 -7 Buffers and Buffering capacity .

Biochem 6 1. It resists changes in [H+] on addition of acid or alkali 3. The buffering capacity of a solution is determined by the acid-base concentration and the pKa of the weak acid • • Maximum buffering effect occurs when: o [weak acid] = [conjugate base] When the buffer effect is at its maximum: o pH of the solution = pKa of the acid 4. Buffering effect is seen on a titration curve for a weak acid • The shape of the curve is the same for all weak acids . A solution that contains a mixture of a weak acid and its conjugate base 2.

the pH = pKa The buffering region extends one pH unit above and below the pKa What acid-base pair is an effective buffer in physiologic fluids? What acid-base pair is the principal buffer in plasma and extracellular fluid (ECF)? .Biochem 7 • • At the midpoint of the curve.

and HPO42What acid-base pair is the principal buffer in plasma and ECF? • CO2-H2CO3-HCO3. even though the pKa is only 6. for 4 reasons: . CO2 is an acid.1.Biochem 8 1.system (carbon dioxide-carbonic acid-bicarb) • CO2 + H2O –carbonic anhydrase H2CO3  H+ + HCO3• Note: carbonic anhydrase converts CO2 to H2CO3 in RBCs • In this system. so H-H equation is: o pH = 6.0301)PCO2 • This system is effective around physiologic pH of 7. What acid-base pair is effective buffer in physiolog fluids? • H2PO4. 2.1 + log [HCO3-] / (0.4.

so effective concentration of CO2 is very high Equilibration of CO2 with H2CO3 is very rapid CO2 removal by lungs allows for rapid changes in [H2CO3] Kidney can retain or excrete HCO3-.Biochem 9 o o o o Supply of CO2 from oxidative metabolism is unlimited. thus changing the concentration of the conjugate base Acid-Base Disorders: Acidosis and Alkalosis .

Alkalosis .Biochem 10 1. can lead to coma and death Respiratory acidosis: pCO2 ↑ as a result of hypoventilation Metabolic acidosis: [HCO3-] ↓ as a result of the addition of an acid stronger than H2CO3 to the ECF • • 2.35 Results in CNS depression When severe. Acidosis • • • Occurs when pH of blood and ECF falls < 7.

. oral antacids) Diabetic ketoacidosis .g.Biochem 11 • • • • • Occurs when pH of blood and ECF is >7. can result in tetany Respiratory alkalosis: pCO2 ↓ as result of hyperventilation Metabolic alkalosis: [HCO3-] ↑ as a result of excess acid loss (e..g. vomiting) or addition of a base (e.45 Leads to neuromuscular hyperexcitability When severe.

Biochem 12 1. hyperglycemia  ↑ fatty acid oxidation ↑ fatty acid oxidation  excessive production of acetoacetic and 3-hydroxybutyric acids and acetone (ketone bodies) Acids dissociate at body pH and release H+  metabolic acidosis . Combination of high blood levels of ketone bodies and a metabolic acidosis 2. Pathogenesis • • • Uncontrolled insulin-dep DM (type 1)  ↓ glucose utilization.

dehydration. Therapy: correct the hyperglycemia. & acidosis • Insulin – to correct the hyperglycemia • Fluids (physiologic saline) – to treat dehydration • In severe cases: sodium bicarbonate – to correct acidosis Amino acids grouped by the properties of their R-groups • • Dehydration Lethargy • • Vomiting Drowsiness • Coma .Biochem 13 3. Clinical picture 4.

nonpolar • Phenylalanine • • Glycine Alanine • • • Valine Leucine Tyrosine • • • Isoleucine Proline Tryptophan . Aromatic. nonpolar (hydrophobic) 2. Aliphatic.Biochem 14 1.

Basic. mildly polar (uncharged. polar 6. hydrophilic) 5. Sulfer-containing 4. polar • • Aspartic acid Asparagine • Lysine • Serine • • • • Threonine Arginine Glutamic acid Glutamine • Histidine Pg. 7 for structures • Cysteine • Methionine Secondary structures of proteins and collagen .Biochem 15 3. Acidic. Hydroxyl.

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1. Secondary structure = arrangement of H bonds between peptide nitrogens & carbonyl oxygens of different amino acids 2. Helical coils

Hydrogen-bonded nitrogens & oxygens are on nearby amino acids Right-handed alpha helix – most common

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3. Beta sheets (pleated sheets) – may run parallel or antiparallel
4. Left-handed helical strands
• Hydrogen bonds between residues on neighboring peptide chains Wound into a supercoiled triple helix in collagen Collagen – major structural protein in the body

o Alpha-keratin in hair and nails o Myoglobin – has several alpha-helical regions Proline, glycine, and asparagine – “helix breakers”

o o
o

Primary structure: repeating glycine-X-Y sequences X and Y are freqeuntly proline or lysine Contains hydroxyproline & hydroxylysine

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Protein Denaturation Agents

1. Extremes of pH (e.g., strong acid or alkali) 2. Ionic detergents (e.g., sodium dodecylsulfate/SDS) 3. Chaotropic agents (e.g., urea, guanidine)

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4. 5. 6. 7.

Heavy metal ions (e.g., Hg++) Organic solvents (e.g., alcohol or acetone) High temperature Surface films (e.g., as when egg whites are beaten)

Caused by mutant sickle cell hemoglobin (Hgb S) • Hydrophobic valine replaces hydrophilic glutamate at position 6 of the beta-chain of normal hemoglobin A (Hgb A) .Biochem 20 Sickle cell anemia 1.

Sickle cell trait Individuals with heterozygous genotype (AS) Have both Hgb A and Hgb S in their RBCs Symptoms o Usually asymptomatic o Episodes of hematuria . Sickle cell disease • • • Individuals with homozygous genotype (SS) Have only Hgb S in their RBCs Symptoms o o Severe anemia: deoxy Hgb S produces fibrous precipitates  formation of sickle cells  shorter life span  severe anemia Acute episodes of vaso-occlusion – “sickle cell crisis” ⇒ ⇒ • • • Sickle cells can’t pass thru capillaries  vasocclusion Disabling pain that requires hospitalization 3.Biochem 21 2.

Biochem 22 Scurvy .

Defective collagen synthesis resulting from a vitamin C (ascorbic acid) deficiency 2. Ascorbic acid is required for hydroxylation of proline and lysine during post-translational modification of collagen 4. O2. Consequences of abnormal collagen • • • Defective wound healing Defective tooth formation Loosening of teeth • • Bleeding gums Rupture of capillaries 3. Pathogenesis • Hydroxylating rxn requires hydroxylase.Biochem 23 1. & Fe2+ • Vit C is required to maintain iron in its oxidation state (Fe2+) • Hydroxyproline forms H-bonds that stabilize collagen helix .

Biochem 24 • Symptoms of scurvy are thus the result of weakend collagen when these hydrogen bonds are missing Free energy change .

The ∆ G of a rxn A + B  C + D is: • ∆ G = ∆ G0’ + RTln ([C][D]) / [A][B]) o where ∆ G0’ is the standard free-energy change (when concentrations of all reactants and products are 1M and pH = 7). The quanitity of energy from chemical reactions that is available to do work (∆ G) 2.987 cal/molK) and T is the absolute temperature 3. R is the gas constant (1.Biochem 25 1. When the rxn has reached equilibrium: • ∆ G0’ = –RTlnKeq .

Biochem 26 Thermodynamic spontaneity: Exergonic and Endergonic Rxns .

is greater than that of the reactants.Biochem 27 1. Endergonic rxns are nonspontaneous (rxn goes to the left) • Keq < 1 • ∆ G0’ is positive • Final concentration of the reactants. Exergonic rxns are spontaneous (rxn goes to the right) Keq > 1 ∆ G0’ is negative Final concentration of the products. is greater than that of the products. A and B. C and D. A and B 2. C and D • • • .

Biochem 28 3. entropy. Note: ∆ G0’ CANNOT predict spontaneity under intracellular conditions • Intracellular spontaneity is a function of actual concentrations as well as Keq. ∆ G. and free-energy change . NOT ∆ G0’ Enthalpy.

Biochem 29 1. when a solute diffuses from • a more concentrated to a less concentrated solution. and when a protein is denatured ↓ when a complex molecule is synthesized from smaller substrates . Entropy (∆ S) • Measure of the change in randomness or disorder of system • ↑ when a salt crystal dissolves. Enthalpy (∆ H) • The amount of heat generated or absorbed in a rxn 2.

Free-energy change (∆ G) • Is related to enthalpy and entropy as follows: o ∆ G = ∆ H .Biochem 30 3.T ∆ S (where T = absolute temp in Kelvins) Catalysts and the Rate of Reaction .

it first goes through an energy barrier called the transition state.Biochem 31 1. Rate of reaction • The ∆ G0’ provides no info concerning the rate of conversion from A to B • When A is converted to B. A-B± • The activation energy (∆ G±) = energy required to scale the energy barrier and form the transition state .

Catalysts (mostly enzymes) result in a: • Lower ∆ G± • Faster reaction rate • Michaelis-Menten equation . the lower the rate of the rxn converting A to B 2.Biochem 32 ± The greater the ∆ G .

Velocity (v) of product formation is related to [ES]: o v = k3[ES] where k3 is also called kcat • . S=substrate. k1-3 = rate constants 3. In enzyme-catalyzed rxns: k1 k3 E + S  ES  E + P k2 Where E=enzyme. P=product.Biochem 33 1. Describes the kinetics of enzyme rxns 2.

Km = [substrate] at which v = ½Vm ([S] = Km) 6. Michaelis-Menten eq predicts velocity if [enzyme] is constant: Vm[S] v = Km+[S] 5. A plot of velocity versus [S] is a rectangular hyperbola • Where Vm = max velocity & Km is the Michaelis constant Lineweaver-Burk Equation .Biochem 34 4.

Form of the Michaelis-Menten eq. which is sometimes known as the double-reciprocal equation: 1 = Km + [S] = Km x 1 + 1 v = Vm[S] Vm [S] Vm 2.Biochem 35 1. The slope is Km/Vm .

The X-intercept is –1/Km Enzyme Regulation: How doe Inhibitors affect the Lineweaver-Burk plots? . The Y-intercept = 1/Vm 4.Biochem 36 3.

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1. Competitive inhibitors • ↑ apparent Km • Vm remains the same • ↑ slope • X-intercept has smaller absolute value • Y-intercept is unchanged

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2. Noncompetitive inhibitors • ↓ Vm • Km unchanged • ↑ slope • X-intercept is unchanged • Y-intercept is larger 3. Uncompetitive inhibitors (bind only to ES complex) • Both Km & Vm are different  lines on the plot are parallel

Allosteric regulation of enyzmes: Definition, How do they affect Km, and Example of Hexokinase

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1. Low-molec wgt effector binds to enzyme at a specific site other
than active site (the allosteric site) & alters its activity 2. Allosteric enzymes usually have >1 subunit and >1 active site 3. Effectors may have a + or – effect on activity
• • Active sites that interact cooperatively: velocity vs, [S] = sigmoid Binding of 1 substrate facilitates binding of substrate at other sites

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4. Example: muscle hexokinase

• • • • •

Positive effectors ↓ the apparent Km Negative effectors ↑ the apparaent Km Hexokinase catalyzes 1st rxn in use of glucose my muscle cells: o Glucose + ATP  glucose-6-P + ADP Hexokinase has a low Km compared to blood [glucose], so it is saturated and operates at its Vm When glycolysis slows down, gluc-6-P accumulates  gluc-6-P allosterically inhibits hexokinase (keeps gluc-6-P in balance)

Other mechanisms of enzyme regulation: 1. Induction/repression of enzyme synthesis

Covalent modificataion 3. Induction/repression of enzyme synthesis • Cytochrome P450 enzymes in the liver (degrade and detoxify drugs) are induced by the drugs themselves 2. Protein-protein interaction 1.Biochem 41 2. Covalent modificataion .

Biochem 42 Phosphorylase (enzyme that breaks down glycogen) is activated by phosphorylation of a specific hydroxyl group • This phosphorylation is stimulated by hormones that elevate blood glucose. Protein-protein interaction between enzyme & regulatory protein • Pancreatic lipase (digests dietary fat) is assisted by colipase • Colipase anchors lipase to the surface of fat droplets • Mechanism and Treatment of Methanol & Ethylene glycol Poisoning . such as glucagon and Epi 3.

the 1st oxidation is carried out by alcohol dehydrogenase . Mechanism of poisoning • Toxicity is caused by the action of their metabolites • In both cases.Biochem 43 1.

Biochem 44 Methanol  formaldehyde + formic acid ⇒ Eyes very sensitive to formaldehyde  blindness o Ethylene glycol  glycoaldehyde. Treatment • Initial infusion of ethanol  competitive substrate  displaces methanol or ethylene glycol from active site of alcohol dehydrogenase • Prevents continued production of toxic metabolites o Citric acid cycle: . oxalate. and lactate ⇒ Deposition of oxalate crystals in kidney  kidney failure 2.

Pathway.Biochem 45 Location. Location • Mitochondria (found in all cells except RBCs) 2. and Initial Substrate 1. Pathway .

& proteins o Glucose catabolism eventually produces pyruvate  o o acetyl CoA via pyruvate dehydrogenase Fatty acids generate acetyl CoA via β -oxidation Some amino acids are degraded to acetyl CoA • . Initial Substrate: Acetyl Coenzyme A (ACETYL CoA) • Condenses with oxaloacetate (OAA) to begin the cycle 4.Biochem 46 It is the final common pathway of oxidiative metabolism 3. Where does acetyl CoA come from? • The catabolism of carbs. fats.

Biochem 47 What are the products of one revolution of the citric acid cycle? 1. 2 CO2 (most CO2 from metabolism) .

Regeneration of one mole of OAA 3. 3 NADH & 1 FADH2  11 ATPs (via oxidative phosphorylation) 4. 1 GTP  1 ATP Oxidative Phosph: 1 NADH = 3 ATP 1 FADH2 = 2 ATP TOTAL OF 12 ATPs/acetyl CoA .Biochem 48 2.

Pyruvate carboxylase in the liver & kidney: .Biochem 49 Describe the anaplerotic rxns that provide OAA and other citric acid cycle intermediates 1.

+ NAD(P)  Malate + NAD(P)+ 4. Malic enzyme in many tissues: • Pyruvate + HCO3. Glutamate dehydrogenase in the liver: • Glutamate + NAD(P)+ + H2O  α -ketoglutarate + NAD(P)H + NH4+ . Phosphoenolpyruvate (PEP) carboxykinase in heart and skeletal muscle: • PEP + CO2 + GDP  OAA + GTP 3.Biochem - 50 • Pyruvate + ATP + HCO3  OAA + ADP + Pi 2.

Biochem 51 Regulation of the citric acid cycle .

NADH 3. NADH Regulated mainly by need for ATP.Biochem 52 1. Step: Isocitrate + NAD+ α -ketoglutarate + NADH + CO2 • Enzyme: isocitrate dehydrogenase • Allosteric activator: ADP • Inhibitors: ATP. long-chain acyl-CoA 2. Step: α -ketoglutarate + NAD+ + CoASH  succinyl CoA + NADH + CO2 • Enzyme: α -ketoglutarate dehydrogenase (note: requires same cofactors as the pyruvate dehydrogenase complex) • Inhibitors: succinyl CoA. Step: Acetyl CoA + OAA  citrate • Enzyme: citrate synthase • Inhibitors: ATP (↑ Km). & therefore by supply of NAD+ .

Biochem 53 Electron Transport Chain (ETC) & Oxidative Phosphorylation (BOTH in MITOCHONDRIA) .

Oxidative phosphorylation: uses energy derived from flow of electrons thru ETS to drive synthesis of ATP from ADP and Pi NADH NADH Q dehydrogenase Ubiquinone-c oxidoreductase (Cytochrome bc1) cytochrome c ATP ATP synthase-.Biochem 54 1. ETS: electrons pass from NADH or FADH2 to ultimately reduce O2 and produce H2O 2.Proton gradientO2 Cytochrome H 2O oxidase .

= Complex I. Cytochrome bc1 = Complex III. = Complex II (where FADH2 enters – not pictured here). Cytochrome oxidase = Complex IV Chemiosmotic hypothesis .Biochem 55 NADH dehydrog. Succinate dehydrog.

hydrogens are pumped across inner membrane to intermembrane space • The [H+] in the intermembrane space ↑ relative to matrix • This generates a proton-motive force as result of 2 factors: o Difference in pH (∆ pH) o Difference in electrical potential (∆ ψ ) between the intermembrane space and the mitochondrial matrix 3. III. Respiratory complexes as proton pumps: • As electrons (e-) pass thru complexes I. Describes coupling of electron flow thru ETS to ATP 2. ATP synthase complex (complex V) . & IV.Biochem 56 1.

pair from FADH2 to O2 (bypass I) 2ATP Uncouplers and Inhibitors of ETS . drive the synthesis of ATP o Passage of pair of e. and in doing so.Biochem 57 • Hydrogen ions pass back into the matrix thru complex V.from NADH to O2  3ATP o Passage of e.

Biochem 58 1. Uncoupling • • • • Carry H+ across inner mit membrane w/o going thru complex V This short-circuits the proton gradient and uncouples electron flow from ATP synthesis Energy.4-DNP) – former diet drug ⇒ Caused blindness (retina has ↑ rate of oxidativ metblism) . instead of used to make ATP. is dissipated as heat Uncoupling agents: o Dinitrophenol (2.

Amytal Antimycin A (antibiotic) Cyanide.Biochem 59 o 2. Piericidin A (antibiotic). Carbon monoxide Oligomycin Thermogenin – helps to maintain normal body temp ⇒ Found normally in brown fat of newborn mammals Carbohydrate digestion and absorption . Rotenone (insecticide). Hydrogen sulfide.flow thru complexes or direct action) Complex I Complex II Complex IV ATP synthase Amobarbital (barbiturate). Inhibitors (via blocking e.

fructose) Starch: storage from of carbs in plants . Digestion • • Disacharides (sucrose).oligosacharides (dextrins).& polysacharides (starch) are cleaved into monosaccharides (glucose.Biochem 60 1.

maltotriose. Absorption • • . and α -dextrins by α -amylase in saliva and pancreatic juice Disaccharides & oligosaccharides o Hydrolyzed to monosaccharides by enzymes on the surface of epithelial cells in the small intestine Monosaccharides absorbed directly by carrier-mediated transport These sugars (primarily glucose) travel via portal vein to liver for: o Oxidation to CO2 and H2O for energy o Storage as glycogen o Conversion to triglyceride (fat) o Release into general circulation (as glucose) 2.Biochem 61 o • Hydrolyzed to maltose.

found chiefly in liver & muscle] 1. Glycogenesis (glycogen synthesis) .Biochem 62 Glycogen metabolism [Glycogen: carb storage.

6 linkages Stimulator: insulin (via dephosphorylation in muscle. phosphorylase (liver). liver. Ca2+ (muscle) 2.4 links Branching enzyme amylo (14) to (16) transglycosylase creates branches w/α -1.Biochem 63 • • • • • Activated substrate: Uridine diphosphate-glucose Glycogen synthase adds to nonreduc end of chains in α -1. Glycogenolysis (glycogen breakdown) • Phosphorylase releases units of glucose 1-P from nonreducing • • • end Phosphoglucomutase converts glucose 1-P to glucose 6-P Debranching system releases glucose residues from α -1. Epi (muscle & liver). cAMP. & fat) Inhibitors: glucagon (liver).6 bonds Stimulators: sames as inhibitors of glycogenesis .

and fat) Glycolysis: Location. liver. Anaerobic and Aerobic .Biochem 64 • Inhibitor: insulin (via dephosphorylation in muscle.

Aerobic: • Glucose + 6O2  6CO2 + 6H2O + 36-38 ATP • Charactersitic of the brain • NADH produced is oxidized by the mitochondrial ETS • ATP is generated by oxidative phosphorylation . Anaerobic (without oxygen) • Glucose  2Lactate + 2ATP • Characteristic of skeletal muscle after prolonged exercise • Lactate dehydrogenase converts pyruvate to lactate 3. Location: cytosol in most tissues of the body 2.Biochem 65 1.

Biochem 66 Describe the first step in glycolysis .

Biochem 67 1. Phosphorylation – involves rxn of glucose in presence of hexokinase OR glucokinase to form glucose 6-phosphate • Hexokinase is found in the cytosol of most tissues: o Low specificity (catalzyes phosphorylation of a wide variety of hexoses) o Low Km (it’s saturated at normal blood [glucose]) o Inhibited by glucose 6-P (prevents cells from accumulating too much glucose since phosphorylation traps glucose inside cells) • Glucokinase is present in the liver & pancreas (β -cells): o High specificity for glucose .

Biochem 68 o o High Km (above the normal blood [glucose]) Inhibited by fructose 6-P (ensures glucose will be phosphorylated only as fast as it is metabolized) What happens in the “2 phases” of glycolysis? .

In the second phase (5 reactions): • Two moles of glyceraldehyde 3-P are oxidized to 2 moles of pyruvate • 4 moles of ATP and 2 moles of NADH are generated for each mole of glucose .Biochem 69 1. In the first phase (5 reactions): • 1 mole of glucose is converted to 2 moles of glyceraldehyde 3-P • 2 moles of ATP are consumed for each mole of glucose 2.

Malate-aspartate shuttle . Glycerol phosphate shuttle 2.Biochem 70 What do the following do: 1.

& liver) . Malate-aspartate shuttle (heart.Biochem 71 NADH produced in the cytosol DOES NOT pass through the mitochondrial inner membrane. but is instead “shuttled” in by: 1. muscle. Glycerol phosphate shuttle (most tissues) • Transfers electrons from cytosolic NADH to mitoch FADH2 • • • It generates 2 ATP/cytosolic NADH = 36 moles of ATP/glucose Transfers electrons to mitochondrial NADH It generates 3 ATP/cytosolic NADH = 38 ATP/glucose 2.

Biochem 72 Gluconeogenesis .

3. 4. separate rxns occur: • Conversion of pyruvate to PEP bypasses pyruvate kinase • Conversion of fructose 1.6-bisphosphate to fructose 6-phosphate by fructose 1.6-bisphosphatase bypasses phosphofructokinase • Conversion of glucose 6-P to glucose by glucose 6-phosphatase bypasses hexokinase . 2.Biochem 73 1. Occurs primarily in the liver & kidney Synthesis of glucose from small noncarb precursors (such as lactate and alanine) Involves the reversible rxns of glycolysis To bypass nonreversible steps of glycolysis.

Glucose from gluconeogenesis is released into the bloodstream for transport to tissues such as the brain and exercising muscle Gluconeogenic substrates: • Lactate • Pyruvate • Glycerol • Substances that can be converted to oxalacetate via the citric acid cycle (such as amino acid carbon skeletons) Cori cycle . 6.Biochem 74 5.

Biochem 75 1. Shuttling of gluconeogenic substrates between RBCs and muscle to liver. Lactate from exercising or ischemic muscle is carried by the circulation to the liver and serves as a substrate for gluconeogenesis . allowing muscle to function anaerobically (net 2 ATP) 2.

Biochem 76 3. The liver releases the resynthesized glucose into the circulation for transport back to the muscle Regulation of glycolysis .

citrate • o Rate-limiting step D-glucose  glucose-6-P via hexokinase/glucokinase* .Biochem 77 1.6-BP via phosphofructokinase o Stimulators: AMP.6-BP (in liver) o Inhibitors: ATP. All are the irreversible steps: • Fructose 6-P  fructose-1. fructose 2.

Biochem 78 Inhibitors: glucose-6-P PEP  pyruvate via pyruvate kinase o Inhibitors: ATP. NAD. Induced by insulin o • Gluconeogenesis regulation . NADH.6-BP (in muscle) • Pyruvate  acetyl CoA via pyruvate dehydrogenase o Stimulators: CoA. ADP. alanine o Stimulators: fructose-1. pyruvate o Inhibitors: ATP. acetyl CoA 2.

All are the irreversible steps: • Pyruvate  OAA via Pyruvate carboxylase (mitochond) • o Requires biotin.Biochem 79 1. ATP o Activated by acetyl CoA OAA  PEP via PEP carboxykinase .

6.6-BP  fructose-6-P via Fructose-1. intestinal epithel Muscle cannot participate in gluconeogenesis Hypoglycemia is caused by a deficiency of these key enzymes Induced by glucocorticoids. cAMP Suppressed by insulin Pnemonic: Pathway Produces Fresh Glucose Pyruvate dehydrogenase complex . o Requires GTP • Fructose-1. 4. 5. 3.6-BPase • Glucose-6-P  glucose via Glucose-6-phosphatase These enzymes are only found in liver.Biochem 80 2. kidney. glucagon.

Contains 3 enzymes that require 5 cofactors: • • • • Pyrophosphate (from thiamine) Lipoic acid CoA (from pantothenate) FAD (riboflavin) .Biochem 81 1.

Biochem 82 2. Cofactors are the first 4 B vitamins plus lipoic acid: • B1 (thiamine. Reaction: • Pyruvate + NAD+ + CoA  acetyl-CoA + CO2 + NADH • NAD (niacin) 3. similar substrate and action) 4. TPP) • B5 (pantothenate  CoA) • Lipoic acid • B2 (FAD) • B3 (NAD) Pentose phosphate pathway . The complex is similar to the a-ketoglutarate dehydrogenase complex (same cofactors.

Biochem 83 1. adrenal cortex – all sites of fatty acid or steroid synthesis 2. liver. The irreversible oxidative portion generates NADPH . Begins with glucose 6-P 3. Sites: lactating mammary glands.

can be formed from glucose 6-P by either arm Major regulatory enzyme: glucose 6-P dehydrogenase – • Glucose 6-P  6-phosphogluconolactone Stimulators: NADP+. maintaining reduced glutathione inside RBCs The reversible nonxidative portion rearranges the sugars so they can reenter the glycolytic pathway Ribose 5-P. 5.Biochem 84 • 4. NADPH needed for: fatty acid and cholesterol (steroid) synthesis. insulin Inhibitors: NADPH Sucrose and Lactose Metabolism . which is needed for nucleotide synthesis. 8. 7. 6.

Sucrase converts sucrose to glucose and fructose • Hexokinase can convert fructose  fructose 6-P (muscle.Biochem 85 1. kidney) .

Biochem 86 • • • Fructose enters glycolysis by a different route in the liver Dihydroxyacetone phophate (DHAP) enters glycolysis directly After glyceraldehyde is reduced to glycerol. it is phosphorylated and then reoxidized to DHAP 2. Lactase converts lactose to glucose + galactose • Galactokinase converts galactose  galactose 1-P • Galactose 1-P  glucose 1-P  glycolysis .

Biochem 87 Glycogen Storage Diseases Result in abnl glycogen metabolism & ↑↑ glycogen in cells DEFFECT TISSUE SIGNS. ETC. .

Ketosis.Biochem Von Gierke’s (type I) Pompe’s (type II) Cori’s (type III) Anderson (type IV) McArdle (type V) Hers’ (type VI) Type VII Type VIII Glucose 6-P Liver & kidney Lysosomes.4-glucosidase Debranch enzyme Branching enzyme Phosphorylase Phosphorylase Phosphofructokinase Phosphorylas kinase 88 Hepatomegaly. Failure to thrive. Hyperuricemia. Hyperlipidemia Failure of heart & lungs Death <2 yo Similar to I. All organs Muscle & liver Liver & spleen Muscle Liver Muscle Liver α -1. but milder Liver cirrhosis. mild hypoglycemia . Hypoglycemia. but milder Similar to type V Mild hepatomegaly. death <2 y Painful muscle cramps w/exercise Similar to type 1.

Biochem 89 Hereditary enzyme deficiencies in lactose and sucrose metabolism 1. Hereditary enzyme deficiences in sucrose metablism: .

growth failure.Biochem 90 • • Fructokinase deficiency  essential fructosuria o Benign disorder Fructose 1-P aldolase deficiency  hereditary fructose intolerance o Characterized by severe hypoglycemia after ingesting fructose (or sucrose). Asians) Galactokinase deficiency  mild galactosemia o Early cataract formation Galactose 1-P uridyltransferase deficiency  severe galactosemia (AUTOSOMAL RECESSIVE) o Cataract. retardation. cirrhosis 2. hepatosplenomeg. jaundice. Inherited enzyme deficiencies in lactose metabolism: • Lactase deficiency  milk intolerance • • o Develops in adult life (age-dep) or hereditary (blacks. death o Treatment: exclude galactose & lactose from diet .

Biochem 91 Pyruvate dehydrogenase deficiency .

Causes backup of substrate (pyruvate & alanine). resulting in lactic acidosis 3. Treatment: ↑ intake of ketogenic nutrients (Lysine & Leucine are the only purely ketogenic amino acids) .Biochem 92 1. Pyruvate dehydrogenase deficiency  neurologic defects 2.

Biochem 93 Glucose-6-phosphate dehydrogenase deficiency .

Pathogenesis: • Poor RBC defense against oxidizing agents (fava beans. primaquine) and antituberculosis drugs 5. Background: • G6PD is the rate limiting enzyme in HMP (hexose • monophosphate) shunt. Heinz bodies: altered Hemoglobin precipitates w/in RBCs . sulfonamides. Manifestations of disease: • ↓ NADPH in RBCs  hemolytic anemia 4. which includes the pentose phosphate pathwy (which yields NADPH) NADPH is necessary to keep glutathione reduced. More prevalent among blacks 6. which in turn detoxifies free radicals and peroxides 3. X-linked recessive 2.Biochem 94 1.

Biochem 95 Lipid digestion .

D. In mouth: 2.E. Mixed micelles form. In the duodenum: 3.Biochem 96 1. K • Bile acids 4. which contain: 5. producing a mix of diacylglycerols & FFAs Lipids are emulsified by bile salts (made from cholesterol in liver) Emulsified fats are hydrolyzed by pancreatic lipase Phospholipids are hydrolyzed by phospholipase A Cholesterol esters are hydrolyzed by cholesterol esterase Fatty acids Diacylglyc • • Monoacyl Phospholipi • • Cholesterol VitA. In small intestine: • • • • • • • • Medium-chain triacylglycerol (TGs) are hydrolyzed by lipase Continues in stomach. Micelles absorbed in small intestine  further metabolized  • • Medium-chain TGs are hydrolyzed Medium-chain fatty acids (8-10 carbons) pass into portal vein .

Biochem 97 • Long-chain fatty acids (>12 carbons) are reincorporated into TGs TGs go into chylomicrons  lymphatics  circulation via thoracic duct • How are lipids transported to tissues? .

phospholipids. and specific apoproteins . Lipids are transported to tissues in the blood plasma primarily as lipoproteins: • Spherical particles w/a core that contain varying proportions of hydrophobic triacylglycerols & cholesterol esters • Outer layer of cholesterol.Biochem 98 1.

Biochem 99 Lipoprotein absorption .

Biochem 100 1. yielding low-density lipoproteins (LDLs) 2. except for medium-chain fatty acids. . Exogenous lipid (from intestine). is released into the plasma as chylomicrons • Chylomicrons contain a high proportion of TGs • TG is hydrolyzed to FFAs and glycerol by lipoprotein lipase on the surface of capillary endothelium in muscle and adipose tissue • The cholesterol rich chylomicron remnants travel to the liver. where they are taken up by receptor-mediated endocytosis (RME) Endogenous lipid (from liver) is released into blood as VLDLs • VLDL TG is hydrolyzed by lipoprotein lipase to FFAs and glycerol.

but mostly in liver) LDL cholesterol: o Inhibits HMG CoA reductase (RLS in cholesterol synthesis) o Down-regulates LDL receptor synthesis  ↓ LDL uptake High density lipoproteins (HDLs) are made in the liver Lipoprotein functions and associated apolipoproteins: Chylomicrons .Biochem 101 • • • LDLs are removed from circulation by RME in tissues that contain LDL receptors (tissues that need cholesterol.

Delivers dietary triglycerides to peripheral tissues and dietary cholesterol to liver 2.Biochem 102 1. Secreted by intestinal epithelial cells 3. Associated apolipoproteins: . eruptive xanthomas 4. lipemia retinalis. Excess causes pancreatitis.

Biochem 103 • • • • B-48 mediates secretion As are used for formation of new HDL C-II activates lipoprotein lipase E mediates remnant uptake by liver Lipoprotein functions and associated apolipoproteins: VLDL .

Delivers hepatic triglycerides to peripheral tissues Secreted by liver Excess causes pancreatitis Associated apolipoproteins: • B-100 mediates secretion • C-II activates lipoprotein lipase . 3. 4.Biochem 104 1. 2.

Biochem 105 • E mediates remnant uptake by liver Lipoprotein functions and associated apolipoproteins: LDL .

Excess causes atherosclerosis. Taken up by target cells via RME 4. Formed by lipoprotein lipase modification of VLDL in peripheral tissue 3. xanthomas.Biochem 106 1. and arcus corneaa (senilis?) . Transports hepatic cholesterol to peripheral tissues 2.

Associated apolipoproteins: • B-100 mediates binding to cell surface receptor for endocytosis Lipoprotein functions and associated apolipoproteins: HDL .Biochem 107 5.

Mediates centripetal transport of cholesterol (i. i.e. from periphery to liver. Acts as a repository for apoC & apoE (which are needed for chylomicron and VLDL metabolism) 3.Biochem 108 1. reverse cholesterol transport.e. Secreted from both liver and intestine . transports cholesterol from periphery to liver) 2.

Associated apolipoproteins: • A’s help form HDL structure • A-I in particular activates LCAT (which catalyzes • esterification of cholesterol) CETP mediates transfer of cholesteryl esters to other lipoprotein particles Pneumonic: HDL is Healthy.Biochem 109 4. LDL is Lousy Oxidation of fatty acids .

Fatty acids must first be activated to their acyl CoA thioesters • Long-chain (LC) fatty acids (>12) activated in cytosol  LC acyl CoAs are shuttled into mitoch matrix by carnitine transport syst . Occurs in mitochondrial matrix.Biochem 110 1. The overall process is: RCH2CH2COOH β -oxidation CH3COSCoA Citric acid cycle CO2+ H2O 2.

which can: o Enter the citric acid cycle (after carboxylation to succinyl CoA in a 3-rxn sequence requiring biotin and Vit B12) o Be used for gluconeogenesis . Fatty acyl CoA is then oxidized to CO2 and H2O by β oxidation: • • • Continues in cycle until it’s completely converted to acetyl CoA Each cycle generates 5 ATPs via ETS and 12 ATPs via combined action of citric acid cycle and ETS Terminal 3 carbons of odd-numbered fatty acids yield propionyl CoA as the final product.Biochem 111 • MCFAs pass directly into the mitoch & are activated in the matrix 3.

Biochem 112 Ketogenesis 1. The formation of acetoacetate and β -hydroxybutyrate from metabolism of acetyl CoA in the liver .

How is acetoacetate used in the body? • Extrahepatic tissues (especially heart) can activate acetoacetate at the expense of succinyl CoA and burn acetoacetyl CoA for energy • Glucose-starved brain can use acetoacetate for fuel (b/c its freely soluble in blood and easily crosses the BBB) . Reaction: • Acetyl CoA + acetoacetyl CoA  hydroxymethylglutaryl CoA (HMG CoA) • HMG CoA  acetoacetate and acetyl CoA • Acetoacetate  β -hydroxybutyrate (requires NADH) 3.Biochem 113 2.

Carried out by fatty acid synthase.Biochem 114 Fatty acid synthesis 1. a cytosolic complex .

Palmitate is the precursor for longer & unsaturated fatty acids • o It’s transported to cytosol by citrate-malate-pyruvate shuttle Malonyl CoA: formed by biotin-linked carboxylation of actyl CoA • • Chain-lengthening occurs in the mitoch and ER (C16C18etc) Desaturating system is also present in the ER o Requires NADPH and O2 o Inserts double bonds no further than 9 carbons from the carboxylic acid group . mainly by pyruvate dehydrogenase 3. Primary substrates: • Acetyl CoA: formed in mitoch. 7 cycles lead to production of palmityl:enzyme.Biochem 115 2. which is hydrolyzed to yield products – palmitate & fatty acid synthase 5. The acetyl and malonyl moieties are transferred from the sulfur of CoA to activate sulfhydryl groups in the fatty acid synthase 4.

Biochem 116 What do the limitations of the desaturating system result in? .

Biochem 117 1. The limitations of the desaturating system impose a dietary requirement for essential fatty acids (those w/double bonds >10 carbons from the carboxyl end) • Lineoleic acid o Precursor for arachidonic acid (which is beginning of cascade that synthesizes prostaglandins. thromboxanes. and eicosanoids) • Linolenic acids .

Biochem 118 Glycerolipid synthesis .

which is mainly produced by reducing dihydroxyacetone phosphate w/NADPH 3. adipose tissue.Biochem 119 1. This process is carried out by the liver. which can then be converted to a variety of lipids: • Triacylglycerol (from transfer of acyl group from acyl CoA) • Phosphatidyl choline & phosphatidyl ethanolamine (from transfer of base from its cytidine diP/CDP derivative) • Phosphatidylserine (from exchange of serine for choline) • Phosphatidylinositol (from reaction of CDP-diacylglycerol with inositol) . Succesive transfers of acyl groups from acyl CoA to carbons 1 and 2 of glycerol 3-phosphate produce phosphatidate. Pathways begin w/glycerol 3-P. and the intestine 2.

Biochem 120 Sphingolipid synthesis .

Begins with palmityl CoA and serine • Produces dihydrosphingosine and sphingosine 2.Biochem 121 1. Sphingosine can then by acylated to produce ceramide • Additional groups may be added to the C1-OH of ceramides .

Biochem 122 Cholesterol synthesis .

Biochem 123 1. Overall reaction: Acetoacetyl CoA + acetyl CoA –HMG CoA synthase  HMG CoA – HMG CoA reductase  mevalonic acid cholesterol . Key intermediate = HMG CoA • HMG CoA reductase: regulatory enzyme that catalyzes HMG CoA + NADPH  mevalonic acid • Increasing amounts of intracellular cholesterol lead to inhibition of HMG CoA reducate and accelerated degradation of the enzyme 3. Cholesterol is made by the liver and intestinal mucosa from acetyl CoA in a multistep process 2.

Biochem 124 What are the fates of the products of cholesterol synthesis? .

vit K.Biochem 125 1. and natural rubber 2. which include vit A. Mevalonic acid • Precursor of a number of natural products called terpenes. coenzyme Q. placenta. and testes • Majority is oxidized to bile acids in the liver • 7-dehydrocholesterol is the starting point for synthesis of vit D . Cholesterol • Converted to steroid hormones in the adrenal cortex. ovary.

Biochem 126 Lipid malabsorption .

Occurs for a variety of reasons: • Bile duct obstruction o ~50% of dietary fat appears in the stools as soaps (metal salts of LCFAs) • o Absence of bile pigments leads to clay-colored stools o Deficiency of the ADEK vitamins may result Pancreatic duct obstruction o Stool contains undigested fat o Absorption of ADEK vitamins is not sufficiently impaired to lead to deficiency symptoms Diseases of the small intestine (e. abetalipoproteinemia. celiac disease. IBD) • . nontropical sprue.g.Biochem 127 1.. Leads to excessive fat in the feces (steatorrhea) 2.

Biochem 128 Hyperlipidemias .

early death from CAD Tx: HMG CoA reductase inhibitors (“statins”) 2.Biochem 129 1. Mixed hyperlipidemias • BOTH serum cholesterol & serum triglycerides are ↑ • lipolysis of VLDL triglycerides Findings: cholesterol levels may be mildly ↑ . Familial hypercholesterolemia • • • Results from defective LDL receptors Findings: severe atherosclerosis. Hypertriglyceridemia • Can result from either overproduction of VLDL or defective 3.

Biochem 130 • • There is both overproduction of VLDL and defective lipolysis of triglyceride-rich lipoproteins (VLDL and chylmicrons) There is a danger of acute pancreatitis Inheritied defects and deficiencies that disrupt fatty acid oxidation .

Inherited deficiencies in the acyl CoA dehydrogenase.Biochem 131 1. Inherited defects in the carnitine transport system. butterfat) is helpful in some cases. b/c MCFAs can bypass carnitine transport system 2.. which have widely varying symptoms: • Hypoglycemia • Muscle wasting w/accumulation of fat in muscle • Feeding fat w/medium-chain triacylglycerols (e.g. the most common being medium-chain (C6-C12) acyl CoA dehydrogenase deficiency .

Biochem 132 • • Hypoketotic hypoglycemia and dicarboxylic aciduria occur. and coma This is believed to account for the condition called “Reyelike syndrome” Sphingolipid Storage Diseases . lethargy. with vomiting.

bone erosion. MR MR. metachromasia. nerves stain yellowish brown w/crystal violet . kidney failure. MR Rash. red spot on macula. myelin absent (also called “Krabbe’s” disease) MR.Biochem 133 Disease Tay-Sachs Gaucher’s Fabry’s Niemann-Pick Globoid cell leukodystrophy Metachromatic Accumulated Substance Ganglioside GM2 Glucocerebroside Ceramide trihexoside Sphingomyelin Galactocerebroside Sulfatide Clinical Manifestations Mental retardation (MR). blindness. lower extremity pain Hepatosplenomegaly. death by 3rd yr Hepatosplenomeg.

thick skin Urea Cycle . skeletal abnormalities Same as Tay-Sachs.Biochem 134 leukodystrophy Gen gangliosidosis Sandhoff’s Fucosidosis Ganglioside GM1 Ganglioside GM2. globoside Pentahexosylfucoglycolipd MR. but more rapid course Cerebral degeneration. hepatomegaly. spasticity.

3. Converts NH4+ (which is toxic. 2. 4.Biochem 135 1. esp to CNS) to urea Occurs in the liver Urea is excreted in the urine NH4+ + CO2 –carbamoyl phosphate synthetase I  carbamoyl P + ornithine –ornithine transcarbamoylase  citrulline + aspartate + ATP –argininosuccinate synthetase  argininosuccinate –argininosuccinate lyase  fumarate + arginine + H20 –arginase  UREA + ornithine .

Biochem 136 Urine byproduct How does detoxification of NH4+ occur in peripheral tissues? .

In most tissues: • Glutamine synthetase incorporates NH4+ into glutamate to • form glutamine. In skeletal muscle: • Glutamate dehydrogenase and glutamate-pyruvate aminotransferase  incorporate NH4+ into alanine . glutaminase hydrolyzes glutamine back to NH4+ and glutamate 2. which is carried by circulation to the liver In the liver.Biochem 137 1.

Biochem 138 • Alanine is carried to the liver. where transdeamination results in converstion of alanine back to pyruvate and NH4+ Hyperammonemia .

Enzyme defects . coma.Biochem 139 1. and death 3. seizure. May be caused by insufficent removal of NH4+. resulting from disorders that involve one of the enzymes in the urea cycle 2. Signs and Symptoms • • Blood NH4+ concentrations above the normal range (30-60 µ M) Mental retardation.

Treatment • • • Carbon skeletons of amino acids . OR arginase  blood levels of metabolite preceding defect ↑↑ o NH4+ levels may also rise Restriction of dietary protein Intake of mixes of keto acids that correspond to essential amin acid Eating benzoate & phenylacetate: alternate path for NH4+ excretion 4. argininosuccinase.Biochem 140 • • Low activity of carbamoyl P synthetase or ornithinecarbamoyl transferase  [NH4+] in blood & urine ↑↑  NH4+ intoxication Defective argininosuccinate synthetase.

leucine. Amino acids can be grouped into families based on the point where their carbon skeletons enter the TCA cycle AcetylCoA/Ketogenic fam(blue:keto-& glucogenic. red:ketogen only) • Isoleucine. 2. lysine. tryptophan.Biochem 141 1. and tyrosine • Phenylalanine  tyrosine via phenylalanine hydroxylase . phenylalanine.

glycine. can be converted to GABA Succinyl CoA family (isoleucine. 7. 4.glutamate.proline) • Histidine – precursor of histamine • Glutamate – excitatory neurotransm. Dopamine.threonine. Tyrosine is starting compound for: o Epi and NE. 6.serine.cysteine.Biochem 142 • 3. tryptophan) Essential amino acids . T3 and T4.gluatmine. 5. methionine. valine) • Methyl of methionine participates in methylation rxns as Sadenosylmethionine (SAM) Fumarate family (phenylalanine and tyrosine) Oxaloacetate family (asparagine and aspartate) Pyruvate fam (alanine. Melanin α -Ketoglutarat fam (arginine.histidine.

Leucine . Isoleucine 2.Biochem 143 1.

6.Biochem 144 3. 4. 8. 5. 7. 9. Lysine Phenylalanine Tryptophan Histidine Methionine Valine Threonine .

Biochem 145 Phenylketonuria (PKU) 1. Results from a deficiency of: • Phenylalanine (Phe) hydroxylase OR .

Findings • ↑↑ Phe in the blood (hyperphenylalaninemia) • • 3. tyrosine is an essential amino acid 5. resulting in CNS damage with mental retardation ↑↑ Phe inhibits melanin synthesis  hypopigmentation . An alternative pathway for Phe breakdown produces phenylketones. Treatment: restricting dietary protein (phenylalanine) Phe builds up to toxic concentrations in body fluids. In those affected. which spill into th eurine 4.Biochem 146 • Dihydropteridine reductase 2.

Have little or no melanin and are: . No tyrosinase (1st enzyme on pathway to melanin) 2.Biochem 147 Albinism 1.

Biochem 148 • • • Easily sunburned Very susceptible to skin carcinoma Photophobic b/c of lack of pigment in iris of eye .

May result from several defects: • Cystathionine synthase (CS) deficiency .Biochem 149 Homocystinuria 1.

pyridoxal phosphate (PLP) (may respond to megadoses of pyridoxine/vit B6) Methyl tetrahydrofolate homocyst methyltransferase deficiency Vit B12 coenzyme deficiency (may respond to vit B12) 2. appears in urine 3. Finding: homocysteine accumulation in blood.Biochem 150 • • • • • • • • • ↓ affinity of CS for its coenzyme. Pathologic changes Dislocation of optic lens Mental retardation Osteoporosis and other skeletal abnormalities Atherosclerosis and thromboembolism Synthetic diets low in methionine Betaine (trimethylglycine) – alternative methyl group donor 4. Pts unresponsive to vitamin therapy may be treated with: .

Biochem 151 Maple-syrup urine disease .

Findings: branched chain keto acids derived from isoleucine. leucine. Elevated keto acids cause severe brain damage. Results from a deficiency in the branched-chain 2keto acid decarboxylase 2. Treatment • A few respond to megadoses of thiamine (vitamin B1) • Those that don’t: synthetic diets low in branched-chain amino acids . giving it a maple syrup-like odor 3.Biochem 152 1. with death in the first year of life 4. and valine appear in the urine.

Biochem 153 Histidinemia .

Biochem st 154 1. Deficiency in histidine-α -deaminase (the 1 enzyme in histidine catabolism) 2. Symptoms: • Mental retardation and speech defects (both are rare) 4. Treatment: not usually indicated . Characterized by elevated histidine in blood plasma and excessive histidine metabolites in urine 3.

Biochem 155 C 6: respiratory C O2 Origin of the atoms in the purine ring aspartate C N C N C 4. N9: glutamine N C NH N-formyl tetra hydrofola te . N7: glycine C C N-formyl tetra hydrofola te N3. C5.

Biochem 156 .

Biochem 157 PURINE nucoleotide synthesis .

Inosine monophosphate (IMP). Involves 2 enzymes: • Hypoxanthine-guanine phophoribosyltransferase (HGPRT) o Comp inhibited by IMP and GMP • Adenine phosphoribosyl transferase o Inhibited by AMP . GMP. & GMP inhibit PRPP synthetase • • PRPP activates glutamine PRPP amidotransferase Inhibited by end products (IMP.Biochem 158 De novo synthesis: PATHWAY: (remember: purines = adenine and guanine) Ribose 5-P –PRPP synthetase PRPP—glutamine PRPP amidotransferase 5phosphoribosyl-1-amine –9 rxns IMP + Asp + GTP  AMP  IMP + Gln + ATP + NAD  GMP 1. AMP) of the pathway 2. AMP. Committed step: conversion of PRPP to 5’-phosphoribosyl-1-amine Purines made by salvage of preformed purine bases: 1.

Biochem 159 Regulation of purine synthesis .

Reciprocal substrate effect: GTP is a substrate in AMP synthesis. Regulation provides a steady supply of purine nucleotides 2. GMP and AMP inhibit 1st step in their own synthesis from IMP 3. Interconversion among purines ensures control of their levels • AMP deaminase converts AMP back to IMP • GMP reductase converts GMP back to IMP • IMP is the starting point for synthesis of AMP and GMP .Biochem 160 1. and ATP is a substrate in GMP synthesis • Balances supply of adenine and guanine ribonucleotides 4.

C5. C 6. N1 : aspartate C N C .Biochem 161 Origin of the atoms in the pyrimidine ring C2. N3: carbamoyl phosphate C N C C4.

Biochem 162 .

Biochem 163 De novo pyrimidine synthesis .

which stands for the names of the enzymes • • CO2 + glutamine – CAP synthetase II  carbamoyl-P (CAP) Synthesis of dihydroorotic acid is a 2-step process: o Committed step: aspartate + CAP –aspartate transcarbamoylase  carbamoyl aspartate o Carbam aspartate –dihydrorotase dihydroorotic acid + H2O 2. In mammals. Dihydroorate forms UMP • Dihydroorate  orotic acid • Orotic acid + PRPP  orotidylate (OMP) • Decarboxylation of OMP  uridylate (UMP) • These 2 steps occur on 1 protein (if defected: orotic aciduria) 3.Biochem 164 1. 1st 3 steps occur on one multifunctional enzyme called CAD. Synthesis of remaining pyrimidines involves UMP .

Biochem 165 • • Phosphorylation of UMP  UDP + UTP Addition of amino group from glutamine to UTP  CTP Regulation of pyrimidine synthesis .

Biochem 166 1. CAP synthetase II regulation • Inhibited by UTP • Activated by ATP and PRPP 2. CTP itself inhibits CTP synthetase .

Biochem 167 Salvage of pyrimidines .

which can use orotic acid. but NOT CYTOSINE . uracil or thymine.Biochem 168 Accomplished by the enzyme pyrimidine phosphoribosyl transferase.

Biochem 169 Deoxyribonucleotide synthesis .

Biochem 170 Formation of deoxyribonucleotides (for DNA synthesis) involves reduction of sugar of ribonucleoside diphosphates: 1. CDP. GDP. or UDP to deoxyribonucs Its reducing power is from 2 sulfhydryl groups on thioredoxin Using NADPH + H+. Thymidylate synthase . thioredoxin reductase converts oxidized thioredoxin back to the reduced form Regulation – controls the overall supply of deoxyribonucleotides o Rxn proceeds only in presence of nucleotide triphosphate o dATP: allosteric inhibitor o Other deoxynucleosides interact w/enzyme to alter specificity 2. Ribonucleotide reductase • • • • Leads to reduction of ADP.

Biochem 171 • • Catalyzes formation of dTMP (deoxythymidylate) from dUMP Coenzyme: N5. N10-methylene tetrahydrafolate (regenerated after each rxn by dihydrofolate reductase) Nucleotide degradation .

Purine degradation (product: Uric acid is exreted in urine) • • • • Sequential actions of 2 groups of enzymes (nucleases and nucleotidases) lead to hydrolysis of nucleic acids to nucleosides Deaminase converts adenosine/deoxyadenosine to deoxy-/inosine Purine nucleoside phosphorylase splits inosine and guanosine to ribose 1-P and free bases hypoxanthine and guanine Guanine is deaminated to xanthine Hypoxanthine & xanthine –xanthine oxidase uric acid • 2. NH4+) • Degraded to free bases uracil or thymine .Biochem 172 1. CO2. Pyrimidine degradation (products = β -amino acids.

and β -alanine and thymine to CO2.Biochem 173 • • A 3-enzyme rxn (reduction. NH4+. & β -aminoisobutyrate THUS: urinary β -aminoisobutyrate is an indicator of DNA turnover (may be ↑ during chemo or radiation therapy) Disorders caused by deficiencies in enzymes involved in nucleotide metabolism . deaminationdecarboxylation) converts uracil to CO2. ring opening. NH4+.

Anemia Synthetic cytdine or uridine (UTP formed acts as inhib of carbamoyP synthetase II) Impaired T-cell function T.↓ . Gene therapy Allopurinol .Biochem 174 Hereditary orotic aciduria Purine phosphorylas deficiency SCID Lesch-Nyhan Orotate phosphoribosyl transferase and/or OMP decarboxylase ↑ purine ↓ uric acid formation Adenosine deaminase HGPRT Retarded growth.& B-cell dysfunction w/early death from infection ↑↑ purine synthesis.

but doesn’t ameliorate neuro symptoms Anticancer drugs that interfere w/nucleotide metabolism . self-mutilation) deposition of sodium urate crystals.Biochem 175 (deficient or absent) hyperuricemia. MR. severe neuro problem (spastic.

Biochem 176 1. Fluoredeoxyuridylate • Inhibits thymidylate synthetase (enzyme that converts dUMP to dTMP) . Aminopterin and methotrexate • Inhibit dihydrofolate reductase (enzyme that converts dihydrofolate to tetrahydrofolate) 3. Hydroxyurea • Inhibits nucleoside diphosphate reductase (enzyme that converts ribonucleotides to deoxyribonucleotides) 2.

Biochem 177 Gout .

May result from a disorder in purine metabolism 2. Secondary gout • Due to radation therapy. CA chemo (b/c they ↑ cell death) . Primary gout: overproduction of purine nucleotides • Mutations in PRPP synthetase  loss of feedback inhibition by purine nucleotides • A partial HGPRT deficiency  less PRPP is consumed by salvage enzyes  ↑ PRPP activates PRPP amidotransferase 4. Is associated w/hyperuricemia 3.Biochem 178 1.

hypoxanthine & xanthine levels rise (is OK. b/c they don’t form crystals) Energy expenditure (3 components) . Treatment: allopurinol • • Xanthine oxidase catalyzes oxidation of allopurinol to alloxanthine.Biochem 179 5. which is a potent inhibitor of the enzyme Result: uric acid levels fall.

Biochem 180 1. Basal energy expenditure (BEE) • “resting energy expenditure” • Energy used for metabolic processes at rest • Represents >60% of total energy expenditure • Related to the lean body mass 2. Activity-related expenditure . Thermic effect of food • Energy required for digesting and absorbing food • Amounts to ~10% of energy expenditure 3.

Biochem 181 • 20-30% of daily energy expenditure Caloric yield from foods and what % they should be in diet .

Carbs: 4 kcal/g • 50-60% of caloric intake 2. Proteins: 4 kcal/g • 10-20% of caloric intake (0.Biochem 182 1.8 g/kg body weight/day) 3. Fats: 9 kcal/g • No more than 30% of caloric intake 4. Alcohol: 7 kcal/g .

and Excess storage .Biochem 183 Fats: Essential fatty acids. Deficiency.

Deficiency • Mainly seen in low-birth-weight infants maintained on artificial formulas and adults on TPN • Characteristic system: scaly dermatitis 3. Essential fatty acids (EFAs): • Linoleic acid • Linolenic acid 2.Biochem 184 1. Excess fat • Stored as triacylglycerol .

Biochem 185 Marasmus vs. Kwashiorker .

including both calories and protein Depleted subQ fat Liver ketogenesisbrain&heart fuel Muscle wasting (break ↓ protein for gluconeogenesis & protein synthes) Frequent infections Low body temp Kwashiorker Starvation with edema often due to protein deficient diet Pitting edema Flaky paint dermatosis: dark patches on skin that peel Large liver due to fatty infilatration Muscle wasting less severe Frequent infections .Biochem 186 Marasmus Insufficient food.

Biochem 187 Micronutrient deficiencies Slowed growth(<60% expected wgt) Death when energy & protein reserves exhausted Other nutrient deficiencies Growth failure(>60% expected wgt) Poor appetitie (anorexia) Watery stools w/undigested food Mental changes (apathetic) Vitamin A .

Biochem 188 1. Xerophthalmia (cornea keratinizes: Bitot spots) o Leading cause of child blindness in 3rd world nations • • Follicular hyperkeratosis (rough. Deficiency signs and symptoms: • Night blindness. Functions: • • • • 11-cis-retinal – prosthetic group of rhodopsin Beta-carotene – antioxidant – NOT TOXIC at high doses Retinyl phosphate – mannose acceptor/donor in glycoprotein synth Retinol & retinoic acid – regulate tissue growth & differentiation 2. tough skin) Anemia .

000 equivalents/day) 4. Clinical usage: For acne and psoriasis Vitamin D • Bone pain. hepatosplenomegaly.Biochem 189 3. nausea. Toxicity (prolonged ingestion of 15. scaly dermatitis.000-50. diarrhea • • ↓ resistance to infection ↑ susceptibility to cancer .

Biochem 190 1. ↑ blood Ca+ by: ↑ bone demineralization by stimulating osteoblastic activity o Simulates Ca+ reabsorption by distal renal tubules Sources: o • • Major: skin (UV: 7-dehydrocholesterol  Vit D3/cholecalciferol) Diet (vit D3) and foods fortified w/vit D2 . Stimulates synth of Ca+-binding protein  aids absorption In combo w/PTH. Functions: regulation of Ca+ metabolism • • 2.

metast calcification. Toxicity: (hyperCa+.25(OH)2D3 (stimulated by PTH) Deficiency Rickets (kids): soft bones.Biochem 191 3.D to its active form) Vitamin E . • • • • • Liver: Vit D3  25(OH)D3 Kidney: 25(OH)D3  active 1. stunted growth Osteomalacia (adults): pathologic fractures Bone demineraliz may also result from vit D  inactive forms by steroids 5. Activation 4. bone demineraliz. kidney stones) • Seen in sarcoidosis (epithelioid macroph convert vit.

Function • • Protection of membranes & proteins from free-radical damage Includes isomers of tocopherol: o Tocopherol + free radicals  tocopheroxyl radical  vit C reduces tocopheroxyl radical  tocopherol is regenerated 2. Deficiency .Biochem 192 1.

abetalipoproteinemia) Signs & Symptoms: o Ataxia o Impaired reflexes o Myopathy o Muscle weakness o Hemolytic anemia (b/c of ↑ fragility of RBCs) o Retinal degeneration Vitamin K . pancreatic insufficiency. celiac disease.Biochem 193 • • Secondary to impaired lipid absorption (cystic fibrosis. chronic cholestasis.

Function • Post-translational carboxylation of glutamyl residues in Ca+binding proteins: factors VII. IX.Biochem 194 1. & X 2. Deficiency (↑ PT. but nl bleeding time) . ↑ aPTT.

Vitamin K in infants • Neonates are born w/low stores of vit K • Vit K crosses placental barrier poorly • Newborns given single injection of vit K • High doses: anemia. hyperbilirubinemia. kernicterus • • The B vitamins .Biochem 195 Impaired blood clotting  ↑ bruising. ↑ bleeding Causes: o Fat malabsorption o Drugs that interfere w/vit K metabolism (warfarin) o Antibiotics that suppress bowel flora 3.

Biochem 196 1. B1 = Thiamine 2. B3 = Niacin . B2 = Riboflavin 3.

Biochem 197 4. B12 = cobalamin Thiamine (vitamin B1) . B6 = Pyridoxine (pyridoxamine. B5 = Pantothenate (pantothenic acid) 5. pyridoxal) 6.

Biochem

198

1. Thiamine pyrophosphate (TPP): required for nerve
transmission & is coenzyme for several key enzymes:

Biochem

199

Pyruvate & α -ketoglutarate dehydrogenase(glycolysis, TCA) • Transketolase (pentose phosphate pathway) • Branched-chain keto-acid dehydrogenase (valine, leucine, isoleucine metabolism) 2. Deficiency leads to beriberi, which occurs in 3 stages: • Early: loss of appetite, constipation, nausea, periph neuropathy, irritability, fatigue • Moderately severe: Wernicke-Korsakoff syndrome (mental confusion, ataxia, ophthalmoplegia) • Severe (in addtion to polyneuritis): o Dry: atrophy & weakness of muscles o Wet:edema,high-output cardiac failure,pulm congestion

Biochem

200

Riboflavin (vitamin B2)

Biochem

201

1. Function: • Converted to re-dox coenzymes FAD & FMN 2. Deficiency signs & symptoms: • Angular cheilitis • Glossitis (red and swollen tongue) • Scaly dermatitis (esp at nasolabial folds & around scrotum) • Corneal vascularization

Biochem 202 Niacin (vitamin B3) .

Deficiency • Causes: o Hartnup disease o Malignant carcinoid syndrome o INH • Mild deficiency: glossitis • Severe deficiency: pellagra – the 3 D’s o Dermatitis o Diarrhea o Dementia 3. Function:converted to redox coenzymes NAD & NADP 2. High doses • Vasodilation (very rapid flushing) .Biochem 203 1.

Biochem 204 • Metobolic changes: ↓ blood cholesterol & LDLs Vitamin B6 (pyridoxine. & pyridoxal) . pyridoxamine.

and trans-sulfuration (rxns of amino acid metabolism) 2. nose.g. glossitis. Function • Coenzyme involved in transamination (e. decarboxylation. chapped lips. depression • Severe: periph neuropathy. seborrheic dermatitis around ears. Clinical usefulness: • High doses: tx homocystinuria (defective cystathione β synthase) . angular stomatitis 3. occasional sideroblastic anemia • Other symptoms: eczema. ALT & AST).Biochem 205 1. nervousness. and mouth. convulsions.. Deficiency (inducible by INH) • Mild: irritability.

Biochem 206 Vitamin B6: Pantothenic acid .

Deficiency (very rare) • Vague presentation. enteritis. adrenal insufficiency . little concern to humans • Dermatitis.Biochem 207 1. alopecia. Function • Essential component of coenzyme A (CoA) and of fatty acid synthase • Cofactor for acyl transfers 2.

Biochem

208

Biotin

Biochem

209

1. Function • Covalently linked biotin = prosthetic group for carboxylation enzymes (e.g. pyruvate carboxylase, acetyl CoA carboxylase) (NOT decarboxylations) 2. Deficiency (rare) • Signs and symptoms:
o o o o Dermatitis Hair loss Atrophy tongue papilla Gray mucous memb o o o Paresthesa,muscle pain Hypercholesterlemia ECG abnormalities

Causes o Antibiotic use (since intestinal bacteria make biotin) o Eating Avidin (raw egg whites)

Biochem

210

⇒ Binds biotin in a nondigestible form ⇒ If you eat >20 eggs/day

Folic acid

Biochem

211

1. Function
• Polyglutamate derivatives of tetrahydrofolate serve as coenzymes in 1-carbon transfer rxns: o Purine & pyrimidine synthesis o Thymidylate synthesis o Conversion of homocysteine to methionine o Serine-glycine interconversion Signs & symptoms: o Megaloblastic anemia o Neural tube defects o ↑ blood homocysteine – associated w/atherosclerotic disease

2. Deficiency

Biochem 212 • Can be caused by several drugs: o o o Methotrexate (chemo) Trimethoprim (antibact) Pyrimethamin(antimalari) o o Diphenylhydantoin (anticonvulsant) Primidone (anticonvuls) Vitamin B12 (cobalamin) .

Functions • • Coenzyme for methylmalonyl CoA  succinyl CoA (methylmalonyl CoA mutase) in propionyl CoA metabolism Coenzyme for methyl transfer between tetrahydrofolate & methionine (homocysteine methyl transferase) 2. optic neuropathy.Biochem 213 1. Deficiency: • Signs & Symptoms: o o o Megloblastic anemia Paresthesia. subacute combined degenerat Prolonged deficiency  irreversible nervous system damage .

absence of terminal ileum/Crohn’s) Use Schilling test to detect deficiency Vitamin C (ascorbic acid) . enteritis. Causes: o Intake of no animal products (vegans) o Achlorhydria. latum. D. ↓ intrinsic factor (impaired absorption) o Malabsorption (impaired pancreatic function.Biochem 214 • 3. sprue.

Biochem 215 1. Functions • Coenzyme for re-dox rxns. including: o o o o Post-translational hydroxylation of proline & lysine in maturation of collagen Carnitine synthesis Tyrosine metabolism Catecholamine neurotransmitter synthesis • Antioxidant .

↓ immune function o Severe: scurvy (↓ wound healing. swollen gums.Biochem 216 • Facilitator of iron absorption 2. osteoporosis. teeth may fall out) y Symptoms of Mineral Deficiencies . anemia. Deficiency • Signs & symptoms: o Mild: capillary fragility w/easy bruising & petechiae (pinpoint hemorrhages in skin). hemorrhage.

bone pain Osteomalacia (as in vit D deficiency) Goiter Cretinism Iodine .Biochem 217 Mineral Calcium Deficiency-Associated Conditions Paresthesia Tetany Bone fractures.

scaly skin Mental lethargy Imparied taste & smell. tachycardia.Biochem 218 Iron Magnesium Phosphorus (as phosphate) Zinc Anemia Fatigue. poor appetite . paresthesia Depressed PTH release Deficiency rarely occurs Growth retardation & hypogonadism Dry. dyspnea Neuromusc excitability.

Biochem 219 .