Biochemistry Exam 1 Review

Intro to Biomolecules:

Evolutionary Timeline:

Energy Charge:

High = anaerobic (all ATP)

ATP generating pathway is
inhibited and ATP utilizing pathway
is activated
Low = catabolic (all AMP)

Salivary Buffering:

pH = -log[H+]
Each increase in 1 unit of pH is 10-fold difference in H+ concentration
Henderson Hasselbalch:

Isoelectric Point: (pK1 + pK2)/2

750 ml saliva produced daily
o Submandibular: 60%
o Parotid: 30%
o Sublingual: <5%
Xerostomia: dry mouth gingivitis + caries
Saliva:
o Contains amylase + lipase
o Secretions stimulated by sympathetic and parasympathetic
o 99.5% water with electrolytes
o Mucus
o Anitmicrobial compounds (lactoferrin, IgA, lysozyme
o Opiorphin: pain-killing protease inhibitor
Saliva Buffering:

Amino Acid:

Non-polar side chain:

o Glycine
o Alanine
o Valine
o Leucine
o Isoleucine
o Phenylalanine
o Tryptophan
o Methionine
o Proline (pyrrolidene ring)
Uncharged Polar side chain:
o Serine
o Threonine
o Tryosine
o Asparagine
o Glutamine
o Cysteine
Acidic Side Chain:
o Aspartic Acid
o Glutamatic Acid
Basic Side Chain:
o Histidine
o Lysine

o Arginine
Hydrogen Bond can be formed by:
o Ser
o Thr
o Asn
o Gln
Cysteine forms disulfide bonds
Amino acids and glucose are transported together with Na+ (from lumen to blood)
o Ex: Na+/Lysine Symporter (2 Na+ in, 1 Lys in)
Zwitterionic:
o Acidic Amino Acids: have +1 charge
o Basic Amino Acids: have -1 charge
Phosphorylation can be done with OH side groups:
o Tyrosin
o Serine
o Threonine
Lysine can be acetylated or methylated
Glutamate can have a carboxyl group added to help blood glotting
N-terminals of amino acids can be acetylated
Histone proteins have modified histamine that was acetylated

Protein Structure and Folding:

Primary (sequence)
o Linear arrangement of AA
Secondary (local folding):
o Alpha helix: stabilized by H bonds
o Beta sheets:
Held by H bonds
Parallel or antiparallel
o Motifs:
EF Hand
Zinc Finger (part helix part pleated sheet)
Tertiary (overall conformation)
o Hydrophobic interactions
o Difsulfide Bridges
o H-bond
o Electrostatic interactions
Quaternary (multimeric structure)
o Ionic bond
o Hydrogen bond
o Hydrophobic (va der waals)
-turn:

o mainly glycine and proline that are stabilized by h bonds

o reverse direction of polypeptide backbone
Rotation can occur between peptide groups in proteins
o Rotated around alpha Carbon
o Phi angle has nitrogen
o Psi angle has carbonyl
Protein folding promoted by chaperone proteins Hsp70, Hsp90 (heat shock)
Ubiquitin:
o If protein damaged, ubiquitin helps with proteolysis
o Damaged protein is labelled with ubiquitin
o Ubiquitin allows proteasome to recognize misfiled protein
o Labelled protein gets cleaved into smaller peptides
Sequence of amino acids of a protein will determine how it will fold. Will go towards native
state (lowest free energy)
Misfolded Protein Diseases:
o Alzheimers
o Prion (mad cow disease and Creutzfeldt-Jakob) abnormal prion protein

Enzyme Catalysis:

Enzyme Nomenclature:
o Oxidoreductases: oxidation-reduction reactions
o Transferases: transfers C, N, or P groups
o Hydrolases: cleavage by addition of water
o Lyases: cleaves of C-C
o Isomerases: forms isomer
o Ligases: forms bond between carbon and another compound (CO2 added to pyruvate)
Coenzymes:
o Apoenzymes: inactive
o Holoenzyme: active
Cofactors: metal ions
Equilibrium constant: [product]/[reactant]
Exergonic: energy releasing
Endergonic: energy absorbing
Delta G = negative spontaneous reaction
Delta G conditions:
o 298K

o 1 atm
o pH 7.0
o Initial concentrations of 1M for all reactants and products
Reaction rate increases linearly with temperature until certain point, then decreases
Substrate binding in active site of trypsin-like serine proteases:
o Catalytic triad: ASP-102, HIS-57, SER-195
o HIS-57 deprotonates deprotonates serine
o Hydroxyl group of series mediates catalysis
o Oxygen from serine attacks peptide bond
o Aspartic Acid stabilizes peptide with negative carboxyl group
o Water comes in and hydrolyzes peptide bond
o *Specific site is only for Lysine or Arginine

Enzyme Kinetics:

Michaelis-Menton:

Vmax is proportional to enzyme amount (more enzyme, higher Vmax)

Km = substrate concentration when reaction velocity is Vmax
o Does not change with changing enzyme
o Smaller Km = higher affinity for enzyme
Low concentration of substrate [S] < Km first order reaction
High concentration of substrate [S] > Km zero order reaction
Lineweaver-Burk plot: (double reciprocal plot)
o Competitive Inhibitor:
Vmax doesnt change (y intercept same)
Km changes (x-intercept changes)
Drugs: statin, pravastatin
o Non-competitive Inhibitor:
Vmax changes (y-intercept changes)
Km stays the same (x-intercept same)
Drugs: Etravirine (HIV reverse transcriptase inhibitor)

Enzyme Inhibition and Drug Discovery:

Fluoride concentration too high = dental fluorosis

o Changes in cosmetic: white yellow
Hexafluorosilicic Acid: commonly used for water fluoridation
Optimal Fluoride Levels: 0.7mg/L
Fluoride has 2 mechanisms to prevent caries:
o Inhibits Enolase:
Reduces lactate formation by mouth bacteria (less
caries)
o Fluoroapatite (Ca5(PO4)3F) is teeth exposed to fluoride ions
Prevents decay
Does not dissolve in acids produced by bacteria

Aspirin: (acetylsalicylic acid):

o Irreversible inhibitor of Cyclooxygenase (COX)
o Blocks synthesis of prostaglandins + thromboxanes
o Inhibits: IKK
o Activates: AMP-activated Protein Kinase
o Antithrombotic: prevents platelet formation, treats blood clots
Bortezomib (BTZ)
o Anticancer drug for multiple myeloma + mantle cell lymphoma
Multiple Myeloma: hematological neoplasm derived from plasma cells that
proliferate into bone marrow
o Reversible Proteasome inhibitor
26s proteasome has 6 catalytic Thr residues on subunit
o Causes accumulation of misfolded IgG in Multiple Myeloma cells
Cell cycle is arrested
Inhibits activation of pro-survival transcription factor: NFB
Proteasome Inhibitors (BTZ) and Salicylates (aspirin) block NFB Pathway:
o Blocks IKK (kinase)
o Activators of IKK
Virus
Ionizing Radiation
TNF
Bacteria and Fungi
o I sequesters p65 and p50 (p65 and p50 = NFB) in cytoplasm
IKK once activated phosphorylates I
Once phosphorylated I is ubiquitinated and sent for proteasome
degredation
P65 and p50 fall off phosphorylated I and head into nucleus
o P60 and p50 in nucleus: (NFB in nucleus)
NFB turns on genes for adhesion proteins, inflammatory cytokines, enzymes,
IKK, chemokines
o Inhibitors block NFB
Tetrahydrofolate (THF):
o Coenzyme for purine + methionine synthesis
o Folic Acid Dihydrofolic Acid THF
o Both enzymes used above is Dihydrofolate Reductase
Methotrexate:
o Competitive inhibitor of Dihydrofolate reductase
o Cancer drug
o Works as competitive inhibitor b/c of similar structure to THF
Azythromycin (Zithromax):
o Antibiotic
o Interferes with bacterias protein synthesis
o Binds to 50s subunit of bacterial ribosome inhibits translation of mRNA

o 7th most prescribed

Omeprazole (Prilozec):
o Antacid gastric proton pump inhibitor
o Irreversible inhibitor of stomach parietal cell H+/K+ ATPase
o Usually acidic in stomach due to proton pump
Protons (H+) in cytosol comes from dissociation of
H2O
H+ pumped against gradient into stomach lumen
K+ pumped against gradient into cytosol
OH- of dissociation of H2O binds with CO2 and
forms HCO3- (bicarbonate) by carbonic anhydrase
o Irreversible b/x forms disulfide bond with cysteine in ATPase
Pravastatin (Pravachol) + Simvastatin
o Competes with HMG-CoA for active site of HMG-CoA reductase
o For high cholesterol levels
Hydrocodone:
o Derived from codeine
o Agonist for opioid receptor

Glycolysis:

10 reactions
Aerobic: pyruvate acetyl CoA
Anaerobic lactic acid
Insulin regulates GLUT4, which takes in glucose to adipose/muscle
1 oxidative step where NAD becomes NADH
o G3P oxidized to 1,3-BPG

Hexokinase:
o Primary enzyme for first step
o High affinity for glucose
o In Liver/pancrease, glucokinase has high Km (low affinity)
Rate Limiting Steps:
o 3 reactions involving
Hexokinase
PFK (most important)
Inhibitors: ATP, citrate
Activators: AMP, F 2,6-BP
Pyruvate Kinase: activated by F 1,6-BP
Net ATP: 2
Pasteur Effect: inhibition of glycolysis by oxygen
o Rate of glycolysis greater in anaerobic than aerobic conditions
Warburg Effect: cancer cells have high rates of glycolysis and decreased Pasteur Effect

Anaerobic Conditions:

Gluconeogenesis:

2 pyruvates (3 carbon compound) glucose

Rate Limiting Step:
o Pyruvate Carboxylase
o PEP Carboxykinase
o F 1,6-BP
o Glucose 6-Phosphatase
Requires energy, unlike glycolysis
Occurs in Liver and Kidney, whereas glycolysis in all cells of body
Pyruvate Carboxylase is in mitochondrial matrix:
o Requires coenzyme Biotin
o Activated by acetyl CoA (regulatory mechanism)
o Turns pyruvate oxaloacetate
o OAA Malate (leaves mito into cytosol) OAA PEP
Starvation:
o Lots of beta-oxidation increased acetyl CoA
o Acetyl CoA activates pyruvate carboxylase increased gluconeogenesis
Energy Requirement:
o 6 ATP
o 2 NADH
Substrates for Gluconeogenesis:
o Lactate
o Pyruvate
o Glyerol (broken down from triglycerides)
o Amino Acids:
Except: lysine, leucine
Gluconeogenesis from Glycerol:
o Liver has Glycerol Kinase (glycerol glycerol 3-phosphae)
o Glycerol 3-phosphate DH (glycerol 3-phosphate DHAP)
o DHAP is intermediate for both gluconeogenesis and glycolysis
Reciprocal Control:
o Insulin:
glycolysis
gluconeogenesis
o Glucocorticoids and Glucagon:
gluconeogenesis
glycoslysis
o F 2,6-BP:
glycolysis (activate PFK)
gluconeogenesis (inhibits F 1,6-BPase)
Controlled by PFKFB
2 active sites (1 kinase, 1 phosphatase)
Unphosphorylated (kinase activity) F 2,6-BP

Phosphorylated (phosphatase activity) 2,6-BP

Diabetes:
o Type 1: low levels of insulin
o Type II: resistant to insulin
o Starvation increased gluconeogenesis increased glucose
Insulin cannot stop this
o Muscle/adipose insulin dependent

Pentose Phosphate Pathway:

G-6-P has 3 pathways:

o Glycogen
o PPP
o Glycolysis
o Gluconeogenesis
Function of PPP:
o Provide NADPH for fatty acid synthesis and reduction of glutathione (drug
metabolism and riding reactive oxygen species)
o Provide pentose phosphate for nucleic acid synthesis
Oxidative Reactions:
o First 2 steps
o Irreversible
Nonoxidative Reactions:
o Reversible
o Produce intermediates of glycolysis (F-6-P and G-3-P)
o Prevents accumulation of Ribulose 5-Phosphate
Transaldolase: transfers 3 carbons
Transketolase: transfers 2 carbons
If you want to convert G-6-P to glycolysis intermediates, you need at least 3 G-6-Ps
o Product: 2 F-6-P and 1 G-3-P
Glucose 6-Phosphate DH:
o First enzyme used to convert G-6-P to 6-Phophogluconate
o Low levels of this provides resistance to malaria

Glycogen Function and Location:

o In well fed person, concentration highest in Liver
o Liver storage depleted within 24 hrs of fast
o Muscle storage is less readily depleted
o More total storage in uscles
o Brain has low glycogen concentration
Glycogen Structure:
o Glucosyl residues joined by glycosidic links
1-4 are main backbone
1-6 are branches at every 8-12 linkage
o 1-4 are seen in cellulose
o If just 1-4 linkage than it would be starch
Glycogen Synthesis:
o G-6-P is initially used to become Glucose 1-Phosphate (reversible)
Enzyme: phophoglucomutase
o G-1-P becomes UDP-glucose with addition of UTP
Enzyme: UDP-glucose pyrophosphorylase
o UDP-glucose glycogen
Backbone formed by Glycogen Synthase
1-6 branches formed by Amylo 1-4, 1-6 Transglucosylase
o Formation of glycogen from UDP-glucose releases UDP (uridine diphosphate)
Glycogen Breakdown:
o 1-4 broken down by Glycogen Phosphorylase becomes G-1-P (10 per glucose)
Phosphorolytic cleavage
o 1-6 broken by Glycogen Debranching Enzyme free glucose
Hydrolytic recation
Has transferase activity oligosaccharide near branch point to 1-4 chain
Regulation of Glycogen Metabolism:
o Glycogen Synthase (build): (dephosphorylated form is active)
Activated: Protein Phosphatase:
Insulin activates
Inactivated: Protein Kinase
o Glycogen Phosphorylase (break): (phosphorylated form is active)
Activated: Protein Kinase
Glucagon: activates from liver
Epinephrine: activates from muscles
Inactivated: Protein Phosphatase

Epinephrine and Glucagon use GPCR Pathway:

o Adenylyl cyclase
o cAMP (degraded by phosphodiesterase to 5AMP)
Phosphodiesterase inhibited by caffeine
5AMP can activate glycogen phosphorylase without phosphorylation
During anoxia or depletion of ATP
o Catalytic subunit from cAMP can activate Glycogen Phosphorylase Kinase
Ca2+ can activate by binding to calmodulin, a subunit of glycogen
phosphorylase kinase, which then activates glycogen phosphorylase to cause
glycogen degradation

Tricarboxylic Acid Cycle:

Oxidation of carbs, fats, and amino acids via acetyl CoA

Products:
o CO2
o NADH
o FADH2
o GTP
Acetyl CoA:
o Activator of Pyruvate Carboxylase (for gluconeogenesis)
o Produced by
Metabolism of amino acids
Monosaccharides
Glycerol, fatty acids
o 2 carbons come off as CO2
Pyruvate Acetyl CoA:
o Enzyme: Pyruvate Dehydrogenase Complex
o 1st Step:
Enzyme: Pyruvate Decarboxylase
Pyruvate binds to TPP (coenzyme)
CO2 released from Pyruvate
nd
o 2 Step:
Enzyme: Dihydrolipoyl Transacetylase
Now binds with oxidized, sulfhydryl form of lipoic acid
rd
o 3 Step:
Coenzyme: CoA
Acetyl CoA formed
th
o 4 Step:
Enzyme: Dihydrolipoyl DH
Coenzyme: FAD
FAD oxidizes sulfhydryl form of lipoic acid
FAD gest reduced to FADH2
NAD+ oxidizes FADH2 to FAD

Pyruvate Dehydrogenase Complex:

o Inhibitors:
Acetyl CoA (end product)
NADH
o Phosphoprotein Phosphatase: activates
Activates: Ca2+
o Protein Kinase: inactivates (phosphorylates active form)
Activates:
ATP
Acetyl CoA
NADH
Inactivates:
CoA
Pyruvate
NAD+
End Products:
o 3 NADH (oxidative step since NAD+ NADH)
o 1 FADH2 (oxidative step)
o 2 CO2
o ATP/GTP
Competing Reactions:

Anaplerosis (filling up):

o Pyruvate Carboxylase occurs in gluconeogenesis in liver/kidneys
o Pyruvate Carboxylase catalyzes reaction between pyruvate and CO2 to make
Oxaloacetate
o Thus, high levels of Oxaloacetate in Liver + Kidneys
o Pyruvate Carboxylase is used to OAA concentrations high
Regulation of Tricarboxylic Acid Cycle:
o Pyruvate DH:
Inhibitor: ATP, NADH, Acetyl CoA
o Citrate Synthase:
Inhibitor: ATP
o Isocitrate DH:
Inhibitor: ATP, NADH
Activator: ADP
o -Ketoglutarate DH:
Inhibitor: NADH, Succinyl CoA

Allosterism and Regulation of Enzyme Activity:

Substrate Concentration vs. Reaction Velocity

o Enzyme following Michaelis-Menton hyperbolic curve
o Allosteric Enzyme sigmoid curve
Shows cooperativity
Hemoglobin:
o Tetramer (2, 2)
o Heme molecule noncovalently bonded to each subunit
o Heme allows oxygen binding
o Allosteric
Single oxygen molecule bounded = easier to bind more
Affinity for last O2 is 300x than affinity for 1st O2
o Can bind 4 oxygen molecules
o Carries oxygen unloads oxygen, takes up CO2

o P50 value: 26 torr

Partial pressure of oxygen that will cause 50% saturation
Higher partial pressure in lungs than capillaries of muscles
EF Hand
o Structure of enzyme than binds Ca2+
o Calmodulin:
Binds 4 calcium ions
Calmodulin-dependent enzymes:
cAMP phosphodiesterase: degredation of cAMP
Myosin light chain kinase: smooth muscle contraction
Calcineurin: phosphatase that takes phosphate off protein
Calcium/calmodulin depended protein kinase II
Plasma membrane Ca2+ ATPase
Ras:
o Monomeric guanine nucleotide binding protein
o >50% chance of cancers have mutated Ras
Activated on state allows unregulated cell proliferation
o GTPase switch:
Inactive Ras: bound to GDP
Guanine Exchange Factor (GEF) allows GTP to replace GDP
Activator Protein
GTPase Activator Protein (GAP) allows Ras to hydrolyze GTP to GDP
Inactivator Protein

Enzyme Regulation: phosphorylation +

dephosphorylation
o Kinase puts phosphate to target protein (active) through hydrolyzing ATP to ADP
o Phosphatase takes off phosphate (inactive)
Feedback inhibition:
o Usually end product of reaction acts as inhibitor of previous enzyme
o Rate limiting enzyme often affected
o Ex: PFK-1 and Citrate:
Citrate is final product of glucose metabolism
Citrate inhibits Phosphofructokinase-1, which converts F-6-P to F 1,6-BP
ATP is also a feedback inhibitor (high ATP = no need to metabolize glucose)
Enzyme Regulation: Hormones

o Insulin:
Stimulates glycolysis
Released after meal
Receptor: tyrosine kinase receptor
o Glucagon:
Inhibits glycolysis
Released in starvation
Receptor: G-protein coupled receptor
o Both Insulin and Glucagon act on:
Glucokinase
Phosphofructokinase
Pyruvate Kinase
Enzyme levels often elevated in plasma levels after damage to tissues
Markers of Liver Disease:
o Alanine Aminotransferase (ALT)
o Aspartate Aminotransferase (AST)
o Increased Bilirubin = liver disease
Markers of Heart Disease:
o Creatine Kinase Isozyme: rise after myocardial infarction
o Isozyme can be placed in electrophoresis:
Isozyme has 2 forms: muscle and brain
2 b subunits and 2 m subunits

o Both
Creatine Kinase MB and Cardiac Troponin are
increased in plasma after myocardial infarction

Metabolic Compartmentalization:

Series of Centrifugations: (each round at faster speed)

o Heavier substance is filtered out first

o From first to last to filter out:
Nucleus
Mitochondria
Ribosomes
Cytosol
Organization of Eukaryotic Cell:
o Plasma Membrane:
Receptors for hormones/cytokines
Transport mechanisms
o Cytosol:
Glycolysis
Pentose Phosphate Pathway
Lipid Synthesis
o Mitochondria
Fatty Acid Oxidation
TCA Cycle
Electron Transport
Oxidative Phosphorylation
Evolutionarily is like prokaryotes:
Eukaryote engulfed mitochondria
Endosymbiotic Relationship
Has double membrane
o Lysosome:
Contain hydrolytic enzymes (hydrolases)
o Peroxisome:
Hydrogen Peroxide forms here
Catalase needed to eliminate hydrogen peroxide
Long Chain Fatty Acid Oxidation occurs in peroxisome, NOT mitochondria
Defect in fatty acid oxidation Adrenoleukodystrophy (ALD)
o Endoplasmic Reticulum:
Drug metabolism with cytochrome P450 system (xenobiotic metabolism)
Ribosomes are sites where protein synthesis occurs
o Golgi:
Posttranslational mechanisms:
Glycosylation (sugars covalently link)
Sulfation
o Nucleus:
DNA synthesis
Contains genetic info, but so does mitochondria
Mitochondria DNA can only be passed on by mothers
RNA synthesis
Movement of Metabolites Across Cell Membrane:

o Small molecules can use simple diffusion (urea)

o Amino acid transport can be either facilitated or active
o Na+/K+ transport is energy demanding (20% total ATP expenditure)
Electron Shuttle Between Cytosol and Mitochondria:
o NADH generated from Citric Acid Cycle in matrix is used for oxidative
phosphorylation
H+ from NADH is transported from mitochondrial matrix through inner
membrane and into intermembrane space
o Inner mitochondrial membrane is impermeable to NADH
o For NADH to come from cytosol, 2 mechnisms:
Glycerol Phosphate Shuttle:
Cytosol: NADH oxidized to NAD
Mitochondria: FAD reduced to FADH2 (used for electron transport)

Malate-Aspartate Shuttle
Redox Couple: Malate and Oxaloacetate (does redox with
NADH/NAD)

Yield of ATP from Oxidation of 1 Glucose:

o NADH = 2.5-3 ATP
o FADH2 = 1.5-2 ATP
o Complete Oxidation Yields:
2 ATP
2 GTP
10 NADH
2 FADH2
o Complete Oxidation = 30-38 ATPs
o Net ATP from Anaerobic Glycolysis = 2 ATP

ATP
NADH
FADH2
GTP
CO2

Glycolysis
2
2
-

Pyruvate Acetyl CoA

2
2

Citric Acid Cycle

6
2
2
4

Total
2
10
2
2
6

Oxidative Phosphorylation:

Takes place in mitochondrial matrix

Takes H+ from NADH and FADH2 to pump across membrane
into intermembrane space
At end of ETC, oxygen is reduced to H2O
Theoretically, 7 ATP would be produced from oxidation of NADH,
but really only 2.5-3
Electron Transport Chain Complex:
o Complex 1: NADH-CoQ Reductase Compelx
NADH transfers 2 electrons
NADH reduced to NAD+ and H+
FMN (flavinmononucleotide) is involved
Reduces CoQ (ubiquinone)
o Complex 2: Succinate CoQ Reductase + CoQ
Reduces CoQ
FADH2 from glycerol phosphate shuttle contributes 2 e Succinate contributes 2 eo Complex 3: CoQH Cytochrome c Reductase:
Electrons from NADH and FADH2 arrive here
o Between Complex 3 and 4: Cytochrome C
Mobile electron carrier, same with CoQ
o Complex 4: Cytochrome c Oxidase
Copper ions present
Protons (H+) are transported through in Complex I, III, IV

H+

concentration accumulates in intermembrane space

On inner membrane:
o ATP synthetase
H+ goes back into matrix and ATP forms
o ATP/ADP antiporter
ATP out
ADP in
o Phosphate Transporter:
OH- out (combines with H+ in intermembrane space to form H2O)
HPO42- in
Inhibitors of Oxidative Phosphorylation:

o Complex 1: Rotenone
o Complex III: Antimycin A
Complex 1 + 2 are reduced (upstream)
Complex c + 3 + 4 are oxidized (downstream)
o Complex IV: Carbon Monoxide + Cyanide
o Complex V (ATP synthase): Oligomycin
o ATP/ADP Translocase (antiporter): Atractyloside
Uncouplers of Oxidative Phosphorylation:
o Dissipates proton gradient across inner membrane to prevent ATP synthesis
Protons are still moved into matrix by uncoupler protein NOT ATP synthetase
o BUT permits electron transport
o Energy is released as heat
o Ex:
2,4-DNP
Uncoupling Protein 1 (thermogenin) seen in brown adipose in babies
Diseases in Cell Respiration and Oxidative Phosphorylation:
o Result in Lactic Acidosis, Muscle and Nerve Pathology
o Ex:
Lebers Heriditary Optic Neuropathy
Defect in mitochondrial gene
Maternal inheritance
Blindness in teens and 20s
Optic Nerve affected
Leigh Syndrome:
Muscle and neurological problems
Lactic acidosis
Anaerobic conditions predominate thus lactic acid will accumulate

Fatty Acid Oxidation:

3 Lipids:
o Cholesteryl ester (CE) cholesterol
o Phosphatidylcholine (phospholipid PL) Glycerlphophocholine
o Triacylglycerol (TAG) 1-Monoacylglycerol
Glycocholic Acid:
o Bile salt (derivative of cholesterol)
o Cholic acid conjugated to glycine

Hormonal Control of Lipid Digestion:

o Stomach:
Cholecystokinin (CCK):
Ihibits gastric motility
Stimulates release of pancreatic enzymes to release lipids
Simulates gallbladder to release bile
o Upper Small Intestine:
Secretin:
Stimulates pancreas to release bicarbonate increases pH of lumen
enzymes more effective
o CCK and Secretin both released by gut endocrine cells when dietary lipids enter small
intestines
Fatty Acid Abosorption:
o Intestinal mucosal cells absorb lipids
o 2-Monoacylglycerol gets reconverted back to Triacylglycerol (TAG)
o Lipids go into Chylomicron:
TAG
Cholesteryl ester
Apolipoprotein B-48
Phospholipids
o Chylomicron goes into lymphatic system which eventually enters blood
Fatty Acid Structure:
o 2-4 Carbons: short chain
o 6-12 Carbons: medium chain
4-10 carbons seen in milk
o 14-20 Carbons: long chain
Fatty acids have at least 16 carbons
o >22 Carbons: very long-chain
o Palmitic Acid is written as 16:0 16 carbons with 0 unsaturated bonds
o Oleic Acid written as 18:1(9) 18 carbons, 1 unsaturated bond at 9th carbon
o Essential Fatty Acids: Linoleic acid + -Linolenic acid
o Formic Acid is simplest with 1 carbon
Cis vs Trans Fatty Acids:
o Double bond = unsaturated fat
o No double bond = saturated
o Trans fat = trans double bond
Arachidonic acid:
o 20:4(5,8,11,14)
o Precursor for prostaglandins
o End of fatty acid = omega
o Also known as Omega-6 because double bond is sixth to last carbon
Lipolysis of Triacylglycerols (TAG):

o 3 enzymes responsible for breakdown:

Adipose Triglyceride Lipase (ATGL)
Hormone Sensitive Lipase (HSL)
Monoacylglycerol Lipase (MGL)
o Enzymes initiate free fatty acid flux from white adipose tissue to liver
o ATGL removes one acyl group from TAG
o Successive removal (TAG DAG MAG)
o Free fatty acids go through receptors on liver into liver and activated with Acyl-CoA
o TAG is reformed in liver and is hydrolyzed back to free fatty acids by the 3 enzymes
o Free fatty acids in liver go to nucleus for gene expression

G-Protein Coupled Receptors:

o Activated when alpha subunit dissociates
o Effector protein is usually adenylyl cyclase
Makes cAMP from ATp
cAMP rises in response to epinephrine or glucagon
o Turn off: hydrolyze GTP to GDP
o cAMP:
2 regulatory subunits + 2 catalytic subunits
cAMP binds to regulatory subunits dissociates from
catalytic subunit
catalytic subunit phosphorylates protein substrate to
activate protein (PKA)
To inactivate protein, phosphatase
dephosphorylates protein

Hormonal Regulation of Fat Breakdown in Adipoytes:

o Epinephrine increases cAMP activates PKA activates

hormone sensitive lipase
o Insulin reverses epinephrine effect stimulates phosphatase to
inactivate HSL
Carnitine Shuttle:
o Net effect: long chain fatty aceyl-CoA is transported from outside
to inside mitochondria
o Steps:
Fatty acid from digestion in cytosol combines with CoA to
become Fatty Acyl CoA
Acyl CoA synthetase is enzyme
Once combined it can go through outer membrane into
intermembrane space
Needs carnitine to go through inner membrane
Transferase 1 on outer membrane gets rid of CoA from fatty acyl coA
Fatty acid is combined with carnitine
Goes through translocase into matrix
Transferase II takes carnitine off
Carnitine is transferred back into intermembrane space by translocase
o Beta oxidation begins once fatty acid is in matrix
Heart uses beta-oxidation of fatty acids for energy to pump blood
Cannot do beta-oxidation:
o Brain
o Erythrocytes

Steps of -oxidation: (for even # carbons)

o OHOT (oxidation, hydration, oxidation, thiolysis cleavage)
o Takes 2 carbons off during each cycle
o Energy is created by formation of FADH2 and NADH
o End Product: Acetyl CoA used in Citric Acid Cycle with Pyruvate

Energy Yield from Beta-Oxidation of Palmitoyl-CoA (16:0)

o Divide carbon amount by 2 = 8
o 8-1 = FADH2 and NADH amount (7 each)
o 8 Acetyl CoA forms
o Each Acetyl CoA goes to Citric Acid Cycle 12 ATP each
12 * 8 = 96 ATP
o 7 NADH * 3 = 21 ATP
o 7 FADH2 * 3 = 14 ATP
o Total: 131
o Costs 2 ATP to form Fatty Acyl CoA from CoA and Fatty Acid
o Net: 129 ATP
Oxidation of Fatty Acids with Odd Carbons:
o End Product: Propionyl Coenzyme A
o Propionyl Coenzyme A gets converted to Succinyl CoA to go into
Citric Acid Cycle
Oxidation of Unsaturated Fatty Acids:
o Needs to deal with cis-double bonds
o New enzymes involved:
Reductase
Isomerase
Medium Chain Fatty Acyl CoA Dehydrogenase Deficiency (MCAD):
o Issue with degrading fatty acids 6-10 carbons long
o Fatty acids accumulate hypoglycemia + hypoketonemia
o 4 distinct Acyl CoA Dhydrogenase in mitochondria for short, med, long, very long
fatty acids
o Important for infants: need to digest breast milk high in medium chain fatty acids
Ketone Bodies:
o Alternative fuel for cells made in liver mitochondria
o 3 types:

 Acetoacetate
3HB
Acetone
o 2 Acetyl CoA forms Acetoacetyl CoA
o Moved back to muscles and reverted back to 2 acetyl CoA
o Used in starvation, brain also uses ketone bodies

Ketone Bodies produced excessively in Diabetic patients

o Insulin decreases
o Epinephrine/Glucagon increases
More lipolysis
More free fatty acid in plasma
More hepatic output of ketone bodies
Result Ketoacidosis

Fatty Acid Synthesis, Obesity, and Cancer:

Carbs and proteins in exess can be converted to fatty acids stored as TAG
Fatty acid synthesis occurs in liver and lactating mammary glands
o In cytosol, whereas beta-oxidation is in mitochondria
o Grows 2 carbons at a time
o ATP and NADPH needed to synthesize fatty acid
o NADPH from pentose phosphate pathway
Metabolic Pathway in Liver:
o Glucose enters liver from GLUT-2
o Glucose becomes G-6-P by glucokinase
o G-6-P goes to PPP or to Pyruvate
o Pyruvate goes to Citric Acid Cycle or Fatty Acid Synthesis
o Inhibition of Isocitrate DH in CAC allows use of Acetyl CoA Carboxylase for fatty
acid synthesis
o High levels of Citrate will allosterically activate fatty acid synthesis

Acetyl CoA Carboxylase:

o Rate limiting step in fatty acid synthesis
o Inactive form: protomers
o Active: polymer
o Activated by Citrate
o Inactivated by end product: Long chain fatty acyl CoA
o Forms Malonyl CoA from Acetyl CoA (adds CO2)
o Allosterically regulates malonyl CoA
Regulation of Acetyl CoA Carboxylate:
o Done by covalent regulation (phosphorylation) by AMP Kinase
(AMPK)
o Insulin activates protein phosphatase to activate acetyl CoA
carboxylase
o AMPK inactivates acetyl CoA carboxylase
o AMPK is increased during starvation by glucagon and
epinephrine

Formation of cytosolic acetyl CoA

o OAA not permeable out of matrix gets converted to Citrate
o Oxaloacetate + Acetyl CoA = Citrate in mitochondrial matrix
o Citrate transporter moves citrate into cytosol
Especially when ATP levels high after a meal
o Citrate in cytosol is reconverted back to Acetyl CoA and OAA
OAA L-Malate Pyruvate (NADH produced from malate to pyruvate)
Acetyl CoA Palmitate (fatty acid synthesis)

Structure of Fatty Acid Synthase (FAS) Complex:

o Each FAS monomer is a multi-catalytic polypeptide with 7 enzymatic domains
o Dimer
o In addition to 7 domains, has ACP, 4-phosphopantetheine
o Efficient way of organizing fatty acid synthesis
o Acyl groups are transferred between cysteine side chain and phophopantetheine of
other subunit

During synthesis:
o Ketone groups reduced to hydroxyl groups by NADPH
o Reduce double bonds to single bonds uses NADPH
o Adds 2 carbons at a time
o NADPH is generated by
PPP
When Malate turns to Pyruvate
Uses of NADPH:
o Reductive synthesis: fatty acids, steroids, sterols
o Cytochrome P450 system
o Detox of reactive oxygen intermediate
Further elongation of fatty acid occurs in smooth ER
o Can add cis double bonds to produce oleic acid (18:1(9))
Fatty acids regulate gene expression by binding to nuclear transcription factors: peroxisome
proliferator-activated receptors (PPARs)