ADENOSINE TRIPHOSPHATE (ATP) TRANSPHOSPORYLATIONS BET.

NUCLEOTIDES
• ↑ATP:ADP = constant ratio o ATP source:
• HIGH ENERGY PHOSPHATES – ↑ -ΔG’° ▪ Glycolysis
o Source of phosphporyl grp ▪ Oxidative phosphorylation
▪ Phosphoenol pyruvate ▪ Photophosphorylation
▪ Phosphocreatine o Nucleoside triphosphates & deoxynucleoside
▪ 1,3 bisphosoglycerate triphosphates = ATP (in terms of energy)
▪ Oxidative phosphorylation ▪ Synthesized from ATP by
▪ Glycolysis: 2 phosphates • nucleoside diphosphokinases
▪ Krebs/citric/TCA cycle: 1 phosphate • nucleoside monophosphokinases
o Acetyl-CoA o UTP (uridine): combine sugars
o Thioester o CTP (cytosine): lipid synthesis
• ATP hydrolysis o GTP (guanodine): protein synthesis
o Exergonic o ↑phosphate grps, spontaneity, rxtive (repulsion),
o ↑ activation energy energy
o *ATP is stable pag walang enzymes o Muscle contraction → ↑ADP
• Iba-iba ΔG for ATP among cells ▪ ↑ATP demand ↓ADP conc
• SN2 ▪ Adenylate kinase: ADP→ATP
o 3 positions on ATP for attack by nucleophile
▪ α: adenylyl transfer PHOSPHOCREATINE
▪ β: pyrophosphoryl transfer o Utilized when ↓ADP stores
▪ γ: phosphoryl transfer o Creatine kinase: catalyzes

▪
RNA SYNTHESIS
o adenylate (AMP) INORGANIC POLYPHOSPHATE
o guanylate (GMP) o Potential energy source
o cytidylate (CMP) o PPi form: reservoir of phosphoryl grp
o uridylate (UMP)
DNA SYNTHESIS PHOSPHAGENS
o Deoxy analogs of ↑↑↑ o Storage forms of grp transfer potential
ACTIVE TRANSPORT o phosphocreatine and arginine phosphate (in
o Transport ions across conc. gradient using ions invertebrates)
o Channels: proteins (amino acids) o ↑ATP demand (how to maintain ratio?) → get
▪ Open/close depending on electrostatic interaxn phosphate grp from phosphocreatine orarginine
w/in molecule phosphate
o Phosphorylation: Na- dependent o If ↓ATP ~ phosphorylate creatine para pag
o Dephosphorylation: K+ dependent dumating emergency na need may stored na
• CONTRACTION phosphate grp

BIOLOGICAL REDOX
• Electron flow – responsible for work done by
organisms
• Heterotrophs – source of electrons: reduced
o compounds
o ATPase: ATP→ADP + Pi
• Autotrophs – initial e- donor is a species excited by
o Myosin: may ATP binding site
light absorption
o Myosin head + ATP → kakalas myosin from actin
• Oxygen – final e- acceptor; converted to H2O (final
once bound → ATP hydrolysis → conformational
product in ETC)
change → myosin attaches to next actin → Pi
release → power stroke conformational change! →
BIOLOGICAL OXIDATION
ADP release
o Dehydrogenation catalyzed by dehydrogenases
 o ↑ oxidation state ↑ energy • Niacin: vit B3; source of nicotinamide moiety
o Caloric content: glucose < fatty acids • Enzymes use EITHER NAD+/NADPH
o e- transfer • B1: thiamine
▪ as electrons • B2: riboflavin
▪ as H+ • B6: pyridoxine
▪ as hydride • Pellagra
▪ direct combination w/ O2 o ↓niacin
• REDUCTION POTENTIALS o Neurological disorder
o Measure affinity for e- o Diets low in TRP [corn]
o Dermatitis, diarrhea, dementia, death
o Risk: alcoholics – ↓ intestinal absorption of
niacin
▪ FMN, FAD
• Flavine Monocucleotide
• Water-soluble coenzyme; reversible REDOX
• Tightly bound (prosthetic grps in flavoproteins)
• Flavin nucleotides
• From vit B2 riboflavin
• Provide a means para flavoprotein can tempo
hold e- while catalyzing e-
o ↑-E° ↑energy for ATP generation • Has isoalloxazine ring (undergoes reversible
o ↑+E° ↑reduced reduction)
UNIVERSAL ELECTRON CARRIERS • FADH2, FMNH2 – reduced forms
o Reduction of e- carriers: conservation of free • Special types:
energy o Cryptochromes: mediate effects of blue
▪ NAD, NADPH lights, circadian rhythms
• Nicotinamide Adenide Dinucleotide o Photolyases: uses absorbed light energy to
• Water-soluble coenzyme; reversible REDOX repair chem fx in DNA
• Pyridine nucleotides ▪ Ubiquinone, plastoquinone
• Oxidoreductases/dehydrogenases catalyzes: • Lipid-soluble, e- carriers, H+ donors
• non-aq envi of membranes
▪ Iron-sulfur proteins, cytochromes
ENERGY BALANCE
• Move readily from one enzyme to another
o Resting Metabolic Rate / basal metabolic rate
o 60-70% of total energy expenditure & O2
consumption
o Excess sa BMR na di mo ginamit → fat!
o Para mamaintain wt: ganito karaming calories
intake (BMR: kayang iburn ng katawan mo)
o ↑ BMR ↑pwedeng kainin
o Wanna lose fat??? Consume less than BMR! Kasi
kung ano man di mo napunan sa BMR, yung stores
• NAD+: oxidation rxns (catabolic: energy
mo sa energy, yun ang madedeplete! EH LIPIDS
producing); + ay galing sa N moiety
ANG FIRST NACCONSUME WHEN YOU FAST
• NADPH: reduction rxns (anabolic: biomolecules)
SO! !!

METABOLISM
• All chem transformations in an organism
o ANAbolism: need energy (simple→biomolecules)
▪ Divergent (iba-ibang biomolecules)
 o CATAbolism: produce energy (NADH / ATP
synthesis)
▪ Convergent
o Acetyl-CoA: common denominator
• Intermediary metabolism – ↓ MW, products, interm,
rxtants, metabolites
• Precursors of macromolecules
o H2O, CO2, NH4+, NO3, N2
• Goal: capture energy from sun and fuels (food);
concert inorg compounds → macromolecules (which
degrade w/ regard to fxn of cells)
• Cells maintain a dynamic steady state :: constant
rate of conversion from one product to another
• Eat → ↑ blood sugar level (not prolonged kasi insulin
transports blood glucose back to cell)
• Cellular differentiation/specialization – permanent
changes
o RBC – no nucleus, no mitochondria; hemoglobin only
• Compartmentalization – one pathway, diff locations
• Control points – irreversible rxns (efficient pathway)
• Kinetic control – stop production pag marami na
o Substrate control: amt of substrate helps in
forward rxn
o Separate pools of anabolic/catabolic intermediates
• Oxidative phosphorylation (in lipids, inner
mitochondrial membrane)
• Krebs/citric/TCA cycle (matrix)
• Fatty acid synthesis (cytosol)
• Feedback inhibition – keeps production and
utilization of each metabolic intermediate in balance
• Change in conc of metabolite [intermediate end
product of metabolism] → ripple effect (affect
other metabolism)
REGULATION
o Substrate availability
o Allosteric regulation
▪ Changes in local conc of small molecule
(substrate, product, metabolites, cofactor):
determine if magproceed pa metabolism
▪ Second messengers: allosteric regulators
• AMP, Ca2+
• Respond to extracellular signals
• Extracellular signals
o Hormonal (insulin, epinephrine)
o Neuronal (acetylcholine)
o Growth factors/cytokine
• Transcription factor
o Nuclear proteins that bind to response elements in
DNA regions → activate/repress rxns by
synthesizing proteins
▪ Activation may be due to de/phosphorylation
• mRNA
o stability varies
o ↑ mRNA =/= ↑ protein product
• Proteins have finite lifetime (degrades)
• Regulate enzyme by sequestering (store) to alter its
effectivity
o Enzyme synthesis: depends on ano need mo
• Liver: most adaptable tissue
o Carb-degrading enzymes → fat-degrading enzymes
ENZYME REGULATION
▪ Concentration of substrate
▪ Allosteric effectors
▪ Covalent modifications
o De/phosphorylation
o Alter electrostatic changes [polar/nonpolar]
→ interaxn w/in protein changes
[conformational changes] → affects Vmax
o Reversible (inefficient if irreversible)
▪ Binding of regulatory proteins
o Not mutually exclusive
o Rxns far from equilibrium: common pts of
regulation
▪ ~naffavor one product~irreversible rxn~
▪ ↑Solute conc sa cell = death <3
o Metabolic regulation
▪ Maintain homeostasis (dynamic state)
▪ Cellular parameter at a steady level over time
o Metabolic control
▪ External force so that metabolism can attack
• Stress, exposure to chem → metabolism
changes
▪ Based on conc of NADH & ADP
• [AMP] – sensitive indicator of cell’s energetic state
o AMPK: AMP→ATP
o ↑ AMP ↑ ATP consumption ↑ AMPK ↓ ATP balance
[response: create ATP!]
 ▪ Inner mitochondrial membrane
TRICARBOXYLIC ACID CYCLE / KREBS / CITRIC ACID • TCA cycle enzymes: in the matrix
CYCLE • CoASH
• Energy producing! Need ATP? TCA! o Acylation coenzyme; reduced CoA; from B5
• Intermembrane space (cytosol) pantothenate
• To conserve energy from oxidative process by o Synthesis & oxidation of fatty acids, pyruvate
transferring e- to NAD+ and FAD o Energy ng hydrolysis ng CoA used to
• NADH, FAD(2H) oxidation in ETC helps forward rxn ▪ Forward rxn
• Products ▪ GDP→GTP
o 3 NADH
o 1 FADH2
o 1 GTP [guanosine triphosphate—ATP analog w/
same energy]
o 2 CO2
REGULATION
o ATP utilization (ADP levels)
o NADH:NAD+
o Rate of FADH2 oxidation
o Ca2+ concentration
▪ Activates pyruvate DH complex
• Bawat glucose [6C] = 2 cycles ng Krebs [pyruvate 3C]
• First u need: ACETYL-COA
o Shuttled in Krebs to combine w/ oxaloacetate
o Sources
▪ Acetate
▪ Ketone bodies
▪ Pyruvate [glycolysis prod]
• pyruvate dehydrogenase complex produces
acetyl-coA
o 3 subunits
▪ TPP
▪ Lipoate
▪ FAD
o dephosphorylation (active) [pyruvate DH
phosphatase]
o phosphorylation (deactivated) [pyruvate DH
kinase]
▪ Fatty acids
• Β oxidation
▪ Amino acid degradation
• If impaired
o X generate ATP from fuel oxidation • FAD
o ↑ TCA precursors o Transfer/accept 1 e- from diff carbons w/in
▪ (x) pyruvate oxidation → reduced to lactate→ enzyme lang
lactic acidosis o Half reduce [FADH]
• ETO NA o Prosthetic grp
o Cindy ISO Kinky she SUCked Crocs and ATE o No conc sa soln
Flowers More Often o X regulate pathway directly
• DH (redox) produce energy • NAD
o Succinate DH o Transfer/accept 2 e- (as hydride)
▪ Has covalently bound FAD o Palipat-lipat (loosely held by enzyme)
 o After kumuha e- peds umalis o Net flux of oxaloacetate towards malate during
o Present sa soln fasting
o Indicator • Synthesis by metabolites
• TCA forward rxns (-ΔG’°) ~regulators!~ o Citrate: fatty acid
o Citrate synthase o α-KG: amino acid (neurotransmitter—GABA,
▪ X allosteric sites but inhibited by amt of citrate glutamate)
(negative feedback inhibition) o succinyl CoA: heme
o Isocitrate DH o malate: gluconeogenesis
▪ Inhibited by NADH o oxaloacetate: amino acid
▪ U need NADH to produce ATP
▪ ↑ADP ↑produce ATP so activate Krebs ANAPLEROTIC RXNS
▪ Has allosteric site for ATP o To replenish enzymes
▪ Activated by amt of ADP, ↑ Ca2+ ▪ Pyruvate carboxylase
o Alpha-ketoglutarate DH • B7 biotin
▪ Inhibited by NADH • High conc in kidney cortex and liver
• E1: α-keto acid decarboxylase containing TPP* • Oxaloacetate synthesis
o *thiamine pyrophosphate; B1 thiamine • B5 pantothenic acid: CoA
• E2: transacylase* with lipoate** ▪ Amino acid degradation
o **transfers acyl grps • Ser
converted to pyruvate
o *lipoate: coenzyme that doesn’t need a vit • Ala
▪ Sources: fats, carbs, amino acids • Leu
converted to succinyl CoA
• Iso

▪ Disulfide accepts e-
• E3: dihydrolipoyl DH with FAD
• Complex advantages:
o Product of one enzyme to be transferred to
another without energy loss
o ↑ rate of catalysis
• TCA reversible rxns
o Aconitase – rapid in both directions
o [products]/[substrate]~k
o [citrate]= 20 x [isocitrate]
o Keq of malate DH favors malate over oxaloacetate • 12 H+ = 3 ATP
CLINICAL RELEVANCE
o Beriberi – ↓ B1 thiamine
▪ Alcoholism (Wet Beriberi) – impaired thiamine
absorption; inhibited alpha-keto acid DH in heart
→ ↑ alpha-keto acids→ cardiomyopathy
o Leigh’s disease – ↓ pyruvate carboxylase
• Subacute necrotizing encephalopathy
• Delayed development
• Lactic acidemia
• Mental retardation
o Lactate Accumulation – anaerobic respiration
o Iron Deficiency Anemia
▪ Iron-containing compounds: heme, aconitase,
succinic DH, heme proteins of ETC
o Exercise
▪ ↑ heart pumping efficiency = ↑ cardiac output; ↓
beats per minute at a lower rate of oxygen
utilization
▪ Lungs extract ↑ oxygen = ↓ respirations per unit
activity
▪ ↑ Vasodilatory capacity in skeletal muscles
• ↑ oxygen delivery; ↓ lactate accumulation
OXIDATIVE PHOSPHORYLATION
• Energy producing
• Location: matrix & intracellular membrane [ETC]
• 4H+ = 1 ATP
• 2.5 mol ATP : NADH
• 1.5 mol ATP : FADH2
• Generation of ATP requires:
o Electron donor (NADH or FADH2)
o Electron acceptor (O2)
o Inner mitochondrial membrane
• Regulated by the rate of ATP utilization
• Fully oxidized CoQ accepts e-→reduced to CoQH2
• ATP synthase + protein complexes: inner
mitochondrial membrane
POISONS
• Dinitrophenol
o ETC v fast; no proton gradient
o Energy from ETC released as heat (not for ATP
synthesis)
o ↓ ATP prod
• Amytal, Rotenone, Sodium azide, CN-
o Site specific inhibitors
o Bind to chain→block redox→e- passage blocked
electron flow from substrate to O2
▪ Amytal/Rotenone
• Blocks NADH DH (complex I)
• impairment of Complex I→impairment of
mitochondria metabolism→↑ free radicals→cell
death→release of toxic compounds and
destruction of other cells
• * block e flow from NADH to CoQ→no ATP is
formed from NADH; 2 ATPs formed per
FADH2
• prevent the utilization of NADH as a substrate
▪ sodium azide
• inhibit Hem groups of cytochromes in
Cytochrome Oxidase (Complex IV)→ ↓
intracellular ATP
▪ CN-
• binds to Fe3+ in Hem groups in cytochrome
Oxidase (Complex IV)
• redox reactions in the respiratory chain will
stop → energy x released → proton pumps x
function → x return through Complex IV → x
ATP prod
• Barbiturates
o inhibit NADH DH (complex I)
• ↑ H2O2 inhibits
o Aconitase
▪ Citrate –x-->isocitrate
▪ Glutamate fuels Krebs, NADH unaltered
o Alpha-KG DH
▪ ↓ NADH
AMINO ACIDS IN PROTEINS
• @pH 7.4
o Amino acids in ionized form (carboxyl group is
dissociated)

• L-amino acids dominate in proteins

• peptide formation
o amino acid + amino acid
 o possesses partial double bond bc N is adjacent to ▪ Hydroxylation of Pro in collagen: H-bonding bet.
carbony carbon [sp2] Polypeptide strands of fibrous protein
o Carboxylation
▪ Glu: attach clot to surface (mediated by Ca 2+)
• **selenocysteine**
o Inserted into protein during synthesis
• sequence of amino acids: determined by genetic code
o 21st amino acid
• side chains: determines folding pattern, ligand
binding, environment interaxn
CLINICAL RELEVANCE
o Gly: small! compact structures (collagen)
• Sickle-Cell Anemia
o Pro: large! kink!
o Point-mutation
o Essential AA: PVT TIM HALL
o polar Glu→ nonpolar Val in β-globin chain of
▪ Except Tyr: created from hydroxylation of
hemoglobin [hydrophobic interaxn]
phenylalanine
o Malaria immunity
o Fold a peptide in aq medium:
▪
▪ Hydrophobic side chain core
• Myocardial Infarction
▪ H-bonding/polar side chain labas
o Creatine kinase: diagnostic aid
o Met: transfer methyl grps
o Troponine-T: better diagnostic aid; slow to elevate
o Cysteine→cystine: oxidation
o ↑ myocardial infarction ↑ creatine kinase
o Cystine→cysteine: reduction
• Cystinuria
• AA sa acidic → +
o Dapat cystine from tubular lumen→renal tubular
• Hydropathy index
cells kaso
o Glycophilicity
o ↓ renal tubular cell transport proteins so stuck sa
o Hydrophilicity
bladder ang cystine
▪ ↑ Hydropathy ↑ nonpolar (lipids)
o Tx: alkalinize urine para maexcrete
▪ ↓ Hydropathy ↑ hydrophilic
• Insulin
• pKa: tells u predominant form @ given pH
o Human insulin
▪ Bound to Zn (magcreate ng depot sa slow release)
POSTTRANSLATIONAL MODIFICATIONS
▪ Secreted as zinc hexamer
• after buo ng peptide, dun pa lang kakabit conjugate
• *type of fatty acid depends san makikita
• Carbohydrate Addition
o Glycosylation
▪ O-glycosylation
▪ N-glycosylation
• N-link glycosides
o Protect cells from immune attacks
o Recognition sites
▪ ~blood sugar test~ o Lispro
• Fasting blood sugar tells u abt ▪ X bind to Zn so absorbed more quickly
current/apparent blood sugar level ▪ Lysine (B29 position)→ moved to B28
• Glycosylated hemoglobin [5-7% HbA1c] ▪ Proline (B28 position)→ moved to B29
• Lipid Addition
o Palmitoylation: C16 plasma membrane STRUCTURE-FXN R/S OF PROTEINS
o Myristoylation: C14 intreacellular vesicles PROTEIN STRUCTURE
o Prenylation • Denaturation
• Regulation o Nonenzymic
o Phosphorylation o Temp, pH, solvent
o Acetylation • Dynamic & Structural Fxns of Proteins
o ADP-ribosylation o Reaction catalysis (enzymes)
• Modified Amino Acids o Transport (e.g. hemoglobin and myoglobin)
o Oxidation
 o Metabolic control (hormones, e.g. insulin, LH, FSH, ▪ Arrangements of secondary structure that
hGH) occur in more than one protein
o Gene transcription and translation (e.g. histone • TERTIARY STRUCTURE
proteins, repressor, enhancer factors) o 3D structure
o Contraction (actin and myosin filaments) ▪ Domain
o Structural roles (e.g. collagen, elastin) ▪ Folds
• Supersecondary structure (motif)
o Actin fold
o Nucleotide binding fold
o β-sheets rotate if part ng domain (discrete part of
protein may sariling set ng AA peptide chain)
o Whole fxn of protein
▪ Lactate DH
▪ G-Actin

• PRIMARY STRUCTURE
o Peptide chain (AA sequence)
o Folding pattern
o Rotation @ angles
o Trans configuration for peptide bond
o Proline
▪ Has 2° amino grp (imino acid)
▪
▪ Globular proteins: water soluble [hydrophobic
core, hydrophilic labas]
• QUATERNARY STRUCTURE
o Association bet 3D structures (noncovalent)
o Hemoglobin
• SECONDARY STRUCTURE
o Maximizes H-bonding STRUCTURAL CLASSIFICATION
▪ Regular/repeating • Transmembrane
• α-helix o Β-adrenergic receptor
o protruding R groups ▪ Phosphorylation sites: regulate protein activity
▪ max interaxn ▪ Not necessary na continuous yung peptide na
▪ prevent steric hindrance mabubuo
o H-bonding w/in peptide ▪ Extracellular signal causes conformational change
▪ Every 4th residue (AA) w/in protein → transmit cascade of rxns
o Rigid • Globular Proteins
• β-pleated sheets o Myoglobin
o H-bonding bet. diff peptides ▪ Bind 1 O2
▪ parallel ▪ Bound in skeletal muscle of heart
▪ anti-parallel ▪ Found in tissues
• prevent torsional angle strain ▪ Single polypeptide
• max interaxn ▪ Stores O2 for exercise
o nonplanar ▪ Bind oxygen→second diffusive pathway for
▪ Non-regular/nonrepeating oxygen through cytosol
• Loops, bends, turns ▪ Becomes abnormal (positive high) 1h after
o Flexibility; less rigid myocardial necrosis and can clear within 24h
▪ Β-turn: connects β-sheets
o Structural motifs
 ▪ Normal conditions: myoglobin circulates in the
blood bound to plasma globulins which are
maintained at 0-0.003 mg/dL (intracellular)
▪ ↑ myoglobin sa plasma if may infection
o Hemoglobin
▪ Bind 4 O2
▪ Tetramer
▪ Facilitates O2, CO2, NO, carbonic acid transport
▪ RBCs only
▪ His residues: usually napprotonate/deprotonate
bc of pKa
▪ Pag nasisira ion pair: tensed state → relaxed
• Proton-dissociation breaks ion-pair present in T
o
state)
• Factors affecting binding capacity of Hgb
▪ Once magbind O2 and hemoglobin, kukunin ng
o ↑ pO2 ↑ affinity
myoglobin→mitochondria→cytochrome oxidase
▪ Marami nang oxygen so no need to release
(complex IV)
o ↑ pCO2 ↓ affinity
OXYGEN BINDING CURVE
▪ CO2 → carbonic acid
• Tensed → relaxed once magbind O2 sa hemoglobin
▪ Apparent sa actively metabolizing cells
o Merong portion sa hemoglobin na nagoopen capable
▪ tissues need O2 kaya irrelease yung O2
of binding more O2 atoms
o ↓ pH ↓ affinity
• ↓ pressure ng O2 na need ng myoglobin kaysa
hemoglobin para masaturate hemoglobin

▪ ↓ pH ↑ pCO2: shift →
• • ↑ req pO2 para masaturate hemoglobin
• ↑ pO2 sa lungs, ↓ pO2 sa tissues • Bohr Effect
• ↑ affinity ng cytochrome oxidase sa O2 vs affinity sa o Deoxygenated Hgb: ↑ affinity for protons
myoglobin o His has ↑ pKa
• Cooperativity o ↑ H+ ↓ pH ↓ pO2 ↑ ionic bonds (salt bridges—
o 1st binding mahirap pero once magbind, madali na stabilizes deoxy Hgb) ;; O2 affinity →
for other O2 atoms stabilize T state
• Narrelease ng myoglobin at hemoglobin yung O2 na o His grps → protonated l→ salt bridges→
nakabind sa kanila as pressure goes down kasi sila stabilize the deoxyHgb
nawawalan ng O2 pag ↓ pO2 (mas need kasi xmpre nung o Salt bridges are destroyed para relaxed na
system) once O2 binds

o
 o ↑ 2,3-bisphosphoglycerate ↓ affinity

▪ 2,3-BPG binds only to T bc pocket made by beta

chains is larger
▪ Destroys ionic interaxn w/in molecule CARBON MONOXIDE BINDING
▪ Once u bind BPG → conformational changes kasi • Carboxyhemoglobin
nagrelease O2
▪ COPD
• ↑ 2,3-BPG para marelease agad kas inga
nahihirapan huminga onti lang oxygen
ISOHYDRIC TRANSPORT
• CO2 (as bicarbonate) from tissues → lungs

HALDANE EFFECT
• Amt of CO2 bound to Hgb is displaced bc ↑ O2
• Dissociation/removal ng CO2 from Hgb

HEMOGLOBIN TYPES
• HbA: adult
• HbF: fetal
o ↑ affinity to O2 kasi ↓pO2 sa womb

CARBAMINO-HGB
• CO2 (as bicarbonate) from tissues → lungs
• Nonenzymic o
• CO2 binds w NH2 terminal amino grps of Hgb • HbA2
• HbA1c minor Hgb
• What if mataas glycolysation anyare sa ibang
proteins
HEMOGLOBINOPATHIES
• Sickle Cell Anemia (Hb S)
o Homozygous recessive
 o Pain!!!!!!!! ▪ 3 constant domains
o Chronic hemolytic anemia – hyperbilirubinemia [↑ ▪ 1 variable domain
dead RBCs] o Light chain
o ↑ infection ▪ 1 constant domain
o <20 days RBC life ▪ 1 variable domain
HEATSHOCK PROTEINS
o Hsp70: prevent premature folding
o Hsp60: template for protein folding (capsule thing)
• Fibrous Proteins
o α helix: tough, insoluble
o β conformation: soft flexible filaments
o collagen triple helix: high tensile strength
o o α-keratin
• Hemoglobin C ▪ strength; only in animals
o Lys→Glu ▪ outer layer of skin
o Mild chronic hemolytic anemia ▪ right handed alpha helix
o No therapy ▪ rich in hydrophobic residues (otherwise sasama
• Hemoglobin SC sa H2O)
o ↓ Hgb than normal but ↑ than sickle cell • Collagen
• Methemoglobinemias o Most abundant protein
o Once Fe is oxidized → methemoglobin (cant bind o Produced by fibroblasts
O2 anymore) o Tensile strength (tendons, cartilage, etc)
o ↓ NADH-cytochrome b5 reductase [Fe3+→Fe2+] o Left handed alpha helix
o Chocolate cyanosis o Vit ABC: regenerate collagen *body produces
o Tx: methylene blue (oxidized as Fe3+ is reduced) less oxygen as we age*
• Thalassemia Syndrome o Clockwise twist
o Beta
▪ α-globins ppt → premature cell death!
o Alpha – mas Malala
▪ ↓ α-globin synthesis
▪ Hydrops fetalis
▪ Fetal death
o Tx: Fe chelation, blood transfusion o Gelatin: hydrolyzed collagen; poor in protein
o ↓ hemoglobin ↓ RBCs o Collagen Types
IMMUNOGLOBULIN
• Anti-body
• Variable: antigen binding site

▪ Fibril-forming
• Rope-like: strength
• Binding pattern in electron microscope

o Heavy chain
 • Type I– osteogenesis imperfecta tarda
• Type II– osteogenesis imperfecta
congenita; death by pulmonary hypoplasia
in utero (womb)
• Replacement of Gly with bulky side chains
• Prevents formation of required triple
helical conformation
• ↑ twists ↑ strength
• What if Cys (not bulky) ang kumabit?
▪ Elastin
• Most abundant • Rubber-like
• Found in ECM (loose connective tissues, o Desmosine cross-link
bone, tendons, skin, blood vessels and
cornea)
• 33% glycine, 21% proline and
hydroxyproline
▪ Network-forming
• 3D mesh
• Filtration
▪ Fibril-associated
• Bind to surface of collagen fibrils
• Links fibrils to one another and to ECM
o Collagen Structure
▪ Rich in • Insoluble polymer
• Pro: facilitates helical structure • Made of small and nonpolar AA
formation • ↑ Pro and Lys ↓ hydroxylated parts
• Hydroxylated to maximize H-bonding • Synthesized from tropoelastin (linear
• prolyl hydroxylase [proline → polypeptide of small & nonpolar [Gly, Ala, Val]
hydroxyproline*] o Elastin Disorders
• activated by Fe ▪ Marfan Syndrome
• dapat acidic otherwise maooxidize • Impaired structural integrity of
& ppt as hydroxides connective tissues
• lysyl hydroxylase [lysine → • Abnormal fibrillin protein + normal
hydroxylysine*] fibrillin protein
• Scurvy
• ↓ Vit C [vit C needed for proline to
hydroxyproline]
• Ascorbid acid -- cofactor
• Gly: fits sa 3rd residue
o Collagenopathies
▪ Ehlers-Danlos Syndrome
• ↓ collagen processing enzymes
• Type III collagen gene mutations:
collagen containing mutant genes
degraded/accumulated in intracellular •
• Alpha-1 anitrypsin
compartments
o Inhibits proteases (elastase – catalyzes
• Lethal vascular problems
breakdown of elastin)
▪ Osteogenesis Imperfecta
o ↓ Alpha-1 antitrypsin → emphysema (cant
• Brittle Bone syndrome
breathe)
• Kyphosis: humped-back
• ↓ alpha 1 and alpha 2 chains
 o Specific alpha-1 AT methionine is required
for the binding of inhibitor to its target
proteases
o Smoking causes oxidation and inactivation of
methionine residue* (*req for binding ng
inhibitor sa elastase)
o Affected diffusion ng O2
o ↑ elastase ↑ elastin
ENZYMES
• Not all biological catalysts are enzymes
CLASSIFICATION OF ENZYMES
• Oxidoreductases
o Dehydrogenases
▪ Transfer of e- (hydride form)
▪ NAD+ / NADH
o Hydroxylases: add hydroxyl groups to substrate
o Oxidases: incorporates O2 to substrate & H2O or
both sa H2O
o Oxygenases: O2 atoms incorporated into acceptor
• Transferases
o Kinase: high-energy phosphate is transferred
o Glycosyltransferase: carb residue
o Acyltransferase: fatty acyl
o Transaminase: N grp → alpha-keto acid
o Synthases : synthesis
• Hydrolases
• Lyases: structure of substrate requires a carbonyl
carbon (electron sink) to stabilize carbanion
transiently formed when C-C bond breaks
• Isomerases
o Mutases: pinagpalit position ng phosphate grp
• Ligases
o Synthetase: derive energy for new bond formation
from cleavage of high-energy phosphate bonds;
synthases use a different source of energy
PROPERTIES OF ENZYMES
• Active sites
o Lock and Key - rigid
o Induced Fit – dynamic protein! Once sub binds to
enzyme → conformational changes; right IMF
• Catalytic efficiency
o Turnover number = amt of product/time
• Specificity
o Substrate-binding
• Holoenzymes
o Enzyme + nonprotein moiety [coenzyme, cofactor]
HOW DO ENZYMES WORK?
• Alt pathway w/ lower activation energy
• No change in ΔG
CHEMISTRY OF ACTIVE SITE
• TS (species w/ highest energy) stabilization
• Provides catalytic grps ↑ TS formation
FACTORS AFFECTING RXN VELOCITY
• Substrate concentration
o ↑ [S] ↑ rate of rxn ((only until Vmax))
• Temperature
• pH
o depends sap Ka ng residues and optimum activity
o ionizable grps provide interaxn
o CHYMOTRYPSIN
▪ Digestive enzyme
▪ Hydrolyzes peptide bonds on carbonyl side of
denatured Phe, Tyr, Trpin denatured proteins
FXNAL GRPS ON ENZYMES
• Active sites contain residues that provide catalytic
power sa enzyme
COENZYMES IN CATALYSIS
• Polar AA (nucleo) – participate directly; stabilize
polar side chains (dipole/ionic interaxns)
• Ser, Cys, Lys, His: covalent catalysis
• His: donate and accept proton @ neutral pH; protein
reservoir
• ↓ activity, ↓ specificity w/o enzymes
• Synthesized from vitamins
o Activation-transfer coenzymes
▪ Covalent bond w/ substrate → tightly held w/c is
deactivated for transfer
▪ Specific moiety/chemical grp involved in binding • Biotin (B7)
to enzyme o Does not have a phosphate group
▪ Separate & diff fxnal grp involved in catalysis o Bound to Lys in carboxylases
▪ Depend on enzyme for specificity and catalytic o Functional group is a nitrogen atom that
power covalently binds CO 2 group
• Thiamine pyrophosphate o Functions only in carboxylation reactions
o Pyrophosphate chelate Mg2+ which binds
tightly to the enzyme
o Functional group contains dissociable proton
o Reactive carbon forms covalent bond with
substrate keto group while cleaving the
o
adjacent C-C bond
• Pyridoxal phosphate (B6)
o Reactive aldehyde functions in catalysis by
forming covalent bond with amino groups
o Positive ring nitrogen withdraws electrons
from a bond resulting in bond cleavage
o Enzyme participates by removing protons
from substrate and by keeping amino acid and
pyridoxal group in a single plane to facilitate
electron transfer
o Oxidation-reduction coenzymes
▪ Do not form covalent bond with substrate
▪ Has functional group that accepts and donates
electrons and is specific in the form of electron
it transfers
• Hydride ions
• Hydrogen atoms
• Oxygen
▪ A different portion of coenzyme binds the
enzyme
• CoA
▪ Not good catalysts without the enzyme
o 3’,5’-BP binds reversibly but tightly on the
• Lactate DH
enzyme
• Catalyze transfer of electrons from lactate to
o Sulfhydryl group always attacks carbonyl
NAD+
groups and forms acyl thioesters
• ADP– binds tightly to the enzyme
• Contains histidine which bind dissociable proton
on lactate making it easier for NAD+ to pull off
other hydrogen with both electrons
• NADH dissociates

•
• Metals in catalysis
o Electrophiles
o Stabilize developing anions (anion TS)
o Accept and donate electrons in redox
o Bind multiple ligands in their coordination sphere
to participate in binding substrates or coenzymes
to enzymes
o Alter charge distribution
NONCATALYTIC ROLE OF COENZYMES
• Structural role (tertiary)
SUMMARY OF COENZYME ACTIVITY

LINEWEAVER-BURK PLOT
MICHAELIS-MENTEN EQ
• Assumptions
o [S] >>> [E] konti lang substrate na bound sa enzyme
o Steady state: ES formation = ES breakdown
o Vinitial measured as soon as magsama S & E
▪ ↓ product (backward rxn can be ignored)
• Km: conc of substrate to reach ½ Vmax
• ↑ Km ↓ enzyme affinity to substrate
o Need marami substrate to reach Vmax
• ↓ Km, konting sub lang saturated na enzyme

INHIBITION OF ENZYME ACTIVITY

• Competitive
o ↑ Km; same Vmax
o shift to right
o mahirap maachieve ½ ng Vmax kasi may competition
• Noncompetitive
o same Km; ↓ Vmax
o no shift
• Uncompetitive
• ↑ Km; ↓ Vmax
▪