Biochem Final Exam Cards

Light reactions are specialized reactions that occurs in the thylakoid membrane of a chloroplast. Specialized pigments capture light and become oxidized. In other words, water gets oxidized to produce O2.

2H₂O -> O₂ + 4H·

Site of photosynthesis in eukaryotes.

• Inner membrane containing concentrated solutions of enzymes
• 

• A membrane that contains proteins involved in harvesting light energy, transporting electrons, and synthesizing ATP.
• 

This is the Clavin Benson Cycle and it occurs in the stroma. NADPH provides electrons ATP provides energy to reduce CO2 and incorporate Carbon into 3C precursors.

Process in which e^- from excited chlorophyll is passed through a series of acceptors that convert electronic energy into chemical energy.

• They pass energy of the absorbed energy from molecule to molecule until it reaches the photosynthetic reaction center where the primary reactions of photosynthesis take place.
• 

Electromagnetic radiation is propogated by discrete packets of light known as photons.

E = hv = hc / λ

• 1) Internal Conversion
• 2) Fluorescence
• 3) Excitation / Energy  Transfer
• 4) Photooxidation

Electronegative energy converted to heat (energy drops to lowest energetic state)

• 
• (green = internal conversion)

Molecule gets electronically excited, and as it decays, it emits a photon at a longer wavelength

• 
• (red = fluorescence)

Excited molecule directly transfers energy to nearby unexited molecule with similar electromagnetic properties.

Like in the antenna complex, the light energy is funneled into reaction center, which has a lower excitation energy than surrounding chlorophyll, so the energy stays in reaction center.

This is oxidation caused by light.

Electron is less tightly bound to the donor when in excited state, reducing a nearby molecule.

• 
• 1) Photon gets absorbed by special pair and electron delocalized over BChl molecules (assistant but does not get reduced)
• 2) P960 transfers e- to BChl - > BPheo b-
• 3) e- migrate to menaquinone (Q_A)
• 4) Q_B gets reduced twice to become Q_B^2-
• 5) Q_B^2- takes up 2 protons and become QH₂
• 6) Electron transport from QH₂ to cytochrome bc to cytochrome c and finally to P960+
• 

• 
• -Q_A: Menaquinone
• -Q_B: Ubiquinone
• -L subunit left and M subunit to the right (Electrons primarily transferred through L subunit)
• -Special pair made of 2 BChl molecules that are closely associated with Mg-Mg distance apart (P870 and P960)

• It reduces its photooxidezed special pair with electrons derived from water.
• 
• Oxidation of 2H₂O to O₂ and 4H⁺ eventually produce NADPH as the electrons are transferred by photosystem II.

12 protons enter the lumen for every O2 produced

• Photosystem II: 
• λ < 680 nm for oxidtion of H2O to O2

• Photosystem I:
• λ < 700 nm reduces NADP+ to NADPH

A proton gradient is generated. 

• The mobile electrons carrier Q get reduced to QH₂ allowing for flow of electrons to b₆f complex. As a result, for every electron transferred, 2 protons are translocated into thylakoid membrane. Sine 4 electrons are transferred from H²O oxidation, this leads to * H⁺ entering thylakoid membrane.
• 

Noncyclic: reduce NADP+ to NADPH

Cyclic: contribute to proton gradient

Reduce NADP+ to NADPH

Process: Two reduced Fd molecules successfully deliver 1 e- to FAD of ferredoxin reductase; FAD transfers 2e- and 1 H+ to NADP+ producing NADPH(Z Scheme)

2 NADPH produced for every 2 water molecules

Contribute to proton gradient

Process: e- passed on to ferredoxin returned to heme of cytochrome b6f, allowing translocation of protons across thylakoid membrane, increasing proton gradient.

• -Two BChl molecules that are closely associated at an Mg-Mg distance
• -Named after maximum wavelength absorbance (P870 and P960)

Process: Photon absorbed by special pair is rapidly delocalized, and e- gets transferred to BPheo

Plastocyanin: peripheral membrane protein in thylakoid lumen that mediates electron transfer between cytochrome b₆f and PSI

• -Has a Cu center that changes from Cu(I) to Cu(II) oxidation states
• -Cu(II) in square planar, and strain causes it to easily reduce to Cu(I) and form a tetrahedral
• -Cu is a great electron carrier

NADPH build up clogs up NADPH reductase promoting generation of proton gradient via cyclic pathway.

• -12 protons enter lumen per O₂ created
• -4 ATP produced per O₂ created
• -4 electrons liberated per water molecule
• -2 photons per electron so 8 photons per water molecule

-9 ATP equivalents produced total (2 NADPH made and they are 2.5 ATP equivalents)

• PSII exclusively between closely stacked grana
• PSI exclusively in contact with stroma to access NADP+
• b6f scattered throughout

If PSII was close to PSI, PSII (P680) would absorb photon of PSI (P720) via exciton transfer.

• Light
• -PSII absorbs more light than PSI
• -PSI is slower as a result and plastoquinone primarily in reduced state
• -LHC associate with PSI funneling more light to it

• Darkness
• -In darker lighting, PSI takes up electrons faster and plastoquinone primarily oxidized
• -PHC gets dephosphorylated as a consequence and moves to PSII, funneling more light to it

A light dependent reaction because it takes energy captured from chloroplasts. It's primary purpose is to fix carbon.

• 1) Pentose carboxylated by Rubisco
• 2) Products converted to two G3P (glyceraldehyde-3-phosphate)
• 3) pentose regenerated using ATP and NADPH from light reactions (NADPH used to make GAP and GAP can either regenerate Ru5P or make carbohydrate byproducts)

3 Ru5P used to make 6 GAPs and only one is used for carbohydrate products.

9 ATP and 6 NADPH used from 3 CO₂ molecules.

The energy from light reactions used in Calvin Cycle to GAP

GAP can be converted to...

F6P which can be converted to G1P (uses ATP) to make α-amylose

F6P and UDP-glucose can combine to form sucrose (eventually). The sucrose is used to transport carbohydrates through plant.

Prevents plants from using ATP and NADPH in the night time, where no light is there to make ATP or NADPH.

Light stimulates calvin cycle and deactivates glycolysis.

• -during the day time, pH increases from 7 to 8, and RuBP most active at pH 8
• -proton influx in thylakoid membrane increases [Mg2+] in stroma
• -CA1P binds to RuBP at night and inhibits it

• Activated by:
• -increased pH (light)
• -increased MG2+
• -increased NADPH
• -activated by reduced thioredoxin as a result of influx of light (thioredoxin inhibits PFK, a key enzyme in glycolysis for phosphorylating F6P)

FBPase is a key enzyme in gluconeogenesis and it converts F-1,6-BP to F6P.

SBPase is a key enxyme in Calvine Cycle for Carbon fixation

Opposite of photosynthesis in which O₂ is consumed and CO₂ is produced.

(O₂ consumed to produce CO₂)

O₂ competes for CO₂ in which high levels of O₂ cause RuBisCO to favor photorespiration.

It produces 3PG and wasteful 2-phosphoglycolate which to convert to something useful, it costs 1 ATP and 1 NADH.

BUT it may prevent photoxidative damage.

It is very slow. Around 3 CO2 per second...

It also needs Mg²⁺ to stabilize carbanion. But Mg²⁺ binds poorly to RuBisCO

3 CO₂ + 9 ATP + 6 NADPH -> GAP + 9 ADP + 8 P_i + 6 NADP⁺

FBPase and SBPase are activated by reduced thioredoxin.

Thioredoxin reduced by ferrodoxin-thioredoxin reductase.

Ferradoxin-thioredoxin responds to redox state of ferradoxin in stroma.

Stomata close to prevent water loss. Results in depleated CO₂ and high O₂ levels.

• Low CO2 Levels:
• -RuBP builds up
• -NADPH builds up as it is not used to make GAP
• -ATP builds up as it is not used by Calvin Cycle
• -light energy not dissipated resulting in photooxidative damage (photorespiration)

C4 plants concentrate CO2 in bundle sheath cells, away from mesophyll cells that are exposed to environment.

This prevent photorespiration.

• Consequence:
• 2 extra ATP  used resulting in use of 5 ATP rather than 3 from just Calvin Cycle.

They absorb CO₂ by night preventing H₂O loss.

NADPH

Pentose Phosphat Pathway

From glycolysis, 3 G₆P molecules use 6 NADP⁺ molecules to make 6 NADPH and Ru5P. (Feedback inhibition where NADPH inhibits G6P)

• Overall Reaction for PPP:
• 3 G₆P + 6 NADP⁺ + 3 H₂O ↔ 6 NADPH + 6 H⁺ + 3 CO₂ + 2 F₆P + GAP

3 Ru₅P ↔ R₅P + 2 Xu₅P

• Favorability of either one depends on what the cell needs. 
• Ru5P: cells needs needs nucleotides for biosynthesis
• Xu5P: cell needs key glycotic intermediates
• 

• Overall Reaction for PPP:
• 3 G₆P + 6 NADP⁺ + 3 H₂O ↔ 6 NADPH + 6 H⁺ + 3 CO₂ + 2 F₆P + GAP

2 Xu5P and 1 R5P converted into 2 F6P and 1 GAP (transaldolase and transketolase)

• Overall Reaction for PPP:
• 3 G6P + 6 NADP⁺ + 3 H₂O ↔ 6 NADPH + 6 H⁺ + 3 CO₂ + 2 F₆P + GAP

Every 3 G6P molecules yield 3 Ru5P molecules which yield 2 Xu5P and 1 R5P that can be used to create 2 F6P and 1 GAP.

It fits the Carbon count.

Transketolase: uses thiamine pyrophosphate (TPP). Thiamin ring very acidic and stabilizes the carbanion formed

Transaldolase: stabilizes the movement of electrons to N

High NADP⁺ concentration increases rate of G6PD (step 1) promoting regeneration of NADPH. NADPH inhibits PPP.

Pentose Phosphate pathway is an oxidative pathway and no phosphorylation or dephosphorylation

Calvin cycle is a reductive pathway

Highly branched structure permits rapid glucose mobilization and simultaneous release of glucose units.

It is also not as dense – if it was linear, it would be tightly packed and harder to access.

• The storage form of glucose. It is removed at the non-reducing ends.
• 

Glucose mobilization occurs in a series of conversion of glycogen to glucose-1-phosphate to glucose-6-phosphate.

Glycogen Phosphorylase catalyzes bond cleavage of glycogen by substitution of phosphate group.



Phosphoglucomutase converts G1P to G6P. No ATP needed since it is already phosphorylated.

G6P is actually incapable of passing through the cell membrane.

G6P has to be translocated into the endoplasmic reticulum in which glucose-6-phosphatase converts G6P to glucose.

Glucose leaves liver via transport proteins.

Glucose-6-phoshate is converted to glucose-1-phosphate, then to UDP-glucose and finally to glycogen.

UDP-Glucose Pyrophosphorylase activates glucose through the addition of a UTP producing UDPG, which then gets added to glycogen chain.

• Entire Process:
• Glucose-6-phoshate is converted to glucose-1-phosphate, then to UDP-glucose and finally to glycogen.

Glycogen Synthase UDPG is transferred to C4-OH group of glycogen's non-reducing end.

ATP is then used to restore UDP to UTP.

• Entire Process:
• Glucose-6-phoshate is converted to glucose-1-phosphate, then to UDP-glucose and finally to glycogen.

The direct conversion of G1P to glycogen and P_i is thermodynamically unfavorable (ΔG > 0) under physiological conditions. By combining G1P with UTP, the overall process becomes exergonic. The free energy that comes from the hydrolysis of PP_i can be used to drive the reaction to completion. This process is irreversible.

Glycogenin preps glycogen for the addition of glycogen residue by adding in a primer.

Phosphorylase catalyzes glycogen phosphorolysis (bond cleavage with addition of phosphate group).

It has to be at least 5 units away from the branching point.

Rate-controlling step.

• Allosteric Regulation:
• Muscle Glycogen Phosphorylase is inhibited by ATP and G6P and activated by AMP

Debranching enzyme removes branches making additional glucose residues accessible for glycogen phosphorylase to start adding phosphate groups and cleaving.

Slower the glycogen phosphorylase.

Responsible for converting G1P to G6P

Glycogen synthase is responsible for transferring UDPG to non-reducing end of glycogen.

• Regulation:
• Activated by G6P and ATP (high energy environment)

The branching enzyme is responsible for creating more branches on the glycogen. It transfers a 7 residue segment from end of chain to glycogen residue.

Phosphorylase catalyzes glycogen bond cleavage through addition of phosphate group.

MUSCLE:

• Phosphorylated:
• T State: somewhat active
• R-State: completely active
• (via phosphorylase kinase)

• Unphosphorylated:
• T State: inactive
• R-State: somewhat active

Inhibited by ATP and G6P while activated by AMP.

LIVER:

Completely active in R state. Regulated by glucose casing it to shift to T state (NOT AMP because liver doesn't change with changing energy levels).

Phosphorylated: less active

Un-phosphorylated: more active

Phosphorylase kinase activate glycogen phosphorylase by phosphorylating it.

• Phosphorylated: more active
• -Occurs in alpha and beta subunit
• (Phosphorylation occurs by Protein Kinase A which is activated by cAMP, which is activated by G protein)

Un-phosphorylated: less active (Dephosphorylation by PP1)

Ca2+ binds to phosphorylase kinase and activates it by binding to gamma subunit.

Protein phosphatase is responsible for removing phosphate group on phosphoryl kinase.

1 phosphorylation: active

2 phosphorylation: inactive

Protein phosphatase is responsible for removing phosphate group on phosphoryl kinase.

It is regulated by glucose in the liver.

Low glucose means PP1 is bound to phosphorylase inactivating PP1 and allowing for glycogen breakdown.

High glucose levels cause phosphorylase to shift to inactive T state and PP1 dissociates from it, activating glycogen synthase.

Glucagon: activates glycogen metabolism in the lives

Insulin: activates glycogen synthesis

Epinephrine: stimulate phosphorylation by binding to receptors and sending out cAMP that activates PKA for phophorylation

To be metabolised, fatty acids must be activated.

Fatty acids are activated by Acetyl-CoA Synthetase which attaches coenzyme A to the fatty acid.

This process preserves the high energy thioester bond as well as the endergonic hydrolysis of pyrophosphate fuels the reaction with energy.

Once the fatty acid is activated to fatty acyl-CoA, it is transported into mitochondria for β-oxidation to take place.

For reaction 1, FAD is thought to act as a prosthetic group to acyl-CoA dehydrogenase. FAD is the reduced to FADH2. Electrons are then transferred to ETF, which are then transferred to ETF: ubiquinone oxidoreductase which transfers the electron pair to the electron transport chain by reduction of coenzyme Q.

Results in synthesis of approximately 1.5 ATP.

Fatty acids are activated in cytosol but oxidized in mitochondria.

A long chain fatty acyl cannot cross the mitochondrial membrane

• Solution:
• Carnitine palmitoyl transferase I and II catalyze the addition of a carnitine to fatty acid (Located along external and internal surfaces of mitochondria)

K = 1 for the reaction indicating acyl-CoA hydrolysis similar in free energy to acyl-CoA’s thioester bond

• Oxidation
• Hydration
• Oxidation
• Thiolysis

The end product has 2 less carbons meaning that if the product is not 2-acyl CoA, then the chain can go through the cycle again.

• β-oxidation produces:
• 1 FADH₂
• NADH
• Acetyl-Coa
• Fatty acid chain with 2 less C

• Further oxidation of acetyl CoA via CAC:
• FADH₂
• 3 NADH

Enoyl-CoA Isomerase: converts cis Δ3 double bond to a trans Δ2 form allowing the product through one more round of β-oxidation 

2.4-dienoyl-CoA reductase: reduces Δ4 double bond or in other words a conjugated double bond into 1 double bond

3,5-2,4-dienoyl CoA isomerase: 20% of the time, 3,2-enoyl-CoA isomerase will have an unaniticipated isomerization. This fixed by the isomerization of a 3,5 diene to a 2,4 diene.

Liver mitochondria capable of converting acetyl-CoA into ketone bodies.

Then liver sends ketone bodies to other body parts.

Ketone Bodies are important fuel for heart and skeletal muscles.

In starvation mode, the brain will use ketone bodies.

Ketone bodies can be broken down to acetyl-CoA and acetoacetate.

Acetoacetate can be broken down to D-β hydroxybutyrate which can decompose into CO2 and acetone.

Reverse can occur and Succinyl-CoA can be made from acetyl-CoA.

Fatty acid biosynthesis occurs through condensation of C2 units in reverse β-oxidation process.

Instead of CoA added, the reaction involves addition of ACP

Malonyl-CoA and Bicarbonate.

The acetyl-CoA used to make malonyl-CoA comes from oxidative decarboxylation of pyruvate, or oxidation of fatty acids.

Biotin is a necessary substrate for synthesizing malonyl-CoA by acetyl carboxylase

β-oxidation: occurs in mitochondria

Fatty acid biosynthesis: occurs in cytoplasm

ACP creates a thioester bond with an acyl group.

Connection made with ser-OH not AMP

• Condensation
• Reduction
• Dehydration
• Reduction

Process is NADPH dependent (2 per acetyl-CoA)

Fatty Acid Synthase is responsible for the entire process of fatty acid synthesis. 

Also two fatty acids can be synthesized at once.

12 is max

Elongases

Terminal Desaturases are responsible for desaturating fatty acid chains.

• Δ9-, Δ6-, Δ5-, Δ4-
• Y – only saturated
• X – can be saturate (5+)

Palmitic acid is the shortest available fatty acid.

Linoleic acid (12 bonds) is essential for creation of key precursors of prostaglandis and eicosanoids (essential for skin permeability)

Pyruvate gets converted to oxaloacetate, the acetyl-CoA combines to form citrate, leaves the mitochondria.

Citrate gets converted to oxaloacetate, then malate, finally pyruvate, only to be transferred back into mitochondria.

Fatty acids are derived from lipase-catalyzed hydrolysis of triacylglycerols, which are composed of a glycerol backbone esterified with three fatty acids.

Triaglycerols are major metabolic energy storage for humans.

• Epinephrine – phosphorylates and inactivates
• Glucagon - phosphorylates and inactivates
• Insulin - dephosphorylates and activates

Ubiquitination: ATP requiring process that is independent of lysosome activity.

Proteins get marked by ubiquitin covalently that indicates degradation.

In order for a protein to be degraded, it must be linked to a chain of at least 4 ubiquitin molecules.

There are destabilizing signal residues on the N-terminal residues that increase chance of residue getting ubiquitinated.

PLP coenzyme

When PLP accepts a N it becomes PMP. This is a reversible process.

• WHY ADD IT?
• To act as an electron sink, stabilizing a carbanion via resonance throughout the molecule (stabilize negative charge on α-carbon)

Facilitates bond cleavage during tautomerization

• Stage I
• Converts amino acid to α-keto acid
• Transamination: Amino acids nucleophilic amino group attacks Enzyme-PLP Schiff base, forming amino acid-PLP Schiff base
• Tautomerization: amino acid-PLP Schiff base tautomerizes to an α-keto acid-PMP (stabilized via resonance)
• Hydrolysis: α-keto acid-PMP Schiff base hydrolyzed to PMP and an α-keto acid

• Stage 2
• Converts α-keto acid into an amino acid (to complete the cycle, PMP must be converted back to enzyme-PLP Schiff base which is same reaction on reverse).

-PMP reacts with α-keto acid to form Schiff base

-Α-keto acid-PMP Schiff base tautomerizes to form amino acid-PLP Schiff base

-Amino group of enzyme attacks amino acid-PLP Schiff base in transamination reaction and releases the amino acid

Transamination does NOT result in net deamination.

Glutamate dehydrogenase is capable of catalyzing oxidative deamination of glutamate yielding ammonia and an α-ketoglutarate

Catalyzes deamination.

Only enzyme capable of accepting either NAD+ or NADP+ as a redox coenzyme

Allosterically inhibited by GTP and NADH (signally abundant energy)

Activated by ADP and NAD+ (signaling need of energy)

Since α-ketoglutarate is an intermediate of the citric acid cycle, glutamate dehydrogenase stimulates citric acid cycle

• Occurs in three different ways:
• 1 – simply excrete ammonia (aquatic animals)

2 – convert ammonia to urea (terrestrial vertebrates). Conversion occurs in the liver via urea cycle then transported to the bloodstream, and finally sequestered by kidneys to be excreted in urine

3 – convert ammonia to uric acid (terrestrial reptiles and birds)

• Carbamoyl phosphate synthetase (CPS) catalyzes condensation and activation of NH3 and HCO3- to for carbamoyl phosphate with a 2 ATP commitment.
• 

• CPS I: uses ammonia as its N donor and participate in urea biosynthesis
• -Rate limiting, irreversible
• -All occurs in 100 Å tunnel (channeling)

• 1 - ATP activates HCO3-
• 2 – ammonia attacks carboxyphosphate, displacing phosphate
• 3 – second ATP phosphorylates carbamate

• CPS II: uses glutamine as its N donor and involved in pyrimidine biosynthesis

Step 1 and 2 of urea cycle occur in the mitochondria

Ornithine and must be transported into membrane

• Citrulline must be transported out of mitochondrial membrane
• All other steps occur in cytosol

• Process:
• Arginosuccinate to arginine

• What does it do?
• Produces fumerate that can be converted to malate, then to oxaloacetate and used for gluconeogenesis

By substrate build up.

CPS I allosterically regulated by N-acetylglutamate (made from glutamate and acetyl CoA)

Glucogenic amino acids: amino acids that degrade into glucose precursors (green)

Ketogonenic Precursors: amino acids that degrade to fatty acids and ketone bodies (red)

• Tetrahydrofolate:
• Adds single carbon unit to molecules. The C is acquired from converting Ser to Gly.

More versatile than SAM because it can transfer methyl group in several oxidation states.

Has a biotin prosthetic group.

• S-adenosylmethionine (SAM):
• Results from methionine degradation in presence of ATP.

Methyl donor

Synthesizes homocysteine (rates depend on SAM)

Synthesized from methionine

• Carbon skeletons for amino acid biosynthesis comes from: 
• -Glycolysis
• -Pentose phosphate pathway
• -Citric acid cycle

• Essential: have to be obtained from plants
• Nonessential: amino acids that can be synthesized by mammals

Regulated by allostery and adenylation

• Inhibited by (use glutamine)
• His
• Trp
• Carbamoyl phosphate
• Glucosamine-6-phosphate
• AMP
• CTP

• Inhibited by (use nitrogen):
• Ala
• Ser
• Gly

• Activated by:
• ATP 
• α-ketoglutarate

High glutamine levels deactivate as well as low N environments. But low N environments lead to irreversible damage of enzyme.

3 step reaction involved in reducing N2 to NH3.

• 2 protein complex:
• -Fe-protein (reductase) with a 4Fe-4S cluster and 2 ATP binding sites
• -MoFe-protein (nitrogenase)

Nitrogenase: reduces N₂ to NH₃

Fe-protein (reductase) with a 4Fe-4S cluster and 2 ATP binding sites

MoFe-protein (nitrogenase)

Role of MoFe dimer:

• Electron transfer: Electrons stored at P cluster (FeMo αβ dimer)) and transferred to FeMo cluster (nitrogen reduction center)
• Extremely sensitize to O2

• Electron transfer occurs 3 times per N2 molecule (requires 12 ATP)
• 

12 ATP

To store nutrients in form of protein

Eliminate abnormal proteins

Eliminate excess proteins and regulatory proteins

Formed from activation of ribose with an ATP molecule to form PRPP.

• Glutamine
• Glycine
• Aspartate

• Aspartate
• Glutamine

Nucleoside diphosphates and triphophates are synthesized via phosphorylation of monophosphates

Nuceloside monophosphates must be converted to nucleoside triphophates in order to be used for nucleic acid synthesis

PRPP activates IMP production. It is inhibited by ADP and GDP (5-phosphoribosylamine activated by PRPP)

• IMP competitively inhibited by AMP and GMP in order to prevent over creation of GTP or ATP (balance)
• (Rate of AMP production increases with GTP / Rate of GMP production increases with ATP)

Class I ribonucleotide reductases are responsible for catalyzing the formation of deoxyribonucelotides via reduction of specific ribonucleotides.

I.e. Reduce NDPs to dNDPs

Have a Fe and MN prosthetic group. The tyrosyl radical is generated by Fe³⁺-O₂^--Fe³⁺ center

Reduced form Cys 225 and 462 in SH forms Cys 462 buried in hydrophobic pocket

Oxidized form Cys 335 and 46s in disulfide link

Thioredoxin reduces oxidized RNR. NADPH serves as a reducing agent.

• Importance:
• When substrate is bound the radical gets transferred to it

If substrate binds and is unable to react due to enzymes oxidized state, then the radical could potentially destroy entire enzyme and substrate

Thymidylate synthase transfers methyl group to dUMP to form thymine

Transferred methylene group reduced to methyl group at expense of oxidation of THF cofactor to DHF

No other folate requiring reaction alters oxidation state of cofactor

dTMP synthesis critical for cancer cells

interrupting dTMP synthesis can kill proliferating cells

Inhibition of DHFR blocks dTMP synthesis

DHF analogs bind to DHFR to stop proliferation of cells

• Ring is catabolized to:
• -Malonyl CoA (fatty acid synthesis)
• -Methylmalonyl CoA (succinyl CoA in CAC)

Increase in glucose relative to the cells around it. As the glucose goes through glycolysis, instead of going through the CAC, it ferments glucose to lactate under aerobic conditions.

• 1) Rapid ATP synthesis
• 2) provides precursors for biosynthesis
• 3) Enforce favorable tumor environment
• 4) Controls reactive oxygen species

• Pro:
• There is an increase in ATP dependent ion pumps

• Con:
• There is actually less ATP requirements in a proliferating cell in comparison to a regular cell

• Pro:
• -There has been observed increase in serine production from 3-PG (3-phosphoglycerate)
• -It has revealed that formation of serine from Gly increase N5,N10 methylene THF. This is important for synthesis of deoxynucleotides
• -Maybe cancer needs in energy in form of reducing power
• -Biosynthesis of NADPH from ribose-5-phosphate

• Con:
• -Most of the carbon ends up in lactate
• -There is a very little change in the number of mitochondria
• -Increasing glycolysis enzymes is inefficient (Cell is already extremely packed)

• Pro:
• -Lactate export decreases surrounding pH
• -Decreasing pH increases invasiveness
• -Increased glucose uptake in cancer can starve surrounding cells

• Con:
• -Warburg effect in cells is turned on very early, not when cells become invasive
• -Unicellular yeast prefers aerobic glycolysis and they are not cancer

Less mitochondrial use, means that the electron transport chain utilization is lowered resulting in fewer oxygen species

Cell life damaged less frequently because oxygen radicals are very damaging

Acetylation of PKM2 has shown to decrease PKM2 activity

Acetylation increases lysozyme affinity to PKM2

Overexpressed in proliferating cells

Pyruvate dehydrogenase (PDH) controls overexpression or pyruvate to acetyl-CoA

Phosphorylation of PDH by PDK decreases PDH activity, switching from mitochondrial respiration to cytoplasmic glycolysis

PKM1 is expressed in most adult tissues, while PKM2 is exclusively expressed during embryonic development. Notably, most tumor cells switch from PKM1 to PKM2 expression may be beneficial to tumor cells. Indeed, switching from PKM2 to PKM1 reverses aerobic glycolysis, providing the selective growth advantage of PKM2 expression for tumor cells in.

Overexpression of PKM2 leads to decrease in PK activity

Inhibition of PK increases glycolytic metabolites that can be used for biosynthesis

In dimeric form, PKM2 can be transported into nucleus to become PK

Phase I metabolism of drugs:

• Role of cytochrome P450 enzymes (CYPs):
• Biotransformation of drugs into less lipid soluble forms
• RH + O₂ + 2H+ + 2e^- → ROH + H₂O
• (adds hydrocrbon)

• Phase II metabolism of drugs:
• Conjugation of the drug, which is adding a large anionic group
• Increases molecular weight, and makes it so they have to be actively transported out.

• Role of UDP-glucuronosyl transferases (UGTs)
• Catalyzes the addition of glucuronic acid moiety to xenobiotics (Major pathway in foreign chemical removal)

Low Phase 1 rate may increase effect of chemotherapy because the drug does not get fully broken down before it reaches the cancer cell

If it is broken down too fast it can’t reach the cancer cell fast enough to have an effect