Biochem Sem 2 Ses 9-11 (Quiz 3)

Metabolism

Highly coordinated cellular activity

Metabolism Goals

• Obtain chemical energy

• Convert nutrient m. to cells characteristic molecules (form metabolic intermediate)

• Degrade (turnover) biomolecules (reuse m.)

Anabolism

Simple to complex molecule building, requiring energy. (carbon reduction)

Catabolism

Complex to simple molecule breakdown, releasing energy. (carbon oxidation)

Human Metabolic Map

• Maintain homeostasis

• Interdependent, enzyme coordinates activity

Homeostasis

Stable biochemical environment

Oxidoreductase

Enzyme that catalyzes the transfer of electrons.

Transferase

Enzyme that catalyzes group transfer reactions.

Hydrolase

Enzyme that catalyzes hydrolysis reactions using water.

Lyase

Enzyme that catalyzes the addition of groups to double bonds or removal of groups to form double bonds.

Isomerase

Enzyme that catalyzes the transfer of groups within a molecule to yield isomeric forms.

Ligase

Enzyme that catalyzes the formation of CC, CS, CO, CN bonds by condensation reaction coupled to ATP cleavage.

Compartmentalization Metabolic Processes

Benefits of Compartmentalization

• To increase efficiency → since substrate maintained at certain concentration

• If the reaction produces toxic byproducts, it wont harm the rest of the reaction

What happens if there is no compartmentalization?

• Interference of pathways (intermediates for 1 pathway can be consumed by another)

• Substrate competition (enzymes might compete for same substrate, disrupts the metabolic balance)

• Enzyme inhibition (regulatory m. and inhibitors might interact with enzyme, disrupt metabolic regulation)

• Misrouting metabolites (metabolite might not reach the target organelle)

Bioenergetics

Quantitative study of energy transduction in living cells and the nature and function of chemical processes underlying the transductions.

Non-biological system

Heat energy for work

Biological system

Chemical energy for living processes

Starvation

Energy reserves depleted

Obesity

Excess storage surplus energy damages health

Cell = Open System

• Heat exchange = metabolic reactions generate heat

• Matter exchange = nutrient enter, waste product exit dr plasma membrane

First Law of Thermodynamics

Energy cannot be created or destroyed, only converted to other forms.

Second Law of Thermodynamics

All energy transformations are inefficient, every reaction leads to an increase in entropy and loss of usable energy as heat.

Consequence Thermodynamic Laws

• System move dr ordered to disordered

• All processes tend to move toward equilibrium

• Entropy same for reversible processes + increase irreversible processes

Gibbs Free Energy (G)

Energy for cells to do work.

Enthalpy (H)

Heat content of a reacting system.

Exothermic

Reactions that release heat (ΔH -) (∆G -)

Endothermic

Reactions that absorb heat (ΔH +) (∆G +)

Entropy (S)

Randomness/disorder of system

• a+b < c+d, ΔS positive = entropy ↑, product less complex, more disordered

Equilibrium Constant Formula

Free energy change (not at equilibrium) formula

Is there free energy change at equilibrium?, whats the formula?

No, the formula for this is  T∆S = ∆H

How much is 1 cal in Joules?

1 cal = 4184 J

What are the units of absolute temperature? T

Kelvin (K)

25^oC = 298 K
25^oC, RT = 2.478 kJ/mol = 0.592 kcal/mol

Units for Thermodynamics

• faraday constant = 96480 J/V.mol = 96.5 kJ/V.mol!!!

∆G

Actual free energy change, unit is J/mol or kJ/mol or cal/mol

• ∆G+ = non spontaneous, non-favorable, endergonic

• ∆G- = spontaneous, favorable, exergonic

∆G⁰ (kJ/mol)

Free energy difference in standard conditions (T = 25^oC, P = 1 atm, any pH).

∆G^’0 (kJ/mol)

Standard free energy change at transformed conditions (T = 37 or 25^oC, pH= 7).

∆G^’0 and the Direction of a Reaction

∆G Formula

*can change the ∆G⁰ for ∆G^’0 (tergantung condition)

R = 8.315 J/mol.K = 0.008315 kJ/mol.K

T = celsius to kelvin = +273

Practice Question 1

Answer:

Additive Free Energy Changes

Practice Question 2

• What is the reaction? exergonic/endergonic? spontan/non spontan? is it favorable?

• Make the additive free energy

Answer:

ATP

Major energy currency of the cell, connecting catabolism and anabolism.

• Ribonucleotide

• Produced in exergonic, consumed in endergonic

• Consists of: adenine, ribose, phosphate

ATP Hydrolysis

1. Hydrolysis dr charge separation (relieve electrostatic repulsion)

2. Pi stabilized by resonance hybrid

3. ADP^2- ionizes at pH 7 ,release proton, lowering pH

4. Greater solvation of Pi and ADP relative to ATP

Phosphorylation Potential (∆GP)

Standard free energy of ATP hydrolysis.

(∆G_’0) = -30.5 kJ/mol

Practice Question 3

Answer:

How does ATP donate Phosphoryl, Pyrophosphoryl, and Adenylyl Groups?

ATP drive unfavorable reaction by coupling group transfer (phosphoryl, pyrophosphoryl, or adenylyl) to a substrate/enzyme

- The 3 phosphates are susceptible to nucleophilic attack

Phosphoryl Group Transfer

• 2 step reaction

• ATP conc far above equilibrium conc. = maintain high group transfer potential → By energy yielding reactions (catabolism)

• ATP → ADP + Pi → ATP (ATP/ADP cycle)

• ATP = donor high energy phosphate

• ADP = accept high energy phosphate, to form ATP

Cellular Roles of ATP

• Power anabolic reactions

• Active transport m. and ions across membranes

• Other energy intensive processes (muscle contraction)

• ATP → ADP = motion, active transport, biosyntheses, signal amplification

• ADP → ATP = oxidation fuel m./ photosynthesis

OIL RIG (REDOX)

Oxidation is losing electrons, reduction is gaining electrons.

• Reducing agent = oxidation

• Oxidized agent = reduction

Reduction Potential (E)

Tendency of a reaction to occur as a reduction reaction (thermodynamic reactivity)

• Reduction potential = measure of electron affinity

• Dependent on conc. reactant and product

Explanation:
yg 2O2 itu reduction = gain e- di product
yg ethanol itu oxidation = lose e- di product

What happens when you combine 2 reactions in REDOX?

• When you combine 2 reactions:

• Large reduction potential = reduction

• Smaller reduction potential = oxidation

Idiot explanation:

• Higher e sel (E⁰’) = reduction

• Lower e sel (E^0’) = oxidation

• Yg reduction itu yg E^’0 nya lbh gede (V)

• Klo misal dia reduction tp reactionny rn itu oxidation, gausah flip the reaction or e sel nya. Asal tau aja dia itu oxidation or reduction buat rumus delta e sel

oxidation = anode = donor

reduction = cathode = acceptor

ekat-eano

What is the reduction potential (E⁰) for standard and in human? (e selnya)

• E^o standard = 25^oC, 1 M

• E^o in human = 37^oC

Reduction Potential Formulas (E^0') (e sel)

• klo misal reactionny di flip jdny symbol ke flip jdnya rumus deltaE0’ nya juga ganti jd E kat + E ano (E red + E ox)

Hubungan Reduction Potential and Free Energy Formulas

Practice Question 4

Answer:

Glucose Oxidation

Source of energy klo complete

Reaction:

• Multiple steps, catalyzed by specific enzymes

• Oxidation and reduction 2 major carrier e- =  NAD⁺/NADP⁺ and FAD/FMN

NAD⁺ and NADH

As reducing agents:

• Substrate = double dehydrogenation (oxidation)

• NAD⁺/NADP⁺ = accept hydride ion (H^-), release H⁺ to environment

FAD, FMN, Flavoproteins

• Flavoproteins = enzymes yg use FMN/FAD cofactor in redox reactions

• FAD/FMN = either accept 1/2 hydrogens (1/2 e-) → more versatile dr NAD⁺/NADP⁺

• Fully reduced forms = FADH₂ and FMNH

Stages Catabolism

• Stage 1 = large m. food breakdown jd small unit (digestion)

• Stage 2 = small m. degraded jd simple units → play central role in metabolism → jd acetyl-CoA

• Stage 3 = ATP produced dr complete oxidation acetyl unit acetyl-CoA

Digestion of Carbohydrates

Sugar → Intestine wall → Bloodstream → Cells in body

• End product = monosaccharides → transported thru passive diffusion transmembrane proteins

Major Pathways of Glucose Utilization

Glycolysis

• Metabolic pathway

• m. glucose degraded in series of 10 enzyme catalyzed reactions to yield 2 m. of 3C compound pyruvate

• Greek, glykys = sweet/sugar, lysis = splitting

• Major fuel most organism = rich in potential energy 

  • Complete oxidation glucose → CO₂ + H₂O (∆G⁰ = -2.840 kJ/mol)

• 1 Glucose = 2 pyruvate 

• Free energy released in form of ATP and NADH

• Glycolysis in the cytosol of cells

Glycolysis Phases

• Linear metabolic pathway, reversible irreversible

• 2 phases = preparatory, payoff

• Important steps: 1,3,10

Phosphorylated Intermediates in Glycolysis

• 9 glycolytic intermediates between glucose and pyruvate = phosphorylated

• pH 7 = phosphate group ionized, glycolytic intermediates net negative charge

• Phosphorylation traps intermediates inside the cell (impermeable due to negative charge).

• Conserves energy via phosphate ester formation.

• Enables ATP generation by transferring phosphate to ADP.

• Lowers activation energy and increases enzyme specificity by binding phosphate groups to enzyme active site.

IN A NUTSHELL

• Traps glucose inside the cell (prevents it from exiting)

• Prepares it for further breakdown by making it more reactive

Preparatory Phase Glycolysis

Each m. glucose:

• Hasil akhir = 2 glyceraldehyde 3-phosphate

• Consume = 2 ATP

Steps:

1. Phosphorylation glucose

2. Conversion glucose 6-phosphate → fructose 6-phosphate

3. Phosphorylation fructose 6-phosphate → fructose 1,6-bisphosphate

4. Cleavage fructose 1,6-bisphosphate → dihydroxyacetone phosphate + glyceraldehyde 3-phosphate

5. Interconversion triose phosphate jd glyceraldehyde 3-phosphate

Step 1 - Phosphorylation glucose

• Phosphorylate glucose C6 → form glucose 6-phosphate 

  • ATP phosphoryl donor = active glucose for reactions

• Hexokinase = high affinity (low K_m) for glucose → phosphorylate all glucose in cell, maintain large glucose gradient

• Irreversible under physiological conditions

Step 3 - Phosphorylation of fructose 6-phosphate to fructose 1,6-bisphosphate

• Regulate PFK-1 (phosphofructokinase-1)

  • ATP supply depleted or ADP/Pi excess → PFK-1 activity increase

  • Cell many ATP, supplied by other fuels kek fatty acids → PFK-1 activity decreased

• Irreversible

Payoff Phase Glycolysis

2 glyceraldehyde 3-phosphate:

• Hasil akhir = 2 pyruvate

• Produce =

  • 4 ATP (net yield 2 ATP per m. glucose jd pyruvate)

  • 2 NADH

Steps:

6. Oxidation glyceraldehyde 3-phosphate + Pi → 1,3-bisphosphoglycerate

7. Phosphoryl transfer 1,3-bisphosphoglycerate → ADP forming ATP + 3-phosphoglycerate

8. Conversion 3-phosphoglycerate → 2-phosphoglycerate

9. Dehydration 2-phosphoglycerate → phosphoenolpyruvate

10. Transfer phosphoryl group PEP → ADP to form ATP + pyruvate

Step 10 - Transfer phosphoryl group dr PEP to ADP

• Phosphoenolpyruvate + ADP → pyruvate + ATP w/ pyruvate kinase

• Product pyruvate (enol) undergo tautomerization jd pyruvate (keto form, pH 7)

Balance Sheet Glycolysis

Fates of Pyruvate

• regenerate NAD⁺ dr NADH → to lanjut glycolysis

Lactate Fermentation and Cori Cycle

• Hypoxic/ anaerobic condition = NADH gbs reoxidized

• Lactate dehydrogenase = use NADH to reduce carbonyl pyruvate to secondary alcohol in lactate

• Cori cycle = lactate produced in muscle balik jd glucose in liver

Alcohol Fermentation

• To make alcohol drinks, industrial ethanol, CO2 to rise bread (yeast)

• Alcohol dehydrogenase = metabolize ethanol to acetaldehyde to be further metabolized

Energy Efficiency Anaerobic Fermentation

Breakdown Glycogen to Supply Glucose

• Glycogen = sugar in muscle

• Glycogen phosphorylase = catalyze attack w/ inorganic phosphate on terminal glucosyl residue at nonreducing end glycogen m.

  • Release glucose 1-phosphate

  • Glycogen m. shortened by 1 glucose residue

  • Phosphorolysis reaction = break linkage + add phosphate m.

Metabolic Regulation Glycolysis

• Non-equilibrium, exergonic, irreversible reactions

Step 1 Metabolic Regulation Glycolysis

• Step 1: Hexokinase = glucose + ATP → glucose 6-phosphate + ADP

• Inhibited by glucose 6-phosphate (negative feedback)

• PFK-1 inactive, fructose 6-phosphate accumulate → jd glucose 6-phosphate (inhibit hexokinase)

Step 3 Metabolic Regulation Glycolysis

• Step 3: Phosphofructokinase-1 = fructose 6-phosphate + ATP → fructose 1,6-bisphosphate + ADP

• Most important regulatory point (pacemaker glycolysis)

• Glucose 6-phosphate = synthesize glycogen

• PFK-1 activity = first committed step catabolic pathway glycolysis

Step 10 Metabolic Regulation Glycolysis

• Step 10: Pyruvate kinase = PEP + ADP → Pyruvate + ATP

• Inhibited by ATP = allosteric inhibition

• Inhibited by alanine = to signal udh cukup building blocks (dr TCA cycle)

• Activated by = fructose 1,6-bisphosphate = allosteric activation biar keep up sm pathway

Glycolysis Regulation in Muscle Fibers

Regulation PFK

• Activated by AMP, inhibited by ATP = bound to allosteric sites

  • ATP/AMP ratio = energy state cell

• Inhibited by low pH = lactic acid accumulation (anaerobic resp)

How does DM1 Interfere with Glycolysis

DM1 = high glucose + ketone in blood = ketoacidosis

Gluconeogenesis

DEF: metabolic pathway, regenerates glucose dr non-carb carbon substrates

• Gluco = glucose, neo = new, genesis = synthesis

• Useful klo starvation, kerja in liver

• Major inputs:

  • Lactate dr glycosis (lactate dehydrogenase)

  • AA dr protein breakdown (starvation)

  • Glycerol dr lipid breakdown

• Fatty acid gbs make glucose in mammals → krn lack of glyoxylate cycle

• Function:

  • Maintain blood glucose lvl

  • Ensure glucose supply ke high demanding tissues (muscle,brain)

  • Alleviate starvation

Steps Gluconeogenesis

Difference w/ glycolysis 

• Gluconeogenesis g use reaction 10

• Uses diff enzymes to reverse reaction 1 and 3

Reaction 1 Gluconeogenesis

Reaction 1 - glucose 6-phosphatase

• Mg²⁺ dependent, irreversible

• Enzyme g ada di brain and muscle, tissues can't make glucose (glucose dr blood)

• Glucose 6-phosphate + H₂O → glucose + Pi

Reaction 3 Gluconeogenesis

Reaction 3 = fructose 1,6-bisphosphatase (FBPase-1)

• Mg²⁺ dependent, irreversible

• Remove phosphate

• Fructose 1,6-bisphosphate + H₂O → fructose 6-phosphate + Pi

Reaction 10 Gluconeogenesis

1. Pyruvate ke mitochondria/ make pyruvate dr alanine in mitochondria

2. Pyruvate carboxylase = ubah pyruvate → oxaloacetate (need ATP+biotin)

   • Pyruvate + HCO^-₃ + ATP → oxaloacetate + ADP +Pi (irreversible)

3. Oxaloacetate back ke cytosol 

4. PEP carboxykinase. Use GTP to push along

   • Oxaloacetate + GTP → phosphoenolpyruvate + CO₂ + GDP

Gluconeogenesis Locations

• In the Mitochondria

  • Pyruvate + ATP → Oxaloacetate + ADP + P

  • Oxaloacetate + NADH → Malate + NAD⁺ 

  • Convert malate = m. keluar mitochondria

  • In cytoplasm balik lg jd oxaloacetate

• In Cytoplasm

  • Malate + NAD⁺ → Oxaloacetate + NADH

  • Oxaloacetate + GTP → PEP + GDP

• In Endoplasmic Reticulum

  • G6P → glucose (catalyst: glucose 6-phosphatase

  • Glucose transporter keluarin glucose ke extracellular space

Cori Cycle

• Fast twitch muscle fiber = fast rate contraction, use O2 quick, anaerobic glycolysis metabolism

• Lactate transferred by RBC

Gluconeogenesis dr AA + Protein Mobilization

• Protein mobilization = 

  • Most dietary AA

  • Structural protein last source material gluconeogenesis

  • Glucogenic AA enter gluconeogenesis (dr pyruvate/TCA cycle intermediates)

Gluconeogenesis from Lipids

• Fat mobilization = 

  • During shortage liver glycogen (long starvation)

  • Glycerol kinase expressed

• Dihydroxyacetone phosphate (DHAP) = glycolytic intermediate 

  • Synthesize glucose dr gluconeogenesis = maintain blood glucose levels

Glucoseneogenesis vs Glycolysis Energy Expenses

Pentose Phosphate Pathway (PPP) Roles

Role of PPP:

• To make NADPH (nicotinamide adenine dinucleotide phosphate)

  • To put reducing equivalents to biosynthetic pathways

  • Catabolism = carbon oxidation, anabolism = carbon reduction

  • Perlu buat di cells synthesizing fatty acid/steroids

• To make 5C sugars

  • Ribose synthesis RNA DNA

  • Increase activity growing tissue + tumor (rapid cell division)

Nonoxidative Phase PPP

• Shuffle three 5C sugars to two 6C sugars + glyceraldehyde 3-p

• For tissues generating NADPH

Metabolic Control of PPP by NADPH

• NADPH = regulate partitioning glucose 6-phosphate between glycolysis and PPP 

• When NADPH form faster than kepake for PPP:

• NADPH rises, inhibit first enzyme in PPP (G6PD)

• Results in more glucose 6-phosphate for glycolysis

Pathway Integration in an Active Muscle

Cellular Respiration

• Klo ada O2 (aerobic conditions) → more energy didapet dr pyruvate (ATP)

• Aerobic condition = pyruvate dr cytoplasm → mitochondria → jd acetyl coA + CO2

  

Aerobic vs Anaerobic Respiration (Fate of Glucose)