Chapter 5 the Working Cell

Chapter 5 Working Cell

Thermodynamics Metabolism Anabolism – synthetic pathways Catabolism – degradation pathways

Role of ATP – cell’s fuel source

Enzymes – special proteins (3-dimensional conformation = tertiary structure) that function to catalyze (make reactions go faster) the bio-reactions that occur in the cell Lock and key theory Active site: that is the location where the substrate binds with the enzyme Competition (between substrates)

Energy Light (from sun) -> 1% of light energy transformed into chemical energy via photosynthesis Sound Kinetic – energy of motion Potential – energy of “inertia”/build-up Electrical Chemical Heat Mechanical Nuclear Energy Total Energy = Kinetic + Potential

Laws of Thermodynamics (heat flow)

Zeroth Law: If A is in thermal equilibrium with B and B is in thermal equilibrium with C, A is in thermal equilibrium with C

First Law: energy can neither be created nor destroyed Total energy of universe is constant Conservation of Energy

Second Law: can transform one energy form to another but NOT at 100% efficiency

Enthalpy, H -> heat Entropy, S -> degree of order; degree of chaos Higher entropy, the lower the order Lower entropy, the higher the order Gibbs Free Energy, G Temperature, T (in degrees Kelvin) K = C + 273.15

Third Law: S = k ln(W) k = Boltzmann’s constant

ΔG = ΔH –TΔS 2nd law of thermodynamics

In the cell, we will have chemical reactions Reactants Products A + B -> C + D Reactants Products Substrates

ΔG < 0, reaction occurs spontaneously Exergonic reactions (energy released)

ΔG > 0, reaction does not occur spontaneously Endergonic reactions (energy required)

Endergonic reactions are coupled with exergonic reactions

ΔH < 0, exothermic reaction (heat released) ΔH > 0, endothermic reaction (heat required)

Energy of reactants versus energy of products

Example of Endergonic reaction Example of Exergonic reaction

Coupled reactions In cell, one reaction provides energy (exergonic) and will be coupled to a reaction that requires energy (endergonic)

Cellular respiration Glucose + oxygen -> carbon dioxide + water + energy

Glucose: carbon dioxide /water More organized less organized More potential energy less potential energy Less stable (entropy) more stable (entropy) [many reactions just to accomplish the overall reaction] Glycolysis, Krebs Cycle, Electron Transport Chain, Chemiosmosis]

Photosynthesis Carbon dioxide + Oxygen + energy-> glucose + water

[many reactions just to accomplish the overall reaction] Electron Transport Chain, Chemiosmosis, Calvin Cycle

ATP: Adenosine Triphosphate Synthesis of ATP ADP + Pi -> ATP Adding that phosphate: phosphorylation ATP functions to have … Chemical work ( reactants to products and reverse: products to reactants) Mechanical work ( motion) Transport work ( molecules across the membrane)

ATP Cycle ADP + Pi ATP

Hydrolysis: breaking ATP -> releasing energy for endergonic reactions Coupled reactions

Phosphorylation -> energy will be received from exergonic reactions

Enzymes – biological catalysts of the cell -Speed up a reaction in the cell -Made up of protein -The tertiary structure of the enzyme helps to determine its functionality -Reduce the energy barrier -optimal T conditions Below optimal T – rate of enzymatic reaction is lower Above optimal T – rate of enzymatic reaction is lower -optimal pH Below optimal pH – rate of enzymatic reaction is lower Above optimal pH– rate of enzymatic reaction is lower -change optimal conditions Add heat; add cold; add salt; add H+ Can lead to denaturation of the protein’s structure (changed the 3-dim structure of the protein/enzyme)

-suffix “ase” DNAase, RNAase, Lipase, Endopepsidase, Glucose-6- Phosphatase Not all have “ase” suffix: Pepsin, Trypsin

Metabolic Pathways

E1 E2 E3 E4 E5 E6 A -> B -> C -> D -> E -> F -> G

Enzyme reacts as follows:

S + E -> E-S -> P + E

Substrate + enzyme -> enzyme substrate complex 3-dimensional shape of the enzyme is fashioned to fit the substrate Enzyme has an “active site”: site where the substrate will bind to the enzyme

Enzymes are specific for their substrate

Enzymes are proteins and they have specific amino acid sequence (Note: amino acid sequence is not correct -> enzyme’s activity can be affected)

Cofactors and coenzymes (“A little help from my friends” – see Sgt Pepper’s Lonely Heart Club Band – The Beatles)

Co-factors: non-protein in structure; inorganic elements/ions: zinc, calcium, magnesium, iron

Co-factor: organic -> co-enzyme (e.g., Vitamin B6) Presence of Salts -> salt concentration can influence the activity of an enzyme

Enzyme Inhibition

Competitive: another substrate, which is similar to the substrate that the enzyme normally binds to, will bind with the enzyme

S1 (normal) S2 (similar in structure to S1)

Both S1 and S2 are competing to enter into the enzyme’s active site To overcome this type of inhibition – flood the enzyme with more S1 (normal substrate) Non-competitive: another substrate will bind to another site on the enzyme (not the active site), thus changing the conformation of the enzyme (shape) and then precluding the normal substrate from binding to the “active site” Feedback inhibition Biochemical pathway –from S1 to S6, all of which is enzyme mediated E1 S1 -> S2 -> S3 -> S4 -> S5 -> S6

Once S6 accumulates, then it will combine with the enzyme responsible for S1

Poisons, pesticides, drugs that can act as enzyme inhibitors KCN, HCN, CO Enzyme denaturation – shape of the enzyme has changed such that it can no longer combine with its intended substrate (3-dimensional conformation/tertiary structure has changed) reversible

Native structure – denatured structure

Oxidation-Reduction and Flow of Energy

Photosynthesis (green plants)

6CO2 + 6H2O + ENERGY C6H12O6 + 6O2

Coenzyme: NADP+ Nicotinamide adenine dinucleotide phosphate

NADP+ + 2e- + H+ NADPH

Cellular Respiration (eukaryotic organisms)

Coenzyme: NAD+ Nicotinamide adenine dinucleotide Flavin adenine dinucleotide

C6H12O6 + 6O2 6CO2 + 6H2O + ENERGY

NAD+ + 2e- + H+ NADH + - + 2FAD + 2e + 2H 2FADH2 Oxidation: loss of electrons [loss of hydrogen ion] Reduction: gain of electrons [addition of hydrogen ion]

Electron Transport Chain cytochromes

ATP Production ATP synthetase complexes Chemiosmosis – production of ATP due to a hydrogen ion gradient across a membrane

Membrane Structure Semi-permeable Plasma lemma Cyto-membrane

Allows for selective permeability of materials (small organic molecules, macromolecules, ions, water)

Phospholipid Bilayer Phospholipids – phosphorylated fatty acids

Embedded in the phospholipids bilayer are proteins Receptor proteins Transport proteins Enzymes Signalling proteins

Embedded in the phospholipids bilayer: cholesterol

Under the PM (interior to the cell) – check out the microfilaments that “support” the PM

On the surface of the PM (outside the cell) – glycolipids, glycoproteins Hydrophilic heads Hydrophobic tails Fluid Mosaic Model of the plasma membrane Mosaic – because of small fragments/parts that make up the membrane Fluid – presence of the proteins that “sort of float”

Types of Proteins

Channel Proteins: allows particular molecules/ions to cross plasma membrane freely

Carrier Proteins: selectively interacts with specific molecule/ion so that it can cross PM (e.g., sodium-potassium pump) Cell Recognition proteins: major histocompatibility complex – made of glycoproteins that are different for each person

Receptor proteins: shaped in such a way that a specific molecule can bind to it

Enzymatic proteins: catalyzes a specific reaction. E.g. ATP metabolic enxymes

Signal Transduction

Types of Transport Across the Cell Passive transport – does not involve the use of energy (ATP) Active transport – does involve the use of energy (ATP) a) Passive transport – diffusion across a membrane High concentration to a low concentration Start out on one side of the “membrane” with high concentration of a solute (molecule) -> over time the molecule will move toward an area that is less concentrated with that solute Eventually – both sides will have the same amount of the material – equilibrium is achieved

Example – oxygen and carbon dioxide entering and leaving the blood cells b) Facilitated Passive Transport Use the transport protein embedded in the PM – it will serve as a channel Sugars, ions are examples of materials that flow through the transport protein channels

Osmosis – diffusion of water across a membrane

Low concentration | High concentration Of Solute | of Solute W A T E R -> (High water area) (low water area) Isotonic Solution -> equal on both sides of the membrane Water in at the same rate as water out Cell volume does not change

Hypotonic Solution: solution has a solute concentration that is lower than that of the cell Water will enter cell by osmosis Outside the cell | Inside the Cell Solute Low | Solute High Water is High | Water is Low Water -> ->

Cells swells, increasing in volume Cell can lyse (burst open)

If plant cell – becomes turgid

Hypertonic Solution: solution has a solute concentration that is higher than that of the cell

Outside the cell | Inside the Cell Solute High | Solute Low Water is Low | Water is High <- <- Water Cell shrink, shrivel

If plant cell – becomes shriveled Osmoregulation – regulation of water uptake

Active Transport – need ATP Sodium-Potassium Pump 1- solute binding to transport protein with certain shape 2- phosphorylation: ATP split and phosphate attaches to carrier 3- transport: protein changes shape – release of molecule (sodium ions outside cell) 4- potassium ions enter protein with changed shape 5- phosphate detaches 6- protein reverts to original shape, potassium ions released from carrier into cell Vesicle Formation – structure is like PM Exocytosis – (large) particles leave the cell Endocytosis – cell takes in (large) macromolecules -> forms vesicles from its PM Phagocytosis – type of endocytosis

Pinocytosis – type of endocytosis; cell takes in liquids Modification of Cell Surfaces Allow cells to communicate, adhere to each other Animals: Anchoring/adhesion junctions Desmosome – single point of attachment between adjacent cells Intermediate filaments

Tight junctions: zipperlike fastening; serve as barriers -> prevent leakage Blood-brain barrier Kidney cells/tubules – keep urine within

Gap junction – allows cell communication Heart muscle and smooth muscle -> flow of ions

Extracellular Matrix Collagen and Elastin Fibronectins and laminins – adhesive proteins – form highways Cartilage – flexible Bone – hard

Plant Cell Walls Plasmodesmata – numerous narrow membrane-line channels that pass through cell wall

Tight Junction Gap Junction

Anchoring Junction - intermediate filaments involved

Plasmodesmata – plant cells