Cell Molec Unit 3

Oxidation of Sugar

Process where sugars are converted into CO2 and H2O to produce energy.

This occurs stepwise in small steps by enzymes, as it creates more energy energy in usable forms (ATP, NADH) overall

If it occured in one step, most energy would be lost as heat

Oxidation

An atom loses an electron, charge becomes more positive

Reduction

An atom gains an electron, charge becomes more negative

Redox Reactions

Reactions where carbons are oxidized and reduced via loss and gain of double bonds.

Cells go through a series of these reactions in order to extract energy from glucose.

Glycolysis

Anaerobic metabolic pathway where glucose is broken down into two pyruvate and energy through 10 enzyme catalyzed steps

Requires energy input but has higher energy payoff

Glucose → 2 pyruvate + ATP + NADH

Occurs in cytosol

Glycolysis Steps 1-3

Steps stage of glycolysis where energy investment occurs (2 ATP)

Glycolysis Steps 4-5

Steps stage of glycolysis where glucose splits into two 3-carbon molecules

Steps 6-10 of Glycolysis

Steps stage of glycolysis where energy generation occurs (4 ATP + 2 NADH).These steps occur twice.

Final Products: 2 Pyruvate, 2 ATP, and 2 NADH

Glycolysis Step 6

Specific step of glycolysis where the oxidation of G3P releases energy to drive formation of NADH and produce 1,3-bisphosphoglycerate

Glycolysis Step 7

Specific step of glycolysis where 1,3-BPG transfers its high-energy phosphate to ADP, producing ATP

Reaction Coupling

Phenomenon where energy released by favorable reactions drives the reaction of unfavorable reactions

Fate of pyruvate after glycolysis

With oxygen it enters the mitochondria, is converted into acetyl-CoA, and enters the Krebs cycle

Without oxygen it undergoes fermentation

Lactate Fermentation

Anaerobic fermentation metabolic pathway where pyruvate is converted into lactate.

Occurs in muscle cells, red blood cells, and microorganisms

Alcoholic Fermentation

Anaerobic fermentation metabolic pathway where pyruvate is converted into ethanol.

Done by yeasts and bacteria

Outer Membrane

Part of mitochondrial structure which encloses the mitochondrion

Intermembrane Space

Part of mitochondrial structure between inner and outer membranes

Inner Mitochondrial Membrane

Part of mitochondrial structure which contains the electron transport chain and ATP Synthase. It is folded into cristae to increase surface area

Matrix

Part of mitochondrial structure which contains enzymes for pyruvate oxidation and the citric acid cycle

Rise of Oxygen on Earth

Photosynthesis evolved, which released O2 into the environment. It reacted with dissolved Fe2+, but once all of it was reacted O2 joined the atmosphere. This led to the evolution of aerobic respiration due to the excess O2.

Key Concept of Mitochondiral structure

The specialized compartments of mitochondria enable efficient ATP production through oxidative phosphorylation

Evolution of Proton Gradient Mediated ATP Synthesis

Stage 1:ATP hydrolysis was used to drive proton pumping

Stage 2: Electron transport evolves to drive proton pumping

Stage 3: These 2 methods are combined, using proton gradient flow to drive ATP synthesis via ATP Synthase. The proton gradient links electron transport to ATP production

Transport across membranes

Drives the uptake of nutrients and export of certain substances through membrane transport proteins

Flagellar Rotation

Process which powers tje rotation of bacteria flagella, enabling cell movement

Mitochondria Fission

Process by which mitochondria divide, very similarly to bacterial cell division

Mitochondria replicate independently from the rest of the cell.

Endosymbiant Theory

Theorized origin of mitochondria and chloroplasts

Based upon the presence of their own DNA, ribosomes resembling those of bacteria, and division by fission

Mitochondria from an ancestral aerobic bacteria

Chloroplast originated from photosynthetic bacteria related to cyanobacteria

Endosymbiosis

Process where formerly independent bacteria became permanent residents inside ancestral eukaryotic cells.

Pyruvate Oxidation

Process by which pyruvate is converted into Acetyl-CoA and CO2, and NAD+ is reduced to NADH

Occurs in the mitochondrial matrix, and is performed by the Pyruvate dehydrogenase complex (PDC)

Reaction intermediates pass through Pyruvate dehydrogenase, Dihydrolipoyl transacetylase, and Dihydrolipoyl dehydrogenase, allowing Acetyl-CoA to enter the TCA cycle

Phagocytosis

Process where a host cell engulfs a bacterium

Molecular Phylogeny

Proposed evidence for endosymbiosis, where COX3, which encodes a protein that is part of cytochrome c oxidase, has high similarity in both bacteria and mitochondria.

Ribosomes and Endosymbiosis

Evidence for endosymbiosis where chloroplast and mitochondria have very similar ribosomes

Genome Structure

Evidence for endosymbiosis, where mitochondria and chloroplast have circular chromosomes like bacteria do.

Citric Acid Cycle

Process in the mitochondria that produces NADH and FADH2, which carry high-energy electrons

Electron Transport Chain

Process that moves electrons to oxygen and uses the released energy to pump protons across the inner mitochondrial membrane

Proton Gradient

Concentration gradient that stores energy across membranes

ATP Synthase

An enzyme that uses the energy of proton flow to synthesize ATP from ADP and inorganic phosphate

Proton-motive force drives rotation of the enzyme which causes conformational changes in the catalytic subunits, allowing ADP and Pi to be converted into ATP

Electron Transfer

Electrons from NADH pass through three respiratory enzyme complexes ultimately teaching oxygen, the final electron acceptor

Ubiquinone (Q) and Cytochrome (C)

Mobile carriers for the ETC

Supercomplex Formation

Three complexes of ETC come togetehr to further facilitate electron transfer

NADH Dehydrogenase

Complex of ETC that receives electrons from NADH and pumps hydrogen across the membrane

Cytochrome Reductase

Complex in ETC that receives ubiquinol and turns it into cytochrome c. It also pumps H into the membrane

Cytochrome c Oxidase

ETC Complex that, receives cytochrome, pumps H+, and turns hydrogen and oxygen into water

Role of NADH and FADH2

Carry high-energy electrons produced during cellular respiration.

Act as electron donators by transferring hydride ions with two electrons to the ETC.

They are oxidated, losing two electrons and a proton. This regenerates them, and they are able to undergo the process again once they grab more hydrogen

TCA Cycle

Process including the citric acid cycle and krebs cycle.

Acetyl CoA is oxidized, releasing CO2, and producing NADH, FADH2, and some ATP and GTP

Occurs in inner membrane of the mitochondria

Fatty Acid Oxidation

Alternate source of Acetyl-CoA where stored fats such as triacylglycerols are broken down by lipases into fatty acids which combine with CoA and ATP to form fatty acyl-CoA

It is then beta-oxidated in the mitochondrial matrix, removing 2 carbons as acetyl-CoA and creating 1 NADH and 1 FADH2 per cycle.

The NADH and FADH2 go on to feed electrons in ETC

Entry of Acetyl CoA

Oxaloacetate (4C) combines with Acetyl-CoA (2C)

Citric Acid Cycle

Acetyl-CoA enters and combines with oxaloacetate to produce 6C of citrate, which are then oxidized into CO2. Oxaloacetate is then regenerated to begin another cycle

Produces 3 NADH, 1 FADH2, and 1 GTP or ATP

Discovery of the cycle

We know it is a cycle because when all intermediates were added to the cycle in the presence of a malonate block, the products before the block will be created and build up. Products added that are after the block will become the product before the block.

This shows that all intermediates will travel around the cycle and become other products in a cyclic process.

Purpose of glycolysis and citric acid cycle for metabolism

They provide precursors for biosynthesis, creating metabolic intermediates such as amino acids, nucleotides, lipids, and sugars used to make cellular macromolecules

Gluconeogenesis

Metabolic process that is mostly a reverse of glycolysis.

Has reciprocal regulation that helps to coordinate glucose breakdown and synthesis

Uses hydrolysis to make Fructose 6-phosphate, which can then be used for glycolysis

Electron Transfer and Proton Transfer relationship

Principle where electron transfer can often be coupled with proton transfer, where electron carriers carry electrons together with protons

Water serves as a source or acceptor of protons during these reactions

If an oxidized electron carrier is reduced, what did it gain?

An oxidized electron carrier gained an electron and a proton

If a reduced electron carrier is oxidized, what did it gain?

A reduced electron carrier lost an electron and a proton

Membrane-embedded Electron Carriers

Protein complexes that can pick up and release protons on opposite sides of the membrane

The middle protein will gain an electron from another protein, allowing it to bring in a proton from water outside the membrane. It then donates the electron, which releases the hydrogen on the other side

Redox Potential (E’o)

(E’o) Tendency to accept electrons, measured in volts

Lower (E’o), or more negative value, means lower electron affinity, and is a better electron donor

Higher (E’o), or more positive value, means higher electron affinity, and is a better electron acceptor

Electron Flow

The spontaneous movement from lower to higher redox potential

Ex. NADH/NAD+ → O2/H2O

How does redox potential change during ETC?

Redox potential increases as electrons flow from lower to higher redox potentials. These increases mostly occur in the three protein complexes as energy releasing steps drive protons across the membrane

Proton-motive Force

Combination of electrical force (delta V) and chemical force (delta pH) that drives H+ across the gradient.

Increased concentration of hydrogen in the intermembrane makes it more acidic and more positively charged, and these differences drive proton movement across the membrane

ATP Synthesis

Process where ATP synthase uses the proton-motive force to convert ADP and Pi into ATP

Hydrogen moves from intermembrane space to the intermembrane space through the pinwheel shaped enzyme

Energy requiring (Positive gibbs free energy)

ATP Hydrolysis

Process where ATP Synthase converts ATP into ADP and Pi to pump H+ against its concentration gradient back into the intermembrane space

Energy releasing (negative gibbs free energy)

Development of Chemiosmotic Hypothesis

Prevailing idea in 1950s for ATP production was a direct phosphate transfer from a high energy intermediate to ADP

Peter Mitchell proposed that the intermediate was actually an electrochemical gradient made by ETC. He believed this because uncoupling agents added to the mitochondria dissipated H+ gradient, which ceased ATP production.

Further experimentation showed the requisite parts of ETC were all needed, as with just one piece missing ATP was not generated.

Additional processes of the proton gradient

The H+ concentration gradient moves metabolites across the membrane in addition to the proton motive force.

ATP/ADP exchange is driven by