Modue 4-5 Cell Biology

Cellular Respiration

A series of metabolic pathways which generates energy that the cell can use ATP

The energy stored in glucose is converted in to the energy stored in ATP

Metabolism

Sum of the chemical reactions that take place within a cell

Energy

Required for synthesizing molecules (like macromolecules: proteins and nucleic acids) 

Required for life sustaining processes like active transport 

Molecules such as those found in food are store energy in chemical bonds 

• When bonds are broken, energy is released into cells 

• Cells can then use that energy immediately or store it by forming new chemical bonds 

• There are different forms of energy and energy can transform from one type into another 

Exergonic (Metabolism + Energy) 

Release energy 

This is because the products of the reactions have LESS energy than than the reactants 

Endergonic (Metabolism + Energy) 

Require energy 

This is because the products of the reactions have MORE energy than the reactants 

Exergonic and Endergonic reactions are paired: The energy release in exergonic reactions is used to power endergonic reactions 

Enzymes

Speed up the rate of both anabolic and catabolic chemical reactions

Without enzymes reactions would occur much to slow for organisms to function

Enzymes act on substrates (specific molecules that an enzyme acts on to cause a chemical reaction) to make products

ATP & ADP

Main forms of chemical energy in a cell, energy is stored in the energy-rich chemical bonds between their phosphate groups 

ATP= adenosine triphosphate

• ATP has 3 phosphate groups 

• ATP is made when the cells has extra energy 

ADP= adenosine diphosphate 

• ADP has 2 phosphate groups so it has less energy than ATP 

• ADP is made when the cell uses the energy in ATP (by removing one of its phosphate groups) 

Oxidation & Reduction

In metabolism, chemical bonds are broken & built, chemical bonds are made of electrons 

Oxidized: When a molecules loses electrons 

• Can generate a positively- charged ion 

Reduced: When a molecules gains electrons 

• Can generate a negatively-charged ion

Redox Reactions

A type of chemical reaction that involved transfer of electrons from one reactant another 

Have two parts: A reduced part and an oxidized part and they always occur together 

Play a central part in a cellular respiration and other metabolic pathways such as photosynthesis 

Electron Carriers

Capture the energy from one chemical reaction and transport it to a different part of the cell to be used 

In cellular respiration the primary electron carriers are NAD+/ NADH and FAD/ FADH2 

• NAD+ (empty/release/ready to receive) 

• NADH (loaded) 

Electron carriers are reduced when carrying electrons and oxidized when they do not carry electrons.

Cellular Respiration (Steps and Processes)

The process of extracting energy from glucose and other molecules and storing it in ATP 

When glucose is oxidized the energy stored in its covalent bonds is released 

• This energy is then captured in the chemical bonds of newly formed ATP molecules 

Ultimately, energy-poor electrons are given to oxygen 

• This means oxygen is reduced 

Cellular Respiration: The Big Picture

C6H12O6 + 6 O2 → 6 CO2 + 6 H2O + 36 ~36 ATP

Energy-rich glucose is broken into energy-poor carbon dioxide 

Two forms of energy are created: ATP & energized electron carriers (NADH & FADH2) 

The energy of electron carriers is also transformed into ATP using the Electron Transport Chain

Overview of Cellular Respiration

Step 1: Glycolysis

• Split the glucose into pyruvate molecules 

Step 2: Pyruvate oxidation 

• Move the pyruvate into the mitochondria and process them 

Step 3: The Citric Acid (Krebs) cycle 

• Remove energy-rich electrons from the processed pyruvate 

Step 4: Oxidative phosphorylation 

• Use the energy from those high energy electrons to build ATP

Mitochondrial Structures 

The outer membrane divide it from the cytoplasm 

The inner membrane is the location of the electron transport chain 

The inter membrane space (between the membrane) where the ETC H+ ions into 

• As H+ re-enter the matrix through the ATP synthase enzymes, ATP is built

The matrix is the central fluid filled are the mitochondria site of citric acid (Krebs) cycle 

Step 1: Glycolysis

The initial glucose-breaking process 

• Covalent bonds are broken, extracting high energy electrons 

• Oxygen is NOT required for this process

• Occurs in the cytoplasm 

• Glucose is broken down in a series of steps, each requiring a specific enzyme, into 2 pyruvates 

Reactants: glucose + 2 ATP + 2 NAD+ 

Products: 2 pyruvate + 2 NADH + 2 ATP (net)

* Glycosis generates 4 ATP molecules but since the first step requires 2 ATP, the overall net gain is 2 ATP

Location:  The cytoplasm 

Step 2: Pyruvate Oxidation

Each 3-carbon pyruvate still has A LOT of energy in the form of electrons

• The pyruvate are transported into the mitochondria so that energy can be harvested 

Reactants: 2 pyruvate + 2 NAD+ + 2 Coenzyme A complexes 

Products: 2 acetyl coenzyme A (acetyl CoA) + 2 CO2 + 2 NADH

Location: the mitochondrial matrix 

Step 3: The Citric Acid (Krebs) Cycle

Breaks the remaining covalent bonds in Acetyl Coenzyme A (Acetyl CoA)

Each time a bond is broken, electrons are transferred to electrons carriers- NADH and FADH2 

• One glucose molecules makes two Acetyl CoA’s 

Reactants: 2 Acetyl CoA + 6 NAD+ + 2 FAD (+ oxaloacrtate) 

Products: oxaloacetate + 4CO2 + 2 ATP + 6 NADH + 2 FADH2 

Location: the mitochondrial matrix 

A closer look: 

The cycle begins with 4 carbon molecule (oxaloacetate) 

2 carbons are added when the acetylCoA enters the cycle 

Those 2 carbons leave the cycle as CO2 molecules, generating NADH 

As remaining 4 carbons rearrange their structure, ATP & more energized electron carriers are made 

At the end of the cycle as 6 carbons have been separated from one another & released as CO2

Where’s the energy?

At the end f the Citric Acid Cycle, only 4 ATP have been made

• 2(net) ATP from glycolysis 

• 2 ATP from the Citric Acid Cycle 

The rest of the energy is stored in electron carriers 

• 10 NADH (from glycolysis, pyruvate oxidation & the citric acid cycle) 

• 2 FADH2 (from the Citric Acid Cycle) 

Oxidative phosphorylation transforms the energy in those electron carriers into ATATP

Step 4: Oxidative Phosphorylation

Builds most of the ATP generated through cellular respiration

First the Electron Transport Chain creates an H+ concentration gradient across the inner mitochondrial membrane 

Then during chemiosmosis ATP synthase uses the gradient to build ATP

The Electron Transport Chain

Electrons (from NADH & FADH2) travel through each of the ETC protein complexes 

Their energy is used by the proteins to pump H+ ions (aka protons) into the inter membrane space 

By the end of the ETC, the electrons no longer store any energy & are combined with O2

Chemisomosis

ATP synthase is the ATP generating protein of oxidative phosphorylation

The concentration of H+ (protons) is very high in the inter membrane space and much lower in the matrix 

• ATP synthase- which is embedded in the inner mitochondrial membrane- allows protons to move back into the matrix 

• The energy that is released when these protons move back in is called proton motive force 

ATP synthase uses the power of the proton motive force to create new ATP 

• It takes the movement of 4 protons (H+) to make 1 molecules of ATP 

Building ATP

Most of the ATP is generated via oxidative phosphorylation

Oxidative phosphorylation uses the Electron Transport Chain (ETC) and chemiosmosis 

• First the ETC creates a proton (H+) concentration gradient across the inner mitochondrial membrane 

• Then ATP synthase uses the energy of that gradient to build ATP in a process called chemiosmosis 

The role of oxygen

Oxidative phosphorylation is the only cellular respiration process that requires oxygen (O2) 

O2 is the final electron acceptor at the end of the Electron Transport Chain (ETC)

• Energy-poor electrons are donated to O2, making space for the other electrons to continue to move through the ETC 

• If oxygen is not present, electrons would build up in the Electron Transport Chain and electrons carriers would remain permentantly reduced 

Building ATP (further) 

ATP is built by phosphorylating ADP 

• This means a new chemical bond is built between ADP and phosphate group 

• This energy of ATP is stored in that chemical bond 

In glycolysis and the citric acid cycle ATP synthesis occurs using substrate level phosphorylation 

• A phosphate groups is removed from one molecule ( the substrate) 

• It is then directly attacked to ADP

Oxygen and Cellular Respiration

The only part of cellular respiration that directly uses oxygen is the Electron Transport Chain

• O2 removes low-energy electrons from the ETC allowing new electrons to constantly enter it 

Electrons in the ETC come from NADH and FADH2

• Donating electrons to the ETC oxidizes the carriers to NAD+ and FAD the form needed for all the other parts of cellular respiration 

• If the electron carriers can’t be oxidized ALL cellular respiration stops 

Fermentation

Cells use fermentation when there is no oxygen present

The goal of fermentation is to regenerate the oxidized electron carrier NAD+

• Without the carrier, glycolysis cannot occur and,,,

• Without glycolysis, a cell has no ways to make ANY ATP

Alcohol Fermentation

Used by yeast to regenerate NAD+

• The pyruvate (made by glycolysis) is transformed into ethanol 

• This transformation requires electrons, which NADH provides, oxidizing it back into NAD+ 

Used in brewing and wine-making 

• This process generates a lot of CO2

• Fermentation tanks have valves to help relive the pressure this gas creates 

Lactic Acid Fermentation

Used to regernate NAD+ in bacteria, fungi, and mammals

• The pyruvate (made by glycolysis) is transformed into lactic acid 

• This transformation requires electrons, which NADH provides, oxidizing it back into NAD+ 

Used to make many different foods 

• Examples: yogurt, cheese, sourdough, bread 

• Lactic acid leads to a tangy taste in these foods 

Regulating Cellular Respiration

The steps of cellular respiration are regulated using feedback inhibition

• This means that the product of chemical reactions can inhibit the continuation of chemical reaction

Many of the enzymes involved in respiration are sensitive to ATP

• If A LOT of ATP is present, they are inactive

• if A LITTLE ATP is present, they are active

Other factors (like pH changes due to lactic acid buildup) can also influence enzyme activity

Autotrophs, Phototrophs, Chemotrophs, Heterotrophs. 

Autotrophs- Self feeders, organisms that CAN build their own energy-rich molecules

Phototrophs- plants, use the energy of light to do this 

Chemotrophs- (like some bacteria) use energy of inorganic molecules (like sulfur or ammonia) 

Heterotrophs( other feeders), animal fungi, most bacteria 

Photosyntehsis

The process used by plants to transform light energy (and carbon dioxide and water) into glucose

6CO2 (carbon dioxide) + 6H2O (water) → C6H12O6 (sugar) + 6O2 (oxygen)

6CO2- Reduced (accepts electrons), 6H2O- Oxidized (loses electrons) 

Endergonic (requires energy) 

Anabolic

Part 1- Light Reactions

Goal: Capture the energy of sunlight and storing it in ATP & NADPH

Light dependent reaction: Occurs in photosystems that are embedded in the thylakoid (coin stacked) membranes of chloroplasts

Energy Harvest

Part 2- Calvin Cycle

Goal: Building sugar using the energy of ATP and NADPH

Light independent reactions: Occurs in the storm of chloroplasts 

Energy Synthesis 

Photosynthesis (Starting Materials + Ending Materials)

Starting Materials

• CO2 absorbed through stomata (aka holes) in plant’s leaves 

• H2O absorbed through the plant’s roots 

• Sunlight, absorbed by the pigments in the leaves 

Ending Materials 

• Glucose (C6H12O6) stored as cellulose and starch 

• O2 released as a waste product 

The energy of light

Light reactions of photosynthesis convert light energy into energy stored in chemical bonds

Light is made of photons that travel in waves 

• Light with shorter wavelengths (blue & purple) have more energy 

• Light with longer wavelengths (red) have less energy 

The color of an object (like a leaf) is determined by which wavelengths of light are reflected off its surface 

Photosynthetic Pigments

To capture as much light as possible, plants use multiple pigment proteins that each absorb different wavelengths of light 

Chlorophyll a is the primary pigment protein in plants 

Accessory pigments (like Chlorophyll b & B-carotene) absorb light & transfer that energy to Chlorophyll a 

Photosystems

Inside a chloroplast, the photosynthetic pigments group together in photsystems

• Photosystems are found in the thylakoid membranes 

• Each photosystem has central reaction center with a Chlorophyll a molecule & a pair of special electrons 

During the light reactions, all pigments in the photosystem collect light energy 

• This energy is funneled toward the reactions center 

• Ultimately it energizes Chlorophyll a’s special electrons 

• These energized special electrons then travel throng ETC proteins are ultimately donated to NADP+

Light Reactions (Steps)

1) Light energy entering Photosytem II (PSII) is funneled to the reaction center, energizing the electrons there

• Electrons carriers then shuttle these electrons through an Electron Transport Chain

• Water is split to provide new special electrons to PSII → Waste product is oxygen

2) As the electrons move through the chain, their energy helps pump H+ into the lumen of the thylakoids

3) When the electrons reach the end of the ETC they are transferred to Photosystems I (PSI)

4) When light energy is absorbed by PSI, these electrons are energized again, and are used to reduce NADP+ to NADPH 

5) ATP synthase uses the energy of H+ moving back across the thylakoid membrane to generate ATP (through chemiosmosis)

Allows for electrons to be excited to a higher energy to then be stored by NADPH to then be used in the Calvin Cycle

Inputs: Sunlight, H2O, NADP+, ADP + Pi

Outputs: O2, NADPH, ATP

The Calvin Cycle

The goal of the Calvin Cycle is to perform carbon fixation 

• Carbon fixation: Attaching carbon atoms to other molecules to generate organic molecules 

• The process of carbon fixation is done by the enzyme Rubisco 

• Carbon dioxide (CO2), with 1 carbon goes into the cycle 

• It is attached to a 5-carbon compound (RuBP)

• The new compound is split into 2 G3P (glyceralehyde-3 phosphate) molecules, each with 3 carbons 

• Combining 2 G3P molecules builds 1 glucose, with 6 carbons 

Each time all the steps of the Calvin cycle are completed, only ONE carbon is fixed 

This means: 

• The Calvin Cycle must run 3 times to generate one new molecule of G3P

• The Calvin Cycle must run 6 times to generate one new molecules of glucose