UNIT 2: Cell Processes

ATP

Adenosine Triphosphate

Redox Reaction

• oxidation and reduction coupled reaction

Oxidation reaction

loss of electron, proton or gain of oxygen

Reduction Reaction

gain of electrons, proton or loss of oxygen

LEO said GER

Loss of

Electrons

Oxidation Reaction

Gain

Electrons

Reduction Reaction

Reducing agent

molecule that donates electrons

Oxidizing agent

molecule that accepts electrons

1. Reducing agent

2. Oxidation reaction

3. Oxidizing agent

4. Reduction reaction

Steps of cellular respiration

1. Glycolysis (anaerobic)

2. Pyruvate oxidation and citric acid cycle (aerobic)

3. Oxidative Phosphorylation (aerobic)

Anaerobic

• does not require oxygen

aerobic

• requires oxygen

Glycolysis

• splitting of glucose into pyruvate

• occurs in cytoplasm

• ancient reaction that harvests energy

• creates insufficient energy (2 ATP for every glucose)

Evolution of glycolysis

• prokaryotes with nit membrane bound organelles evolved glycolysis

• anaerobic atmosphere (without oxygen)

• all cells still use glycolysis

Steps of glycolysis

1. Glucose priming

   • endergonic (2 ATP → 2 ADP + 2 phosphate (attached to glucose))

2. Chopping stage

   • glucose is split in half

3. Energy harvest

   • exergonic ( 2 ADP + 2 phosphate (attached to glucose) → 2 ATP)

Net yield from glycolysis

• 2 pyruvate

• 2 H₂O

• 2 ATP

• 2 NADH

Cancer and glycolysis

• cancer is able to grow anywhere (does not need to be near blood source) because it preforms glycolysis to gain energy anywhere

Why is mitochondria the powerhouse of the cell

It creates ATP that powers the rest of the cell

1. intercellular space

2. cristae

3. matrix

4. inner membrane

5. outer membrane

pyruvate oxidation

1. pyruvate enters mitochondria through transport protein

2. 2 CO₂ are released from pyruvate as it enters the mitochondria

3. pyruvate oxidizes to form Acetyl CoA

   • and 2 NADH

Citric Acid/Krebs Cycle

• After pyruvate oxidation Acetyl CoA enters the matrix

• In 8 steps Acetyl CoA gets oxidized and turns into CO₂, NADH, FADH₂ and ATP

• happens 2 time per glucose (one per pyruvate)

Net gain of pyruvate oxidation and citric acid cycle

• 2 ATP

• 8 NADH

• 2 FADH₂

• 6 CO₂ (which are released from mitochondria)

How does the citric acid cycle favour the laws of thermal dynamics

• 1st law: Energy is not created or destroyed it is only transferred in coupled reactions

• 2nd law: an increase in enthropy is favoured in the universe. Bigger molecules are transformed into smaller ones (CO₂ + ATP + NADH +FADH₂)

Methods of Generating ATP

1. Substrate Level Phosphorylation

2. Chemiosmosis Generation of ATP

Substrate Level Phosphorylation

• ATP is formed from an enzyme catalyzed reaction

• occurs is glycolysis and citric acid cycle

• Phosphate containing group transfers a phosphate directly to ADP

• 30.5 kJ/mol of potential energy is also transferred

Chemiosmosis

• Movement of H+ ions through ATP synthase to generate ATP

• H+ diffuse from an area of high [ ] to low [ ]

• increase in entropy through diffusion

• release of energy through diffusion is used to generate ATP by combining ADT + P

What components are apart of Oxidative Phosphorylation

1. electron transport chain

2. chemiosmosis

Where does oxidative phosphorylation take place

mitochondria - cristae membrane

Oxidative Phosphorylation generates the _____ amount of ATP

most

Steps for oxidative phosphorylation

1. Oxygen (1/2 O₂ ) rips electron from C4

   • ½ O₂ + 2 e^- + 2 H⁺ → H₂O

2. C4 rips oxygen from C3 via shuttle molecule Cytochrome C (CytC)

   • C4 gains energy and pumps protons from matrix into inter membrane space

3. C3 rips electron from C2 or C1, via ubiquinone

   • C3 gains energy to pump protons across matrix to inter membrane space

4. If C2 loses and electron, it will gain an electron from FADH₂ . FADH₂ oxidizes into FAD and complex 2 reduces

5. If C1 loses an electron it will gain electrons from NADH. NADH oxidizes into NAD+, C1 reduces (gains electrons)

   • C1 gains energy and pumps H+ across into inter membrane space

Chemiosmosis:

6. Proton gradient in intermembrane space has been created. H+ diffuse across ATP synthase (exergonic -releases energy), ADP phosphorylates into ATP (endergonic)

Purpose of Oxidative Phosphorylation

1. Generate a lot of ATP

2. Recycle NAD+ and FAD to be used again in citric acid cycle

3. Get rid of potentially harmful Oxygen

1 NADH = _ ATP

3

1 FADH = _ ATP

2

Final ATP count from 1 glucose molecule

• Glycolysis: 2 ATP, 2 NADH

• Entry + Citric Acid Cycle: 2 ATP, 8 NADH, 2 FADH

• Oxidative Phosphorylation: 38 ATP (Total)

What is the role of oxygen in cellular respiration

• acts as the final electron acceptor in electron transport train

• Oxygen atom pulls electrons from the control centers push protons into the intermembrane space

• Creates H₂O

What happens if there is insufficient Oxygen

• oxidative phosphorylation shuts down because there is no longer a electron acceptor

• Pyruvate Oxidation and Citric acid cycle shut down (no NAD+ and FAD recycled)

• Glycolysis can continue because it has a way to recycle the NAD+

How is shivering related to the cellular respiration?

• causes muscle contractions

• ATP is required for muscle contractions - activating cellular respiration

• some energy released will be in the form of heat and not used in reduction reactions

What is brown fat

• Found in newborns, hibernating mammals, migratory birds

• generates body heat

• higher levels of mitochondria, that have high levels on uncoupling proteins

• lots of capillaries to bring in oxygen

What is an uncoupling protein channel?

• Transport chain for H+ that does not got through ATP synthase

• energy from diffusion is not used to generate ATP

• instead energy is released in the form of heat

How is cellular respiration controlled?

• Allosteric inhibition by ATP, NADH and Citrate

• Allosteric Activation by ADP

Thermodynamics

study of how energy moves

Metabolism

all chemical reactions occurring in an organism

Anabolism

chemical reactions that require energy to make new chemical bonds

Catabolism

chemical reaction that releases energy when bonds are broken

Energy

ability to do work (Joules or Calories)

Kinetic energy

energy of motion

Potential energy

stored energy

First Law of Thermodynamics

The total amount of energy in the universe is constant, it cannot be created or destroyed only transferred into different forms

Enthalpy of Reaction

the heat content of a substance

$\Delta H$ (Change in enthalpy)

overall heat change of a reaction

Exothermic Reaction

Energy is released

Endothermic Reaction

Energy is absorbed

Second Law of Thermodynamics

Entropy (S) (disorder/chaos) is favoured and constantly increasing in the universe

What does entropy favour

• solids → liquid/gas

• Bigger reactant → multiple smaller products

• high concentration → low concentration

Spontaneous reaction

reaction that only requires a little bit of energy to get started and will continue to occur on its own once it has started

Gibbs free energy

the maximum amount of usable energy released by a chemical system at constant temperature and pressure, determining if a process is spontaneous

\Delta G<0

• reaction is spontaneous

• exergonic

\Delta G>0

• reaction is not spontaneous

• endergonic

$$\Delta G=0$$

• reaction is at equilibrium

• no net change

• no tendency to proceed

• system is balanced

Exothermic reaction (Cellular respiration)

• reaction that releases heat

Endothermic Reaction (Photosynthesis)

Cellular respiration chemical equation

C₆H₁₂O₆ + O2 → 6 CO₂ + 6 H₂O +Energy (38 ATP)

cellular respiration reaction characteristics

$\Delta G$ = -2870 kJ/mol of glucose

• releases energy

• increase in entropy

• proceeds spontaneously

Photosynthesis chemical equation

6 CO₂ + 6 H₂O +Energy (from sun) → C₆H₁₂O₆ + O2

Characteristics of photosynthesis reaction

$\Delta G$ = 2870 kJ/mol of glucose

• absorbs energy

• decrease in entropy

• does not proceed spontaneously - energy is needed to derive the reaction

Equation for photosynthesis:

6 CO₂ + 6 H₂O + light energy → C₆H₁₂O₆ + 6 O₂

Purpose of the cuticle on a dicot leaf

• protects cell against UV radiation

• Prevents against loss of water in the leaf

In what part of the leaf does photosynthesis take place

palisade mesophyll cell

1. cell wall is made of cellulose

2. leaves have waxy cuticle that prevents water loss

3. chloroplast have chlorophyll that have a plant a green pigment

4. contain guard cells

Guard cell

Guard cells come in ____

pairs

What are guard cells

• Cells that open/close to regulate oxygen, carbon dioxide and water

How do guard cells open?

• triggered by K+ ions

1. K+ enters cell and which pulls water molecules into the cell with osmosis

2. Cell swells up (turgid) and the stroma opens

What happens as the guard cell closes

• K+ ions leave the cell, followed by water

• cell becomes flaccid (shrivels) and stomata closes

Which is guard cells open/close

1. close

2. open

What are the thylakoids?

• flattened membrane sacs in granum

• contain light pigment molecules (chlorophyll) and ETC on membranes

• Give leaf green colour

What is the significance of thylakoids?

increase surface area for capturing light

What are granum

• interconnected systems of thylakoids

How many granum are in a chloroplast?

approximately 60

What is the stroma?

• protein-rich fluid within the chloroplast

Label the chloroplast

1. outer membrane

2. granum

3. Lumen

4. inner membrane

5. stroma

6. thylakoids

Light is…

electromagnetic radiation

light travels in ____ packets called ____

• wave

• photons

Light from the sun is…

a mixture of photons of different energies called wavelengths (measured in nanometers)

the smaller the wave =

more energy

photon

a wave packet of energy

pigment

a material that has selective absorption of light

what are the most abundant photosynthetic pigments in photosystems

• chlorophyll a and b

What is chlorophyll?

• green coloured pigment

• absorbs light energy for photosynthesis

What is the chemical difference between Chlorophyll A and B

one R-side chain

Why are plants green

• chlorophyll a and b absorb violet-blue light and red regions of light - reflects green light

What is the main pigment in a photosystem

chlorophyll A

role of chlorophyll A

• absorbs light energy and transfers energy directly to photosynthesis reaction

role of chlorophyll B

• accessory pigment that absorbs remainder of light

role of accessory pigments (including chlorophyll B)

• absorb different ranges of energy to maximize the total absorption of light energy for photosynthesis

• chlorophyll a collects energy for accessory pigments and transfers it to trigger photosynthesis

Where can pigments be found

within the photosystem

Why are leaves different colours in the fall?

• production of chlorophyll stops

• other colours become visible due to accessory pigments

Photosynthesis equation

6 CO₂ + 6 H₂O + light energy → C₆H₁₂O₆ + 6 O₂

Roles of photosynthesis:

1. Make food: sugars for plants (autotrophs) and consumed by other animals (heterotrophs)

2. Remove CO₂ from the atmosphere

3. produces oxygen for aerobic organisms

steps of photosynthesis

1. Light dependent reactions

   • non-cyclic phosphorylation

   • cyclic phosphorylation

2. Light independent reactions

   • Calvin-Benson cycle

Goal of light dependent reactions

• Produce: ATP, NADPH and O₂