IB Biology - Respiration

ATP name

adenosine triphosphate

ATP

a molecule that functions to distribute energy within cells → acts as an immediate source of chemical energy that is used to power cellular processes

ATP structure

ribonucleotide consisting of an adenine base + 3 phosphate groups attached to the central ribose sugar → 3 covalently linked phosphate groups → store potential energy in their bonds

When ATP is hydrolysed

hydrolysed to release the outermost phosphate → the energy stored in the phosphate bond is released to be used by the cell

Life processes within cells that ATP supplies with energy

• biosynthesis

• active transport

• movement

Life processes within cells that ATP supplies with energy - biosynthesis

The synthesis of macromolecules requires ATP → ATP provides energy for anabolic reactions that build large, complex molecules from smaller molecules

Life processes within cells that ATP supplies with energy - active transport

ATP provides energy to move substances against their concentration gradient across membranes → e.g. nerve cells use ATP to establish a resting potential → e.g. ATP is also used in vesicular transport (endocytosis + exocytosis)

Life processes within cells that ATP supplies with energy - movement

TP provides energy for the movement of whole cells or cell components → e.g. moving chromosomes during mitosis + meiosis → e.g. contraction of muscle cells

What processes require energy in cells?

• Building mRNA

• Moving chromosomes during mitoses 

• Active transport 

• Forming polypeptides during translation

Phosphorylation

The addition of a phosphate group to a molecule → during ATP synthesis, a phosphate is added to ADP to form ATP → energy is stored during ATP synthesis + released during ATP hydrolysis

ATP hydrolysis

ATP + H₂O → ADP + phosphate + energy

• A water molecule is added to break off the 3rd phosphate from ATP → an exergonic reaction (energy is released) → the released energy is used for work/processes within the cell

ATP synthesis

ADP + phosphate + energy → ATP

• Energy is required to add a phosphate to ADP to form ATP → an endergonic reaction (energy is required) → energy is temporarily stored in ATP

Respiratory substrate

Any organic molecule that can be broken down during cell respiration to release energy for ATP production

Examples of respiratory substrates

Glucose + fatty acids are the principal respiratory substrates → other organic compounds → e.g. amino acids, can also be used

Cell respiration

metabolic processes within cells that break down organic compounds to release energy + produce ATP

Gas exchange

movement of respiratory gases between an organism + its environment → e.g. oxygen enters the blood + carbon dioxide leaves the blood

Aerobic respiration

Aerobic respiration → uses oxygen to release energy from glucose + produce ATP

glucose + oxygen → carbon dioxide + water (+ ATP)

Anaerobic respiration

releases energy from glucose without oxygen + produces ATP

In humans:
glucose → lactate (+ ATP)

Differences between aerobic and anaerobic respiration

Anaerobic vs aerobic stages

Factors affecting the rate of cell respiration

• Temperature → affects the activity of enzymes involved in respiration

• pH → affects enzyme activity

• Inhibitors → can reduce enzyme activity

• Glucose availability → glucose is a major respiratory substrate

• Oxygen availability → required for aerobic respiration

Respirometer

A respirometer measures the rate of aerobic respiration by measuring oxygen consumption

• A living organism → e.g. germinating seeds/invertebrate, is placed in a sealed container

• Soda lime/another alkali absorbs the CO₂ produced

• As O₂ is consumed + CO₂ is absorbed → the gas pressure decreases

• This causes the liquid in the manometer to move

• Greater movement over a given time → higher rate of respiration

Why is CO₂ absorbed in a respirometer?

CO₂ is absorbed by an alkali → e.g. soda lime so that any decrease in gas volume/pressure is due to oxygen consumption → the change can be used to determine the rate of aerobic respiration

Controls in a respirometer experiment

• Water bath → keeps temperature constant

• Glass beads → control with the same volume/mass as the living organisms

• Sealed apparatus → prevents outside gases entering or leaving

Calculating rate of cell respiration

rate of respiration = change in measurement ÷ time

Redox reaction

Respiration involves the movement of electrons (oxidation + reduction; always together)

Dehydrogenation

The removal of hydrogen from a substrate

• Hydrogen carries electrons, so removing hydrogen causes the substrate to lose electrons → substrate is oxidized

Electron carrier

they carry electrons from place to place → electron carriers accept/give up electrons as required → linking oxidations + reductions in cells

NAD

NAD is an electron carrier that transfers hydrogen + electrons during cell respiration.

• NAD accepts hydrogen/electrons from a substrate

• When NAD gains hydrogen → reduced to form reduced NAD (NADH)

• NADH can later give up the hydrogen/electrons

The reason why we need electron carriers

Where does glycolysis occur

in the cytoplasm of the cell (outside the mitochondria) → first stage of aerobic and anaerobic respiration

Glycolysis

converting glucose to pyruvate

Glycolysis end products

• 2 pyruvate (3C)

• net yield of 2 ATP

• 2 reduced NAD (NADH)

Stages in glycolysis

1. Phosphorylation → 2 ATP are used to add phosphates to glucose

2. Lysis → the phosphorylated glucose is split into two 3-carbon molecules

3. Oxidation → the 3-carbon molecules lose hydrogen/electrons

4. NAD is reduced → hydrogen/electrons are accepted by NAD, forming reduced NAD (NADH)

5. ATPx formation → ADP is phosphorylated to form ATP

6. 2x pyruvate are formed

Why must NAD be regenerated during anaerobic respiration?

During glycolysis, NAD accepts hydrogen/electrons → becoming reduced NAD (NADH)

• Without oxygen, reduced NAD cannot be oxidised by the electron transport chain → NAD must be regenerated so it can continue accepting hydrogen/electrons → allows glycolysis to continue

Conversion of pyruvate to lactate

In anaerobic respiration in humans: pyruvate → lactate

• Reduced NAD (NADH) gives its hydrogen/electrons to pyruvate → pyruvate is converted into lactate → reduced NAD is oxidised → regenerating NAD → allows glycolysis to continue without oxygen → continues producing ATP

ATP production during anaerobic respiration

net yield is 2 ATP per glucose

Anaerobic respiration in yeast

In the absence of oxygen, yeast carries out anaerobic respiration

Glucose → ethanol + carbon dioxide + ATP

Similarities between anaerobic respiration in humans and yeast

• Use glycolysis to convert glucose → pyruvate

• Regenerate NAD so glycolysis can continue

• Produce a net yield of 2 ATP per glucose

Difference between anaerobic respiration in humans and yeast

Humans: pyruvate → lactate
Yeast: pyruvate → ethanal → ethanol + carbon dioxide

Stages of anaerobic respiration in yeast

• Glycolysis:
  glucose → 2 pyruvate

  • net 2 ATP

  • reduced NAD (NADH) produced

• Pyruvate → ethanal

  • Decarboxylated → CO₂ is removed from pyruvate

• Ethanal → ethanol

  • reduced NAD (NADH) gives hydrogen/electrons to ethanal

  • NAD is regenerated

  • regenerated NAD allows glycolysis to continue

Wheres does the link reaction take place

In the mitochondria’s matrix

Steps of the link reaction

• Pyruvate (3C) enters the mitochondrial matrix

• Pyruvate is oxidised → hydrogen/electrons are removed

• NAD accepts the hydrogen/electrons → forming reduced NAD (NADH)

• Pyruvate is decarboxylated → CO₂ is removed

• An acetyl group (2C) is formed

• Acetyl group joins coenzyme A → forming acetyl-CoA

• Acetyl-CoA carries the acetyl group to the Krebs cycle

How many times does the link reaction happen

twice per glucose because glycolysis produces 2 pyruvate

Role of coenzyme A in the link reaction

Coenzyme A attaches to the acetyl group (2C) → forming acetyl-CoA.

Coenzyme A carries the acetyl group into the Krebs cycle

Starting materials for link reaction

• pyruvate (3C)

• NAD⁺

• coenzyme A (CoA)

End products of link reaction

Per glucose:

• 2 acetyl-CoA

• 2 reduced NAD (NADH)

• 2 CO₂

• 0 ATP

Where does the Kerb Cycle take place

In the mitochondria’s matrix

Stages of the Kerb cycle

1. Acetyl CoA (2C) from link reaction combines with a 4 carbon compound (oxaloacetate), making a 6 carbon compound (citrate)

2. Citrate (6C) is oxidized (NAD+ is reduced to NADH) and decarboxylated (carbon dioxide is released) to form a 5 carbon compound

3. The 5 carbon compound is oxidized and decarboxylated to form a 4 carbon compound. This forms carbon dioxide and another NADH

4. The 4 carbon compound is further oxidised

a. FAD to reduced FAD/FADH2

b. NAD to reduced NAD/NADH

ATP is produced by the phosphorylation of ADP

Every 1 glucose molecule produces per Kerb cycle:

• 6x NADH (reduced NAD) (oxidation + reduction)

• 4x CO2 (decarboxylation)

• 2x FADH2 (reduced FAD) (oxidation and reduction)

• 2x ATP (phosphorylation)

How many time oxidisation and decarboxylation happen in the Kerbs Cycle

• Per turn of the Krebs cycle → 4 oxidations (dehydrogenation) + 2 decarboxylations

• Oxaloacetate (4C) is regenerated so the cycle can repeat

Where is the electron transport chain

inner mitochondrial membrane → inner membrane is arranged into folds (cristae) → increases the surface area available for the transport chain

How does reduced NAD transfer energy to the electron transport chain?

• Reduced NAD (NADH) + reduced FAD (FADH) is oxidised back to NAD + FAD → both return to the matrix

• Both H atoms split into H+ and e-

• The electrons move down the electron transport chain via electron carriers (membrane proteins), losing energy at each one

• The electrons transfer energy to the electron transport chain

Where does the reduced NAD used in the electron transport chain come from?

• Glycolysis

• Link reaction

• Krebs cycle

How is a proton gradient formed in the electron transport chain

1. As electrons pass through the chain, they lose energy

2. This energy is used to provide the carriers with energy to pump protons (H+) into the intermembrane space from the matrix

3. A concentration gradient of protons builds up

Chemiosmosis

The movement of H⁺ through ATP synthase:

• H⁺ ions move down their electrochemical gradient from the intermembrane space into the mitochondrial matrix

• H⁺ can only cross the inner mitochondrial membrane through ATP synthase

How does chemiosmosis produce ATP?

• H⁺ ions move through ATP synthase down their electrochemical gradient

• This releases energy → causes ATP synthase to rotate/change shape

• ATP synthase uses this energy to phosphorylate ADP → creates ATP

What is the role of oxygen in the electron transport chain?

• Oxygen acts as the terminal electron acceptor → accepts de-energised electrons from the electron transport chain → allows electrons to continue flowing along the electron transport chain

How is water formed during aerobic respiration?

• Oxygen accepts electrons from the electron transport chain

• Oxygen combines with H⁺ (protons) from the mitochondrial matrix → forms water (H₂O)

Why do lipids produce more energy per gram than carbohydrates

• Lipids contain less oxygen + more oxidizable hydrogen and carbon than carbohydrates → more oxidation can occur → releases more energy per gram

How are carbohydrates used in cell respiration

• Carbohydrates are broken down into monosaccharides → e.g. glucose

• Glucose enters glycolysis

• Carbohydrates can be used for both aerobic + anaerobic respiration

• Glycolysis and anaerobic respiration only occur when carbohydrate is the respiratory substrate

How are lipids used in cell respiration

• Fatty acids are broken down into 2C acetyl groups

• Forms acetyl-CoA → enters the respiration pathway at the Krebs cycle

• This bypasses glycolysis → lipids cannot be used for anaerobic respiration

Pho

the process by which cells synthesise organic compounds → e.g. glucose from inorganic molecules → CO₂ + H₂O in the presence of sunlight and chlorophyll

What organisms photosynthesize

• plants

• algae

• cynobacteria

How chemical energy is used

Photosynthetic organisms contain pigments that capture the light energy from the sun to create chemical energy (ATP) → used to synthesise organic compounds via anabolic reactions for life processes

What happens to water during photosynthesis

Water is split during the light-dependent reactions, providing hydrogen that is carried by NADPH → photolysis

NADPH later used to help convert carbon dioxide into glucose

Where does the oxygen produced during photosynthesis come from

Photolysis → oxygen comes from the splitting of water during photosynthesis

What is the by-product of photosynthesis

Oxygen → is released from the chloroplast

Chromatography

technique used to separate and identify different components in a mixture → e.g. photosynthetic pigments

Formula for Rf value

Rf = distance travelled by pigment ÷ distance travelled by solvent front

Types of photosynthetic pigment:

• Chlorophyll

• Xanthophyll

• Carotenoid

• Anthocyanin

Photoactiviation

the absorption of light energy (photons) by photosynthetic pigments → e.g. chlorophyll in a photosystem → boosts their electrons to a higher energy level

Why do photosynthetic pigments only absorb specific wavelengths of light

Electrons in each pigment have specific energy levels → they can only absorb wavelengths of light that provide the correct amount of energy to excite them

What happens when a photosynthetic pigment absorbs light?

• Light energy is absorbed by the pigment

• Electrons within the pigment become excited to a higher energy level

• The energy from the excited electrons is used to produce chemical energy (ATP) → photophosphorylation

How is light energy transformed into ATP in photosynthesis?

Light is absorbed by photosynthetic pigments → photoactivation occurs, where electrons become excited to a higher energy level → the energy from these excited electrons is used to produce chemical energy (ATP)

Absorption spectrum

how much light a photosynthetic pigment absorbs at different wavelengths

x-axis: wavelength of light (nm) + corresponding colour
y-axis: amount of light absorbed by the pigment

Which wavelength does chlorophyll a absorb the most

1. Blue

2. Red

Red wavelength

(600 - 700 nm) → most abundant

Blue wavelength

(400 - 500 nm) → most energy

Action spectrum

Shows the rate of photosynthesis at different wavelengths of light

How can the rate of photosynthesis be measured for an action spectrum

By measuring:

• rate of O₂ production

• rate of CO₂ consumption

The similarities between absorption and action spectra

• Both vary with wavelength of light

• Both generally have high values in the blue + red regions

• Both generally have low values in the green/yellow region

Why are absorption + action spectra similar

Wavelengths that are strongly absorbed by photosynthetic pigments provide more energy for photosynthesis → produce a higher rate of photosynthesis

Main limiting factors of photosynthesis

• CO₂ concentration

• Light intensity

• Temperature

How can CO₂ concentration be varied experimentally

Use different concentrations of sodium bicarbonate solution → provides CO₂

How can light intensity be measured

using a lux meter

CO₂ enrichment

Experimentally increasing the CO₂ concentration above normal atmospheric levels to investigate its effect on photosynthesis + plant growth

Why CO₂ enrichment experiments are carried out

Predicts how future increases in atmospheric CO₂ may affect:

• Rate of photosynthesis

• Plant growth

Types of CO₂ enrichment experiments

• Enclosed greenhouse experiments

• Free-Air CO₂ Enrichment (FACE) experiments

How are enclosed greenhouse CO₂ enrichment experiments carried out

CO₂ concentration is artificially increased inside an enclosed greenhouse → its effects on photosynthesis + plant growth are measured

Advantage and disadvantage of enclosed greenhouse CO₂ enrichment experiments

Advantage: Variables → e.g. temperature + light can be carefully controlled

Disadvantage: Conditions are less representative of the natural environment

How are FACE experiments carried out

Pipes release CO₂ around plants in an open, natural environment → sensors monitor CO₂ concentration + adjust its release

Advantage and disadvantage of FACE experiments

Advantage: More representative of natural conditions → can study larger plants/ecosystems

Disadvantage: Environmental variables → e.g. temperature, rainfall + light are harder to control

Diagram of chloroplast

Photosystem

A molecular array of chlorophyll + accessory pigments pigments with a special chlorophyll as the reaction centre that absorb light energy + emit excited electrons during photosynthesis

Where are photosystems located

• In the thylakoid membranes of chloroplasts

• In the membranes of cyanobacteria

Why do photosystems contain different pigments

Different pigments absorb different wavelengths of light → grouping them together allows the photosystem to absorb a wider range of wavelengths

Types of photosystems

• Photosystem I (PSI) → 700nm

• Photosystem II (PSII) → 680nm

Can a single pigment molecule perform photosynthesis

No → a single molecule of chlorophyll or any other pigment cannot perform any part of photosynthesis on its own

Why is the structured arrangement of pigments important

Allows energy absorbed by pigments to be transferred towards the reaction centre → enabling sufficient energy transfer for photosynthesis