AP Biology - Unit 3

Cellular Energetics

What is an Enzyme?

A type of protein

What is the structure of an enzyme?

It is folded into a 3 dimensional shape with an active site

What is an active site?

The bonding location of an enzyme

What does the function of an enzyme depend on?

To it’s role in chemical reactions

What is a substrate?

The reactant that an enzyme acts on

When an enzyme bonds to it’s substrate…:

A temporary molecule called the enzyme-substrate complex is formed

Where does the substrate bind?

The active site

What is a catalyst?

A chemical agent that speeds up a reaction

How do enzymes work?

By lowering activation energy

How can an enzyme lower activation energy (E_a)?

• Orienting substances correctly

• Straining substrate bonds

• Providing a favorable microenvironment

• Covalently bonding to the substrate

What can affect Enzyme function ?

• Environmental factors

• Temperature

• pH

• Chemicals

What other factors can affect the rate of reaction?

• Amount of enzymes present

• Concentration of substrate

• Presence of cofactors/coenzymes

• Presence of enzyme inhibitors

What are the types of enzyme inhibition?

• Competitive

• Non-competitive

How does competitive inhibition work?

Competitive inhibitors bind to the active site of an enzyme and compete with the substrate.

How do non-competitive inhibitors work?

Noncompetitive inhibitors bind to another part of an enzyme and cause the enzyme to change shape, making the active site less effective

How does allosteric regulation work?

• The binding of an activator stabilises the active form of the enzyme

• The binding of an inhibitor stabilises the inactive form of the enzyme.

What is cooperativity?

A form of allosteric regulation

How does cooperativity work?

The binding of a substrate to one active site stabilises favorable conformational changes to all other subunits

What is feedback inhibition?

When an end product of a metabolic pathway shuts down the pathway

Why is feedback inhibition useful?

Because it prevents a cell from wasting chemical resources by synthesising more product than is needed.

What is metabolism and what makes it?

It is the totality of an organisms chemical reactions and arises from interactions between molecules within the cell

What is a metabolic pathway?

• a series of interconnected, enzyme-catalyzed chemical reactions within a cell that convert one molecule (substrate) into another (product), essential for life by managing energy and building blocks

What is a catabolic pathway?

• A set of metabolic reactions that break down complex, large molecules, into simpler ones

• They release energy

What are anabolic pathways?

• A set of metabolic pathways that build complex compound molecules from simpler ones

• They consume energy

What is energy?

The capacity to cause change

What are some forms of energy that can preform work?

• Kinetic energy - associated with motion

• Thermal energy - kinetic energy associated with random movement of atoms or molecules

• Potential energy - Energy that matter possesses because of it’s location or structure

• Chemical energy - potential energy available for release in a chemical reaction

What is heat?

Thermal energy in transfer between objects

What is the first law of thermodynamics?

• The energy of the universe is constant

• Energy can be transferred and transformed

• Energy cannot be created or destroyed

What is the second law of thermodynamics?

• During every energy transfer or transformation, some energy is unusable, often lost as heat

• Every energy transfer or transformation increases the entropy of the universe

What is entropy?

A measure of molecular disorder, or randomness

What are exergonic reactions?

• Chemical reactions that release free energy, occurring spontaneously, because their products have lower energy than their reactants

• Exothermic

What are endergonic reactions?

• Chemical reactions that absorb surrounding energy, occurring non-spontaneously because their products have more energy than their reactants

• Can sometimes be (but not necessarily) endothermic (only if it absorbs surrounding heat)

What are redox reactions?

Chemical reactions that transfer electrons between reactants

What is oxidation?

A chemical reaction where a substance loses electrons

• In organic chemistry, it can also mean to gain oxygen and/or lose hydrogen

What is reduction?

A chemical reactions where a substance gains electrons

• Is reduced (the amount of positive charge is reduced)

• In organic chemistry can also mean the gain of hydrogen atoms

What is a cell’s energy source?

ATP (Adenosine triphosphate)

What is ATP composed of?

• A ribose (a sugar)

• Adenine (a nitrogenous base)

• Three phosphate groups

How is energy released from ATP?

• When the terminal phosphate bond is broken

• The release of energy comes from the chemical change to another state of lower free energy

How can the bonds between the phosphate groups of ATP’s tail be broken?

By hydrolisis

What kinds of work does a cell do?

• Chemical work - pushing endergonic reactions

• Transport work - pumping substances against the direction of spontaneous movement

• Mechanical work - Such as contraction of muscle cells

What is energy coupling?

The use of an exergonic process to drive an endergonic process

How is energy coupling mediated?

By ATP - ATP hydrolisis

What is photosynthesis?

A complex series of reactions that convert solar energy into chemical energy

Which organisms use photosynthesis?

• Plants

• Algae

• Some prokaryotes

What are autotrophs?

Organisms that sustain themselves without eating things derived from other organisms

What are photoautotrophs?

Organisms that use solar energy to make organic molecules from water and carbon dioxide

Where does photosynthesis in plants mostly occur?

In the leaves - which contain chlorophyll

What is chlorophyll, and what role does it play in photosynthesis?

• A green pigment in chloroplast

• It absorbs light energy

What are the stomata and what role do they play in photosynthesis?

• Microscopic pores on leaf surface

• CO₂ enters and O₂ exits from the stomata

What are chloroplasts and where are they located?

• The interior tissue of the leaf

• Found mainly in the mesophyll

  • There are typically 30-40 chloroplasts in a mesophyll cell

What are thylakoids and what role do they play in photosynthesis?

• Membranes containing chlorophyll

• They convert solar energy into ATP

What are Grana?

Stacks of thylakoid membranes

What is Stroma?

Dense fluid that surrounds thylakoid

What is the process of photosynthesis?

• Redox process

  • Water is oxidized

  • Carbon dioxide is reduced

• Light reactions

  • in thylakoids

  • Split water

  • release O₂

  • Produce ATP

  • form NADPH

• Calvin cycle

  • In stroma

  • forms sugar from CO_2, using ATP and NADPH

  • Begins with carbon fixation

  • Incorporating CO₂ into an organic molecule

What are pigments?

Substances that absorb visible light

How do pigments absorb visible light?

Pigments absorb specific wavelengths and wavelengths that are not absorbed are reflected or transmitted

What is the main photosynthetic pigments?

Chlorophyll A

What are examples of photosynthetic accessory pigments and how are the useful?

• Chlorophyll b - broaden the spectrum used for photosynthesis

• Carotenoids - Absorb excessive light that would damage chlorophyll

What are photosystems consisted of?

A reaction centre surrounded by light-harvesting complexes

What are light-harvesting complexes?

Pigment molecules bound to proteins that funnel the energy of photos to the reaction center

What is the first step of light reactions?

Primary electron acceptor in reaction centre accepts an excited electron from chlorophyll a

• Solar-powered transfer of an electron from a chlorophyll a molecule to the primary electron acceptor

What are the two types of photosystems in the thylakoid membrane?

• Photosystem II

  • Functions first (the numbers reflect the order of discovery)

  • Best at absorbing a wavelength of 680nm

• Photosystem I

  • Best at absorbing a wavelength of 700nm

How do both photosystems work together?

They use light energy and produce ATP and NADPH

What are the two routes for electron flow?

Cyclic and noncyclic

What is the noncyclic electron flow?

• The primary pathway

• Involves both photosystems

• produces ATP and NADPH

What is the cyclic electron flow?

• Uses only photosystem I

• Produces only ATP

• generates a surplus of ATP

• Satisfying the higher demand in the Calvin cycle

What is the role of water in Photosynthesis?

• Water is split by the photosystem II on the side of the membrane facing the thylakoid space

• The diffusion of H+ from the thylkoid space back to the stroma powers ATP synthase

• ATP and NADPH are produced on the side facing the stroma, where the Calvin cycle takes place

What are the 3 phases of the Calvin cycle?

• Carbon fixation (catalyzed by rubisco)

• Reduction

• Regeneration of the CO₂ acceptor (RuBP)

How does the Calvin cycle work?

• It regenerates it’s starting material after molecules enter and leave the cycle

• Build sugar from smaller molecules by using ATP and the reducing power of electrons carried by NADPH

• Carbon enters the cycle as CO₂ and leaves as a sugar named glyceraldehyde -3-phosphate (G3P)

How many times must the Calvin cycle take place for the net synthesis of one G3P?

Three times, fixing three molecules of CO₂

What are problems that plants face that affect photosynthesis?

• Dehydration due to hot and dry conditions

  • Plants close stomata, which conserves water but limits photosynthesis

    • Reduces access to CO_2, O₂ buildup

    • Photorespiration

What are the different plant types?

• C3 plants

• C4 plants

• CAM plants

What are C3 plants?

• The most common type of plant that preforms photosynthesis by fixing CO₂ into a 3 carbon compound first

• They are efficient in moderate climates

What is photorespiration?

• a light-dependent process in plants where the enzyme Rubisco mistakenly adds oxygen (O2) instead of carbon dioxide (CO2) to RuBP

• consumes energy and releases CO2 without producing ATP or sugar

• makes photosynthesis less efficient, especially in hot, dry conditions when stomata close

What are C4 plants?

• Plants that minimize the cost of photorespiration by incorporating CO₂ into four-carbon compounds in mesophyll cells

• These compounds are then exported to bundle-sheath cells

• They release CO₂ that is then used in the Calvin cycle

What are CAM plants?

• Plants that open their stomata at night, and close them in the day

• They incorporate CO₂ into organic acids

• CO₂ released from organic acids and is used in the Calvin cycle

What happens in cellular respiration?

• fuel (ex glucose) is oxidised

• Oxygen is reduced

What are the 4 stages of cellular respiration?

• Glycolysis

• Pyruvate Oxidation

• The citric acid cycle

• Oxidative phosphorylation

What happens in glycolysis?

Glucose is broken down into two molecules of pyruvate

What happens in pyruvate oxidation?

Pyruvate is converted to beginning molecule for next cycle.

What happens in the citric acid cycle?

The breakdown of glucose is completed.

What happens in oxidative phosphorylation?

• This is where most ATP is synthesised

• It is powered by redox reactions

What are the two major phases of glycolysis?

• Energy investment phase

• Energy payoff phase

Where does glycolysis occur?

In the cytoplasm

How does pyruvate get converted to beginning molecule of next cycle?

• In the presence of O_2, pyruvate enters a mitochondrion

• Pyruvate must be converted to acetyl coenzyme A, which links glycolysis to the citric acid cycle

What are the 3 main reactions of pyruvate oxidation?

• Oxidation of pyruvate and release of CO₂

• Reduction of NAD+ to NADH

• Combination of the remaining two-carbon fragment and coenzyme A to form acetyl CoA

How many steps are there in the citric acid cycle?

8

What is the 1st step of the citric acid cycle?

The acetyl group of acetyl CoA joins the cycle by combining with oxaloacetate, forming citrate

What happens in the next 7 steps of the citric acid cycle?

The citrate is decomposed back to oxaloacetate

How is ATP produced through the citric acid cycle?

NADH and FADH₂ produced by the cycle relay electrons extracted from food to the electron transport chain which powers ATP synthesis via oxidative phosphorylation

What is the electron transport chain (ETC) (Oxidative phosphorylation)

a series of protein complexes in cell membranes (mitochondria in eukaryotes) that transfers electrons from donors (like NADH) to acceptors (like oxygen), releasing energy used to pump protons and create a gradient, which then powers ATP synthase to produce the majority of ATP during cellular respiration

What is the function of the Elctron Transport chain?

To break large free-energy drop from food to O₂ into smaller steps that release energy in manageable amounts

Where does the ETC take place?

In the cristae of the mitochondrion

What happens to electrons as they go down the ETC?

They drop in free energy, until they are finally passed to O_2, forming water

• ETC PRODUCED NO ATP DIRECTLY!

What is chemiosmosis?

The use of energy in a H+ gradient to drive cellular work

What is an example of Chemiosmosis?

• Electron transer in the ETC causes proteins to pump H+ from the mitochondrial marix to the intermembrane space

• H+ then moves back across the membrane, passing through channels in ATP synthase

• ATP synthase uses the exergonic flow of H+ to drive phosphorylation of ATP

What is the sequence of energy flow for cellular respiration?

Glucose → NADH → ETC → Proton-motive force → ATP

Approximately what percent of energy in a glucose molecule is transferred to ATP during cellular respiration?

40%

Approximately how much ATP is made in cellular respiration?

38 ATP

What does fermentation consist of?

Of glycolysis plus reactions that regenerate NAD+