AP Biology - Cellular Energies

Bioenergetics

The study of how cells release energy from bonds when they require that energy and store it when they don’t

First Law of Thermodynamics

“Energy cannot be created or destroyed. In other words, the sum of energy in the universe is constant.”

Second Law of Thermodynamics

Energy transfer —> less organization. Means that the universe is less organized.

Entropy

Disorder

Exergonic Reactions

Energy is given off during the reaction. Products have less energy than reactants. Ex: Oxidizing of molecules in mitochondria

Energy Diagram

Energy represented along y-axis

Energonic Reactions

Products have more energy than reactants. Ex: plants using carbon dioxide + water to make sugar

Transition State

Reactants have to turn into a high energy molecule before becoming the products.

Activation Energy

The energy required to reach the transition state. Required in order to break bonds before reforming them, like what happens in a reaction

Enzyme

Biological catalyst used to start the reaction. Lower the activation energy + help transition step molecule form.

Enzyme Specificity

Each enzyme only catalyzes one kind of reaction

Substrates

For enzyme reactions, these are the targeted molecules

Active Site

The place on the enzyme where the enzyme-substrate complex is formed

Enzyme-Substrate Complex

The state when the enzyme and substrate(s) are attached

Enzymes Do

Increase rate of reaction due to lowering the activation energy. Make an enzyme-substrate complex that is temporary. Doesn’t change the structure of the enzyme

Enzymes Don’t

Change the reaction. Make a reaction happen that wouldn’t happen normally

Induced Fit

Sometimes the enzyme has to change its shape to make room for the substrates

Cofactors

What an enzyme uses to help catalyze a reaction, could be either organic, inorganic or an ion. Inorganic coenzymes tend to be metals. Vitamins are organic coenzymes.

Heat

This factor will speed up a reaction up until a point

Denatured

When enzymes are damaged by heat and are no longer able to catalyze reactions. Most enzymes best function at 37 degrees celsius, which is body temperature

Q₁₀

Measure of temperature sensitivity of a physiological process or enzymatic reaction. Formula: Temperature must be in either celsius or kelvin and that temperature unit must be used throughout. Reaction rates must be in the same unit. Q₁₀ isn’t a unit, the more temperature dependent a reaction is, higher Q₁₀. If Q₁₀ = 1, temperature independent

pH disruption

Optimal pH is 7 for most enzymes, but some enzymes function best at different pHs. Ex: Pepsin, found in the stomach, works best at pH of 2. At the wrong pH, hydrogen bonds making up the enzyme can change and potentially be altered.

Saturation Point

Increase in substrate concentration, at the beginning will speed up reaction, but once all of the enzymes are occupied the reaction will slow back down

Allosteric Sites

Other sites on the enzyme that aren’t the active site

Competitive Inhibition

When a substance blocks a substrate from entering the enzyme’s active site.

Allosteric Inhibitor

Inhibitor binds to allosteric site

Noncompetitive Inhibitor

Binds at an allosteric site, a substrate can still bond at active site, but this changes the shape of the enzyme, so that it can’t react

Adenosine Triphosphate (ATP)

One adenosine bonded with three phosphate. Lots of energy put into the phosphate bonds. Energy from exergonic reactions like ATP hydrolysis are used to power endergonic reactions

Cellular Respiration

The process of breaking down sugar and creating ATP

Photosynthesis

Where sugar is created in autotrophs. Begins with photons hitting a leaf, which excites electrons + activates chlorophyll. Electrons get passed along electron carriers, which eventually makes ATP + NADPH.

Equation of Photosynthesis

6CO₂ + 6H₂O —> C₆H₁₂O₆ + 6O₂

Theory with evidence

Prokaryotic photosynthesis may have contributed to the oxygen in the atmosphere, also prokaryotic photosynthesis made it so that eukaryotic photosynthesis can happen now

Light Reactions

Also known as light dependent reactions

Dark Reactions

Also known as light independent reactions

Photons

Energy units

Chloroplast

Primary site of photosynthesis

Stroma

Inside the membrane of a chloroplast

Grana

Inside stroma, small structures that look like coin structures

Thylakoids

Structures that make up the grana, have chlorophyll within them.

Chlorophyll a

A light-absorbing pigment in photosynthesis (a)

Chlorophyll b

A light-absorbing pigment in photosynthesis (b)

Carotenoids

A light-absorbing pigment in photosynthesis (c). Absorb blue-green light, plants with lots of these are orange, yellow or red

Reaction Center

The place where the molecule that can transform light energy to chemical energy

Antenna Pigments

Bounce light off themselves to bring to the reaction center

Photosystem I (PS I)

The main type of chlorophyll present in this structure is P700

P700

Best absorbs light at a wavelength of 700 nanometers, reaction center in photosystem I. This excites the electrons that will be used to produce NADPH

Photosystem II (PS II)

Main type of chlorophyll present in structure is P680

P680

Reaction center in Photosystem II, best absorbs light at 680 nanometers. This excites the electrons that will be used to produce ATP.

Photophosphorylation

When light energy is used to make ATP

Absorption Spectrum

Model representing how well a pigment absorbs electromagnetic radiation. Light absorbed plotted as a function of radiation waves

Emission Spectrum

Opposite of absorption spectrum. Tells which wavelengths are being given off by a pigment

Photolysis

When water is split into oxygen, hydrogen ions and electrons to make more electrons to replace the ones in photosystem II

In the grana of chloroplasts, where the thylakoids are

Where do light reactions occur?

Cyclic Photophosphorylation

Only ATP and no NADPH produced. Only uses photosystem I

Carbon Fixation

Turning CO₂ into carbohydrates. Happens in stroma.

Calvin-Benson Cycle

Also known as the dark reactions, happens in stroma. ATP + NADPH are necessary, CO₂ is fixed in order to make

Stomata

Pores on leaf surface that let CO₂ in and O₂ + water out

Photorespiration

Not great process which plants use when they don’t have as much access to CO₂ and oxygen is building up. Uses ATP + O₂, produces CO₂ and doesn’t produce sugar

CAM plants

These live in hot environments, separate carbon fixation and the Calvin cycle. Open stomata at night and bring CO₂ into organic acids. During day, close stomata + release CO₂ from acids, letting light reactions run

C4 Plants

Changed their leaf anatomy, so they can fix carbon in a different part of the leaf from the rest of the Calvin cycle. Stops photorespiration, C₄ plants make a four carbon molecule during carbon fixation and then perform cyclic electron flow in light reactions

C6H12O6 + 6O2 -> 6CO2 + 6H2O + ATP

Equation for cellular respiration

Aerobic Respiration

Four stages: Glycolysis, Formation of Acetyl-CoA, Krebs (citric acid) cycle, oxidative phosphorylation

NADH

Electron carrier that unloads their electrons (N)

FADH2

Electron carrier that unloads their electrons (F)

Glycolysis

The splitting of glucose, first stage of aerobic respiration

Glucose

Six carbon molecule that gets split during glycolysis

Pyruvic Acid

Three carbon molecule that gets made during glycolysis

Glucose + 2 ATP + 2 NAD+ -> 2 Pyruvic Acid + 4 ATP + 2 NADH

Equation for glycolysis

In the cytoplasm

Where does glycolysis happen?

Net gain of 2 ATP

What is the net production of ATP

2 pyruvic acids

How many pyruvic acids formed?

2 NADH

How many NADH produced?

Acetyl Coenzyme A

Also known as acetyl CoA, two carbon molecule,

2 Pyruvic Acid + 2 Coenzyme A + 2 NAD+ -> 2 Acetyl-CoA + 2 CO2 + 2 NADH

Equation of Formation of Acetyl-CoA

Pyruvate Dehydrogenase Complex

The enzyme that makes the formation of Acetyl-CoA reaction happen

Krebs Cycle

Also known as citric acid cycle. Where the carbons in the Acetyl CoA eventually get converted to CO₂

Matrix

Inside of the inner membrane of the mitochondria

Oxaloacetate

Four carbon molecule which Acetyl CoA combines with

Citric Acid

Also known as citrate. Acetyl CoA combines with oxaloacetate to form this six-carbon molecule

1 ATP, 3 NADH, 1 FADH2

What are the three types of energy produced in the krebs cycle and how much of each one is produced?

Electron Transport Chain

When NADH and FADH2 bring electrons around the membrane of the mitochondrial matrix.

Cytochrome C

One of the carrier molecules in the electron transport chain

pH gradient

This is formed when hydrogen ions get pumped into the mitochondrial matrix (pH)

proton gradient

This is formed when hydrogen ions get pumped into the mitochondrial matrix (pro)

Chemiosmosis

Pumping of ions and diffusion of ions to create ATP

ATP Synthase

The channel that hydrogen ions go through to diffuse across the inner membrane

Oxidative Phosphorylation

When protons flow across the channel give the energy in order to combine ADP and P, creating ATP

Anaerobic Respiration

What the cell goes into if it doesn’t have access to oxygen. Glycolysis can still run, but the krebs cycle and oxidative phosphorylation can’t.

Lactic Acid

What gets produced in muscles during anaerobic respiration

Ethanol

What gets produced in yeast during anaerobic respiration

Fermentation

Either produces ethanol or lactic acid, only done in emergencies.