Cell Energy

Metabolism

All the combined chemical reactions of an organism. Manages the material and energy resources of the cell

Catabolic Pathway

The release of energy by breaking down complex molecules to simpler compounds. An example includes digestion

Anabolic Pathway

consume energy to build complicated molecules from simpler ones. An example is linking together amino acids to form muscle protein(monomers to polymers)

Energy

The capacity to do work

Kinetic energy

the energy of moving objects

chemical potential energy

The energy stored in the chemical bonds of molecules.

electrical potential energy

the energy available when you have an electrical gradient across a semipermeable membrane

Thermodynamics

study of energy transformations that occur in matter.

1st law of thermodynamics

states that the energy of the universe is constant and that energy can be transferred an transformed, but it cannot be created or destroyed.

2nd law of thermodynamics

every energy transfer increases entropy, or the amount of heat loss/disorder or randomness

Free Energy

usable energy available for an organism to do work (ΔG)

Exergonic Reaction

chemical reaction that releases free energy

Endergonic Reaction

chemical reaction that absorbs free energy; that is they require the investment of free energy

Energy Coupling

Using an exergonic reaction to power an endergonic reaction

ATP

Adenine Triphosphate. They are molecules that deliver immediately available energy to run cellular processes(mitosis, active transport, etc.) Most biological energy consuming processes have an ATPase attached.

Phosphates

Phosphate groups are negatively charged. They are often added (phosphorylation) or removed (dephosphorylation) to manipulate free energy in a living system.

ATPase

An enzyme (protein) that catabolizes ATP into ADP and phosphate.

ATP synthase

An enzyme (protein) that anabolizes ATP using the flow of H+ ions to bind ADP and a phosphate group together.

Feedback Inhibition

When the end products of long metabolic pathways become allosteric inhibitors . Increases the efficiency of the pathway by turning it off when the end product accumulates in the cell

fermentation (anaerobic respiration)

The partial degradation of sugars that occur without the use of oxygen

Aerobic Respiration

the most prevalent and efficient catabolic pathway in which oxygen is consumed as a reactant along with organic fuel(most commonly glucose but other foods are sources)

Redox Reactions

Oxidation and reduction reactions (LEO says GER) coupled to transfer electrons (energy) in a chemical reaction.

Reduction

Reactants gain of one or more electrons (energy). They typically lose O and add H. [GER]

Oxidation

the loss of one or more electrons (energy) from a reactant. They typically lose H and gain O. [LEO]

NAD+ and NADH

NAD+ is a derivative of the B vitamin Niacin. It gains two electrons plus the stabilizing hydrogen ion to form NADH(it is reduced, therefore has gained energy)

Glycolysis

Location is the cytoplasm/cytosol.

Needs 2 ATP to make glucose more reactive

Enzyme reactions produce 4 ATP through substrate level phosphorylation

Glucose(six Carbon) is converted to two pyruvate(3 carbons each)

Products:2 net ATP and 2 NADH

No oxygen is needed

Oxidation of Pyruvate

A transport protein moves pyruvate from the cytosol into the matrix of the mitochondria

Carbon is removed in the form of CO2, electrons are stripped from the pyruvate to form 2 NADH, and coenzyme A joins with the remaining two carbons

2 acetyl are produced per glucose molecule

Krebs/Citric Acid Cycle

location: mitochondrial matrix

2 cycles each:

removes CoA from acetyl

release 2 carbon as CO2

production of 1 ATP through substrate level phosphorylation

production of 3 NADH

production of 1 FADH2

overall products are: 4 CO2, 6 NADH, 2 FADH2, and 2 ATP

Electron Transport Chain

In the inner membrane of the mitochondria

powered by electrons from NADH and FADH2.

O2 is the final electron acceptor.

The loss of energy through the electrons causes the proton gradient.

At the end, the electrons combine with 2 hydrogen ions and oxygen to form water.

Proton gradient

Electrical potential energy created by the electron transport chain (ETC) during Oxidative phosphorylation and the Light Dependent Reactions (LDR).

FAD+ and FADH2

a B vitamin coenzyme that is an electron acceptor in the citric acid cycle as well as an electron donor in the ETC

Oxidative Phosphorylation

oxygen is used to convert ADP into ATP via two processes: ETC and Chemiosmosis.

Chemiosmosis

energy coupling that uses energy from the H+ ion gradient to drive cellular work, which in this case is ATP synthesis

Anaerobic Respiration

Produce ATP and recycle NAD+ without consuming oxygen (fermentation).

Fermentation

the recycling of NAD+ under anaerobic conditions

Alcohol Fermentation

pyruvate is converted to ethanol, releasing CO2 and oxidizing NADH in the process to create more NAD+

Lactic Acid Fermentation

pyruvate is converted to lactate and oxidizing NADH in the process to create more NAD+

facultative anaerobes

can make ATP via cellular respiration if oxygen is present or fermentation if oxygen is not present

Obligate Aerobe

Organisms that require oxygen for cellular respiration to survive.

Chloroplast

They are the organelle of photosynthesis

Stroma-plasma of the chloroplast (location of Calvin Cycle)

Thylakoids-pigment filled membranes (location of light dependent reactions)

Chlorophyll

located in the thylakoid membranes and is the light absorbing pigment that drives photosynthesis and gives plants their green color

Stomata

tiny pores, usually on the lower epidermis of the leaf;

gas exchange happens here (CO2 in; O2 and H2O out)

Photosynthesis Reaction Formula

Light Dependent Reactions

occur in and around the thylakoid membrane;

stores chemical energy in the form of NADPH, and ATP;

oxygen gas is the waste product

Carbon Fixation

when CO2 from the air is incorporated into organic molecules

Photons

discrete particles of light, which is electromagnetic energy

Pigments

substances that absorb light

Absorption Spectrum

a graph plotting a pigment's light absorption versus wavelength

Action Spectrum

graphs the effectiveness of different wavelengths of light in driving the process of photosynthesis

Photosystem II (P680)

Photosystem II (aka P680) is the first photosystem in the light dependent reactions; it provides e- to the electron transport chain and hydrolyzes H2O for the e- and H+

Photosystem 1 (P700)

Photosystem I (aka P700) is the second photosystem in the light dependent reactions; it provides e- to NADP+ in linear e- flow OR e- to the electron transport chain for cyclical e- flow.

Linear(noncyclic) electron flow

Produces an electrochemical gradient in the first electron transport chain (ETC) and NADPH in the final ETC.

PS2 --> ETC1 --> PS1 --> ETC2 --> NADPH

cyclic electron flow

Produces an electrochemical gradient in the first electron transport chain (ETC) over and over and over again.

PS2 --> ETC1 --> PS1 --> ETC1 --> PS1 --> ETC1 --> ...

Chemiosmosis in Chloroplasts

uses the electrochemical gradient across the thylakoid membrane (created by the ETC), to power ATP synthase to phosphorylate ADP into ATP

Calvin Cycle

Makes sugar from CO2 in three stages:

1. Carbon Fixation

2. Reduction

3. Regeneration of RuBP

Carbon Fixation (Calvin Cycle)

Rubisco attaches CO2 to RuBP.

RuBP

ribulose biphosphate;

in the calvin cycle these are attached to CO2 molecules

Rubisco

an enzyme is supposed to fix CO2 to RuBP;

sometimes it fixes O2 to RuBP (photorespiration), this is bad for the plant

Reduction (Calvin Cycle)

ATP AND NADPH are used to convert molecules into pre sugars (G3P)

G3P

the product of reduction (Calvin Cycle) that are the building blocks of all sugars

Regeneration (Calvin Cycle)

New RuBPs are generated from the remaining G3P's.

Impact of Hot Dry Days on Photosynthesis

On hot days, plants close their stomata to conserve water; this means no CO2 uptake and no O2 release; this leads to an increase in photorespiration

Photorespiration

rubisco will bind to O2 instead of CO2 to RuBP; this is a highly inefficient energy consuming process.

C4 photosynthesis

mesophyll cells perform the light reactions, while bundle sheath cells perform the calvin cycle; this reduces the rate of photorespiration

CAM Photosynthesis

crassulacean acid metabolism;

stomata are closed during the day and light dependent reactions occur; at night, the stomata open and CO2 is fixed into malate, which is the carbon source for the Calvin Cycle

Structure of Chlorophyll

magnesium center

has a hydrocarbon tail to make it lipophilic for membrane attachment

Leaf Structure

photosynthesis takes place in the mesophyll cells; stomata are small pores for gas exchange; the epidermis is the outer protective layer (sometimes there is a waxy cuticle layer too); veins transport reactants to the leaf, and products out of the leaf

Paper Chromatography

technique for separating and identifying pigments from cell extracts

solvents move up by capillary action

Rf Values

ratio of the movement of the pigment(B) over the migration of the solvent(F)