# Energy and Work

Energy and organic molecules are required by every living organism, and are used in two ways;
    Building blocks for making other organic molecules that the organism needs.
    Chemical potential energy which can be released by breaking down the molecules in respiration.
This chemical potential energy is used in the following ways;
    Muscle contraction and other cellular movements
    Active transport of substances
    Synthesis of complex substances (anabolic reactions) from simple ones.
Energy yielding reactions in all organisms generally produce an intermediary energy molecule, ATP.

# ATP (Adenosine Triphosphate)

ATP consists of adenine (organic base) and ribose (pentose sugar), making adenosine (a nucleotide), which is then combined with three phosphate groups to make ATP, a nucleotide. It is a small water-soluble molecule, allowing easy transport. When a phosphate group is removed, [known as Hydrolysis] ADP is formed and it produces 30.6kJ of energy, and is a reversible reaction that allows for interconversion between ATP and ADP - the formula is below: known as phosphorylation.
    ATP + H$_2$O ↔ ADP +H$_3$PO$_4$ ΔG = ± 30.6kJ

### Energy Currency

The cells energy yielding reactions synthesise ATP, and ATP is used by the cell in all forms of work. and the cell trades in ATP rather than using intermediates. Energy lost during energy transfers is converted to thermal energy, as well as any excess energy, if too much is produced to create ATP for example. Energy currency is immediate donor of energy to cell's energy-requiring reaction, and a storage molecule is a short-term (glucose) or long term (glycogen) store of chemical energy. ATP losses a phosphate group and forms ADP

### Synthesis

Most ATP is synthesised using electrical potential energy, the energy from the transfers of electrons by electron carriers in mitochondria and chloroplasts. It's stored as a difference in hydrogen ion concentration across the membrane (the membranes of mitochondria and chloroplasts are basically impermeable to hydrogen ions). Hydrogen ions are then allowed to flow down their concentration gradient through a transport protein, and part of this protein is ATP synthase, an enzyme that, surprisingly, synthesises ATP. The transfer of three hydrogen ions results in the production of one ATP molecule provided that ADP and a phosphate group is present inside the organelle.

## Roles

ATP is required for various biological processes in animals including; Active Transport, Secretion, Endocytosis, Synthesis and Replication of DNA and Movement.

### Active Transport

Active Transport is the movement of molecules defined as the energy-consuming transport of molecules or ions across a membrane against a concentration gradient, made possible by transferring energy from ATP. Most cells have sodium/potassium pumps and these are maintained by ATP, for many many things.

### Muscle Contraction

Muscle contraction goes as such;
A sarcomere contracts by sliding the thin actin filaments over the thick myosin filaments (molecules with a flexible head, an ATPase molecule, hydrolyses ATP to ADP and phosphate)
    1. Calcium ions are released from the sarcoplasmic reticulum, allowing the myosin head to bind to the portion of actin filament next to it.
    2. This head then tilts at 45 degrees, moving the actin filament about 10nm in relation to the myosin towards the centre of the sarcomere
    3. Millions of fibres doing this at the same time makes the muscle contract, releasing ADP and phosphate
    4. Another ATP binds to the head and is again hydrolysed, and the head tilts back to it's original position
    5. When contraction ends, ATP is used to pump calcium ions back into the sarcoplasmic reticulum.
During contraction, ATP is continually regenerated using creatine phosphate, which provides a phosphate group to ADP, allowing it to become ATP and creatine. The limited supply of creatine phosphate must be replenished via ATP from respiration. The muscle may not be able to keep up with it and a lactate pathway is used to allow continued formation of ATP, but the cells incur an oxygen debt.

# Respiration
### Glycolysis

This is the splitting of glucose, that eventually results in two molecules of pyruvate. ATP is used in the first stage, where glucose is phosphorylated using ATP, which allows the reaction to be easier. Glucose breaks down to hexose phosphate, which breaks down to hexose biphosphate, which breaks down to 2 molecules of triose phosphate. Hydrogen is then removed and transferred to NAD, producing two molecules of reduced NAD for each glucose molecule. The process produces 4 ATP molecules in total, in addition to the two molecules of reduced NAD, but requires 2 ATP molecules.
In summary. Glucose > Glucose-6-phosphate > Fructose-1-phosphate > Hexose-1,6-bi(s)phosphate > 2x Triose Phosphate > 2x Intermediate Compound > 2x Pyruvate.
Pyruvate is then actively transported to the mitrochrondrial matrix for the link reaction. Thus ultimately producing;
* 2 ATP Molecules
* 2 Pyruvate Molecules
* 2 Molecules of Reduced NAD [NADH]

### Link reaction

Pyruvate and NAD enter the link cycle which takes place in the mitochondrial matrix, where it is decarboxylated, dehydrogenated and combined with Coenzyme A to give acetyl coenzyme A. CO$_2$ is produced and NAD is reduced. Acetyl coenzyme A acts as a carrier of acetyl groups to the krebs cycle. The hydrogen removed from pyruvate is now transferred to NAD.
Thus ultimately; [as 2 molecules of Pyruvate]
* 2NADH produced
* 2 Co$_2$ produced

### Krebs cycle

The krebs cycle(also known as Citric acid cycle or tricarboxylic acid cycle)is a closed pathway of enzyme-controlled reactions;
    1. Acetate [from Acetyl CoA] combines with a four-carbon compound (oxaloacetate) to form a six-carbon compound (citrate)
    2. Citrate is decarboxylated and dehydrogenated (the hydrogens reduce both NAD and FAD), yielding CO$_2$ and NADH and FADH.
    3. ATP is produced via SLP [Substrate Level Phosphorylation]
    4. Oxaloacetate is regenerated to combine with another acetyl coenzyme A from the link reaction.
For each turn of the krebs cycle, three NAD molecules and one FAD are reduced,2 carbon dioxide molecules are produced and one ATP molecule is generated via an intermediate compound. The hydrogen released is used in oxidative phosphorylation to provide energy to make ATP.The reactions of Krebs cycle do not make use of oxygen.However,Oxygen is required in the final stage(i.e. Oxidative phosphorylation).

### Oxidative phosphorylation

The electron transport chain provides the energy for the phosphorylation of ADP to ATP, and this takes place in the mitochondrial membranes. Reduced NAD/FAD are passed to the electron transport chain where hydrogens are removed from the two hydrogen carriers and is split into hydrogen ions and an electron. The electron is passed to a series of electron carriers whilst the hydrogen ion remains in the mitochondrial matrix. Once the electron is tranferred to oxygen, a hydrogen ion will be draw from the solution to reduce the oxygen to water.
The transfer of electrons along the series of electron carriers, passing from a higher carrier to a lower one, releasing energy, making it available to convert ADP + Phosphate to ATP. Each reduced NAD molecule produces 2.5 molecules of ATP (an average) and each reduced FAD produces 1.5 molecules of ATP (on average).

#### Chemiosmosis

The energy from the electron transport chain is used to pump hydrogen ions from the mitochondrial matrix into the area between the plasma membrane and the cristae - the concentration of hydrogen ions becomes higher than that in the matrix, a concentration gradient exists. Hydrogen ions are then allowed to pass that through protein channels that have the enzyme ATP synthase on the end, as the ions pass through their electrical energy is used to synthesise ATP. The energy of three hydrogen ions are used to phosporylate one ADP to ATP.

# Anaerobic respiration
### In Mammals

Pyruvate > Lactic Acid
Pyruvate is dehydrogenated via Lactate Dehydrogenase producing Lactic Acid in mammals. Pyruvate accepts 2H, allowing NADH > NAD + 2H. This is very useful biologically for mammals, as during anaerobic respiration, the Link Reaction, Krebs Cycle and Oxidiative Phosphorylation cannot occur; as they all rely on O$_2$ or the products of a process that does. The biological use is that NAD is reoxidised which means it now can accept 2H in Glycolysis, this allows for 2ATP's to be released via glycolysis allowing the mammal to continue to respire and produce ATP without the presence of oxygen.

### In Yeast

Pyruvate > Ethanal > Ethanol
* Pyruvate is decarboxylated via Pyruvate decarboxylase to produce Ethanal [CO2 as a biproduct]
* Ethanal accepts 2H atoms from NADH thus going to Ethanol and reoxidising NAD.
Yeast is a 'facultative anaerobe' it can survive without oxygen although it is killed if the ethanol conc. exceeds 15%

# Respiratory Substrates

The main respiratory substrates for all cells are carbohydrate usually in the form of hexose sugars such as glucose. Although glucose is not essential for all cells - a lot of cells can oxidise lipids and amino acids.

### Energy Values

The energy liberated in aerobic respiration usually comes from the oxidation of hydrogen to water when reduced NAD and reduced FAD are passed into the electron transport chain. So the more hydrogen bonds to break, the more energy - lipids have a energy density more than double that of carbohydrates, because of their long fatty acid tails.

### Respiratory quotient

The overall equation for aerobic respiration shows that oxygen used = carbon dioxide produced, and so they are in a 1:1 ratio. Other substrates do not do this, and it is possible to show what is being used for energy by using the respiratory quotient, which is;
$Respiratory\,Quotient={\frac {volume\,of\,carbon\,dioxide\,per\,unit\,time}{volume\,of\,oxygen\,per\,unit\,time}}$
High RQ values usually indicate that anaerobic respiration is taking place.
| Respiratory Substrate | Respiratory Quotient |
| Carbohydrates | 1 |
| Fat | 0.7 - 0.72 |
| Proteins | 0.8 - 0.9 |
| Carboxilic Acids acid | 1.33 - 4.0 |