What is ATP
ATP is a nucleotide because it consists of a nitrogen containing base which is adenine, it contains a five carbon sugar which is ribose, and three phosphate groups. The phosphate groups are in a chain and each of them is negatively charged.
ATP is often described as the energy currency of the cell, it is used for temporary storage of energy and for energy transfer between processes and between different parts of the cell.
The quantity of ATP with a cell at any time is very small without ATP cells start to degrade within minutes. This damage is quickly irreparable and leads to cell death
Properties of ATP
-ATP is soluble in water so it can move freely through the cytoplasm and other aqueous solutions in the cell
-ATP is stable at pH levels close to neutral the same as in the cytoplasm
-ATP cannot pass freely through the phospholipid by layer of membranes. This means it cannot diffuse out of the cell and its movement between membrane bound organelles within cells can be controlled.
-The third phosphate group of ATP can easily be removed and reattached by hydrolysis and condensation reactions
-Hydrolysing ATP to ADP and phosphate releases a small amount of energy. This is enough for many processes within the cell. If more energy was released, there would be an excess of energy.
Main types of cellular activity that need energy
- Synthesis macro molecules.
Anabolic reactions that link monomer together into large polymers would be endothermic and therefore unlikely to happen without coupling them to conversion of ATP to ADP. One or more ATP molecule is used every time a monomer is linked to a growing polymer.. - Active transport
Pumping of ions or other particles across a membrane against the concentration gradient requires energy from ATP. the energy is used to cause reversible changes in the shape of the pump protein. When the pump is in one shape the particle can enter it from one side of the membrane. When the pump is in the other confirmation shape, the particle can exit on the other side of the membrane. One of the two shapes is more stable than the other. ATP is used to cause the change from the more stable to the less stable confirmation. Change back to the more stable confirmation happens without the need for energy. - Movements.
Cells require energy from ATP for movement. Components of cells are moved larger amounts of energy and therefore more ATP molecules are needed to change the shape of a cell. Some cells use changes of shape for movement from place to place the energy for these movements is provided by ATP..
Energy transfers during interconversions between ATP and ADP
ATP contains more chemical potential energy than ADP. Therefore, energy is released when ATP is converted to ADP and a phosphate. The amount of energy released is relatively small but sufficient for many processes within the cell. In some cases the phosphate group is linked to another molecule such as a protein pump in a membrane or a substrate in a metabolic reaction. When the phosphate detach from the molecule energy is released, this energy causes a change in the molecule for example, a confirmational change in a membrane pump or a chemical change the comfort substrate into a product.
Energy is required to convert ADP and phosphate back to ATP this energy can come from:
-Cell respiration
-Photosynthesis
-Chemosynthesis
There is a continual regeneration of ATP from a DP and phosphate in the cell.
Energy transfers during interconversions between ATP and ADP are not 100% efficient so some of the energy is transformed into heat.
Cell respiration definition
Cell respiration is a function of life that is performed by all living cells. In respiration carbon compounds are oxidised to release energy and this energy is used to produce ATP glucose and fatty acids are the main respiratory substrate is used in cell cells. In humans the food we eat is the source of respiratory substrate. Plants use carbohydrates or lipids previously made by photosynthesis.
In many cells respiration uses oxygen and produces carbon dioxide. It is therefore necessary for oxygen to enter cells through the plasma membrane while at the same time carbon dioxide exit the cell. Together these movements are known as gas exchange although they do not involve direct one for one swapping of molecules. Instead, both carbon dioxide and oxygen move across the plasma membrane independently by simple diffusion.
Gas exchange and cell respiration are different processes but they are interdependent without gas exchange cell respiration could not continue because there would soon be lack of oxygen and a harmful excess of carbon dioxide inside the cell. Without cell respiration gas exchange could not continue because the use of oxygen and production of carbon dioxide and respiration create the concentration gradient which causes gases to the fuse .
Anaerobic and aerobic cell respiration chem composition
So respiration can be performed using a variety of alternative metabolic pathways. Some pathways are aerobic meaning that they use oxygen while others are an aerobic where no oxygen is needed.
Aerobic respiration is in humans and in many other animals as well as plants use glucose and oxygen to change ADP to ATP and release carbon dioxide and water .
And aerobic respiration in humans and other animals and some bacteria use glucose to turn ADP into ATP and release lactate.
An aerobic respiration and yeast and other fungi use glucose to turn ADP into ATP and release ethanol plus carbon dioxide
Anaerobic and aerobic cell respiration features compared
In aerobic cell respiration, oxygen is used as an electron acceptor in oxidation reactions. Carbohydrates such as glucose and lipids including fats and oils as well as amino acid after deamination can be used. Carbon dioxide and water or waste products. The yield of ATP is much higher, more than 30 ATP molecules per glucose. Initial reactions are in the cytoplasm but more occur in the mitochondria including the use of oxygen.
In an aerobic cell respiration oxygen is not used, other substances act as oxygen acceptor and oxidation reactions. Only carbohydrates can be used. Carbon dioxide plus either lactate or ethanol or waste product and water is not produced. The yield of ATP is lower only two ATP is per glucose . All reactions happen in the cytoplasm the mitochondria are not required.
Anaerobic respiration in muscles
In humans the lungs and the blood system supply oxygen to most organs of the body rapidly enough for aerobic respiration sometimes however an aerobic cell respiration is used in muscles. The advantage of anaerobic respiration is that it can supply ATP very rapidly over a short time period. It is used when we need to maximise the power of muscle contractions.
Lactic acid is a waste product of anaerobic respiration muscles. There is a limit to the concentration that the human body can tolerate in this restricts how much and aerobic respiration can be done. This is the reason for the short time scale over which the power of muscle contraptions can be maximised. We can only sprint for a short distance not more than 400 meters . After vigourous muscle contraction the lactate must be broken down and this requires oxygen it can take several minutes for enough oxygen to be absorbed to breakdown all the lactate the demand for oxygen that builds up during a period of anaerobic respiration is called oxygen debt.
Variables affecting the rate of cell respiration
The rate of cell respiration can be determined from several types of measurement.
-Oxygen uptake
-Carbon dioxide production
-Consumption of glucose or other respiratory substrates
Oxygen uptake is usually used to determine the rate of aerobic respiration. It cannot be measured by finding how much air is breathed into the lungs because air contains other gases and oxygen.
To measure oxygen uptake, there are many different apparatus’s that are known as respirometers, they all have the following parts:
-A sealed glass or plastic container in which the organism or tissue is placed with enough air for it to remain healthy
-Alkali such as potassium hydroxide to absorb carbon dioxide produced during respiration
-A capillary tube containing fluid connected to the container to measure changes in the volume of air inside the respirometer
Carbon dioxide production normally adds to the volume of air in the atmosphere as oxygen intake reduces it. Inspirometer all carbon dioxide is absorbed by the base so any volume changes should be due to the oxygen intake alone. Volume changes recorded by movements of the fluid in the capillary tube are therefore a measure of oxygen consumption.
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Role of NAD
Oxidation and reduction are chemical processes that always occur together. This happens because they involve transfer of electrons from one substance to another oxidation is the loss of electrons from a substance reduction is a gain of electron.
Electron carriers are substances that need help and lose electrons reversibly. They often link oxidation and reduction in cells. The main electron carrier and respiration is NAD. The structure of NAD is similar to that of a nucleotide as it has an adenine base connected to a ribose sugar connected to 2 phosphates connected to another ribose sugar connected to a nicotinamide base.
NAD initially has one positive charge and exists as NAD+. Substances are oxidised in respiration by removing two hydrogen atoms. Each hydrogen consist of an electron and a proton. NAD+ accepts two electrons and one proton from the hydrogen atom becoming NADH which is reduced NAD and the other proton H+ is released.
Reactions involving NAD show that reduction can be achieved by accepting atoms of hydrogen because they hold an electron.
Oxidation can therefore be achieved by losing hydrogen atoms. Oxidation and reduction can also occur through a gain or loss of atoms of oxygen. There are fewer examples of this in biochemical processes. Adding oxygen atoms to a molecule or ion is oxidation because the oxygen atoms have a high affinity for electrons and tend to draw them away from other parts of the molecule or ion. The similar way losing oxygen atoms is reduction.
Glycolysis stages
Glycolysis is the first part of aerobic respiration when glucose or another monosaccharide is the substrate. It happens in the cytoplasm of cells. In glycolysis glucose is converted to pyruvate by a chain of reactions each of which is catalysed by a different enzyme. A useful outcome of glycolysis is the production of a small yield of ATP without any oxygen being consumed. For this reason the first stage of glycolysis may seem rather inefficient as ATP is used rather than produced.
Stage 1: phosphorylation of glucose
Phosphorylation is the addition of phosphate to a molecule. This requires energy but makes a molecule more unstable and therefore more likely to participate in subsequent reactions. In cells many phosphorylations are carried out by transfer of phosphate from ATP.
In the first stage of glycolysis glucose is Foss related. The reaction is usually shown with with a phosphorylation of glucose coupled by the conversion of ATP to ADP. This term is the glucose into glucose six phosphate. The six indicating that the phosphate is linked to the sixth carbon atom of the glucose molecule.
In the next reaction glucose is converted to fructose creating a symmetrical molecule that can be split in half. Then there’s a second phosphorylation on the first carbon of the fructose molecule creating fructose 16 biphosphate.
Stage 2: Lysis
Fructose biphosphate is now split to form two molecules of triose phosphate
Stage 3: Oxidation
Each of these triose phosphates is oxidised by removing their hydrogen atoms, these are taken by NAD which then becomes reduced NAD. Oxidation of a sugar produces an organic acid. The organic acid released is Glycerate. Energy is released by the oxidation of triose and allows for a second phosphate group to become attached (because an inorganic phosphate is released) so the product is bisphosphoglycerate.
Stage 4: ATP formation
ATP is produced in the final reactions of glycolysis by transfer of phosphate groups to ADP. This can happen twice because bisphosphoglycerate has two phosphates. In these reactions, the glycerate is converted to another organic acid pyruvate. This is the end of glycolysis.
To bisphosphoglycerate molecules are produced per glucose and each of them yields to ATPs. Therefore four ATP’s are produced per glucose in the final reactions of glycolysis but because two ATPs are used there is a net yield of two ATPs per glucose.
In the end one glucose containing six carbon atoms is converted into two pyruvates each containing three carbon atoms, and two any de molecules are converted into reduced NAD.
Conversion of pyruvate to lactate in anaerobic cell respiration for NAD regeneration
For glycolysis to happen of glucose, ADP and NAD must be replenished.
-glucose should not run out as long as there are stores in a cell or does transported from elsewhere
-ADP will only run out if all of it has been converted to ATP in which case there is no need to carry out glycolysis
-NAD will run out unless it is regenerated by oxidation of reduced NAD
There are several methods of regenerating NAD. In each case, two hydrogen atoms are transferred to another molecule oxidising reduced NAD. In some human cells and also some other animals and bacterial cells hydrogen is transferred from reduced NAD to pyruvate converting it to lactate and this happens in the cytoplasm of the cells .
Two NAD molecules are used as each glucose is converted by glycolysis to pyruvate and two pyruvate are produced so each of them can convert a reduced NAD back to NAD to regenerate it. As long as glucose is available, lactic concentrations do not rise too high and any aerobic respiration carried out this way should be able to continue indefinitely.
Anaerobic respiration by glycolysis with conversion of pyruvate to lactate is called lactic fermentation.
Anaerobic cell respiration in yeast
NAD used in glycolysis can also be regenerated by conversion of pyruvate to ethanol and carbon dioxide instead of lactate. This is a two stage process. In the first stage carbon dioxide is removed from the pyruvate in a decarboxylation reaction where the product is ethanal. In the second stage two hydrogen are transferred from reduced NAD to ethanal converting it to ethanol. The number of NEDs regenerated is the same number used for glucose and glycolysis so this process allows production of ATP by anaerobic respiration to continue indefinitely as long as glucose is available and ethanol concentrations do not rise too high.
An aerobic respiration by glycolysis which converts pyruvate to ethanol and carbon dioxide is known as ethanol fermentation or alcoholic fermentation. It is used in baking and brewing. In both cases the organism that carries out the fermentation is yeast. Yeast is a unicellular fungus that occurs naturally in habitats work glucose or other sugars are available such as the surface of fruits. Yeast is a facultative and a robe this means it can respire either aerobically or anaerobically.
Ethanol fermentation with yeast in the production of brewing and baking
bread is made by adding water to flower needing the mixture to make dough and then baking it. To give bread a lighter texture something must be added to the dough to create bubbles of gas. Yeast is often added for this purpose. If the dough is kept warm the yeast will grow and respire. Initially it requires aerobically but once all the oxygen in the dough has been used up, the yeast starts to respire and aerobically. Because the dough is very viscous the carbon dioxide produced by an aerobic respiration cannot escape. Instead it forms bubbles within the dough and these bubbles caused the dough to swell. Ethanol is also produced by anaerobic cell respiration but evaporates during baking.
Yeast is also used when brewing drinks such as beer and wine. Here however the aim is to produce ethanol rather than carbon dioxide. One is made from grape juice which naturally has a high sugar concentration. Beer is made from beer grains mixed with water. Grains contain large amounts of starch but little sugar the starch must be first converted to sugar using amylase because yeast cannot metabolise starch. Brewing of wine or beer is carried out in large tanks so diffusion of oxygen into the liquid in the tank is limited. The yeast’s rapidly use up any oxygen present and then respire and aerobically. The ethanol produced remains dissolved but most of the carbon dioxide bubbles to the surface and escapes. Depending on the amount of sugar present at the start ethanol fermentation ends either when all the sugar has been used up or when the ethanol concentration becomes toxic to the yeast.
As well as brewing drinks, ethanol fermentation can also be used to produced bioethanol a renewable energy source. Any plant matter can be utilised as a feed stock but most bioethanol is produced from sugarcane and corn using yeast. Sugars are converted into ethanol enlarged fermenters. The ethanol is purified by distillation and bioethanol is used as fuel and vehicles sometimes in pure state and sometimes mixed with gasoline.
Link reaction in aerobic cell respiration
If oxygen is available, pyruvate can be oxidised to carbon dioxide and water. This gives a much higher yield of ATP than an aerobic cell respiration. Most of the reactions are part of the curb cycle, but an initial reaction is conversion of Purva from glycolysis into two carbon acetyl groups. This conversion forms a link between glycolysis and the Krebs cycle.
In the link reaction a complex of three enzymes carry out these processes:
-Decarbonation by removal of carbon dioxide to change three carbon pyruvate into a two carbon molecule
-Oxidation by removal of two electrons, these electrons are accepted by an AD converting it to reduced NAD
-Binding of the acetyl group to a complex carrier molecule called coenzyme A, the product is acetyl coenzyme A
Pyruvate is produced by glycolysis in the cytoplasm but both the link reaction and the Krebs cycle take place in the matrix of the mitochondria. A transporter protein in the outer membrane of the mitochondria moves pyruvate from the cytoplasm to the mitochondria matrix.
Krebs cycle
Acetyl groups produced by the link reaction are oxidised in a cycle of reactions that happens in the matrix of the mitochondrion. This cycle is called the Krebs cycle. Acetyl groups are fed into the cycle by transfer from coenzyme A to oxaloacetate producing the organic acid citrate.
Oxaloacetate has four carbon atoms and citrate has six. Citrate is converted back to oxaloacetate by a series of enzyme catalyse reactions. The number of carbon atoms is decreased by two decarboxylation reactions in which carbon and oxygen are removed producing carbon dioxide. In aerobic cell respiration all the carbon in substrate such as sugars or fat is removed by decarboxylation in the Krebs cycle or in the link reaction. Carbon dioxide is a waste product in those cell cells and is excreted.
Four reactions in the Krebs cycle are oxidations and release energy. Much of the release energy is held by the electrons that are removed in the oxidations. These electrons are transferred either to NAD or 2FAD. Both of these molecules act for carriers of electrons, they also accept protons, so they are hydrogen carriers as well. FAD functions in a similar way to ND when either of these molecules except a pair of electrons they become reduced reduced NAD and reduced FA transfer electrons and the energy they are holding to the electron transport chain in the inner mitochondrial membrane.
The net effect of one turn in the Krebs are:
-One acetyl group is consumed
- Three NEDs are converted to reduced NAD and one FAD to reduced FAD
-Two molecules of carbon dioxide are released
-One ADP is converted to ATP
Electron transport chain transfer transfer of energy from reduced NAD
In the inner mitochondria membrane there are groups of proteins that act as electron carriers by accepting and then passing on pairs of electrons. Together the sequence of carriers formed the electron transport chain. The first carrier and the chain excepts a pair of electrons from reduced NAD. This changes the carrier from an oxidised state to a reduced state and converts the reduced NAD back to NAD. The carrier gains chemical energy by this transfer of electrons.
Reduced NAD is produced in glycolysis, the link reaction and the Krebs cycle. Oxidation reactions in these processes are the source of the energy that is transferred by reduced NAD to the electron transport chain. The Krebs cycle also produces reduced FAD which transfers a pair of electrons to the electron transport chain. The electrons transferred by a reduced FAD carry less energy than those from reduced NAD so they are accepted by a carrier part along the chain which has a higher affinity for electrons than the first carrier.
Generation of proton gradient along the electron transport chain
Electrons brought to the mitochondria membrane by reduced NAD are accepted by the first carrier of the electron transport chain. They then pass along the chain from carrier to carrier energy is released at every stage in this flow of electrons.
The three main carriers in the electron transport chain each act as a proton pump. They use energy released by the flow of electrons to pump protons across the inner mitochondria membrane, from the matrix to the membrane space between the inner and outer mitochondria membranes. The first and second main electron carriers each pump for protons per pair of electrons the third carrier pumps two. This gives a total of 10 protons pumped from the matrix to the inter membrane space Per pair of electrons from reduced NAD.
Electrons brought by reduced FAD also fuel proton pumping however these electrons are fed into the chain after the first carrier so only six protons are pumped per pair of electrons rather than 10
Energy is needed to pump protons across the inter mitochondrial membrane because they are being moved against the concentration gradient. This energy is not lost. It is stored temporarily in the form of the proton gradient. The stored energy can then be used to generate ATP.
So the role of the electron transport chain is to generate and maintain a proton gradient across the inner mitochondrial membrane. It does this by pumping protons across the membrane using energy released by the flow of electrons. The electrons from which this energy is obtained are brought to the electron transport chain by reduced NAD and reduced FAD.
Chemosmosis
ATP synthase is a large and complex protein that phosphorus ADP to produce ATP. This is an endergonic reaction meaning an energy absorbing reaction so a source of energy is needed. This energy is provided by the proton gradient created by the electron transport chain. The process used to cover the proton gradient to synthesis of ATP is called chemosmosis.
In osmosis a concentration gradient causes water to move across a membrane but the energy released in this process is not utilised. In chemosmosis protons move down their concentration gradient from the high concentration in the membrane space to the lower concentration in the matrix and the energy released during this process is used to link a phosphate group to ADP producing ATP.
ATP synthase has two main regions. One of these is made of transmembrane subunits that are embedded in the inner mitochondrial membrane. This region allows protons to pass across the membrane releasing energy. The other main region is globular and project into the matrix. It has active sites that use energy released by the protons to catalyse production of ATP.
The role of oxygen as a terminal electronic acceptor in aerobic cell respiration
ATP production by mitochondria can only continue when there is electron flow and proton pumping. This depends on reduced NAD supplying pairs of electrons to the start of the electron transport chain and the electrons being removed at the end of the chain. Each electron carrier in the electron transport chain has a stronger affinity for electrons than the previous one, so removal of electrons from the last electron carrier can only be done by a substance that has very strong affinity for electrons. Most organisms use molecular oxygen for this purpose. It is known as the terminal electronic acceptor molecules of oxygen except electrons from the final electron carrier and hydrogen ions from the matrix producing water.
Use of oxygen is the last stage in a aerobic cell respiration. However, all the previous stages apart from glycolysis depend on oxygen. If oxygen runs out, electrons are not removed from the end of the electron transport chain so all the carriers and the electron transport chain. This means electrons cannot be accepted from reduced NAD at the start of the electron transport chain. Reduced NAD therefore accumulates. When all the NAD in the mitochondria and has been converted to reduced NAD oxidation in link reactions and the Krebs cycle are impossible so these processes stop. Anaerobic cell respiration can continue in the cytoplasm by regenerating NAD without using oxygen however the yield of ATP is far smaller.
Differences between lipids and carbohydrates as respiratory substrates
Both lipids and carbohydrates can be used as substrate in respiration. This is why they are both suitable as energy yielding foods in the diet and also as energy stores in the body. Both lipids and carbohydrates are oxidised in respiration to release energy. However, there are differences in the metabolic pathways and in the energy yield pre gram:
In carbohydrates, the first stage of respiration with sugars such as glucose and fructose as the substrate is glycolysis, which generates some ATP and does not require oxygen. And aerobic respiration is therefore possible. Pyruvate can be converted into acetyl groups by the link reaction and the acetyl groups can then be fed into the Krebs cycle. These stages can only happen if oxygen is available.
The energy yield program of carbohydrates is only 17 kJ perg. This is about half that of lipids. And it is released from a substrate by oxidising carbon hydrogen and carbohydrates more than 50% of the mass is oxygen which does not yield energy.
In lipids on the other hand the first stage of respiration with lipids such as fats and oils is the breakdown of fatty acids into acetyl groups in the matrix of the mitochondria. Acetyl groups are then fed into the Krebs cycle. These stages only happen when oxygen is available so an aerobic respiration is not possible with lipids.
The energy yield program of lipids is 37 kJ perg. This is nearly twice as much as that of carbohydrates. Nearly 90% of the mass of lipids is carbon hydrogen from which there is a yield of energy and respiration.
