5.2.2 Respiration

ATP

ATP

Adenosine triphosphate

ADP

adenosine diphosphate

why do living organisms need to respire?

it releases the energy stored in organic molecules such as glucose

this energy is immediately used to synthesis molecules of ATP from ADP and inorganic phosphate

the ATP can then be hydrolysed to release energy needed to drive biological processes

all living organisms respire to obtain energy

so why do living organisms need energy

energy is the capacity to do work

energy is sorted in complex organic molecules is potential energy

it is also chemical energy converted from light by photosynthesis

when energy is released it drives biological processes such as

active transport

endocytosis/exocytosis

synthesis of large molecules such as collagen

DNA replication

cell division

movement

activation of chemicals- glucose is phosphorylated at the beginning of respiration so that it become more reactive and able to be broken down to release more energy

so why do living organisms need energy- metabolic reactions

metabolic reactions are the collective name for all the chemical reactions inside living cells

there are two types; anabolic and catabolic

when larger molecules are made from smaller ones it is anabolic

when smaller molecules are made by the hydrolysis of larger ones it is catabolic

the role of ATP

ATP is the intermediary between energy-releasing and energy consuming metabolic reactions

ATP is relatively stable in solutions in cells, however, it can be readily hydrolysed by enzyme catalysis

the energy releasing hydrolysis of ATP is coupled with an energy consuming metabolic reaction

this makes ATP an immediate energy source

when ATP is hydrolysed to ADP and Pi, a small quantity of energy is released

this means the cell obtains energy in small manageable amounts

ATP is often referred to as the universal energy currency as all living things use it

some energy is released by hydrolysis of ATP as heat

whilst this may appear wasteful it helps keep living organisms warm and helps with enzyme reactions

respiration formula

C₆H₁₂0₆+60₂ → 6CO₂+6H₂O + 32 ATP

respiration definition

respiration is a series of reactions in which energy is transferred from organic compounds, such as carbohydrates, to the temporary energy store, ATP

glycolysis

the first stage of respiration

a biochemical pathway that occurs in the cytoplasm of all living organism that respire, including prokaryotes

it is anaerobic as it doesn’t require oxygen

oxidative phosphorylation

the formation of ATP using energy released in the electron transport chain and in the presence of oxygen. it is the last stage in aerobic respiration

4 stages of respiration

glycolysis (in both aerobic and anaerobic respiration), link reaction, Krebs cycle, electron transport chain (only in aerobic respiration)

mitochondria

found in all cell types

found in higher numbers in cells that have higher energy demands#

1um diameter, 10um long

where does glycolysis occur

cytoplasm of the cell

where does the link reaction occur

the matrix of the mitochondria

where does the krebs cycle occur

the matrix of the mitochondria

where does the electron transfer chain occur

utilises proteins found in the membrane of the crista

glycolysis

this is the first stage

it occurs in the cytoplasm

first stage of aerobic respiration and anaerobic respiration

doesn’t need O₂ so this stage is anaerobic

occurs in the cytoplasm of all living cells

there are 2 stages of glycolysis

1. phosphorylation

2. oxidation

it is a pathway involving a sequence of 10 reactions, each catalysed by a different enzyme, some with the help of the coenzyme, NAD

the main points;

1. phosphorylation of glucose to hexose bisphosphate

2. splitting each hexose bisphosphate molecule into two triose phosphate molecules

3. oxidation of triose phosphate to pyruvate

cofactor

enzymes involved in catalysing oxidation and reduction reactions need the help of coenzymes (a type of cofactor) to accept the hydrogen atoms removed during oxidation

NAD is a non-protein molecule that helps dehydrogenase enzymes to carry out oxidation reactions

NAD oxidises substrate molecules during glycolysis, the link reaction and the Krebs cycle

NAD in the living cells synthesised from nicotinamide (vitamin B₃), the five carbon sugar ribose, the nucleotide base adenine and two phosphoryl groups

stage 1- phosphorylation

glucose is phosphorylated by adding 2 phosphates from 2 molecules of ATP

glucose is split using water (hydrolysis)

2 molecules of triose phosphate are created and 2 molecules of ATP are used up

as glucose is very stable it needs to be activated before it can be split into two three carbon compounds

one molecule of ATP is hydrolysed and the released phosphoryl group is added to glucose to make hexose monophosphate

another molecule of ATP is hydrolysed and the phosphoryl group is added to the hexose phosphate to form a molecule of hexose bisphosphate. it now had phosphates on carbon 1 and 6

the energy from the hydrolysed ATP activates the sugar

the hexose bisphosphate is then split into two three carbon molecules, triose phosphate. each has a phosphate group attached

stage 2- oxidation

4 ATP are produced, but 2 were used at the start, so there’s a net gain of 2ATP

coenzyme NAD collects the hydrogen ions forming 2 Reduced NAD

the triose phosphate is oxidised (loses hydrogen), forming 2 molecules of pyruvate

the sums

the ned products of glycolysis are pyruvate and reduced NAD

energy is released during this reaction

4 molecules of ADP + Pi converted to 4 molecules of ATP

so net gain of 2 molecules of ATP

2 pairs of hydrogen atoms produced

2 molecules of pyruvate

the fate of pyruvate

this depends on the availability of oxygen

the stages of respiration

the link reaction, the Kerbs cycle and oxidative phosphorylation only happen in aerobic conditions

under aerobic conditions, the pyruvate molecules from glycolysis are actively transported into the mitochondria for the link reaction

in the absence of oxygen, pyruvate is converted in the cytoplasm to lactate or ethanol

cristae

inner highly-folded mitochondrial membrane

mitochondrial matrix

fluid filled inner part of mitochondria

how the structure enables function

the matrix is where the link reactions and the Kerbs cycle takes place

the matrix contains:

-enzymes that catalyse the stages of these reactions

-molecule of the coenzymes NAD and FAD (flavine adenine dinucleotide)

-oxaloacetate- the four-carbon compound that accepts the acetyl group from the link reaction

-mitochondrial DNA- some of which codes for enzymes and other proteins

-mitochondrial ribosomes- structurally similar to prokaryotic ribosomes

the outer membrane

the phospholipid composition of the outer membrane is similar to that of the membranes around other organelles

proteins from channels to allow passage of molecules such as pyruvate into the mitochondrion

the inner membrane

the lipid composition of the inner membrane differs from the outer

this bilayer is less permeable to small ions such as hydrogen

the folds give a large surface area for the electron carries and ATP synthase enzyme embedded in them

the electron carriers are protein complexes arranged in electron transport chains. electron transport chains are involved in the final stage of aerobic respiration

the intermembrane space

this space is also involved in oxidative phosphorylation

the inner membrane is in close contact with the mitochondrial matrix, so the molecules of reduced NAD and FAD can easily deliver hydrogen to the electron transport chain

electron transport chain

each electron carrier protein contains a haem group

the iron ion can accept and donate electrons as it can alternate between Fe₂+ (reducing- gaining an electron) and Fe₃+ (oxidised giving an electron to the next carrier)

these carrier proteins are oxido-reductase enzymes

the electron carriers also have a coenzyme that pumps protons from the matrix to the intermembrane space using energy released from the electrons

this leads to a build up of protons in the intermembrane space and a proton gradient forms

this leads to a flow of protons through the channels in the ATP synthase enzymes to make ATP

decarboxylation

removal of a carboxyl group from substrate molecule

dehydrogenation

removal of hydrogen atoms from a substrate molecule

substrate-level phosphorylation

production of ATP from ADP and Pi during glycolysis and the Krebs cycle

symport

a transport protein that transports two ions or molecules in the same direction

aerobic respiration

if 0₂ is present ₃C pyruvate passes into mitochondria

here it is completely oxidised forming CO₂ and the H₂0

the second stage of aerobic respiration is the link reaction

link reaction- pyruvate

this is transported via a specific pyruvate-H+ symport

pyruvate is converted to a two-carbon acetyl group during the link reaction

the acetyl group is oxidised during the Krebs cycle

the link reaction

links glycolysis to the Krebs cycle

the end product of the link reaction can enter the Krebs Cycle

-one carbon atom is removed from pyruvate in the form of CO₂

-the remaining 2-carbon molecule combines with coenzyme A to produce Acetyl Coenzyme (acetyl CoA)

-another oxidation reaction occurs when NAD+ collects more hydrogen ions. this forms reduced NAD

-no ATP is produced in this reaction

the link reaction occurs twice for every glucose molecule

for each glucose molecule used in glycolysis, two pyruvate molecules are made

but the link reaction uses only one pyruvate molecules, so the link reaction and the Krebs cycle happen twice for every glucose molecule which goes through glycolysis

overall equation for one link reaction

pyruvate + NAD + CoA → acetyl CoA + reduced NAD + CO₂

what are the products of the link reaction that go to the Krebs Cycle and the ETC

for each glucose molecules:

-2 acetyl coenzyme A (go into the Krebs cycle)

-2 carbon dioxide (released as waste products)

-2 reduced NAD (go to the electron transport chain)

what is the krebs cycle also known as

also known as citric acid cycle or the tricarboxylic acid cycle

where does the Krebs cycle take place?

the matrix of mitochondria

how many times does the Krebs cycle go around

twice per glucose molecule as from one glucose molecule you get 2 pyruvate

what is the definition of the Krebs cycle

it is a series of enzyme-catalysed reactions that oxide the acetate from the link reaction to 2 molecules of carbon dioxide whilst conserving energy by reducing the coenzymes NAD and FAD

what happens after the coenzymes are reduced

the reduced coenzymes (NAD,FAD) then carry the hydrogen atoms to the electron transport chain on the cristae where they will produce more ATP

what are the krebs cycle stages

1. the acetyl group released from acetyl CoA combines with a four carbon compound, oxaloacetate, to form a six carbon compound citrate

2. citrate is decarboxylated and dehydrogenated, producing a five carbon compound, one carbon dioxide and one reducing NAD

3. this 5 carbon compound is further decarboxylated and dehydrogenated, producing a four carbon compound, one carbon dioxide and one reduced NAD

4. at this stage, substrate level phosphorylation takes place. this produces one molecule of ATP

5. the 4 carbon compound is dehydrogenated producing a different 4 carbon compound and molecule of reduced FAD

6. rearrangement of the atoms in the four carbon molecule, catalysed by an enzyme, followed by further dehydrogenation, regenerate a molecule of oxaloacetate, so the cycle continues

what are the products of the Krebs cycle

2 CO₂ molecules

1 ATP molecules (per acetate)

4 pairs of hydrogen atoms

what products have been made after glycolysis and the link reaction

although oxygen is not directly used, these stages cannot happen in the absence of oxygen

by the end of the krebs cycle, the production of carbon dioxide from glucose is completed

glucose is not the only substrate that can be respired aerobically

what other substances enter the krebs cycle and how?

fatty acids are broken down to many molecules of acetate that enter the krebs cycle via acetyl CoA

glycerol may be converted to pyruvate and enter the krebs cycle via the link reaction

amino acids may be deaminated and the rest of the molecule can enter the krebs cycle directly or be changed to pyruvate

chemiosmosis

flow of protons, down their concentration gradient across a membrane, through a channel associated with ATP synthase

oxidative phosphorylation

the formation of ATP using energy released in the electron transport chain and in the presence of oxygen. it is the last stage of aerobic respiration

how much ATP does NAD and FAD produce

1 NAD= 2.5 ATP

1 FAD= 1.5 ATP

ETC

1. reduced NAD and reduced FAD are reoxidised when they deliver their hydrogen atoms to the electron transport chain

2. the hydrogen atoms released from the reduced coenzymes split into proteins and electrons

3. the protons go into solution in the mitochondrial matrix

4. the electrons from the hydrogen atoms pass along the chain of electron carriers

5. each electron carrier proteins has an iron ion at its core. these iron ions gain an electron, becoming reduced (Fe

6. the reduced iron ion then donates the electron to the next iron ion in the chain

7. as the electrons pass along this chain some energy is used to pump protons across the inner mitochondrial membrane

8. the electrons are passed down the chain of protein complexes from I to IV, each complex binding electrons more tightly than the previous one

9. altogether 10 protons are pumped across the membrane for every hydrogen from NADH (or 6 proteins for FADH)

chemiosmosis

in complex IV the electrons are combined with protons and molecular oxygen to form water. the oxygen diffuses in from the tissue fluid

oxygen is only involved at the very last stage of respiration as the final electron acceptor

the energy of the electrons is now stored in the form of a proton gradient across the inner mitochondrial membrane

the ATP synthase enzyme has a proton channel through it, and as the protons ‘fall down’ this channel their energy is used to make ATP

this method of storing energy by creating a proton gradient across a membrane is called chemiosmosis

why is oxygen important? (anaerobic respiration)

so that the H atoms produced in glycolysis and Krebs cycle can be converted to water and drive the production of ATP

what happens in the absence of oxygen

oxygen cannot act as the final electron acceptor. the protons cannot combine with electrons and oxygen to make water

the proton gradient reduces and oxidative phosphorylation stops

Krebs cycle and electron transport chain can’t take place and pyruvate builds up in the cell

anaerobic process of glycolysis is the only source of ATP

what has to be done to keep glycolysis going

glycolysis can take place but the reduced NAD needs to be reoxidised

what ways do anaerobic respiration happen

can happen in 2 different ways

fungi and plants use the ethanol fermentation pathway

mammals use lactate fermentation pathway

takes place in the cytoplasm

how does the production of lactate in animals occur

human cells convert pyruvate to lactate. this reaction uses reduced NAD by oxidising it to NAD once more. the enzyme lactate dehydrogenase catalyses this

NAD is now available again to accept electrons and protons so glycolysis continues

if NAD is not regenerated, even glycolysis would have to stop, because there would be no oxidised NAD available to accept these electrons and protons

pyruvate + reduced NAD

lactate + NAD

what happens to the lactate

the lactate produced in the muscle tissue is carried away from the muscles to the liver

when oxygen is available lactate may be either

converted to pyruvate, which may enter the Krebs cycle via the link reaction

recycled to glycose and glycogen

if the lactate were not removed from the muscle tissues, the pH would be lowered and this would inhibit enzyme action

how does the production of ethanol in plants and some microorganisms occur

pyruvate loses a molecule of carbon dioxide and accepts hydrogen from reduced NAD to produce ethanol

pyruvate + reduced NAD → ethanol + carbon dioxide + NAD

respiratory substrate

an organic substance that can be oxidised by respiration, releasing energy to make molecules of ATP

apart from carbohydrates, what else can also be used as respiratory substrates

lipids and proteins

how can lipids and proteins be oxidised

in the presence of oxygen to produce molecules of ATP, carbon dioxide and water

they each have a difference relative energy value

what cells can only use glucose for respiration

some mammalian cells (brain and erythrocytes)

what is used to store glucose until it is hydrolysed for respiration

glycogen

plants store it as starch

what are monosaccharides changed by to be used for respiration

monosaccharides such as fructose and galactose can be changed by isomerase enzymes to glucose for respiration

what are lipids often used by

muscle cells

what happens to triglycerides to use for energy

they are hydrolysed by lipase to glycerol and fatty acids

the glycerol is then converted to triose phosphate and respired

lipids→ fatty acids

the fatty acids are long-chain hydrocarbons with a carboxylic acid group

this makes them a good source of protons for oxidative phosphorylation and so fats produce much more ATP than an equivalent mass of carbohydrates

fatty acid process

1. with the aid of some energy from the hydrolysis of one molecule of ATP to AMP, each fatty acid is combined with coenzyme A

2. the fatty acid-CoA complex is transported into the mitochondrial matrix, where it is broken down into the two-carbon acetyl groups, each attached to CoA

3. this beta-oxidation pathway generates reduced NAD and reduced FAD

4. the acetyl groups are released from CoA and enter the Krebs cycle by combining with the four-carbon oxaloacetate

for each oxidised acetyl group in the Krebs cycle, three molecules of reduced NAD, one molecule of reduced FAD and one molecule of ATP by substrate level phosphorylation are made

proteins

excess amino acids are deaminated in the liver

the keto acid, enters the respiratory pathway as pyruvate, acetyl CoA or a Krebs cycle acid such as oxaloacetic acid

during fasting and starvation, proteins in the muscles can be hydrolysed to amino acids and then respired

energy values

the majority of ATP is produced during oxidative phosphorylation

more proteins for chemiosmosis means more ATP

respiratory substrate = mean energy value (KJg-1)

carbohydrates = 15.8

lipid = 39.4

protein = 17

as the protons ultimately combine with oxygen atoms to form water, the greater the proportion of hydrogen atoms in the molecule, the greater the need for oxygen

respiratory quotient

RQ = CO₂ produced/O₂ consumed

if the RQ value is greater than 1, anaerobic respiration is also taking place as more carbon dioxide is produced that oxygen used