The roles of ATP in living cells and the mechanisms of production of ATP Flashcards
What is anabolism?
- simple molecules put together to form complex molecules
- complex molecules will then be stored as energy
- think A = Adding molecules together
What do anabolism terms end in?
- genesis
- e.g. glycogenesis (glucose to glycogen)
What is an example of anabolism?
- glycogenesis (glucose into glycogen)
What is catabolism?
- breakdown of complex molecules into simple molecules
- think C for catabolism = Cut up molecules
What is an example of catabolism?
- glycogen to pyruvate
What do all terms used to describe catabolism end in?
- lysis
what is catabolims and anabolims together referred to as?
- metabolism
When catabolic reactions something is released and captured and used later in anabolic reactions, what is this?
- adenosine triphosphate (ATP)
If organisms do not work to produce energy what will happen to them?
- they will die
What are a few examples of how energy is requried in the body?
- muscle contraction
- ions/molecules transport across membranes
- biosynthesis of essential metabolites, growth and replace damaged cells
- thermoregulation
Energy in the body, called free energy must come from somewhere, where is this?
- nutrients that we consume.
What is Gibbs Free Energy?
- thermodynamic calculation
- used to calculate the maximum reversible work that may be performed by a thermodynamic system at a constant temperature and pressure.
There are 3 parts to Gibbs Free Energy, what is enthalpy?
- the heat content of the reacting system
- referred to as H
There are 3 parts to Gibbs Free Energy, what is entropy?
- the randomness or disorder in a system
- referred to as S
There are 3 parts to Gibbs Free Energy, what is Gibbs Free Energy?
- energy capable of doing work at constant temperature and pressure
- referred to as G
In cells what does the change in enthalpy (/_H)_ relate to?
- types and numbers of chemical bonds broken and formed
In cells if the change in enthalpy (_/_H) is positive (+ve) is this an endothermic or exothermic reaction? A positive change in energy indicates that energy is required to produce something. Ball rolling down or up a slide for example:
- ball rolling down = reduced enthalpy (energy released from glucose through breaking the bonds of glucose)
- ball rolling back up = increased enthalpy (energy required to make bonds, such as glucose to glycogen)
- endothermic (anabolism = adding/building)
- energy has to be invested to make new bonds
In cells what does the change in entropy (_/_S) refer to?
- describes the formation of large complex molecules from smaller molecules or vice versa
- (e.g. DNA formation/protein formation)
In cells a postive (+ve) change in entropy (_/_S) refer to what?
- when randomness increases (i.e. breaking up a big molecule to smaller molecules)
- breaking fown glucose into ATP
What is the formula for determining change in gibbs free energy?
- _/_G = _/_H - T x _/_S
- _/_G = Change in Gibbs Free Energy
- _/_H = Change in enthalpy
- _/_S = Change in entropy
When we are looking at Gibbs Free Energy, if a random reaction is to occur, what must the _/_G (Change in Gibbs Free Energy be?
- negative (i.e. energy is released by the reaction)
- also referred to as an exergonic reaction
- catabolic reactions release energy
What is an exergonic reaction in thermodynamics?
- a chemical reaction where the change in the free energy is negative (there is a net release of free energy)
- reactants are turned into products
Following an exergonic reaction in thermodynamics, do products or reactants have more energy?
- reactants
- reactants become more stable than the reactants
- formation of product is “downhill” (spontaneous)
An example of an exergonic reaction is breaking down (burning) glucose into pyruvate, is this a anabolic or catabolic reaction?
- catabolic
- releasing energy
What is an endergonic reaction?
- reactants are turned into products
- glucose into glycogen is an example
In an endergonic reaction energy is invested to turn reactants into products, such as the formation of glucose into glycogen. Are the reactants or the products more stable?
- reactants are more stable
Why is coupling of reactions important in metabolism?
- endergonic reactions can be driven in the forward direction by coupling it to an exergonic reaction
- anabolic reactions can drive catabolic reactions
Coupling of reactions is important in metabolism. Endergonic reactions can be driven in the forward direction by coupling it to an exergonic reaction (catabolic reactions can drive anabolic reactions). An example of this is:
- coupled with a exergonic reaction (catabolic)
- ATP + H2O = ADP + Pi
- this provides _/_G of -30.5 kJ/mol
- -30.5 - 13.8 = -16.7 meaning reaction will occur as _/_G is negative and it will be spontaneous
What is the principle of coupling reactions?
- couple a reaction that requires energy with one that produces energy
- catabolic = produces energy
- anabolic = requires energy
In thermodynamics the hydrolysis of ATP is able to drive the an unfavourable reaction, which is essentially one where Gibbs Free Energy is not negative. What does the hydrolysis of ATP do then to help?
- releases free energy
- energy released ensures Gibbs Free Energy is negative
Adenosine triphosphate has 3 phosphate groups, hence the tri in its name. If it has one or two phosphate groups attached, what are these called?
- one = adenosone monophosphate
- two - adenosine diphosphate
Adenosine triphosphate has 3 phosphate groups. What are the names of these phosphate bonds moviong away from the adenosine?
- first = alpha
- second = beta
- third = gamma
Adenosine triphosphate has 3 phosphate groups. The generation of energy from ATP is driven by breaking the bonds between the alpha (1st), beta (2nd) and gamma (3rd) phosphates. Which bond is generally broken providing the majority of energy for the cell?
- gamme bond
What is phosphorylation?
- adding a phosphate group to a molecule
What is substrate level phosphorylation (SLP)?
- adding a phosphate group direclty to ADP
- phosphate provided by a substrate
- ADP + phosphate group = ATP
Substrate level phosphorylation (SLP) involves adding a phosphate group direclty to ADP from a substrate, which then forms ATP. What is required for this process to take place?
- soluble enzymes and chemical intermediates
What is an enzyme?
- biological catalysts that accelerate the rate of chemical reaction
- creates a new pathway for the reaction; one with a lower activation energy
In the image below, the _/_G requires an enzyme to accelerate the rate of reaction to get it over the hump. What is the energy known as that the enzyme will release that will determines if the substrate is able to spontaneously roll down the hill becoming the products?
- Ea = activation energy provided by enzymes
Do enzymes influence the Gibbs free energy (_/_G) of a reaction as depicted in the image below?
- no _/_G remains constant
- enzymes lower the activation energy
Are enzymes able to react and act alone or do they require something else?
- they require co-factors
The iron in heme is a metal ion, and is an example of what?
- a co-factor
Co-factors can be co-enzymes. What are the 2 main groups of co-enzymes?
1 - Co-substrates
2 - Prosthetic groups
Where do most co-enzymes come from?
- vitamins in the diet
What are non-protein cofactors?
- metal cations
- iron and sodium
Co-substrates, which are a subgroup of cofactors are able to diffuse between enymes and generally carry what?
- electrons
Co-substrates, which are a subgroup of cofactors able to diffuse between enymes carry electrons. Becuase they carry electrons they co-substrates flux between oxidised and reduced forms, what does oxidised and reduced mean in terms of electrons?
- oxidation = loss of electron (NAD+)
- reduced = addition of electron (NADH)
Prosthetic groups are a subgroup of co-enzymes, what are they?
- non-protein cofactors that are covalently bound to the enzyme
Prosthetic groups are a subgroup of co-enzymes, that are non-protein cofactors that are covalently bound to the enzyme. During the enzymatic reaction are they released from the enzyme?
- no
- they act as a temporary store for electrons or reaction intermediates
B2 also referred to as Riboflavin is an important vitamin that is consumed in the diet and is important for maintaining energy pathways withing the cells. What are the 2 co-enzymes that are required to extract energy from the dietary source of B2?
- FAD – flavin adenine dinucleotide
- FMN – flavin mononucleotide
B2, also referred to as Riboflavin is an important vitamin that is consumed in the diet and is important for maintaining energy pathways withing the cells. Flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) are the 2 co-enzymes that are required to extract energy from the dietary source of B2. Are FMN and FAD classed as a prosthetic group or co-substrate?
- prosthetic group
Niacin is an important vitamin that is consumed in the diet and is important for maintaining energy pathways withing the cells. What is the co-enzymes that is required to extract energy from the dietary source of niacin?
- Nicotinamide adenine dinucleotide (NAD+)
Niacin is consumed in the diet. Nicotinamide adenine dinucleotide (NAD+) is the co-enzymes that is required to extract energy from the dietary source of niacin. Is NAD+ classed as a Prosthetic group or Co-substrate?
- Co-substrate
Hydrogens and electrons are transferred to co-factors that does what to them?
- reduces co-factors
What is the major difference between NAD+ and NADH vs. NADPH and NADP+?
- NAD+ and NADH do not contain a phosphate group
-
Out of NAD+, NADH, NADPH and NADP+, which are used for anabolic reactions?
- NADPH and NADP+?
Out of NAD+, NADH, NADPH and NADP+, which are used for catabolic reactions?
- NAD+ and NADH
Is NADH or NADPH used for ATP synthesis?
- NADH
Is NADH or NADPH used for reductive biosyntheses
- NADPH
What is oxidative phosphorylation?
- metabolic pathway in which cells use enzymes to oxidize nutrients (removal of electron produces energy)
- stored chemical energy in the nutrients is released producing adenosine triphosphate
How do cells cecycle NADH and FADH2?
- via the respiratory chain in the mitochondria
For every NADH and FADH2, how many ATP are synthesised?
- NADH = 2.5 ATP molecules
- FADH2 = 1.5 ATP molecules
What is glycolysis?
- metabolic pathway that converts glucose (C₆H₁₂O₆) into pyruvic acid (CH₃COCOOH)
- free energy is released forming ATP and reduced NAH+
Does glycolysis take place in the cells cytoplasm or in the mitochondria?
- cytoplasm
What does glucose-6-phosphate (G-6-P) actually mean?
- a glucose molecule has been phosphorylated
- phosphorylation occurs at carbon 6
What enzyme converts glucose to glucose-6-phosphate (G-6-P) in the priming phase of glycolysis?
- hexokinase
Hexokinase is the enzyme that converts glucose to glucose-6-phosphate (G-6-P) in the priming phase of glycolysis, but what else is required to initiate this reaction?
- ATP is converted to ADP releasing a phosphate group
- phosphate group is added to glucose at 6th carbon
- glucose-6-phosphate (G-6-P) is formed and can no longer leave the cell
In glycolysis the second priming step is the conversion of glucose-6-phosphate through phosphorylation into what?
- fructose-6-phosphate
- isomerase is used to do this
In glycolysis what is the step where the cell is commited to glycolysis?
- conversion of fructose-6-phosphate into fructose1,6-bisphosphate
- ATP phosphorylated into ADP
- phosphate group added to fructose-6-phosphate at the first carbon becoming fructose1,6-bisphosphate )phosphate at number 1and 6 carbons of the glucose
In glycolysis the commited step where the cell is committed to the glycolysis pathway is the conversion of fructose-6-phosphate into fructose1,6-bisphosphate. What enzyme is responsible for this conversion?
- Phosphofructoskinase-1
In the priming (investing) phase of glycolysis how many ATP are needed?
- 2 ATPs
In glycolysis the commited step where the cell is committed to the glycolysis pathway is the conversion of fructose-6-phosphate into fructose1,6-bisphosphate. Phosphofructoskinase-1 is responsible for this conversion. Fructose1,6-bisphosphate is then broken down into two 3 carbon molecules called dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (G-3-P). Out of these 2 which is the only one that continues on in the glycolysis pathway?
- G-3-P
In glycolysis the commited step where the cell is committed to the glycolysis pathway is the conversion of fructose-6-phosphate into fructose1,6-bisphosphate. Phosphofructoskinase-1 is responsible for this conversion. Fructose1,6-bisphosphate is then broken down into two 3 carbon molecules called dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (G-3-P). Onlp G-3-P continues on in glycolysis, what happens to DHAP?
- isomerase re-arranges it into G-3-P
In the glycolysis payoff reactions how is the first ATP produced?
- Glyceraldehyde-3-phosphate (G-3-P) from the priming stage of glycolysis is converted into 1,3-bisphosphoglycerate (1,3 BPG)
- 1,3 BPG has 2 phosphate groups so 1 is added to ADP forming ATP
In the glycolysis payoff reactions the first ATP is produced during the conversion of glyceraldehyde-3-phosphate (G-3-P) from the priming stage of glycolysis, into 1,3-bisphosphoglycerate (1,3 BPG). 1,3 BPG has 2 phosphate groups and therefore donates 1 to ADP forming ATP. But what enzyme is responsible for converting G-3-P into 1,3 BPG?
- Phosphoglycerate kinase (PGK)
Although it occurs in glycolysis there are 2 instances where a phosphate group is added to ADP forming ATP. What is this process referred to as?
- substrate level phosphorylation
Pyruvate is fromed from phosphoenolpyruvate. What enzyme is responsible for this?
- pyruvate kinase
Pyruvate kinase is responsible for converting phosphoenolpyruvate into pyruvate. During this conversion what does pyruvate also do?
- takes phosphate group from phosphoenolpyruvate
- then phosphorylates ADP, creating an ATP molecule
During the glycolysis payoff reactions why do we need to multiply what we create by 2?
- becuase each molecule of glucose creates 2 lots of Glyceraldehyde-3-phosphate (G-3-P)
- each G-3-P molecule enters the glycolysis payoff reaction
At the end of the glycolysis payoff reaction how many ATP and NADH molecules will we create?
- 4 ATP (2 per cycle)
- 2 NADH (1 per cycle)
In glycolysis how many ATP are required to initiate the reaction?
- 2 ATP
Pyruvate is the end product of glycolysis. Here there are 2 things that can happen to pyruvate, what are they?
- aerobic conditions it is oxidation and complete degradation in the Krebs cycle
- hypoxic (anaerobic) conditions, it can be reduced to lactate
How many membranes does the mitochondria have?
- 2
- inner and outer membrane
The mitochondrian has folds designed to increase the surface area of the mitochondria. What is this called?
- cristae
What is the area within the mitochondria that is contained within the inner membrane?
- matrix
Where does the respiration chain sit within the mitochondria?
- on the innner membrane
What is decarboxylation?
- a chemical reaction that removes a carboxyl group and releases carbon dioxide
How does pyruvate cross the mitochondrial membrane?
- undergoes oxidative decarboxylation
- pyruvate dehydrogenase complex facilitates this
- Acetyl CoA is formed
The pyruvate dehydrogenase complex converts pyruvate into Acetyl CoA so that is can cross the mitochondrial membrane. This is the link between glycolysis and the citric acid cycle. Is this reaction reversible?
- no
- it is irreversible, so it a rate limiting step
During each cycle of the Krebs cycle, how many GTP (ATP), NADH and FADH2 are created?
- 3 NADH
- 1 GTP
- 1 FADH
During each cycle of the Krebs cycle, 3 NADH, 1 GTP and 1 FADH are created. Why do we need to multiply all of these by 2, meaning we have 6 NADH, 2 GTP and 2 FADH for each molecule of glucose?
- glycolysis creates 2 glyceraldehyde-3-phosphate (G-3-P)
- each G-3-P creates 1 pyruvate, so 2 pyruvate in total
- each pyruvate enters the citric acid cycle
What are the 2 key regulation steps of the TCA cycle?
1 - conversion of pyruvate to acetyl-CoA by pyruvate dehydrogenase complex allowing entry into mitochondria matrix
2 - citrate synthase reaction controls entry of acetyl-CoA into the TCA cycle
- BOTH ARE IRREVERSIBLE
Once NADH & FADH2 leave the citric acid cycle, how are they re-oxidized?
- through a series of coupled oxidation & reduction reactions occuring whilst electrons are passed along a series of carriers
- carriers are in the electron transport chain (ETC)
- essentially donating their electrons to the ETC
How many complexes are in the electron transport chain?
- 4
Once NADH and FADH have released their electrons into the electron transport chain, what are the 2 electron carrier proteins which facilitate the electon transport chain?
1 - ubiquinone also known as Coenzyme Q
2 - cytochrome C
As electrons move along the electron transport chain, what do they pump into the intermembrane space?
- H+ protons
- creates concentration of H+ protons
In the electrong transport chain, what 2 things are used that are also very important for maintaining membrane potential to create ATP?
1 - electrical energy (positive electrical charge gradient created)
2 - chemical potential energy (concentration gradient created)
What is the proton motive force?
- build up of protons (H+)
- separation of charge between the intermembrane space and mitochondrial matrix
- drives the synthesis of ATP using ATP synthase
- low H+ proton concentratio in matrix
- high H+ proton concentration in intermembrane space
What is ATP synthase?
- a protein on the inner membrane of the mitochondria
- catalyzes the formation of the energy storage molecule ATP using ADP and inorganic phosphate (Pi)
ATP Synthase is composed of 2 structures. In the image below, which number denotes the F0 and F1 portions of ATP synthase?
1 = F1 projects into matrix of mitochondria
2 = F0 resides in the inner membrane of the mitochondria
What happens when H+ protons flow from the intermembrane space through the membrane, the cylinder within the F0 portion of the ATP synthase?
- the g-shaft rotates
- the turning causes conformational changes in the F1 part of the ATP synthase
As the y-shaft interacts with each of the B subunits of F1 portion, they change conformation and facilitate the formation of what?
- ATP from ADP and Pi
