Biochemistry Revision Flashcards
What is anabolism and what does it end in?
- building of something (glycogen)
- end in enesis like glycogenesis
What is catabolism and what does it end in?
- breaking of something (glycogen into glucose)
- end in lysis like glycogenolysis
In catabolic reactions what is created?
- energy
- ATP
What is an endergonic reaction and does this produce or require energy?
- reaction that is not spontaneous
- requires energy to occur
What is an exergonic reaction and does this produce or require energy?
- reaction that is spontaneous
- energy is created (exits the reaction)
The addition of a phosphate group to glucose, forms glucose-6-phosphate (G-6-P) facilitated through the enzyme hexokinase or glucokinase (liver only). The reactants here are glucose and phosphate and the product is G-6-P. Is this an endergonic or exergonic reaction and does this produce positive or negative energy?
- endergonic reaction as G-6-P is built
- requires energy from ATP as reactants have lower energy than products
- forming G-6-P needs 13.8 kJ
Is the dephosphorylation of an ATP molecule to ADP and phosphate, required during the formation of glucose to glucose-6-phosphate (G-6-P) an endergonic or exergonic reaction and does this produce positive or negative energy?
- exergonic reaction released from the ATP
- releases energy from ATP as reactants (ATP and H2O) have higher energy than the products (ADP+Pi)
- produces -30.5 kJ
The formation of glucose-6-phosphate requires aprox 13.8 kJ of energy. The dephosphorylation of ATP creates aprox 30.5 kJ. What is the net energy and what is the grouping of energonic and exergonic reactions together in this way called?
- coupling reactions
- -30.5 - 13.8 = -16.7 kJ
- negative energy so reaction occurs spontaneously
We need to know a lot of co-enzymes which are important in the transduction of energy from food. What is the role of NAD+ and NADH?
- generate electrons during glycolysis, TCA cycle and pyruvate decarboxylation
- then transfer these electrons to the electron transport chain
We need to know a lot of co-enzymes which are important in the transduction of energy from food. What is the role of Coenzyme Q / Ubiquinol (QH2)?
- lipid soluble electron carrier inside inner mitochondrial membrane
- carries electrons from complex 1 and 2 to 3
We need to know a lot of co-enzymes which are important in the transduction of energy from food. What is the role of Cytochrome C?
- single electron carrier between complex 3 and complex 4
We need to know a lot of co-enzymes which are important in the transduction of energy from food. What is the role of FAD / FADH2?
- carres electrons to electrong transport chain from KREBs cycle
- transfers electrons to complex II
In the glycolysis pathway, there is a junction where a specific step of glycolysis can enter glycogenesis or the penthose pathway?
- glucose-6-phosphate
What is the start and end of glycolysis?
- start = glucose
- end = pyruvate
Following the production of 2 pyruvate molecules from one glucose molecule in glycolysis, a molecules is produced, what is this molecule called?
- acetyl-CoA
Following the production of 2 pyruvate molecules from one glucose molecule in glycolysis, acetyl-CoA is produced. This is a junction where a number of things can happen, what are the 3 things that could happen to the acetyl-CoA, depending on the needs of the cell?
1 - fatty acid sysnthesis and lipogenesis
2 - ketone production
3 - KREBs cycle and then electron transport chain
In glycolysis how many ATP are invested and generated, and how many NADH are generated?
- 2 ATP invested
- 4 ATP generated (net 2 ATP)
- 2 NADH generated
In glycolysis, there are 3 irreversible enzymatic actions that also act to regulate glycolysis, what are they?
1 - hexokinase
2 - phosphofructokinase
3 - pyruvate kinase
Phosphfructosekinase 2 (PFK-2) is an enzyme that is involved in regulating glycolysis and gluconeogenesis. PFK-2 is able to phophorylase a step of glycolysis. Which step is this and what is created?
- fructose 6 phosphate
- creating fructose 2,6 biphosphate (F-2,6-BP)
Phosphfructosekinase 2 (PFK-2) is an enzyme that is involved in regulating glycolysis and gluconeogenesis. PFK-2 is able to phophorylase fructose 6 phosphotase into fructose 2,6 biphosphate (F-2,6-BP). What is the importance of F-2,6-BP in glycolysis and and gluconeogenesis?
- most potent allosteric activator of PFK-1
- glycolysis = increased PFK-1 activity by F-2,6-BP (insulin high)
- gluconeogenesis = decreased PFK-1 activity as F-2,6-BP is inhibited (glucagon high)
Phosphfructosekinase 1 (PFK-1) is heavily regulated within the cell to control glycolysis and gluconeogenesis. What is the role of ATP on the activity of PFK-1?
- if lots of ATP we do not need glycolysis
- high ATP = inhibition of PFK-1
Phosphfructosekinase 1 (PFK-1) is heavily regulated within the cell to control glycolysis and gluconeogenesis. What is the role of AMP on the activity of PFK-1?
- AMP (breakdown product of ATP) is a marker of low ATP
- high ATP = activation of PFK-1 as need more ATP
Phosphfructosekinase 1 (PFK-1) is heavily regulated within the cell to control glycolysis and gluconeogenesis. What is the role of H+ on the activity of PFK-1?
- H+ can increase if we work just anaerobically
- high H+ can decrease pH of the blood
- high H+ inhibits PFK-1 to stop more pyruvate and lactate
Phosphfructosekinase 1 (PFK-1) is heavily regulated within the cell to control glycolysis and gluconeogenesis. What is the role of fructokinase-6-phosphate (G-6-P) on PFK-1?
- high G-6-P indicates lots of glucose around
- high G-6-P activates PFK-1 to take the glucose and create ATP
Phosphfructosekinase 1 (PFK-1) is heavily regulated within the cell to control glycolysis and gluconeogenesis. What is the role of fructokinase-2,6-biphosphate (G-2,6-BP) on PFK-1?
- high G-2,6-BP has been made from G-1,6-P, so indicates lots of glucose in system that can be used in glycolysis
- high G-2,6-BP activates PFK-1
Phosphfructosekinase 1 (PFK-1) is heavily regulated within the cell to control glycolysis and gluconeogenesis. What is the role of citrate on PFK-1?
- citrate is the first molecule of the KREBs cycle
- lots of citrate indicates the KREBs cycles is slow or dysfunctional
- high citrate inhibits PFK-1 to relieve pressure on KREBs cycle
If muscles are working purley anaerobically, what happens to pyruvate and what enezyme is responsible?
- turned into lactate
- lactate dehydrogenase
If muscles are working purley anaerobically, pyruvate is turned into lactate by lactate dehydrogenase. Lactate can then be recyled back to the liver and converted into what, facilitated by what enzyme?
- pyruvate
- facilitated by lactate dehydrogenase
If muscles are working purley anaerobically, pyruvate is turned into lactate by lactate dehydrogenase. Lactate can then be recyled back to the liver and converted into pyruvate and be used in gluconeogenesis for the formation of glucose. In addition lactate is able to recycle the NADH back into the NAD+ which allows glycolysis to continue. How many ATP can the recyling of NADH back into glycolysis create?
- 2 ATP
What enzyme if responsible for converting pyruvate into acetyl-CoA, and what 2 things are generated by this?
- pyruvate dehydrogenase
- creates a CO2 and NADH in the process
What enzyme is responsible for converting acetyl-CoA into citrate, the first step of the KREBs cycle?
- citrate synthase
Following the production of pyruvate there are 2 irreversible enzymatic steps that ensure regulation of the fatty acid synthesis and entry into the KREBs cycle, what are these 2 irreversible enzymes?
1 - pyruvate dehydrogenase
2 - citrate synthase
In the KREBs cycle how many molecules of GTP which is converted into ATP, NADH and FADH2 molecules from 1 molecule of glucose, keeping in mind there are two 3 carbon molecules of pyruvate that will be turned into acetyl-CoA and citrate before entering the KREBs cycles, so everything needs to be doubled.
- GTP = 2
- NADH = 6
- FADH2 = 2
The mnemonic Citrate Is Krebs Starting Substrate For Making Oxaloacetate can be used for remembering the steps of the KREBs cycle, what does each word refer to?
- Citrate = Citrate.
- Is = Iscitrate.
- Krebs = α-ketoglutarate.
- Special = Succinyl-CoA.
- Substrate = Succinate.
- For = fumarate.
- Making = malate.
- Oxaloacetate = Oxaloacetate
How many ATP are generated from one partial turn (1 third) and one
full turn of the ATP synthase?
- 1 third turn = 1 ATP
- 1 full turn = 3 ATP
How many H+ are required to move between each alpha-beta pair and one full turn of the ATP synthase?
- 3 H+ moves to next alpha-beta pair
- 9 H+ make one full turn
- BUT 1 need 1 H+ to transport ADP into matrix
- so 10 H+ in total for a full turn of ATP synthase
NADH that are generated in glycolysis can enter the mitochondrial matrix to be used as part of the elctron transport chain via what pathway?
- malate aspartate shuttle
NADH that are generated in the KREBs cycle can enter the mitochondrial matrix to be used as part of the elctron transport chain via what pathway?
- glyceraldehyde 3-phosphate shuttle
What do uncoupling agents/proteins do to the electron transport chain?
- allow H+ to cross the innermembrane layer
- lose the potential gradients provided by H+
Are uncoupling agents/proteins, which create energy from heat by allowing H+ to cross the inner membrane and into the matrix always bad?
- no
- thermogenin is a protein that uncouple the ETC. The energy release provides heat contributing to themrogenesis in new born babies
Are uncoupling agents/proteins, which create energy from heat by allowing H+ to cross the inner membrane and into the matrix. DNP is an uncoupling agent that was used in a diet drug, why?
- causes uncoupling and allows H+ to flow into the matrix
- ETC works harder to increase H+ pumped out ATP generated
- metbaolism increases to try and increase ATP synthesis
How many respiratory proteins are encoded in the mitochondrial genome?
- 13
Reactive oxygne species (ROS) are created primarily in the matrix of the mitochondria. What is present in the matrix that can then be damaged by these ROS?
- mitochondrial genome
What is the threshold for mitochondrial mutations?
- 70%
In the genetic bottleneck of mitochondrial mutations, mutations begin in primordial germ cells in the oocyte (cells that havent specialised yet, but will eventually become oocytes in females). Is the level of mutation in oocytes pre-determined or is this random?
- random
In the genetic bottleneck of mitochondrial mutations, mutations begin in primordial germ cells in the oocyte (cells that havent specialised yet, but will eventually become oocytes in females). Does the level of mutation present in oocytes match that of the mother?
- could be completely different due to random effect
- children could have anything from 10-75% level of mutation in mitochondria
Leber’s hereditary optic neuropathy (LHON) is a single base change in the mt gene ND4, (results in Arg to His substitution) in a polypeptide of which complex?
- Complex I
Leber’s hereditary optic neuropathy (LHON) is a single base change in the mt gene ND4, (results in Arg to His substitution) in a polypeptide in complex 1, which causes what?
- partially defective in electron transport from NADH to Ubiquinone
- reduced H+ transported into innermembrane space
Myoclonus epilepsy with ragged-red fibre (MERRF) is caused by a point mutation in the mt gene encoding a tRNA specific for lysine (tRNALys). What can this cause?
- disrupts synthesis of proteins essential for oxidative phosphorylation (ATP synthesis)
What is glycogen metabolism, also called glycogenesis?
- formation fo glycogen
What is the first step of glycogenesis (glycogen synthase), this is also a major cross roads step in the glycolysis pathway?
- glucose is converted into glucose-6-phosphate
- hexokinase or glucokinase (liver) facilitates this
The converstion of glucose into glucose-6-phosphate (G-6-P) via hexokinase or glucokinase (liver) is the first step of glycogenesis (glycogen metabolism). What is the next step and which enzyme facilitates this?
- conversion of G-6-P into G-1-P
- phosphoglucomutase
Phosphoglucomutase is able to convert Glucose-6-Phosphate into Glucoe-1-Phosphate in the 2nd stage of glycogenesis. Is this reaction irreversible, and why is this important?
- yes
- so glycogen can be converted back into glucose as required
What enzyme is responsible for converting glucose-1-phosphate into glycogen?
- glycogen synthase
What enzyme is responsible for converting glycoen into glucose-1-phosphate?
- glycogen phosphorylase (adds phosphate to glucose)
Which bonds form long chains and branches on glycogen?
- chains = a1-4 glycosidic bonds
- branches = a1-6 glycosidic bonds
Why is the a1-4 and a1-6 arrangement, in addition to storage, important for fast acting energy requirements?
- so glycogen synthase can add more glucose quickly in times of high sugar
- so glycogen phosphorylase can remove more glucose quickly in times of low sugar
If glycogen is broken down in the liver is the glucose produced used for itself or transported into the blood?
- released in the blood as glucose
If glycogen is broken down in the skeletal muscle, is the glucose produced used for itself or transported into the blood?
- just for the muscle
When comparing glycogenolysis (glycogen breakdown) in the liver and muscle the first 2 steps are identical:
- step 1 = converstion of glycogen into G-1-P via Glycogen phosphorylase
- step 2 = converstion of G-1-P into G-6-P via phosphoglucomutase
In muscle the G-6-P can then enter the oxidation or lactate metabolism pathways. What does the liver posses that allows glucose to be released straight into the blood?
- glucose 6 phosphotase
- G-6-P is converted straight into glucose
- glucose is released into the blood
I glycogenolysis (glycogen breakdown) the a1-4 and a1-6 glycosidic bonds of glycogen need to be broken down. What 2 enzymes are responsible for this?
- glycogen phosphorylase breaks down a1-4 bonds
- debranching enzyme breaks down a1-6 bonds
In glycogenesis, the steps are almost the reverse of glycogenolysis:
- step 1: glucose to G-6-P via hexakinase or glucokinase (liver)
- step 2: G-6-P to G-1-P via phosphoglucomutase
After this there is an additional step and enzyme before glycogen is formed, what is this?
- Uridine triphosphate converts G-1-P into uridine biphosphate glucose
- this can then be turned into glycogen by glycogen synthase
Glycogen synthase is not able to start building glycogen from scratch. Instead there is protein that possesses its own catalytic activity and is able to add glucose molecules onto itself. After a 7-8 glucose molecule has been made glycogen synthase can start adding glucose to glycogen at a1-4 glycosidic bonds. What is this protein that starts the formation of glycogen called?
- glycogenin
Glycogen synthase is able to add further glucose to glycogen in a chain via a1-4 glycosidic bonds. But what enzyme is able to create branches in glycogen?
- branching enzyme creates a1-6 glycosidic bonds
Glycogen phosphorylase is the enzyme that breaks down glycogen into G-1-P. This enzyme is heavily regulated. If there is a lot of glucose in the cell what will this do to glycogen phosphorylase acvtivity?
- inhibit
- if glucose is present we dont need to break down glycogen
Glycogen phosphorylase is the enzyme that breaks down glycogen into G-1-P. This enzyme is heavily regulated. If there is a lot of G-6-P in the cell what will this do to glycogen phosphorylase acvtivity?
- inhibits
- G-6-P indicates that there is a lot of glucose in the cell so no need to break down glyocgen
Glycogen phosphorylase is the enzyme that breaks down glycogen into G-1-P. This enzyme is heavily regulated. If there is a lot ofATP in the cell what will this do to glycogen phosphorylase acvtivity?
- inhibits
- lots of ATP means we dont need to break down glycogen
Glycogen phosphorylase is the enzyme that breaks down glycogen into G-1-P. This enzyme is heavily regulated. If there is a lot of AMP in the cell what will this do to glycogen phosphorylase acvtivity?
- activates
- AMP is an ATP breakdown product, indicating ATP is low
Glycogen synthase is the enzyme that makes glycogen from G-1-P. This enzyme is heavily regulated. If there is a lot of G-6-P in the cell what will this do to glycogen synthaseacvtivity?
- activate
- lots of G-6-P indicates lots of glucose, so cell tries to replenish glycogen stores
What will high levels of insulin do to glycogen synthase (build glycogen) and glycogen phosphorylase (break down glycogen)?
- glycogen synthase = increased activity
- glycogen phosphorylase = decreased activity
What will high levels of glucagon do to glycogen synthase (build glycogen) and glycogen phosphorylase (break down glycogen)?
- glycogen synthase = decreased activity
- glycogen phosphorylase = increased activity
In glycogen storage disorders, such as Von Gierkes disease, what does this do to the glycogen stored in the liver?
- glycogen is broken down by glycogen phosphorylase into G-1-P and then into G-6-P
- Von Gierke disease patients do not posses G-6-Phosphotase so G-6-P cannot be turned into glucose and released into plasam
In gluconeogeneis, which is the formation of glucose from non carbohydrates sources, requires specific substrates, what are the main 3?
1 - lactate (recylced from pyruvate)
2 - alanine (protein breakdown)
3 - glycerol (fats)
In gluconeogeneis, which is the formation of glucose from non carbohydrates sources, requires specific substrates, the main are
1 - lactate (recylced from pyruvate)
2 - alanine (protein breakdown)
3 - glycerol (fats)
Each of these requires a specific enzyme, what are the enzymes?
1 - lactate = lactate dehydrogenase
2 - alanine = pyruvate carboxylase
3 - glycerol = phosphoenolpyruvate carboxykinase
There are 3 enzymatic reactions in glycolysis, which gluconeogenesis must overcome. What are the 4 enzymes that are able to overcomr these 3 irreversible steps?
1 - pyruvate carboxylase (reverse pyruvate formation)
2 - phosphoenolpyruvate carboxykinase (reverse pyruvate formation)
3 - fructose 1,6 biphosphotase
4 - glucose-6-phosphotase
Phosphofructokinase-2 (PFK-2) creates fructose 2,6 biphosphate is able to increase the activity of PFK-1 and increase glycolysis. However, in gluconeogenesis, what happens to the activity of PFK-2?
- inhibit
