Metabolism Flashcards
(187 cards)
1
Q
What is composition of an amino acid?
A
They have an amine group, a carboxylic acid group, a hydrogen and an R-group which changes based on the amino acid.
2
Q
What is chirality?
A
Amino acids have 4 different group bonded to the central carbon (except for glycine which has two hydrogens), so they have optical isomers (enantiomers). All amino acids in proteins are L-isomers.
3
Q
Which amino acids are hydrophobic?
A
Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, Methionine, Tryptophan and Phenylalanine.
4
Q
Which amino acids are hydrophilic?
A
Serine, Threonine, Tyrosine, Asparagine, Glutamine and Cysteine.
5
Q
Which amino acids have positively charged side chains?
A
Arginine, Lysine and Histidine.
6
Q
Which amino acids have negatively charged side chains?
A
Aspartate and Glutamate.
7
Q
How do amino acids bond?
A
The -OH on the carboxylic acid bonds covalently to the hydrogen on the amine group of another amino acid to form a peptide bond.
8
Q
What bonds and interactions hold a protein together?
A
Proteins are held together by covalent bonds disulfide bridges, hydrogen bonds, ionic interactions, Van der Waals forces and hydrophobic interactions.
9
Q
What are the disulfide bridges in a protein?
A
Disulfide bridges are strong covalent bonds between to sulfur atoms. These bonds are only between two cysteines.
10
Q
What are hydrogen bonds in proteins?
A
These occur between amino acids that have a partially positive hydrogen atom and a partially negative atom.
11
Q
What are the ionic interactions in proteins?
A
These arise between charged amino acids. They are strong bonds when the ion pairs in the interior. When on the exterior of the protein they are easily neutralised by salts.
12
Q
What are the Van der Waals forces in proteins?
A
They are weak electrostatic interactions due to the fluctuating electron clouds. They are very weak but due to the large number of electrons present, they can have a large impact on the protein’s stability.
13
Q
What are the hydrophobic interactions in proteins?
A
They are based on whether an amino acid is charged or not. They are crucial to protein folding. Because proteins are mostly in aqueous environments, they fold with hydrophilic amino acids on the outside and hydrophobin inside.
14
Q
What is the primary structure of a protein?
A
This is the linear sequence of the amino acids in the chain.
15
Q
What is the secondary structure of a protein?
A
This is the initial folding into local structures within a protein such as alpha-helices and beta-pleated sheets.
16
Q
What is the alpha-helix structure in a protein?
A
They are right-handed helices formed by hydrogen bonds between C=O of one residue and the N-H of another. The side chains face outwards from the helices.
17
Q
What are beta-pleated sheets in an amino acid?
A
This is when proteins fold into an almost 2D shape with the NH and C=O at right angles to the backbone. It is held together by hydrogen bonds. They can be parallel or antiparallel.
18
Q
What is the tertiary structure?
A
This is the arrangement of the secondary local structures into a compact globular structures called domains.
19
Q
What is the quaternary structure?
A
This is the 3D structure of a multimeric protein with several subunits.
20
Q
Why do polypeptides fold into structures?
A
Polypeptides fold in order to have the most energetically stable form. This happens independently although sometimes they can be guided by chaperone proteins.
21
Q
What is electrophoresis?
A
It is the process of separating molecules based on their charge to identify them.
22
Q
How can electrophoresis be used to detect mutated proteins?
A
Proteins with single mutations might have a different charge composition which means they would travel a different distance on the electrophoresis plate.
23
Q
What is the first law of thermodynamics?
A
Energy can neither be created nor destroyed. It can only be transferred from one form to another.
24
Q
What is the second law of thermodynamics?
A
In an isolated system, entropy (the degree of disorder) will always increase.
25
What is Gibbs Free energy?
It is the amount of energy within a molecule that could perform useful work at a constant temperature, denoted by G. It combines both laws of thermodynamics because changes in G (delta-G) measure the change in entropy of a reaction.
26
How do cells make energetically unfavourable reactions occur?
Reactions happen spontaneously when delta-G is negative. So cells do energetically unfavourable reactions by coupling it with a reaction which has a negative change in G, such as hydrolysis of ATP.
27
What is the structure of ATP?
ATP is composed of Adenine bonded to a ribose sugar which is bonded to three phosphate groups. There is a phosphoanhydride bond which links the terminal phosphate groups with a large negative delta-G. Hydrolysing this bond releases 31 kJ/mol.
28
What are enzymes?
Enzymes are biological catalysts which increase the rate of a reaction without being altered by it.
29
Why are enzymes important in biological reactions?
Even with the use of ATP, reactions won't happen at a fast enough rate to be useful. Enzymes increase the rate by lowering the activation energy required for the reaction, thus allowing more of them to happen.
30
What is the transition state and how does it link to enzymes function?
The transition state is the conformation of the substrate where the atoms are rearranged geometrically and electronically so the reaction can proceed
31
How does the transition state link to enzyme function?
Enzymes function by putting stress on particular bonds so the substrate goes into the transition state easier.
32
What is the active site of an enzyme?
This is the part of the enzyme where the substrate fits in. Key residues in this site make or break bonds in the substrate by altering the arrangement of electrons in redox reactions.
33
What is the lock and key model proposed by Emil Fischer?
This model says that the shape of the active site is specific to a substrate and this explains why most enzymes only catalyse one substrate.
34
What is the induced fit model proposed by Daniel Koshland Jr?
In this model, the substrate induces a change in the enzyme to form the correct active site. When the substrate becomes product, the enzyme changes shape back and the product leaves the site. This model is now held to be more valid than the Lock and Key hypothesis.
35
What is lysozyme?
It is a component of tears and nasal secretions. It is an enzyme which hydrolyses the polysaccharide in bacterial cell walls to break them down and it was discovered by Sir Alexander Fleming.
36
How does lysozyme work?
It hydrolyses alternating polysaccharide copolymers of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) which is the unit polysaccharide in many bacterial cell walls. It cleaves at the Beta(1-4) glycosidic bond connecting C1 of NAM to the C4 of NAG.
37
What is the effect of pH on enzyme activity?
Enzymes have an optimum pH they work at. Below and above that level, the amino acids' ionic properties maybe be changed which affects the enzyme conformation and thus their function.
38
What is the effect of temperature on enzyme activity?
As temperature increases, reaction rate increases. All enzymes have an optimum temperature they work at. In humans this is at about 37 degrees celsius. Beyond that, enzymes become denatured and it becomes inactive.
39
What is the effect of substrate concentration on enzyme activity?
As the substrate concentration increases, enzyme activity increases upto a point because more substrates fit into active sites. Beyond a certain point all active sites become saturated and increasing the substrate concentration would have no effect.
40
What is a coenzyme?
This is a non-protein compound which is necessary for enzymes to function.
41
What is NAD+?
NAD+ (Nicotinamide adenine dinucleotide) is a coenzyme in many dehydrogenation reactions. It work by accepting one hydrogen and two electrons.
42
What is lactate dehydrogenase?
During intense exercise, pyruvate turns into lactate to regenerate NAD+. The lactate is taken to the liver where the lactate dehydrogenase enzyme uses the abundance of NAD+ to convert it back to pyruvate.
43
What is glycolysis?
It is the first stage of cellular metabolism. It is an anaerobic process where one 6 carbon molecule (glucose) is split into two 3 carbon molecules (pyruvate). It takes place in the cytoplasm.
44
What are the two stages of glycolysis?
Glycolysis can be split into 10 reactions. The first 5 reactions use ATP to form a high energy compound and the latter 5 split the high energy compound to form more ATP than inputted.
45
What is the first reaction in glycolysis?
A glucose molecule is converted to glucose-6-phosphate using a hexokinase enzyme and this converts 1 ATP into ADP. Kinase enzymes transfer phosphates from a donor such as ATP to a substrate. This reaction is irreversible and traps the glucose in the cell due to the negative charge on the product.
46
What is the second reaction in glycolysis?
Glucose-6-phosphate is converted to fructose-6-phosphate using the phosphoglucose isomerase enzymes. This is so that fructose can be split into equal halves later.
47
What is the third reaction in glycolysis?
Fructose-6-phosphate is converted to fructose-1,6-bisphosphate using the phosphofructokinase enzyme and it converts an ATP into ADP. This is to generate a highly symmetrical and energetic compound.
48
What is the fourth reaction in glycolysis?
Fructose-1,6-bisphosphate is split into glyceraldehyde 3-phosphate and dihydroxyacetone phosphate by the enzyme aldolase. This generates two high energy compounds.
49
What is the fifth reaction in glycolysis?
Dihydroxyacetone phosphate is converted to glyceraldehyde 3-phosphate by the enzyme triose phosphate isomerase (TPI). Deficiency in TPI is a very rare metabolic disease (only 100 cases reported in 35 years) and it leads to a life expectancy of 6 years.
50
What is substrate level phosphorylation?
This is the production of ATP by transferring a phosphate from a substrate to ADP.
51
What is the sixth reaction in glycolysis?
Glyceraldehyde 3-phosphate is converted to 1,3-bisphosphoglycerate using the glyceraldehyde 3-phosphate dehydrogenase enzyme. It also generates an NADH molecule from NAD+ and inorganic phosphate.
52
What is the seventh reaction in glycolysis?
1,3-bisphosphoglycerate is converted to 3-phosphoglycerate using the phosphoglycerate kinase enzyme. This generates an ATP by transferring a phosphate to an ADP.
53
What is the eighth reaction in glycolysis?
3-phosphoglycerate is converted to 2-phosphoglycerate by the phosphoglycerate mutase enzyme.
54
What is the ninth reaction in glycolysis?
2-phosphoglycerate is converted to phosphoenolpyruvate by the enolase enzyme.
55
What is the tenth reaction in glycolysis?
Phosphoenolpyruvate is converted to pyruvate by the enzyme pyruvate kinase. This phosphate is transferred to an ADP to form an ATP.
56
What is the net result of glycolysis?
Two ATP molecules are used to generate two molecules of pyruvate, 4 molecules of ATP (2 net ATP molecules) and 2 molecules of NADH.
57
What happens to pyruvate during alcoholic fermentation?
Pyruvate is converted to acetaldehyde by pyruvate decarboxylase, which generates CO2. Acetaldehyde is converted to ethanol by alcohol dehydrogenase. This converts the NADH back into NAD+ to be used in glycolysis again.
58
How is lactate generated from pyruvate?
Pyruvate is converted to lactate using lactate dehydrogenase which converts NADH into NAD+. This process is reversible.
59
Why is regeneration of NAD+ essential?
NAD+ is essential for glycolysis to continue during oxygen deprivation since glycolysis is an anaerobic process.
60
How can lactate dehydrogenase be used as a diagnostic tool?
It is present in many tissues including heart, liver, kidney, skeletal muscle, brain and lungs. So elevated levels would indicate several disorders such as stroke, myocardial infarction, hepatitis, muscular dystrophy, pulmonary infarction.
61
What is creatine kinase?
Muscles only store a small amount of ATP. During prolonged contraction, creatine phosphate is converted to creatine and ATP to provide energy. The enzyme that does this is creatine kinase.
62
How can creatine kinase (CK) be used as a diagnostic tool?
Muscle damage causes leakage of CK into the blood. Elevated levels of a specific isoenzyme can diagnose myocardial infarction and the extent of the damage.
63
How is pyruvate used in aerobic respiration?
Pyruvate reacts with HS-CoA to form Acetyl CoA and CO2. This occurs in the mitochondria and produces one NADH from NAD+. The enzyme used for this is the pyruvate dehydrogenase complex.
64
What is the pyruvate dehydrogenase complex?
It is a massive complex containing 3 different enzymes (pyruvate decarboxylase, lipoamide reductase-transacetylase and dihydrolipoyl dehydrogenase) as well as 5 different prosthetic groups (Thiamine pyrophosphate, lipoamide, FAD, CoA and NAD+). There 60 proteins in it altogether.
65
What is the composition of Acetyl CoA?
It contains an acetyl (2 carbon) group which has a high energy thioester bond to Coenzyme A. This molecule has a ribose sugar and adenine which suggests RNA ancestry.
66
What is the Krebs Cycle?
The Krebs Cycle, also known as the Tricarboxylic Acid (TCA) cycle is a continuous set of eight reactions that happen in the matrix of the mitochondria. It is the second stage of cellular metabolism.
67
What is the first reaction in the TCA?
A 4 carbon molecule called oxaloacetate reacts with acetyl CoA to form the 6 carbon molecule citrate and HS-CoA. This is catalysed by citrate synthase.
68
What is the second reaction in the TCA?
Citrate is isomerised to isocitrate by aconitase.
69
What is the third reaction in the TCA?
Isocitrate is oxidised to the 5 carbon molecule alpha-ketoglutarate by isocitrate dehydrogenase. This reaction produces one NADH and CO2.
70
What is the fourth reaction in the TCA?
Alpha-ketoglutarate is oxidised to a 4 carbon molecule called succinyl-CoA through a reaction with HS-CoA. It is catalysed by an alpha-ketoglutarate dehydrogenase complex. The reaction forms an NADH and CO2.
71
What is the fifth reaction in the TCA?
Succinyl-CoA is converted to Succinate by displacing the CoA with a phosphate which is then transferred to a GDP to form GTP. Succinyl CoA synthetase is the enzyme.
72
What is GTP?
GTP is a Guanosine Triphosphate. It is produced primarily in tissues with anabolic reactions like the liver. another form of succinyl CoA synthetase produces ATP mainly in skeletal and cardiac muscle.
73
What is the sixth reaction in the TCA?
Succinate is oxidised to fumarate by succinate dehydrogenase. This also produces FADH2 from FAD.
74
What is the seventh reaction in the TCA?
H2O is added to fumarate to form malate by breaking a double bond by the fumarase enzyme.
75
What is the eighth reaction in the TCA?
Malate is dehydrogenated to oxaloacetate, the first reactant in the cycle, by malate dehydrogenase. This reaction produces one NADH from NAD.
76
What are the net products of the TCA?
Each turn produces two CO2 (waste products), 3 NADH, 1 GTP and 1 FADH2.
77
Where are the enzymes in the TCA located?
All enzymes in the TCA are located in the mitochondrial matrix except for succinate dehydrogenase which is in the inner mitochondrial membrane.
78
How many ATPs are yielded from the TCA and its products?
Each NADH forms 3 ATP and each FADH2 form 2 ATP. Therefore 12 ATP molecules are derived from the TCA.
79
What is meant by degradation of amino acids?
This involves removing the amino group from the molecule and using the carbons in either glycolysis or the TCA.
80
What are the seven metabolic products formed from amino acids?
Pyruvate, Acetyl CoA, acetoacetyl CoA, alpha-ketoglutarate, succinyl CoA, fumarate and oxaloacetate.
81
What is protein metabolism?
It's when an amine group is transferred from an amino acid to a keto acid to form a new amino acid and a new keto acid.
82
How is alanine used in metabolism?
Alanine reacts with alpha-ketoglutarate to form pyruvate and glutamate by aminotransferase. Alpha-ketoglutarate is reformed from glutamate by glutamate dehydrogenase, which also generate NH4+ to form urea.
83
How is NADH from glycolysis transferred to the mitochondrial matrix for the final stage of cellular metabolism?
Skeletal muscle and the brain uses the Glycerol Phosphate Shuttle. The liver, kidney and heart uses the Malate-Aspartate Shuttle.
84
What is the first step in the Glycerol Phosphate shuttle?
Cytoplasmic glycerol 3-phosphate dehydrogenase transfers the electrons from NADH to dihydroxyacetone phosphate (DHAP) to form Glycerol 3-phosphate.
85
What is the second stage in the Glycerol Phosphate shuttle?
Membrane bound Glycerol 3-phosphate dehydrogenase transfers electron from glycerol 3-phosphate to FAD to form FADH2. These are then transferred to coenzyme Q in the electron transport chain.
86
How does the malate-aspartate shuttle work?
H- is transferred from cytoplasmic NADH to oxaloacetate to give malate by the enzyme malate dehydrogenase (MDH). Malate is transferred to the mitochondrial matrix where it is rapidly oxidised to oxaloacetate by NAD+ to form NADH. This is catalysed by MDH in the mitochondria.
87
What transporters does the malate-aspartate shuttle use?
The alpha-glutarate transporter lets malate in in exchange for alpha-glutarate.
The glutamate/aspartate transporter lets glutamate in in exchange for aspartate.
88
What is the Warburg effect?
In cancer cells, mutations in isocitrate dehydrogenase, succinate dehydrogenase and fumarase has shown to decrease TCA activity and increase aerobic glycolysis, generation of lactate from pyruvate even with ample oxygen. This is the Warburg effect. Forcing them to carry out oxidative phosphorylation could make them into non-malignant cells.
89
What is the structure of mitochondria?
Mitochondria has two membranes: the outer membrane which limits the size of the organelle and the inner membrane which is called the cristae. The inside is called the matrix and the gap between the membranes is the intermembrane space.
90
What is the function of the mitochondria?
Mitochondria is the powerhouse of the cell. It is where the majority of the ATP is produced through oxidative phosphorylation.
91
How is mitochondria suited to its function?
The cristae of the mitochondria contains all the enzymes and cofactors for oxidative phosphorylation and it is folded to to increase surface area.
92
What is the evidence for the endosymbiont theory?
1. Mitochondria can only grow from pre-existing ones.
2. They have their own circular genes with no histone proteins, resembling prokaryotes.
3. They have their own protein synthesising machines, resembling prokaryotic ribosomes.
4. The first amino acid in mitochondrial transcription is formylated methionine, same as bacteria. Eukaryotes have methionine.
5. Some antibiotics that affect bacterial protein synthesis also affects mitochondria.
93
What is the mitochondrial karyotype?
Mitochondria have only 37 genes found in a circular genome. They have several copies of the genome.
94
WHat is the inheritance pattern of mitochondrial DNA (mtDNA)?
mtDNA is only inherited through the ovum and thus any mtDNA mutation related diseases are only found in the maternal offspring.
95
How does mitochondria generate ATP?
The enzymes and cofactors in the inner mitochondrial membrane reoxidises NADH and FADH2. Those reactions have a delta-G of -223 and -170 kJ/mol respectively. This energy is used to synthesis several ATP molecules.
96
Define the chemiosmotic theory.
The chemiosmotic theory says the transfer of electrons down the electron transport chain pumps H+ ions into the intermembrane space. As H+ ions accumulate, a proton gradient is established. When H+ ions diffuse back into the matrix, the energy released is used to generate ATP.
97
Define oxidative phosphorylation.
Oxidative phosphorylation is the final stage in cellular metabolism. It uses the oxidation of reduced coenzymes and the transfer of electrons along the electron transport chain to phosphorylate an ADP molecule.
98
What is the first step in the electron transport chain?
The first enzyme in the inner membrane is the NADH dehydrogenase complex which has a higher affinity for electrons than NADH. So it accepts two electrons from NADH, oxidising it back to NAD+. The electron are passed down the proteins in the complex which pumps H+ ions into the intermembrane space.
99
What is the second step in the electron transport chain?
The electrons are transferred from the NADH dehydrogenase complex to an electron carrier called ubiquinone (coenzyme Q). This transfers the electron to the second membrane bound enzyme, cytochrome b-c1 complex.
100
What is the third step in the electron transport chain?
Cytochrome b-c1 complex and the enzyme following it have increasing electron affinities which keeps the electrons flowing in one direction. The energy of the electron is again used to pump H+ ions out of the matrix.
101
What is the fourth step in the electron transport chain?
The electrons are passed to the second electron carrier, cytochrome c. The carrier takes the electrons, now with reduced energy, to the final enzyme, the cytochrome oxidase complex.
102
What is the fifth step in the electron transport chain?
The cytochrome oxidase complex uses the final energy of the electrons to pump more H+ ions out of the matrix and then holds onto the electrons.
103
What is the endpoint for the electrons in the electron transport chain?
When four electrons are collected at the cytochrome oxidase complex, they are taken by 4 H+ ions and one O2 molecule to form 2 water molecules. Thus oxygen is the final electron acceptor which is why this process is aerobic.
104
What is redox potential?
The ability of a redox couple (the reduced and oxidised form of a molecule) to accept or donate electrons is the redox potential.
105
What does a negative and positive redox potential suggest?
A negative potential implies the redox couple tends to donate more electrons (lower reducing power than hydrogen) .
A positive potential implies the couple tends to accept electrons (less reducing power than hydrogen).
106
What is the structure of ATP synthase?
It is a multimeric protein. It has an F0 part which is embedded in the inner membrane and an F1 part which projects into the matrix.
107
How does ATP synthase work?
Whan proton gradient builds up in the intermembrane space, ATP synthase allows the H+ back into the matrix. This rotates the F0 part of the enzyme which is attached to the F1 part by a rotor. the rotation causes a conformational change in the F1 part, which drives ATP production.
108
How does the direction of proton flow affect ATP synthase?
When H+ ions flow into the matrix, ATP is synthesised. If the proton gradient reverses and the electrons flow out, the rotor, the moving part of the enzyme, turns the other way and ATP is hydrolysed.
109
What is the oxygen electrode?
It is a device which measures the oxygen concentration of a solution.
110
How does the oxygen electrode work?
It is housed in a small container with a platinum cathode and silver anode. When a voltage of 0.6 V is applied, oxygen is reduced to water. The resulting current is proportional to oxygen concentration, thus allowing us to calculate it.
111
How can an oxygen electrode help to understand mitochondrial respiration?
Prepare a suspension of mitochondria and place it into a chamber with an oxygen electrode. If the current is monitored over time while various substrates and enzyme inhibitors are added, the effect they have can be determined.
112
What is the structure of fatty acids?
Fatty acids are composed of a hydrophilic carboxylic acid head and a hydrophobic hydrocarbon tail.
113
What is the difference between saturated and unsaturated fatty acids?
Saturated fatty acids have all single covalent bonds in their hydrocarbon tail while unsaturated fatty acids have one or more C=C double bonds.
114
How are fatty acids stored in living things?
They are stored in the cytoplasm of cells as triacylglycerol which has a glycerol molecule with three fatty acid chains bonded to it. In plants, the fatty acids are unsaturated (thus liquid) while animal fats are saturated (thus solid).
115
Where do mammals store fatty acids?
Mammals store fatty acids as triacylglycerol in specialised cells called adipocytes.
116
What is the role of fatty acids in energy release?
Over 50% of the body's energy needs. excluding the brain, comes from metabolising fatty acids since they have double the energy as same weight of carbohydrates.
117
What is the process of fatty acid metabolism?
The process is called beta-oxidation and it occurs in the mitochondria. The end result is acetyl CoA which is used in the TCA.
118
What is the first step in beta-oxidation?
The fatty acid reacts with HS-CoA and two ATP molecules to produce Acyl CoA and two ADP. This is catalysed by Acyl CoA synthetase. This process occurs on the outer mitochondrial membrane.
119
What is Carnitine Shuttle?
It is the process of moving the Acyl CoA into the matrix. Acyl CoA is coupled to carnitine by carnitine acyltransferase I on the cytoplasmic side to form acyl carnitine and then moved to the matrix side by a translocase channel. Then, carnitine acyltransferase II on the matrix side splits the molecule again to release Acyl CoA.
120
What are the steps in the beta-oxidation cycle?
The Acyl CoA molecule undergoes oxidation, hydration, oxidation and thiolysis, in that order. Each turn produces a molecule with two fewer carbon atoms.
121
What are the products of the beta-oxidation cycle?
Each turn forms one Acetyl CoA, one NADH and one FADH2. For fatty acids with even number of carbons, the final turn produces two acetyl CoA. For odd fatty acids, the final turn makes Propionyl CoA which undergoes reactions to become Succinyl CoA and enters the TCA cycle.
122
What are the exact products formed by the complete metabolising of Palmitic Acid?
Palmitic acid has 16 carbon atoms. It goes through 7 cycles of beta-oxidation. The reaction also uses 7 FAD, 7 NAD+, 7 H20 and 7 CoA. The products are 8 acetyl CoA, 7 FADH2 and 7 NAD.
123
What are the enzymes involved in lipogenesis?
Acetyl CoA Carboxylase and Fatty acid synthase (FAS). The latter is a polypeptide with seven different enzymatic functions.
124
What are the substrate molecules involved in lipogenesis?
Acetyl CoA and Malonyl CoA.
125
What is the first step in lipogenesis?
Acetyl CoA is converted to 3C Malonyl CoA using the enzymes Acetyl CoA carboxylase.
126
What are the second and third steps in lipogenesis?
Malonyl from Malonyl CoA and Acetyl from Acetyl CoA are transferred to acyl carrier proteins (ACP) to form Malonyl and Acetyl ACP molecules.
127
What are the next four steps in lipogenesis?
Acetyl and Malonyl ACP undergo a cycle of: decarboxylative condensation (CO2 is released); reduction with NADPH; dehydration; reduction again with NADPH. The end result is a a 4C ACP which is hydrolysed to form a fatty acid.
128
What are the similarities between beta-oxidation and lipogenesis?
Beta oxidation does oxidation, hydration, oxidation and cleavage while lipogenesis is a chemical reversal of that process.
129
What are the differences between beta-oxidation and lipogenesis?
Beta-oxidation uses CoA carrier; lipogenesis uses ACP.
Beta-oxidation occurs in mitochondrial matrix; lipogenesis occurs in cytoplasm.
Beta-oxidation uses FAD/NAD for oxidation; lipogenesis uses NADPH for reduction.
130
What alterations are made to a 16C fatty acid after lipogenesis in the cytoplasm?
Elongation longer than 16 carbons long occurs separately in the mitochondria or ER. Fatty acids can be desaturated by the enzyme fatty acyl-CoA desaturases.
131
How is de novo lipogenesis linked to cancer?
De novo lipogenesis in adults occurs in liver, adipose tissue, lactating breasts and certain cancer cells.
132
What length of fatty acid chain can each Acyl CoA dehydrogenase bind to in beta-oxidation?
Short chain <6C; medium chain 6-12C; long chain 13-21C; very long chain >22C.
133
What is Medium Chain Acyl-CoA Dehydrogenase Deficiency?
MCADD is an autosomal recessive condition seen in 1 in 10 000 births in the UK primarily among caucasians. It is fatal if undiagnosed. Patients are unable to metabolise fatty acids. So they should have a high carbohydrate diet and never fast for more than 12 hours.
134
What is primary carnitine deficiency?
It is an autosomal recessive disorder seen in 1 in 100 000 births in USA (1 in 500 in the Faroe Islands). It is due to a reduced ability of cells to absorb carnitine for beta-oxidation. It causes encephalopathies, cardiomyopathies, muscle weakness and hypoglycaemia.
135
What is cholesterol?
Cholesterol is a steroid found primarily in cell membranes to increase or decrease membrane stiffness.
136
What the three stages of de novo cholesterol synthesis?
De novo synthesis of cholesterol occurs in the liver.
Stage 1: Synthesis of isopentenyl pyrophosphate in the cytoplasm.
Stage 2: condensation of 6 of those molecules to form squalene in the cytoplasm.
Stage 3: cyclisation and demEthylation of squalene to form cholesterol in the ER.
137
What is the first step of stage 1 of cholesterol synthesis?
Two Acetyl CoA molecules are condensed by beta-ketothiolase to form Acetoacetyl CoA.
138
What is the second step of stage 1 of cholesterol synthesis?
Another Acetyl CoA is condensed to the molecule by HMG CoA synthase to form HMG CoA.
139
What is the third step of stage 1 of cholesterol synthesis?
HMG CoA is reduced to mevalonate by HMG CoA reductase. This step is part of the negative feedback loop controlled by cholesterol, mevalonate and bile salts.
140
What is the fourth step of stage 1 of cholesterol synthesis?
Mevalonate undergoes three phosphorylations (2 at carbon-5 and and 1 at carbon-3) by kinases followed by decarboxylation to form 3-isopentenyl pyrophosphate (a 5 carbon molecule).
141
What is the first step of stage 2 of cholesterol synthesis?
Isopentenyl pyrophosphate undergoes isomerisation by the enzyme isopentenyl pyrophosphate isomerase to form dimethylallyl pyrophosphate.
142
What is the second step of stage 2 of cholesterol synthesis?
Another isopentenyl pyrophosphate is added to Dimethylallyl pyrophosphate bt geranyl transferase enzyme to form 10 carbon geranyl pyrophosphate.
143
What is the third step of stage 2 of cholesterol synthesis?
Another isopentenyl pyrophosphate is added to geranyl pyrophosphate to form 15 carbon farnesyl pyrophosphate by the geranyl transferase enzyme.
144
What is the fourth step of stage 2 of cholesterol synthesis?
Two farnesyl pyrophosphate are condensed by squalene synthetase to form 30 carbon squalene.
145
What is the first step of stage 3 of cholesterol synthesis?
Squalene is reduced to squalene epoxide by the enzyme squalene monooxygenase in the presence of NADPH and oxygen. This changes the C=C bond distribution.
146
What is the second step of stage 3 of cholesterol synthesis?
Squalene epoxide is converted to Lanosterol by the enzyme squalene epoxide lanosterol cyclase.
147
What is the third step of stage 3 of cholesterol synthesis?
Lanosterol is reduced and three methyl groups are added in 19 steps to form cholesterol. This release methanoic acid and two CO2.
148
What is the hormonal purpose of cholesterol?
Cholesterol is converted to pregnenolone by the enzyme desmolase. This molecule is the basis for all 5 groups of steroid hormones.
149
What are the steps in the synthesis of Vitamin D3 from cholesterol?
Under UV light, 7-dehydrocholesterol is converted to previtamin D3 and then cholecalciferol (Vitamin D3).
150
What are bile salts?
Bile salts are molecules generated by the liver with a hydrophobic face and a hydrophilic face. They are stored in the gallbladder.
151
What is the purpose of bile salts?
Bile salts are released into the intestine during digestion where they act as emulsifiers. They aid in digestion and absorption of fats as well as fat-soluble vitamins A, D E and K. Bile salts deficiency leads to steatorrhea (fatty stool).
152
How is cholesterol used in the synthesis of bile salts?
Half of the 800mgo of cholesterol synthesised by the liver is broken down in a series of reactions to form primary bile salts glycocholate and taurocholate.
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What are lipoproteins?
Since lipids are insoluble in aqueous solutions, they are transported in the blood by packaging them into lipoproteins. These are made of a phospholipid monolayer with cholesterol and apoproteins. They contain cholesterol esters and triacylglycerols.
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How are cholesterol esters synthesised?
They are made in the plasm from cholesterol and a chain of lecithins catalysed by the enzyme lecithin cholesterol acyltransferase (LCAT).
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What is the purpose of cholesterol esters?
They are more hydrophobic than cholesterol and thus allows tighter packing inside lipoproteins.
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What are the five categories of lipoproteins?
Lipoproteins are categorised based on density and they all have different apoproteins to allow recognition by different cells. The groups are: chylomicrons (CM); very low density (VLDL); intermediate density (IDL); low density (LDL); high density (HDL).
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What is the function of HDLs?
HDLs (good cholesterol) take cholesterol from peripheral tissue to the liver for use or disposal, thus reducing total serum cholesterol.
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What is the function of LDLs?
LDLs (bad cholesterol transports cholesterol from the liver to peripheral tissues. Prolonged elevation of LDL leads to atherosclerosis (hardening of the arteries).
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What is familial hypercholesterolaemia?
FH is a monogenic dominant trait. Heterozygotes have 2-3 times the normal cholesterol levels, making the susceptible to atherosclerosis in middle age
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What is familial hypercholesterolaemia?
FH is a monogenic dominant trait. Heterozygotes have 2-3 times the normal cholesterol levels, making the susceptible to atherosclerosis in middle age. Homozygotes have 5 times the normal levels, leading to severe atherosclerosis and coronary infection in adolescence.
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What is the cause of FH?
Cholesterol as LDL is taken up by receptor molecules called LDL receptors, which severely lacked function in FH patients.
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What are the treatments for FH?
The two treatments are: HMG CoA reductase inhibitors (statins); resins or sequestrants (cholestyramine) which bind to bile acid-cholesterol complexes and prevent reabsorption into the intestine.
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What is the first stage in dietary fat digestion?
Lingual, gastric and pancreatic lipases digests lipids to form monoacylglycerols (MAG), diacylglycerols (DAG) and free fatty acids (FA).
164
What are the five classes of mutations in LDL receptor gene resulting in FH?
Class I: In the LDLR promoter - LDLR not synthesised.
Class II: In the coding region - LDLR not transported from ER to Golgi, leading to low cell surface expression.
Class III: In the N-terminus region - LDLR doesn't bind to LDL properly.
Class IV: In the cytoplasmic domain - the complex doesn't cluster, preventing endocytosis.
Class V: In the EGFP domain - LDL not released from receptor and thus LDLR not recycled.
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What is the second stage in dietary lipid digestion?
Bile salts solubilize fatty acids to form micelles that also contain cholesterol, lysophosphatidic and fat soluble vitamins.
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What is the final stage in the digestion of dietary lipids?
The micelles are taken up by enterocytes which resynthesise triacylglycerols and incorporate them into chylomicrons. These are then transported in the lymphatic system to the right destination.
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How are proteins directed to the right compartment?
Proteins have a signal sequence on them which direct them to the right organelle.
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What are the three types of intracellular transport?
Gated transport, transport across membranes and vesicular transport.
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Describe an example of gated transport.
Import of nuclear proteins is an example of gated transport. Nuclear proteins pass through nuclear pores which have a meshwork of nuclear fibrils to prevent passage of large molecules. Nuclear import receptors recognise signal sequences on nuclear proteins and deliver them into the nucleus.
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What are the two populations of ribosomes in the cytoplasm?
Some ribosomes are free in the cytoplasm and synthesis cytoplasmic proteins. Others are bound to the ER and synthesis proteins to be translocated into the ER.
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Describe an example of transport across membranes.
Proteins synthesised with an ER sequence are recognised by ribosomes. They attach to the ER and form a polyribosomes which synthesises the protein directly into the ER.
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What modifications does the ER make to the polypeptide?
Folding the polypeptide, formation of disulfide bridges, initial glycosylation, specific proteolytic cleavages, assembly of multimeric proteins.
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What happens to misfolded proteins in the ER?
They are kept in the ER rather than being transported to the Golgi. They are then send to to the cytosol to be degraded.
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What causes Cystic Fibrosis (CF)?
A mutation in the Cystic Fibrosis transmembrane conductance regulator (CFTR) gene at the 508th position leads to loss of phenylalanine. This results in misfolding and thus the protein is degraded. This leads to CF.
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Describe examples of vesicular transport.
Endocytosis and exocytosis are examples of vesicular transport. They are carried out by vesicles.
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Define endocytosis.
The absorption of matter by a cell by invagination of its membrane to form a vacuole.
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Define exocytosis.
The process by which the contents of a cell are released through fusion of vesicles with the plasma membrane.
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What are the steps in outward secretory and inward endocytic pathways?
Outward pathway: Proteins pass from the ER to the Golgi to the plasma membrane via vesicles.
Inward pathway: extracellular molecules are ingested in vesicles and delivered to endosomes or lysosomes by vesicles.
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What are the two faces of the Golgi Apparatus?
Golgi has a cis face where the proteins enter and a trans face where the proteins exit.
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What is the purpose of the Golgi Apparatus?
Proteins undergo further modifications in the Golgi. Complex oligosaccharides are added and removed by enzymes in the Golgi as the protein moves through.
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What are the two types of secretion from the Golgi?
Constitutive secretion means a steady stream of vesicles bud off from the Golgi and are released. This happens in all cells.
Regulated secretion means products are concentrated and stored in the vesicles until an extracellular signal stimulates secretion. This only happens in some cells.
182
Describe the process of exocytosis and endocytosis.
Exocytosis occurs via budding of the vesicles at the membrane. The vesicles have a protein coat where the membrane invaginates. A protein called dynamin forms a loop around deeply invaginated vesicle and causes it to pinch off. Then then protein coat is removed.
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How are vesicles moved inside cells?
Vesicles bind to motor proteins which transport them along microtubules in the cytoskeleton.
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What are the three forms of endocytosis?
Receptor mediated endocytosis, pinocytosis and phagocytosis.
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What is phagocytosis?
This is when cells take in particles. An example is white blood cells ingesting a bacterium.
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What is receptor mediated endocytosis?
This is when a molecule binds to a receptor on a membrane which causes endocytosis An example is the absorption of LDL.
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What are the consequences of faulty membrane trafficking?
Over 75 genetic conditions are due to mutations in membrane trafficking genes. Many pathological infections also target membrane trafficking.
