Metabolism Flashcards
What is composition of an amino acid?
They have an amine group, a carboxylic acid group, a hydrogen and an R-group which changes based on the amino acid.
What is chirality?
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.
Which amino acids are hydrophobic?
Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, Methionine, Tryptophan and Phenylalanine.
Which amino acids are hydrophilic?
Serine, Threonine, Tyrosine, Asparagine, Glutamine and Cysteine.
Which amino acids have positively charged side chains?
Arginine, Lysine and Histidine.
Which amino acids have negatively charged side chains?
Aspartate and Glutamate.
How do amino acids bond?
The -OH on the carboxylic acid bonds covalently to the hydrogen on the amine group of another amino acid to form a peptide bond.
What bonds and interactions hold a protein together?
Proteins are held together by covalent bonds disulfide bridges, hydrogen bonds, ionic interactions, Van der Waals forces and hydrophobic interactions.
What are the disulfide bridges in a protein?
Disulfide bridges are strong covalent bonds between to sulfur atoms. These bonds are only between two cysteines.
What are hydrogen bonds in proteins?
These occur between amino acids that have a partially positive hydrogen atom and a partially negative atom.
What are the ionic interactions in proteins?
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.
What are the Van der Waals forces in proteins?
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.
What are the hydrophobic interactions in proteins?
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.
What is the primary structure of a protein?
This is the linear sequence of the amino acids in the chain.
What is the secondary structure of a protein?
This is the initial folding into local structures within a protein such as alpha-helices and beta-pleated sheets.
What is the alpha-helix structure in a protein?
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.
What are beta-pleated sheets in an amino acid?
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.
What is the tertiary structure?
This is the arrangement of the secondary local structures into a compact globular structures called domains.
What is the quaternary structure?
This is the 3D structure of a multimeric protein with several subunits.
Why do polypeptides fold into structures?
Polypeptides fold in order to have the most energetically stable form. This happens independently although sometimes they can be guided by chaperone proteins.
What is electrophoresis?
It is the process of separating molecules based on their charge to identify them.
How can electrophoresis be used to detect mutated proteins?
Proteins with single mutations might have a different charge composition which means they would travel a different distance on the electrophoresis plate.
What is the first law of thermodynamics?
Energy can neither be created nor destroyed. It can only be transferred from one form to another.
What is the second law of thermodynamics?
In an isolated system, entropy (the degree of disorder) will always increase.
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.
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.
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.
What are enzymes?
Enzymes are biological catalysts which increase the rate of a reaction without being altered by it.
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.
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
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.
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.
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.
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.
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.
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.
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.
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.
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.
What is a coenzyme?
This is a non-protein compound which is necessary for enzymes to function.
What is NAD+?
NAD+ (Nicotinamide adenine dinucleotide) is a coenzyme in many dehydrogenation reactions. It work by accepting one hydrogen and two electrons.
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.
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.
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.
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.
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.
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.
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.
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.
What is substrate level phosphorylation?
This is the production of ATP by transferring a phosphate from a substrate to ADP.
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.
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.
What is the eighth reaction in glycolysis?
3-phosphoglycerate is converted to 2-phosphoglycerate by the phosphoglycerate mutase enzyme.
What is the ninth reaction in glycolysis?
2-phosphoglycerate is converted to phosphoenolpyruvate by the enolase enzyme.
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.
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.
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.
How is lactate generated from pyruvate?
Pyruvate is converted to lactate using lactate dehydrogenase which converts NADH into NAD+. This process is reversible.
Why is regeneration of NAD+ essential?
NAD+ is essential for glycolysis to continue during oxygen deprivation since glycolysis is an anaerobic process.
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.
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.
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.
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.
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.
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.
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.
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.
What is the second reaction in the TCA?
Citrate is isomerised to isocitrate by aconitase.
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.
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.
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.
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.
What is the sixth reaction in the TCA?
Succinate is oxidised to fumarate by succinate dehydrogenase. This also produces FADH2 from FAD.
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.
