Test 2 part 1 Flashcards

Question

Energy - Greater order

Answer 1

Where there is greater order there is lower entropy and greater instability. For example - someone at the top of a diving board, a drop of dye, molecule of glucose.

Answer 2

Less order, higher entropy, more stability. Someone jumping into the water, the dye diffused in water, glucose broken down into carbon dioxide and water. There is a tendency for increased disorder and less structure.

Answer 3

A measure of somethings stability. Something with a higher free energy has greater instability and greater order. The change in free energy is abbreviated as Delta G. The final state minus the starting state is the free energy equation. Reactants are the starting state, products are the final state. The starting state has a higher free energy and the final state has a lower free energy.

Answer 4

Anything with a negative delta G value (less than zero) is a reaction that will occur spontaneously. This is an exergonic reaction - spontaneous. Energy is released.

Answer 5

An endergonic reaction. Have to have an energy input for the reaction to occur. Non spontaneous reaction. You can couple the endergonic and exergonic reactions to make sure that the endergonic reactions occur. Energy coupling.

Answer 6

Reactions in the cell don't typically come to equilibrium. When you have delta G values not equal to zero, that enables things to do work. If a reaction is at equilibrium the delta G values are at zero. Typically the product of one reaction becomes the substrate for another. Example of a catabolic pathway. The free energy that is released can be used to power an anabolic pathway.

Answer 7

ATP: Adenosine triphosphate Nitrogenous base: adenine, ribose sugar: adenosine, triphosphate - 3 phosphate groups.

Answer 8

ATP can be hydrolysed - you can cleave off the terminal phosphate group to make ADP. This reaction has a negative delta G value. Hydrolysis of ATP (Delta G) - 7.3 kcal per mol. For each mol of ATP thats hydrolysed there will be 7.3 kcal of energy released. This is an exergonic reaction.

Answer 9

Hydrolysis is any chemical reaction in which a molecule of water breaks one or more chemical bonds.

Answer 10

ATP is less stable than ADP and inorganic phosphate. We are breaking ATP down into its constituent parts - going to a more stable situation. The ATP has higher free energy the bottom one has lower free energy - the difference in those free energy levels is -7.3 kcal per mol. The other thing that is important is the charge on ADP relative to ATP so this relates to the stability of these molecules. On ATP is 4 negative charges and on ADP there are three negative charges. If you have 4 negative charges there is going to be some repulsion/repelling between the negative charges - they don't want to be close to each other. Less stable than ADP because in ADP there are only 3 negative charges repelling each other.

Answer 11

* A phosphate is joined to another molecule or protein forming a phosphorylated intermediate. Instead of the phosphate and energy being released as heat energy because cells can't use heat energy for work. * The hydroxyl group of ATP will be joined onto the phosphate group. * The phosphorylated intermediate will be more reactive - we’ve increased the free energy - that will enable the molecule to potentially do work.

Answer 12

Conversion of glutamic acid to glutamine - need to add an ammonia to glutamic acid —\> endergonic reaction. Occurs by couple reactions. We couple the hydrolysis of ATP to the conversion of glutamic acid to glutamine. Cleave off the terminal phosphate from ATP to phosphorylate the glutamic acid, raising its free energy and making it more reactive and therefore less stable. Now it is more likely to react with ammonia to form glutamine. The ammonia can come in and join with the glutamic acid and the phosphate is released. hen you add both reactions together there is a net delta G that is negative -3.9 kcal per mol.

Answer 13

a cell membrane and a transport protein responsible for moving things across a membrane. That may need an energy input - what happens is the protein becomes phosphorylated making the protein more reactive and it may change its shape and allow things to move across the membrane.

Answer 14

Motor proteins - things which walk along a skeletal track and can transport things around a cell. The reason they can walk is because parts of the protein become phosphorylated which powers conformational changes. Motor protein: Myosin moves along actin microfilaments present in your muscle cells causing your muscles contract.

Answer 15

To make ATP we will add a phosphate to ADP - endergonic reaction - positive delta G value. Same value as ATP hydrolysis → +7.3 kcal per mol, except it’s a positive value rather than negative. To make ATP we need to put energy in.

Answer 16

Catabolic pathways. Energy from catabolism - exergonic, energy-releasing processes (oxidation of food stuff). Use the energy produced from those processes to power the addition of the phosphate to ADP to get ATP. Can use this to fuel cellular work.

Answer 17

Enzymes are biological catalysts - they don't change the equilibrium position for a reaction, only the rate in which equilibrium is attained (this would refer to an isolated enzyme, reactions typically don't come to equilibrium themselves because the product becomes the reactant for the next reaction and so on). Typically substrate specific. Highly regulated: Regulation - the control of its activity - that is what enabled the control of the metabolic pathways.

Answer 18

There are exceptions - rubisco - the enzyme important for photosynthesis. Rubisco is a slow enzyme and not very substrate specific. But the key enzyme in carbon fixation.

Answer 19

activation energy for a reaction. Exergonic reaction - the free energy of the products is lower than those of the reactants. This reaction has a negative delta G value - would occur spontaneously. There's actually a hill that has to be overcome as the reactants change into what's called the transition state (halfway between the reactants and the products - that has to be overcome for the reaction to occur. That may occur naturally if you leave it for long enough but inside a cell you can't afford to wait around for these reactions to occur so we have enzymes to control when and how fast the reaction will occur.

Answer 20

The enzyme as the lock and the substrate as the key - match the shape - shape specific. The shape can change.

Answer 21

Hexokinase - the enzyme that catalyses the very first reaction in glycolysis. There is a slight change of the protein when the substrate binds - it's trying to exclude water because you don't want water in the active site. That's called induced fit: change of shape as the substrate enters. Then it forms an enzyme substrate complex.

Answer 22

The substrate molecules bind to the active site and forming an enzyme substrate complex. Then in the active site, various things occur to lower the activation energy so the substrate can be converted to products. The active site can lower activation energy by: Acting as a template for substrate orientation. It can position the substrate relative to one another. Stressing the substrates and stabilising the transition state. Stressing - bending them a bit. Providing a favourable microenvironment (could change the charge distribution on the substrate molecules) and/or Participating directly in the catalytic reaction. You may get amino acids binding to the substrate molecules. Then: 4) substrates are converted to products 5) the products are released 6) the active site will go back to its original conformation so ti can accept more substrate. Called the catalytic cycle.

Answer 23

A) Positioning them close together so it encourages a reaction between them. B) Charges on the enzyme - positively charged residue and a negatively charged residue - separation of the charge in the enzyme can lead to charge redistribution on the substrate molecule. So electrons may move to one charge and that may be necessary for the reaction to occur. Creation of a favorable microenvironment. C) Bending - change the substrates shape slightly. D) Enzymes may form covalent bonds with the substrate itself. Amino acid residues in the enzyme may bind to the substrate.

Answer 24

Lysozyme - in your eyes. If theres dust in your eyes to prevent an eye infection you need to stop the bacteria reproducing - you need to get rid of them Red - substrate. Blue - lysozyme. The red thing - polysaccharide from the bacterial cell wall. The lysozyme will bite it in half. So compromising the bacterial cell wall - the bacteria are less able to produce in your eye and the bacteria may die.

Answer 25

The oligosaccharide is the substrate - has 6 sugars. The Oligosaccharide goes into the active site of the lysozyme. In the enzyme substrate complex, we've got a glutamic acid and an aspartic acid which are parts of the lysozyme. The substrate comes in and there is a straining of the molecule - being twisted. The amino acid residues will do some chemistry on the molesulce of the Oligosaccharide. The aspartic acid residue is joined with its carbon (covalent bonding between the enzyme and the substrate). A water molecule will be positioned relative to the Oligosaccharide and the charge distribution will be affected by the glutamic acid and the carbon group - the positioning of the substrates and the electrons around the water will be affected by the enzyme and that will mean that the water will - part of it will join onto the carbon so we get hydroxylation there. The other proton in the water will join onto the glutamic acid.

Answer 26

reaction rates.

Answer 27

Theres an optimal temperature where the reaction will go faster. If you go lower than the optimum then you get lower rates of reaction - the enzyme and substrate are vibrating a lot less because there is less thermal energy so you're less likely to get the substrate entering the active site. If you go above the temperature optimum you are going to have more thermal energy so they are moving around more frequently - so more substrate entering the active site. But at high temperatures the shape of the enzyme is likely to change. The active site may not have the correct conformation to catalyse the reaction. You can denature proteins if you heat them up. Heat tolerant enzymes - bacteria 77℃

Answer 28

pH - optimal pH can be determined in the part of the body that you find the enzyme in. Pepsin - you find in the stomach - very acid so the optimum pH is 2. If you go either side of this optimum pH you've got lower rates of reaction because the shape of the enzyme is changing. The active site may change how some of the amino acid residues are and may not be able to catalyse the reaction as well. Trypsin - intestinal enzyme. Slightly basic so a basic enzyme optimum. Most of the enzymes in your cells are around 7 pH.

Answer 29

The protein making the enzyme may not be sufficient for catalysis to occur. You need additional things in the active site - cofactors. You can have 2 different cofactors Inorganic ions - iron, copper and zinc. Important in respiration because the enzymes are removing the electrons from food material and you need somewhere for those electrons to go - and the inorganic ion will accept those electrons. Complex organic molecules - vitamins (cofactors required for enzyme catalysis), NAD and FAD.

Answer 30

Enzymes can be inhibited. Inhibitors can be drugs or toxins or normal metabolites. Irreversible inhibitors - irreversible - once bound, its bound forever - cant be removed. Reversible inhibitors - bound more weakly and can be removed from the enzyme. Inhibitors can be competitive - bind to the active site. Competitive inhibitors have similar shape to the normal substrate and compete with the substrate to the active site. Non-competitive inhibitors - (metabolic control) - using metabolites to regulate activity/metabolism - they will bind at a site, away from the active site - not actually competing with the substrate. When they bind to the enzyme they change the shape of the active site so that the substrate can no longer come into the active site.

Answer 31

Sarin - very lethal nerve gas. You can't detect it - odourless and colourless. Sarin inhibits the enzyme acetylcholinesterase. This enzyme is important in communication between nerve cells. Diagram - two nerve cells. We've got a nerve impulse which needs to be transmitted to the cell below - there's a release of neurotransmitter which diffuses between the cells and binds the protein and the signal is propagated. The neurotransmitter (acetylcholine) is recycled very quickly - need to break down the transmitter very quickly for the next transmission. Acetylcholinesterase is the enzyme that does this. Breaks down acetylcholine for the next signal. If you inhibit this enzyme, your neurotransmission breaks down and nerve cells aren't able to communicate properly. You rapidly get paralysis and asphyxiation.

Answer 32

Penicillin - kills bacteria because it inhibits the enzyme transpeptidase and this creates cross-links in the bacterial cell wall.

Answer 33

Viagra - will inhibit the enzyme phosphodiesterase and it improves blood flow. It also has significant effects in plants. You can put viagra in the water with roses and they will stay more upright - it works on similar enzymes in plants. It has a role in plant reproduction - you can grow pollen tubes and add viagra and it will change its direction of growth. If you inhibit them then you change the way that the pollen tubes grow.

Answer 34

You can control whether an enzyme is there or not - more enzyme = more substrate into product - this control occurs at the genetic level. You can control how active the enzymes are - can occur at different levels. Allosteric control - relatively fast. Covalent control - relatively fast. Proteolytic activation - digestive enzymes because you don't want them to actively produce them because you'd start eating your own body

Answer 35

Allosteric regulation occurs when a molecule binds to part of an enzyme, away from the active site. You can have different forms: Can act as activators - stimulate the enzyme. Can stabilise active form - switch a metabolic pathway on. Or as an inhibitor - stabilise an inactive form of the enzyme effectively switching the enzyme off. Similar to reversible non-competitive inhibition. Inhibitor often is the end product of a metabolic pathway.

Answer 36

is a slight change in shape. With an allosteric activator you get binding of the activator at an allosteric site. This site is something away from the active site - a regulatory site on the enzyme. In this example we have a tetrameric protein - comprised of 4 subunits. The subunits are identical - often enzymes don't exist as monomers - you can have dimers, tetromers etc. so we have binding of the activator and its locking the enzyme in this active form. So catalysis can occur. The allosteric inhibitor will lock the enzyme in an inactive formation. This is a way that enzymes can control the activity of enzymes by using allosteric regulation - allosteric inhibitors and activators. The allosteric inhibitors are often the end product of a metabolic pathway. Using metabolites to control the enzymes. This is called feedback inhibition.

Answer 37

* The end product of a metabolic pathway inhibits an enzyme that catalyses an earlier reaction in the pathway. * The pathway is switched on and you build up levels of the isoleucine inside the cell - this can be wasteful to keep making the isoleucine. * The isoleucine can act as the allosteric inhibitor and inhibit the very first enzyme in this pathway. * Isoleucine binds to the allosteric site - makes a conformational change in the enzyme, changing the shape of the active site and then it is switched off. * That way you aren't wasting the initial substrate.

Answer 38

* The end product of a metabolic pathway can inhibit the expression of enzyme that catalyse reactions in a metabolic pathway * Genetic level inhibition: Tryptophan inhibits the trp operon as well as enzyme 1 in this metabolic pathway - tryptophan binds to the repressor protein and the repressor protein changes shape. Now it can bind to the operator region of DNA - which is upstream of the genes encoding the enzymes responsible for tryptophan synthesis. * Tryptophan can switch off production of the enzymes. * In a situation when you need to produce tryptophan, you want to have lots of these regions around where the operator region is free and the RNA polymerase can move along the gene and can be transcribed. * When you have tryptophan you don't want to produce it so you switch off the production of these enzymes. With the tryptophan bound to the repressor protein the RNA polymerase cant move along the DNA.

Answer 39

* Adding or removing a phosphate group to an enzyme. * Proteins can be phosphorylated and dephosphorylated and that can switch them on and off - controlled by proteins called kinases and phosphatase.

Answer 40

* Certain enzymes created in an inactive form: precursor forms → zymogen or proenzyme. * Enzymes produced with an additional bit added onto it which needs to be cleaved off before the enzyme becomes active. * Digestive enzymes: pancreas → breaks down proteins in digestion. If it was produced in an active form it would start to break down proteins in the pancreas - transported to the stomach and then becomes active.

Answer 41

The wood frog can withstand very cold temperatures when it hibernates - it essentially freezes and shuts down. This is because of urea produced in the bloodstream and also is releasing glucose from its liver. Glycogen stored in your liver. As the temperature decreases they start to release glucose from the glycogen in the liver. Theres an enzyme in the liver called glycogen phosphorylase and it cleaves off individual glucose units from glycogen. The control of the glycogen phosphorylase is very carefully controlled - allosteric and covalent control. The covalent control involves phosphorylation of the glycogen phosphorylase via a kinase enzyme.

Answer 42

The study here where [protein kinase a and phosphorylase was studied in two populations of wood frog. One population from alaska and one from ohio. Compare the protein kinase and glycogen phosphorylase active in these two populations of wood frog. Why can the alaskan frogs be able to survive better in the very cold temps in alaska. As things are frozen for long periods of time the alaskan frogs have much greater protein kinase A activity. With increasing time of freezing - the glycogen phosphorylase is being switched on more in the frogs from the colder environments. Because of the control of the glycogen phosphorylase being regulated more than they are better able to survive in freezing temperatures in alaskan frogs.

Answer 43

* Kinases will transfer phosphate from ATP onto a protein. * Phosphorylation can activate some enzymes and deactivate others.

Answer 44

* Phosphatase's will remove phosphate from a protein