Enzymes Enzymes Enzymes

What is denaturation?

             

It is the process in which the folding structure of a protein is altered due to exposure to an excess of certain chemical or physical factors. This causes the protein to become inactive because it loses its properties

What does a graph for increasing substrate concentration of an enzyme look like? Describe it

It increases but begins to slow down until it reaches a plateau

Compare competitive/Noncompetitive inhibition  

Competitive inhibition is where an inhibitor is physically and structurally similar to the substrate. Because of its similarities, the inhibitor binds to the active site of the enzyme where the substrate would normally bind. This binding of the inhibitor to the enzyme means the substrate cannot bind and it must wait for its turn.

Non-competitive inhibition is when inhibitor binds to a site on the enzyme other than the active site. The binding of the inhibitor to the enzyme cause the enzyme to change shapes. This alters the active site and the substrate can no longer bind.

Discuss lock key vs. induced fit.

Induced fit is where an enzyme alters it shape to fit the substrate.

Lock and key states that an enzyme’s active site is the exact shape of the substrate, and that the substrate neatly fits in.

Both are substrate specific, just one model states that the enzyme molds to fit the substrate whereas the other says that the site is like a puzzle piece that does not change.

Don't forget about the Link reaction!

What happens during the Link Reaction you ask???

Well....

Once the pyruvate molecules form glycolysis are in the mitochondrion, enzymes in the matrix of the mitochondrion remove hydrogen and carbon dioxide from the pyruvate. This is called oxidation (removal of hydrogen or addition of oxygen) and decarboxylation (removal of carbon dioxide). Therefore, the process is called oxidative decarboxylation. The hydrogen removed is accepted by NAD+. The link reaction results in the formation of an acetyl group. This acetyl group is then accepted by CoA and forms acetyl CoA! 

Krebs is very fun

Steps of the Krebs cycle

Step 1

Acetyl CoA is combined with oxaloacetate to form a six carbon molecule of citrate.  The acetyl coenzyme A acts only as a transporter of acetic acid from one enzyme to another. Once combined, CoA is released that it may combine with another acetic acid molecule to begin the Krebs cycle again.

Step 2

Citrate undergoes an isomerization.  A hydroxyl group and a hydrogen molecule are removed from the citrate structure in the form of water.  The two carbons form a double bond until the water molecule is hadded back.  The Hydroxyl group and hydrogen molecule are in different positions so isocitrate is formed.

Step 3

Isocitrate molecule is oxidized by a NAD molecule.  The NAD molecule is reduced by the hydrogen atom and the hydroxyl group.   The NAD binds with a hydrogen atom and carries off the other hydrogen atom leaving a carbonyl group.  A molecule of CO2 is released creating alpha-ketoglutarate.

Step 4

Coenzyme A, returns to oxidize the alpha-ketoglutarate molecule.  A molecule of NAD is reduced again to form NADH and leaves with another hydrogen.  A carbon group is released as carbon dioxide and a thioester bond is formed in its place between the former alpha-ketoglutarate and coenzyme A to create a molecule of succinyl-coenzyme A complex.

Step 5

A water molecule sheds its hydrogen atoms to coenzyme A.  Then, a free-floating phosphate group displaces coenzyme A and forms a bond with the succinyl complex.  The phosphate is then transferred to a molecule of GDP to produce an energy molecule of GTP.  It leaves behind a molecule of succinate.

Step 6

Succinate is oxidized by a molecule of FAD. The FAD removes two hydrogen atoms from the succinate and forces a double bond to form between the two carbon atoms, thus creating fumarate.

Step 7

An enzyme adds water to form malate.   The malate is created by adding one hydrogen atom to a carbon atom and then adding a hydroxyl group to a carbon next to a terminal carbonyl group.

Step 8

The malate molecule is oxidized by a NAD molecule.  The carbon that carried the hydroxyl group is now converted into a carbonyl group.  The end product is oxaloacetate which can then combine with acetyl-coenzyme A and begin the Krebs cycle all over again.

Steps of Glycolysis

Steps of Glycolysis

The enzyme hexokinase adds a phosphate group to glucose producing glucose 6-phosphate. This phosphate group comes from ATP and it is converted to ADP.

The enzyme phosphoglucoisomerase converts glucose 6-phosphate into its isomer fructose 6-phosphate.

The enzyme phosphofructokinase uses another ATP molecule to transfer a phosphate group to fructose 6-phosphate to form a hexose-bisphosphate.

The enzyme aldolase splits the molecule into two sugars that are isomers of each other.

First the enzyme triose phosphate dehydrogenase transfers a hydrogen (H-) from the molecule NAD+ to form NADH via oxidation. Next triose phosphate dehydrogenase adds a phosphate (P) from the cytosol to the oxidized molecule. This occurs for both molecules created by lysis

The enzyme phosphoglycerokinase transfers a phosphate from the molecule to a molecule of ADP to form ATP.  The process yields two 3-phosphoglycerate molecules and two ATP molecules.

The enzyme phosphoglyceromutase relocates the P from 3-phosphoglycerate from the third carbon to the second carbon to form 2-phosphoglycerate.

The enzyme enolase removes a molecule of water from 2-phosphoglycerate to form phosphoenolpyruvic acid (PEP). This happens for each molecule of 2-phosphoglycerate.

The enzyme pyruvate kinase transfers the final phosphate from PEP to ADP to form pyruvic acid and ATP. This happens for each molecule of PEP. This reaction yields 2 molecules of pyruvic acid and 2 ATP molecules.

Warm Up #2

The structure of a Mitochondrion and its function

Cristae- Folds of the inner membrane which increase the surface area available for the electron transport chain

Inter membrane- Contains the electron transport chains and ATP synthase which create ATP by carrying out oxidative phosphorylation

Outer membrane- Separates the contents of the mitochondrion from the rest of the cell, creating the perfect environment for aerobic respiration

Space between the inner and outer membranes- Protons are pumped into this small space by the electron transport chain. Because the space is so small, a high proton concentration can be easily achieved

Matrix- Fluid inside the mitochondria which contain enzymes for the Krebs cycle and the link reaction

Ribosomes- 70s ribosomes and a naked loop of DNA are present in the matrix

Warm up #1

What is oxidative decarboxylation?

·          Biochemical that coverts pyruvate into a two carbon and CoA compound called acetyl-CoA

·         Pyruvate loses a carbon forming Co2

·         Oxidation cause electrons to be transferred from the pyruvate to NAD+ producing NADH

·         And CoA is added

What is substrate-level phosphorylation?

It occurs during glycolysis and the Krebs Cycle
It is the source for the majority of the ATP produced in aerobic respiration
It is the addition of a free phosphate to ADP to form ATP by direct donation.

What are the products of Krebs Cycle?

·         8 NADH

·         2 ATP

·         6 Co2

·         2 FADH2

What are the products of Glycolysis?

·         2 Pyruvate

·         2 Net ATP

·         2 NADH