Lecture 10

The intermediate products F and I act as _________on e1 and e10. The final product K is a __________________ for both pathways.

positive feedback stimulators; negative feedback inhibitor f

Chymotrypsin is an example of a ______________,An enzyme that breaks the bonds in proteins to form smaller units

protease

CO2 is carried in the blood in what form?

- carbonic acid - bicarbonate and hydrogen ions

How does CO2 induce the tense state of hemoglobin? (2 things)

-CO2 lowers pH -CO2 binds to the N-terminus of each amino (NH3+) group of the 4 polypeptides, forming carbamate,stablizing deoxyhemoglobin

Chymotrypsin cleaves peptide bonds on the ___________ side of large, __________________amino acids.

Carboxyll; hydrophobic

How does decreased pH affect histidine to promote the tense form of hemoglobin?

Decreased pH induced protonation and charge on histidine, which promotes salt bridge formation and stabilizes the tense form of hemoglobin.

1. Name the three amino acids that form the catalytic triad for chymotrypsin

The catalytic triad is: Aspartate, histidine, and serine

Describe the 8 steps of how chymotrypsin cleaves peptide bonds

Step 1: First, serine of chymotrypsin is deprotonated. The proton is donated to histidine of chymotrypsin. Now histidine has a positive charge. Oxygen of Serine is now a nucleophile and can attack the carbonyl carbon in step 2. Step 2: The oxygen of serine attacks the carbonyl carbon of the peptide bond. Step 3: The proton that was given to histidine is donated to the nitrogen of the peptide bond. The bond is cleaved between the carbonyl carbon and the amino group of the peptide bond. Step 4: The free amino group is released from the peptide bond. Step 5: A molecule of water donates a proton to Histidine. Histidine is now positively charged. There is now OH- hydroxyl free in solution. Step 6: OH- bonds to carbonyl where the peptide bond once existed Step 7: Positively charged histidine donates proton to serine. Step 8: Release of Carboxylic Product carboxyl group is released

Describe the structure of the heme group that is associated with each hemoglobin subunit. Also, describe, generally, how binding of molecular oxygen (O2) to the heme group affects the heme group's structure and both the structure and function of hemoglobin.

The ability of myoglobin and hemoglobin to bind to oxygen depends on the presence of a heme group. Structure of heme The heme group consists of a central iron atom Fe2+. Attached to Fe2+ are four pyrrole rings linked together to form a tetrapyrrole ring. The iron atom lies in the center of the tetrapyrrole ring, bonded to the four pyrrole nitrogen atoms. Usually, the iron ion is in the Fe2+ oxidation state. The iron ion can form 2 bonds. One on each side of the heme plane. These binding sites are called the 5th and 6th coordination sites. The 5th coordination site is occupied by the imidazole ring of a histidine residue. In deoxyhemoglobin and deoxymyoglobin, the sixth coordination site remains unoccupied, and this position is available for binding oxygen.

cooperativity of hemoglobin is similar to the cooperativity of allosteric enzymes because...

The binding of Oxygen to hemoglobin disrupts the Tense state<-----> R-state equilibrium in the favor of the relaxed state, which is associated with oxyhemoglobin. Hemoglobin will bind to more oxygen in the relaxed state.

Explain why the graph showing myoglobin and hemoglobin's O2 binding capacity shows how they function in carrying and releasing oxygen and the reasons for the differences between myoglobin and hemoglobin.

The graph of hemoglobin is an s shaped (sigmoidal) curve, whereas myoglobin shows a hyperbolic curve. the reason why both myoglobin and hemoglobin have lowered fractional saturation at lower partial pressures of oxygen is because oxygen must be transported in the blood from the lungs where the partial pressure of oxygen is high to the tissues where the partial pressure of oxygen is lower the cooperativity of hemoglobin enhances oxygen delivery. Because of cooperativity between O2 binding sites hemoglobin delivers more O2 to tissues than would myoglobin. On the graph we can see that in the lungs hemoglobin becomes nearly saturated with oxygen such that 98% of the oxygen binding sites are occupied. When hemoglobin moves to the tissues, the oxygen saturation level drops to 32%. Thus 66% or 98 - 32 of the potential oxygen binding sites release oxygen in the tissues. If myoglobin with its high affinity for oxygen were a transport protein for oxygen it would release a mere 7% of its oxygen under these conditions.

How many bonds can the iron atom of heme form? Where do these bonds form , what are the binding sites called? What bonds form at these sites?

The iron ion can form 2 bonds. One on each side of the heme plane. These binding sites are called the 5th and 6th coordination sites. In hemoglobin and myoglobin, the 5th coordination site is occupied by the imidazole ring of a histidine residue. In deoxyhemoglobin and deoxymyoglobin, the sixth coordination site remains unoccupied, and this position is available for binding oxygen. In oxyhemoglobin and oxymyoglobin, the oxygen binds at the sixth coordination site

How does hemoglobin bind to histidine?

The iron of heme is covalently bonded to the side chain of histidine

1. Name two irreversible enzyme inhibitors, indicate generally how they function and on which enzymes, and explain why their inhibitory effects on their target enzymes are irreversible.

The two irreversible enzyme inhibitors are: DIPF: DIPF is irreversible inhibitor of Acetylcholine Esterase. Serine's hydroxyl of Acetylcholine-Esterase will covalently bind to the phosphate group on DIPF, and because the covalent bond formed is so strong, it will not be reversible. This bond formation results in an inactivated enzyme. Penicillin: Penicillin is an irreversible inhibitor of bacterial transpeptidase. Penicillin will bind to the hydroxyl on serine in the Transpeptidase's active site. Transpeptidase is the enzyme that makes peptidoglycan. When transpeptidase is inhibited, bacteria can't make cell walls. This is because Penicillin binds to bacterial transpeptidase, forming a "penicilloyl-enzyme complex" which is enzymatically inactive. The complex is so stable that it cant be reversed.

competitive inhibition(draw graph)

This graph shows...

CO2 reacts with terminal ___________ groups of globin polypeptides to form charged_______________ groups that stabilize _____________________________

amino; carbamate;deoxyhemoglobin

Carbon Dioxide (CO2) is carried in the cells in the form of...

bicarbonate (HCO3-)

Co2 is a waste product of...

cellular respiration

Glycolosis is a part of the biochemical process _____________.

cellular respiration

If CO2 builds up in the blood.... oxygen affinity of hemoglobin__________________ and pH_____________________

decreases;decreases

The tense state of hemoglobin is also called _________________________. The Relaxed form of hemoglobin is called _______________________________

deoxyhemoglobin; oxyhemoglobin

define allostery,

enzymes' catalytic properties can be changed by the binding of effector molecules to places other than the active site.

define Irreversible inhibition

involves a permanent interaction between inhibitors and enzymes, essentially destroying the enzyme.

Binding of molecular oxygen (O2) to the heme group affects the _______________________ structure of hemoglobin

quaternary

How is oxygen binding in hemoglobin modulated?

•Cooperativity (first oxygen binding makes the next bindings easier). •2, 3-BPG binding (through interactions with charged AAs) allosterically regulates O2 binding. •CO2 lowers the pH of the environment, which reduces O2 binding. Protonation of histidines stabilizes T-state. -CO2 binds to N terminus of each amino group of the 4 polypeptides

Describe how CO2 is released from the tissues into the lungs

1. From body tissue to blood capillary · CO2 is produced by tissue cells. The increase in CO2 in the tissues will push the reaction to the right · It passes through the endothelium, into the red blood cells of the blood capillaries as CO2. · In the red blood cells, CO2 reacts with water to form carbonic acid(H2CO3) in a reaction catalyzed by the enzyme carbonic anhydrase. Carbonic acid dissociates to form (carbamate) HCO3- and H+, resulting in a decrease in pH (caused by hydrogen ions) inside the red blood. When there is a high CO2 concentration in the cells, the reaction will be pushed to the right, making more bicarbonate and H+ outside of the red blood cell. · This creates a concentration gradient, and bicarbonate(HCO3-) wants to form CO2 2. From blood capillary to the lungs · From here, HCO3- is pushed back into the bed blood cell, and forms C O2 · CO2 is passed through the alveoli of the lungs, where it is then exhaled. 3. exhalation1. . in lungs, there is a decrease in co2 of alveoli since excess co2 is exhaled. concentration of co2 in blood and alveoli, down the concentration into alveoli. The co2 in the blood diffuses out into the alveoli. CO2 levels drop in the blood now. Reaction is pushed left, Co2 will form in the blood and RBCs, pushing the reaction to the right again 1. From body tissue to blood capillaryry

Describe the mechanism by which 2,3 BPG affects hemoglobin function. Also, draw a graph showing the results of an experiment to test the effects of 2,3-BPG on oxygen saturation of hemoglobin

1. Pure hemoglobin binds oxygen more tightly than does hemoglobin in red blood cells. This difference is due to the presence of 2/3 BPG in red blood cells. 2/3 BPG is a regulatory molecule that decreases the affinity of hemoglobin to oxygen. When 2-3 BPG binds to hemoglobin it reduces its oxygen affinity so that more oxygen is released. This is because 2/3 BPG stabilizes the tense state of hemoglobin. This will reduce hemoglobin's oxygen affinity, leading to the release of oxygen. In order for structural transition from T2R to take place the bonds between hemoglobin and 2/3 BPG must be broken and 2/3 BPG must be expelled.

On which coordination site does oxygen bind to the heme group of myoglobin and hemoglobin

6th

Describe how the concept of reaction equilibrium is important for driving the efficient elimination of the waste product CO2 in the lungs.

After exhilation: CO2 in the blood will diffuse out of the capillaries and across the endothelium, across the lining of the lung and into the alveolus. · After exhaling, the concentration of CO2 in the alveoli goes down, this will create a concentration gradient. · The reaction goes backwards. As there is a lack of carbonic acid (H2CO3) , it will be formed from bicarbonate (HCO3-) and a proton. Then CO2 and water are created in reverse, then to CO2 · When CO2 is formed from the reverse reaction, it is diffused out into the lungs to be released.

Define Protease

An enzyme that breaks the bonds in proteins to form smaller units

How binding of molecular oxygen (O2) to the heme group affects the heme group's structure and both the structure and function of hemoglobin(cooperativity)

Binding of O2 to a heme shifts the position of the iron atom into the plane of the tetrapyrole ring. The histidine bound in the 5th coordination site moves with it. This histidine is part of an alpha Helix which also moves. Heme groups cooperativity: Following The movement of Fe 2+, other subunits follow suit resulting in changes in quaternary structure. The T to R state transition of 1 heme group will affect other heme groups in favor of the R state.

describe the structure of heme-where is it found?

Fe2+ exists in the center of heme. Each hemoglobin has a heme group. Heme has a tetrapyrrole ring (has 4 pyrrole groups), and iron is attached to the nitrogen of each pyrrole.

Describe the specific roles of the Aspartate in the catalytic triad of chymotrypsin

It forms hydrogen bonds with Histidine, which maintains histidine in its proper position(stabilizing it).

Compare the structures of myoglobin and hemoglobin and indicate how differences in their structures account for differences in their functions.

Myoglobin is a single polypeptide containing a single O2 binding heme group. It consists largely of alpha helices that are linked together and form a globular structure. Myoglobin can exist as deoxymyoglobin (the oxygen-free form) or as oxymyoglobin which has an oxygen bound. Hemoglobin has a quaternary structure of 4 polypeptides (two alpha globin and two beta globin subunits) with a total of four O2 binding heme groups. Deoxyhemoglobin corresponds to the T state of hemoglobin whereas oxyhemoglobin corresponds to the R state. The T state is less biochemically active than the R state. This is because the T state has a lower affinity for oxygen. Due to cooperativity between oxygen binding sites, hemoglobin delivers more oxygen to tissues than would myoglobin. Cooperativity refers to the effect where when one oxygen is bound to a heme group, other heme groups more readily bind to oxygen. (Like a domino effect) This is why Hemoglobin functions as an oxygen carrier from the lungs to the entire body, and myoglobin functions as a storer of oxygen in the muscle cells.

How is the heme group of hemoglobin bonded to the globin?

On the fifth coordination site, Fe 2+ covalently binds to imidazole of the histidine residue of the globin molecule