Biochem Exam 2

Explain why 2,3-bisphosphoglycerate reduces hemoglobin’s affinity for oxygen. Your answer must include the molecular interactions that occur between all relevant structures or molecule

Hemoglobin is made up of 4 unites and is a tetramer, with each subunit containing a heme group that bonds one molecule of oxygen. The heme group contains an iron porphyrin ring that is in the ferrous state. When oxygen binds, the iron moves into the plane with the heme, and the structural change goes to the other units. When 2,3-BPG binds, it binds to the center of the tetramer and favors the T state and the release of oxygen

How does 2,3 BPG make hemoglobin less affinic for oxygen

2,3 BPG binds to the center of hemoglobins tetramer and only in the T state. DUring the transition of T-to-R, this pocked collapses and 2,3 BPG is released. in order for the structural transition from T to R to take place, the interactions between BPG and hemoglobin have to be disrupted. Stays in the T state until higher oxygen concentrations are reached

Whats the difference between fetal and adult hemoglobin

Fetal hemoglobin is composed of 2 alpha chains and two gamma chains, while adult hemoglobin has two alpha subunits and two beta subunits.

why does fetal hemoglobin have a greater affinity for oxygen

Instead of having a histidine at the 2,3-BPG site, they have a serine due to their gamma subunits. The gamma subunit does not bind to 2,3 BPG and is less sensitive to it, so the baby takes up the oxygen the it released by the mothers hemoglobin 

Why is carbon monoxide dangerous

it binds to hemoglobin 200fold more tightly than oxygen and can prevent delivery of oxygen to tissues. it can also force hemoglobin into the R state and never let it deliver to its tissues

Bohr effect

Hyrdrogen ions and co2 promote the release of oxygen from hemoglobin. Hydrogen and Co2 behave as allosteric effectors that push for the T state.

What two molecules are produced by metabolism that lead to the boost of oxygen delivery to the rest of the body

h+ and co2

Why does hydrogen have an effect on hemoglobin

An added proton onto the hemoglobin results in a salt bridge between histidine and aspartate that promotes the T state and release of oxygen

How does Carbon dioxide effect hemoglobin (2 ways)

Carbon dioxide reacts with water to form the bicarbonate ion, resulting in a drop in pH that stabilizes the T state. A direct interaction between carbon dioxide and hemoglobin results in oxygen release.

What is the direct interaction between carbon dioxide and hemoglobin

Carbon dioxide reacts with terminal amino groups on hemoglobin to form carbamate groups, which are negatively charged. The carbamate forms a salt bridge that stabilize the T state.

how is carbon dioxide carried to the blood in humans

bicarbonate ion

How does bicarbonate work

co2 and h2o form to make carbonic acid. carbonic acids dissociate into h+ and bicarbonate. The H+ release results in a drop in pH and favors the T state formation. 

How is CO2 eventually exhaled

Co2 enters a red blood cell from the tissue. Co2 reacts with water in the red blood cell to form bicarbonate. Bicarbonate leaves the RBC and exchanged bicarbonate for Cl. Bicarbonate travels through the plasma and enters the RBC at the lung, exchanging for Cl. At the lung, bicarbonate is turned into H+ and carbonic acid. Carbonic anhydrase converts carbonic acid to water and CO2. CO2 exits through the cell into the alveolus and is exhaled

What causes sickle cell anemia

A mutation that results in the substitution of valine for glutamate at position 6 of the beta chains. As a result, the blood cells become sickle shaped and do not bind oxygen as well

What are the effects of sickle cell anemia

Aggregrates form that deform the red blood cell. The hydrophobic val side chain associates with another hemoglobin, which associates with another hemoglobin, and so forth. As a result, a large fibrous agregrate deforms the red blood cell by clogging small capilarries. This results in the red blood cell being deformed and lysing. Sickle cells can also plug up capillaries and deprive tissues of oxygen.

what is the mutated form of hemoglobin

hemoglobin S

what do the alleles have to be to have sickle cell anemia

both alleles are mutated

what is a benefit of a heterozygous sickle cell anemia

do not have sickle cell anemia and have resistance to malaria

what is thalassemia

the absence or underproduction of one of the hemoglobin chains.

alpha thalassemia

not enough alpha chain of hemoglobin is produced, and hemoglobin tetramers form that contain only the beta chain. These tetramers bind to oxygen with high affinity and no oxygen release

beta thalassemia

not enough of the beta chain is produced. alpha chains form an insoluble aggregate that precipitates inside of immature red blood cells 

what does it mean to be a catalyst

a catalyst is an agent that enhances the rate of a chemical reaction without being affected itseld

covalent catalyst

the active site contains a nucleophile that is covalently modified

general acid base catalysis

a molecule other than water donates or accepts a proton

catalysis by approximation

the enzyme brings two substrates together in an orientation that facilitates catalysis

metal ion catalysis

metal ions serve as an electrophillic catalyst

what are the properties of an enzyme

determine the patterns of reactions, mediate the transformation of energy to different forms, display high specificity, and have million fold catalytic power

are all catalysts enzymes

no, there is catalytic RNA

what do enzymes do to reactions speed wise

they can accelerate reactions by facotrs of a billion or more

do reactions happen often without a catalyst

no

what does carbonic anhydrase do

allows transfer of co2 from tissues to lungs

how are enzymes specific

enzymes are specific in reactions that they catalyze and in the substrates that they bind to. An enzyme will catalyze a single chemical reaction or a set of reactions that are similar to one another

what enzyme catalyze the hydrolysis of a peptide bond

protease

are all enzymes absolutely specific

no, they bind to chemically and structurally similar molecules. ADH can bind to ethanol and methanol

cofactors

non protein molecules that are needed to perform reactions that amino acids can not do alone

apoenzyme

enzyme in the absence of a cofactor

how are enzymes named

they are assigned an EC number, which is a series of numbers that are based on the reactions they catalyze. They are also names for the reaction that they catalyze or have a common name

what does G have to be for a reaction to occur spontaneously without an input of energy, and what kind of reaction is this called

Delta G has to be negative, exergonic

What is delta G when a reaction is at equillibrium

zero

What is delta G when a reaction is nonspontaneous and what kind of reaction is it

Positive, endergonic

What is the relationship between delta G and the reaction

It is only dependent on the free energy between the products and the reactants, it does not matter how the reaction occurs

what is the relationship between delta G and the rate of the reaction

there is no relationship

what is the difference between delta G, delta G knot, and delta Gknot’

Delta G is a measure of the energy that is capable of converting reactions into profucts. G knot is the standard free energy change, and Gknot ‘ is the standard free energy change at pH 7.

How do the reactans and products affect delta G

If there is a high concentration of reactants, delta G is more negative, favoring the forward reaction. If there is a high concentration of products, delta G is more positive, favoring the reverse reaction. 

what kind of reactions have a large K

exergonic

What kind of reaction has a small K value

endergonic

Activation energy

the energy required to form the transition state from the substrate. also known as the difference in energy between the transitions state and substrate

what do enzymes alter and what do they not

enzymes alter the reaction rate, not the reaction equillibrium

How does activation energy influence reaction rate

the higher the activation energy, the slower the reaction rate

what does an enzyme do to delta G and activation energy

an enzyme can not change delta G. An enzyme lowers the activation energy

why do enzymes lower activation energy

the combination of a substrate and an enzyme creates a reaction pathway whos transition state energy is lower than that of the reaction without an enzyme. Since the activaiton energy is lower, more molecules have to energy required to reach the transition state

What is a holoenzyme

an enzyme combined with a cofactor

what are cofactors composed of

metal ions or derivatives of vitamins

What is the enzyme substrate complex

enzymes bind substrates together to form an enzyme substrate complex on the active site of the enzyme

what is the active site of an enzyme

three dimensional cleft or crevice created by amino acids from different parts of the primary structure

what is released when enzyme and substrate bind

free energy

what are five properties that active sites share

active site takes up a small volume of an enzyme, they create unique environments, the interaction os enzyme and substrate uses multiple weak interactions, enzyme specificicty depends on molecular structure of active site, and substrate has induced fit inside of active site

First order reaction

Rate of reaction is directly proportional to the reactant concentration, units of s-1

Bimolecular or second order reaction

Include two reactants. Can be 2A - P, or A+ B= P. M-1s-1

Pseudo first order

bimolecular reactions with a large excess of one reactant and the rate is proportional to the concentration of the limiting reactant

zero order

rate is independent of reactant concentrations, when at maximal velocity

mixed order

between first and zero order

velocity is directly proportional to [S] when

first order. if [s] is small, most enzymes are unoccupied and will quickly take them

Where are the orders located on an enzyme curve

the first steep part of the curve is first order, in between is mixed because reaction order is changing, and then zero is at the maximal velocity.

vmax

the fastest rate of a reaction, all of the active sites are filled

Km

[S] at half maximal velocity and a measure of binding affinity between enzyme and substrate

Turnover number

the number of substrate that has turned to product over time

sequential reaction

all substrates bind to the enzyme before any product is released, most enzymes using nad+ or NADH display this

Double Displacement

Products released before all substrates bind enzyme, seen in enzymes that shuffle functional groups

what kind of enzymes do not obey michaelis menten kinetics

allosteric enzymes

Temperature affect on enzymes

The reaction rate doubles for every 10 degree rise in temperature up to the optimum temperature. Above the optimal temperature, the temperature change breaks noncovalent bonds and the ezyme becomes denatured from changes in structure and active site

pH effects on enzymes

at low pH ionizable groups are protonates, at high pH deprotonated. Attractive forces are messed up an alter the shape of active site and enzyme to the point where substrate cant fit

Irreversible enzyme inhibitors

bind covalently or non covalently to th enzyme, but with a dissociation constant

Reversible inhibition

rapid dissociation of the enzyme-inhibitos complex

What are the three reversible inhibition

Competitive inhibition, uncompetitive inhibition, non competitive inhibition

Competitive inhibition

the inhibitor is structurally similar to the substrate and can bind to the active site, preventing the actual substrate from binding.

Uncompetitive inhibition

the inhibitor binds only to the enzyme substrate complex and even though the substrate can go into the active site, nothing occurs

non competetive inhibition

the inhibitor binds the substrate at an allosteric site or the enzyme substrate complex and changes shape of active site

What do competitve inhibitors do to Vmax and Km

Vmax stays the same, Km increases because you needs more substrate to bind to be able to reach Vmax

For competetive inhibition, where is the line with inhibitors

the one that is steeper and is closer to the ordinate

On a Lineweaver burt plot what is km and what is vmax

The place at which the line crosses x is 1/km, and the place at which the line goes through y is 1/vmax

Uncompetetive inhibition relationship with Km and Vmax

Km and Vmax become greater with the inhibitor. parallel lines on a lineweaver burt plot

non competitive inhibition with vmax and km

vmax changes, but km stays the same

irreversibly inhibitors

Form a stable covalent bond with the enzyme

what can irreiversible inhibitors be used for

mapping the active site of an enzyme

what are the three classes of irreversible inhibitors

group specific, substrate analogs, and suicide inhibitors

group specific inhibition

Group specific reagents react with specific amino acid side chains. Example: DIPF reacts with a primary alcohol on serine in acetylcholine esterase, forming a covalent bond and killing the enzyme. could be used to map serines

Affinity labels (substrate analogs)

Covalently modify active site residues and resemble the substrate, can be used to map the active site. Affinity labels inhibit the enzyme by covalently modifying an amino acid in the active site and made the enzyme inactive.

Suicide inhibitors

Metabolized by enzyme to a reactive compound that covalently binds to the active site. 

Why are transition state analogs good inhibitors

they are designed to mimic the unstable, high energy transition state of the substrate, which the enzyme will bind to over the substrate.

induced fit

the modification of the shape of an active site in an enxyme that occurs upon substrate binding

Covalent catalysis features

The active site has a reactive group that becomes temporarily covalently attached to a part of the substrate.

What is an example of covalent catalysis

Proteolytic Chymotrypsin.

General Acid Base Catalysis features

A molecule other than water is the proton donor or acceptor. These include histidine, aspartate, and phosphate group on myosin and kinesin

Catalysis by approximation Features

Two substrates are brought together along a single binding surface on an enzyme. Example: carbon anhydrase binds carbon dioxide and water in adjacent sites

Metal ion catlysis

metal ions facilitate the formation of reactive species, serve to stabilize a negative charge on a reaction intermediate, and serve as a bridge between enzyme and substrate

Chymotrypsin catalysis mechanism acetylation step

Substrate enters the active site, and histidine removes a proton from serine 195 and generates a nucleophile out of serine. Serine as now an alkoxide ion attacks the carbonyl carbon of the target peptide bond. This forms a tetrahedral intermediate, but the oxygen on the substrate is unstable so the oxyanion hole stabilizes its negative charge. When the tetrahedral intermediate collapses, the acyl enzyme is generated, which is facilitates by the transfer of the proton at histidine to the new amino group. The amino group that broke off departs from the enzyme, completing the acylation step.

What makes the catalytic triad

histidine, serine, and aspartate

Deacetylation step of chymotrypsin

When the amino group leaves, there is room for water in the active site for water. Water molecule attaches to the active site. Histidine draws a protein away from the water molecule, and the hydroxyl ion attacks the carbonyl group of the acyl enzyme. Another unstable tetrahedral intermediate is made, and an oxyanion hole stabilizes negative charge. tetrahedral intermediate collapses and the alcohol on the serine is regenerated, and the h atom in the histidine is taken by the carboxylic terminus of the substrate. 

three classes of proteases and their active sites

cysteine (histidine active site), Apartyl (aspartate active site), and metallo (metal activated water)