enzymes

if a catalyst lowers the activation energy, what does that imply about the stability of our transition state

lower energy transition state, so it is a more stable transition state

ultimate goal of sodium potassium pump

maitnain high extracellular sodium and low extracellular potassium maintain high intracellular potassium and low intracellular sodium

6 overarching concepts of enzymes

1) increase rate of reaction 2) transform unsuable energy to usable energy 3) require functional help from cofactors and coenzymes 4) highly specific 5) not all enzymes are proteins 5) remain unchanged at the end of the reaction

when an antibody binds its antigen, three possible outcomes can occur

1) neutralization --pathogen is unable to exert its effect on the body 2) opsonization --marking the pathogen for destruction by other WBC 3) agglutination--clumping together the Ag and Ab into large insoluble protein complexes that can be phagocytozed and digested by macrophages

which model of Enzyme substrate specificity would agree with the fact that no alteration of tertiary or quartneary structure is necessaryupon binding of the substarate

lock and key

draw an antiobdy and label its parts

2 identical heavy chains 2 identical light chains disulfide linkages and noncovlaent interactions hold heavy and light chains together antigen binding site at the tip of the Y constant region vs variable region

fat soluble vitamins

A, D, E, K

write a sample reaction equation using an ezyme where the reactant AB is combined with C to form BC and A in the presence of a catalyst

A-B + C ---> [A---B---C]---> B-C + A

whys is the transition state higher in energy in the abscence of an enzyme

A-B + C ---> [A---B---C]---> B-C + A the transition state is the intemrediate formed. this essentially occurs when one reactant begins to have its bond broken and form a new bond with another reactant therefore, the electron densities between AB are pushed away (bond partially broken) and electron density between BC is starting to come together. These electron densities do not overlap well, thus increasing overall energy

water soluble vitamins

B and C must be readily replenished because they are excrreted easily

Which vitamin is a precursor for NAD and which vitamin is a precursor for CoA

B3=Niacin which is a precursor for NAD B5 is precursor for CoA

B7

Biotin

which mineral may act as a cofactor but also act as a strong payer in the role of healthy bone and teeth

Ca2+

B12

Cyanocobalamin

during DNA replication when two DNA polymers are joined to form a single strand is catlyzed by what enzyme (name and type)

DNA ligase

at physiological pH, describe the interaction between DNA polymerase's cofactor and DNA what happens if the pH is reduced

DNA polymerase uses the cofactor Mg2+ to stabilize the the highly negatively charged DNA molecule. at phsiologically pH, the aspartate residues are negatively charged (amino group is protonated, but its carboxylic acid and carboxyl R group are deprotonated yielding a -1 charge). therefore Mg2+ is able to interact with the negatively charged aspartates if the pH is dropped below the pKA of the carboxyl side chain group of apsratic acid, then Mg2+ can't stabilize and DNA Polymerase function will decrease

what is the equation for an enzyme catalyzed reaction in terms of the enzyme-substrate complex

E+S--> ES-->[E-X]-->EP1P2-->E+ P1+P2 substrate is denoted as x during transition state because it isn't quite a reactant nor is it quite a product at this point

True or false, if I use an enzyme to decrease the Ea of a certain reaction, in the process I am able to decrease the free energy of the same reaction

FALSE. gibbs free energy only depends on the energy of the reactants and the energy of products and is INDEPENDENT of the pathway taken to get from reactant to product enzymes do not impact the gibbs free energy value

water and carbon dioxide make carbonic acid, what sis the chemical equation

H2O + CO2 --> H2CO3 --> HCO3- + H+ all in equilibirum

although the majority of enzymes are proteins, __________ molecules can also act as enzymes

RNA molecules

What does histone acetylation do?

Relaxes DNA coiling, allowing for transcription Acetylation makes DNA Active

at a constant concentration of enzyme, the enzyme activity will continue to rise until certain value. This _________________ represents the condition in which all the active sites are filled with appropriate substrate

Vmax

sodium-potassium pump

a carrier protein that uses ATP to actively transport 3 sodium ions out of a cell and 2 potassium ions into the cell

What could permit a binding protein involved in sequestration to have a low affinity for its substrate and still have a high percentage of substrate bound?

a high concentration of BP compared to a low concentration of substrate would allow for all the substrate to by bound despite a low affinity

structural proteins generally have a highly repeptive secondary structure and a super secondary structure. what is this super secondayr structure

a repeptive organization of secondary structural elements together referrred to as a motif (gives these proteins fibrous nature)

which type of enzyme would be beneficial to help sped up a ketone-enol tautomerization what is a characteristic of this type of enzyme

acid/base catalysis trasnfer of proton from carbon to oxygen proton carrier

makes up microfilaments and thin filaments in myofibrils the most abundant protein in the human body

actin

this protein has a negative side and a positive side that allows motor proteins to travel unidirectionally across its filament

actin

motor proteins have transient interactions with what two strucutral proteins

actin and microtubules (tubulin)

the amount of energy needed to be input into a reaction to get it going

activation energy

Antibodies are part of the _____________ immune system whose main job is to bind ___________ and prepare them for destruction

adaptive foreign antigens as we know, the Ab affinity for its antigen it super duper high

what is glycosylation? is this an example of co or post transnational modification on what proteins do these typically occur and what is the overall purpose

adding a carbohydrate to a protein post typically occurs on proteins embedded in the cell membrane used to identify different types of cells

what is lipidation?

adding a lipid to a protein

what are the implications of lysine acetylation

adding an acetyl group to a lysine residue on an amino acid removes its positive charge at physiological pH and changes its acid/base characteristics. this will also impact lysine's electrostatic interactions with other molecules

Lyases

addition of groups to double bonds, or formation of double bonds by removal of groups need to generate double bond or ring structure essentially the cause the decompsotion of a reactant without water like a hydrolase and without the transfer of electrons like an oxidoreductase

binding a substrate at places other than its active site

allosteric binding (can bind regulators at these sites) causes enzyme conformational shape thus altering enzymatic function regulators can be activators or inhibitors

enzymes do not change the amount of product formed because they do not change the gibbs free enerrgy of a reaction. however, by lowerin the Ea, they do what to the reaction?

allow equilbirum between reactant and product to be reached quicker, but DO NOT CHANGE THE EQULIBRIUM (it is just reached quicker) same concentration of products and reactants is formed regardless if there is an enzyme or not

enzyme found in the mouth responsible for breaking down complex carbs such as starch into sugar what pH does this enzyme function best at

alpha amylase pH of about 7

the conversion of alpha ketoglutarate and aspartate (as a pair) to glutamate and oxalocatetate uses what enzyme and what mechanism

aminotrasnferase moves the amino group from aspartate to alpha ketoglutarate

what is a ligase

an enzyme that combines A and B to form a complex AB

What is a suicide inhibitor?

an inhibitor that covalenttly bonds to an enzyme and then never unbinds

proteins produced by B cells that function to neutralize targets in the body such as toxins, bacteria and then recruit other cells to help eliminate the threat

antibodies/immunoglobulins

when an enzyme is not bound to its cofactor it is called

apoenezyme

during the urea cycle, arginosuccinate is broken down into arginine and succinate by what enzyme? what type of enzyme is this

arginnosuccinate lyase

proteins that serve a stabilizing function by transporting or sequestering molceules are referred to as what and what are some examples

binding proteins hemoglobin calcium-binding proteins DNA binding proteins (transcription factors)

group of glycoproteins that mediate calcium dependent cell adhesion (typically hold similar cell types together)

cadherin

in general what does an enzyme do to a substrate in its active site

enzyme creates a suitable micro environment in active site and when it brings in the substrate it forms the enzyme-substrate complex. The enzyme is able to stabilize the partially broken bonds and partially formed bonds of the transition state to lower its energy this stimulates the breakage of the old bonds and formation of new bonds to form the products

enzymes greatly increase the rate of reaction of a ton of processes in our bodies. What would happen if we did not have carbonic anhydrase

carbonic anhydrase catlyzes the conversion of non polar CO2 into carbonic acid which dissociates into polar HCO3-. the polarity of HCO3- allows this molecule to dissolve in the blood and be transported to the lungs. then HCO3- is removed from red blood cells via the chloride shuttle and converted back to CO2 where it is expelled. if we did not have Carbonic anhydrase, we would have a build up of CO2 which is acid, so we would experience a drop in physiological pH (acidosis)

what is the purpose of the carbonic anhydrase reaction

carry CO2 from tissues to lungs so we can expel it

Oxidoreductases

catalyze oxidation-reduction reactions that involve the transfer of electrons an oxidase is used to strip electrons away from a molecule whereas a reductase gives electrons to a molecule

isomerase

catalyzes the rearrangement of bonds within a single molecule

why is a GPI anchor useful

cell membrane is composed of hydrophillic outside and hydrophobic inside, so maybe a protein has various portions of polar and non polar parts and can't bind the cell membrane effectivelty, but because the lipid is built like the lipid bilayer it can plunge into the hydorphobic portion and anchor itself in

proteins found on the surface of most cells and aid in binding the cell to the extracellular matrix of other cells

cellular adhesion molceules (this is a broad class that can be broken down into three subgroups)

how do we shuttle HCO3- out of red blood cell so it can travel to lungs

chloride shuttle

chymotrypsin only cleaves peptide bonds of F, W, and Y what does these have in common

chymotrypsin must be specific for aromatic rings

what is a transferase

class of enzymes that enact the transfer of specific functional group from one molecule to another. A + BX --> AX +B

Hydrolases

cleave bonds on molecules with the addition of water

NADH is an electron carrier, is it an example of a coenzyme or cofactor

coenezyme NADH --> <-- NAD+ + H:-

which coenzyme is an acyl carrier

coenzyme A

_______________ are organic carrier molecules

coenzymes predominately carbon based hold on to certain things for the enzyme to make catalysis run more smoothly

Cofcators/coenzymes are directly involved (directly participate) in the enzyme's catalytic mechanism

cofactors (maybe aiding in stabilization for example such as MG2+ working with DNA polymerase to stabilize the negatively charged phosphate groups of DNA)

enzymes typically do not act alone, they need

cofactors which are

this strucutral protein has a characteristic trihelical fiber (3 left handed helices woven together to form a secondary right handed helix) and makes up most of the extracellular matrix of connective tissue (provides strength and flexibility)

collagen

what may result in the improper folding of collagen leading to cell death and bone fragility

collagen forms a unique and specific secondary helical structure thanks to the abundance of the flexible glycine amino acid. removal of glycine or replacement with another AA would cause improper collagen folding

primary strucutral proteins in the body

collagen, keratin, elastin, actin, tubulin

In a decarboxylation reaction a covalent bond is fromed between the enzyme and the substrate. This is a reaction that can be facilitated by which type of catalysis? what is a characteristic of this type of enzyme

covalent catalysis electron sink/carrier

what is the basis for the enzyme microenvironment

create a non polar area to increase the proximity and oteintation of substrates to more easily react. this also decreases the likelihood that other reactions will take place (thus limiting unwanted products)

How do cytoskeletal proteins differ from motor proteins?

cytoskeletal proteins tend to be fibrous with repeating domains while motor proteins tend to have ATPase activity and binding heads both types of proteins function in cellular motility

this type of structural protein can be thoguht of as a 3D web or scaffolding system for the cell

cytoskeleton

at equilbirum, what is the value for gibbs free energy

delta G = 0. the forward and reverse reactions occur at the same rate and the reaction is neither spontaneous nor non-spontenous

the difference between the energy level of the reactant and the transition state

delta G double dagger (free energy of activation) the amount of energy the reactant needs to get over the barrier to become the product

co translational modification occur to the protein when? what is an example

during translation acetylation the first amino acid (typically methionine) is removed and replaced with an acetyl group

this motor protein is involved in the sliding movement of cilia and flagella

dynein

a patient comes into the ER with pneumonia. Upon examination you notice a buildup of mucous in the lungs. what protein is most likely disrupted?

dynenin which is responsible for the production of cilia. this could be classified as primary ciliary dyskinesia

this structural protein is involved in the extracellular matrix of connective tissue and its primary role is to stretch and recoil which restores the origianl shape of the tissue

elastin

DNA polymerase is an enzyme used in DNA replication that uses an active site metal (Mg2+) to stabilize the highly negative DNA molecules. what type of enzyme is DNA polymerase

electrostatic catalyst good for charge stabilization

DNA replication, the TCA cycle and the expression of genes can all be sped up by which type of protein

enzyme/catlytic protein

trypsin is a digestive enzyme produced in the pancreas which binds to polypeptides (single substrate) and carries out two closely related reactions (catalyzes cleavage of peptide bonds on carboxyl end of lysine and arginine). what porperty of an enzyme does this represent

enzymes are highly specific and highly effecient

molecules must __________ and be properly _____________ in order for them to react. enzymes are able to help with both therefore increasing the frequency of successful collisions

enzymes help with the proximity and orientation of reactants

true or false, in a reaction that has not reached equilibrium, the gibbs free energy mustbe negative and therefore spontaneous

false, if it hasn't reached equilbrium, gibbs free energy can either be negative or positive

true or false, protein kinases can only phosphorylate one enzyme

false, protein kinases are known for their amplifaction effect. they can regulate many enzymes and have various downstream effects

true or false, the coenzyme/cofactor just needs to be in the vicinity of the enzyme for it to work properly

false, the conezyme/cofactor must bind directly to the enzyme for it to function properly

true or false, isomerases can onyl catalyze the reactions between constiutional isomers and not stereoisomers

false, they can catalyze the isomerazition between stereoisomers and constitutional isomers

true or false, at the transition state, the enzyme and substrate exhibit their weakest bond together

false, this is where the enzyme and substrate are the most tightly bound

temperature changes impact protein ___________ and _____________

folding and geometry

B9

folic acid

ABO blood grouping takes advantage of what type of post translational protein modifcation

glycosylation

many post translational modifications occur in what two organelles

golgi apparatus and endoplasmic reticulum

what is the name of the enzyme that catalyzes the first step of glycolysis and what does its name mean

hexokinase adds a phosphate group to a 6 carbon sugar Glucose + ATP--> Glucose-6-P + ADP

for a transport protein, when there is high concentration of a ligand, the protein will have___________ affinity for the ligand and when there is low ligand concentration, the transport protein will have ___________ affinity for the ligand

high low

proteins found in chromosomes that help package DNA in a very tight manner

histones

when an enzyme is bound to its cofactor it is called

holoenezyme

phosphatases, lipases, peptidases, nucleaseas are all examples of what class of enzyme

hydrolase

describe a spontenous reaction in terms of gibbs free energy. what is one common type of spontaneous reaction

if spontaneous, delta G is less than 0 and the reaction is said to be exergonic. combustion reactions are a common example

phosorphorylation occurs ____________ the cells where ATP concentrations are high. Proteins found ____________ the cell are not phosphorylated in the extracellular environment

inside outside phosphrylation occurs inside the cell

group of proteins that have 2 membrane spanning chains (alpha and beta) play important role in cellular signlaing and can greatly impact cellular function by promoting cell division, apoptosis, or orther processes

integrin

3 subgroups of CAMS

integrins, selectins, cadherins

what type of protein allows small charged particles to enter and exit a cell

ion channel

what are four broad examples of protein fucntions that are not enzymes

ion channels/receptors motor antibodies transport

is the sodium concentration typically higher or lower inside the cell

it is typically higher otuside the cell, so sodium wants to flow in, that's why we need the active transporter NA/K ATPase to pump 3 sodium ions out

intermediate filament proteins found in epithelial cells, contribute to mechanical integrity of the cell and function as reguatory protein primary protein making up hair and nails

keratin

____________are the enzymes responsible for phosphorylation

kinases

this motor protein plays key roles in aligning chromosomes during metaphase and depolymerizing microtubules during anaphase of mitosis

kinesin

3 types of motor proteins

kinesin (intracellular transport), myosin (contracting muscles), and dynein (intracellular transport--> helps with cilia)

both kinesin and dynein are important for vesicle transport in the cell, but they differ in their polarities, how?

kinesin brings vesicles towards the positive end of the microtubule and dyneins bring vesicles towards the negative end

the activation energy of a reaction describes how quickly the reaction will take place, therefore the activation energy describes the kinetics/thermodynamics of the reaction

kinetics

the transfer of electrons from NADH to pyruvate with the help of _______________ to form lactic acid and NAD+

lactate dehydrogenase

some enzymes are able to bind more thna one substrate. During the formation of lactic acid, lactate dehydrogenase binds what two enezymes? what is the chemical equation for the formation of lactic acid

lactate dehydrogenase binds NADH (reducing agent) and pyruvate pyruvate + NADH -->lactic acid + NAD+

after eating a piece of pizza, blood glucose levels rise causing the secretion of insulin from beta cells of the pancreas. insulin is a _________ that binds its __________on the exterior of a cell to cause an intracellular cascade leading to glucose uptake

ligand receptor

cofactors come in two flavors

metal ions and organic molecules

____________are inorganic cofactors (not cofactor and coenzyme, just cofactor)

minerals

movement at the neck of this motor protein is responsible for the power stroke of sarcomere contraction

myosin

what is the primary motor protein that interacts with actin

myosin

tubulin, like actin, has polarity where is the negative end and positive end typically located

negative end of microtubule located adjacent to the nucleus whereas the positive end is usually in the periphery of the cell

B3

niacin

ATP synthesis is an example of a non-spontaneous/spontenous process and is therefore endergonic/exergonic

non spontenous and energonic therefore delta G is > 0 so this reaction will not take place unless we input a certain amount of energy

do enzymes alter the equilbirum constant

nope. they just help equilbirim be reached quicker

organic molecule cofactors have a special name and can bind weakly or strongly to an enzyme. what is this thing called when it is bound tightly to an enzyme

organix molecules that help enzymes function are called coneznymes. when these coenzymes are tightly bound, they are called prosthetic groups

B5

pantothenic acid

enzyme found in the stomach that breaks down proteins into peptides what pH does this enzyme function best at

pepsin pH of about 2

___________ are proteins that reverse the effects of protein kinases

phosphatases we need a different enzyme because the kinase reaction is so thermodynamically favorable (products are way more stable) that the reaction is essentially a one way street, so this necessitates the use of a whole other enzyme

which enzyme catalyzes the isomerization of glucose 6 phosphate to fructose 6 phosphate

phosphoglucose isomerase

what is the basic mechanism for a protein kinase

protein kinases catalyze the transfer of a terminal phosphoryl group from ATP onto a hydroxyl containing residue (therefore serine, threonine or tyrosine) of the target protein

a zymogen is an inactive form of an eznyme. what is one potential way to activate a zymogen

proteolysis

B6

pyridoxal phosphate

enzymes typically bind substrates reversibly/irreversibly through covalent/non covlane tforces

reversibly non covalent H bonds, van der Wals, hydrophobic effect

B2

riboflavin

bind to carb molecules that project from other cell surfaces (forming the weakest bonds of all 3 CAMS) expressed on WBC

selectins

There is a dipeptide formed between K-A, and after the addition of water, the peptide bond holding these amino acids together is broken what is the class of enzyme most likely to cause these

serine hydrolase (protease) serine is a key residue responsible for breaking peptide bond

net change in energy levels between a reactant and product

standard free energy change energy released into environment once reaction is over

the reverse reaction of a lyase can also be accomplished by the same enzyme, when the reverse process occurs, what is typically the name given to these enzymes

synthases

Ubiquination

targets a protein for degradation by a proteasome

what is the function of a GPI anchor

tether a protein to a cell membrane this is an example of a lipidation post translational modification

I am examining a spontaneous reaction but it takes forever to occur, what gives

the activation energy (kinetics) must be super high

what is the cofactor necessary for the proper functioning of carbonic anhydrase

zinc

how does phosphorylation impact hydorgen bond capability

the addition of two new negatively charged oxygen atoms increases the amount of H bond acceptors which can increase the specificity of the enzyme's interaction with its substrate

compare and contradt the lock and key model with the induced fit model

the lock and key model states that the substrate fits perfectly and precisely in the active site due to their complementary shapes the induced fit model states that the enzyme active site and substrate are not precisely complementary, but once the substrate binds to the active site, the binding causes the active site to become complementary to the substrate

what happens when two potassium ions are bound to the extracellular portion of the sodium potassium pump

the receptor is dephosphorylated causeing a confomational shift allowing the influx of two potassium ions

the active site is a 3D crack in the enezyme that contains the catalytic groups. what do these catalytic groups do

the residues that come from different parts of the enzyme and which catalyze the actual reaction these are responsible for lowering the energy of the transition state (stimulate the breaking and forming of bonds in the transition state)

what is the general basis of what occurs before, during and after an enzyme and substrate bind

they come close, they bind with semi-strong bonds, conformational (induced fit--really tight) after the reaction, the enzyme loosens its grip and realles the substrate in its product form

what is the overarching concept for how enzymes lower the activation energy of a reaction (specific examples would be acid/base, covalent, electrostatic catalysis)

they lower the energy of the transition state, therefore making it more stable therefore lowering the Ea

B1

thiamine

when a phsophate group is added toa hydroxyl group of an AA residue in an enzyme, a net negative charge is produced. why is this useful

this gives the enzyme an extra 2 negative charges (PO3 2-) which can disrupt old interactions and form new interactions thereby altering the active site and catalytic activity of the enzyme

the transfer of amino acids to the growing polypetide chain via tRNA during protein translation is an example of a process that uses what kind of enzyme what is the name of this enzyme

transferase peptidyl transferase

6 types of enzymes

transferse,lyase, hydrolase, isomerase, oxidoreductase,, ligase

the photosynthetic reaction CO2 + H2O + light --> C6H12O6 + O2 what is the overacrhcing concept that the enzyme is accomplishng here

transforming unusable energy into usable energy (light energy converted into usable energy stored in chemical bonds of glucose)

highest energy point on a reaction coordinate diagram

transition state

where will you find the most instability throughout the entire enzymatic reaction

transition state

hemoglobin picks up O2 from the lungs where it is plentiful and moves the oxygen to the muscle cells where is is less plentiful. what type of protein is hemoglobin

transport

what type of protein binds small molecules and sends them to other locations in a mutlicelluar organism

transport protein

what occurs when the NA+/K+ ATPase is full of intracellular sodium (meaning it has bound 3 sodium ions)

triggers the breakdown of ATP into ADP and Pi the phosphate attaches itself to the protein (phosphorylation) causing a conformational shift allowing for the release of the 3 sodium ions to the extracellular space

true or false: the process of breaking down ATP into ADP and Pi is exergonic and therefore the products are lower in energy than the reactants, thereby this process releases a ton of free energy

true

True or false, enzymes are not unchancged at the end of the reaction, but they may participate in the reaction

true, enzymes will remain net unchanged. they can be used up in the reaction, but will be regenerated

true or false, the kinetics of phospphorylation reactions are highly adjustable

true. depending on the physiological conditions of the cell, these reactions can occur at varying rates

tryposnigen is a zymogen released from the pancrease and shipped to the intestine. inside the intestine trypsinogen is covalently modified by an enzyme enterokinase to form the biologically active trypsin. why does this process occur

trypsinogen is inactive, so this prevents it from breaking down crucial pancreatic proteins, because we really want trypisin to help with the digestion in the intestines

protein that makes up microtubules which are important for providing structure, chromosome sepratation in mitosis and meiosis and intracellular transport with kinesing and dynein

tubulin

enzymes create micorenvironments to help stabilize the tranisition state. are these micoreneviornemnts typically polar or non polar

typically non polar, the only time we would see water in the microenvironment is if water is needed as a reactant

_______________ are considered organic cofactors and coenzymes

vitamins

dietary cofactors and coenzymes

vitamins and minerals

carbonuc anhydrase catalyzes the reaction to form carbonic acid from what two reactants

water adn carbon dioxide Carbonic anhydrase makes carbonic acid turn into CO2 and H2O much faster in our saliva and other tissues.

CO2 cannot be easily carried by hemoglobin, so how do we get it from the tissue to the lungs

we convert CO2 and water into H2CO which readily dissolves into HCO3- and H+. HCO3- can dissolve in bloodstream allowing us to trasnport it

what are the typical x and y axes for a reaction coordinate diagram

x=reaction progress y=energy

is an ATPase an example of a motor protein

yes, they power the conformational change necessary for motor function