Enzymes

shape

The enzyme (molecule) responds to the presence of a substrate chemically by changing its … slightly

induced fit

An … is where you see a slight change in the active site that brings the substrates closer and further helps catalyze the reaction. It helps overcome the activation energy that is needed for the reaction to occur 

all the time

This is important because it is happening … in all metabolic pathways and cells

catalytic

Enzymes have a protein structure and an active site which contains both a binding site and a … site

protein

Most enzymes/biological catalysts are of … structure 

larger

Sometimes a substrate is a bit … than the little piece needed to intact with the catalytic site so that a reaction can occur 

facilitator

Enzymes do this by acting as a ... They position substrates together because of the mainly secondary structure of the overall composition protein that the enzyme is made of. The secondary structure has groups of amino acids that provide the optimal environment for that reaction to occur

stable

The shape of the enzyme (caused by contorted movement) puts stress and strain on the bonds of the substrate. Making it less …

transition

When it becomes unstable, the enzyme can bring a substrate to a high level … state where it is energetically really reactive.

unchanged

Catalyst/enzymes are … by these reactions. Once they release their substrates, then they go into the next reaction

good conditions

So it is not the reaction that changes enzymes, but a lack of … or a change of conditions to where the enzyme can’t do its optimum performance which would then impact metabolic processes

difference

One step in the metabolic process that is either changed or slowed down can make a huge … 

stable

Because of the vast diversity of protein structure in general, (specifically enzymes) we find that enzymes are more … than others

Glycolysis

… is the first part of cellular respiration 

10

There are … enzymatic steps that catalyze the steps in glycolysis 

6

There are … major classes of enzymes and they are important for metabolic processes 

Oxygen

… is the final electron acceptor in the electron transport chain

superoxide radicals

Interaction of oxygen with other molecules (specifically those that have an affinity/liking for electrons and carry them or transport them throughout the cell) can accidentally react with oxygen, causing it to become a reactant or a reactant structure/species They are called ... This can react with different components of the cells  including proteins, cellular components and DNA itself. This can cause damage to these structures and their functions

iron

In catalase, it four protein subunits that have joined together as a functional unit. Within each, there is an … ion that’s attached to an heme group (iron/porphyrin)

oxidoreductase

When you have reactive oxygen species (like a catalase) they are presented in the form of hydrogen peroxide. As a result of this in the heme groups’s iron ions are facilitating the change from hydrogen peroxide to oxygen and water which is harmless to the cells including proteins. With this, you have a loss of an electron, and oxidation. The iron ions that are bonded there actually contribute an electron to the second hydrogen peroxide molecule which then results in its breakdown

superoxide

The … mutates deals with reactive oxygen species and converts them to hydrogen peroxide

oxygen and water

Hydrogen peroxide is then metabolized by the catalase to …

reactive oxygen species

Oxidoreductases catalase is a very abundant enzyme. It makes up 25% of the protein inside a cell that is constantly dealing with …. and those that have really high rates of metabolism (like lung tissue)

Transferase

… are enzymes which catalyze an atom or a functional group to be transferred between 2 molecules

Kinase

… means that we are adding a phosphate group

reversible

In glycolysis, a double-sided arrow means that the reaction is …. 

Hexokinase

… is not reversible 

Hydrolases

…. has water involved. Bonds are cleaved. In this, you have product formation and the addition of hydrogen and hydroxyl groups (ex: lactase)

molecules

Hyrolases break down larger … into smaller molecules so they can be used by the cell

related

Lyases and Isomases are closely … to each other in glycolysis 

Aldolase

… in glycolysis allows the production of glyceraldehyde 3 phosphate (G3P) and DHAP. They are important in the production of ATP

TPI

Triode phosphate isomerase (…) allows the conversion of DHP to G3P. This is important bc G3P is the only thing of the two that can proceed through glycolysis and result in ATP production

Decarboxylase

… can be used in alcoholic fermentation, where you have in the absence of oxygen, you have pyruvste being converted into acetal aldehyde (catalyzed by a decarboxylase, it removes a carboxyl group)

amino acids

Decarboxylase changes the structure of the … into other molecules. (ex: L-tyrosine through Decarboxylase (through the removal of a carboxyl group) turns into tyramine which is a precursor to dopamine))

Ligases

… glues one component to another. They are closing gaps

lagging

DNA replication, you have a … strand and a leading strand

DNA polymerase

… adds nucleotides on the 3 prime end and goes in a direction. If it has to go the opposite direction it can’t.

DNA ligase

There is a group of other enzymes that are needed in order to replicate DNA in the other direction on the lagging strand. Bc of this, you have little fragments being created and the thing that is joining the fragments together is …

bacterial cells

This is important in BIO technology bc it can piece things together and be able to sequence or genes that are in …

Radiation

… influences can damage protein/enzyme structures

optimal temperature

As temperatures increases particles are moving more quickly (increase in kinetic energy) as it speeds up, you have reached the … for the enzyme and it maintained constantly through homeostasis 

Different

… organisms have different optimal temperature 

PCF

… (polymerase chain reaction) is where you use the DNA polymerase from the emus aquaticus to catalyze a reaction because you are constantly changing the temperature of the reaction in order to synthesize DNA. We use it bc if we use the human DNA polymerase, it will just denature bc it is not the optimal temperature 

enzyme

The substrate concentration will increase the rate of reaction and the limiting factor is the … because you can continue to increase the substrate concentration, but at a certain point, all the enzyme molecules are saturated which would then level off the reaction rate

rate

But if you have more and more enzyme and the substrate is limited, then it is going to limit the … of reaction too.

regulated

Enzymes can be … by other molecules. They can interact directly with the active site of the enzyme or other sites within the structure of the enzyme

Allosteric inhibition/activation

When you have a molecule bind to an enzyme 

Salivary amylase

Salivary amylase in your mouth breaks down starch through the saliva. The optimal pH for that is around 7

Pepsin’s

… optimal pH is much lower. It is acidic

pancreas

Enzymes in the … is higher than both of them

preventing

There are different ways to regulate an enzyme. It can be through binding or … binding through inhibitors, activators, cofactors, and coenzymes

Enzyme inhibition

Something trying to prevent the action of an enzyme

Competitive inhibitors

binds directly to the active site of an enzyme to prevent binding. It’s competing for the active site with the normal substrate of an enzyme

increases

As substrate concentration …, the effect of the competitive inhibitor is not as strong because your have a high substrate concentration

noncompetitive inhibitor

A … binds to the enzyme’s allosteric site and changes the shape of the main active site of an enzyme to not allow it to be the right shape for its substrate so it can’t bind or the binding is limited thus decreasing the maximum rate

maximum rate

normal rate under optimal conditions

zero

The maximum rate is not … in non competitive inhibitors because not all enzymes are bound to an allosteric inhibitor or a non competitive inhibitor at the same time

down

When you have an inhibitor present, it brings … the rate of reaction in the enzyme

Allosteric inhibitors

… stabilize an inactive form. It is not at the active site it is somewhere on the surface of a protein on the surface of the enzyme. It influences it

more

A molecule can serve as an allosteric activator by binding somewhere else in the surface of the enzyme and stabilizes the enzyme and make it more likely to interact with its substrate (makes it … active, greater optimize reaction)

steric activator

Affinity for the substrate increases where you have an …

PFK

… (phosphofructokinase) catalyzes a reaction where instead of one phosphate group on fructose, you have two resulting in fructose-1, 6-phosphate

ATP

… interacts with PFK. As glycolysis continues, more ATP is being produced

cellular respiration

In order to generate …, you generate more ATP

slowing

ATP is a very reactive molecule, it can degrade really fast in the cell. So when there is an excessive amount of ATP being produced, that excess ATP can bind it PFK and reduce its function thus … down glycolysis

myokinase

When ATP is low, ADP can be used indirectly to produce energy through the action of … enzyme which yields ATP and AMP. AMP activates PFK by binding to a site other than the active site

AMP

… serves as the signaling molecule that kicks PFK back into gear and gets glycolysis going again

conditions

An enzyme can be modified in two different ways in order to control cell metabolism using different molecules (ATP and AMP) in direct response to the … of the cell

vitamins

A lot of coenzymes are … that we get from our vitamins 

Cofactors

… are a lot of organic compounds function in order to help/make enzyme activity possible in different cases 

present

Cofactors and coenzymes can contribute different functional groups that are not necessarily … in the enzyme itself and then participate in the catalytic reaction that makes the reaction happen. It is a contributing factor.

conformation

Cofactors and coenzymes can help orient the substrates bc the proper … so that a reaction occurs 

mineral ions

An example of cofactors is the … that we get in our diet (ex: DNA polymerase requires magnesium (a type of cofactor) for its polymerase action in order to add nucleotides on during DNA replication. Zinc (a type of cofactor) is really important in the same process but more for the purpose of DNA repair) 

Coenzymes

… are organic molecules and some of them are more important for electron transport/transfer (ex: vitamin K is important for clotting factors in the blood).

inhibiting

When drugs are created to address different diseases, that they’re actually … an enzyme in a pathway (ex: ace inhibitors are inhibiting the production of the enzyme that produces angiotensin (narrows blood pressure, blood vessels and increases blood pressure).

Exergonic reactions

… are spontaneous reactions because they can occur without the addition of energy

spontaneous

… reactions do not necessarily occur quickly

exergonic

Products of these reactions will have less free energy than the substrates Delta G < 0 These reactions are classified as …

endergonic

If a chemical reaction requires an input of energy, then ΔG>0. Products of these reactions will have more free energy than the substrates. These reactions are classified as …

transition state

It causes reactant(s) to become contorted and unstable, which allows the bond(s) to be broken or made. This unstable state is called the … Once in it, the reaction occurs very quickly

substrates

The 3D shape of the enzyme and reactants (aka …) determines this specificity.

active site

Substrate molecules interact at the enzyme’s …

induced fit

At the active site, there is a mild shift in shape that optimizes reactions. This is called …

maximizes

The slight changes at the active site … the catalysis

positioning 2 substrates

The enzyme can help the substrate reach its transition state by … so they align perfectly for the reaction

providing an optimal environment

The enzyme can help the substrate reach its transition state by …, i.e. acidic or polar, within the active site for the reaction

contort/stress

The enzyme can help the substrate reach its transition state by … the substrate so it is less stable and more likely to react

temporarily react with the substrate

The enzyme can help the substrate reach its transition state by … (chemically change it) making the substrate less stable and more likely to react.

released

After a catalyzed reaction, the product is … and the enzyme becomes available to catalyze another reaction

O2

… is a great electron acceptor in cellular respiration, but it is very reactive

superoxide radical

Interaction with electron carrier molecules can transfer an electron to oxygen, making it an unstable …

interacting

O2 is a great electron acceptor in cellular respiration, but it is very reactive, this can cause damage in the cell by … with, proteins, cell components and even DNA

iron-porphyrin

Catalase (which is an oxidoreductases) contains 4 protein subunits, each with an … (heme) group

H2O2

Extremely efficient and stable enzyme: each catalase enzyme can decompose millions of … molecules every second.

superoxide mutase

Works closely with enzyme …, which converts superoxides to H2O2.

abundant

Catalase is a very …. enzyme

Hexokinase

… is a type of transferases and kinase that adds a phosphate group from ATP to glucose in the first step of glycolysis

cell membrane

The hexokinase group is reactive, and chemically unable to pass through the …

Traps

The hexokinase … glucose in the cell for use in glycolysis and cellular respiration

pathways

Many kinases are in biochemical/metabolic ..