ENZYMES

Biological Catalysts Enzymes are complex proteins,

usually having either tertiary or quarternary structure, and are responsible for mediating chemical reactions in organisms

Dissolving awayFor example, think about

hydrolysis reactions that use water to break apart major macromolecules

If hydrolysis reactions were that easy to initiate, that means you would dissolve every time you contacted water!

CatalystsMost reactions in organisms cannot

happen without the help of enzymes

These enzymes accelerate the rate of reactions and push them forward

Therefore, enzymes are known as catalysts –they lower the energy required to initiate a chemical reaction, increasing the likelihood that the reaction occurs

Lock and KeyEnzymes, structurally, are

designed to fit specific SUBSTRATES – the reactants in the biochemical reactions

This is known as a “lock and key” mechanism where each enzyme is specialized

Enzyme + substrate enzyme substrate complex

The substrate binds on the ACTIVE SITE of the enzyme where the chemical reaction will occur

Other binding sites might be present on the enzyme that are secondary to the active site. These are known as ALLOSTERIC SITES and generally do not result in the formation of a new product via a chemical reaction

Tertiary and Quarternary structureNotice, therefore, that enzymes are

complex proteins – often having at least tertiary structure and sometimes quarternary structure

The complex possibilities seen in protein folding produces a large number of structural shapes necessary to produce specialized enzymes for each possible chemical reaction

Specificity is keyBecause they are so specific,

each enzyme is designed to accelerate only one type of chemical reaction

http://highered.mcgraw-hill.com/sites/0072495855/student_view0/chapter2/animation__how_enzymes_work.html

Enzymes are custom madeOn top of being specific to

certain reactions, enzymes are also designed to function optimally under certain conditions

The following factors can affect enzyme function:◦pH◦Temperature◦salinity

Why the sensitivity?Enzymes are located everywhere in

living organismsEach living organism must survive

in ecosystems that can affect their internal systems (for example, crustaceans living in high temperature sea vents)

Even organisms that have their internal systems well shielded from the external enviornment (like us)

Specialists in special systemsFor example, within a human being, pH

levels can vary within the digestive system

The stomach is a highly acidic area (pH = 1) whereas the duodenum is a more basic area thanks to the pancreas (pH = 5-6)

Therefore, enzymes that function in the stomach must be able to function in low pH vs. those that function in the duodenum that must function in higher pH

Why?This comes back down to

understanding the biochemistry of enzymes

Remember that functional groups in amino acids create enzymes that can be more basic, acidic, hydrophilic or hydrophobic

These characteristics help an enzyme to survive better in certain environments

Coming undoneEnzymes can “denature” - acidic/basic

environments or increased temperatures can interfere with basic bonds (disulfide bridges, Vanderwaals interactions, etc.) that will cause the enzyme to unfold

Remember: a loss of structure = loss of function

An enzyme that cannot hold its 3D shape loses its ability to “fit” with a substrate

http://www.sumanasinc.com/webcontent/animations/content/proteinstructure.html

http://www.lew-port.com/10712041113402793/lib/10712041113402793/Animations/Enzyme_activity.html

Pepsinhttp://www.biotopics.co.uk/JmolA

pplet/pepsin.htmlPepsin will denature at pH levels

of more than 5.0This means that as food moves

from your stomach to your duodenum pepsin is inactivated by the increase in pH – this allows other proteases in the duodenum to take over protein digestion

TemperatureIn regard to temperature, the

ideal temperature for most enzymes is dependent on the average internal temperature of the organism

Human enzymes function optimally at internal body temperature = 370

However, as mentioned before, there are some enzymes that can function well at more extreme temperatures

Enzyme kineticsEnzymes are used widely in the

production of various chemical substances in manufacturing, or for laboratory tests because they are such efficient ways to speed up chemical reactions

Enzymes can be used over and over again to catalyze numerous reactions (they will degrade eventually though)

Therefore, the knowledge of optimal ranges of enzyme function are beneficial for this reason

Enzyme kineticsTherefore, enzyme kinetics is the study

of enzymatic function – how fast an enzyme can catalyze a reaction

The speed at which an enzyme can catalyze a reaction is best illustrated by how much product is produced in the chemical reaction over time

Substrate + enzyme product + enzyme

Vmax and KmVmax = fastest rate at which

substrate can be produced by the enzyme

Km is a rate constant - it describes how much the enzyme “wants” to binds to the substrate – it usually is related numerically to half of Vmax

Why does it plateau?In general it makes sense that if

you add more substrate to a given concentration of enzymes, you should get more product

However, you should notice that the curve plateaus eventually

Why?

Think about functionRemember that in order to carry

out a reaction, the enzyme must bind to a substrate

If a small concentration of substrate is added to a group of enzymes, it makes sense that more product can be produced as the concentration increases – because you are engaging more and more enzymes in the reaction process

Think about functionBut if the concentration of

enzyme is not increased, and more and more substrate is added, the rate of product production starts to slow down

If each enzyme in the reaction is attached to a substrate, adding more substrate will not increase the rate of reaction since each enzyme is already occupied with a substrate

Think about functionTherefore it can be said that the

enzyme concentration is the limiting factor

Increasing the amount of substrate will not cause the rate of the reaction to in increase unless enzyme concentration increases

InhibitionInhibition occurs when enzyme function

is tampered with – this is sometimes necessary to control enzymatic function

This can occur two ways:COMPETITIVE INHIBITION: another

substance binds to the active site of the enzyme

NON-COMPETITIVE INHIBITION: another substance binds to a non-active site – an allosteric site that prevents the binding of the main substrate

The most common form of non-competitive (allosteric) inhibition occurs when the binding of an inhibitor to an allosteric site causes a conformational change in the enzyme making it unable to bind with the usual substrate

Why does Vmax and Km change?

Binding the active site will make the enzyme less “desirous” to bind the substrate – since it is already bound to something else – this affects Km

Binding an allosteric site might not change the enzyme’s desire to bind the substrate, but it will affect its ability to carry out chemical reactions, therefore affecting Vmax