IB Biology - 2.5 Enzymes

catalyst

a chemical that can help a reaction occur with less energy, without being used in the reaction itself

Enzymes

a class of proteins that catalyses chemical reactions.

Lactose

a disaccharide (C12H22O11) found in milk that may be hydrolysed to yield glucose and galactose.

Hyaluronidase

a family of enzymes that break down hyaluronic acid and increase tissue permeability. Often used during eye surgery to administer local anesthetics faster.

enzyme-substrate specificity

a feature of an enzyme activity with regard to the kind of substrate reacting with an enzyme to yield a product

Enzyme activity

a measure of the ability of an enzyme to catalyse a specific reaction.

enzyme

a protein produced by a living organism which acts as a catalyst to bring about a specific biochemical reaction

active site

a region on an enzyme that binds to a protein or other substance during a reaction

Denaturation

a structural change in a protein that alters its three-dimensional shape and causes the loss of its biological properties.

induced fit model

active site is not a rigid fit for the substrate and changes its conformation to better accommodate the substrate

Metabolism

all of an organism's chemical processes.

Catalase

an enzyme found in the blood, and in most living cells, that catalyses the decomposition of hydrogen peroxide into water and oxygen.

Hydrolysis

decomposition of a chemical compound by reaction with water.

denatured

destroy the characteristic properties of (a protein or other biological macromolecule) by heat, acidity, or other effect which disrupts its molecular conformation.

lock and key model

substrate is drawn to closely matching cleft on enzyme molecule

induced fit model

the current theory of the action of an enzyme binding to a substrate

products

the end result

How does heat cause denaturation?

vibrations within the molecule breaks inter molecular bonds or interactions

Methods of production of lactose-free milk

- lactase (enzyme) digests lactose into glucose/galactose - lactase is fixed to an inert surface (eg. alginate beads) - milk is passed over this surface to become lactose free

effects of pH on rate of reactions

- most acidic or basic have the smallest rate of reaction

Advantages of lactose-free milk

- provides a source of dairy for lactose-intolerant people - increases sweetness of milk (less ned for sweeteners) - reduces crystallization and production times for cheese

Immobilised enzymes are often used in industrial practices: examples

- used for medical diagnostic tests - used in food production - eg. lactose- free milk

List the three main processes cells use energy for

Cell movement Active transport Anabolism

What's the essential idea?

Enzymes control the metabolism of the cell

Explain how enzymes affect equilibrium in a reaction

Enzymes do not change equilibrium. Enzymes lower the activation energy to catalyze the reaction, but the end result is the same with or without the enzyme

Immobilized enzymes

Enzymes used in industry that are usually attached to another material or into aggregations that restrict enzyme movement

List the advantages of lactose-free milk

Lactose-intolerant individuals can still consume dairy Glucose and galactose are sweeter than lactose, so less sugar needs to be added to dairy products Glucose and galactose are more soluble than lactose, so the texture of ice cream will be less gritty The production of yogurt and cottage cheese is faster because bacteria ferment glucose and galactose faster than lactose

Describe how enzymes are affected by pH

Most enzymes have an optimum pH at which their activity is highest, so increasing or decreasing the pH from this value will decrease enzyme activity

What would be true if the lock and key hypothesis were actually true?

One enzyme would only catalyze one reaction. in actuality, some enzymes can catalyze multiple reactions.

List the three ways enzymes can lower activation energy

Re-orient the substrates Induce physical strain Alter chemical groups

Enzymes, substrates, and active sites; steps v2

Substrate: reactant in a biochemical reaction enzyme: globular protein which acts as a catalyst for biochemical reactions active site: region on the surface of an enzyme to which substrates bind and which catalyze the reaction * polar regions of amino acids attract substrate and active site of the enzyme * once a substrate has been lock into the active site, the reaction is catalyzed * the products are released and the enzyme is used again

What are substrates?

Substrates are the substances that enzymes convert into products

Reducing pH by one unit makes the solution...

Ten times more acidic This is because the pH scale is logarithmic

How is the substrate and the active site matched structurally according to the lock and key hypothesis?

The 3D structure of the active site is specific to the substrate. substrates that don't fit, won't react.

Activation energy (Ea)

The amount of energy needed to put the reactants into a transition state

Collision

The coming together of a substrate molecule and an active site A substrate molecule can only bind to the active site if it moves very close to it

Explain how enzymes use reorientation to catalyze reactions

The enzyme arranges specific atoms in the substrate so that bonds can form more easily

Substrate

reactant of an enzyme-catalyzed reaction

exothermic

reactions that give out energy

endothermic

reactions that need energy to occur

effects of temperature on rate of reactions

- if temperature is too low or too high than there is a smaller rate of reaction

Outline how lactose-free milk is produced

-Lactase is purified from yeast or bacteria and then bound to an inert substance (such as alginate beads) -Milk is then repeatedly passed over this immobilized enzyme, becoming lactose-free

Induced Fit model

-enzyme or reactants (substrate) changes their shape slightly -reactants become bound to enzymes by weak chemical bonds -reaction proceeds more readily

What is an active site?

An active site is a special region on the surface of the enzyme where substrates bind.

Pepsin

An enzyme found in human stomachs that breaks down proteins into smaller peptides and aids in digestion It functions best in acidic environments

Isozyme

An isomer of an enzyme that has a different composition so it can adapt to changes in the environment

Breaking bonds requires/releases energy

Breaking bonds requires energy

What are enzymes?

Enzymes are globular proteins that work as catalysts - they speed up chemical reactions without being altered. - they lower the activation energy necessary for a reaction.

Competitive Inhibition

Inhibitor have similar shape to substrate and will collide with active site

What does the induced-fit model do better?

It better explains enzyme activity

immobilized enzymes

held in place in tiny pores on bead of substance called calcium alginate

substrate

substances that enzymes convert into products in these reactions (the reactants)

Induced Fit

- Enzyme active site change shape slightly to fit (Mould) - As it change shape puts strain on substrate - This distorts the bonds and lower activation energy needed to break the bond

Outline the steps necessary for an enzyme-catalyzed reaction to occur.

- Enzyme-catalyzed reactions occur in solutions (such as the cytoplasm). - Components of the solution are in constant, random motion. - For a reaction to occur, the substrate must collide with and bind to the active site of the enzyme. - A collision with another region of the enzyme will not result in a reaction occurring. - For a reaction to start energy input is needed. - Binding to the active site lowers the amount of energy needed to start the reaction (activation energy).

Outline how enzyme catalysis involves molecular motion and the collision of substrates with the active site

- The coming together of a substrate molecule and an active site is known as a collision - most enzyme reactions occur when the substrates are dissolved in water - All molecules dissolved in water are in random motion, with each molecule moving separately - If not immobilized the enzyme can move too, however enzymes tend to be larger than the substrate (s) and therefore move more slowly - collisions are the result of the random movements of bot substrate and enzyme - the substrate may be at any angle to the active site when the collision occurs - successful collisions are ones in which the substrate and active site happen to be correctly dinged to allow binding to take place

lock and key model

- The shape of the active site must be complementary to the shape of the substrate. - Therefore, only the correct substrate can fit onto the active site. - The substrate chemically interacts with amino acids comprising the active site. The substrate and the active site must also chemically fit together.

enzyme-catalysis reaction

- When a substrate binds to the enzyme's active site, an enzyme-substrate complex is formed - The enzyme catalyses the conversion of the substrate into product, creating an enzyme-product complex - The enzyme and product then dissociate - as the enzyme was not consumed, it can continue to catalyse further reactions

Immobilised enzymes are often used in industrial practices: methods

- aggregations of enzymes bonded together - attached to a surface - eg. glass - entrapped in gels - eg. alginate gel beads

Factors affecting enzyme activity: pH level

- enzyme activity is highest at an optimal pH range - activity decreases outside of this range (due to denaturation)

Immobilised enzymes are often used in industrial practices: advantages

- enzyme is not dissolved - so concentration of substrate can be increased - enzymes can be recycled many times, saving money and time - collection of products is straight forward - increases enzyme stability to changing temp and pH

Factors affecting enzyme activity: Temperature

- increases enzyme activity (more kinetic energy = more collisions) - enzyme activity peaks at optimum temperature - higher temperatures decrease activity ( causes denaturation)

Factors affecting enzyme activity: substrate concentration

- increases enzyme activity (more particles = collisions) - at a certain point, activity plateaus (saturation of active sites)

effects of substrate on rate of reaction

-the more substrates the more possible reactions can occur -levels off at a certain rate because there are a certain amount of enzymes and surplus substrates so no more reactions can occur

Steps of induced fit model (anabolic reaction)

1. 2 substrate molecules are drawn into the cleft of the enzyme 2. The enzyme changes shape, forcing the substrate molecules to combine 3. The resulting end product is released by the enzyme which returns to its normal shape, ready to undergo more reactions

Steps of lock and key model

1. Substrate drawn into active sites of enzyme 2. Substrate shape is compatible with enzyme's active site in order to fit and be reacted upon 3. enzyme modifies substrate

Lactase

A digestive enzyme that breaks lactose into glucose and galactose. Low levels of lactase can result in lactose intolerance.

Topoisomerase

A family of enzymes that act on the coiled structure of DNA. They cut the DNA to alter the coiled structure.

Enzyme

A globular protein which speeds up the rate of a chemical equation by lowering activation energy (eg. it is a biological catalyst)

Non-Competitive Inhibition

A molecule that binds to an enzyme at a location outside the active site and inhibits the enzyme's function, which changes the enzyme active site shape.

Zymase

A naturally occurring enzyme in yeasts, widely used in the baking industry to ferment sugar into ethanol and carbon dioxide.

Enzyme

A type of protein that speeds up a chemical reaction in a living thing

What does and enzyme do?

An enzyme stresses the bond in the substrate, reducing the activation energy required for a reaction to occur.

Describe how enzyme are altered via denaturation

An unfavorable change in temperature or pH will alter the active site so the substrate can no longer bind Or, if the substrate does bind, the reaction that the enzyme normally catalyzes will not occur In many cases, denaturation causes enzymes that were dissolved in water to become insoluble and form precipitate

What is the induced-fit model?

As the substrate approached the enzyme, it induces a conformational change in the active site - it changes shape to fit the substrate - this stressed the substrate, reducing the activation energy of the reaction - the enzyme reverts to its original shape

Forming bonds requires/releases energy

Forming bonds releases energy

Describe the two ways in which enzymes are affected by temperature

Heat will give the particles more kinetic energy, so the enzyme and substrate molecules will move faster which causes the chance of collision and enzyme activity to increase Too much heat may cause bonds in the enzyme to vibrate and cause denaturation. This will change the structure of the protein and denature it so enzyme activity will fall

Describe how enzymes are affected by substrate concentration

Initially, a higher substrate concentration will result in increased enzyme activity as active sites are filled more rapidly. As substrate concentration rises, however, the active sites will become saturated with substrates and enzyme activity will plateau

What is activation energy?

It's the amount of energy that must be put into a reaction to make it occur

Outline the advantages of enzyme immobilization

The enzyme can be separated from the products, stopping the reaction at the ideal time and preventing contamination of the procucts The enzymes may be able to be recycled after use to save money Immobilization of enzymes increases the stability of enzymes to changes in temperature and pH, reducing the rate they are degraded and have to be replaced Substrates can be exposed to higher enzyme concentration than with dissolved enzymes, speeding up reaction rates

Explain how enzymes use physical strain to catalyze reactions

The enzyme causes the bonds in the substrates to stretch and destabilize, making the reaction occur more easily

Lock and Key Hypothesis

The idea that enzymes are specifically shaped to fit only one type of substrate. This suggested that enzyme is rigid and does not change shape.

What is the lock and key hypothesis?

The lock and key hypothesis is that the substrate and the active site match each other in 2 ways - structurally - chemically

Transition state

The reactive condition of a substrate after activation energy has been provided

Explain how enzymes add chemical groups to catalyze reactions

The side chains of amino acids in the active site transfer hydrogen ions to or from the substrate to destabilize bonds

Active site

The special region on the surface of the enzyme where the substrate binds and catalysis occurs

Induced fit

When an enzyme changes shape after binding to a substrate

What are the steps of the lock and key hypothesis?

The steps of the lock and key hypothesis are: a) there is a large globular protein enzyme b) is has an active site where the substrate combine to the enzyme c) the substrate then fits into the enzyme d) the sum is now the activated complex. the substrate is weakened to all for the reaction e) the unchanged enzyme is then re-used at low concentrations f) there are then the products of the reactions that leave the enzyme active site after going through the reaction

How is the substrate and the active site matched chemically according to the lock and key hypothesis?

The substrates that are not chemically attracted to the active site won't be able to react.

Metabolism

The sum of all catalyzed biochemical reaction occurring in an organism at a given time

Enzyme-substrate specificity

The term used to describe how enzymes only catalyze one biochemical reaction

Enzyme substrate complex (ES)

The term used to describe the active site once substrates have bonded to it

Most enzyme-catalyzed reactions occur in...

Water This way, all of the particles can move separately

Effect of Denaturation on Enzyme Activity

like all proteins, enzyme structure can be modified by external factors such as high temperatures and extreme pH - these factors disrupt the chemical bonds which are necessary to maintain the tertiary structure of the enzyme - resulting in loss of shape/function

Lactase

the enzyme responsible for catalysing the split of lactose into galactose and glucose.

low specificity

the enzyme will bind with a range of related substrates (e.g. lipases hydrolyze any fatty acid chain)

high specificity

the enzyme will only bind with a single type of substrate

lock and key model

the first theory of the action of an enzyme binding to a substrate

activation energy

the minimum quantity of energy which the reacting species must possess in order to undergo a specified reaction

esterase

the name of a hydrolase enzyme that splits esters into an acid and an alcohol in a chemical reaction with water called hydrolysis

amylase

the name of the enzyme that helps digest carbohydrates

lactase

the name of the enzyme that is produced by the body to break down lactose

lipase

the name of the enzyme which breaks down fats so they can be absorbed in the intestines

protease

the name of the enzyme which breaks down proteins and peptides

Active site of an enzyme

the region of an enzyme that attaches to a substrate

Active site

the specific portion of an enzyme that attaches to the substrate.

Substrate

the substance on which an enzyme works.

Enzymes are proteins and denaturation is a key

to how enzyme activity is affected by temperature and pH