IB Biology C1.1 Enzymes and Metabolism HL

What is a catalyst? What are enzymes?

Catalyst - substance that increases the rate of a chemical reaction but is not used up by the reaction; can catalyze reactions many times

Enzymes - biological catalysts, proteins made by cells to speed up biochemical reactions

What would happen if cells didn't make enzymes?

Life-dependent chemical reactions would happen too slowly for life to continue.

What is metabolism? How do they occur?

Sum of all body's chemical reactions, complex network of interdependent and interacting chemical reactions occurring in living organisms. Can be linear chains or cycles

Almost ___ _______ ____ are catalyzed by what?

all metabolic reactions are catalyzed by enzymes.

What is enzyme specificity and what does it cause?

Enzymes are specific to one reaction or a group of reactions. Because of enzyme specificity, many different enzymes are required by living organisms. Control over metabolism and by making more or less of a specific enzyme they can control the rate of reaction.

Compare and contrast ANABOLIC vs. CATABOLIC [5]

Description

Anabolic-build up smaller molecules into larger ones, Catabolic-break down larger molecules into smaller ones

Energy

Anabolic - requires energy

Catabolic - releases energy

Condensation or Hydrolysis

Anabolic-condenstaion of monomers into macromolecules

Catabolic-Hydrolysis of macromolecules into monomers

Examples

Anabolic- protein synthesis, glycogen formation, and photosynthesis

Catabolic- digestion of food, cell respiration

More Detailed Example

Anabolic- carbon dioxide and water are combined to produce glucose using light energy in PHOTSYNTHESIS

Catabolic-glucose is broken down into carbon dioxide and water, producing ATP, CELL RESPIRATION

What shape are enzymes? Structure?

Globular proteins with a precise three dimensional structure and chemical properties

What is the region called where reaction is catalyzed?

The active site is where the substrate(s) bind to catalyze a reaction.

What are the 3 steps to enzyme catalysis?

1. The shape and chemical properties of the substrate and the active site match each other allowing the substrate to bind to the active site

2. While the substrate is bound to the active site, it's converted to products

3. The products are released leaving the active site free to catalyze another reaction.

The active site is composed of __ ____ what, but interactions between these within the overall 3-D structure ensure what?

a few amino acids, but the interactions overall ensure that the active site has the necessary properties for catalysis.

How would you describe a substrate's direction of movement? but, when a...

RANDOM, but when a substrate is close enough to interact, the chemical properties of the enzyme surface attract the substrate molecule toward the active site.

Define Induced Fit Binding. [3]

Interactions between the substrate and active site causes bond angles and bond lengths to be altered, changing the 3D moleuclar shapes of both substrate and active site.

Changes to substrate molecules allow bond breakage in turn converting substrates to products

products are detached from the active site and the enzyme reverts to its original state for more catalysis.

In liquid, molecules constantly are in what?

RANDOM MOTION

What is it called when a substrate comes together with the active site of an enzyme?

Substrate-active site collision

What will increase the rate substrate-active site collision?

If there is a higher concentration of substrate or enzyme molecules, the rate will increase (more opportunity for collision)

IF what increases, there is more kinetic energy in the system causing what?

Temperature increases, molecules will move more quickly increasing the rate of reaction.

There is some variation in the molecular motion of substrates and enzymes [3]

1. Can happen in the liquid of the cytoplasm and both the enzyme and substrate are free to move (substrate is usually smaller than enzyme, more movement)

2. Large substrate molecules are immobilized and the enzyme moves to it (DNA replication and transcription)

3. Enzymes are immobilized by being embedded in membrane, substrate moves to it

What property of the enzyme's active site allows substrate molecules to bind but not to other substances?

Enzyme-substrate specificity

Some enzymes are specific to __ substrate, while others are ___ specific and can bind to a variety of substrates.

one, less

Describe the effects of denaturation on enzymes.

Enzymes are proteins, so they can be denatured by heat, pH, salts, and heavy metals. Even if a small change happens far from the active site, interactions within the enzyme are likely to affect the active site. Binding will no longer work

What is pH? [3]

the measure of acidity due to the presence of hydrogen ions (protons).

LOWER pH indicates higher hydrogen ion concentrations and greater acidity

pH scale is logarithmic, reducing pJ by one unit makes it 10 times more acidic.

Describe the effects of temperature graph (enzymes) [3]

Particles are in random motion, and when heat is applied they gain kinetic energy causing rapid movement. The increase in kinetic energy increases the chances of a substrate colliding with the active site which in turn increases enzyme activity.

However, the likelihood of bonds breaking increases as temperature increases. Denaturation will no longer allow substrates to bind.

The highest temperature prior to denaturation is called the optimum temperature

Describe the effects of pH graph (enzymes) [3]

Most enzymes have an optimum pH at which their activity is highest

If pH is increased or decreased from optimum, ionic bonds are altered which can denature

Not all enzymes have the same optimal pH, wide range of optimum pH is due to the environment in which the enzyme works

Describe the effects of substrate concentration graph (enzymes)

If concentration of molecules is increased, substrate-active site collisions will occur more frequently and rate of reaction increase.

However there's a point where active sites will be all occupied until products have been released. As concentration increases, more sites are occupied and the rate of reaction plateaus and doesn't reach a maximum.

There's a transition state during chemical reactions, what is required to reach this state?

Activation energy is required to reach this transition state and is used to break bonds between substrate bonds.

An enzyme _______ for a reaction to occur

lowers the activation energy needed

Describe reactions without and with an enzyme [2 parts with 2 points (4)]

Without an enzyme

- The reaction is exothermic because there's a net release of energy

-the energy released as new bonds are made is GREATER than the activation energy needed to break bonds and reach transition state.

With an enzyme

-The net amount of energy released is unchanged but the activation energy is smaller. Bonds in the substrates are weakened as it binds to the active site, less energy needed to break

-rate of reaction increases

Compare and Contrast intracellular enzymes and extracellular enzymes [4]

INTRACELLULAR

synthesized by: ribosomes

where synthesized: free ribosomes in cytoplasm

where used: used inside the cell

examples: used for glycolysis and Krebs Cycle

EXTRACELLULAR

synthesized by: ribosomes

where synthesized: membrane bound attached to ER

where used: released from cell and work around it

examples: used for chemical digestion in gut

The conversion of energy from one form to another is never 100% efficient. In metabolic reactions , the _____ contain ____ what than the reactants.

products, less energy

What happens to additional energy?

converted to heat. Animals depend on this heat production for maintenance of constant body temperature.

Sometimes metabolism releases more heat, then what happens?

Body uses evaporative cooling to dissipate excess metabolic heat. In cold conditions human body will shiver to produce heat through muscle contraction

Most enzyme-catalyzed reactions cause what amount of change in a substrate?

SMALL change, large chemical transformations happen in sequences of small steps forming a METABOLIC PATHWAY

Define Linear and cyclical pathways.

Linear: Most metabolic pathways involve a chain of reactions. Glycolysis converts glucose into pyruvate, this metabolic pathway involves nine different chemical reactions

Cyclical: More unusually, reactions can occur in cycles. Every intermediate is a product of one reaction and a substrate of another. Examples include Krebs and Calvin cycle

What is the second active site called?

Allosteric site, which is where a different specific substance can bind and unbind.

Binding causes interactions within an enzyme that lead to what?[2]

CONFORMATIONAL CHANGES which alter the active site enough to prevent catalysis. Binding is reversible.

Allosteric sites allow the activity of an enzyme to regulated as well

What are non-competitive inhibitors?

Substances that inhibit an enzyme by binding to the allosteric rather than active site don't compete with substrates.

What are competitive inhibitors?

Substances that bind to the active site, distrupting the substrate's ability to bind and the enzyme can't catalyze

What are some characteristics of competitive inhibitors?

Structurally similar to the substrate so they can bind to the same active site. However, they are not converted into products and so remain bound for longer than the substrate.

What are Statins? example too

Medicines that use competitive enzyme inhibition. Ex. used to treat high cholesterol

Statins bind to the active site of an enzyme that catalyzes a reaction used to synthesize cholesterol in liver cells. As a result, it lowers enzyme activity producing less cholesterol

Compare and Contrast competitive and non-competitive inhibition [2]

If the inhibitor concentration is relatively low and substrate concentration is increased...

Competitive: the extent of inhibition will reduce until the enzyme is effectively uninhibited. With many more substrate than inhibitor, substrates almost always arrive at active site first

Non: increases in substrate concentration cannon prevent a non-competitive inhibitor from binding, and rate of reaction will be somewhat inhibited

What is feedback inhibition?

Regulatory system used by metabolic pathways to ensure that they produce enough of a substance but not too much. The product of the last reaction in the pathway, the end product inhibits the FIRST reaction

Having too little, too much; what affects feedback inhibition? [4]

-Inhibited enzymes have an allosteric site, and binding changes shape of the active site preventing catalysis

-NON-COMPETITIVE inhibition and also NEGATIVE feedback

-If too much of the end product is made, it will increasingly inhibit the first enzyme in the pathway. This switches OFF the whole pathway and prevents the synthesis of more end-product

-If too little of the end product is made there will be minimal inhibition/change. The metabolic pathway will be open to produce more end products.

Regulating a metabolic pathway example and importance

Regulation is efficient, and products do not accumulate if end product is not being used.

Conversion of threonine and isoleucine is an example of feedback inhibition.

-5 reactions amino acid threonine is converted to isoleucine

-As concentration of isoleucine builds it binds to allosteric site of first enzyme

-As a result its a non-competitive inhibitor

Inhibition can also be IRREVERSIBLE because....

Heavy metals such as mercury and lead are NON-SPECIFIC inhibitors of a wide range of enzymes because they bind IRREVERSIBLY to amino acid cysteine in the structure of the enzyme

Because of this, heavy metals are...

VERY TOXIC if they enter the body and are dangerous pollutants of the environment.

Targeting irreversible inhibitors do what?

Target one specific enzyme, and are structurally similar to the substrate, so they bind to the enzyme's active site.

Substrate converted to a product and released leaving the active site open, but inhibitors permanently bind to active site by the formation of a COVALENT BOND

What is mechanism-based intuition? [3]

STABLE INHIBITOR-ENZYME COMPLEX that can never work as a catalyst again

Causes harm to an organism because every molecule of inhibitor can permanently inactivate one enzyme molecule.

The inhibitor may kill an organism if the function of the inhibited cycle is vital

Outline the process of mechanism-based enzyme inhibition killing bacteria with penicillin [5]

- Transpeptidase cross-links strands of carbohydrate into one molecule that forms the entire cell wall

-When bacteria grows, one enzyme breaks these links. Transpeptidase remakes the links

-Penicillin is a mechanism-based inhibitor

-Penicillin binds to the active site of transpeptidase enzyme, preventing the substrate of the enzyme from binding. Penicillin forms a permanent covalent bond, binding IRREVERSIBLY

-The enzyme that breaks cross links in the bacterial cell wall works but the transpeptidase enzyme can't reform. The cell wall is weakened and bacteria are killed by lysis