C1.1 Enzymes and metabolism

Define catalyst

A substance is a substance that increases the rate of chemical reaction

What is the role of enzymes in chemical reactions ?

Enzymes are biological catalysts, they speed up biochemicals reactions

What do enzymes do ?

Convert substrates into products

What's an example of an inorganic catalyst ?

Platinum
- used to help convert unburned hydrocarbons in exhaust gases to carbon dioxide and water

Define metabolism

network of interdependent and interacting chemical reactions that occurs in living organisms

Where do reactions occur ?

Most occur in cells but there are some extracellular reactions such as digestion

Define specificity

Each enzyme catalyses one specific reaction or a specific group of reactions

How is control of metabolism regulated by enzymes ?

If a cell produces an enzyme it can drive a reaction that would otherwise happen slowly

What mechanisms are there for stopping enzymes ?

Particular enzymes can be stopped from working if a reaction is not required for a while

Compare anabolic and catabolic reactions

Anabolic reactions build up smaller molecules into larger ones using energy whereas catabolic reactions breaks down larger molecules and releases energy

What type of reactions are anabolic reactions?

Condensation reactions that require energy ( from ATP ) producing macromolecules from monomers

Give examples for 3 anabolic reactions

- protein synthesis by ribosomes ( translation )
- DNA synthesis ( replication )
- Synthesis of complex carbohydrates

Give examples for 3 catabolic reactions

- digestion of food
- cell respiration
- digestion of complex carbon compounds

Outline properties of globular proteins

- 3D structure
- irregular amino acid sequences
- spherical
- soluble
- sensitive to changes in temperature and pH

What is the relationship between enzyme structure and specificity ?

Each enzyme is specific to a reaction. The structure of the active site of the enzyme and the substrate are dependent on each other. This allows the substrate to bind to the enzyme while most other substances can't

Outline the stages of enzyme catalysis of a chemical reaction

A substrate will undergo random movements until it approaches the enzyme. The chemical properties of an enzyme surface will attract the substrate towards the active site. Bonds will cause the substrate to turn into its products and the products will then detach.

Describe the induced fit model of enzyme binding.

When the active site and the substrate interact the bond lengths and angles of both to change which alters the 3D shape

What do changes to the substrate allow ?

Make it easier for the bonds within them to break and new bonds to form converting substrates into products

What is substrate active site collisions ?

When a substrate and active site come together

Explain the role of random collisions in the binding of the substrate with the enzyme active site

Both the substrate and the enzyme will be randomly travelling at altering directions. The molecules will occasionally come into contact with each other. Successful collisions are the ones in which the substrate and active site are aligned.

What variation is there in the molecular motion of substrates and enzymes ?

- Many happen in cytoplasm and both molecules are dissolved in water and therefore free to move
- Some substrates are large and don't move much in these cases the enzyme will move in relation to the substrate
- Some enzymes are embedded in membranes and cannot move ( immobilized ) so the substrate has to move

What is enzyme substrate specificity ?

The shape and chemical properties of an enzymes active site allow substrate molecules to bind but not other substances

Discuss variation in specificity of different enzymes

Some enzymes are very specific and always binds to the same singular substrate.
Whereas some enzymes can catalyse any molecule in a certain group ( eg. any hexose sugar )

Define denaturation

The irreversible, structural change in an enzyme that makes it unable to catalyse due to the substrate no longer fitting its active site.

What does the enzyme structure depend on ?

Relatively weak interactions between amino acids within the protein

Outline the causes and effects of denaturation on enzyme structure and function

Causes: heat and acidity
Effects to active site: prevent binding of substrates, prevent catalysis after binding

What is the acidity in enzymes due to ?

Due to the presence of hydrogen ions

Explain the effect of temperature on rate of enzyme activity

When heated particles gain kinetic energy and therefore move around quicker and the chance of active site to substrate collision is increased which increases enzyme activity.

Enzyme activity can also decrease because as they are heated the bonds vibrate more and the bonds are more likely to break which causes structural changes

Explain the effect of pH on rate of enzyme activity

Enzymes have an optimum ph which they're activities highest if pH increases or decreases from the optimum, Ionic bonds between amino acids in the enzyme are altered this will cause the structure of the enzyme to change.

What does it mean that the pH scale is logarithmic ?

Each unit of pH is 10 times more or less acidic than the next

Explain the effect of substrate concentration on rate of enzyme activity

If the concentration of substrate molecules increases, more collisions will occur more frequently and the rate at which the enzyme catalyzes reactions will increase

However if substrate concentration increases, the rate at which catalysis occurs decreases as more active sites will be occupied

Identify the independent variable in enzyme catalysed reactions

The factor being investigated ( manipulated )

temperature substrate concentration, enzyme concentration or pH

Identify the dependent variable in enzyme catalysed reactions

the results of an experiment ( responding )

The quantity that is measured to calculate the reaction rate

Identify the control variable in enzyme catalysed reactions

Factors that are kept constant

All factors apart from the independent variable

State the unit for enzyme reaction rate

The reaction rate is the amount of reaction over time.

Amount of reaction / per unit time.

State two methods for determining the rate of enzyme reaction rates

1. Allow reaction to happen for a set amount of time and measure the amount of substrate used or product

2. ​Start with known amount of substrate and measure time taken for all substrates to convert to products

Describe three investigative techniques for measuring the activity of an enzyme

Define activation energy

Energy required to reach the transition state before substrates are converted to products

What is activation energy used for ?

Break bonds in substrate molecules to form products

Explain the role of enzymes in lowering the activation energy of a reaction

It weakens the bonds so when it binds to the active site less energy of needed to break it

Compare the location of synthesis of enzymes used within and outside of a cell

Extracellular enzymes are synthesized by ribosomes attached to the endoplasmic reticulum whilst intracellular enzymes are synthesized by free ribosomes in the cytoplasm

What are extracellular enzymes ?

Exoenzymes - enzymes that are released from the cell and work outside it

What are intracellular enzymes ?

Enzymes that act within cells

State an example of an intracellular metabolic reaction

Glycolysis
This reaction is catalyzed by the enzyme hexokinase in the cytoplasm

State an example of an extracellular metabolic reaction.

Digestive system where solid food is digested by extracellular enzymes then passed through the plasma membrane to enter cells

How do unicellular heterotrophic archaea , bacteria and fungi take in macromolecules ?

They secrete exoenzymes that work outside the cell to convert the macromolecules into monomers which can then be absorbed across the plasma membrane

How is heat energy generated by the reactions of metabolism

The products contain less energy than the reactants the additional energy is converted to heat

Describe how birds and mammals maintain a body temperature greater than that of their environment

They use heat generated by metabolism to maintain a temperature greater than that of their environment

Give an example of maintaining temperature using heat generated by metabolic reactions

Emperor Penguins huddled together to use the metabolic heat released by their neighbors

State the reason for metabolic pathways.

They allow for a greater level of regulation

How can mammals raise their overall metabolic rate when basal metabolism doesn't release enough energy ?

Shivering - involuntary muscle contractions

Mammals with brown fat tissue will have large numbers of mitochondria that carry out uncoupled respiration which allows them to generate heat by oxidizing substrates without producing ATP

Compare linear metabolic pathways with cyclical reaction pathways.

Linear sequences our chain reactions with a distinct beginning and end whereas cycles involve the end product starting the next cycle these are less common than linear

State an example of a linear metabolic pathway

Chain reactions

Glycolysis is nine different chemical reactions that are catalyzed by nine different enzymes one molecule or substrate is converted to one molecule of product this is then the substrate for the next reaction in the chain

State an example of a cyclic metabolic pathway.

Every intermediate is a product of one reaction and a substrate of another reaction

Outline the structure and function of an allosteric site

A second active site or a difference specific substance can bind and unbind

Define enzyme inhibitor

Substances that bind to enzymes and lower their activity as it prevents catalysis

What do allosteric sites allow ?

The activity of an enzyme to be regulated

Describe mechanism of non-competitive enzyme inhibitors.

Substances that inhibit an enzyme by binding to the allosteric site rather than the active site

Describe mechanism of competitive enzyme inhibitors.

They bind to the active site of an enzyme meaning the substrate cannot bind and the enzyme cannot catalyze its reaction.

They are structurally similar to the enzyme

Outline the function of statins as an example of a competitive inhibitor.

They are used to treat high blood cholesterol statins bind to the active site of the enzyme HMG-CoA reductase this enzyme catalyzes a reaction used to synthesize cholesterol if statins lower the rate, less cholesterol will be produced by the body

Explain why the rate of reaction with increasing substrate concentration is lower with a non-competitive inhibitor compared to a competitive inhibitor.

If inhibitor concentration is low and substrate concentration is increased the extent of inhibition will reduce until the enzyme is uninhibited
With more substrates than inhibitors the substrates usually bind to the active site first
However with non-competitive inhibitors, increases in substrate concentration does not prevent non-competitive inhibitors from binding to the allosteric site

Outline the mechanism of feedback inhibition

The product of the last reaction in the pathway (end product) inhibits the first reaction

Outline the benefit of feedback inhibition

The products of the intermediate steps in the metabolic pathway do not accumulate in the cell if the end product is not being used

Compare reversible and irreversible enzyme inhibition

Reversible inhibition can release inhibitors and be used by substrates

Irreversible inhibitors bind forever

Outline the cause of mechanism-based inhibition.

If irreversible molecules such as heavy metals bind to the enzymes active site and becomes permanently bound by the formation of a covalent bond

Outline the consequence of mechanism-based inhibition

A stable inhibitor enzyme complex is formed that can never work as a catalyst again