Unit 3 - Practicals Flashcards
What is an enzyme?
It is a protein molecule that acts as a catalyst in a biochemical reaction.
What are proteins made of?
Proteins are made of amino acids.
What is the structure of an amino acid molecule?
In an amino acid, there is a central alpha carbon with four chemical groups attached to it:
- a hydrogen atom
- an amino group
- a carboxyl group
- a variable R group (side chain).
How many R groups and amino acids are there?
There are 20 different R groups and so there are 20 different amino acids.
Draw the structure of an amino acid molecule.
See revision guide pg 59 for diagram.
How do amino acids join together?
- A condensation reaction (water is produced) occurs between two amino acids.
- H2O molecule removed via condensation.
- A branch forms between the two amino acids linked by a peptide bond.
Draw the condensation reaction between two amino acids.
See revision guide pg 59 for diagram.
What is a dipeptide?
It is formed by two amino acids linked by a peptide bond.
What do amino acids form when joined together?
- Lots of amino acids joined together form long-chain molecules i.e. polymers.
- 3 amino acids form a tripeptide.
- Many amino acids join to form a polypeptide.
- A polypeptide with more than 50 amino acids is called a protein.
What is the active site?
It is the part of the enzyme where the biochemical reaction takes place. The active site has a specific shape that only the substrate will fit.
What are the lock and key mechanisms of enzyme action?
- The substrate enters the active site of the enzyme.
- The substrate binds to the active site of the enzyme.
- Only specific substrates will bind to a particular enzyme’s active site.
- After the reaction, the substrate is broken down into products and is released.
- The active site is then available to catalyse further reactions.
What happens when an enzyme catalyses a reaction?
When an enzyme catalyses a reaction, the reaction takes place on the active site of the enzyme.
What is the active site made of?
The active site consists of a small number of amino acids which form a specific shape because of the protein’s secondary and tertiary structure.
What is the role of the enzyme?
Enzymes work specifically to catalyse one type of biochemical reaction e.g. the enzyme, amylase only breaks down starch.
What can cause an enzyme to denature?
- If the temperature is too high, e.g. above 40°C, the hydrogen bonds will break.
- This means the enzyme changes its shape.
- So the active site loses its shape.
- The enzyme is denatured and can no longer act as a catalyst.
What is the secondary structure of enzymes?
- Secondary structure:
- The secondary structure is made of polypeptide chains which are arranged into alpha-helix or beta-pleated sheets.
- Secondary structures are held together by hydrogen bonds (weak bonds) between the -NH of one peptide link and -C=O of another amino acid.
What is the tertiary structure of enzymes?
- Tertiary structure:
- The secondary structure folds into three-dimensional shapes to make the tertiary structure.
- The tertiary structure is held together by other types of bonds e.g. ionic bonds.
- It is the tertiary structure that gives the enzyme the shape of the active site.
Enzymes:
Biological catalysts
What is a catalyst?
It is a substance that speeds up a reaction and is left unchanged at the end of the reaction.
What is the collision theory?
- The collision theory states that for a reaction to occur:
- particles must collide.
- particles must have enough energy to react.
- The energy of the collision depends on the speed of the particle and the angle they collide.
What is activation energy?
It is the minimum energy needed for particles to react.
What happens when the enzyme lowers the activation energy needed?
- This causes:
- more particles to have the required energy to react.
- there are more successful collisions.
- there is a faster reaction.
What is the catalytic activity?
It is the increase in the rate of a reaction caused by the inclusion of an enzyme.
What is a substrate?
It is the molecule that is affected by the action of the enzyme.
What is the active site?
The active site is the area of an enzyme where a substrate binds.
What is denatured?
It is when the tertiary structure of the enzyme is changed.
How to measure the rate of reaction?
- Enzyme reactions can be measured by:
- measuring decrease in substrate.
- measuring increase in product.
- It is easier to measure the increase in product as the starting measurement for the product is 0.
Why is it important to record the initial rate of an enzyme-catalysed reaction?
It is important to record the initial rate of reaction because the rate will decrease as the substrate is used up and its concentration decreases.
Enzymes:
Factors affecting activity
What are the factors affecting the activity of enzymes?
- Temperature
- pH
- Substrate concentration
- Enzyme concentration
What happens if certain factors are not present during an enzyme-catalysed reaction?
If these factors are not present then the reaction may slow down or not work at all.
How does temperature affect the rate of reaction of enzymes?
As the temperature increases up to the optimum temperature, the rate of reaction also increases.
What is the optimum temperature?
It is the temperature at which an enzyme works the fastest.
What happens when the enzyme is below the optimum temperature?
- Particles have less energy.
- There are fewer collisions.
- There is a slower reaction.
What happens when the enzyme is above the optimum temperature?
- Hydrogen bonds in enzyme break.
- Enzyme and active site lose their shape so the enzyme can no longer do its job.
- It has been denatured.
Draw a graph showing the effect of temperature on enzyme-catalysed reaction.
See revision guide pg 62 for graph.
What is the optimum temperature for enzymes in humans?
For enzymes in humans, the optimum temperature is 40°C.
What is the optimum pH for enzymes?
- It is between 7 and 8 as this is the pH of most body cells and blood.
- However, some enzymes have a more extreme optimum pH e.g. pepsin, a stomach enzyme that has an optimum pH of 1.
How does pH affect the rate of reaction of enzymes?
- pH affects the charge on the active site.
- If pH changes then the charges on the active site change and the substrate may no longer bind to it.
- The shape of the active site is very sensitive to pH.
Draw a graph showing the effect of pH on enzyme-catalysed reactions.
See revision guide pg 62 for graph.
How does substrate concentration affect the rate of reaction of enzymes?
If there is an increase in substrate concentration, then there is an increase in the rate of collisions which increases the rate of reaction.
How does enzyme concentration affect the rate of reaction of enzymes?
If there is an increase in enzyme concentration, then there is an increase in the rate of collisions which increases the rate of reaction.
What happens if the substrate concentration is too high?
- If the substrate concentration is too high then there will be no more active sites for them to bind to.
- At this point, increasing the substrate concentration will no longer affect the rate of reaction.
What happens if the enzyme concentration is too high?
If the enzyme concentration is too high, there are too many free available active sites compared to substrate molecules so the rate of reaction will no longer increase.
Draw a graph showing the effect of substrate concentration on enzyme-catalysed reaction.
See unit 3 enzymes 3 video on youtube for graph.
Draw a graph showing the effect of enzyme concentration on enzyme-catalysed reaction.
See unit 3 enzymes 3 video on youtube for graph.
Practical 2:
Diffusion of molecules
What is diffusion?
Diffusion is the movement of a substance from an area of high concentration to an area of low concentration.
Where can diffusion occur?
- Diffusion can happen in liquids and gases because their particles are moving randomly from place to place.
- It can also occur across a membrane as long as the molecules are small enough to pass through the membrane then the diffusion will occur.
What is dynamic equilibrium?
There will be the same number of molecules in areas of low concentration and high concentration so they are evenly spread. This is described as dynamic equilibrium.
What are the factors affecting rate of diffusion?
- Size of molecules = Larger molecules move slowly than smaller ones so the rate of diffusion decreases.
- Temperature = At higher temperature, the energy of molecules increases, so they move faster, increasing the rate of diffusion.
- Distance through a substance = The greater the distance that the molecules have to travel through a substance, the slower the rate of diffusion.
- Surface area = As surface area increases, the area of which molecules can spread is increased so the rate of diffusion increases.
- Shape of the surface of the molecule = The shape of the surface of the molecule that is diffusing can affect the rate of diffusion e.g. shape of a cell can affect its surface area which affects the rate of diffusion of molecules in or out of cell.
What is the kinetic theory?
It explains the properties of different states of matter.
What are the properties of solids?
- Fixed shape.
- Particles are arranged close together with a regular pattern so they cannot flow.
- The particles vibrate in a fixed position.
- It cannot be compressed or squashed.
What are the properties of liquids?
- It takes the shape of a container.
- Particles are arranged close together in a random motion so they can flow and move randomly.
- Particles can move around each other.
- Cannot be compressed or squashed.
