Proteins and Enzymes Flashcards
What is the monomer that proteins are made from?
Amino acids
amino acids are combined to from polypeptides, many polypeptides combine to form proteins
What is the structure of an amino acid?
- Central Carbon atom
- Amino group (H2N)
- Carboxyl group (COOH)
- Hydrogen atom (H)
- R group
Each amino acid has a different R group
What is the bond between amino acids?
Peptide bond
How does a peptide bond form?
Condensation reaction which removes a water molecule (made from combining an -OH from the carboxyl groups of amino acid A with the -H from the amino group of amino acid B) to form a peptide bond.
What is the primary structure of proteins? + how are they formed
Polypeptides - formed through many condensation reactions so many amino acid (monomers) are joined together through polymerisation.
The sequence of amino acids in a polypeptide chain is a proteins primary structure.
What does primary structure determine?
The shape and therefore function of a protein. A change in one amino acid can lead to a change in shape of the protein.
-> shape is specific to function
What is the secondary structure of proteins? + how is it formed
There are weak hydrogen bonds between the amino acids that make up a polypeptide, which causes a long polypeptide chain to be twisted into a 3D shape called an alpha helix.
What is the tertiary structure of proteins?
Alpha helix can be twisted and folded to form a more complex and specific 3D structure of a protein which is the tertiary structure of a protein.
What are the bonds which maintain a tertiary structure?
Disulfide bridges- Strong and not easily broken
Ionic bonds- Formed between any carboxyl and amino groups which do not form peptide bonds, easily broken by pH changes
Hydrogen bonds- easily broken
What is the quaternary structure of proteins?
Large proteins which form complex molecules containing a number of polypeptide chains linked in different ways. There can also be a non-protein group within the molecule (like iron containing harm group in haemoglobin|)
What determines the 3D shape of a protein?
Sequence of amino acids (primary structure)
What is the test for proteins?
Biuret test- detects peptide bonds
- Place sample test tube and add an equal volume of hydroxide solution at room temperature
- Add drops of dilute copper sulphate solution and mix
- Purple solution indicates the presence of peptide bonds. If no proteins are present, solution will stay blue
What are the two basic molecular shapes of proteins?
Fibrous Proteins (like collagen) - structural functions
Globular proteins (like enzymes and haemoglobin) - metabolic functions
What do fibrous proteins form?
Long chains that run parallel to each other
What is the structure of collagen?
- Primary structure- unbranched polypeptide chain
- Secondary structure- polypeptide is tightly wound
- Lots of Amino acid
- Tertiary structure- chain is twisted into a second helix
- Quaternary structure- 3 polypeptide chains which are wound together like a rope
Where is collagen found and what is its function?
Found in tendons, these join muscles to bones. When muscles contract the bone moves to the direction of the contraction.
Why is collagen’s quaternary a suitable molecule for a tendon?
Individual polypeptide chains in fibres are held together by bonds between amino acids of adjacent chains.
What is an enzyme and what does it do?
Globular proteins which lower the activation energy for a reaction to take place.
What is the structure of an enzyme?
Tertiary structure - have a specific 3D shape due to their sequencing of amino acids in their primary structure
Active site is specific and made up of amino acids
Substrate fits into active site to form an enzyme-substrate complex
What is the induced fit model of enzymes?
Enzyme can change shape in order to fit substrate.
Enzyme colliding with a substrate is a change in the environment which causes a change in shape
Enzyme puts strain on substrate when changing shape, causing bonds to be distorted and activation energy to be lowered (needed to break the bond)
What are the stages of the induced fit model?
Enzyme-substrate molecule->
Enzyme-substrate complex->
Enzyme + product molecule
What is the lock and key model?
A substrate will only fit the active site of one particular enzyme
They both fit each other exactly
What are the limitations of the lock and key model?
Enzymes structure is not rigid, as suggested in the model, it is flexible and will change shape when other molecules bind to it, at places other than the active site therefore the induced fit model is more accurate.
What factors are needed for an enzyme to work?
- Needs to come into physical contact with substrate
- Have an active site that fits the substrate
How are enzyme-catalysed reactions measured?
(How long the reaction takes)
- The formation of products of reaction
- Disappearance of the substrate
Explain an enzyme-catalysed reaction graph
- Lots of substrate at first but no product
- Therefore it is easy for substrate molecules to come into contact with empty active sites/enzyme molecules
- All enzyme active sites are filled with substrates, which are rapidly broken down into products
- This decreases substrate concentration but increases product concentration
- The more the reaction goes on, there less substrate but more product
- So it is more difficult for enzyme-substrate complexes to form
- As a result, it takes more time for substrate molecules to be broken down by the enzyme so rate of disappearance/formation slows and graph begins to level off
- Rate of reaction continues to slow down until there is no substrate left, so the graph levels off as no new product can be produced
How is rate of change measured?
- Draw a tangent on curve
- Find the gradient using the straight lines which form a right angled triangle (change of y / change in x)
How does temperature affect enzyme action?
- Rise in temperature increases kinetic energy of molecules
- Therefore molecules move around and collide with each other more often
- There are more effective collisions and thus more enzyme-substrate complexes being formed
- As temperature begins to increase more, hydrogen bonds begin to break, causing a change in shape. At around 60 C, the enzyme becomes denatured.
How does pH affect enzyme action?
pH - measure of hydrogen ion concentration
Increasing/decreasing pH reduces the enzyme action
-Change in pH alters the charges on amino acids in primary structure of enzyme so an enzyme-substrate complex cannot be formed as the active site changes shape.
How does enzyme concentration affect the rate of reaction?
- Increase in amount of enzyme, increases the rate of reaction as long as there is enough substrate to bind to form an enzyme substrate complex.
- This is because there is always more substrate than enzymes so excess substrate can be acted upon by increasing the concentration of enzymes
What happens if the substrate is limiting?
The increase in enzyme concentration will not affect the rate of reaction and so graph will level off
How does substrate concentration affect the rate of enzyme action
- The rate of reaction increases as substrate concentration increases
- This is because at low substrate concentrations, active sites are not working at full capacity but as more substrate is added, more active sites are filled until they are working as fast as possible
What happens when all active sites are filled but more substrate is added ?
The rate of reaction does not change, there will be an excess of substrate so the graph will level off.
What are enzyme inhibitors?
Substances which directly and indirectly interfere with the functioning of the active site and therefore reduce activity.
What is a competitive inhibitor?
Bind to active site of an enzyme
What is a non competitive inhibitor?
Bind to the enzyme on a part other than the active site
How do competitive inhibitors work?
They have a molecular shape similar to substrate so they are able to fit the active site of the enzyme. Therefore they have to compete with substrates for available active sites.
They are not permanent
What happens when substrate concentration is increased?
The effect of a inhibitor is reduced
What happens when the concentration of competitive inhibitor increases?
The longer it will take for substrates to occupy all active sites
How do non-competitive inhibitors work?
Attach themselves to a part of the enzyme which is not the active site
This changes the tertiary structure of the enzyme and therefore the active site so substrate molecules are no longer able to fit it
As a result the enzyme cannot function + fewer enzyme substrate complexes
Does an increase in substrate concentration have an effect on the non-competitive inhibitor?
No because they are not competing for the same site
