Biological molecules (PROTEINS) Flashcards
Describe the biuret test for proteins
1) Add sodium hydroxide to test solution
2) Add copper sulfate
Positive test result - solution turns from blue to lilac
What monomer is the polymer protein formed from
Amino acids
Describe the structure of amino acids
Horizontal: N-C-C
Attached to the N - two Hs
Attached to C - one R and one H
Attached to C - double bond O and another OH
What makes up an amino acids
Amino group - H2N
Carboxyll group - COOH
What does the R mean in an amino acid
Variable group
What is a dipeptide
2 amino acids joined together via a condensation reaction
What is a polypeptide
2 or more amino acids joined together via a condensation reaction
What is the bond called between amino acids
Peptide bond - forms between the OH of carboxyll and H of amino group
What are the 4 levels of proteins
Primary structure
Secondary structure
Tertiary structure
Quaternary structure
What is the primary structure of a protein
The type, number and sequence of amino acids linked by peptide bonds
Describe the secondary structure of a protein
The folding shape that the polypeptide chain forms as a result of hydrogen bonding into either a alpha helix or beta pleated sheet
Give the two types of secondary structure
Coil into an alpha helix
Fold into a beta pleated sheet
Describe the tertiary structure
The overall specific 3d shape of the polypeptide chains formed by further folding
Give the 2 types of tertiary structure proteins
Globular proteins
Fibrous proteins
Give the 3 bonds present in the tertiary structure
cHydrogen bonding
Disulphide bonding - form between cysteine molecules (specifically the sulphur atoms)
ionic bonds - form from ionised amine and ionised carboxyll group
Also: hydrophobic interactions
Describe the quaternary structure
(not all proteins have this, although all proteins have the first 3 structures)
protein made from more than 1 polypeptide chains in the tertiary structure
Give an example of a protein that has a quaternary structure
Haemoglobin
What happens if the primary structure of an enzyme is changed
Structure is determined by the position of amino acids. If the primary structure is changed, so is the sequence of amino acids in the polypeptide so it will cause the hydrogen/ ionic/ disulphide bonds of tertiary structure to change location so the overall 3d shape changes. This changes the shape of the active site so the enzyme is no longer functional
What is an enzyme
Enzymes are tertiary structure proteins which catalyse reactions, providing an alternative pathway with a lower activation energy
Enzymes are also globular
Describe the lock and key model for enzymes
The enzymes active site is complimentary to the substrate.
Enzyme and substrate collide and bond to form an enzyme substrate complex
Substrates bonds get distorted and strained, therefore lowering the activation energy
Products are then formed and released so enzyme returns to its original shape
What makes the active site unique in an enzyme
The specific folding and bonding in the tertiary structure of the protein
When an enzymes active site bonds to a substrate, what does it form
An enzyme substrate complex
Describe the induced fit model of an enzyme
The enzymes active site is initially not complimentary to substrate
Once substrate and enzyme collide and bond to form an enzyme substrate complex, the active site changes shape so its complimentary to the substrate
This puts strain on the substrates bonds, distorting and weakening them, therefore lowering the activation energy
Products are then formed and released so enzyme returns to its original shape
Which model is the accepted model for enzyme action
The induced fit model
Enzymes are….
Specific - usually only catalyse one type of reaction
What happens if the primary structure of an enzyme is changed
The sequence of amino acids within the polypeptide chain of the enzyme will change
This will change the location of the ionic / disulphide / hydrogen bonds within the tertiary structure
This changes the shape of the active site
Therefore enzyme substrate complexes will not be able to form as the substrate is not complimentary to active site shape
Enzyme is no longer FUNCTIONAL
Give the effect of temperature on enzyme activity
If temperature is too low - there is not enough kinetic energy for successful collisions between enzyme and substrate so less enzyme substrate complexes form
Optimum temperature - many successful collisions and many enzyme substrate complexes due to more kinetic energy
If temperature is too high - enzymes denature and active site changes shape so enzyme substrate complexes cannot form
What happens to the bonds holding the enzyme in shape once an enzyme denatures
They break due to the vibration of the enzyme
Give the effect of pH on enzyme activity
Too high OR too low - enzyme can denature, active site change shape and less enzyme substrate complexes forming
—> this is because the changed OH- or H+ ions can interfere with the ionic and hydrogen bonds found in the enzymes tertiary structure
Do all enzymes have an optimum pH of 7
No
—> all enzymes have different optimum pH it depends on where they are naturally occurring
When do you use the -log[H+] equation
-log[H+] is used to calculate the pH from the hydrogen ion concentration of a solution
At low substrate concentration, what is the limiting factor
Substrate concentration - not enough substrate molecules to collide with enzymes
Describe the effect of increasing substrate concentration on enzyme activity
Higher the substrate concentration = faster rate of reaction
—> more substrate molecules so more collisions between enzymes active site so more enzyme substrate complexes
—> This is only true up to the ‘saturation point’
What happens at the saturation point / V max for a graph investigating the rate of reaction with increasing SUBSTRATE concentration
The line plateaus as enzyme concentration becomes the limiting factor.
—> all the active sites become occupied (CANNOT say used up)
NOTE: in exams, specify this concentration
Describe the effect of enzyme concentration on enzyme activity
Increasing enzyme activity increases the rate of reaction as substrates are more likely to collide with enzymes forming enzyme substrate complexes
—> however this is only true for a certain point - if the substrate concentration does not increase then enzyme concentration has no affect on rate or reaction
—> there is empty active sites due to insufficient substrate concentration so less enzyme substrate complexes
What does the graph of rate of reaction against increasing ENZYME concentration initially show
Initially shows a linear relationship ( a straight line)
—> can use the gradient to determine the rate of reaction at a specific point
What will a graph show if enzyme / substrate concentration increases alongside substrate / enzyme concentration
A straight line -no plateau
What do inhibitors do
Stop the enzyme from functioning and producing product
What are the two types of inhibitors
Competitive
Non competitive
Describe how the competitive inhibitor works
Competitive inhibitor has similar shape to substrate and can bind to active site
This prevents enzyme substrate complexes from forming and reaction from occurring
What does increasing substrate concentration do to competitive inhibitors
Reduces the chance of competitive inhibitors from binding to enzymes active site as they can knock them out of the active site
NOTE: on a graph for rate or reaction, the line with no inhibitor and a competive inhibitor must end at the same point
Describe how non competitive inhibitors work
Non competitive inhibitors bind to the enzyme AWAY from the active site (called allosteric site)
This causes a change in the tertiary structure
This changes the shape of the active site so the substrate and enzyme can no longer bind as they are not COMPLIMENTARY
What happens to the rate of reaction if you increase substrate concentration with non competitive inhibitors
Nothing - there is no effect
regardless of how much substrate you add, the enzymes active site is no longer complimentary so enzyme substrate complexes cannot form
In a results table, which way do the dependant and independent variables go
Independent variable ( the one that changes) goes first ( on the left) and the dependant variable ( the actual results ) goes on the right
What is it called when an enzyme breaks down the substrate into products
we say the substrate has been HYDROLYSED (or digested) into its products
When bread becomes stale, the structure of some of the starch is changed. This changed starch is called retrograded starch.
Scientists have suggested retrograded starch is a competitive inhibitor of amylase in the small intestine.
Assuming the scientists are correct, suggest how eating stale bread could
help to reduce weight gain
The similar shape of the competitive inhibitor stops enzyme substrate complexes from occurring so less hydrolysis of starch into maltose so less digestion of glucose
Formation of an enzyme-substrate complex increases the rate of reaction.
Explain how.
It reduces activation energy as substrates bonds become stressed, distorted and bended
How to work out initial rate of reaction from a graph
Draw a tangent when t = 0. Work out gradient of tangent. Remember to add unit ( unit will be unit of y divided by unit of x)
