3.1.4 Proteins

Question 1

What are amino acids?

Answer 1

Amino acids are the basic monomer units which combine to form a polypeptide. These are then combined to form proteins. The type and order of amino acids used determines the protein that is made.

The order of amino acids determines the structure of
the protein and therefore it’s properties and function.

100 amino acids have been identified of which 20 occur naturally in proteins and are common in all organisms

Simple: Basic monomer units to form polypeptides which then fold to form proteins
Have very specific order which determines function/properties of protein
20 occur naturally

Question 2

What do all amino acids have in common?

Answer 2

central carbon atom attached to four
different chemical groups:

Amino group (-NH2)

Carboxyl group (-COOH) the acidic
group

Hydrogen atom (-H)

R group (varies and is different for
each amino acid)

Question 3

How do dipeptides formed/peptide bonds?

Answer 3

Water is made by combining the –OH from the carboxyl group from one amino acid with an –H from the amino group of another amino acid
Water molecule is removed
The two amino acids become linked by a peptide bond between the carbon of one and the nitrogen of the other

Question 4

Primary structure e.g what is it, name of process/product, what it determines

Answer 4

Many amino acid monomers are joined together in a series of condensation reactions resulting in a polypeptide in a process called polymerisation
Different proteins contain different amino acid sequences
This sequence is the primary structure
The primary structure of a protein determines its ultimate shape and its function
A change in shape may result in a change in function.
A protein’s shape is specific to its function

Question 5

Secondary structure and two types of helix

Answer 5

There is –NH and –C=O on either side of every peptide bond
The hydrogen of –NH is +ve
The oxygen of –C=O is –ve
These 2 groups readily form weak hydrogen bonds causing the polypeptide chain to be coiled or folded
The resulting secondary structure depends on the arrangement of hydrogen bonds formed

alpha helix- coiled beta helix- folded

Question 6

Tertiary structure and what proteins between

Answer 6

The a-helices of the secondary protein structure can be twisted and folded even more to give the complex, and often specific, 3-D structure of each protein This is known as the tertiary structure. This structure is maintained by a number of diff bonds. Where the bonds occur depends on the primary structure of the protein.

 disulfide bridges - which are fairly strong and therefore nor easily broken. • 	 ionic bonds- which arc formed between any carboxyl and amino groups that are not involved in forming peptide bonds. They are weaker than disulfide bonds and arc easily broken by changes in pH. • 	 hydrogen bonds - which are numerous bur easily broken

cystines

Question 7

Quaternary Structure

Answer 7

Many proteins are made from more than one polypeptide chain.
The chains are simply linked together by interactions between polypeptide chains.
There may also be non-protein (prosthetic) groups associated with the molecules
An example of such a protein would be haemoglobin.

Question 8

Protein test

Answer 8

The Biuret Test - detects peptide bonds
Place sample in test tube and add equal volume of sodium hydroxide solution at room temperature
Add a few drop of very dilute copper (II) sulphate solution and mix gently
A purple colour shows a presence of peptide bonds (a protein)

NOTE: in exam just say Biuret Reagent

Question 9

Protein funct+ shape Fibrous

Answer 9

e.g Collagen
Structural function
Form long chains which run parallel to each other 
Simple secondary structure 
Insoluble in water

Question 10

Protein shape and function- Globular

Answer 10

Enzymes Haemoglobin
Metabolic (in reactions) function
Soluble in water
Complex secondary structure

Question 11

Why are reactions able to take place at normal body temperature and how?

Answer 11

Enzymes lower activation energy

the enzyme is flexible and can mould itself around the substrate in the way that a glove moulds itself to the shape of the hand.
The enzyme has a certain general shape, just as a glove has, but this alters in the presence of the substrate.
As it changes its shape, the enzyme puts a strain on the substrate molecule. This strain distorts a particular bond or bonds in the substrate and consequently lowers the activation energy needed to break the bond.

Question 12

Conditions for a reaction to occur naturally

Answer 12

Molecules need to collide with enough energy to break old bonds and form new ones

The energy of the products should be less than the energy of the reactants

A minimum amount of energy is needed to start the reaction. This is the activation energy

Question 13

Enzymes structure

Answer 13

Enzymes are globular proteins so their function is controlled by their complex 3D structure

Active Site-Made up of a few catalytic amino acids

The tertiary structure brings them together

The substrate binds here, the rest of the enzyme is support

Enzymes are specific- The substrate and complex are complementary

Combine to form enzyme-substrate complexes

The substrate is held by temporary bonds between
amino acids on active site and groups on substrate

Question 14

Lock and Key Model-

What limitations are there?

Answer 14

Lock and key model- A substrate will only fit the active site of one particular enzyme

Enzyme considered to be a rigid structure – scientists observed other molecules could bind to enzyme at sites other than active site and altered the activity of the enzyme
A flexible not rigid structure

Question 15

Induced Fit Model

Answer 15

The generally accepted theory

The active site forms as the enzyme and substrate interact

The proximity of the substrate leads to a change in the enzyme that forms the functional active site

The enzyme is flexible and can mould itself around the substrate (think glove and hand)!

The enzyme has a general shape but this changes in the presence of the substrate

As the enzyme changes its shape it puts a strain on the substrate molecule and distorts bonds 🡪 lowers the activation energy needed to break the bond

Question 16

Why is induced fit better?

Answer 16

It explains
How other molecules can affect enzyme activity
How the activation energy is lowered

Enzymes are sensitive to temperature and pH so a change in the enzymes environment is likely to change its shape

Question 17

Measuring enzyme-catalysed reactions: explain the graph

Answer 17

Lots of substrate but no product

Easy for substrate molecules to come into contract with active sites

All active sites are filled and the substrate is rapidly broken down

The amount of substrate decreases and there is an increase in the amount of product

There is less and less substrate and more and more product

Now more difficult for substrate molecules to come into contact – there are fewer and product getting in the way

Takes longer for the substrate to be broken down so the graph tails off

Rate of reaction continues to slow until there is so little substrate

The graph flattens because all the substrate has been used up

Question 18

Factors effecting enzyme action

Answer 18

Temperature, pH, substrate concentration, enzyme concentration

Question 19

Effect of temp on enzymes

Answer 19

Enzymes have an optimum temperature at which they work fastest In humans this is approx 37˚C

Kinetic energy- Increasing temperature increases kinetic energy.
Increases number of collisions.
Increasing rate of reaction.

Denaturation- Increasing temperature vibrates molecules violently breaks hydrogen bonds and other cohesive forces 3D shape altered
Active site no longer fits substrate
Approx 60˚C in humans

Question 20

Effect of pH on enzymes

Answer 20

H is a measure of hydrogen ion concentration

Each enzyme works best at a particular pH (optimum), normally 7.

A change in pH affects the charge of the amino acids at the active site.

What impact would this have? Change in pH can denature enzymes. The bonds maintaining the structure break so the shape changes

Question 21

Effect of substrate concentration

Answer 21

Low concentration There are not enough substrate molecules to occupy all of the active sites.
Therefore the rate of reaction is only half the maximum rate possible

Intermediate concentration Most of the active sites are filled as there are many substrate molecules. The rate of reaction is at its maximum (Vmax)

High concentration Although there are more substrate molecules, there is no change to the rate of reaction as all the active sites are full

Question 22

Effect of enzyme concentration

Answer 22

Enzymes are not used up in the reaction so can work efficiently at low concentrations

Once the active site has worked on a substrate it is free to work on another substrate molecule

At certain point, increase has no effect as already enough active sites to accommodate available substrates

Question 23

Competitive Inhibitors

Answer 23

Compete with substrate molecules

Have similar structure to substrate

Reduce number of enzyme-substrate complexes being formed.

Same final amount of product formed, it just takes longer.

If equal amount of substrate and inhibitor, rate is halved.

Increase in concentration of substrate reduces effect of inhibitor.

Question 24

Non-competitive inhibitors

Answer 24

Bind to enzyme away from active site – allosteric site.

Change the overall shape of the molecule including the active site.

There is no competition for the active site.

Reduce the amount of active enzyme molecules = decrease the maximum rate of reaction.

Increase on concentration of substrate does not reduce effect of inhibitor.