Biological Molecules 1.4

Question 1

Proteins

Answer 1

Usually very large molecules
Each organism has numerous proteins that differ from species to species
The shape of one differs from all other types
One group of proteins, enzymes, is involved in almost every living process

Question 2

Amino acids

Answer 2

The basic monomer units which combine to make up a polymer called polypeptide
Polypeptides can be combined to form proteins
About 100 amino acids have been identified, of which 20 occur naturally in proteins

Question 3

What about amino acids provides indirect evidence for evolution

Answer 3

The fact that the same 20 amino acids occur in all living organisms

Question 4

Amino acid structure

Answer 4

Every amino acid has has a central carbon atom to which four diff chemical groups are attached:

• amino group (-NH2)
• carboxyl group (-COOH)
• hydrogen atom (-H)
• R side group

Question 5

Amino group

Answer 5

-NH2

A basic group from which the amino part of the name amino acid is derived

Question 6

Carboxyl group

Answer 6

-COOH

an acidic group which gives the amino acid the acid part of its name

Question 7

R group

Answer 7

A variety of diff chemical groups
Each amino acid has a different R group
These 20 naturally occurring amino acids differ only in their R group

Question 8

Amino acid structure diagram

Answer 8

H     H   O-H
 |      |     |
N - C - C
 |      |     ||
H     R    O

Question 9

The formation of a peptide bond

Answer 9

Forms between two amino acids to form a Dipeptide
Condensation reaction - removal of a water molecule
Water is made by combining an -OH from the carboxyl group of one amino acid with an -H from the amino group of another amino acid
The 2 amino acids then become linked by a new peptide bond between the carbon atom on one and nitrogen atom on the other

Question 10

Test for protein

Answer 10

Biuret test
Add sodium hydroxide solution
Add very dilute Copper sulphate solution
Colour change from blue to purple (peptide bonds, hence protein)

Question 11

Primary structure of proteins

Answer 11

The sequence of amino acids in the polypeptide chain

Determines the proteins final 3D shape and ultimately its biological function

Question 12

Secondary structure of proteins

Answer 12

Hydrogen bonds form between amino acids in the chain (between charged C=O and -NH groups either side of a peptide bond) causing it to fold into an alpha helix or beta pleated sheet

Question 13

Tertiary structure of proteins

Answer 13

alpha helixes fold further to create a complex, often specific 3D tertiary structure
Bonds help maintain structure: H bonds are numerous but easily broken/weak ionic bonds exist between carboxyl and amino groups, but are easily affected by pH/strong disulfide bridges form, connecting one sulphur atom to another

Question 14

Quaternary structure of proteins

Answer 14

Combination of a number of different polypeptide chains and associated non-protein groups into a large, complex protein molecule e.g, haemoglobin

Question 15

Two shapes of protein and functions

Answer 15

Fibrous proteins, such as collagen, have structural functions
Globular proteins, such as enzymes and haemoglobin, carryout metabolic functions

Question 16

Fibrous proteins

Answer 16

Form long chains which run parallel to one another. These chains are linked by cross bridges and so form very stable molecules
One example is collagen

Question 17

Collagen molecular structure

Answer 17

The primary structure is an unbranched polypeptide chain
In the secondary structure the polypeptide chain is very tightly wound
Lots of the amino acid, glycine helps close packing
In the tertiary structure the chain is twisted into a second helix
Its Quaternary structure is made up of three such polypeptide chains wound together in the same way as individual fibres wind together in a rope

Question 18

Where is collagen found

Answer 18

In tendons
Tendons join muscles to bones
When a muscle contracts the bone is pulled in the direction of the contraction

Question 19

Enzymes

Answer 19

Globular proteins that act as catalysts

Question 20

Catalysts

Answer 20

Alter the rate of chemical reactions without undergoing permanent changes themselves
They can be used repeatedly and are therefore effective in small amounts
Enzymes don’t make reactions happen; they speed up reactions that already occur

Question 21

Enzyme structure

Answer 21

Globular protein
Has a specific 3-D shape that is the result of the sequence of amino acids (primary protein structure)
A specific region of the enzyme is functional, this is known as the active site, it’s made up of a relatively small number of amino acids
The active site forms a small depression within the much larger enzyme molecule
The Molecule on which the enzyme acts is called the substrate, this fits neatly into the depression and forms an enzyme substrate complex
The substrate molecule is held within The active site by bonds that temporarily formed between certain amino acids of the active site and groups on the substrate molecule

Question 22

Induced fit model of enzyme action

Answer 22

Proposes that the active site forms as the enzyme and substrate interact. The proximity of the substrate (the change in the environment of the enzyme) leads to a change in the enzyme that forms the functional active site
So the enzyme is flexible and can mould itself around the substrate
The enzyme has a certain general shape but this alters in the presence of the substrate. As it changes the 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 bonds
Any change in an enzymes environment is likely to change its shape. The very act of colliding with its substrate is a change in its environment and so its shape changes – induced fit

Question 23

For an enzyme to work it must:

Answer 23

Come into physical contact with its substrate

Have an active site which fits the substrate

Question 24

Two changes most frequently measured in enzyme-catalysed reactions:

Answer 24

The formation of the products of the reaction

The disappearance of the substrate

Question 25

Measuring rate of change

Answer 25

We can measure the change in the rate of reaction at any point on the curve of the graph
We do so by measuring the gradient of our chosen point. The gradient is equal to the gradient of the tangent to the curve at that point

Question 26

Effect of temperature on enzyme action

Answer 26

Rise in temperature increases the kinetic energy of the molecules
As a result the molecules move around more rapidly and collide with each other more often
In an enzyme catalysed reaction this means that the enzyme and substrate molecules come together more often in a given time
There are more effective collisions resulting in more enzyme substrate complexes being formed and so the rate of reaction increases

However a temperature rise also begins to cause the hydrogen and other bonds in the enzyme molecule to break
This results in the enzyme, including its active site, changing shape
At first the substrate fits less easily into the changed active sites, slowing the rate of reaction
At some point the enzyme is so disrupted that it stops working altogether. It said to be denatured

Question 27

What temperature is our body at

Answer 27

37°C

Question 28

Effect of pH on enzyme action

Answer 28

The pH of the solution is a measure of its hydrogen ion concentration
Each enzyme has an optimum pH, that is a pH at which it works fastest
An increase or decrease in pH reduces the rate of enzyme action. If the change in pH is more extreme then, beyond a certain pH, the enzyme becomes denatured

Question 29

The pH affects how an enzyme works how?

Answer 29

A change in pH alters the charge of the amino acids that make up the active site of the enzyme. As a result, the substrate can no longer become attached to the active site and so the enzyme substrate complex cannot be formed

Depending on how significant change in pH is, it may cause the bonds maintaining the enzymes territory structure to break. The active site therefore changes shape

Question 30

Effect of enzyme concentration on the rate of reaction

Answer 30

Once an active site on an enzyme has acted on its substrate, it is free to repeat the procedure on another substrate molecule
This means that enzymes, being catalysts, are not used up in the reaction and therefore work efficiently at very low concentrations
In some cases, a single enzyme molecule can act on millions of substrate molecules in one minute

Question 31

Effects of substrate concentration on the rate of enzyme action

Answer 31

If the concentration of enzyme is fixed and the substrate concentration is slowly increased, the rate of reaction increases in proportion to the concentration of substrate’s
This is because at low substrates concentrations, the enzyme molecules have only a limited number of substrate molecules to collide with, and therefore the active sites of the enzymes are not working to full capacity
As more substrate is added, the active sites gradually become filled, until the point where all of them are working as fast as they can. The rate of reaction is at its maximum
After that, the addition of more substrate will have no effect on the rate of reaction

Question 32

Enzyme inhibitors

Answer 32

Substances that directly or indirectly interfere with the functioning of the active site of an enzyme and so reduce its activity

Question 33

Two types of enzyme inhibitor

Answer 33

Competitive inhibitors– which bind to the active site of the enzyme
Non-competitive inhibitors– which bind to the enzyme at a position other than the active site

Question 34

Competitive inhibitors

Answer 34

Have a molecular shape similar to that of the substrate
This allows them to occupy the active site of an enzyme
So they compete with the substrate for the available active sites
It is the difference between the concentration of the inhibitor and the concentration of the substrate that determines the effect this has on enzyme activity

Question 35

Non-competitive inhibitors

Answer 35

Attach themselves to the enzyme at a binding site which is not the active site
Upon attaching to the enzyme, the inhibitor alters the shape of the enzyme and its active site in such a way that substrate molecules can no longer occupy it, and so the enzymes cannot function

Question 36

What are the building blocks for proteins?

Answer 36

Amino acids

Question 37

What makes an enzyme specific

Answer 37

has a specific active site shape, only complementary substrates ​ can bind to the active site to form enzyme-substrate complexes

Question 38

The shape of the active site is determined by what

Answer 38

Tertiary structure of the polypeptide

Question 39

Pepsin

Answer 39

a protease enzyme that functions in the stomach