AQA AS bio 3.1 biological molecules

What are proteins made up of?

Amino acids are the monomers from which proteins are formed

What are proteins important as?

Enzymes, chemical messengers, and components of the blood

Draw the general structure of an amino acid

What does the NH₂ in an amino acid represent?

amine group

What does the COOH in an amino acid represent?

carboxyl group

What does the R in an amino acid represent?

side chain

How many different amino acids are common in all organisms?

There are 20 amino acids that are common in all organisms

How do the 20 amino acids common in all organisms differ from each other?

They differ only in their side group

What type of bond does a condensation reaction between two amino acids form?

peptide bond

(one water molecule is eliminated)

Draw a diagram for the condensation reaction between two amino acids

How are dipeptides formed?

By the condensation of two amino acids

How are polypeptides formed?

By the condensation of many amino acids

What is a functional protein?

A protein that affects the functional operations of a cell

What is a structural protein?

A protein that provides physical stability and movement, like collagen

How many polypeptides may a functional protein contain?

one or more polypeptides

How many levels of protein structure are there?

4; primary, secondary, tertiary, quaternary

What is the primary structure of proteins?

The sequence (order) of amino acids

What is the secondary structure of proteins?

The shape that the chain of amino acids forms, stabilised by hydrogen bonding between different parts of the polypeptide chain

Name the two shapes that can form within proteins due to hydrogen bonds

α-helix

β-pleated sheets

How do hydrogen bonds form in the secondary structure of proteins?

The hydrogen in the -NH has a weak positive charge

The oxygen in the -C=O has a weak negative charge

hydrogen bonds form between the oxygen of the carboxyl group of one amino acid and the H in the amine group of another amino acid

What is the tertiary structure of a protein?

The 3D shape of the protein formed from further twisting and folding

Leads to additional bonds forming to maintain the structure

Name the three types of bond that help maintain the tertiary structure of a protein

Hydrogen bonds (weakest)

Ionic bonds

Disulphide bonds (strongest)

How do hydrogen bonds form in the tertiary structure of a protein?

Between R groups of amino acids within polypeptide chains

How do ionic bonds form in the tertiary structure of a protein?

Between charged R groups

(between carboxyl and amine groups not involved in the peptide bond)

How do disulphide bridges (type of covalent bond) form in the tertiary structure of a protein?

Only occur between sulphur in the R group of the amino acid cysteine

What is the quaternary structure of a protein?

Occurs in proteins that have more than one polypeptide chain

Each polypeptide chain in the quaternary structure is referred to as a...

Subunit of the protein

How does denaturing affect a protein?

The bonds which hold the tertiary and secondary structure in shape will break

The unique 3D shape of the protein (e.g. enzyme's active site) is changed

Name two conditions that can cause a protein to denature

Too high a temperature (too much kinetic energy)

Too high/low a pH (too many H+ or OH- ions)

Describe the impact of a change in primary structure of proteins

There is a change in the sequence of amino acids that form a chain (primary structure)

The ionic, hydrogen and disulphide bonds will form in a different location

This results in a different 3D shape

Describe the impact of a change in primary structure of enzymes

The enzyme's active site will be a different shape so the enzyme will not work

Describe the impact of a change in primary structure of a carrier protein

Carrier proteins will have a different shaped binding site, so molecules are no longer complementary and cannot be transported across cell membranes

Describe how to test for proteins in a sample

1) grind up the food sample in a pestle and mortar with distilled water

2) filter the solution through a funnel and filter paper in order to remove any remaining undissolved solid

3) place 3cm^3 of the food sample into a test tube

4) add 3cm^3 of Biuret's reagent

Describe the result for a positive test for proteins

The solution will turn from blue to purple/lilac

Describe the result for a negative test for proteins

The solution would remain blue

What is a T-test for?

comparing 2 means

What is an enzyme?

A biological catalyst (speeds up chemical reactions without being used up or changed)

Describe the structure of an enzyme

Globular proteins with a tertiary structure

There is a specific 3D shape on the surface called an active site where reactions take place

How does an enzyme catalyse a reaction?

Enzymes lower the activation energy of the reaction by providing an alternate pathway for the reaction to occur

What does it mean that enzymes are specific?

The tertiary structure of the active site is specific to the structure of the substrate molecule

This means the active site can only fit complementary substrate(s) and combine with them to form an enzyme substrate complex

Name two models of enzyme action

lock and key model

induced fit model

Describe the lock and key model for enzyme action

Suggests that the tertiary structure of the active site is fixed so the active site doesn't change shape

Due to random collisions, the substrate binds to an enzyme's active site to form an enzyme-substrate complex

Temporary bonds form between the substrate molecule and the amino acids on the surface of the active site, distorting the bonds in the substrate and lowering the activation energy

The substrate is broken down into products which are released

Describe the induced fit model of enzyme action

The active site is not complementary to (doesn't fit) the substrate

As the substrate binds to the active site, the shape of the active site changes slightly to mould itself tightly around the substrate so it fits perfectly

This distorts the bonds in the substrate, lowering the activation energy

Which model of enzyme action is believed to be correct?

Induced fit model

Name five factors which affect the rate of enzyme controlled reactions

Temperature

pH

Substrate concentration

Enzyme concentration

Concentration of competitive and non-competitive inhibitors

What does the rate of an enzyme controlled reaction depend on?

The frequency of successful collisions between the substrate and the active site of the enzyme

Draw the graph showing the effect of temperature on the rate of an enzyme controlled reaction

How does temperature affect enzyme activity, up to the optimum temperature?

The rate increases as the temperature increases:

The kinetic energy of the enzyme and substrate increases

This increases the frequency of successful collisions between the substrate and the active site

This increases the number of enzyme-substrate complexes that form

How does temperature affect enzyme activity, past the optimum temperature?

The rate of reaction decreases with temperature:

The enzymes are vibrating more rapidly, causing bonds (e.g. hydrogen bonds) within the enzymes to break

This changes the enzyme's tertiary structure; as the shape of the active site changes, it is no longer complementary to the substrate, so the substrate cannot fit.

The enzyme is denatured and no longer functions.

Can an enzyme renature if it has denatured due to high temperatures?

No - it's tertiary structure has changed so much that it cannot be reversed

Draw the graph showing the effect of pH on the rate of enzyme controlled reactions

How does pH affect enzyme activity?

Enzyme activity decreases as the pH moves away from the optimum pH

H+ ions bond with the R groups of the amino acids in the active site, preventing the R groups from bonding with the substrates

H+ ions also bond with R groups of amino acids in the rest of the enzyme molecule

This breaks the bonds holding the tertiary structure of the enzyme in place.

The tertiary structure of the enzyme changes so the shape of the active site changes and is no longer complementary to the substrate - the enzyme has denatured

How can you calculate the pH of a solution using the concentration of hydrogen ions?

pH = -log[H+]

Draw the graph showing the effect of enzyme concentration on enzyme activity

How does enzyme concentration affect enzyme activity?

At first the rate of reaction is directly proportional to enzyme concentration: the number of active sites available for substrates to collide with increases

This increases the frequency of collisions between the substrate and the active sites

Eventually the rate of reaction will level off as substrate concentration becomes the limiting factor: there will not be enough substrate molecules to collide with all the available active sites, so increasing enzyme concentration will have no effect

Draw the graph showing the effect of substrate concentration on enzyme activity

How does substrate concentration affect enzyme activity?

At first, the rate of reaction is directly proportional to the substrate concentration: more substrate molecules increases the frequency of collisions between the substrate and the active site

Eventually the rate of reaction will level off as enzyme concentration becomes the limiting factor: all active sites are occupied so increasing substrate concentration will have no effect

What is a competitive inhibitor?

molecule with a similar shape to the substrate, allowing it to occupy the active site of the enzyme

It competes with the substrate to bind in the active site of an enzyme.

Describe how competitive inhibitors impact enzyme activity

they have a similar shape to that of the substrate molecules

they compete with the substrate to bind to the active site of the enzyme

They prevent the actual substrate from colliding with the active site, reducing the frequency of collisions between the substrate and the active site

This reduces the rate of reaction

How can you reduce the effect of a competitive inhibitor?

increasing substrate concentration

There will be a greater chance that the substrate will occupy the active site instead of the competitive inhibitor

What is a non-competitive inhibitor?

A molecule that binds to a different site (allosteric site) on the enzyme, causing the tertiary structure of the enzyme to change

Describe how non-competitive inhibitors impact enzyme activity

When it binds to the allosteric site, it causes the tertiary structure to change

the active site changes shape and is no longer complementary to the substrate, so enzyme-substrate complexes can't be formed

This reduces the rate of reaction

Does increasing substrate concentration reduce the effect of non-competitive inhibitors?

No

As the shape of the active site has changed, the substrate molecule still cannot bind with the active site

Give a method to investigate the effect of temperature on the rate of an enzyme controlled reaction

1) take three test tubes and measure 5cm³ of milk into each. Draw a cross on each with a black marker, then place in water bath at 20°C for 10 minutes to equilibrate

2) add 5cm³ of trypsin to each test tube simultaneously and start the timer

3) record how long it takes for the milk samples to completely hydrolyse and become colourless (you are able to see the cross)

4) repeat at temperatures of 30°C, 40°C, 50°C and 60°C

5) find the mean time for the milk to become hydrolysed at each temperature, then work out the rate of reaction using:

rate of reaction = 1 / mean time

6) plot a graph of rate of reaction against temperature

What statistical test should be used for comparing two means?

T-test

What are monosaccharides?

The monomers from which larger carbohydrates are made

Name three common monosaccharides

glucose, fructose, galactose

What type of bond does a condensation reaction between two monosaccharides form?

A glycosidic bond

What is a disaccharide?

Two monosaccharides joined together by a glycosidic bond

How is a disaccharide formed?

by the condensation of two monosaccharides

Give three examples of disaccharides

maltose, lactose, sucrose

How is the disaccharide maltose formed?

By the condensation of two glucose molecules

Give the word equation for the condensation reaction that forms maltose

glucose + glucose → maltose + water

How is the disaccharide lactose formed?

By the condensation of a glucose molecule and galactose molecule

Give the word equation for the condensation reaction that forms lactose

glucose + galactose → lactose + water

How is the disaccharide sucrose formed?

by condensation of a glucose molecule and a fructose molecule

Give the word equation for the condensation reaction that forms sucrose

glucose + fructose → sucrose + water

What is an isomer?

molecules with the same molecular formulae but different structural formulae (same atoms but arranged differently)

Name two isomers of glucose

α-glucose and β-glucose

Give the structure for α-glucose

Give the structure for β-glucose

What are polysaccharides?

Polymers formed by the condensation of many glucose units

Name three polysaccharides

starch, glycogen, cellulose

How is the polysaccharide starch formed?

By the condensation of α-glucose

How is the polysaccharide glycogen formed?

By the condensation of α-glucose

How is the polysaccharide cellulose formed?

By the condensation of β-glucose

What is the function of starch?

glucose storage in plants

What is the function of glycogen?

glucose storage in animals (mainly in muscle and liver cells)

What is the function of cellulose?

structural component of plant cell walls

What two polysaccharides make up starch?

amylose and amylopectin

What type of bonds can be found within amylose?

1,4 glycosidic bonds between α-glucose molecules

Describe the shape of amylose

Unbranched helix-shaped chain

Recognise the structure of amylose

What type of bonds can be found within amylopectin?

1,4 and 1,6 glycosidic bonds between α-glucose molecules

1,6 glycosidic bonds form branches

Describe the shape of amylopectin

Branched molecule

Recognise the structure of amylopectin

Describe how the structure of starch relates to its function

Amylose's helix shape is compact, so a lot can be stored in a small space

Amylopectin's branches result in many terminal glucose molecules that can be acted on by enzymes simultaneously, increasing the rate at which the glucose can be hydrolysed for use

Insoluble, so it has no osmotic effect and large amounts can be stored without affecting water balance

What type of bonds can be found within glycogen?

1,4 and 1,6 glycosidic bonds between α-glucose molecules

1,6 glycosidic bonds form branches

Describe the shape of glycogen

Highly branched molecule

(there are even more 1,6 glycosidic bonds than amylopectin)

Describe how the structure of glycogen relates to its function

Branching results in many terminal glucose molecules that can be acted on by enzymes simultaneously, increasing the rate at which the glucose can be hydrolysed for use

(Important for animals as they have a high respiration rate and their energy needs can change rapidly)

High number of branches makes glycogen a compact molecule, so a lot can be stored in a small space

Insoluble, so it has no osmotic effect and large amounts can be stored without affecting water balance

Large and cannot diffuse out the cell