3.6 Structure of Proteins

Question 1

Structure of a generic amino acid:

Answer 1

H R O
N—–C——C
H H OH

Question 2

What does the R group represent in an amino acid?

Answer 2

The part of the structure that differs for each amino acid (one of 20 different ones)

Question 3

What are peptide bonds?

Answer 3

Form between proteins to make dipeptides, in a CONDENSATION reaction

Question 4

Stages of protein formation:

Answer 4

Primary
Secondary
Tertiary
Quaternary

Question 5

Define peptides =

Answer 5

polymers made up of amino acid molecules

Question 6

Define proteins and the monomers that form them =

Answer 6

Made of many amino acid monomers
Consist of one or more polypeptides arranged as macromolecules that have specific biological functions

Question 7

How many types of amino acid are non-essential?

Answer 7

5 - the body makes them

Question 8

How many types of amino acids are essential?

Answer 8

9 - can only be obtained from food

Question 9

How many types of amino acids are conditionally essential?

Answer 9

6 - only needed by infants and young children

Question 10

Describe the formation of a dipeptide:

Answer 10

Amine group (NH2) interacts with the carboxylic acid group of another amino acid (COOH)
Condensation reaction
Peptide bond forms
Water is produced as a waste product

Question 11

What forms when many amino acids are bonded together?

Answer 11

A polypeptide is formed

Question 12

What is the condensation reaction catalysed by?

Answer 12

An enzyme called peptidyl transferase present in ribosomes

Question 13

What happens to the R groups in polypeptides during their formation reactions?

Answer 13

Differing R groups interact with each other which leads to long chains of amino acids (polypeptides) folding into complex proteins

Question 14

Why is the shape of proteins important?

Answer 14

Specific shapes of proteins are vital for many functions

Question 15

Describe the primary stage of protein synthesis:

Answer 15

Chain of amino acids
Long polypeptide chain
Only contains peptide bonds
Particular amino acids influence how polypeptide folds to give the protein’s final shape that determines its function

Question 16

Describe the secondary stage of protein synthesis:

Answer 16

Twisted chain of amino acids
Held together with hydrogen bonds which pull it together into 2 different shapes
Depends on which amino acids are present

Question 17

2 different structures of polypeptides in the secondary stage of protein synthesis:

Answer 17

Alpha helix
Beta pleated sheets
Multiple of each one occur un one chain

Question 18

Describe the tertiary stage of protein synthesis:

Answer 18

Folding of protein into its final shape - critical for function
All held in place by interactions between R groups (polar charges interact - O, H , OH)
Disulphide bonds - covalent bonds between R groups containing sulfur (strongest)
Hydrogen bonds - weak
Hydrophobic/hydrophyllic interactions - polar and non-polar R groups

Question 19

Hydrophobic and hydrophillic definitions:

Answer 19

Hydrophobic = typically inside molecule as they repel water
Hydrophillic = typically outside molecule as they attract water

Question 20

Describe the quaternary stage of protein synthesis:

Answer 20

Made of 1 polypeptide chain
Same bonds as tertiary
Made of multiple tertiary chains bonded together
Can be conjugated proteins (contain prosthetic groups that aid its function) e.g. haemoglobin

Question 21

Bonds present in primary stage:

Answer 21

Peptide bonds

Question 22

Bonds present in secondary stage:

Answer 22

Peptide bond
Hydrogen bonds

Question 23

Bonds present in tertiary and quaternary stage:

Answer 23

Peptide bonds
Hydrogen bonds
Disulphide bonds
Hydrophobic/hydrophyllic interactions

Question 24

Stationary phase to separate amino acids using thin layer chromatography:

Answer 24

Stationary phase: thin layer of silica gel (or other adhesive) added to a rigid surface e.g. sheet of glass/metal

Question 25

Mobile phase to separate amino acids using thin layer chromatography:

Answer 25

organic solvent that travels up silica gel

Question 26

How TLC of amino acids works?

Answer 26

Amino acids are added to one end of the gel This end is submerged in an organic solvent which moves through the silica gel Different amino acids are separated due to differing solubilities in the solvent/ the interactions with the stationary phase (hydrogen bonds)

Question 27

What is the test for protein and results?

Answer 27

Biuret reagent Colour change from blue to purple shows that protein is present

Question 28

What is the Biuret Reagent made from?

Answer 28

Copper sulfate Sodium hydroxide

Question 29

Hazards of copper sulfate

Answer 29

Dangerous if ingested Harmful to environment

Question 30

Hazards of sodium hydroxide

Answer 30

Corrosive alkali (can causes irritation or eye damage)

Question 31

Steps of the Biuret test;

Answer 31

1) Add 2cm3 of water into a test tube with 1cm3 Biuret Reagent 2) Add 2cm3 of sample into a test tube with 1cm3 Biuret Reagent 3) Hold each test at a 45 degree angle to add the Reagent so it forms a layer on top and record the colour 4) Mix each one by shaking each test tube and record colour

Question 32

Why does the biuret solution turn purple?

Answer 32

The copper sulfate reacts with the peptide bonds in proteins which produces a purple colour

Question 33

Why is it important to create a layer on top of the sample with the biuret reagent?

Answer 33

Ensures that no colour from the food sample is obscuring the result e.g. dark coloured foods

Question 34

What are some drawbacks of the biuret test?

Answer 34

Food sample must be liquid/in solution Subjective Difficult to distinguish colour change with coloured foods

Question 35

What is the enzyme that breaks down peptides?

Answer 35

Protease

Question 36

What kind of reaction does protease catalyse?

Answer 36

A hydrolysis reaction that breaks down peptides into their amino acids by breaking the peptide bonds using water Reforming the amine and carboxyl groups