Biological molecules proteins 2.1.2

Question 1

What are peptides?

Answer 1

• Peptides are polymers made up of amino acid molecules. Proteins consist of one or more polypeptides arranged as complex macromolecules and they have specific biological functions.

Question 2

What elements do proteins contain?

Answer 2

Carbon, hydrogen, oxygen, nitrogen, sulphur. (CHONS)

Question 3

What is a gene?

Answer 3

• A gene is a stretch of DNA that codes for proteins.
• DNA is NOT made out of proteins

Question 4

What are the monomers of proteins?

Answer 4

amino acids

Question 5

How many amino acids are there within proteins in nature?

Answer 5

• There are 20 aas within proteins in nature
• Plants and microorganisms can synthesise all of these amino acids
• Animals can only synthesise non essential amino acids.

Question 6

Structure of amino acids

Answer 6

*look on pp

Question 7

Condensation reaction of 2 amino acids

Answer 7

*look on pp

Question 8

What is the Buiret test?

Answer 8

The biuret test is used to test for proteins. Firstly, a sample of the solution is placed
in a test tube and subsequently an equal amount of NaOH is added. Afterwards, a few drops of dilute copper (II) sulfate solution is added and gently mixed. In the presence of a protein, the solution turns lilac/ as an indicator of peptide bonds. In the absence of protein, the solution remains blue

Question 9

How to find rf value

Answer 9

distance travelled by solute / distance travelled by solvent

Question 10

What is the purpose of chromatography?

Answer 10

Chromatography is used to seperate a mixture of solutes disolved in a solvent. This allows identification of the solutes in the mixture using retention factors (Rf)

Question 11

What are the 2 types of chromatography?

Answer 11

1. Paper chromatography, uses chromatography paper.
2. Thin layer chromatography (TLC0 uses an inert surface (glass, metal or plastic) which is coated with material such assilica gel or cellulose.

Question 12

The process of chromatography

Answer 12

• A spot of the mixture is placed near the bottom of a piece of chromatography paper/plate
• The paper/plate is then placed upright in a suitable solvent
• As the solvent moves up the paper or plate it carries the mixture with it.

Question 13

What are the 2 phases of chromatography?

Answer 13

• The mobile phase = the solvent
• The stationary phase = the paper or plate that the solvent moves up

Question 14

Why do solutes move at different rates?

Answer 14

1. Solubility in the mobile phase.
   The more soluble the compound is in the solvent, the further it will travel.
   Hydrophilic compounds travel faster in water, hydrophobic compounds travel faster in organic solvents.
2. Adsorption by the stationary phase
   Adsorption = attraction of the chemical component to the surface of the stationary phase. The higher the rate of adsorption, the slower rate of movement.

Question 15

What is a retention factor?

Answer 15

The retention factor of a particular material in a particular solvent is the ratio of the distance the spot moved above the origin to the distance the solvent front moved above the origin. Retention factors are always less than 1.

Question 16

Seperating amino acids using thin layer chromatography

Answer 16

• A technique used to seperate the individual components of a mixture.
• The rate at which amino acids in the organic solvent move through the silica gel depends on the interactions (hydrogen bonds) they have with the silica in the stationary phase.

Question 17

Primary structure of proteins

Answer 17

• The sequence of amino acids in the polypeptide chains are joined together by peptide bonds.
• Determined by genetic code on the DNA/gene or the base sequence of the DNA.
• The particular amino acids will influence how the polypeptide folds to give the protein’s final shape, this in turn dtermines the function.
• The only bonds in the primary structure are peptide bonds.

Question 18

Secondary structure

Answer 18

• Initial local folding of polypeptide chain
• 2 regular shapes (alpha helices and beta pleated sheets)
• These 2 regular shapes form due to hydrogen bonds between the: carboxyl group (slightly electronegative) and the amine group (slightly electropositive) of the peptide bonds of different neighbouring aas.
• Secondary structure is the result of hydrogen bonds and forms at regions along protein molecules depending on the amino acid sequences.

Question 19

Tertiary structure

Answer 19

• Further folding of the polypeptide chain to give the final 3 dimensional structure of the polypeptide.
• The alpha helices and beta sheets of secondary structure are brought together by bonds formed between side chains/R groups of aas

Question 20

Hydrophobic interactions

Answer 20

Occur in:
- Interior of proteins (hydrophobic environment) where it is not in contact with water.
- Parts of membrane proteins in contact with the phospholipid bilayer.

Hydrophillic groups are on the outside of the protein whereas hydrophobic groups are on the inside of the molecule, shielded from the water in the cyptoplasm.

Question 21

Interactions between R groups

Answer 21

• Hydrophobic and hydrophillic interactions = weak interactions between polar and non polar groups.
• Hydrogen bonds = these are the weakest of the bonds formed.
• Ionic bonds = these are stronger than hydrogen bonds and form between oppositely charged R groups
• Disulphide bonds (aka disulphide bridges) = these are covalent and the strongest of the bonds but only form between R-groups that contain sulphur atoms.

Question 22

Quaternary structure

Answer 22

• Association of 2 or more polypeptide chains to form a fully functional protein
• The same bonds that fold the tertiary structure are used to maintain the quaternary structure of the protein.
• Many proteins require the quaternary structure to be functional e.g. haemoglobin, all fibrous proteins.
• Some proteins only require the tertiary structure as do not need to associate into a complex to be functional and are made from just 1 polypeptide chain e.g. many enzymes.

Question 23

How is secondary structure different to tertiary structure?

Answer 23

• It is only formed from hydrogen bonds (which occur between carboxyl and amine groupsof nearby peptide bonds)
• There are no R groups involved in the secondary structure.

Question 24

What bonds are involved in each of the protein structures?

Answer 24

• Primary = peptide
• Secondary = hydrogen
• Tertiary = hydrogen, ionic, hydrophobic, disulphide
• Quaternary = hydrogen, ionic, hydrophobic, disulphide

Question 25

Summary of hierarchy of structures in a protein

Answer 25

- Primary structure = amino acid sequence - Secondary structure = contains alpha helices and beta sheets, R groups not involved. - Tertiary structure = Final 3D structure of polypeptides, involving bonds between R groups. - Quaternary structure = Interaction of more than 1 pp chain to form a protein.

Question 26

Breakdown of peptides

Answer 26

- Peptides are created by amino acids linking togther in condensation reactions to form peptide bonds. - Protease are enzymes that catalyse the reverse reaction , turing peptides back into their constituent amino acids. - A water molecules is used to break the peptide bond in a hydrolysis reaction, reforming the amine and carboxylic acid groups.

Question 27

Globular proteins

Answer 27

- All proteins which are soluble in water and carry out the cell's metabolic functions - They are compact, water soluble, and usually roughly spherical in shape. - They form when proteins fold into their tertiary structures in such a way that hydrophobic R groups on the amino acid are kept away from the aqueous environment. - can have tertiary or quaternary structure -

Question 28

Insulin

Answer 28

- A globular protein - Involved in the regulation of blood glucose concentration, hormones are transported in the blooodstream so they need to be soluble. - Has quaternary structure - Hormones also have to fit into specific receptors on the cell surface membrane to have their effect and therfore need to have precise shapes.

Question 29

Conjugated proteins

Answer 29

- Globular proteins that contain a non protein component called a prosthetic group, proteins without a prosthetic group are called simple proteins

Question 30

Haemoglobin

Answer 30

- Has quaternary structure - 2 alpha sub units/pp chains, 2 beta sub units/pp chains - The protein part is called globin - It has a non protein part attatched (haem with an iron ion in the middle) this is where oxygen binds. - Has a prosthetic group

Question 31

Catalase

Answer 31

- An enzyme, each enzyme is specific to a particular reaction or type of reaction. - Catalase is a quaternary protein containing 4 haem prosthetic groups. - The presence of iron II ions in the prosthetic groups allow catalase to interact with hydrogen peroxide and spped up its breakdown.

Question 32

Denaturation

Answer 32

- The loss of the exact 3D structure of a protein. Primary structure remains intact. - 4, 3, 2 are affected and lost in order. - Occurs because rise in temp above optimum breaks H bonds and change in pH breaks ionic bonds.

Question 33

Fibrous proteins

Answer 33

- Long chain structural proteins which make up hair, skin, bone, tendons, ligaments. Also integral to lots of tissues such as alveoli and blood vessels. - High proportion of hydrophobic and small amino acids, range of aas are small - Insoluble in water, long pp chains, strong, all have quaternary structure - Many H bonds or covalent cross links between polypeptides to give added strength.

Question 34

Elastin

Answer 34

- Made by linking many soluble tropoelastin protein molecules to make a very large, insoluble, and stable cross linked structure - Is a fibrous protein which is found in elastic fibres - Quaternary protein made from tropoelastin

Question 35

Keratin

Answer 35

- Present in hair, skin and nails - Has a large proportion of the amino acid cysteine, this reults in many strong disulphide bonds (disulphide bridges) forming strong, inflexible and insoluble materials - The degree of disulphides determines the flexibility

Question 36

Collagen

Answer 36

- Connective tissue found in skin, tendons, ligaments and the nervous system - All are made up of 3 polypeptides wound together in a triple helix structure, every 3rd amino acid in the structure is glyscine. - Many hydrogen bonds form between the polypeptide chains forming long quaternary proteins with staggered ends. - In Collagen also contains highproportions of the amino acids proline and hydroxyproline. The R groups in these amino acids repel each other and this adds to the stability of collagen.

Question 37

At which levels of protein structure do ionic bonds occur?

Answer 37

Tertiary and quaternary

Question 38

What bond holds togther alpha helix or beta pleated sheet?

Answer 38

Hydrogen

Question 39

Which bonds are the last to break when an enzyme is heated?

Answer 39

disulphide

Question 40

At which level of protein structure do hydrophobic interactions occur?

Answer 40

Tertiary and quaternary

Question 41

What makes haemoglobin a globular protein?

Answer 41

It has has hydrophobic groups on the inside and hydrophillic groups on the outside

Question 42

What will break an ionic bond between amino acids?

Answer 42

pH change