Protein Structure

Question 1

Role of proteins

Answer 1

• Catalyst - enzymes
• Transporters
• Receptors
• Ligands in cell signalling
• Structural support
• Muscular contraction

Question 2

Feature of proteins

Answer 2

• polypeptides - macromolecules made from a.a
• a.a sequence encoded by gene - nucloetide sequence
• polypeptide chain folds into complex, highly specific 3d structure - determined by sequence, chemical and physical properties of aa

Question 3

How are a.a classified?

Answer 3

According to chemical properties of R groups

Question 4

What is an amino acid residue?

Answer 4

What remains of an a.a after it has been joined by a peptide bond to form a protein

Question 5

What are the different chemical properties of R groups?

Answer 5

• Hydrophobic
• Hydrophilic
• Polar
• Non-polar
• Acidic
• Basic
• Neutral

Question 6

What are the different physical properties of R group?

Answer 6

• Aliphatic
• Aromatic

Question 7

State the relationship between pK and pH values

Answer 7

• If pH < pK, group will be protonated
• If pH > pK, group will be deprotonated

Question 8

Define primary structure or protein

Answer 8

The linear amino acid sequence of the polypeptide chain

Question 9

Define secondary structure

Answer 9

The local spatial arrangement of polypeptide backbone

Question 10

Define tertiary structure

Answer 10

The overall 3d configuration of protein

Question 11

Define quatenary structure

Answer 11

The association between different polypeptides to form a multi-subunit protein

Question 12

Define peptide bond

Answer 12

The linking of two a.a, accompanied by abstraction of a molecule of water

Question 13

Properties of peptide bonds

Answer 13

• planar
• rigid - peptide C-N has partial double bond, prevent rotation
• trans conformation
• bonds on either side of peptide bond (psi and phi) free to rotate

Question 14

What is the importance of amino acids in proteins?

Answer 14

Determines

• the way polypeptide chain folds
• physical characteristics of protein

Question 15

Define Isoelectric point of a protein

Answer 15

the pH at which there is no overall net charge on protein

Question 16

What are conjugated proteins?

Answer 16

Proteins that are covalently linked to other chimal components

Eg; lipoproteins, glycoproteins

Question 17

How is protein function determined?

Answer 17

function determined by structure which is determined by sequence and angle of peptide bond

Question 18

State the characteristics of a-helix

Answer 18

• H bonds between N-H and C=O (4aa away) stabilise the structure
• 3.6aa per turn
• 0.54nm pitch - 1 complete turn

Question 19

State the chracteristics of B-strand

Answer 19

• R groups alternate between opposite sides
• Antiparallel B-sheet : adjacent B-s run in opposite directions
• Parallel (not stable)
• Mixed

Question 20

List examples of proteins with secondary sturctures

Answer 20

• ferritin : Iron storage, largely a-helix
• fatty acid binding protein : largely B-sheet

Question 21

Give examples of tertiary structured proteins

Answer 21

• fibrous - collagen
• globular - carbonic anhydrase

Question 22

State the role and characteristics of fibrous & globular proteins

Answer 22

Fibrous

• Role : support, shape and protection
• Characteristic : long strands of sheets, single type of repeating sec. structure

Globular

• Role : catalysis, regulation
• Characteristic : compact, several types of ss

Question 23

Describe a collagen protein

Answer 23

• made from a-helix chains
• triple helical arrangement of collagen chains
• H bonds stabilises interactions between chains
• formed from covalently cross-linked collagen molecules

Question 24

Describe globular proteins

Answer 24

consist of

• Motifs : folding patterns containing 1 or more elements of sec structure
• Domains : part of polypeptide chain that fold into a distinct shape. Has specific role

Question 25

How are water soluble porteins folded?

Answer 25

Polypeptide chains fold so that **hydrophobic chains** are folded to face **inwards** while **hydrophilic chains** arefolded to face **outward**

Question 26

List examples of quatenary structures

Answer 26

* Haemoglobin : 2 a subunits and 2 B subunits * Ribosome : 55 protein subunit and 3 RNA molecules

Question 27

What are the bonds involved in maintaining protein structures?

Answer 27

* Primary : Covalent * Secondary : H bonds * Tertiary : Covalent, H bonds, Ionic, Van der waals, Hydrophobic (interaction between hydrophobic side chains due to displacement of water) * Quatenary : Covalent, H bonds, Ionic, Van der waals, Hydrophobic

Question 28

Proteins with what bonds are normally secreted out of cell and why?

Answer 28

* Proteins with disulphide bonds. Eg; ribonuclease * outside environment is more harsh, protein need to be robust, disulphide bonds hold a.a together

Question 29

What is protein denaturation?

Answer 29

Disruption of protein structure caused by breaking of forces that hold the proteins together

Question 30

What causes protein denaturation?

Answer 30

* Heat : increases vibrational energy * pH : Changes ionic/h binds * detergents : disrupt hydrophobic interations

Question 31

Describe the characteristics of protein folding

Answer 31

* Information needed for folding contained in primary sequence * Protein folding cannot be random * Folding process must be ordered : each step involves localised folding & stable confirmations maintained

Question 32

What are the examples of diseases caused by protein misfolding?

Answer 32

* Transmissible spongiform encephalopathies * Amyloidoses