L02- PROTEIN STRUCTURE AND FUNCTION

Question 1

Describe the primary structure of a protein

Answer 1

• Linear structure/ order of amino acids
• bonds = covalent peptide bonds between AA
• From the N terminus to the C terminus
• Can have projecting AA side chains

Question 2

Describe the types of projecting AA side chains

Answer 2

• Non polar, aliphatic side chain e.g glycine
• Polar, uncharged e.g Serine
• Positively charged
• Negatively charged
• Aromatic

Question 3

Which AA groups tend to be found on the inside of a protein?

Answer 3

• Non polar, aliphatic amino acids

Question 4

Which AA groups tend to be found on the outside of a protein?

Answer 4

• Polar, uncharged amino acids

Question 5

Which terminal does the primary structure start at?

Answer 5

Amino terminal (n terminus)

Question 6

Describe the secondary structure of a protein

Answer 6

• folds in the amino acid chain –> beta sheet, alpha helices
• hydrogen bonds between atoms in peptide bond
• bonds not covalent
• R groups influence shape of secondary structure as they influence where bonds are formed

Question 7

Which way do R groups face in the alpha helices?

Answer 7

Outwards

Question 8

Describe the tertiary structure

Answer 8

• Final 3D structure
• Further folding - more H bonds, ionic bonds, disulphide bridges
• most stable/ lowest amount of energy - there are not two negatively charged molecules near each other or a hydrophilic and hydrophobic near each other

Question 9

Describe H bonding in tertiary proteins

Answer 9

Can have H bonding between different R groups, between R groups and peptide bonds, and between different peptide atoms​

Question 10

Quaternary?

Answer 10

multiple polypeptide chains

Question 11

Name 4 different types of tertiary structures

Answer 11

• Fibrous - long, elongated , collagen
• Globular - round balls, enzymes
• Helix - interacting with other proteins
• Beta pleated sheet - involved in protein folding

Question 12

How to determine protein shape?

Answer 12

• X- ray crystallography
• NMR

Question 13

What are heteromers and homomers?

Answer 13

Hereromers = protein with two or more different polypeptide chains
Homomers = protein with two or more identical polypeptide chains

Question 14

Charcteristics of proteins (2)

Answer 14

• flexible, can change their conformity e.g enzymes
• Ability to be phosphorylated

Question 15

Functions of proteins (4)

Answer 15

• Binding, (receptors, ligands, antibodies)
• Catalysis, (enzymes)
• Switching things on and off, (cell signalling pathways)
• Structural support, (cytoskeleton)

Question 16

What is the name of proteins that help other proteins to fold?

Answer 16

Chaperone proteins

Question 17

Which factors regulate the function of proteins? (4)

Answer 17

• Synthesis - has the protein been made or not
• Localisation - Is the protein in the correct location to carry out its function or not
• Modification - is the protein active or inactive
• Degradation - is the protein needed anymore

Question 18

How are proteins localised ? (3 steps)

Answer 18

• produced in the RER
• have a sorting signal which tells them where to go
• are transported from cytosol into organelles via transporter vesicles

Question 19

Explain what type of reaction is needed to regulate protein function

Answer 19

Phosphorylation - A phosphate group is covalently attached to amino acid side chains which have a hydroxy group.

They can inhibit or activate a protein and they induce a conformational change

Question 20

What enzyme catalyses a phosphorylation reaction?

Answer 20

Kinase enzyme which uses ATP

Question 21

Which protein is responsible for dephospho rylation?

Answer 21

Phosphatase

Question 22

What is unfolded protein response (UPR)?

Answer 22

This is a homeostatic mechanism and it tries to keep folding in the cell in balance with the cell’s needs.

Question 23

What can happen if there is an imbalance in the UPR process?

Answer 23

It results in the ER becoming stressed. It causes an increase in unfolded proteins. It can inhibit translation and cause potential cell death

Question 24

Give 3 consequences as a result of a lack of protein folding

Answer 24

• Sickle cell anaemia
• Type II diabetes
• Cataract