FoM:L5 - Protein structure

Question 1

How can amino acids be grouped?

Answer 1

• properties of side chain
• charged polar (basic and acidic)
• uncharged polar (amide, hydroxyl, sulfhydryl)
• non-polar neutral (hydrophobic)

Question 2

How are amino acids joined together?

Answer 2

• amide linkage called peptide bond
• condensation reaction (loss of H2O)

Question 3

How are the 3D structure of proteins found out?

Answer 3

X-ray crystallography

Question 4

What are the 4 levels of protein structure?

Answer 4

primary: type, number and order of aas
secondary: H bonding between carbons of polypeptide backbone
tertiary: interactions between R groups and folding
quaternary: interactions between multiple polypeptides

Question 5

Outline secondary structure of proteins

Answer 5

• conformation of lowest energy
• a single stable conformation
• can change when proteins interact
• side chains not involved in H bonding

Question 6

Outline protein folding

Answer 6

• constrained
• peptide bond is not fully flexible: partial double bound, no free rotation
• stability and shape determined by many non-covalent bonds
• help of chaperones

Question 7

Why do proteins fold?

Answer 7

• minimise disruption to H bonds in H2O
• polar side chains outside, non-polar inside
• determined by distribution of polar and non-polar amino acids

Question 8

Outline H bonding in an alpha helix

Answer 8

N-H of every peptide bond is hydrogen-bonded to the C=O of a neighbouring peptide bonded located 4 peptide bonds away (same chain)

Question 9

What is myoglobin?

Answer 9

• binds and stored O2 in muscles
• 153 amino acids
• 8 alpha helices

Question 10

Outline the H bonding in beta pleated sheets

Answer 10

Held together by H bonding between peptide bonds in different strands

Question 11

Outline the structure of antibodies

Answer 11

• 2 heavy 2 light chains
• 2 beta sheets packed tightly against each other in beta barrel (immunoglobulin fold)

Question 12

What are protein domains?

Answer 12

• substructure
• part of polypeptide that can fold independently into stable conformation
• modular units

Question 13

Outline quaternary structure of proteins

Answer 13

• more than one polypeptide
• each chain = subunit
• subunits arranged together and nature of contacts
• non-covalent interactions

Question 14

What are fibrous proteins?

Answer 14

• structural
• long strands
• insoluble
• elongated 3D structure

Question 15

What are globular proteins?

Answer 15

• knot-like shape
• dynamic functions

Question 16

What are disulphide bonds?

Answer 16

• S-S
• formed in ER
• 2 cysteine amino acids

Question 17

Give 6 examples of globular proteins

Answer 17

• enzymes
• hormones
• antibodies
• transport
• binding
• membrane

Question 18

Why do membrane proteins contain alpha helices?

Answer 18

• short regions (20 aa) span membranes
• non-polar side chains

Question 19

How is protein folding regulated?

Answer 19

• co-translational
• molecular chaperone (heat-shock proteins)

Question 20

What do exposed hydrophobic regions cause?

Answer 20

• aggregation and precipitation out of solution

Question 21

How are proteins transported?

Answer 21

• gated transport
• transmembrane transport : needs signal peptide
• vesicular transport

Question 22

What are localisation signals?

Answer 22

• direct proteins to specific organelles
• signal peptides or patches
• signal recognition particles guide proteins

Question 23

What is post-translational modification?

Answer 23

• proteolysis (cleavage)
• addition of carbohydrates
• addition of lipids
• phosphorylation, methylation, acetylation