Amino acids, peptides, proteins and enzymes

Question 1

Optical activity of AAs

Answer 1

• at least 1 chiral center ⇒ can have enantiomers/ diastereoisomers
• enantiomeres can be L or D
• almost all proteins ⇒ L configuration (except glycine)

Question 2

Hydropathy index

Answer 2

• represents hydrophobic or hydrophilic properties of the side chain of AA
• hydrophibic ⇒ +
• hydrophilic ⇒ -

Question 3

Isoelectric point

Answer 3

• no net charge
• isoelectric species: zwitterions
• isoelectric pH is the pH midway between the pKA values on either side of the point
  pH= pI= (pKa1+pKa2)/2

Question 4

Configuration

Answer 4

geometric relationship between given set of atoms

Question 5

Conformation

Answer 5

• spatial arrangement of proteins
• achieved without breaking covalent bonds
• due to rotation of single bonds
• the chosen conformation usually ⇒ lowest Gibbs free energy⇒ most thermodynamically stable

Question 6

Primary protein stucture

Answer 6

• genetically determined
• stabilizing forces: covalent bod, peptide bond
• sequence of amino acids in polypeptide chain
• determines its function

Question 7

Ramachandran Plot

Answer 7

• helps predict secondary structure of protein

- shows possible rotations of alpha1 and alpha2 carbons

Question 8

Secondary protein structure

Answer 8

• alpha helix
• beta sheet
• beta turn
• stabilizing forces: H bonds between peptide groups
• stability base on: minimized steric repulsion between side chains, maximized H-bonds between peptide groups

Question 9

Alpha helix

Answer 9

• spiral structure consisting of coiled polypeptide backbone core with side chains oriented outwards and hydrophilic elements inward
• completer turn: 3,6A
• stability: H bonds between peptide bond carbonyl oxygens and amide hydrogens
• van der Waals interactions in core of helix
• right handed or left handed

Question 10

Decrease of Stability of proteins structure

Answer 10

• electrostatic interactions of side chains
• bulkiness of side chains
• positive or negative charged AAs at C- or N-terminal
• proline
• interaction between AA residues at end of helical segment and electric dipole inherent to helix

Question 11

Beta Sheet

Answer 11

• all peptide bonds involved in H-bonding
• consist of 2 or more polypeptide chains
• parallel sheets
• antiparallel sheets
• right handed twist

Question 12

Beta turn

Answer 12

• reverses direction of polypeptide chain ⇒ compact globular shape
• H-bond between 1st and 4th AA

Question 13

Tertiary protein structure

Answer 13

• Interactions: disulfide bridges, hydrophobic, polar, H-bonds, salt bridges, electrostatic
• Hydrophobic pocket
• Domains: structural and functional units of the polypeptides

Question 14

Quaternary protein structure

Answer 14

• proteins consisting of 2 or more polypeptide chains

- Interactions: hydrophobic, polar, ionic, H-bond

Question 15

Proteins assisting in proteins folding

Answer 15

• Chaperons: during protein synthesis, help move hydrophobic inside. Heat shock proteins
• Proteins disulphide isomerase: catalyze formation and breakage of disulphide bonds
• Proline-cis, trans- isomerase: cis-trans isomerization of peptidyl-prolyl bond

Question 16

Alpha keratin

Answer 16

• location: hair, nails, horns, hooves, quills etc
• intermediate filaments
• right handed alpha helix
• regular inter-chain H-bonds

Question 17

Silk Fibroin

Answer 17

• protein of silk
• produced by insects and spiders
• mainly beta-sheets
• not stretch

Question 18

Collagen

Answer 18

• location: tendons, cartilage, bone, skin etc
• fibrous protein
• provides structural function to the body
• Primary structure: Gly, Pro, hydroxyproline
• Post translational modification: proline/lysine ⇒ hydroxyproline or hydroxylysine
• Secondary structure: collagen helix

Question 19

Procollagen and tropocollagen

Answer 19

• 3 collagen helices ⇒ triple helix with globular part ⇒ Procollagen
• stabilizing forces: H-bonds
• function of globular part: promote folding + inhibit fiber formation
• procollagen peptidase: remove globular part ⇒ Tropocollagen ⇒ can polymerize ⇒ fiber

Question 20

Alpha Keratin

Answer 20

• location: hair, nails, claws, hooves etc.
• intermediate filaments
• right handed alpha helix

Question 21

Silk fibroin

Answer 21

• produced by insects and spiders
• beta sheet ⇒ polypeptide chain
• highly flexible

Question 22

Myoglobin

Answer 22

• monomer
• compact
• 75% alpha helices
• non-polar side chains inside, polar side chains outside
• contains a heme

Question 23

DIPF

Answer 23

irreversible inhibitor of Ser-proteases

Question 24

Specific inhibitors

Answer 24

SH-enzymes: monoiodoacetate

OH-enzymes: DIPF

Question 25

Non-specific inhibitors

Answer 25

denaturation of enzymes heavy metal ions heat