Amino acids & Proteins

Question 1

Define amino acids.

Answer 1

monomeric units of protein.

Question 2

Which carbon is the alpha carbon?

Answer 2

The carbon attached to the carboxyl group.

Question 3

What does the identity & properties of an amino acid depend on?

Answer 3

R group.

Question 4

Give the 4 main amino acid groups.

Answer 4

• hydrophobic with non polar R groups
• polar amino with neutral R groups that have an uneven charge distribution
• positively charged amino acids with R groups that have a positive charge at physiological pH
• negatively charge amino acids with R groups that have a negative charge at physiological pH.

Question 5

Which is the only non-chiral amino acid & its key structural feature?

Answer 5

glycine.

super flexible so provides flexibility where other side chains are too bulky.

Question 6

Are amino acids cations or anions?

Answer 6

neither, zwitterions.

Question 7

What kind of proteins is proline found in & why?

Answer 7

Prolines side chain bonds to the amine. Tight constraints in proteins so found in rigid proteins, eg in turns of globular proteins.

Question 8

What part of the protein is histidine usually found in & why?

Answer 8

Histidine found in many active sites, only amino acid with pKa of side near neutral pH (6.7). Important because it can alter its charge at physiological pH, can be influenced by other residues. R group has an imidazole ring which releases protons during reactions.

Question 9

What role does cysteine have in proteins & why?

Answer 9

Cysteine contains sulphur (free thiol group). Forms covalent bond with other cysteine residues to stabilize protein. pKa of 8.4. Sulphur is good ligand with iron.

Question 10

What conformation are the peptide chains in proteins & why?

Answer 10

Peptide chains in proteins in trans conformation so R groups are on different sides of the chain to avoid steric clashes. Only exception is Proline.

Question 11

Give the directionality of amino acid sequences.

Answer 11

N terminal residue > C terminal residue

Question 12

Define the primary structure of proteins.

Answer 12

sequence of amino acids

Question 13

Define the secondary structure of proteins.

Answer 13

simple, repetitive motifs that are found in almost all proteins

Question 14

Define the tertiary structure of proteins.

Answer 14

overall fold of a protein

Question 15

Define the quaternary structure of proteins.

Answer 15

several proteins folded together

Question 16

Why is the partial double bond character of the peptide bond significant?

Answer 16

provides rigidity in protein structure, prevents significant movement around the peptide bond.

Question 17

Why are the pure single bonds in a polypeptide important?

Answer 17

so rotation can occur.

Question 18

Give the 2 important pure single bonds in polypeptides & why they are important.

Answer 18

• Phi is the angle of rotation of the N - a-Carbon .
• Psi is the angle of rotation of the a-Carbon – carbonyl carbon.
• these angles determine the oath of the polypeptide chain.

Question 19

What did Ramachandran et al., 1963 recognise?

Answer 19

many combinations are forbidden due to steric clashes, allowed values plotted on 2-dimensional plot called a Ramachandran Plot.

Question 20

What limits the no. of structures accessible to unfolded form sufficiently enough to allow protein folding to take place?

Answer 20

igidity of peptide unit & restricted set of allowed Phi and Psi angles

Question 21

How is secondary structure formed & maintained?

Answer 21

H bonding between NH & CO groups

Question 22

Describe an alpha helix.

Answer 22

• right handed helix
• No. residues/turn = 3.6
• H bonding arranged so C=O bond of nth residue points along the helix towards N-H group of the (n+4)th residue.
• R groups all point outwards.

Question 23

Residues facing outward tend to be _ and those facing inwards tend to be _.

Answer 23

Residues facing outward tend to be hydrophilic and those facing inwards tend to be hydrophobic.

Question 24

Describe a beta sheet.

Answer 24

• beta strands
• at least 2 polypeptide chains
• can be parallel or antiparallel
• successive R groups, 2 residue repeat of 7.0 A
• rippled or pleated
• H bonding between C=O of one chain to N-H of other chain
• Typically 4 or 5 strands combine, can be a mix of parallel & antiparallel or purely one of those.
• B-turn, CO group of residue i is H bonded to NH group of i+3. This interaction stabilises abrupt changes in direction.

Question 25

Define the structure of loops.

Answer 25

do not have regular periodic structure, often rigid & well-defined.

Question 26

Give the position & function of turns & loops in proteins.

Answer 26

lie on the surfaces & participate in interactions with other molecules.

Question 27

Define 'super secondary structure'.

Answer 27

elements of secondary structure link together into their own combinations, forming mini-domains that have stability in their own right.

Question 28

What was the first protein to have its full structure determined by Watson & Kendrew 1950’s?

Answer 28

Myoglobin.

Question 29

Describe the structure of myoglobin

Answer 29

- single polypeptide of 153 amino acids - binds heme (prosthetic group) - dimensions: 45 x 35 x 25 A - 70% is 8 a helices, rest is turns & loops.

Question 30

Give an example of a protein with a secondary structure completely made of beta sheets.

Answer 30

Concanavalin A.

Question 31

Define domain.

Answer 31

section of protein that can fold independently. Some have many, all have at least one.

Question 32

Describe the quaternary structure of human hemoglobin.

Answer 32

- a2 B2 tetramer - 4 heme groups - 4 separate proteins folded together

Question 33

What is the effect of faults in protein folding?

Answer 33

Diseases such as cystic fibrosis caused by misfolding of a protein involved in Cl- transport across membranes.

Question 34

How are proteins held together & limitations of this?

Answer 34

- accumulation of weak forces & are only marginally stable - only work in conditions if organism they are in - easily denatured by extreme pH, rise in temperature and are not usually stable in organic solvents that strip away the essential layer of water molecules.

Question 35

Why do are folded proteins in their most energetically favourable conformation?

Answer 35

Unfolded: contact between polypeptide & water is maximised. Folded: more compact structure reduces contact with water.

Question 36

Give the 5 forces that hold the protein in its folded state.

Answer 36

- hydrophobic interactions - ionic interactions - Van der Waals interactions - hydrogen binds - disulphide bonds.

Question 37

Describe hydrophobic interactions.

Answer 37

- amino acid has a methyl group on side chain or a ring structure - trying to get away from the water solvent - water molecules surrounding hydrophobic residue, so they can’t interact with other water molecules (very ordered around it) and therefore entropy is decreased. ‘Clathrate’ structure. - if hydrophobic residues are aggregated less water molecules are stuck in this structure (surface area decreased).

Question 38

Describe ionic interactions.

Answer 38

- electrostatic interaction occurs between a positively charged amino acid & a negatively charged amino acid - single interactions or multiple clusters of interactions

Question 39

Describe Van der Waals.

Answer 39

- non-covalent interactions between electrically neutral molecules arising from electrostatic interactions between permanent dipoles and/or instantaneous induced dipoles - weaker than ionic but there is a large collective of them - they have a positive & negative component

Question 40

Describe hydrogen bonds.

Answer 40

- electrostatic attractions between a weakly acidic donor group & an acceptor atom that bears a lone pair of electrons - h atom sandwiched between 2 electronegative atoms - ideal bond length is 2.7-3.1 A - many H bonds in alpha helices & beta sheets - H bonding in alpha helix arranged so C=O bond of nth residue points along helix towards N-H group N+4th residue - H bonds in water, in unfolded state H bonds will from with solvent, in folded state H bonds form between residues (one bond compared to two so entropy increases because two water molecules are liberated) - H bonds by themselves make weak contributions to stability of the molecule

Question 41

Describe disulphide bonds.

Answer 41

- covalent bind between two cysteine amino acids in the protein chain - only covalent bond found to hold the protein chain in its correct fold - found mainly in proteins that are exported from the cell or those that must be stable in high temperatures