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BIO1332 Biochemistry > Amino acids & Proteins > Flashcards

Amino acids & Proteins Flashcards

1
Q

Define amino acids.

A

monomeric units of protein.

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2
Q

Which carbon is the alpha carbon?

A

The carbon attached to the carboxyl group.

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3
Q

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

A

R group.

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4
Q

Give the 4 main amino acid groups.

A
  • 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.
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5
Q

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

A

glycine.

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

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6
Q

Are amino acids cations or anions?

A

neither, zwitterions.

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7
Q

What kind of proteins is proline found in & why?

A

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

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8
Q

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

A

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.

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9
Q

What role does cysteine have in proteins & why?

A

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.

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10
Q

What conformation are the peptide chains in proteins & why?

A

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.

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11
Q

Give the directionality of amino acid sequences.

A

N terminal residue > C terminal residue

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12
Q

Define the primary structure of proteins.

A

sequence of amino acids

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13
Q

Define the secondary structure of proteins.

A

simple, repetitive motifs that are found in almost all proteins

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14
Q

Define the tertiary structure of proteins.

A

overall fold of a protein

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15
Q

Define the quaternary structure of proteins.

A

several proteins folded together

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16
Q

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

A

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

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17
Q

Why are the pure single bonds in a polypeptide important?

A

so rotation can occur.

18
Q

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

A
  • 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.
19
Q

What did Ramachandran et al., 1963 recognise?

A

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

20
Q

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

A

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

21
Q

How is secondary structure formed & maintained?

A

H bonding between NH & CO groups

22
Q

Describe an alpha helix.

A
  • 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.
23
Q

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

A

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

24
Q

Describe a beta sheet.

A
  • 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.
25
Q

Define the structure of loops.

A

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

26
Q

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

A

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

27
Q

Define ‘super secondary structure’.

A

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

28
Q

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

A

Myoglobin.

29
Q

Describe the structure of myoglobin

A
  • 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.
30
Q

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

A

Concanavalin A.

31
Q

Define domain.

A

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

32
Q

Describe the quaternary structure of human hemoglobin.

A
  • a2 B2 tetramer
  • 4 heme groups
  • 4 separate proteins folded together
33
Q

What is the effect of faults in protein folding?

A

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

34
Q

How are proteins held together & limitations of this?

A
  • 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.
35
Q

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

A

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

36
Q

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

A
  • hydrophobic interactions
  • ionic interactions
  • Van der Waals interactions
  • hydrogen binds
  • disulphide bonds.
37
Q

Describe hydrophobic interactions.

A
  • 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).
38
Q

Describe ionic interactions.

A
  • electrostatic interaction occurs between a positively charged amino acid & a negatively charged amino acid
  • single interactions or multiple clusters of interactions
39
Q

Describe Van der Waals.

A
  • 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
40
Q

Describe hydrogen bonds.

A
  • 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
41
Q

Describe disulphide bonds.

A
  • 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

BIO1332 Biochemistry (12 decks)

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