Amino Acid Chemistry + Protein Structure Flashcards
Understand concepts introduced in Week Two of the course
True or False:
In a protein side-chain, the amino acid Ile will typically have a positive charge.
(Ile = isoleucine)
False
Its R group is a non-polar hydrocarbon.
True or False:
An acidic amino acid has a side chain with a pKa of 5.
At pH 7, its ratio of protonated : deprotonated form is 100:1.
False
pH 7 is more basic than pH 5 (the pH at which the p : d ratio is exactly 1 : 1), and so the deprotonated form would actually dominate.
True or False:
Alanine, Valine, and Asparagine are all hydrophobic.
False
Alanine and valine both have hydrocarbon groups as part of their R side-chain and so are hydrophobic.
However, asparagine has an amide side-group and so is polar and can form hydrogen bonds.
True or False:
Every amino acid with a ϕ,ψ value of -50,-50 will be in an alpha helix.
False
The sequence of amino acids before and after the one in those regions will determine what kind of structure it is a part of.
However, ‘all amino acids of an α-helix will be roughly in that region
True or False:
Hydrophobic collapse stabilises secondary structures in proteins.
False
Hydrogen bonding between amino acid side-chains stabilises secondary structures (e.g α-helices and β-sheets).
Proline is an ‘α-helix breaker’.
True
Glycine is also known for undermining α-helical structures becuase of its small R group (i.e. a single hydrogen).
Proline disrupts these secondary structures becuase of its irregular geometry.
True or False:
An aspartic acid side chain will typically be protonated at pH 7.
False
Aspartic acid has a side chain pKa of 3.9, and so the comparatively more basic environment will lead to it donating its hydrogen (i.e. deprotonating).
True or False:
An lysine side chain will typically be deprotonated at pH 7.
False
Lysine has a side chain pKa of 10.5, and so the comparatively more acidic environment will lead to it accepting hydrogens (i.e. being protonated).
True or False:
The higher the pKa of an acid, the more likely it is to be a strong acid.
False
An acid with a higher pKa will have a lower tendency to donate protons.
Complete the Sentence:
Most buffers consist of…
…a weak acid and its conjugate base.
What are TWO key features of the buffer zone?
(of a titration)
- Roughly equivalent concentrations of weak acid and conjugate base.
- Resistance to dramatic changes in pH.
At the buffer zone midpoint, [acid] = [conj. base] i.e. roughly equal molar concentrations.
What are the THREE ‘rough guidelines’ for charged amino acid side-chains?
(According to the BIOL244 Lectures)
- Carboxylic Acids: pKa ~ 4
- Basic Side-Chains: pKa > 9
- Slightly Basic (His): pKa ~ 6
(Note: This is at physiological pH 7).
Which weak acid is typically used in biochemical contexts and why?
Phosphoric Acid - it is triprotic and is utilised as an acid-catalyst, sequestering agent, etc.
ALthough it has buffers for three different pH levels, biochemists tend to only concern themselves with the one around physiological pH 7 ranges.
‘Sequestering agents’ form bonds with divalent atoms such as Mg, Fe (II), etc.
Name ONE important buffer system in biological systems.
The bicarbonate buffer system.
The linked equilibria buffer the pH away from pKa (whereas other buffers work more optimally when the system pH is close to the pKa of the weak acid).
In humans (and other species) this is a vital homeostatic mechanism that prevents the blood from becoming too alkaline/acidic.
Describe:
The FOUR universal structural components of an amino acid.
- A tetrahedral, chiral carbon.
- A carboxyl side group.
- An amino side group.
- An ‘R’ side group
The R side group is what gives each amino acid its unique properties (depending on the charge and polarity of this group).
What is the attractive force that holds amino acids together in a sequence?
Peptide bonds.
These form via dehydration polymerisation reactions between the carboxyl group of one amino acid and the amino group of another.
The carboxyl group loses an OH, and the amino group loses an H to form a water molecule as a byproduct.
Which amino acid is the exception to the general tetrahedral shape of these molecules.
Proline
(and all its derivatives)
It has a secondary amine group (imine) which forms a ring-structure in the molecule with its three-carbon R group.
This means proline is rotationally constrained / has a constrained phi (ϕ) angle.
It is also known as an ‘imino acid’.
List:
The TWO acidic amino acids.
(i.e. polar, charged)
- Aspartic Acid (Asp, D)
- Glutamic Acid (Glu, E)
Under typical physiological conditions of pH ~7, these are deprotonated and have a negative charge.
List:
The THREE basic amino acids.
(i.e. polar, charged)
- Lysine (Lys, K)
- Arginine (Arg, R)
- Histidine (His, H)
Under typical physiological conditions of pH ~7, these are protonated and have a positive charge.
List:
The SIX polar, uncharged amino acids.
Note: There are some amino acids that are sometimes counted but is overall a special case.
- Glutamine (Gln, Q)
- Serine (Ser, S)
- Asparagine (Asn, N)
- Threonine (Thr, T)
- Cysteine (Cys, C)
- Tyrosine (Tyr, Y)
Tyrosine is considered a ‘special case’ due to its ring-structure in its R side chain.
Cysteine is labelled this due to its S atom in the R side chain (i.e. weaker polar bond between S-H). Its hydophobicity is ‘ambiguous’ when it comes to protein structure.
List:
The NINE nonpolar amino acids.
- Alanine (Ala, A)
- Leucine (Leu, L)
- Valine (Val, V)
- Methionine (Met, M)
- Tryptophan (Trp, W)
- Phenylalanine (Phe, F)
- Isoleucine (Ile, I)
- Proline (Pro, P)
- Glycine (Gly, G)
Which conformation is the peptide bond usually found in?
Trans-conformation.
(i.e. the two α-carbons are on opposite sides of the peptide bond).
Which amino acid can form disulfide bonds/bridges?
Cysteine
It has a thiol group (SH) as its R side chain, which forms disulfide linkages with other cysteines, which may play an important role in protein structure.
Describe:
The amide plane.
(In relation to peptide bonds)
Due to the partial double-bond character of the peptide bond, the six atoms of this peptide group lie within the same plane.
This has important connotations for the three-dimensional folding of proteins.
Define:
Secondary protein structure.
Localised structures formed and stabilised by hydrogen bonding between different amino acid side chains of the polypeptide backbone.
(e.g. α-helices and β-sheets)
List:
FOUR examples of how you may visualise the tertiary structure of a protein.
- Backbone only.
- Backbone + sidechains.
- Ribbon structures.
- Space-filling structures.
Where can rotation occur in a peptide bond?
(i.e. in a polypeptide chain of amino acids)
About the two bonds either side of the ** α-carbon** connecting to its amide planes.
These are called the phi (φ) and psi (ψ) bonds.
Phi (φ) = the bond with the nitrogen of the amino group.
Psi (ψ) = the bond with the carbon of the carboxyl group.
What restricts the values of Phi (φ) and Psi (ψ), and thus reduces the degrees of freedom in secondary/tertiary protein structure?
Steric hindrance caused by atoms of neighbouring side-chains/groups in the polypeptide.
The image above shows some of the ‘disallowed’ bond angle combinations.
Which of the two main types of β-sheets are slightly more stable?
Parallel or Antiparallel?
Antiparallel β-sheets have slightly more optimal hydrogen bonding.
This is because the geometry of the parallel β-sheets leads to the hydrogen bond occurring at an angle that makes its length slightly longer (and thus slightly weaker).
