Proteins (BIOC1001)

Proteins have many roles to play in nature. This roles fall into 4 major functional groups: [blank_start]binding[blank_end] (even though every role involves a binding event), [blank_start]catalysis[blank_end] (enzymes speed up reactions that turn [blank_start]substrates[blank_end] into metabolites), [blank_start]switching[blank_end] (receptors that bind [blank_start]ligands[blank_end] changing conformation and triggering internal response) and [blank_start]structural[blank_end] (such as collagen in [blank_start]extracellular[blank_end] matrix or keratin in your hair and nails).

Proteins are composed of amino acids linked by amide bonds.

Nonionic forms can NEVER exist in nature. This statement is:

All amine and carboxylic groups are charged.

R groups can also be [blank_start]charged[blank_end] since they also have pKa which depends on [blank_start]molecular structure[blank_end] and [blank_start]environment[blank_end] of amino acid. In proteins, the [blank_start]pKa[blank_end] of the [blank_start]amino[blank_end] and [blank_start]carboxyl[blank_end] groups can be ignored since they cancel each other out at N and C terminus. Thus, only [blank_start]side-chain[blank_end] pKa's influence [blank_start]charge[blank_end] of protein, which is, therefore, [blank_start]pH[blank_end] dependent.

Which ones are FALSE?

In nature, amino acids can exist as two mirror images: L and D stereoisomeres.

Which amino acids have aliphatic R groups?

Amino acids with hydrocarbon side-chains are non-polar and thus [blank_start]hydrophobic[blank_end]. The higher the aliphatic complexity the more [blank_start]hydrophobic[blank_end] and, therefore, tend to be in the [blank_start]center[blank_end] of the protein sequestered away from the solvent. The most hydrophobic amino acids are [blank_start]Leucine[blank_end] and [blank_start]Isoleucine[blank_end], the latter having [blank_start]4 stereoisomers[blank_end] due to the 2 chiral centers, whereas the least complex, [blank_start]glycine[blank_end], tends to be in [blank_start]sharp turns[blank_end] due to imparted structural flexibility. There are, however, a few exceptions where you can find aliphatic side-chains on the protein surface, for instance if it binds to hydrophobic substrate/ligand or other hydrophobic protein.

Name the following acidic R groups (carboxylic and amide side-chains)?

Acidic R groups ([blank_start]aspartate[blank_end] and [blank_start]glutamate[blank_end]) have carboxylic side-chains which confer them a [blank_start]negative[blank_end] charge at physiological pH (due to their [blank_start]deprotonation[blank_end] turning them into conjugate bases) and thus are very [blank_start]hydrophilic[blank_end]. This means that they are commonly found in the [blank_start]surface[blank_end] of proteins and in [blank_start]active[blank_end] sites of enzymes (since they are used in catalysis as a [blank_start]base[blank_end]).

Which is the most basic amino acid?

[blank_start]Basic[blank_end] R groups (acyclic with basic N containing side-chains) are very [blank_start]hydrophilic[blank_end] and thus are found at the [blank_start]surface[blank_end] of proteins and as binding sites. At pH=7, they are [blank_start]positively[blank_end] charged ([blank_start]Arginine and Lysine[blank_end]), with the exception of Histidine. Arginine is the most basic amino acid. [blank_start]Histidine[blank_end] can be either a base or an acid (pKa~7), key for acid-base catalysis in [blank_start]enzimes[blank_end], and binds to [blank_start]metal ions[blank_end] such as Zn2+, key for protein structure and function (glutamate and sometimes aspartate also bind to metal ions).

Which of the following amino acids contain side-chains with sulphur groups?

Sulfur containing side-chains are [blank_start]hydrophobic[blank_end] ([blank_start]methionine[blank_end]) but [blank_start]cysteine[blank_end] is extremely reactive (sometimes can be found in [blank_start]active[blank_end] sites), polarisable and can loose H+ to become S- ion. It is also responsible for the formation of [blank_start]dissulphide bonds[blank_end] (covalent), which give proteins [blank_start]stability[blank_end] and conformational rigidity), especially found in proteins required to be [blank_start]tough[blank_end] or to stabilize folding of [blank_start]long[blank_end] polypeptides.

Which of the following statements about side-chains with alcohols are FALSE?

Which of the following amino acid side-chains have N heterocycles?

Which amino acids are responsible for protein's optical density (absorb UV light) at 280nm?

[blank_start]Proline[blank_end] is a special amino acid whose side-chain contains a [blank_start]N heterocycle[blank_end], like Tyrosine, Phenilalanine and Tryptophan. Nevertheless, it is unique in that it has no free [blank_start]amino[blank_end] group to form H-bond with [blank_start]carboxyl[blank_end] group further down the chain. Thus, it halts [blank_start]helice[blank_end] formation and, hence, is called [blank_start]helice breaker[blank_end]. Furthermore, whereas normally [blank_start]trans[blank_end] configuration of peptide bonds is favored (alpha-carbon substituents as far apart as possible, facing [blank_start]opposite[blank_end] sides), in amide bonds involving [blank_start]proline[blank_end] there is higher probability of forming [blank_start]cis[blank_end] configuration (facing [blank_start]same[blank_end] side), giving rise to strange configurations.

Why are peptide bonds so strong?

Under physiological conditions, the peptide bond is planar which restricts it to 2 possible configurations: cis and trans. To minimize steric crowding due to close proximity between bulky groups on C and N the trans form is always favored.

The peptide bond is [blank_start]planar[blank_end] (no rotation) but the C-C and C-N bonds on either side are [blank_start]flexible[blank_end], thus determining shape of polypeptide which is key for complex protein structure. The torsion angles around C-C and C-N are the [blank_start]psi[blank_end] and [blank_start]phi[blank_end] angles, respectively. Rotation is determined by nature of [blank_start]R[blank_end] groups. [blank_start]Ramachandran[blank_end] plotted allowed [blank_start]phi[blank_end] and [blank_start]psi[blank_end] angles (the degrees of freedom of bonds in proteins) according to [blank_start]steric hinderance[blank_end] (physical size of atoms/groups of atoms limits possible torsion angles). If all [blank_start]phi[blank_end] and [blank_start]psi[blank_end] angles are the same, peptide assumes repeated structure, such as a-[blank_start]helix[blank_end] or B-[blank_start]sheet[blank_end].

Missense mutations can be silent.

Label the levels of protein structure.

Which of the following are determined by a protein's primary structure?

Which of the following questions about the peptide bond are FALSE?

Chemical reactivity of a polypeptide chain is determined by the nature and location of the [blank_start]peptide[blank_end] bonds ([blank_start]primary[blank_end] structure), the carbonyl [blank_start]O[blank_end] and amide N ([blank_start]secondary[blank_end] structure) and the [blank_start]R[blank_end] groups attached to the alpha-C. The combination of these re reactivities determines folding and folded structure of proteins. Although proteins are linear polymers, they don´t form random conformations. Most are [blank_start]globular[blank_end] with [blank_start]hydrophobic[blank_end] core and the amino acid chain takes up conformations with regular patterns of torsion angles [blank_start]phi[blank_end] and [blank_start]psi[blank_end]. The resultant regular segments make up the [blank_start]secondary[blank_end] structure.

The carbonyl and amide groups of peptide bond determine the primary and secondary structures.

Which one is TRUE?

Secondary structures are formed by H-bonds between [blank_start]amide[blank_end] N and carbonyl [blank_start]O[blank_end] of peptide groups in polypeptide chains. Hence, not surprisingly, the 2 most common configurations, [blank_start]alpha-helices[blank_end] and [blank_start]B-sheets[blank_end], are the ones which [blank_start]maximize[blank_end] H-bonding. Alpha-helices are formed by repeated pattern of H-bonding between carbonyl [blank_start]O[blank_end] and close [blank_start]amide[blank_end] N [blank_start]4[blank_end] residues further down the same chain. All polar [blank_start]amide[blank_end] and carbonyl groups are H-bonded except [blank_start]first[blank_end] N and last [blank_start]O[blank_end]. [blank_start]B-sheets[blank_end] have no fixed pattern since the H-bonds occur between distant groups. However, these are always present (no free polar amide or carbonyl groups), apart from the [blank_start]edge[blank_end] strands.

Which one is FALSE regarding alpha-helices?

Which ones are TRUE about B-sheets?

B-turns are...

Which interactions play a role in tertiary structure?

The [blank_start]tertiary[blank_end] structure of a protein is the final folded polypeptide chain held together by mostly [blank_start]non-covalent[blank_end] interactions in its most [blank_start]stable[blank_end] structure. The interaction between [blank_start]R[blank_end] groups and between these and [blank_start]water[blank_end] dictates the [blank_start]tertiary[blank_end] structure. The fact that those [blank_start]non-covalent[blank_end] interactions are relatively [blank_start]weak[blank_end], and therefore break and reform easily, allows for structural [blank_start]flexibility[blank_end] which is key to protein [blank_start]function[blank_end]. Flexible regions are often [blank_start]loops[blank_end] (long stretches of amino acids between secondary structure elements) that protrude into the solvent being involved in [blank_start]function[blank_end] and, since they don´t contribute to [blank_start]stability[blank_end], are more prone to [blank_start]mutation[blank_end] which provides a mechanism for molecular [blank_start]evolution[blank_end]. Apart from the [blank_start]flexible[blank_end] functional regions, often there are inflexible/rigid [blank_start]framework[blank_end] regions which can require additional stabilization provided by: 1-[blank_start]dissulfide bonds[blank_end] (covalent bonds between [blank_start]Cysteine[blank_end] residues); 2-coordinate covalent bonds with [blank_start]metal ions[blank_end] (mainly Ca2+ and Zn2+, distinct from metal ions in [blank_start]active[blank_end] sites) and 3-stabilization by [blank_start]co-factor[blank_end] binding (required by some proteins to exhibit activity and for stability). Hence, tertiary structure can exhibit various distinct [blank_start]domains[blank_end] with particular shapes and functions. [blank_start]Post-translational modifications[blank_end] (phosphorylation, glycolisation, ubiquitination...) also change an stabilize tertiary structure, as well as [blank_start]water[blank_end], whether forming an [blank_start]hydration shell[blank_end] that exerts pressure providing stability or the molecules trapped [blank_start]inside[blank_end] the protein which can be important for structure and activity.

The interaction between R groups is the major determinant in protein folding.

Which one is TRUE?

The [blank_start]Hydrophobic[blank_end] effect, the clustering of hydrophobic side-chains in the protein's [blank_start]core[blank_end], is the major driving force behind [blank_start]folding[blank_end]. Non-polar [blank_start]R[blank_end] groups are sequestered away from the solvent to [blank_start]minimize[blank_end] contact area with [blank_start]water[blank_end] because, as they cannot form [blank_start]H-bonds[blank_end], they would disrupt H-bonded network of water. This also brings polarisable [blank_start]hydrophobic[blank_end] groups together allowing [blank_start]Van der Waals[blank_end] interactions. Hence, generally polar side-chains tend to be on the [blank_start]surface[blank_end] of the protein whereas [blank_start]non-polar[blank_end] ones tend to be on the core. Nevertheless, not only polar residues, as well as water, can be dragged away (or trapped) to the [blank_start]core[blank_end] and tend to H-bond with other [blank_start]polar[blank_end] elements, but hydrophobic residues can also cluster on the [blank_start]surface[blank_end], either because this unfavorable structure is compensated by overall [blank_start]favorable[blank_end] interactions or because those clusters form [blank_start]binding[blank_end] sites or interact with other non-polar groups.

Which is FALSE?