Where would you expect to find polar amino acids in a protein in an aqueous environment?

From The School of Biomedical Sciences Wiki

Polar Amino Acids There are twenty amino acids that occur naturally, these amino acids can be separated into two groups; non-polar amino acids and polar amino acids. The polar group consist of 10 amino acids, two are negatively charged - aspartic acid and glutamic acid, 3 have a positive charge - arginine, lysine and histidine, and 5 are uncharged - asparagine, glutamine, serine, threonine and tyrosine.[1] The properties of the amino acid are due to the properties of the side chain or R-group. These properties are extremely important when it comes to forming protein structure as different R-groups allow different non-covalent bonds to form between amino acids in the polypeptide chain. For example only amino acids with charged R-groups can form ionic bonds with each other or with other charged molecules [2].
All polar amino acids have either an OH or NH2 group (when in aqueous environment), and can therefore make hydrogen bonds with other suitable groups [3].

Polarity of the amino acids affects the overall structure of a protein. Polar amino acid residues have a tendency to be on the outside of a protein, due to the hydrophilic properties of the side chain [4].
A mutation which causes an amino acid substitution can have a great affect on protein structure and therefore protein function. For example the point mutation which substitutes valine for the polar amino acid glutamate causes haemoglobin to change its shape, due to the new hydrophilic region, leading to the condition known as sickle cell anaemia [5]

References

  1. ↑ Alberts B., Johnson A., Lewis J., Raff M., Roberts K. and Walter P. (2008) Molecular Biology of the cell, 5th edition, New York: Garland Science. (Pg 127)
  2. ↑ Gupta P.K. (2009) Cell and Molecular Biology, 2nd edition, New Delhi: Rastogi Publications, p. 43
  3. ↑ Alberts B, Johnson A, Lewis J, Raff M, Roberts K and Walter P (2008) Molecular Biology of the Cell, 5th edition, New York: Garland Science, p. 125 - 129
  4. ↑ Alberts B, Johnson A, Lewis J, Raff M, Roberts K and Walter P (2008) Molecular Biology of the Cell, 5th edition, New York: Garland Science, p. 125 - 129
  5. ↑ Chen, Harold (2006) Atlas of genetic diagnosis and counseling, Totowa, N.J. : Humana Press

  1. Biology
  2. University of Illinois at Chicago
  3. Cell Biology
  4. Question #1601597

Anonymous Student

8 months ago

The sequences for three different tripeptides are written out below. Indicate whether you expect to find them in the inner core or on the surface of a cytosolic protein, and explain your answer. A. Serine-Threonine-Tyrosine B. Alanine-Glycine-Leucine C. Proline-Serine-Alanine

    All replies

    Expert Answer

    8 months ago

    The presence of hydrophobic and polar amino acids in the polypeptide determines which part of the protein will be exposed to the aqueous environment such as towards the periphery of the cytosolic protein or in the inner core of the cytosolic protein.

    1. Serine-Threonine-Tyrosine: This tripeptide comprises polar amino acids that do not carry any charge. Therefore, this peptide sequence can be found on the surface of the protein exposed to the cytosol (aqueous region).
    2. Alanine-Glycine-Leucine: This tripeptide comprises amino acids with hydrophobic side chains. These non-polar amino acids will be present in the inner core of the protein where they interact with other non-polar amino acids via the formation of the hydrophobic bonds. This tripeptide sequence will avoid any possible interactions with the aqueous or cytosolic environment as it is energetically unfavorable.
    3. Proline-Serine-Alanine: This tripeptide comprises a mix of polar (serine) and non-polar (proline and alanine) amino acids. Based on the nature of each amino acid, the serine amino acid is most likely to be exposed to the outer surface of the protein facing the cytosol. As proline posses limitations in terms of conformation freedom, it is mostly found in the turns or loop structures of polypeptide chains. The chances are that the proline might be partly exposed to the cytosol whereas the alanine residue will be completely buried inside the core of the protein as it is a non-polar amino acid residue.

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    Where would you expect to find polar amino acids in a protein in an membrane environment?

    Polar amino acids tend to be located on the protein surface (capable of interacting with water molecules)

    Where are polar amino acids found in proteins?

    Polar amino acids are those with side-chains that prefer to reside in an aqueous (i.e. water) environment. For this reason, one generally finds these amino acids exposed on the surface of a protein.

    Where are polar charged amino acids found?

    Six amino acids have side chains that are polar but not charged. These are serine (Ser), threonine (Thr), cysteine (Cys), asparagine (Asn), glutamine (Gln), and tyrosine (Tyr). These amino acids are usually found at the surface of proteins, as discussed in the Proteins 2 module.

    Are polar amino acids soluble in water?

    Amino acids are generally soluble in water and insoluble in non-polar organic solvents such as hydrocarbons. This again reflects the presence of the zwitterions. In water, the ionic attractions between the ions in the solid amino acid are replaced by strong attractions between polar water molecules and the zwitterions.