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You can see the side chains vary significantly among the 20 major amino acids Some, like tryptophan, are large, creating steric forces that limit the possible conformations available to the peptide chain Others, like glycine and alanine, are small, allowing the possibility of tightly packed conformations Some amino acid side chains are hydrophilic, either uncharged polar or charged (ionized) at neutral pH Others are nonpolar and hydrophobic Three
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of the 20 amino acids are aromatic Phenylalanine and tryptophan are aromatic and hydrophobic, whereas tyrosine is aromatic but polar owing to a hydroxyl group on the aromatic ring
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Factors Influencing Protein Structure
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In this section we list and discuss the factors influencing protein structure These factors include the forces affecting the conformation of biomolecules (Chap 6) as they apply specifically to amino acids and peptide chains We begin with a discussion of charge interactions Charges occur in proteins due to the ionization of the amine and carboxyl groups of amino acids at the ends of the polypeptide chain, or due to the ionization of various amino acid side chains Charges cause the protein to fold in a way that maximizes the distance between like charges, while bringing opposite charges as close together as possible, all of which minimizes the free energy and stabilizes the protein structure
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Ionization of Amine and Carboxyl Groups
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The functional groups that define an amino acid are the amine and carboxyl groups on the a-carbon Both of the groups are easily ionized at physiological pH, the amine group by the addition of a proton, and the carboxyl group by the loss of a proton See Fig 9-1 The result is a zwitterion, an ionized molecule that has both a positive and a negative charge on it, but a net charge of zero
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O H C C O R (side chain)
+ NH3
Amino acid zwitterion
FIgure 9-1 Amino acid amine and carboxyl groups are easily ionized
In a polypeptide chain, the amine and carboxyl groups participate in the covalent peptide bonds, eliminating the possibility of ionizing these groups except at the ends of the chain Nonetheless that still means each polypeptide chain in a protein will have a positive charge at one end and a negative charge at the other; this can influence the folded structure of the protein Most proteins consist of a single polypeptide chain; however, many proteins contain more than one polypeptide chain bound together in a quaternary structure
chapter 9 p r o t e i n B i o p h y s i c s
Ionization of Amino Acid Side Chains
Five of the 20 major amino acids have side chains that carry a charge (ionize) at physiological pH Notably aspartate and glutamate each carry a negative charge, while histidine, lysine, and arginine carry a positive charge (see Table 9-1)
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What s the difference between polar versus charged When we use the word charged, we mean that the molecule is ionized ions contain a unit charge (the amount of charge on an electron or proton) or they contain a multiple of a unit charge in contrast, the word polar is used in various ways strictly speaking, polar means the presence of both positive and negative charges on the same molecule, but these can be either unit charges or partial charges in the case of an ionized molecule, polar would imply that the molecule is a zwitterion But ionized amino acid side chains typically contain only a positive or negative charge still, scientists sometimes refer to such single charge ions as polar, because ions prefer (energetically) to be in a polar environment that is, an environment containing polar molecules such as water Another use of the word polar is this: we say that a molecule or bond is polar when the electrons are distributed unevenly, so there is some charge, but it is a partial charge According to this use of the word polar, charged side chains contain more charge than polar side chains recall from chap 6 that the attractive or repulsive force between two charges (and the energy of their interaction) is proportional to product of the amount of each charge therefore the Gibbs energy change associated with the interaction of charged (ionized) side chains is stronger than that associated with polar side chains
These charged amino acid side chains can influence protein structure in a number of ways They can form salt bridges A salt bridge is a single ionic bond between a positive and negative ion In addition to salt bridges that hold parts of the molecule together, like charges will repel and tend to push certain parts of the polypeptide chain away from each other Positive charges can participate in a cation-pi attraction with an aromatic side chain (see Chap 6) Similarly a negative charge will result in repulsion from the side of an aromatic group, causing negatively charged side chains to be positioned away from aromatic side chains
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