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BIOCHEMISTRY | PROTEIN STRUCTURE AND FUNCTION | AMINO ACIDS | NOTED BY FAKHRY (IG @SFAKHRYM)
v STRUCTURE
£ There are only 20 (among >300 different AAs [amino acids] described in nature) are commonly found as constituents of mammalian proteins
• These are the only AAs that are coded for by DNA
• These AAs are used for the synthesis of proteins by the mRNA-directed process that occur on ribosomes
• Other AAs exist for which there is no genetic code
§
example, in the urea cycle or in proteins where they are generated by posttranslational modifications (such as
hydroxyprolone in collagen)
Selenocysteine
•
§ It is known as the 21st amino acid
§ It is unique in that a serine residue is converted to selenocysteine while attached to a transfer RNA
...

• Hydroxyl groups found on serine and threonine can form hydrogen bonds
• A distinctive side chain ("R group"): bonded to the α-carbon atom
...
Its α-carbon contains two hydrogens
§ It is useful to classify the aas according to the properties of their side chains
§
Proline
• It differs from other aas
• Differ in its side chain, and α-amino N form a rigid (five-membered ring structure)
• Has secondary amino group - refers to "imino acid"
• The unique geometry of proline contributes to the formation of the fibrous structure of collagen and often
interrupts the α-helices found in globular proteins
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(Its α-carbon has two hydrogen substituents)
•
§ AAS with an asymmetric center at the α-carbon can exist in two forms, designated D and L
• The two forms in each pair are termed stereoisomers, optical isomers, or enantiomers
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BIOCHEMISTRY | PROTEIN STRUCTURE AND FUNCTION | AMINO ACIDS | NOTED BY FAKHRY (IG @SFAKHRYM)
v CLASSIFICATION
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CLASSIFIED ACCORDING TO THE CHARGE AND POLARITY OF THEIR SIDE CHAINS at ACIDIC pH

BIOCHEMISTRY | PROTEIN STRUCTURE AND FUNCTION | AMINO ACIDS | NOTED BY FAKHRY (IG @SFAKHRYM)
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AAS with nonpolar side chains
• Include: Alanine, glycine, isoleucine, leucine, methionine, phenylalanine, proline, tryptophan, and valine
• Does not gain or lose protons or participate in hydrogen or ionic bonds
• A property that promotes hydrophobic interaction: The side chains can be thought of as "oily" or lipid-like
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5), so it is not hydrophobic in
•
this pH range
• Location of nonpolar aas in proteins:
§ Hydrophobic effect: The side chains tend to cluster together in the interior of the protein in aqueous solutions (polar
environment), thus, fill up the interior of the folded protein and help give it its three-dimensional shape
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§ In hydrophobic environment (such as membrane), nonpolar R groups are found on the outside surface of the protein, interacting
with the lipid environment
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§ Serine, threonine, and tyrosine: each contain a polar hydroxyl group that can participate in hydrogen bond formation
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§ Amide group of aspargine, as well as the hydroxyl group of serine or threonine, can serve as a site of attachment for
oligosaccharide chains on glycoproteins

BIOCHEMISTRY | PROTEIN STRUCTURE AND FUNCTION | AMINO ACIDS | NOTED BY FAKHRY (IG @SFAKHRYM)
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AAS with acidic side chain
§ Include: Aspartic acid and glutamic acid (aspartate or glutamate): proton donors
§ At physiologic pH: the side chains are fully ionized, containing (-COO-)
§ They are negatively charged at physiologic pH

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AAS with basic side chain
§ Include: Histidine, lysine, and arginine: The side chains accept protons
§ At physiologic pH, the R groups of lysine and arginine are fully ionized and positively charged (-NH3+)
§
Histidine is weakly basic, the free aa is largely uncharged at physiologic pH
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• This is an important property of histidine that contributes to the buffering role, it plays in the functioning of proteins
such as hemoglobin
• Histidine is the only aa with a side chain that can ionize within the physiologic pH range
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e
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This flexibility has two effects
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The second is that it is an ideal residue
for protein functional centres
Proline and Glycine
§ Proline: Secondary alpha amino group
§ Glycine: no chirality (simplest side chain)
§ Very flexible (free rotation)
§ Both of them have effect on alpha helix - secondary structure (alpha helix breaker)
Cysteine
§ Has -thiol group: make disulfide bridge
Selenocysteine
§ It is known as the 21st amino acid (also proteinogenic, - they are incorporated in translation)
§ Its R group contain selenol group
§ It's the only amino acid containing an essential dietary micronutrient (selenium) as a constitutive component (essential
dietary = have to get from diet)
§ the only amino acid encoded by a UGA codon and the only one synthesized on its tRNA in all domains of life
§ It is used in selenoproteins, a protein that has selenocysteine in it
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g
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The
net charge of the entire molecule is zero
§ Amino acids are the best-known examples of zwitterions
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The -NH2 group is the stronger base, and so it picks up H+ from the -COOH group to leave a zwitterion (i
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the
amine group de-protonates the carboxylic acid)
§ When an amino acid dissolves in water, the zwitterion interacts with H2O molecules – acting as both an acid and a base
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If you dissolve the amino acid in water, a simple solution
also contains this ion
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78)
§ Can be used to calculate how the pH of a physiologic solution responds to changes in the concentration of a weak acid and/or
its corresponding "salt" form
• Example: calculating the abundance of ionic forms of acidic and basic drugs (see in pharm chapter)

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Buffers (it is a solution that resists change in pH following the addition an acid or base)
§ Amino acids in aqueous solution contain weakly acidic α-carboxyl group and weakly basic α-amino grups

BIOCHEMISTRY | PROTEIN STRUCTURE AND FUNCTION | AMINO ACIDS | NOTED BY FAKHRY (IG @SFAKHRYM)
Thus, both free amino acids and some amino acids combined in peptide linkages can act as buffers
• See aas histidine
Can be created by mixing a weak acid (HA) with its conjugate base (A-)
§ If an acid such as HCl is added to a buffer, A- can neutralize it, being converted to HA in the process
§ If a base is added, HA can neutralize it, being converted to A- in process
Maximum buffering capacity occurs at a pH equal to the pKa, but a conjugate acid-base pair can still serve as an effective buffer when
the pH of a solution is within +-1 pH unit of the pKa
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To that end, you will each be assigned a single unknown amino acid to identify
by titration versus a standardized solution of NaOH (link)
§ Ionizable groups on AAs carry protons at low pH (high [H+]), which dissociate as the pH increases
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Once the pH is above the pKa, the group will be protonated
§ See video for example (example of titration curve of alanine, glycine, and histidine)

BIOCHEMISTRY | PROTEIN STRUCTURE AND FUNCTION | AMINO ACIDS | NOTED BY FAKHRY (IG @SFAKHRYM)

BIOCHEMISTRY | PROTEIN STRUCTURE AND FUNCTION | AMINO ACIDS | NOTED BY FAKHRY (IG @SFAKHRYM)
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Titration of Amino acids



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