Lecture 5 Chapter 4 Amino Acids

Amino acid structure General properties Peptide bonds Classification and characteristics Acid-base properties Nomenclature Stereochemistry Nonstandard amino acids Amino acid derivatives D-amino acids Biologically active amino acids

Amino Acids The building blocks of proteins

Backbone of an amino acid is composed of the N, C, and C. Amino acid structures and sequences are written from left to right, starting with the N-terminus (amino) and finishing with the Cterminus (carboxyl) The thing that differentiates each amino acid is the R group C is chiral, except in Gly

Amino acids
The amino acid, Alanine (Ala, A) is shown below in line, stick, ball and stick, and CPK (space filling) representations.

Representative Amino acids

Asn

Tyr

Leu

Cys

Glu

Arg

His

Models of Amino Acids - Ball and Stick & Space filling

(1) A I F (2) Q (3)

Amino acids - polypeptides

Amino acids can be connected together via peptide bonds to form polypeptide chains Tripeptide (ADF) below in stick (left) and CPK (right) representations quite a different impression, huh?!

Amino acids can form peptide bonds CO-NH linkage

Amino acid residue Dipeptides, tripeptides, oligopeptides Polypeptides Proteins consist of one or more PP

Peptides are linear polymers that range from 8 to 4000 amino acid residues Twenty (20) different naturally occurring amino acids

Linear arrays of amino acids can make a huge number of molecules

Consider a peptide with two amino acids
AA1 AA2

20
AA1

20
AA2

= 400 different molecules

AA3

20 x

20 x

20 =

8000 different molecules

For 100 amino acid protein the # of possibilities are:

20100 = 1.27 x10130

The total number of atoms in the universe is estimated at

9 x1078

Cystine consists of two disulfide-linked cysteine residues

Cys residues have SH groups at the end of their side chains. Two of these groups can be oxidized to form an S-S (disulfide) bond.

Protein structure - example

DNA polymerase I Adds nucleic acids to the end of a DNA strand (shown in red) The protein undergoes a substantial conformational change during reaction (blue and black are open and closed conformations)

Protein structure - example

The crystal structure of the hexameric ATPase HP0525 from Helicobacter pylori

Amino Acids:
The building blocks of proteins
pKR pK1

pK2

-amino acids because of the -carboxylic and -amino groups pK1 and pK2 respectively pK is for R group pKs Remember these values for the pK1 2.2 while pK2 9.4 pKas of the termini for ALL AAs
R

In the physiological pH range, both carboxylic and amino groups are completely ionized!!
Hint: draw the structures of an amino acid at several pH values

Acid - Base properties of amino acids

[A - ] pH = pK + log [HA]
Isoelectric point: the pH where a protein carries no net electrical charge

1 pI = ( pK i + pK j ) 2

For a monoamino-monocarboxylic residue pKi = pK1 and pKj = pK2 ; For D and E, pKi = pK1 and pKj = pKR ; For R, H and K, pKi = KR and pKj = pK2

The observed pKa of an amino acid side chain is dependent on its environment in the protein standard pKas can be substantially shifted by the protein environment!!

Isoelectric point
pI = 0.5(pKi + pKj); for 2 ionizable groups If amino acid has ionizable side chain, then it must be taken into account when computing pI If the side chain is negatively charged when ionized (Asp, Glu), then pI = 0.5(pK1 + pKR) (remember pK1 is the pKa of the Cterminus, -COOH)
e.g., pI of Asp = 0.5(2.20 + 3.90) = 3.05 (the total charge from the side chain and C-term at pH=3.05 is 1 which balances with the +1 charge of the Nterm to give a total charge of 0)

If the side chain is positively charged when ionized (Arg, Lys, His), then pI = 0.5(pKR + pK2) (remember pK2 is the pKa of the Nterminus, -NH2)
e.g., pI of Lys = 0.5(10.54 + 9.4) = 9.97

COOH H-C-CH2-COOH NH3 +

COO-

COOH-C-CH2-COONH3 +

COOH-C-CH2-COOK2 NH2

K1 H-C-CH2-COOH KR
NH3 +

+1

-1

-2

Nomenclature

The tetrapeptide Ala-Tyr-Asp-Gly or AYDG

Nomenclature
Glx means either Gln or Glu; same for Asx (Asn or Asp) Long name - drop -ine and add -yl and put amino acids in order (e.g. alanine alanyl, lysine lysyl, etc.) The standard method to write an amino acid sequence is from the N-terminus to the C-terminus N-terminus-AA1-AA2-AA3-AA4-AAn-C-terminus The protein is different, if named backwards!! KCAT (Lys-Cys-Ala-Thr) is different from TACK Order DOES count

Greek alphabet

Greek lettering used to identify atoms in lysine or glutamate

All naturally occurring amino acids that make up proteins are in the L conformation

In the Fischer projection all bonds in the horizontal direction is coming out of the plane of the paper, while the vertical bonds project behind the plane of the paper

True / False or ll-in: In the tripeptide Arg-Pro-Tyr, the Cterminal residue is Arg? At a pH below its pK, the -amino group of Lys is ________. At a pH below its pK, the -carboxylate group of Asp is _____________.

Stereochemistry
Optical activity - The ability to rotate plane - polarized light
Asymmetric carbon atom (i.e. carbon with 4 different groups) Chirality - Not superimposable Mirror image - enantiomers (+) Dextrorotatory - right - clockwise (-) Levorotatory - left counterclockwise Operational definition only Cannot predict absolute configurations

The Fischer Convention Absolute configuration about an asymmetric carbon

related to glyceraldehyde (+) = D-Glyceraldehyde (-) = L-Glyceraldehyde

All naturally occurring amino acids that make up proteins are in the L conformation

In the Fischer projection all bonds in the horizontal direction is coming out of the plane of the paper, while the vertical bonds project behind the plane of the paper

An example of an amino acid with two asymmetric carbons

Cahn - Ingold - Prelog system

Can give absolute conguration nomenclature to multiple chiral centers. Priority Atoms of higher atomic number bonded to a chiral center are ranked above those of lower atomic number. With the lowest priority away from you R (rectus right) highest to lowest = clockwise, S (sinistrus left) highest to lowest = counterclockwise SH>OH>NH2>COOH>CHO>CH2OH>C6H5>CH3>H

Side Chain Modifications in Proteins: Non-standard amino acids

Post-translationally modified amino acids These transformations are made after the amino acids are already incorporated into a protein Typical alterations include: hydroxylation, methylation, acetylation, carboxylation, and phosphorylation Addition of PO32- to a Ser, Thr, or Tyr is a common theme in signal transduction

Figure 4-14

Biologically Active Amino Acids: Non-standard amino acids

Neurotransmitters GABA: glutamine decarboxylation product Dopamine: tyrosine derivative Local mediator of allergic reactions Histamine: histidine decarboxylation product Thyroid hormone that stimulates vertebrate metabolism Thyroxine: tyrosine derivative About 250 amino acids have been found in various plants and fungi Figure 4-15

Oxidation and Reduction of Glutathione

2 GSH

Oxidation -2H - 2eReduction +2H + 2e-

GSSG

2 GSH + X oxidized

GSSG + X reduced