Functions of Proteins:
1) Serve as structural components of cells and tissues
2) May transport and store small molecules (i.e. transport of O2 by hemoglobin)
3) May be involved in the transmission of information between cells.
4) May provide a defense against infection (i.e. antibodies)
5) Most enzymes are proteins.
Each protein consists of a unique sequence of amino acids. The physical and chemical properties of a protein molecule depend on the sequence and in particular how the chain of amino acids folds up in 3 dimensional space. All the information needed to define the 3D structure of a protein is inherent in the amino acid sequence.
The 20 naturally occurring amino acids are built on a common theme.
A free amino acid has the general structure:
See Figure in Text
NH2 - amino group at one end
COOH - a carboxyl group at one end
an alpha C - both groups are attached to the alpha carbon
(also attached to the carbon:
a H atom
an R group (side chain)
Therefore, the R group is the only thing that varies from one amino acid to another. Amino acids are considered to be Zwitterionic (possessing both - and + charge) and amphoteric (able to act as an acid or as a base)
Amino acids can act as buffers in a pH range which is + or - 1 pH unit from their pk values.
The charge of an amino acid will depend upon the pH of the surrounding solution. In the zwitterionic form, an amino acid will have both a negative and positive charge which will yield no NET CHARGE.
Please review related information from Amino Acids as Buffers Lab
Amino acids are joined together to form a protein by peptide bonds.
Peptide bonds are created by the condensation of the carboxyl (COOH) group of one amino acid with the amino (NH2) group of the next. Remember, the formation of the peptide bond involves the removal of one water molecule (condensation reaction or dehydration synthesis)
Since peptide bonds are covalent, they are relatively stable, and in the living cell are broken only rarely, usually as the result of a specific enzymatic action. Peptide bonds are broken in a process which is functionally the opposite of the condensation reaction. This process involves the addition of H2O and is termed hydrolysis.
Electrons are shared by the O,C, & N atoms in such a way the bond has a stiffness which resists rotation. As a result, each peptide bond lies in a flat plane. Rotations must occur at the alpha carbon. Articulated chain of flat plates. A peptide consisits of a small number of amino acids connected by peptide bonds.
A longer chain of amino acids joined in this manner is called a polypeptide.
We can define the direction of a polypeptide chain according to the orientation of the peptide bonds. The amino acid at one end of the chain must have a free NH2 group and thus defines the amino- or N terminal end.
The amino acid at the other end must have a free COOH group and thus defines the carboxy- or C terminal end.
Protein sequences are conventionally written from N-terminus (at the left) to C-terminus (at the right).
The peptide bonds form a zig-zag backbone, from which the side-groups (denoted R) protrude. The R group is different for each amino acid and determines the nature of its contribution to the overall protein structure.
Just twenty different amino acids are used to synthesize proteins. They are described by 3 letter abbreviations or 1 letter abbreviations.
glycine Gly G
alanine Ala A
arginine Arg R
Classified by their ionic charges, the amino acids fall into four groups:
lysine, arginine, and histidine BASIC
Addition of a hydrogen ion converts the free (second) amino group of lysine or arginine to the positively charged form NH3+. A proton can similarly be added to the histidine ring making it positively charged. Important point: charge of the side group will depend upon the pH of the surrounding solution.
lysine and arginine exist in the + charged form within the cell
histidine can be either uncharged or charged at physiological pH so it frequently plays an active role in enzymatic reactions involving the exchange of H ions.
See Figures in Text
The basic amino acids are hydrophilic and would normally be found on the outer surface of a protein.
aspartic acid and glutamic acid ACIDIC
Because the carboxyl group can lose a hydrogen ion to exist in the negatively charged form O=C-O-. Both exist in - charged form within the cell. These amino acids are also hydrophilic and ; therefore, would be found on the outer surface of a protein.
See Figures in Text
aspartic acid glutamic acid
See Figures in Text
Five other amino acids are classified as POLAR Like the basic and acidic amino acids, the polar amino acids are hydrophilic and able to hydrogen bond with water.
serine
threonine
tyrosine
All have OH groups in their side chains
asparagine
glutamine
Have polar amide groups [ O=C-NH2]
See Figures in Text
The NON-POLAR NEUTRAL amino acids are HYDROPHOBIC (water-repelling).
There are 10 amino acids with hydrophobic side chains. They tend to interact with one another and with other hydrophobic groups and would be expected to be located within the interior of a protein. Typically have primarily C and Hs in the R group.
The simplest of course is glycine, which has a single H as its side group:
alanine, valine, leucine, and isoleucine have hydrocarbon chains consisting of up to 4 carbon atoms.
Proline also contains a hydrocarbon side chain but it forms a ringed structure:
See Text for Figures of all Non-Polar Amino Acids
As a result, a proline residue disrupts the usual organization of the backbone of a polypeptide chain, causing a sharp transition in the direction of the chain. The presence of proline therefore interrupts the formation of any regular repeating structure.
The side chains of cysteine and methionine contain sulfur atoms. Methionine is very hydrophobic, cysteine is less so.
See Figures in Text
Phenylalanine and tryptophan both have side chains containing very hydrophobic aromatic rings.
See Figures in Text
In addition to the standard 20 amino acids, certain others are occasionally found in proteins. They are created by modifying one of the standard amino acids after it has been incorporated into the protein. We won't go in to these modifications right now.