Proteins are linear polymers of amino acids, Architecture of protein molecules, The many biological functions of proteins

Biochemistry

Properties of Living Systems, Biomolecules, Biomolecular Hierarchy

Properties of biomolecules & fitness, Organization and structure of cells, Viruses

Water, pH and Ionic Equilibria

Basic Thermodynamic Concepts, Physical Significance of Thermodynamic Properties

Effect of Concentration on Net Free Energy Changes, High-energy Biomolecules, Complex Equilibria Involved in ATP Hydrolysis

Amino acids: Building Blocks of Proteins, Acid-Base Chemistry of Amino Acids, Reactions of Amino Acids

Optical activity & stereochemistry of amino acids, Spectroscopic properties of amino acids, Separation and analysis of amino acids

Proteins are linear polymers of amino acids, Architecture of protein molecules, The many biological functions of proteins

Chemical groups in proteins, Purification of proteins, Amino acid sequencing

Forces influencing protein structure, Primary and secondary structure

Protein Folding and Tertiary Structure, Subunit Interactions and Quaternary Structure

Carbohydrates

Lipids

Proteins are linear polymers of amino acids, Architecture of protein molecules, The many biological functions of proteins

Amino acids are the monomeric building blocks of protein molecules

The chemical bond that joins two amino acids involves an amide bond (also known as a "peptide bond") between the carbonyl group of the first amino acid and the amino group of the second amino acid.
Bond formation involves the subsequent release of a water molecule

The joining of two amino acids results in the formation of a "dipeptide"

The carboxyl group of the dipeptide (now known as the carboxyl terminus) is available for formation of a peptide bond with another amino acid
Three amino acids connected by peptide bonds is referred to as a "tripeptide", next would come "tetrapeptide" and so on. "Polypeptide" or "Peptide" is a general term for any such polymeric molecule of non-defined length, and a "Protein" is generally "a long polypeptide". There is no clear distinction of when a polypeptide might become a protein. General, when people talk about "Peptides" they mean short polymers of 2-50 amino acids, and "Proteins" would be larger than 50 amino acids in length

The peptide bond (as drawn above) looks like it is a single bond, and therefore, free to rotate. However, the peptide bond has partial double bond character due to a resonance structure:

The resonance structures have the following consequences:

Rotation around the peptide bond is restricted (88 kJ/mol energy required to rotate), therefore, it can be considered rigid

The carbonyl oxygen is positioned trans to the amide hydrogen

The amide nitrogen valence electron geometry has some sp³ character, and is therefore intermediate between tetrahedral and trigonal planar. The

O-C-N-H atoms in the peptide bond are usually considered to be co-planar

There is a partial positive charge on the amide nitrogen (+0.28), and a partial negative charge on the carbonyl oxygen (-0.28)

While the peptide bond is rigid, there is a single bond between the C

(

)

and C atoms and the N and C(2) which are free to rotate. Thus, while the C

(1) - C (O) - N (H) - C

(2) atoms are all planar, this planar peptide bond has two degrees of rotational freedom.

These two rotation angles are known by the greek letters

(phi) and

(psi).

Y is the rotation angle about the C_a (1) - C bond

and

is the rotation angle about the N - C_a (2) bond

. These are also referred to as "main chain" angles.

It is these two degrees of rotational freedom that allows polypeptides to fold up into unique conformations

"Proteins" may consist of a single polypeptide, or a complex of two or more polypeptides

If two identical polypeptides associate, that complex is termed a "homo-dimer". If two different polypeptides associate, that complex is termed a "hetero-dimer"

A complex of three polypeptides is termed a "trimer", four a "tetramer", then "pentamer", "hexamer", etc.

Greek letters are used to describe the composition of polypeptides in a complex assembly. (NOTE: this nomenclature says nothing about the structure of the proteins)

Subunit organization	Meaning	Example
ab	The protein is composed of two separate polypeptide chains, and each has a different amino acid sequence (a heterodimer)	Insulin Chain 'A' has 21 amino acids Chain 'B' has 30 amino acids
a₂	The protein is composed of two separate polypeptide chains, and they are identical (a homodimer)	Lambda phage Cro repressor Each monomer has 66 amino acids
abg	The protein is composed of three separate polypeptide chains, and each is uniquely different (a heterotrimer)	Chymotrypsin Chain a has 13 amino acids Chain b has 132 amino acids Chain g has 97 amino acids
a₂b₂	The protein is composed of four separate polypeptide chains. However, these can be described as two sets of identical pairs of polypeptide chains (a dimer of homodimers)	g-globulin Chain a has 214 amino acids Chain b has 446 amino acids

Amino acid compositions of polypeptides :

Peptide bonds can be hydrolyzed by strong acid (typically 6N HCl, boiling overnight). This method can allow the quantitation of the relative proportions and amounts of each amino acid in a polypeptide. There are a few problems with this method:

Tryptophan is utterly destroyed by acid. Its presence in the polypeptide must be determined by other methods (e.g. UV absorption)
Asparagine and Glutamine are converted to Aspartic acid and Glutamic acid by treatment with acid. Therefore, it will be unclear whether the original protein contained asparagine or aspartic acid, and glutamine or glutamic acid. In the three-letter amino acid code, the results for aspartic acid/asparagine are listed as Asx, and glutamine/glutamic acid as Glx
Molar ratios of the amino acids can be determined by dividing the raw data by the lowest concentration amino acid

Amino Acid	Amino acid concentration from hydrolysis (n moles)	Normalized Concentration (moles)	Probable Composition
Ala	570	12.7	13
Cys	58	1.3	1
Asx	400	8.9	9
Glx	690	15.3	15
Phe	300	6.7	7
Gly	520	11.6	12
His	410	9.1	9
Ile	275	6.1	6
Lys	725	16.1	16
Leu	700	15.6	16
Met	110	2.4	2
Pro	180	4.0	4
Arg	120	2.7	3
Ser	240	5.3	5
Thr	97	2.2	2
Val	255	5.7	6
Tyr	45	1.0	1
Total amino acids: 127

Architecture of Protein Molecules

There are three very general categories of proteins in the body:

Globular. These are water soluble, and the polypeptide chain folds up in such a way as to

place the hydrophobic residues within the core region

and removed from solvent exposure. As their name implies, they are more or less spherical in shape.

Fibrous. Often long polymeric chains of

simple repeating motifs

of a small set of amino acids. Often forming long, intertwined strands of such polypeptides that result in high tensile strength (e.g. silk). Generally insoluble. Function in a

structural role

in biological assemblies.

Membrane. Found associated with lipid membranes (often bilayers of fatty acids). Solubility in non-polar membrane environment is achieved by folding up so as to

expose non-polar residues on the surface

of the protein. Thus, membrane proteins are insoluble in aqueous environment, and require detergent to be solubilized in water.

Levels of Protein Structure

There are four "levels" of protein structure: primary, secondary, tertiary and quaternary

Primary. The primary sequence of a protein refers to the specific order of amino acids in the polypeptide chain. The amino terminal is the "start" and the carboxyl terminal is the "end"

Secondary. Although each amino acid is different, the "backbone" atoms of a polypeptide chain represent a repeating motif of identical peptide bonds (excluding the imino acid proline). We have seen that there are two rotational degrees of freedom for each amino acid in the polypeptide, and the "main chain" is flexible. Furthermore, the main chain carboxyl groups are potential hydrogen bond acceptors, and the main chain amide groups are potential hydrogen bond donors.

The main chain is therefore able to adopt simple repeating orientations that allow hydrogen bonds to form between main chain groups

. The two most common such structural motifs are called the "

a-helix" and the "b-sheet"

In the

-helix the peptide "coils up" in a right-handed helix of approximately 3.6 amino acids per turn, stabilized by main chain hydrogen bonds between the O(i) and N(i+4) groups (in the example below, side chain atoms have been deleted for clarity, and the hydrogen bonds are shown in broken green lines)

click here for a vrml file of a helix (need cosmo player plugin)

-sheet structures come in two general types: parallel and anti-parallel.

-sheets form between two different polypeptide chains (or two different regions within a polypeptide chain) via hydrogen bonds between opposing main chain amide and carbonyl groups. In the example below the top strand runs from right to left and the bottom strand runs left to right. This is called an "anti-parallel"

-sheet.

Tertiary structure.

The unique three-dimensional conformation that a protein folds up into is called the tertiary structure

It determines the unique functionality of the protein

. Since showing all the atoms in a large protein can be complicated, the tertiary structure is often represented by a simple ribbon diagram that shows the arrangement of the secondary structure elements to form the tertiary structure. The following diagram is for an enzyme known as 2,5-diketo-D-gluconate reductase (it is a single polypeptide chain folded up into a soluble globular protein). In the ribbon diagram the

-helices are colored red and the

-sheets are colored yellow. Many protein structures exhibit some degree of symmetry in their tertiary structure and are very beautiful. A major challenge in modern biochemistry is to understand how the information in the primary sequence determines the tertiary structure (this is the "protein folding" problem)

Quaternary structure. Sometimes individual proteins associate together in a stable multi-protein complex.

The specific arrangement of the proteins in forming the complex is known as the quaternary structure

The Biological Functions of Proteins

Enzymes.

Enzymes are catalysts that speed up reaction rates by lowering the energy barrier between reactant and product

. They do not alter the free energy difference between the reactant and products. Therefore, in thermodynamic terms,

they affect only the rate of the reaction and not the

G or the equilibrium

. Likewise, the protein enzymes are not destroyed during the reaction that they catalyze. One protein enzyme can therefore catalyze many reactions. The naming of enzymes is often a clue to the specific reaction that they catalyze.

Regulatory proteins. These do not perform any chemistry (as do enzymes) but rather, they are involved in molecular communication and control of biochemical pathways. They can, for example, turn enzymes on and off.

Transport proteins. Biological systems are "open" thermodynamic systems that exchange heat and matter with the surroundings. Various proteins have a specific role in binding and transporting molecules into and out of the cell. Many of these are membrane proteins, as well as globular proteins. Hemoglobin is a transport protein for oxygen.

Storage proteins. Proteins contain N, C, H, O, and S. Thus, they can also serve as raw materials for other biochemical reactions. Egg white contains the protein ovalbumin, and is a source of nutrients for the developing bird embryo. Likewise, the protein casein is present in high concentration in mammalian milk, and provides infant mammals with a source of amino acids.

Contractile and motile proteins. Certain proteins and protein tertiary structures are capable of movement and contraction. Often such assemblies involve fibrous proteins, due to their tensile strength. Such assemblies also require the input of energy to perform the work that they do (i.e. energy for work is obtained by coupling to the hydrolysis of high-energy molecules).

Structural proteins. Much of the "glue" and "fibers" that keeps you together involves fibrous proteins. Tendons, cartilage, hair, nails, leather (skin) is composed of structural proteins (typically fibrous proteins). In fact horse hooves are composed of such structural proteins, and when boiled down make a great glue (Elmer's glue) or Jello (sometimes its best not to ask where some foods come from. Soylent Green for example).

Scaffold proteins. Large tertiary complexes sometimes involve the assembly of regulatory and enzyme proteins onto a protein scaffold. The scaffold protein's role is therefore not functional per se, but rather structural.

Protective and exploitive proteins. Some proteins protect against invading viruses or disease causing bacteria. Other proteins protect an organism against extremes of temperature, or pH or toxic molecules.

Exotic proteins. Some proteins affect taste, are useful rubber substitutes; spider silk is stronger than steel and can be used to make very thin bullet proof vests, some proteins convert energy into light (as with fireflies and luminescent jelly fish), some proteins are powerful glues (used by barnacles to stick to boats). Materials science is a rich area with proteins, if only we had a better understanding of how to design them.

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