Primary through Quartenary structure

This is a molecule of hexokinase, a metabolic protein found in almost all living organisms. This protein is composed of approximately 6000 atoms and weighs 48 kiloDaltons (kDA). It also has a glucose molecule bound to it, but that is nearly impossible to see.

Primary Structure

Protein have multiple levels of structure. The most basic is its primary structure. A protein's primary structure is simply the order of its amino acids. Note that this order is always written from amino end to carboxyl end (by convention). An example of a protein primary structure is:

            5        10        15        20        25        30
  1 A A S X D X S L V E V H X X V F I V P P X I L Q A V V S I A
 31 T T R X D D X D S A A A S I P M V P G W V L K Q V X G S Q A
 61 G S F L A I V M G G G D L E V I L I X L A G Y Q E S S I X A
 91 S R S L A A S M X T T A I P S D L W G N X A X S N A A F S S
121 X E F S S X A G S V P L G F T F X E A G A K E X V I K G Q I
151 T X Q A X A F S L A X L X K L I S A M X N A X F P A G D X X
181 X X V A D I X D S H G I L X X V N Y T D A X I K M G I I F G
211 S G V N A A Y W C D S T X I A D A A D A G X X G G A G X M X
241 V C C X Q D S F R K A F P S L P Q I X Y X X T L N X X S P X
271 A X K T F E K N S X A K N X G Q S L R D V L M X Y K X X G Q
301 X H X X X A X D F X A A N V E N S S Y P A K I Q K L P H F D
331 L R X X X D L F X G D Q G I A X K T X M K X V V R R X L F L
361 I A A Y A F R L V V C X I X A I C Q K K G Y S S G H I A A X
391 G S X R D Y S G F S X N S A T X N X N I Y G W P Q S A X X S
421 K P I X I T P A I D G E G A A X X V I X S I A S S Q X X X A
451 X X S A X X A

This is the sequence of hexokinase, yeast hexokinase from the yeast species Saccharomyces cerevisiae to be specific. To find out more about this protein, jump to the Brookhaven Protein Data Bank 3D browser and enter hexokinase in the textbox, or SCOP (Structural Classification of Proteins) and use the PDB reference number 1HKG.

Secondary Structure

Protein secondary structure refers to certain common repeating structures found in proteins. There are two types of secondary structures: alpha-helix and beta-pleated sheet.

An alpha-helix is a tight helix formed out of the polypeptide chain. The polypeptide main chain makes up the central structure, and the side chains extend out and away from the helix. The CO group of one amino acid (n) is hydrogen bonded to the NH group of the amino acid four residues away (n +4). In this way every CO and NH group of the backbone is hydrogen bonded.

Here are three models of an alpha-helix. The first shows only the alpha-carbon of each amino acid. The second shows all of the atoms that make up the backbone of the polypeptide. The third shows all of the hydrogen bonds that hold alpha-helices together.The third, and most complete, model is also shown here.

A-helices are most commonly made up of hydrophobic amino acids, because hydrogen bonds are generally the strongest attraction possible between such amino acids. a-helices are found in almost all proteins to various extents. For more information read Stryer's Biochemistry, page 27.

B-pleated sheets are the other type of secondary structure. They can be either parallel or anti-parallel. Anti-parallel beta-pleated sheets generally look like

At the turns they have the structure:

where amino acid n hydrogen bonded to amino acid (n +3) in a hairpin turn.

There is a special type of molecular model used to highlight protein secondary structure. Follow this link to view an example. This common type of protein model represents segments of beta-pleated sheets as ribbon arrows, and it represents a-helices as helical ribbons. The remainder of the polypeptide chain is referred to as random coil, and is represented as a thin line. Please note that random coil is somewhat of a misnomer; the protein is definitely highly organized, but the random coil regions do not show any easily categorized secondary structure components.

Tertiary Structure

Tertiary structure is the full 3-dimensional folded structure of the polypeptide chain. There are a number of examples of tertiary in your textbook, and the hexokinase image used as the icon in this module is a complete structure.

Quartenary Structure

Quartenary structure is only present if there is more than one polypeptide chain. With multiple polypeptide chains, quartenary structure is their interconnections and organization. This is an image of hemoglobin, a protein with four polypeptides-- two alpha-globins, and two beta-globins. The red patches are heme groups (iron complexes bound to the protein, which bind oxygen).