Structure in biology is the “arrangement ororganisation” of any living thing, be it cells or whole organ systems, whilefunction is the specific “physiological activity” of a living thing (2).Structure is extremely important to any function carried out in biology and inmost cases the structure has been developed in such a specific and attuned waythat deviation from it will result in complete loss or, at the very least,reduced function.
This extensively researched and explored when it comes to themacromolecules; proteins. Loss of protein function due to structural changes isroot cause of many conditions and diseases, and emphasises the strongrelationship structure has with function in biology (Salvador et al).Proteins are essential to every singlefunction carried out by a living organism whether that be maintainingstructure, catalysing reactions or communication. These functions are extremelyspecific in multicellular and unicellular organisms; therefore, proteins musthave a structure that is unique to their assigned function, which occurs infour stages. The primary structure of the protein is the first stage and it isthe amino acid sequence of the protein. Amino acids are organic compounds witha central carbon attached to a carboxyl group, an amine group and a side chainthat gives each acid its unique properties. There are 20 amino acids withvarying properties such as being hydrophobic, polar or containing ioniccharges. The sequence is coded for by the DNA bases making up the gene for theprotein and these bases are grouped in to 3 to produce codons – one codon forevery amino acid added.
During transcription the DNA sequence of the gene istranscribed as RNA and is then transported to the ribosome, position on theendoplasmic reticulum that is surrounding the nucleus, where the amino acidsequence is assembled. The codons are complementary to a particular tRNAmolecule which itself is attached to an amino acid. In this fashion the codonis read, the tRNA molecule is retrieved and the amino acid adds on to the chainwith adjacent acids forming peptide bonds, until a stop codon is reached (Albertset al). Then follows the secondary structure which isthe folding of the amino acids, whether that is coiling as seen in an alphahelix or folding in to sheets in beta sheets. Many proteins share either typeof folding depending on their function and this type of folding is onlyreserved to the two types because it doesn’t concern the side chains on theamino acids. Instead it is focused on the way the amine group and carboxylgroup on the polypeptide chains interact to form hydrogen bonds. In the alphahelix the polypeptide chains twist on itself and a hydrogen bonds is formedevery fourth N-H and C=O.
This type of folding is common in areas like nails aswell as in transmembrane proteins as the hydrophilic polypeptide backbones areshielded in this helical structure when placed in a hydrophobic lipid membrane.For beta sheets, either hydrogen bonds are formed between adjacent sheetsrunning in parallel direction or a polypeptide chain folded over backwards withthe chain now running in antiparallel. These are found in parts like silk andfeathers. A protein can contain more of one structure or a mixture of bothdepending on its amino acid sequence and corresponding function (Alberts et al).The tertiary structure is extremely vital tothe final protein shape as it determines the bonding holding together thepolypeptide chain and is inherently tied to the side chains on the amino acidsthat form the base of the protein. There are 4 types of bonding:hydrophobic/hydrophilic interactions, disulphide bonding, hydrogen bonding andvan der waals interactions. The side chains on the amino acid determines theseinteractions and affects how the protein is shaped which is why the preciseamino acid sequence is very important.
The final folding of a protein is sothat the molecule exists at the lowest possible energy state to make it stableand any disruption in this state through environmental changes such as changesin temperature result in the protein denaturing; potentially irreversibly. Thisis because these changes affect the bonding’s in the tertiary and secondary structureof the protein. Most proteins also have a quaternary structure which is thestructure made from multiple polypeptide chains as well as containing otherfeatures such as an inorganic prosthetic groups which is a nonprotein part ofthe protein.
An example of such a structure is haemoglobin (Alberts et al).The generic structure of the protein and howit potentially differs depending on its function is explored above, but tobetter understand this a specific example of haemoglobin can be used. Thefunction of blood is to transport nutrients and oxygen to cells and rid thecells of carbon dioxide and other waste.
To carry out the particular functionof transporting the gases, blood contains the protein haemoglobin which is acarrier protein that is able to bind with oxygen and carbon dioxide dependingon the amount of hydrogen ions present in blood. This conjugated protein isuniversal in all mammals with their being alterations in its affinity foroxygen depending on the organism’s requirements, such as fetal haemoglobinhaving higher affinity for oxygen than adult. To function optimally as a carrier, theprotein’s structure is highly specific. The base of this structure is globularproteins; four identical polypeptide chains: two alpha and two beta, with eachcontaining a ‘heme pocket’. The alpha and beta chains are paired together asa1b1 and a2b2 and are dimers (two structurally similar molecules linkedtogether by weak or strong bonds) which makes the haemoglobin molecule atetramer.
The heme pocket is a prosthetic group consisting of an organicporphyrin ring with conjugated double bonds which are held in place by phenylamine;a side chin on the polypeptide chains. In the centre of this ring is the ironatom, held there by the bonds it makes with the four nitrogen atoms part of thering. It contains two other free bonding sites due to the iron being in theFe+2 state, but one is occupied by the polar histidine’s (present to give theactive site the correct shape) and the other is where the oxygen binding takesplace. This forms the active site that allows the protein to bind with oxygen.The polypeptide dimers interact with each other to form two states ofhaemoglobin: when deoxygenated the dimers are held by inter and intra subunitsalt bridges making them tense (T state) and R state when these bridges arebroken in an oxygenated haemoglobin. These two states affect the positioning ofthe iron in the porphyrin ring. In the deoxygenated T state, the iron is in theplane of the ring, making it more accessible to oxygen allowing for easybinding.
This cause a 15 degrees’ rotation between the dimers, allowing theoxygen to bind with the other exposed irons. When oxygen is released from oneiron, the rotation shifts back and the other iron are made inaccessible tooxygen, regaining the deoxygenated structure as the other oxygen molecules arereleased. The structure of haemoglobin is integral for this mechanism and isimportant for the function as it allows oxygen to be carried and released progressively.Sickle cell anaemia is a condition whicharises when the haemoglobin is unable to perform its function due to a changein its structure caused by mutations in the protein gene. Mutations are achange in DNA sequences, the effects of which can range from being silent (not resultingin any noticeable change in function) to potentially being fatal. There is asingle base pair mutation found in the beta globin chain of the adulthaemoglobin where the base adenine is replaced by thymine in the 6th codonwhich results in there being glutamic acid instead of valine on the 6thposition. This mutation doesn’t affect the haemoglobin function whenoxygenated, however when the haemoglobin is deoxygenated the valine on 6thposition on the beta chain “buries” itself in an adjacent beta chain that ishydrophobic.
Multiple molecules then join together to form an insoluble fibremade from fatty haemoglobin molecules. This eventually results in the cellshape changing from biconcave to that of a sickle which can then aggregatetogether and cause loss of function throughout the organism. Blocked vesselswould mean reduced nutrient supply throughout the organism which acts as adomino effect causing other cells to lose function as well as blocked vesselsresulting in supply being cut to organs like kidneys – disrupting theirfunction.
The way structure and function is interlinked in proteinscan be seen quite evidently with the example of sickle cell anaemia and ringstrue for many other single gene disorders. However not all conditions are amanifestation of a mutation in a single gene that reduces the resultingproteins function and in turn affect the function of the whole cell. Loss offunction in an organism can arise from a whole array of factors such as theenvironment of the organism, other genetic conditions or random events based onchance. Further research must be conducted to see what really causes proteinsto have structural changes.
One particular field of research is looking attranscription factors which are proteins that ensure genes are expressed in thecorrect order. Mutations in these proteins can then affect other proteins thatare expressed and causes loss of function.