so, where were we? Ah yes, those little antibodies.
The basic structure off the antibody protein. It is composed of multiple protein chains, and has a characteristic ‘Y’ shape. These can be embedded in immune cell membrane, or released into the surrounding environment (typically the blood).
Antibodies have a specific region which contains the binding site which actually latches onto, and holds onto invaders. This is the part that binds the antigen (interesting point: antigens are derived from Antibody Generating. An antigen is anything that causes an immune response). The specific part of the antigen which the antibody recognises is called the epitope. This is a stretch (or stretches) of amino acids (the building blocks of every protein). The chemical properties conferred to this region of antigen are conferred to it by the amino acids which construct it, and this contributes to the overall 3-D folding of the protein which makes up the antigen. As mentioned before, the shape of the binding site needs to complement the shape of the epitope. At the atomic level, this binding is mediated by non-covalent forces. The most common forces at work are Hydrogen bonds and van der vaals forces. Hydrogen bonding occurs between hydrogen and the highly electronegative moieties; nitrogen, oxygen and fluorine. Fluorine isn’t incorporated in proteins so isn’t particularly relevant in this context, but oxygen and nitrogen are present in abundance in proteins. The correct pattern of Hydrogen bond donors in the specific shape of the antibody binding site, must match the pattern of hydrogen bond acceptors in the antigen, and vice versa.
Nitrogen is highly electronegative. One reason for this is that it has two electrons orbiting it which aren’t usually involved in neutral bonding. (they can be involved in bonding, but when this occurs, nitrogen becomes positively charged). These electrons are known as a ‘lone pair’. The presence of a lone pair makes the nitrogen very electronegative. Hydrogen is relatively positive compared to nitrogen; particularly ionised Hydrogen, or hydrogen that has been bonded to a structure. This is because hydrogen is simply a proton and an electron. In its ionised or bonded form, the electron is either absent (ionised hydrogen) or in use in maintaining a bond. This leaves, in essence, a single proton available for intermolecular interaction. Protons are positively charged subatomic particles, and the relative difference in charge between a single proton and electronegative nitrogen means there is a very strong attraction between the two atoms (rule of thumb – opposites attract). This strong attraction is about as strong as intermolecular attractions get without them actually forming a covalent or ionic bond. Oxygen has 2 lone pairs, which makes it very electronegative, and also makes it highly prone to generating hydrogen bonds.
Examples of hydrogen bonding (using amino acids as models) The dotted line denotes the hydrogen bond. Hydrogen bonds are crucial throughout biology, and are one of the forces that enable proteins to exist - in doing so, enable life to exist.
Amino acids all contain oxygen and nitrogen, and some contain more Hydrogen bond generating groups than others. The content and arrangement of amino acids in the antigen binding site, and on the antigen itself is important in not only determining the shape of both of these sites – but also in determining the extent of hydrogen bonding which will occur. More hydrogen bonding will mean the attraction between the antibody and antigen will be much stronger, and will be more liable to elicit downstream immune effects.
Van der vaals interactions are much less specific, operate under short distances, and are very weak. Van der vaals forces can arise from any atom and are the basic, weak attractive forces between atoms which arise from the subatomic properties of the protons and electrons which help make up atoms. Stronger interactions probably bring the molecules together first, and the van der vaals forces probably add to the pre-existing strength of attraction between antibody and antigen.
The grey, red and blue atomic structure is the antigen binding portion of the antibody. The Green structure is the epitope of the antigen. The small yellow lines indicate hydrogen bonds between antibody and epitope. The shapes of both the antigen and antibody determine how the pattern of H-bond donors and acceptors will line up and give a stronger interaction. This interaction will result in a global change in the structure of the antibody which will mediate downstream effects which will produce the response.
The region of the antibody which binds the antigen can also be called the Complementarity Determining Region (CDR), and it is this region which is variable throughout antibodies produced against different antigens. The protein structure in this region is physically and chemically different for different antigens, and new CDR’s can be generated, to bind other epitopes. How is this complexity achieved? How does the seemingly fixed genetic code achieve production of an almost limitless potential in invader antigen detection?
It seems that the region of DNA that makes up the genetic code in the gene which codes for the CDR is chopped up and rearranged for the different B lymphocytes in the latent pool I mentioned earlier. Lots of small stretches of DNA are cut out and reshuffled, to be stuck together in a different order to produce a new genetic code. This is known as genetic recombination. Each different B lymphocyte has a different recombination of the CDR portion of the gene. The subsequent code then goes on to form a novel CDR (or antigen binding site, if you prefer that term) which may or may not bind to an antigen that may enter the body. It’s a blind process which tried to churn out as many variations as possible, in the hopes that some antibody-antigen binding will occur (different invaders may bear similar epitopes, so there may be some antibody binding from an antibody already primed to tackle a previous foe).
This genetic recombination of the CDR is precisely what puts the ADAPTIVE in adaptive immune system. It means that we don’t only have the defences we’re born with, but we can generate new ones without having to wait generations to evolve them. What’s more, these antibodies that we develop in our lifetimes have the potential to be passed on to our offspring. At least for mothers anyway. The colostrum, which is the initial breast milk produced following childbirth is packed full of useful proteins, some of which include the mothers antibodies which confers the newborn baby with extra immunity. It’s not particularly long lived immunity as the baby hasn’t received the Memory cells (remember them from the previous post?), but it’s a good start to life. For the budding biologist/medic out there - it may seem a bit odd. The baby drinks the protein concoction of colostrum - surely the proteins, including the antibodies would just be digested? Well, the newborn digestive system has limited capacity to take up whole proteins without digesting them, in a cellular process known as endocytosis, but that’s all complicated shit and another story for another day.
Soooooooooooooo. How on earth did such a system evolve? The adaptive immune system, in all its complexity evolved a very long time ago (about 500 million years ago) in the common ancestor of all jawed vertebrates (the gnathostomes) – birds, reptiles, mammals, amphibians etc. This common ancestor would’ve been some sort of fish like creature. The non-jawed vertebrates, the agnathans, appear to have a primordial version of the gnathostome adaptive immune system, but it does seem to be lacking a few key components which prevent it from reaching the versatility and complexity of gnathostome immune systems.
The basic phylogenetics of the immune system. The metazoans are all of the multicellular organisms. Agnathans are on the borderderline of exclusive innate immunity and adaptive immunity. Invertebrates have various complexities of innate immunity, but lack adaptive immunity as we know it.
The adaptive immune system has been largely conserved throughout all jawed vertebrates since then. Antibodies seem to have been adapted from pre-existing cell surface receptors, as many cell surface proteins bear structural similarities to antibodies (the immunoglobins), and the fact that antibodies can be cell surface bound. On a molecular level, this crucial genetic recombination mechanism which underpins our ability to adapt, develop and remember invaders, seems to have arisen as a result of peculiar genetic phenomenon known as a transposon. Transposons are stretches of DNA that principally exist for the sole purpose of existing. They may be remnants of early viral invasion in which some viral genes got left behind in the host genome and just kinda stayed there. Transposons are nothing more than special sequences of DNA which probably shouldn’t be there, and code for proteins which exist to cut out the transposon and stick it elsewhere in the genome, where it may be copied by some passing DNA replication machinery. Sometimes, transposons can stick themselves on the middle of an important gene and cause a disease state though this isn’t common. We have transposons in our genome. Irksome things, they are - largely pointless aspects of our biology that troll the genome.
An example of how transposons work. They will code for an enzyme such as a transposase which cuts out the transposon, resticks the host DNA, carries it to another region of DNA, cuts the DNA in that region and sticks in the transposon.
A couple of transposons known as RAG 1 and RAG 2 are thought to have inserted themselves in the region of DNA which coded for the primordial antibody, which may have initially been some sort of general receptor for invaders (so a part of the innate immune system), and helped construct enzymes which cut up and restick DNA together. This makes sense as transposons code for enzymes which cut their own selves out of the genome and stick them elsewhere. Turns out their cut & paste-trolling came in handy in the antibody coding genes where the enzymes they coded for seemed adept at cutting up and reshuffling these antigen recognition sites, helping to induce variability in the CDR’s of antibodies.
And that’s that. I like to think these two posts have covered the immune system right from the subatomic physical, through chemical and biological - right up to the systems level and what it means for life in general. I hope. The immune system is a shining example of the perpetual evolutionary arms race and warfare on the biochemical level. It involves reshuffling genetic code, matching shapes and differentiating between the biochemistry of ones’ own ‘self’ and ‘non-self’. The immune response extends from against other species to against cells from other members of the same species. The female immune system will even mount an immune response against incoming male sperm, and even against a developing foetus if it has the chance (luckily, the placenta is an awesome piece of engineering and makes sure maternal and foetal blood don’t mix - but it’s a fallible system).
It’s all about those important proteins presented on the cell surface. It’s a formidable defence which has helped to keep vertebrates alive against the odds. As a percentage of life on Earth, vertebrates make up a miniscule minority in comparison to the single cellular organisms we share this planet with. It may seem like a pretty shitty thing to do, to go and invade someone else’s body. But look at it from the point of view from the invader - just as much as we have the immune system to help us survive, they want to survive too. In light of this, not only will they have evolved mechanisms to get themselves into our bodies – but they’ll also have systems to exploit the weaknesses of and deceive our bodily defences. Survival is a constant struggle for all of us, even if we’re not aware of it.
These immunology posts were in response to a question by the venerable Shizumataka. Hope it was helpful! :D