What Is an Antibody? — Millions of Keys Cut in Advance, and the Ones That Fit

A Virus Seen for the First Time

Every year when winter arrives, a virus with a new name appears on the news. That virus did not exist in the world when we were born. Yet the body usually overcomes that virus after being sick for a few days.

We also often hear that once we catch a certain disease when we are young, we do not catch it again, or even if we do, it passes lightly. This means the body remembers that disease.

One of the tools the body uses to catch an unfamiliar opponent is an antibody. The strange thing is that the body has already prepared to make antibodies that fit before it ever encounters the opponent. This article starts with the shape of antibodies, following how the body makes countless types in advance, how it selects and grows the matching ones, and the process by which that event remains as memory.

A Y-Shaped Key

A single antibody is too small to see with an ordinary microscope, but its shape resembles the letter Y. Antibodies are Y-shaped proteins produced by B cells that lock precisely onto specific targets. B cells are white blood cells that make antibodies, and each cell makes antibodies that fit only one target.

An antigen is a target recognized by the immune system, usually a piece of an invader or a foreign substance. An antibody forms a Y shape by pairing two long chains and two short chains (PMID 15618007). The variable region is the part at the tips of the two arms of the Y that grips the target, and its shape differs from one antibody to the next. The reason antibodies can recognize almost any kind of antigen is that these tips are extremely diverse (PMID 32031242).

B cells first carry the antibodies they will make on their surfaces, and later release those same antibodies outward (PMID 27793570). The way B cells recognize opponents is different from T cells. T cells are white blood cells that roam around checking protein fragments displayed on the surfaces of other cells to recognize invaders or infected cells. In contrast, B cells recognize opponents in their original shape without breaking them apart (PMID 27793570).

This article compares antibodies to keys and the shape of antigens to locks. Just as the cuts on a key blade must match a lock to fit inside, the shape of the variable region must match the shape of the antigen for an antibody to bind. However, antibodies do not open locks. They grab and block targets, or leave a mark so other immune cells can recognize them.

Antibodies belong to adaptive immunity. Adaptive immunity is immunity that singles out and recognizes specific opponents, remembers the opponents it has met, and responds faster and more efficiently upon the next encounter. How this layer connects with the immunity we are born with is followed in "How Does the Immune System Tell 'Self' from 'Other'? — Guards at the Gate, and a Patrol That Remembers Faces".

An antibody is a key that grips one shape with the tips of its two arms, and a single B cell makes only one such key.

Millions of Keys Inside One Person

B cells together make millions of different antibodies, and each and every one recognizes a different antigen (PMID 15618007). Yet the number of genes that make these antibodies is limited (PMID 33679727). This means that millions of antibodies cannot be written down one by one in the genes.

Australian virologist and immunologist Frank Macfarlane Burnet offered a bold answer to this puzzle. The idea is that the body first makes all sorts of shapes of antibodies, one for each B cell, and when an opponent enters, it selects and multiplies only the B cell that matches. A clone is a group of identical cells created when a single cell divides and divides again. This idea of Burnet's is called the clonal selection theory.

Clonal selection is the process by which a B cell with an antibody matching the entered antigen is selected and expands into clones with the same antibody. The backbone of this idea is a structure in which the body continuously makes countless proteins that stick to opponents, and selects only some of them to expand further (PMID 2497040).

Burnet's idea required something unprecedented for the time. A part of the genes determining antibodies had to mix randomly in each cell. Half a century of subsequent research backed up this guess (PMID 18180793).

This diversity is prepared as if anticipating the countless threats the body will encounter in the future (PMID 30690255). And it is from a very early time. The proteins that B cells and T cells of a baby in the mother's womb use to recognize opponents are already extremely diverse by the end of the second trimester of pregnancy (PMID 28466095).

To put it in terms of keys, it is a method of cutting all sorts of shapes of keys in advance without knowing what kind of lock will come, and when a lock arrives, finding the matching key and copying only that one. This analogy has one limitation. In reality, there is no locksmith who designs the keys knowing the locks that will come in the future. The cutting is random, and the selection is done by the entering opponent.

Before meeting an opponent, the body randomly makes millions of antibodies, and selects and multiplies only the B cells that match the entered opponent.

Pick and Stitch Gene Pieces

In cells that make antibodies, the structure of the antibody genes differs from that of other cells in the body. In 1976, Japanese molecular biologists Nobumichi Hozumi and Susumu Tonegawa compared antibody genes from two types of mouse cells. One was a very early embryo cell, and the other was an antibody-producing tumor cell. What the two researchers examined were short-chain genes. In the embryo cell, the gene determining the tip of the arm and the gene determining the rest were on two different DNA segments. In the antibody-producing tumor cell, the two genes were together on a single, smaller DNA segment (PMID 824647). The authors interpreted that the two separated genes are joined together as they grow into an antibody-producing cell (PMID 824647).

The framework of this stitching is now pictured as follows. The gene determining the tip of the arm is divided into pieces like V, D, and J, with multiple similar versions lined up for each piece (PMID 32031242).

V(D)J recombination is the process where a growing B cell randomly picks one V, D, and J gene piece each, cuts out the DNA between them, and stitches them together to make the gene for the variable region. This recombination is the core mechanism that generates antibody diversity (PMID 32031242). Because there are many pieces to choose from, this single process accounts for a large share of the diversity (PMID 12045092).

Differences arise even further from there. The junctions where the pieces are stitched together are not precise every time, adding small variations at the seams, and differences also arise from which pairs the long chains and short chains form (PMID 30690255, PMID 9122742). In terms of a key, it is like dividing the blade into three sections, picking one piece from each drawer containing multiple options to connect them, and fusing those seams slightly differently every time.

Among the cells in the body, B cells and T cells are the only ones that rewrite their own genes in this way (PMID 11444378). Breaking and rejoining chromosomes is also dangerous. If this process goes wrong, chromosome pieces can attach in the wrong places, and some cancers originating in B cells and T cells are linked to such miswirings (PMID 15242404, PMID 26104458). However, this process is usually regulated so precisely that bad outcomes are very few or unnoticeable (PMID 15242404).

The reason antibodies differ from one B cell to another is that they randomly pick and stitch together gene pieces while growing.

Copying the Right Key and Filing It Down to Fit Better

When a virus enters the body, among countless B cells, a few whose surface antibodies catch that virus wake up. The awakened B cells multiply, acquire mutations to make antibodies that bind more tightly, and also change the type of antibody they produce (PMID 9122742).

There is a dedicated place where this happens. The germinal center is a temporary, small zone that forms in places like the lymph nodes after an infection or vaccination, where awakened B cells multiply and refine their antibodies. Inside it, B cell multiplication, mutation, and selection all take place in one location (PMID 22224772).

Somatic hypermutation is a process where mutations accumulate at a very high frequency in the genes of the variable region while the awakened B cells are multiplying. Mutations are entered into the genes one letter at a time (PMID 17328676), and as a result, variant antibodies with varying strengths of binding to the antigen are created (PMID 32323268).

Affinity is the degree to which an antibody tightly holds onto an antigen. Among the variants, B cells with increased affinity receive signals from other immune cells, such as helper T cells, get selected, and multiply further (PMID 32323268). This process of variation and selection does not end once, but is repeated multiple times (PMID 11138628).

Affinity maturation is the process where the affinity of antibodies gradually increases as mutation and selection are repeated. Given that well-fitting variants survive out of randomly altered ones, this process is compared to Darwinian evolution (PMID 35113731). It also resembles the picture painted by the clonal selection theory later refined by Burnet (PMID 18180793).

To put it in terms of a key, it is the process of copying a roughly fitting key while randomly filing down its teeth with a file, and keeping only the ones that fit the lock better. The hand doing the filing does not look at the lock. Trying the key against the lock is what the selection step does.

At the end of this process, B cells split into two paths. They become cells that pour out antibodies, and cells that remember the opponent for the future (PMID 32323268).

Matching B cells multiply in the germinal center and repeat mutation and selection, producing antibodies that bind more and more tightly.

Keeping the Blade, Changing the Stem

The very first antibody that appears when meeting a new opponent is IgM (PMID 33066119). Immunoglobulin is another name for antibodies, which are divided into various types like IgM, IgG, and IgA depending on the shape of their stem. Because IgM is a large clump of five or six Y-shapes tied together, it has 10 or 12 arm tips to grab opponents (PMID 33066119). Even though the gripping force of each individual arm is usually weaker than that of IgG, many arms attach all at once to hold on tightly (PMID 33066119).

After that, the B cell changes the type of antibody. Class switching is when a B cell changes the stem side while keeping the arm tips of the antibody the same, resulting in the production of a different type of antibody. When the stem changes while aiming at the same antigen, what the antibody does changes to suit the elimination of the opponent (PMID 35169260, PMID 32031242).

The initial response is led by IgM, and in a body that remembers an opponent it has met once, stem-changed antibodies become dominant (PMID 29664567). The power to defend the body from an already-met opponent is deeply connected to making IgG suited to that opponent (PMID 29664567). IgA and IgE also defend the body depending on the nature of the opponent and the route through which it enters (PMID 29664567).

IgE is a type of antibody mainly involved in allergic reactions. What happens when IgE is produced against harmless substances like pollen is followed up in "What Is Allergy? — A False Alarm, and Why It Rings More Often".

In terms of a key, it is like keeping the blade the same while swapping out only the handle. The handle is the part that other immune components grab, and that story continues in the section after next.

Cells That Pump Out, Cells That Remember

Some of the awakened B cells focus entirely on making antibodies. Plasma cells are transformed B cells, and they are cells that churn out large quantities of antibodies without a break. Plasma cells are called the antibody factories of the body (PMID 24700574), and they continually send out large amounts of antibodies (PMID 9122742).

There are short-lived plasma cells and long-lived plasma cells. Short-lived plasma cells stay outside the germinal centers within the lymph nodes and spleen. Some cells move from places like the lymph nodes to the bone marrow and become long-lived plasma cells (PMID 24700574). Inside the bone marrow, there are special niches that support the long lifespan of these cells (PMID 24700574).

Some others remain as memory. Memory B cells are B cells that survive for a long time carrying antibodies suited to an opponent they have met once, and they wake up right away when they encounter the same opponent again. When the same opponent returns, memory B cells quickly produce antibodies that match that opponent and bind tightly to it (PMID 9122742). Memory B cells play a major role in protecting the body from repeated infections, especially mutant viruses with slightly changed shapes (PMID 37400644).

Vaccines are a way to leave behind this memory. They show the appearance of the opponent in advance in a form that does not cause disease, allowing the body to select and refine the right key and keep spare copies of it. Antibodies formed after a vaccine or after an infection play an essential role in blocking various infections (PMID 39162394). One review considers knowing how high-quality memory B cells that bind broadly even to variants are formed to be essential for vaccine development (PMID 37400644).

Plasma cells that pump out antibodies and memory B cells that remember the opponent are generated together in the same process.

What Antibodies Do

A virus cannot multiply on its own; it must latch onto a human cell and get inside. What the tips of the antibody's arms block is this exact path. Neutralization is when an antibody sticks to an invader like a virus, stopping it from entering cells or doing harm. An antibody can block the stage where the virus clings to a cell, the stage where it goes inside, the stage where it merges with the cell, and the stage where newly made viruses escape the cell (PMID 39162394).

The stem side calls over other immune components. One of them is complement. Complement is a group of proteins floating constantly in the blood, part of the immune side we are born with, which turns on even where antibodies have attached to burst invaders or help other immune cells. The antibody stem sticks to complement and to proteins on the surfaces of various immune cells that grab antibody stems, bridging the innate immune system we are born with and the antibody side of immunity (PMID 39162394). IgM, which has many arms, is especially good at calling over complement, making it efficient at bursting cells (PMID 33066119). Invaders with antibodies attached to them also become easier for other immune cells to swallow up (PMID 27793570).

Antibodies sometimes work together with other components like complement, and sometimes work without them (PMID 26104200). Inside the body, many of these jobs likely happen all at once or one after another (PMID 26104200). While there are functions that stop an invader from taking hold or causing disease, such as neutralizing viruses, there are also cases where antibodies instead help the invader multiply or worsen the disease (PMID 26104200).

Finding a certain antibody through a blood test is usually a matter of looking for traces that the body has already met that counterpart or seen its likeness through a vaccine. However, the mere fact that antibodies are present does not fully explain how well the body is protected. Looking at COVID-19, most people who are infected or vaccinated make neutralizing IgG aimed at the virus surface protein, but having those antibodies alone does not fully explain the power to block disease, and the work of calling on complement and other immune cells operates together as well (PMID 37778697).

Antibodies grab invaders with their arm tips to block them, and use their stems to call complement and other immune cells to get rid of the invaders.

The Day an Unseen Virus Arrives

Let us follow what we saw earlier in a single continuous scene. Suppose a brand-new virus enters through the nose.

Among the millions of B cells in the body, there is one whose surface antibody grabs onto some part of that virus. This is because antibodies, made in advance by randomly stitching together gene fragments, are diverse enough to recognize almost any kind of antigen (PMID 32031242, PMID 30690255). The B cell that has grabbed the virus wakes up and multiplies (PMID 9122742).

The antibody that appears first is IgM, which has many arms (PMID 33066119). Meanwhile, in the germinal center, mutation and selection repeat, leaving behind B cells that bind more tightly to the virus (PMID 32323268). In this reaction, many B cells switch their stems to produce IgG or IgA (PMID 38143767).

At the end of this, plasma cells pour out antibodies, and memory B cells remain (PMID 32323268). When the same virus enters again later, memory B cells quickly churn out tightly binding antibodies (PMID 9122742).

What can be said of this scene goes only as far as this: the reaction of the second encounter starts faster and with a better-fitting antibody than the first. How well it actually protects the body depends on the various jobs that the virus and the antibodies do. As we saw earlier, the mere presence of antibodies does not explain everything; calling upon the complement system and other immune cells works together as well.

The Same Randomness Also Cuts Keys Aimed at Us

It is estimated that as many as 70% of the antibodies in newly made B cells stick to the body's own substances (PMID 31556969). There are studies showing that even looking at the entire pool of newly equipped B cells, more than half do so (PMID 20727040). When you cut things at random, a key that fits the lock of our own house is bound to appear.

Autoimmunity is when the immune system, which protects the body, mistakenly recognizes the body's own cells as enemies and attacks them. Therefore, the body has multiple stages to filter out these B cells. More than 75% of growing B cells die because they joined gene segments incorrectly or recognized the body's own substances (PMID 15618007).

The B cells that survive also have safety devices. B cells that stick to the body's own substances have their antibody genes rewritten, disappear, or are locked into a non-responsive state (PMID 16477212, PMID 12633668). There are research results showing that B cells locked in a non-responsive state can undergo mutation in the germinal center, move away from the body's own substances, and turn into cells that target only outside intruders (PMID 31556969).

Mutations in the germinal center also carry risks. Because mutations can create new B cells that stick to the body's own substances, the response in the germinal center is strictly regulated (PMID 30410492). Restricting the signals of helper T cells while an immune response is taking place is one way to suppress such B cells (PMID 16477212).

There are cracks in these safety devices, too. In certain situations, B cells that were locked in a non-responsive state can wake up again and release antibodies that harm the body (PMID 31556969). "Why Doesn't the Immune System Attack Us? — The Brakes on the Patrol" follows how the body manages T cells that target the body's own substances, and what kind of disease occurs when those mechanisms break down.

The randomness that diversifies antibodies also makes antibodies that stick to the body's own substances, and the body filters them out at multiple stages.

Where to Look Further

The details of cut-and-paste and refinement still hold unresolved questions. A 2020 review noted that it is still not clear how V(D)J recombination, class switching, and somatic hypermutation occur at the gene level (PMID 32031242). A 2024 review notes that we still do not know how to design vaccines that provide long-lasting protection against certain pathogens (PMID 38670066).

You can see how the body recognizes a first-time invader, and how the immunity we are born with connects to the immunity tailored and grown to match a met enemy, in "How Does the Immune System Tell 'Self' from 'Other'? — Guards at the Gate, and a Patrol That Remembers Faces". "Why Doesn't the Immune System Attack Us? — The Brakes on the Patrol" continues with how the body manages T cells that target its own body, and "What Is Allergy? — A False Alarm, and Why It Rings More Often" follows with what IgE causes.

The story of how the molecule called mRNA, which came to be used in vaccines as well, took decades to become a medicine can be seen in "The Rejected Molecule — The Decades It Took for mRNA to Become Medicine". How to sort out what was reported after a vaccine and what the vaccine caused is covered by "Between Reported and Caused — What Vaccine Safety Surveillance Caught, and What It Cleared".

Source Papers

• "Evidence for somatic rearrangement of immunoglobulin genes coding for variable and constant regions." (1976) — PMID 824647 — In mouse embryonic DNA, the variable (V) and constant (C) region genes of the kappa light chain were on two separate segments, whereas in tumor cells making the kappa chain, only a single smaller segment joining V and C was visible. The authors interpreted that these join together during lymphocyte development to form a continuous stretch.
• "V(D)J recombination, somatic hypermutation and class switch recombination of immunoglobulins: mechanism and regulation." (2020) — PMID 32031242 — The extreme diversity of the variable region, the random selection, cleavage, and joining of V, D, and J fragments are core mechanisms of diversity, along with class switching and somatic hypermutation, while the genetic mechanisms remain unclear.
• "Antibody diversification by somatic mutation: from Burnet onwards." (2008) — PMID 18180793 — Half a century of research has supported the randomization process required by Burnet's clonal selection theory, showing primary diversity generated by RAG and secondary diversity and in-body evolution driven by somatic hypermutation after encountering an antigen.
• "B-cell development and differentiation." (1997) — PMID 9122742 — Inaccurate recombination is the source of diversity, followed by proliferation, mutation, and class switching after antigen stimulation, leading to memory B cells that live long and rapidly produce high-affinity antibodies, and plasma cells that constantly secrete large quantities of antibodies.
• "B cells." (2005) — PMID 15618007 — B cells make millions of different antibodies, their receptors have two heavy chains and two light chains, and over 75% of developing B cells die due to improper recombination or self-antigen recognition.
• "Antigen Presentation to B Cells." (2016) — PMID 27793570 — Unlike T cells, B cells recognize antigens in their native shape, and the same receptor is secreted to initiate phagocytosis, complement activation, and neutralization.
• "Dynamic 3D Locus Organization and Its Drivers Underpin Immunoglobulin Recombination." (2020) — PMID 33679727 — A very diverse receptor repertoire must be generated from a limited number of genes.
• "The B cell repertoire." (1989) — PMID 2497040 — A mechanism that continually produces numerous receptors and selects and proliferates a subset of them, driving affinity changes and the restriction of autoreactive cells.
• "Affinity war: forging immunoglobulin repertoires." (2019) — PMID 30690255 — Fragment assembly, junctional randomness, and heavy-and-light-chain combinations create proactive diversity anticipating diverse threats, followed by strong selection.
• "Survival of the fetus: fetal B and T cell receptor repertoire development." (2017) — PMID 28466095 — The B and T cell receptor repertoires of the fetus are already highly diverse by the end of the second trimester.
• "V(D)J recombination: RAG proteins, repair factors, and regulation." (2002) — PMID 12045092 — With many segments to choose from, V(D)J recombination accounts for a large share of immune response diversity.
• "Regulation of antigen receptor gene assembly in lymphocytes." (2001) — PMID 11444378 — Somatic alteration of the mammalian genome occurs exclusively in B and T cells.
• "How to keep V(D)J recombination under control." (2004) — PMID 15242404 — Chromosome cleavage is dangerous and tightly regulated, and negative consequences are usually minor or unapparent, whereas mispairing leads to lymphoid tumor-associated translocations.
• "V(D)J Recombination: Mechanism, Errors, and Fidelity." (2014) — PMID 26104458 — Aberrant rearrangements caused by recombination enzymes are linked to tumorigenesis.
• "Germinal Centers." (2022) — PMID 35113731 — Germinal centers are the site of B cell clonal expansion and affinity maturation, driving Darwinian diversification and affinity-based selection.
• "Germinal Center Reaction." (2020) — PMID 32323268 — A transient structure formed in response to immunization or pathogens, generating variants with differing affinities through rapid proliferation and hypermutation, selecting high-affinity cells with the help of Tfh and other cells, and differentiating into memory B cells and plasma cells.
• "Germinal centers." (2012) — PMID 22224772 — Germinal centers are sites where B cell clonal expansion, somatic hypermutation, and affinity-based selection occur to produce high-affinity antibodies.
• "Molecular mechanisms of antibody somatic hypermutation." (2007) — PMID 17328676 — Somatic hypermutation involves the sequential introduction of single-nucleotide substitutions into V genes, serving as the basis for affinity maturation.
• "Germinal center reaction." (2001) — PMID 11138628 — The primary purpose of the germinal center is the formation of B cell memory through repeating cycles of receptor diversification and optimal selection.
• "Structure, Function, and Therapeutic Use of IgM Antibodies." (2020) — PMID 33066119 — IgM forms pentamers or hexamers with 10 to 12 binding sites, functioning as the first antibody secreted after antigen exposure; its individual affinity is lower than that of IgG, but it binds strongly via multivalency and efficiently activates complement.
• "The role of chromatin loop extrusion in antibody diversification." (2022) — PMID 35169260 — Class switching expresses other constant region isotypes that optimize the function of antigen-specific antibodies.
• "Memory control by the B cell antigen receptor." (2018) — PMID 29664567 — Primary responses are led by IgM, memory responses are dominated by class-switched isotypes, defense against reinfection is linked to the production of pathogen-specific IgG, and IgA and IgE also contribute depending on the microbe and route of infection.
• "Tracking plasma cell differentiation and survival." (2014) — PMID 24700574 — Plasma cells are the antibody factories of the body, comprising short-lived plasma cells and long-lived plasma cells residing in bone marrow survival niches.
• "Memory B cells." (2024) — PMID 37400644 — Memory B cells are central to repeated infections, particularly in defending against mutant viruses, and forming high-quality memory B cells with broad neutralization breadth is key to vaccine development.
• "Antibody-mediated control mechanisms of viral infections." (2024) — PMID 39162394 — Antibodies generated after vaccination or natural infection are crucial for defending against various infections, neutralization blocks attachment, internalization, fusion, and release steps, and the Fc region connects innate and adaptive immunity through complement and Fc receptors on immune cells.
• "Functions of Antibodies." (2014) — PMID 26104200 — Antibodies act on pathogens with or without effector molecules like complement, multiple functions likely occur simultaneously or sequentially in the body, and while they have functions that prevent pathogen acquisition and pathogenesis like neutralization, they can also promote proliferation or contribute to disease (reviews tend to focus on beneficial functions).
• "Non-neutralizing functions in anti-SARS-CoV-2 IgG antibodies." (2024) — PMID 37778697 — Most infected or vaccinated individuals produce spike-neutralizing IgG, but its presence alone does not fully account for protection, involving functions that recruit complement, NK cells, and macrophages.
• "Human IgM-expressing memory B cells." (2023) — PMID 38143767 — Many B cells undergo class switching to IgG and IgA during T cell-dependent responses.
• "Molecular underpinning of B-cell anergy." (2010) — PMID 20727040 — Over half of the primary repertoire consists of autoreactive B cells, most of which are silenced by anergy.
• "Clonal redemption and clonal anergy as mechanisms to balance B cell tolerance and immunity." (2019) — PMID 31556969 — Up to 70% of immature B cell antibodies are estimated to be autoreactive, anergic B cells can under certain circumstances reawaken to produce disease-causing autoantibodies, and mutations in germinal centers can steer cells away from self-reactivity and turn them into cells specific for foreign antigens (clonal redemption).
• "B-cell tolerance." (2006) — PMID 16477212 — Autoreactive B cells are rendered tolerant through checkpoints such as receptor editing, deletion, anergy, and growth factor competition, and risks are suppressed during immune responses through limited T cell help and strict germinal center regulation.
• "Antigen receptor selection by editing or downregulation of V(D)J recombination." (2003) — PMID 12633668 — Autoreactive receptors undergo secondary recombination to destroy or replace receptor genes (receptor editing).
• "Regulation of the Germinal Center Response." (2018) — PMID 30410492 — Germinal center mutations can generate autoreactive clones, making regulation of the germinal center response essential.
• "Exploring new perspectives in immunology." (2024) — PMID 38670066 — Although clonal selection theory, receptor diversity, and immunological memory are pillars of modern immunology, how to design vaccines that confer long-lasting protection against certain pathogens remains unknown.