The Central Dogma of Life

All cells within a complex multicellular organism such as a human being contain DNA. All the DNA together make up that organisms genome. There are many different types of cells within a complex organism. What, then makes a cardiomyocyte different than a hepatocyte? The answer lies within how each cell controls its genome. DNA consists of genes, which are short sequences of nucleic acids that code for particular molecular structures or protein that carries out a specialized function. Each cell can control its unique set of genes. Some are expressed, and others are repressed. This dictates cellular morphology and function. That is how a myocyte differs from a hepatocyte. Its not the DNA itself. All cells contain the same DNA. Rather, it’s how each cell is individualized, and controls how it uses the set of DNA. This expression and repression is highly regulated by cues both within and extrinsic to the cell. This article will serve to cover the first part of what DNA actually is and how it codes for specific polypeptides that carry out downstream functions. This is the central dogma of life.

Nucleic Acids

Nucleic acids are what transfers genetic material as well as participate in cell signaling and other metabolic processes. Often considered the building blocks of cells. There are two main categories of nucleic acids; Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Both DNA and RNA are polymers of nucleotides. Both RNA and DNA structures are similar in that they consist of a sugar (either Ribose, or deoxyribose) with a nitrogen containing base (either a pyrimidine or purine) bonded to a phosphate group, except that DNA does not have a hydroxide group at Carbon-2, where as RNA does.

Bases

Nitrogenous bases are categorized as either a pyrimidine or a purine. A pyrimidine is a heterocyclic aromatic ring structure, whereas a purine is a two ringed heterocyclic aromatic ring. The pyrimidines are Uracil, which only exists in RNA, thymine, which only exists in DNA, and cytosine which coexists. The purines are adenine and guanine, which coexist in both DNA and RNA. Base-pairing is what creates the characteristic double-helix feature of DNA, and the single-stranded RNA structure. Each base-pair consists of one pyrimidine and one purine which are called base complements. In DNA, thymine always binds adenine (T-A), and guanine always binds to cytosine (G-C) through double or triple hydrogen bonds.

DNA molecule

DNA being a double helix is proven to be advantageous in multiple ways; the nitrogenous base which contains the nucleic information is locked within the complex, facing each other in the centre of the molecule, as opposed to in RNA, where the nucleic acid base is exposed to the cellular environment which provides more opportunity for it to be mutated. DNA is more chemically stable than RNA and less susceptible to degradation. Having two complementary strands allows for greater proof-reading mechanisms. Thymine is much more stable than uracil (RNA). Due to deamination cytosine is often changed to uracil, which in DNA is quickly corrected because uracil is not supposed to be there. In RNA, it’s impossible for the cell to know if it’s truly supposed to be there or not.

DNA replication

DNA replication is the biological process of producing two identical copies of DNA from a single original DNA molecule. This process occurs in all living organisms. It beings at specific locations within the genome called origins of replication. These origins of replication are areas of high T-A base pairing. This is important because there are less hydrogen bonds between the A-T bases so the strand is easier to break at those points. This is known as initiation and at this point the DNA strand is unwound by proteins and enzymes known as helicases, which expose the two strands and result in replication forks that are bi-directional from the origin. Topoisomerases are enzymes used to temporarily break the strands of DNA to relieve tension. These two strands then serve as a template for the leading and lagging strands which will be created as a DNA polymerase will match complementary nucleotides to the templates. DNA is always synthesized in the 5′ to 3′ direction and because at the replication fork the template strands are oriented in opposite directions the leading strand is the strand of nascent DNA which is being synthesized in the same direction as the growing replication fork and replication is continuous in the 5′ to 3′ direction. Within the lagging strand the nascent DNA being synthesized is in the opposite direction, and because of this replication lags and is fragile. Primase is an enzyme that synthesizes a short RNA primer with a free 3′ OH group which is then elongated by a DNA polymerase. The leading strand only receives one RNA primer, while the lagging strand receives several. The leading strand is continuously extended by a DNA polymerase, while the lagging strand is extended discontinuously from the multiple primers forming Okazaki fragments. DNA clamp proteins form a sliding clamp around the DNA, this allows the DNA polymerase to maintain constant contact with the template strands, and enhancing processivity. Once DNA polymerase reaches the end of the template strands and runs into double-strand DNA the sliding clamp protein complex undergoes a conformational change and releases the DNA polymerase. RNase then removes the RNA primers and is replaced by DNA ligase which joins together the multiple parts of the DNA.

DNA replication occurs at multiple points within the chromosome of an organism and because of the linear nature of chromosomes these replication forks are unable to reach the terminal ends and as a consequence a small amount of DNA is lost each replication cycle. Telomeres are regions of repetitive DNA close to the ends of the chromosomes that help mitigate the loss of genomic material during replication. These telomeres are finite and thus each cell has a terminal number of replications. This is otherwise known as the Hayflick limit. When DNA is passed down the germ cell line telomerase is an enzyme that extends the repetitive sequences of the telomere region. Telomerase can become mistakenly up-regulated in somatic cells, which can sometimes lead to cancer.


This is the first release of a 3 part series of articles dedicated to the Central Dogma of life. This article covered what RNA, DNA and DNA replication are.

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B-Cells and T-Cells

These specialized cells are a critical part of the bodies humoral immune system. They recognize foreign antigens or invaders and mount a quick response. B-cells act quickly by developing antibodies to the antigen epitopes. T-cells react based on what serological class they are in. If it is a CD8 T-cell, its cytotoxic and can quickly fight and phagocytize the antigen, if it is a CD4 T-cell, it works in conjunction with B-cells and other T-cell subclasses to defend the host. This article will dive into B-cells, and every subclass of T-cells and how they work together to form the humoral branch of the immune system.

B-Cells

B-cells also known as B lymphocytes are a type of lymphocyte that functions as part of the humoral component of the adaptive immune system. It’s role is to secrete antibodies, but it also functions as an antigen-presenting cell (APC) that secretes cytokines. It possesses a B-cell receptor (BCR) on its surface that allows it to bind to a specific target antigen and initiate an immune response. B-cells develop from hematopoietic stem cells (HSCs) that originate within the bone marrow. They then develop into multipotent progenitor cells (MPP), which further differentiates into the common lymphoid progenitor (CLP). Development further progresses through several stages through various gene expression patterns and arrangements. Before maturation occurs, positive selection takes place to make sure that the pre-BCR and BCR can recognize and bind to specific ligands through antigen-independent signaling. If the cells are unable to bind, these B-cells cease to develop. Negative selection occurs through binding of self-antigen with the BCR. If the BCR is able to bind self-antigen it undergoes four fates; clonal deletion, receptor editing, anergy, or ignorance. Clonal deletion is the destruction of the B-cell through programmed cell death, in other words known as apoptosis. This is only for those B-cells that have expressed receptors for self-antigens. Receptor editing is exactly what the name suggests; editing of the BCR during the maturation process in an attempt to change the specificity the receptor to not recognize self-antigens. Anergy is used to describe lack of reaction by the bodies immune system. Its a way of saying that the B-cells that express BCRs for self-antigen will simply not be used. The last fate; ignorance means that the B-cell ignores the signal and continues through natural development. When negative selection is complete, the B-cells are now in a state of central tolerance. These mature B-cells do not bind with self antigens. From the bone marrow, B-cells migrate to the spleen as transitional B-cells. Within the spleen they become Follicular B-cells or Marginal zone B-cells depending on the signal received through the BCR. Once completely differentiated, they are now called naive B-cells.

B cell

B-Cell Activation

Activation usually occurs within the secondary lymphoid organs, such as the spleen and the lymph nodes. This is where naive B-cells are positioned once mature. When these naive immunocompetent B-cells encounter an antigen through its BCR, the antigen is internalized by receptor-mediated endocytosis, digested, and positioned on MHC II molecules on the B-cell surface. This allows the B-cell to act as an antigen-presenting cell to T-cells. T-cell dependent activation requires a T-cell helper, most commonly a follicular T-helper cell, to bind to the antigen-complexed MHC II molecule on the B-cell surface through its T-cell receptor (TCR) which drives T-cell activation. These T-cells express the surface protein CD40L and secrete cytokines IL-4, and IL-21 which bind to CD40 on the B-cell surface and act as co-stimulatory factors for B-cell activation. The co-stimulatory factors promote proliferation, immunoglobulin class switching, and somatic hypermutation. Activated T-cells then provide a secondary wave of activation that cause the B-cells to proliferate and form germinal centers. During the production of these germinal centers, activated B-cells may differentiate into plasma blasts, which can produce weak IgM antibodies. Within the germinal centers, B-cells differentiate into high affinity memory B-cells or long-lived plasma cells. The primary function of plasma cells is the secretion of clone-specific antibodies. There are very few antigens that can directly provide T-cell independent B-cell activation. Some components of bacterial cell walls (lipopolysaccharide), and bacterial flagellin are some to name a few. One other mechanism through which B-cell activation is enhanced is through the activity of CD21, CD19, and CD81; all three are surface proteins that form a complex. When the BCR binds to an antigen that is tagged with the complement protein C3, CD21 binds to C3, and downstream signaling lowers the activation threshold of the cell.

Memory B-cell Activation

Activation begins through detection and binding of the target antigen. When the antigen binds, it is taken up by the B-cell through receptor-mediated endocytosis, degraded, and presented onto the MHC II molecule within the B-cell surface. The memory B-cell then acts as an antigen-presenting cell that presents the antigen:MHC II complex to T-cells. Most commonly memory follicular T-helper cells that bind through their TCR. The memory B-cell is then activated and differentiates into either plasmablasts and plasma cells or generate germinal centers.

T-Cells

A T-cell is another lymphocyte, which is a subset of white blood cells. They are called T-cells because they mature in the thymus from thymocytes. There are several subsets of T-cells, each with a specific role in the immune system. These T-cells, just like B-cells originate from hematopoietic stem cells in the bone marrow. These lymphoid progenitor cells populate the thymus and expand by cell division to immature thymocytes. The earliest thymocytes do not express either CD4+ or CD8+ and are classified as double negative cells. Through progression they become double positive and then eventually differentiate into single positive cells, either becoming CD8+, or CD4+. Its interesting to note that there is a small population of double positive T-cells within the peripheral circulation, although their function is unknown. About 98% of thymocytes undergo apoptosis during the development process by failing either positive selection or negative selection. The 2% that survive leave the thymus and become mature immunocompetent T-cells. Lets review positive and negative selection again. Positive selection selects for T-cells that are capable of interacting with MHC molecules. During positive selection signals by double positive precursors express either MHC class I or II receptors. A thymocytes fate is determined during positive selection. Double positive CD4+/CD8+ cells that interact with MHC class II molecules eventually become CD4+ cells, and on the contrary thymocytes that interact well with MHC class I molecules mature into CD8+ cells. Negative selection removes thymocytes that are capable of strongly binding with self MHC peptides.

Difference-Between-T-cells-and-B-cells-

T-Helper Cells

T-helper cells do just what their name suggests, they help other cells in immunological processes. This is evident in the activation of B-cells talked about previously. These cells are also most well known as CD4+ T-cells because the highly express CD4 glycoprotein on their surfaces. These T-cells become activated when they are presented with peptide antigens or epitopes by MHC class II molecules, usually present on antigen-presenting cells. Once activated, these cells proliferate rapidly and secrete multiple cytokines. T-helper cells differentiate into several subtypes; TH1, TH2, TH3, TH17, TH9, and THF, each secreting different cytokines to facilitate different pathways of the immune response. This is an article for another time.

TCellSubsets3-01

Cytotoxic T-Cells

These killer T-cells destroy virus-infected cells and tumor cells. These cells are known as CD8+ T-cells since they express the CD8 glycoprotein on their surface. These cells recognize targets by binding to antigen epitopes that are associated with MHC class I molecules. Cytotoxic T-cells are highly regulated by Regulatory T-cells through IL-10, adenosine, and other molecules. They can be inactivated to an anergic state, which prevents autoimmune diseases.

T-cell CD8

Memory T-Cells

These memory T-cells are long-lived and when presented with an antigen that is recognized they can quickly expand and differentiate into large numbers of effector T-cells. These memory T-cells can either be CD4+ or CD8+ T-cells. There are four subtypes of memory T-cells that will be discussed below.

Central memory T-cells express CD45RO, C-C chemokine receptor type 7 (CCR7) and L-selectin which are all surface protein markers. They have high expression of CD44, and is commonly found within the lymph nodes.

Effector memory T-cells express CD45RO, but lack expression of CCR7 and L-selectin. These T-cells also have high expression of CD44, but are not found in the lymph nodes. These T-cells are found in the peripheral circulation and tissues.

Tissue resident memory T-cells occupy tissues without recirculating. The one specific surface marker that is associated with these cells is integral aeB7.

Virtual memory T-cells differ from all other memory subsets in that they do not originate from a clonal expansion event. These cells reside at low frequencies.

Natural Killer T-cells (NK)

First off, it should be mentioned that these cells should not be confused with natural killer cells of the innate immune system. Unlike conventional T-cells that recognize antigen epitopes presented on MHC I/II molecules, NKT cells recognize glycolipid antigens presented by a molecule called CD1d. When these cells are activated, these cells perform functions from both T-helper cells and cytotoxic T-cells. These cells specialize in recognizing tumor cells and cells infected with herpes viruses.