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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Acid-Base Balance

An acid is any compound that can donate H+ when dissolved in water. A base is any compound that can donate OH- ions. A buffer system is a combination of a weak acid or base and its salt or conjugate that resists changes in pH. The human body has incredible mechanisms to maintain an acid-base balance. Changes in pH put the body in different physiological states that can cause an array of problems. Acidosis is when the pH falls below the reference range of 7.34. Alkalosis is when the pH increases above the reference range of 7.44.

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The most important buffer system in the body is the bicarbonate (HCO3)/carbonic acid (H2CO3) system. Carbonic acid works to allow the human body to rid of toxic CO2 via respiration to maintain a normal pH of 7.4. There normally is a 20:1 ratio of bicarbonate to carbonic acid.

The red cells pick up CO2 from tissues and throughout its travel through the blood vessel its converted to carbonic acid. That carbonic acid is then broken down into bicarbonate and hydrogen. The excess hydrogen ions are buffered by hemoglobin. Bicarbonate leaves the red cell and goes into circulation. Bicarbonate enters the plasma through an exchange mechanism with chloride to maintain a state of electroneutrality in the cell. When the red cells reach the lung the hemoglobin will release the excess hydrogen ions by the binding of oxygen to hemoglobin. The excess hydrogen ions bind to bicarbonate to form carbonic acid. Carbonic acid then dissociates into H20 and CO2 which is expelled.

As mentioned above, an individual can be in a state of acidosis or alkalosis. This can be caused by ventilation and is called respiratory acidosis or respiratory alkalosis or it can either be caused by HCO3-. This is called metabolic acidosis or alkalosis.

Respiratory acidosis is an increase in PCO2. Conversely respiratory alkalosis is a decrease in PCO2. Metabolic acidosis is a loss of HCO3- or an addition of H+. Metabolic alkalosis is a loss of H+ or an increase of HCO3-. The body will naturally compensate for the pH changes. Some of the compensatory mechanisms are increasing respiration in metabolic acidosis. Hyperventilation increases the amount of CO2 that is expelled and raising the pH. In respiratory acidosis the kidney will increase its reabsorption of HCO3-.

Metabolic acidosis can be caused by multiple different disease states. Excessive loss of HCO3- by diarrhea can cause metabolic acidosis. Diabetic ketoacidosis can cause it. Other causes are ingestion of acids or renal tubular failure where there is no renal reabsorption of HCO3-.

Metabolic alkalosis is caused by excess or an overdose of HCO3-. Excessive vomiting causes a loss of hydrochloric acid with the stomach contents. Vomiting also results in hypokalemia and hyponatremia which are both positively charged ions (acids) leading to an increase in the pH. Excessive diuretic use can sometimes initially cause an increase in chloride, but most commonly results in hyponatremia and causing a contractile alkalosis.

Respiratory acidosis is most commonly caused by CO2 retention usually due to ventilation failure. Decreased cardiac output and hypotension also cause acidosis. Less blood is pumped to the heart so less CO2 is getting transported to the lungs to be expelled. Chronic lung conditions such as COPD result in an inability to ventilate properly and to expel CO2. Certain drugs cause depression of the respiratory center in the brain and can cause respiratory acidosis. Some of these drugs are barbiturates, opiates and ethanol (alcohol).

Respiratory alkalosis is primarily caused by hyperventilation (increased alveolar ventilation). This results in a decreased arterial PCO2. Any condition which decreases pulmonary compliance causes a sensation of dyspnea. Dyspnea is not a single sensation and there are at least three distinct sensations including air hunger, work/effort, and chest tightness. These sensations cause a state of hypoxia which is caused by the hyperventilation.

-Caleb

General Endocrinology

Hormones make up the endocrine system and act on almost every tissue in the body. Hormones are substances that are produced by a specialized cell that circulates in the blood. The best example of this is insulin which is secreted by the beta cells in the pancreas.

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Credit for the photo goes to Pearson Education, Inc.

There are multiple forms of chemical signaling that hormones utilize. The first is autocrine where the cell targets itself. Signaling across gap junctions occurs when a specialized cell targets another cell that is connected via a gap junction. Paracrine is when the targeted cell is nearby. Endocrine which will be the primary focus for today is when the cell produces hormones or chemical signals that have to travel through the blood stream to act on distant cells. Depending on the receptor type to these hormones distinguishes the action it has on the recipient tissue or cell. Receptors can by cytoplasmic, ion channels, tyrosine kinase receptors, or a G-protein coupled receptor. There can also be different types of hormones. Protein hormones utilize calcium as a secondary messenger. The action potential of protein hormones is quick as opposed to steroid hormones. The action of steroid hormones is slow as steroids are not as membrane permeable as protein hormones. Its important to note that hormones are released in pulses. Each pulse has an amplitude and period.

The endocrine system needs feedback control loops to function properly. Negative control loops maintain hormonal balance. Positive control loops are actually what causes physiological changes in the tissues involved.

The endocrine system starts in the hypothalamus. The hypothalamus releases releasing hormones to stimulate the anterior and posterior pituitary to secrete effector hormones that act on various sites of the body.

The anterior pituitary otherwise known as the adenohypophysis secretes the majority of the hormones. Releasing hormones are secreted by the hypothalamic neurons into the hypothalamopituitary portal system. These hormones are then carried down the pituitary stalk by this portal system into the adenohypophysis. The anterior pituitary secretes adrenocorticotropic hormone (ACTH), thyroid-stimulating hormone (TSH), growth hormone (GH), prolactin (PRL), follicle-stimulating hormone (FSH), and luteinizing hormone (LH). These all act on their respectable tissues/cells to secrete specific hormones. ACTH acts on the adrenal gland, which sits on top of the kidneys. The adrenal gland is responsible for secretion of catecholamines (epinephrine/norepinephrine) that influences the flight or fight response as well as glucocorticoids such as cortisol which have physiological effects throughout the entire body. TSH acts on the thyroid gland to secrete the thyroid hormones T3 and T4. These hormones also have wide-spread physiological function throughout the body. GH acts on the liver and influences bone, muscle, and tissue growth. PRL acts on the mammary glands such as the breast glands to stimulate growth and to start lactation. FSH and LH act on the testes of males to secrete inhibin and testosterone as well on the ovaries in females to secrete estrogen, progesterone, and inhibin. Decreased or elevated levels of any of these hormones can have detrimental effects on normal physiological processes. These discrepant levels can either be from primary disease (In the organ where the hormones are produced) or it can be secondary disease, i.e. from the hypothalamus, or pituitary.

Oxytocin and vasopressin (ADH) are the hormones secreted by the posterior or neurohypophysis pituitary. These are synthesized in the paraventricular supraoptic nuclei of the hypothalamus and are carried down the pituitary stalk by axonal transport. These hormones are then released into the general circulation in the neurohypophysis. Oxytocin works in females and males. It effects the uterine smooth muscle and mammary glands in females and in males it effects the smooth muscle in the ductus deferens and the prostate gland. Vasopressin or ADH promotes water retention in the distal tubules and collecting ducts of the kidneys. SIADH is excess ADH secretion and results in concentrated urine, and a low serum concentration. In other words there is low serum sodium which is bad! Diabetes insipidus on the other hand is deficiency in ADH.

-Caleb

Overview of the Immune System; Part One

The overall function of the immune system is to prevent or limit infection. It is essential for survival. Multiple organ systems, cells, and proteins are involved in the immune response. It is the most complex system that the human body has. The immune system is differentiated into two directions. Innate or non-specific immunity or Acquired (specific) immunity.

The Innate immune system consists of many components. The skin acts as a mechanical barrier and is typically the first line of defense against foreign substances. Mucous membranes consist of the bodies normal microbiota which compete with invading microbes. The mucous membranes are also lined with mucous and cilia which act in an elevator type motion to push foreign substances away. Physiological barriers such as temperature, pH and the complement system. The more acidic environment that a lower pH offers disrupts bacterial growth. Antimicrobial proteins and peptides are present in different epithelial locations in the body. Lysozymes are present in the tears and saliva and cleave the peptidoglycan cell wall present in bacteria. Secretory phospholipase A2 is present in the gut and can enter the bacterial cell and hydrolyze lipids in the cell membrane. Lectins target gram positive bacteria and forms pores in the membranes. Defensins integrate into the lipid and form pores which causes loss of membrane integrity. These defensins are present in PMNs (neutrophils) and lamellar bodies in the gut. Cathelicidins are present in neutrophils and macrophages in the lungs and intestines and distrupt membranes. Histatins are constitutively produced by the glands in the oral cavity and are active against pathogenic fungi.  Inflammation plays a huge role in the Innate immune system. Inflammation induces vasodilation and increase in capillary permeability causing an influx of immune cells like PMNs and macrophages. Inflammation can be observed by the four cardinal signs; rumor (redness), tumor (swelling), color (heat), and dolor (pain). The innate immune response is a rapid response.

Innate Immunity

The complement system recognizes features of microbial surfaces and marks them for destruction by coating them with C3b. There are three distinct pathways; the classical pathway, the lectin pathway, and the alternative pathway. All pathways generate a C3 convertase which cleaves C3, leaving C3b bound to the microbial surface and releasing C3a. In the classical pathway the activated C1s cleaves C4 to C4a and C4b which binds to the microbial surface. C4b then binds C2, which is cleaved by C1s to C2a and C2b forming the C4b2b complex. C4b2b on the microbial surface is an active C3 convertase which cleaves C3 to C3a and C3b. This results in opsonization of the bacterial surface by C3b. The C4b2b3b complex is an active C5 convertase leading to the development of the membrane-attack complex. Each complement component (C4a/b, C2a/b, C3a/b) have different functions, but that is another discussion for another time. The lectin pathway of complement activation is when mannose-binding lectin (MBL) and ficolins recognize and bind to carbohydrates on the pathogen surface. Ficolins are similar to MBLs, but have a different carbohydrate binding domain. MBLs bind with high affinity to mannose and fucose residues. Conversely ficolins bind oligosaccharides containing acetylated sugars. When MBL binds to a pathogen surface MBL-associated serine protease (MASP)-2 is activated and cleaves C4 and C2 similar to the classical pathway. The alternative pathway is an amplification loop for C3b formation that is accelerated by properdin (factor P) in the presence of pathogens. Properdin stabilizes the C3bBb complex. C3 undergoes spontaneous hydrolysis to C3(H20) which binds to factor B, allowing it to be cleaved by factor D into Ba and Bb. The C3(H20)Bb complex is essentially a C3 convertase which cleaves more C3 into C3a and C3b. C3b molecules result in opsonization of bacterial surfaces. Its important to recognize that all pathways lead to generation of a C5 convertase. C4b2a4b in the classical pathway, C4b2a3b in the lectin pathway, and C3b2Bb in the alternative pathway. C5 is cleaved into C5a/b that initiates the assembly of the terminal complement components. These are the terminal complement components that form the membrane-attack complex.

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The membrane attack complex consists of an assembly of C6, C7, and C8. This complex undergoes a conformational change that results in polymerization of C9 which generates a large pore in the cell membrane. Host cells contain CD59 which prevents the assembly of the C9 molecules preventing the formation of the membrane-attack complex.

C3a, C4a, and C5a are unique in that these complement components are called anaphylatoxics. They initiate a local inflammatory response when systemic injection of these molecules occurs. They induce smooth muscle cell contraction and increased vascular permeability. They induce adhesion molecules and activate mast cells that invade and populate submucosal tissues to release inflammatory mediators such as histamine and TNF-a.

The Acquired or adaptive immune system is all about specificity. The Humoral branch of the acquired immune system is executed by the B lymphocytes that produce antibodies to specific antigens. The cell-mediated branch consists of antigen presenting cells (APC) such as the dendritic cells processing foreign substances and presenting proteins of those substances as antigens through the major histocompatibility complex (MHC) to CD8 T lymphocytes. These are cytotoxic T-cells that kill these foreign antigens. The acquired immune response is a slow response because it takes the body time to produce antibodies. An important aspect of the adaptive response is memory. Once antibodies have been produced to an antigen, these responses last and the time it takes to produce an antibody on subsequent exposures is rapidly decreased.

These two different systems work in conjunction to produce an adequate and sustained response. When foreign antigens are processed and expressed on the surface of APCs as MHC peptides, pro-inflammatory cytokines such as IL-12p70, IL-18, and IFN-a are secreted. These attract NK cells which primarily attack viruses as well as PMNs and macrophages that phagocytize these antigen peptides to destroy them. Adaptive immunity is also started with dendritic cells that also undergo antigen uptake and processing. This is also called the maturation signal. This signal is augmented by IFN-y and TNF-a secreted by macrophages and NK cells. These dendritic cells either present the antigen to B lymphocytes which are the antibody producers or they present the antigen to CD4/CD8 T-cell lymphocytes.

There are multiple classes of antibodies. IgD is typically expressed on B-cell lymphocytes during differentiation with IgM. IgD is also present in the serum in low concentrations. IgM is a pentamer and the largest immunoglobulin. It is the first antibody that is produced in the immune response. IgA is in high concentration in the mucosal linings, saliva, and tears. Typically part of first line defenses. IgG is present in high concentrations in the serum. IgG is unique in that it can cross the placenta. IgE is involved in allergic reactions. It binds to mast cells and basophils causing degranulation.

-Caleb

Non-Malignant Leukocyte Disorders

Non-Malignant simply means that it is localized to the leukocytes. Leukocytes are another name for the white blood cells, more specifically in the case of these disorders, the granulocytes. These disorders are fairly uncommon and are inherited. The following are ones that are found to distinct morphological features and affect the granulocyte functionality.

Alder Reilly Anomaly

Alder Reilly Anomaly is a recessive trait defect that causes incomplete degranulation of mucopolysaccharides. Large, darkly staining metachromatic cytoplasmic granules which can be seen and are partially digested mucopolysaccharides. These granules are characteristically referred to as Alder Reilly bodies. These can sometimes resemble toxic granulation, but it is important to note that in toxic granulation neutropenia, dohle bodies, and a left shift is seen. In Alder Reilly Anomaly none of those are present. Its also important to mention that the functionality of the granulocytes is not impaired.

Alder Reilly

Pelger Huet Anomaly

Pelger Huet Anomaly is an autosomal dominant syndrome characterized by decreased nuclear segmentation. This is caused by a mutation in the Lamin B receptor gene. Lamin B is an inner nuclear membrane protein that plays a role in normal leukocyte nuclear shape change during maturation. Morphological changes include hyposegmented neutrophils or neutrophil lobes connected by a thin nuclear filament. Pseudo or acquired PHA can be observed in the granulocytes in individuals with MDS, AML, or chronic myeloproliferative neoplasms.

Pelger Huet

Chediak Higashi Syndrome

Chediak Higashi Syndrome is characterized by an abnormal fusion of granules. These present as large and are dysfunctional. This is caused by a mutation in the LYST, or CHS1 gene that encodes for proteins involved in vesicle fusion or fission. The mutated protein causes loss of lysosomal movement and loss of phagocytosis. Thus leaving the individual susceptible to an increased number of infections without the innate immune system to fight them off. One of the characteristic findings is neutropenia.

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May-Hegglin Anomaly

May-Hegglin Anomaly is a rare autosomal dominant platelet disorder that is characterized by variable thrombocytopenia, giant platelets, and dohle bodie like inclusions in the granulocytes. MHA is caused by a mutation in the MYH9 gene that causes a dysfunctional and disarray production of myosin heavy chains type IIa which affects the megakaryocytic maturation process as well as platelet fragmentation. Though most cases are clinically asymptomatic, the individual may present with mild bleeding tendencies.

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Chronic Granulomatous Disease

In CGD, mutations in proteins that make up the NADPH oxidase complex. The mutations lead to failure of the phagocytes to generate the oxygen-dependent respiratory burst following phagocytosis. Normal phagocytosis of a microorganism leads to phosphorylation of cytosolic P47 and P67. Antibacterial neutrophil elastase and cathepsin G from the primary granules and cytochrome complex gp91 and gp22 from the secondary granules migrate to the phagolysosome. NADPH oxidase is formed when P47 and P67 combine with P40, RAC2, and the cytochrome complex. Majority of cases of CGD is due to mutations in P47 or gp91.

Leukocyte Adhesion Disorders

Normal recruitment of leukocytes to a site of inflammation involves capture of leukocytes from peripheral blood, followed by a process known as rolling along a vessel wall. Rolling involves binding of integrins to endothelial cell receptors which is high-affinity which ultimately leads to diapedesis of leukocytes into tissues from peripheral blood. With Leukocyte Adhesion disorders there are mutations that result in the inability of neutrophils and monocytes to adhere to endothelial cells, and the consequence is potentially fatal bacterial infections.

Leukocyte Adhesion Disorder I is caused by a mutation in the genes responsible for B2 integrin subunits. This leads to a decreased amount of the truncated form of the B2 integrin which is essential for endothelial cell adhesion. Patients typically present with neutrophilia, lymphadenopathy, splenomegaly, and characteristic skin lesions.

Leukocyte Adhesion Disorder II is caused by a mutation in the SLC35C1 gene. This gene encodes for a fucose transporter that moves fucose from the endoplasmic reticulum to the Golgi region. Fucose is needed for the synthesis of selectin ligands. The defective fucose transporter leads to the inability to produce functional selectins and causes defective leukocyte recruitment and reoccurring infections. LADII is much more rare than LADI. Clinical presentation is growth retardation, coarse facial features, and other physical deformities.

Leukocyte Adhesion Disorder III is even more rare than LADII and is caused by a mutation in the Kindlin-3 gene. The mutations impair leukocyte rolling and activation of B integrin. With LADIII there is also decreased platelet integrin GPIIbIIIa resulting in bleeding similar to that of Glanzmann Thrombasthenia.

-Caleb