Table of contents
Humans, like other animals, have mechanisms to stop bleeding. These mechanisms that normally occur due to a blood vessel trauma are collectively called hemostasis (not to be confused with homeostasis).
The first step in the process is vasospasm (caused by endothelin), during which the smooth muscles at the area around the injury constrict.
When platelets/thrombocytes, anucleate cytoplasmic fragments of a blood cell (megakaryocyte), come in contact with the collagen layer below the endothelium of the vessel, they change shape and become “sticky”. This part of hemostasis is platelet plug formation. The platelets slow down blood drainage by sealing the blood vessels, and activate other platelets.
The next step is blood coagulation, during which a clot/thrombus/coagulum/cruor forms. This process is quite complex and includes many players. The most important ones include calcium, vitamin K, platelets, prothrombin and fibrinogen found in the blood. Platelets help the conversion of a blood clotting factor into its active form and this includes the ones at the end of the cascade. For instance, the inactive form of thrombin, prothrombin, turns into the active form via thrombokinase, an enzyme liberated from platelets. Thrombin, with the help of calcium, converts fibrinogen (inactive soluble form of fibrin) into insoluble fibrin. Fibrin then forms a mesh with the platelets. The mesh can trap other formed elements slowing down the flow of blood until the vessel is repaired. Once the vessel is healed, fibrinolysis commences.
Although coagulation is a normal physiological process excessive coagulation called thrombosis can occur which can block blood flow leading to necrosis in the tissue in the site in question. A special thrombus that can travel in the circulation is called an embolus causing embolism. Haemophilia is when hemostasis fails to take place. These disorders may be due to inherited or acquired factors (or even both) (that e.g. cause abnormal haematopoietic processes). A mutation can cause the conformation of one of the cofactors to change rendering the cofactor unfunctional, so the whole cascade fails. An increase (e.g. thrombocytosis, hypercalcaemia, hyperfibrinogenemia, hyperprothrombinemia) or decrease (even lack) (e.g. thrombocytopenia, hypocalcaemia, hypofibrinogenemia, hypoprothrombinemia) in any of the players of hemostasis may lead to thrombosis or haemophilia respectively.
[Other haematological disorders include anaemia, polycythemia, leukocytopenia & leukocytosis.]
Human transport of respiratory gases involves 3 steps: ventilation (air in and out - alveoli of the lungs and the outside environment), external gas exchange & internal gas exchange.
Respiratory gases diffuse along their partial pressure gradient which is directly proportional to their concentration. The greater the surface area & partial pressure difference, the greater the rate at which the gases diffuse (Fick's Law).
At the alveoli, external gas exchange occurs between the alveoli of the lungs and blood.
A special red pigment, haemoglobin, is responsible for gas transport. Haemoglobin is made of 4 polypeptide chains (it is 1 metalloprotein with a quaternary structure), 2 alpha & 2 beta, each with a haem prosthetic group. The haem group is a porphyrin skeleton made of 4 pyrrole heterocycles and a ferrous ion in the middle (Heme binds oxygen so that each haemoglobin molecule can bind up to four oxygen molecules. When all of the heme units in the blood are bound to oxygen, haemoglobin is considered to be saturated.)
Once oxygen binds to deoxyhaemoglobin, a hydrogen ion is released. The ability of haemoglobin to bind H+, renders it a great buffer. Some oxygen is also found dissolved in the blood plasma. Bicarbonate enters the red blood cell as a chloride ion exits. This is called the chloride shift. The H+ reacts with bicarbonate forming carbonic acid (in the lungs). Carbonic acid dissociates to form carbon dioxide and water. The carbon dioxide then diffuses into the alveoli. The H2CO3 ⇌ CO2+H2O reaction is faster thanks to carbonic anhydrase. Another “source” of carbon dioxide is the plasma (dissolved form) and carbaminohaemoglobin. So carbon dioxide is transported in blood by three different mechanisms: as dissolved carbon dioxide, as bicarbonate, or as carbaminohaemoglobin.
Internal respiration occurs between the blood and the cells. There, oxyhaemoglobin has a lower affinity for oxygen due to the acidic environment. This is called the Bohr effect.
The Bohr effect shows how the oxygen-haemoglobin dissociation curve can be changed by the pH. Higher temperatures can also lead to a decrease in oxygen saturation of haemoglobin.
“An oxygen–haemoglobin saturation/dissociation curve is a common way to depict the relationship of how easily oxygen binds to or dissociates from haemoglobin as a function of the partial pressure of oxygen. As the partial pressure of oxygen increases, the more readily haemoglobin binds to oxygen. At the same time, once one molecule of oxygen is bound by haemoglobin, additional oxygen molecules more readily bind to haemoglobin. Other factors such as temperature, pH, the partial pressure of carbon dioxide, and the concentration of 2,3-bisphosphoglycerate can enhance or inhibit the binding of haemoglobin and oxygen as well. Foetal haemoglobin has a different structure than adult haemoglobin, which results in foetal haemoglobin having a greater affinity for oxygen than adult haemoglobin.
The less saturated haemoglobin is and the lower the partial pressure of oxygen in the blood is, the more readily haemoglobin binds to carbon dioxide. This is an example of the Haldane effect.” quoted from:
openstax.org/books/anatomy-and-physiology/pages/22-chapter-review
Haemoglobin unloads oxygen. At the same time, CO2 enters and combines with water forming carbonic acid(with the help of carbonic anhydrase). Carbonic acid dissociates into bicarbonate which leaves as chloride enters. The resulting H+ as well as some CO2 binds to haemoglobin forming carbaminohaemoglobin.
Image from: Openstax archives
The digestive system is the organ system responsible for processing the food we ingest. To most of us, it sounds like all that this system does is just take the nutrients in our food and then get rid of the waste. However, the digestive system is more than a mere food delivery driver. There is no better way to illustrate the genius behind this system than on the example of a Muslim observing Ramadan.
If you ever stopped to wonder what happens in your body as you fast. The simple answer is a lot. But if you are a science buff, like myself, look no further than this article.
Regulation of the metabolic rate, appetite & thirst
Metabolism is defined as all the chemical reactions (transformations of chemicals) taking place in the body to sustain its functions (e.g. make energy). The energy use of the body is defined by its total metabolic rate. The metabolic rate is mainly regulated by a region in the brain called the hypothalamus (region responsible for the body's “internal equilibrium”).
Did you know that even relaxing our muscles requires energy?
This explains why after a while, the cadaver of a person becomes rigid (rigor mortis). Physicians (pathologists) use this, together with the estimated surrounding temperature, to determine the time of death.
*An enzyme (biocatalyst made of proteins) is like motivation for students; it (e.g. a score) makes them prepare for an exam. Students could potentially prepare for an exam without motivation but it would take forever. Just like scores, enzymes speed up chemical transformations that would otherwise not take place (they would need years to take place without enzymes).
Enzymes, like students, won’t do their job properly if they are not provided with the proper conditions. Each student likes a subject but won’t study other subjects. The pH and temperature of the body are like subjects. So each enzyme requires an optimum condition.
During the day, the empty stomach of a faster secretes ghrelin, a hormone (a hormone is a “chemical message” released into the bloodstream to communicate with a target tissue) made of a few amino acids (amino acids are the building blocks of proteins). Ghrelin stimulates the hypothalamus to release neuropeptide Y (a neurotransmitter [a signal secreted by nerve cells] made of tens of amino acids), thereby signalling hunger. Neuropeptide Y is also regulated by the activity of fat cells. These cells secrete adipokines (e.g. leptin) which are hormones that tell the hypothalamus “what is up with the fat''. When there is fat, more of these hormones are released, thereby slowing down the release of neuropeptide Y and stimulating the release of hormones, which decrease appetite (e.g. melanocortins, see later). Insulin (released by the pancreas) also stops the release of neuropeptide Y & thus decrease appetite.
The blood pressure of the faster decreases and so starts to experience thirst. Low blood pressure means that blood perfusion in the kidneys decreases. As a result, the kidneys (juxtaglomerular apparatus) then secrete the enzyme renin*. This enzyme (renin) converts a protein in the blood plasma (called angiotensinogen) into another protein (angiotensin I). This other protein is then converted to another protein (angiotensin II) by an enzyme produced in the lungs (called ACE or angiotensin-converting enzyme). Angiotensin II increases blood pressure (by stimulating the release of the hormone aldosterone and making the lumen of blood vessels smaller; vasoconstriction), stimulates thirst and stimulates the release of antidiuretic hormone (responsible for making the Ramadan observer urinate less). Antidiuretic hormone is made by the hypothalamus and secreted by the neurohypophysis/posterior pituitary, while aldosterone is secreted by the zona glomerulosa of the adrenal cortex. Doctors may control (e.g. using drugs that inhibit an enzyme in the pathway) this renin-angiotensin pathway to treat hypertension.
When the sun goes down and we break our fast, we start feeling satiated because the intestines release peptide YY that tells the hypothalamus to stop secreting neuropeptide Y, which stimulates appetite, & to release appetite-suppressants (melanocortins like melanocyte-stimulating hormone). Cholecystokinin, released by the initial horse-shoe shaped part of the intestine, the duodenum, in response to the presence of fats, signals satiety and suppresses appetite. Pancreatic polypeptide (PP) also exhibits a similar effect.
Breaking one’s fast also leads to a sense of pleasure (euphoria) by activating a reward circuit similar to the one activated in drug addicts; the dopamine reward circuit.
The adrenal gland is made up of the adrenal medulla and cortex. The adrenal medulla is, among other things, responsible for releasing adrenaline :)
Ingestion, digestion & elimination of a date
Muslims break their fast either with dates (or with water). It appeared to me as if explaining the process of digesting such a small fruit would be easy, but it turned out that finding the right words to convey my message with scientific accuracy was a mission impossible. Which is why I decided to leave out some steps (like absorption, see later) in order to simplify things for you, the reader.
Dates are rich in antioxidants (phytochemicals) that destroy oxidants, reactive molecules such as free radicals. Oxidants damage DNA, proteins, and unsaturated fatty acids by stealing their electrons. Oxidants are generated by radiation, alcohol, tobacco, etc. Dates are also rich in fibre. Dietary fibre (roughage; indigestible carbohydrates like cellulose) decreases cholesterol concentration in the blood and decreases the risk for cardiovascular disease and diabetes. Fibre also stimulates the feeling of satiety and the peristaltic movement (peristalsis, by the muscle layers, are unidirectional waves of muscular contractions that push the food in the gastrointestinal tract) of the bowel (which helps avoid constipation).
Ingestion includes masticating/chewing & swallowing the date. These two processes involve the mouth (buccal/oral cavity) & the teeth.
A quadrant of human dentition is made up of 2 incisors, 1 canine, 2 premolars & 3 molars. These teeth pierce, cut, tear, crush and grind the food into bolus.
Digestion (breaking down bigger molecules in the food into smaller ones our cells can use) of the date starts in the mouth. Here, the starch (large molecule made up of 100s of glucose [simple carbohydrate] units) contents of the date are broken into malt sugar (a disaccharide made up of 2 glucose units) by salivary amylase. Saliva also moistens the food.
Swallowing (deglutition) is a complex neuromuscular reflex involving the soft palate, pharynx & larynx. The tongue propels the date bolus pushing the soft palate to the back, thus closing the path to the nose. The pharynx is also connected to both the oesophagus & the larynx, which is connected to the airways and consequently the lungs. As the bolus is propelled, the laryngeal muscles push the larynx upwards. As a result, a cap-like structure called the epiglottis closes the glottis (part of the larynx).
Now, we can voluntarily push the date down the oesophagus until it reaches the part we can’t control. The oesophagus is a muscular tube that moves the bolus into the stomach even when standing upside down. So you won’t have to worry about your date not reaching the stomach while praying Maghrib. Since the stomach was empty the whole day it was folded into a hot dog. As the date bolus enters, the stomach unravels. As food distends your stomach gastrin is released. Gastrin stimulates churning & the glands lining the walls of the stomach. These glands (made of so called parietal and chief cells) release stomach acid (HCl), a substance needed for vitamin B12 absorption called the intrinsic factor & pepsin (the enzyme that will break down the protein content of the date into the smaller molecules called peptides).
There are several ways that protect the stomach from its acid.
The stomach secretes a layer of alkaline mucus to neutralise the acidity of the acid along its lining.
Moreover, its cells fit tightly together, like a jigsaw puzzle to stop the acid from leaking between them and into the underlying tissue.
If some of the cells become damaged, they are quickly replaced. So each minute about a half million of these cells are exfoliated and replaced.
Now, the dates exit the stomach in the form of the fluid-like chyme. Here [in the small intestine], the chyme will face chemical transformations like it has never seen before, as this is where most of digestion takes place. Bile, produced by the liver (the largest secreting organ; largest gland) & concentrated by the gallbladder, emulsifies the fat globules into droplets in the same way a detergent washes oil from dishes. Emulsification greatly increases the surface area of fat exposed to lipase (a fat digesting enzyme released by the small intestine and pancreas). Bile also activates the enzyme lipase. The products of fat & oil digestion include larger and smaller building blocks - they can even be absorbed without digestion since the conditions in the intestine aren’t exactly perfect (see *).
In addition to mechanical digestion, the liver is responsible for controlling the amount of nutrients in the blood & storing them. Most importantly the liver detoxifies alcohol and other drugs (which are not allowed in Islam).
Liver cells repackage cholesterol and fats. These fats are bound to proteins and are transported as high-density lipoproteins, or HDLs (“good” cholesterol), but most are transported by low-density lipoproteins, or LDLs (“bad” cholesterol). LDLs deliver cholesterol to the cells. LDL enters the cell, and its cholesterol and other components are used. When cholesterol levels are high, HDLs collect the excess cholesterol and transport it to the liver. HDLs decrease risk for cardiovascular disease. Cholesterol is a component of animal cell membranes, but when excess cholesterol in blood forms plaques on artery walls, thereby increasing the risk of cardiovascular disease. Omega-3 (found in dates) decreases LDL levels, decreasing the risk for heart disease.
The pancreas is a gland that secretes digestive enzymes, which break sugars, proteins & fats, and hormones, which regulate the level of glucose in the blood. The pancreatic ducts secrete an alkaline solution to provide the optimal environment for the enzymes in the small intestine. Pancreatic enzymes include trypsin, carboxypeptidase and chymotrypsin, which digest larger peptides to shorter peptides; pancreatic lipase, which degrades fats; pancreatic amylase, which breaks down complex carbohydrates, except cellulose, to carbohydrates made of 2 units; and nucleases, which split the nucleic acids (e.g. DNA) into their building blocks called nucleotides. Trypsin, secreted in an inactive form by the pancreas, is activated by an enzyme called enterokinase. The trypsin then activates chymotrypsin and carboxypeptidase and more trypsin. Dipeptidases, released by the duodenum, then split the small peptides into amino acids. The protein content of the date has been digested. The duodenum also releases enzymes that break carbohydrates (disaccharides made of two carbohydrate units) into a single carbohydrate unit. Now, the duodenum secretes a hormone called glucose-dependent insulinotropic peptide in response to glucose. This hormone stimulates the release of insulin. Insulin acts like a spoon for cells. It allows the cells to take in glucose from the blood. It is the only hormone that does this.
The duodenum also secretes other hormones. For instance, cholecystokinin is released in response to the protein & fat contents of the date (now, chyme). Cholecystokinin, in addition to signalling satiety, stimulates the release of digestive juices in the pancreas and gallbladder. There are other enzymes that can stop the stomach from emptying its contents (e.g. secretin).
The final step would be absorption. Folds in the wall of the intestine (villi, and microvilli) increase the surface area of the small intestine by about 600 times. If we could unfold and spread out the lining of the small intestine, its surface would approximate the size of a football stadium. The digested molecules can now be absorbed by the (lymph & blood) vessels lining the intestine to be delivered to the liver. Due to the lack of space this article will not discuss the very interesting process of absorption. But if you are dying to know about it, check out this link: bit.ly/3DHtWcV. Most of the water you drink to hydrate your dry throat after 14 hours of fasting is absorbed in the small intestine. The concentration of water is higher in chyme than it is in cells lining the intestine. Meaning, water moves down its concentration gradient from the chyme into cells. The remaining water is then absorbed in the large intestine (it is large because of its diameter).
The large intestine, which consists of the cecum, colon, rectum, and anus, is responsible for eliminating/egesting (defecation) undigested wastes. As chyme passes, it assumes the consistency of faeces (its brownish colour is due to bile). Bacteria in the large intestine feed on the undigested materials of the chyme. In exchange, they produce large amounts of vitamin K and certain B vitamins for us to use.
Teeth evolution: youtu.be/wrPEjEqURJg
Videos 3 to 8 are perfect for the part of HL Biology regarding ‘evolutionary novelties’: https://youtube.com/playlist?list=PL8dPuuaLjXtNRgJI4gHRLFtOD_r4hfJaF
When acids and salts interact, a chemical reaction usually occurs when the acid is stronger than the acid from which the salt was formed. This is why carbon dioxide gas is formed when hydrochloric or acetic acid reacts with limestone (descaling your kettle with vinegar) or baking soda (childhood volcano 🌋 experiment). These acids are stronger than carbonic acid. And BTW the decomposition of the carbonic acid formed in the reaction produces carbon dioxide gas. For example: CaCO3 + 2HCl = CaCl2 + CO2 + H2O.
This principle is the basis for the laboratory production of many gases. CO2 is produced from carbonates and bicarbonates with an acid stronger than carbonic acid (hydrochloric acid, sulphuric acid, acetic acid); SO2 from sulphites (e.g. Na2SO3) with an acid stronger than sulphurous acid (hydrochloric acid, acetic acid); H2S from sulphides (e.g. FeS) with an acid stronger than hydrogen sulphide (hydrochloric acid, acetic acid); acetylene (C2H2) can be produced from its salts (e.g. CaC2) with a stronger acid (H2O, HCl).
As with acids, a strong base "displaces" the weaker base from its salt. For instance, NH3 can be produced in the laboratory from an ammonium salt (that was derived from the neutralization of a strong acid by NH3, a weak base; see hydrolysis of salts) (e.g. NH4Cl) with sodium hydroxide: NH4Cl + NaOH = NH3 + NaCl + H2O.
This explains why many metal chalcogenides (oxides) dissolve in acids -> water is the weaker acid. Or why non-metal oxides react with bases. In reality, these are just anhydrides that can form bases or acids when dissolved in water: https://chem.libretexts.org/Bookshelves/Inorganic_Chemistry/Supplemental_Modules_and_Websites_(Inorganic_Chemistry)/Descriptive_Chemistry/Main_Group_Reactions/Compounds/Oxides
Did you know?
Metals of the s-block (alkali metals & alkaline earth metals) are said to be alkaline, as they form base anhydrides/basic oxides. This explains why many of them form hydroxides. (Oxides of the p-block elements are mostly acidic & binary).