Chemical Composition of Living Things PDF

Chemical Composition of Living Things INORGANIC COMPOUNDS This presentation is designed for 1st year students of JFMED CU in Martin It is for internal use only and not to be distributed Copping is prohibited!!!!! ...

Chemical Composition of Living Things INORGANIC COMPOUNDS This presentation is designed for 1st year students of JFMED CU in Martin It is for internal use only and not to be distributed Copping is prohibited!!!!!  What is Life Wikipedia: There is currently no consensus regarding the definition of life. One popular definition is that live organisms are: ▪ open systems that maintain homeostasis, ▪ composed of cells, ▪ have a life cycle, ▪ undergo metabolism, ▪ can grow, ▪ adapt to their environment, ▪ respond to stimuli, ▪ reproduce ▪ evolve.  Levels of Organisation of Living Things The first Image of a Hyderogen Atom´s Orbitel Structure Posted by Shailesh Prasad https://lifeboat.com/blog/2016/02/the-first-image-ever-of-a-hydrogen-atoms- orbital-structure Atom Molecule Three molecules of benzen rings connected by carbon atoms https://www.extremetech.com/extreme/157048-the-first-ever-images-of-a-molecule-as-it-makes-and- breaks-atomic-bonds The black dots are glycogen, scattered among several Macromolecule mitochondria https://www.sciencephoto.com/media/214945/view/tem-of-glycogen-in-salamander-liver-cell https://shoptr4.lastbornfoundation.org/content?c=organisation+of+organisms&id=33  Atoms and Elements ▪ Organisms are composed of matter, which is anything that takes up space and has mass. ▪ Matter exists in many diverse forms, each with its own characteristics. ▪ Matter consists of chemical elements in pure form and in combinations called compounds. ▪ An element is a substance that cannot be broken down to other substances by chemical reactions. Today, chemists recognise around 100 elements occurring in nature. ▪ About 25 of the natural elements are known to be essential to life – biogenic elements.  Atoms and Elements Macroelements are found in all living things. ▪ Four of these – carbon (C), oxygen (O), hydrogen (H), and nitrogen (N) – make up 96 % of living matter. ▪ Phosphorus (P), sulphur (S), calcium (Ca), potassium (K), and few other elements account for most of the remaining 4 % of an organism’s weight. Microelements (trace elements) (less than 0.01%): boron (B), chromium (Cr), cobalt (Co), copper (Cu), fluorine (F), iodine (I), iron (Fe), manganese (Mn), molybdenum (Mo), selenium (Se), silicon (Si), vanadium (V), and zinc (Zn).  Structure of Atoms ▪ An atom is the smallest unit of matter that still retains the properties of an element. ▪ Physicists have split the atom into more than a hundred types of particles, but only three kinds of particles are stable enough to be of relevance: neutrons, protons, and electrons. ▪ Neutrons and protons are packed together tightly to form an atomic nucleus. Electrons, moving at nearly the speed of light, form a cloud around the nucleus. ▪ Electrons and protons are electrically charged. Each electron has one unit of negative charge, and each proton has one unit of positive charge. ▪ A neutron is electrically neutral. Protons give the nucleus a positive charge, and it is the attraction between opposite charge that keeps the rapidly moving electrons in the vicinity of the nucleus. https://awo.aws.org/glossary/electron-shell/  Structure of Atoms Each element is identified by three numbers: atomic number, mass number, atomic weight. ▪ The atomic number is the number of protons and is written as a subscript to the left of the symbol for the element. The abbreviation 2He, for example, tells us that an atom of the element helium has two protons in its nucleus. Unless otherwise indicated, an atom is neutral in electrical charge, which means that its protons must be balanced by an equal number of electrons. Therefore, the atomic number tells us the number of protons and also the number of electrons in an electrically neutral atom. ▪ The mass number is the sum of protons plus neutrons in the nucleus of an atom. The mass number is written as a superscript to the left of an element’s symbol. For example, we can use this shorthand to write an atom of helium as 4 He. Almost all of an atom’s mass is concentrated in its nucleus, because the 2 contribution of electrons to mass is negligible. ▪ Because neutrons and protons each have a mass very close to 1 Dalton, the mass number is an approximation of the total mass of an atom, usually called its atomic weight.  Structure of Atoms ▪ An atom’s electrons vary in the amount of potential energy they possess. The different states of potential energy for electrons in an atom are called energy levels, or electron shells. ▪ The first shell is closest to the nucleus, and electrons in this shell have the lowest energy. Electrons in the second shell have more energy, electrons in the third shell more energy, and so on. ▪ An electron can change its shell, but only by absorbing or losing an amount of energy equal to difference in potential energy between the old shell and the new one. ▪ The three-dimensional space where an electron is found 90% of the time is called an orbital. ▪ No more than two electrons can occupy the https://historyoftheatomictheory.files.wordpre https://sites.google.com/site/chem1403/atomic- orbitals same orbital. ss.com/2014/12/bohr-03.png  Structure of Atoms ▪ The chemical properties of an atom depend mostly on the number of electrons in its outermost shell. ▪ We refer to those outer electrons as valence electrons, and to the outermost electron shell as the valence shell. ▪ Atoms with a completed valence shell are unreactive. They are termed inert elements. ▪ The reactivity of atoms arises from the presence of unpaired electrons in the valence shell. http://breakingawesomechem.weebly.com/valence-shells--core- electrons/the-difference-between-valence-shell-electrons-and-core-electrons  Isotopes ▪ All atoms of a given element have the same number of protons, but some atoms have more neutrons than other atoms of the same element. These different atomic forms are referred to as isotopes of the element. ▪ In nature, an element occurs as a mixture of its isotopes. ▪ For example, consider the three isotopes of the element carbon, which has the atomic number 6. The most common isotope is carbon 126C, which accounts for about 99 % of the carbon in nature. It has 6 neutrons. Most of the remaining 1% of carbon consists of atom of the isotope 13 C, with 7 neutrons. A third, even rare isotope 14 C has 8 neutrons. 6 6 Both 12C and 13C are stable isotopes, meaning that their nuclei do not have a tendency to lose particles. The isotope 14C is unstable, or radioactive.  Application of Isotopes Radioactive isotopes have many useful application in biology and radioactive tracers have become important diagnostic tools in medicine. ▪ One of the well known application of radioisotope is the method called carbon dating. Radioactive carbon with 14 neutrons decays into nitrogen 14 with a very long half-life (over 5,000 years). Therefore, in organic materials that were once alive, the amount of carbon 14 will steadily decrease over time. Calculating backwards, we can measure the amount of carbon 14 in a dead organism and determine when the organism died.  Application of Radioisotopes in Medicine ▪ Based on the fact, that chemical properties of radioisotope and it´s nonradioactive form are exactly the same, radioisotope can be substituted for a stable isotope in required molecules thus they become labelled. Radiation emitted by the radioisotope can be detected using the appropriate apparatus and the progress of those atoms through the body can be traced. ▪ For that reason, labelled molecules are called tracers. ▪ Tracers (radioisotopes) can be directly injected into blood stream or ingested by the organisms (if they are administered per oral) and consequently, it is possible to monitor internal processes and conditions inside the human body.  Application of Radioisotopes in Medicine ▪ The most common radioisotopes used for the study of function of thyroid gland are iodine-123 and iodine-131. Following the injection of very small amount of radioactive iodine within few minutes, it will begin to concentrate in the thyroid gland. By monitoring of distribution and concentration of tracer, it is possible to determine whether it´s function is pathological. ▪ Other radioisotopes allow monitoring of different organs and tissues. For example, cobalt-57 is used for observation of absorption, storage, and metabolism of vitamin B12; chromium-51 and iron- 59 help with determination of the survival rate of http://encyclopedia.lubopitkobg.com/Basic_Chemistry.html red blood cells and strontium-87 allows monitoring of bone metabolism. ▪ Radiation emitted by radioisotopes as cobalt-60 and cesium-137 can also be used in treatment of certain types of illnesses, especially cancerous tumours.  Atoms in Medicine ▪ X-Rays are a type of electromagnetic radiation with wave length ranging from 0.01 to 10 nanometres, which can pass through an opaque object. ▪ X-Rays were discovered by German physicist Wilhelm Roentgen in 1895 and already in one month, they were being used to diagnose broken bones. ▪ For taking of radiograph (x-ray image), the patient must be placed in front of an x-ray detector and then exposed to a short x-ray pulse. ▪ Bones contain high amount of calcium (element of high atomic number), which absorbs majority of rays. This absorption reduces the amount of rays reaching detector behind bones, making them bright and visible on the radiograph. ▪ Because of different absorption ability of different tissues in the body, it allows to analyse and distinguish normal and pathological cases. ▪ X-rays can be used in the detection of skeleton disorders as well as of some pathological processes of soft tissue. It allows detection of lung inflammation and tumours, intestinal obstructions, gall bladder stones, kidney stones etc. https://emergencyfoundation.org.au/software-halves-time-to-diagnose-broken-bones/  Atoms in Medicine ▪ Computerised tomography (CT) is an imaging technique that combines x- rays and computers. ▪ CT allows making high-resolution images based on a series of x-rays through cross sections of any part of the living body. ▪ Comparing with simply x-rays, CT gives more precise image of analysed tissue and can be used for detection of tumours, blood clots, or https://www.medicalnewstoday.com/articles/153201 other abnormalities in all kinds of tissues.  Atoms in Medicine http://img.medscapestatic.com/pi/meds/ckb/48/15748tn.jpg ▪ Nuclear magnetic resonance (NMR) uses magnetic field to alter the normal spin of the protons in certain atoms in the body and to change their natural magnetic fields. ▪ This temporary alteration causes the protons to give off a faint signal that can be detected and can show the presence and concentration of the analysed chemicals. ▪ This technique enables to watch blood flow through vessels in given tissues and organs, to diagnose blood clots, tumours, clogged vessels, damaged nerves, brain and joints. Figure shows spinal stenosis  Atoms in Medicine ▪ Positron emission tomography (PET) is one of relatively new imaging techniques, which uses emission of positively charged electrons, called positrons. Whereas positron is actually an antimatter particle, after collision with electron, both particles are (by annihilation) converted into the high energy gamma radiation which is detected. ▪ Isotopes that emit positrons used in medicine are carbon-11 and fluorine-18, both with short half live (20.4 and 110 minutes, respectively). ▪ They can be incorporated into sugar molecules and introduced to patient. Radioactive sugar travels throughout the body. Patient is then scanned by sensors that detect arising gamma radiation. Intensity of gamma ray emission shows tissues that metabolise sugar faster than other tissues. Because fast-metabolising tissue with high intake of sugars is one sign of tumours, this technic allows detection of primary tumours as well as metastasis. PET can also detect early warning signs of diseases. https://www.neurologyadvisor.com/topics/alzheimers-disease-and-dementia/amyloid-pet-scan-associated-with-changes-in-mci- and-dementia-clinical-management/ http://www.physicsinfo.co.uk/?page=view&id=2679  Compounds and Molecules ▪ A compound is a substance consisting of two or more different elements combined in a fixed ratio. ▪ For example, in water, there are two H atoms and one O atom. This composition does not change. ▪ When atoms interact chemically to form molecules, the atoms are held together by electrical forces called chemical bonds. ▪ Atoms with incomplete valence shell interact with certain other atoms in such way that each partner completes its valence shell. Atoms do this by either sharing or transferring valence electrons. ▪ Five important types of chemical bonds are: covalent bonds ionic bonds hydrogen bonds hydrophobic interactions van der Waals forces  Compounds and Molecules Covalent Bonds ▪ A covalent bond is the sharing of a pair of valence electrons by two, or more atoms. ▪ An example of covalent bonding involves carbon atoms. Since carbon atom has four electrons, but requires a total of eight to fill its outer shell, it must borrow four electrons from other atoms. It can do this by combining with four hydrogen atoms (each H atom requires one electron to fill its outer shell) to form CH4 (methane). ▪ Other elements require different numbers of electrons to fill their outer shells, which determines the number of covalent bonds that the element can make. ▪ The dash between two atoms represents two shared electrons (C–H), a single bond. Sometimes electrons are shared in groups of four, called double bonds (C=O).  https://www.britannica.com/science/covalent-bond https://www.usgs.gov/media/images/strong-polar-bond-between-water-molecules-creates-water-cohesion ▪ In covalent bonds, between identical atoms such as H-H, the electrons are shared equally – non-polar covalent bond. Non-polar covalent bonds also exist between different atoms, such as C-H, since both atoms have a similar attraction for electrons. ▪ If one atom has a much greater attraction for electrons than the other one, the electrons are shared unequally – polar covalent bond. Then, one part of the molecule has a positive charge and another part has a negative charge. ▪ All covalent bonds are strong bonds. Therefore, covalent bonds do not break unless they are exposed to strong chemicals or are supplied with large amounts of energy, generally as heat. ▪ Since biological systems cannot tolerate high temperatures, they utilise the protein catalysts called enzymes, which can break these covalent bonds at temperatures at which life can exist.  Compounds and Molecules Ionic Bonds ▪ If electrons from one atom are attracted very strongly by another atom which is nearby, the electrons completely leave the first atom and become a part of the outer electron shell of the second one, without any sharing. This bond is termed an ionic bond. ▪ Ionic bonds are attractions between oppositely charged ions. ▪ Ionic bonds within a salt crystal are strong. However, if the crystal of salt is dissolved in water, each of the individual ions becomes surrounded by water molecules, which inhibit oppositely charged ions from approaching one another closely enough to form ionic bonds. Since cells are composed primarily of water, the interaction between ions of opposite charge is minimal and ionic bonds can be considered weak.  Compounds and Molecules https://www.assignmentpoint.com/science/chemistry/ionic-bonding.html ▪ An atom can fill its outer shell by either gaining electrons or by losing electrons and in this way becomes either negatively or positively charged, respectively. Such charged atoms are termed ions. ▪ When the charge is positive, the ion is specially called a cation. Conversely, negatively charged ion is called an anion. ▪ Examples of cations are sodium (Na+), potassium (K+), hydrogen (H+), calcium (Ca2+) and iron (Fe3+). ▪ Some anions are chloride (Cl-), hydroxyl (OH-), sulphate (SO43-), phosphate (PO43-), and carboxyl (COO-).  Compounds and Molecules Hydrogen Bonds ▪ A hydrogen bond is a weak bond, which occurs when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom. ▪ In living cells, the electronegative partners involved are usually oxygen or nitrogen atoms. ▪ An example is hydrogen bonding between water (H2O) and ammonia (NH3). The polar covalent bonds of water result in the oxygen atom having a slight negative charge and the hydrogen atoms having a slight positive charge. In ammonia, an electronegative nitrogen atom has a small amount of negative charge because of its pull on the electrons it shares covalently with hydrogen.  Compounds and Molecules Hydrogen bond. If the slight positive charges on the hydrogen atoms in a water molecule attract the slight negative charges on the oxygen atoms of other water molecules. https://chemistryonline.guru/hydrogen-bond/ If a water molecule and an ammonia molecule are close together, a weak attraction will occur between the negatively charged nitrogen atom and a positively charged hydrogen atom of the adjacent water molecule. https://www.quora.com/What-are-the-different-types-of-hydrogen-bonds  Compounds and Molecules Hydrophobic Interactions ▪ Hydrophobic interaction is a very important weak force that help to hold a protein´s shape. ▪ It is a force that causes hydrophobic molecules or nonpolar portions of molecules to aggregate together rather than to dissolve in water. ▪ A nonpolar molecule cannot form hydrogen bonds with water, so it distorts the usual water structure, forcing the water to make a cage of https://celestemohan.wordpress.com/2013/02/25/tertiary-level-of-protein-structure/ hydrogen bonds around it.  Compounds and Molecules Van der Waals Interactions ▪ Van der Waals forces are nonspecific interactions caused by transient dipoles in all atoms. ▪ Momentary random fluctuations in the distribution of the electrons of any atom given rise to a transient unequal distribution of electrons – a dipole. ▪ If two non-covalently bonded atoms are close enough, the transient dipole in one atom will perturb the electron cloud of the other one. ▪ This perturbation generates a transient dipole in the second atom, and the two dipoles will attract each other weakly. https://socratic.org/questions/why-do-van-der-waals-forces-hold-molecules-together  Compounds and Molecules pH Scale ▪ The pH scale ranges from 0 to 14. The numbers indicate the hydrogen ion concentration [H+] and also the hydroxide ion concentration [OH-]. ▪ The pH of water (pH = 7) is neutral pH because pure water breaks up or dissociates in this manner: H – O – H → H+ + OH- ▪ In any quantity of water, most of the water molecules are intact but some have dissociated to give an equal number of H+ and OH- ions. The fraction of water molecules that dissociate is 10-7 (or 0.0000001) which is called a pH of 7. ▪ In other words, the pH scale was devised to simply discussion of the hydrogen ion concentration [H+].  http://acidsandbases-101.weebly.com/ph--poh.html https://www.scienceabc.com/pure-sciences/can-ph-have-values-out-of-the-0-14-range.html  Compounds and Molecules Acids and Bases ▪ Acids are substances that increase the [H+] of a solution. For example, hydrochloric acid (HCl) dissociates in manner: HCl → H+ + Cl- ▪ In the pH scale, the numbers 0 to 7 indicates an acidic pH, each lower unit has 10 times higher number of hydrogen ions as the number above. ▪ Bases are substances that increase the [OH-] of a solution. For example, sodium hydroxide (NaOH) dissociates in manner: NaOH → Na+ + OH- ▪ In the pH scale, the numbers 7 to 14 indicate a basic pH, each higher unit has 10 times higher number of hydroxide ions as the number below.  Compounds and Molecules Buffers ▪ All living things need to maintain the hydrogen ion concentration, or pH, at a constant level. ▪ For example, the pH of the blood is held constant at about 7.4, otherwise we become ill. ▪ The presence of buffers helps to keep the pH constant. ▪ A buffer is a chemical or a combination of chemicals that can take up excess hydrogen ions or excess hydroxide ions. ▪ When an acid is added to a buffered solution, a buffer takes up excess hydrogen ions, and when a base is added to a buffered solution, a buffer takes up excess hydroxide ions. ▪ Therefore, the pH changes minimally whenever a solution is buffered. ▪ One of buffer systems involves carbonic acid (H2CO3) and bicarbonate (HCO3–) anion.  Free Radicals ▪ Reactive chemical species called free radicals are being implicated in dozens of disorders, from wrinkled skin to cancer and premature senility. ▪ Free radicals, essentially molecules orbited by an unpaired electron, can form when molecular oxygen (O2), hydroxyl ions (OH-), nitrogen dioxide (NO2), or other groups of covalently bonded atoms undergo certain types of chemical reactions and in the process, they lose an orbiting electron. ▪ In their new, unstable state, they can quickly steal an electron from a nearby molecule. https://pierredieregesondheid.wordpress.com/2018/12/09/free-radicals-ii/#jp- carousel-1196  Free Radicals ▪ If the free radical steal an electron from a protein such as the collagen in connective tissue of joints or skin, the result can be increased wrinkling or intensified arthritis. ▪ If the electron donor is a molecule of fat in the delicate boundary that encloses a cell, a hole can form in that boundary, and the results can be damaged blood cells and damaged lung or eye tissue. ▪ If free radicals rob electrons from DNA, the “thefts“ may alter genes and lead to cancer. ▪ And finally, if free radical attacks a nerve transmitter substance in the brain, it may contribute to Alzheimer´s dementia. https://sciencesamhita.com/role-of-free-radicals-in-aging/  Free Radicals ▪ Several factors may contribute to formation of free radicals: very heavy exercise tobacco smoking exposure to x-rays strong sunlight pesticides cancer-causing substances heavy air pollutions certain kinds of drugs eating cured meats fatty food foods containing rancid fats ▪ Avoiding these is clear one way to reduce wear and tear by free radicals, and so is consuming more foods (not supplements) rich in vitamin A, C, and E, since these molecules scavenge unpaired electrons from free radicals before they can do damage.