HA1 Lecture: The Chemistry of Life PDF

⚛️ HA1 Lecture: The Chemistry of Life Atoms make up all matter What are atoms? Atoms are defined as “the basic building blocks of matter”. Atom is the basic of all matter....

⚛️ HA1 Lecture: The Chemistry of Life Atoms make up all matter What are atoms? Atoms are defined as “the basic building blocks of matter”. Atom is the basic of all matter. They are very small and consist of even tinier particles. What are the subatomic particles? Neutrons, Protons, and Electrons are the basic particles making up the atom. They join together with other atoms and create matter. What is matter? Matter is something that occupies space and has mass. All matter is composed of elements, substances that cannot be broken down or transformed chemically into other HA1 Lecture: The Chemistry of Life 1  substances. Every matter contains atoms and atoms make up the matter. Energy is defined as the ability to do some sort of work. According to Einstein's theory of Relativity, energy can be converted into matter and matter can be converted into energy. Energy and matter are one and the same thing but in different contexts. Glucose Breakdown: Glucose is broken down in the presence of oxygen into carbon dioxide and water. The breaking of chemical bonds in glucose releases energy, which is then captured in the form of adenosine triphosphate (ATP), the energy currency of the cell. What are elements? An element is a substance that cannot be broken down into any other substance. Every element is made up of its own type of atom. This is why the chemical elements are all very different from each other. What are the elements found in the human body? Some elements are much more common than others. The human body is approximately 99% comprised of just six elements: Oxygen, hydrogen, nitrogen, carbon, calcium, and phosphorus. Another five elements make up about 0.85% of the remaining mass: sulfur, potassium, sodium, chlorine, and magnesium. What are trace elements? Trace elements (or trace metals) are minerals present in living tissues in small amounts. Some of them are known to be nutritionally essential, others may be essential (although the evidence is only HA1 Lecture: The Chemistry of Life 2  suggestive or incomplete), and the remainder are considered to be nonessential. An element is considered a trace element when its requirement per day is below 100 mg. The deficiency of these elements is rare but may prove fatal. Examples include copper, iron, zinc, chromium, cobalt, iodine, molybdenum, and selenium What is iron and what does it do? Iron is a mineral that the body needs for growth and development. The human body uses iron to make hemoglobin, a protein in red blood cells that carries oxygen from the lungs to all parts of the body, and myoglobin, a protein that provides oxygen to muscles. What is iodine and what does it do? Iodine is a mineral found in some foods. The body needs iodine to make thyroid hormones. These hormones control the body's metabolism and many other important functions. The body also needs thyroid hormones for proper bone and brain development during pregnancy and infancy. What does the thyroid gland do? The thyroid gland produces hormones that regulate the body's metabolic rate, growth and development. It plays a role in controlling heart, muscle and digestive function, brain development and bone maintenance. Its correct functioning depends on a good supply of iodine from the diet. HA1 Lecture: The Chemistry of Life 3  Hypothyroidism is a common condition where the thyroid doesn't create and release enough thyroid hormone into your bloodstream. This makes your metabolism slow down. Also called underactive thyroid, hypothyroidism can make you feel tired, gain weight and be unable to tolerate cold temperatures. What is fluorine and what does it do in the body? For the past several decades, fluoride has been added to community water supplies and oral care products such as toothpaste and mouth rinse. Fluoride works by strengthening the tooth's hard outer surface called enamel. Isotopes Differentiate atomic number and mass number Atomic number and mass number both consider the number of protons present in a given element. The atomic number is simply the number of protons in the given element (Z), and the mass number is the number of protons + neutrons in an atom of the element (A). What are isotopes? Atoms with the same number of protons but different numbers of neutrons are called isotopes. They share almost the same chemical properties, but differ in mass and therefore in physical properties. There are stable isotopes, which do not emit radiation, and there are unstable isotopes, which do emit radiation. Describe carbon dating and carbon-14. HA1 Lecture: The Chemistry of Life 4  Radiocarbon dating, or carbon-14 dating, is a scientific method that can accurately determine the age of organic materials as old as approximately 60,000 years. When a living organism—like a plant or an animal—is alive, it takes in carbon from its environment, including a tiny amount of a special type of carbon called carbon-14. This carbon-14 is radioactive, which means it slowly breaks down over time at a known rate. When the organism dies, it stops taking in new carbon, so the carbon-14 it has starts to decrease as it breaks down. Scientists can measure how much carbon-14 is left in the remains of the organism. Since they know how fast carbon-14 breaks down, they can calculate how long it's been since the organism died. This helps them estimate the date of death, giving us a way to determine how old ancient remains are. What are radioisotopes? An unstable form of a chemical element that releases radiation as it breaks down and becomes more stable. Radioisotopes may occur in nature or be made in a laboratory. In medicine, they are used in imaging tests and in treatment. What are the dangers of radioactive isotopes? Radioactive isotopes pose significant dangers to human health and the environment, as was starkly demonstrated in the nuclear disasters at Fukushima (2011) and Chernobyl (1986). Radioactive Contamination: Fukushima: HA1 Lecture: The Chemistry of Life 5  The Fukushima Daiichi nuclear disaster, triggered by a massive earthquake and tsunami, led to the release of radioactive isotopes like iodine-131, cesium-134, and cesium-137 into the environment. These isotopes contaminated the air, water, and soil in the surrounding area, leading to long-term environmental damage. Chernobyl: The explosion and fire at the Chernobyl reactor released a vast amount of radioactive material, including iodine-131, cesium-137, and strontium-90. The radioactive cloud spread across Europe, causing widespread contamination. Health Risks: Fukushima: Iodine-131: This isotope has a short half-life (about 8 days) but is dangerous because it concentrates in the thyroid gland when inhaled or ingested, increasing the risk of thyroid cancer, especially in children. Cesium-137: With a half-life of about 30 years, cesium-137 can contaminate food and water sources, leading to long-term exposure. It distributes evenly in soft tissues, increasing the risk of cancers. Chernobyl: Acute Radiation Syndrome (ARS): Many workers and firefighters at Chernobyl were exposed to lethal doses of radiation, leading to ARS, characterized by nausea, vomiting, and severe organ damage, leading to death in some cases. Long-term Effects: The widespread exposure to radioactive isotopes led to increased rates of HA1 Lecture: The Chemistry of Life 6  thyroid cancer, particularly in children exposed to iodine-131, and elevated risks of other cancers in the affected population. Environmental Impact: Fukushima: The release of radioactive isotopes into the Pacific Ocean caused concerns about contamination of marine life. Radioactive cesium was found in fish, leading to restrictions on fishing in the region. The long- term effects on the marine ecosystem remain a concern. Chernobyl: The "Chernobyl Exclusion Zone," a 30-kilometer radius around the plant, remains heavily contaminated. The environment has been severely impacted, with forests, wildlife, and water bodies still containing significant levels of radioactivity. However, the absence of human activity has allowed some wildlife to thrive in unexpected ways. Socioeconomic and Psychological Impact: Fukushima: The disaster led to the evacuation of tens of thousands of people, many of whom have not been able to return to their homes. The displacement caused significant social and economic disruption, as well as psychological stress, including anxiety and depression. Chernobyl: The Chernobyl disaster resulted in the evacuation and resettlement of over 300,000 people. The psychological impact was profound, with many suffering from stress, anxiety, and a sense of loss. HA1 Lecture: The Chemistry of Life 7  The disaster also led to long-term economic hardships for the affected regions. Chemical Bonds What are chemical bonds? A chemical bond is an attraction between two or more atoms, and is what forms a chemical. This is an electrostatic attraction - an attraction between positive and negative charges. In each atom, there are positively charged protons in the nucleus and negatively charged electrons orbiting around the outside. What are compounds? a substance made from two or more different elements that have been chemically joined. Examples of compounds include water (H2O), which is made from the elements hydrogen and oxygen, and table salt (NaCl), which is made from the elements sodium and chloride. Discuss the electron distribution diagram. Chemical bonds form when atoms interact to achieve more stable electron configurations, typically by filling their outer electron shells. The type of bond formed depends on how the electrons are shared or transferred between the atoms. Maximum number of electrons in a shell is 2n^2. K Shell: 2 x (1)^2 = 2 L Shell: 2 x (2)^2 = 8 M Shell: 2 x (3)^2 = 18 HA1 Lecture: The Chemistry of Life 8  Note: Outermost orbit: maximum of 8 electrons (with few exception such as transition elements). Kung M shell ang outermost orbit, it will follow the octet rule. What are the different types of bonds? Covalent Bond A covalent bond is a chemical bond that involves the sharing of electrons to form electron pairs between atoms. formed between two non-metals that have similar electronegativities. Neither atom is "strong" enough to attract electrons from the other. For stabilization, they share their electrons from outer molecular orbit with others Polar Covalent Bond Unequal sharing of bonds. In polar molecules, such as water (H2O) and ammonia (NH3), there is an uneven distribution of electrons, leading to the presence of partial positive and partial negative charges on different atoms within the molecule. Non-polar Covalent Bond Equal sharing of bonds. Non-polar molecules, such as oxygen (O2), nitrogen (N2), and carbon dioxide (CO2), have equal distribution of electrons, resulting in no significant separation of charge. Electronegativity is a chemical property that describes the tendency of an atom or a functional group to attract electrons toward itself. HA1 Lecture: The Chemistry of Life 9  Polarity Electronegativity diference range Ionic 1.8 and above Polar covalent 0.5 - 1.7 Non-polar covalent 0.0 - 0.4 Ionic Bond An Ionic bond is the bond formed by the complete transfer of valence electron to attain stability. An ionic bond is formed between a metal and a non-metal. Non-metals(-ve ion) are "stronger" than the metal(+ve ion) and can get electrons very easily from the metal. Hydrogen Bond Hydrogen bonded with Nitrogen, Oxygen, and Fluorine. Properties of Water What makes water unique? 1. It has one very electronegative oxygen — keeping oxygen slightly negative charge because of the electrons are spending more time to it than the hydrogen. 2. It gives hydrogen a slightly positive charge. HA1 Lecture: The Chemistry of Life 10  This means water molecules have an easy time bonding together. Why? Because the hydrogen of one water molecule with its slightly positive charge can bond to another water molecule’s oxygen with slightly negative charge. The structure of water resulting to polarity: 1. Each hydrogen in a water molecule is bound to the oxygen with a hydrogen bond. 2. It’s a covalent bond because the hydrogen and oxygen share an electron. 3. It’s polar because they don’t share them equally. 4. The result is that water is a polar (charged) molecules and it is an excellent solvent. How many molecules of water stick together? 1. They are held together by hydrogen bonds. 2. Hydrogen bonds are attractions between between the positive end of the molecule and the negative end of another molecule. 3. This results in water’s cohesive and thermal properties. whereas water’s polarity is very good for its solvent properties. Cohesive Properties: Cohesion is when molecules of the same type are attracted to each other. The hydrogen bonds between water molecules (cohesion) explains the following: 1. Surface tension that allows some organisms to rest or move on top of the water’s surface → important for many insects HA1 Lecture: The Chemistry of Life 11  2. Allows water to move as a column (group of water molecules) through the stems of plants. Adhesive Properties: Adhesion is an attraction between two unlike molecules. 1. The water moves up the stems of plants because in addition to being attracted to itself (cohesion), it is also attracted to the side of the stem (adhesion). 2. Water is so highly attracted to the sides of the stem that it pulls itself up against the force of gravity without any energy input from plant. Thermal Properties: Water has a very high specific heat (the amount of energy required to raise the temperature). It resists changes in temperature. Specific heat: the measurement of heat that is needed to be absorbed or lost to change its temperature. This means that water can absorb lots of energy before becoming too hot. It also means that water must loose a lot of energy to drop in temperature. That is why in a very hot summer, the pavements may be really really hot but the water is still cool. Example 1: cells can withstand a lot of heat energy release from their metabolic reaction. Example 2: sweat on skin can absorb a lot of heat energy before it evaporates, cooling an organism. HA1 Lecture: The Chemistry of Life 12  Water’s high specific heat is useful in the following: 1. Aquatic organisms who can’t survive extreme temperature changes. 2. Plants have openings in their leaves called stomata to let vaporizing water out in order to cool down the leaf. Solvent Properties: The formation of hydrogen bond is super important for cohesion and adhesion but it is really water’s polarity that makes it an excellent solvent. With water being polar makes it a powerful solvent Solvent → solvent, substance, ordinarily a liquid, in which other materials dissolve to form a solution. Almost all metabolic reactions in cells must take place with the reactants in aqueous solutions (dissolved in liquid). Example: Salt after being dissolved. The fact that water surrounds them keeps sodium and chlorine from joining together. Example: Sodium-Potassium Pump Since water is an excellent solvent, it allows for a wide variety of reactants to be dissolved, leading to their ability to collide and undergo metabolic reactions. Chemical compounds that are important to living organisms HA1 Lecture: The Chemistry of Life 13  Monomer: they are atoms or small molecules that bond together to form more complex structures such as polymers. Small, repeating parts. Polymer: it is a generic name for long molecules made of many repeating parts. Polymerization: any process in which relatively small molecules, called monomers, combine chemically to produce a very large chainlike or network molecule, called a polymer. Macromolecules: they are large polymers that are assembled from small repeating monomer subunits. Types of Macromolecules: 1. Carbohydrates → monosaccharides 2. Lipids → glycerol and fatty acids 3. Proteins (polypeptides) → amino acids 4. Nucleic Acids → nucleotides Example Category Building Blocks Subcategory molecules Glucose, Simple sugar/ galactose, Carbohydrates Monosaccharide Monosaccharide fructose, ribose Maltose, Disaccharide lactose, sucrose Starch, glycogen, Polysaccharide cellulose, chitin Fat stored in Lipids Fatty Acids Triglycerides adipose tissue Phospholipids Lipids forming a bilayer in HA1 Lecture: The Chemistry of Life 14  cell membranes Steroids Some hormones Enzyme, antibodies, Proteins Amino Acids peptide hormones Nucleic Acids Nucleotide DNA and RNA Carbohydrates Carbohydrates are found in a wide array of both healthy and unhealthy foods—bread, beans, milk, popcorn, potatoes, cookies, spaghetti, soft drinks, corn, and cherry pie. They also come in a variety of forms. The most common and abundant forms are sugars, fibers, and starches. Immediate source of energy. 1:2:1 ratio of carbon, hydrogen, and oxygen. Monosaccharide Monosaccharides are also called simple sugars, are the simplest forms of sugar and the most basic units (monomers) from which all carbohydrates are built. Monosaccharides are carbohydrate molecules that cannot be broken down by hydrolysis There are several monosaccharides you should know: a. Glucose is the main type of sugar in the blood and is the major source of energy for the body's cells. Glucose comes from the foods we eat or the body can make it from other substances. It nourishes the brain. b. Galactose is a milk sugar. Galactose serves as a substrate for cerebrosides, gangliosides and mucoproteins in the brain and nervous system, which supports its neural and immunological role HA1 Lecture: The Chemistry of Life 15  c. Fructose is a fruit sugar. It is commonly found in honey. Disaccharide Disaccharides also called double sugar, any substance that is composed of two molecules of simple sugars (monosaccharides) linked to each other. Condensation reaction is a reaction in which two or more molecules combine to form a larger molecule, with the simultaneous loss of a small molecule such as water or methanol. They are are molecules formed by condensation reactions between two monosaccharides. They are sharing an oxygen, forming a glycosidic bond. (HO-OH → -O-). Glucose + fructose yields to sucrose. Through condensation reaction, water is released, creating a glycosidic bond → sucrose. There are several important disaccharides that you must know: a. Maltose → glucose + glucose (source: hydrolyzed starch) b. Lactose → glucose + galactose (source: mammalian milk) HA1 Lecture: The Chemistry of Life 16  c. Sucrose → glucose + fructose (source: plants) Polysaccharide Polysaccharides are long chains of carbohydrate molecules, composed of several smaller monosaccharides. These complex bio-macromolecules functions as an important source of energy in animal cell and form a structural component of a plant cell. There are several polysaccharides that you must know: a. Cellulose, a tough, fibrous, and water-insoluble polysaccharide, plays an integral role in keeping the structure of plant cell walls stable. nice-to-know: Humans do not have the enzymes needed to break down cellulose. Cellulose is also an insoluble fiber and does not dissolve in water. When consumed, insoluble fibers can help push food through the digestive system and support regular bowel movements. b. Starch/ Starchy foods are our main source of carbohydrate and have an important role in a healthy diet. Starchy foods – such as potatoes, bread, rice, pasta, and cereals – should make up just over a third of the food you eat. It is the storage of extra glucose in plants c. Glycogen is the stored form of glucose that's made up of many connected glucose molecules. Glucose (sugar) is your body's main source of energy. Lipids All fatty acids have a methyl group (CH3) on one end and a carboxyl group (COOH) on the other end. In the middle is a chain of anywhere between 11-23 CH2 groups (H3C-CH2-COOH). Fatty acids are categorized into two: HA1 Lecture: The Chemistry of Life 17  a. Saturated fatty acids (SFA) contain no double bond; this type of fat can be synthesized by the body and its major dietary source is food from animal sources, such as full- fat dairy products, red meat, and poultry. Moreover, there are numerous types of SFA according to length of their chain (contains 4–16 carbon atoms). Straight molecule (not bent) Said to be saturated because the carbons are carrying as many hydrogen atoms as they can. Solid at room temperature. b. Unsaturated fatty acids are hydrocarbon chains containing at least one carbon–carbon double bond b.1. Monounsaturated fatty acids contain one double bond. Bent molecule (why? hydrogen don’t like each other which causes the repelling forces to not equal out). Source: plants/ animals (i.e. fish) and are liquid at room temperature. b.2. Polyunsaturated fatty acids (PUFAs) contain many double bonds. It has many bends and liquid at room temperature. b.1.1. Trans The hydrogens are on the opposite side of the double bond, so the molecules is straight. Many processed foods are made with hydrogenated fats. These fatty acids that were previously unsaturated fats with many double bonds, but hydrogen atoms have been added in (hydrogenated), eliminating the double bonds and straightening the molecules. This process results to products lasting longer but they are less healthy → caused bad cholesterol. HA1 Lecture: The Chemistry of Life 18  b.1.2. Cis Hydrogens are on the same side of the double bond and they repel each other so there is a bend i n shape. Polyunsaturated fats that are naturally curved, Includes omega-3-fatty acids, named for double bond on the third carbon. Cis products are healthy and mostly found in fish. Is Fat Good for you? When looking at nutrition label, you must consider the following: The total amount of fat: Note: even if you are eating healthy fats, it is still fat. Fat has more calories per gram. (fats= 9 calories per gram; carbohydrates= 4 calories per gram). Too many fats can lead to excessive weight. The type of fat Trans fat and saturated fats are not as healthy as cis polyunsaturated fats Condensation reactions result in the formation of Triglyceraldehyde Lipids. Lipids are result of condensation reaction between glycerol and three fatty acids. Energy Storage in Humans The energy in food is used to generate ATP, which is used to power many cell processes. HA1 Lecture: The Chemistry of Life 19  If there are is already a sufficient ATP, humans and other animals will store energy in the following ways: Glycogen in the liver and muscle tissue Triglyceraldehyde in fat cells (adipose) Storing Carbohydrates vs Lipids Lipids have two main advantages over carbohydrates: They have twice the energy content (they make ATP twice). They are not soluble in water, meaning they don’t mess up the osmotic balance of cells and surrounding tissues. Proteins Proteins are large, complex molecules made up of amino acids. They play various roles in the body, such as catalyzing metabolic reactions (enzymes), providing structural support, regulating cell processes, and more. Proteins are made of 20 standard amino acids. Each amino acid consists of an amino group (-NH₂), a carboxyl group (-COOH), a hydrogen atom, and a distinctive side chain (R group) attached to a central carbon (carbon). Proteins have four levels of structure: 1. Primary Structure sequence of amino acids in a polypeptide chain. 2. Secondary Structure Local folding of the polypeptide chain into structures like alpha-helices and beta-pleated sheets, stabilized by hydrogen bonds. 3. Tertiary Structure HA1 Lecture: The Chemistry of Life 20  The overall 3D shape of a single polypeptide, determined by interactions like hydrogen bonds, hydrophobic interactions, disulfide bridges, and ionic bonds. 4. Quaternary Structure Association of multiple polypeptide chains (subunits) to form a functional protein. Note: The hierarchical structure determines a protein's stability, specificity, and interaction with other molecules. Misfolding or errors at any level of the protein can lead to loss of function or diseases (e.g., Alzheimer's, prion diseases). Function of the proteins Enzymatic catalyze biochemical reactions (e.g., amylase). Structural provide support (e.g., collagen in connective tissues). Transport carry substances in the bloodstream or across membranes (e.g., hemoglobin). Signaling act as hormones or receptors (e.g., insulin). Immune Response form antibodies that target pathogens (e.g., immunoglobulins). Nucleic Acid Nucleic acids are biopolymers essential for all known forms of life. They store and transmit genetic information and are HA1 Lecture: The Chemistry of Life 21  involved in protein synthesis. The two main types are DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). The building block of nucleic acids, each nucleotide consists of three components: Phosphate group Pentose sugar (Deoxyribose in DNA and ribose in RNA) Nitrogenous base Functions of nucleic acid: Genetic Information Storage DNA stores the genetic blueprint of an organism. Gene Expression and Regulation RNA plays a crucial role in gene expression, splicing, and regulation. Catalytic Activities Some RNA molecules, like ribozymes, have catalytic functions. HA1 Lecture: The Chemistry of Life 22