Chemistry of Life Notes (Chapter 2) PDF

Chapter 2 notes Chemistry of life Water - The best way to get rid of water in the body is urine. - Sweat is another way to get rid of water in the body but not main job to get rid water in the body - 50% of the body weight is water 96% of the human bo...

Chapter 2 notes Chemistry of life Water - The best way to get rid of water in the body is urine. - Sweat is another way to get rid of water in the body but not main job to get rid water in the body - 50% of the body weight is water 96% of the human body consists of oxygen, carbon, hydrogen, and nitrogen. Matter - Definition: anything that has mass and occupies space - Matter have substance that can be either elements and compounds - Can be measure - Can be either elements and compound Elements - Definition: a substance that cannot be separated into substances different from itself - A pure substances - Cannot be broken - For example, oxygen cannot be broken or decomposed into anything except for oxygen itself Compounds - Definition: chemical combination of two or more elements - For example, the water is the compound of hydrogen and oxygen Basic Structures of Life - Major Elements - Oxygen(O), contain 65% of the body weight - Water(H2O) is very important to the human body because the body requires a chemical mixture to happen, it needs water. For example, when you mix something, you need water such as flour, powder, and so on. Atoms - Definition: the smallest part of an element; consists of a nucleus containing protons and neutrons surrounded by electrons - Atoms also have protons, neutrons, and electrons. - Atom is neutral when there is an equal amount of proton and electron - Protons carry a positive charge. - Electrons carry a negative charge. - Neutrons are electrically neutral. - Proton, electron, and neutron made up the atoms - Atom is the smallest matter - Electrons - Definition: minute particles with a negative charge that revolves around the nucleus of an atom - Electrons are whirling around the nucleus are one or more concentric cloud - - An electron's negative charge cancels out the proton's positive charge, making the atom electrically neutral. - The first ring(concentric cloud) can only hold two electrons. The second energy level(concentric cloud) and so on, can only hold eight electrons. - Protons and neutrons are packed together in the center of the atom, called the nucleus - Proton are positive charge - Neutrons are neutral - The number of proton= atomic number - proton+neutrons = atomic weight  - Proton differentiates the element from other because number of proton determines the element atomic weight*** Chemical Bonds - Valence electrons - Most atoms are not stable, and they are drawn to others atoms as they attempt to gain, lose, or share the electrons in their outer shells - Molecules - Definition: a combination of two or more atoms held together by chemical bond - 3 type of chemical bond: ionic bonds, covalent bond, and hydrogen bonds - Ionic bonds - Definition: Bond formed when one atom transfers an electron from its outer shell to another atom. - Because the electrons are negatively charged, when an atom gains or loses an electron, its overall changes from neutral to either positive or negative. - Ions are electrically charged atoms when atoms gain or lose electrons. - Atom having positively charged are called cations; atom having negative charge are anions - For example, salt NaCl - Salt help with wound care - - Covalent Bonds - Sugar and alcohol are example of covalent bonds - Definition: bond formed between two atoms when the atoms share one or more pairs of electron(**mostly focus on outer shell)  - - Hydrogen Bonds - Definition: a weak attraction between a slightly positive hydrogen atom in one molecule and slightly negative oxygen or nitrogen atom in another. - In the process of bonding, it become a polar molecule - Refer to page 22 for more details - - Hydrogen have positive charge Energy - Definition: the capacity to do work - Ability to perform work - Putting matter into motion - Two types of energy: potential energy and kinetic energy - Potential energy - Definition: the energy stored in the bonds of molecules - Energy is ready to use when it needed - Energy stored - Potential energy is what in you like ur potential  - Kinetic energy - Definition: energy in motion - Electrons moving around the nucleus is an example of kinetic energy. - Energy ready to use - Chemical reactions release the energy, making it available to do work - For example, put a gas in the car, you start the car and drive the car, while driving the car, the car is using the gas→ release energy Metabolism - Definition: the sum of all the chemical reactions in the body - Needs water for chemical reactions to happen in the body**** - Two type of metabolism: catabolism and anabolism - Catabolism - Definition: phase of metabolism during which complex substances are converted to simpler ones, resulting in the release of chemical energy - Breaking down large complex compound into simpler ones - The breaking of the chemical bonds release energy - For example, driving a car, the gas in your car have to be broken down - Anabolism - Definition: the constructive phase of metabolism during which cells use nutrients and energy for growth and repair ** - Involves building larger and more complex molecules( such as carbohydrates, lipids, protein, nucleic acid) from small subunits - Require energy input - Obtains energy from ATP - The energy needed for anabolic reaction is obtained from ATP molecules. - Protein synthesis is an example of anabolism - For example, newborn babies such as first year newborn will not be in the same size when it come to second year Chemical Reactions - Types of chemical reactions: synthesis, decomposition, exchange, and reversible. - Synthesis  - Two or more substances combine to form a different, more complex substance. - A+B→AB - For example, production of collagen-rich scar tissue in a healing wound - Decomposition - A complex substance breaks down into two or more simpler substances - Because the bond is broken, the energy is released - AB→A+B - For example, breakdown of a complex nutrients within a cell to release energy for other cellular functions - Exchange - Two molecules exchange atoms or groups of atoms, which form two new compounds - AB+CD=AC+BD - For example, when hydrochloric acid(HCl) and sodium bicarbonate(NaHCO3) meet in a small intestine, the sodium and chlorine atoms exchange, producing salt and bicarbonate: NaHCO3+ HCl→ NaCl + H2CO3 - Reversible reactions - It can go in either direction under different circumstance - These reactions are symbolized by arrow in both directions - Sodium and potassium is an example of reversible reaction - Inorganic molecules - Inorganic molecules essential to human life include water, oxygen, and carbon dioxide as well as acid and base. - Inorganic molecules include water, oxygen, carbon dioxide, and acid-bases.** - Inorganic compounds do not contain carbon.*** -  - Water - Water is very important to the human body and contains 50% or more of an adult’s body weight.** - The body need water so chemical reaction can happen - Characteristic of water - Water is a solvent- water dissolves more substances than any other liquid. - Because of its polar nature, water can ionize, or break down, large chemical compounds and then transport them to the body’s cell, which need them to functions - Create an solution - Sometime can dissolve in it, - For example, add salt into the water to create solution - Water is a lubricant- water clings to the body’s tissue and forms a lubricating film on membranes - Water clinging to the pleural and pericardial membranes helps reduce friction as the lungs and heart expand and contract. Also, fluid within the joint cavities prevents friction as the bones move. - Lubricant means a substance (such as grease) capable of reducing friction, heat, and wear - Water changes temperature slowly -water can absorb and release large amounts of heats without changing temperature. - This allows the body to maintain a stable body temperature. It allows the body to cool off when it's overheated. Specially, when water in form of sweat changes from liquid to a vapor, it carries large amount of heat - Lose temperature Body Fluids - The fluids in the body consists of chemicals dissolved or suspended in water - Suspended in water means mixed in liquid but do not dissolved - Two type of body fluids: mixture and compound - Compound  - When two more elements combine to create a new substance that has its own chemical properties. - For example, the elements Na and Cl, when they combine , they create the compound table salt→ which is essential for life - For example, water is a molecular compound, resulting from the chemical combination of hydrogen and oxygen. - Mixture - Substance that results when two or more substances blend rather than chemically combine. - Substances are not combine, the substances can be separated - For example, when you cook scrambled eggs and ur adding salt, ur creating mixture. The egg still tastes like egg and it retains all the properties of an egg; they just have an additional taste of salt. Types of Mixtures - Mixtures of substances in water can be solutions, colloids, and suspensions. - Solution - Definition: a liquid mixture in which the minor component (the solute) is evenly distributed within the more abundant substance( the solvent). - A solution consists of particles of matter called the solute, dissolved in a more abundant substance-usually in water- called solvent - A solution can be solid, liquid, or gas - The solvent must be clear and the particles cannot be separated out of the solvent(water) **when the solution is allowed to stand. - For example, the sugar in water; glucose in blood; adding sugar in the coffee - Collid - Definition: Usually mixture of protein and water; can change from liquid to gel - The particles are small enough to stay permanently mixed, but large enough so that the mixture is cloudy - For example, gelatin; thyroid hormone(as stored in the thyroid gland)  - - Suspension - Definition: Mixture containing large particles that tend to settle when left undisturbed - Making the suspension cloudy or even opaque. - If allowed to stand, the particles will separate and settle at the bottom of the container. - For example, salad dressing; blood cells in plasma Acid, Bases, and pH - Acid(HCl, acidic) - Definition: any substance that release hydrogen ion(H+) when dissolved in water - The more hydrogen ions(H+) produced, the stronger the acid.  - Banana, lemon, wine, vinegar, coffee, bread, milk, and saliva - Sometime its called proton donors - Strong acid - A strong acid(like HCI) separate into H+ and an ion - Weak acid - It produces few H+ ions which make it a weak acid. - It don't separate - Stomach is more acidic - If you're throwing up, you're releasing acid which is hydrogen, then now your body has more alkaline. - Releasing more hydrogen ion - Bases(alkaline compounds) - Definition: any substance that combines with hydrogen ions - Accept hydrogen - Also called proton acceptors - Bases balance out acids by accepting excess hydrogen ions - A common base called sodium hydroxide(NaOH) dissociates into Na+ and OH- when dissolved in water. - The greater the concentration of OH- ions, the stronger the base. - The intestine is more alkaline - If you are pooping, your releasing alkaline, left with acidic in the body - Releasing more hydroxide(OH-)c - Acid+Base - If acid-like HCl enters the base, the HCl will separate into H+ and Cl-. The solution would then have H+,Cl-, Na+, and OH-. Then the OH- ions would accept the H+ forming H2O which reduces the acidity of the solution. The Na+ and Cl- ions would also combine, forming NaCl(salt). - The pH scale(power of hydrogen) - Definition: a measure of the hydrogen ion concentration of a solution - The pH scale range from 0 to 14 - Normal pH in human blood is 7.35 to 7.45, slightly alkaline** - A solution with a pH less than < 7 is acidic. - The lower the pH value, the more H+ ions the solution has and the more acidic it is.  - A solution with a pH of 7 is neutral, containing equal numbers of H+ and OH- ions - Solutions with a pH greater than > 7 are basic(alkaline). - The higher the pH value, the more OH- ions the solution has, and the more alkaline it is. - Substances called buffers help the body by donating or removing H+ ions in order to keep the pH in a normal range. Organic Compounds - 4 major groups of organic substances are carbohydrates, lipids, protein, and nucleic acids. - Organic compound contain carbon*** - Carbohydrates - Definition: Group of organic compounds known as starches or sugars that serves as the body’s primary source of energy - Body’s main energy source - The body obtains carbohydrates by eating food such as potatoes, vegetables, rice, etc. Through metabolism, the body breaks down carbohydrates to release stored energy - All carbohydrates consist of carbon, hydrogen, and oxygen - The chains consist of sugar called saccharide units. - Carbohydrates are classified according to the length of their sugar units or carbon chain as being either monosaccharides, disaccharides, and polysaccharides. - Monosaccharides - Contain one sugar units - Have three primary monosaccharides: glucose, fructose, and galactose. - Glucose: the primary source of energy used by most of the body’s cell - Fructose: found in fruits; its converted to glucose in the body - Galactose: found in dairy products; its also converted to glucose in the body - The insulin convert glycogen back to glucose - Disaccharides - Contain sugar units  - 3 important disaccharides - sucrose(table sugar)= glucose + fructose - Lactose (milk sugar)= glucose + galactose - Maltose(found in germinating wheat)= glucose+ glucose - Polysaccharides - Consists of many sugar units joined together by chains or complex shapes. (glycogen, starch, and cellulose) - Glycogen: the stored form of glucose - Insulin converted back to glucose - When glucose levels are high after eating, the liver converts excess glucose into glycogen. - When glucose level drop, the liver converts glycogen back to glucose - The muscle also store glycogen to meet their energy needs - Starch: the form in which plants store polysaccharides - Rice, potatoes, and corn are examples of food high in starch. - When consumed, digestive enzymes split the starch molecule, releasing glucose. - Cellulose: produced by plants cells as part of their cell wall. - Human cant digest cellulose and don't obtain nutrients from it. - Cellulose supplies fiber in the diet, which helps move materials through the intestines. - Lipids - Definition: group of fats characterized by their insolubility in water - Insoluble in water - Lipid have many roles includes: being a reserve supply of energy, providing structure to cell membrane, insulating nerves, serving as vitamins, and acting as a cushion to protect organs***  - A reserve energy supply - Provide structure to cells - Insulate nerves - Serve as vitamins - Cushion organs - Proteins - Definition: very large molecules consisting of smaller chemical subunits called amino acids. - Protein are most abundant and most important organic compounds in the body - Proteins are the most abundant and important organic compound in the body. - The structure and metabolic function of every cell depends on proteins. - Proteins consist of amino acids. - The body do not store protein - Kidney have remove excess wastes, remove protein - Because the kidney's job is to filtrate, remove protein, remove excess wastes but if a patient has kidney cancer then the kidney is not working, the patient goes to dialysis to remove protein from the body. - People who have kidney cancer(renal cancer), have too much backup protein, blockage - Apple juice is good for kidney, should not be on high protein - Too much protein in the body then they go to dialysis. - Protein have subunit called amino acids - Amino acids contain carbon, oxygen, hydrogen, and nitrogen. - All amino acids have a central carbon atom with an amino group(NH3) and a carboxyl group(COOH) bonded to it. - What differentiates the amino acids from others is the R group. - 2 types of amino acids: essential amino acids and nonessential amino acids. - Essential amino acids: amino acids that must be obtained through food.  - Nonessential amino acids: amino acids that the body can manufacture and therefore do not need to be obtained through food - Protein structure - Amino acids link to each other through peptide bonds - The peptide bond forms when the carboxyl group(COOH) of one amino acid links to the amino group(NH3) of another amino acid. In this process, the water is released. - A short chain of amino acids linked by peptide bonds is called polypeptide. - Each protein have three unique shape and the protein shape determine it functions - Structure of protein: primary structure, secondary structure, tertiary structure, and quaternary structure. - Primary structure consists of a sequence of amino acids in a chain. - - - Nucleic acid - Definition: complex organic substances, especially DNA and RNA - Two type of nucleic acids: DNA and RNA - The nucleic acids consist of thousands of smaller molecules called nucleotides. - The nucleotides are made of a five-carbon sugar(pentose), phosphate group, and one of several nitrogen bases. - DNA sugar is deoxyribose - DNA is the largest molecule in the body. It carries the genetic code for every hereditary ranging from eye color to nose shape. - RNA sugar is ribose - RNA copies the genetic code of DNA to direct protein synthesis - ATP*** - Definition: stores energy released from the breakdown of nutrients and provides it to fuel cellular reactions. - Food provides the body with energy - ATP stores the energy released from the breakdown of nutrients and provides it to fuel cellular reactions. - ATP consists of base, a sugar, and three phosphate group - Step 1 of ATP - The phosphate groups are connected to each other with high-energy bonds. - Step 2 of ATP - When one of these bonds is broken through a chemical reaction, energy is released that can be used for work(such as muscle movement) - Step 3 of ATP - After the bond is broken, adenosine triphosphate becomes adenosine diphosphate and single phosphate. - Di means two - Step 4 of ATP - Meanwhile, the cell uses some of the energy released from the breakdown of the nutrients in food to reattach the third phosphate to ADP, again forming ATP. - Refer to page 33 for image of the steps