Basic Principles of Biological Chemistry PDF

High Heat of Vaporization Allows water to regulate the Earth’s climate: Solar heat absorbed by ocean water is dissipated when surface water evaporates. As warm tropical air moves towards poles, water vapor releases heat as it condenses into rain....

High Heat of Vaporization Allows water to regulate the Earth’s climate: Solar heat absorbed by ocean water is dissipated when surface water evaporates. As warm tropical air moves towards poles, water vapor releases heat as it condenses into rain. Stabilizes temperature in aquatic ecosystems. Helps keep organisms from overheating. Temperature Regulation Apart from liquid metals, water has the highest thermal conductivity of any liquid. Thermal conductivity is the rate at which heat passes a material. This is the reason why large bodies of liquid water (lakes and oceans) have a nearly uniform vertical temperature profile. Water exists as a liquid from 0 - 100° C. This range allows water molecules to exist as a liquid in most places on our planet. Insulation/Cooling Because water can take on a lot of heat before it increases in temperature, water serves as a good insulator and a good coolant Good insulator to retain temperature when your body gets too cold. Good coolant to cool you when your body temperature increases. Example: sweating to cool down body At night, oceans are good insulators, as energy that the sun spent heating the water all day is slowly released throughout the night. How does sweat cool you? Sweating is a type of evaporative cooling Increases in temperature cause increases in the movement of water molecules (kinetic energy goes up) With enough movement, some water molecules will bump out of the liquid surface (this is evaporation) and form water vapor. When the molecules evaporate, the average kinetic energy of the remaining liquid goes down and the temperature drops.  Water as a Solvent A solvent is a dissolving agent. A solute is a substance being dissolved. Polar solutes can “stick” to water. Because of its polarity, water can dissolve lots of things and is referred to as universal solvent. http://avonapbio.pbworks.com/w/page/9429553/Water's%20Versatility%20as%20a%20Solvent Water as a Solvent Substances that dissolve well with water are called hydrophilic (water loving) Acids Alcohols Salts Substances that do not dissolve with water are called hydrophobic (water hating/repelling). Lipids Water as a Solvent For Hydrophilic Solutions: Water Molecules Solute within Water Forces between solvent molecules are the same as forces between solvent and solute A substance cannot dissolve in water if it cannot overcome the forces of water. The molecules are pushed out from the water and don’t dissolve. pH of water Water in a pure state has a neutral pH pure water is neither acidic nor basic Naturally, water is not pure Water changes its pH when substances are dissolved in it. Rain pH = 5.6 (contains natural derived carbon dioxide and sulfur dioxide) Acids, Bases, and Buffers Organisms are sensitive to changes in pH When acidic substances dissolve in water, they make that solution more acidic When basic substances dissolve in water, they make that substance more basic What is pH? pH is a measure of the concentration of hydrogen ions (H+) in a solution The pH scale ranges from 0 to 14 pH is defined as the negative log of the hydrogen ion concentration: pH = -log [H+] p=potenz (potential to be) H= for hydrogen http://water.usgs.gov/edu/phdiagram.html  Disassociation of Water Water molecules split to form a negative hydroxyl (OH-) ion and a positive hydrogen (H+) ion The OH- is alkaline while the H+ is acidic Experimentally, it has been calculated that in disassociated water: [H+] = [OH-] = 10-7 pH = -log [H+]…..so pH of pure water is 7. https://kentuckychemistry.files.wordpress.com/2013/04/water-dissociation1.png?w=470&h=182  Acids and Bases (alkalis) When dissolved in water, a chemical that has: [H+] > [OH-] ACID (pH < 7.0) [H+] < [OH-] BASE (pH > 7.0) http://water.usgs.gov/edu/phdiagram.html Acids Acids can donate a proton (an H+ ion) in a reaction Characteristics of Acids Taste sour Corrosive to metals Change litmus paper to red Become less acidic when mixed with bases. Bases (Alkalis) Bases can accept a hydrogen ion (H+) in a reaction. When dissolved in water, bases can release/donate hydroxide ions (OH- ) into a solution. Characteristics of Bases Feel slippery Change litmus paper to blue Become less basic when mixed with acids. Strong/Weak Acids and Bases Strong acids and bases can completely dissociate in water, (donates all of its H+ or OH- ions) Strong Acids Strong Bases hydrochloric acid (HCl) sodium hydroxide (NaOH) nitric acid (HNO3) potassium hydroxide (KOH) sulfuric acid (H2SO4) Weak acids and bases cannot completely dissociate in water,(only donate some of its H+ or OH- ions) Weak Acids Weak Bases formic acid (HCOOH) ammonia (NH3) acetic acid (CH3COOH) ammonium hydroxide (NH4OH) Hydrogen sulfide (H2S) Neutralization Neutralization occurs when you mix an acid and base together. The acid releases a H+ ion and the base releases a OH- ion that would combine together to make a molecule of water. H+(aq) + OH-(aq) ➔ H2O Salts Salts are compounds that release ions other than H+ and OH- in a solution. When you neutralize an acid with a base, you always produce water and a salt. Acid + Base ➔ Water + Salt HCl + NaOH ➔ H2O + NaCl HBr + KOH ➔ H2O + KBr Strong acids (6 main) HCl: Hydrochloric acid HNO3: Nitric acid H2SO4: Sulfuric acid HBr: Hydrobromic acid HI: Hydroiodic acid (also known as hydriodic acid) HClO4: Perchloric acid HClO3: Chloric acid Properties of strong acids A strong acid is one which completely dissociates in its solvent. Under most definitions, the acid dissociates into a positively-charged hydrogen ion (proton) and a negatively-charged anion. Strong Bases LiOH - lithium hydroxide NaOH - sodium hydroxide KOH - potassium hydroxide RbOH - rubidium hydroxide CsOH - cesium hydroxide Ca(OH)2 - calcium hydroxide Sr(OH)2 - strontium hydroxide Ba(OH)2 - barium hydroxide Properties of Strong Bases The strong bases are excellent proton (hydrogen ion) acceptors and electron donors. The strong bases can deprotonate weak acids. Aqueous solutions of strong bases are slippery and soapy. Concentrated solutions can produce chemical burns. Dilution of acids Using concentrated acids and diluting them down as required helps to save space in the lab and gives you the flexibility to make up any concentration you need. The drawback is that working with concentrated acids can be very hazardous. When performing dilutions it is vital to work safely and always add acid to water, not the other way around! WHY?...heat is generated After measuring out your concentrated acid and water, the acid must always be added to the water. This is because when the two mix, heat is generated – this is called the “Enthalpy of solution” or “enthalpy of dissolution”. On an atomic level this heat is caused by acid-water attractions being created in the solution as the two species mix. You can observe this when you perform the dilution – as you add the concentrated acid into the water, you will feel the solution getting warm. Dilution of acids Water absorbs the heat safely As the heat is generated, it has to go somewhere. If you add water into concentrated acid, the heat will go into the still very concentrated acid. This can cause it to fume, spatter or even boil – giving off corrosive fumes and droplets. If you add acid into water, the heat is absorbed by the water which just warms slightly but remains un-reactive. This is due to the hydrogen bonding in water, which means a lot of energy is needed to make it boil – the heat from a dilution is usually not enough to do this. Buffers Buffers are compounds that resist pH change despite the addition of an acid or base. Two kinds of buffers Weak acid and the base that forms as the acid dissolves in water, or Weak base and the acid that forms as the base dissolves Buffers A buffer solution is an aqueous solution consisting of a mixture of a weak acid and its conjugate base, or vice versa. Its pH changes very little when a small amount of strong acid or base is added to it. Buffer solutions are used as a means of keeping pH at a nearly constant value in a wide variety of chemical applications. In nature, there are many systems that use buffering for pH regulation. For example, the bicarbonate buffering system is used to regulate the pH of blood Buffering Some Common Buffers Buffers must be chosen for the appropriate pH range that they are called on to control. Some common buffers and their useful pH ranges are listed below: Buffer pH Range MES (2-N-morpholino ethanesulfonic acid) 5.5-6.7 PIPES (piperazine-N,N-bis(2-ethanesulfonic acid) 6.1-7.5 HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) 6.8-8.2 Tris-HCl (tris(hydroxymethyl)aminomethane) 7.0-9.0 Buffers in cell biology Most cells in our bodies operate within a very narrow window of the pH scale, typically ranging only from 7.2 to 7.6. If the pH of the body is outside of this range, the respiratory system malfunctions, as do other organs in the body. Cells no longer function properly, and proteins will break down. Deviation outside of the pH range can induce coma or even cause death. Buffers in Biology pH changes in living cells can have dangerous consequences! Denature proteins and DNA that results in cell death As a result, biological systems have built-in buffering systems  Carbonate/Carbonic Acid System Buffer system in blood: CO2 + 2H2O H2CO3 H2O HCO3- + H+ + bicarbonate Carbon Carbonic Dioxide Acid One example of how the body uses this buffering system in the body Lactic acid production in muscles Lactic acid (a weak acid) enters the blood and donates a proton → makes more H+ More H+→ more H2CO3 → more CO2 CO2 carried to your lungs and is removed from body through exhaling Protect against accidental spill Animal cells contain pouches called lysosomes. These pouches are the recycling center of the cell. The insides of these pouches are acidic, having a pH of 5, and contain many enzymes that digest proteins, fats, sugars and DNA. The acidic environment inside a lysosome helps break down molecules for recycling. However, if one or more of these pouches accidentally breaks open inside the cell, the acidic contents will spill into the rest of the cell and make the whole cell acidic. The cell has buffers that protect itself in case these spills happen. Since buffers resist a change in pH, a few lysosomes that break open will not make the pH inside a cell more acidic. Changing the pH can make stem cells? In 2014, the journal “Nature” reported a very exciting discovery from Japanese stem-cell researchers. Normal adult cells such as skin cells and brain cells can be turned into stem cells when placed in an acidic environment. Stem cells are cells that have the potential to become any type of cell in the body, which makes them very promising as cures for medical problems. Dead, missing, or broken cells can be replaced by new cells. Stem cells can be taken from an embryo, which is very controversial when it comes to human embryos, so being able to turn adult cells into stem cells is an exciting step for biomedical science. What this study tells us is that buffers inside a cell also likely prevent the cell from forgetting its adult identity and becoming a stem cell. NEXT LECTURE… Intro to Organic Chemistry