Unit 2.1 Biochemistry PDF

Unit 2.1: Biochemistry Content Outline: Chemistry of Life– Part 1 I. Matter A. Anything that takes up space and has mass to it. II. Element A. The simplest form of a substance that cannot be broken apart and still have the properties of that element. I...

Unit 2.1: Biochemistry Content Outline: Chemistry of Life– Part 1 I. Matter A. Anything that takes up space and has mass to it. II. Element A. The simplest form of a substance that cannot be broken apart and still have the properties of that element. III. Compound A. Two or more elements bonded together resulting in new chemical properties to emerge for the compound. B. An example: Water (H20) – a stable liquid and can sometimes be used to out a fire. Hydrogen by itself is a flammable gas; Oxygen by itself is also a flammable gas. IV. CHNOPS (The most common elements in all life forms.) and Trace elements (present in small amounts) V. Atom A. The smallest unit of matter with set chemical properties. Atoms maintain their original properties because the subatomic parts are all present. VI. Subatomic Particles (Small parts that make up atoms.)(“sub” means “below” or “lower”) A. Proton (These particles carry a positive charge. They are located in the nucleus of an atom.) 1. The number of protons never changes in an element. (This allowed the Periodic Chart to be created.) B. Neutron (These particles carry no charge, which is called neutral. They are also located in the nucleus of an atom.) 1. The number of neutrons can change. (Atoms with different numbers of neutrons than the normal amount for that element are called Isotopes.) C. Electrons (These particles carry a negative charge. They are located outside the nucleus in the “Electron cloud”. The electrons moving, which is called kinetic energy, is why they are associated with energy and batteries. It is potential energy when they are bonded. 1. The number of electrons can change. (Atoms with different numbers of electrons than the normal amount for that element are called Ions.) 2. The cloud is divided into energy levels. The first energy level holds two electrons. The second and third hold eight electrons. D. Atoms are weighed in units called Daltons or Atomic Mass Units (AMU”S). 1. Each proton or neutron (these are the largest sub-atomic particles) is equal to 1 Dalton or 1AMU. (Electrons are basically 1/1000 of a Dalton.) VII. Molecule A. Two or more atoms bonded together. (They maybe the same type of atom or they maybe different atoms.) VIII. Atomic Number A. This is usually shown as subscript on the Periodic Table. B. It refers to the number of protons only in that element. IX. Mass Number A. Usually shown as superscript on the Periodic Table. (“Super” means “above” or “greater”) B. It basically refers to the number of protons and neutrons together in that element or molecule. 1. These are the two subatomic particles that have “significant mass or weight” associated with them. Remember electrons have very little mass, so you can just add protons and neutrons. 2. It can also be referred to as Atomic Weight. X. Isotopes A. Atoms that possess different numbers of neutrons than the normal amount for that element and thereby have different mass numbers. B. These usually have the same chemical properties as the normal element, but the physical properties maybe different. C. Most isotopes are radioactive.  Chemistry of Life – Part 2 I. Energy (represented by the symbol “E”) A. Energy comes from the rapid movement of electrons (e-) normally, but it could be neutrons too. B. Potential Energy (PE) – Energy of position. (Usually refers to electrons “locked” in a chemical bond.) C. Kinetic Energy (KE) – Energy of movement. (Usually refers to electrons that can move freely.) II. Chemical Properties A. An element’s or molecule’s properties are usually associated with the number of electrons it has. B. Periods (Run horizontally on the Periodic Table. Horizontal is “side to side”) 1. Elements behave differently as you go across a period. 2. Think of it as a sentence, different words convey different things. Also what is usually at the end of a sentence… a period. C. Columns or Families (Run vertically on the Periodic Table. Vertical is “up and down”) 1. Elements behave similarly as you go down a column or family. III. Chemical Bonds (These occur between elements or molecules.) A. Covalent Bonds 1. This type is the strongest type of chemical bond. a. Results from sharing electrons between elements or molecules to fill both outer shells. 2. They always create a molecule. (The size of the molecule may differ though.) a. Two or more atoms together of any kind. 3. Polar molecules carry an electrical charge at opposite poles(poles refers to the “ends” of the molecule) and non-polar molecules do not have an electrical charge. D. Structural Formula (Used to show the shape of the molecule) E. Molecular Formula (Tells the elements, and number of atoms of each, that make up a molecule) 1. A.K.A. Chemical Formula F. Ionic Bonds 1. These are fairly strong bonds while dry – but are weak in water so they dissolve into ions. 2. These bonds are created by gaining or losing electrons between elements so that each element can fill its’ outer most shell. 3. When dissolved in water Ions are created. (Gatorade is an ion loaded drink.) a. Cations – possess a positive charge because it has more protons than electrons. b. Anions – possess a negative charge because it has more electrons than protons. c. These love water because water is a polar molecule too. 4. Ionic Compounds a. A cation bonded to an anion to make a salt when dry. G. Hydrogen Bonds 1. Fairly weak bonds. (It is “like” a magnet) (A positive Hydrogen attracted to a negative “Substance”…usually oxygen.) 2. These are the most important biological bonds. IV. Chemical Reactions A. To make a bond requires energy to be consumed. (The bond requires “catching” an electron.) B. To break a bond gives off energy. (The electrons are “released” to move again.) C. Reactants (Located on the left side of an equation.); Products (Located on the right side of an equation.) 1. Demonstrates the Law of the Conservation of Mass 1. Matter is neither created nor destroyed just transferred or transformed. 2. If an element is on one side of an equation it must be on the other side too! 3. Equilibrium ( ↔ ) a. Chemical reaction is going both ways at equal rates. Unit 2.1: Biochemistry Content Outline: Water Properties– Part 1 I. Life and Water A. Water, mainly found inside of cells, makes up 70 –95% of the organisms body for all life forms on earth. II. Water is a Polar Molecule (has a positive and a negative end) A. Oxygen has a slightly negative charge because it is more electronegative (it has a stronger hold on the electrons because it has eight positive protons). B. Hydrogen has a slightly positive charge because it is less electronegative (it has a weaker hold on the electrons because it only has one positive proton). C. Water’s polarity allows for it to make Hydrogen bonds easily. D. This polarity makes it possible to conduct electricity very well. (Remember, electricity is flowing electrons.) E. The polarity allows for a single water molecule to bind to 4 other water molecules at a time. III. Cohesion A. This term refers to water molecules binding to other water molecules. B. This property is made possible because of Hydrogen bonds. C. This is important in how water moves up a plant. IV. Adhesion A. This term refers to water molecules binding to something other than water molecules. B. This property is made possible because of Hydrogen bonds. V. Surface Tension A. This is the linking together of water molecules on the surface of a body of water. B. This property is made possible because of Hydrogen bonds. VI. Water helps with temperature regulation in organisms and on the earth. A. Water is the only substance on earth to be found in all 3 states naturally. (solid, liquid, and gas) B. Water can act as a huge heat “piggy” bank. (Such as when the sunlight hits the oceans and other water bodies and the water heats up slowly as it absorbs the light energy.) C. This property is made possible because of Hydrogen bonds. D. It takes tremendous amounts of E to break all four hydrogen bonds at once and turn liquid water to a gas. E. This is a important worldly effect as it helps to keep the temperature of earth stable (the water absorbs the energy of sunlight, so we don’t fry, and then releases that same energy at night, so we don’t freeze… remember that one side of earth is always in the sun and the other side is dark so temperature is stable.) F. Kinetic E terms associated with water. 1. Heat – This measurement is the total amount of kinetic E in a substance. 2. Temperature – This measurement is the intensity of all the heat in a substance as the molecules move. (The faster they move… the hot it gets and the slower they move… the colder it gets.) G. Ice cubes and cold drinks (The hot drink molecules lose energy as they try to warm up the frozen water molecules thereby causing the drink to “cool”.) VII. Evaporative Cooling A. Putting heat E into water, causing the water to evaporate and carry the heat E away from the body thus providing a cooling of the organism to occur as the E leaves. B. Wind increases the effect of cooling by carrying the water vapor away from the body. Humidity, water vapor in the air, decreases the effect because water can’t evaporate into the air as it is already full of water vapor. VIII. Expansion of Water when it freezes A. Water condenses down to 4% Celsius; after that, the colder it gets, the more it expands. B. Life was and still is able to survive under the floating ice that occurs at the poles and during winter.  Water Properties – Part 2 I. Water is the Universal Solvent (It can dissolve most things) A. Solvent – Liquid that is doing the dissolving of another substance. B. Solute – Substance being dissolved in the solute. C. Solution – Substance possessing equal distribution of material. (Kool-aid is a good example.) D. Hydrogen bonds of water make each situation possible. E. Hydration shell – Water surrounding a molecule. Substance is dissolved and “disappears”. F. Oils, grease, and fat are non-polar and therefore water can’t grab and dissolve. (Need salt to make a molecular bridge to dissolve… most dishwashing liquids are just saltwater with coloring.) II. Hydrophobic “hydro” means water; “phobic” means fear of A. Water cannot attach to the substance because the substance is non-polar. B. The substance “hates” water’s polarity. III. Hydrophilic “philic” means love of A. Water can attach to the substance because the substance is polar. B. The substance “loves” water’s polarity. IV. “WET” Chemistry Terminology A. Dissociation 1. Refers to water breaking apart into H+ (Proton) and an OH- (Hydroxide Ion). 2. Acid – a substance that gives away H+. (Measured on a pH scale.) a. Scale goes from 0 to 14. b. 7 neutral c. On the pH scale: 7 – Substance is a base 3. Base – a substance that gives away OH-. (Measured on a pOH scale.) a. On the pOH scale: < 7 – substance is a base; > 7 – substance is an acid B. Buffer 1. A substance that can resist changes in pH or pOH. 2. It can take on or gives off a H+ or OH- to maintain the pH or pOH concentration. 3. Good example is Human Blood –The buffer is Bicarbonate ( HCO₃¯ ). a. Bicarbonate helps keeps blood at a pH of 7.4 ideally b. It is needed because of the food, drink, air or other substances we put into our bodies c. HCO3- can take on H+ from the blood to become H2CO3 (carbonic Acid) to raise blood pH. i. The H2CO3 then travels to the lungs where it is converted to H2O (water) and CO2. + + d. OR H2CO3 can give off a H to become HCO3- and H to lower blood pH. C. Acid Precipitation (Refers to Rain, Snow, Sleet, Ice, or Fog with a low pH.) 1. Water falling in the environment that has a pH of less than 5.6. 2. Mainly because of SO (Sulfur Oxide) and NO (Nitrous Oxide) in the air to combine with water. a. Both are found in fossil fuels when burned. (Such as oil, gasoline, or diesel fuel. Unit 2.1: Biochemistry Content Outline: Carbon Properties I. Organic Chemistry A. Branch of science dealing with the element carbon and its many properties. B. It is usually associated with all living organisms. 1. About 30% of an organism’s dry weight (called Biomass) is Carbon in organic molecules. a. Helps to make the organic molecules: Carbohydrates, Lipids, Proteins, and Nucleic Acids. b. The original source for Carbon in all life forms is Carbon Dioxide. (CO2 in Photosynthesis) C. Inorganic refers to most compounds not containing Carbon. (CH4 (Methane gas) and CO2 or CO are exceptions. They contain Carbon but are classified as inorganic.) II. Carbon’s e- configuration A. Carbon has versatility in four directions because of its four unpaired electrons in its outer shell. B. These four unpaired electrons allows carbon to act like an intersection in the building of an organic molecule by using those to form covalent bonds with other atoms. 1. This allows cells to build an almost infinite number of different molecules. C. Covalent bonding capabilities of Carbon 1. Single Bond between Carbon atoms.(shown as: C-C) 2. Double Bond between Carbon atoms. (shown as: C=C) 3. Triple Bond between Carbon atoms. (shown as: C=C) III. Hydrocarbons A. Molecules containing mostly Carbon and Hydrogen. B. Most hydrocarbons are energy sources. (Some examples are: Fossil fuels, Oils, And Fats) 1. The more Hydrogen atoms in a molecule; the more energy there is in the molecule. C. Hydrocarbons are important parts of cell membranes. (The tails of phospholipids) D. All hydrocarbons are extremely hydrophobic because they are nonpolar molecules. (“Afraid of” water’s polarity.) IV. Functional Groups Associated with Organic Molecules A. These are the sites of most organic molecules chemical reactions or properties. (They have a function to do.) B. Hydroxyl s (-OH) 1. This group allows molecules to act as an alcohol or polar molecule. 2. Name usually ends with “ol”. C. Carbonyls (Only has one double bonded oxygen.) (It takes one stroke to make a lower case “n”.) 1. Aldehydes (A is at one end of the alphabet.)(Carbonyl is located on the end of the molecule.) 2. Ketones (K is in the middle of the alphabet.)(Carbonyl is located in the middle of the molecule.) D. Carboxyl (Has two oxygens…one double bonded and one singled.)(It takes two strokes to make an “x”) 1. These molecules can act as an acid by losing a Hydrogen atom and can also possibly polar too. E. Amine (Contains Nitrogen) 1. Can act as bases by picking up free H+. F. Sulfhydrls (Contains Sulfur) 1. Sulfur can make Di-Sulfide bridges for “pockets” in protein formation. G. Phosphate (Contains Phosphorus) 1. These molecules are usually involved in E Transfers, such as associated with ATP. It can also act like an Anion, a negative ion. Unit 2.1: Biochemistry Content Outline: Molecules of Life – Part 1 I. Macromolecules – “Macro” means “large” A. Polymers “poly” means ‘many”; “mer” means “unit”. 1. These are formed from individual units called monomers (“Building Blocks”). 2. Monomers are linked together by covalent bonds. Organisms need these to stay intact so the strongest type of bond is used. 3. These are another example of the theme: Structure = Function. B. Macromolecules are formed by Dehydration or Condensation Reactions. 1. Hydroxyl (OH) is removed from one molecule and Hydrogen (H) is removed from another This combination forms water. This orientation of molecules and making of a bond requires E. 2. Enzymes (most are proteins) help speed up the rate of the reaction. C. Macromolecules are broken apart into individual monomers by Hydrolysis reaction. “lysis” means “split”. 1. This process releases E in the bond breakage. 2. The process needs water (hydroxyl and hydrogen) to fill the open bonds on the monomers. 3. Enzymes speed up the rate of the reaction here too. II. Carbohydrates “Carbo” refers to Carbon; “hydrate” refers to water. A. These molecules are mainly sugars. 1. Monosaccharides (Are the monomers or “building blocks”.) “sacch” means “sugar”. 2. Disaccharides – two monosaccharides linked together. “di” means “two”. 3. Polysaccharides (Are the polymers.) – Many sugars linked together. B. The chemical composition is: Carbon = Oxygen; 2x as many hydrogen also present. C. The names usually end with “ose”. Such as Fructose, Glucose, Sucrose. D. These are primary E sources for cells. E. Carbohydrates can also be sources of stored E in cells or organisms. 1. Starch - E storage molecule in plants. 2. Glycogen – E storage molecule in Animals. 3. Cellulose – Structural component of plant cell walls. a. Cellulose is the most abundant organic compound on Earth. 4. Chitin – This is the exoskeleton of some animals and also Fungi cell walls. III. Lipids A. These macromolecules are fats, oils, waxes, and steroids. B. Most lipids are hydrophobic molecules. “Hydro” means “water”; “phobic” means “fear of”. C. Lipids are mainly composed of Hydrocarbons (All of the bonded hydrogens cause more energy to be released when they are broken off of the carbon. D. Two Main parts 1. Fatty Acid tails (The Hydrocarbon unit.) 2. 3 Carbon Glycerol molecule (alcohol) to hold the whole molecule together. E. Major Types of lipids 1. Triglycerols or Triglycerides – your basic fat or oil. a. There are saturated fats. These fatty acids are saturated with hydrogen atoms. The molecule has no open bonds to put any more Hydrogen on. (These are solid at room temp.) (They usually are associated with animals.)These are the bad types of fat when it comes to our diet. b. There are unsaturated fats. These have double or triple bonds that “could be broken” to add more Hydrogen to the fatty acid. (These are liquids at room temp.) (They usually are from plants, such as vegetable oil, sunflower oil, or peanut oil.) c. There are also Polyunsaturated fats. These have numerous double or triple bonds in the fatty acid portion. (These are also liquids at room temp.) (They are also usually from plants.) d. Hydrogenated or Trans fats (These are oils turned solid by adding Hydrogen by breaking the double or triple bonds so in order to transform it into a saturated fat) 2. Phospholipids a. These molecules replace a single fatty acid with a single Phosphate ion. (This part of the molecule is Hydrophilic. “philic” means “lover of” It loves water because the phosphate carries a negative charge. Remember water is polar. So the negative phosphate will be attracted to the positive hydrogen portion of water.) b. They still have 2 Fatty Acid tails. (These are the Hydrophobic portion of the molecule. They carry a neutral charge. Therefore are not attracted to water.)  c. Phospholipid Bi-layers (having 2 layers) are common for cell and organelle membranes. 3. Waxes a. These lipids are made by combining alcohols with unsaturated oils. Such as girls lipsticks which also have coloring added to make the different shades. 4. Steroids, Hormones, and Cholesterol a. A steroid has 4 carbon rings with the top ring looking like a house. b. Cholesterol is also a steroid molecule, but it helps with cell membrane flexibility. All membranes need to have some cholesterol to remain flexible. Cholesterol in excess is bad for your health though. F. Lipids are stored in Adipose Tissue in animals. This can lead to obesity or even Atherosclerosis (Clogged Arteries). Unit 2.1: Biochemistry Content Outline: Metabolism and Enzymes – Part 1 I. Metabolism A. The sum of all the chemical reactions occurring in an organism. B. The collective process has two separate phases. 1. Catabolism – This refers to the breaking down of a molecule. a. This process releases “potential” E found in the chemical bond between monomers. b. This is an exergonic reaction because it releases heat to the environment c. Think Catastrophe; breaking up things. 2. Anabolism –This is the assembly of molecules. a. This process requires “Kinetic” E to position molecules in away so as to create a chemical bond between monomers. b. This is an endergonic reaction because it absorbs energy from the environment. c. Think Anabolic steroids; these build muscle. II. Energy (represented by “E”) A. Has the ability to facilitate transformation. B. There are two types of E mainly, as living organisms are concerned. 1. Kinetic E (represented as “KE”) - This is the energy of movement. (Usually refers to the movement of electrons or protons in Biology.) 2. Potential E (represented as “PE”) – This is the energy of position. (Usually referring to the chemical bonds associated with those electrons and protons.) C. For living organisms, the chemical E of life is found in chemical bonds. 1. The processes of Cellular Respiration and Digestion release the E for use by cells. 2. Source of all E for Earth? (It is the sun) The process of photosynthesis allows plants to store this solar energy in the form of chemical energy (sugar). III. Thermodynamics A. The study of Heat E (Thermo) and its properties (dynamics). B. First Law of Thermodynamics (Also called the Principle of the Conservation of E) 1. E cannot be created nor destroyed only transformed or transferred. C. Second Law of Thermodynamics 1. Every E transfer increases the entropy of the universe. a. Entropy- means disorder; unable to do work because it is in a low state of order. 2. Sunlight(high quality E) going in and heat (low quality E)coming out; it can’t do work. IV. Gibbs Free E (represented as “G”) A. It is referred to as “free” because E is available to perform work. (Mainly making ATP or GTP in a cell.) B. Not all E is available. (Some is lost as waste…like when we defecate…same goes for cells too.) 1. Most E is lost as Heat as a byproduct of the bonds being broken. V. Types of work performed by living cells: (Most are achieved by using proteins and enzymes.) A. Mechanical – work outside of the cell B. Transport across the membrane C. Metabolic processes – Catabolism and Anabolism VI. ATP (Adenosine Tri-Phosphate) A. Made from Ribose sugar (RNA sugar) and the nitrogen base Adenine. B. Has 3 negative phosphates linked together which makes it highly unstable like a “compressed spring”. Unstable, means it has the capacity do perform work remember. C. ATP converting to ADP gives off energy; ADP being converted to ATP requires energy.(The energy needed to make this bond comes from the “free” e in our food as it is broken down.)(ADP is recycled back to ATP.) D. Phosphorylation 1. The attaching of an unstable phosphorus ion to another molecule to make it unstable and thereby able to perform work. (Take the phosphorus off and it quits working.)  Metabolism and Enzymes – Part 2 I. Enzymes A. These molecules are Biological Catalysts. 1. Proteins that speed up and control the rate of a chemical reaction. B. They are recycled; they are not consumed by the reaction. C. Enzymes are selective in what they will work with. We used to say they had a “lock and key fit” (old term); we now say it “fits like a glove or has an induced fit”. (new term) 1. This is like putting on a latex glove… it stretches to conform to the shape of your hand. D. Enzyme names usually end with “ase”. II. Free E of Activation A. This refers to the Free E used to start a chemical reaction in motion. (Essentially is the energy for getting the molecules moving and positioned so that it is possible to combine or be torn apart.) B. The energy of activation is lowered by the action of enzymes. (Enzymes reduce by grabbing the molecule and positioning it correctly… we don’t have to wait for nature to do it.) 1. Enzymes also replace the need for heat in most chemical reactions (remember heat can make molecules move faster) so that organisms don’t burn up during metabolism. III. Substrate A. This refers to the molecule that is being affected by the enzyme. (What the enzyme is grabbing and working on.) IV. Active Site A. This refers to the location where the chemical reaction(s) is taking place between the enzyme and substrate. B. It is an Induced Fit , which creates the Enzyme-Substrate Complex. (Complex meaning “more than one piece in the unit”.) C. The two parts are mainly held together by weak Hydrogen bonds D. By orienting the substrate molecules, the reaction rate speeds up. V. Environmental factors that can affect enzymes ability to work optimally. (“optimal” means “best” or “Fastest”) A. Temperature – freeze/cold (cold things don’t move quickly) or Heat causing it to Denature (“unfold”). B. pH of the environment C. Salt concentrations D. The Optimal Conditions for most human enzymes: 1. 98.6˚F (35 - 40⁰C) 2. pH usually between 7.2 and 7.6 (The human body’s pH of blood is an average of 7.4.) 3. Remember, this is an unstable (dynamic) environment. There is an upper limit and a lower limit for enzymes. Beyond the limits, bad things begin to happen. So it is basically, trying to stay between the limits. The limits of “life”. VI. Inhibitors A. The name implies that these molecules negatively affect an enzymes ability to work optimally. These slow down or stop the rate of the chemical reaction. B. Two types of Inhibitors exist, based on the location of the enzyme that is affected: 1. Competitive- These molecules compete for the active site. (This is because of similar shape.) a. These molecules slow down the reaction rate. (These molecules will be removed.) 2. Non-competitive –These molecules attach somewhere other than the active site causing the shape of the active site to change so the substrate can’t fit into it. a. These molecules cause the reaction to stop completely VII. Feedback Inhibition A. A product in excess shuts down the reaction that is taking place at an earlier point in the pathway. B. Prevents “waste” of precious materials and energy b