All Notes 1.1-1.4 PDF

Lesson 1.1 - Chemical Fundamentals Chemical Fundamentals ​ Molecules (lipids, nucleic acids, proteins, and carbohydrates) play big role in living things ​ The understanding of chemistry behind biologically important molecules is biochemistry Isotopes ​ When 2 atoms have same number...

Lesson 1.1 - Chemical Fundamentals Chemical Fundamentals ​ Molecules (lipids, nucleic acids, proteins, and carbohydrates) play big role in living things ​ The understanding of chemistry behind biologically important molecules is biochemistry Isotopes ​ When 2 atoms have same number of protons and electrons but different number of neutrons they are isotopes ○​ Atomic mass differs ​ In radioisotopes, nucleus in isotope spontaneously decays ​ Radioisotope has half-life ○​ Amount of time it takes for half of nuclei to decay ​ Used in radiometric dating and as radioactive tracers Chemical Behaviour ​ Electrons move around atomic nucleus at distance determined by amount of energy electron has ​ Further it is from nucleus, greater its potential energy ​ Found around nucleus in energy levels ○​ n = 1 ​ Electrons in outermost energy level are called valence electrons ​ Valence electrons determine chemical behaviour of atom Chemical Bonding ​ Intramolecular forces (between atoms) ○​ Ionic and covalent bonds ​ Intermolecular forces (between molecules) ○​ Hydrogen bonds, hydrophobic interactions, and other weak forces Intramolecular Forces ​ Ionic bond is force of attraction between positive and negative charges ○​ E.g. Sodium Chloride (NaCl) ​ Since cell is aqueous environment are considered free, dissociated (Na+) since they dissolve in water  ​ Covalent bond forms when two atoms share one or more pairs of valence electrons ○​ E.g. Water (H2O) Intramolecular Forces – Polarity ​ Polar Covalent Bonds ○​ Unequal sharing of electron pair results in one atom attracting pair more strongly than other atom ○​ Due to difference in electronegativity ○​ Atoms will take on partial positive (δ +) or partial negative (δ -) charge Molecule Shape Molecular Polarity ​ To be considered polar molecule ○​ Contain polar covalent bonds ○​ Have asymmetrical arrangement of bonds (shape) Water ​ Polar molecule with many unique properties ​ Called universal solvent because of ability to dissolve many ionic and polar compounds ​ Hydrogen bonding (strongest of intermolecular forces) gives water properties that support life on earth Density of Water Importance of Water – Solubility of Molecules in Cell ​ Water is key to life ○​ Cells of living things operate in water environments ​ Polar molecules will usually be soluble in water if they are not too complex ○​ Molecules are hydrophilic (water-loving) ​ Non-polar molecules are not soluble in water ○​ Molecules are hydrophobic (water-hating) Intermolecular Forces ​ Hydrogen bonding ○​ Weak force of attraction between slightly positive hydrogen atom and slightly negative charge on neighbouring molecule’s oxygen, nitrogen, or fluorine ​ Hydrophobic interactions ○​ Interactions resulting from tendency of nonpolar molecules to band together in water Biochemical Reactions ​ Neutralization  ​ Condensation ​ Hydrolysis ​ redox Neutralization Reaction ​ Acid and bases react to form water and salt ○​ HCl(aq) + NaOH(aq) → H2O(l) + NaCl(aq) Acid ​ Substance that produces hydrogen ions when dissolved in water ○​ Since water is polar it attracts hydrogen ion ot make hydronium ion ​ E.g. hydrogen chloride (HCl) is gas ○​ When mixed with water, it form hydrochloric acid ​ HCl(g) + H2O(l) → H3O+ + Cl- Base Buffers ​ Buffer – substance that helps reduce major pH level fluctuations ​ E.g. human blood operates best at pH of 7.4 (acceptable blood pH range: 7.35-7.45) ○​ Natural buffers in body able to maintain optimal pH levels by reacting to neutralize excess acid or excess base ○​ Important buffer in human body (in blood and extracellular fluid) is ​ Carbonic acid – Bicarbonate buffer system Carbonic Acid – Bicarbonate Buffer System  ​ If blood becomes too basic ○​ CO2 and H2O in blood react to form carbonic acid (H₂CO₃) ○​ H₂CO₃ dissociates into bicarbonate ion (HCO₃-) and hydrogen ions (H+) to decrease blood pH ​ If blood becomes too acidic ○​ Excess hydrogen ions in blood will combine with bicarbonate ions to make more carbonic acid ○​ Works to raise pH in two ways ​ Carbonic acid is weak acid, which raises pH of blood ​ Carbonic acid is converted to H2O and CO2 ​ As CO2 is expelled from body there is drive to make more carbonic acid in reaction ​ To make more carbonic acid, excess hydrogen ions in blood are used, raising pH of blood Base ​ Substance that produces hydroxide ions when dissolved in water ​ E.g. sodium hydroxide (NaOH) is solid ○​ When mixed with water it forms base ​ NaOH(s)+H2O(l) → Na+ + OH- + H2O(l) Lesson 1.1b - The Chemicals of Life – Functional Groups as Linakes Why are organic molecules made out of carbon? ​ Carbon is able to form stable bonds with carbon atoms ​ Carbon is best electron sharer ○​ Can form bonds with 4 other atoms ○​ Bonds are covalent and therefore strong ○​ Strong bond holds energy Building Hydrocarbons ​ Compounds composed of H and C ​ Combinations of H and C form non-polar molecules, but store lots of energy ​ In order to be useful to living things, hydrocarbons need to be able to interact with water How is this achieved ​ At strong polar functional group to carbon backbone ○​ Stearic acid has carboxyl functional group Functional Groups Group Chemical Structural Ball-and-stick Found in formula formula model Hydroxyl —OH —OH Alcohols (e.g. ethanol) Carboxyl —COOH Acids (e.g. vinegar) Amino —NH2 Bases (e.g. ammonia) Sulfhydryl —SH Rubber Phosphate —PO4 ATP  Carbonyl —COH Aldehydes (e.g. formaldehyde) Ketones (e.g. —CO— acetone) Organic Molecules React Condensation Reaction (dehydration synthesis) ​ Creates covalent bond (or linkage) between interacting functional groups ​ Energy is absorbed into new bond ​ Also called ANABOLIC reaction ○​ Producing larger molecules from smaller subunits ​ Examples ○​ Monomers (smaller molecules) will combine to form (polymers) very large molecules through condensation reactions Hydrolysis Reaction (hydration) ​ Water molecule used to break covalent bond ​ Releases energy (bonds are broken) ​ Also called catabolic reaction break larger macromolecule into smaller subunits Common Biological Linkages ​ hydroxyl + hydroxyl ether ​ hydroxyl + carboxyl ester  ​ amino + carboxyl amide (peptide) ​ phosphate + hydroxyl phosphate ester Lesson 1.3 - Macromolecules Nutrients ​ Humans eat to build their bodies, gain strength, for taste, to live, etc. ​ Food → ENERGY → allows us to do WORK ​ To be healthy, body requires approximately 50 nutrients ​ Nutrients can be grouped into 3 broad categories  ○​ vitamins/minerals ○​ Water ○​ Macromolecules ​ Protein ​ Carbohydrates ​ Fat (lipids) ​ Nucleic acids Macromolecules ​ Large molecules composed of repairing subunits ​ Four major classes: carbohydrates, proteins, lipids, and nucleic acids ​ Dehydration Synthesis (Condensation Reaction) ○​ Two subunits link together through removal of water molecule ○​ Dehydration synthesis is anabolic reaction that absorbs energy ​ Hydrolysis reaction ○​ Two subunits break apart through addition of water molecule ○​ Hydration synthesis is catabolic reaction that releases energy Carbohydrates ​ Used for energy, building material, and cell identification and communication ​ Contain carbon, hydrogen, and oxygen 1:2:1 ratio ​ Classified into 3 groups ○​ Monosaccharides ○​ Oligosaccharides ○​ Polysaccharides Monosaccharides ​ Subunit of carbohydrate ​ Two types ○​ Aldose ​ All carbons have hydroxyl groups attached, with exception of carbonyl group found on terminal carbon  ○​ Ketose ​ All carbons have hydroxyl groups attached, with exception of carbonyl group found on central carbon ​ When dissolved in water, sugars with 4 or more carbons form rings structures ​ When dry, they form linear structures Disaccharides ​ 2 subunits of simple sugars combine ​ Condensation reaction (dehydration synthesis) forms glycosidic linkage between two monosaccharides to make oligosaccharide ​ Maltose (α 1-4); Sucrose (α 1-2) Polysaccharides ​ Many subunits (100’s to 1000’s) ​ Four types: starch, glycogen, cellulose, chitin ○​ Starch ​ Composed of amylose (α 1-4 links) and amylopectin (α 1-4 links but α 1-6 links where it branches) ​ Energy storage for plants ○​ Glycogen ​ Composed of α1-4 links but α1-6 links where it branches ​ More branched than starch ​ Animal energy storage ○​ Cellulose ​ Composed of ß1-4 links ​ Every other glucose subunit becomes inverted to accommodate link ​ Not coiled or branched ​ Used in plant cell walls ​ Cellulose structure ○​ Chitin ​ Cellulose-like polymer of N-acetylglucosamine ​ Monomer is glucose molecule with nitrogen containing group attached at second C position ​ Used in insect and crustaceans to form hard exoskeleton Lipids ​ Hydrophobic molecules ​ Generally nonpolar and are insoluble in water ​ Includes fats, phospholipids, steroids, and waxes ​ Gram of fat stores 9 calories of energy ○​ Compared to 4 calories in carbohydrates and proteins ​ Used for energy storage, cushioning, and insulation ​ Animals convert excess carbohydrates into fat and store fat as droplets in cell od adipose (fat) tissue Fats ​ Fats (e.g. triglycerides) ○​ Backbone is glycerol which has 3 hydroxyls ○​ Each fatty acid has terminal carboxylic acid and between 16 and 18 carbons ○​ Condensation reaction attaches 3 fatty acids to glycerol making ester linkages (esterification) Saturated Fats ​ Come from animals ​ Used for long-term energy storage, insulation, protection, and helps dissolve fat soluble vitamins ​ No double bonds between carbon atoms in fatty acids ​ Solid at room temperature due to straight chains → fatty acids are closer together → more intermolecular forces Unsaturated Fats ​ From plant oils ​ One or more double bonds between carbon atoms in fatty acids ​ Double bonds form kinks, producing more space between fatty acids thus reducing number of intermolecular interactions ​ Liquid at room temperature Phospholipids ​ Composed of one glycerol, two fatty acids, and a highly polar phosphate group ​ Form cellular membranes (phospholipid bilayer) ​ Phospholipid bilayer is virtually impermeable to macromolecule, relatively impermeable to charged ions, and quite permeable to small, lipid soluble molecules ​ O2 and CO2 diffuse through with very little resistance Steroids ​ Hydroponic molecules ​ Four fused hydrocarbon rings with several functional groups attached ​ Cholesterol is converted, by body, into bile salts and vitamin D ​ Other steroids include sex hormone ○​ E.g. estrogen, testosterone, progesterone Waxes ​ E.g. beeswax, paraffin, cutin ​ Consists of alcohol or carbon rings with ester linkage to fatty acid ​ Hydrophobic ​ Acts as waterproof coatings on various plant and animal parts Nucleic Acids ​ Found in DNA, RNA, ATP, and nucleotide coenzymes (NAD+, NADP+ and FAD) ​ DNA and RNA are nucleotide polymers ​ Nucleotides consist of nitrogenous base, five-carbon sugar and phosphate group ○​ Nitrogenous bases are ​ Adenin A ​ Guanine G ​ Cytosine C ​ Thymine T ​ Uracil U ​ In DNA, A bonds with T with 2 hydrogen bonds, and G bonds with C with 3 Hydrogen bonds ​ Two strands are antiparallel ○​ One strand is upside down compared to the others Nucleotides Nitrogenous Bases Sugars Proteins ​ Involved in almost everything cells do ​ Can be enzymes, immunoglobulins, hemoglobin, keratin, fibrin, etc. ​ Proteins are made up of many amino acids ○​ Each is called a residue Amino Acids ​ Proteins are made of one or more amino acids ​ 20 amino acids differ in R groups they contain ○​ 8 amino acids are essential ​ Side chains can make amino acid polar (hydrophilic), non-polar (hydrophobic), or charged (acidic/basic) Nonpolar Amino Acids Polar Amino Acids Acid and Basic Amino Acids Protein Structure ​ Amino acids are monomers that make up proteins ​ Bonds that hold amino acids together are called peptide bonds ​ Peptide bonds are formed by dehydration synthesis reaction ​ Also called conformation ​ Depends on amino acids it contains, and interaction between those amino acids Primary Structure ​ Polypeptide chain → many amino acids in chain connected by peptide bonds ​ Sequence of amino acids is determined by nucleotide sequence of a particular gene ​ In protein with X number of amino acids, number of possibilities is 20x Secondary Structure ​ Folding and coiling of polypeptide chain as it grows ​ Formed by hydrogen bonds between oxygen atoms of carboxyl group and hydrogen atoms of amino group ​ Two types ○​ α helix – tight coil produced by H-bonds every 4 peptide bonds repeated ○​ ß pleated sheets – H-bonds formed between parallel stretches of a polypeptide Tertiary Structure ​ Polypeptide chain undergoes additional folding due to side chain (R-group) interaction Quaternary Structure ​ Two or more polypeptide chains come together, such as in collagen and hemoglobin Denaturation ​ Temperature and pH changes can cause protein to unravel ○​ Denature ​ Due to disruption hydrogen bonds, etc ​ Denatured protein is unable to carry out its biological function  Lesson 1.4 - Enzymes What is an Enzyme ​ Protein catalysts that speed up biochemical reaction ​ NOT used up during reaction – can be used over and over again → catalytic cycle ​ Specific to particular substrate (reactant) ​ Classified according to type of reaction they catalyze ​ Named specifically for reaction they catalyze and usually end in “ase” How do Enzymes Work ​ Lower activation energy of reaction How do Enzymes Lower Activation Energy ​ They form enzyme-substrate complexes ​ Substrates bind to a region on the surface of enzymes known as the active site, to form an enzyme-substrate complex ​ The active site undergoes a slight conformational change to better accommodate the substrate (induced fit) How does the enzyme-substrate complex lead to lowering activation energy? ​ In catabolic reactions the interactions between the substrate and enzyme causes stress or distorts the bonds in the substrate, allowing bonds to break  ​ In anabolic reactions the enzyme stress or distorts bonds to encourage a link between two substrates to allow bonds to form between them Factors that Affect Enzyme Activity Temperature ​ As temperature rises, reacting molecules gain more kinetic energy increases chances of successful collisions. ​ There, the rate of the reaction increases. ​ Eventually, at a set OPTIMAL temperature, the enzyme’s activity is at its greatest. E.g. In humans, the optimal temperature of all enzymes is 37ºC ​ As temperature increases, higher than the optimal temperature, the enzyme denatures. pH ​ Enzymes work within a very small pH range ​ Optimal pH is the level at which an enzyme’s activity is the greatest ​ pH levels outside of the optimal range can cause denaturing of the enzyme Concentration of substrate and enzyme ​ The rate of reaction will increase with an increase of either substrate or enzyme concentration ​ However, with an increase in substrate concentration, eventually all of the active sites of the enzymes become occupied all at once (point of saturation). ​ Before any more reactions can occur an enzyme/substrate complex has to dissociate to free up an active site Inhibition ​ Competitive Inhibitors are so similar to an enzyme’s substrate that they can bind to the active site and block the normal substrate ​ Non-competitive Inhibitors bind to the enzyme at an allosteric site (not the active site) and cause a conformational change in the enzyme, preventing the normal substrate from binding ​ Feedback inhibition ○​ A method used by cells to control metabolic pathways involving a series of reactions ○​ A product formed later in a sequence of reactions allosterically inhibits an enzyme that catalyzes the reaction earlier on Allosteric Regulation ​ Cells control enzyme activity to coordinate cellular activities ​ Activators may bind to allosterically controlled enzymes to stabilize its shape and keep all active sites available ​ Allosteric inhibitors may bind to allosterically controlled enzymes to stabilize the inactive form of the enzyme. Cofactors and Coenzymes ​ Required by some enzymes to function ​ They bind to the active sites of enzyme ○​ Cofactors are inorganic, non-protein components, usually attract electrons in the substrate to assist in breaking bonds (Zn2+ and Mn2+) → MINERALS. ○​ Coenzymes are organic, non-protein molecules, such as the derivatives of many VITAMINS ​ They often shuttle molecules from one enzyme to another. (e.g. vitamin B3 is a coenzyme of NAD+)