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Chapter 2
Biol 2113 Giesecke
| Term | Definition |
|---|---|
| Atomic Numbers | number of protons |
| Number of Protons | equals number of electrons |
| Elements | most basic chemical, determined by atomic number |
| Carbon, C | Primary component of all organic molecules, which include carbohydrates, lipids (fats), proteins and nucleic acids. |
| Hydrogen, H | Component of all organics. Ion H+ influences pH of body fluids |
| Oxygen, O | Major component of organic and inorganic molecules. As a gas, needed for production of cellular energy ATP |
| Nitrogen, N | A component of proteins & nucleic acids (genetic material) |
| Elements that make up 96% of body | Carbon, Hydrogen, Oxygen, Nitrogen |
| Calcium, Ca | salt in bones & teeth. Ionic Ca2+ for muscle contractions, conduction of nerve impulses & blood clotting |
| Phosphorus, P | salt in bones & teeth, nucleic acid, ATP |
| Potassium, K | major cation inside cells; used for conduction of nerve impulses; muscle contraction |
| Sulfur, S | proteins, especially muscle proteins |
| Sodium, Na | major ion found in extracellular fluid, water balance, conduction of nerve impulses, muscle contractions |
| Magnesium, Mg | in bone, cofactor in several metabolic reactions |
| Iron, Fe | in hemoglobin, which transports oxygen within red blood cells, in enzymes |
| States of Matter | solid, liquid, gas |
| Energy | capacity to do work or put matter into motion |
| Kinetic Energy | energy in action |
| Potential Energy | stored energy, inactive energy |
| Forms of Energy | Electrical, Chemical, Mechanical, Radiant/Electromagnetic |
| Electrical Energy | movement of charged particles. Charged ions move along or across cell membranes are nerve impulses. Example: current across heart causes it to pump |
| Chemical Energy | energy is stored in bonds. When reactions occur, potential energy is released or energy is stored. Example: Energy in food is stored in ATP. When ATP bonds break, energy is released to do cellular work. |
| Mechanical Energy | Energy directly involved with moving matter. Example: riding a bike; legs push petals |
| Radiant / Electromagnetic Energy | travels in waves that vary in length. Visible light, infrared waves, radio waves, ultraviolet waves, x-rays. Example. Visible light stimulates eyes |
| Isotope | Same number of protons & electrons, different number of neutrons |
| Atomic Mass | Average of relative weights of all isotopes, weighted by abundance in nature |
| Isotope | heavier isotopes are unstable and decompose spontaneous into more stable forms |
| Molecule | two or more atoms held together by chemical bond |
| Molecule of an element | two or more atoms of the same element held together by chemical bond |
| Compound | two or more atoms of different elements held together by chemical bond |
| Mixture | combination of elements or compounds physically mixed but not bound by bonds. Example: air |
| Types of Mixtures | Solution, Colloid, Suspension |
| Solution | transparent mixture, solute very small, does not scatter light, does not settle out, homeogeneous. Example: mineral water |
| Solute | thing mixed in, smaller amount |
| Solvent | base of solution, larger amount, usually liquid |
| Colloid | also called emulsions, particles larger, scatter light, does not settle out, sol-gel transformation, Example: jello, cytosol |
| Suspensions | solute very large, settles out, may scatter light, Example: blood |
| Inert elements | full valence shell |
| Reactive elements | valence shell incomplete |
| Ionic Bonds | -donating / receiving electrons; attraction of opposite charges; metal + nonmetal; most are salts which form crystals |
| Calcium phosphate | salt in bones |
| Sodium Chloride | table salt |
| Covalent Bonds | sharing of electrons; shared electron spends time at both atoms |
| Polar Covalent Bonds | unequal sharing of electron, creates dipole with slight negative side and slight positive side; dissolves in water; does not freely diffuse through cell membrane. Examples: water, sugar, some amino acids, most proteins |
| Non-Polar Covalent Bonds | equal sharing of electrons due to equal pulling ability; do not dissolve in water; fat soluble; easily diffuse through cell membranes; all compunds with only C & H or identical atoms; examples: CO2, O2, fats, some amino acids |
| Water dissolves | ionic compounds, polar covalent bonds, Examples: sugar, some amino acids, most proteins |
| Water does not dissolve | non-polar covalent compounds; examples: CO2, O2, fats (many C-H bonds), some amino acids |
| Transportation of Non-polar compounds | surround non-polar with polar |
| Transportation of fats | surround with proteins and phospholipids |
| lipoproteins | LDL & HDL |
| Transportation of gasses CO2 and O2 | hemoglobin |
| Hydrogen Bonds | Weakest bond, attraction of oppositely charged parts, creates surface tension in water, affect shape and properties in DNA and protein. |
| anabolism | endergonic, uses energy to build structures; A + B -> AB |
| catabolism | exergonic; releases energy to power body; AB -> A + B |
| Metabolism | chemical reactions in body; anabolism & metabolism; changes throughout life |
| Exchange Reactions | bonds are made and broken; parts of the reactant molecules change partners; AB + C -> AC + B & AB + CD -> AD + CB |
| Oxidation-Reduction Reactions | decomposition reaction; breaking down of food; reactants exchange electrons; ionic & covalent; by losing electrons & combining with Oxygen. Cellular respiration |
| oxidized | lose electrons, electron donor |
| reduced | takes up electron, electron acceptor |
| exergonic | reactions that release energy |
| endergonic | reactions that absorb energy |
| Factors influencing rate of reactions | Temperature; concentration; particle size, and catalysts. |
| Biochemistry | study of the chemical composition and reactions of living matter. |
| Organic compounds | contain carbon; covalently bonded; may be large |
| Inorganic compounds | all other chemicals that are not the other type; include water, salts, and many acids and bases. |
| Percentage of water in cell | 60-80% |
| Properties of water for life | High heat capacity; high heat of vaporization; Polar solvent properties; Reactivity; cushioning |
| High heat capacity of water | can absorb and release large amounts of heat without changing in temperature. Prevents sudden temperature changes from external (sun) or internal (muscle activity) sources. As part of blood, distributes heat evenly to maintain homeostasis. |
| High heat of vaporization of water | must absorb large amounts of heat for hydrogen bonds to break; perspiration evaporates from body removing large amounts of heat. |
| Polar Solvent properties of water, polar | called universal solvent in body; water molecules are polar; ionic compounds and small reactive molecules, acids and bases, dissociate in water; forms hydration layers; body's major transport medium. |
| Reactivity of water | involved in hydrolysis reactions in breaking down of food; dehydration synthesis in building large carbohydrate or protein molecules; |
| Hydrolysis reactions | Water molecule breaks apart and bonds during a decomposition reaction |
| Dehydration synthesis | Two smaller molecules come together and form larger molecule + water. Parts of water are taken away from the initial molecules; the "lose" water. |
| Cushioning of water | helps protect organs from physical trauma. Example: cerebrospinal fluid surrounding brain. |
| Salt | ionic compound containing cations other than H+ and anions other than OH-; when they dissolve in water, they dissociate in to component ions. |
| Electrolytes | ions, substances that conduct an electrical current in solution |
| Common Salts in body | NaCl; CaCO3; KCl; CaPO3 |
| Kidneys | maintain ionic balance in body fluids |
| Acids | sour taste, react with metals, release H+ |
| Common acids in body | Acetic acid HC2H3O2 or HAc; Carbonic acid H2CO3 |
| Bases | bitter taste, feel slippery, release OH- |
| Important bases in body | Bicarbonate ion HCO3- in blood; Ammonia NH3 waste product protein breakdown |
| Acidic values | ph below 7 |
| Basic values | ph above 7 |
| acid + base -> | salt + water; neutralizes pH |
| Regulates acid-base balance | kidneys & lungs; buffers |
| normal blood pH range | 7.35 - 7.45 |
| buffer | resist abrupt and large swings in pH; releases H+ when pH rises; binds H+ when pH drops. Acts as weak acid with dynamic equalibrium |
| Electroneutral | property of Carbon; never gains or loses electrons |
| Carbon's 4 electrons in valance shell | able to form long chains (fats) or rings(carbohydrates & steroids) |
| Polymer | chainlike molecules made of many similar or repeating units (monomers) |
| Carbohydrates | sugars & starches; contain C, H, O. H:O ratio = 2:1 as in water; -saccharide; larger molecule the less soluble in water |
| Monosaccharides | simple sugars; single-chain or single-ring structure containing 3 - 7 carbon atoms; C:H:O ratio 1:2:1; Examples: glucose C6H12O6 blood sugar; deoxyribose C5H10O5; |
| Isomers | same molecular formula but different arrangement; Example: galactose and fructose c6H12O6 |
| Disaccharides | double sugar; two monosaccharides are joined by dehydration synthesis; 2C6H12O6 -> C12H22O11 + H2O; examples: sucrose; lactose; maltose. Too large to pass through cell membranes; must be broken into simple sugars by hydrolysis |
| Polysaccharides | polymers of simple sugars linked together by dehydration syntheses. Large, insoluble molecules; ideal for storage; lack sweetness. Examples: starch and glycogen |
| Starch | storage of carbohydrate formed by plants; |
| Glycogen | Stores carbohydrate of animal tissues; stored in skeletal muscle and liver cells; highly branched very large molecule; liver cells break down molecule to release glucose when blood sugar levels drop sharply |
| Carbohydrate functions | provide ready, easily used source of cellular fuel; most cells only use a few types of simple sugar; mostly glucose; break down of glucose in cell produces energy to make ATP; when enough ATP are made; dietary carbohydrates diverted to glycogen or fat |
| Lipids | insoluble in water; contain carbon, hydrogen, oxygen; oxygen much lower. Phosphorus found in some complex molecules. Examples: triglycerides; phospholipids. |
| Triglycerides | neutral fats; composed of fatty acids and glycerol in 3:1 ratio; 3 fatty acids attach to 1 glycerol by dehydration synthesis; e shaped molecule; glycerol same in all; fatty acids result in different kinds of fats; 100+ atoms; nonpolar; |
| Fatty acid | linear chain of carbon and hydrogen with organic acid group -COOH at end. |
| Glycerol | modified simple sugar - a sugar alcohol |
| Saturated fats | fatty acid chains with only single covalent bonds between carbon atoms; molecules packed closely together; solid at room temperature; common in animal fats |
| Unsaturated fats | fatty acids that contain one or more double bonds between carbon atoms; double bonds kink; can not be packed close together; liquid at room temperature; typical of plant lipids |
| Trans fat | oils that have been solidified by addition of H atoms at carbon double bonds |
| Omega-3 fatty acids | found naturally in cold-water fish decrease risk of heart disease and inflammatory diseases |
| Phospholipids | modified triglycerides; diglycerides with a phosphorus containing group and 2 instead of 3 fatty acid chains; Phosphorus containing part is polar; hydrocarbon tail is nonpolar; polar end attracts water or ions; used in building cellular membranes |
| Steroids | flat molecules made of four interlocking hydrocarbon rings; fat soluble; contain little oxygen; cholesterol most important steroid; required for cell membranes, synthesis of Vitamin D, steroid hormones, bile salts. |
| Eicosanoids | diverse lipids from 20-carbon fatty acid (arachidonic acid) found in cell membranes. play role in various body processes including blood clotting, regulation of blood pressure, inflammation, labor contractions; blocked by drugs NSAIDS and COX inhibitors. |
| Protein | composes 10-30% of cell mass; basic structural material of the body, Not all are construction materials. vital role in cell function; include enzymes, hemoglobin, contractile proteins of muscle with varied functions; contain C, O, H, N and many contain S. |
| Amino acids | building blocks of protein; 20 common types; contain a basic group, amine -NH2 & organic acid group -COOH; may act as a base or acid. all are identical except for R group |
| Peptide bond | proteins are long chains of amino acids joined by dehydration synthesis; amine end of one amino acid link to acid end of the next; most proteins contain from 100 to 10,000 amino acids |
| Structural Levels of Proteins | primary: linear sequence of amino acids; secondary: most commonly alpha helix coil: stabilized primary with H bonds between NH and CO groups; beta pleated sheet side H bonds; tertiary: alpha or beta folds upon itself: globular shape; quaternary: aggregate |
| Proteins are classified by shape | Fibrous or Globular |
| Fibrous Proteins | extended and strand-like; insoluble in water; very stable; provide mechanical support and tensile strength to tissues. Example: collagen, keratin, elastin; also known as structural proteins |
| Globular Proteins | compact, spherical proteins that have at least tertiary structure; water soluble; chemically active; play crucial role in all biological processes. Also called functional proteins. Examples: antibodies; protein-based hormones; enzymes |
| Denatured Proteins | condition where protein unfolds and loses shape; H-bonds are fragile & break when pH drops or temperature rises; regains structure when conditions are restored unless severely damaged. |
| Molecular chaperones | help proteins achieve their functional three-dimensional structure. Folding process requires this help to ensure folding is quick & accurate |
| Enzymes | globular proteins; biological catalyst; regulate & accelerate rate of biochemical reactions; not used up or changed in reaction; |
| Substrate | substance on which enzyme acts |
| Characteristics of Enzymes | some protein, others made of parts: holoenzyme = apoenzyme + cofactor; some control 1 reaction; others act on several; named for type reaction: hyrolases add water, oxidases oxidize reactants, have -ase suffix; some created inactive; bucket brigade |
| Enzyme action | substrate fits to active site = enzyme-substrate complex; complex rearranges to form products; releases products of the reaction |
| Nucleic Acids | composed of Carbon, oxygen, hydrogen, nitrogen, phosphorus; largest molecules in body; |
| Nucleotides | structural units of nucleic acids; complex; 3 parts: nitrogen-containing base; pentose sugar; phosphate group |
| Nucleotide bases | Adenine, A; guanine, G; Cytosine, C; thymine, T; uracil, U |
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