2. The Chemistry of Life
2. The Chemistry of Life BISC 102
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Date Created: 09/08/16
2. The Chemistry of Life 2.1. Atoms Make up All Matter - Matter = material that takes up space and has mass • occurs in 3 forms - solid Smallest mass to largest - liquid 1. Electron - gas 2. Proton - Energy = ability to do work (moving matter) 3. Atom • energy used by most ecosystems from the sun • heat, light and chemical bonds A. Elements are Fundamental Types of Matter - Matter consists of elements - Element = pure substance, cannot be broken down • oxygen, carbon, nitrogen, sodium, hydrogen - Scientists noticed patterns in chemical behavior in mid 1800s - Dmitry Mendeleyv invented the periodic chart - 92 naturally occurring elements - 25 elements essential to life - bulk elements required in large amounts (96% of human body) • carbon • hydrogen • oxygen • nitrogen - 3.5% of body consists of other bulk phosphorus • sulfur • • sodium • magnesium • potassium • calcium - Trace elements required in small amounts—> 0.5% of body • iron • zinc B. Atoms are particles of elements - Atom = smallest piece of an element that retains charc. of element • contains three particles - proton: + charge - neutrons: uncharged - both form nucleus • - charged electrons surround nucleus - atoms take up a lot of space, but when they are moving, like a fan, they take up mass - Atomic Number: number of protons in nucleus • periodic table has elements arranged sequentially by atomic number • protons = electrons, the atom is electrically neutral • ion: atom that has gained or lost electrons therefore has a net - or + charge C. Isotopes have different numbers of neutrons - Atoms mass number = protons + neutrons (in nucleus) - atomic number - mass = number of neutrons - Isotope: atoms of the same element that differ in number of neutrons—> same protons, diff. mass numbers • radioactive isotopes: excess neutrons = unstable - emit energy as rays when they break down into more stable forms - half-life = time for half to decay to stable form - used in x-rays - excessive exposure can lead to sickness and mutations - Atomic weight: average mass of all isotopes 2.2. Chemical Bonds Link Atoms Atoms in organisms arranged into molecules - Molecules: two or more chemically joined atoms - Compound: molecule composed of 2 or more diff. elements - Molecular formula: representation of atoms in a compound; CH4 (methane) A. Electrons determine bonding - Orbitals: describe location for an election relative to its nucleus • Energy shell: group of orbitals; ﬁrst holds 2 electrons, after that it can hold up to 8; outer shells have higher energy • valence: outermost energy shell; no. of electrons determine chemical reactivity of atom - if full (with 8) = stable; octet rule • number of orbitals in each shell determines the amount of electrons it can hold - Electronegativity: measures atoms ability to attract electrons (high = strip from others) - Chemical bond: transfer of electrons from one atom to another, holds atoms together B. In an ionic bond, one atom transfers electrons to another atom - Ion: an atom that has lost or gained electrons - Ionic: a highly electronegative atom ﬁlls its valence by taking electrons from another atom • donator has + charge after atom that accepts has - charge • • held together through opposite charges C. In a covalent bond, atoms share electrons - Covalent: two atoms share electrons to complete outer shell - Double: share two pairs of electrons (O2) - Polar: one nucleus exerts stronger pull on shared electrons; diff. electronegativity values - Non polar: 2 atoms exert approx. equal pull Ionic, polar and non polar represent points along a continuum. • so electronegative, rips electrons, = ionic bond form • atom tugs at shared electrons more than the other = covalent bond is polar • 2 atoms with similar electronegativity share equally = non polar D. Partial changes on polar molecules create hydrogen bonds - Hydrogen: partially + H atom in 1 water molecule attracted to partially - O atom in another molecule; opposite partial charges on adjacent molecules attract each other - WATER IS POLAR - allows it to form hydrogen bonds 2.3 Water is Essential to Life The polarity of a water molecule and the hydrogen bond b/w water molecules account for its unique properties A. Water is Cohesive and Adhesive - Cohesion: ability of molecules to cling to each other due to hydrogen bonding • stops water evaporating instantly surface tension: hold together at its surface - • Adhesion: ability of polar water molecules to cling to polar surfaces (e.g. glass), due to + and - poles B. Many substances dissolve in water - Solvent: chemical in which other substances (solvents) dissolve - Solution: one or more solutes (aqueous solution) - Hydrophilic substances: polar or charged, readily dissolve in water (e.g. salt) - Hydrophobic: non polar; do not dissolve or form hydrogen bonds with water (fats) C. Water regulates temperature - Resists temp. changes - Heat is needed to raise water’s temp than other liquids, as hydrogen bonds counteract ability to absorb energy and move faster - Evaporation: conversion of liquid into a vapor D. Water expands as it freezes - Ice formation • liquid water = unstable H bonds = molecules close together • freezes = H bonds expand and become more stable • ICE LESS DENSE, so ﬂoats in liquid water • if it were denser, sink and ponds would freeze solid bottom up - can be deadly: expansion of ice kills outer membrane in cell - mammals have thick layers of fur to stay warm - pond surface freezes, when temp drops, it retains heat in water below E. Water participates in life’s chemical reactions - In a chemical reaction 2 or more molecules ‘swap’ atoms to yield diff. molecules - Reactants: molecules that enter reaction - Molecules formed from reaction = products 2.4 Cells Have an Optimum pH - H+ ions = important substance dissolved in water - Determine whether a solution is acidic or basic by examining proportion of hydrogen and hydroxide ions in the solution • Acid: increase the H+ concentration of a solution —> pH < 7 - dissociate in water and release H+ (lemon juice, vinegar) • Bases (BLUE): decrease H+ or increase OH- —> pH > 7 - either take up H+ or release OH- (milk of magnesia) • Neutral: (water) equal number of H+ and OH- - Measure through pH scale - Buffer: chemical or a combo, that keeps pH within normal limits (e.g. blood) 2.5 Cells Contain Four Major Types of Organic Molecules - Organic: chemical compounds contain both carbon and hydrogen—> contain core of carbon atoms, other attach - Molecular connectors: (diagram) each reactive group of atoms occur in 1 or more organic molecules - Living organisms composed of biological molecules: • carbs • lipids • proteins • nucleic acids A. Large organic molecules are composed of small subunits - Polymer: (protein, nucleic acid, carbs) chains of small molecular subunits called monomers (individual subunits) - Common examples that act as molecular to hook one subunit of organic to another • hydroxyl • carboxyl • amino • phosphate - Dehydration synthesis: chemical reaction used by cells to link monomers into polymers - Enzyme reaction: water molecule, -OH and an -H is removed - Functional groups: determine an organic molecules chemical properties - Hydrolysis: breaks the covalent bonds that link monomers 4. Carbohydrates include simple sugars and polysaccharides - monosaccharides - Organic molecules that consist of carbon, hydrogen, oxygen—> 1:2:1 - Energy source for cells - Sugars (simple carbs): • monosaccharides (monomer): contain 5 or 6 carbon atoms, simple sugars (glucose) • disaccharide: 2 mono. joined by dehydration synthesis (maltose, sucrose, lactose) • polysaccharides (polymer): may sugars joined (starch- store energy) (cellulose- structural building materials) - Complex Carbs chains of mono. • poly. are huge molecules consisting of many mono. monomers • - long chains of glucose - e.g. cellulose: plant cell walls C. Proteins are complex and highly versatile - amino acids - Variable structures and functions - Structure shows functions • collagen = protein ﬁbre; structural support • Actin = muscle proteins; contractile (contraction in muscles) • Membrane channel proteins = transport • enzyme = digestive protein - monomers (building blocks) of proteins are amino acids (20) • form a repeating part of amino acids R group of amino acids is variable • - join 2 amino (buliding blocks) together - remove h2o through dehydration to synthesis (build) new molecule, to form a peptide bond or depitide - A polypeptide must properly fold into a protein or it cant do its job (denature) - Protein structure has 4 levels (each fold): • primary • secondary • tertiary • quaternary - If you change pH or apply heat, it will undo and change its structure and hence change its function—> called denaturation loss of function D. Nucleic Aids Store and Transmit Genetic Information - nucleotides - Nucleic acid is a polymer consisting of monomers called nucleotides - Cells contain 2 types of NA: • deoxyribonucleic acid (DNA) • ribonucleic acid (RNA) - Monomer consists of: • centre is a 5 carbon sugar (ribose in RNA, deoxyribose in DNA) • at least one phosphate attached to each carbon • opposite side has nitrogenous base - Uses dehydration and hydrolysis E. Lipids are hydrophobic and energy rich - glycerol, fatty acids - includes triglycerides (fatty acids) and steroids - hydrophobic, hard to dissolve in water - Not built from chains of monomers - dehydration links three fatty acids to a glycerol molecule, forming triglyceride - hydrolysis separates fatty acids from glycerol - saturated = all possible numbers of hydrogens around the carbons it can have, forming straight carbon chains • all carbons of a saturated fatty acids are bonded to 4 other atoms • solid at room temp. and of animal origin - unsaturated fatty acid contains at least 1 double bond, so at least 2 carbons are only bonded to 3 other atoms • poly: more then one double bond • mono: one double bond • double bonds create kinks in fatty acids that prevent them from packing close together • unsat. like oils are therefore liquids - steroids are lipid molecules - cholesterol is in animal cell membranes, and several hormones are derived from it - trans fats • unsaturated fats, originally from plant origin • industry has modiﬁed the fats by putting the hydrogen on the opposite side to each other to make trans fat; hydrogenated oils - behave like saturated fat, being solid at room temp. - increases shelf life of product - not good for digestive system and overall health - steroids • 4 interconnected carbon rings (vitamin D) • cholesterol is a key part of animal cell membranes
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