Atoms. Chapter 2: Fundamentals of Chemistry. The main subatomic particles Atomic Model. Isotopes. Building blocks of matter

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1 You need to know this for the Chemistry Quiz Atoms Chapter 2: Fundamentals of Chemistry Dr. Amy Rogers Bio 139 Microbiology Some figures courtesy of Biology: A Guide to the Natural World by Krogh Building blocks of matter Invisible but not indivisible: Made up of subatomic particles Can only be broken down by extraordinary means (for example, particle accelerators) The main subatomic particles Atomic Model Charge Location Proton Positive Nucleus Mass Neutron Neutral Nucleus Mass Electron Negative Orbital shell Space/Volume If drawn to scale, electrons would be 1/3 mile away! Atomic Number = # of protons This defines an element Hydrogen: one proton (+ one electron) Gold: 79 protons (+79 electrons) Isotopes Same element, different number of Neutrons Atomic Weight: sum of protons & neutrons Mole (also called gram molecular weight): the weight of a substance in grams equal to total atomic weight of all the atoms in a molecule of the substance e.g. Glucose (C 6 H 12 O 6 ) molecular weight = Mole glucose = 180 grams Some isotopes are unstable and undergo radioactive decay 1

2 Interactions between atoms: Chemical Bonding Matter is transformed from pure elements into everything else by joining atoms together This is called Chemical Bonding Stable energy states Energy always seeks its lowest state Bonding converts the atoms to a lower, more stable energy state Stable energy state = Filled outer electron shell Electrons are responsible for atoms bonding together Outer Shells Electrons move within defined energy levels outside the nucleus The volume of each energy level, or shell, fits a specific number of electrons First shell: Second shell: Third shell: 2 electrons 8 electrons 8 electrons Unstable atoms: Highly reactive Outer electron shells are unfilled (fewer than 2 or 8 valence electrons) Stable atoms: Largely inert Outer electron shells are full (2 or 8 valence electrons) Ionic Bonding: Give and Take Electrons are given from one atom to another, leading to a net transfer of charge. This charge separation creates ions, which are attracted to one another electrostatically. Cation: positively charged ion; lost electron(s) ex. Na+ Anion: negatively charged ion; gained electron(s) ex. Cl- 2

3 Covalent Bonding: Share and share alike Electrons are NOT transferred, but shared. Polar Covalent Bonding: Sharing of the electrons is unequal, leading to slight charge separation (polarity). Oxygen has greater electronegativity Carbon more electronegative but molecule is symmetric Hydrogen Bonds: A special kind of weak electrostatic attraction that results from polar covalent bonds involving hydrogen Critically important for biology Hydrogen bonds form from attraction between partial + and - charges of polar molecules Hydrogen bonds are WEAK but MANY of them together are a significant force Hydrogen bonds are very important for: Protein folding DNA base pairing Receptor/ligand interactions Properties of water Metabolism: Forming & Breaking chemical bonds Metabolism: Forming & Breaking chemical bonds Catabolism: breaking of bonds (digestion) Anabolism: synthesis (bond creation) X Y X + Y + energy X + Y + energy X Y exergonic reaction endergonic reaction 3

4 Some Biologically Important Properties of Water Solubility: The solution to many problems Solvent: for Polar & charged solutes (hydrophilic) Specific Heat: high Reactant in biochemical reactions Solute Solvent Solution Water as a Solvent: Water is polar & forms hydrogen bonds (with itself and with solutes) Hydrophobic molecules Do not dissolve in water Crucial for maintaining biological compartments Hydrophilic: water loving interacts with or dissolves in water Polar or Ionic Solutes Nonpolar molecules Hydrocarbons, lipids Specific Heat: The amount of energy required to raise the temperature of a substance by 1 o C Heat buffering by water maintains (relatively) stable temperatures on planet earth and in animals bodies Specific Heat of Water: Why so high? Heat is the kinetic energy of moving molecules It takes a lot of energy to get water molecules moving because: Hydrogen Bonds must be broken 4

5 Water as a reactant Most biochemical reactions take place in water Water is often not only a solvent, but also a reactant X Y + H 2 O X H + HO Y Hydrolysis (often exergonic) X H + HO Y X Y + H 2 O Dehydration synthesis (often endergonic) (ex. anabolic formation of organic polymers such as complex carbohydrates, some lipids, and proteins) (ex. catabolism of complex carbohydrates, lipids, proteins to simple sugars, fats, amino acids) Acids & Bases: All things in moderation Opposite of acidic is alkaline (basic) Alkaline/Basic = low [H+] or Low [H+] = high ph high [OH-] OH - (hydroxide ion) is a strong base: It accepts H+ to yield water ph is a measure of concentration of hydrogen ions (H+, or protons) in a solution More hydrogen ions = more acidic High acidity = low ph OH - + H + H 2 O ph On the ph scale, 7 is neutral Carbon: The primary ingredient of life 0 is highly acidic 14 is highly basic/alkaline Logarithmic scale: one change in ph unit = 10x change in [H+] e.g., ph 5 = 100 times more acidic than ph 7 Organisms use buffers to maintain appropriate ph (usually 6-8) ph extremes can denature proteins & disrupt membranes 5

6 Carbon Carbon Structures: Hydrocarbons Atomic number = 6 4 valence electrons; wants 8 Most stable with 4 covalent bonds per carbon Stability, Variety, Complexity of organic molecules Propane C 3 H 8 Hydrocarbons are reduced: saturated with hydrogen, no oxygen atoms present Lots of energy stored in these bonds; can be released by oxidation Functional Groups drastically alter chemical properties Functional Groups Change Everything Ethane (hydrocarbon gas) Nonpolar Won t dissolve in water Ethanol (liquid alcohol) Polar Water soluble Complex organic molecules: Carbohydrates Main energy source for most living things Monosaccharides (simple sugars): carbon ring with several alcohol groups (+ one aldehyde or ketone) Some are isomers (same molecular formula but different structures) e.g., glucose & fructose (C 6 H 12 O 6 ) Most common monosaccharide: Glucose Groups of atoms that confer a special property on a carbon-based molecule Other examples: ribose & deoxyribose 6

7 Disaccharides e.g., lactose, maltose, sucrose (table sugar) two monosaccharides connected by the removal of water and the formation of a glycosidic bond Polysaccharides (complex carbohydrates) Starch Glycogen Cellulose energy storage in plants energy storage in animals structural role (cell walls) These 3 examples are all very long (thousands of subunits) polymers of glucose Example of dehydration synthesis! Polymers large molecules made up of many similar or identical chemical subunits Polymer Polysaccharides & Complex carbohydrates Monomer Subunits Monosaccharides or simple sugars Proteins Amino acids Nucleic acids Nucleotides Lipids Fatty acids: Long hydrocarbon chains with carboxyl group at end Diverse category including fats, phospholipids, steroids Relatively more hydrogen & less oxygen than carbohydrates; therefore more energy-rich Hydrophobic Many important functions including Energy storage Cell membranes 7

8 Saturated fatty acid: maximum hydrogen content; all single bonds between carbons. Usually solid at room temp. Fats 3 carbon glycerol head + 1 to 3 fatty acid tails Unsaturated fatty acid: one or more double bonds; not saturated with hydrogen; kink in chain. + Often liquid at room temp, esp. if polyunsaturated (more than one double bond) If: 3 fatty acids: triacylglycerol (or triglyceride) 2 fatty acids: diacylglycerol 1 fatty acid: monoacylglycerol Formation of triacylglycerols Phospholipids Diacylglycerols (glycerol head + 2 fatty acids tails) + a charged phosphate group R = long hydrocarbon chain (do NOT need to be all the same) Dehydration synthesis forming three ester bonds Phospholipids Hydrophobic end (nonpolar fatty acid tails) Hydrophilic end (charged phosphate group) In an aqueous environment, phospholipids will spontaneously form structures to hide their hydrophobic parts VERY IMPORTANT property Principle component of all cell membranes 8

9 Lipids: Steroids e.g. cholesterol, steroid hormones, vitamin D Proteins are polymers of Amino Acids Basic structure of all steroids: Four carbon rings Specific steroids have various side chains, bond arrangements. Here: cholesterol Proteins begin as polypeptide chains Peptide bonds form between Amino acids differ in the structure of their side chain (R group) Examples at left (do NOT memorize) carboxyl group of one amino acid and amino group of another amino acid Note similarity of basic structure despite variety of R groups This tremendous chemical diversity is linked like letters of the alphabet into protein words Dehydration synthesis again! Polypeptides fold into complex shapes Protein folding: Telephone cord analogy Final protein has a very specific 3-D conformation critical to its function Most folding is mediated by hydrogen bonds At high temperature or extreme ph, these bonds are broken and the protein unfolds or denatures 9

10 Nucleotides: Subunits of nucleic acids Energy carriers DNA & RNA: polymers of nucleotides 3 components: Phosphate(s) Sugar (ribose or deoxyribose) Base (ATGCU) ATP: adenosine triphosphate High energy bonds between 2 outer phosphate groups DNA Double stranded Deoxyribose Bases: Adenine Guanine Cytosine Thymine RNA Single stranded Ribose Bases: Adenine Guanine Cystosine Uracil 10