Bio10 Cell and Molecular Lecture Notes SRJC

Transcription

1 Basic Chemistry Atoms Smallest particles that retain properties of an element Made up of subatomic particles: Protons (+) Electrons (-) Neutrons (no charge) Isotopes Atoms of an element with different numbers of neutrons Behave the same way in chemical reactions Radioisotopes emit particles and energy as they decay, eventually becoming a different element Mass Number (Atomic Mass) Number of protons +number of neutrons Examples: H = 1 P +, 0 N 0 atomic mass = 1 C = 6 P +, 6 N 0 atomic mass = 12 Electrons Carry a negative charge Repel one another Are attracted to protons in the nucleus Move in orbitals (volumes of space that surround the nucleus) Electron Orbitals Orbitals can hold up to two electrons Atoms differ in the number of electrons in orbitals Orbitals closest to nucleus are lower energy and are filled first Shell Model First shell Lowest orbital Holds 2 electrons Second shell 4 orbitals hold up to a total of 8 electrons Unfilled shells make atoms likely to react The number and arrangement of their electrons determines whether atoms will interact Chemical Bonds, Molecules, and Compounds Bond is union between electron structures of atoms Atoms bond to form molecules Molecules may contain atoms of only one element: O2 Compounds contain more than one element: H2O Important Bonds in Biological Molecules Ionic bonds Covalent bonds Hydrogen bonds A Carranza Page 1 7/24/2015

2 Ionic Bonding One atom loses electrons, becomes positively charged ion Another atom gains these electrons, becomes negatively charged ion Charge difference attracts the two ions to one another Formation of NaCl Sodium atom (Na) outer shell has one electron Chlorine atom (Cl) outer shell has seven electrons Na transfers electron to Cl, forming Na+ and Cl- Ions remain together as NaCl (sodium chloride) Covalent Bonding Atoms share a pair or pairs of electrons to fill outermost shell Polar or Nonpolar Bonds Nonpolar if atoms share electrons equally Hydrogen gas (H - H) Polar if electrons spend more time near nucleus with most protons Water Electrons more attracted to O nucleus than to H nuclei Water is polar, covalent molecule Molecule has no net charge Oxygen end has a slight negative charge Hydrogen end has a slight positive charge Hydrogen Bonding Atom in one polar covalent molecule is attracted to oppositely charged atom in another such molecule or in same molecule Properties of Water Polarity Stabilizes temperature Adhesion Cohesion Capillarity Capacity to dissolve substances Polarity Hydrophilic substances Polar covalent bond Hydrogen bond with water Example: sugar Hydrophobic substances Nonpolar covalent bond Repelled by water Example: oil A Carranza Page 2 7/24/2015

3 Temperature-Stabilizing Effects Liquid water can absorb much heat before its temperature rises Energy first disrupts hydrogen bonding before increasing the movement of molecules Evaporative Cooling As energy causes molecules to break free, they carry away some energy. Evaporative water loss is used by mammals to lower body temperature Cohesion and Evaporation Cohension is the hydrogen bonding among water molecules The force is strong enough to force water up treetops, but weak enough that thermal energy will break the hydrogen bonds causing evaporation Water Adhesion The hydrogen bonding between water and other polar substances Hydrogen bonding holds polar molecules together Capillarity Cohesion and adhesion together create this property Water climbs narrow tubes Hydrogen Ions: H+ Unbound protons Important biological functions Form when water ionizes The ph Scale Measures H+ concentration of fluid Change of 1 on scale means 10X change in H+ concentration Highest H+ Lowest H Acidic Neutral Basic Examples of ph Pure water is neutral with ph of 7.0 Acidic Stomach acid: ph Lemon juice: ph 2.3 Basic Seawater: ph Baking soda: ph 9.0 Acids and Bases Acids Donate H+ when dissolved in water Acidic solutions have ph < 7 Bases Accept H+ when dissolved in water Acidic solutions have ph > 7 A Carranza Page 3 7/24/2015

4 Buffer System Minimizes shifts in ph Is a partnership between a weak acid and the base it forms when dissolved The weak acid and base work as a pair to counter shifts in ph Carbonic Acid Bicarbonate Buffer System When blood ph rises, carbonic acid dissociates to form bicarbonate and H+ H2C > HC03- + H+ When blood ph drops, bicarbonate binds H+ to form carbonic acid HC03- + H > H2C03 Salts Compounds that release ions other than H+ and OH- when dissolved in water Example: NaCl releases Na+ and Cl Many salts dissolve into ions that play important biological roles Molecules of Life Most Common Elements in Living Organisms Oxygen Hydrogen Carbon Nitrogen Organic Compounds Hydrogen and other elements covalently bonded to carbon Carbohydrates Lipids Proteins Nucleic acids Methane Simplest organic molecule A greenhouse gas Main component of natural gas Produced by bacteria in vertebrate gut Found in deep ocean deposits as the world s single largest carbon store Hydrocarbon Bonding Patterns and Nomenclature Carbon number Compound Root Name 1 Methane 2 Ethane 3 Propane 4 Butane 5 Pentane 6 Hexane 7 Heptane 8 Octane A Carranza Page 4 7/24/2015

5 Carbon s Bonding Behavior Outer shell of carbon has 4 electrons; can hold 8 Each carbon atom can form covalent bonds with up to 4 other atoms Bonding Arrangements Carbon atoms can form chains or rings Other atoms project from the carbon backbone Functional Groups Atoms or clusters of atoms that are covalently bonded to carbon backbone Give organic compounds their different properties Examples of Functional Groups Methyl group CH3 Hydroxyl group OH Amino group NH3+ Carboxyl group COOH Phosphate group PO3- Sulfhydryl group SH Types of Reactions Functional group transfer Electron transfer Rearrangement Condensation Cleavage (hydrolysis) Condensation Reactions Form polymers from subunits Enzymes remove OH from one molecule, H from another, form bond between two molecules Discarded atoms can join to form water Hydrolysis A type of cleavage reaction Breaks polymers into smaller units Enzymes split molecules into two or more parts An OH group and an H atom derived from water are attached at exposed sites Carbohydrates Monosaccharides Simple sugars Glucose, fructose, ribose Oligosaccharides Short-chain carbohydrates Sucrose Polysaccharides Complex carbohydrates Glycogen, starch, cellulose, chitin a) Structure of glucose b) Structure of fructose c) sucrose glucose fructose A Carranza Page 5 7/24/2015

6 Lipids Tend to be insoluble in water Some have fatty acid tails Fats Phospholipids Waxes Sterols: have a fused carbon ring Fatty Acids Carboxyl group at one end Carbon backbone Saturated or unsaturated Saturated Monounsaturated Polyunsaturated Fats Fatty acid(s) attached to glycerol Triglycerides are most common Phospholipids Main component of cell membranes Hydrophilic head Hydrophobic tails linolenic acid Sterols and Derivatives No fatty acids Rigid backbone of four fused carbon rings Cholesterol: most common type in animals Waxes Long-chain fatty acids linked to long-chain alcohols or carbon rings Firm consistency, repel water Important in waterproofing A Carranza Page 6 7/24/2015

7 Amino Acid Structure Amino group Carboxyl group R group Protein Synthesis Peptide bond Condensation reaction links amino group of one amino acid with carboxyl group of next Water forms as a by-product Primary Structure Sequence of amino acids Unique for each protein Two linked amino acids = dipeptide Three or more = polypeptide Backbone of polypeptide has N atoms: -N-C-C-N-C-C- N-C-C-N Second and Third Levels Hydrogen bonding produces helix or sheet Domain formation Fourth-Level Structure Some proteins are made up of more than one polypeptide chain A Carranza Page 7 7/24/2015

8 Nucleotide Structure Sugar At least one phosphate group Nitrogen-containing base Adenosine Triphosphate (ATP) base three phosphate groups sugar Nucleotide Bases Adenine (A) Guanine (G) Thymine (T) Cytosine (C) Nucleotide Functions Energy carriers Coenzymes Chemical messengers Building blocks for nucleic acids DNA Double-stranded Sugar-phosphate backbone Covalent bonds in backbone H bonds between bases RNA Usually single strands Four types of nucleotides Unlike DNA, contains the base uracil in place of thymine Three types are key players in protein synthesis A Carranza Page 8 7/24/2015