Ch 2 Chemistry of Life

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Information about Ch 2 Chemistry of Life

Published on January 5, 2008

Author: Breezy


Chapter 2: The Chemical Level of Organization:  Chapter 2: The Chemical Level of Organization Atoms:  Atoms All matter is composed of atoms. Protons (+) and neutrons (neutral) are found on the atom’s nucleus, while electrons (-) circle the nucleus. Atomic number - number of protons Atoms with the same atomic number belong to the same element, and thus have the same inherent properties. Atoms:  Atoms Atomic Weight:  Atomic Weight Mass refers to the amount of a substance. Weight refers to the force exerted on a substance by gravity. Atomic mass of an atom refers to the sum of the masses of protons and neutrons. measured in Daltons 1 Proton – 1.009 Daltons 1 Neutron – 1.007 Daltons 1 Electron – 1/1840 of a dalton - negligible Isotopes:  Isotopes Isotopes - Atoms of an element that possess a different number of neutrons.Have the same atomic # b/c # of protons stays the same Radioactive isotopes - Spontaneously decay into elements of lower atomic number. emit energy and/or subatomic particles Half-life refers to the amount of time necessary to decay half the atoms of a given sample. Electrons:  Electrons Atoms with the same number of protons as electrons are electrically neutral. Ions - Atoms in which the number of protons and electrons differ. Cation - Contains more protons than electrons, and carries a positive charge. Anion - Contains fewer protons than electrons, and carries a negative charge. Electrons and Atomic Behavior:  Electrons and Atomic Behavior Orbital refers to the area around a nucleus where an electron is most likely found. Chemical behavior of an atom is determined by the number and arrangement of its orbitals. Electrons are attracted to the positively charged nucleus, thus it takes energy to hold electrons in place. potential energy of position Atomic Energy Levels (Orbitals):  Atomic Energy Levels (Orbitals) Electrons can absorb energy and release energy 8e 8e 2e Slide9:  Electrons of various atoms Elements? Electrons and Atomic Behavior:  Electrons and Atomic Behavior During some chemical reactions, electrons are transferred between atoms, while still retaining their energy of position. Oxidation - loss of an electron Reduction - gain of an electron Kinds of Atoms:  Kinds of Atoms Ninety-two naturally occurring elements Periodic table arranged by grouping atoms based on valence electrons (electrons in the outer energy levels). Octet rule Most atoms important to life can contain no more than 8 electrons Inert atoms have outer level filled. Reactive atoms do not have outer level filled. Periodic Table of the Elements:  Periodic Table of the Elements Elements in the Human Body:  Elements in the Human Body Table 2–1 Chemical Bonds:  Chemical Bonds A molecule refers to a group of atoms held together by energy in a stable association. O2 Compound is composed of two or more different types of atoms bond together. NaCl Atoms in a molecule are joined by chemical bonds. Chemical Bonds:  Chemical Bonds Ionic bonds are formed because ions of opposite charge attract one another. table salt Sodium Na+ Chlorine Cl- Slide16:  Covalent bonds are formed when two or more atoms share pairs of valence electrons. Strength depends on number of shared electrons. Share one = single bond, share two = double bond = share three = triple bond Hydrogen Bonding:  Hydrogen Bonding In a water molecule, both the oxygen and hydrogen atoms attract the shared electrons in the covalent bond (electronegativity). Oxygen atom is more electronegative than the hydrogen atoms. Chemical Reactions:  Chemical Reactions A chemical reaction occurs during the formation or breaking of chemical bonds. Chemical reactions can be influenced by: temperature concentration of reactants and products catalysts Energy:  Energy Energy: the power to do work Work: a change in mass or distance Forms of Energy Kinetic energy: energy of motion Potential energy: stored energy Chemical energy: potential energy stored in chemical bonds Break Down, Build Up:  Break Down, Build Up Decomposition reaction (catabolism): AB A + B Synthesis reaction (anabolism): A + B AB Exchange reaction (reversible): AB A + B Water In, Water Out Hydrolysis: A—B—C—D—E + H2O A—B—C—H + HO—D—E Dehydration synthesis (condensation): A—B—C—H + HO—D—E A—B—C—D—E + H2O How do enzymes control metabolism?:  How do enzymes control metabolism? Activation Energy Chemical reactions in cells cannot start without help Activation energy gets a reaction started Materials in Reactions Reactants: materials going into a reaction Products: materials coming out of a reaction Enzymes: proteins that lower the activation energy of a reaction Energy In, Energy Out:  Energy In, Energy Out Exergonic reactions: produce more energy than they use Endergonic reactions: use more energy than they produce What is the difference between organic and inorganic compounds?:  What is the difference between organic and inorganic compounds? Organic and Inorganic Molecules Organic: molecules based on carbon and hydrogen Inorganic: molecules not based on carbon and hydrogen Essential Molecules Nutrients: essential molecules obtained from food Metabolites: molecules made or broken down in the body Why is water so important to life?:  Why is water so important to life? Properties of Water Solubility: water’s ability to dissolve a solute in a solvent to make a solution Reactivity: most body chemistry uses or occurs in water High heat capacity: water’s ability to absorb and retain heat Lubrication: to moisten and reduce friction KEY CONCEPT:  KEY CONCEPT Most of our body weight is water Water is the key structural and functional component of cells and their control mechanisms, the nucleic acids Aqueous Solutions:  Aqueous Solutions Figure 2–8 Polar water molecules form hydration spheres around ions and small polar molecules to keep them in solution Electrolytes:  Electrolytes Inorganic ions which conduct electricity in solution Electrolyte imbalance seriously disturbs vital body functions Molecules and Water:  Molecules and Water Hydrophilic: hydro = water, philos = loving reacts with water Hydrophobic: phobos = fear does not react with water Solutions Colloid: a solution of very large organic molecules Suspension: a solution in which particles settle (sediment) Concentration: the amount of solute in a solvent (mol/L, mg/mL) What is pH and why do we need buffers?:  What is pH and why do we need buffers? pH: the concentration of hydrogen ions (H+) in a solution Neutral pH: a balance of H+ and OH— pure water = 7.0 Acids and Bases Acid (acidic): pH lower than 7.0 high H+ concentration, low OH— concentration Base (basic): pH higher than 7.0 low H+ concentration, high OH— concentration pH Scale:  pH Scale Figure 2–9 Has an inverse relationship with H+ concentration: more H+ ions mean lower pH, less H+ ions mean higher pH pH of body fluids measures free H+ ions in solution Excess H+ ions (low pH): damages cells and tissues alters proteins interferes with normal physiological functions Excess OH— ions (high pH) also cause problems, but rarely Acid and Alkaline:  Acid and Alkaline Acidosis: excess H+ in body fluid (low pH) Alkalosis: excess OH— in body fluid (high pH) Controlling pH Salts: positive or negative ions in solution contain no H+ or OH— (NaCl) Buffers: weak acid/salt compounds neutralizes either strong acid or strong base Slide32:  What kinds of organic compounds are there, and how do they work? Slide33:  Functional Groups Molecular groups which allow molecules to interact with other molecules Carbohydrate Functions:  Carbohydrate Functions Table 2–5 Monosaccharides: simple sugars with 3 to 7 carbon atoms (glucose) Disaccharides: 2 simple sugars condensed by dehydration synthesis (sucrose) Polysaccharides: Chains of many simple sugars (glycogen) Carbohydrates are quick energy sources and components of membranes Lipids:  Lipids Mainly hydrophobic molecules such as fats, oils, and waxes Made mostly of carbon and hydrogen atoms Lipids have many functions, including membrane structure and energy storage Classes of Lipids Slide36:  Fatty acids may be: saturated with hydrogen (no covalent bonds) unsaturated (1 or more double bonds) Types of Eicosanoids Leukotrienes: active in immune system Prostaglandins: local hormones, short-chain fatty acids Slide37:  Figure 2–15 Glycerides: are the fatty acids attached to a glycerol molecule Triglyceride: are the 3 fatty-acid tails, fat storage molecule Steroids Cholesterol: component of cell membranes Estrogens and testosterone: sex hormones Corticosteroids and calcitrol: metabolic regulation Bile salts: derived from steroids Slide38:  Phospholipids and Glycolipids Have hydrophilic heads and hydrophobic tails Are structural lipids, components of cell membranes Protein Structure:  Protein Structure Proteins are the most abundant and important organic molecules Basic elements: carbon (C), hydrogen (H), oxygen (O), and nitrogen (N) Basic building blocks: 20 amino acids Protein Functions 7 major protein functions: support: structural proteins movement: contractile proteins transport: transport proteins buffering: regulation of pH metabolic regulation: enzymes coordination and control: hormones defense: antibodies Amino Acid Structure:  Amino Acid Structure central carbon hydrogen amino group (—NH2) carboxylic acid group (—COOH) variable side chain or R group Peptide Bond:  Peptide Bond A dehydration synthesis between: the amino group of 1 amino acid and the carboxylic acid group of another amino acid producing a peptide Primary Structure:  Figure 2–20a Primary Structure Polypeptide: a long chain of amino acids Secondary Structure Hydrogen bonds form spirals or pleats Tertiary Structure:  Figure 2–20c Tertiary Structure Secondary structure folds into a unique shape Quaternary Structure Final protein shape: several tertiary structures together Shape and Function:  Shape and Function Protein function is based on shape Shape is based on sequence of amino acids Denaturation: loss of shape and function due to heat or pH Protein Shapes Fibrous proteins: structural sheets or strands Globular proteins: soluble spheres with active functions Enzymes:  Enzymes Enzymes are catalysts: proteins that lower the activation energy of a chemical reaction are not changed or used up in the reaction How Enzymes Work Substrates: reactants in enzymatic reactions Active site: a location on an enzyme that fits a particular substrate Enzyme Helpers:  Enzyme Helpers Cofactor: an ion or molecule that binds to an enzyme before substrates can bind Coenzyme: nonprotein organic cofactors (vitamins) Isozymes: 2 enzymes that can catalyze the same reaction Enzyme Characteristics Specificity: one enzyme catalyzes one reaction Saturation limits: an enzyme’s maximum work rate Regulation: the ability to turn off and on Nucleic Acids:  Nucleic Acids Large organic molecules, found in the nucleus, which store and process information at the molecular level DNA and RNA Deoxyribonucleic Acid (DNA) Determines inherited characteristics Directs protein synthesis Controls enzyme production Controls metabolism Ribonucleic Acid (RNA) Codes intermediate steps in protein synthesis Complementary Bases:  Complementary Bases Complementary base pairs: purines pair with pyrimidines: DNA: adenine (A) and thymine (T) and cytosine (C) and guanine (G) RNA: uracil (U) replaces thymine (T) The Bases Nucleotides:  Nucleotides Are the building blocks of DNA Have 3 molecular parts: sugar (deoxyribose) phosphate group nitrogenous base (A, G, T, C) High Energy Compounds - ADP and ATP:  High Energy Compounds - ADP and ATP adenosine diphosphate (ADP): 2 phosphate groups adenosine triphosphate (ATP): 3 phosphate groups Phosphorylation • Adding a phosphate group to ADP with a high-energy bond to form the high-energy compound ATP ATPase: the enzyme that catalyzes phophorylation

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