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Chapter 2: An Introduction to the Chemical Level of Organization Chemistry
o Is the science of changeo Topics of this chapter include:
The structure of atoms The basic chemical building blocks How atoms combine to form increasingly complex structures
2-1 Atoms and Atomic Structure Matter
o Is made up of atoms Atoms join together to form chemicals with different characteristics Chemical characteristics determine physiology at the molecular and
cellular levels
2-1 Atoms and Atomic Structure Subatomic Particles
o Proton Positive charge, 1 mass unit
o Neutron Neutral, 1 mass unit
o Electron Negative charge, low mass
2-1 Atoms and Atomic Structure Atomic Structure
o Atomic number Number of protons
o Nucleus Contains protons and neutrons
o Electron cloud Contains electrons
2-1 Atoms and Atomic Structure Elements and Isotopes
o Elements are determined by the atomic number of an atom Remember, atomic number = number of protons Elements are the most basic chemicals
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2-1 Atoms and Atomic Structure Elements and Isotopes
o Isotopes are the specific version of an element based on its mass number Mass number = number of protons plus the number of neutrons Only neutrons are different because the number of protons determines
the element
2-1 Atoms and Atomic Structure Atomic Weight
o Exact mass of all particles Measured in moles
o Average of the mass numbers of the isotopes
2-1 Atoms and Atomic Structure Electrons and Energy Levels
o Electrons in the electron cloud determine the reactivity of an atomo The electron cloud contains shells, or energy levels, that hold a maximum
number of electrons Lower shells fill first Outermost shell is the valence shell, and it determines bonding The number of electrons per shell corresponds to the number of atoms
in that row of the periodic table
2-2 Molecules and Compounds Chemical Bonds
o Involve the sharing, gaining, and losing of electrons in the valence shello Three major types of chemical bonds
1. Ionic bonds o Attraction between cations (electron donor) and anions
(electron acceptor)2. Covalent bonds
Strong electron bonds involving shared electrons3. Hydrogen bonds
Weak polar bonds based on partial electrical attractions
2-2 Molecules and Compounds Chemical Bonds
o Form molecules and/or compounds Molecules
Two or more atoms joined by strong bonds Compounds
Two or more atoms OF DIFFERENT ELEMENTS
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joined by strong or weak bonds Compounds are all molecules, but not all molecules are compounds
H2 = molecule only H2O = molecule and compound
2-2 Molecules and Compounds Ionic Bonds
o One atom—the electron donor—loses one or more electrons and becomes a cation, with a positive charge
o Another atom—the electron acceptor—gains those same electrons and becomes an anion, with a negative charge
o Attraction between the opposite charges then draws the two ions together
2-2 Molecules and Compounds Covalent Bonds
o Involve the sharing of pairs of electrons between atoms One electron is donated by each atom to make the pair of electrons Sharing one pair of electrons is a single covalent bond Sharing two pairs of electrons is a double covalent bond Sharing three pairs of electrons is a triple covalent bond
2-2 Molecules and Compounds Covalent Bonds
o Nonpolar covalent bonds Involve equal sharing of electrons because atoms involved in the bond
have equal pull for the electronso Polar covalent bonds
Involve the unequal sharing of electrons because one of the atoms involved in the bond has a disproportionately strong pull on the electrons
Form polar molecules — like water
2-2 Molecules and Compounds Hydrogen Bonds
o Bonds between adjacent molecules, not atomso Involve slightly positive and slightly negative portions of polar molecules being
attracted to one anothero Hydrogen bonds between H2O molecules cause surface tension
2-2 Molecules and Compounds States of Matter
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o Solid Constant volume and shape
o Liquid Constant volume but changes shape
o Gas Changes volume and shape
2-3 Chemical Reactions In a Chemical Reaction
o Either new bonds are formed or existing bonds are broken Reactants
Materials going into a reaction Products
Materials coming out of a reaction Metabolism
All of the reactions that are occurring at one time
2-3 Chemical Reactions Basic Energy Concepts
o Energy The power to do work
o Work A change in mass or distance
o Kinetic energy Energy of motion
o Potential energy Stored energy
o Chemical energy Potential energy stored in chemical bonds
2-3 Chemical Reactions Types of Chemical Reactions
o Decomposition reaction (catabolism)o Synthesis reaction (anabolism) o Exchange reactiono Reversible reaction
2-3 Chemical Reactions Decomposition Reaction (Catabolism)
o Breaks chemical bonds o AB A + Bo Hydrolysis A-B + H2O A-H + HO-B
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Synthesis Reaction (Anabolism) o Forms chemical bondso A + B ABo Dehydration synthesis (condensation reaction)
A-H + HO-B A-B + H2O
2-3 Chemical Reactions Exchange Reaction
o Involves decomposition first, then synthesiso AB + CD AD + CB
2-3 Chemical Reactions Reversible Reaction
o A + B ↔ AB o At equilibrium the amounts of chemicals do not change even though the
reactions are still occurring Reversible reactions seek equilibrium, balancing opposing reaction
rates Add or remove reactants
Reaction rates adjust to reach a new equilibrium
2-4 Enzymes Chemical Reactions
o In cells, cannot start without help Activation energy is the amount of energy needed to get a reaction
started Enzymes are protein catalysts that lower the activation energy of
reactions
2-4 Enzymes Exergonic (Exothermic) Reactions
o Produce more energy than they use Endergonic (Endothermic) Reactions
o Use more energy than they produce
2-5 Inorganic and Organic Compounds Nutrients
o Essential molecules obtained from food Metabolites
o Molecules made or broken down in the body Inorganic Compounds
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o Molecules not based on carbon and hydrogeno Carbon dioxide, oxygen, water, and inorganic acids, bases, and salts
Organic Compoundso Molecules based on carbon and hydrogeno Carbohydrates, proteins, lipids, and nucleic acids
2-6 Properties of Water Water
o Accounts for up to two-thirds of your total body weighto A solution is a uniform mixture of two or more substances
It consists of a solvent, or medium, in which atoms, ions, or molecules of another substance, called a solute, are individually dispersed
2-6 Properties of Water Solubility
o Water’s ability to dissolve a solute in a solvent to make a solution Reactivity
o Most body chemistry occurs in water High Heat Capacity
o Water’s ability to absorb and retain heat Lubrication
o To moisten and reduce friction
2-6 Properties of Water The Properties of Aqueous Solutions
o Ions and polar compounds undergo ionization, or dissociation, in watero Polar water molecules form hydration spheres around ions and small polar
molecules to keep them in solution
2-6 Properties of Water The Properties of Aqueous Solutions
o Electrolytes and body fluids Electrolytes are inorganic ions that conduct electricity in solution Electrolyte imbalance seriously disturbs vital body functions
2-6 Properties of Water The Properties of Aqueous Solutions
o Hydrophilic and hydrophobic compounds Hydrophilic
hydro- = water, philos = loving Interacts with water
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Includes ions and polar molecules Hydrophobic
phobos = fear Does NOT interact with water Includes nonpolar molecules, fats, and oils
2-6 Properties of Water Colloids and Suspensions
o Colloid A solution of very large organic molecules For example, blood plasma
o Suspension A solution in which particles settle (sediment) For example, whole blood
o Concentration The amount of solute in a solvent (mol/L, mg/mL)
2-7 pH and Homeostasis pH
o The concentration of hydrogen ions (H+) in a solution Neutral pH
o A balance of H+ and OH
o Pure water = 7.0
2-7 pH and Homeostasis Acidic pH Lower Than 7.0
o High H+ concentrationo Low OH concentration
Basic (or alkaline) pH Higher Than 7.0o Low H+ concentrationo High OH concentration
pH of Human Blood o Ranges from 7.35 to 7.45
2-7 pH and Homeostasis pH Scale
o Has an inverse relationship with H+ concentration More H+ ions means lower pH, fewer H+ ions means higher pH
2-8 Inorganic Compounds Acid
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o A solute that adds hydrogen ions to a solutiono Proton donoro Strong acids dissociate completely in solution
Base o A solute that removes hydrogen ions from a solution o Proton acceptoro Strong bases dissociate completely in solution
Weak Acids and Weak Bases o Fail to dissociate completelyo Help to balance the pH
2-8 Inorganic Compounds Salts
o Solutes that dissociate into cations and anions other than hydrogen ions and hydroxide ions
2-8 Inorganic Compounds Buffers and pH Control
o Buffers Weak acid/salt compounds Neutralize either strong acid or strong base Sodium bicarbonate is very important in humans
o Antacids Basic compounds that neutralize acid and form a salt Alka-Seltzer, Tums, Rolaids, etc.
2-9 Carbohydrates Organic Molecules
o Contain H, C, and usually Oo Are covalently bondedo Contain functional groups that determine chemistry
Carbohydrates Lipids Proteins (or amino acids) Nucleic acids
2-9 Carbohydrates Carbohydrates
o Contain carbon, hydrogen, and oxygen in a 1:2:1 ratio Monosaccharide — simple sugar Disaccharide — two sugars Polysaccharide — many sugars
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2-9 Carbohydrates Monosaccharides
o Simple sugars with 3 to 7 carbon atomso Glucose, fructose, galactose
Disaccharides o Two simple sugars condensed by dehydration synthesis o Sucrose, maltose
Polysaccharideso Many monosaccharides condensed by dehydration synthesiso Glycogen, starch, cellulose
2-10 Lipids Lipids
o Mainly hydrophobic molecules such as fats, oils, and waxeso Made mostly of carbon and hydrogen atomso Include:
Fatty acids Eicosanoids Glycerides Steroids Phospholipids and glycolipids
2-10 Lipids Fatty Acids
o Long chains of carbon and hydrogen with a carboxyl group (COOH) at one end
o Are relatively nonpolar, except the carboxyl groupo Fatty acids may be:
Saturated with hydrogen (no covalent bonds) Unsaturated (one or more double bonds)
Monounsaturated = one double bond Polyunsaturated = two or more double bonds
2-10 Lipids Eicosanoids
o Derived from the fatty acid called arachidonic acido Leukotrienes
Active in immune system o Prostaglandins
Local hormones, short-chain fatty acids
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2-10 Lipids Glycerides
o Fatty acids attached to a glycerol moleculeo Triglycerides are the three fatty-acid tails
Also called triacylglycerols or neutral fats Have three important functions
1. Energy source2. Insulation3. Protection
2-10 Lipids Steroids
o Four rings of carbon and hydrogen with an assortment of functional groupso Types of steroids
Cholesterol Component of plasma (cell) membranes
Estrogens and testosterone Sex hormones
Corticosteroids and calcitriol Metabolic regulation
Bile salts Derived from steroids
2-10 Lipids Phospholipids and Glycolipids
o Diglycerides attached to either a phosphate group (phospholipid) or a sugar (glycolipid)
o Generally, both have hydrophilic heads and hydrophobic tails and are structural lipids, components of plasma (cell) membranes
2-11 Proteins Proteins
o Are the most abundant and important organic moleculeso Contain basic elements
Carbon (C), hydrogen (H), oxygen (O), and nitrogen (N) o Basic building blocks
20 amino acids
2-11 Proteins Seven Major Protein Functions
1. Support Structural proteins
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2. Movement Contractile proteins
3. Transport Transport (carrier) proteins
4. Buffering Regulation of pH
5. Metabolic Regulation Enzymes
6. Coordination and Control Hormones
7. Defense Antibodies
2-11 Proteins Protein Structure
o Long chains of amino acidso Five components of amino acid structure
1. Central carbon atom2. Hydrogen atom3. Amino group (—NH2)4. Carboxyl group (—COOH)5. Variable side chain or R group
2-11 Proteins Hooking Amino Acids Together
o Requires a dehydration synthesis between: The amino group of one amino acid and the carboxyl group of another
amino acid Forms a peptide bond
Resulting molecule is a peptide
2-11 Proteins Protein Shape
o Primary structure The sequence of amino acids along a polypeptide
o Secondary structure Hydrogen bonds form spirals or pleats
o Tertiary structure Secondary structure folds into a unique shape
o Quaternary structure Final protein shape — several tertiary structures together
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2-11 Proteins Fibrous Proteins
o Structural sheets or strands Globular Proteins
o Soluble spheres with active functions o Protein function is based on shape
Shape is based on sequence of amino acids
2-11 Proteins Enzyme Function
o Enzymes are catalysts Proteins that lower the activation energy of a chemical reaction Are not changed or used up in the reaction Enzymes also exhibit:
1. Specificity — will only work on limited types of substrates2. Saturation Limits — by their concentration3. Regulation — by other cellular chemicals
Chapter 3: An Introduction to Cells Sex Cells (Germ Cells)
o Reproductive cells o Male spermo Female oocyte (a cell that develops into an egg)
Somatic Cells o Soma = bodyo All body cells except sex cells
3-1 Plasma Membrane Extracellular Fluid (Interstitial Fluid)
o A watery medium that surrounds a cello Plasma membrane (cell membrane) separates cytoplasm from the
extracellular fluid o Cytoplasm
Cytosol = liquid Intracellular structures collectively known as organelles
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3-1 Plasma Membrane Functions of the Plasma Membrane
o Physical Isolation Barrier
o Regulation of Exchange with the Environment Ions and nutrients enter Wastes eliminated and cellular products released
3-1 Plasma Membrane Functions of the Plasma Membrane
o Sensitivity to the Environment Extracellular fluid composition Chemical signals
o Structural Support Anchors cells and tissues
3-1 Plasma Membrane Membrane Lipids
o Phospholipid bilayer Hydrophilic heads — toward watery environment, both sides Hydrophobic fatty-acid tails — inside membrane Barrier to ions and water — soluble compounds
3-1 Plasma Membrane Membrane Proteins
o Integral proteins Within the membrane
o Peripheral proteins Bound to inner or outer surface of the membrane
3-1 Plasma Membrane Membrane Proteins
o Anchoring proteins (stabilizers) Attach to inside or outside structures
o Recognition proteins (identifiers) Label cells as normal or abnormal
o Enzymes Catalyze reactions
3-1 Plasma Membrane Membrane Proteins
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o Receptor proteins Bind and respond to ligands (ions, hormones)
o Carrier proteins Transport specific solutes through membrane
o Channels Regulate water flow and solutes through membrane
3-1 Plasma Membrane Membrane Carbohydrates
o Proteoglycans, glycoproteins, and glycolipids Extend outside cell membrane Form sticky “sugar coat” (glycocalyx)
o Functions of the glycocalyx Lubrication and Protection Anchoring and Locomotion Specificity in Binding (receptors) Recognition (immune response)
3-2 Organelles and the Cytoplasm Cytoplasm
o All materials inside the cell and outside the nucleus Cytosol (intracellular fluid)
o Dissolved materials Nutrients, ions, proteins, and waste products
o High potassium/low sodiumo High proteino High carbohydrate/low amino acid and fat
Organelles o Structures with specific functions
3-2 Organelles and the Cytoplasm The Organelles
o Nonmembranous organelles No membrane Direct contact with cytosol Include the cytoskeleton, microvilli, centrioles, cilia, ribosomes, and
proteasomeso Membranous organelles
Covered with plasma membrane Isolated from cytosol Include the endoplasmic reticulum (ER), the Golgi apparatus,
lysosomes, peroxisomes, and mitochondria
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3-2 Organelles and the Cytoplasm Nonmembranous Organelles
o Six types of nonmembranous organelles1. Cytoskeleton 2. Microvilli 3. Centrioles 4. Cilia 5. Ribosomes 6. Proteasomes
3-2 Organelles and the Cytoplasm The Cytoskeleton
o Structural proteins for shape and strength Microfilaments Intermediate filaments Microtubules
3-2 Organelles and the Cytoplasm The Cytoskeleton
o Microfilaments — thin filaments composed of the protein actin Provide additional mechanical strength Interact with proteins for consistency Pair with thick filaments of myosin for muscle movement
3-2 Organelles and the Cytoplasm The Cytoskeleton
o Intermediate filaments — mid-sized between microfilaments and thick filaments
Durable (collagen) Strengthen cell and maintain shape Stabilize organelles Stabilize cell position
3-2 Organelles and the Cytoplasm The Cytoskeleton
o Microtubules — large, hollow tubes of tubulin protein Attach to centrosome Strengthen cell and anchor organelles Change cell shape Move vesicles within cell (kinesin and dynein) Form spindle apparatus
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3-2 Organelles and the Cytoplasm The Cytoskeleton
o Thick filaments Myosin protein in muscle cells
3-2 Organelles and the Cytoplasm Microvilli
o Increase surface area for absorptiono Attach to cytoskeleton
Centrioles in the Centrosomeo Centrioles form spindle apparatus during cell divisiono Centrosome: cytoplasm surrounding centriole
Ciliao Small hairlike extensions
Cilia move fluids across the cell surface
3-2 Organelles and the Cytoplasm Ribosomes
o Build polypeptides in protein synthesiso Two types
1. Free ribosomes in cytoplasmo Manufacture proteins for cell
2. Fixed ribosomes attached to ERo Manufacture proteins for secretion
Proteasomeso Contain enzymes (proteases)o Disassemble damaged proteins for recycling
3-2 Organelles and the Cytoplasm Membranous Organelles
o Five types of membranous organelles1. Endoplasmic reticulum (ER)2. Golgi apparatus3. Lysosomes4. Peroxisomes5. Mitochondria
3-2 Organelles and the Cytoplasm Endoplasmic Reticulum (ER)
o Endo- = within, plasm = cytoplasm, reticulum = networko Cisternae are storage chambers within membranes
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o Functions1. Synthesis of proteins, carbohydrates, and lipids2. Storage of synthesized molecules and materials3. Transport of materials within the ER4. Detoxification of drugs or toxins
3-2 Organelles and the Cytoplasm Endoplasmic Reticulum (ER)
o Smooth endoplasmic reticulum (SER) No ribosomes attached Synthesizes lipids and carbohydrates
o Phospholipids and cholesterol (membranes)o Steroid hormones (reproductive system)o Glycerides (storage in liver and fat cells)o Glycogen (storage in muscles)
3-2 Organelles and the Cytoplasm Endoplasmic Reticulum (ER)
o Rough endoplasmic reticulum (RER) Surface covered with ribosomes
o Active in protein and glycoprotein synthesiso Folds polypeptide protein structureso Encloses products in transport vesicles
3-2 Organelles and the Cytoplasm Golgi Apparatus
o Vesicles enter forming face and exit maturing faceo Functions
1. Modifies and packages secretionso Hormones or enzymeso Released through exocytosis
2. Renews or modifies the plasma membrane3. Packages special enzymes within vesicles for use in the cytoplasm
3-2 Organelles and the Cytoplasm Lysosomes
o Powerful enzyme-containing vesicles Lyso- = dissolve, soma = body
o Primary lysosome Formed by Golgi apparatus and inactive enzymes
o Secondary lysosome Lysosome fused with damaged organelle
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Digestive enzymes activated Toxic chemicals isolated
3-2 Organelles and the Cytoplasm Lysosomes
o Functions1. Clean up inside cells2. Autolysis
3-2 Organelles and the Cytoplasm Clean Up Inside Cells
o Break down large moleculeso Attack bacteriao Recycle damaged organelleso Eject wastes by exocytosis
3-2 Organelles and the Cytoplasm Autolysis
o Auto- = self, lysis = breako Self-destruction of damaged cells
Lysosome membranes break down Digestive enzymes released Cell decomposes Cellular materials recycle
3-2 Organelles and the Cytoplasm Peroxisomes
o Are enzyme-containing vesicles Break down fatty acids, organic compounds Produce hydrogen peroxide (H2O2) Replicate by division
3-2 Organelles and the Cytoplasm Membrane Flow
o A continuous exchange of membrane parts by vesicles All membranous organelles (except mitochondria) Allows adaptation and change
3-2 Organelles and the Cytoplasm Mitochondria
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o Have smooth outer membrane and inner membrane with numerous folds (cristae)
o Matrix Fluid around cristae
o Mitochondrion takes chemical energy from food (glucose) Produces energy molecule ATP
3-2 Organelles and the Cytoplasm Mitochondrial Energy Production
o Glycolysis Glucose to pyruvic acid (in cytosol)
o Citric acid cycle (also known as the Krebs cycle and the tricarboxylic acid cycle, or TCA cycle)
Pyruvic acid to CO2 (in matrix)o Electron transport chain
Inner mitochondrial membrane
3-2 Organelles and the Cytoplasm Mitochondrial Energy Production
o Called aerobic metabolism (cellular respiration) Mitochondria use oxygen to break down food and produce ATP Glucose + oxygen + ADP carbon dioxide + water + ATP
3-3 Cell Nucleus Nucleus
o Largest organelleo The cell’s control centero Nuclear envelope
Double membrane around the nucleus o Perinuclear space
Between the two layers of the nuclear envelope o Nuclear pores
Communication passages
3-3 Cell Nucleus Contents of the Nucleus
o DNA All information to build and run organisms
o Nucleoplasm Fluid containing ions, enzymes, nucleotides, and some RNA
o Nuclear matrix Support filaments
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3-3 Cell Nucleus Contents of the Nucleus
o Nucleoli Are related to protein production Are made of RNA, enzymes, and histones Synthesize rRNA and ribosomal subunits
o Nucleosomes DNA coiled around histones
3-3 Cell Nucleus Contents of the Nucleus
o Chromatin Loosely coiled DNA (cells not dividing)
o Chromosomes Tightly coiled DNA (cells dividing)
3-3 Cell Nucleus Information Storage in the Nucleus
o DNA Instructions for every protein in the body
o Gene DNA instructions for one protein
o Genetic code The chemical language of DNA instructions
o Sequence of bases (A, T, C, G) Triplet code
o 3 bases = 1 amino acid
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