Chemistry Comes Alive

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Chemistry Comes Alive
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The Chemistry of Life

• Atoms, Ions and Molecules
• Water and Mixtures
• Energy and Chemical Reactions
• Organic compounds

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Matter

• The stuff of the universe
• Anything that has mass and takes up space
• States of matter
• Solid has definite shape and volume
• Liquid has definite volume, changeable shape
• Gas has changeable shape and volume

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The Chemical Elements

• Element
• simplest form of matter with unique chemical
  properties
• Each element has unique physical and chemical
  properties
• Physical properties those detected with our
  senses
• Chemical properties pertain to the way atoms
  interact with one another

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Major Elements of the Human Body

• 98.5 of body weight consists of
• Oxygen (O)
• Carbon (C)
• Hydrogen (H)
• Nitrogen (N)

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Lesser and Trace Elements of the Human Body

• Lesser elements make up 3.9 of the body and
  include
• Calcium (Ca), phosphorus (P), potassium (K),
  sulfur (S), sodium (Na), chlorine (Cl), magnesium
  (Mg), iodine (I), and iron (Fe)
• Trace elements make up less than 0.01 of the
  body
• They are required in minute amounts, and are
  found as part of enzymes

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Periodic Table of the Elements

• Atomic number of each element
• number of protons in its nucleus
• Periodic table
• letter symbols of elements arranged by atomic
  number

http//pearl1.lanl.gov/periodic/default.htm
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Atomic Structure

• Nucleus - center of atom contains
• protons positive charge, mass of 1 amu
• neutrons neutral charge, mass of 1 amu
• atomic mass total of protons neutrons
• Electron shells
• electrons negative charge
• of electrons of protons, atoms have neutral
  charge
• electrons further from nucleus have higher energy
• valence electrons are in the outermost shell
• interact with other atoms
• determine chemical behavior
• octet rule - atoms react to obtain a stable
  number of 8 valence electrons

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Bohr Planetary Model of an Atom
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Models of Some Elements
p represents protons, no represents neutrons
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Isotopes and Radioactivity

• Isotopes
• elements that differ in the number of neutrons
• 1H, 2H, 3H
• extra neutrons result in increased atomic weight
• heavy water
• have no change in chemical behavior
• same valence electrons
• Atomic weight
• Average atomic mass of the mixture of isotopes of
  an element found in a sample

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Isotopes of Hydrogen

• radioisotopes decay to stable isotopes releasing
  radiation

• radioisotopes decay to stable isotopes releasing
  radiation

Figure 2.3
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Radioisotopes and Radioactivity

• Isotopes
• same chemical behavior, differ in physical
  behavior
• Radioisotopes
• unstable isotopes
• Radioactivity
• radioisotopes decay to stable isotopes releasing
  radiation

Marie Curie
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Ionizing Radiation

• High energy
• Ejects electrons from atoms
• Destroys molecules and produces free radicals
• sources include
• UV light, X rays, nuclear decay (?, ?, ?)
• ? particle -
• 2 protons 2 neutrons cant penetrate skin
• ? particle -
• free electron - penetrates skin a few millimeters
• ? particle -
• high energy, penetrating very dangerous

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Ionizing Radiation 2

• Physical half-life
• time for 50 of atoms to decay
• 90Sr - 28 yr.
• 40K - 1.3 billion years
• Biological half-life
• time for 50 of atoms to disappear from the body
• function of decay and physiological clearance
• Cesium 137 - physical half-life -- 30 years
  - biological half-life -- 17 days
• Radiation exposure
• background radiation
• radon gas from decay of uranium in granite
• cosmic rays

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Molecules and Chemical Bonds

• Molecules
• two or more atoms of same element covalently
  bonded
• Compounds
• two or more atoms of different elements
  covalently bonded
• Molecular formula
• itemizes each element present and its quantity
• Structural formula
• shows arrangement of atoms
• needed to show structural isomers

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Concentration of Solutions

• Percent, or parts per 100 parts
• Molarity, or moles per liter (M)
• Mole Avagadros number of molecules
• 6.02 X 1023
• A mole of an element or compound is equal to its
  atomic or molecular weight (sum of atomic
  weights) in grams

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Types of Chemical Bonds

• Ionic
• Covalent
• Hydrogen

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Chemical Bonds

• Electron shells, or energy levels, surround the
  nucleus of an atom
• Bonds are formed using the electrons in the
  outermost energy level
• Valence shell outermost energy level containing
  chemically active electrons
• Octet rule except for the first shell which is
  full with two electrons, atoms interact in a
  manner to have eight electrons in their valence
  shell

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Chemically Inert Elements

• Inert elements have their outermost energy level
  fully occupied by electrons

Figure 2.4a
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Chemically Reactive Elements

• Reactive elements do not have their outermost
  energy level fully occupied by electrons

Figure 2.4b
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Ions

• Ions - carry a charge, unequal numbers of
  protons and electrons

• Ionization - transfer of electrons from one atom
  to another (? stability of valence shell)

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Anions and Cations

• Anion - atom gained electron, net negative charge
• Cation - atom lost an electron, net positive
  charge

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Ionic Bonds

• Attraction of oppositely charged ions to each
  other forms an ionic bond - no sharing of
  electrons
• Ionic bonds are weak and dissociate in water
• These compounds tend to form crystals...

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Formation of an Ionic Bond
Figure 2.5a
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Covalent Bonds

• Formed by sharing valence electrons
• Types of covalent bonds
• single covalent bond
• double covalent bond
• Triple covalent bond

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Polar and Nonpolar Molecules

• Electrons shared equally between atoms produce
  nonpolar molecules
• Unequal sharing of electrons produces polar
  molecules
• Atoms with six or seven valence shell electrons
  are electronegative
• Atoms with one or two valence shell electrons are
  electropositive

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Comparison of Ionic, Polar Covalent, and Nonpolar
Covalent Bonds
Figure 2.8
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Hydrogen Bonds

• Weakest of the bonds
• Attraction between polar molecules no sharing
  of electrons
• Greatest physiological importance
• properties of water
• shapes of complex molecules
• proteins, DNA

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Hydrogen Bonding in Water
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The Chemistry of Life

• Atoms, Ions and Molecules
• Water and Mixtures
• Energy and Chemical Reactions
• Organic compounds

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Adhesion and Cohesion

• Adhesion - attraction between one substance and
  another substance
• Cohesion - attraction between one substance and
  itself
• water is very cohesive due to hydrogen bonds
• Surface tension
• elastic surface film caused by the attraction of
  molecules at the surface from those below

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Thermal Stability of Water

• Heat capacity amount of heat required to raise
  the temperature of 1g of a substance by 1C
• Calorie amount of heat required to raise the
  temperature of 1g of water by 1C
• Water stabilizes internal temperature of the body
• high heat capacity
• its hydrogen bonds inhibit increased temperature
  (molecular motion) caused by increased heat
• effective coolant
• 1 ml of perspiration removes 500 calories from
  the body

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Properties of Water

• Reactivity is an important part of hydrolysis
  and dehydration synthesis reactions
• Cushioning resilient cushion around certain
  body organs

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Mixtures and Solutions

• Mixtures two or more components physically
  intermixed (not chemically bonded)
• Solutions homogeneous mixtures of components
• Solvent substance present in greatest amount
• Solute substance(s) present in smaller amounts

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Solvency

• Solvency - ability to dissolve matter
• Hydrophilic - charged substances that dissolve
  easily in water
• Hydrophobic - neutral substances that do not
  easily dissolve in water
• Water is the universal solvent, important for
  metabolic reactions and transport of substances

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Water as a Solvent

• Water molecules overpower the ionic bond above
  between NaCl- by forming hydration spheres.
• Note orientation of water molecules negative
  pole faces Na, positive pole faces Cl-

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Mixtures

• Substances that are physically blended but not
  chemically combined
• Solutions
• Colloids
• Suspensions

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Solutions

• Solute lt 1nm
• pass through membranes
• Transparent
• e.g. copper sulfate solution

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Colloids

• Particles 1 to 100nm
• to large to pass through membranes
• Cloudy
• e.g. milk protein

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Suspensions

• Particles gt100nm
• Cloudy or opaque
• Separate on standing
• e.g. blood cells

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Measures of Concentration

• Weight per Volume
• weight of solute in a given volume of solution
• e.g. IV saline contains 8.5 g/L NaCl
• Percentages
• weight or volume of solute in solution
• e.g. IV D5W (5 w/v dextrose in distilled water)
• 5 grams of dextrose in add 100ml water
• Molarity
• number of moles of solute/liter in solution
• physiologic effects of a chemical based on the
  number of molecules in solution

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Salts

• Inorganic compounds
• Contain cations other than H and anions other
  than OH
• Are electrolytes they conduct electrical currents

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Acids and Bases

• Acids release H and are therefore proton donors
• HCl ? H Cl
• Bases release OH and are proton acceptors
• NaOH ? Na OH

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Acid-Base Concentration (pH)

• Acidic solutions have higher H concentration and
  therefore a lower pH
• Alkaline solutions have lower H concentration
  and therefore a higher pH
• Neutral solutions have equal H and OH
  concentrations

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pH

• pH - based on the molarity of H on a logarithmic
  scale
• pH -log H
• for molarity of H 100,10-1,10-2,etc.
• pH - log 100 0, - log 10-1 1, etc.
• a change of one number on the pH scale therefore
  represents a 10 fold change in H concentration
• Our body uses buffers to resist any change in pH

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pH Scale
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Buffers

• Systems that resist abrupt and large swings in
  the pH of body fluids
• Carbonic acid-bicarbonate system
• Carbonic acid dissociates, reversibly releasing
  bicarbonate ions and protons
• The chemical equilibrium between carbonic acid
  and bicarbonate resists pH changes in the blood

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The Chemistry of Life

• Atoms, Ions and Molecules
• Water and Mixtures
• Energy and Chemical Reactions
• Organic compounds

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Work and Energy

• Energy - the capacity to do work
• Kinetic energy - energy of motion
• Potential energy- inherent energy due to an
  objects position or internal state
• Chemical energy - potential energy stored in the
  molecular bonds
• Electromagnetic energy - kinetic energy of
  photons
• light, infrared, UV, X rays ? rays

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Chemical Reactions

• Occur when chemical bonds are formed, rearranged,
  or broken
• Are written in symbolic form using chemical
  equations
• Chemical equations contain
• Number and type of reacting substances, and
  products produced
• Relative amounts of reactants and products

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Examples of Chemical Reactions
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Patterns of Chemical Reactions

• Combination reactions Synthesis reactions which
  always involve bond formation
• A B ? AB
• Decomposition reactions Molecules are broken
  down into smaller molecules
• AB ? A B
• Exchange reactions Bonds are both made and
  broken
• AB C ? AC B

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Energy Flow in Chemical Reactions

• Exergonic reactions reactions that release
  energy
• Endergonic reactions reactions whose products
  contain more potential energy than did its
  reactants

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Metabolism

• All the chemical reactions of the body
• Catabolism
• energy releasing (exergonic) decomposition
  reactions
• Anabolism
• energy releasing (endergonic) synthesis reactions

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Reaction Rates

• Basis for chemical reactions is molecular motion
  and collisions
• Reaction Rates affected by
• concentration
• more concentrated, more collisions, faster rx
• temperature
• higher temperature, greater collision force,
  faster rx
• catalysts
• speed up reactions without permanent change to
  itself
• biological catalysts are enzymes

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Oxidation-Reduction (Redox) Reactions

• Reactants losing electrons are electron donors
  and are oxidized
• Reactants taking up electrons are electron
  acceptors and become reduced

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Energy Flow in Chemical Reactions

• Exergonic reactions reactions that release
  energy
• Endergonic reactions reactions whose products
  contain more potential energy than did its
  reactants

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The Chemistry of Life

• Atoms, Ions and Molecules
• Water and Mixtures
• Energy and Chemical Reactions
• Organic compounds

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Organic Compounds

• Molecules unique to living systems contain carbon
  and hence are organic compounds
• They include
• Carbohydrates
• Lipids
• Proteins
• Nucleic Acids

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Organic Molecules Carbon

• Bonds readily with other carbon atoms, hydrogen,
  oxygen, nitrogen, sulfur
• needs 4 more valence electrons
• Can form rings or long carbon chains that serve
  as the backbone for organic molecules

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Functional Groups

• Groups of atoms attach to carbon backbone
• Determine the properties of organic molecules

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Monomers and Polymers

• Monomers
• subunits of macromolecules
• DNA has 4 different monomers (nucleotides)
• proteins have 20 different monomers (amino acids)
• Polymers
• series of monomers bonded together
• Polymerization
• the bonding of monomers together to form a
  polymer
• caused by a reaction called dehydration synthesis

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Monomers and Polymers

• Monomers
• subunits of macromolecules
• DNA has 4 different monomers (nucleotides)
• proteins have 20 different monomers (amino acids)
• Polymers
• series of monomers bonded together
• Polymerization
• the bonding of monomers together to form a
  polymer
• caused by a reaction called dehydration synthesis

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Hydrolysis

• Splitting a polymer (lysis) by the addition of a
  water molecule (hydro)
• Digestion consists of hydrolysis reactions

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Carbohydrates

• Contain carbon, hydrogen, and oxygen
• Their major function is to supply a source of
  cellular food
• Examples
• Monosaccharides or simple sugars

Figure 2.13a
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Organic Molecules Carbohydrates

• Hydrophilic organic molecule
• General formula
• (CH2O)n , n number of carbon atoms
• for glucose, n 6, so formula is C6H12O6
• Names of carbohydrates
• word root sacchar- or the suffix -ose often used
• monosaccharide or glucose

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Monosaccharides

• Simplest carbohydrates
• General formula is C6H12O6
• structural isomers

• Three major monosaccharides
• glucose, galactose and fructose
• mainly produced by digestion of complex
  carbohydrates

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Disaccharides

• Pairs of monosaccharides
• Three major disaccharides
• sucrose
• glucose fructose
• lactose
• glucose galactose
• maltose
• glucose glucose

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Polysaccharides

• Starch, cellulose and glycogen
• long chains of glucose form these polysaccharides
• Starch produced by plants is digested by amylase
• Cellulose gives structure to plants, fiber to our
  diet

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Polysaccharides

• Glycogen is an energy storage polysaccharide
  produced by animals
• Liver cells synthesize glycogen after a meal to
  maintain blood glucose levels

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Carbohydrate Functions

• Source of energy
• Conjugated carbohydrates
• glycolipids
• external surface of cell membrane
• glycoproteins
• external surface of cell membrane
• mucus of respiratory and digestive tracts
• proteoglycans
• carbohydrate component dominant
• cell adhesion, gelatinous filler of tissues (eye)
  and lubricates joints

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Lipids

• Contain C, H, and O, but the proportion of oxygen
  in lipids is less than in carbohydrates
• Examples
• Neutral fats or triglycerides
• Phospholipids
• Steroids
• Eicosanoids

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Fatty Acids

• Chain of usually 4 to 24 carbon atoms

• Carboxyl (acid) group on one end and a methyl
  group on the other

• Polymers of two-carbon acetyl groups

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Fatty Acids

• Saturated fatty acid - carbon atoms saturated
  with hydrogen
• Unsaturated fatty acid - contains CC bonds that
  could bond more hydrogen

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Fatty Acids

• Saturated fatty acid - carbon atoms saturated
  with hydrogen
• Unsaturated fatty acid - contains CC bonds that
  could bond more hydrogen

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Triglyceride Synthesis (2)

• Triglycerides called neutral fats
• fatty acids bond with their carboxyl ends,
  therefore no longer acidic

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Triglycerides

• Hydrolysis of fats occurs by lipase enzyme
• Triglycerides at room temperature
• liquid called oils, often polyunsaturated fats
  from plants
• solid called fat, saturated fats from animals
• Function - energy storage
• also insulation and shock absorption for organs

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Phospholipids

• Amphiphilic character
• Hydrophobic tails similar to neutral fats with
  two fatty acids attached to glycerol
• Hydrophilic head differs from neutral fat with
  the third fatty acid replaced with a phosphate
  group attached to other functional groups

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A Phospholipid - Lecithin
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Steroids

• Cholesterol
• other steroids derive from cholesterol
• cortisol, progesterone, estrogens, testosterone
  and bile acids
• required for proper nervous system function and
  is an important component of cell membranes
• produced only by animals
• 85 naturally produced by our body
• only 15 derived from our diet

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Eicosanoids

• Derived from arachidonic acid (a fatty acid)
• Function as chemical signals between cells
• Includes prostaglandins
• role in inflammation, blood clotting, hormone
  action, labor contractions, control of blood
  vessel diameter

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Cholesterol

• All steroids have this 4 ringed structure with
  variations in the functional groups and location
  of double bonds

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Representative Lipids Found in the Body

• Neutral fats found in subcutaneous tissue and
  around organs
• Phospholipids chief component of cell membranes
• Steroids cholesterol, bile salts, vitamin D,
  sex hormones, and adrenal cortical hormones
• Fat-soluble vitamins vitamins A, E, and K
• Eicosanoids prostaglandins, leukotriens, and
  thromboxanes
• Lipoproteins transport fatty acids and
  cholesterol in the bloodstream

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Organic Molecules Proteins

• Polymer of amino acids

• 20 amino acids
• identical except for -R group attached to central
  carbon
• amino acid properties determined by -R group
• The amino acids in a protein determine its
  structure and function

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Amino Acids

• Building blocks of protein, containing an amino
  group and a carboxyl group
• Amino acid structure

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Amino Acids
Figure 2.15a-c
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Amino Acids
Figure 2.15d, e
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Peptides

• A polymer of 2 or more amino acids
• Named for the number of amino acids they contain
• dipeptides have 2, tripeptides have 3
• oligopeptides have fewer than 10 to 15
• polypeptides have more than 15
• proteins have more than 100
• Dehydration synthesis creates a peptide bond that
  joins amino acids

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Dipeptide Synthesis
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Protein

• Macromolecules composed of combinations of 20
  types of amino acids bound together with peptide
  bonds

Figure 2.16
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Structural Levels of Proteins

• Primary amino acid sequence
• Secondary alpha helices or beta pleated sheets

Chemistry of Life Proteins Secondary Structure
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Structural Levels of Proteins

• Tertiary superimposed folding of secondary
  structures
• Quaternary polypeptide chains linked together
  in a specific manner

Chemistry of Life Proteins Tertiary Structure
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Chemistry of Life Proteins Quaternary Structure
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Fibrous and Globular Proteins

• Fibrous proteins
• Extended and strandlike proteins
• Examples keratin, elastin, collagen, and certain
  contractile fibers
• Globular proteins
• Compact, spherical proteins with tertiary and
  quaternary structures
• Examples antibodies, hormones, and enzymes

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Protein Denuaturation

• Reversible unfolding of proteins due to drops in
  pH and/or increased temperature

Figure 2.18a
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Protein Denuaturation

• Irreversibly denatured proteins cannot refold and
  are formed by extreme pH or temperature changes

Figure 2.18b
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Characteristics of Enzymes

• Most are globular proteins that act as biological
  catalysts
• Holoenzymes consist of an apoenzyme (protein) and
  a cofactor (usually an ion)
• Enzymes are chemically specific
• Frequently named for the type of reaction they
  catalyze
• Enzyme names usually end in -ase
• Lower activation energy

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Characteristics of Enzymes
Figure 2.19
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Mechanism of Enzyme Action

• Enzyme binds with substrate
• Product is formed at a lower activation energy
• Product is released

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How Enzymes Work
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Nucleic Acids

• (C), thymine (T), and uracil (U) Composed of
  carbon, oxygen, hydrogen, nitrogen, and
  phosphorus
• Their structural unit, the nucleotide, is
  composed of N-containing base, a pentose sugar,
  and a phosphate group
• Five nitrogen bases contribute to nucleotide
  structure adenine (A), guanine (G), cytosine
• Two major classes DNA and RNA

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Deoxyribonucleic Acid (DNA)

• Double-stranded helical molecule found in the
  nucleus of the cell
• Replicates itself before the cell divides,
  ensuring genetic continuity
• Provides instructions for protein synthesis

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Structure of DNA
Figure 2.21a
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Structure of DNA
Figure 2.21b
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Ribonucleic Acid (RNA)

• Single-stranded molecule found in both the
  nucleus and the cytoplasm of a cell
• Uses the nitrogenous base uracil instead of
  thymine
• Three varieties of RNA messenger RNA, transfer
  RNA, and ribosomal RNA

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Adenosine Triphosphate (ATP)

• Source of immediately usable energy for the cell
• Adenine-containing RNA nucleotide with three
  phosphate groups

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Adenosine Triphosphate (ATP)
Figure 2.22
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How ATP Drives Cellular Work
Figure 2.23