The Chemical Basis for Life Chapter 2

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The Chemical Basis for LifeChapter 2
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Matter

• Anything that occupies space and has mass.
• Can exist as
• Gas
• Liquid
• Solid
• Is composed of elements
• What are examples of each type of matter?

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• Element- any of 116 known substances that can not
  be separated into smaller substances.
• 92 occur in nature
• 2 are hypothetical
• And 2 are not known to exist
• Are referred to by a chemical symbol and are
  organized in the Periodic Table of Elements.
• Nitrogen (N), Oxygen (O), Hydrogen (H), and
  Carbon (C) make up 96 of the matter found in all
  living organisms

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Elements in Animal Body

• Major Elements
• Oxygen (O)
• Necessary for cellular energy
• Carbon (C)
• Primary component of organic molecules
• Hydrogen (H)
• Component of water and organic molecules,
  necessary for energy transfer and respiration
• Nitrogen (N)
• Component of all proteins and nucleic acid

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• Minor Elements
• Calcium (Ca)
• Bones, teeth, muscle contraction, nerve impulse
  transmission
• Phosphorus (P)
• Energy transfer
• Potassium (K)
• Important in nerve function. Principle positive
  ion within cells
• Sulfur (S)
• Component for most proteins
• Sodium (Na)
• Ion in extracellular fluid, important in nerve
  function.
• Chlorine (Cl)
• Most abundant neg ion in extracellular fluid
• Magnesium (Mg)
• Component of energy-transferring enzymes

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• Trace Elements
• Silicone (Si)
• Aluminum (Al)
• Iron (Fe)
• Manganese (Mn)
• Fluorine (F)
• Vanadium (V)
• Chromium (Cr)
• Copper (Cu)
• Boron (B)
• Cobalt (Co)
• Zinc (Zn)
• Selenium (Se)
• Molybdenum (Mo)
• Tin (Sn)
• Iodine (I)

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Atoms

• The smallest unit of an element that retains the
  unique properties of that element.
• Composed of
• Protons
• Neutrons
• Electrons

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More about atoms-Protons and Neutrons

• Protons and Neutrons are found in the nucleus.
• Each proton and neutron has an atomic mass of 1.
• Together protons and neutrons determine the
  atomic weight of the atom.
• Protons have positive charge.
• Neutrons have no electrical charge and are
  considered neutral.
• Net charge of atoms are neutral because have
  equal numbers of protons and electrons.

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Electrons

• Tiny particles that remain in constant motion
  around the nucleus.
• So tiny that their mass does not contribute to
  the atomic weight of the atom.
• Have negative charge.
• Orbit around nucleus but not necessarily in a
  planetary manner, more in an orbital manner so
  that electrons exist in a cloud and they can move
  closer to one side of the atom or the other.

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Atoms continued

• The number of protons gives an atom its atomic
  number.
• If an atom loses or gains an electron, then it
  becomes positively or negatively charged, thereby
  becoming an ion.
• If an atom has a different number of neutrons,
  then they are called isotopes of the element

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Atomic Number
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Isotopes
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Ions
e-
Na atom 11 e, 11 p
Na ion 10 e, 11 p
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Rate of Decay

• The time rate of disintegration of radioactive
  material, generally accompanied by emission of
  particles or gamma radiation.

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Electron Shell

• Area around the nucleus where the electrons are
  most likely to be.
• Electrons energy level determines which electron
  shell it will inhabit.
• Lower energy electrons will be closer to nucleus
  in lower shells.
• If shells are not full, then atoms will be more
  active.
• Helium and Neon have full electron shells so are
  chemically inert.

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How the Shells work.

• First shell can contain 2 electrons.
• Second shell on can contain 8 electrons.

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Molecules and Compounds

• Molecules- when atoms are joined together by
  chemical bonds. Are the smallest particle of a
  substance that retains the properties of the
  substance.
• Molecule of the element- when two or more atoms
  of the same element are joined together.
• Bonds- how atoms are attached to one another.
• Compounds- A substance made up of two or more
  elements.

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Chemical Bonds

• Means that the atoms are sharing or transferring
  electrons between them.
• Trying to fill their shells or give up extra
  electrons to another atom.
• Remember that atoms are constantly trying to
  become more stable.
• Types of chemical bonds
• Covalent
• Ionic
• Hydrogen

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Covalent Bonds

• Bonds formed when atoms share electrons.
• Electrons spend part of time in outer electron
  shell of each atom.
• Classified depending on how many electrons are
  being shared.
• single covalent bond one electron is shared
• double covalent bond two electrons are shared
• triple covalent bond three electrons are shared
  
• May be shared equally (nonpolar) or unequally
  (polar).

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Polar Water Molecule

• Shared electrons in a covalently bonded molecule
  may spend more time near one atom than the other
• Shared electrons in water molecule spend more
  time near O atom than H atoms
• Created poles
• Gives molecule a slight positive charge on H side
  of molecule and slight negative charge on O side
  of molecule

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http//www.youtube.com/watch?vqmgE0w6E6ZI
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Ionic Bonds

• Formed when electrons are transferred from one
  atom to another.
• Formed most often between two different types of
  atoms.
• Usually between with fewer than 2 electrons in
  outer shell and those that are nearly full.
• Transfer causes a positive charge on one atom and
  a negative charge on the other. Keeps attraction
  to one another called electrostatic attraction.

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Electron transferred
Attraction betweenopposite charges
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Types of Ions

• Cations- Ions with a net positive charge.
• Anions- Ions with a net negative charge.
• Ions are important in contraction of muscle
  fibers, transmission of nerve impulses, and
  maintenance of water balance.

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Hydrogen Bonds

• A specific type of a weak ionic bond.
• Weaker than ionic or covalent bonds.
• Bond between hydrogen atoms already covalently
  bonded in a molecule to oppositely charged
  particles.
• Since Hydrogen wants to donate electron, will
  have outer electron going toward other nucleus.
  This will make Hydrogen have an overall positive
  charge.
• Positive charge will cause electrostatic
  attraction to a negative molecule.
• Found in water or DNA to stabilize shape.

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Chemical Reactions

• The formation and breaking of chemical bonds.
• Require energy input or release of energy.
• Chemical Equation- reaction is described in
  written form.
• X Y ? Z
• (reactants) (products)
• Arrow indicates direction of the reaction

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Types of Chemical Reactions

• 1. Synthesis Reaction- new and more complex
  molecule is made from simpler chemicals.
• XY?XY
• O O O2
• 2. Decomposition Reaction- single complex
  chemical is broken down into multiple, simpler,
  chemicals.
• XY?XY
• 2H20?2H2 O2
• 3. Exchange Reaction- certain atoms are
  exchanged between molecules. Combination of
  synthesis and decomposition reaction.
• WX YZ ? WY XZ
• NaHCO3 HCl ? NaCl H20 C02

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Chemical Reactions Continued

• Synthesis reactions require energy.
• Decomposition reactions expend or release energy.
• Exchange reactions have no net energy
  requirements. Energy released from decomposition
  portion, helps with synthesis portion.

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Chemical Reactions Continued

• Factors that influence reaction rates
• Concentration of reactants
• Temperature of environment
• Activation energy- the energy required for the
  reaction to happen.
• Some reactions require presence of a catalyst or
  enzyme
• Reaction speed is increased when catalyst is
  present
• Protein (enzyme)

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Chemical Components of Living Organisms Organic
and Inorganic Compounds

• Inorganic compounds- do not contain hydrocarbon
  groups (H and C bonded together) and often have
  ionic bonding.
• Water
• Salts
• Acids and Bases
• Organic compounds- contain hydrocarbon groups and
  are usually covalently bonded

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Water

• Water is the universal solvent
• Solutes- chemicals added to water
• Solution- resulting chemical and water mixture
• Hydrophilic (water loving)- chemicals that
  dissolve well or mix with water.
• Hydrophobic (water hating)- chemicals or
  molecules that do not mix well with water.
• Water is an ideal transport medium
• Blanketing power allows molecules in water to
  move around and be cushioned from one another.
• Blood
• Urine
• Water has a high heat capacity and a high heat of
  vaporization
• Easily able to absorb heat.
• Wont evaporate easily.
• Water is used for lubrication.

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Salts

• Mineral compounds that have ionic bonds
• Principal form of minerals that enter and are
  stored in the body.
• In ionic form are called electrolytes-substances
  that have ability to transmit an electrical
  charge.

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Acids and Bases

• Acids- ionically bonded substances that when
  added to water freely release hydrogen ions.
• Called H donors or proton donors
• Bases- alkaline in nature release a hydroxyl ion
  (OH-).
• Called proton acceptors
• Acids and Bases are also electrolytes as they can
  transmit electricity when ionized in water.

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The pH Scale

• Ranges from 1-14.
• Lower numbers are the most acidic, higher numbers
  are more alkaline.

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Buffers

• A substance that minimizes the change of the
  acidity of a solution when an acid or base is
  added to the solution.
• By not allowing excessive hydrogen or hydroxyl
  ions to accumulate, buffers help cell maintain a
  neutral pH.

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Organic Molecules

• Molecules that contain carbon.
• Why carbon?-4 outer electrons in outer shell,
  trying to share this to complete outer shell.
• Divided into 4 groups
• Carbohydrates
• Glycogen
• Ribose
• Lipids
• Triglycerides
• Phospholipids
• Steroids
• Prostaglandins
• Proteins
• Globular
• Fibrous
• Nucleic Acids
• DNA
• RNA
• Adenosine triphosphate (ATP)

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Carbohydrates

• Used for energy, storage of energy, and cellular
  structures.
• Simple Sugars-monosaccharides.
• Glucose and Fructose
• Disaccharide- when two monosaccharides are joined
  together in synthesis reaction.
• Polysaccharides- combinations of many
  monosaccharides.
• Glycogen and cellulose

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Some terminology

• Glycoprotein- when a macromolecule is formed out
  of a carbohydrate attached to a protein.
• Anabolism- process of building molecules needed
  for cellular functioning.
• Catabolism- Decomposition of nutrients.

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Lipids

• Used for energy and stored in fat.
• 4 classes of Lipids
• 1. Neutral fats
• 2. Phospholipids
• 3. Steroids
• 4. Eicosanoids

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Lipids continued..

• Neutral Fats
• Also called triglycerides or fats.
• Contains three fatty acids and a glycerol
  molecule.
• Saturated fatty acids- all bonds in the
  hydrocarbon chain are single bonds.
• Unsaturated fatty acids- when there are some
  double bonds between the carbon and hydrogen
  atoms.
• Lipoproteins- macromolecule composed of proteins
  and lipids
• Hydrolysis- when triglycerides are decomposed.

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• Phospholipids
• Have a glycerol backbone
• Have a lipid bilayer when placed in water.
• Hydrophilic are facing water, while hydrophobic
  tails line up with one another.

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• Steroids
• Take form of four interlocking hydrocarbon rings.
• Are hydrophobic.
• Examples include
• Cholesterol
• Cortisol

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• Eicosanoids
• Lipids formed from a 20 carbon fatty acid and
  ring structure. (hairpin structure)
• Include
• Prostaglandins- in inflammation
• Thrombaxone- platelet function
• Leukotrienes- bronchoconstriction and increased
  mucus production.

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Proteins

• Most abundant organic molecules in the body.
• Have widest variety of functions.
• Catalyze- speed up reactions occurring in the
  body.
• Transport ions and other molecules into and out
  of the cell and around the body.
• Made chiefly of carbon, oxygen, hydrogen, and
  nitrogen.
• Composed of amino acids

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Amino Acids

• 20 different amino acids used by the body.
• Central carbon is attached to hydrogen atom, an
  amino group (NH2), a carboxyl group (COOH), and a
  side chain.
• Include
• Alanine    Arginine    Asparagine    Aspartic
  acid    Cysteine    Glutamic acid    Glutamine
     Glycine   Histidine    Isoleucine
     Leucine    Lysine    Methionine
     Phenylalanine   Proline    Serine
     Threonine    Tryptophan    Tyrosine
     Valine

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Structure of Proteins

• Shape of protein directly determines its
  function.
• Antibodies- fit together like puzzle to foreign
  invaders.
• Structure is described in four layers
• Primary Structure- sequence and number of amino
  acids that link together to form the peptide
  chain.
• Secondary Structure- the natural bend of parts of
  the peptide chain as it is formed in three
  dimensions.
• Tertiary Structure- overall shape of a single
  protein molecule.
• Quaternary Structure- when two or more protein
  chains join to form a complex macromolecule.

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• http//www.youtube.com/watch?vOz2x_yxPXwwfeature
  related

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Structural Proteins

• Stable, rigid, water-insoluble proteins that are
  used for adding strength to tissues or cells.
• May also be called Fibrous proteins.
• Important in structural framework and physical
  movement.
• Examples include
• Collagen
• Keratin
• Actin and Myosin

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Functional Proteins

• Generally are water-soluble and have a flexible,
  three-dimensional shape, which can change under
  different circumstances
• May also be called Globular proteins.
• Function in chemical reactions, transport of
  molecules, regulation of metabolism, and immune
  system.
• Include
• Hormones
• Antibodies
• Protein-based hormones
• Enzymes

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Enzymes

• Proteins that catalyze or speed up chemical
  reactions.
• Will end in ase
• Are essential in the body for catalyzing
  (speeding up) chemical reactions without being
  destroyed themselves during the process.
• Substrates the substance that the enzyme acts
  upon.

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Nucleic Acids

• Largest molecule of body composed of Carbon,
  Oxygen, Hydrogen, Nitrogen, and Phosphorus.
• 2 classes of Nucleic Acids
• DNA (deoxyribonucleic acid)
• Exists mainly in the nucleus but also
  mitochondria.
• Contains all instructions needed by cell to build
  proteins.
• Coded in segments called genes.
• RNA (ribonucleic acid)
• Transfers the instructions out of the nucleus and
  into the cytoplasm and builds proteins.
• Exists as mRNA, tRNA, and rRNA.

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Nucleotides

• The molecular building blocks of nucleic acids.
• Are 5 different nucleotides, but all have the
  same structure.
• Are all composed of a 5-Carbon pentose sugar.
• Sugar in DNA is deoxyribose.
• Sugar in RNA is ribose.
• Nucleotides are named for their nitrogen base.

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Nucleotides

• Adenine-both DNA and RNA
• Guanine-both DNA and RNA
• Cytosine-both DNA and RNA
• Thymine-Only in DNA
• Uracil- Only in RNA

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Nucleic Acid Formation

• Occurs when sugar and phosphate groups join in a
  long chain with nitrogenous base open.
• Information needed to produce proteins is based
  on order of the nucleotides.
• C-G-T makes amino acid alanine.
• Chromosomes-long chains of genes combined with
  proteins.

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DNA

• Consists of two parallel strands of nucleotides
  adenine, guanine, cytosine and thymine.
• Connected by hydrogen bonds between specific
  pairings of nucleotides.
• Adenine and Thymine
• Guanine and Cytosine
• Once bound, these two strands twist around one
  another to form a double helix.
• Order of nucleotides is what makes unique genetic
  code of each individual.

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RNA

• Consists of only one strand of nucleotides.
• Does not have thymine, but instead has uracil.
• Pairings are
• Guanine and Cytosine
• Adenine and Uracil
• Exists in three forms
• tRNA- Transfer RNA
• Copies information in the DNA molecule
• mRNA- Messenger RNA
• Carries information out of the nucleus
• rRNA-Ribosomal RNA
• Creates the proteins needed by the body

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ATP

• Adenosine Triphosphate- energy of the cells.
• Cells need ATP to fuel or carry out any work.
• Cellular Respiration- when the cells use up the
  nutrients
• ATP is a RNA nucleotide containing adenine with
  two additional phosphate groups attached.
• When bonds (high energy bonds) between phosphate
  groups are broken, energy is released.
• When phosphate group is lost, resulting molecule
  is adenosine diphosphate (ADP).

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Why is it so important?

• Since we know how these bonds work, we can
  understand how certain things such as drugs and
  chemical reactions in the body occur.
• Will help us later on in digestion of food,
  growth of the body, cellular signaling, and
  transmission of nerve impulses.