The Chemical Basis of Life

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The Chemical Basis of Life

• Chapter 2

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Atoms and Molecules

• Chemicals play many roles in an organisms life
• DNA is a combination of chemical elements
• Every cell has DNA
• Every living thing contains cells
• Organisms use chemical signals for many things
  including
• Muscle movement, mating, and defense
• This chapter deals with the place of chemicals in
  organisms

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Studying the Role Of Chemicals in Organisms

• Since chemicals play such an important role in
  organisms lives we use a reductionistic attitude
  to study it
• Reductionism- In order to understand the whole,
  we study the parts
• We reduce the biological hierarchy first

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Biological Hierarchy

• Start at the organ level
• Organ Flight muscle of moth
• Cell and Tissue Muscle cell and tissue
• Organelle Microfibril
• Molecule Actin (protein)
• Elements
• Atoms

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Elements

• A chemical element is a substance that cannot be
  broken down to other substances by ordinary
  chemical means
• About 25 of the 92
• naturally occurring
• elements are
• essential to life
• Goiters are caused
• by iodine deficiency

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Essential Elements

• Carbon, hydrogen, oxygen, and nitrogen make up
  the bulk of living matter, but there are other
  elements necessary for life

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Compounds

• Compound a substance containing two or more
  elements in a fixed ratio
• More common than pure elements
• Example NaCl (salt)
• Most compounds in living organisms contain at
  least 3 or 4 different elements
• Carbon, hydrogen, oxygen, and nitrogen
• Proteins like actin are made of these

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Atoms

• Elements consist of one kind of atom that is
  different form all other atoms of other elements
• Smallest unit of matter that still retains the
  properties of the element in question
• An atom consists of three basic types of
  subatomic particles
• Protons, electrons, and neutrons

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Atoms

• Protons and neutrons are located in the core of
  the atom called the nucleus
• Electrons surround the nucleus in a sort of orbit

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Atoms

• Protons are positively charged
• Electrons are negatively charged
• Neutrons are__?__?__
• The atom is held together by the attraction
  between the positively charged protons and the
  negatively charged electrons
• The number of protons and the number of electrons
  are equal

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Isotopes

• Atoms of each element are distinguished by a
  specific number of protons, this is the elements
  atomic number
• Mass number- is the number of protons and
  neutrons in its nucleus

Isotopes of Carbon Isotopes of Carbon Isotopes of Carbon Isotopes of Carbon
Mass Number Carbon 12 Carbon13 Carbon14
Protons 6 6 6
Neutrons 6 7 8
Electrons 6 6 6

• The number of neutrons may vary
• Varying numbers of neutrons create isotopes

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Radioactive Isotopes

• Radioactive isotopes are unstable, and give off
  energy as the nucleus decays spontaneously
• Radioactive isotopes can be useful tracers for
  studying biological processes
• The body cannot tell the difference between
  regular carbon and radioactive carbon and the
  body takes up the compounds and uses them, thus
  leaving a radioactive trace

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Radioactive Isotopes

• Photographic film or Geiger counters can detect
  radioactivity
• These are used to study basic chemical processes
  in organisms, such as photosynthesis and in
  diagnosis using radioactive anatomical imaging

PET scan
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Electrons

• Arranged only at certain energy levels called
  shells
• Inner shell holds 2 electrons
• Outer shells hold 8 elections
• The number of electrons in the outer shell
  determines the chemical reactivity of the element
• If the shell is not full (2 or 8) then the
  element will interact with other elements in
  order to fill its outer shell

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Electrons
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How does an electron fill its out shell?

• When two atoms with incomplete outer shells
  react, they either give up or receive electrons,
  causing a bond
• Chemical bond Two types of chemical bonds
• Ionic Bonds
• Convalent bonds

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Ionic Bonds

• Attractions between ions of opposite charge hold
  them together
• Ion- molecule with an electrical charge
• from loosing or gaining an electron

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Covalent Bonds

• Two atoms share electrons
• Two or more atoms held together by covalent bonds
  are called molecules
• Single bonds
• Double bonds

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Polar Molecules

• Consists of two hydrogen molecules covalently
  bonded to a single oxygen atom
• Shared electrons
• An atoms attraction for the shared electrons is
  called its electronegativity
• If the molecule shares the electron equally it is
  called nonpolar
• If the electrons are pulled more closely to one
  atom than to the others, the stronger pulling
  atom becomes slightly negative and the other
  slightly positive, this makes the molecule polar

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Water

• Due to its polarity, water has some unusual
  properties
• The partially charged atoms are attracted to
  neighboring molecules and form weak bonds called
  hydrogen bonds

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Water

• Water exists on earth in all three physical
  states
• What are they?
• Where are they?
• Life exists on earth because of the properties of
  water and its abundance

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Water

• Cohesive nature of water
• Allows plants to uptake water from the roots
• Surface tension of water allows small insects to
  walk on water
• Makes it more difficult to heat and cool water
• Takes up a lot of heat when the atmosphere is
  hot, therefore cools the atmosphere and releases
  heat in cold times as it cools and warms the
  atmosphere
• Evaporative Cooling- perspiration

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Water

• Frozen water is less dense than liquid water
• Fewer molecules in ice than an equal volume of
  liquid
• Ice floats

Ice
Water
ICE Hydrogen bonds are stable
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Water as a Solvent

• Solution- liquid consisting of a homogenous
  mixture of two or more substances
• Solvent- dissolving agent
• Solute- substance being dissolved
• Aqueous solution- solution where water is the
  solvent
• Because of its polarity, water is an excellent
  solvent

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Acidic and Basic Solutions

• In aqueous solutions some of the water molecules
  dissociate (come apart) and form ions
• Hydrogen ions (H)
• Hydroxide ions (OH-)
• For chemical processes to function within
  organisms the right balance of (H) and (OH-)
  ions
• Pure water is a neutral solution

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Acidic and Basic Solutions

• Acid- chemical compound that donates H ions
• Base- chemical compound that donates OH- ions
• pH scale measures acidity
• 0-7 is acidic, 8-14 is basic
• Buffers- resist changes in pH by accepting H ions

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Chemical Reactions

• The structure of atoms and molecules determines
  the way they behave
• Chemical reactions rearrange molecules and ions
  and change the way they behave
• Chemical reaction- process leading to chemical
  changes in matter

Reactants
Products
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Living Cells and Chemical Reactions
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The Molecules of Cells

• Chapter 3

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ORGANIC COMPOUNDS AND THEIR POLYMERS

• Nearly all molecules created by cells are
  composed of carbon molecules
• Carbon can be bonded to itself or to elemental
  atoms
• Organic Compounds-compounds synthesized by cells
  and containing carbon
• Carbon has the ability to synthesize large,
  diverse molecules

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Carbon

• Carbon has only four electrons in its outer
  shell that holds eight
• Very reactive with many other atoms
• The shape of a molecule, which depends partly on
  its bond angles, usually helps to determine its
  angles
• The chain of carbon atoms in organic molecules is
  called the carbon skeleton

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Carbon

• Carbon can form four covalent bonds
• It can join with other carbon atoms to make
  chains or rings
• Over 2 million organic, carbon-containing
  compounds are known

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Forms of Carbon Skeletons

• Straight of Branched
• Vary in length
• Arranged in Rings
• Hydrocarbons- Compounds containing only H and C
• Compounds with the same of H and C but with
  different forms are called Isomers

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Functional Groups

• The groups of atoms that usually participate in
  chemical reactions
• Attached to the carbon skeleton
• Can be polar, which makes them water soluble
• Compounds can contain several functional groups

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Functional Groups
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Functional Groups

• Hydroxyl group (-OH)- oxygen is bonded to the
  carbon skeleton
• Compounds containing a hydroxyl group are called
  alcohols
• Amino group (-NH2)- nitrogen bonded to carbon
  skeleton and hydrogens bonded to nitrogen
• Compounds containing an amino group are called
  amines

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Carbonyl Groups

• Carbon atom linked by a double bond to an oxygen
  atom
• Ketone- carbonyl group within the chain
• Aldehyde- carbonyl group at the end of the chain
• Carboxylic Acid- carbonyl group at the end of the
  chain, and attached to a hydroxyl group

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Macromolecules

• Most organic molecules are large macromolecules
  made up of smaller molecules
• Thousands of connected atoms
• Examples
• Proteins
• DNA
• Lipids

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Polymers

• Polymer- a large molecule consisting of many
  identical or similar units strung together
• Monomer- The units that serve as the building
  blocks of polymers
• Essentially universal between organisms
• The diversity of polymers accounts for the
  uniqueness of each organism

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Dehydration Synthesis

• Monomers are linked together to form polymers by
  a process called dehydration synthesis

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Hydrolysis

• Breakdown of polymers, break the bonds between
  polymers by adding a water molecule

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Four Classes of Large Molecules

• Carbohydrates
• Proteins
• Nucleic Acids
• Lipids

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Carbohydrates

• A class of molecules ranging from small sugar
  molecules to large polysaccharides
• Monosaccharides- carbohydrate monomers,
  single-unit sugars
• Disaccharides- two monosaccharides linked
  together, double-sugars
• Polysaccharides-hundreds to thousands of
  monosaccharides linked together

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Monosaccharides

• Molecular formulas that are some multiple of CH2O
• Sugars have two trademark elements
• A number of hydroxyl groups (-OH) and a Carbonyl
  Group
• Monosaccharides are the fuels for cellular work

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Disaccharides

• Disaccharides are formed when two monosaccharides
  link together
• The two monosaccharides link by dehydration
  synthesis
• Sucrose
• fructose glucose

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Polysaccharides

• Polymers of many monosaccharides linked together
  by dehydration synthesis
• Starch- Storage polysaccharide in plant tissues
  as granules
• Glycogen- Storage polysaccharide in animals,
  stored in liver and muscle tissue as granules
• Cellulose- Building material in plants, most
  abundant organic material on earth, cannot be
  hydrolyzed by animals

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Polysaccharides
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Lipids Fats

• Consist of mainly C and H atoms linked by
  non-polar covalent bonds
• Not attracted to water (hydrophobic)
• Fat- large lipid made from one glycerol and
  molecule and 3 fatty acid molecules
• Energy storage- stores more than twice the amount
  of energy as a carbohydrate
• Glycerol and fatty acids linked by dehydration
  synthesis

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Fats

• Fats are also called triglycerides
• The three fatty acids are often of different
  kinds
• Fatty acids sometimes contain double bonds
• Unsaturated Fats- fatty acids with double bonds
• Saturated Fats- fatty acids without double bonds
• The double bonds prevent the fatty acids from
  packing together and solidifying at room
  temperature

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Fats
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Lipids Phospholipids, waxes and steroids

• Phospholipids Similar to fats, but contain
  phosphorous and only 2 FA chains, important in
  membranes
• Waxes FA linked to alcohol. Very hydrophobic,
  protective coatings from pathogens and drying out
• Steroids carbon skeleton bent to form rings,
  cholesterol, hormones

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Proteins

• Polymer constructed from amino acid monomers
• Thousands of proteins in the human body
• Unique 3D structure the corresponds to a specific
  function
• Seven major classes of proteins

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Protein Classes

• Structural- hair, fiber in ligaments or tendons
• Contractile- provide muscular movement
• Storage- Ovalbumin, in egg whites
• Defensive- antibodies that fight infection
• Transport- hemoglobin, conveys oxygen
• Signal- coordinate bodily activities
• Enzymes- chemical catalyst

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Amino Acids

• Proteins are made up of multiple variations of 20
  different amino acids
• AAs have an amino group and a carboxyl group
  attached to the central (?) carbon
• ? carbon also is bonded to an H and an R group
• The R group is a chemical group which
  characterizes the amino acid

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Amino Acids
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Amino Acid Linkage

• AAs are linked together by dehydration synthesis
• Carboxyl group of one AA must be positioned next
  to the amino group of another AA, the resulting
  linkage is called a peptide bond
• A chain of AAs is called a polypeptide

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Amino Acid Linkage
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Protein Shape

• A proteins specific, 3D shape is what determines
  its function
• Proteins usually bond to another molecule to
  perform their function

Lysozyme
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Protein Structure

• Primary structure- AA sequence
• Secondary structure- folding or coiling
• Coiling- ? helix
• Folding- pleated sheet
• Maintained by regularly spaced hydrogen bonds
  between the carbonyl and amino groups of amino
  acids

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Protein Structure

• Tertiary structure- overall 3D shape of a
  polypeptide
• Globular or fibrous
• Quaternary structure- when a protein contains
  more than one chain the way the subunits form is
  called the quaternary structure
• Results from bonding interactions between the
  subunits

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Protein Structure
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Nucleic Acids

• Polymers that serve as the blueprints for
  proteins
• Two types
• DNA-deoxyribonucleic acid
• RNA- ribonucleic acid
• Genetic material that you inherit from your
  parents consists of genes
• Genes are specific stretches of genes along the
  DNA that program AA sequences
• They ultimately control the life of a cell

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Nucleic Acids

• The monomers that make up nucleic acids are
  called nucleotides
• Nucleotides have three parts a phosphate group,
  a sugar, and a nitrogenous bases (adenine A,
  guanine G, cytosine C, and thymine T or
  uracil U
• DNA sugar deoxyribose nitrogenous bases are A,
  T, C, and G
• RNA sugar ribose nitrogenous bases are A, U,
  C, and G

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Nucleic Acids
Nucleotide Monomer
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DNA

• DNA consists of two polynucleotide strands
  twisted around each other in a double helix
• RNA has only a single polynucleotide strand
• The sequence of the four kinds of nitrogenous
  bases in DNA carries genetic information

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How DNA Works

• Stretches of a DNA molecule called genes program
  the amino acid sequences of proteins
• DNA information is transcribed into RNA, a
  single-stranded nucleic acid
• RNA is then translated into the primary structure
  of proteins
• Actions of proteins control the functions of the
  cell