AP BIOLOGY

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• AP BIOLOGY CHEMISTRY/BIOCHEMISTRY
• I. Chemical Elements
•     A. Matter
•         1. Matter takes up space and has mass.
          2. All matter (living and nonliving) is
  composed of basic elements.             a.
  Elements cannot be broken down to substances with
  different chemical or physical properties.
              b. Six elements (C, H, N, O, P, and
  S) are commonly found in living things.

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•     B. Atomic Structure
•  
•         1. Chemical and physical properties of
  atoms (e.g., mass) depend on the subatomic
  particles.             a. Different atoms
  contain specific numbers of protons, neutrons,
  and electrons.             b. Protons and
  neutrons are in the nucleus of atoms electrons
  move around the nucleus.             c. Protons
  are positively charged particles neutrons have
  no charge both have about 1                
  atomic mass unit of weight.             d.
  Electrons are negatively charged particles.
          2. Isotopes have different mass.
              a. Isotopes are atoms with the same
  number of protons but differ in the number of
  neutrons e.g.,                  a carbon atoms
  has six protons but may have more or less than
  usual six neutrons.             b. Isotopes have
  many uses                 1)  Determine diet of
  ancient peoples by determining proportions of
  isotopes in mummified or                
  fossilized human tissues.                 2)
  Used as tracers of biochemical pathways.
                  3) Determine age of fossils
  using radioactive isotopes.                 4)
  Radiation used in medical treatment.
                  5) Source of radiation used in
  medical diagnostic procedures including PET scan.

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•     C. Energy Levels
•         1. Protons are positively charged
  electrons are negatively charged. Oppositely
  charged protons and electrons are            
  attracted to each other.         2. An atom's
  proton number determines its number of electrons
  and its chemical properties.         3.
  Arrangement of an atom's electrons is determined
  by total number of electrons and electron shell
  they occupy.             a. Energy is the
  ability to do work.             b. Electrons
  with least amount of potential energy are located
  in K shell closest to nucleus electrons having
                  more potential energy are
  located in shells farther from the nucleus.
              c. Atomic Configurations
                  1) Bohr model helps determine
  number of electrons in outer shell.
                  2) Inner shell contains up to
  two electrons additional shells contain eight
  electrons.                 3) Elements are
  arranged in rows in periodic table according to
  number of electrons in outer shell.            
  d. How atoms react with one another depends upon
  the number of electrons in outer shell.
                  1) Atoms with filled outer
  shells do not react with other atoms.
                  2) In atom with one shell, outer
  shell is filled when it contains two electrons.
                  3) For atoms with more than one
  shell, the octet rule applies outer shell is
  stable when it                     contains
  eight electrons.                 4) Atoms with
  unfilled outer shells react with other atoms so
  each has stable outer shell.                 5)
  Atoms give up, accept, or share electrons in
  order to have a stable outer shell.            
  e. Electron Orbitals                 1) Orbital
  is a volume of space where rapidly moving
  electrons are predicted to be found.
                  2) An orbital has a
  characteristic energy state and a characteristic
  shape.                 3) At first energy level
  (K shell), there is only one spherically shaped
  orbital where at most two electrons
                      are found about the nucleus.
                  4) At second energy level (L
  shell), there is one spherically shaped orbital
  and three dumbbell shaped orbitals
                      the second energy level
  contains at most eight electrons.
                  5) Higher energy levels may
  contain more orbitals however, outer shells have
  a maximum of four orbitals                    
  and eight electrons.

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•      4.Chemical Formulas and Equations
              a. A chemical formula indicates the
  number of atoms in each substance H2O has TWO
  Hydrogen                 (H) Atoms and ONE
  Oxygen (O) Atom.             b. The formula also
  indicates the number of molecules 6H2O is six
  molecules of water.             c. A chemical
  equation is always balanced the same number of
  each type of atom is on both sides.
• II. Compounds and Molecules
•     A. Molecules
•         1. Molecules are atoms held together by
  chemical bonds.         2. Molecules form when
  two or more atoms react with one another (e.g.,
  O2).         3. Two or more different elements
  react or bond together to form a compound (e.g.,
  H2O).         4. Electrons possess energy bonds
  that exist between atoms in molecules contain
  energy.

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•     B. Ionic Bonding
•  
•         1. Ionic bonds form when electrons are
  transferred from one atom to another.         2.
  Losing or gaining electrons, atoms participating
  in ionic reactions fill outer shells, and are
  more stable.         3. Example sodium with one
  less electron has positive charge chlorine has
  extra electron that has negative            
  charge. Such charged particles are called ions.
          4. Attraction of oppositely charged ions
  holds the two atoms together in an ionic bond.

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• C. Covalent Bonding
•         1. Covalent bond results when two atoms
  share electrons so each atom has octet of
  electrons in outer shell.         2. Hydrogen
  can give up electron to become hydrogen ion (H)
  or share with another atom to complete its
              outer shell of two electrons.
          3. Structural formulas represent shared
  atoms as a line between two atoms e.g., single
  covalent bond (H-H),             double covalent
  bond (OO), and triple covalent bond (N three
  lines N).         4. Three dimensional shape of
  molecules is not represented by structural
  formulas but is critical in understanding
              the biological action of molecules
  action of insulin, HIV receptors, etc.

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•     D. Nonpolar and Polar Covalent Bonds
•         1. In nonpolar covalent bonds, sharing of
  electrons is equal.         2. With polar
  covalent bonds, the sharing of electrons is
  unequal.             a. In water molecule (H2O),
  sharing of electrons by oxygen and hydrogen is
  not equal the oxygen atom with                
  more protons dominates the H2O association.
              b. Attraction of an atom for
  electrons in a covalent bond is called
  electronegativity an oxygen atom is more
                  electronegative than hydrogen
  atom.             c. Oxygen in water molecule,
  more attracted to electron pair, assumes small
  negative charge.         3. Hydrogen Bonding
              a. Hydrogen bond is weak attractive
  force between slightly positive hydrogen atom of
  one molecule and                 slightly
  negative atom in another or the same molecule.
              b. Many hydrogen bonds taken
  together are relatively strong.             c.
  Hydrogen bonds between complex molecules of cells
  help maintain structure and function.

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•   B. Properties of Water
•         1. The temperature of liquid water rises
  and falls more slowly than that of most other
  liquids.             a. Calorie is amount of
  heat energy required to raise temperature of one
  gram of water 1 degree C.             b. Because
  water holds heat, its temperature falls more
  slowly than other liquids this protects
  organisms                 from rapid temperature
  changes and helps them maintain normal
  temperatures.         2. Water has a high heat
  of vaporization.             a. Hydrogen bonds
  between water molecules require a large amount of
  heat to break.             b. This property
  moderates earth's surface temperature permits
  living systems to exist here.             c.
  When animals sweat, evaporation of the sweat
  takes away body heat, thus cooling the animal.
          3. Water is universal solvent,
  facilitates chemical reactions both outside of
  and within living systems.             a. Water
  is a universal solvent because it dissolves a
  great number of solutes.             b. Ionized
  or polar molecules attracted to water are
  hydrophilic.             c. Nonionized and
  nonpolar molecules that cannot attract water are
  hydrophobic.         4. Water molecules are
  cohesive and adhesive.             a. Cohesion
  allows water to flow freely without molecules
  separating, due to hydrogen bonding.            
  b. Adhesion is ability to adhere to polar
  surfaces water molecules have positive, negative
  poles.             c. Water rises up tree from
  roots to leaves through small tubes.
                  1) Adhesion of water to walls of
  vessels prevents water column from breaking
  apart.                 2) Cohesion allows
  evaporation from leaves to pull water column from
  roots.         5. Water has a high surface
  tension measured by how difficult it is to break
  the surface of a liquid.             a. As with
  cohesion, hydrogen bonding causes water to have
  high surface tension.             b. Permits a
  rock to be skipped across pond surface supports
  insect walking on water surface.         6.
  Unlike most substances, frozen water is less
  dense than liquid water.             a. Below 4
  degrees C, hydrogen boding becomes more rigid but
  more open, causing expansion.             b.
  Because ice is less dense, it floats therefore
  bodies of water freeze from the top down.
              c. If ice was heavier than water,
  ice would sink and ponds would freeze solid.

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• . Acids and Bases
•         1. Covalently bonded water molecules
  ionize the atoms dissociate into ions.        
  2. When water ionizes or dissociates, it releases
  a small but equal number of H and OH- ions
              thus its pH is neutral.         3.
  Water dissociates into hydrogen and hydroxide
  ions H - O - H  H    OH-.         4. Acid
  molecules dissociate in water, releasing hydrogen
  ions (H) ions HCl  H     Cl-.         5.
  Bases are molecules that take up hydrogen ions or
  release hyroxide ions. NaOH  Na OH-.        
  6. The pH scale indicates acidity and basicity
  (alkilinity) of a solution.             a.
  Measure of free hydrogen ions as a negative
  logarithm of the H concentration (-log H).
              b. PH values range from 0 most
  acidic to 14 most basic.                 1) One
  mole of water has 10 to the 7 moles/liter of
  hydrogen ions therefore, has neutral pH of 7.
                  2) Acid is a substance with pH
  less than 7 base is a substance with pH greater
  than 7.                 3) As logarithmic scale,
  each lower unit has 10 times the amount of
  hydrogen ions as next higher pH unit
                      as move up pH scale, each
  unit has 10 times the basicity of previous unit.
          7. Buffers keep pH steady and within
  normal limits in living organisms.            
  a. Buffers stabilize pH of a solution by taking
  up excess hydrogen or hydroxide ions.
              b. Carbonic acid helps keep blood pH
  within normal limits H2CO3  H    HCO3-.

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• IV. Organic Molecules
•     A. Definitions
•         1. Most common elements in living things
  are carbon, hydrogen, nitrogen, and oxygen.
          2. These four elements constitute about
  95 of your body weight.         3. Chemistry of
  carbon allows the formation of an enormous
  variety of organic molecules.         4. Organic
  molecules have carbon bonded to other atoms and
  determine structure and function of living
  things.         5. Inorganic molecules do not
  contain carbon and hydrogen together inorganic
  molecules (e.g., NaCl) can play            
  important roles in living things.

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•     B. Carbon Skeletons and Functional Groups
•         1. Carbon has four electrons in outer
  shell bonds with up to four other atoms (usually
  H, O, N, or another C).         2. Ability of
  carbon to bond to itself makes possible carbon
  chains and rings these structures serve as the
  backbones of organic molecules.         3.
  Functional groups are clusters of atoms with
  characteristic structure and functions.
              a. Polar molecules (with /-
  charges) are attracted to water molecules and are
  hydrophilic.             b. Nonpolar molecules
  are repelled by water and do not dissolve in
  water these are hydrophobic.             c.
  Hydrocarbon is hydrophobic except when it has an
  attached ionized functional group such as
  carboxyl (acid)                 (--COOH) then
  molecule is hydrophilic.             d. Cells
  are 70-90 water the degree organic molecules
  interact with water affects their function.
          4. Isomers are molecules with identical
  molecular formulas but differ in arrangement of
  their atoms                 (e.g.,
  glyceraldehyde and dihydroxyacetone).

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• C. Building Polymers
•         1. Four classes of polymers
  (polysaccharides, triglycerides, polypeptides,
  and nucleic acids)             provide great
  diversity.         2. Small organic molecules
  (e.g., monosaccharides, glycerol and fatty acid,
  amino acids, and nucleotides)             serve
  as monomers, the subunits of polymers.

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•     D. Condensation and Hydrolysis
•         1. Polymers are the large macromolecules
  composed of three to millions of monomer
  subunits.         2. Polymers build by different
  bonding of different monomers mechanism of
  joining and breaking             these bonds is
  condensation and hydrolysis.         3. Cellular
  enzymes carry out condensation and hydrolysis of
  polymers.         4. During condensation
  synthesis, a water is removed (condensation) and
  a bond is made (synthesis).             a. When
  two monomers join, a hydroxyl (--OH) group is
  removed from one monomer and a hydrogen
                  is removed from the other.
              b. This produces the water given off
  during a condensation reaction.         5.
  Hydrolysis reactions break down polymers in
  reverse of condensation a hydroxyl (--OH) group
  from water             attaches to one monomer
  and hydrogen (--H) attaches to the other.

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• V. Carbohydrates
•     A. Monosaccharides and Disaccharides
•         1. Monosaccharides are simple sugars with
  a carbon backbone of three to seven carbon atoms.
              a. Best known sugars have six
  carbons (hexoses).                 1) Glucose
  and fructose isomers have same formula (C6H12O6)
  but differ in structure.                 2)
  Glucose is commonly found in blood of animals is
  immediate energy source to cells.
                  3) Fructose is commonly found in
  fruit.                 4) Shape of molecules is
  very important in determining how they interact
  with one another.         2. Ribose and
  deoxyribose are five-carbon sugars (pentoses)
  contribute to the backbones of RNA            
  and DNA respectively.         3. Disaccharides
  contain two monosaccharides joined by
  condensation.             a. Lactose is composed
  of galactose and glucose and is found in milk.
              b. Maltose is two glucose molecules
  forms in digestive tract of humans during starch
  digestion.             c. Sucrose is composed of
  glucose and fructose and is transported within
  plants.

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•     B. Polysaccharides are chains of glucose
  molecules or modified glucose molecules (chitin).
  
•         1. Starch is straight chain of glucose
  molecules with few side branches.         2.
  Glycogen is highly branched polymer of glucose
  with many side branches called "animal starch,"
              it is storage carbohydrate of
  animals.         3. Cellulose is glucose bonded
  to form microfibrils primary constituent of
  plant cell walls.             a. Cotton is
  nearly pure cellulose.             b. Cellulose
  is not easily digested due to the strong linkage
  between glucose molecules.             c.
  Grazing animals can digest cellulose due to
  special stomachs and bacteria.         4. Chitin
  is polymer of glucose with amino acid attached to
  each it is primary constituent of crabs and
              related animals like lobsters and
  insects.

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Construct linear glucose
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Good morning!Go to lab tables, construct one
linear glucose and one linear fructose per lab
table. What is an isomer?
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Convert to ring glucose bya. Disaasembling the
double bond to oxygen on 1Cb. Take the hydroxide
(-OH) group off 5Cc. Bond the O that was
double bonded to 5Cd. Attach the OH group to 1C
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Construct ring fructosea. Detach the double
bond from the O of 2Cb. Detach the OH from
5Cc. Bond the O to 5Cd. Attach OH group to
opening in 2C
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5. Make sucrose Condensation Reactiona. Orient
molecules as seen belowb. Remove OH group from
1C on a-glucosec. Remove H from hydroxide group
of 5C on fructosed. Bond O to 1C of glucose,
H2O is released
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• VI. Lipids
•     A. Lipids are varied in structure.
•         1. Many are insoluble in water because
  they lack polar groups.         2. Fat provides
  insulation and energy storage.         3.
  Phospholipids from plasma membranes and steroids
  are important cell messengers

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•     B. Fats and Oils
•         1. A fatty acid is a long hydrocarbon
  chain with a carboxyl (acid) group at one end.
              a. Because the carboxyl group is a
  polar group, fatty acids are soluble in water.
              b. Most fatty acids in cells contain
  16 to 18 carbon atoms per molecule.            
  c. Saturated fatty acids have no double bonds
  between their carbon atoms.             d.
  Unsaturated fatty acids have double bonds in the
  carbon chain where there are less than
                  two hydrogens per carbon atom.
              e. Saturated animal fats are
  associated with circulatory disorders plant oils
  can be substituted                 for animal
  fats in the diet.         2. Glycerol is a
  water-soluble compound with three hydroxyl
  groups.         3. Triglycerides are glycerol
  joined to three fatty acids by condensation.
          4. Fats are triglycerides containing
  saturated fatty acids (e.g., butter is solid at
  room temperature).         5. Oils are
  triglycerides with unsaturated fatty acids (e.g.,
  corn oil is liquid at room temperature).        
  6. Animals use fat rather than glycogen for
  long-term energy storage fat stores more energy

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• C. Waxes
•         1. Waxes are a long-chain fatty acid
  bonded to a long-chain alcohol.         2. Solid
  at room temperature, waxes have a high melting
  point and are waterproof and resist degradation.
          3. Waxes form a protective covering that
  retards water loss in plants, and maintains
  animal skin and fur.

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•     D. Phospholipids
•         1. Phospholipids are like neutral fats
  except one fatty acid is replaced by phosphate
  group or a             group with both phosphate
  and nitrogen.         2. Phosphate group is the
  polar head hydrocarbon chains become nonpolar
  tails.         3. Phospholipids arrange
  themselves in a double layer in water, so the
  polar heads face outward             toward
  water molecules and nonpolar tails face toward
  each other away from water molecules.         4.
  This property enables them to form an interface
  or separation between two solution (e.g., the
  interior             and exterior of a cell)
  the plasma membrane is a phospholipid bilayer.

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•     E. Steroids
•         1. Steroids differ from neutral fats
  steroids have a backbone of four fused carbon
  rings             vary according to attached
  functional groups.         2. Functions vary due
  primarily to different attached functional
  groups.         3. Cholesterol is a part of an
  animal cells membrane and a precursor of other
  steroids, including             aldosterone and
  sex hormones.         4. Testosterone is the
  male sex hormone.

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At each lab table, construct three fatty acids
and one glycerol molecule
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2. Combine to form a triglyceride
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• VII. Proteins
•     A. Protein Functions
•         1. Support proteins include keratin,
  which makes up hair and nails, and
  collagenfibers, which support many organs.
          2. Enzymes are proteins that act as
  organic catalysts to speed chemical reactions
  within cells.         3. Transport functions
  include channel and carrier proteins in the
  plasma membrane and hemoglobin             that
  carries oxygen in red blood cells.         4.
  Defense functions include antibodies that prevent
  infection.
•         5. Hormones include insulin that
  regulates glucose content of blood.         6.
  Motion is provided by myosin and actin proteins
  that make up the bulk of muscle.

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•     B. Amino Acids
•         1. All amino acids contain an acidic
  group (---COOH) and an amino group (--NH2).
          2. Amino acids differ in nature of R
  group, ranging from single hydrogen to
  complicated ring compounds.         3. R group
  of amino acid cysteine ends with a sulfhydryl
  (--SH) that serves to connect one chain of amino
              acids to another by a disulfide bond
  (--SS).         4. There are 20 different amino
  acids commonly found in cells.
•   
•  
•  
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•  
•  
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•  
•  

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• C. Peptides
•         1. Peptide bond is a covalent bond
  between amino acids in a peptide.         2.
  Atoms of a peptide bond share electrons unevenly
  (oxygen is more electronegative than nitrogen).
          3. Polarity of the peptide bond permits
  hydrogen bonding between parts of a polypeptide.
          4. A peptide is two or more amino acids
  joined together.         5. Polypeptides are
  chains of many amino acids joined by peptide
  bonds.             a. Protein may contain more
  than one polypeptide chain it can have large
  numbers of amino acids.

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• D. Levels of Protein Structure
•         1. Shape of a protein determines function
  of the protein in the organism.         2.
  Primary structure is sequence of amino acids
  joined by peptide bonds.             a.
  Frederick Sanger determined first protein
  sequence, with hormone insulin, in 1953.
              b. First broke insulin into
  fragments and determined amino acid sequence of
  fragments.             c. Then determined
  sequence of the fragments themselves.
              d. Required ten years research
  modern automated sequencers analyze sequences in
  hours.             e. Since amino acids differ
  by R group, proteins differ by a particular
  sequence of the R groups.         3. Secondary
  structure results when a polypeptide takes a
  particular shape.             a. The alpha helix
  was the first pattern discovered by Linus Pauling
  and Robert Corey.                 1) In peptide
  bonds oxygen is partially negative, hydrogen is
  partially positive.                 2) This
  allows hydrogen bonding between the CO of one
  amino acid and the NH of another.
                  3) Hydrogen bonding between
  every fourth amino acid holds spiral shape of an
  alpha helix.                 4) Alpha helices
  covalently bonded by disulfide (--SS--) linkages
  between two cysteine amino acids.             b.
  The beta sheet was the second pattern discovered.
                  1) Pleated beta sheet
  polypeptides turn back upon themselves hydrogen
  bonding occurs between                    
  extended lengths.                 2)
  Beta-keratin includes keratin of feathers,
  hooves, claws, beaks, scales, and horns silk
  also is protein                     with beta
  sheet secondary structure.         4. Tertiary
  structure results when proteins of secondary
  structure are folded, due to various interactions
              between the R groups of their
  constituent amino acids.         5. Quaternary
  structure results when two or more polypeptides
  combine.             a. Hemoglobin is globular
  protein with a quaternary structure of four
  polypeptides.             b. Most enzymes have a
  quaternary structure.

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• E. Denaturation of Proteins
•         1. Both temperature and pH can change
  polypeptide shape.             a. Examples
  heating egg white causes albumin to congeal
  adding acid to milk causes curdling.            
  b. When such proteins lose their normal
  configuration, the protein is denatured.
              c. Once a protein loses its normal
  shape, it cannot perform its usual function.
          2. The sequence of amino acids therefore
  causes the proteins final shape.

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Construct an amino acid
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• VIII. Nucleic Acids
•     A. Nucleic Acid Functions
•         1. Nucleic acids are huge polymers of
  nucleotides with very specific functions in
  cells.         2. DNA (deoxyribonucleic acid) is
  the nucleic acid whose nucleotide sequence stores
  the genetic             code for its own
  replication and for the sequence of amino acids
  in proteins.         3. RNA (ribonucleic acid)
  is a single-stranded nucleic acid that translates
  the genetic code of DNA             into the
  amino acid sequence of proteins         4.
  Nucleotides have metabolic functions in cells.
              a. Coenzymes are molecules which
  facilitate enzymatic reactions.             b.
  ATP (adenosine triphosphate) is a nucleotide used
  to supply energy.             c. Nucleotides
  also serve as nucleic acid monomers.

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