Announcements

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Announcements

• On-line quiz Chapter 2 deadline ..midnight
  tonight!
• Review guidelines for on-line quizzes, they are
  on the BIO 121/122 website.
• Note Once you begin taking the quiz, be sure to
  complete it. Otherwise a grade of zero will be
  submitted to the database.

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Life and ChemistryLarge Molecules
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Life and Chemistry Large Molecules

• Theories of the Origin of Life
• Macromolecules Giant Polymers
• Condensation and Hydrolysis Reactions
• Proteins Polymers of Amino Acids
• Carbohydrates Sugars and Sugar Polymers
• Lipids Water-Insoluble Molecules
• Nucleic Acids Informational Macromolecules That
  Can Be Catalytic
• All Life from Life

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Life on Earth
Source http//pubs.usgs.gov/fs/2001/fs084-01/imag
es/reef2.jpg
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The Building Blocks of Organisms

• MONOMER ? MACROMOLECULE ?
  LIFE
• Amino Acid Protein
• Nucleotide Nucleic Acid
• WERE DID THE MONOMERS COME FROM???

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Theories of the Origin of Life

• There are two theories for the origin of life
• Life from extraterrestrial sources
• Chemical evolution

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Meterorite ALH 84001 Mars to Antarctica 11,000
years ago Polycyclic aromatic hydrocarbons
formed by decaying organisms Magnetite iron
oxide mineral made by living things Water water
is required by life, as we know it Other
meteorites contained water, purines, pyrimidines,
and amino acids.
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Figure 3.1 Synthesis of Prebiotic Molecules in
an Experimental Atmosphere
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The Building Blocks of Organisms

• MONOMER ? MACROMOLECULE ?
  LIFE
• Amino Acid Protein
• Nucleotide Nucleic Acid

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Macromolecules Giant Polymers

• There are four major types of biological
  macromolecules
• Proteins
• Carbohydrates
• Lipids
• Nucleic acids

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Table 3.1 The Building Blocks of Organisms
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Macromolecules Giant Polymers

• The functions of macromolecules are related to
  their shape and the chemical properties of their
  monomers.
• Some of the roles of macromolecules include
• Energy storage
• Structural support
• Transport
• Protection and defense
• Regulation of metabolic activities
• Means for movement, growth, and development
• Heredity

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Condensation and Hydrolysis Reactions

• Macromolecules are made from smaller monomers by
  means of a condensation or dehydration reaction
  in which an OH from one monomer is linked to an H
  from another monomer.
• Energy must be added to make or break a polymer.
• The reverse reaction, in which polymers are
  broken back into monomers, is a called a
  hydrolysis reaction.

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Figure 3.3 Condensation and Hydrolysis of
Polymers (Part 1)
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Figure 3.3 Condensation and Hydrolysis of
Polymers (Part 2)
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Proteins Polymers of Amino Acids

• Proteins are polymers of amino acids. They are
  molecules with diverse structures and functions.
• Each different type of protein has a
  characteristic amino acid composition and order.
• Proteins range in size from a few amino acids to
  thousands of them.
• Folding is crucial to the function of a protein
  and is influenced largely by the sequence of
  amino acids.

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Proteins Polymers of Amino Acids

• An amino acid has four groups attached to a
  central carbon atom
• A hydrogen atom
• An amino group (NH3)
• The acid is a carboxyl group (COO).
• Differences in amino acids come from the side
  chains, or the R groups.

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Source http//www.hcc.mnscu.edu/programs/dept/che
m/V.27/amino_acid_structure_2.jpg
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Proteins Polymers of Amino Acids

• Amino acids can be classified based on the
  characteristics of their R groups.
• Five have charged hydrophilic side chains.
• Five have polar but uncharged side chains.
• Seven have nonpolar hydrophobic side chains.
• Cysteine has a terminal disulfide (SS).
• Glycine has a hydrogen atom as the R group.
• Proline has a modified amino group that forms a
  covalent bond with the R group, forming a ring.

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Table 3.2 The Twenty Amino Acids Found in
Proteins (Part 1)
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Table 3.2 The Twenty Amino Acids Found in
Proteins (Part 2)
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Table 3.2 The Twenty Amino Acids Found in
Proteins (Part 3)
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Proteins Polymers of Amino Acids

• Proteins are synthesized by condensation
  reactions between the amino group of one amino
  acid and the carboxyl group of another. This
  forms a peptide linkage.
• Proteins are also called polypeptides. A
  dipeptide is two amino acids long a tripeptide,
  three. A polypeptide is multiple amino acids long.

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Figure 3.5 Formation of Peptide Linkages
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Proteins Polymers of Amino Acids

• There are four levels of protein structure
  primary, secondary, tertiary, and quaternary.
• The precise sequence of amino acids is called its
  primary structure.
• The peptide backbone consists of repeating units
  of atoms NCCNCC.
• Enormous numbers of different proteins are
  possible.

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Proteins Polymers of Amino Acids

• A proteins secondary structure consists of
  regular, repeated patterns in different regions
  in the polypeptide chain.
• This shape is influenced primarily by hydrogen
  bonds arising from the amino acid sequence (the
  primary structure).
• The two common secondary structures are the a
  helix and the b pleated sheet.

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Proteins Polymers of Amino Acids

• The a helix is a right-handed coil.
• The peptide backbone takes on a helical shape due
  to hydrogen bonds.
• The R groups point away from the peptide
  backbone.
• Fibrous structural proteins have a-helical
  secondary structures, such as the keratins found
  in hair, feathers, and hooves.

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Proteins Polymers of Amino Acids

• b pleated sheets form from peptide regions that
  lie parallel to each other.
• Sometimes the parallel regions are in the same
  peptide, sometimes the parallel regions are from
  different peptide strands.
• This sheetlike structure is stabilized by
  hydrogen bonds between N-H groups on one chain
  with the CO group on the other.
• Spider silk is made of b pleated sheets from
  separate peptides.

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Figure 3.6 The Four Levels of Protein Structure
(Part 1)
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Figure 3.6 The Four Levels of Protein Structure
(Part 2)
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Figure 3.6 The Four Levels of Protein Structure
(Part 3)
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Proteins Polymers of Amino Acids

• Tertiary structure is the three-dimensional shape
  of the completed polypeptide.
• The primary determinant of the tertiary structure
  is the interaction between R groups.
• Other factors can include the location of
  disulfide bridges, which form between cysteine
  residues.

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Figure 3.4 A Disulfide Bridge
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Proteins Polymers of Amino Acids

• Other factors determining tertiary structure
• The nature and location of secondary structures
• Hydrophobic side-chain aggregation and van der
  Waals forces, which help stabilize them
• The ionic interactions between the positive and
  negative charges deep in the protein, away from
  water

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Proteins Polymers of Amino Acids

• It is now possible to determine the complete
  description of a proteins tertiary structure.
• The location of every atom in the molecule is
  specified in three-dimensional space.

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Figure 3.7 Three Representations of Lysozyme
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Proteins Polymers of Amino Acids

• Quaternary structure results from the ways in
  which multiple polypeptide subunits bind together
  and interact.
• This level of structure adds to the
  three-dimensional shape of the finished protein.
• Hemoglobin is an example of such a protein it
  has four subunits.

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Figure 3.8 Quaternary Structure of a Protein
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Proteins Polymers of Amino Acids

• Shape is crucial to the functioning of some
  proteins
• Enzymes need certain surface shapes in order to
  bind substrates correctly.
• Carrier proteins in the cell surface membrane
  allow substances to enter the cell.
• Chemical signals such as hormones bind to
  proteins on the cell surface membrane.
• The combination of attractions, repulsions, and
  interactions determines the right fit.

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Proteins Polymers of Amino Acids

• Changes in temperature, pH, salt concentrations,
  and oxidation or reduction conditions can change
  the shape of proteins.
• This loss of a proteins normal three-dimensional
  structure is called denaturation.

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Figure 3.11 Denaturation Is the Loss of Tertiary
Protein Structure and Function
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Announcements

• On-line Quiz Chapter 3 Deadline Monday

44
Life and Chemistry Large Molecules

• Theories of the Origin of Life
• Macromolecules Giant Polymers
• Condensation and Hydrolysis Reactions
• Proteins Polymers of Amino Acids
• Carbohydrates Sugars and Sugar Polymers
• Lipids Water-Insoluble Molecules
• Nucleic Acids Informational Macromolecules That
  Can Be Catalytic
• All Life from Life

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Carbohydrates Sugars and Sugar Polymers

• There are four major categories of carbohydrates
  
• Monosaccharides (e.g., glucose, fructose)
• Disaccharides, which consist of two
  monosaccharides (e.g., sucrose, lactose)
• Oligosaccharides, which consist of between 3 and
  20 monosaccharides
• Polysaccharides, which are composed of hundreds
  to hundreds of thousands of monosaccharides

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Carbohydrates Sugars and Sugar Polymers

• The general formula for a carbohydrate monomer is
  multiples of CH2O, maintaining a ratio of 1
  carbon to 2 hydrogens to 1 oxygen.
• During the polymerization, which is a
  condensation reaction, water is removed.

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Figure 3.13 Glucose From One Form to the Other
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Carbohydrates Sugars and Sugar Polymers

• Different monosaccharides have different numbers
  or different arrangements of carbons.
• Most monosaccharides are optical isomers.
• Hexoses (six-carbon sugars) include the
  structural isomers glucose, fructose, mannose,
  and galactose.
• Pentoses are five-carbon sugars.

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Figure 3.14 Monosaccharides Are Simple Sugars
(Part 1)
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Figure 3.14 Monosaccharides Are Simple Sugars
(Part 2)
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Carbohydrates Sugars and Sugar Polymers

• Monosaccharides are bonded together covalently by
  condensation reactions. The bonds are called
  glycosidic linkages.
• Disaccharides have just one such linkage
  sucrose, lactose, maltose, cellobiose.

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Figure 3.15 Disaccharides Are Formed by
Glycosidic Linkages
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Carbohydrates Sugars and Sugar Polymers

• Polysaccharides are giant polymers of
  monosaccharides connected by glycosidic linkages.
  
• Cellulose is a giant polymer of glucose joined by
  b-1,4 linkages.
• Starch is a polysaccharide of glucose with a-1,4
  linkages.

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Figure 3.16 Representative Polysaccharides (Part
1)
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Figure 3.16 Representative Polysaccharides (Part
2)
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Lipids Water-Insoluble Molecules

• Lipids are insoluble in water.
• This insolubility results from the many nonpolar
  covalent bonds of hydrogen and carbon in lipids.
• Lipids aggregate away from water, which is polar,
  and are attracted to each other via weak, but
  additive, van der Waals forces.

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Lipids Water-Insoluble Molecules

• Roles for lipids in organisms include
• Energy storage (fats and oils)
• Cell membranes (phospholipids)
• Capture of light energy (carotinoids)
• Hormones and vitamins (steroids and modified
  fatty acids)
• Thermal insulation
• Electrical insulation of nerves
• Water repellency (waxes and oils)

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Lipids Water-Insoluble Molecules

• Fats and oils store energy.
• Fats and oils are triglycerides, composed of
  three fatty acid molecules and one glycerol
  molecule.
• Glycerol is a three-carbon molecule with three
  hydroxyl (OH) groups, one for each carbon.
• Fatty acids are long chains of hydrocarbons with
  a carboxyl group (COOH) at one end.

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Figure 3.18 Synthesis of a Triglyceride
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Lipids Water-Insoluble Molecules

• Saturated fatty acids have only single
  carbon-to-carbon bonds and are said to be
  saturated with hydrogens.
• Saturated fatty acids are rigid and straight, and
  solid at room temperature. Animal fats are
  saturated.

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Lipids Water-Insoluble Molecules

• Unsaturated fatty acids have at least one
  double-bonded carbon in one of the chains the
  chain is not completely saturated with hydrogen
  atoms.
• The double bonds cause kinks that prevent easy
  packing. Unsaturated fatty acids are liquid at
  room temperature. Plants commonly have
  unsaturated fatty acids.

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Figure 3.19 Saturated and Unsaturated Fatty Acids
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Lipids Water-Insoluble Molecules

• Phospholipids have two hydrophobic fatty acid
  tails and one hydrophilic phosphate group
  attached to the glycerol.
• As a result, phospholipids orient themselves so
  that the phosphate group faces water and the tail
  faces away.
• In aqueous environments, these lipids form
  bilayers, with heads facing outward, tails facing
  inward. Cell membranes are structured this way.

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Figure 3.20 Phospholipid Structure
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Figure 3.21 Phospholipids Form a Bilayer
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Nucleic Acids Informational MacromoleculesThat
Can Be Catalytic

• Nucleic acids are polymers that are specialized
  for storage and transmission of information.
• Two types of nucleic acid are DNA
  (deoxyribonucleic acid) and RNA (ribonucleic
  acid).
• DNA encodes hereditary information and transfers
  information to RNA molecules.
• The information in RNA is decoded to specify the
  sequence of amino acids in proteins.

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Nucleic Acids Informational MacromoleculesThat
Can Be Catalytic

• Nucleic acids are polymers of nucleotides.
• A nucleotide consists of a pentose sugar, a
  phosphate group, and a nitrogen-containing base.
• In DNA, the pentose sugar is deoxyribose in RNA
  it is ribose.

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Figure 3.24 Nucleotides Have Three Components
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Nucleic Acids Informational MacromoleculesThat
Can Be Catalytic

• DNA typically is double-stranded.
• The two separate polymer chains are held together
  by hydrogen bonding between their nitrogenous
  bases.
• The base pairing is complementary At each
  position where a purine is found on one strand, a
  pyrimidine is found on the other.
• Purines have a double-ring structure. Pyrimidines
  have one ring.

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Figure 3.25 Distinguishing Characteristics of
DNA and RNA
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Nucleic Acids Informational MacromoleculesThat
Can Be Catalytic

• The linkages that hold the nucleotides in RNA and
  DNA are called phosphodiester linkages.
• These linkages are formed between carbon 3 of the
  sugar and a phosphate group that is associated
  with carbon 5 of the sugar.
• The backbone consists of alternating sugars and
  phosphates.
• In DNA, the two strands are antiparallel.
• The DNA strands form a double helix, a molecule
  with a right-hand twist.

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Nucleic Acids Informational MacromoleculesThat
Can Be Catalytic

• Most RNA molecules consist of only a single
  polynucleotide chain.
• Instead of the base thymine, RNA uses the base
  uracil.
• Hydrogen bonding between ribonucleotides in RNA
  can result in complex three-dimensional shapes.

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Figure 3.26 Hydrogen Bonding in RNA
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Nucleic Acids Informational MacromoleculesThat
Can Be Catalytic

• Nucleotides have other important roles
• The ribonucleotide ATP acts as an energy
  transducer in many biochemical reactions.
• The ribonucleotide GTP powers protein synthesis.
• cAMP (cyclic AMP) is a special ribonucleotide
  that is essential for hormone action and the
  transfer of information by the nervous system.