Orgainic/inorganic pg. 14 sg

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Orgainic/inorganic pg. 14 sg

• Some cpds which contain carbon are inorganic.
• Examples include carbon dioxide, carbonates,
  and hydrogen carbonates.
• All cpds which contain no carbon are inorganic
• Three types of organic cpds are found in living
  things, carbohydrates, proteins, lipids

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Structure
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• Carbon atoms can share electrons -notable being
  other carbon atoms, hydrogen atoms and oxygen
  atoms.
• The simplest organic molecules are defined as
  being comprised of only carbon and hydrogen
  hydrocarbons

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• Hydrocarbons are non-polar, hydrophobic
  compounds. (water hating)
• Compounds that have no charges on them will not
  mix with polar water.

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• Hydrophilic comes from the Latin roots "hydro"
  (water) and "philia" (love).
• Compounds are polar, and so dissolve easily in
  the polar solvent water.

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• Structural formulas of some simple hydrocarbons.
• Methane CH4

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Hydrocarbons

• A simple chain of carbons with its full
  complement of hydrogens is said to be saturated.
• known as alkanes.
• name ends with 'ane'.

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• Hydrocarbons with double bonds in them are said
  to be unsaturated.
• contain at least one double bond.
• Alkenes

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Branching chains

• Sometimes two hydrocarbon molecules can have the
  same numbers of the same atoms but have different
  arrangements of these atoms. We say they are
  isomers.

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Role of hydrocarbons in fats

• A fat molecule consists of a small, non
  hydrocarbon component joined to three hydrocarbon
  tails. The tails can be broken down to provide
  energy. Mammalian adipose cells stockpile fat.

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Functional Groups Parts of the molecules of life.

• Part of your homework tonight is to go to this
  web site Building Biomolecules The Functional
  Groups
• Review each of the functional groups and do the
  self quiz.

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Functional groups
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Adenosine triphosphate or ATP
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Phosphate groups

• In biology this is an important group found in
  ATP.

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• Structurally, ATP consists of the adenine
  nucleotide (ribose sugar, adenine base, and
  phosphate group, PO4-2) plus two other phosphate
  groups.

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Exergonic / Endergonic Reactions

• Energy releasing processes, ones that "generate"
  energy, are termed exergonic reactions.
• Reactions that require energy to initiate the
  reaction are known as endergonic reactions

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ATP The primary energy transferring molecule in
cells
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Macromolecules page 15sg

• Monomers make polymers. Polymers are long
  molecules consisting of many similar or identical
  building blocks linked by covalent bonds.

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Condensation Reaction

• Monomers are connected by a reaction in which two
  molecules are covalently bonded to each other
  through loss of a water molecule, also known as
  condensation reaction (also called dehydration
  synthesis .
• Dehydration Synthesis-Hydrolysis

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Hydrolysis

• Means - to break with water. Bonds between
  monomers are broken by the addition of water
  molecules, a hydrogen from the water attaching to
  one monomer and a hydroxyl group attaching to the
  adjacent monomer. This occurs in the digestive
  tract. Dehydration Synthesis-Hydrolysis
• Biology I Interactive Animations (go to
  biochemistry section)

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Carbohydrates fuel and building molecules pg 15
sg

• Carbohydrates have the general molecular formula
  CH2O
• The simplest CHO are monosaccarides.
• Disaccharides are double sugars (formed by
  dehydration synthesis)
• Polysaccharides are made of many sugars

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Monosaccharides

• Glucose is the most common monosaccharide and is
  vital to life
• Three common sugars share the same molecular
  formula C6H12O6. Because of their six carbon
  atoms, each is a hexose.

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Name 2 monosaccharides p 15 sg

• Glucose
• Fructose
• Galactose
• Ribose

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Glucose has the trademarks of a sugar pg 14 sg

• A hydroxyl group is attached to each carbon
  except one, here you find a double bond to oxygen
• Used as major nrg source for cells
• (2.2.8)

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Glucose comes in different shapes

• Linear and ring forms

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Draw the ring structures of glucose and ribose pg
14 sg

• Ribose ( 5 carbons)

• Glucose (6 carbons)

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• Most names for sugars end in ose
• In aqueous solutions, glucose molecules as well
  as most other sugars, form rings.

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Disaccharide

• Consists of two monosaccharides joined together
  by a glycosidic linkage, a covalent bond formed
  during dehydration reactions Dehydration
  Synthesis-Hydrolysis (go to carbohydrate
  synthesis)

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Common Disaccharides (name two disaccharides) pg
15 sg
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Storage Polysaccharides

• Starch is a common PolySac of plants. Consisting
  of glucose molecules

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Glycogen another storage molecule

• Stored mainly in liver and muscle, hydrolysis of
  glycogen releases glucose

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Storage of starch in plants

• Plants store starch as granules within cellular
  structures called plastids inside the
  chloroplasts

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Another structural poly sac is cellulose sg 15

• Found in plant cell walls- structural support

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• Due to the distinctive structures of starch and
  cellulose, cellulose is indigestible to humans .
• While cellulose is not a nutrient for humans it
  remains as an important fiber.

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Yet another structural poly sac

• Chitin used by arthropods (insects, spiders,
  crustaceans to form exoskeleton, also found in
  cell wall of fungi)

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• Tutorial 3.2 Macromolecules ( ann go to
  animations, then cho )

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Lipids- Diverse hydrophobic molecules pg 15 sg

• Fat molecules are made up of four parts
• a molecule of glycerol (on the right) and
• three molecules of fatty acids.

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Structure of Fatty Acid

• Has a long carbon chain, at one end is a carboxyl
  group. Attached to this is a long hydrocarbon
  tail. The non polar C-H bond in the tails make
  them hydrophobic

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The glycerol and fatty acid join

• One molecule of water is removed for each fatty
  acid joined to the glycerol.
• This results in a ester linkage.

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Saturated Fatty Acid

• Contain the maximum possible amount of hydrogens,
  thus saturated fats. The hydrocarbon chains in
  these fatty acids are, fairly straight and can
  pack closely together, making these fats solid at
  room temperature.

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Unsaturated Fatty Acid

• some of the carbons share double bonds, theyre
  not bonded to as many hydrogens as they could if
  they werent double. Therefore these oils are
  called unsaturated fats. They remain liquid

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Look at the difference
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Function of fats pag 15 sg

• energy storage molecules Fats possess more energy
  per molecule and less hydration compared with
  carbohydrates, resulting in fats possessing much
  more energy stored per unit mass or volume fats
  have 9cal/gram CHO and proteins have 4 cal/gram
• Stored as fats in animals and oils in plants
• In animals such as ourselves, fats are stored in
  adipose cells
• Buoyancy lipids are less dense than water
  allowing animals to float

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Phospholipids

• Major component of cell membranes
• Structure Phospholipids are made from glycerol,
  two fatty acids, and (in place of the third fatty
  acid) a phosphate group
• The hydrocarbon tails of the fatty acids are
  hydrophobic
• the phosphate group end of the molecule is
  hydrophilic because of the oxygens with all of
  their pairs of unshared electrons.
• This means that phospholipids are soluble in both
  water and oil.

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• Phospholipids have the special property of having
  both hydrophobic and hydrophilic parts
• A molecule that is both hydrophilic and
  hydrophobic is called amphipathic.

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Structure of phospholipids
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Function of Phospholipids

• Found in cell membranes. Act as barrier .
• When phospholipids are added to water they self
  assemble, with hydrophobic parts inward and
  hydrophilic parts outward.
• http//telstar.ote.cmu.edu/Hughes/tutorial/cellmem
  branes/orient2.swf

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Another group of lipids are Steroids

• A lipid characterized by a carbon skeleton
  consisting of four fused rings. One common
  steroid is cholesterol.
• Many hormones are steroids, including sex hormones

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• Tutorial 3.2 Macromolecules ( ann go to
  animations then to lipids)

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Proteins

• Proteins are a major constituent of most cells
  (gt50 dry weight)
• All proteins consist of polymers that are folded
  into specific conformations
• This conformation plus the chemistry of
  well-placed functional groups control a protein's
  function (another example of function follows
  form)
• Proteins are made up of 20 different types of
  amino-acid monomers

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Polymers of amino acids are called peptides pg 14
sg

• Remember the structure of an amino acid. Carboxyl
  and amino group. A protein consists of polymers
  of amino acids, folded and coiled into a specific
  configuration.

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• The side group determines characteristics, making
  it hydrophobic or hydrophilic, acidic or basic.

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Coming together to make a peptide bond.

• amino acid basics
• Animation of Peptide Bond Formation
• Animation - Amino acid condensation
• The carboxyl group of one is adjacent to the
  amino group of the other, an enzyme can join the
  amino acids by dehydration reaction.

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Several function of proteins. Pg 68 sg

• Structural proteins act as support. Examples
  include the silk fibers of spiders and insects,
  collagen in animal connective tissue, and keratin
  found in hair, horns, feathers.

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Storage proteins

• Storage of amino acids. Examples are egg whites,
  casein, found in milk, and plants have storage
  proteins in their seeds.

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Transport proteins

• Transport of other substances, Hemoglobin is an
  example, transporting oxygen from the lungs to
  other parts of the body. McGraw-Hill Online
  Learning Center TestltBLURTgt

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Hormonal Proteins

• They perform by coordinating of an organism's
  activities. An example is insulin.

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Movement Proteins

• Used for movement. Examples are actin and myosin
  found in muscle tissue.

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Defensive Proteins

• Protection from disease. Antibodies are an
  exampe.

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Enzymatic Proteins

• Selective acceleration of chemical reactions. We
  will be discussing enzymes in detail later.

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A proteins function depends on its conformation.

• A polypeptide is not the same as a protein.
• The chain of amino acids known as a polypeptide
  must be twisted and folded.
• Most proteins are globular (roughly spherical)
  others are fibrous in shape.

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Shape is everything

• In order for a protein to function properly it
  must be able to be recognized and fit properly to
  another molecule. (This is important to remember
  when we speak of enzymes)

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Polar and non polar amino acids (aa) pg 68 sg

• Polar aa have hydrophilic R groups
• Found on surface of proteins make them water
  soluble
• Make channels for hydrophilic substances
• Positive charged R groups allow ions through

• Positive charged R groups allow ions through
• Integral or transmembrane proteins

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• Transmembrane protein p 68sg

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Non polar aa/pg 68

• In center of water soluble proteins stabilize
  structure

• Remain embedded
• Peripheral proteins

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A proteins function depends on its conformation.
Pg 66 sg

• A polypeptide is not the same as a protein.
• The chain of amino acids known as a polypeptide
  must be twisted and folded.
• Most proteins are globular (roughly spherical)
  others are fibrous in shape.

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2 types you need to know pg. 66sg

• Globular - clumped into a shape of a ball. Major
  examples include insulin, hemoglobin, and most
  enzymes.
• http//student.ccbcmd.edu/gkaiser/biotutorials/pr
  oteins/images/u4fg1b3.jpg

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• Fibrous proteins Keratins - in wool, hair skin,
  fur, claws, nails, hooves, horns, scales, beaks,
  feathers, actin and mysin in muscle tissues and
  fibrinogen needed for blood clots.

• tropomycin

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Four levels of protein structure all driven by
chemical bonds/67 sg

• Primary structure determined by base structure
  of the gene that codes fro the polypeptide.
• A chain of amino acids

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Secondary Structure p 6667

• Regular repeating structure including beta
  sheets, and alpha helices stabilized by hydrogen
  bonds between groups in the main chain of the
  polypeptide.

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Two types of secondary structure

• Alpha - Helix the first structure. It has a rod
  shape. The peptide is coiled around an imaginary
  cylinder and stabilized by hydrogen bonds formed
  between components of the peptide bonds

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The second type

• Beta - pleated sheets the amino acids adopt the
  conformation of a sheet of paper and the
  structure is stabilized by hydrogen bonds between
  amino acids in different polypeptide strands.

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Lyzozyme
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Tertiary structure pg 67

• The three dimensional conformation of a
  polypeptide.
• Stabilized by intramolecular bonds that form
  between aa in the
• Bonds form, ionic, hydrogen, hydrophobic
  interactions and disulfide bridges.

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Quaternary Structure

• Linking together of 2 or more polypeptides to
  form a single protein

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Hemoglobin pg 67

• Prosthetic groups a non polypeptide structure
  contained in a protein
• Heme group linked to each of the four
  polypeptides in hemoglobin.
• Proteins with a prosthetic group are called
  conjugated proteins

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Protein folding

• Interactive Concepts in Biochemistry -
  Interactive Animations
• http//www.stolaf.edu/people/giannini/flashanimat/
  proteins/protein structure.swf
• Proteins Structure Animation

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• Tutorial 3.2 Macromolecules ( go to proteins )

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Nucleic acids are informational proteins

• First type of nucleic acid is deoxyribonucleic
  acid of DNA. The second type is ribonucleic acid
  or RNA.

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• DNA is structurally different than RNA.
• The sugar in DNA is deoxyribose and in RNA the
  sugar is ribose

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Nucleic acids are made of the monomer called
nucleotides

• Nucleotides are made of three parts.
• 1. nitrogenous base
• 2. pentose ( a five carbon sugar)
• 3. a phosphate group

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Found in DNA and RNA
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The Nitrogenous bases are 5 in type

• 1. Cytosine (C)
• 2. Thymine (T) found in DNA only
• 3. Uracil (U) found only in RNA
• 4. Adenine (A)
• 5. Guanine (G)

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There are two families of nitrogenous bases

• The pyrimidines
• Has a six- membered ring or carbon and nitrogen .
  
• These include cytosine, thymine, and uricil

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• And Purines
• Larger, with the six membered ring fused to a
  five membered ring.
• Includes Adenine and guanine

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Found in DNA and RNA
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Building a Polynucleotide

• Polynucleotides are joined by covalent bonds
  between the phosphate sugar Forms phosphodiester
  bond
• This results in the backbone of DNA and RNA

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Looks like this
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DNA- you must be able to draw this pg. 60 sg

• All along the appendages are attached the
  nitrogenous bases

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• Tutorial 3.2 Macromolecules ( go to nucleic
  acids )

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This all fits together

• The central dogma in molecular biology is
• DNA?RNA?protein
• You must be able to draw DNA and RNA