Organic Chemistry

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Organic Chemistry

• All living things are mostly composed of 4
  elements H, O, N, C honk
• Compounds are broken down into 2 general
  categories
• Inorganic Compounds
• Do not contain carbon
• Organic compounds
• Contain significant amounts of carbon.
• Often found with common "functional groups"

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Carbon The Swiss Army Knife of Chemistry. 

• Carbon is essential to life for several reasons
• It can form strong stable (usually non-polar)
  covalent bonds
• It can form up to 4 chemical bonds
• It can form multiple bonds

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Organic Compounds

• Organic Compounds often form Polymers
• Long chains of smaller molecules (not atoms)
  called monomers, bind to form huge Macromolecules
  
• 4 Types Carbohydrates, Lipids, Proteins
  Nucleic acids

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Carbohydrates

• Includes Sugars, starches, cellulose glycogen
• Made of Carbon ( C ), Hydrogen ( H ), and Oxygen
  (O )
• Following ratio of elements CnH2nOn
• Sugars Provide immediate energy for cells
• Simple sugars include Glucose Fructose since
  these are made of only 1 Carbohydrate molecule
  they are known as Monosaccharides

Glucose A Monosaccharide
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Dehydration Synthesis

• Monosaccharides can be linked together through
  the process of Dehydration Synthesis
• Water is removed from 2 monocaccharides -
  resulting in a covalent bond between the 2
  molecules
• Sucrose (table sugar) is made of 2 sugars linked
  together and these are called Disaccharides
• Require some digestion to be used by cells

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Hydrolysis

• Dehydration synthesis is a reversible process
  Called Hydrolysis.
• A water molecule is inserted where the monomers
  join. Breaking their bonds.

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Dehydration Synthesis Simplified
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Hydrolysis Simplified
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Polysaccharides

• Starches are many monosaccharides linked together
  in a single chain. These are called
  Polysaccharides.
• Plants use Starch for energy storage e.g.
  Potatoes
• Two types of starches
• Amylose - Long strait unbranched chains
• Pectins - many linked short Amylose chains

Starch
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Cellulose

• Cellulose is made of long polysaccharide chains
• Plants use this for structure (e.g. Wood) - not
  very digestible
• Due to the reverse orientation of the
  monosaccharide subunits, digestive enzymes cannot
  hydrolyze the bonds between them

Cellulose
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Glycogen

• Glycogen is a moderately branched polysaccharide
• Animals use this for short-term energy storage.
• Mostly stored in the human liver until converted
  to fat

Glycogen
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Lipids

• Lipids are macromolecules including Fats, Waxes
  and Oils.
• Primary function is energy storage.
• Energy is stored in C-H bonds.
• More efficient in storing energy
• Lipids are made of 2 parts
• Glycerol - an alcohol - Serves as backbone of the
  molecule
• 3 Fatty acids - Long hydrocarbon chains

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Dehydration Synthesis of a Lipid
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Hydrolysis of a Lipid
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Types of fats

• Saturated fats have long chains with no
  double-bonds
• Unsaturated fats have double bonds
• Polyunsaturated fats have many double bonds
• Each time a double bond is encountered, the
  molecule "Bends" slightly, resulting in a lower
  density of the lipid. This makes the molecule
  more likely to remain liquid at room or body
  temperatures. And thus, less likely to clog
  cardiac arteries.

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Other Lipids

• 4 Other types of biologically important Lipids
• Phospholipids - Important for membrane structure
• Steroids - eg. Cholesterol testosterone.
  Provide membrane support / serve as hormones
• Terpenes - serve as important components of
  pigments
• Prostaglandins - appear to act like localized
  hormones to induce cellular/tissue responses

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Proteins

• Proteins are made of Amino Acids
• There are 20 different amino acids. Each having a
  similar general structure - Differ only in their
  R groups

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Peptide Bonds

• Amino acids form proteins via dehydration
  synthesis forming peptide bonds
• Two amino acids linked together are called
  dipeptides
• More than 2 linked together are called
  polypeptides - polypeptides can be thousands of
  amino acids long

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Dehydration synthesisof a protein
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Hydrolysis of a Protein
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Protein Structure

• Protein types include globular proteins which are
  usually enzymes and Fiberous proteins which
  usually serve for structure (eg. Hair)
• Proteins Exhibit 4 levels of structure.

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Primary Structure

• Primary Structure of a protein is its sequence
  of amino acids
• Primary Structure dictates all further levels of
  protein structure

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Secondary Structure

• The Sequence (primary structure) causes parts of
  a protein molecule to fold into sheets or bend
  into helix shapes - this is a proteins Secondary
  Structure.

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Tertiary Structure

• The protein then can compact and twist on itself
  to form a mass called its Tertiary Structure

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Quaternary Structure

• Several Proteins then can can combine and form a
  proteins Quaternary Structure
• Various conformations are usually caused by the
  formation of hydrogen or disulfide bonds.
• PH, changes or heat can disrupt these bonds,
  permanently denaturing the protein.

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Nucleic Acids

• Two types of Nucleic acids
• DNA (Deoxyribonucleic Acid)
• RNA (Ribonucleic acid)
• DNA is Formed of in a "Double Helix" - like a
  spiral staircase.

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Nucleotides

• DNA is formed from Nucleotides
• These are made of 3 components
• A 5-Carbon Sugar
• A Nitrogenous base
• A Phosphate group
• Nucleotides form a backbone through linkages from
  the OH group of the 3rd carbon to a phosphate
  group of the adjoining nucleotide. These are
  called Phosphodiester bonds

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Types of Nucleotides

• For DNA There are 4 different Nucleotides
  categorized as either Purines (double ring) or
  Pyramidines (single ringed). These are usually
  represented by a letter. These Are
• Adenine (A)
• Cytosine (C)
• Guanine (G)
• Thymine (T)

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Base Pairing Rules

• Each "Rung" of the DNA "staircase" is formed by
  the linking of 2 Nucleotides through Hydrogen
  Bonds.
• These Hydrogen bonds form only between specific
  Nucleotides. This is known as Base Pairing. The
  rules are as follows
•  Adenine (A) will ONLY bond to Thymine (T)
• Cytosine (C) will ONLY bond to Guanine (G)

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Summary of DNA Structure
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RNA

• AKA ribonucleic acid
• RNA differs from DNA in several important ways.
• It is much smaller
• It is single-stranded
• It does NOT contain Thymine, but rather a new
  nucleotide called Uracil which will bind to
  Adenine.

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ATP

• Short for Adenosine Tri-Phosphate. ATP is closely
  related to nucleic acids.
• Composed of Ribose, Adenine a phosphate group
• Phosphate group has ability to bind/release
  additional phosphate group allowing it to store
  or release energy