Organic Chemistry

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Outline

• Organic vs Inorganic
• Functional Groups and Isomers
• Macromolecules
• Carbohydrates
• Lipids
• Proteins
• Nucleic Acids

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Organic Molecules

• Inorganic Chemistry of elements other than
  carbon
• Organic Carbon-based chemistry

Organic
Inorganic
Always containcarbon and hydrogen
Usually with - ions
Alwayscovalent bonding
Usuallyionic bonding
Often quite large, withmany atoms
Always withfew atoms
Usually associatedliving systems
Often associated with nonliving matter
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Carbohydrates as structural materials
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Carbon Atom

• Carbon atoms
• Contain a total of 6 electrons
• Only four electrons in the outer shell
• Very diverse as one atom can bond with up to four
  other atoms
• Often bonds with other carbon atoms to make
  hydrocarbons
• Can produce long carbon chains like octane
• Can produce ring forms like cyclohexane

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Octane Cyclohexane
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Functional Groups and Isomers

• Functional groups
• Specific combinations of bonded atoms
• Attached as a group to other molecules
• Always react in the same manner, regardless of
  where attached
• Determine activity and polarity of large organic
  molecules
• Many functional groups, but only a few are of
  major biological importance

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Biologically ImportantFunctional Groups
Compound
Structure
Group
Significance
Alcohols
Hydroxyl
Polar, forms H-bonds some sugarsand amino acids
Example Ethanol
Polar, forms H-bonds some sugarsand amino
acids Example Ethanol
Aldehydes
Polar some sugarsExample Formaldehyde
Carbonyl
Polar some sugarsExample Formaldehyde
Polar some sugarsExample Acetone
Ketones
Polar some sugarsExample Acetone
CarboxylicAcids
Polar, acidic fats and amino acidsExample
Acetic acid
Carboxyl
Polar, acidic fats and amino acidsExample
Acetic acid
Polar, basic amino acidsExample Tryptophan
Amino
Amines
Polar, acidic some amino acidsExample
Adenosine triphosphate
Polar, basic amino acidsExample Tryptophan
Thiols
Sulfhydryl
Disulfide Bonds some amino acidsExample
Ethanethiol
Disulfide Bonds some amino acidsExample
Ethanethiol
OrganicPhosphates
Polar, acidic some amino acidsExample
Adenosine triphosphate
Phosphate
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Isomers

• Isomers - organic molecules that have
• Identical molecular formulas, but
• Differing internal arrangement of atoms

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Macromolecules

• Some molecules called macromolecules because of
  their large size
• Usually consist of many repeating units
• Resulting molecule is a polymer (many parts)
• Repeating units are called monomers
• Some examples

Subunit(s)
Example
Category
Glycerol fatty acids
Fat
Lipids
Monosaccharide
Polysaccharide
Carbohydrates
Amino acid
Polypeptide
Proteins
Nucleotide
DNA, RNA
Nucleic Acids
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Common Foods
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Dehydration and Hydrolysis

• Dehydration - Removal of water molecule
• Used to connect monomers together to make
  polymers
• Polymerization of glucose monomers to make starch
• Hydrolysis - Addition of water molecule
• Used to disassemble polymers into monomer parts
• Digestion of starch into glucose monomers
• Specific enzymes required for each reaction
• Accelerate reaction
• Are not used in the reaction

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Synthesis and Degradationof Polymers
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Four Classes of Organics1 - Carbohydrates

• Monosaccharides
• Single sugar molecule
• Glucose, ribose, deoxyribose
• Disaccharides
• Contain two monosaccharides joined during
  dehydration reaction
• Sucrose
• Polysaccharides
• Polymers of monosaccharides
• Starch, cellulose, chitin

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Popular Models for RepresentingGlucose Molecules
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Synthesis and Degradationof Maltose, a
Disaccharide
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Carbohydrates ExamplesMonosaccharides

• Single sugar molecules
• Quite soluble and sweet to taste
• Examples
• Glucose (blood), fructose (fruit) and galactose
• Hexoses - Six carbon atoms
• Isomers of C6H12O6
• Ribose and deoxyribose (in nucleotides)
• Pentoses Five carbon atoms
• C5H10O5 C5H10O4

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Carbohydrates ExamplesDisaccharides

• Contain two monosaccharides joined by dehydration
  reaction
• Soluble and sweet to taste
• Examples
• Sucrose
• Table sugar, maple sugar
• One glucose and one fructose joined by
  dehydration
• Maltose
• Malt sugar
• Two glucoses joined by dehydration

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Carbohydrates ExamplesPolysaccharides (1)

• Polymers of monosaccharides
• Low solubility not sweet to taste
• Examples
• Starch
• Polymer of glucose
• Used for short-term energy storage
• Plant starch
• Often branched chain
• Amylose, corn starch
• Animal starch
• Unbranched
• Glycogen in liver and muscles

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Carbohydrates ExamplesPolysaccharides (2)

• More polysaccharide examples
• Cellulose
• Long, coiled polymer of glucose
• Glucoses connected differently than in starch
• Structural element for plants
• Main component of wood and many natural fibers
• Indigestible by most animals
• Chitin
• Polymer of glucose
• Each glucose with an amino group
• Very resistant to wear and digestion
• Arthropod exoskeletons, cell walls of fungi

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StarchStructure and Function
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GlycogenStructure and Function
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CelluloseStructure and Function
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Four Classes of Organics2 - Lipids

• Insoluble in water
• Long chains of repeating CH2 units
• Renders molecule nonpolar
• Types of Lipids

Human Uses
Organismal Uses
Type
Butter, lard
Long-term energy storage thermal insulation in
animals
Fats
Cooking oils
Long-term energy storage in plants and their seeds
Oils
No-stick pan spray
Component of plasma membrane
Phospholipids
Medicines
Component of plasma membrane hormones
Steroids
Candles, polishes
Wear resistance retain water
Waxes
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Blubber
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Types of LipidsTriglycerides
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Types of LipidsTriglycerides (1)

• Triglycerides (Fats)
• Long-term energy storage
• Backbone of one glycerol molecule
• Three-carbon alcohol
• Each has an OH- group
• Three fatty acids attached to each glycerol
  molecule
• Long hydrocarbon chain
• Saturated - no double bonds between carbons
• Unsaturated - ?1 double bonds between carbons
• Carboxylic acid at one end
• Carboxylic acid connects to OH on glycerol in
  dehydration reaction

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Dehydration Synthesis of Triglyceridefrom
Glycerol and Three Fatty Acids
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Types of LipidsPhospholipids (2)

• Phospholipids
• Derived from triglycerides
• Glycerol backbone
• Two fatty acids attached instead of three
• Third fatty acid replaced by phosphate group
• The fatty acids are nonpolar and hydrophobic
• The phosphate group is polar and hydrophilic
• Molecules self arrange when placed in water
• Polar phosphate heads next to water
• Nonpolar fatty acid tails overlap and exclude
  water
• Spontaneously form double layer a sphere

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Phospholipids Form Membranes
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Types of LipidsSteroids Waxes (3)

• Steroids
• Cholesterol, testosterone, estrogen
• Skeletons of four fused carbon rings
• Waxes
• Long-chain fatty acid bonded to a long-chain
  alcohol
• High melting point
• Waterproof
• Resistant to degradation

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Steroid Diversity
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Waxes
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Four Classes of Organics3 -Proteins

• Functions
• Support Collagen
• Enzymes Almost all enzymes are proteins
• Transport Hemoglobin membrane proteins
• Defense Antibodies
• Hormones Many hormones insulin
• Motion Muscle proteins, microtubules

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Protein SubunitsThe Amino Acids

• Proteins are polymers of amino acids
• Each amino acid has a central carbon atom (the
  alpha carbon) to which are attached
• a hydrogen atom,
• an amino group NH2,
• A carboxylic acid group COOH,
• and one of 20 different types of R (remainder)
  groups
• There are 20 different amino acids that make up
  proteins
• All of them have basically the same structure
  except for what occurs at the placeholder R

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Structural Formulas for the20 Amino Acids
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ProteinsThe Polypeptide Backbone

• Amino acids joined together end-to-end
• COOH of one AA covalently bonds to the NH2 of the
  next AA
• Special name for this bond - Peptide Bond
• Two AAs bonded together Dipeptide
• Three AAs bonded together Tripeptide
• Many AAs bonded together Polypeptide
• Characteristics of a protein determined by
  composition and sequence of AAs
• Virtually unlimited number of proteins

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Synthesis and Degradation of a Peptide
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Protein MoleculesLevels of Structure

• Primary
• Literally, the sequence of amino acids
• A string of beads (up to 20 different colors)
• Secondary
• The way the amino acid chain coils or folds
• Describing the way a knot is tied
• Tertiary
• Overall three-dimensional shape of a polypeptide
• Describing what a knot looks like from the
  outside
• Quaternary
• Consists of more than one polypeptide
• Like several completed knots glued together

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Levels of Protein Organization
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Examples of Fibrous Proteins
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Protein-folding Diseases

• Assembly of AAs into protein extremely complex
• Process overseen by chaperone molecules
• Inhibit incorrect interactions between R groups
  as polypeptide grows
• Defects in these chaperones can corrupt the
  tertiary structure of proteins
• Mad cow disease could be due to mis-folded
  proteins

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Four Classes of Organics4 -Nucleic Acids

• Polymers of nucleotides
• Very specific cell functions
• DNA (deoxyribonucleic acid)
• Double-stranded helical spiral (twisted ladder)
• Serves as genetic information center
• In chromosomes
• RNA (ribonucleic acid)
• Part single-stranded, part double-stranded
• Serves primarily in assembly of proteins
• In nucleus and cytoplasm of cell

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The Nucleotides ofNucleic Acids

• Three components
• A phosphate group,
• A pentose sugar (ribose or deoxyribose), and
• A nitrogenous base (4 kinds in DNA, 3 kinds in
  RNA, 3 common to both
• Nucleotide subunits connected end-to-end to make
  nucleic acid
• Sugar of one connected to the phosphate of the
  next
• Sugar-phosphate backbone

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Nucleotides
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DNA Structure
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RNA Structure
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Comparison of DNA RNA

• Table 3.4

RNA
DNA
Feature
Ribose
Deoxyribose
Sugar
Cytosine, guanine adenine, uracil
Cytosine, guanineadenine, thymine
Bases
Mostly single stranded
Double-stranded Pairing across strands
Strands
No
Yes
Helix
Interprets genetic info protein synthesis
Heredity cellular control center
Function
Cell nucleus and cytoplasm
Chromosomes of cell nucleus
Where
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Other Nucleic Acids

• ATP (adenosine triphosphate) is composed of
  adenine, ribose, and three phosphates
• In cells, one phosphate bond is hydrolyzed
  Yields
• The molecule ADP (adenosine diphosphate)
• An inorganic phosphate molecule pi
• Energy
• Other energy sources used to put ADP and pi back
  together again

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ATP
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Review

• Organic vs Inorganic
• Functional Groups and Isomers
• Macromolecules
• Carbohydrates
• Lipids
• Proteins
• Nucleic Acids

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