DR. K REVIEWS . . . : DR. K REVIEWS . . . PRESENTATION 3
ORGANIC CHEMISTRY jammasterk.com
ORGANIC CHEMISTRY : ORGANIC CHEMISTRY ORGANIC CHEMISTRY IS THE CHEMISTRY OF BIOLOGICAL MOLECULES = THE MOLECULES OF LIFE
ORGANIC CHEMISTRY IS THE CHEMISTRY OF ORGANIC COMPOUNDS
ORGANIC COMPOUNDS ARE CHARACTERIZED BY COVALENTLY BONDED CARBON ATOMS
CARBON ATOMS COVALENTLY BONDED TO OTHER CARBON ATOMS
CARBON ATOMS COVALENTLY BONDED TO OTHER ATOMS
ORGANIC MOLECULES: CARBON SKELETON : ORGANIC MOLECULES: CARBON SKELETON THE STRUCTURE OF ANY ORGANIC MOLECULE IS BUILT UPON A CARBON BACKBONE
CARBON ATOMS COVALENTLY BONDED TO OTHER CARBON ATOMSWITH ASSOCIATED HYDROGENS = A “HYDROCARBON CHAIN”
THE HYDROCARBON CHAIN CAN BE LINEAR
THE HYDROCARBON CHAIN CAN BE BRANCHED
THE HYDROCARBON CHAIN CAN BE A RING
THE HYDROCARBON CHAIN CAN FEATURE SINGLE BONDS BETWEEN THE CARBONS
HYDROCARBON CHAIN CAN FEATURE DOUBLE BONDS BETWEEN THE CARBONS
ORGANIC MOLECULES: FUNCTIONAL GROUPS : ORGANIC MOLECULES: FUNCTIONAL GROUPS THE PROPERTIES OF AN ORGANIC MOLECULE ARE DETERMINED BY ITS FUNCTIONAL GROUPS
FUNCTIONAL GROUP = A SMALL ARRANGEMENT OF ATOMS THAT CONFERS PROPERTIES ON THE OVERALL MOLECULE
FUNCTIONAL GROUPS INCLUDE:
HYDROXYL GROUPS
CARBONYL GROUPS
CARBOXYL GROUPS(ACID GROUPS)
SULFHYDRYL GROUPS
AMINO GROUPS
PHOSPHATE GROUPS
ORGANIC MOLECULES: OTHER FEATURES : ORGANIC MOLECULES: OTHER FEATURES ORGANIC MOLECULES CAN BE LARGE = MACROMOLECULES
SOME ORGANIC MOLECULES ARE LONG CHAINS OF REPEATING UNITS = POLYMERS/MONOMERS
POLYMERS ARE MADE THROUGH CONDENSATION REACTIONS
POLYMERS ARE BROKEN THROUGH HYDROLYSIS REACTIONS
MAKING POLYMERS: CONDENSATION REACTIONS : MAKING POLYMERS: CONDENSATION REACTIONS A CONDENSATION REACTION CREATES A LINKAGE BETWEEN TWO MONOMERS THROUGH THE CREATION OF WATER
H FROM ONE MONOMER
OH FROM THE OTHER MONOMER
A CONDENSATION REACTION IS ALSO CALLED A DEHYDRATION SYNTHESIS
BREAKING POLYMERS: HYDROLYSIS REACTIONS : BREAKING POLYMERS: HYDROLYSIS REACTIONS A HYDROLYSIS REACTION BREAKS A POLYMER INTO ITS COMPONENT MONOMERS THROUGH THE ADDITION OF WATER
H ADDED TO ONE MONOMER
OH ADDED TO THE OTHER MONOMER
ORGANIC MOLECULES: ISOMERS : ORGANIC MOLECULES: ISOMERS STRUCTURAL ISOMERS = SAME CHEMICAL FORMULA, DIFFERENT STRUCTURE
C6H12O6 = GLUCOSE
C6H12O6 = FRUCTOSE
GEOMETRIC ISOMERS = PLACEMENT OF HYDROGENS ASSOCIATED WITH A DOUBLE BOND
CIS CONFIGURATION = HYDROGENS ON SAME SIDE OF THE DOUBLE BOND
TRANS CONFIGURATION = HYDROGENS ON OPPOSITE SIDES OF THE DOUBLE BOND
ENANTIOMERS = MIRROR IMAGE ISOMERS
LEFT-HANDED MOLECULE = L-ENANTIOMER
RIGHT-HANDED MOLECULE = R-ENANTIOMER
CARBOHYDRATES : CARBOHYDRATES COMPOSITION: CARBON, HYDROGEN, OXYGEN… 1:2:1
COMMONLY CALLED SUGARS OR CARBS
TYPES
MONOSACCHARIDES
DISACCHARIDES
POLYSACCHARIDES
CARBOHYDRATES: MONOSACCHARIDES : CARBOHYDRATES: MONOSACCHARIDES SIMPLE SUGARS
SINGLE UNIT SUGARS
LINEAR OR RING FORM
EXAMPLES
GLUCOSE
FRUCTOSE
CARBOHYDRATES: DISACCHARIDES : CARBOHYDRATES: DISACCHARIDES TO MONOSACCHARIDES LINKED
LINKAGE = GLYCOSIDIC BOND
GLYCOSIDIC BOND FORMED THROUGH CONDENSATION REACTION
EXAMPLES
MALTOSE (GLUCOSE-GLUCOSE)
SUCROSE (GLUCOSE-FRUCTOSE)
CARBOHYDRATES: POLYSACCHARIDES : CARBOHYDRATES: POLYSACCHARIDES A POLYSACCHARIDE IS A POLYMER OF MULTIPLE MONOSACCHARIDE MONOMERS
GLYCOSIDIC BOND LINKAGES
THE BIOLOGICAL BIG THREE
STARCH = ENERGY STORAGE IN PLANTS
GLYCOGEN = ENERGY STORAGE IN ANIMALS
CELLULOSE = STRUCTURAL POLYSACCHARIDE = CELL WALLS
LIPIDS: GENERAL INFORMATION : LIPIDS: GENERAL INFORMATION HIGH MOLECULAR WEIGHT
NONPOLAR/HYDROPHOBIC
VARIABLE
TRIGLYCERIDES
PHOSPHOLIPIDS
STEROIDS
WAXES
LIPIDS: TRIGLYCERIDES : LIPIDS: TRIGLYCERIDES TRIGLYCERIDE = TRIACYLGLYCERIDE
GLYCEROL (-OH GROUPS)
3 FATTY ACIDS
FORMED THROUGH CONDENSATION REACTION
INCLUDES FATS AND OILS
FATTY ACIDS
SATURATED = ALL SINGLE BONDS
UNSATURATED = ONE OR MORE DOUBLE BONDS
THE FATTY ACIDS CHARACTERIZE THE TRIGLYCERIDE
PRACTICAL TRIGLYCERIDES : PRACTICAL TRIGLYCERIDES FATS
ARE SATURATED TRIGLYCERIDES
ARE CHARACTERIZED BY SATURATED FATTY ACIDS
ARE GENERALLY SOLID AT ROOM TEMPERATURE
ARE GENERALLY OF ANIMAL ORIGIN
OILS
ARE UNSATURATED TRIGLYCERIDES
ARE CHARACTERIZED BY UNSATURATED FATTY ACIDS
ARE GENERALLY LIQUID AT ROOM TEMPERATURE
ARE GENERALLY OF PLANT ORIGIN
PHOSPHOLIPIDS : PHOSPHOLIPIDS GLYCEROL
2 FATTY ACIDS (NONPOLAR, HYDROPHOBIC)
1 PHOSPHATE (POLAR, HYDROPHILIC)
NATURE OF THE MOLECULE
HYDROPHILIC HEAD
HYDROPHOBIC TAILS
SPONTANEOUSLY ORGANIZES INTO A BILAYER IN AQUEOUS SOLUTION
PRIMARY STRUCTURE OF BIOLOGICAL MEMBRANES
STEROIDS : STEROIDS STEROIDS = STEROLS
CHEMICAL STRUCTURE OF 4 FUSED RINGS
EXAMPLES
TESTOSTERONE
ESTROGEN
PROGESTERONE
CORTISOL
CHOLESTEROL (PRIMARY ORIGIN)
WAXES : WAXES EXTREMELY HYDROPHOBIC
PLANT MOLECULES = CUTICLE
PROTEINS: GENERAL INFORMATION : PROTEINS: GENERAL INFORMATION COMPOSED OF AMINO ACIDS
AMINO ACIDS LINKED BY PEPTIDE BONDS
AMINO ACID CHAIN = POLYPEPTIDE
AMINO ACIDS : AMINO ACIDS BASIC STRUCTURE
CENTRAL CARBON
AMINO GROUP
CARBOXYL (ACID) GROUP
HYDROGEN
SIDE CHAIN = R GROUP (VARIABLE)
PEPTIDE BOND FORMATION : PEPTIDE BOND FORMATION CONDENSATION REACTION
AMINO GROUP (H)
CARBOXYL (ACID) GROUP (OH)
PROTEIN STRUCTURE: 4 LEVELS : PROTEIN STRUCTURE: 4 LEVELS PRIMARY STRUCTURE
SECONDARY STRUCTURE
TERTIARY STRUCTURE
QUATERNARY STRUCTURE
PROTEINS: PRIMARY STRUCTURE : PROTEINS: PRIMARY STRUCTURE SEQUENCE OF AMINO ACIDS
IDENTITY
ORDER
DETERMINES SECONDARY STRUCTURE
PRIMARY STRUCTURE IS A FEATURE OF POLYPEPTIDES
PROTEINS: SECONDARY STRUCTURE : PROTEINS: SECONDARY STRUCTURE DUE TO INTERACTION OF AMINO ACIDS IN PRIMARY STRUCTURE
ALPHA HELIX
BETA PLEATED SHEET
SECONDARY STRUCTURE IS A FEATURE OF POLYPEPTIDES
PROTEINS: TERTIARY STRUCTURE : PROTEINS: TERTIARY STRUCTURE THREE-DIMENSIONAL FOLDING OF SECONDARY STRUCTURE
INFLUENCE OF AMINO ACID SIDE CHAINS
DISULFIDE BONDS
HYDROGEN BONDS
IONIC BONDS
TERTIARY STRUCTURE IS A FEATURE OF POLYPEPTIDES
PROTEINS: QUATERNARY STRUCTURE : PROTEINS: QUATERNARY STRUCTURE A 3-DIMENSIONAL ASSEMBLAGE OF MULTIPLE POLYPEPTIDES
A PROTEIN IS A COMPOSITION OF ONE OR MORE POLYPEPTIDES
EXAMPLE: HEMOGLOBIN = 4 POLYPEPTIDES
QUATERNARY STRUCTURE DETERMINES FUNCTION
PERFECT QUATERNARY STRUCTURE = PERFECT FUNCTION
QUATERNARY STRUCTURE IS A UNIQUE FEATURE OF PROTEINS
DENATURATION/RENATURATION : DENATURATION/RENATURATION DENATURATION = NEGATIVE CHANGE IN PROTEIN STRUCTURE
RENATURATION = POSITIVE CHANGE IN PROTEIN STRUCTURE
FACTORS
PH
SALT CONCENTRATION
TEMPERATURE
DENATURATIONCAN BE REVERSIBLE, OR IRREVERSIBLE
DENATURATION/RENATURATION CAN REGULATE PROTEIN ACTIVITY
NUCLEIC ACIDS: GENERAL INFORMATION : NUCLEIC ACIDS: GENERAL INFORMATION ARE GENERALLY POLYMERS OF NUCLEOTIDES
DNA
RNA
ATP (RESEMBLES A NUCLEOTIDE)
FOCUS ON NUCLEOTIDE STRUCTURE : FOCUS ON NUCLEOTIDE STRUCTURE FIVE-CARBON SUGAR
DEOXYRIBOSE (DNA)
RIBOSE (RNA)
PHOSPHATE GROUP
NITROGENOUS BASE
ADENINE (DNA/RNA) = PURINE (BIG, 2-RING)
THYMINE (DNA) = PYRIMIDINE (SMALL, 1-RING)
URACIL (RNA) = PYRIMIDINE
CYTOSINE (DNA/RNA) = PYRIMIDINE
GUANINE (DNA/RNA) = PURINE
FOCUS ON DNA STRUCTURE & FUNCTION : FOCUS ON DNA STRUCTURE & FUNCTION DEOXYRIBOSE SUGAR
DOUBLE HELIX
“RAILS” = SUGAR-PHOSPHATE STRANDS
ANTI-PARALLEL (3’-5’)
“RUNGS” = NITROGENOUS BASE PAIRS
A = T
C = G
COMPLEMENTARY
HYDROGEN BONDS
PERMANENT GENETIC LIBRARY
FOCUS ON RNA STRUCTURE & FUNCTION : FOCUS ON RNA STRUCTURE & FUNCTION SINGLE-STRANDED MOLECULE
RIBOSE SUGAR
URACIL REPLACES THYMINE
TEMPORARY USE IN PROTEIN SYNTHESIS
FOCUS ON ATP STRUCTURE & FUNCTION : FOCUS ON ATP STRUCTURE & FUNCTION ADENOSINE TRIPHOSPHATE
ADENINE
RIBOSE
3 PHOSPHATE GROUPS
ENERGY CONTAINING MOLECULE
IMMEDIATE AND UNIVERSAL USE IN THE CELL
HIGH ENERGY BOND TO THIRD PHOSPHATE