Download ORGANIC CHEMISTRY: Molecules of Life

ORGANIC CHEMISTRY: Molecules of Life
Organic Chemistry = deals with substances with element “C”
 4th most abundant element on Earth
 Nonmetal  forms up to FOUR covalent bonds
 Found in all living organisms
 4 v e Can form double & triple bonds with itself or other
elements
 Can form straight chains, branches, or ring structures
(form tubes or coils)
 C bonded to H  Hydrocarbons } bond stores much
energy, therefore good fuels
C – H } Nonpolar covalent due to low difference
between electronegativities (2.5 – 2.1 = 0.4)
 Single bonded C to C bonds = Alkanes
 At least one double bond between C to C = Alkenes
 At least one triple bond between C to C = Alkynes
FUNCTIONAL GROUPS = have definite chemical properties
Other Organic chemistry Vocabulary:
ISOMERS = same molecular or empirical formula but exists
in differ forms of molecule
Structural isomers = differences in actual structure
Stereoisomers = same carbon structure but differ in
how groups attach
enantiomers = “mirror “ images of each other
C6H12O6
POLYMER = large molecule by linking many smaller
molecules EX: Carbohydrates
MONOMER = small subunits of polymers
EX: Monosaccharides
DEHYDRATION REACTION = bonding two monomers
releasing –OH from one monomer and –H from another
monomer
HYDROLYSIS REACTION = the breaking of two monomers
by adding water
FOUR MACROMOLECULES NEEDED for LIFE:
(C based compounds)
1. Carbohydrates
2. Nucleic acids
3. Proteins
4. Lipid
POLYMERS
SEE hand-Out Chart!
CARBOHYDRATES:
 All carbohydrates come from plants!!!!
 Contain elements: C, H, O in a molar ratio of 1:2:1
EX: C6H12O6 Glucose (hexose = 6-C sugar)
Ribose  5-C sugar = pentose
 Release energy when breaking C-H (oxidation )
 “building blocks” or monomers = monosaccharides
 Monosaccharides (3-7 C backbone)  contain hydroxyl (-OH)
making the sugar an alcohol and a carbonyl (-C=O) making the sugar
either an aldehyde (glucose) or ketone (fructose)
NOTE: Enzymes that act on different sugars can distinguish between
structures and isomers. (α – glucose and β-glucose = differ in position of
–OH group)
 Mono + mono = Disaccharide
EX: glu + glu = maltose  long chains of glucose = STARCH
glu + fru = sucrose (table sugar)
glu + galactose = lactose (sugar in milk)
 POLYSACCAHRIDES (polymers of monosaccharides)
- Serve as energy storage because they are NOT soluble in watertoo large to pass thru cell membrane
o Starch = (found in plants) α – glucose linked in long chains
(~6000)
 Simplest structure = amylose (unbranched chains)
 Complex structure = amylopectin = (branched chains)
o Glycogen= starch in animals
o Cellulose = β-glucose linked in chains




Most abundant polysaccharide
Humans cannot break down  lack enzyme
Becomes “fiber” of digestive tract
Cows break down by way of symbiotic bacteria &
enzymes
o CHITIN = polymer of N-acetylglucosamine (substituted version
of glucose, has a amino group)
 Seeds are coated with chitin to protect against fungi
attacks
 Has antiviral and antibacterial properties  good in
medicine
 Found in fungi and arthropods
 Serves as an exoskeleton
o PEPTIDOGLYCAN = polymer found in bacteria; each
monomer has a amino group + an amino acid chain
NUCLEIC ACIDS:
 Made up of elements: C, H, O, P, N
 DNA (deoxyribonucleic acid) = genetic material in cell
and RNA (ribonucleic acid) = copy of DNA
CENTRAL DOGMA of Biology:
DNA  RNA  Proteins
 Monomers = NUCLEOTIDES} 3 components: N-Base (organic
nitrogen), Phosphate, 5-C sugar (pentose) ribose
 NUCLEOTIDES:
o DNA, RNA, Adenosine triphosphate (ATP =energy molecule),
nicotinamide adenine dinucleotide (NAD+), flavin adenine
dinucleotide (FAD)}electron carriers in cellular processes
 BOND two Nucleotides =
o The phosphate of one nucleotide binds to the hydroxyl end of
another nucleotide at pentose (5-C sugar)
 5’ -3’ (5th C in ribose bonded to phosphate group)
 3’-5’ (3rd C in ribose bonded to phosphate group)
o See diagram below
Dehydration
rxn
DNA 
 double helix, one strand hydrogen bonded to another strand
at the nitrogen bases = complimentary
 genetic material (original= “blueprint”) made up of
specific N-Bases
 N-Bases: Adenine (A), Thymine (T), Cytosine (C),
Guanine (G)
 CANNOT ever leave nucleus
RNA 
 Differs from DNA with 5-C sugar ribose has a with a
hydroxyl group of C-2
 Three types:
o messenger RNA (mRNA) = copy (complimentary) of
DNA
o ribosomal RNA (rRNA) = part of ribosome, “hold”
tRNA and mRNA together
o transfer RNA (tRNA) = carries amino acids to
ribosome
 N-bases:
o N-Bases: Adenine (A), Uracil (U), Cytosine (C),
Guanine (G)
PROTEINS:
 Most diverse group (both chemically & functionally) of biological
macromolecules
 FUNCTIONS of Proteins in organisms:
o Enzyme catalyst = increase the chemical rxn rate by lowing the
Ea  very specific “Lock n Key” model
o Defense = use structure to “recognize” foreign substances
o Transport = carries small molecules or ions to a specific cell or
across cell membranes
o Support = play structural roles like collagen in skin
o Motion = contractile proteins - actin & myosin allow for
contraction of muscles; cytoskeleton in cell allow cell to move
substances in/out
o Regulation = small proteins, hormones, serve as intercellular
messengers; turns on/off genes
o Storage = calcium and iron are stored in body by binding to
storage proteins
 Made up of: C, H, O, N
 Monomers = Amino Acids (AA) (found in appendix 2)
o 20 Amino Acids
o All AA contain a hydroxyl and a carboxyl group
o Differs AA  R’ Group
o Specific order of AA determines protein structure
& Function
o AA are bonded together by a peptide bond
 Structures of Proteins:
o Primary (linear), Secondary (H-bonding between
amino acids creates α & β pleated sheets),
Tertiary (folded sheets = globular proteins w/
DISULFIDE BONDS), Quaternary (subunits of
globular proteins)
 Nonpolar parts of proteins are found together in the
“middle” of structure with the polar ends on outside
 Proteins have “motifs” (reoccurring part) and
“domains” (substructure within the tertiary structure)
ANALOGY: Amino acids are letters, motifs are words, and domains are
paragraphs
 Proteins have “chaperones” to help them fold correctly
 Improper folding  theory for diseases
 DENATURATION = process that changes the shape
of a protein due to temperature and pH, or ionic
concentration changes; usually causes inactive protein
 Small proteins structures can renature (renaturation)
LIPIDS: (fats, phospholipids, steroids)
 Differs from the other three macromolecules: INSOLUABLE in
water
 Made up of element: C, H, O (P) }not in a 1:2:1 RATIO
 FATS: Long-term energy; STEROIDS: plasma membrane &
hormones; PHOSPHOLIPIDS: Plasma Membrane; WAXES:
protect, prevention of water loss (ex: Plants cuticle)
 Monomers = Glycerol & Fatty Acids (FA)
FATTY ACIDS (FA):
- Long chain C with a carboxyl end
GYCEROL:
- 3 C polyalcohol  has 3- hydroxyl groups
FATS: provide insulation, long-term energy storage
- Most lipid molecules contain 3-FA and a glycerol bonded together
TRIGLYCERIDES
- SATURATED (single bonds) vs Unsaturated FA (at least one
double bond)
Unsaturated:
SATURATED:
 “bad” fat
 Solid at room temperature
 Single bonds – having as
many Hydrogen bonds as
possible
 “better” fat
 Liquid at room temp
 Double bonds (at least one –
Mono; more than one polyunsaturated
IMPORTANT: the energy from the C-H bond in fats gives twice the
amount of energy than carbohydrates (glycogen has more C-OH bonds) =
9 kcal/g
READ: Article “Everyone Needs a Little Fat, Right?”
“HYDROGENATED” Fats  done chemically, produces double bonds
with a trans configuration known as
Why “hydrogenate” fats?
It’s the processing of pure vegetable oils – a good source of
heart-friendly unsaturates – that creates harmful trans fats!
During manufacturing, these liquid oils have hydrogen
bubbled through them in a process called hydrogenation to
improve their texture, flavour and shelf life. The resulting
product is a more solid fat, called hydrogenated fat or
hydrogenated vegetable oil, which goes on to be used as an
ingredient in many processed foods.
PHOSPHOLIPIDS =
 found in plasma (cell) membrane
 the only lipid with a phosphorous – makes one end POLAR (head) =
HDROPHILIC end & the other end is still NONPOLAR (tail) =
HYDROPHOBIC end
 structure: similar to a triglyceride but substitute one fatty acids with
a phosphate group
 Polar end = Phosphate group fatty acid chains “tails”
 Membranes= double layer with nonpolar ends toward each other and
the polar ends on inside or outside of membrane
STEROIDS:
 Structure= four fused C rings and differ by the functional groups off
C structure
ESTROGEN
WAXES:
 Structure: long chain fatty acids bonded with a long chain alcohol
 Used for plants to prevent water loss, earwax repels insects and dust
& dirt, beeswax used to make honeycomb for storing honey
CHEMICAL BONDING of Macromolecules for Life:
CARBOHYDRATE: monomer + monomer = glycoside bond
NUCLEIC ACIDS: monomer + monomer = phosphodiester linkage
PROTEINS: monomer + monomer = peptide bond (polypeptide bond)
LIPID: glycerol + fatty acids = ester bonds