Organic Chemistry
deals with organic compounds
Cell composition
70 – 95% water, the rest is carbon based compounds
Major elements in living things:
C, O, H, N, S, P
Organic compounds-
compounds containing
carbon bonded to carbon–only formed within living things (usually also has H)
Inorganic compounds-
compounds that do not contain
carbon bonded to carbon–found in living + non living world
Carbon
4 valence electrons. Most likely to share electrons in covalent bonds- can form four directions of bonds
What different shapes can carbon compounds can take on?
straight (chain), branched, closed rings
Assume H are bonded to the extra Cs
Hydrocarbons-
contain only
C and H. Major component of
fossil fuels. Store large amounts of
organic compounds
Isomers-
compounds that have the same molecular formula but
different structural formulas
Structural isomers-
differ in arrangement of atoms
Geometric isomers
same arrangement, but
subtle differences in shape or in spatial arrangement
Stereoisomers
mirror images- one is
active and inactive
Functional Groups
Groups of atoms attached to
carbon skeletons; Most commonly involved in
chemical reaction; Each gives unique properties to the molecule
Polymer-
large molecule consisting of many identical or similar subunits strung together
monomer
each individual subunit
one nucleotide/monomer of a dna molecule
sugar+phosphate+base
Condensation/ dehydration synthesis-
links monomers together
by removing one
water molecule for each monomer added
synthesis
build up
how does condensation work
One molecule contributes the
H and the other contributes the OH. Each monomer bonds each other covalently. Requires energy.
Hydrolysis
reverse of above- breaking bonds in a
polymer by adding water. H from water attaches to one molecule
OH from water attaches to adjacent molecule
releases energy
Carbohydrates (sugars, starches) shape
rings
Monosaccharides
carbohydrate sugars; singular; have formula of
CH2O in multiples.
- If these monosaccharides are not used immediately, they can form larger sugars for long term storage (humans–be stored in the liver as glycogen)
Monosaccharides ex
Glucose (C6H12O6) Major nutrient for cells. During cellular respiration-cells release energy stored in glucose molecules
Disaccharides:
double sugar consisting of 2 monosaccharides joined by a covalent bond
Polysaccharides
macromolecules- polymers in which
a few 100 to a few 1000 monosaccharides are linked together
molecules of life
carbs, lipids, nucleic acids, proteins
Storage polysaccharides
starch, glycogen
Starch-
polymer of only glucose. Storage unit synthesized in plants; helical shape; major source of starch-potatoes, grains
Glycogen-
polymer of only glucose. Stored in
liver and muscle cells of animals; very branched; Depleted in about
a day if not replenished by food
Structural polysaccharides:
cellulose, chitin
cellulose
major component of cell walls of plants; Parallel cellulose molecules are held together by hydrogen bonds- arranged in units called microfibrils, eventually form super coiled fibrils
wood main ingredient
cellulose
digestion of cellulose
Few organisms can digest cellulose- important roughage in the human diet,
moves everything along, and stimulates the digestive tract to secrete mucus. Some bacteria and microorganisms can digest it- cow has this bacteria inside a pouch called a rumen connected to the stomach and gets energy from the grass
Chitin
Found in exoskeletons of
arthropods (insects, lobsters…)Also found in
fungi
lipids
have little or no affinity for water
types of lipids
triglycerides, phospholipids, steroids
Triglycerides (fats): composition
3 fatty acids + 1 glycerol
fatty acids
Long carbon skeleton
o At one end- head consisting of a carboxyl group
o Attached to head is long hydrocarbon tail
how does glycerol attach to fatty acid
attaches to fatty acid by covalent bonds
Saturated Fats:
No double bonds between carbon atoms composing the tail of the fatty acids; As many hydrogen atoms as possible are bonded to the carbon skeleton
ex and dangers of saturated fats
animal fats–butter, lard. Can contribute to atherosclerosis because deposits called
plaque develop on internal lining of blood vessels arteries get more narrow
blocking blood flow
Unsaturated Fats:
Contains one or more double bond in the tail, formed by the removal of H atoms from the carbon skeleton. Has “kink” in shape wherever the double bond occurs. Prevents molecules from packing together close enough to solidify.
o Liquid at room temp
ex unsaturated fats
oil
function of triglycerides
energy storage– Gram of fat stores more than–g of fats more than 2x energy of g of polysaccharides (1 g of fat is 9kcal and 1 g of ps is 4 kcal)
o Humans store fat in adipose cells- can
swell and shrink depending on how much fat is stored in the cells
phospholipids
Have two fatty acids and a
negatively charged phosphate group attached to the glycerol. Hydrocarbon tail is
hydrophobic. Phosphate group is
hydrophilic bc it’s charged so water attracted
function phospholipids
major components of cell membranes. Arranged in bilayer, Hydrophilic heads are on outside in contact with water, hydrophobic tails are sandwiched in the interior away from water
steroids + ex
Lipids characterized by four interconnected rings (no fatty acids), Component of
membranes of animal cells, Precursor from which most other steroids are synthesized (like sex hormones)
ex: cholesterol
Carotenoids:
Orange-yellow pigment found in plants, - Plays role in photosynthesis
Proteins
Account for more than 50% of nonwater part of cells
- Used for structure, storage, transport, signaling, movement,
defense
- Most structurally sophisticated- each has
a unique 3d shape
Amino Acids:
Contain both a carboxyl group and an amino group; - Each amino acid has one carbon in center, bonded to a H atom, carboxyl group, amino group, variable chain represented by R
20 kinds of amino acids make up proteins
acidic v basic in ionic bonds
proton donor–acidic
proton receiver–basic
R group
side chain/variable that makes each amino acid different
Examples of R group variations
Nonpolar side chains (hydrophobic)
o Polar side chains (hydrophilic)
o Acidic amino acids
o Basic amino acids
acidic amino acids
side chains that are negative in charge
Basic amino acids-
side chains that are positive in charge
Polypeptide chains:
Amino acids join one another by dehydration synthesis, forming a
covalent bond called peptide bond. - Backbone is composed of
central Carbon, carboxyl group, amino group, side chains stick out
Polypeptide chain-
polymer of many amino acids linked by peptide bonds
Protein Conformation:
Protein consists of one or more polypeptide chain twisted, wound,
and folded upon itself to form a
macromolecule with a 3d shape, or conformation(shape). Protein’s function depends on conformation.
Globular v fibrous proteins
Globular proteins–glob shaped; ex–enzymes
Fibrous proteins–used for structure
ex–keratin
conformation proteins process
they form based on bonds
if two both have hydrophobic or hydrophilic side chains they might bond and then the entire proteins folds into a shape based on all those bonds. if one is replaced the protein folds the wrong way.
Primary structure proteins
Sequence of amino acids. Even slight change in primary structure can affect
the protein’s ability to function
ex of primary structure issue
sickle cell anemia, one amino acid is substituted for another in the primary structure of hemoglobin, preventing hemoglobin from forming properly
Secondary structure proteins
Segments of polypeptide chains are repeatedly coiled or
folded in patterns due to
hydrogen bonds along the back bone. Weak positive charge of H attached to N has an attraction to
the weak negative of an O on a nearby carboxyl group
two possible shapes–secondary structure proteins
alpha helix and beta pleated sheet
alpha helix and beta pleated sheet
two shapes that can emerge (don’t have to, can coexist)
Alpha helix-
coiled shape
ex–
all alpha helix example–hair. Proteins with these are more
elastic bc the H bonds can break and reform
beta pleated sheet
chain folds back and forth, and
two regions of the chain lie parallel to one another. Found in fibrous proteins-fibroin (found in silk). proteins with these are stronger.
- Tertiary structure
Irregular contortions from bonding between
the side chains of the amino acids due to hydrophobic interaction. Amino acids with
hydrophobic side chains congregate at the core of the protein to avoid contact with water. Also due to H bonds and ionic bonds
reinforced by disulfide bonds.
Disulfide bonds
help reinforce the conformation- form
where two amino acids with sulfhydryl groups bond to each other
Quaternary structure
Two or more subunits join together into one functional macromolecule;
subunit
each polypeptide chain in quaternary structures
ex quaternary structure
Ex- collagen- helical subunits supercoiled into a larger triple
helix, giving it great strength; Hemoglobin consists of
2 kinds of polypeptide chains w 2 of each
Factors determining conformation:
Conformations occur spontaneously as
the protein is being synthesized in the cell; If pH, salt, temp, or other environmental aspects are changed, the
protein may denature.
Protein can sometimes re-form its original shape when
returned to its normal environment
denature
protein unravels and becomes inactive
factors that disrupt conformation
Organic solvents (ether, chloroform) turn proteins inside out
o Chemicals can disrupt bonds
o Heat can disrupt conformations
ex of heat disrupting conformation
(ex-
cooking an egg denatures proteins in egg whites and makes it solidify
Nucleic Acids (+ex)
nucleotides are connected, forming a chain
ex–DNA, RNA
Nucleotides
monomers that compose the polymers of nucleic acids
parts to nucleotide
nitrogenous base
5 carbon sugar
phosphate group
what kind of polymer is a nucleic acid?
polynucleotide
polynucleotide
Nucleotides are joined by covalent bonds called phosphodiester
linkages between
the phosphate of one nucleotide and sugar of next, resulting in repeating sugar-phosphate-sugar-phosphate
DNA (deoxyribonucleic acid)
Contains deoxyribose sugar (missing a ribose group)
Genetic material that organisms
inherit from their parents
Very long, consisting of
thousands of genes
Sequence of the bases in DNA
encode instructions for all cell activities
RNA (ribonucleic acid)
o Contains a ribose sugar. Acts as messenger by bringing the genetic info found in the DNA in the nucleus to the ribosome where proteins are made. There, proteins are formed, from the encoded instructions in the RNA.
Bases:
pyrimidines, purines, form H bonds w one another
pyrimidines
a single ring–Cytosine, Thymine, Uracil
purines
double ring–Adenine, Guanine
James Watson and Francis Crick
discovered the shape of DNA molecule, double helix
double helix
Consists of two polynucleotide chains that
spiral around an imaginary axis
- Phosphate and sugar are on
outside of the helix and the bases form the rungs
- Two strands are held together by
H bonds between the paired bases
bases that always bond
Adenine always bonds thymine, guanine pairs with
cytosine.
uracil
uracil only found in RNA and thymine only found in DNA
Uracil is the RNA replacement for Thymine
nucleotides that don’t form polynucleotides
ATP, coenzymes, Chemical messengers between cells
ATP
(adenosine triphosphate)
o Made up of sugar, base, 3 phosphate groups ; can transfer a phosphate group to another molecule thereby giving off energy–energy currency in cells
coenzymes/enzyme helpers +ex
o Accepts hydrogen atoms and electrons from one molecule
and transfers them to different sites
(ex–NAD+, FAD)
ex of Chemical messengers between cells
Ex- cyclic AMP, or cAMP- called a second messenger- can
activate proteins within the cell
polarity rules for r groups
polarity: O > N > C = H.
