The Chemistry of Organic Molecules
Scientists used to believe cells contained something “extra”
that other matter did not; a vital force of some kind.
They divided chemistry up into “living” (organic) and
“nonliving” (inorganic) chemistry.
“organic molecules” were thought to relate specifically to
life processes.
We now know that the chemical reactions of life are
just like any other chemical reaction.
The most abundant “life-specific” materials, however, are
carbon and hydrogen.
Therefore: “Organic molecules” are molecules
containing carbon and hydrogen. Inorganic
Molecules do not.
Matter
Is made of…
Elements
That combine to form…
Molecules & Compounds
Made from a carbon backbone and …
Which Include…
Organic Compounds
Nucleic Acids
Functional Groups
Lipids
hydroxyl
amino
carbonyl
phosphate
Proteins
carboxyl
Sugars
sulfhydryl
Which, together with backbone
structure lead to specific…
Hydrophobic
Chemical Properties
Hydrophilic
Acidic
Alkaline
Polar
Nonpolar
Organic Compounds: carbon + hydrogen
ALL complex organic molecules are built from the
same basic carbon scaffold idea.
What makes them different?
– Carbon skeleton’s structure
– Functional Groups
Cells contain 4 major classes of
organic compounds:
– Proteins (made of amino acids)
– Carbohydrates (sugars)
– Lipids (fats, oils, etc.)
– Nucleic Acids (DNA, RNA)
We name organic compounds
according to their functional groups
and chemical properties.
Because of the carbon atom’s unique structure, it
is capable of forming a great diversity of
different structures.
It is this property of carbon that contributes to life’s
rich diversity on all levels of the biosphere
Key concept:
FORM FOLLOWS FUNCTION
Show inner life of the cell
A chemical anagram
Isomers share the same chemical formula –
they are composed of the same atoms – but
have different architecture.
Form follows function… different shapes are going
to have different functional implications.
Andrew Ippolito
Warden, I Lit Poop
Isomers of C3H8O
1-Propanol
n-propyl alcohol
H H H
H C C C O H
H H H
Both compounds
have the same
number of C, H, and
O atoms; however,
they are arranged
differently.
2-Propanol
isopropyl alcohol
H
H OH
H C C C H
H HH
Why do isomers have different names?
We name chemical compounds by how their
atoms are arranged,
Because different
arrangements have different chemical effects.
If chemical properties were not affected by the
atomic arrangement, we wouldn’t care about
how they were arranged – and so we wouldn’t
have different names.
The chemical and physical “rules” that molecules
follow due to their unique nature.
Chemical Properties we will be concerning
ourselves with include:
Solubility (how soluble the molecule is in water)
Alkalinity (measure of how acidic/basic a molecule is)
Reactivity (how likely a molecule is to undergo a
chemical reaction)
Structure (is it long and bendy, clumpy and gooey, or
flat and stiff)
Keep in mind why everything revolves around water.
The ability of a molecule or compound to dissolve in
water.
– Hydrophobic: (phobia) – the molecule is afraid of water;
it does not dissolve.
– Hydrophilic: (phila, love) – the molecule loves water, and
dissolves in it.
Solubility is influenced by the functional groups
present in an organic molecule
Molecules are soluble in water if they are polar (they
are imbued with an electrical charge – not neutral)
– Examples:
Basic concept (no pun intended): pH is really a measure of
how chemically “reactive” the environment is.
– This reactivity depends on two factors
The hydrogen ion concentration (H+)
The hydroxyl ion concentration (OH-)
– Why? These are the breakdown products of water.
Substances that contribute to an increase in the H+
concentration (or a decrease in OH- concentration!) are
considered acidic.
– Example: add HCl to water and the H+ concentration shoots up.
Substances that contribute to an increase in OHconcentration (or a decrease in H+ concentration!) are
considered basic (or “alkaline”)
The reactivity of an organic molecule depends
upon the electron configuration of it’s functional
groups.
Nearly all organic compounds react with other
compounds in one way or another.
Hydration, an example chemical reaction
– Functional groups are parts of a molecule.
– They have chemical properties that are independent
on what the Rest of the molecule is made out of.
An arm is an arm, whether it’s on your shoulder or a robotic car.
It still grasps, it still has finger-like appendages.
– They are not “functional groups” until they are actually
attached to a molecule. If they are free, they are ions!
(wanderers, remember?)
“hydroxyl ion” “hydrogen ion”, “phosphate ion”, etc.
– Functional Groups contribute to the name of a
molecule (ethane vs. ethanol)
– The functional groups of a molecule influence the
molecules chemical properties.
Example: [Rest of molecule]—OH
– “OH” is the hydroxyl functional group. When a
hydroxyl group is present in a molecule it increases
the negative charge of a molecule (and therefore
increases its polarity)
– When a single hydrogen in Ethane (C2H6) is replaced
by a hydroxyl group, the molecule ceases to be
ethane and becomes Ethanol (C2H3O).
– Ethane is insoluble in water because it is
hydrophobic, but ethanol, because of its polar
hydroxyl group, is hydrophillic.
– An abbreviation for ethanol in chemical “shorthand” is
EtOH.
Carbohydrates
Proteins
Lipids
Nucleic Acids
monomer
polymer
Monomeric compounds
Polymeric compounds
Macromolecules can be thought of as chains of
smaller molecules.
– Each link in the chain is called a monomer.
– The chain itself is called a polymer.
Organic macromolecules found in all living cells
are classified into 4 groups:
–
–
–
–
Proteins
Nucleic Acids
Lipids
Carbohydrates
Sugars
– Can be monomeric (monosaccharide) or polymeric
(polysaccharide).
Lipids
– Any organic, fat-soluble (hydrophobic) molecule.
Highly diverse family of molecules broken down into
further classifications.
Proteins
– One or more polypeptide chains composed of amino
acids, folding into complex structures
Nucleic Acids
– Chains of nucleotides or deoxynucleotides.
Two types: simple + complex
Simple:
– A carbon backbone with a ratio of C:H:O of 1:2:1
(usually, not always).
– simple sugars are called monosaccharides, and are
universally used as immediate energy source to cells.
– two simple sugars can link together by dehydration
reactions to produce disaccharides
C6H12O6 (generic hexose) is the simplest sugar
(monosaccharide) we will deal with right now.
– This compound has 3 different, common structures of its carbon
backbone (isomers).
– these are GLUCOSE, FRUCTOSE, AND GALACTOSE.
– Different pairs of these produce the variety of disaccharides:
Glu + Glu = Maltose (used in brewing)
Glu + Fru = Sucrose (table sugar, made in plants)
Glu + Gal = Lactose (milk)
plants transport sugars in the form of disaccharides
The common isomers of Glucose (6-carbon monosaccharide)
link
Polysaccharides are long chains of monosaccharides.
POLYSACCHARIDES are used for two things:
– storing energy in the short-term (they don't freely enter a cell
membrane), and
– structural components (crab shells)
Energy Storage Polysaccharides:
– Starch = Plants
– Glygoen = Animals
– Both are polymers of glucose; not fructose or galactose.
Starch can either be branched or unbranched in plants. In animals, it is
always branched.
– Unbranched starch (only in plants) is called amylose.
– Branched starch (in plants) is called amylopectin.
Glycogen is HIGHLY branched compared to amylopectin.
The shape of these polysaccharides is helical. This allows the
connecting bonds to stick out in the environment, where enyzmes
have access to break them.
Glycogen's release depends on hormones. insulin from the pancreas
promotes the storage of glucose as glycogen.
Figure 3.8aa
Figure 3.8ba
Lipids: a diverse class of organic compounds that
all share the same general chemical property:
they are insoluble in water.
– Lipids are made from 2 subcomponents:
Glycerol (3 carbons with 3 OH groups; an alcohol)
Fatty acid (a hydrocarbon chain with a carboxyl group at the
very end)
Lipids store more energy than sugars per unit mass. They
are more “energy dense”
CH bonds (predominant bonds in lipids) are stronger than
CO bonds (predominant bonds in sugars)
– Why? Oxygen’s hogging the electrons, so the bond is weak.
This is why sugars are used as “fast energy” molecules –
the bonds are much easier to break than lipids!
Why are saturated fats worse for you than Unsaturated
fats?
– Circulatory disorders. Solids at high temperatures clog your
arteries
Website: The Lipid Library
Triglyceride: A compound consisting of
1 glycerol attached to 3 fatty acids
Triglycerides are the subunits of fats and oils.
– Fats have triglycerides containing fully saturated fatty
acids.
– Oils have triglycerides containing unsaturated fatty
acids – those containing double carbon bonds at
various places along the chain.
Fats are solid because their fatty acids are saturated with
hydrogens, making the hydrocarbon chains linear.
– Linear chains stack on each other in a highly ordered way
Oils are liquid because their fatty acids are unsaturated,
meaning that some carbons in the hydrocarbon chain
are double bonded to each other – not hydrogen. This
bond creates a kink in the chain.
– Kinks allow a greater amount of movement in the chain, and are
therefore less ordered, keeping them in a looser, liquid
configuration
Solid fats in your blood vessels inhibit blood flow.
Triglyceride
Glycerol
C—O—C
Fatty Acid
C—O—C
Fatty Acid
C—O—C
Fatty Acid
Fat
Glycerol
C—O—C
Saturated
C—O—C
Saturated
C—O—C
Saturated
Oils
Glycerol
C—O—C
Un
C—O—C
Un
C—O—C
Un
Lipid droplets are the lipid storage organelles of all
organisms.
Their important role in cellular and organismic
energy storage becomes most prominent in
cases where lipid droplet biology is
misregulated.
– This is for example the case in several major
lipid storage diseases such as atherosclerosis,
diabetes or obesity.
For a long time it was thought that lipid droplets
only act as storage depots.
More recent data, however, support the idea that
lipid droplets are highly dynamic organelles
which participate in several cellular
processes and interact with various other cellular
compartments.
Despite their multifariousness of functions, all lipid
droplets share a simple, stereotyped structure of
a hydrophobic core built of the storage lipids
(mainly triacylglycerols), surrounded by a
phospholipid monolayer to which numerous
proteins are attached (Fig. 1).
Although the central role of lipid droplets for
energy storage was demonstrated, little is
known about their cellular biology such as
biogenesis, mechanism of protein
association or size and number control
inside cells.
Phospholipids
– Heads that dissolve in water and tails that don’t.
If left to their own devices in an aqueous solution,
they will move around and align such that the
heads are all facing the same way, and the tails
are all facing the other way.
++++++++++++++++++++++++++++++++++++
---------------------------------------------------------------P
P
P
P
P
P
P
++++++++++++++++++++++++++++++++++++
---------------------------------------------------------------P
P
P
P
P
P
P
The Plasma Membrane
a.k.a. The Lipid Bilayer
Outside of the cell = Extracellular Environment
Outer Leaflet
Intermembrane Space
Inner Leaflet
Inside the Cell: Cytoplasm
THE SAME IS TRUE FOR MANY OTHER MEMBRANES
Nucleus, Endoplasmic Reticulum, Golgi Apparatus, etc.
Phospholipids are constructed the same way as
triglycerides, except a single phosphate
functional group replaces a fatty acid.
Phospholipid
O
C—O—P
C—O—C O R
CCCCC
C—O—C
CCCCC
C—O—C
C—O—C
Glycerol
Glycerol
O
CCCCCC
O
C—O—P O R
Saturated
CCCCCCC
C—O—C
Saturated
CCCCCCC
O
Characterized by their structure:
4 Fused Carbon rings
What makes steroids different from each other?
The function groups attached to the carbon rings.
Basic structure of many steroids
Beethoven Pneumonic: SIX SIX SIX FIIIIVE
A basic steroid that serves as both a structural
component and a precursor for more complex
steroids.
When inserted into a plasma membrane, cholesterol
increases a plasma membrane’s rigidity.
– Think of a stabilizing fin in a boat.
Diets high in both cholesterol and fats lead to a build
up of solid material in the blood vessels, leading to
all sorts of trouble!
Membrane in a gel state with
straightened chains. The green
chains are hydrocarbons, the
blue elements are cholesterol,
and the red spheres are the
head-group atoms of the lipids.
The cholesterol is removed to
show the lipid chains more
clearly in the visualization on
the right.
Membrane in a fluid state.
Unlike the membrane in a gel
state, the membrane in a fluid
state has a low cholesterol
concentration (one
cholesterol molecule to 16
lipid molecules), and the
hydrocarbon chains appear
highly disordered. The
cholesterol is removed in the
visualization on the right.
Website
Cholestrol is also precursor to:
– Testosterone = Testes; Estrogen = Ovaries
Primarily – not exclusively! There are other places these are
formed…
Figure 3.13a
Whereas a triglyceride is a small alcohol (glycerol)
attached to 3 fatty acids, waxes are a long
alcohol attached to a very long fatty acid.
Waxes = Long fatty acids + long alcohols
Cuticle in plants decreases water loss
Skin and fur maintenance.
– Earwax has cerumin, which repels or kills insects!
– Traps dust & dirt before it reaches the eardrum
Bees make a honeycomb to store the breakdown
products of sucrose
– Remember sucrose is a disaccharide of glucose and
fructuose
Proteios, “first place” – the most important organic
molecule in the cell
Also the most diverse
As much as 50% of the dry weight of cells is
protein
Over 100,000 identified so far
Support
Enzymes
Transport
Defense
Hormones
Motion
Points of confusion:
–
–
–
–
Amino acid
Peptide
Polypeptide
Protein
Additional reading
Amino Acids are the building blocks of proteins.
Peptides are two or more amino acids joined
together by a peptide bond.
Polypeptides are chains of peptides.
Peptide Bond Dynamics (Draw it)
Dehydration
Hydrolysis
H2O
The stupid picture in the book
Phospho-acceptors (can be phosphorylated)
– Serine
– Threonine
– Tyrosine
Highly charged
– Glutamic Acid (acidic)
– Aspartic Acid (acidic)
– Histidine (basic)
Structurally Important
– Alanine
– Glycine
– Proline
(3.16 has mistake)
Primary structure (“what is the protein’s
sequence?”)
– The sequence of amino acids in the polypeptide chain
Secondary (the “local” structure of a portion of the
polypeptide chain)
– Stretches of amino acids will tend to form repeating
units such as helices, sheets, fingers, etc.
Alpha helix
Beta pleated-sheet
Zinc finger
– Reinforced by hydrogen bonding
Tertiary
– The global shape of the entire polypeptide chain.
Usually classified as “globular” and “filamentous”.
– Globular polypeptides have hydrophobic centers for
the same reason that phospholipids form a bilayer; it’s
the net sum of all forces on the molecule that causes
them to spontaneously settle into a stable structure.
In this case, the polar areas of the chain will react
with the surrounding aqueous environment, while the
hydrophobic regions will aggregate towards the
inside. Thus, “hydrophobic interactions” are truly a
misnomer.
– Reinforced inter-chain crosslinks (disulfide bonds)
Quaternary
– When multiple polypeptide chains (that
have their own tertiary structure) come
together and interact in a stable
complex, they will exhibit a higher order
structure called Quaternary structure.
– Short version: The overall shape of 2 or
more polypeptide chains interacting with
each other.
A protein consisting of a single polypeptide chain is said to
be a monomeric protein (or simply (“monomer”)
Proteins with two polypeptide chains are dimeric proteins
(“dimer”)
– Each polypeptide in a dimeric protein is generally refered to as a
subunit
There are trimeric (trimer), quatrameric (quatramer),
etc… proteins.
Proteins with many subunits are called multimeric
proteins (multimer)
– DNA and RNA polymerase complexes, nuclear pores, ion
channels, and many gene regulatory proteins are multimeric
protein complexes.
Primary: Sequence of amino acids
Secondary: folding of localized regions
sheet
helix
Tertiary: folding of the entire polypeptide
Quaternary: interaction of 2 or more polypeptides
Denaturation: When a polypeptide’s tertiary
struture collapses (melts)
Aggregation: when a polypeptide does not fold
properly, but jumbles into a mess.
Watch video?
Not all proteins can form their proper shapes
spontaneously. Many need help as they are
being synthesized.
Proteins that help other proteins fold correctly are
called protein chaperones.
Proteins that incorrectly fold can form huge,
clumpy messes called protein aggregates.
Polymers of nucleotides
Nucleotides are compounds composed of three
modules:
– Phosphate
phosphoric acid
– A pentose sugar
sugar with 5 carbons
– A nitrogenous base
A nitrogen-containing molecule having the chemical properties
of a base
phosphate
Nitrogenous Base
(deoxy)Ribose
NUCLEOTIDE
phosphate
Nitrogenous Base
(deoxy)Ribose
PO4
Phosphate provides high-energy chemical bonds.
phosphate
Nitrogenous Base
(deoxy)Ribose
Ribose is simply a 5-carbon sugar (a pentose).
When you remove a hydroxyl functional
group from the 2’ carbon, it becomes
deoxyribose.
(very weak bond)
(very strong bond)
phosphate
Nitrogenous Base
(RNA only)
(deoxy)Ribose
The 3rd component, the base, is either a purine
or pyramidine.
adenine
Uracil
Thymine
guanine
cytosine
Purines are bigger than
U
AG
adenine
guanine
Thymine
cytosine
Uracil
pyramidines
T
C
Nucleotides are found as
– polymers DNA and RNA, which serve as information
carriers
– monomers as coenzymes and energy carriers (ATP)
Coenzymes are essential factors that ensure enzymes can
carry out their biochemical functions
Adenosine Tri-Phosphate (ATP). Stores energy in
chemical bonds that can be extracted by the cell
to perform work.
A pairs with T
G pairs with C
So, one big always binds with one small
A and T form 2 hydrogen bonds
G and C form 3 hydrogen bonds
– GC is therefore harder to pull apart than AT
A
G
A
G
A
G
A
A
T
C
Why does A
always pair
with T, and G
always pair
with C?
T
C
T
C
T
T
So the helix is
of uniform
thickness
Benzopyrene, the major mutagen in tobacco smoke, in an adduct to DNA.[52]
Deoxyribonucleic acid (DNA)
– Very stable molecule.
– Primary function is to store information, such as the primary sequence
of proteins
Ribonucleic acid (RNA)
– Not as stable as DNA
– RNA does many things. Different classes of RNA are specialized to
their own tasks. The two most characterized are:
Messenger RNA (mRNA) encodes a protein sequence
There are transfer RNAs (tRNA) specific for each of the 20 amino acids
rRNA (ribosomal RNA) is an essential component of Ribosomes, which help
translate the language of Genes to the language of Proteins.
– Each kind of RNA has its own kind of genes. The genes we normally
talk about are actually genes that encode mRNA.