Download Organic Chemistry

Atoms, molecules, and life
•An 18-th century chemists proved that all matter, living and
nonliving is composed of particles called atoms, and discovery had
a profound and permanent effect on the study of biology. In the
decades that followed, biologists recognized that every organisms
contains the same two dozen types of atoms arranged in different
ways. The glorious diversity of life on our planet – the millions of
kinds of plants, animals, fungi, and microbes could now be seen to
stem from the myriad ways that specific atoms combine and
interact.
•A natural question arose from the pioneering work of Lavoisier and
Dalton: are living things made up of the same elements as rocks,
planets, and stars, or is our chemical makeup difference? Living
things, it turns out, display a special subset of the 92 naturally
occurring elements in the earth’s crust, but the elements occur in
very different proportions. 98% of the atoms in the earth’s crust are
the elements oxygen, silicon (Si), aluminum (Al), iron (Fe), calcium
(Ca), sodium (Na), potassium (K), and magnesium (Mg), with the first
three predominating
• In a typical organisms, however, 99% of the atoms
are the markedly different subset carbon, hydrogen,
nitrogen and oxygen, with sodium and calcium,
phosphorus (P), and sulfur making up most of the
remaining 1%, plus a few other elements present in
trace amounts. Biologists called the first ones – macro
elements and the other – microelements.
Microelements are present as ions in the structure of
enzymes, vitamins and hormones. Other inorganic
materials are water and mineral salts.
•Biologists are not certain why the chemical subsets of
living and nonliving things are so different, but they do
know that atomic architecture determines the physical
properties of elements and , in turn, the properties of
living organisms.
Most frequent partners hydrogen, oxygen, and
nitrogen
Hydrogen
Oxygen
Nitrogen
Carbon
Mineral
Sources
Calcium (Ca) dairy products, dark
green vegetables,
legumes
Function
bone and tooth formation, blood
clotting, nerve and muscle function
Minerals
Phosphorus dairy products, meat, bone and tooth formation, acid-base
(P)
grains
balance, nucleotide synthesis
Sulfur (S)
proteins
part of some amino acids
Potassium
(K)
meat, dairy products, acid-base balance, water balance,
many fruits and
nerve function
vegetables, grains
Chlorine (Cl) table salt
acid-base balance, formation of
gastric juice, nerve function, water
balance
Sodium (Na) table salt
acid-base balance, water balance,
nerve function
helps with ATP use
Magnesium
(Mg)
whole grains, green
leafy vegetables
Mineral
Iron (Fe)
Sources
Function
meat, eggs, legumes, whole
part of hemoglobin, used in
grains, green leafy vegetables respiration
Minerals
Fluorine (F) drinking water, tea, seafood
Zinc (Zn)
meat, seafood, grains
maintenance of tooth (and
bone?) structure
part of some digestive
enzymes and proteins
Copper (Cu) seafood, nuts, legumes, organ part of iron metabolism,
meat
melanin synthesis, in
respiration
Manganese nuts, grains, vegetables, fruit, enzyme functioning
(Mn)
tea
Iodine (I)
seafood, dairy products,
part of thyroid hormones
iodized salt
Cobalt (Co) meat, dairy products
part of vitamin B12
Selenium
seafood, meat, whole grains
(Se)
Molybdenu legumes, grains, some
m (Mo)
vegetables
antioxidant that works with
vitamin E
enzyme functioning
The idea that the
laws that govern
life the same as
those that govern
inorganic
processes and
molecules.
7major functional groups
Elements
•Need between 1 mg and
OH
2500 mg of each every
dayYou need more than
-C=O
200 mg each of:
Calcium Ca
•Phosphorus P
•Sulfur S
•Potassium K
•Chlorine Cl
•Sodium Na
•Magnesium Mg
•
-C=O
OH
H-N
H
-S-H
-PO4
-CH3
Functional Groups
Hydroxyl -OH
• alcohols
• gives a compound
polar qualities
• form hydrogen
bonds
Carbonyl -C=O
• ketones and
aldehydes
• found in most
sugars
Functional Groups
Carboxyl - COOH
•organic acids
•polar
•gives a molecule
acidic properties
•key part of amino
acids, the building
blocks of proteins
Amino
•-NH2
•called amines
•gives a compound
basic properties
•key part of amino
acids, the building
blocks of proteins
Phosphate -PO4; organic phosphates
•negative charge; hydrophilic
•when it reacts with water energy is
released; critical for many chemical
reactions in the body
Functional Groups
Methyl -CH3
Sulfhydryl -SH
•methylated
•called thiols
compounds
•two of these
functional groups can •effects gene
expression when it
interact to form
attaches to DNA
sulfur bonds very
•helps determine
important for
the function of
maintaining the
some male and
shape of proteins
female hormones
Organic Chemistry
• The study of compounds that contain
carbon
• Can be very simple molecules or very
complex ones
• Most organic compounds also contain
hydrogen
carbon can form covalent bonds with many
different elements
Carbon: The Backbone of Life
•Although cells are 70–95% water, the rest
consists mostly of carbon-based compounds
•Carbon forms large, complex, diverse molecules
•
•
•
•
Proteins
DNA
Carbohydrates
Lipids
What is carbon’s valence?
What does this mean?
What are the shapes of organic compounds?
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Carbon Compounds
•Carbon chains form the skeletons of most
organic molecules
•Carbon chains vary in length and shape
Organic compounds
• Just as a novel is made up of words and words are made up
of individual letters, the phenomenon we call life is written in a
language of molecules and atoms. And just as atomic structure
underlines the properties of molecules and compounds, the
shapes and behaviours of biological (organic)molecules
account for the physical characteristics and activities of living
organisms.
• The fundamental components of biological molecules
• Carbon: the indispensable element
While some biological molecules are small and relatively
simple, many of the carbohydrates, lipids, proteins, and nucleic
acids are macromolecules – extremely large molecules with
molecular weights of about 10,000 Daltons or more. Most of
the compounds that make up living things, however, share one
thing in common: they contain carbon. In fact, life on earth can not be
separated from carbon and its unique chemistry. Any compound that
contains carbon and has molecule weight over 10,000 Daltons or
more is called an organic compounds.
Substances in living organisms by weight
Macromolecules
•
Large biological molecules
• Carbohydrates
• Proteins
• Lipids
• Nucleic Acids
w ater
proteins
nucleic acids
carbohydrates
lipids
inorganic ions
•
•
Most made of chains of repeating units called
polymers
Lipids are a bit of an exception
•The unique structure of the carbon atom ultimately accounts
for the great diversity of molecules in living things. Carbon’s
unique properties allow it to bond with up to four other atoms
and form the ring or chain skeletons of macromolecules.
Macromolecules are polymers formed by linking of many
monomers by means of condensation reactions. The
splitting of polymers into their component monomers occurs
through hydrolysis.
•Macromolecules that are synthesized in the sell are called
biopolymers. Biopolymers can be divided into homopolymers
and heteropolymers. Homopolymers are built up of equal
monomers and heteropolymers are built up of different
monomers. Heteropolymers have structural and storage
function the cells. These are for example polysaccharides.
Heteropolymers are proteins and nucleic acids.
•Organic compounds are four main types : carbohydrates,
lipids, proteins and nucleic acids. All organisms are built up
of these four types of organic compounds. This proves the
Lipids
fats, steroids, oils, waxes, etc
Fats are lipids that store energy
Some lipids make up
the plasma
membrane of cell
membranes.
Carbohydrates sources of stored energy
• A carbohydrate is composed of C, H and O in the ratio 1:2:1 (CH2O).
This formula gives the group its name, “hydrate of carbon ”.
Carbohydrates consist of a carbon backbone with various functional
groups attached. The basic carbohydrate subunits are sugar
molecules called monosaccharides (single sugar); they functions as
monomers that can be joined together to form more complex
disaccharides (two sugars) and polysaccharides (many sugars).
• Monosaccharides: simple sugars
• Monosaccharides serve as energy sources for living tings and as
building blocks for carbohydrate polymers and other biological
molecules. Each simple sugar has a structure based on a short
carbon backbone. The monosaccharides glucose, fructose, and
galactose are the most important carbohydrate monomers, since
those units make up the complex carbohydrates in starch, wood, and
other biological materials. These monomers are referred to as sugars
and some do have a sweet taste. Fructose, for example, gives many
of fruit their sweet flavour. Glucose is the universal cellular fuel,
broken down by virtually all living things to release energy stored in
its bonds.
Forming and Digesting Polymers
•
•
•
•
Dehydration synthesis:
process that bonds
monomers together
Hydrolysis: process that
breaks polymers.
Bonds based on
functional groups at
ends of monomers
Enzymes speed this up.

Carbohydrate: molecule composed of carbon,
hydrogen, and oxygen with simplified formula
Cn(H20)n
 raw materials for amino acids, fats- fuel source
 many isomers
- end in –ose
 ring structure common when in water
The sub-unit (building blocks) of carbohydrates are
single sugars, called monosaccharides.
Carbohydrates

Range from small sugar molecules to the long
starch molecules we consume in pasta and
potatoes.
Key source of energy
found in most foods — especially fruits, vegetables,
and grains
Monosaccharide: single sugar unit
Examples:Glucose (C6H12O6);Fructos;Galactose
Deoxyribose(C5H10O5)Ribose (C5H10O5)
Disaccharides : sugars built of two
monosaccharides
•Real diversity in shape and properties can arise when
monosaccharide monomers are linked into larger
molecules. Disaccharides are the common form in
which sugar are transported inside plants. For
example, glucose bonds to fructose to yield sucrose,
or table sugar. Sucrose is abundant in the saps of
sugarcane, maple trees, and sugar beets. Honey has
also glucose and fructose. The predominant sugar in
milk is lactose , galactose bonded to glucose. Maltose
– two joined glucose subunits – gives barley seeds a
sweet taste and their utility to the beer industry.
Formation of a disaccharide
Polysaccharides storage depots and
structural scaffolds
•Living organisms form the long-chain carbohydrates
called polysaccharides by linking large numbers of single
sugars, or monosaccharides, into polymers. The most
important polysaccharides are starch, glycogen, and
cellulose. Other biologically significant polysaccharides
include chitin, a major component of the shells of insects
and crustaceans such as lobsters and crabs. Starch is the
major nutrient reserve in most plants. Glycogen is a
storage from for glucose in the living animal cells. It has a
branched molecule which allows the rapid break down and
release of energy that animals often require. Cellulose is
polysaccharide as chitin and gives strength and rigidity to
plant cells and wood.
Polysaccharides
Starch- Helical (spiral) structure
Cellulose
•long, straight chain, never
branched
•h-bonds between parallel
polymers
•makes fibers. Only some fungi
and prokaryotes can digest
cellulose (also symbionts:
termites, cows, etc)
•Glycogen (animals only) has
many branches
•Branched carbs better for rapid
glucose release (more places
for an enzyme to attack)
Lipids: energy interfaces, and signals
• The second group of biological molecules, the lipids, makes
certain foods oily, keep us warm , and prevent the watery contents
of cells from leaking out. Lipids include the fats, such as bacon
fat, lard, and butter; the oils, such as corn, coconut, and olive oils;
the waxes, like beeswax and earwax; the phospholipids, which are
Important components of cell membranes; and steroids, including
certain vitamins, hormones, and cholesterol(the heart and blood
vessel cloggier ). Like carbohydrates, lipids can serve as energy
storage molecules or as waterproof coverings around cell.
Fats and oils are common compounds in animals and plants, and
the reason again is based on molecular structure. When an
organism burns stored fats or oils, more calories of heat energy
are released than when it burns an equivalent amount of sugar or
polysaccharide. When we consume more calories than we burn
our body stores the extra energy in concentrated form as fat.
• Waxes are a variation on oils. Their molecules are made up of a
long – chain alcohol linked to the carboxyl group of a fatty acid.
Large numbers of wax molecules packed together form a
waterproof outer layer on the leaves of plants, the bills and
feathers of some birds, and other structures in living organisms.
Waxes serve as structural materials in honeycombs of beehives;
and as protective coatings for the ear canal.
The phospholipids contain nitrogen and phosphorus as well
as the carbon, hydrogen, and oxygen atoms in fats and oils. These
additional elements give phospholipids their ability to maintain a
cell’s waterproof boundary. The overall shape of a phospholipids
molecule is something like a head with two long, thin tails
streaming from the nape of the neck; the glycerol phosphate
forms the hydrophilic head, while the fatty acid chains form the
hydrophobic tails. The behaviour of phospholipids is rooted in
this shape. Since the tails are hydrophobic and the head is
hydrophilic the molecules have an ambivalent approach to water.
This behaviour of phospholipids accounts for the structure of cell
membranes, which are double – layered phospholipids barriers
surrounding living cells.
•Steroids, the third type of lipids, are much less abundant
in living cells than are fats, oils, and phospholipids, but
they are no less important. Steroids are no polar and
hydrophobic; they are insoluble in water, can dissolve in
oils or in lipid membranes, and can move into and out
many cells. Some steroids act, as vitamins, while others,
such as estrogen and testosterone, are hormones.
Cholesterol , another common steroid, has important
beneficial effects on the fluidity of many cellular
membranes. But this steroid, which is regularly
manufactured in the body, may build up in the blood
vessels and contribute to heart disease.
Lipids
• Not polymers, only sort of “macro”
molecules
• Hydrophobic
– nonpolar
• Mostly hydrocarbons
• Fats/oils: glycerol + 3 fatty acids
(triglycerol)
• Great for energy storage
– 2x as much as proteins/carbs
– Stationary plants can have
starches, animals need higher
density fuel (fat)
• Insulation and cushioning
Lipids
fats, steroids, oils, waxes, etc
Fats are lipids that store energy
Some lipids make up
the plasma membrane
of cell membranes.
Lipids
• Saturated
– C bonds always single
– solid at room temp
• Unsaturated
– has a double bond between C
atoms
– liquid at room temp
• Polyunsaturated
– has more than one double
bond
Cholesterol
• Associated with Heart disease
– HDL (good); LDL (bad)
• 4 carbon rings w/ a short C chain
http://www.healthytimesblog.com/2010/12/understanding-cholesterol-the-goodthe-bad-and-the-ugly/
Hydrocarbons
• Contain huge amounts of energy
– released when bonds between carbon and
hydrogen are broken
Functional Groups
• Properties of organic
molecules depend on:
– Carbon structure
– Atoms and molecular parts
attached to them
• Functional groups are
characteristic sets of
atoms that attach to
carbon skeletons
– give specific bonding
patterns and chemical
behaviors to compounds
The idea that life
necessary for the
creation of
organic
compounds.
Enantiomers
• Very important in pharmaceuticals
– Thalidomide: one enantiomer reduces morning
sickness, the other causes severe birth defects
Isomers
• Compounds with the same
molecular formula but different
structures and properties:
– Structural isomers have different
covalent arrangements of their
atoms
– (Geometric) Positional isomers
have the same covalent
arrangements but differ in spatial
arrangements
– Enantiomers are isomers that are
mirror images of each other