Download Biology * Introduction to Organic Chemistry

Biology –
Introduction to
Organic Chemistry
Life’s Diversity is
due to being
carbon-based.

Almost all the molecules a
cell makes are composed
of carbon atoms bonded to
one another and to atoms
of other elements.

Carbon is unparalleled in its
ability to form large and
complex molecules, which
build the structures and
carry out the functions
required for life.

Carbon-based molecules
are called organic
compounds, and they
usually contain hydrogen
atoms in addition to
carbon.
Life’s Diversity is
due to being
carbon-based.

The number of
electrons in the
outermost shell
determines an atom’s
chemical properties. A
carbon atom has 4
electrons in a valence
shell that holds 8.

Carbon completes its
outer shell by sharing
electrons with other
atoms in four covalent
bonds.

Here you see a methane (CH4)
molecule. It forms a tetrahedron
shape.

The tetrahedral shape occurs
wherever a carbon atom
participates in four single bonds.

In molecules with more than one
carbon, each carbon atom is a
connecting point from which a
molecule can branch in up to four
directions.
Life’s Diversity is
due to being
carbon-based.

In addition, different shapes occur
when carbon atoms form double
bonds.

Thanks to the geometry of
carbon’s single and double
bonds, large organic molecules
can have very elaborate shapes.

A molecule’s shape usually
determines its function.
Life’s Diversity is
due to being
carbon-based.

Carbon chains form the
backbone of most organic
molecules.

The diagram illustrates four
ways in which such “carbon
skeletons” (shaded in the
figure) can vary.

They may differ in length and
can be straight, branched, or
arranged in rings.

Carbon skeletons may also
include double bonds, which
can vary in number.
Hydrocarbons

Hydrocarbons are composed of only carbon
and hydrogen.

The majority of naturally occurring
hydrocarbons are found in crude oil and
natural gas and provide most of the world’s
energy.

Hydrocarbons are rare in living organisms, but
hydrocarbon chains are found in regions of
some molecules.

For instance, fats contain hydrocarbon chains
that provide fuel to your body.
Hydrocarbons
This inherent ability
of hydrocarbons to
bond to
themselves is
known
as catenation, and
allows
hydrocarbons to
form more
complex
molecules.

The hydrocarbons easily bond with other hydrocarbons making long
chains or rings, because H and C have very similar
electronegativties AND C-C bonds share their electrons completely
equally since they have the same electronegativity value.

In other words, the bond between carbon atoms is entirely nonpolar, in that the distribution of electrons between the two elements
is somewhat even due to the same electronegativity values of the
elements (~0.30).
ELECTRONEGATIVITY

Electronegativity = the tendency of an atom to
attract electrons towards itself.
ELECTRONEGATIVITY
Hydrocarbons

Recall that C can form 4 bonds.

We know from C position on the periodic table, that it is in group 4.
all group 4 elements react in such a way that they can form up to 4
bonds.

The atomic number of C is 6.

The first shell can hold up to 2 electrons.

The second shell can hold up to 8 electrons.

Atoms have a tendency to ionize in such a way that their outer-most
shell is filled. They can do this either by gaining or losing electrons,
but it will always take the “path of least resistance”.
https://www.youtube.com/watch?v=1UE3hZ7cOP0
Hydrocarbons

Hydrocarbons
are hydrophobic like lipids.
They are “afraid” of water!
Hydrocarbons as an energy source

Hydrocarbons are the world's leading source of electrical and
thermal energy, due to the amount of energy produced when
burnt.

This burning is a combustion reaction in which oxygen from the air
becomes a reactant with the hydrocarbon, to form a new chemical
product.
Common properties of
hydrocarbons

they produce

steam

carbon dioxide

Heat
Common properties of
hydrocarbons
#1 example, methane undergoes the following combustion reaction:
CH4 + 2 O2 → 2 H2O + CO2 + energy (OR if low O2) 2 CH4 + 3
O2 → 2 CO + 4 H2O
The burning of hydrocarbons releases heat energy. For this reason it is
considered to be an “exothermic” chemical reaction.
Functional
Groups

Small changes in in size
and structure, can
greatly change the
properties of an
organic compound.

There are 5 functional
groups:

Hydroxyl group

Carbonyl group

Carboxyl group

Amino group

Phosphate group
Functional
Groups

Functional groups
participate in chemical
reactions.

These groups are polar.

They are hydrophilic
(water-loving)

They are water-soluble.
Hydroxyl Group

A hydroxyl group consists of a hydrogen atom bonded to an
oxygen atom, which in turn is bonded to the carbon skeleton.
Ethanol, shown in the table, and other organic compounds
containing hydroxyl groups are called alcohols.
Polymers
Cells link monomers together to form
polymers by a dehydration reaction, a
reaction that removes a molecule of
water as two molecules become
bonded together.
 Each monomer contributes part of the
water molecule that is released during
the reaction. One monomer loses a
hydroxyl group and the other
monomer loses a hydrogen atom to
form H2O.
 As this occurs, a new covalent bond
forms, linking the two monomers.



Cells not only make
macromolecules but also
have to break them down.
Most of the organic
molecules in your food are in
the form of polymers that
are much too large to enter
your cells.
Breaking
Polymers



You must digest these
polymers to make their
monomers available to your
cells.
This digestion process is
called hydrolysis. Essentially
the reverse of a dehydration
reaction, hydrolysis means to
break (lyse) with water
(hydro-).
The bond between
monomers is broken by the
addition of a water
molecule, with the hydroxyl
group from the water
attaching to one monomer
and a hydrogen attaching
to the adjacent monomer.
Breaking
Polymers
Carbohydrates

Carbohydrates are the class
of molecules that range from
small sugar molecules, such
as those dissolved in soft
drinks, to large
polysaccharides, such as the
starch molecules we
consume in pasta and
potatoes.

Simple sugars, or
monosaccharides (from the
Greek monos, single, and
sacchar, sugar), are the
monomers of carbohydrates.
Carbohydrates

Monosaccharides generally
have molecular formulas that
are some multiple of CH2O.

The formula for glucose, a
common monosaccharide of
central importance in the
chemistry of life, is C6H12O6.

All sugars will have a number
of hydroxyl groups (¬OH) and
a carbonyl group (7 C“O,
highlighted in blue).

Monosaccharides generally have molecular formulas that are some
multiple of CH2O. For example, the formula for glucose, a common
monosaccharide of central importance in the chemistry of life, is
C6H12O6.

Monosaccharides, particularly glucose, are the main fuel molecules for
cellular work. Because cells release energy from glucose when they
break it down, an aqueous solution of glucose (often called dextrose)
may be injected into the bloodstream of sick or injured patients; the
glucose provides an immediate energy source to tissues in need of
repair. Cells also use the carbon skeletons of monosaccharides as raw
material for making other kinds of organic molecules, such as amino
acids and fatty acids. Sugars not used in these ways may be
incorporated into disaccharides and polysaccharides,
Artificial
Sugars

As you can see above, the
sugar substitute aspartame,
found in Equal, Nutrasweet,
and many diet soft drinks
and chewing gums, is not a
sugar at all.

It is a dipeptide (two amino
acids joined together, as in
a protein). But it's is a very
slightly modified dipeptide.

180 times as sweet as sugar
(sucrose).
Artificial Sugars

In this case, the artificial sweetener
sucralose looks very similar to the
natural sugar sucrose.

Sucralose is in some soft drinks and
is marketed as an alternative to
aspartame.

600 times as sweet as sugar.
Disaccharides

Cells construct a disaccharide from two monosaccharide
monomers by a dehydration reaction.

Maltose, also called malt sugar, is formed from two
glucose monomers.

One monomer gives up a hydroxyl group and the other
gives up a hydrogen atom.

As H2O is released, an oxygen atom is left, linking the two
monomers.

Malt sugar, which is common in germinating seeds, is
used in making beer, malt whiskey, and malted milk
candy.

Sucrose is the most
common disaccharide. It
is made of a glucose
monomer linked to a
fructose monomer.
Transported in plant sap,
sucrose provides a
source of energy and
raw materials to all the
parts of the plant. We
extract it from the stems
of sugarcane or the roots
of sugar beets to use as
table sugar.
Disaccharides
high-fructose corn syrup

What is high-fructose
corn syrup (HFCS)?
Let’s start with the corn
syrup part.

The main
carbohydrate in corn
is starch, a
polysaccharide built
from glucose
monomers.

Industrial processing
hydrolyzes starch into
these monomers,
producing corn syrup.
high-fructose corn syrup

Glucose, however, does not taste as sweet to us as sucrose.

Fructose, on the other hand, tastes much sweeter than both glucose
and sucrose.

When a new process was developed in the 1970s that used an enzyme
to rearrange the atoms of glucose into the sweeter isomer, fructose, the
high-fructose corn syrup industry was born.

(High-fructose corn syrup is a bit of a misnomer, because the fructose is
combined with regular corn syrup to produce a mixture of about 55%
fructose and 45% glucose, not much different from the proportions in
sucrose.)
https://www.youtube.com/watch?v=6-uL2oW4dcY
high-fructose corn syrup

MAYO CLINIC - Research has shown that high-fructose corn syrup is
chemically similar to table sugar. Controversy exists, however, about
whether the body handles high-fructose corn syrup differently than
table sugar.

At this time, there's insufficient evidence to say that high-fructose
corn syrup is any less healthy than other types of sweeteners.

It is known, however, that too much added sugar of all kinds — not
just high-fructose corn syrup — can contribute unwanted calories
that are linked to health problems, such as weight gain, type 2
diabetes, metabolic syndrome and high triglyceride levels. All of
these boost your risk of heart disease.
http://www.mayoclinic.org/healthy-lifestyle/nutritionand-healthy-eating/expert-answers/high-fructosecorn-syrup/faq-20058201
high-fructose corn syrup

And although HFCS consumption has declined somewhat in recent
years, obesity rates continue to rise, with almost 36% of U.S. adults
now considered obese. Alternative hypotheses for our increasing
obesity abound, including the fact that, from 1980 to 2000, the U.S.
per capita daily caloric intake increased 23%.

There is solid evidence, however, that overconsumption of sugar
and/or HFCS along with dietary fat and decreased physical activity
contribute to weight gain. In addition, high sugar consumption
tends to replace eating more varied and nutritious foods.
Reece, Jane B.; Simon, Eric J.; Taylor, Martha R.; Dickey, Jean L.; Hogan, Kelly A.. Campbell Biology: Concepts & Connections (Page 38). Pearson Education.
Kindle Edition.
http://www.mayoclinic.org/healthy-lifestyle/nutritionand-healthy-eating/expert-answers/high-fructosecorn-syrup/faq-20058201
Polysaccharides

Polysaccharides are
macromolecules, polymers of
hundreds to thousands of
monosaccharides linked
together by dehydration
reactions. Polysaccharides may
function as storage molecules or
as structural compounds.

three common types:
starch, glycogen,
and cellulose.
Glycogen

Animals store glucose in a
polysaccharide called
glycogen. Glycogen is more
highly branched than starch,
as shown in the figure. Most
of your glycogen is stored as
granules in your liver and
muscle cells, which hydrolyze
the glycogen to release
glucose when it is needed.
Cellulose

Cellulose, the most abundant organic compound on Earth, is a major
component of the tough walls that enclose plant cells. Cellulose is also
a polymer of glucose, but its monomers are linked together in a
different orientation.

Humans (and some other animals) do not have enzymes that can
hydrolyze the glucose linkages in cellulose. Therefore, cellulose is not a
nutrient for humans, although it does contribute to digestive health. The
cellulose that passes unchanged through your digestive tract is referred
to as “insoluble fiber.” Fresh fruits, vegetables, and whole grains are rich
in fiber.

Cows and termites house such microorganisms in their digestive tracts
and are thus able to derive energy from cellulose. Decomposing fungi
also digest cellulose, helping to recycle its chemical elements within
ecosystems.
Chitin

Chitin is a structural
polysaccharide used by insects
and crustaceans to build their
exoskeleton, the hard case
enclosing the animal. Chitin is
also found in the cell walls of
fungi.
carbohydrates are hydrophilic

Almost all carbohydrates are
hydrophilic owing to the many
hydroxyl groups attached to their
sugar monomers. Thus, cotton bath
towels, which are mostly cellulose,
are quite water absorbent due to the
water-loving nature of cellulose.
Lipids

Fats are energy storage molecules – stored energy as lipids

They do not mix well with water. In contrast to carbohydrates and
most other biological molecules, lipids are hydrophobic (waterfearing). You can see this chemical behavior in an unshaken bottle
of salad dressing. The oil (a type of lipid) separates from the vinegar
(which is mostly water).
Phospholipids

Phospholipids are the major
component of cell
membranes.

Phospholipids are structurally
similar to fats, except that
they contain only two fatty
acids attached to glycerol
instead of three.

Hydrophillic (polar) heads
and hydrophobic (non-polar)
tails.
Phospholipids

Phospholipids spontaneously
form a double-lipid bilayer
(like the cell membrane) in
water.

Chemistry may have brought
forth “life”.

The structure of phospholipids
provides a classic example of how
form fits function.

The two ends of a phospholipid
have different relationships with
water, resulting in the aggregation
of multiple phospholipid molecules
into a membrane (Figure 3.10B).

The hydrophobic tails of the fatty
acids cluster together in the center,
excluded from water, and the
hydrophilic phosphate heads face
the watery environment on either
side of the membrane.
PROTEINS

Nearly every dynamic
function in your body
depends on proteins.

A protein is a polymer of
small building blocks called
amino acids.

Of all of life’s molecules,
proteins are structurally and
functionally the most
elaborate and varied.
Protein structure and its link to
function.

The primary structure of a protein is the precise sequence of amino
acids in the polypeptide chain.

Segments of the chain then coil or fold into local patterns called
secondary structure.

The overall three-dimensional shape of a protein is called tertiary
structure.

Proteins with more than one polypeptide chain have quaternary
structure.

Prion diseases SEE https://en.wikipedia.org/wiki/Prion

PROTEINS
Peptide bonds are formed by a dehydration
reaction.
Nucleic Acids

DNA and RNA are built from single units
(monomers) of nucleic acids.

DNA = Deoxyribonucleic acid

RNA = Ribonucleic acid