MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
Carbon & The chemical basis of life
“Carbon chemistry rules Life …”
“All forms of life on planet Earth are carbon-based creatures ..”
Introduction

In the second chapter you have read that the chemical element carbon (C) is the
third most abundant chemical element in biological organisms

Carbon indeed plays a center role in the build-up, formation and maintenance of all
life forms on planet Earth

In this chapter you will learn and understand the important reasons which explains
carbon’s crucial function for all biological organisms on Earth

You also will understand why and how chemical elements, most importantly carbon,
can form a huge number of molecules due to chemical reactions between chemical
reactions partners
Definition: Chemical Reactions
Chemical reactions lead to chemical changes in matter (= chemical elements) to form
novel entities (= molecules & compounds)
e.g.
2 H2 + O2  2 H2O

chemical reactions do not destroy or create matter, they only rearrange linkages

chemical reactions are dependent on so-called activation energy which triggers the
reaction (see Chapter 5)

there are thousands of chemical reactions occurring simultaneously and in an
extremely organized manner in a living cell (see Chapters 6 & 7)

most of these chemical reactions involve carbon-based or so-called organic
molecules, which are catalyzed by highly specialized proteins, called enzymes
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MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
Carbon-based molecules & Life

all biological organisms are made up of (bio)molecules in which carbon (= C) is the
most abundant chemical element

it is the unique atomic & chemical properties of the carbon atom which greatly
explains its outstanding position in the living universe

the capacity of carbon to interact with 4 different atomic reaction partners
greatly explains the huge diversity of (bio)molecules and last not least the
tremendous variety in body shapes and structures of biological organisms
according to the Bohr atomic model, carbon needs 4 electrons to fill up its
outermost electron shells to reach the noble gas configuration

Another explanation for carbon’s outstanding position amongst other atoms lays in
its four unique, so-called hybrid sp3-orbitals which have a defined 3-dimensional
arrangement in space, by forming a so-called tetrahedral structure
- as a result of carbon’s tetrahedral structure its four atomic reaction partners are
arranged in a defined 3-dimensional orientation
- each hybrid sp3 orbital is clearly aligned in space and each orbital is forming a
109 degree angle towards the other one
“Carbon-based molecules are not only boring carbon pearls on a string but rather
have an intricate and defined 3-dimensional structure … “

Therefore, when each of the four hybrid sp3 orbitals of carbon forms a single
covalent bond with four other atoms, they are arranged at the corners of an
imaginary pyramid-like, so-called tetrahedral, structure with bond angles near 109
degrees.

Finally, carbon can make covalent bonds with another carbon atom, which
1. can create long carbon chains serving as the backbones of multiple organic
molecules
2. can serve to store high amounts of energy
- e.g. the C-C covalent bond contains 83.1 Kcal (kilocalories) per mole
- the C=C double covalent bond has 147 Kcal/mole
- e.g. energy from sunlight is converted into the C-C covalent bond energy
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MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
The hybrid sp3 orbital and the tetrahedral structure of the C-atom
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MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.

When several carbon atoms undergo covalent bond formation with other carbons,
long carbon chains form. Carbon chains form the skeletons (or carbon backbones)
of most organic molecules.
- the skeletons may vary in length and can be straight, branched, or even
in closed rings, such as in benzene

Carbon can also share two or three sp3 orbitals with just one other carbon atoms to
form double and triple covalent bonds. Therefore carbon skeletons of molecules may
also include double and triple bonds as we will see later
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MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.

Isomers are compounds that have the same molecular formula but different
structures and therefore different chemical properties. For example, butane and
isobutane have the same molecular formula C4H10, but butane has a straight
skeleton and isobutane has a branched skeleton. The two butanes shown below are
structural isomers, molecules with the same molecular formula but differ in the
covalent arrangement of atoms.

Carbons unique hybrid sp3 orbitals and its special arrangement in space is also
responsible for enantiomer formation. Enantiomers are possible if there are four
different atoms or groups of atoms bonded to a central carbon. Under these
circumstances the four groups will arrange in space in two different ways that are
mirror images to each other. The resulting enantiomers are like left-handed and
right-handed versions of each other.
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MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
- usually only one of the two enantiomers is biologically active, the other is often
inactive.

Even the.
One enantiomer of.
The L-Dopa isomer
is an effective treatment
of Parkinson’s disease,
but the D-Dopa isomer
is inactive.
The subtle 3D-structural differences in two enantiomers have important
functional significance in biological systems because of emergent properties from
the specific arrangements of atoms.
- for example, one of the enantiomers of the drug Thalidomide which was
prescribed in the 1960s to reduce morning sickness in pregnant women showed
its desired effect, but the other isomer caused severe birth defects, e.g.
missing fingers and even limbs
- e.g. only the L-Dopa enantiomer is effective to reduce the symptoms in
patients suffering from Parkinson Disease (PD), the D-Dopa isomer is biologically
inactive
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MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.

Due to its atomic electron arrangement and orbital structure the carbon atom
(= C ) can interact with four different atom reaction partners
whenever a central carbon atom (= C) forms a covalent bond with four different
atomic reaction partners, left- and right-handed or so-called stereoisomer
molecules are the outcome
Examples:
e.g. Ethanol (= alcohol)
H
I
H3C - C – OH
ı
H
e.g. Serine (= amino acid)
H
I
HO – CH2 - CH2 - C - COOH
ı
NH2
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MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
CARBON IS THE BASIS OF THE ORGANIC MOLECULES OF LIFE

The above described unique properties help explain why carbon ( C ) and not any
other similarly abundant chemical element, such as silicone, is the central atom for
all biologically relevant molecules!
carbon-based compounds or so-called organic compounds are next to water the
most common substances in living matter

the strong tendency of the C-atoms outer-shell electrons to form covalent bonds,
explains the enormous variety of C-based molecules in nature
over 2 million biologically or chemically synthesized organic compounds are
known today

If more than one C-atom are covalently linked together, the C-atoms build a
characteristic, so-called carbon skeleton; this carbon chain can be:
1. branched carbon skeletons
 e.g. certain amino acids
2. unbranched carbon skeletons
 e.g. in fatty acids (see section below)
The functional groups of carbon molecules

the unique physico-chemical properties of organic compounds depend not only on
the carbon skeleton but also on groups covalently linked to the C-atom, so-called
functional groups

the 4 major functional groups important for biological molecules (see Figure
below)
Definition: Functional groups
Functional groups are clusters of atoms with characteristic structure and chemical
properties
Examples of functional groups
 e.g.
– OH
- COOH
- SH
- NH2
HydroxylCarboxylSulfhydrylAmino-
group
group
group
group

the most important feature of functional groups is the presence or absence of socalled electrical net-charges of its atomic members in aqueous solutions
 e.g. – COO- or
– Sor – Oor – N+

polar molecules bear positive (+) and/or negative (-) net charges in its functional
groups which are strongly attracted to water molecules; these molecules are also
called hydrophilic
 e.g. nucleic acids, carbohydrates, most amino acids
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MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.

molecules with no or minor surface net charges of its atoms are called non-polar
molecules; these molecules, which are repelled by water and do not dissolve in it;
are called hydrophobic
 e.g. alkanes, fatty acids, lipids

if a molecule consists of a hydrophilic and a hydrophobic part then we speak of a socalled amphiphilic molecule
 e.g. bile acids in our gall bladder
Structural formulas, models and examples of important functional groups of
(bio)molecules
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MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
The carbon-based molecules of life

all important structures and components of biological organisms are formed by
molecules based on the chemical element carbon

cells make a huge number of large molecules from a relatively little set of small
molecules
 cells combine the functional groups of the biomolecules in different variations
 a similar strategy is nowadays used by many pharmaceutical companies in a
laboratory synthesis process called combinatorial chemistry

many of life’s molecules, e.g. DNA, proteins or polysaccharides are so-called
macromolecules

most macromolecules are so-called polymers
 polymers are large molecules which consist of many structurally identical or
similar building blocks, called monomers
 The chemical process of polymer formation is called dehydration synthesis
(= linkage by removal of water), in which hydroxyl-groups play a prominent
role

nature creates a huge structural variety on the basis of only a few molecular units:
1.
2.
3.
proteins from only 20 amino acids
DNA/RNA from only 5 nucleotides (A, T, G, C, U)
Storage carbohydrates (e.g. starch, glycogen) from mainly 3 sugars
 this enormous number of structural variety is achieved by variation in sequence,
also called rearrangement

Five major classes of carbon-based molecules have been found in literally all
forms of life on planet Earth and characterized by biochemists
1.
2.
3.
4.
5.

-

Carbohydrates
Lipids and Fats
Proteins
Nucleic Acids
Signaling & Communication molecules
most of the cellular macromolecules are constructed by covalently bonding more
simple precursor molecules, so-called monomers by so-called condensation
reactions
typical precursor molecules for biological synthesis (= biosynthesis) of
macromolecules are hexose/pentose sugars, nucleotides, amino acids and fatty
acids
during biochemical condensation reactions water is released after chemical
reaction of functional groups of the monomers
 Condensation is also called dehydration synthesis because
water is removed (dehydration) while a new bond is created (= synthesis)
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MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.

during dehydration synthesis between two monomers, a hydroxyl (- OH) group
is removed from one monomer and a hydrogen (H) is removed from the other (see
Graphic below)
The reaction principle of chemical dehydration synthesis of polymers
Monomer 1
+
M1
HO
Monomer 2
O
Dimer
M2
H
M1
O
HO
H
H
O
(H2O)
Polymer
+
M2
O
O
M3
H
etc.
O
Covalent bonds

during condensation reactions, many monomers are joined together to form socalled polymers; polymers are large macromolecules made of three to millions of
monomer sub-units

four classes of macromolecules or bio-polymers (= polysaccharides, triglycerides,
polypeptides, nucleic acids) perform a variety of vital functions in cells
1. Carbohydrates (Sugars & Polysaccharides)
1.1. Mono sugars

Monosaccharides, particularly glucose and fructose, are the major fuel for cellular
work. They both are the “cell’s gasoline”. They also function as the raw material for
the synthesis of other carbon-based monomers, such as amino acids and fatty
acids. In aqueous solutions, such as the interior of a cell, they exist mostly in ringform.
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MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.

Carbohydrates are assembled from small sugar monomers or monosaccharides to
larger units, called polysaccharides
 e.g. potato starch or liver glycogen, which are also called storage carbohydrates;
 another storage carbohydrate is honey; it consists of glucose and fructose
molecules

Glucose and fructose are so-called isomers
 they have an identical molecular formula = C6H12O6, but a different chemical
structure
 both molecules exist in linear or ring form in nature

glucose/fructose are so-called hexose sugars (in contrary to so-called pentose
sugars), which means they have a carbon skeleton with 6 C-atoms

hexoses are the main fuel molecules of the cell, while pentose sugars are essential
components of DNA/RNA molecules (see end of this chapter)
Hexoses
(= sugars with 6 C-atoms)
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MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
Trioses
Pentoses
Disaccharides

Disaccharides are sugars formed by a so-called glycosidic linkage between two
monosaccharides (= mono-sugars) after dehydration synthesis. In the case of
maltose (the “beer sugar”), two glucose molecules are linked together via a
glycosidic bond.

The mono-sugars in disaccharides can be the same or different ones
e.g.
glucose + glucose
glucose + fructose
glucose + galactose



maltose (‘beer malt’)
sucrose (‘sugar cube’)
lactose (‘milk sugar’)
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MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
Chemical structures of important Disaccharides
Polysaccharides

Polysaccharides are complex sugars made up from hundreds to millions of monosugars linked together via glycosidic (covalent) bonds

Polysaccharides are found in huge amounts in many plants where they play major
roles as structural components in form of cellulose or as storage carbohydrates in
form of starch in tubers, stems, fruits and other plant parts

Especially the latter polysaccharide starch is the major sugar source for our world
civilizations and plays a crucial role in world nutrition

Important agricultural plants which store huge amounts of starch in different plant
parts are:
Agricultural plant
1. sugar cane
2. sugar beet
3. corn
4. rice
5. potato
6. jam
Examples of polysaccharides (PS):
Plant part of starch storage
stems
tuber
endosperm of kernel
endosperm of kernel
tuber
tuber
function and use in living organisms
1. Starch
- a storage polysaccharide composed entirely of glucose monomers.
- most monomers are joined by alpha-1-4 linkages between the glucose molecules.
- one unbranched form of starch, amylose, forms a helix, while branched forms, like
amylopectin, are more complex.
- starch serves as storage polysaccharides in plants.
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MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
2. Glycogen
- a more branched and coiled polysaccharide than starch;
- it serves as storage polysaccharide in liver and muscle of higher animals which
can be mobilized in form of glucose in times of starvation
- usually found as glycogen granules within the cells
- they only have about a one day supply.
3. Cellulose
- linear structured polysaccharide made up from beta-1,4 glycosidic bonded
glucose molecules.
- it is synthesized in plant cells where it makes up the major component of the
tough wall of plant cells.
- it serves cell protection and support of cellular structure
- cellulose is the single most abundant organic compound on Earth
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MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
Chemical structures of biologically important Polysaccharides
Pllaannttss)
Chemical structure of starch (P
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MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
Pllaannttss)
Chemical structure of cellulose (P
•
The human enzymes that digest starch, e.g. amylase, cannot hydrolyze the beta-1,4
linkages in cellulose. Therefore, cellulose in our food (e.g. in a salad or a carrot)
passes through the digestive tract and is eliminated in feces as “insoluble fiber”. As it
travels through the digestive tract, it abrades the intestinal walls and stimulates the
secretion of mucus. It also helps to detoxify the human body by absorbing otherwise
poisonous molecules from our body.
•
Some microbes can digest cellulose to its glucose monomers through the use of
cellulase enzymes. Many eukaryotic herbivores, like cows, rhinos, giraffes and
termites, have symbiotic relationships with cellulolytic microbes, allowing them
access to this rich source of metabolic energy.
Fats & Lipids

The word fat is not “a vogue” in our public opinion and truly not a fashionable word
in our modern societies, fats and its close molecular relatives lipids are enormously
important bio-molecules for biological organisms

Fats and lipids are a diverse group of compounds and are macromolecules primarily
composed of fatty acids

a fatty acid is a molecules which consists of an unbranched, nonpolar
hydrocarbon chain (= a chain mainly made of C- and H-atoms) with a terminal
carboxyl group
- when the C- and H-atoms are linked together via single covalent bonds and as
even-numbered multiples of CH2-units, we call these fatty acids saturated
- unsaturated fatty acids have one or more C=C double bonds in their carbon
chain
- the carbon atom at the end of the CH2-chain has a polar hydroxyl-group ( COH) and a carbonyl-group ( C=O); it forms an acidic ( fatty acid!) carboxylgroup
- the hydrocarbon portion of the molecule can contain 4-36 carbons
- most of the fatty acids in biological organisms have a even-numbered chain
length of 14 to 20 carbon atoms
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MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
e.g. the C16 fatty acid palmitic acid or the C18 fatty acid stearic acid (see
picture below)
 the Figures below shows the space-fill models and chemical structures of the
unsaturated fatty acids palmitic acid and stearic acid, with the red-colored
oxygen atoms of the carboxyl groups

fat is a lipid consisting of a glycerol backbone and covalently attached fatty acids;
- in the case of three attached fatty acid, we also speak of a so-called triglyceride
Since long-term high levels of triglycerides (TGs) can contribute to arteriosclerotic
plaque formation in human blood vessels and strokes, routine monitoring of the
blood plasma levels of TGs is important in our modern, high caloric and sessile
societies

-
the main function of fat is the storage of high-energy-containing molecules (=
fatty acids!) in specialized cells (= adipocytes) of fat tissues
 especially adipocytes of overweight and obese human individuals have huge
amounts of stored fat in form of fat droplets
-
the biological function of fat reserves and deposits is manifold but includes:
1. protection from cold and hypothermia in infants, hibernating mammals
and whales
2. energy reserve for periods of food scarcity and mal-nutrition
3. storage and deposit of lipophilic (= fat-loving) metabolic wastes, such
as drugs, poisons, hormones ?
oil is a type of fat with a slightly different composition of its lipids
 the lipids of oil contain a higher content of so-called unsaturated fatty
acids, which gives it a more viscous appearance at room temperature.
Space-fill models and chemical structures of the unsaturated fatty acids
palmitic acid (top) and stearic acid (bottom)
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MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
C
Chheem
miiccaall ssttrruuccttuurree ooff aa ttyyppiiccaall ttrriiggllyycceerriiddee ((== ffaatt))
3 x fatty acids

+
1 x glycerol

Phospholipids and cell membranes

Phospholipids is a diverse group of biomolecules which – albeit their structural
similarity to fats – have more diverse biological functions in living organisms

phospholipids consist of only two fatty acids (usually one saturated and one
unsaturated = blue-colored part of the Figure below), which are covalently linked to
the glycerol backbone (see pink-colored part); the third component can be:
1. a phosphate group (see orange-color part in the Figure below)
2. a phosphate derivative
3. a choline
4. an ethanolamine
5. or a sugar (e.g. inositol)
 which are linked to the third hydroxyl-group of glycerol (see picture below)

phospholipids are the major components of the biological membranes of all cells on
planet Earth

phospholipids help to form the so-called lipid bilayer of the cell membrane (see
Chapter 4), which separates the outside world from the cell interior

phospholipids and especially certain enzymatic cleavage products, such as the
unsaturated fatty acid arachidonic acid, play a crucial role in diverse intracellular
communication processes, the so-called signal transduction events

waxes are structurally very similar to lipids and are compounds where one fatty acid
is linked with an alcohol; structurally different waxes have a variety of different
biological functions in different organisms
 e.g. bee wax for sealing
coating waxes of fruits
cuticule of plant leaves
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MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
Space-fill model and chemical structure of typical phospholipids
P
Phhoosspphhaattee ggrroouupp
G
Gllyycceerrooll
 2 x FFaattttyy A
Acciidd

phospholipids brought into water spontaneously arrange themselves as a socalled phospholipid bilayer structure (see Figure below)

this phenomenon is explained by the amphiphilic nature of the phospholipids
molecules, which means that they have a water-loving (= hydrophilic or polar)
“head part” and a water-hating (= hydrophobic or non-polar) tail region
Definition: Hydrophilic/Hydrophobic
- Hydrophilic refers to electrically (+ or -) charged (polar) chemical groups
or molecules which will interact with the polar water molecule
- hydrophilic molecules dissolve in water
- Hydrophobic refers to non-charged (unpolar) chemical groups or
molecules which will not interact with the polar water molecule
- hydrophobic molecules do not dissolve in water but in organic solvents, such
as hexane, chloroform or ethanol

a phospholipid bilayer membrane is formed by arrangement of the polar head
groups of the phospholipids with the polar water molecules forming the outer
sheet of the bilayer and by tail end-to- tail end alignment of the non-polar fatty
acid tails in the middle of the bilayer structure to create a hydrophobic core
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MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
Polar and non-polar parts of a typical phospholipids molecule
A
Arrrraannggeem
meenntt ooff pphhoosspphhoolliippiiddss iinn aa bbiioollooggiiccaall ((== cceellll)) m
meem
mbbrraannee
( Lipid bilayer diagram)
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MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.

The membranes of cells or organelles of biological organisms are made up from
more than just a simple phospholipid bilayer; cell and organelle membranes are
usually filled with inserted or associated macromolecules, such as proteins,
glycoproteins and cholesterol (see Graphic below), which play important
structural functions or play a role in cell communication
Schematic picture of a segment of a biological cell membrane
STEROIDS

steroids are 4-ringed lipid-like molecules which are the starting material for the
synthesis of many important biological molecules

many steroids are potent, so-called lipophilic hormones which control a huge
variety of important biological processes, such meiosis, carbohydrate
metabolism, fat storage, muscle growth, immune function, and nerve cell
membrane function

the class of molecules called steroids comprises the gonadal androgens,
estrogens, and progestogens as well as the anabolic/catabolic glucocorticoids
- e.g. the female and male sexual hormons (estrogen, testosterone
- e.g. cholesterol, which is an important component of biological membranes
- e.g. vitamine D, which plays an important role in bone formation
- e.g. cortisone: a glucocorticoid, which is a regulating molecule of immunological
responses in the human body and has strong anti-inflammatory effects
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MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
Chemical structures of important steroids

many synthetic variations of steroids are used today as drugs for treatment of
many diseases
- e.g. testosterone derivatives are used in modern animal farming as so-called
anabolics for increasing muscle growth in cattle
- testosterone or derivatives thereof are also widely (mis-)used as anabolic
steroids for accelerated athletic muscle build-up, a habit which – in the longterm - can lead to health complications, such as heart muscle damage

steroid molecules are also synthesized by plants where they have many
diverse – an mostly – unknown biological functions
- e.g. the foxglove plant (Digitalis purpurea) produces the well-known
cardiotonic digitalis steroid
Amino acids, polypeptides and proteins

amino acids are the fundamental monomer building blocks of one of the most
complex and diverse class of biological macro-molecules, called proteins

proteins itself are the structural building blocks of almost all major cellular
components and structures, such as enzymes, ribosomes, cytoskeleton,
centrosomes, proteasome, etc.; cell and organism life without the presence of
functional proteins is not imaginable

amino acids have characteristic chemical and structural features:
1. they have an amino group (-NH2) plus a carboxyl group (-COOH) as
functional groups (see red part in the Figure below)
2. both functional groups are covalently attached to the first (so-called
‘alpha’) carbon atom (or α- C atom)
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MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
3. have a variable residual part (= R group)
 see blue-colored parts below
 the R-group is covalently linked to the alpha C-atom
 this R-residue gives the amino acid its unique chemical properties
Chemical structures of 2 important amino acids
Cysteine

Serine
rreedd
= conserved amino and carboxy group involved in peptide bond
formation
bblluuee
= unique part or “R- group” of the amino acid
20 amino acids have been identified in all forms of life on planet Earth, which –
according to their different chemical structures - have been organized in groups of
so-called:
 basic amino acids
 acidic amino acids
and their amides
=
arginine, histidine, lysine (see Graphic below))
=
 aliphatic a. acids
=
 sulfur-containing
 aromatic a. acids
 non-aromatic a. acids
=
=
=
glutamic acid, aspartic acid, asparagine,
glutamine
glycine (see picture), alanine, leucin,
isoleucine, valine
cysteine (see picture) and methionine
tyrosine, phenylalanine, tryptophan
serine (see picture above), threonine

special amino acids, such as tyrosine and tryptophan have a so-called aromatic ring
structure attached to the alpha C-atom
 the free hydroxyl-group of the tyrosine R-group plays an important role in the
regulation of the function of important proteins in the cell
 a phosphate group can become attached to the tyrosine in a cellular process
called tyrosine phosphorylation

cysteine and methionine have a so-called sulfhydryl group in their variable group
 these sulfhydryl groups play an important role in the build-up of the 3-dimensional
structure of proteins
24
MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
G
Geenneerraall ssttrruuccttuurree aanndd ffuunnccttiioonnaall ggrroouuppss ooff aann aam
miinnoo aacciidd
O
O  C
C  O
OH
H

R
R  C N
NH
H222

H
G
Grreeeenn
ppiinnkk
rreedd
bblluuee
bbllaacckk
=
=
=
=
=
Carboxyl – group
Amino – group
Hydrogen
R- group
α C-atom

amino acids in the cell are also linked together by dehydration synthesis (see
previous section above) and form so-called peptide bonds (see Graphic below)

the product of the chemical reaction between two amino acids is called a dipeptide

the product of multiple amino acids linked together is called a polypeptide (-chain)
 examples of biologically important polypeptide chains are insulin or growth
hormones

if the number of amino acids in a polypeptide chain goes into the hundreds, we then
speak of a protein
25
MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
Amino acids differ in its R - groups
 = Carbon
 = Oxygen
 = Sulfur
 = Hydrogen
 = Nitrogen
26
MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
Peptide bond formation through dehydration synthesis
Polypeptides & Proteins

formation of multiple peptide bonds via dehydration synthesis creates a linear polypeptide chain, in which the amino acids are arranged one after another like pearls
on a chain
 the linear arrangement of the amino acids (or so-called amino acid sequence) in
a given polypeptide chain refers to the so-called primary structure of a protein
Amino acid 1
Amino acid 2
Amino acid 3
→
→
→
… etc.

for a polypeptide chain to become biologically functional in form of a protein, it
has to be folded into the correct 3-dimensional (or tertiary) structure
27
MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
PROTEINS

the word protein originates from the greek word ‘proteos’, which means ‘in first
place’

proteins are huge macromolecules found in all forms of life on planet Earth

chemically, proteins are polymers made of linear strings of amino acids,
connected via peptide bond formation (see above)
 many proteins have other molecules tightly attached with or loosely bound to it
(= co-factors or co-enzymes)
 some proteins have single atoms, e.g. zinc, selenium, copper, etc. bound to it,

proteins are the most diverse of all of life’s molecules regarding structure and
function
 the huge diversity is primarily based on differing, so-called arrangement
combinations of the universal set of 20 amino acids
 each amino acid can basically form a peptide bond with either itself or with any
other of the remaining 19 amino acids

in the living cell, however, the peptide bond formation is not a random event, but
happens in a highly regulated fashion in a cellular process called protein
translation
 the cell does not allow the 20 amino acids to interact with each other by
random, but assembles (= polymerizes) them in certain defined sequences
 therefore, each cellular protein has a defined so-called linear amino acid
sequence, consisting of a defined number of amino acids
 the cellular peptide bond formation is catalyzed by a highly complex ‘protein
synthesis machinery’, called ribosomes (see Chapter 10-2)

along the synthesis of the polypeptide chain at the ribosome and along the way
into the endoplasmic reticulum (see UNIT 3), the amino acid strand folds into a
unique 3-dimensional structure

The 3-dimensional structure of a protein is strongly dependent on:
1. the linear sequence of its amino acids and
2. the chemical properties of the side groups (R) of its amino acids
“The 3-dimensional protein structure determines the protein’s unique
biological function …”
 most of the proteins have a globular structure and are so-called globular proteins
 but many structural proteins e.g. actin, myosin have a long and thin fibrous
structure
28
MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.

7 major classes of proteins are categorized according to their functions
1. structural proteins
e.g. keratin
e.g. actin
e.g. collagen
 in hairs, silk
 cell support, movement, cytoskeleton
 skin matrix
2. contractile proteins
e.g. myosin
e.g. tubulin
 muscle contraction
 cytoskeleton, flagella, mitosis, meiosis
3. storage proteins
e.g. ovalbumin
 egg white
4. transport protein
e.g. serum albumin
e.g. transferring
e.g. coeruloplasmin
e.g. GLUT4
 fatty acid transport
 iron transport
 copper transport
 glucose transport
5. defense proteins
e.g. immunoglobulin G (IgG)
e.g. complement protein C5
 antibody, immune sustem
 immune system
6. signaling proteins
e.g. insulin receptor (responsible for glucose transport into cell)
7. enzymes (or so-called ‘bio-catalysts’)
e.g. amylase, protease

the characteristic shape and topography of the surface of a protein determines
further:
1. with which molecules it interacts and which molecules will bind
 in the case of an enzyme we speak of the interaction site also as the
‘active site’ or of the ‘catalytic center’;
 the interacting molecule is called the ‘substrate’ (see Chapter 6)
2. with which other proteins it will interact
 these protein-protein interactions play a crucial role in the transmission of
cellular signals, in a process called signal transduction
3. the place in the cell where a synthesized protein will be located
 some proteins have surface structures which helps them to move into or
close to the cell membrane e.g. so-called receptor proteins
29
MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.

the 3-dimensional structure of a protein can be destroyed
 e.g. by treatment of the protein with heat or acid
 the process which leads to the destruction of a protein’s structure is called
denaturation
Denaturation of a protein, e.g. by heat or acids, usually leads to the loss of its
biological function
-
but some rare proteins are highly resistent to e.g. heat, such as a class of
enzymes called Taq-Polymerases
this unique feature gained tremendous importance in modern biotechnology
and medicinal analytics
today, the heat-resistent Taq-Polymerase is the ‘molecular working horse’ of
a biological technique called polymerase-chain-reaction or PCR

the 3-dimensional structure of a protein and its biological function can also be
distorted or (in the worst case) destroyed by so-called mutations
 mutated proteins are the primary cause of many human diseases, such as
sickle cell anemia or cancer (see UNIT 11)

four structural levels determine the 3-dimensional appearance or
conformation of a protein
1. the primary structure
 the primary structure is defined by the so-called linear sequence of amino
acids
 thousands of linear sequences of proteins are known today and they are
archived in so-called protein data banks, e.g. SwissProt
2. the secondary structure
 coiling or folding of parts of the polypeptide chain in 2 characteristic microstructures:

Alpha-helix (plural alpha-helices)

Beta-sheet (or pleated sheets)
 both secondary structures are maintained/stabilized by regular spaced
hydrogen bonds between the - N – H groups and the – C = O groups at
the alpha C-atom
 the R-groups of the amino acids are NOT involved!
30
MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
Alpha-helical structure (= A
Allpphhaa hheelliixx) of a protein
 Hydrogen bond formation between residues of the
peptide bonds of amino acids forms a rigid,
rod-like molecular cylinder
R-Groups
Hydrogen
Bonds
31
MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
Beta sheet structure (= pplleeaatteedd sshheeeett) of a protein
 Hydrogen bonding between backbone atoms of amino acids of adjacent -sheets form
a rigid, planar, sheet-like structure in proteins
Hydrogen
Bonds
R-Groups
Polypeptide 1
Polypeptide 2
Pleated or beta
in a protein
32
MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
3. the tertiary structure
- is the overall 3-dimensional shape of the folded polypeptide chain of a
protein (see Figure below)
 the tertiary structure is determined by the arrangement of alternating
reedd parts in the Figure below) and beta-sheets (y
yeelllloow
alpha-helices (r
w
parts in the Figure below), which are connected via loop-domains
 the tertiary structure of proteins can be solved by two highly sophisticated
technologies, called X-ray crystallography or nuclear magnetic resonance
(= NMR)
 many 3D-structures of proteins have been successfully unraveled with the
help of these two methods
 the retrieved data are archived in the so-called Brookhaven Data Bank
(PDB), where they can be visualized with the help of special computer
software
3-Dimensional (= tertiary) structure of a protein
 computer-assisted ribbon model of the mitochondrial IDH protein showing the
“run” of the polypeptide chain including:
1. beta sheets ( yyeelllloow
w)
2. alpha helices ( ppuurrppllee )
blluuee)
3. turns or loops (b
 this protein plays an important role in the metabolism of glucose molecules in
cells; it has catalytic activity and works as an enzyme (see Chapter 6)
33
MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.

this so-called tertiary protein structure (= the 3D-structure) of a poly-peptide
chain is mediated and stabilized weak forces, most importantly hydrogen bonds
formed between certain side groups or R-groups of its amino acids

many proteins are in close association with ions, such as zinc or magnesium ion
or other – often smaller – molecules, such as NAD+, biotin or thiamin (see
Figure below)
Computer-assisted stick model of the IDH protein with an associated/
bound NAD+ molecule
-
IDH protein is shown with blue-colored ribbons symbolizing the covalent
bonds of the polypeptide chain
the molecule NAD+ is shown as red-colored ribbons associated with IDH
Without the bound NAD+ molecule the IDH protein would not the biologically
fucntional
4. the quarternary structure (see Figure below)
 is the interaction of multiple polypeptide chains or so-called sub-units
of a protein e.g. insulin receptor, hemoglobin, to form the final functional
protein complex
 if two sub-units of a protein couple together we speak of a dimer
 if the sub-units are identical we call the complex a homo-dimer,
 if they are different we speak of a hetero-dimer
 many of these sub-unit interactions are mediated via so-called disulphide
bridges, involving the side chain group of the amino acid cysteine
34
MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
The quarternary structure of a protein
(= interaction of multiple polypeptide chains)
 Graphic shows a simplified model of the protein hemoblobin
Nucleotides & Nucleic Acids

nucleic acids are the biological polymers that harbor the so-called genetic code
of all living organisms;
 nucleic acids are the blueprints of life and explain the biological phenomenon
heredity (see also Chapters 8 & 9)

2 types of nucleic acids are known:
1. DNA (= deoxyribonucleic acid)
 harbors the genetic information of biological organisms in of a digital
molecular code (see: The genetic code  Chapter 10)
2. RNA (= ribonucleic acid)
 has multiple functions in the transmission of the genetic information from
the DNA to the intact protein (see UNIT 8)

Nucleic acids are polymers made up from only 4 different monomers by
dehydration synthesis

the monomeric units or monomers of nucleic acid are called nucleotides
35
MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.

The nucleotides found in nucleic acids consist of 3 molecular elements
1.
a nitrogenous base
 the base can be either:
Adenine (A)
Thymine (T)
Cytosine (C)
Guanine (G)
Uracil (U)
2.
a pentose (sugar)
 deoxyribose (for DNA)
 ribose (for RNA)
3.
a phosphate group
→
→
→
→
→
found in DNA and RNA
only found in DNA !
found in DNA and RNA
found in DNA and RNA
only found in RNA !

nucleic acid monomers form a so-called polynucleotide chain by dehydration
synthesis
 in biological systems this synthesis is catalyzed by specific enzymes, called
DNA- or RNA-polymerases (see Chapter 10)
 a new polynucleotide strand is formed in a strict 5’-3’ direction with the help
of an older, so-called parent DNA strand as template
 RNA usually consists of a single polynucleotide strand and forms
characteristic 3-dimensional structures, the so-called hairpin loops
 DNA forms the so-called double helix (Watson-Crick helix), which consists
of two polynucleotide strands wrap around each other (see Figure below)

in the next Chapter we will hear more about the place, where all these biological
molecules are found and where they perform their life-essential functions
Chemical structure of a typical nucleotide
P
Phhoosspphhaattee G
Grroouupp
D

DN
NA
A ==
←
N
Niittrrooggeennoouuss B
Baassee
←
S
Suuggaarr ((DDNNAA == DDeeooxxyyrriibboossee))
((R
RN
NA
A == R
Riibboossee))
36
MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
Components and architecture of D
DN
NA
A ((== D
DeeooxxyyrriibbooN
Nuucclleeiicc A
Acciidd))
↑
↑
Sugar- Base
Phosphate
Strand 1
↑
Base
↑
SugarPhosphate
Strand 2
33--D
Diim
meennssiioonnaall m
mooddeell ooff aa ffrraaggm
meenntt ooff tthhee D
DN
NA
A ddoouubbllee hheelliixx
37
MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
Comparison of the RNA and DNA molecules
Sugar
Nucleotides
R
Riibboossee
(A, U, G, C)
D
Deeooxxyyrriibboossee
(A, T, G, C)
38
MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
Signaling & Communication molecules
-
carbon-based molecules found in biological organisms not only play important
roles as food molecules (carbohydrates, fats, proteins), the maintenance of
structures (= phospholipids, proteins, cellulose) or serve as storage forms of
enerhy (fats, starch, glycogen), but also play an enormously important role in
communication and signaling
-
different classes of signaling and communication molecules can be
classified, each which a huge array of different biological functions
Peptido-hormones

peptide hormones are small molecules which signal cells to change their activity
and status

peptide hormones are short poly-peptide chains which exert important
biological functions, e.g. growth control, sugar uptake, control of metabolism,
immune response, etc. in living organisms

important molecules are, e.g. insulin (see Figure below), glucagon, NGF, EGF,
interferons, Prolactoliberin, Prolactin, Somatostatin, Vasopressin (ADH),
Erythropoetin (EPO),
-
Ribbon model of insulin
in humans, the peptido hormone insulin signals cells to take up glucose
from the surrounding blood stream
the blood glucose-level decreasing hormone insulin contains 51 amino
acids, arranged in two short poly-peptide chains
it binds to a “cell antenna”, the so-called insulin receptor, which (upon
insulin activation) signals the cell to activate a glucose transporting protein
absence of insulin in humans leads to diabetes 1
39
MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
Neurotransmitter molecules

neurotransmitters comprises a diverse group of small signaling molecules
which affect nerve cells in the central nervous system (CNS)

they ferry information from the end of one nerve cell to the "beginning" of
another by activating so-called a receptor proteins on the synapse

examples of important neurotransmitters are:
1.
2.
3.
4.
5.
6.
7.
Acetylcholine
Epinephrine
GABA
L-Dopa
Dopamine
Glutamate
Glycine
Second messenger molecules

are small molecules that are produced and/or released by living cells in
response to external stimuli, such as light, heat, stress and hormones

they activate so-called signaling cascades in the cell interior which usually
leads to activation of genes in the cell nucleus

important cellular signaling molecules are:
1. Nitric oxide (NO)
 the gas NO affects smooth muscle cells and plays an important role in
the control of the vascular system of the human body
 Sildenafil (Viagra), a recently-approved erection facilitator, may affect the
enzymes responsible for generating NO
2. Inositols and prostaglandins
 are both small signaling molecules released from phospholipids of cell
membranes after injury or cell activation
 inositols are sugars with potent inner cellular signaling function, such as
release of calcium from cell stores
40
MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.

prostaglandins are derivatives of the unsaturated fatty acid arachidonate
which play an important role in the regulation of the vascular system and
in inflammatory processes
3. Cyclic adenosine mono-phosphate (cAMP)
 cAMP is a small signaling molecule which works as a so-called second
messenger molecule, which helps to transducer signals from the
surface of a cell into the nucleus
 levels of cAMP increase in cells after activation with hormones, such as
the stress hormone adrenaline or in the presence of the coffee bean
alkaloid caffeine
Chemical structure of the cAMP molecule
Plant hormones

Plants also produce a vast variety of carbon-based signaling molecules of
which many function as hormones

Plant hormones play an integral role in controlling the growth and
development of plants and mediate potent signaling effects

Important discovered plant hormones are:
1. Auxins
- produced in plant stem tips from the amino acid tryptophan
- promote stem elongation
- maintain apical dominance by inhibiting growth of lateral buds
- produced in the stem, buds, and root tips
- e.g. Indole Acetic Acid (IA)
2. Gibberillins (GA)
- not produced in stem tip but also promote stem elongation
41
MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
3. Cytokinins
- promote cell division
- produced in growing areas, such as meristems at tip of the shoot
- e.g. Zeatin in corn (Zea maize)
4. Abscisic acid (ABA)
- inhibits plant cell growth and promotes seed dormancy
- also involved in opening and closing of stomata in wilting leaves
5. Ethylene
- gas produced by ripe fruits of angiosperm plants from the amino acid
methionine
- triggers and synchronizes the ripening process, e.g. of fruits
6. Nitric oxide (NO)
- plants produce the gas NO as a biological weapon against invading
pathogens
- infection of the plant triggers the formation of NOS enzyme, that
makes NO from the amino acid arginine
7. Secondary metabolites
- Secondary metabolites are derivatives from simple ancestral
molecules (= primary metabolites)
- They are usually stored in the central vacuoles of specialized cell
type located in, e.g. scent glands of flowers, called osmophores
- They fulfill several important functions in plants:
1. plant defense
- against, e.g. herbivores and plant viruses
2. attraction of pollinators
3. communication between plants
- e.g. salicylic acid in silver willow
42
MESA COLLEGE, SAN DIEGO
SCHOOL OF MATHEMATICS & NATURAL SCIENCES
General Biology Lecture (BIOL 107); Instructor: Elmar Schmid, Ph.D.
Chemical structure of important signaling &
communication molecules in plants
Auxins
Cytokinins
Abscisic Acid
Ethylene
Gibberillins
N=O
.
 “radical”
Nitric Oxide
43