LECTURE 8:
CHEMISTRY OF LIFE
Simple to Complex – Life’s Levels of
Organization
Our journey begins here.
Chemistry and Life
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Apa perbedaan antara
atom dan molekul?
Apa yang membuat atom
membentuk molekul?
Does shape matter?
To Understand the Big,
You’d Better Know the Small
Atoms and Atomic Structure
• Atom merupakan unit
terkecil dari element kimia
• Elements merupakan
substansi yang tidak dapat
dipecah menjadi substansi
yang lebih sederhama
melalui reaksi-reaksi
kimia.
INTRODUCTION
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Botany is the scientific study of plant life. It is
also called plant science, phytology, or plant
biology.
Biology is the study of life. The word biology is
composed of 2 Greek roots
“bio” which mean “life”
“logi” which mean “study of”
Biology as a science is concerned with all lifeplant and animal, but botany is interested in
plant life in particular.
 INTRODUCTION
Plant life
means
• Organization: Tersusun dari satu atau
lebih sel, yang merupakan unit dasar dari
kehidupan.
• Metabolism: Konsumsi energi melalui
pengubahan non-living material menjadi
cellular components (anabolism) dan
mendekomposisinya menjadi bahan
organik (catabolism)
• Growth: Mempertahankan laju synthesis
lebih tinggi daripada catalysis
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Cells are the basic and fundamental unit
of structure, physiology, and organization
of all living organisms.
Mengetahui komposisi sel dan
bagaimana sel bekerja merupakan
fundamental bagi semua ilmu biologi
(biological sciences)
Biology Systems

Biology organizes living things along
certain levels. That is living things can be
viewed and organized
•
•
•
at a chemical level, looking at the biochemistry of
organisms, or
at a cellular level where interest in the structure
and functions of cells and cell physiology is
considered, or
at the levels of tissues or organs.
MOLECULAR PLANT
COMPOSITION
Organic Compounds
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The major groups of organic compounds as
far as life is concerned are:
Carbohydrates
Lipids
All built around carbon atoms
Protiens
Nucleic acids
Hydrogen, oxygen and nitrogen are frequently
found bonded to carbon. Organic compounds
made up of carbon and hydrogen are known as
hydrocarbons, this includes what common
materials?
Carbohydrates
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“Fuel molecules” consist of
carbon, hydrogen and
oxygen atoms (CH2O).
Carbohydrates are further
classified as
Monosaccharides 
Glucose
Disaccharides
Polysaccharides  starch
dan chitin
Lignin
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The major noncarbohydrate, polyphenolic
structural constituent of wood and other plant
material that encrusts the cell walls and
cements the cells together
A highly polymeric substance, with a complex,
cross-linked, highly aromatic structure of
molecular weight about 10,000 derived
principally from coniferyl alcohol (C10H12O3) by
extensive condensation polymerization
Cellulose
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Tersusun dari rantai panjang ß-glucose yang
berikatan satu sama lain (repeating unit C6H10O4)
Penyusun utama bagi kerangka struktural kayu
dan sel-sel biomassa yang lain
The b-linkages membentuk rantai linear yang
sangat stabil dan resisten terhadap serangan
bahan kimia karena tingkat ikatan hidrogen yang
tinggi yang terjadi di antara rantai cellulose,
menghambat peregangan molekul yang terjadi
dalam perombakan hidrolisis adri iakatan
glycosidic
• Hydrolysis dapat mereduksi cellulose menjadi
cellobiose (repeating unit C12H22O11) dan
akhirnya menjadi glucose, C6H12O6
Hemicellulose
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Tersusun dari rantai gula yang berbeda,
pendek dan bercabang
Mengandung gula 5-C (biasanya D-xylose
dan L-arabinose) dan gula 5-C (D-galactose,
D-glucose, dan D-mannose) dan uronic acid
Gula mudah disubstitusi dengan acetic acid
Secara alami Hemicellulose tak berbentuk
dan relatif mudah dihidrolisis menjadi gula
dibandingkan dengan cellulose
Starch
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Tersusun dari rantai panjang molekul α-glucose yang
saling berikatan (repeating unit C12H16O5 )
Ikatan terjadi dalam rantai α-1,4 linkages dengan
cabang yang terbentuk sebagai hasil dari α-1,6
linkages
Distribusinya luas dan disimpan dalam semua biji
dan umbi (tubers)
Karena α linkages dalam starch, polymer ini sangat
tidak berbentuk, dan lebih mudah dirombak oleh
sistem enzim menjadi glucose
Proteins
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Berperan utama dalam fungsi struktural dan
pengaturan. Seperti: enzymes (mengatur
ribuan rekasi kimia internal, enzim sebagai
biologic catalyst),
Proteins terdiri dari hydrogen, carbon,
nitrogen, oxygen dan biasanya sulfur. Ini
tergabung dalam cara yang berbeda untuk
membentuk lebih dari 20 amino acids yang
berbeda
Tanaman dapat mensintesis semua asam
amino yang dibutuhkan, tetapi hewan tidak
dapat.
Nucleic Acids
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Large complex molecules. Two classes are
ribonucleic acids (RNA) and
deoxyribonucleic acid (DNA).
Nucleic acids tersusun dari molecular units
disebut nucleotides, setiap nucleotide terdiri
dari:
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•
•
A 5 carbon sugar, apakah ribose atau deoxyribose,
A phosphate group,
A nitrogenous base yang mempunyai a double ringer
purine atau a single ringed pyrimidine
Nucleic Acids
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DNA mengandung purine adenine (A), dan
guanine(G) dan pyrimidines cytosine (C) dan
thymine (T) bersama-sama dengan sugar
deoxyribose dan phosphate
RNA mengandung purines adenine dan guanine
dan pyrimidines cytosine dan uracil (U) bersamasama dengan sugar ribose and phosphate.
Adenosine triphosphate (ATP) merupakan
nucleic acid yang menyediakan energy secara
teratur dalam semua cells, tersusun dari adenine,
ribose dan tiga phosphates.
FORMATION OF
MOLECULAR
COMPOSITION OF PLANTS:
ATOM
What causes atoms to form molecules?
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Basically, all things that happen spontaneously
are energetically favorable (a book dropping)-You
never see a book spontaneously rise
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Something must be energetically favorable about
atoms coming together as molecules
Molekul penyusun tanaman disintesis dari
molekul yang sangat sederhana, yaitu inorganic
molecules (CO2, H2O and nutrient elements)
Pembentukan hampir semua molekul kehidupan
terjadi melalui reaksi yang dikatalissasi oleh
enzymes dan berdasarkan karakteristik
constituent dasar dari molecules (atom)
Atomic Models
electron cloud
Atoms and Atomic Structure
In a simplified yet useful view of an atom, electrons orbit a nucleus
composed of protons and neutrons.
Atoms Come in Different Forms Called Isotopes
1.
2.
3.
Isotopes of a given element have the same number
of protons but different numbers of neutrons.
Many isotopes are unstable, making them
radioactive.
Radioactive isotopes (radioisotopes) play an
important role in health, medicine and biological
research.
Three isotopes of hydrogen.
Some Atoms are Sociable, Others
Aren’t
•
Atoms “want” (are most stable) to have a filled
outer electron shell.
•
Atoms without a filled
outer shell will share
electrons with other
atoms to accomplish
this “goal.”
Filling outer electron
shells controls which
atom will pair with
which others and in
what combinations.
•
Filling Electron
Shells
An important rule: the
innermost shell holds two
electrons; subsequent
shells hold 8 electrons.
Pairing for the Greater Good
When atoms come together by sharing
electrons the bond is a covalent bond.
A molecule is
formed when
two or more
atoms are
bound
together
covalently.
H2
Drawing It Out
The sharing of a pair of electrons between
atoms (a covalent bond) is shown as:
H-H (for H2)
or
H-O-H (for H2O)
or
(for CH4)
Water - A Most Important
Molecule
Note how bonding fills all outer electron shells.
Valence Electrons
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The electrons found in the outer “shell” of an
atom are known as valence electrons
The valence of an atom is the number of
electrons an atom must receive to become
chemically stable (i.e., less reactive)
For many atoms Valence = 8 - # valence
electrons
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Oxygen: 6 valence electrons, valence = 2
Nitrogen: 5 valence electrons, valence = 3
Carbon: 4 valence electrons, valence = 4
Valence Electrons
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In Biology (even in chemistry) there are
always exceptions:
• Hydrogen: 1 valence electron, valence = 1
• Phosphorus: 5 valence electrons, valence = 5
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These ideas of valence electrons and an
atom’s valence will take on more
meaning as we discuss chemical bonds
and molecular structure
Valences of Various Elements
1
4
3
5
2
1
Polar and Non-Polar
Covalent Bonding
Polar and Non-Polar Covalent
Bonding
A polar substance is one in which the molecule
has a negative side and a positive side
Some atoms have an equal
affinity for electrons.
If so, the shared electrons
spend equal amounts of time
around each atom and the
covalent bond is non-polar.
The covalent bonds of H2 and CH4 are nonpolar and so are the molecules.
Polar and Non-Polar Covalent
Bonding
Some atoms have an unequal affinity for
electrons.
If so, the shared electrons spend more time around
one atom relative to another and the covalent bond
is polar.
H2O
Oxygen draws electrons
to itself much more
strongly than hydrogen.
Therefore, the covalent bonds of H2O
are highly polar and so is the molecule.
Polar and Non-Polar Covalent
Bonding
Polar and Non-Polar Covalent
Bonding
The polar versus non-polar distinction determines
which molecules will dissolve in a particular solute.
For example, sugar dissolves in
water, but fat doesn’t.
The general rule is like dissolves
like.
The familiar case of oil and water
Water = polar molecule
Fat = non-polar molecule
Soap = polar and non-polar molecule
Some Atoms Do Almost Anything to Fill
Electron Shells
Sodium donates a lonely electron to chlorine to
complete its outer electron shell. Chlorine is only too
happy to accept.
The result is ion formation.
An ion is an atom or molecule with one or more
full positive or negative charges.
Ions and Ion Formation
IONIC BONDING
Ionic Bonds
Two oppositely charged ions bind together.
This type of chemical bond is an ionic bond.
Salts are
solids held
together by
ionic bonds.
Ionic bonds
are common
and important
in biology.
Ionic bonding
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High electronegativity
difference strips
valence electrons
away from another
atom
Electron transfer
creates ions (charged
atoms)
Cation (positive ion);
anion (negative ion)
Ex: Salts (sodium
chloride)
Ionic Bonds
Ionic Bonding
Ionic bonds result from
one atom essentially
giving an electron to
another atom
 Ionic bonds represent an
extreme of polarity and
are represented in
biological systems as the
salt bridges within proteins
Ionic bonding
Ionic bonding involves 3 steps (3 energies)
1) loss of an electron(s) by one element,
2) gain of electron(s) by a second element,
3) attraction between positive and negative
Ionization energy
Na
Cl
Cl–
+
+
e–
Na+
e– +
Electron affinity
Lattice energy
Na+
Cl–
Cl–
Na+
Ionic bonding: energies

By convention, a requirement for energy is given a
+ sign (we have to put energy in) and is called
endothermic, a release of energy is given a – sign
and is called exothermic.
Ionization energy
Na
Cl
Cl–
+
+
e–
Na+
e– + Na+
Electron affinity
Lattice energy
Cl–
Cl–
+ 496
– 349
Na+ – 766
Strong Bonds in Solid
In solid phase
ionic bonds
can be very
strong
But in aqueous
phase ionic
bonds tend to
be weaker than
covalent bonds
Hydrogen Bonding
Oxygen and nitrogen are much more “hungry”
for electrons than hydrogen.
Bonds between nitrogen or
oxygen and hydrogen are
highly polar.
This allows bonds to form
between partially positive
and partially negative
atoms in different or (in
large molecules) the same
molecule.
The result is a
hydrogen bond.
Hydrogen Bonding Gives Water
Unique Properties
Relative Bond Strengths
>
Covalent
>
Ionic
Hydrogen
Molecular Shape
Molecules have distinct shapes – and shape matters.
Molecular Shape
A regulatory protein
molecule (yellow)
binding to DNA.
Without
complementary
shapes, binding
would not occur.
Molecular Shape Matters
We perceive and
distinguish odors
because of the
particular shape of
the odorant (the
molecule we smell)
and receptor
molecules on nose
cells.
Biological Chemistry Takes Place in
Solutions
Molecules are often
described as
hydrophilic (waterloving) or hydrophobic
(water-fearing) on the
basis of their solubility
in water.
The End