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LECTURE 8:
CHEN!STRY OF L!FE
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SimpIe to CompIex - Life's LeveIs of
Organization
Our journey begins here.
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Chemistry and Life
Apa perbedaan antara
atom dan molekul?
Apa yang membuat atom
membentuk molekul?
Does shape matter?
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%o Understand the Big,
You'd Better Know the SmaII
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toms and tomic Structure
Atom merupakan unit
terkecil dari element kimia
Elements merupakan
substansi yang tidak dapat
dipecah menjadi substansi
yang lebih sederhama
melalui reaksi-reaksi
kimia.
%#ODUC%O
otany is the scientific study of plant life. t is
also called pIant science, phytoIogy, or pIant
bioIogy.
iology is the study of life. The word biology is
composed of 2 Greek roots
"bio which mean "life
"logi which mean "study of
iology as a science is concerned with all life-
plant and animal, but botany is interested in
pIant Iife in particuIar.
%#&%
!Iant Iife means
Organization: Tersusun dari satu atau
lebih sel, yang merupakan unit dasar dari
kehidupan.
MetaboIism: 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
ells 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)
BioIogy Systems
BioIogy organizes Iiving things aIong
certain IeveIs. That is living things can be
viewed and organized
at a chemicaI IeveI, looking at the biochemistry of
organisms, or
at a ceIIuIar IeveI where interest in the structure
and functions of cells and cell physiology is
considered, or
at the IeveIs of tissues or organs.
Organic Compounds
%he major groups of organic compounds as
far as Iife is concerned are:
Carbohydrates
Lipids
!rotiens
ucIeic acids
ydrogen, 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?
II buiIt
around
carbon
atoms
Carbohydrates
"Fuel molecules consist of
carbon, hydrogen and
oxygen atoms (
2
O).
arbohydrates are further
classified as
Monosaccharides
GIucose
Disaccharides
!oIysaccharides starch
dan chitin
Lignin
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 (1012O3)
by extensive condensation polymerization
igher heating value: '111 tu/lb
CeIIuIose
Tersusun dari rantai panjang -glucose yang
berikatan satu sama lain (repeating unit 10O4)
Penyusun utama bagi kerangka struktural kayu dan
sel-sel biomassa yang lain
The .-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
ydrolysis dapat mereduksi cellulose menjadi
cellobiose (repeating unit 1222O11) dan
akhirnya menjadi glucose, 12O
igher heating value: ' 7500 tu/lb
emiceIIuIose
Tersusun dari rantai gula yang berbeda,
pendek dan bercabang
Mengandung gula 5- (biasanya D-xylose
dan L-arabinose) dan gula 5- (D-galactose,
D-glucose, dan D-mannose) dan uronic acid
Gula mudah disubstitusi dengan acetic acid
Secara alami emicellulose tak berbentuk
dan relatif mudah dihidrolisis menjadi gula
dibandingkan dengan cellulose
Starch
Tersusun dari rantai panjang molekul d-glucose yang
saling berikatan (repeating unit 121O5 )
katan terjadi dalam rantai d-1,4 linkages dengan
cabang yang terbentuk sebagai hasil dari d-1,
linkages
Distribusinya luas dan disimpan dalam semua biji
dan umbi (tubers)
Karena d linkages dalam starch, polymer ini sangat
tidak berbentuk, dan lebih mudah dirombak oleh
sistem enzim menjadi glucose
Gross heat of combustion: Qv (gross)750 tu/lb
!roteins
erperan 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. ni
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.
ucIeic cids
Large complex molecules. Two classes are
ribonucIeic acids (# and
deoxyribonucIeic acid (D.
ucleic acids tersusun dari molecular units
disebut nucleotides, setiap nucleotide terdiri
dari:
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
ucIeic cids
D mengandung purine adenine (A), dan
guanine(G) dan pyrimidines cytosine () dan
thymine (T) bersama-sama dengan sugar
deoxyribose dan phosphate
# mengandung purines adenine dan guanine
dan pyrimidines cytosine dan uracil (U) bersama-
sama dengan sugar ribose and phosphate.
denosine triphosphate (%! merupakan
nucleic acid yang menyediakan energy secara
teratur dalam semua cells, tersusun dari adenine,
ribose dan tiga phosphates.
O#M%O O
MOLECUL#
COM!OS%O O !L%S:
%OM
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hat causes atoms to form moIecuIes?
asically, all things that happen spontaneously
are energetically favorable (a book dropping)-ou
never see a book spontaneously rise
Something must be energetically favorable about
atoms coming together as molecules
Molekul penyusun tanaman disintesis dari
molekul yang sangat sederhana, yaitu inorganic
molecules (O
2
,
2
O and nutrient elements)
Pembentukan hampir semua molekul kehidupan
terjadi melalui reaksi yang dikatalissasi oleh
enzymes dan berdasarkan karakteristik
constituent dasar dari molecules (atom)
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eIectron cIoud
tomic ModeIs
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n a simplified yet useful view of an atom, electrons orbit a nucleus
composed of protons and neutrons.
toms and tomic Structure
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toms Come in Different orms CaIIed sotopes
1. sotopes of a given element have the same number
of protons but different numbers of neutrons.
2. Many isotopes are unstable, making them
radioactive.
3. Radioactive isotopes (radioisotopes) play an
important role in health, medicine and biological
research.
Three isotopes oI hydrogen.
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Some toms are SociabIe, Others
ren'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.
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iIIing EIectron
SheIIs
An important rule: the
innermost shell holds two
electrons; subsequent
shells hold 8 electrons.
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!,iring Ior the Gre,ter Good
hen atoms come together by sharing
eIectrons the bond is a covaIent bond.

A molecule is
formed when
two or more
atoms are
bound
together
covalently.
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Drawing t Out
The sharing of a pair of electrons between
atoms (a covaIent bond) is shown as:
- (for
2
)
or -O- (for
2
O)
or
(for
4
)
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ater - Most mportant
MoIecuIe
ote how bonding fills all outer electron shells.
'aIence EIectrons
The electrons found in the outer "shell of an
atom are known as vaIence eIectrons
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 'alence 8 - # valence
electrons
Oxygen: valence electrons, valence 2
itrogen: 5 valence electrons, valence 3
arbon: 4 valence electrons, valence 4
'aIence EIectrons
n iology (even in chemistry there are
always exceptions:
ydrogen: 1 valence electron, valence 1
Phosphorus: 5 valence electrons, valence 5
These ideas of valence electrons and an
atom's valence will take on more
meaning as we discuss chemical bonds
and molecular structure
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'aIences of 'arious EIements
1
4
3
2
5

!oIar and on-


!oIar CovaIent
Bonding
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!oIar and on-!oIar CovaIent
Bonding
A polar substance is one in which the molecule
has a negative side and a positive side
%he covaIent bonds of

and C

are non-
poIar and so are the moIecuIes.
Some atoms have an equaI
affinity for electrons.
f so, the shared electrons
spend equal amounts of time
around each atom and the
covalent bond is non-poIar.
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!oIar and on-!oIar CovaIent
Bonding
%herefore, the covaIent bonds of

O
are highIy poIar and so is the moIecuIe.
Some atoms have an unequaI affinity for
electrons.
f so, the shared electrons spend more time around
one atom relative to another and the covalent bond
is poIar.
Oxygen draws electrons
to itself much more
strongly than hydrogen.

O
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!oIar and on-!oIar CovaIent
Bonding
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!oIar and on-!oIar CovaIent
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.
%he famiIiar case of oiI and water
ater = poIar moIecuIe
at = non-poIar moIecuIe
Soap = poIar and non-poIar moIecuIe
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Some toms Do Imost nything to iII
EIectron SheIIs
Sodium donates a lonely electron to chlorine to
complete its outer electron shell. hlorine 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.
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ons and on ormation
OC BODG
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onic Bonds
Two oppositely charged ions bind together.
This type of chemical bond is an ionic bond.
Salts are
solids held
together by
ionic bonds.
onic bonds
are common
and important
in biology.
onic bonding
igh eIectronegativity
difference strips
vaIence eIectrons
away from another
atom
EIectron transfer
creates ions (charged
atoms
Cation (positive ion
anion (negative ion
Ex: SaIts (sodium
chIoride
onic onds
onic onding
onic bonds result from
one atom essentially
giving an electron to
another atom
onic bonds represent an
extreme of polarity and
are represented in
biological systems as the
salt bridges within proteins
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onic bonding
onic 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
+
a
e
-
a
+
onization energy
l
e
-
+ l
-
Electron affinity
Lattice energy
+ l
-
a
+
l
-
a
+
+
a
e
-
a
+
+
a
e
-
a
+
a a
e
-
a
+
a
+
onization energy
l
e
-
+ l
-
l l
e
-
+ e
-
+ l
-
l
-
Electron affinity
Lattice energy
+ l
-
a
+
l
-
a
+
+ l
-
l
-
a
+
a
+
l
-
l
-
a
+
a
+
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onic bonding: energies onic bonding: energies
y 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.
+
a
e
-
a
+
onization energy
l
e
-
+
l
-
Electron affinity
Lattice energy
+
l
-
a
+
l
-
a
+
+ 4
34
7
+
a a
e
-
a
+
a
+
onization energy
l l
e
-
+
l
-
l
-
Electron affinity
Lattice energy
+
l
-
l
-
a
+
a
+
l
-
l
-
a
+
a
+
+ 4
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7
S
t
r
o
n
g

o
n
d
s

i
n

S
o
l
i
d
n solid ph,se
ionic bonds
c,n be very
strong
ut in aqueous
phase ionic
bonds tend to
be weaker than
covalent bonds
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ydrogen Bonding
Oxygen and nitrogen are much more "hungry
for electrons than hydrogen.
%he resuIt is a
hydrogen bond.
onds 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.
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ydrogen Bonding Gives ater
Unique !roperties
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#eIative Bond Strengths
CovaIent
onic
ydrogen
> >
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MoIecuIar Shape
Molecules have distinct shapes and shape matters.
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MoIecuIar Shape
A regulatory protein
molecule (yellow)
binding to DA.
Without
complementary
shapes, binding
would not occur.
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MoIecuIar 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.
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BioIogicaI Chemistry %akes !Iace in
SoIutions
Molecules are often
described as
hydrophilic (water-
loving) or hydrophobic
(water-fearing) on the
basis of their solubility
in water.
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The End