The Backbone of Life

- 30% komposisi sel tersusun dari

mikromolekul dan makromolekul
yang tersusun dari unsur karbon
(C) sebagai tulang punggungnya.
- Karena atom Karbon berukuran
kecil, memiliki 4 elektron valensi
dan juga mempunyai 4 (empat)
“peluang” pada kulit elektron
terluarnya; satu atom Karbon
dapat membentuk 4 ikatan
kovalen dengan atom-atom lain.
- Persentase unsur penting yang
terdapat di dalam sel; C-H-O-N-S-P

Perbandingan komposisi sel

In this chapter we will investigate the properties of smaller molecules to
illustrate concepts of molecular architecture that will help explain why carbon
is so important to life.
e.g. various functional groups in cell’s molecules

e.g. four major families of small molecules (Building block) in cell

Monomer
Study of Carbon Compounds: Organic
Chemistry or Biochemistry?
- To study cellular molecules, means to study compounds containing
carbon. Almost all molecules of importance to the cell biologist have a
backbone, or skeleton, of carbon atoms linked together covalently in
chains or rings.
- In its early days, organic chemistry was synonymous with biological
chemistry because the carbon-containing compounds that chemists first
investigated were obtained from biological sources.
“however, because organic chemists have now synthesized an incredible
variety of carbon-containing compounds that do not occur naturally in the
biological world, organic chemistry and biochemistry is separate.”
- Organic chemistry therefore includes all classes of carbon-containing
compounds, whereas biochemistry deals specifically with the chemistry of
living systems.

CH3COOH
Few years later

Acetic acid
In 1828
 Eksperiment yang dilakukan oleh
Stanley Miller pada tahun 1953.

Mencoba membuktikan apakah senyawa

organik dapat disintesis secara spontan oleh
kondisi yang diatur seperti kondisi awal bumi.

- H2O, CH4, NH3 dan H2 mewakili kondisi

atmosfer bumi saat itu.
- Percikan listik mewakili petir/halilintar.
- Kondensor mendinginkan hasil reaksi dan
membuat uap menjadi air mewakili hujan.

Hasil penelitian menemukan bahwa dalam

wadah penampung terdapat senyawa organik
seperti asam amino dan hidrokarbon rantai
panjang.
Versatility of Carbon
The key to an atom's chemical characteristics is its
electron configuration. This configuration determines
the kinds and number of bonds an atom will form with
other atoms.

Tetra-valence of Carbon atom

The Formation of Bond with Carbon

- Carbon atoms are most likely to form covalent - The sharing of one pair of electrons
bonds with one another (C) and with atoms of between atoms results in a single bond
oxygen (O), hydrogen (H), nitrogen (N), and and form a tetrahedron shape. e.g.
sulfur (S). Methane, Ethane.
- One or more electrons are required to
Free rotation
complete the outer orbital. The number of
“missing” electrons corresponds in each case
to the valence of the atom, which indicates, in
turn, the number of covalent bonds the atom
can form.
- Sometimes, two or even three pairs of electrons can be shared by two
atoms, giving rise to double bonds or triple bonds.
e.g. Ethylene and carbon dioxide are examples of double-bonded
compounds.
Triple bonds are rare but can be found in molecular nitrogen, hydrogen
cyanide and acetylene.

Do not allow free

rotation
- Bentuk lain yang dapat dihasilkan oleh ikatan kimia dengan atom Carbon
(C), adalah cincin (ring).
Carbon-Containing Molecules are Stable

- Both the valence and the low atomic weight of carbon give it unique
properties that account for the diversity and stability of carbon-containing
compounds, giving carbon a preeminent role in biological molecules.
- This stability is expressed as bond energy— the amount of energy
required to break 1 mole (about 6 x 1023) of such bonds.
(The term bond energy is a frequent source of confusion. It’s not as energy that is somehow “stored” in
the bond but rather as the amount of energy needed to break the bond.)
- Bond energies are usually expressed in calories per mole (cal/mol), where
a calorie is the amount of energy needed to raise the temperature of 1
gram of water by 1oC.--- 1 kilocalorie (kcal) is equal to 1000 calories.
e.g. C – C ; 83 kcal/mol
C – N ; 70 kcal/mol
C – O ; 84 kcal/mol
C – H ; 99 kcal/mol
C = C ; 146 kcal/mol
C ≡ C ; 212 kcal/mol
The Relationship Between Energy (E ) and Energies of Biologically Important Bonds in
Wavelength ( λ) for Electromagnetic Radiation. Cell or Body (aquaeous).
Molecular Diversity from Carbon Skeleton
Variation

Hydrocarbon
- When only hydrogen atoms are bonded to
carbon atoms in linear or circular molecules,
the resulting compounds are called
hydrocarbons.
- In biology, hydrocarbons play only a limited
role because they are essentially insoluble in
water, the universal solvent in biological
systems. However, they play an important role
in the structure of biological membranes. – The
interior of every biological membrane is a nonaqueous environment
consisting of the long hydrocarbon “tails” of phospholipid
molecules that project into the interior of the membrane from
either surface. This feature of membranes has important
implications for their role as permeability barriers. –

Hydrocarbon in phospholipid nonpolar tail

Isomers

- Compounds that have the same numbers of atoms of the same elements
but different structures and hence different properties, called isomer.
- Structural isomers; differ in the covalent arrangements of their atoms.
The number of possible isomers increases tremendously as carbon
skeletons increase in size. There are only 3 forms of C5H12 but there are 18
variations of C8H18 and 366.319 possible structural isomers of C20H42.
Structural isomers may also differ in the location of double bonds (not
shown).
- Geometric isomers; Geometric isomers have the same covalent
partnerships, but they differ in their spatial arrangements.
The differences arise from the inflexibility of double bonds. Single bonds
allow the atoms they join to rotate freely about the bond axis without
changing the compound. In contrast, double bonds do not permit such
rotation, resulting in the possibility of geometric isomers. If a double bond
joins two carbon atoms, and each C also has two different atoms (or
groups of atoms) attached to it, then two distinct geometric isomers are
possible.
Enantiomers / Stereoisomers
- are isomers that are mirror images of each other.
- are left-handed and right-handed versions of the molecule.
- The middle carbon is called an asymmetric carbon or Chiral center
because it is attached to four different atoms or groups of atoms. The
four groups can be arranged in space around the asymmetric carbon in
two different ways that are mirror images. Because two stereoisomers are possible for
each asymmetric carbon atom, a compound with n asymmetric carbon atoms will have 2n possible
stereoisomers.

Sistem L (levo “left”) & D (dextro “right”)

digunakan untuk membedakan molekul
enantiomer yang hanya memiliki 1 Chiral Carbon.
- Enantiomers yielding two stereoisomers with similar or identical chemical
properties BUT differing in certain physical and biological properties.

Sistem R (rectus “right”) –clockwise &

S (sinister “left”) – counterclockwise
digunakan untuk senyawa yang
memiliki lebih dari 1 Chiral Carbon.

- The three-dimensional structure of biomolecules large and small—the

combination of configuration and conformation—is of the utmost
importance in their biological interactions: reactant with its enzyme,
hormone with its receptor on a cell surface, antigen with its specific
antibody.
Chemical groups: Key to the functioning
of biological molecules

- The distinctive properties of an organic molecule depend not only on the

arrangement of its carbon skeleton but also on the molecular
components attached to that skeleton.

- These groups may participate in chemical reactions or may contribute to

function indirectly by their effects on molecular shape. The number and
arrangement of the groups help give each molecule its unique properties.
Biologically Important Chemical Groups (Functional Groups)
…lanjutan

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