KIMIA ORGANIK REVIEW

BIOKIMIA

KIMIA ORGANIK

Mempelajari senyawa yang mengandung karbon (C) Organisme (mahluk hidup): terutama terdiri dari C, H, O ,N, ( S, P) Biomolekul : Senyawa yang secara alami ada pada mahluk hidup, misalnya : karbohidrat, lipid, protein, asam nukleat mengandung C

PADA SIKLUS KARBON Tanaman melakukan fotosintesis Energi sinar matahari CO2 + H2O -------------> karbohidrat O2 yang terbentuk dilepas ke atmosfir Hewan mendapat makanan dari tanaman sebagai sumber senyawa karbon dan menggunakan O2 untuk mengoksidasi karbohidrat menjadi CO2 , H2O dan energi

MATERI DAN ENERGI

Most of the Universe consists of matter and energy Energy is the capacity to do work. Matter has mass and occupies space. All matter is composed of basic elements that cannot be broken down to substances with different chemical or physical properties.

 Elements are substances consisting of one type of atom, for example : Carbon atoms make up diamond, and also graphite. Pure (24K) gold is composed of only one type of atom, gold atoms. Atoms are the smallest particle into which an element can be divided.

 Proton particle in the nucleus with a positive charge of +1 and a mass of approximately 1 atomic mass unit (amu) Elements differ from each other in the number of protons they have, e.g. Hydrogen has 1 proton; Helium has 2.

PROTON

NEUTRON DAN ELEKTRON The neutron also is located in the atomic nucleus (except in Hydrogen). The neutron has no charge, and a mass of slightly over 1 amu. The electron is a very small particle located outside the nucleus. Because they move at speeds near the speed of light the precise location of electrons is hard to pin down.

 Electrons occupy orbitals, or areas where they have a high statistical probability of occurring. The charge on an electron is -1. Its mass is negligible Electron negatively charged particle (-1) with a mass 1/1837 of that of a proton
Pada atom yang netral jumlah elektron = jumlah proton

 The atomic number is the number of protons an atom has. It is characteristic and unique for each element The atomic mass (also referred to as the atomic weight) is the weighted average of an element in naturally occuring isotopes. Kadang berat atom dinyatakan juga dalam Dalton Berat atom 1 proton = 1 Dalton. Contoh: O :nomor atom 8, massa atom 16 Mass number : Number of protons plus neutrons in an atom Besarnya atomic mass sekitar/ = mass number

 Isotope Atoms of an element that have differing numbers of neutrons (but a constant atomic number) are termed isotopes.
Hidrogen: Nomor atom 1, massa atom 1.008
1H

Tabel periodik elemen

Angka Romawi penunjuk kolom (at least the ones ending in A) : menunjukkan jumlah elektron pada kulit-terluar atom Angka numerik penunjuk baris 1 s/d 7: menunjukkan jumlah kulit-elektron atom Contoh elemen yang ada di alam. H :kolom I A baris 1 mempunyai: 1 elektron dan 1 kulit-elektron P :kolom V A baris 3 mempunyai: 5 elektron pada kulit-terluar 3 kulit-elektron

 MOLECULES Molecules are compounds with elements in definite, fixed ratios. Those atoms are held together by chemical bonds. For example: water, glucose, ATP. Molecular formulas are an expression in the simplest wholenumber terms of the composition of a substance. For example, the sugar glucose has 6 Carbons, 12 hydrogens, and 6 oxygens per repeating structural unit. The formula is written C6H12O6.

C = 6X12 = 72 H = 12X1 = 12 O = 6X16 =96

 SIFAT EEKTRON Electrons determine chemical properties of elements Electrons are outside the nucleus, and determine properties of the atom. Chemical reactions involve sharing or exchanging electrons. Electrons move about the nucleus in atomic orbitals. Absorption of energy can cause an electron to move up to a higher energy level. The atom is stable when the outermost energy level of most atoms has eight electrons.

 Electrons can be transferred carrying energy to another molecule. The H atom can carry electrons for transferring energy. Oxygen has a strong affinity for electrons. Redox reaction transfer of electrons from one molecule (oxidized) to another (reduced).

 Stability can be achieved by adding, losing, or sharing electrons. Bonds are formed until the outer shell electron of an atom are all involved in bonds or until a stable octet outer shell is achieved

 Electronegativity refers to the tendency for atoms to bind electrons. Oxygen (0) with an electronegativity of 3.5 has a strong affinity. Hydrogen (H)(2.1) and carbon (C)(2.5) each have lower affinities.
A bond between C and H will have nearly equal sharing of electrons. Oxygen and hydrogen form a highly polar bond because of the much stronger affinity for electrons by O.

Electronegativity according to Pauling

Electro negativity measures the inclination of an atom to pull the electronic cloud in its direction during chemical bonding with another atom. Pauling's scale is a widely used method to order chemical elements according to their electro negativity.

 Pauling gave the element with the highest possible electro negativity, fluorine, a value of 4,0. Francium, the element with the lowest possible electro negativity, was given a value of 0,7. All of the remaining elements are given a value of somewhere between these two extremes.

Chemical bonds and attractive forces A molecule is two or more atoms linked by a chemical bond. Molecules can contain different types of bonds.

Covalent bonds If atoms are sharing electrons, then the bond between them is covalent.

Methane has four covalent bonds between carbon (C) and hydrogen (H). The figure below shows the methane molecule in four different views.

 Covalent bonds involve a complete sharing of electrons and occurrs most commonly between atoms that have partially filled outer shells or energy levels. The electrons are in hybrid orbitals formed by the atoms involved. Thus if the atoms are similar in electronegativity then the electrons will be shared. Diamond is strong because it involves a vast network of covalent bonds between the carbon atoms in the diamond.

Covalent bonds

Ionic bonds
Ions are produced when atoms can

obtain a stable number of electrons by giving up or gaining electrons. For example Na (sodium) can donate an electron to Cl (chlorine) generating Na+ and Cl-. The ion pair is held together by strong electrostatic attractions.

Non-covalent bonds and other weak forces Non-covalent bonds and other weak forces are important in biological structures. Electrostatic bonds result from the electrostatic attraction between two ionized groups of opposite charge, such as carboxyl (-COO-) and amino (-NH3+). In water, these bonds are very weak. Hydrogen bonds -result from electrostatic attraction between an electronegative atom (O or N) and a hydrogen atom that is bonded covalently to a second electronegative atom. N-H ----- O=C- -O-H----- O=C-

 Van der Waals bonds -are short range attractive forces between chemical groups in contact. Caused by slight charge displacements. Hydrophobic attractions -cause nonpolar groups such as hydrocarbon chains to associate with each other in an aqueous environment. Multiple weak bonds or forces can cause strong interactions Biological recognition results from a three dimensional structure that allows multiple weak forces between molecules

 Bonds contain energy, and a require energy to be broken. Bond energy (expressed as kcal/mole) is the energy required to break a bond. For example, an H-H bond requires 104 kcal/mole to break.

Vanderwaals radius Even when two atoms that are near one another will not bind, they will still attract one another. This phenomenon is known as the Vanderwaals interaction. The Vanderwaals forces cause a force between the two atoms. This force becomes stronger, as the atoms come closer together. However, when the two atoms draw too near each other a rejecting force will take action, as a consequence of the exceeding rejection between the negatively charged electrons of both atoms. As a result, a certain distance will develop between the two atoms, which is commonly known as the Vanderwaals radius.

 Ionic radius Ionic radius is the radius that an ion has in an ionic crystal, where the ions are packed together to a point where their outermost electronic orbitals are in contact with each other. An orbital is the area around an atom where, according to orbital theory, the probability of finding an electron is the greatest.

Polar Covalent Bonds Covalent bond between two atoms of different electronegativities, causing one atom to have a greater attraction for the bonding pair(s) and thus charge separation within the bond Bedanya dengan ionic bond dan covalent bond: An ionic bond is formed by the transfer of electrons between atoms of wideley different electronegativities. In a covalent bond , electrons are shared between atoms of identical or similar electronegativities

 Contoh :
+ + + -

HO

C Cl

N=O

Most CarbonCarbon and CarbonHydrogen bonds are nonpolar

The Chemistry of Water The polarity of water (H2O) Each hydrogen atom is covalently bonded to the oxygen via a shared pair of electrons. Oxygen also has two unshared pairs of electrons. Thus there are 4 pairs of electrons surrounding the oxygen atom, two pairs involved in covalent bonds with hydrogen, and two unshared pairs on the opposite side of the oxygen atom.

 Oxygen is an "electronegative" or electron "loving" atom compared with hydrogen. Water is a "polar" molecule, meaning that there is an uneven distribution of electron density. Water has a partial negative charge near the oxygen atom due the unshared pairs of electrons, and partial positive charges near the hydrogen atoms. An electrostatic attraction between the partial positive charge near the hydrogen atoms and the partial negative charge near the oxygen results in the formation of a hydrogen bond as shown in the illustration.

 The hydrophobic effect, or the exclusion of compounds containing carbon and hydrogen (non-polar compounds) is another unique property of water caused by the hydrogen bonds. The hydrophobic effect is particularly important in the formation of cell membranes. The best description is to say that water "squeezes" non-polar molecules together.

 The ability of ions and other molecules to dissolve in water is due to polarity. For example, in the illustration below sodium chloride is shown in its crystalline form and dissolved in water.

 Many other unique properties of water are due to the hydrogen bonds. For example, ice floats because hydrogen bonds hold water molecules further apart in a solid than in a liquid, where there is one less hydrogen bond per molecule. The unique physical properties, including a high heat of vaporization, strong surface tension, high specific heat, and nearly universal solvent properties of water are also due to hydrogen bonding

 Introduction to Organic Molecules Organic molecules contain carbon Alcohol hydrocarbon with a hydrogen replaced by "OH". Acid hydrocarbon with a hydrogen replaced by a carboxyl "COOH". COOH -> COO- + H+ Amine hydrocarbon with a hydrogen replaced by an amine "NH2". Basic- accepts protons. NH2 + H+ -> NH3+ Phosphate addition of -PO4= (switch) Amino Acid

hydrocarbon with amino and carboxyl groups

MACAM-MACAM SENYAWA ORGANIK

Monosakarida contoh

POLISAKARIDA
Contoh : amilum, glikogen yang merupakan polimer glukosa

Lihat kuliah metabolisme karbohidrat

ASAM AMINO

STRUKTUR PROTEIN

Protein / rantai polipeptida merupakan polimer asam amino

Asam lemak

The fatty acids are composed of CH2 units, and are hydrophobic/not water soluble

(a) dan (b) : asam lemak jenuh

(c) : asam lemak tak jenuh

LIPID Lipid adalah segolongan senyawa yang relatif tak larut dalam air tetapi larut dalam pelarut nonpolar Turunan/berkaitan dengan asam lemak Macam2: Triasilgliserol = trigliserida Kolesterol Fosfolipid Steroid dll

ASAM LEMAK ( RCOOH) O Rumus : R C OH R adalah gugus alkil O R C adalah gugus asil (acyl)

- COO-

CH3 (CH2)n CH2 CH2 COOH 1

 ASAM LEMAK JENUH Tak ada ikatan rangkap Rumus umum CnH2n+1COOH Contoh : asam butirat (C4), asam stearat (C18) asam palmitat (C16) CH3(CH2)14COOH

ASAM LEMAK TAK JENUH mengandung satu atau lebih ikatan rangkap

Contoh: Structure of a phospholipid, space-filling model (left) and chain model (right)

 Specific chemical properties were a result of the presence of particular functional groups. Functional groups are clusters of atoms with characteristic structure and functions. Polar molecules (with +/- charges) are attracted to water molecules and are hydrophilic. Nonpolar molecules are repelled by water and do not dissolve in water; are hydrophobic.

 Hydrocarbon is hydrophobic except when it has an attached ionized functional group such as carboxyl (acid) (COOH), then molecule is hydrophilic. Since cells are 70-90% water, the degree to which organic molecules interact with water affects their function. One of the most common groups is the -OH (hydroxyl) group. Its presence will enable a molecule to be water soluble

 Hydrocarbon is hydrophobic except when it has an attached ionized functional group such as carboxyl (acid) (COOH), then molecule is hydrophilic. Since cells are 70-90% water, the degree to which organic molecules interact with water affects their function. One of the most common groups is the -OH (hydroxyl) group. Its presence will enable a molecule to be water soluble

 NUKLEOTIDA Structure of two types of nucleotide

single-ringed.

ASAM NUKLEAT
Polimer nukleotida merupakan rantai polinukleotida Contoh : DNA (Deoxyribonucleic acid) RNA (Ribonucleic acid)

ISOMER
Isomers are molecules with identical molecular formulas but differ in arrangement of their atoms (e.g., glyceraldehyde and dihydroxyacetone (cari strukturnya!)