Introduction To Biochemistry
Introduction To Biochemistry
Carbon (symbol C) is a tetragen; this means that it is in the 4th group of the periodic system of
elements. Within this group, it is the 1st element and, thus, is in the 2nd period. It has the atomic
number 6 and is a non-metal. It has a melting point of 3550°C and a boiling point of 4827°C.
Chemically pure carbon may be prepared in the laboratory through the thermal decomposition of
sucrose in the absence of oxygen. The physical and chemical properties of carbon are also
dependent on the crystalline structure of the element. Carbon has a relative atomic mass of 12
grams per mol. However, there are 2 additional isotopes of carbon: C13 and C14. C13 is the
more frequent isotope and is considered stable. C14, on the other hand, is very rare and unstable.
Its half-life is 5730 years and it is used for the radiometric dating of organic substances.
Additionally, the density for graphite is estimated to be 2.25 g/cm³ and that for diamond is
approximately 3.51 g/cm³.
Pure carbon mostly exists in crystalline form and forms either graphite or diamonds as a
modification. Diamond is the hardest natural substance and is also used as a cutting material
besides its use as a gem. Under normal pressure and temperature conditions, graphite is the
thermodynamically stable form of pure carbon. Because of its electronic conductivity, it is used
as an electrode in the industry. Equally important is the fact that carbon as a free element has
numerous uses such as its application as a black fume pigment in inks for printers and rims for
motor vehicles. Graphite, an allotrope of carbon, is used as a lubricant, for pencil tips, as an
electrode in dry cells, and as a component for high-temperature crucibles. An amorphous form of
carbon referred to as vegetal carbon is utilized predominantly for industrial purposes for the
manufacture of bleaching agents and as a gas absorbent.
In its less crystalline form, carbon is also known as soot. Mostly, soot forms as a byproduct of
combustive processes. The regular inhalation of soot can lead to pneumoconiosis and cardiac
damages. Moreover, evidence-based studies on workers who come into direct physical contact
with carbon particles have shown that they may experience inflammation on the hair follicles and
oral mucosal lesions. Often, carbon is encountered as a compound with oxygen. Under high
temperatures, these 2 elements form carbon monoxide (CO) or carbon dioxide (CO 2). The latter
is primarily important in the context of respiration and blood circulation.
Electron Configuration and Hybridization of Carbon
Carbon is in the 2nd period of the 4th main group of the periodic system of elements. This means
that carbon has 2 electron shells around its core of 6 protons and neutrons each. This means that
it has 4 valence electrons, which can form bonds. Overall, carbon consists of a core with 6
protons, 6 neutrons, and a 2-layered electron shell with 6 electrons in total.
Hybridization means the fusion of 2-electron energy levels to a single joint level. In the case of
carbon, the 2 energy levels of the 2nd shell can hybridize. This way, the 2s- and 2px-, y-, z-
orbitals become energetically equal sp3-orbitals. These sp3-orbitals can overlap with the sp3-
orbitals of another carbon atom and, thus, form a covalent bond. This bond is also referred to as
sigma-bond. Analogous to this, a tetrahedral form results from the arrangement of the atoms.
This is referred to as the diamond grid of carbon. It is not necessary that all p-orbitals participate
in hybridization. Moreover, only 2 of them can hybridize with the 2s-orbitals. They then form the
3 sp2-orbitals. They arrange in one plane and are thus 2-dimensional. The p-orbital, which does
not participate in hybridization, is oriented rectangular to this plane and forms a droplet form
both over and under the triangle formed by the sp2-orbitals. The sp2-orbitals of carbon can form
covalent bonds with other sp2-hybridized carbon atoms. They then lie in one plane and have a
triangular structure. One is the so-called plane of graphite.
The non-hybridized p-orbitals can interact with each other and form pi-bonds, which are less
energetic compared to the sigma-bonds. Above and below the sigma bond, they form a kind of
electron cloud. Because of this cloud, the rotatability of the molecule is lost. However, the
interactions of the pi-bonds are so weak that the graphite planes can be shifted against each
other. This also is the reason why a pencil, which contains graphite, can be used for writing.
(Note: Sigma- and pi-bonds together form the double bond C = C).
Thus, it is not surprising that there is also the possibility that only 1 of the three 2p-orbitals
participates in hybridization. Together with the 2s-orbital, it then forms the so-called sp1-
orbitals. They are arranged linearly, that is, in series. The 2 non-hybridized p-orbitals are located
both orthogonally to each other and orthogonally to the sp1-orbitals.The sp1-orbitals of carbon
can form covalent bonds with other sp1-hybridized carbon atoms. They are then one-
dimensionally arranged in a line. Together with the non-hybridized p-orbitals, a triple bond (C ≡
C) forms.
Reactive particles are the special form of an atom that mostly occur as unstable intermediate
products with high reactivity. Reactive particles have very short lives and mostly react
immediately.
Carbenium Ion
Carbenium ion is the positively charged carbon ion C+. It is an electrophilic particle since it has
an electron gap due to its positive charge. As an electrophilic particle, the carbenium ion can
attack molecules with notable electron density. This process is called an electrophilic attack.
Hereby, mostly anions, double bonds, or lone electron pairs of electrons are attacked.
The stability of the carbenium ion depends on its substituents. Thus, the methyl cation is the
most unstable form of the carbenium ion. Primary carbenium ions are characterized by their
greater stability. Even more stable, however, are secondary carbenium ions. The tertiary
carbenium ion is the most stable form of the carbenium ion. Note: The more substituents the
carbenium ion has, the more stable it is. However, this rule does not apply to molecules
stabilized by mesomerism (e.g.: benzyl).
Carbanion
Carbanion is the negatively charged carbon ion C–. Due to its lone electron pair, it is a
nucleophilic particle. Carbanions mostly form via splitting off of an alpha-hydrogen proton,
which is a proton that is bound to the C atom next to the functional group. As a nucleophilic
particle, the carbanion preferably attacks molecules with low electron density. This is called a
nucleophilic attack.
Radicals
Radicals are particles with an unpaired electron. They are very unstable and can form additional
radicals out of other components. This mostly leads to a chain reaction. For example, radicals
form under ultraviolet radiation. A homolytic split occurs, and the 2 bonding electrons divide
equally into the products so that each of them has 1 unpaired electron. Primary carbon radicals
are the most unstable carbon radicals. Secondary carbon show higher stability. This stability
increases with tertiary carbon radicals.
Electron effects influence the distribution of the charge of a molecule and, thus, have an effect on
its reactivity.
Inductive Effects
Inductive effects or I-effects are based on sigma-bonds and only have an effect over short
distances. To understand inductive effects, it is important to comprehend the electronegativity of
the affected atoms. Note: The further an element is in the upper-right corner of the periodic table,
the greater is its electronegativity. If a carbon atom has a bond with a substituent that has greater
electronegativity, it pulls the electrons of the sigma-bond closer to it. Such a substituent is called
an I-substituent. Because of the attraction of the 2 bonding electrons, it becomes slightly more
negative, while the carbon becomes slightly more positive. Carbon now has a positive partial
charge δ+.
Mesomeric Effects
Mesomeric effects or M-effects are based on pi-bonds. Their influences affect the whole
molecule. A substituent with a lone pair can act as a +M-substituent if the lone pair participates
in the mesomerism of the molecule. This way, the electron density of the molecule’s core is
increased. Thus, the pi-electrons are not firmly bound to a location but are de-locatable. Vice
versa, -M-substituents can decrease the electron density of a molecule if they pull the pi-
electrons away from the molecule’s core.
Electrometric Effects: The electrometric effect refers to the displacement of electrons from one
atom to another following the advent of reagent attacks within the pi-bond. In the event that the
attacking species is an electrophile, the pi-electrons are drawn towards a positively charged
atom. This occurrence is referred to as the +E effect. Contrariwise, if the attacking component is
a nucleophile, the electrons are delocalized away from the attacking reagent and into the pi-
system. This phenomenon is referred to as the –E Effect. Nonetheless, the term “electrometric
effect” has gradually become obsolete.
DEFINATION OF TERMS
Isotopes: Members of a family of an element that all have the same number of protons but
different numbers of neutrons. The number of protons in a nucleus determines the element's
atomic number on the Periodic Table.
Half-life: In a chemical reaction, the half-life of a species is the time it takes for the
concentration of that substance to fall to half of its initial value
Thermodynamics: branch of physics that deals with heat, work, and temperature, and their
relation to energy, entropy, and the physical properties of matter
Pneumoconiosis: group of lung diseases caused by the lung's reaction inhaling certain dusts.
The main cause of the pneumoconioses is work-place exposure. Environmental exposures have
rarely been related to these diseases. The primary pneumoconioses are: Abestosis – caused by
inhaling asbestos fibers.
Mesomerism: In chemistry, the mesomeric effect (or resonance effect) is a property of
substituents or functional groups in a chemical compound. It is defined as the polarity produced
in the molecule by the interaction of two pi bonds or between a pi bond and lone pair of electrons
present on an adjacent atom.