FUNDAMENTALS OF BIOCHEMISTRY

BIOCHEMISTRY

• Biochemistry also called BIOLOGICAL CHEMISTRY is the study ofchemical processes in living organisms.

• Biochemistry deals with structures and functions of cellularcomponents such as proteins, carbohydrates, lipids, nucleic acids(biomolecules)

• Biochemistry operates at a molecular level and brings to light thehidden secretes of life

BIOCHEMISTRY as molecular logic of life

• Biochemistry asks how the remarkable properties of living organismsarise from the thousands of different lifeless biomolecules.

• When these molecules are isolated and examined individually, theyconform to all the physical and chemical laws that describe thebehavior of inanimate matter—as do all the processes occurring inliving organisms.

• The study of biochemistry shows how the collections of inanimatemolecules that constitute living organisms interact to maintain andperpetuate life animated solely by the physical and chemical laws thatgovern the nonliving universe

AXIOMS OF LIVING MATTER1. A high degree of chemical complexity and microscopic organization

रासायनिक जनिलता और सूक्ष्म संगठि की एक उच्च निग्री

2. Systems for extracting, transforming, and using energy from the environment

पयाावरण से ऊजाा निकालिे, बदलिे और उपयोग करिे के नलए नसस्टम

3. A capacity for precise self-replication and self-assembly

सिीक आत्म-प्रनतकृनत और स्व-समूहि की क्षमता

4. Mechanisms for sensing and responding to alterations in their surroundings

अपिे आस-पास में बदलावों को समझिे और प्रनतनिया देिे के नलए तंत्र

5. Defined functions for each of their components and regulated interactions among them.

प्रते्यक घिकों और उिके बीच नवनियनमत परस्पर प्रभाव के नलए निर्ााररत काया।

6. A history of evolutionary change.

नवकासवादी पररवताि का इनतहास

Major Organic Compounds of Animate Objects

4 major classes of BIOMOLECULES

Carbohydrates

Lipids

Proteins

Nucleic acids

Definitions• Atom: Atoms are the basic building blocks of ordinary matter.

Atoms can join together to form molecules.

Atoms are composed of particles called protons, electrons and neutrons.

The protons and neutrons cluster together in the central part of the atom,called the nucleus, and the electrons 'orbit' the nucleus.

• Element: a pure substance of one type of atom.

It can be solid, liquid or gas.

• Compound: Substance containing more than one type of atoms.

• Molecules: A molecule is the smallest particle in a chemical element orcompound that has the chemical properties of that element or compound.

Molecules are made up of atoms that are held together by chemical bonds.

Most biological molecules are made from 6important elements

1. Oxygen

2. Sulfur

3. Carbon

4. Hydrogen

5. Nitrogen

6. Phosphorous

Name Oxygen Sulfur Carbon Hydrogen Nitrogen Phosphorous

Symbol O S C H N P

Atomic No. 8 16 6 1 7 15

Atomic mass 15.9994 amu

32.066 amu 12.0107 amu 1.00794 amu 14.06674 amu 30.97376 amu

No. of protons/electrons

8 16 6 1 7 15

No. of neutrons 8 16 6 0 7 16

Classification Non metal Non metal Non metal Non metal Non metal Non metal

Crystal structure Cubic Orthorhombic Hexagonal Hexagonal Hexagonal Monoclinic

Color Colorless Yellow Black Colorless Colorless White

Uses Supports life

Matches, gun powder,

medicines

Steel filters Balloons, metal refining

Forms most ofatmosphere

Fertilizers, detergents

Obtained from Liquid naturally Burning with insufficient

oxygen

Mines, oil, gas Liquid air Phosphate rock

TYPES OF BONDS

IONIC BOND

• Ionic bonding is the complete transfer of valence electron(s) between atoms.

• It is a type of chemical bond that generates two oppositely charged ions.

• In ionic bonds, the metal loses electrons to become a positively charged cation, whereas the nonmetal accepts those electrons to become a negatively charged anion.

• Ionic bonds require an electron donor, often a metal, and an electron acceptor, a nonmetal.

• Ionic bonding is observed because metals have few electrons in their outer-most orbitals. By losing those electrons, these metals can achieve noble gas configuration and satisfy the octet rule.

• Similarly, nonmetals that have close to 8 electrons in their valence shells tend to readily accept electrons to achieve noble gas configuration.

• In ionic bonding, more than 1 electron can be donated or received to satisfy the octet rule.

• The charges on the anion and cation correspond to the number of electrons donated or received.

• In ionic bonds, the net charge of the compound must be zero.

EXAMPLES : CHLORIDE SALTS

In this example, the sodium atom is donating its 1 valence electron to the chlorine atom. This creates a sodium cation and a chlorine anion. Notice that the net charge of the resulting compound is 0.

In this example, the magnesium atom is donating both of its valence electrons to chlorine atoms. Each chlorine atom can only accept 1 electron before it can achieve its noble gas configuration; therefore, 2 atoms of chlorine are required to accept the 2 electrons donated by the magnesium. Notice that the net charge of the compound is 0.

COVALENT BONDS

• Covalent bonding is the sharing of electrons between atoms. • This type of bonding occurs between two atoms of the same element or of

elements close to each other in the periodic table. • This bonding occurs primarily between nonmetals; however, it can also be

observed between nonmetals and metals. • If atoms have similar electronegativities (the same affinity for electrons),

covalent bonds are most likely to occur. • Because both atoms have the same affinity for electrons and neither has a

tendency to donate them, they share electrons in order to achieve octet configuration and become more stable.

• In addition, the ionization energy of the atom is too large and the electron affinity of the atom is too small for ionic bonding to occur.

• For example: carbon does not form ionic bonds because it has 4valence electrons, half of an octet. To form ionic bonds, Carbonmolecules must either gain or lose 4 electrons. This is highlyunfavorable; therefore, carbon molecules share their 4 valenceelectrons through single, double, and triple bonds so that each atomcan achieve noble gas configurations.

• Covalent bonds include interactions of the sigma and pi orbitals;therefore, covalent bonds lead to formation of single, double, triple,and quadruple bonds.

In this example, a phosphorous atom is sharing its three unpaired electrons with three chlorine atoms. In the end product, all four of these molecules have 8 valence electrons and satisfy the octet rule.

CO-ORDINATE BOND

• A coordinate bond is a type of covalent bond where both of theelectrons that form the bond originate from the same atom (moregenerally, a "dative" covalent bond).

• Coordinate bonds form between a central electrophile (low electrondensity, such as metal cations) and one or more nucleophiles ( highelectron density, such as the hydroxide anion) oriented around theformer. Nucleophiles acts as "ligands" by supplying two electrons percoordinate bond to the electrophile to satisfy the octet rule.

HYDROGEN BOND

• A hydrogen bond is a partially electrostatic attraction between ahydrogen (H) which is bound to a more electronegative atom such asnitrogen (N), oxygen (O), or fluorine (F), and another adjacent atombearing a lone pair of electrons.

• Hydrogen bonds can occur between molecules (intermolecular) orwithin different parts of a single molecule (intramolecular).

• They are somewhat stronger than a van der Waals interaction, andweaker than fully covalent or ionic bonds.

• Intermolecular hydrogen bonding is responsible for the high boilingpoint of water (100 °C)

• Intramolecular hydrogen bonding is partly responsible for thesecondary and tertiary structures of proteins and nucleic acids.

• It also plays an important role in the structure of polymers, bothsynthetic and natural.

References

• Principles of Biochemistry (5th) Lehninger.