BIF101 Official Handouts

Department of Bioinformatics and Computational Biology, VUP · Module 1: Unit of Life · Cells as the Basic Unit of Life

A cell is the smallest unit of a living thing and is the basic building block of all organisms.

Cells as Building Blocks

A cell is the smallest unit of a living thing. A living thing, whether made of one cell (like bacteria) or many cells (like a human), is called an organism. Thus, cells are the basic building blocks of all organisms. Several cells of one kind that interconnect with each other and perform a shared function form tissues; several tissues combine to form an organ (your stomach, heart, or brain); and several organs make up an organ system (such as the digestive system, circulatory system, or nervous system). Several systems that function together form an organism (like a human being). There are many types of cells all grouped into one of two broad categories: prokaryotic and eukaryotic. For example, both animal and plant cells are classified as eukaryotic cells, whereas bacterial cells are classified as prokaryotic. In general, the classification of cells is associated with the presence or absence of a nucleus, the biggest and at one time until the dawn of the electron microscopy age, the only visible organelle found exclusively in eukaryotic cells. Although the nucleus or “karyon” is the major identifiable characteristic of eukaryotic cells, simple possession of this organelle is not the standalone attribute setting it apart from prokaryotic cells. Organelles are membrane-bound compartments optimized for a function so a cellular business can be more efficiently conducted. Macromolecules are made up of basic molecular units. They include the proteins (polymers of amino acids), nucleic acids (polymers of nucleotides), carbohydrates (polymers of sugars) and lipids (with a variety of modular constituents). The biosynthesis and degradation of biological macromolecules involves linear polymerization, breakdown steps (proteins, nucleic acids and lipids) and may also involve branching/debranching (carbohydrates). These processes may involve multiprotein complexes (e.g. ribosome, proteasome) with complex regulation. Homeostasis: A property of cells, tissues, and organisms that allows the maintenance and regulation of the stability and constancy needed to function properly. Homeostasis is a healthy state that is maintained by the constant adjustment of biochemical and physiological pathways Water is needed to maintain homeostasis. Cells are also made up of macromolecules—nucleic acids, lipids, proteins, carbohydrates. These macromolecules help maintain a cell's structure, help cells communicate with each other, aid in energy storage, etc.

Module 2: Composition of matter

Matter is made of combinations of elements substances such as hydrogen or carbon that cannot be broken down or converted into other substances by chemical means. The smallest particle of an element that still retains its distinctive chemical properties is an atom. However, the characteristics of substances other than pure elements—including the materials from which living cells are made— depend on the way their atoms are linked together in groups to form molecules. In order to understand how living organisms are built from inanimate matter, therefore, it is crucial to know how all of the chemical bonds that hold atoms together in molecules are formed. Each atom has at its center a positively charged nucleus, which is surrounded at some distance by a cloud of negatively charged electrons, held in a series of orbitals by electrostatic attraction to the nucleus. The nucleus in turn consists of two kinds of subatomic particles: protons, which are positively charged, and neutrons. which are electrically neutral. The number of protons in the atomic nucleus gives the atomic number. An atom of hydrogen has a nucleus composed of a single proton; so hydrogen, with an atomic number of 1, is the lightest element.

Electronegativity is the property of an atom which increases with its tendency to attract the electrons of a bond. If two bonded atoms have the same electronegativity values as each other, they share electrons equally in a covalent bond. Usually, the electrons in a chemical bond are more attracted to one atom (the more electronegative one) than to the other. If the electronegativity values are very different, the electrons aren't shared at all. One atom essentially takes the bond electrons from the other atom, forming an ionic bond

Electronegativity Example

The chlorine atom has a higher electronegativity than the hydrogen atom, so the bonding electrons will be closer to the Cl than to the H in the HCl molecule In the O2 molecule, both atoms have the same electronegativity. The electrons in the covalent bond are shared equally between the two oxygen atoms.

Module 3: Molecules of life

Living organisms are composed of several types of substances called biomolecules. According to their molecular weight, substances in living organisms are divided into two groups:

1. Low molecular substances (Mr < 10 000) Water Inorganic (mineral) substances Intermediates of metabolic pathways (carboxylic acids etc.) Final products of metabolic pathways (amino acids, monosaccharides, lipids, nucleotides)
2. High molecular substances (Mr > 10 000) Proteins Polysaccharides Nucleic acids

High molecular substances, which are present in living organisms, are also named as biological macromolecules or biopolymers. The building units of proteins are amino acids, the building units of polysaccharides are monosaccharides, and the building units of nucleic acids are nucleotides. According to their origin, the substances included in the living organisms are divided into inorganic substances (water, carbon dioxide, mineral substances) and organic substances (the most important are nucleic acids, proteins, saccharides, lipids).

Fig.: Average representation of the main groups of substances in organisms Condensation is a chemical process by which 2 molecules are joined together to make a larger, more complex, molecule, with the loss of water.