Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Physical Chemistry Biochemistry is the study of living systems using the methods of chemistry and physics. Physical chemistry deals with the physicochemical phenomena, which are needed to understand biochemistry. Organisms are complicated and highly organized. Each organism consists of many organ systems ( e.g. respiratory and reproductive systems). Each system is formed of many organs which are formed of tissues. The tissues are formed of cells that contain cell organelles. The cell and its organelles are made up from molecules. Cells are composed of different types of molecules: Water 70% Proteins 15% Nucleic acids 7% Polysaccharides 3% Lipids 1% Minerals and others 4% Molecules are formed of elements. Carbon (C), hydrogen (H), oxygen (O), nitrogen (N), phosphorous (P) and sulfur (S) are the main elements that constitute more than 99% of the human body. Elements are substances that cannot be broken down further by ordinary chemical means. Atoms are the smallest unit of matter retaining the properties of an element. Each atom is made up of positively charged protons, neutral neutrons, and negatively charged electrons. Electrons are generally affected by the following three chemical phenomena: 1. Electrons tend to pair. 2. They are negatively charged and so are subject to the electrostatic attraction-repulsion rules. The relative ability of an atom to draw electrons in a bond toward itself is called the electronegativity of the atom. Atoms with high electronegativitiy attract the electrons more than those that have small electronegativity. 3. Atoms tend to fill their outermost electron energy level (orbit) either by transfer or sharing of electrons. These three factors are the basis for the different types of chemical bonds and chemical reactions that occur in nature. 1 Chemical Bonds The components of the system become more stable through the formation of bonds. There are several types of chemical bonds: 2 1- Covalent Bonds Covalent Bonds are formed by sharing of a pair of electrons. Electrons are shared in pairs. Two atoms sharing a single pair of electrons have a single bond, while two atoms sharing two pairs have a double bond and two atoms sharing three pairs have a triple bond. Covalent Bonds are the strongest chemical Atoms bonds, the energy of a single covalent bond can vary from 50 kcal/mol to 110 Sharing a pair kcal/mol depending on the elements of electrons involved. Once formed, covalent bonds rarely break spontaneously at room temperature because of the high amount of energy required. Carbon-carbon bonds (C—C), carbonCovalent bond in a molecule oxygen bonds (C—O) and carbon-hydrogen bonds (C—H) are all examples of covalent bonds. Methane is formed of one carbon atom covalently attached to 4 hydrogen atoms by 4 covalent bonds. 2- Ionic Bonds Ionic bonds are formed when there is a complete transfer of electrons from one atom to another to fill Atoms their outermost energy levels. This electron transfer results in two ions, one positively charged and the Transfer of other negatively charged. These electrons ions become attracted to each other Negatively by the resulting electrostatic charge charged ion differences. Ionic bonds are generally weak. They are often 4-7 Ionic bond in Positively kcal/mol in strength. a molecule charged ion So they can be broken easily when subjected to heat or submerged in water. An example of this process is the formation of a sodium chloride molecule. Ionic bonds are also called electrostatic bonds as they result from the electrostatic attraction between two ionized atoms or groups of opposite charge 3- Hydrogen bonds Hydrogen bonds result from electrostatic attraction between an electronegative atom e.g. oxygen or nitrogen (O or N) and a hydrogen atom that shares its electron with a second electronegative atom. Hydrogen bonds occur between two or more polar molecules. A polar molecule is a molecule that has a slight positive charge at one end and a slight negative charge on the other (giving it poles). The bond is quite weak (5 kcal/mol) and easily broken, unlike covalent bonds. Accumulation of many hydrogen bonds provides specificity and significant stability to macromolecular structures. Hydrogen bonds are frequently found in proteins and nucleic acids in large numbers and serve to keep the protein or nucleic acid structure secure. Perhaps the most famous example of hydrogen bonds is the bond which is formed between oxygen of water molecule and the hydrogen of another water molecules. Each water molecule can form up to 4 hydrogen bonds. H O H Hydrogen bond H O H Hydrogen bond between 2 water molecules 4- Van der Waals interactions Van der Waals interactions are intermolecular forces of attraction that occur when there is a transient asymmetry in the distribution of charge around atoms in a molecule. The consequent charge imbalance affects and attracts adjacent atoms. Van der Waals interactions are very weak bonds (1 kcal/mol) formed between non-polar molecules or non-polar parts of a molecule that have slight transient charge displacements. 3 5- Hydrophobic Interactions Hydrophobic interactions occur between clusters of nonpolar molecules that tend to aggregate so as to minimize the surface area that is exposed to water. Hydrophobic molecules tend to aggregate together in avoidance of H2O molecules. 6- Steric Hindrance Atoms occupy a fixed volume of space that is very difficult to compress, except by covalent bond formation. Thus, atoms cannot overlap in their position. The effect of this on protein structure is called steric hindrance. Bulky side-chains such ( as that found in isoleucine amino acid) restrict the possible side-chain angles in protein structure. Biological Functions where non-covalent interactions play roles 1. Binding specificity Specificity of enzyme substrate binding is due to formation of enough noncovalent bonds to hold the enzyme and substrate together. Also, specificity of antigen antibody reactions is due to formation of enough noncovalent bonds. 2. Protein structure Secondary, tertiary and quaternary protein structures are stabilized by noncovalent bonds. Collagen ,a protein whose function depends on its ability to maintain a long and fibrous structure, is stabilized by noncovalent bonds. 3. DNA base pairing Hydrogen bonding between adjacent base pairs underlies the ability of one strand of DNA to pair with another and serves to hold the two strands of the DNA double helix together. 4