Chemical Bonds and Water Biochemistry_lec 1.pdf

BIOCHEMISTRY [CHM 203]  CHEMICAL BONDS And BIOCHEMISTRY of WATER By Dr. Maha M Salah Assistant Professor of Medical Biochemistry and Molecular Biology  What is Biochemistry? - It is the stud...

BIOCHEMISTRY [CHM 203]  CHEMICAL BONDS And BIOCHEMISTRY of WATER By Dr. Maha M Salah Assistant Professor of Medical Biochemistry and Molecular Biology  What is Biochemistry? - It is the study of the Chemistry of biological organisms. It forms a bridge between Biology and Chemistry by studying how complex chemical reactions and chemical structures give rise to life and life's processes. CHM 203  Chemical Bonds ❑ They refer to the formation of a chemical bond between two or more atoms, molecules, or ions to give rise to a chemical compound. These chemical bonds are what keep the atoms together in the resulting compound ❑ Therefore, chemical compounds are reliant on the strength of the chemical bonds between its constituents; The stronger the bonding between the constituents, the more stable the resulting compound would be. CHM 203  ❑ Types of Chemical Bonds: ✓ The different types of bonds in chemical reactions are formed from the loss, gain, or sharing of electrons between two atoms/molecules. ✓ Accordingly, They are classified into: I. Covalent Bonds II.Non-Covalent Bonds CHM 203 A] Covalent Bonds: ✓ They are the sharing of electrons in the outer atomic orbitals between adjacent atoms. ✓ They are the strongest bonds and tend to be very stable. ✓ Because bond energy is relatively high, considerable energy must be expended to break covalent bonds. CHM 203  ✓ Types of Covalent Bonds Can be classified according to Polarity: i. Polar ii. Non-Polar Can be classified according to number of electron pairs shared: i. Single ii. Double iii.Trible Coordinate Covalent Bonds CHM 203  Polar Covalent Bonds ✓ In this type, electrons are shared unequally due to different Electronegativity (power to attract electrons). So, the more electronegative atom pulls the electron pair closer to itself and away from the less electronegative atom. Water is an example of such a polar molecule. ✓ One end of the molecule tends to be partially positively charged and the other end tends to be partially negatively charged. CHM 203  Water CHM 203  Non-Polar Covalent Bond ✓ In this type, the electrons are equally shared between the two atoms that have the same electronegativity and therefore have equal sharing of electrons. ✓ An example is Methane gas (CH4). CHM 203  ❑ According to the number of electron pairs shared, covalent bonds could be Single, Double or Trible bonds: CHM 203 ❑ Coordinate Covalent Bonds: - They are covalent bonds [sharing of electron pair(s)] in which the two electrons come from the same atom. CHM 203  B] Non-Covalent Bonds ✓ They are much weaker than covalent bonds. ✓ They play an important role in determining many of the properties of biomolecules and how these molecules interact with water and with each other. ✓ They include: i. Hydrogen Bonds ii. Ionic Bonds iii.Van der Waals Forces iv.Hydrophobic Interactions CHM 203  Hydrogen Bonds ✓ It forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom. The atom to which the hydrogen is covalently bonded is called the hydrogen donor, whereas the other atom is termed the hydrogen acceptor. CHM 203  ✓ Examples for Hydrogen Bonding are: 1. Hydrogen bonds between water molecules. 2. Hydrogen bonds between water and other molecules. 3. Hydrogen bonding between amino acids in a linear protein molecule determines the way it folds up into its functional configuration. 4. Hydrogen bonds between nitrogenous bases in nucleotides on the two strands of DNA (guanine pairs with cytosine, adenine with thymine) give rise to the double-helix structure that is crucial to the transmission of genetic information. CHM 203 CHM 203  Ionic Bonds (Salt Bridges) ✓ Ions are electrically charged particles formed when atoms loose or gain electrons. ✓ Ionic bonds occur because of strong electrostatic forces of attraction between oppositely charged groups (NH3+ and COO-) or ions (Na+ and Cl-). CHM 203 CHM 203  Van der Waals Forces ✓ Van der Waals forces are a class of transient electrostatic interactions. ✓ The basis of a Van der Waals interaction is that the distribution of electrons around an atom changes with time. ✓ At any instant, the electron distribution is not perfectly symmetric. CHM 203  ✓ This transient asymmetry in the electron distribution around an atom (transient dipole) acts to induce a complementary asymmetry in the electron distribution (dipole formation) in its neighboring atoms. ✓ These two induced dipoles then attract each other (dipole-dipole interaction). ✓ The attraction between molecules is greatest at a distance called the Van der Waals distance. If molecules approach each other more closely, a repulsive force develops, by the negative charges of their outer electron shells. CHM 203 CHM 203  Hydrophobic Interactions ✓ They refer to the tendency of nonpolar compounds to cluster together in an aqueous medium. ✓ They describe the relation between water and hydro-phobes. ✓ Hydro-phobes are nonpolar molecules and usually have a long chain of carbons that do not interact with water molecules. ✓ Non-Polar molecules can’t form hydrogen bonds with water molecules and tend to cluster together. They are water insoluble. CHM 203  ✓ Water tends to squeeze nonpolar molecules out together. ✓ Nonpolar molecules are driven together in water not primarily because they have a high affinity for each other but because water molecules are strongly bonding to each other by hydrogen bonds, as in case of oil and water. ✓ Hydrophobic Interactions are important for the folding of polypeptide chains of proteins. This is important in keeping a protein stable and biologically active CHM 203  ✓ Besides from proteins, there are many other biological substances that rely on hydrophobic interactions for its survival and functions, like the phospholipid bilayer membranes in every cell. CHM 203  BIOCHEMISTRY OF WATER ❑Water has many unique properties that make it essential for life. It covers 2/3 of the earth surface. ❑The human body is composed of over 70% water, and it is the major component of many body fluids including blood, urine and saliva. CHM 203  ❑ Molecular Structure of Water: ✓ Water has a simple molecular structure. ✓ It is composed of two hydrogen atoms and one oxygen atom attached together by two covalent bonds: 1. Each hydrogen atom of a water molecule shares an electron pair with the central oxygen atom forming covalent bond. 2. The oxygen nucleus attracts electrons more strongly than does the hydrogen nucleus. CHM 203  3. The sharing of electrons between H and O is therefore unequal; the electrons are near the oxygen atom than the hydrogen atom (polar covalent bond). 4. The result of this unequal electron sharing is two electric dipoles in the water molecule. 5. Each hydrogen atom bears a partial positive charge, and the oxygen atom bears a partial negative charge. CHM 203 ✓ The geometry of water molecules is typically referred to as "bent" or "angular". Since the two bonds connecting oxygen to hydrogen are not linear. The bond angle is 104.5ɵ. Therefore, giving a polar trait to water molecules. CHM 203 ❑ Chemical Properties of Water ✓ Because water molecules are dipoles, there is an electrostatic attraction between the oxygen atom of one water molecule and the hydrogen atom of another water molecule forming the Hydrogen Bond. CHM 203 ❑ Thermal Properties of Water ✓ Ice melts at 0o C turning into water which boils at +100o C. Thus, water is a liquid over most of the wide range of temperature found on the earth’s surface, which is essential for life. CHM 203  ✓ Hydrogen Bonding is responsible for Thermal Properties of Water: 1. Each water molecule can form as many as four hydrogen bonds with neighboring water molecules (which occur when water has frozen into ice). 2. When ice is warmed to its melting point, about 15% of hydrogen bonds are broken. As the temperature rises, more hydrogen bonds are broken. 3. When the boiling point is reached, all hydrogen bonds are broken, water molecules free from one another and water vaporizes. CHM 203  ❑ Solvent Properties of Water ✓ The Dipolar structure of water molecules allows water to be the Universal Solvent. ✓ In case of Ionic molecules: They dissolve by formation of Solvation Spheres as follows: 1. When a crystal of the ionic compound, NaCl for example, is placed in water, the sodium and chloride ions are separated in the solvent. 2. The hydrogen atoms of water molecules are positively charged and attract chloride anions. CHM 203  3. Meanwhile, oxygen atoms of water molecules are negatively charged and attract sodium cations. 4. Water molecules shield individual sodium and chloride ions from one another by hydration. CHM 203 ✓ In case of Polar molecules: Due to the dipolar nature of water molecules and its capacity to form hydrogen bond, the polar molecules can be dissolved very easily. Examples: Ketones, Alcohols, Aldehydes, and compounds that have carboxyl or amino groups. CHM 203 CHM 203 ✓ In case of Amphipathic molecules: They are molecules that contain polar (head) and non-polar groups (tail) e.g.: soap and bile salts. The non-polar hydrophobic tail of a molecule aggregates in the center away from water and the hydrophilic heads of molecule form hydrogen bonds with the surrounding water molecules forming Micelles. CHM 203 CHM 203  ✓ In case of non-Polar molecules: They are not soluble in water because they can’t form hydrogen bonds with water molecules. These molecules cannot dissolve in water except in presence of amphipathic molecules e.g.: Fat i.e., Triacylglycerol (TAG) and Cholesterol Esters. They can form an Emulsion, in which the non-polar molecules are surrounded by the amphipathic molecules which can deal with water. CHM 203 CHM 203 # Hydrogen bonds are type of: a) Polar covalent bonds. b) Nonpolar covalent bonds. c) Non-covalent bonds. d) None of the above. # What does a hydrogen atom need to be in for hydrogen bonding to occur? a) A polar covalent bond b) A non-polar covalent bond c) An ionic bond d) An alkaline bond # Which among the following is not a property of Ionic Bonds? a) Losing of electrons b) Gaining of electrons c) Sharing of electrons d) Transfer of electrons THANK YOU