Introduction to Chemistry and Biochemistry PDF

Introduction to Chemistry  Organic vs Inorganic Chemistry ❖ Inorganic chemistry is the study of compounds from non living sources ❖ Organic chemistry is the study of compounds from living sources Modern definitions ❖ Inorganic chemistry is the synthesis and behavior...

Introduction to Chemistry  Organic vs Inorganic Chemistry ❖ Inorganic chemistry is the study of compounds from non living sources ❖ Organic chemistry is the study of compounds from living sources Modern definitions ❖ Inorganic chemistry is the synthesis and behavior of inorganic and organometallic compounds ❖ Organic chemistry is the study of carbon compounds  Matter ❖ Matter is anything that has mass and occupies space ❖ The quantity of matter in a substance - MASS Matter occupies space and has VOLUME ❖ All substances are comprised of matter ❖ Matter is comprised of particles… Solid, Liquid and Gas are the three states of matter ❖ The difference in state is dependent on the arrangement and movement of the particles Matter  Solid Liquid Gas Particles arranged in a lattice Particles arranged in clusters Particles widely spaced Very strong forces of attraction Forces of attraction weaker Negligible forces of attraction than that in a solid and stronger than in a gas Particles are only able to Particles flow over each other Particles move in a rapid and vibrate random motion Particles have a definite shape Definite volume No definite shape and definite volume Since particles are free to move Particles rapidly fill any they do not have a definite container they have no volume shape Negligible compressibility Very little compressibility High compressibility  Structure and Function of Atoms ❖ Particles of matter → Atoms ❖ Atoms → Elements ❖ Elements → Molecules and Compounds ❖ Compounds → Mixtures ❖ An element is a substance that cannot be further decomposed by ordinary chemical means. ❖ Each element has atoms comprised of a proton, neutron and electron.  subAtomic particles Particles Symbol Relative mass Charge (atomic mass unit) Protons p 1.007276 +1 Neutrons n 1.00864 0 Electrons e- 5.485 799 x 10-4 -1  Atomic structure ❖ Protons and neutrons are found in the nucleus of the atom ❖ Electrons are found in orbitals outside the nucleus  Atom ❖ Atoms are neutral because they contain the same number of protons and electrons ❖ Ions are formed if the number of protons are different from the number of electrons, i.e. the number of positive and negative charges are unequal ❖ Positive charge > negative charge = CATION ❖ Positive charge < negative charge = ANION Elements ❖ Each element has an atomic number and an atomic mass Atomic number - number of protons in the nucleus of the atom Atomic mass (mass number) – average mass of an atom compared to the carbon atom which has been assigned 12 atomic units. ❖ An element (M) has the following notation mass number charge M atomic number number of entities ❖ E.g. The element sodium has the symbol Na, the mass number is 23 and the atomic number is 11 23 Na 11 ❖ Magnesium has a charge of 2+ because there are two more positive charges when compared to negative charges Mg 2+ ❖ Nitrogen is a diatomic molecule N2 i.e. the number of entities is 2 ❖ The number of neutrons = mass number – atomic number ❖ The mass number is not a whole number…it is an average of two or three varieties of atoms Chlorine has 2 atoms with mass numbers 35 and 37.  One kind has 17 protons and 18 neutrons the other has 17 protons and 20 neutrons  The two atoms are present in the proportion – 75% 35Cl and 25% 37Cl Chlorine therefore has an atomic wt of 35.5 The two atoms are ISOTOPES of chlorine Isotopes are atoms of the same element having the same atomic number or number of protons but different mass numbers or number of neutrons  Bonding ❖ When elements combine they do so as electrovalent or covalent bonding ❖ Electrovalent bonding is a giving away of an electron forming charged particles. This type of bonding is between a metal and a non metal Sodium and Chlorine = NaCl (common salt) Sodium – Group 1 (metal) Chlorine – Group 7 (non metal) Electrovalent Bonding ❖ In the chemical compound sodium chloride  Na has one electron in its outer shell and chlorine has seven in its outer shell.  The sodium gives up the electron to chlorine and becomes positively charged (Na+)  The Chlorine takes the electron from sodium and becomes negatively charged (Cl-) Electrovalent Bonding  Covalent Bonding ❖ Covalent bonding occurs when elements share their outer (valence) electrons. This type of bonding occurs among non metals  Water – H2O  Oxygen has an atomic number of 8 so it has 2 on the inner shell and 6 in the outer shell  Hydrogen has one electron in its outer shell Covalent Bonding ❖ A compound is a substance that can be decomposed into two or more simpler substances by ordinary chemical means ❖ A molecule is the smallest chemical unit of a substance that is capable of stable independent existence ❖ A mixture is a material composed of two or more substances each of which retains its own characteristic properties ❖ Homogeneous mixture - the component parts are evenly distributed. E.g. homogenized milk and sodium chloride in water Most solutions are homogeneous mixtures ❖ Heterogeneous mixture – the component parts can be easily distinguished. E.g. rocks, granite in water, immiscible liquids e.g. oil and water.  Acids, bases and buffers ❖ There exist different definitions for an acid and a base Arrhenius Definition An acid is a substance that produces hydroxonium ion (H3O+) as the only positively charged ion A base is a substance that produces (OH-) as the only negatively charged ion ❖ The Arrhenius theory accounts for the many acids and bases that exist ❖ One limitation with the theory is that it is only applicable to aqueous solutions. As a result a molecule like ammonia (alkaline gas) would not be classified as a base ❖ A more general definition for acid and base were later proposed by 2 Scientists, Johannes BrØnsted and Thomas Lowry BrØnsted-Lowry Theory An acid is any substance (molecule or ion) that transfers a proton to another substance A base is any substance (molecule or ion) that accepts a proton HA + B → BH+ + A- H+ donor H+ acceptor H+ donor H+ acceptor BrØnsted-Lowry Theory  Acid and Base Strength ❖ A strong acid (strong base) is completely dissociated in aqueous solution ❖ Therefore the acid (base) dissociation equilibrium of a strong acid (strong base) lies entirely to the right and as such only ions are present in the solution HCl (aq) → H+ (aq) + Cl- (aq) NaOH (aq) → Na+ (aq) + OH- (aq) Source: http://wikis.lawrence.edu/display/CHEM/Acids+and+Bases-Davis  Acid and Base Strength  A weak acid (weak base) is partially dissociated in aqueous solution  Only a small fraction of the of the molecule is transferred to ions CH3COOH (aq) CH3COO- (aq) + H+ (aq) Relative Strength of Conjugate Acid-Base Pairs Buffers ❖ A Buffer is a solution containing a weak acid and a conjugate base and is able to resist changes in pH ❖ Buffers do this by neutralizing added acid or base ❖ Blood is a buffer that resists changes in pH. If the pH of blood drops below 7.0 or increase beyond 7.8 we would die ❖ Like all buffers, blood contains significant amounts of both weak acid and conjugate base ❖ Blood contains a carbonic acid- bicarbonate buffer ❖ When additional base is added to blood the acid reacts with the base neutralizing it. In addition if acid is added to blood the conjugate base reacts with the acid neutralizing it H+(aq) + HCO3-(aq) H20(l) + CO2(g) Introduction to Biochemistry  Introduction to Biochemistry ❖ What is Biochemistry? Study of molecules and chemical reactions in living things – Metabolic reactions e.g. digestion, excretion, respiration etc. – Analysis of biomolecules – Characterization of cell components ❖ Molecular level - biochemistry deals mainly with the chemistry of carbon compounds ❖ Carbon compounds are very versatile and can polymerize into large complex structures called macromolecules ❖ Macromolecules are usually in the form of polymers ❖ Polymers – joining together of smaller organic molecules (monomers) via condensation (removal of water molecule) ❖ Macromolecules have properties that are different from their constituent monomers ❖ Example, glucose (carbohydrate monomer) is more soluble and sweeter than starch (carbohydrate polymer)  Biological Macromolecules ❖ The four major organic macromolecules are  Carbohydrates  Proteins  Lipids  Nucleic Acids Macromolecules Monomers Carbohydrates monosaccharides Proteins amino acids Lipids fatty acids and glycerols Nucleic acids nucleotides  Introduction to Biochemistry ❖ Biochemistry is related to nutrition ❖ It is through nutrition that we are able to get important chemical substances into our system ❖ It is through biochemistry that nutrients and trace elements are processed in the body Importance of Biochemistry 1. Understanding the cause of diseases 2. Composition of living cells and molecules present 3. Location of biomolecules in the cell and structure of the cells 4. Function of biomolecules and relationship between structure and function 5. Source of biochemicals in cells  Nutrients  Cellular biosynthesis 6. Relationship between function of biomolecules, biosynthesis and biodegradation of cells 7. Maintaining the concentration of cellular molecules in pathways and metabolic reactions Isomerism  Isomerism ❖ The presence of the chiral (asymmetric) carbon makes it possible for the formation of isomers ❖ There are 2 types of isomers constitutional isomers and stereoisomers (a) Constitutional Isomers ❖ These compounds have the same molecular formula but different structural formula ❖ e.g. Glucose and fructose are both hexose having the formula C6H12O6  (a) Constitutional Isomers  Epimers: two sugars that differ from each other only in configuration around a single asymmetric carbon  (a) Constitutional Isomers ❖ The number of isomers can be deduced by using the formula 2n – Le Bel-van’t Hoff rule n = # of asymmetric carbon ❖ A hexose will have 4 asymmetric carbons therefore the number of isomers that will be formed is 24 = 16 (b) Stereoisomers ❖ These compounds have the same molecular and structural formula but different spatial arrangement ❖ There are two types: Geometric and Optical isomers (b)(i) Geometric Isomers ❖ They are sometimes referred to as cis trans isomers N.B. not applicable to monosaccharides, usually occurs in unsaturated compounds – i.e. those having double bonds Cis- butene Trans-butene  Unsaturated fatty acids Image result for cis fatty acid and trans fatty acid (b)(ii) Optical Isomers: Enantiomers  Optically active compounds rotate plane polarized light  Molecules that rotate plane polarized light to the right are dextrorotary (D)/ (+) Molecules that rotate plane polarized light to the left are levorotary (L)/ (-)  The number of isomers that can be formed is dependent on the number of chiral/asymmetric carbon  (b)(ii) Optical Isomers - Enantiomers ❖ Chiral objects cannot be superimposed on their mirror images —e.g., hands, gloves, and shoes ❖ They are non-superimposable mirror images of each other but are chemically identical ❖ Any carbon atom which is connected to four different groups will be chiral ❖ The D (+) and L (-) form of a compound constitute a pair of enantiomers or enantiomorphs ❖ When equal amounts of D and L forms are present, the resulting mixture becomes optically inactive and is called racemic. ❖ Carbohydrates can exist in either of two conformations, as determined by the orientation of the hydroxyl group about the asymmetric carbon farthest from the carbonyl group. ❖ D- and L- conformations ❖ With a few exceptions, those carbohydrates that are of physiological significance exist in the D-conformation. The mirror-image conformations are in the L- conformation ❖ Living systems contain only one of the possible stereochemical forms of a compound, or they are found in separate systems ❖ D-lactic acid is found in living muscles; D-lactic acid is present in sour milk. ❖ Humans can metabolize D-monosaccharides but not L-isomers; only L-amino acids are used in protein synthesis