Biochemistry LC1: Introduction to Biochemistry (2024) PDF

B. MOLECULES AND COMPOUNDS COURSE OUTLINE Formed when two or more atoms unite in the basis of their electron structure I. BASIC CONC...

B. MOLECULES AND COMPOUNDS COURSE OUTLINE Formed when two or more atoms unite in the basis of their electron structure I. BASIC CONCEPTS Carbon A. Principal Areas in Biochemistry ○ Period 2 and Group IV of the B. Molecules and Compounds Periodic Table of Elements C. Types of Chemical Bonds ○ Tetravalent II. BOND POLARITY AND ○ Has the ability to participate in a ELECTRONEGATIVITY A. Polar Covalent Bonds wide variety of chemical reactions B. Electronegativity and is able to form different C. Bond Polarity compounds with other elements. D. Chemical Reactions E. General Types of Organic C. TYPES OF CHEMICAL BOND Reactions F. Properties of Organic 1. Ionic Bond Compounds involves in the complete transfer of III. MOLECULAR POLARITY electrons from one atom to another, A. Solubility and Miscibility Based resulting in the production of charged on Polarity atoms, known as ions B. Molecule Polarity IV. INTERMOLECULAR FORCES OF these ions can be positively charged ATTRACTION or negatively charged (e.g. Group 1 A. Physical Properties & 2, Group 6 & 7 NaCl) B. Intermolecular Forces of 2. Covalent Bond Attraction (IMFA) results from the sharing of B.1. Types of IMFA electrons between two atoms V. ISOMERISM covalent bonds can be polar or VI. ORIGINS OF LIFE VII. BIOMOLECULES nonpolar VIII. REFERENCES II. BOND POLARITY AND OVERVIEW OF GENERAL AND ORGANIC ELECTRONEGATIVITY CHEMISTRY AND INTRODUCTION TO BIOCHEMISTRY A. POLAR COVALENT BONDS a given bond is either ionic and covalent. I. BASIC CONCEPTS However, the shared electrons in covalent ORGANIC CHEMISTRY bonds tend to be attracted somewhat more Study of carbon and its compound strongly by one atom by the other. Substances that are primarily composed of we call such bonds with asymmetrical carbon electron distribution as polar covalent BIOCHEMISTRY bonds Chemistry of living things Study of biology at the cellular and B. ELECTRONEGATIVITY molecular level Bond polarity is due to differences in electronegativity, the intrinsic ability of an A. PRINCIPAL AREAS IN BIOCHEMISTRY atom to attract electrons in covalent bonds. Structure and function of biomolecules (lipids, carbohydrates, nucleic acids, and proteins) Metabolism -anabolic and catabolic processes Molecular genetics -how life is replicated, regulation of protein synthesis (central dogma of molecular biology: replication, transcription, translation) Figure 1: Electronegativity BIOCHEMISTRY LC1: INTRODUCTION TO BIOCHEMISTRY DR. ESPIRITU, A. DATE: 08/07/2024 C. BOND POLARITY 5. Elimination Nonpolar covalent bonds Formation of double bonds from ○ bonds between atoms with similar saturated compounds or almost the same electronegativities (EN) F. PROPERTIES OF ORGANIC Polar covalent bonds COMPOUNDS ○ bonds between atoms whose The properties of organic compounds are largely electronegativities differ by less influenced by these factors: than 2 units Intermolecular forces of attraction - Ionic bonds force of attraction of one molecule to ○ bonds between atoms whose another molecule electronegativities differ by more Molecular geometry than 2 units Structural effects: Orbital hybridization D. CHEMICAL REACTIONS Steric effects To be able to form new compounds, they Inductive effects -distortion of electron have to participate in chemical reactions. cloud These chemical reactions involve the Resonance - pi electron delocalization disruption and formation of chemical CH Hyperconjugation - sigma electron bonds. delocalization (e.g. alternating double bonds) SITE OF ORGANIC CHEMICAL REACTIONS Multiple Bonds - to form other bonds III. MOLECULAR POLARITY Polar Groups - easily breaking of bonds ➔ distribution of electrons in the whole →e- will form new other bonds molecule Chemical reactions - characteristically involve the disruption and formation of A. SOLUBILITY AND MISCIBILITY BASED chemical bonds. ON POLARITY Lewis Acid and Lewis Base Characteristics “Like dissolves like” the overall solvation capacity of a solvent REACTION INTERMEDIATES depends upon its polarity Carbocation, Cabanions - charged Polar solvents like water dissolves polar organic molecules solutes (hydrophilic) Free Radicals - presence of unpaired ○ Polar bonds - there is unequal electron in its outermost shell distribution of electrons ○ Most reactive of them all ○ Nonpolar bonds - there is equal distribution of electrons E. GENERAL TYPES OF ORGANIC Nonpolar solvent dissolves nonpolar REACTIONS solutes (hydrophobic) 1. Addition Reactions B. MOLECULE POLARITY usually a characteristic of unsaturated compound and usually the polarity of a molecule is dictated by its result to disruption of multiple bonds geometry AND the individual bonds ○ Unsaturated compounds - existing within molecule compound that contain multiple A molecule with nonpolar bonds is most bonds (e.g. double bond, triple likely a nonpolar molecule bond) A polar molecule must contain at least one 2. Elimination Reactions polar bond Reverse of addition, formation of ○ Exception: Carbon dioxide double bonds 3. Substitution Reactions A molecule with polar bonds may not necessarily be Replacement of one substituent by polar. Why? Example: The bonds of carbon dioxide another are polar but the whole molecule is nonpolar. 4. Rearrangement Reactions - It is because of its molecular geometry. Rearrangement of the structure of a The geometry of carbon dioxide is linear. compound In linear geometry, there is equal PREPARED BY: BATCH 2028 1D 2 BIOCHEMISTRY LC1: INTRODUCTION TO BIOCHEMISTRY DR. ESPIRITU, A. DATE: 08/07/2024 distribution of electrons that is why it is The higher the molecular mass, the nonpolar. higher the london dispersion forces The Dipole Moment or total net product of Usually increase with molar mass vectors or charges is considered through (MM); the larger the MM, the stronger their molecular geometry. the LDF Example: Ammonia and Carbon dioxide 2. Dipole-dipole forces * Take note of the symmetry Forces exhibited by polar compounds Only polar compounds have this type of force Polar molecules exhibit dipole-dipole forces aside from LDF. The more polar a molecule, the stronger the dipole-dipole interaction. Note: LDF and Dipole-dipole forces are collectively known as van der Waals forces (vdW). 3. Hydrogen bonding It is a strong IMFA and special type of dipole-dipole force It is present among molecules which contain hydrogen bound to a small, highly electronegative atom such as N, O and F. ○ Example: H2O - Molecular structure of H2O: Tetrahedral/ V shape Figure 2: Molecular Geometry of Ammonia and CO2 IV. INTERMOLECULAR FORCES OF ATTRACTION A. PHYSICAL PROPERTIES Solubility - one of the most important Figure 3: Lewis Structure of H2O properties of organic compounds These properties of organic compounds are 4. Ion-Ion forces generally related to the intermolecular forces Present in ionic organic compounds of attraction or IMFA. Strong force because it is able to produce crystal lattice structure similar B. INTERMOLECULAR FORCES OF to ionic compounds. ATTRACTION (IMFA) Every ionic compound is held in a well-ordered crystalline state. Forces that must be overcome or broken The forces that hold ions together are during melting, evaporation and sublimation. strong electrostatic lattice forces, an Recall that atoms in molecules are associated adequate amount of energy is needed with other atoms by covalent bonds. These to break the orderly structure of the are relatively strong bonds and are called crystal. intramolecular forces. In sodium acetate, an ionic organic We differentiate this from IMFA, which are compound, BP is very high that it tends forces between molecules. to decompose before it boils. TYPES OF IMFAs 1. London Dispersion Forces (LDF) V. ISOMERISM LDF are present in all substances and Isomers are defined as compounds possessing the the only IMFA present in non-polar same molecular formula but different structural substances and noble gasses. formula PREPARED BY: BATCH 2028 1D 3 BIOCHEMISTRY LC1: INTRODUCTION TO BIOCHEMISTRY DR. ESPIRITU, A. DATE: 08/07/2024 Structural/Constitutional isomerism – b. Trans - functional groups are variation in the bonding arrangement of found on the opposite side of the atoms or groups double bond (has a linear 1. Skeletal - same molecular structure) formula, but different carbon skeleton VI. ORIGINS OF LIFE 2. Positional - same molecular Vitalism is the idea that substances and formula, but different functional processes associated with living group position organisms did not behave according to the 3. Functional - same molecular known laws of physics and chemistry. formula, but different functional Evidence group (e.g. Alcohol and ether) ○ Biochemicals can only be produced Functional groups: molecules aside from by living organisms. carbon and hydrogen that gives the ○ Complex bioconversion of chemical molecule additional property/function substances requires living matter. Stereoisomerism – no variation in bonding arrangement, only in orientation in BIOCHEMICAL EVOLUTION space. Urea was synthesized by heating the 1. Geometric inorganic compound ammonium cyanate 2. Conformational - not really an (1828). [Friedrich Wohler] isomer (can revert back to original This showed that compounds found conformation); rotation of single exclusively in living organisms could be bond synthesized from common inorganic 3. Optical - rotation of the molecule substances. DvL: Dextro vs. Levo Dextro rotation: to the right Levo rotation: to the left Figure 5: Wohler Synthesis ORGANIZATION OF LIFE Elements Simple organic compounds Macromolecules Supramolecular structures Organelles Cells Tissues Organism Figure 4: Isomerism VII. BIOMOLECULES Enantiomers - Mirror images, MANY IMPORTANT BIOMOLECULES ARE non-superimposable POLYMERS Diastereomers - non-mirror image, non-identical stereoisomers. Hence, they occur when two or more stereoisomers of a compound have different configurations at one or more (but not all) of the equivalent (related) stereocenters and are not mirror images of each other. Figure 6: Polymers, Biomolecules a. Cis - groups attached to carbon-carbon double bond are found on one side (has a kinky structure) PREPARED BY: BATCH 2028 1D 4 BIOCHEMISTRY LC1: INTRODUCTION TO BIOCHEMISTRY DR. ESPIRITU, A. DATE: 08/07/2024 BIOMOLECULES - STRUCTURE LIPIDS Figure 10: Lipids Figure 7: Biomolecules PROTEINS LINKING MONOMERS Cells link monomers by a process called dehydration synthesis (removing a molecule of water). This process joins two sugar monomers to make a double sugar. Figure 8: Bond Linking Monomers Figure 11: Proteins BREAKING DOWN POLYMERS CARBOHYDRATES Cells break down macromolecules by a process called hydrolysis (adding a molecule of water). Water is added to split a double sugar Figure 12: Carbohydrates NUCLEIC ACIDS Figure 9: Breaking Down Polymers Figure 13: Nucleic Acids PREPARED BY: BATCH 2028 1D 5 BIOCHEMISTRY LC1: INTRODUCTION TO BIOCHEMISTRY DR. ESPIRITU, A. DATE: 08/07/2024 COMMON THEME: Monomers form polymers through condensations. Polymers are broken down through hydrolysis Figure 14: Condensation and Hydrolysis Reference(s): 1. Dr. A. Espiritu (2024). Lecture and Powerpoint Presentation. PREPARED BY: BATCH 2028 1D 6