Biochemistry Module 0 - Introduction to Biochemistry (2024-2025) PDF

BIOCHEMISTRY: MODULE 0 - INTRODUCTION TO BIOCHEMISTRY Gallardo, Joannah Phoebe A. UERM BSN 2024-2025 MODULE 0.1: INTERMOLECULAR FORCES OF ATTRACTION Reference: Chemistry by Brown and LeMay STATES OF MATTER ...

BIOCHEMISTRY: MODULE 0 - INTRODUCTION TO BIOCHEMISTRY Gallardo, Joannah Phoebe A. UERM BSN 2024-2025 MODULE 0.1: INTERMOLECULAR FORCES OF ATTRACTION Reference: Chemistry by Brown and LeMay STATES OF MATTER  The fundamental difference between states of matter is the strength of the intermolecular forces of attraction. Stronger forces bring molecules closer together. Solids and liquids are referred to as the condensed phases. DIFFERENCES IN THE STATES OF MATTER A. Gas a. Assumes both volume and shape of its container b. Expand to fill its container c. Is compressible d. Flows readily e. Diffusion within a as occurs rapidly B. Liquid a. Assumes shape of portion of container it occupies b. Does not expand to fill its container  c. Is virtually incompressible d. Flows readily e. Diffusion within a liquid occurs slowly C. Solid a. Retains its own shape and volume. b. Does not expand to fill its container c. Is virtually incompressible d. Does not flow e. Diffusion within a solid occurs extremely slowly The atoms in a solid are able to vibrate in place. As the temperature of the solid increases, the vibrational motion increases. WHICH STATE OF MATTER? The answer to this question largely relies on the ○ Balance between the kinetic energies of the particles. ○ Interparticle energies of attraction. Comparing Kinetic Energies and Energies of Attraction of States of Matter Gas Kinetic energies >>> energies of attraction Liquid Comparable kinetic energies and energies of attraction  Solid Energies of attraction >> kinetic energies INTERMOLECULAR FORCES The attraction between molecules are not nearly as strong as the intramolecular attractions (bonds) that hold compounds together. Many physical properties reflect intermolecular forces, like boiling points, melting points, viscosity, surface tension, and capillary action. TYPES OF INTERMOLECULAR FORCE Weakest to strongest forces: ○ Dispersion forces ○ Dipole-dipole forces ○ Hydrogen bonding(a simple dipole-dipole force) ○ Ion-dipole forces Note: First two are also referred collectively as van der Waals forces.  DISPERSION FORCES The figure below shows how a nonpolar particle (in this case a helium atom) can be temporarily polarized to allow dispersion force to form. The tendency of an electron cloud to distort is called its polarizability. FACTORS WHICH AFFECT AMOUNT OF DISPERSION FORCE IN A MOLECULE Number of electrons in an atom (more electrons, more dispersion force) Size of atom or molecule/molecular weight Shape of molecules with similar masses (more compact, less dispersion force)’  POLARIZABILITY & BOILING POINT If something is easier to polarize, it has a lower boiling point. Remember: This means less intermolecular force (smaller molecule: lower molecular weight, fewer electrons)  DIPOLE-DIPOLE INTERACTIONS Polar molecules have a more positive and a more negative end-a dipole (two poles δ+ and δ−). The oppositely charged ends attract each other. WHICH HAVE A GREATER EFFECT: DIPOLE-DIPOLE INTERACTIONS OR DISPERSION FORCES? If two molecules are of comparable size and shape, dipole-dipole interactions will likely be the dominating force. If one molecule is much larger than another, dispersion forces will likely determine its physical properties. HYDROGEN BONDING The dipole-dipole interactions experienced when H is bonded to N, O, or F are unusually strong. We call these interactions “hydrogen bonds” A hydrogen bond is an attraction between a hydrogen atom attached to a highly electronegative atom and a nearby small electronegative atom in another molecule or chemical group.  WHAT FORMS HYDROGEN BONDS? Hydrogen bonding arises in part from the high electronegativity of nitrogen, oxygen, and fluorine. These atoms interact with a nearly bare nucleus (which contains one proton). ION-DIPOLE INTERACTIONS Ion-dipole interactions are found in solutions of ions.  The strength of these forces is what makes it possible for ionic substances to dissolve in polar solvents SUMMARIZING INTERMOLECULAR FORCES MODULE 0.2: INTRODUCTION TO AMINO ACID Engr. A Cadiz MSc  WHAT IS AMINO ACID? Building blocks of protein. Acts as precursors - many biologically important molecules are derivative of amino acids. ○ Example: Tyrosine (Y) is the precursor of the hormone thyroxine and the skin pigment melanin. Acts as source of Sulfur - derived from the sulfur containing amino acids. ○ Example: Cysteine ( C ) and Methionine (M) Involved in many metabolic pathways such as in Gluconeogenesis where it is involved in glucose synthesis. The amino acids commonly dealt with are a - amino acids (a carboxyl group and an amine group attached to the a - carbon). FUNCTION OF AMINO ACIDS  For synthesis of proteins the body needs. Precursor of nitrogen containing compounds like N-Bases of nucleic acids (purines/pyrimidines), porphyrins (heme, chlorophyll), folic acid (glutamic), creatine (gly, arg, met), glutathione (glu, cys, gly) Some amino acids and their derivatives function as chemical messengers/neurotransmitters. For glucose synthesis. Function as buffer For detoxification reactions (gly, cys met) ANATOMY OF AMINO ACIDS The name amino acid suggests that these structures have an amine and acid group (amino acid and carboxylic acid group). Since the central carbon has four (4) different groups attached to it, it is a chiral carbon. ○ Because of the tetrahedral arrangement of the bonding orbital around the a-carbon atom, the four different groups can occupy two unique spatial arrangements and thus amino acids have two possible isomers.  Amino acid - an organic compound that contains both an amino (-NH2) and carboxyl (-COOH) groups attached to the same carbon atom. ○ The position of carbon atom is Alpha (a) ○ -NH2 group is attached to the alpha (a) carbon atom. ○ -COOH group is attached to the alpha (a) carbon atom. R = side chain –vary in size, shape, charge, acidity, functional groups present, hydrogen-bonding ability, and chemical reactivity. ○ >700 amino acids are known ○ Based on common “R” groups, there are 20 standard amino acids.  Amino acids have two (2) possible isomers; ○ L and D isomers Nearly all amino acids in biochemistry are of the L-form (L for life); the opposite of sugars, which nearly always occur as the D-isomer. The L-designation has nothing to do with the way they rotate polarized light but is purely structural. This is based on the structure of L-glyceraldehyde. By Fischer’s convention, L and D refer only to the absolute configuration of the four substituents around the chiral carbon, not to optical properties of the molecule. The non - ionic form does not occur in significant amounts in aqueous solutions. The zwitterionic form predominates at normal pH (pH = 7.4). ○ At this pH, the non - ionic form has lost its proton (hydrogen iron) and has a negative charge with the electrons of the double bond shared across the two O atoms. ○ Also attached to the a-carbon is an amine group at pH = 7.4 has an extra proton and so carries a positive charge. ○ These two charges cancel each other out and hence the net charge is  dependent upon the charge carried on their R-group. The amino acids residues in protein molecules are exclusively L - isomers. Cells are able to specifically synthesize the L - isomers of amino acids because the active sites of enzymes are asymmetric, causing the reactions they catalyze to be stereospecific. All of the common amino acids are a-amino. The common amino acids of proteins have been assigned three-letter abbreviations and one-letter symbols, which are used as shorthand to indicate the composition and sequence of amino acids polymerized in proteins.  They have a carboxyl group and an amino group bonded to the same carbon atom (the a-carbon) They differ from each other in their side chains, or R groups, which vary in structure, size, and electric charge, and which influence the solubility of the amino acids in water. In addition to these 20 amino acids there are many less common ones. Some are residues modified after a protein has been synthesized; others are amino acids present in living organism but not as constituents of proteins TABLE OF ABBREVIATIONS OF THE 20 AMINO ACIDS FOUND IN PROTEINS NON POLAR, ALIPHATIC R GROUPS AROMATIC R GROUPS POSITIVELY CHARGED R GROUPS POLAR, UNCHARGED R GROUPS NEGATIVELY CHARGED R GROUPS UNCOMMON AMINO ACIDS AMINO ACID DERIVATIVES NOT FOUND IN PROTEINS BIOLOGICALLY ACTIVE AMINO ACID DERIVATIVES  IMPORTANT FUNCTIONS OF UNCOMMON AMINO ACIDS 4 - hydroxyproline ○ A derivative of Proline, found in plant in cell wall proteins 5 - hydroxylysine ○ Found in collagen, a fibrous protein in connective tissues. 6 - N - methyllysine ○ Is a constituent of myosin, a contractile protein of muscles. 7 - carboxyglutamate ○ Found in the blood clotting protein, prothrombin and in certain other proteins that bind Ca2+ as a part of their biological function. Desmosine ○ A derivative of four (4) Lys residues, which is found in the fibrous protein elastin. Selenocysteine ○ A special case. This rare amino acid residue is introduced during protein synthesis rather than created through a post-synthetic modification. ○ It contains selenium rather than the sulfur of cysteine  ○ Derived from serine, selenocysteine is a constituent of just a few known proteins. Ornithine and Citrulline ○ Deserve special note because they are key intermediates (metabolites) in the biosynthesis of arginine and in the urea cycle. GENERAL PROPERTIES OF a-AMINO ACIDS Optical Activity ○ All amino acids show optical activity except for glycine, the rest of the amino acids contain at least one asymmetrical carbon atom (chiral carbon). Dextrorotatory (+) isomer which has the ability to rotate the plane of polarized light to the right. Levorotatory (-) isomer which has the ability to rotate the plane of polarized light to the left. Therefore, both isomers can rotate the plane of polarized light by the same magnitude but in opposite directions. Acid-Base Properties of Amino Acids ○ When an amino acid is dissolved in water it exists in solution as a dipolar ion or zwitterion (German for “hybrid ion”). Zwitterion can act as an acid (proton donor). Zwitterion can act as a base (proton acceptor) ○ Substances having this dual nature are amphoteric and are often called ampholytes (from “amphoteric electrolytes”) depending on the pH of their media.  CHARACTERISTIC TITRATION CURVES OF AMINO ACIDS Acid-base titration involves the gradual addition or removal of protons. Amino acids vary in their acid-base properties and have characteristic titration curves. The plot has two distinct stages, corresponding to deprotonation of two different groups on glycine. Each of the two stages resembles in shape the titration curve of mono-protic acid, such as acetic acid. At the midpoint of any titration, a point of infection is reached where the pH is equal to the pKa of the protonated group being titrated. pH and pKa are simply convenient notations for proton concentration and the  equilibrium constant for ionization, respectively. The pKa is a measure of the tendency of a group to give up a proton, with that tendency decreasing tenfold as the pKa increases by one unit. The characteristic pH at which the net electric charge is zero is called the isoelectric point or isoelectric pH, designated pI. COMPARISON OF THE TITRATION CURVES OF THREE (3) WEAK ACIDS  MODULE 0.3: AMINO ACIDS, PEPTIDES, AND PROTEINS CLASSIFICATION OF AMINO ACIDS FUNDAMENTALS While their name implies that amino acids are compounds that contain an an —NH2 group and a —CO2H group, these group are actually present as —NH3 and —CO2- respectively They are classified as α, β, γ etc. amino acids according to the carbon that bears the nitrogen. AMINO ACIDS An α-amino acid that is an intermediate in the biosynthesis of ethylene. A β-amino acid that is one of the structural units present in coenzyme A. a γ-amino acid involved in the transmission of nerve impulses. THE 20 KEY AMINO ACIDS More than 700 amino acids occur naturally, but 20 of them are especially important. These 20 amino acids are the building blocks of proteins. All are α-amino acids. They differ in respect to the group attached to the α carbon. TABLE 27.1 The amino acids obtained by hydrolysis of proteins differ in respect to R (the side chain). The properties of the amino acid vary as the structure of R varies. GLYCINE (GLY OR G) Glycine is the simplest amino acid. It is the only one in the table that is achiral. In all of the other amino acids in the table, the α carbon is a stereogenic center.  ALANINE (Ala or A) VALINE (Val or V) LEUCINE (Leu or L) ISOLEUCINE (Ile or I) METHIONINE (Met or M) PROLINE (Pro or P) PHENYLALANINE (Phe or F) TRYPTOPHAN (Trp or W) ASPARAGINE (Asn or N) GLUTAMINE (Gln or Q) SERINE (Ser or S) THREONINE (Thr or T) TO BE FOLLOWED…  27. 2 STEREOCHEMISTRY OF AMINO ACIDS CONFIGURATION OF α-AMINO ACIDS Glycine is achiral. All of the other amino acids in proteins have the L-configuration at their α carbon. 27.7 PEPTIDES Peptides are compounds in which an amide bond links the amino group of one α-amino acid and the carboxyl group of another. An amide bond of this type is often referred to as a peptide bond. TO BE FOLLOWED…