Biochemistry 1 PDF

A. Biochemistry is chemistry of - Resonance structure of peptide bonds life processes Life on Earth is based on Carbon (± 18.5 % of the mass of a human is carbon) The 6 most important chemical elements th...

A. Biochemistry is chemistry of - Resonance structure of peptide bonds life processes Life on Earth is based on Carbon (± 18.5 % of the mass of a human is carbon) The 6 most important chemical elements that make up the biological compounds by covalent bonding C, H, O, N, P, S Covalent bonds (involves the sharing of electron pairs Noncovalent interactions between atoms, 1)Ionic Interactions the strongest of bonds) A charged group on one molecule can attract an oppositely charged group on the same or another molecule. 2)Hydrogen Bonds These interactions are largely ionic interactions between partially positively charged hydrogen and partially negatively charged acceptor atoms. Electronegativity is a chemical property that describes how strongly an atom attracts electrons towards itself. O>N>S>C>P>H The 180-degree angle in hydrogen bonding arises from the linear or nearly linear arrangement of atoms. This configuration minimizes electron pair repulsion, optimizes the interaction between the partially positively charged hydrogen atom and the electronegative resonance structures atom, and contributes to the overall stability of the hydrogen bond. While not an absolute rule, the tendency for this linear geometry enhances the strength of hydrogen bonds. 3)van der Waals Interactions Double bond gives rise to resonance structures. Van der Waals interactions are weak, attractive Not static bonds forces between molecules due to temporary fluctuations in electron distribution, creating Molecules in aqueous solution interact with temporary dipoles. water molecules through the formation of hydrogen bonds and through ionic interactions. A dipole refers to a molecule or a part of a These interactions make water a versatile molecule that has a separation of charge, resulting in a positive pole and a negative pole. solvent, able to readily dissolve many species, This charge separation occurs when there is an especially polar and charged compounds that uneven distribution of electrons within the can participate in these interactions. molecule, leading to regions with a net positive Water can dissociate into a proton and charge and regions with a net negative charge. hydroxide, forming equilibrium. 4)Hydrophobic interactions Interactions between nonpolar compounds Neutral pH 7 through the hydrophobic effect. The interactions of nonpolar molecules with water molecules are not as favorable as are interactions between the water molecules themselves. The water molecules in contact Note; pH is determined by H+. Adding H+ strong with these nonpolar molecules form “cages” acid inc H+ conc and lowers pH, while adding around them, becoming more well-ordered strong base reduces H+ and raising pH. than water molecules free in solution. C. Acid - Base Acids PROTON DONORS dissociate into protons and conjugate bases Order from strongest to weakest; covalent>ionic>hydrogen>VDV>hydrophobic B. WATER (H2O) Water is highly cohesive Water molecules interact strongly with one another through hydrogen bonds. The polar nature of water is responsible for its - Henderson hasselbach eqn high dielectric constant D of 80. Explanation; -if pH equals pKa it means it means that the concentration of the acid and its conjugate base are equal in the solution. -If pH is bigger than pKa it means the concentration of acid is more than conjugate base. -The titration curve occurs to determine the -If pH is smaller than pKa it means the conc of subs in solution and to determine unknown concentration. concentration of conj base is more than acid. - An acid with more then 1 dissociable H+ ex1; H3PO4->phosphoric acid Bases PROTON ACCEPTORS associate with protons to become their conjugate acids Weak Acid acts as buffer at pH around pKa -Buffer; helps maintain stable pH -Weak acids and weak bases can form buffer systems due to Dissociation is partial so it allows dynamic equilibrium which means it shifts back and forth and this causes control of ph better due to it does not have too much hydrogen ions - An acid with more then 1 dissociable or hydroxide ions to give away in the solution. H+ ex2; C2H5NO2->glycine -Strong acids and bases form poor buffers  Qn; what happens to bicarbonate concentration during ventilation? Rate of removal of carbon dioxide is increased. This causes alkalosis that causes decrease in acidity. When there is high acidity(equation shift left to right) you either breathe co2 out or hyperventilate to release bicarbonate from kidneys. D. AMINO ACID Peptide bond formation - An acid with more then 1 dissociable H+ ex3; H2CO3 Hydrophobic Amino Acids Qn; Why is human blood basic if it contains a buffer of carbonic acid (H2CO3) and bicarbonate anion (HCO3-) in order to maintain blood pH between 7.35 and 7.45? The human body regulates pH with buffers and Polar Amino Acids keeps it within the range of 7.2 – 7.5 For example: The carbonic acid – bicarbonate buffer in the blood keeps pH around 7.4 pKa (carbonic acid) = 6.1 Qn; quilibrium of bicarbonate  isomers that differ in spatial arrangement of atoms, rather than order of atomic connectivity In organic chemistry, the Le Bel–Van 't Hoff rule states that the number of stereoisomers of an organic compound containing no internal n planes of symmetry is 2 , where n represents the number of asymmetric carbon atoms. Living systems have ordered matter Involving numerous reversible interactions Positively Charged Amino Acids Entropy is a measure of disorder in a system, like the randomness of molecules. Enthalpy is the total heat content in a process, considering heat absorbed or released. The second law of thermodynamics states that natural processes tend to increase overall disorder or entropy. F. PROTEIN Protein Composition and Structure Negatively Charged Amino Acids Amino Acid structure primary- peptide b Secondary- hydrogen b, peptide b Tertiary- h bonds, disulfide b Quaternary - same as tertiary E. STEREOISOMERS - Myoglobin; The tertiary structure -Myoglobin is an example of a highly compact, globular, mainly helical protein with a heme prosthetic group. It supplies oxygen to cells in the muscle. Remember whale ex - Quaternary structure; haemoglobin Hemoglobin consists of four chains: two identical α chains and two identical β chains. FIGURE 7.6 Quaternary structure of deoxyhemoglobin. Hemoglobin, which is composed of two α chains and two β chains, functions as a pair of αβ dimers. (A) A ribbon diagram. (B) A space-filling model. [Drawn from 1A3N.pdb.]