Biochemisty: Review on Chemistry PDF

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Biochemistry(Lecture)Module 1 Review of General Chemistry MATTER: PURE – Element & Compound MIXTURE - Homogeneous & Heterogenous Element- contains one Compound is a bond between two or more elementHOMOGENOUS – one phase; cannot be determine HETEROGENOUS – two or more; can be determinePROTON ...

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Biochemistry(Lecture) Law of Conservation of Mass: “Matter is neither created nor destroyed” Module 1 Review of General Chemistry MATTER: • •

PURE – Element & Compound MIXTURE - Homogeneous & Heterogenous

Element- contains one Compound is a bond between two or more element HOMOGENOUS – one phase; cannot be determine HETEROGENOUS – two or more; can be determine PROTON – positively charge ELECTRON – negatively charge NEUTRON – neutral -

ATOMIC MASS = p + n ATOMIC NUMBER = p PROTON = ELECTRON

ISOTOPES = is when the number of neutrons are different from the number of protons and electrons e.g: Oxygen = 16 16 8𝑂 STOICHONOMETRY – study of the mass relationships on a given chemical reaction

1.2 Atoms What is matter made of? – Dalton’s Atomic Theory1 Postulates: • All matter is composed of very tiny particles, which Dalton called atoms. • All atoms of the same element have the same chemical properties. Atoms of different elements have different chemical properties. • Compounds are formed by the chemical combination of two or more of the same or different kinds of atoms. • Molecules are a tightly bound combination of two or more atoms that acts as a single unit.

Explanation: If matter is made up of indestructible atoms, then any chemical reaction just changes the attachments among atoms, but does not destroy the atoms themselves

What are atoms made of? Protons, Electrons and Neutrons PROTON – positively charge ELECTRON – negatively charge Carbon monoxide + Lead oxide → Carbon dioxide + Lead (mass = 28) (mass = 223) → (mass = 44) (mass = 207) Total mass = 251 → Total mass = 251 The total mass after this chemical change is the same as the mass that existed before the reaction took place NEUTRON – neutral -

ATOMIC MASS = p + n ATOMIC NUMBER = p PROTON = ELECTRON

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The element’s atomic number is equal to the number of protons and electrons.

1.3 Chemical Bonding

When the valence electrons from two or more elements come together by lowering their total energy, they form a chemical bond. Two major types of chemical bonds: ionic and covalent Ionic - a chemical bond usually formed between a metal and nonmetal; resulting from the attraction between positive and negative ions due to the differences of the electronegativities of a metal and nonmetal. Covalent - formed when electron pairs are shared between two atoms whose difference in electronegativity is less than 1.9; usually formed between two nonmetals. TYPES OF BONDS: • •

IONIC BOND COVALENT BOND = Polar & Non-polar

- Note: to know the type of bond is through electronegative difference.

>0.5 = NONPOLAR 0.5-1.9 = POLAR 1). Ka’s also have a negative logarithm, expressed as pKa.

Module 2 Review of Organic Chemistry

2.1 Hydrocarbons Carbon can form single, double and triple covalent bonds. Because carbon assumes a stable tetrahedral shape, it can form long chain of carbon single bonds without falling apart. Hydrocarbons - compounds made up of only the elements carbon (C) and hydrogen (H). They may be aliphatic or aromatic Four classes of hydrocarbons: 1. Alkanes (aliphatic) 2. Alkenes (aliphatic) 3. Alkynes (aliphatic) 4. Arenes (aromatic) Aliphatic hydrocarbons acylic hydrocarbons that may be long or short chained and may or may not contain a double bond or a triple bond. Aromatic hydrocarbons - compounds that usually contain the phenyl group or other cyclic unsaturated hydrocarbons that satisfy the criteria of aromaticity and Hückel’s Rule. Hydrocarbons - classified whether they are saturated or unsaturated. Saturated - carbon-carbon bonds are single bonds, they are termed as saturated carbons . This means that it is saturated with hydrogen. Unsaturated - When the compound contains double bonds, triple bonds, or both. - molecule has lesser hydrogens. Kekule structures (expanded structural formula) are Lewis structures that uses lines to represent the covalent bonds but still shows all atoms and lone pair electrons. In partially condensed structures, only the bonds with hydrogens are no longer presented. Unlike Kekule and partially condensed, the condensed structure no longer presents any covalent bonds but the atoms are positioned in the same way as the original carbon-carbon backbone.

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Bond-line structures (skeletal or line-angle structures) drawn in a zigzag format ( ), where each corner or endpoint represents a carbon atom. Double bonds are shown with two lines, and triple bonds are shown with three lines

Carbon normally forms 4 covalent bonds and has no unshared pairs of electrons. Nitrogen normally forms 3 covalent bonds and has 1 unshared pair of electrons. Oxygen normally forms 2 covalent bonds and has 2 unshared pairs of electrons. Hydrogen forms 1 covalent bond and has no unshared pairs of electrons. A halogen (fluorine, chlorine, bromine, and iodine) normally forms one covalent bond and has three unshared pairs of electrons. 2.2 Hybridization

Single bonds – is formed by the formation of a σ-bond (sigma bond). A σ-bond can be formed by the overlapping of orbitals in three ways: s-s orbitals, s-p orbitals and p-p orbitals. HYBRIDIZATION- phenomenon of overlapping atomic orbitals. Carbon atom - has two unpaired electron.

Double bond - composed of a σ―bond and a π―bond (pi bond). A π―bond - when the p orbitals in the same axis of two different atoms overlap such as px―px or py―py to form the π bond.

Bond-line structures or skeletal structures structural formula that shows the arrangement and bonding of carbonAn atom contains a π-bond, this atom is sp2 atoms present in an organic molecule but does not show the hydrogenhybridized since it is composed of one’s orbital and atoms attached to the carbon atoms. two p orbitals to hybridize.

When only one s and one p orbital will hybridize (to form spwith chiral centers have an optical activity. Molecules with hybridization) leaving 2 p orbitals unhybridized and availablechiral centers but are all-in-all achiral are called meso to overlap, this will create one σ-bond and two π -bonds. Whencompounds. Since these molecules are achiral, therefore meso two carbons participate in this orientation, this will give rise to compounds will not have an optical activity. We can identify these molecules by drawing a plane of symmetry. If the the triple bond molecule contains a chiral center(s) and does not have a plane Sp σ Triple bond of symmetry, the molecule is chiral Sp2 σπ Double bond Sp3 σππ Single bond 2.5 Organic Reactions Four Basic Classes of Organic Reactions: • Addition, Eliminations, Substitution 2.3 Functional groups Rearrangement Functional groups are atoms or groups of atoms of an organic molecule that undergo predictable chemical reactions. Compounds having the same functional group, in whatever organic molecule it occurs, undergoes the same types of chemical reactions.

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Addition a reaction in which atoms or groups of atoms are added to each carbon atom of a carbon –carbon multiple bond in a hydrocarbon or hydrocarbon derivative.

reochemistry

Stereochemistry - branch of chemistry concerned with the three-dimensional arrangement of atoms in molecules Stereoisomers - isomers where the bonds are in the same connection but differ in their spatial arrangement the two molecules are non-superimposable images of each other. Stereoisomers can be further classified into two groups: enantiomers and diastereomers. Enantiomers - nonsuperimposable mirror images of each other.

Elimination - reaction in which two groups or two atoms on neighboring carbon atoms are removed, or eliminated, from a molecule, leaving a multiple bond between the carbon atoms2. This reaction usually involves breaking of σ-bond and formation of a π-bond. Substitution -

chemical reaction in which part of a small reacting molecule replaces an atom or a group of atoms on a hydrocarbon or hydrocarbon derivative.

Diastereomers - nonsuperimposable mirror images of each other. Carbon is chiral when all of its four bonds are single bonds (sp3 hybridized) and no two pendant groups or atoms attached is the same. In larger molecules, this carbon is a chiral center or a stereogenic center. According to the Le Bel―Van’t Hoff Rule, the number of stereoisomers a molecule has is equal to 2 n , where n is the number of stereogenic centers. Chiral molecules rotate the plane of polarized light. This property is called optical activity. However, not all molecules

Rearrangement is broad class of organic reaction where the chemical bonds or groups rearranges forming its isomer.

INTRODUCTION TO BIOCHEMISTRY

3.1 Importance of Biochemistry

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Biochemistry is the study of chemistry of living organisms. It involves the study of the chemical processes occurring within living systems:

The Greek physician Galen (A.D. 129–199) campaigned for a pharmacological approach using plant and animal products for disease treatment.

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Paracelsus (A.D. 1493–1541) asserted that man is made out of the same material as the rest of creation.

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Chinese physicians discovered in the seventh century A.D. that night blindness could be treated with pig and sheep livers.

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Fredrich Wöhler (1800-1882) demonstrated in 1828 that urea, a compound that had only been associated with living cells, could be synthesized from an inorganic compound outside of the cell.

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1903: Neuberg defined CHEMISTRY OF LIFE

the structure, function and interactions of various biomolecules inside cells the control of information flow through biochemical signaling, and the flow of chemical energy through metabolism. It has three branches, namely: 1. Structural and Functional Biochemistry - focuses initially on discovering the chemical structures and three-dimensional arrangements of biomolecules (protein, carbohydrates, lipids, nucleic acids), those chemicals that are found in living matter 2. Informational Biochemistry - defines the language(s) for storing biological data and for transmitting that data in cells and organisms. 3. Bioenergetics - describes the flow of energy in living organisms and how it may be transferred from one process to another

The Chinese in the fourth century B.C. believed that humans contained five elements: water, fire, wood, metal, and earth.

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When all elements were present in proper balance, good health resulted. An imbalance in the elements caused illness.

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The early Greeks, including Plato (428–348 B.C.), attempted to explain the body in terms of cosmological theories and stressed diet for treatment of disease. The Greek term for digestion, pepsis, a word indicating inner heat, is the origin of the word pepsin, a digestive enzyme.

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Origins of Life •

Big Bang theory is the most widely accepted cosmological theory for the origin of the Universe

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The Universe was composed of Helium, Hydrogen and some Lithium (resulted from the original Big Bang explosion). The rest of the elements were formed from a through the series of cosmological explosions.

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Radioactive dating indicates that the Earth's age is about 4 billion to 5 billion years.

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Carbon, nitrogen, oxygen, phosphorus and sulfur, important biological elements, were formed from nuclear reaction of first-generation stars. Firstgeneration stars are the original stars produced after the formation of the Universe

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The Earth's atmosphere was different from the atmosphere we know today. It had very little free O2 and there was no ozone layer (O3). This created the conditions that lead to the production of simple biomolecules

History of Biochemistry 2 •

Biochemistry

Distinguishing Characteristics of Living Organisms

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Lipid, phospholipid, glycolipid, sterol,

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Vitamin Hormone, neurotransmitter

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Carbohydrate, sugar

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Capable of reproduction

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Capable of metabolism Capable of growth and repair

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Possess a characteristic size and shape Able to adapt

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have regulatory mechanisms

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Amino acids

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Respond to stimulus Have defined systems for extracting, transforming and using energy from the environment Have a certain degree of complexity and organization.

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Nucleotides

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Monosaccharides

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3.2 Biomolecules

Monomers:

Polymers: • • •

Peptides, oligopeptides, polypeptides, proteins Nucleic acids, i.e. DNA, RNA Oligosaccharides, polysaccharides (including cellulose)

Chemicals of Life • • •

Water- Principal component of living cells. Organic compounds- carbohydrates,fats and lipids, proteins, nucleic acids Inorganic compounds- Bulk elements (N, Na, P, S, Cl, K and Ca) and trace elements ( Fe, Mg, Mn, Zn, I, Ar, Br, Mo and V)

Biomolecules •

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Biological molecules. Refers to molecules that are present, produced and utilized by living organisms. Many biomolecules are carbon-containing molecules that have different functional groups. Categorized into 4 families: carbohydrates, lipids, proteins and nucleic acids. Most biomolecules are considered as derivatives of hydrocarbons with one or more hydrogen atoms replaced by a functional group. This enables different chemical properties, forming families of organic compounds. Biomolecules may contain two or more types of functional groups, each with its own chemical characteristics and reactions. The functional groups and their arrangement in three-dimensional space determine the "personality" of a compound.

What is special about carbon? •

Carbon is a tetravalent atom

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Carbon can form single, double, and triple bonds Carbon atoms are able to bond together to form long chains and rings.

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3.3 Water

Water is the solvent for life. It is found inside and outside of cells of the body. The body is about 60% water; water found inside cells comprises the intracellular fluid and that found outside cells comprises the extracellular fluid. The average human body is composed of 60% water, 17% protein, 15% fat and 3% nitrogen. Functions of water: • •

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• Small molecules:

Principal fluid medium in which nutrients, gases, and enzymes are dissolved Extracellular water bathes the cells, serving as medium for transport of nutrients and oxygen to the cells and removing wastes from the cells Intracellular water is the physicochemical medium that allows various metabolic processes to take place Intracellular fluid volume provides form to tissues and organs and ultimately to the body

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Regulation of body temperature

3.4 Acids, Bases, pH and Buffer Importance of pH in living cells: In animals, for example, the maintenance of blood pH (7.35 < pH < 7.45) is crucial for life. Slightly acidic pH (6.95) →coma and death. Slightly basic pH (7.7) → convulsions and muscle spasms.

Chemistry of water :

Water has a boiling point of 100 °C, a freezing point of 0 °C, has maximum density at 4 °C, high specific heat, high heat of vaporization and fusion, and high dipole moment. The presence of dipole moment and its polarity account for the ability of water to form hydrogen bonds making it a good solvent for polar organic molecules in the body such as proteins and carbohydrates which are hydrophilic or water-loving molecules, but not fats or lipids which are hydrophobic or water-fearing molecules and cause hydrophobic aggregation . Water is the Universal Solvent : • •

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H-bonding – bond between H and an electronegative atom such as O or N Ion-dipole - bond between an ion and a molecule with an electric dipole moment such as H2O Dipole-dipole - bond between 2 molecules with electric dipole moments such as H2O and an amide or amine functional group

This implies that... • •

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A solvent is good at dissolving a substance (solute) in solution. Water is polar, so it can dissolve ions and other polar organic molecules such as proteins and carbohydrates which are hydrophilic (water-loving). Like dissolves like. Water is a poor solvent for non-polar molecules which are hydrophobic (waterfearing) such as fats and oils resulting in Hydrophobic aggregation.

Maintaining the pH of cells and tissues is important for maintaining body homeostasis or equilibrium. Blood pH is maintained at 7.35 < pH < 7.45. A slightly acidic pH < 6.95 can lead to coma and death from acidosis, and a slightly basic pH > 7.70 can cause convulsions and muscle spasms from alkalosis. How does the body maintain pH ? Buffers present in physiologic fluids maintain the body’s pH. A Buffer solution is a solution that contains a weak acid or base that is capable of resisting or minimizing the change in pH upon the addition of a strong acid or base. Buffer solutions can be prepared in the laboratory by mixing a weak acid and its conjugate base or a weak base and its conjugate acid. In the video shown in lesson 2.2, buffer systems of the human body were briefly introduced. Blood contains the carbonic acid-bicarbonate buffer system and physiologic fluids in cells contain the phosphate buffer system. The Henderson-Hasselbach equation is helpful in calculating the proportions of weak acid and its conjugate base or weak base and its conjugate acid needed to prepare the buffer. The buffering range for a buffer solution is defined as the pH + 1. This the range in which the capacity of the buffer to resist drastic changes in pH is maximal.

Buffer capacity is affected by • • • •

[salt/acid] ratio Concentration of acid and conjugate base component inflection point is where pH=pKa Equivalence point is the point in the titration where complete deprotonation occurs. This happens when the added amount of titrant (standard solution) is equal to the total

number of ionizable protons of the titrand (analyte, unknown solution). The equivalence point is used to calculate the concentration of the titrand.

Phosphate Buffer System •

Intracellular

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H2PO4- + OH ⇌ HPO42- + H3O+ involves dihydrogen phosphate H2PO4(proton donor) and hydrogen phoshphate HPO42- ( proton acceptor) When there is excess OH- in the cell, it is neutralized by the dihydrogen phosphate, shifting the equilibrium to the right

3.5 Buffer Systems in the Body Major Buffering Systems in the Body •

Carbonic Acid-Bicarbonate Buffer System

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Extracellular CO2 + H2O ⇌ H2CO3 ⇌ H+ + HCO3

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If there are too many H3O+ ions in the blood, the H3O+ binds with the HCO3 to form carbonic acid. This carbonic acid will be dissociated into water and CO2, and will be released out by the lungs If there are too few H3O+ ions in the blood, the carbonic acid will react to form H3O+ and HCO3

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During hyperventilation, CO2 is rapidly excreted in the body, causing the equilibrium to shift to the left, therefore, pH increases During hypoventilation, CO2 builds up in the body causing the equilibrium to the right, consequently decreasing the pH.

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When there is excess H3O+ in the cell, it is neutralized by the hydrogen phosphate, shifting the equilibrium to the left

Protein Buffer Nearly all proteins can...