Biological Foundation 1st Term 1st Year PDF

BIOLOGICAL FOUNDATION CM38 1ST TERM | 1ST YEAR | PROF. CHAN properties of water INTRODUCTION TO CHEMISTRY...

BIOLOGICAL FOUNDATION CM38 1ST TERM | 1ST YEAR | PROF. CHAN properties of water INTRODUCTION TO CHEMISTRY 1. Liquid at normal temperature 2. high boiling point and melting point 3. high heats of fusion and vaporization WATER 4. high heat capacity ○ Molecules are polar molecules which also create 5. surface tension (ex. Diving into the water) hydrogen bonds between water molecules. ○ Water - can interact with other molecules with acids and bases an opposite charge. - acids: proton donor ○ Polar - it is a molecule which has both negative - base: proton acceptor and positive charges. - strong: acids and bases Explanation: molecules will always have a - Weak acids and bases: conjugates target in them, may be neutral or positive or negative charge. Buffers In the case of water it is called - partial, - solution of weak acid (HA) and conjugate base positive and partial negative charges. (A-) ○ covalent bond 0.0965 nm - Resist a large change in pH of a solution ○ hydrogen bond 0.177 nm - the acids “absorbs” base ○ distance the water and oxygen in molecules - The base “absorbs” acid 104.5 buffer capacity hydrogen bonding in water - Molar concentration of acid and base ○ constant breakage and formation of hydrogen - Ratio of acid and base bonds in water - Effective when pH = -+1 unit of pKa ○ water: 2.3 H-bonds ; no oxygen 0 to 100 c ○ Ice: 4 H-bonds ; spaces is the oxygen -273 TO 0 c Henderson-hasselbach equation - equation for determining several aspects of any given buffers Non-covalent interaction − [𝐴 ] 1. Ionic bonds - (+) and (-) molecules 𝑝𝐻 = 𝑝𝐾𝑎 + 𝑙𝑜𝑔 [𝐻𝐴] 2. electrostatic interaction - (+)and (-) ions a. Hydration of Ions in Solution Biological buffers - bicarbonate blood Non-covalent bonding − + 𝐻𝐶𝑂3 + 𝐻 ⇔ 𝐻2𝐶𝑂3 ⇔ 𝐶𝑂2 + 𝐻2𝑂 1. Hydrogen bonds - water, amines, alcohol , carboxylic acids pKa = 6.37, pH of blood = ∼7.4 2. van der Waals forces - unequal distribution of blood pH controlled by respiration and kidneys electrons 3. hydrophobic interactions - occurs only in biological buffers aqueous environment and tendency for - phosphate: intracellular 2− + hydrophobic molecules to coalesce. 𝐻𝑃𝑂4 + 𝐻 ⇔ 𝐻2𝑃𝑂4 − pKa = 7.2 Water: the universal solvent Important for phosphorylation 1. Ionic compounds Proteins: both intracellular and blood (hemoglobin) 2. polar compounds 3. amphipathic molecules Control of Blood pH a. micelles (ex. Waterproof make up the - Lungs and kidneys water based) - Lung excrete carbon dioxide - kidney s excrete H+ by two major routes CM38 BIOLOGICAL FOUNDATION l AUGUST TO NOVEMBER 1 ZALAMEDA  BIOLOGICAL FOUNDATION CM38 1ST TERM | 1ST YEAR | PROF. CHAN 1. Ammonia Matter can also undergo other change called physical 2. Phosphate change. Involved the change of state of matter without - Most bicarbonate is reabsorbed changing the identity of the substance. Ex. evaporation of water PH conditions - pH < 7.35 acidosis the scientific method - systematic way of investigating a - pH > 7.45 alkalosis problem - fact is a statement based on direct experience Respiratory acidosis - Hypothesis is a statement that is proposed - depression of respiratory rate without actual proof, to explain the facts and - increases CO2 in blood their relationship - increases bicarbonate retention in kidney - Theory is the formulation of an apparent - lowers pH relationship among certain observed - hyperventilation phenomena. - lowers CO2 in blood THE SCIENTIFIC METHOD - Lowers protons for kidney excretion 1. Introduction - objectives, scope and limitations - Lowers reabsorption of bicarbonate and sodium etc. - Increases pH 2. method metabolic acidosis 3. result and discussion - something causes the lowering of plasma bicarbonate 4. conclusion - increased metabolism acids (e.g. lactic acid - during Scientific notation: intense workout) −2 −3 1. 𝑎𝑑𝑑 1. 95 × 10 𝑎𝑛𝑑 2. 8 × 10 - increased ketone bodies 5 9 2. 𝑚𝑢𝑙𝑡𝑖𝑝𝑙𝑦 7. 40 × 10 𝑎𝑛𝑑 3. 12 × 10 - loss of bicarbonate (diarrhea) −4 7 - kidney failure resulting to low proton excretion 3. 𝑑𝑖𝑣𝑖𝑑𝑒 1. 63 × 10 𝑎𝑛𝑑 7. 94 × 10 metabolic alkalosis - something causes the increase in plasma Measurement - constantly making measurement on a daily bicarbonate basis - often a result of excessive vomiting measurement consist of 2 parts: number and unit - excessive excretion of protons Units 1. Length - meter MATTER, ENERGY AND MEASUREMENTS 2. volume - liter - Universe is composed of matter, energy and 3. mass - gram empty space. 4. time - seconds or hours 5. temperature - celsius matter - is anything that has mass and occupies space common metric prefixes chemistry - is the science that deals with matter, structure 1. Giga - 10^9 and properties of matter and the transformation for one 2. mega - 10^6 form of matter to another. 3. kilo - 10^3 4. deci - 10^-1 energy can also be used to change from one form of 5. centi - 10^-2 matter to another. This is called chemical change or 6. milli - 10^-3 reaction 7. micro - 10^-6 ex. Burning of hydrocarbons 8. Nano - 10^-9 9. Pico - 10^-12 CM38 BIOLOGICAL FOUNDATION l AUGUST TO NOVEMBER 2 ZALAMEDA  BIOLOGICAL FOUNDATION CM38 1ST TERM | 1ST YEAR | PROF. CHAN Unit conversion 1. A physician recommends adding 100. Mg of Elements - is a pure substance that cannot be broken morphine to 500. cc/h to alleviate a patient’s down into simpler substances by a chemical reaction pain. Determine how many grams per second the patient is receiving. Each element is identified by a one-or two-letter symbol Element - are arranged in the periodic table states of matter - can exist in three states: solid, liquid and Position of an element in the periodic table tells us much gas about the its chemical properties gasses - have no definite shape or volume liquids - are only slightly compressible Classifying matter solids - have definite shape and definite volumes 1. Elements: symbol - they are arranged in that specific order because of their chemical Density - any substance is defined as its mass per unit properties. volume a. Bromine Br ex. If 73.2 mL of a liquid has a mass of 61.5g, what is the b. Calcium Ca density in g/mL? c. Carbon C d. Chlorine CI Specific gravity - numerically the same as density but has e. Chromium Cr no units, the reason is that SG is defined as a comparison f. Cobalt Co of the density of a substance to the density of water. g. Copper Cu Ex. the density of ethanol at 20c is 0.789. What is the h. Fluorine F specific gravity of ethanol? i. Hydrogen H j. Iodine I k. Lead Pb l. Magnesium Mg m. Manganese Mn ANATOMY OF AN ATOM LECTURE 1.2 n. Nitrogen N o. Oxygen O Classifying matter p. Phosphorus P Matter can be divided into two classes: q. Potassium 1. Pure substances - these are matter that r. Sodium Na subdivided into your element and your s. Sulfur S compounds. t. Zinc Zn 2. Mixtures - can also be subdivided into homogenous and heterogenous mixture Elements - periodic table are divided into three groups 1. Metals Class is then subdivided into: 2. nonmetals 1. Elements and compounds for pure substances 3. Metalloids 2. Homogenous and heterogenous mixtures a. Homo - mixture in which the Metal - are located on the left side of the periodic table compounds mix with each other and - They are good conductors of heat and electricity its composition is uniform throughout - Metals are shiny solids at room temperature, the solution except for mercury Hg which is a liquid b. Hetero - mixture in which the composition it not uniform throughout and different compounds are observed CM38 BIOLOGICAL FOUNDATION l AUGUST TO NOVEMBER 3 ZALAMEDA  BIOLOGICAL FOUNDATION CM38 1ST TERM | 1ST YEAR | PROF. CHAN Nonmetal - are located on the right side of the periodic Smallest stable - form of matter in the universe table Atoms - are composed of three subatomic particles - Nonmetals have a dull appearance 1. Proton (+) - positive charge - They are usually poor conductors of heat and 2. Neutrons neutral electricity 3. Electrons (-) negative charge - Nonmetal can be solids, liquid or gasses at room temperature - Solid example: sulfur carbon - Liquid example: bromine - Gas example: nitrogen oxygen Metalloids - are located on the solid line that start at boron B and angles down towards astatine At - They have properties intermediate between metals and nonmetals - Only seven elements are metalloids: 1. Boron b 2. Silicon Si ATOMIC MASS UNITS 3. Germanium Ge 4. Arsenic As - The atomic mass unit (amu) is defined to be −27 5. Antimony Sb 1. 66 × 10 𝑘𝑔 6. Tellurium Te - The amu is also 1/12𝑡ℎ the mass of a carbon 12 7. Astatine At atom - The amu is also called a dalton Da and is used to Compound: pure substance formed by chemically report the mass of molecules and compounds combining two or more elements together Protons - found in the nucleus of the atom Chemical formula consists of: - Have a mass of 1.00728 amu and a positive 1. Element symbols to show the identity of the charge elements forming a compounds - The number of protons also defines what the 2. Subscripts to show the ratio of atoms in the elements is compounds 1. Helium He atoms have 2 protons 2. Hydrogen H atoms have 1 proton 3. Iron Fe atoms have 26 proton Neutrons - found in the nucleus of the atom and help prevent protons from clustering together - Have a mass of 1.000867 amu but no charge - The number of neutrons in an element can vary - Element with the same number of protons but different neutron are known as isotopes Electrons - negatively charged particles with a mass of −4 1/2000th that of a proton (∼ 5. 486 × 10 𝑎𝑚𝑢) CM38 BIOLOGICAL FOUNDATION l AUGUST TO NOVEMBER 4 ZALAMEDA  BIOLOGICAL FOUNDATION CM38 1ST TERM | 1ST YEAR | PROF. CHAN - Reside outside the nucleus - Location outside of the nucleus is dependent on - Atomic number Z is the number of protons in the number of electrons present the nucleus - Impossible to know the speed of an electron simultaneously Subatomic particle summary - Proton and electrons are the only particles that - Every atom of a given elements has the same a have charge (1+) mass of 1.0073 number of protons in the nucleus - Protons and neutrons have essentially the same - Different elements have different atomic mass none (neutral) mass of 1.0087 numbers - The mass of an electrons is negligible so we - A neutral atom has no net overall charge ignore it. Negative (1-) mass of 5.486 x 10^-4 Z = NUMBER OF PROTONS = NUMBER OF ELECTRONS Isotopes - are atoms of the same element that STRUCTURE OF THE ATOM have a different number of neutrons Mass number (A) = the number of proton z (+) the number of neutrons Mass number (A) Atomic number (Z) - # of protons = 17 - # of electrons = 17 - # of neutrons = 35 - 17 = 18 35 - 𝐶𝑙 17 Nucleus - location of proton and neutrons isotopes - superscript represent the total mass of the - Dense core of the atom element - Location of most of the atom’s mass 1. 13^C is an isotope of carbon read as carbon-13 2. 12^C is an isotope of carbon read as carbon-12 Electron cloud - the number 12 and 13 represent the total mass - Location of electrons of the atom - Comprises most of the atom’s volume - the number of proton is factored into the mass - Mostly empty space - the number of neutrons can be calculated by subtracting the total mass from the number of Opposite charges attract while like charges repel each protons other 1. 13^C has 7 neutrons = 13 - 6 = 7 Protons and electrons attract each other but two electrons 2. 12^C has 6 neutrons = 12 - 6 = 6 repel each other atomic weight - is the weighted average of the masses of the naturally occurring isotopes of a particular element reported in atomic mass units. from the periodic table: From the periodic table 1. 6 = atomic number CM38 BIOLOGICAL FOUNDATION l AUGUST TO NOVEMBER 5 ZALAMEDA  BIOLOGICAL FOUNDATION CM38 1ST TERM | 1ST YEAR | PROF. CHAN 2. C = element symbol 1. Law of conservation of mass - state that matter 3. 12.01 = atomic weight (amu) can neither be created nor destroyed, no detectable change in mass in an ordinary how to determine the atomic weight of an element chemical reaction. example: what is the atomic weight of chlorine? 2. Law of constant composition - states that any compound is always made up of elements in the Step = list each isotope it mass in atomic mass units same proportion by mass. and its abundance in nature. - isotope = Cl-35 Cl-37 - mass [amu] = 34.97 & 36.97 - isotopic abundance = 75.78% - 0.7578 / 24.22 - 0.2422 Step = multiple the isotopic abundance by the mass of RUTHERFORD GOLD FOIL EXPERIMENT each isotope and add up the products - the sum is the atomic weight of the element 34.97 x 0.7578 = 26.5003 amu 36.97 x 0.2422 = 8.9541 amu ———————————————— 4 sig. figs 35.4544 amu 35.45 amu [answer] POSTULATES OF DALTON’S ATOMIC THEORY 1. All matter is made up of very tiny, indivisible particles which dalton called atoms 2. All atoms of a given element have the same chemical properties. Conversely, atoms of different elements have different chemical properties - A piece of gold foil was hit with alpha particles 3. In ordinary chemical reaction - no atom of any which have a positive charge most alpha particle element disappears or is changed into an atom went right through. This showed that the gold of another element atoms were mostly empty space. 4. Compounds are formed by the chemical combination of two or more different kinds of atoms, in given compound the relative numbers of atoms of each kind of element are constant DETERMINING THE STRUCTURE OF ATOM and are most commonly expressed as integers 5. A molecule is a tightly bound combination of Electrons - were discovered by J.J Thomson two or more atoms that act as single unit. (1897) Charged - determined by Robert Milikan (1909) Proton - were discovered by Rutherford (1919) EVIDENCE FOR DALTON’S ATOMIC THEORY who earlier determined that atoms have a nucleus. Neutrons - were discovered by Chadwick (1932) CM38 BIOLOGICAL FOUNDATION l AUGUST TO NOVEMBER 6 ZALAMEDA  BIOLOGICAL FOUNDATION CM38 1ST TERM | 1ST YEAR | PROF. CHAN 6A CHALCOGENS O,S,Se,Te,Po THE NUCLEAR ATOM 7A HALOGENS F,CI,Br, I, At 8A NOBLE GASSES (or rare gasses) He,Ne,Ar,Kr,Xe,Rn PROPERTIES Rutherford postulated a very small, dense nucleus with the electrons around the outside 7A = Halogens - exist as two atoms joined together, very of atoms reactive 8A = Noble gasses - very stable and rarely combine with other Most of the volume is empty space elements ELECTRONIC STRUCTURE THE PERIODIC TABLE Electron - is confined to a specific region around the nucleus giving it a particular energy. A row in the periodic table called a period - The regions occupied by electrons are called Column in the periodic table called a group principal energy levels or shells (n) One notices a repeating pattern of properties - The shells are numbered n = 1,2,3,4 etc Main group elements Electron is lower numbered shells are closer to the - They consist of the tall column on the right and nucleus and are lower in energy. left of the periodic table Electron is higher numbered shell are further from the - The groups are numbered 1A to 8A nucleus and are higher in energy. Transition metal elements - These are in the 10 short columns in the middle Shell with larger numbers (n) - are farther from the - The groups are numbered 1B to 8B nucleus and can hold more electrons Inner transition elements The maximum number of electrons in each shell is given by - They consist of the lanthanides and activities 2 - There are no group numbers assigned the formula 2𝑛 where n = shell number SYMBOL - one or two letter abbreviation derived from the element’s english or latin name The distribution of electrons in the first four shells: NAME - the sum of the numbers of protons and neutrons in a Shell (n) number of electrons in a shell specific isotope ↑ 4 32 ATOMIC NUMBER - equal to the number of protons in the ↑ 3 increasing 18 increasing nucleus, as well as the number of electrons in the electrons ↑ 2 energy 8 number of cloud ↑ 1 2 electrons ATOMIC MASS - weighted average of the masses of all the elements isotopes rounding the atomic mass to the nearest Shell - are divided into subshells identified by the letter while number yields the mass number of the most common s,p,d and f isotope. Subshells - consist of orbitals Orbitals - is a region of space where the probability of 5 group names and representative elements finding an electron is high Elements can be classified as metals, nonmetals or metalloids Each orbital can hold two electrons GROUP NAME ELEMENTS Subshell number of orbitals 1A ALKALI METALS Li, Na, K, Rb, Cs, Fr S 1 2A ALKALINE EARTH METALS Be,Mg,Ca,Sr,Ba,Ra P 3 CM38 BIOLOGICAL FOUNDATION l AUGUST TO NOVEMBER 7 ZALAMEDA  BIOLOGICAL FOUNDATION CM38 1ST TERM | 1ST YEAR | PROF. CHAN D 5 F 7 S orbital - has a spherical shape. - Gets larger in size the shell number increases P orbital - has a dumbbell shape The electron configuration shows how the electrons are arranged in an atom’s orbitals. The ground state is the lowest energy arrangement. Rules to Determine the Ground State Electronic Configuration of an Atom Orbital diagram - uses a box to represent each orbital and arrows to represent electrons Rule Electrons are placed in the lowest energy orbital beginning with the 1s orbital. an orbital ↑↓ an electron pair Orbitals are then filled in order of increasing energy ↑ a single unpaired electron Two electrons must have paired spins (opposite Rule each orbital holds a maximum of 2 electrons directions) to fit into the same orbital Rule when orbital are equal in energy: - 1 electron is added to each orbital until all of the orbital are half-filled ELEMENT ORBITAL ELECTRON - Then, the orbital can be completely filled NOTATION CONFIGURATION H (Z = 1) 1 electron ↑ 1 1𝑠 1s He (Z = 2) 2 electrons ↑↓ 2 1𝑠 1s Li (Z = 3) 3 electrons ↑↓ ↑ 2 1 1𝑠 2𝑠 1s 2s C (Z = 6) 6 electrons ↑↓ ↑↓ ↑ ↑ 2 2 2 1𝑠 2𝑠 2𝑝 1s 2s 2p Ne (Z = 10) 10 electrons ↑↓↑↓↑↓↑↓↑↓ 2 2 6 1𝑠 2𝑠 2𝑝 1s 2s 2p CM38 BIOLOGICAL FOUNDATION l AUGUST TO NOVEMBER 8 ZALAMEDA  BIOLOGICAL FOUNDATION CM38 1ST TERM | 1ST YEAR | PROF. CHAN Atom|The smallest unit of matter that retains the properties of an element. VALENCE ELECTRONS Atomic mass|The quantity of matter Chemical properties - an element depend on the number of electrons in the valence shell contained in an atom of an element. Valence shell - the outermost shell (the highest value of n) Valence electrons - electrons in the valence shell Atomic mass unit|Unit of mass used to express atomic and molecular weights. 2 2 Be = 1𝑠 2𝑠 Valence shell: n = 2 Atomic number|The number of protons in Number of valence electrons = 2 the nucleus of an atom. 2 2 6 2 5 CI = 1𝑠 2𝑠 2𝑝 3𝑠 3𝑝 Atomic Theory| Scientific explanation for Valence shell: n = 3 the properties of matter based on atoms. Number of valence electrons = 7 Atoms|The fundamental building blocks of matter, consisting of protons, neutrons, and electrons. Base|A substance that accepts protons or donates electrons in a chemical reaction.Chemical molecules that accept or donate protons in chemical reactions. REVIEWER Biological Buffers|Substances that resist Acid| A substance that donates protons or changes in pH accepts electrons in a chemical reaction. Substances with low pH levels that donate Buffer|A solution that resists changes in hydrogen ions in solutions. pH when an acid or base is added. Acidosis| Excessive acidity disrupts the buffers|Substances maintaining pH levels body's pH balance, leading to health by resisting changes in acid or base complications. chemical formula|a shorthand Acids and Bases|Define acids and bases representation of the elements present in and their characteristics. a compound and their ratios. alkalosis|Disturbance in pH balance Covalent bond|A chemical bond formed causing increased alkalinity in the body. by the sharing of electrons between atoms. CM38 BIOLOGICAL FOUNDATION l AUGUST TO NOVEMBER 9 ZALAMEDA  BIOLOGICAL FOUNDATION CM38 1ST TERM | 1ST YEAR | PROF. CHAN Density|Mass per unit volume of a Metabolic alkalosis|Excessive blood substance. alkalinity due to metabolic factors. electron cloud|region around the nucleus Micelles| Tiny structures formed by bile where electrons are likely to be found. salts to aid lipid absorption. Electrons|Negatively charged subatomic Non-covalent Interaction| Weak particles involved in chemical reactions chemical bond between molecules without and electricity. electron sharing. Energy|The capacity of an organism to do Nucleus|The central organelle in work or produce heat. eukaryotic cells that contains genetic material. Henderson-Hasselbalch equation|An equation used to calculate pH in buffer Periodic table|A visual representation of solutions. elements organized by their atomic number and properties. Hydrogen Bond | Attraction between hydrogen atom and electronegative atom Physical change|Change that does not in another molecule. alter the chemical composition of a substance. Hydrophobic interactions|Exclusion of nonpolar molecules by water due to Polar| Having a partial positive and partial hydrophobicity. negative charge. Ionic bonds|Chemical bonds formed by Polar molecule| A molecule with a partial the complete transfer of electrons from positive and partial negative charge. one atom to another. Scientific method|A systematic approach Isotope|A variant of an element with the used to investigate and understand same number of protons but different natural phenomena. number of neutrons. Atoms of the same element with different numbers of valence electrons|electrons in the neutrons. outermost energy level of an atom Matter|Anything that has mass and takes Van der Waals forces|Weak attractive up space. forces between molecules caused by temporary fluctuations in electron metabolic acidosis|excess acid in body distribution. fluids due to various causes. CM38 BIOLOGICAL FOUNDATION l AUGUST TO NOVEMBER 10 ZALAMEDA  BIOLOGICAL FOUNDATION CM38 1ST TERM | 1ST YEAR | PROF. CHAN Water| Polar molecules that can enter the cell through aquaporins. CM38 BIOLOGICAL FOUNDATION l AUGUST TO NOVEMBER 11 ZALAMEDA