Chapter 2- Chemistry comes alive PDF

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CHEMISTRY COMES ALIVE Matter – anything with mass and occupies space - weight – pull of gravity on mass - solid – with definite shape and volume liquid – with definite volume but changeable shape gas – with changeable volume and shape Energy - capacity to do work or put matter into motion - 2 types – kinetic energy – energy in action potential energy – stored ( inactive ) energy - energy can be transferred from potential to kinetic Forms of energy used by the body: 1. Chemical energy – stored in the chemical bonds - ATP ( energy of the body) 2. Electrical energy - result from movement of charged particles 3. Mechanical energy – energy that directly cause the movement of matter 4. Radiant or electromagnetic energy - energy that travel in waves. - light, infrared waves, radiowaves, untraviolet waves, X-rays Energy - is neither created nor destroyed - can be converted from one form to another form, - some energy is unused in the conversion ( lighting a bulb) Composition of Matters: All matters are made up of elements Elements: - unique substances that cannot be broken into simpler form by ordinary chemical means - 2 properties of elements – physical – anything we can sense or measure - chemical – how atoms interact (bond ) with other atoms Atoms -unique building blocks of elements -give each element its chemical and physical properties -smallest particles of the element that retain the properties of the element - atomic symbols – designated for each element. - usually represented by the first letter or the first 2 letter of the name of the element in English, Latin mainly and rarely in other languages - 118 elements – 92 are naturally occurring 26 are produced from natural element by particle accelerator or nuclear reactor.

- 24 out of 92 naturally occurring are: 4 elements ( O, C, N, H ) – 96.1 of body mass 9 elements ( Ca,P,K,S Na, Cl,Mg, I, Fe ) – 3.9% 11 trace elements ( Cr, Mn, Z. etc….. ) – less than 0.01% - many are part of, or activate enzymes - atomic structures: - nucleus – 99.9% of entire atomic mass - has - proton – positive charge ( 1 amu) - neutron –no charge (1 amu) electron - equal in numbers to protons - negative charge - 1/2000 the mass of proton ( 0 amu) - 2 models : - planetary model - orbital model - Identifying elements of atom: Atomic number – number of protons ( distinguishes the atom of one element from another element) - subscript to the lower left of atomic symbol Mass Numbers – sum of number of protons and number of electrons - subscript to the upper left of the atomic symbol - mass numbers of atoms of an element are not all identical Isotopes – are atoms of the one elements that has the same number of proton but different numbers of neutrons, thus the have the same atomic number but different mass number. Atomic weight – average of mass numbers of all isotopes of an atom 2 types of isotopes: - stable isotope – ( nuclear structure does not change over time) - Ex: O 16, O 17, O 18 - unstable isotope are also called radioisotope - decay or decomposed or change to more stable form ( causing tiny explosion called radioactivity- which can be detected by scanner - Ex. H-3, C14, O15, O19 - maybe used for diagnostic purposes ( I-131) for thyroid cancer

Molecule – combination of 2 or more atoms held by chemical bond - if the combined atoms are of the same elements, - molecules of that element - ex. O2 - if the combined atoms are of different elements – molecules of a compound or simply “ compound “ ex. H2O - smallest particle of a compound that has the specific features of the compound Mixtures – two or more components physically intermixed - 3 types: - 1. solutions – homogenous mixtures - does not settle down - does not scatter light ray - transparent - made up of 2 substances – solvent - greater in amount, -usually liquid ( water ) - solute – lesser in amount - how concentration of solution is expressed: - percent – parts of solute /100 parts of solvent - mg/dl – milligram of solute in 1 deciliter of solvent - molarity or moles/ liter 2. Colloids -

also called emulsion heterogenous compound translucent do not settle down do scatter light rays the solute are larger particles undergo sol-gel transformation cytosol of cell, milk

3. Suspensions:- heterogenous - solutes are larger particles mostly can be seen by naked eye - solutes settles down Compound versus mixtures:

compound - homogenous - chemically bonded - can be separated by breaking the bonds

Chemical bonds: - Note: - electron shell ( 1 to 7) - valence shell- outmost shell

mixtures - homogenous or heterogenous - not chemically bonded but physically intermixed - can be separated physically ex. straining, filtering

- Octet rule - chemically inert elements – stable, unreactive - outermost shell contains 8 electrons except helium ( 2 electrons) -chemically reactive elements – unstable - outer shell not fully occupied - tend to gain, lose or share electrons with other atoms ( form bonds ) to be stable Types of chemical bonds: 1. Ionic bond – atoms gains or loses electrons - formed by transfer of valence electrons between atoms charging both atoms and these opposite charges attract each other forming the ionic bond - electron acceptor – anion ( -) - electron donor – cation (+) - usually solid ( give strength to some tissue like teeth and bones ) 2. Covalent bond – formed by sharing 2 or more valence shell electrons - most common chemical bond in the body - maybe - single covalent bond – 1 pair is shared – H2 - double covalent bond – 2 pairs are shared – O2 - triple covalent bond – 3 pairs are shared – N2 - methane is composed of 4 separate 1 paired covalent bond. - non polar covalent bond – the shared electrons are attached or pulled equally by both atom producing electrically balanced molecules - all covalent bonds of similar atoms are non-polar ex. methane (CH4) - covalent bonds of dissimilar atoms, ex. CO2 - polar covalent bond – the pull of shared electron by the atoms are unequal - atoms with stronger pull have partial negative charge - atoms with weaker pull have partial positive charge - ex. H2O - result to polar molecules. 3. Hydrogen bond – when the hydrogen atom with a partially positive charge (of a molecule ) attract the partially negative charge of the neighboring atoms ( of another molecule) - considered more an simple attraction rather than a bond - weak bond ( 5% of the strength of covalent bond ) - more on intra molecular bond - ex. between molecule of water

Chemical Reactions: - when bonds are formed, rearranged, broken - maybe expressed by chemical equation: 2 or more reactant = products Patterns of chemical reaction: 1. Synthesis- ( combination reaction, endergonic reaction , anabolic ) - small particles are bonded together to form larger more complex molecules - formation of bonds - absorb more energy than release - product have more potential energy than the reactants 2. Decomposition reaction –( exergonic, catabolic, reverse synthesis ) - breaking of bonds - release more energy than absorb - emit energy 3. Exchange reaction – displacement reaction - bonds are made and broken *Oxidation- reduction reaction ( Redox) – a decomposition reaction forming ATP - an exchange reaction because electrons are exchanged between reactants. - electron acceptors are reduced - electron donors are oxidized * Chemical reactions – are theoretically reversible - but most of the biological reactions are irreversible because of energy requirements and the removal of products * A chemical reaction is said to be in equilibrium if neither a forward or reverse reactions is dominant Factors affecting rate of chemical reactions: 1. temperature 2. concentration of reactants 3. particle size 4. presence of catalysts – substances that increase rate of reaction without being chemically changed nor part of the product. - biological catalyst – are ENZYMES. Biochemistry: Study of chemical composition and reaction of living matter. All chemicals in the body fall into 2 types of compound - Organic c. – contains Carbon, covalently bonded and usually large. - ex:. CHO, CHON, Fats, Nucleic acids

- Inorganic c. – has no Carbon, usually smaller - ex. water, salts, acids and bases Inorganic compounds: 1. Water- 60-80% of the volume of the most living cells - most abundant, most important inorganic compound in living organism. - properties: - high heat capacity – ensure temperature homeostasis - high heat of evaporation – require large amount of heat to evaporate, use for cooling. ( sweating ) - polar solvent – universal solvent - dissociate ionic substances into ions - forms hydrated layers around large molecules forming colloids. ( plasma, CSF) - body major transport medium - reactivity – adding water ( hydrolysis or decomposition reaction ) - removing water ( dehydration synthesis ) - cushioning – CSF around the CNS. 2. Salts: - ionic compound that dissolve in water forming ions ( electrolytes) that conducts electrical current - contains cations other than H+ and anions other than OH- ex. NaCl, KCl, CaCO3, CaPO4…. 3. Acid and Bases : are also electrolytes and can conduct current Acid – proton donor - ex; HCl, acetic acid, carbonic acid Base – proton acceptor ex. NaOH, MgOH pH – the acid base concentration - negative logarithm of molecule of H per liter - pH of 2 equals .01 - pH of 3 equals .001 Acid pH - less than 7 Neutral pH – 7 ( pure water ) Alkaline pH – more than 7 Neutralization : Acid-base homeostasis : - changes on acidity ( change in pH) of any body fluid maybe fatal. but this is prevented by : body buffers, lungs ( exhalation of CO2 ) kidneys ( by secreting acidic urine )

Buffers:- are mixtures of compound that resist pH changes - convert strong acid ( completely dissociated ) or strong base into a weak ( slightly dissociated ) ones - Ex. Carbonic acid- Bicarbonate system Organic compounds: - containing carbon ( except CO2, CO which are inorganic ) - usually large molecules but their interaction with other molecules involved only a small part called functional group - unique to living things - are polymers (chains of similar units called monomers or building blocks ) polymers are formed by dehydration synthesis broken down by hydration reaction - includes CHO, CHON, lipids and nucleic acids 1. Carbohydrates: - contain CHO with hydrogen-oxygen ratio to 2:1 - represent 1-2% of the cell mass - sugars and starches - functions - major source of cellular fuel - structural molecules ( ribose sugar of RNA ) - 3 classes: - monosaccharides – simple sugars - contain 3-7 Carbon atoms - pentose sugars: - ribose - deoxyribose - hexose sugars: - glucose - galactose, - fructose - disaccharides –double sugars - too large to pass the cell membrane - ex: maltose, lactose, sucrose mono and di – are sweet and water soluble - polysaccharides – - not sweet, not water soluble - ideal for storage products - ex; starch – CHO of plants cellulose glycogen 2. Lipids: - also contains CHO but less than carbohydrates .The proportion of Oxygen in lipids is much lower. - has phosphorous ( P ) in more complex lipids - insoluble in water but soluble in ether and alcohol

Types of lipids: a. Triglycerides - or neutral fats or simple fat ( solid) or oil ( liquid) - composed of 3 fatty acids bounded to glycerol molecule by dehydration synthesis - see figure 2.16 (a) - found mainly at the subcutaneous layer ( adipose tissue ) - serve as insulator, protection (cushion)and storage of energy. saturated fatty acids – single bonds between C atoms, contains the most number of hydrogens - solid at room temperature - ex: animal fats, unsaturated fatty acids – one or more double bonds between C atoms - liquid at room temperature - mono unsaturated oil – olive, peanut oils - polyunsaturated oil – canola oil, sunflower oil, soy beans oil trans fats – oils that have been solidified by adding H atom at the site of carbon double bonds. ex: margarine and baked products ( unhealthy ) omega- 3 fatty acids – in cold water fish – decrease the risk of heart attack and some inflammatory disease b. Phospholipids – modified triglycerides - has -glycerol part as the backbone -2 fatty acid chains as the tail ( non polar) -phosphorus containing group as the head ( polar ) - component of the cell membrane c. Steroids: - made of 4 interlocking rings of hydrocarbon - ex; cholesterol – found in the cell membrane, - raw material for vitamin D synthesis, hormones, bile acids, d. Eicosanoids – derived from arachidonic acid found in cell membrane - prostaglandins and leukotrienes e. Other lipids – lipoproteins that transport fats in the blood (HDL, LDL ) - fat soluble vitamins ( vit A, D, E, K ) 3. Proteins: - large molecules containing C, H, O, N. Some with sulfur and phosphorus. - polymers of amino acids ( 20 types of AA ) joined by peptide bonds - has 2 important functional group – amine group (base) – protein acceptor - carboxyl group ( acid ) – protein donor - has the center R group that differ among types of amino acid

- formed by peptide bond between the amine group of one AA to the carboxyl group of another AA with loss of water molecule Structural level of proteins: 1. primary structure – sequences of AA forming the polypeptide chain 2. secondary structure – 2 types: - alpha-helix - twisting and bending of polypeptide chain stabilized by hydrogen bond - beta pleated sheet – adjacent strands are held together by hydrogen bond 3. tertiary structure – superimposed on secondary structure 4. quartenary structure - 2 or more polypeptide chain with each own tertiary structure form functional protein Protein can be also classified according to their overall appearance as to: - fibrous (structural) protein – like collagen, keratin, elastin contractile protein of the muscle - strand like, water insoluble, stable - globular (functional) protein – like antibodies, hormones enzymes - compact, spherical, water soluble and sensitive to environmental changes Protein denaturation : - when the protein is exposed to change increase temperature or decrease in pH, the shapes change and active sites are disruption. - reversible if normal condition is restored - irreversible if conditions are extremes ( cooking egg ) Molecular chaperones – are globular proteins whose has several functions ( ex: trigger immune response )

Enzymes: - globular protein acting as biological catalysts - lower activation energy and speed up biological reactions - characteristics: - end with “ ase” - specific to a certain substrate - named after the reaction the speed up ( hydrolases, etc… ) - some are purely proteins - some are functional enzymes with 2 components - apoenzyme ( the protein part ) - cofactor ( if it is a metal) or coenzyme ( if it is a organic molecule like vitamin )

4. Nucleic acids ( DNA and RNA ) – largest molecule of the body - contains C,H,O,N,P - building block or unit is the nucleotide ( made up of deoxyribose sugar molecule, linked to a phosphate group and a base ) - 5 bases: - 2 purines ( adenine and guanine ) they are large double ring bases - 3 pyrimidines ( cytosine, thymine, uracil ) they are single ring bases comparison between DNA/RNA – refer to Table2.4 (page 55) 3 types of RNA – messenger RNA, ribosomal RNA, transfer RNA 5. ATP ( Adenosine Triphosphate ) - an adenosine containing nucleotide with 2 additional phosphate group. - primary the energy transferring molecule in the cell or called the energy currency of the cell ATP + water = ADP + P + energy ( Phosphorylation )...