MHS1101 Lecture 1 Chemistry & Biochemistry PDF

MHS1101: LECTURE 1 CHEMISTRY & BIOCHEMISTRY  LEARNING OUTCOMES By the end of this lecture you should be able to:  Identify the chemical elements of the body  Define the types of chemical bonds  Define acid & base and interpret the pH scale  Define energy & work & describ...

MHS1101: LECTURE 1 CHEMISTRY & BIOCHEMISTRY  LEARNING OUTCOMES By the end of this lecture you should be able to:  Identify the chemical elements of the body  Define the types of chemical bonds  Define acid & base and interpret the pH scale  Define energy & work & describe some types of energy  List & define the fundamental types of chemical reactions  Explain why carbon is able to serve as structural foundation of many biological molecules  Discuss the types & functions of carbohydrates, lipids, and proteins  Explain how enzymes function  CHEMICAL ELEMENTS  simplest form of matter [e.g. hydrogen & oxygen]  atomic number of element - number of protons in the nucleus [periodic table]  each element represented by letters [e.g. Na, Cl] Main chemical elements of human body:  oxygen (O) - 65%  carbon (C) - 18.6%  hydrogen (H) - 9.7%  nitrogen (N) - 3.2% [see Table 2.1, pg 42 Saladin]  Trace elements in minute amounts, but play vital roles  CHEMICAL ELEMENTS  some elements are minerals – all are inorganic [e.g. Ca, Na, K, Mg]  extracted from soil by plants  important for teeth, bones, enzyme functions  electrolytes - mineral salts essential for nerve & muscle function  ATOMS & SUBATOMIC PARTICLES  atoms are smallest stable unit of matter  can not be broken down to simpler substance by chemical means  everything comprises atoms (e.g. air)  cellular physiology is based on interactions of atoms  ATOMS & SUBATOMIC PARTICLES Atom nucleus:  protons (positive charge)  neutrons (neutral, no charge)  electrons (negative charge)  atoms electrically neutral - number of electrons = number of protons  valence electrons orbit outermost shell & determine chemical bonding properties of an atom  circles form electron cloud, shells or energy levels  ELECTRONS & ENERGY LEVELS  electron cloud - orderly series of energy levels  each level holds certain number of electrons  1st = 2 Carbon (C) ,, Nitrogen (N) ,,  2nd & 3rd up to 8 Atomic number = 6 Atomic number = 7 Atomic mass = 12 Atomic mass = 14  outermost level - surface (valence shell)  valence electrons determine chemical bonding properties of the atom Sodium (Na) ,,  if outer shell is filled, atom inert or Atomic number = 11 Atomic mass = 23 ‘noble’ (non-reactive) – i.e. He Figure 2.1 ©McGraw-Hill Education. All rights reserved. Authorized only for instructor use in the classroom. No reproduction or further distribution permitted without the prior  ISOTOPES  varieties of element that differ only in number of neutrons  extra neutrons increase atomic weight  isotopes of an element are chemically similar - same number of valence electrons  MOLECULES & CHEMICAL BONDS  molecule - chemical particle comprising two or more atoms united by chemical bond  compound - molecule comprising two or more different elements  molecular formula - identifies constituent elements & numbers of atoms present  structural formula - identifies location of each atom  MOLECULES & CHEMICAL BONDS  chemical bonds - hold atoms together within molecule or attract one molecule to another Most important types of chemical bonds  ionic  covalent  hydrogen  van der Waal’s forces  CHEMICAL BONDS: IONIC BONDS Ionic bonds  ions - charged particles (atom or molecule) with unequal numbers of protons & electrons  ionisation - transfer of electrons from one atom to another  anion - article that gains electron(s) (net negative charge)  cation - particle that loses electron(s) (net positive charge)  ions with opposite charges are attracted to each other  ions carry +ve [e.g. Na+] or –ve [e.g. Cl-] charge  bond is electrical attraction between +ve & -ve  IONISATION 1) Transfer of electron from sodium atom to chlorine atom Figure 2.4 2) The charged sodium ion and chloride ion that result ©McGraw-Hill Education. All rights reserved. Authorized only for instructor use in the classroom. No reproduction or further distribution permitted without the prior  CHEMICAL BONDS: COVALENT BONDS Covalent bonds  formed by sharing electrons occupying single energy shell common to both atoms  complete the outer shell by sharing electrons with other atoms  single covalent bonds (e.g. H ) 2  double covalent bonds (e.g. CO ) 2  nonpolar covalent bonds - equal sharing of electrons - very strong  SINGLE COVALENT BOND Figure 2.6a DOUBLE COVALENT BOND Figure 2.6b  NONPOLAR & POLAR COVALENT BONDS Nonpolar covalent bond (a) Figure 2.7 Polar covalent bond (b) Copyright © McGraw-Hill Education. Permission required for reproduction or display.  MOLECULES & CHEMICAL BONDS HYDROGEN BONDS  weak attraction between a slightly positive H atom in one molecule & a slightly negative oxygen or nitrogen atom in another  H O molecules are attracted to each other by H bonds 2  +ve charge of hydrogen atom  -ve charge of oxygen, nitrogen or fluorine Figure 2.8  MOLECULES & CHEMICAL BONDS VAN DER WAAL’S FORCES  weak, brief attractions between neutral atoms  fluctuation in electron density within atoms creates brief polarity & attracts adjacent atom for very short time  only 1% as strong as covalent bond but important in physiology (example, protein folding)  WATER & MIXTURES  mixtures - physically blended but not chemically combined  body fluids are complex mixtures of chemicals  most mixtures in body consist of chemicals dissolved or suspended in H2O  H2O is 50% to 75% of body weight  depends on age, sex, fat content, etc.  WATER  has polar covalent bonds & v-shaped molecule  gives H2O set of properties  solvency  cohesion  adhesion  chemical reactivity  thermal stability  WATER  solvency - ability to dissolve other chemicals  H2O is called the universal solvent  hydrophilic - substances that dissolve in H2O  molecules must be polarized or charged (e.g. sugar)  hydrophobic - substances that do not dissolve in H2O  molecules are nonpolar or neutral (e.g. fats)  metabolic reactions depend on solvency of H2O  WATER & HYDRATION SPHERES  attractions to H20 molecules overpower ionic bond in Na+Cl-  H20 forms hydration spheres around each ion & dissolves them  H20’s negative pole faces , its positive pole faces Figure 2.9 Copyright © McGraw-Hill Education. Permission required for reproduction or display.  WATER  Adhesion - tendency of one substance to cling to another  H20 adheres to large membranes reducing friction around organs  Cohesion - tendency of like molecules to cling to each other  H20 very cohesive due to its hydrogen bonds  ‘film’ on surface of H20 due to molecules held together by surface tension  WATER  Chemical reactivity - ability to participate in chemical reactions  H20 ionizes into &  H20 ionizes many other chemicals (acids & salts)  H20 is involved in hydrolysis & dehydration synthesis reactions  Thermal stability - helps stabilize internal body temperature  H20 has high heat capacity - heat required to raise temperature of 1g of substance by 1°C  Calorie - amount of heat that raises temperature of 1g of H20 by 1°C  H bonds inhibit temperature increases by inhibiting molecular motion  Effective coolant  1 mL of perspiration removes 500 calories  SOLUTIONS, COLLOIDS & SUSPENSIONS Solution  particles [solute] mixed with abundant substance (usually H20 ) called solvent  solute can be gas, solid, or liquid  solutions will pass through most membranes Colloids  in body are often mixtures of protein & H20  many can change from liquid to gel state within & between cells  particles too large to pass through semipermeable membrane Suspension  too large to penetrate selectively permeable membranes  example: blood cells in plasma A SOLUTION, A COLLOID & A SUSPENSION Figure 2.10  ACIDS, BASES & PH  acid - proton donor (releases ions in H 0) 2  base - proton acceptor (accepts ions)  many bases release  pH - measure derived from the molarity of  pH of 7.0 is neutral  pH of less than 7 is acidic solution  pH of greater than 7 is basic solution  ACIDS, BASES & PH  pH - measurement of molarity of on logarithmic scale  change of one number on pH scale represents 10-fold change in concentration  solution with pH of 4.0 is 10x as acidic as one with pH of 5.0  Buffers - chemical solutions that resist changes in pH  maintaining normal (slightly basic) pH of blood is crucial for physiological functions  THE PH SCALE  acid-base concentration: relative concentration of H+ ions in fluids  H+ atoms can lose electron & become a H+ ion  extremely reactive - can break chemical bonds & disrupt cell function Figure 2.11  ENERGY & CHEMICAL REACTIONS Energy  capacity to do work e.g. building molecules or contracting muscles  all body activities are forms of work Potential energy  energy stored in an object, but not currently doing work  e.g. H20 behind a dam wall  chemical energy - potential energy in molecular bonds  free energy - potential energy available in system to do work  ENERGY & WORK  Kinetic energy - energy of motion, doing work  e.g. H20 flowing through a dam, generating electricity  heat - kinetic energy of molecular motion  energy releasing process – exergonic  energy conserving process – endergonic  chemical energy – potential energy stored in bonds of molecules – used in chemical reactions  activation energy – energy required to start chemical reaction  CLASSES OF CHEMICAL REACTIONS  chemical reaction - process in which covalent or ionic bond is formed or broken  chemical equation - symbolizes course of a chemical reaction  reactants (on left) products (on right)  Classes of chemical reactions  decomposition reactions  synthesis reactions  exchange reactions  DECOMPOSITION REACTION  large molecule breaks down into two or more smaller ones: AB A + B Figure 2.12a  SYNTHESIS REACTION  two or more small molecules combine to form a larger one: A + B AB Figure 2.12b  EXCHANGE REACTION  two molecules exchange atoms or group of atoms AB+CD ABCD AC + BD  stomach acid (HCl-) & sodium bicarbonate from pancreas combine to form NaCl and Figure 2.12c  METABOLISM, OXIDATION & REDUCTION  Metabolism - all chemical reactions of the body  Catabolism  energy-releasing (exergonic) decomposition reactions  breaks covalent bonds  produces smaller molecules  Anabolism  energy-storing (endergonic) synthesis reactions  requires energy input  production of protein or fat  Catabolism & anabolism are inseparably linked  Anabolism is driven by energy released by catabolism  METABOLISM, OXIDATION & REDUCTION  Oxidation  chemical reaction in which molecule gives up electrons & releases energy  molecule oxidised in this process  electron acceptor molecule is the oxidising agent  oxygen is often involved as the electron acceptor  Reduction  any chemical reaction in which a molecule gains electrons & energy  molecule is reduced when it accepts electrons  molecule that donates electrons is the reducing agent  METABOLISM, OXIDATION & REDUCTION  Oxidation-reduction (redox) reactions  oxidation of one molecule always accompanied by reduction of another  electrons are often transferred as hydrogen atoms ORGANIC COMPOUNDS [MACROMOLECULES]  ORGANIC MOLECULES: CARBON  “What sets the carbon atom apart is that it is shamelessly promiscuous. It is the party animal of the atomic world, latching on to many other atoms (including itself) and holding tight, forming molecular conga lines of hearty robustness – the very trick of nature necessary to build proteins and DNA. As Paul Davies has written: ‘If it wasn’t for carbon, life as we know it would be impossible. Probably any sort of life would be impossible’” (p. 309) Bryson (2003) A short history of nearly everything. Black Swan. CARBON COMPOUNDS & FUNCTIONAL GROUPS  Four categories of carbon compounds  Carbohydrates  Lipids  Proteins  Nucleic acids  CARBON COMPOUNDS & FUNCTIONAL GROUPS  Carbon has four valence electrons  binds with other atoms that can provide 4 more electrons to fill valence shell  Carbon atoms bind readily with each other to form carbon backbones  form long chains, branched molecules & rings  form covalent bonds with hydrogen, oxygen, nitrogen, sulfur & other elements  Carbon backbones carry a variety of functional groups  FUNCTIONAL GROUPS OF ORGANIC MOLECULES Name and Symbol Structur Occurs in  functional groups - small e clusters of atoms attached to Sugars, carbon backbone Hydroxyl alcohols  determine many of the Fats, oils, properties of organic molecules Methyl steroids, amino acids Examples:  hydroxyl Amino acids, Carboxyl sugars,  methyl proteins  carboxyl Amino acids, Amino proteins  amino,  phosphate Phospha Nucleic te acids, ATP Figure 2.13 ©McGraw-Hill Education. All rights reserved. Authorized only for instructor use in the classroom. No reproduction or further distribution permitted without the prior  CARBOHYDRATES  hydrophilic organic molecule  e.g. sugars & starches  General formula  , n = number of carbon atoms  Glucose, n = 6, so formula is  2:1 ratio of hydrogen to oxygen  names often built from root ‘sacchar-’ & suffix ‘-ose’ both meaning sugar, sweet  THE THREE MAJOR MONOSACCHARIDES  Glucose [blood sugar]  Galactose  Fructose  same molecular formula:  all isomers of each other  produced by digestion of complex carbohydrates [starch& disaccharides]  small intestine & liver convert galactose & fructose to glucose Copyright © McGraw-Hill Education. Permission required for reproduction or display. Figure 2.15  CARBOHYDRATES  disaccharide - sugar made of two monosaccharides  Three important disaccharides  sucrose - table sugar  glucose + fructose  lactose - sugar in milk  glucose + galactose  maltose - grain products  glucose + glucose Figure 2.16  CARBOHYDRATES  Oligosaccharides - short chains of 3 or more monosaccharides (at least 10)  Polysaccharides - long chains of monosaccharides (at least 50) Three key examples:  glycogen - energy storage in cells of liver, muscle, brain, uterus, vagina  starch - energy storage in plants that is digestible by humans  cellulose - structural molecule in plants important for human dietary fiber (but indigestible) Figure 2.17 Glycogen  CARBOHYDRATES  Carbohydrates - quickly mobilized source of energy  all digested carbohydrates converted to glucose  oxidized to make ATP  Conjugated carbohydrate - covalently bound to lipid or protein moiety  glycolipids - external surface of cell membrane  glycoproteins - external surface of cell membrane, mucus of respiratory & digestive tracts  Proteoglycans - more carbohydrate than protein  gels that hold cells & tissues together, gelatinous filler in eye, joint lubrication & cartilage texture  LIPIDS  contain carbon, hydrogen & oxygen  hydrophobic molecules with high ratio of hydrogen to oxygen  Ratio 1:2 (carbon to hydrogen) more calories per gram than carbohydrates – better for energy storage  fat is hydrophobic & is a more compact energy storage substance  fat is less oxidised than carbohydrates & contains over twice as much energy: 9 kcal/g for fat; 4 kcal/g for carbohydrates  Lauric acid C12H24O2  LIPIDS  Five primary types in humans  fatty acids  triglycerides  phospholipids  eicosanoids  steroids  LIPIDS  Fatty acids  chains of 4-24 carbon atoms with carboxyl group on one end  Saturated  each carbon atom has 4 single covalent bonds  Unsaturated  One or more bonds are double covalent bonds  Polyunsaturated  multiple double bonds between carbons in chain  essential fatty acids must be obtained from food  LIPIDS  Triglycerides (neutral fats)  three fatty acids linked to glycerol  each bond formed by dehydration synthesis  broken down by hydrolysis  Triglycerides at room temperature  when liquid, called oils - often polyunsaturated fats from plants  when solid, called fat - saturated fats from animals  Primary function: energy storage  also help with insulation & shock absorption (adipose tissue)  TRIGLYCERIDE (FAT) SYNTHESIS Palmitic acid (saturated) Stearic acid (saturated) Linoleic acid (unsaturated) Copyright © McGraw-Hill Education. Permission required for reproduction or display. Figure 2.18a TRIGLYCERIDE (FAT) SYNTHESIS Figure 2.18b  LIPIDS  phospholipids - similar to neutral fats except one fatty acid is replaced by a phosphate group  structural foundation of cell membrane  Amphipathic  fatty acid ‘tails’ are hydrophobic  phosphate ‘head’ is hydrophilic Lecithin – a Representative Figure 2.20 Phospholipid Copyright © McGraw-Hill Education. Permission required for reproduction or display.  LIPIDS  Eicosanoids - 20-carbon compounds derived from arachidonic acid  hormone-like chemical signals between cells  includes prostaglandins - role in inflammation, blood clotting, hormone action, labour contractions, blood vessel diameter Copyright © McGraw-Hill Education. Permission required for reproduction or display.  LIPIDS  steroid - lipid with 17 carbon atoms in four rings  cholesterol - ‘parent’ steroid from which others are synthesized  role in nervous system function & structural integrity of all cell membranes  15% of cholesterol comes from diet & 85% is internally synthesized (mostly liver)  other steroids: cortisol, progesterone, oestrogens, testosterone & bile acids  CHOLESTEROL  ‘good’ & ‘bad’ cholesterol refer to droplets of lipoprotein in the blood  complexes of cholesterol, fat, phospholipid & protein HDL (high-density lipoprotein) – ‘good’ cholesterol  lower ratio of lipid to protein - may help to prevent cardiovascular disease LDL (low-density lipoprotein) – ‘bad” cholesterol’  high ratio of lipid to protein  contributes to cardiovascular disease Figure 2.22  PROTEINS  Protein - a polymer of amino acids  amino acid - central carbon with three attachments amino group (NH2)  carboxyl group  radical (R) group  20 amino acids used to make proteins are identical except for R group  properties of amino acid determined by R group  AMINO ACIDS Some polar amino acids Some nonpolar amino acids Methionine Cystein e Tyrosine Arginine Figure 2.23a  Amino acids differ only in the R group  PROTEINS  Peptide - molecule comprising two or more amino acids joined by peptide bonds  Peptide bond - joins amino group of one amino acid to carboxyl group of next  Formed by dehydration synthesis  Named for number of amino acids  dipeptides - 2  tripeptides - 3  oligopeptides - fewer than 10 or 15  polypeptides - more than 15  proteins - more than 50  PROTEIN STRUCTURE  Conformation - unique, three-dimensional shape of protein  crucial to function  proteins can reversibly change conformation & thus function  examples: muscle contraction, enzyme catalysis, membrane channel opening  Denaturation  extreme conformational change that destroys function  extreme heat or pH  example: cooking an egg  PROTEIN STRUCTURE  Primary structure  sequence of amino acids which is encoded in genes  Secondary structure  coiled or folded shape held together by hydrogen bonds  hydrogen bonds between slightly negative & slightly positive groups  most common secondary structures are:  alpha helix - spring-like shape  beta helix - pleated, ribbon-like shape  FOUR LEVELS OF PROTEIN STRUCTURE Primary structure Sequence of amino acids joined by peptide bonds Secondary structure Alpha helix or beta sheet formed by hydrogen bonding Tertiary structure Folding and coiling due to interactions among R groups and between R groups and surrounding water Quaternary structure Association of two or Figure 2.24 more polypeptide chains with each other Add aemoglobin to bottom Copyright © McGraw-Hill Education. Permission required for reproduction or display.  PROTEIN STRUCTURE  Tertiary structure  further bending & folding of proteins into globular & fibrous shapes due to hydrophobic-hydrophilic interactions & van der Waals forces  globular proteins - proteins within cell membrane & proteins that move freely in body fluids  fibrous proteins - slender filaments suited for roles in muscle contraction & strengthening of skin & hair  Quaternary structure  associations of two or more polypeptide chains due to ionic bonds & hydrophobic-hydrophilic interactions  occurs only in some proteins  example: hemoglobin has four peptide chains  FOUR LEVELS OF PROTEIN STRUCTURE Primary structure Sequence of amino acids joined by peptide bonds Secondary structure Alpha helix or beta sheet formed by hydrogen bonding Tertiary structure Folding and coiling due to interactions among R groups and between R groups and surrounding water Quaternary structure Association of two or more polypeptide chains with each other Figure 2.24 Copyright © McGraw-Hill Education. Permission required for reproduction or display.  PROTEIN FUNCTIONS  Structure  keratin - tough structural protein of nails, skin surface  collagen - deeper layers of skin, bones & cartilage  Communication  some hormones & other cell-to-cell signals are proteins  ligands are molecule that reversibly binds to a protein  Membrane transport  Channel proteins in cell membranes govern what passes  Carriers—transport solutes to other side of membrane  Catalysis - most enzymes are globular proteins  PROTEIN FUNCTIONS  Recognition & protection  glycoproteins are important for immune recognition [antibodies are proteins]  Movement  motor proteins - molecules with the ability to change shape repeatedly  Cell adhesion  proteins bind cells together [e.g. sperm to egg]  keeps tissues from falling apart  ENZYMES & METABOLISM  enzymes - proteins that function as biological catalysts  permit reactions to occur rapidly at body temperature  substrate - substance enzyme acts upon  Naming convention  named for substrate with -ase as the suffix  amylase enzyme digests starch (amylose)  enzymes lower activation energy - energy needed to get reaction started EFFECT OF ENZYME ON ACTIVATION ENERGY Figure 2.26  ENZYME STRUCTURE & ACTION  enzymes are not consumed by the reactions  one enzyme molecule can consume millions of substrate molecules per minute  temperature, pH & other factors can change enzyme shape & function  can alter ability of enzyme to bind to substrate  enzymes vary in optimum pH  salivary amylase works best at pH 7.0, pepsin at pH 2.0  temperature optimum for human enzymes—near body temperature (37°C)  ENZYME STRUCTURE & ACTION Enzyme action  substrate approaches enzyme’s active site  molecules bind together forming enzyme-substrate complex  enzyme–substrate specificity - lock & key  enzyme releases reaction products  enzyme unchanged & can repeat process Figure 2.27  COFACTORS  ± 2/3 of human enzymes require a nonprotein cofactor  some are inorganic (iron, copper, zinc, magnesium & calcium ions)  some bind to enzyme & induce change in shape, which activates the active site  essential to function  coenzymes - organic cofactors derived from water-soluble vitamins (niacin, riboflavin)  accept electrons from enzyme in one metabolic pathway & transfer them to enzyme in another  e.g.  ACTION OF A COENZYME  transports electrons from one metabolic pathway to another  METABOLIC PATHWAYS  chain of reactions, with each step usually catalyzed by a different enzyme  α β γ ABCD  A is initial reactant, B and C are intermediates, & D is end product  Regulation of metabolic pathways  cells can turn pathways on/off when end products are needed/not needed  ATP, OTHER NUCLEOTIDES & NUCLEIC ACIDS  Three components of nucleotides  nitrogenous base (single or double carbon–nitrogen ring)  sugar (monosaccharide)  one or more phosphate groups  ATP  Adenine (nitrogenous base)  Ribose (sugar)  Phosphate groups (3)  OTHER NUCLEOTIDES  Guanosine Triphosphate (GTP)  another nucleotide involved in energy transfer  Cyclic Adenosine Monophosphate (cAMP)  formed by removal of 2nd & 3rd phosphate groups from ATP  formation triggered by hormone binding to cell surface  cAMP becomes ‘second messenger’ within cell  NUCLEIC ACIDS  polymers of nucleotides  DNA (deoxyribonucleic acid)  contains millions of nucleotides  constitutes genes  instructions for synthesizing proteins  RNA (ribonucleic acid) - three types  messenger RNA, ribosomal RNA, transfer RNA  70 to 10,000 nucleotides long  carries out genetic instruction for synthesizing proteins  assembles amino acids in right order to produce proteins  LEARNING OUTCOMES By the end of this lecture you should be able to:  Identify the chemical elements of the body  Define the types of chemical bonds  Define acid & base and interpret the pH scale  Define energy & work & describe some types of energy  List & define the fundamental types of chemical reactions  Explain why carbon is able to serve as structural foundation of many biological molecules  Discuss the types & functions of carbohydrates, lipids, and proteins  Explain how enzymes function NEXT LECTURE THE CELL