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Part 1: Cell biology and energetics Chapter 1: Molecules of life Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-1 Elements • • H, O, N and C constitute 99 per cent of living parts of organisms 12 to 14 other elements of importance to living organisms – P, S, Cl, Na, Mg, K, Ca Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-2 Atoms • Each element is composed of one type of atom • Atoms composed of subatomic particles, which carry a charge – proton (positive) – neutron (neutral) – electron (negative) (cont.) Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-3 Atoms (cont.) • Atomic structure – nucleus composed of protons and neutrons – electrons orbit nucleus • Atomic number – number of protons in nucleus • Atomic mass – number of protons + neutrons in nucleus • Isotopes of element have different numbers of neutrons Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-4 Electrons • Electrons move around the nucleus in orbitals – zones of space in which electrons exist at any one moment • Electrons in orbitals closest to the nucleus have lowest energy levels – those further away have successively higher energy levels – electrons can move between orbitals by gaining or losing energy (cont.) Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-5 Electrons (cont.) • Each orbital contains no more than two electrons • Single orbital at lowest energy level – closest to the nucleus • At higher energy levels, more than one orbital – electron shell Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-6 Fig. 1.3a: Structure of carbon atom Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-7 Fig. 1.3b: Structure of oxygen atom Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-8 Fig. 1.3e: Structure of chlorine atom Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-9 Bonds between atoms • Chemical properties of an element determined by number and arrangement of electrons in outermost shell – atoms gain or share electrons to fill outermost shell • Outermost shell filled with – two electrons in hydrogen (one shell) – eight electrons in other elements (two or more shells) • Sharing electrons to fill outermost shell – forms chemical bonds Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-10 Covalent bonds • Sharing electrons creates covalent bonds – atoms join to form molecules • Hydrogen atoms have one electron in outermost shell – two atoms form molecular hydrogen (H2) by sharing electrons • Molecules formed by electron sharing between atoms of C, O, H, N, P and S are basic constituents of living systems Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-11 Fig. 1.5a: Formation of covalent compounds Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-12 Fig. 1.5b: Formation of covalent compounds Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-13 Non-covalent bonds • Electrical charges bond atoms or molecules – weaker than covalent bonds • Ionic bonds – form between cations and anions • Van der Waals forces – form between temporarily polarised atoms • Hydrogen bonds – form between polar molecules of hydrogen and oxygen, nitrogen or other electronegative atoms Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-14 Ionic bonds • Atoms become charged when they lose or gain an electron from the outer shell – loss of electron creates a positively charged cation (electrons < protons) – gain of electron creates a negatively charged anion (electrons > protons) • Cations and anions bond together by opposite charges – ionic bonds Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-15 van der Waals forces • Charge on an atom is not uniformly distributed at any instant – one part may have slightly negative or positive charge • Attracts neighbouring atom with opposite charge Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-16 Hydrogen bonds • • Hydrogen and oxygen atoms bind covalently to form water molecules Electrons tend to stay closer to the oxygen atom, resulting in polarisation of the molecule – H end positive – O end positive • Polar molecules form hydrogen bonds with similar molecules Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-17 Fig. 1.5c: Formation of covalent compounds Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-18 Water • Ionic compounds separate into constituent anions and cations when dissolved in water – polar molecules of water surround ions and shield them from one another – hydration • • Water also forms hydrogen bonds with other polar molecules Non-polar molecules are repelled Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-19 Acids • Acids are proton donors – release H+ and an anion into solution • HCl → H+ + acid → H+ + anion Cl- pH of acid is < 7 Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-20 Bases • Bases are proton acceptors – accept H+ H+ • + H2O → H3O+ pH of base is > 7 Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-21 Buffers • Substances that maintain stable internal pH • Act as reservoir of H+ – release H+ when pH rises – accept H+ when pH falls CO2 + H2O ↔ H2CO3 ↔ H+ + HCO3OH- + H2CO3 ↔ H2O + HCO3- Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-22 Carbohydrates • Carbohydrates are the most abundant organic molecules in living organisms – chemical energy, structural components – Cn(H2O)n • Monosaccharides – single molecules with three to seven carbon atoms (glucose, fructose, galactose) • Disaccharides – formed by glycosidic linkages of monosaccharides (lactose, sucrose, α, α′-trehalose) • Polysaccharides – long chains of monosaccharides Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-23 Structural polysaccharides • Cellulose (plant and algal cell walls) – molecules group into microfibrils – hydrogen bonds and van der Waals forces between cellulose molecules prevent hydrogen bonding with water • insoluble Pectins (component of plant cell wall matrix) – galacturonic acid with side chains – forms gels • Chitins (fungal walls, arthropod exoskeleton) – forms microfibrils – similar to cellulose Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-24 Storage polysaccharides • Starch (plants) – short-term storage in photosynthetic tissue – long-term storage in tubers, seed endosperm and cotyledons – composed of amylopectin and amylose • Other plant storage polysaccharides – inulins – levans • Glycogen (animals) – storage in all tissues, but most abundant in liver and muscles Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-25 Lipids • Water-soluble biomolecules – structure phospholipids, sterols – energy storage and transport triacylglycerols – photoreceptors carotenoids – coverings waxes – chemical messengers • steroids, glycolipids. isoprenoids Composed principally of C, H and O Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-26 Simple lipids • Simple lipids are composed of – fatty acids with long hydrocarbon chain – alcohol • Triacylglycerols act as energy reserves – calorific content 37.67 kJg-1 more than twice as much than that of carbohydrates and proteins – stored in adipose tissue (animals) and seeds and fruit (plants) Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-27 Biomembranes • Phospholipids – amphipathic molecules hydrophobic non-polar region (hydrocarbon chains) hydrophilic polar region (phosphate and nitrogen compounds) – form micelles and bilayers (basic structural units of all biological membranes) • Glycolipids – amphipathic molecules hydrophobic non-polar region (hydrocarbon chains) hydrophilic polar region (monosaccharides) – involved in cell–cell recognition Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-28 Polyisoprenoid lipids • Steroids – properties depend on degrees of unsaturation of steroid structure and chemical groups at different positions • Cholesterol – amphipathic sterol – membranes, including myelin sheaths – precursor of many hormones • Carotenoids – long-chain polyisoprenoids – photoreception in chloroplasts, animal eyes – vitamins A, E, K Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-29 Proteins • Proteins are the most functionally diverse biomolecules – enzymes – structure collagen, elastin, silk – hormones insulins, growth factors – defence immunoglobulins, fibrinogen – haemproteins haemoglobin, myoglobin, cytochromes – membrane proteins Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-30 Amino acids • Proteins are chains of amino acids – components selected from set of twenty amino acids • All amino acids are composed of – amino group (–NH2), which may gain a proton and become –NH3+ – acidic carboxyl group (–COOH), which may donate a proton and become –COO– various side-chain groups (denoted by R) Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-31 Structure of proteins • Primary structure – sequence of amino acids • Secondary structure – determined by arrangement of R-groups: α-helix and βsheets • Tertiary structure – final shape of protein: globular or extended rods • Quaternary structure – association of several globular proteins to form a functional protein Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-32 Fig. 1.32: Secondary structure of protein Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-33 Fibrous proteins • Keratin (hair, nails, feather, skin) – α-helix, extensible, increasing proportion of cysteine reduces extensibility • Silk – β-sheet protein, strong and flexible, but low extensibility • Collagen (connective tissue, bone, cartilage, skin) – α-helix, primary structure rich in glycine, proline, lysine • Elastin (arteries, skin, ligaments) – α-helix, primary structure rich in glycine, proline, alanine, lysine Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-34 Nucleic acids • • Nucleic acids carry genetic information in all living cells Composed of nucleotides – nitrogenous base pyrimidine (uracil, cytosine, thymine) purine (adenine, guanine) – pentose sugar ribose, deoxyribose – phosphate group Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-35 DNA • Deoxyribose nucleic acid – double-stranded – pentose sugar = 2-deoxyribose – bases = A (adenine), T (thymine), G (guanine), C (cytosine) • Two strands of DNA are joined by hydrogen bonds between complementary bases A — T (U in RNA) G—C Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-36 RNA • Ribose nucleic acid – single-stranded – pentose sugar = ribose – bases = A (adenine), U (uracil), G (guanine), C (cytosine) • Types of RNA – messenger RNA (mRNA) specifies amino acid sequence for given polypeptide – ribosomal RNA (rRNA) major component of ribosomes – transfer RNA (tRNA) carries amino acids to ribosomes to add to polypeptides Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-37 Fig. 1.40b: Structure of DNA Copyright 2005 McGraw-Hill Australia Pty Ltd PPTs t/a Biology: An Australian focus 3e by Knox, Ladiges, Evans and Saint 1-38