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  • 1. BIOCHEMISTRY for health professionals L AURA BATMANIAN JUSTIN RIDGE SIMON WORRALL
  • 2. PART A ly 1 on 1 20 -Biological og ca gic m al hem t mischemistry pAu 1
  • 3. PART A BIOLOGICAL CHEMISTRYAtomic number and Radioactive isotopes can be useful in clinicalatomic mass diagnosis and in therapy. Isotopes that are inten- tionally introduced into the body are called y aThe atoms of different elements have different numbers radiopharmaceuticals. Depending on the type, the ty ly 1of subatomic particles but all the atoms of a single re isotope will collect in one or more areas of the body.element have the same number of protons in their nuclei. Since the isotope emits radiation, it is easily t ion, ea tracked on 1The number of protons is unique for each element and gh h and can be followed through the body and used toanis referred to as its atomic number. The atomic number thy. Radioact check if organs are healthy. Radioactive isotopes are e 20is written as a subscript on the left of the symbol for the also given to cancer patients in an attempt to dam e atients ients att am damage -element. Thus, 6C tells us that an atom of carbon has six ever, radiati ver, radia om decayin cancerous tissue. However, radiation from decaying decayprotons in its nucleus. Since atoms do not carry a net so dam da heal healt sues es isotopes can also damage healthy tissues leading tocharge the carbon atom must also have six electrons. cellular injury, often result y, resul resulting in cellular death. llular ar lia The mass number of an element allows us todetermine the number of neutrons in the nucleus. The How are electro e electrons organised ganisedmass number is written as a superscript to the left of the in atoms? ms? am traelement’s symbol. So, using carbon as an example 12 Ctells us that the nucleus of a carbon atom contains sixprotons (from its atomic number) and six neutrons (mass 6 s Simple models of an atom ov mphasise the size of imple he ple the nucleus re o tom overemphasise mphas relative to the whole atom. For a small who om atom such as helium, if the nucleu was the size of a um,, nucleus nuclnumber – atomic number). The mass number also gives small mmarble then the atom w hen wou have a radius of would pl rs sus a close approximation of the atomic mass (in daltons). altons). ) 50–60 m. At this scale the electrons would only be a 50–6 s elec few millimetres in diameter. From this you can see that fe metres diame res fo AuIsotopes the majority of the volum occupied by an atom does ajority rity volume not contain anything. This means that when two atoms t ntain anythi TAll the atoms of an element have the same number of e am umber mb come together to u e undergo a chemical reaction, theirprotons, but sometimes the number of neu ber neutron varies. neutrons nuclei are widely separated, and that only the electrons wid s rThese different forms of a single element are referred ngle ar red are involved. involv of ieto as isotopes. For example, carbon naturally occurs le, natur natu rs The elelectrons associated with an atom haveas a mixture of three isotopes with atomic masses of sotopeses ato es differing amounts of energy. Electrons close to the di rin12, 13 and 14. The most common form is 12 C which fo nucleus have the lowest amount of energy and are n ro ev 6accounts for 99% of naturally oc occurring carbon. The arbon. strongly attracted by the positively charged nucleus.remaining 1% consists mainly of 13 C (6 protons an nsists mainl 6 otons and Electrons further away from the nucleus are said to7 neutrons) with a small a amount of 14 C (6 protons t 6 pro have higher energy because energy has to be expended - p Elsand 8 neutrons). utrons). to push them against the attraction of the nucleus. Both carbon-12 an carbon-13 are stable isotopes h a and bon-13 -13 stabl is The energy levels of the electrons are not continuouslywhose nuclei do not lose particles. However, carbon-14 no cles. Howe c distributed, instead occurring in discrete steps. If thereis unsta and is radioactive. Radioactive i unstable i oactive. Radioac ive. isotopes have was a continuous distribution of energy levels then the which spontaneously lose particles and give offnuclei wh w aneously ously pa partic electrons would act like a ball rolling down a slope.©energy. Th process is often referre to as radioactive This ocess T referred ref However, because of the discontinuous distribution ofdecay, and can result in a change in the atomic number a n sult c the energy levels, electrons act more like a ball on asuch that a different element is formed. For example, 14C ch erent elemen rent staircase. When a ball rolls down stairs it can spenddecays to produce stable nitrogen. nit time on each step but must drop quickly from step 14 1 14 to step. Similarly, electrons do not spend appreciable 6 C 7 N + e– + energy time between energy levels. Thus, electrons are found In this decay reaction a neutron becomes a proton, in electron shells whose energy is relative to theirwhich remains in the nucleus, an electron, and excess distance from the nucleus (Fig 1-2). Electrons can moveenergy, which is released. from one energy level to a higher one by absorbing6
  • 4. ELEMENTS AND COMPOUNDS, CHEMISTRY AND LIFE 1 Orbital theory Initially electrons were thought to orbit the nucleus rbit th ly 1 in the same way that planets orbit a sun. H rbit However, this planetary model does not give a real p picture of on 1 an atom. Electrons do not circle the at ot t ato atom in fixed, circular orbits. To get a better pict et picture of atomic ic e 20 structure, chemists describe orbitals—regions around escribe orbital gions a und s - the nucleus where an electron is likely to be found n ely fo most of the time. T ime. This orbital model is represented orbit rbit del represente l represe as an electron cloud surrounding the nucleus of the tron su ng he th lia atom that represents th probable region of grea hat at the bable greatest electron density. ronFIGURE 1-2 Electrons exist at different energy levels in atoms. Each electron shell can now be thought of as an ch w though th am traElectrons closest to the nucleus have the lowest energy whereasthose furthest away have the highest. The energy levels are notcontinuously distributed but exist in discrete steps. An electron may ay electron cloud containing electrons wi a specific ectron orbitals a re aining arranged in three-dim g trons with energy level that are distributed in a sp specific number of three-dimensional space (Fig 1-4). ed n three-dimensabsorb energy from the environment and jump one or more levels, vels, (1s The fi electron shell (1s) is sph first ctron n (1s) spherical, the second has pl rs sa process called excitation. Later it can return to its initial state by tate y four orbitals of which one (2 is spherical and three fou tals f on (2s)giving up the energy it previously absorbed. mbbell-shaped (2p are dumbbell-shaped (2p orbitals). The next shell also bell-shaped (2 fo Au s ‘p has one ‘s’ and three ‘p’ orbitals, as well as others with ‘s’ ‘p more complex shapes. The shapes of these orbitals re shapenergy (e.g. light). This process is calle excitation. cal called excita xc are important because they determine the shape of e importan bLater, when the electron returns to its origi rns original energy o y molecules when they are used to form chemical bonds whe s rlevel, the excess energy it possessed is released to the rel rele ot (see below). bel below) of ieenvironment (e.g. as heat).at). Each orbital is occupied by a maximum of two E How electrons are distributed into their shells re stributed i heir shell electrons. The first electron shell can hold two electrons ectrdetermines the chemical reactivit of the atom. The hemical reactivity al he in its s orbital whereas the next shell can hold a maximum ro evdifference between one elemen and the next in the een element hee th of eight electrons in its four orbitals. Each of theseperiodic table of the elements (a table made by arranging e f element le ma arrang electrons basically has the same energy but occupies athe elements according to their atomic number, part of ents nts n nu er, different volume of space. Chemical reactivity arises- p Elswhich is shown in Fig 1-3) is the addition of a proton, an 1 e from the presence of unpaired electrons in one or moreelectron and one or more neutrons. The f tron rons. first electron of their outermost shells.shell can hold on pair of electrons whereas the next two one ctrons whecan h four pairs of electrons. This mea that the first hold ectrons.three levels hold 18 electrons. le ctrons. means Chemical bonds and compounds© The chemical properties of an element largely Th micaldepend on the number of elecdepe e electrons in the outermostshell. These are often referr to as valence electrons.sh referred re Atoms with incomplete valence (outermost) shells canAtoms with the same number of valence electrons he sam n share or transfer valence electrons to or from anotherhave similar properties. Atoms with full outermost ilar per pert atom such that both atoms complete their valence shells.shells are ggenerally unreactive, being unable to easily This normally results in the atoms staying close to eachreact with other atoms. These atoms are also said other (Fig 1-5). This interaction is termed a chemicalto be inert. Atoms with incomplete outer shells are bond, of which covalent and ionic are the strongestreactive. (Table 1-2). 7
  • 5. PART A BIOLOGICAL CHEMISTRY ly 1 on 1 e 20 - lia am tra pl rs s fo Au s r of ieFIGURE 1-3 The initial elements in part of the periodic table of the elements. This figure shows how each element relates to the next. Each s per perio e he ele e ts ts. Th figelement differs from the next by the addition of a proton and a variable number of neutrons. Elements with similar electron distributions such ddition p nd able num nas hydrogen, lithium and sodium, or helium, neon and argon, have similar chemical reactivity. A full periodic table is shown on page XXX. odium,, ne c ro ev[Based on Campbell & Reece, 2005, Biology, 7th Ed ce, 05, Biology, th E Biolog Edition, Pearson Benjamin Cummings] on Cumming Cummi - p Els©FIGURE 1-4 Electrons really occupy defined volumes of space. To better define the behaviour of electrons, the concept of orbitals—volumes in which electrons spend 90% of the time—was developed. Electrons are distributed into shells of differing energies, with electronsin each shell occupying defined orbitals.8
  • 6. ELEMENTS AND COMPOUNDS, CHEMISTRY AND LIFE 1 TABLE 1-2 How atoms interact to make simple that each atom now has two associated electrons, with molecules complete valence shells. Two or more atoms interacting by covalent bonds constitute a molecule (Table 1-3). e (T Distribution Structural Covalent Compound of electrons representations bond type A similar story can be told for the formation of or he for ly 1 a molecule of oxygen (O2) from two oxygen atoms. omm Hydrogen However, since an oxygen atom has six valence electrons m va Single on 1 (H2) in a shell that requires eight to be comp ight ght complete, the two oxygen atoms share two pairs of electr wo ele electrons to completete e 20 Oxygen their valence shells. The sharing of a single pair of o ngle e - Double (O2) electrons is referred to as a single bond, and the sharing o sh sha of two pairs is termed a double bond. e ouble uble Water Two The number of pairs of electrons that an atom need mber ns hat needs ne lia (H2O) single to share to fill its valenc shell, that is, the number of valence valen l, at numbe covalent bonds it generally needs to form to do this, is lent gen ds termed its binding capacity or valence. This c be used rmed bindin d valence. can Methane Four (CH4 ) am tra single to explain the valences of elements such as hydrogen, n en, es e ents s oxygen and nitrogen, but not for some other elements. In fo me o naturally occurring compounds phosphorus often has rring compound p gNote: This table demonstrates how three elements can be used to make ake a valence of five, not three as wo valen , a would be predicted using pl rs smolecules through chemical bond formation. The first two examples show es owmolecules made from two atoms of the same element whereas the last two ast the rule outlined above. This is because a phosphorus ed Tshow molecules made from two different elements atom, which has five electrons in its valence shell, can h e elect fo Au use its three unpaired electrons to make single bondsCovalent bonds but can also use its outermost pair of electrons to make oA covalent bond is formed when two atoms share a n wo oms sh ms a double bond bond.pair of valence electrons. The simplest e est example of this exam l is So far the examples of bonding that have been s ris to look at the formation of a molecule of hydrogen o rog examined are between two atoms of the same element. examin a of ie(H2) from two hydrogen atoms. Hydroge atoms have n oms. Hydrogen Hydro ms hav Howeve atoms of different elements can also interact However, Howa single valence electron in a shell (1s) that can hold two on (1 ) an d to fo form molecules. One of the simplest examples ofelectrons. When two hydrogen at atoms approach each two different elements combining to form a molecule ro evother they reach a point where their electron orbitals ch lectron orbita ctron is water (H2O). In this molecule, oxygen completesoverlap. At this point they can share electrons such s hare ectrons s its valence shell by forming single bonds with two- p Els TABLE 1-3 Representative values for covalent and noncovalent bonds LE 1 Represe alues c Strength (kJ/mole) Class of bond Type of bon pe bond Bond length (nm) In vacuum In water Covalent Cova Covalent ovalent 0.15 380 380© Noncovalent Nonc Ionic 0.25 335 13 Hydrogen 0.30 17 4 van der Waals interaction (per atom) 0.35 0.1 0.1Note: In water, covalent bonds are much stronger than the other attractive forces between atoms. Thus they define the boundaries of one molecule from er, canother. However, many of the important biological interactions between molecules are mediated by noncovalent interactions that are individually quiteweak, but together can create effective interactions between two molecules. These noncovalent forces are ionic bonds, hydrogen bonds and van der Waalsinteractions. The strengths of all noncovalent bonds are less than that of covalent bonds, in both the presence and the absence of water. The strength of abond can be measured as the energy required (kilojoules; kJ) to break all the bonds in one mole of a molecule that contains only one bond, that bond being ofone type only. The values in water are more representative of their relative importance in biological systems, whereas in vacuum values are really the maximumvalue for each bond type. 9
  • 7. PART A BIOLOGICAL CHEMISTRYMolecular shapesAny molecule has a distinctive size and shape that isdependent on the atoms used to make it, and on the ly 1pattern in which they are bonded to each other. As wewill see in later chapters, the functionality of many on 1biological molecules is often determined by their three-dimensional shape. e 20 Molecules made from two atoms such as H2 or O2 -are always linear. However, molecules comprisingthree or more atoms have much more complex shapes. FIGURE 1-9 Examples of simple molecules. A shows the mples s e mole owsTheir shapes are derived from the orbitals used to structure of a molecule of methane. When an atom with valence ecule metha meth vale liaform the bonds between the atoms. When an atom electrons in both the s and p orbitals forms a covalent bond, the oth orbit s valent t orbital hybridises to give four t ridises es teardrop-shaped hybrid orbitals that shaped ped orbit thforms covalent bonds, the orbitals in the valence shell delineate a tetrahedron. In the case of methane the carbon sits at the te etrahedron. hane carb srearrange. An atom with valence electrons in both s and centre of the tetrahedro and the four covalent bonds it makes with re tetrahedron fou alent bon mp orbitals hybridise to form four new hybrid orbitals am trathat are teardrop-shaped and extend from the region ofthe nucleus. These orbitals delineate a volume of space e single hydrogen atom are the four corners. B shows the structure of ngle atoms ato s e ur corn water. Oxyge al makes single bonds with hydrogen atoms (two) ater. Oxygen also w wit and these sit at opposing corners of the tetrahedron. The other two ing orners tetra tcalled a tetrahedron, a shape similar to a pyramid. An corners ar occupied by pairs of electrons that are not used to make are ed y ele t pl rs sexample of a tetrahedral molecule is methane (Fig 1-9A). g 9A). bonds. Thus, water is also a tetrahedral molecule. bonds ater tetrThe carbon nucleus sits at the centre of the tetrahedron trahedron fo Auand the four hydrogen atoms bonded to the carbon sit heat its four corners. Water is also a tetrahedral molecule h ral hydrogen atoms. Each of these sit at opposite corners drogen gen Ethough it is less easy to see why (Fig 1-9B). The sha ig 1-9B) 9B e shape s of the tetrahedron while the other corners are occupied e tetrahedr wof water is derived from the formation of tw single rmation o two on by non-bonding orbitals containing pairs of electrons non-bond s rbonds between the central oxygen atom a and two wo which are totally derived from the oxygen atom. tota of ie ro ev - p Els©12
  • 8. ELEMENTS AND COMPOUNDS, CHEMISTRY AND LIFE 1CHAPTER SUMMARY ly 1 on 1 e 20 - lia am tra pl rs s fo AuContent relating to this chapter is available online at: pter r va e nline : e s rhttp://evolve.elsevier.com/AU/Batmanian/biochemistry/ evier.com/A evier.com/AU atm nian/bioch b of ie ro ev- p Els© 13