1. BIOCHEMISTRY
for health professionals
L AURA BATMANIAN
JUSTIN RIDGE
SIMON WORRALL

2. PART A
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Biological
og ca
gic
m al
hem t
mis
chemistry
p
Au
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3. PART A BIOLOGICAL CHEMISTRY
Atomic number and Radioactive isotopes can be useful in clinical
atomic mass diagnosis and in therapy. Isotopes that are inten-
tionally introduced into the body are called y a
The atoms of different elements have different numbers radiopharmaceuticals. Depending on the type, the ty
ly 1
of 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 1
The number of protons is unique for each element and gh
h
and can be followed through the body and used toan
is referred to as its atomic number. The atomic number thy. Radioact
check if organs are healthy. Radioactive isotopes are
e 20
is 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 decay
protons in its nucleus. Since atoms do not carry a net so dam
da heal
healt sues
es
isotopes can also damage healthy tissues leading to
charge 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 to
determine the number of neutrons in the nucleus. The How are electro
e electrons organised
ganised
mass number is written as a superscript to the left of the in atoms?
ms?
am tra
element’s symbol. So, using carbon as an example 12 C
tells us that the nucleus of a carbon atom contains six
protons (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
nucl
number – atomic number). The mass number also gives small mmarble then the atom w
hen wou have a radius of
would
pl
rs s
us 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 Au
Isotopes 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 T
All the atoms of an element have the same number of
e am umber mb come together to u
e undergo a chemical reaction, their
protons, but sometimes the number of neu
ber neutron varies.
neutrons nuclei are widely separated, and that only the electrons
wid
s r
These different forms of a single element are referred
ngle ar red are involved.
involv
of ie
to as isotopes. For example, carbon naturally occurs
le, natur
natu rs The elelectrons associated with an atom have
as a mixture of three isotopes with atomic masses of
sotopeses ato es differing amounts of energy. Electrons close to the
di rin
12, 13 and 14. The most common form is 12 C which
fo nucleus have the lowest amount of energy and are
n
ro ev
6
accounts 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 to
7 neutrons) with a small a amount of 14 C (6 protons
t 6
pro have higher energy because energy has to be expended
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and 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 continuously
whose nuclei do not lose particles. However, carbon-14
no cles. Howe c distributed, instead occurring in discrete steps. If there
is 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 off
nuclei 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 of
decay, and can result in a change in the atomic number
a n sult c the energy levels, electrons act more like a ball on a
such that a different element is formed. For example, 14C
ch erent elemen
rent staircase. When a ball rolls down stairs it can spend
decays 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 their
which remains in the nucleus, an electron, and excess distance from the nucleus (Fig 1-2). Electrons can move
energy, which is released. from one energy level to a higher one by absorbing
6

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.
ron
FIGURE 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 tra
Electrons closest to the nucleus have the lowest energy whereas
those furthest away have the highest. The energy levels are not
continuously 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-dimens
absorb 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 s
a 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 shap
energy (e.g. light). This process is calle excitation.
cal
called excita
xc are important because they determine the shape of
e importan b
Later, when the electron returns to its origi
rns original energy
o y molecules when they are used to form chemical bonds
whe
s r
level, the excess energy it possessed is released to the
rel
rele ot (see below).
bel
below)
of ie
environment (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
ectr
determines the chemical reactivit of the atom. The
hemical reactivity
al he in its s orbital whereas the next shell can hold a maximum
ro ev
difference between one elemen and the next in the
een element hee th of eight electrons in its four orbitals. Each of these
periodic table of the elements (a table made by arranging
e f element le ma arrang electrons basically has the same energy but occupies a
the elements according to their atomic number, part of
ents
nts n
nu er, different volume of space. Chemical reactivity arises
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which is shown in Fig 1-3) is the addition of a proton, an
1 e from the presence of unpaired electrons in one or more
electron 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 whe
can 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 mical
depend on the number of elec
depe e electrons in the outermost
shell. These are often referr to as valence electrons.
sh referred
re Atoms with incomplete valence (outermost) shells can
Atoms with the same number of valence electrons
he sam n share or transfer valence electrons to or from another
have 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 each
react with other atoms. These atoms are also said other (Fig 1-5). This interaction is termed a chemical
to be inert. Atoms with incomplete outer shells are bond, of which covalent and ionic are the strongest
reactive. (Table 1-2).
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5. PART A BIOLOGICAL CHEMISTRY
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on 1
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am tra
pl
rs s
fo Au
s r
of ie
FIGURE 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 fig
element 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 n
as 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
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©
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 electrons
in 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
g
Note: 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 s
molecules through chemical bond formation. The first two examples show
es ow
molecules made from two atoms of the same element whereas the last two
ast the rule outlined above. This is because a phosphorus
ed T
show 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 bonds
Covalent bonds but can also use its outermost pair of electrons to make
o
A 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 r
is 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,
How
a single valence electron in a shell (1s) that can hold two
on (1 ) an d to fo
form molecules. One of the simplest examples of
electrons. When two hydrogen at atoms approach each two different elements combining to form a molecule
ro ev
other they reach a point where their electron orbitals
ch lectron orbita
ctron is water (H2O). In this molecule, oxygen completes
overlap. At this point they can share electrons such
s hare ectrons s its valence shell by forming single bonds with two
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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 0.1
Note: In water, covalent bonds are much stronger than the other attractive forces between atoms. Thus they define the boundaries of one molecule from
er, c
another. However, many of the important biological interactions between molecules are mediated by noncovalent interactions that are individually quite
weak, but together can create effective interactions between two molecules. These noncovalent forces are ionic bonds, hydrogen bonds and van der Waals
interactions. 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 a
bond 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 of
one type only. The values in water are more representative of their relative importance in biological systems, whereas in vacuum values are really the maximum
value for each bond type.
9

7. PART A BIOLOGICAL CHEMISTRY
Molecular shapes
Any molecule has a distinctive size and shape that is
dependent on the atoms used to make it, and on the
ly 1
pattern in which they are bonded to each other. As we
will see in later chapters, the functionality of many
on 1
biological 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 comprising
three or more atoms have much more complex shapes. FIGURE 1-9 Examples of simple molecules. A shows the
mples s e mole ows
Their shapes are derived from the orbitals used to structure of a molecule of methane. When an atom with valence
ecule metha
meth vale
lia
form 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 th
forms 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 s
rearrange. 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 m
p orbitals hybridise to form four new hybrid orbitals
am tra
that are teardrop-shaped and extend from the region of
the 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
t
called 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 s
example of a tetrahedral molecule is methane (Fig 1-9A).
g 9A). bonds. Thus, water is also a tetrahedral molecule.
bonds ater tetr
The carbon nucleus sits at the centre of the tetrahedron
trahedron
fo Au
and the four hydrogen atoms bonded to the carbon sit
he
at its four corners. Water is also a tetrahedral molecule
h ral hydrogen atoms. Each of these sit at opposite corners
drogen
gen E
though 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 w
of water is derived from the formation of tw single
rmation o two
on by non-bonding orbitals containing pairs of electrons
non-bond
s r
bonds between the central oxygen atom a and two
wo which are totally derived from the oxygen atom.
tota
of ie
ro ev
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©
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8. ELEMENTS AND COMPOUNDS, CHEMISTRY AND LIFE 1
CHAPTER SUMMARY
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am tra
pl
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fo Au
Content relating to this chapter is available online at:
pter
r va e nline :
e
s r
http://evolve.elsevier.com/AU/Batmanian/biochemistry/
evier.com/A
evier.com/AU atm nian/bioch
b
of ie
ro ev
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©
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