Chapte

C er 13: Biocchemistry – fastt factss

B..1 Introd
duction to
t bioche
emistry
Metabolic reaactions involve a complex interplay between
M b man ny
different components
c in highly con
ntrolled enviironments.

• The sum o
of all chemiccal reactions occurring in an organism
m is known as metabolism
m. These reactions occurr in
aqueous solution
s in co
ontrolled environments.
• Anabolism
m refers to metabolic
m patthways of synthesis, cataabolism referrs to metabo
olic pathwayss of
breakdowwn.
• Condensaation reactions occur durring synthesis, and hydro
olysis reactions occur durring breakdown.
• Photosyntthesis synthe
esizes energyy-rich moleccules from CO
O2 and H2O using
u light en
nergy.
• Respiratio
on is the controlled breakkdown of en
nergy-rich mo
olecules in ceells to releasse energy.
• The functions of biom
molecules dep
pend on theiir structures and shapes..

B..2 and B..7 Prote

eins and enzymess
Proteins aree the most diverse of the biopolymers responsiblee for metabo olism and strructural integgrity of livingg
organnisms. Analysses of protein
n activity and
d concentrattion are key areas of biocchemical ressearch.

• 2-amino acids
a are amphoteric and d can exist ass zwitterionss or as cation
ns or anions in
i solution. Their
T charge
depends on
o the pH an nd their isoellectric point.. They can acct as pH bufffers.
• There aree 20 differentt amino acids that differ in their R gro
oup.
• ondensation reactions fo
Amino acids join by co orming peptide bonds, which are amiide links. Theere is an
enormouss variety of protein
p strucctures possib
ble due to thee variety of amino
a acids.

Protein
P struccture Nature of
o interactions

priimary covvalent (amidee / peptide) bonds betweeen amino acids

seccondary hyd
drogen bonds within the polypeptidee chain involvving groups in
i the peptid
de bonds

terrtiary inteeractions bettween side chains

c including hydrophobic interacttions, hydroggen
bonnds, ionic bonds, disulfide bridges

quaternary inteeractions bettween polyp

peptide chain
ns, including the same intteractions ass in the
terttiary structure

• Fibrous prroteins are in

nsoluble and
d have a dom
minant secon
ndary structu
ure. They aree used in struuctural
components. Globular proteins arre soluble annd have a dom
minant tertiaary structuree. They are th
he molecular
tools in ceells.
• The speciffic three-dim
mensional shape of a glob
bular protein mation and iss essential for
n is known ass its conform
its functio
on.
• Enzymes aare biologicaal catalysts th
hat are madee of protein and control every biocheemical reactiion.

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• Enzymes b
bind specificcally to their substrate (reeactant) at a region calle
ed the active site. The forrmation of
enzyme–ssubstrate complex provid des an altern
nate reaction n route that has a lower activation
a en
nergy.
• Enzyme sttudies show saturation kinetics
k as [S]] increases.
• Vmax refers to the
e maximum rate
r of the reeaction undeer the specified condition
ns.
• Km reefers to the substrate
s concentration required forr the rate to be Vmax/2.
• The lower the vaalue for Km th he affinity of the enzyme for its substtrate.
he greater th
• nds on its conformation, and so is sensitive to changes in tem
Enzyme activity depen mperature, pH, and heavyy
metal ions.
• Chemical inhibitors caan regulate enzymes.
e Theere are two main
m types:

Competiitive inhibition Non-comp

petitive inhib
bition

bin
nding site on
n enzyme binds at activee site binds at allostteric site

efffect on Vmax no
ot affected decreased

efffect on Km increased not affected

• Product in
nhibition gen
nerates a feeedback loop that
t can be used
u to regu
ulate the concentration of
o enzymes
accordingg to the need
ds of the cell..
• The aminoo acid compo
osition of a protein
p can be hy and by gel
b analysed by paper chrromatograph
electrophoresis.
• The pH off a buffer solution can bee determined
d from know o its acid/base and by th
wledge of thee pKa or pKb of he
ratio of itss acid/base to
t salt.
[salt]]
pH = pK a + log10
{acid]
• The proteein concentraation in a sollution can bee determinedd using UV-vvis spectrosco
opy and a calibration currve
based on known stand dard concentrations. Thee Beer–Lamb bert law show ws that the absorbance
a o a compound
of
at fixed wavelength
w iss directly pro
oportional to its concentrration.

B..3 Lipidss
Lipids are a broad group of biomo
olecules that are largely non-polar
n and are therefore insolublee in water.

• Lipids are a broad group of non-po

olar biomole
ecules.
• Lipids are more reducced than carb
bohydrates and
a so releasse more energy when oxidized.
• Fatty acid
ds can be saturated or un
nsaturated. Unsaturated
U fats have low
wer melting points than saturated fats;
they are o
often liquids at room tem
mperature annd are knownn as oils.
• Triglycerid
des form by condensatio
on of three faatty acids witth one glycerol molecule
e, and contain ester links.
• The degreee of unsaturration in a faat is known as
a its iodine number.
n
• Lipids are essential co
omponents of o cells, especcially in mem
mbranes, butt excess dietaary fats can cause
c negatiive
health efffects such as circulatory problems.
p Saaturated fat and trans fatts cause the greatest pro
oblems.
• Phospholiipids contain
n two fatty acids and a ph
hosphate gro
oup condenssed to glycerrol. They form
m a bilayer in
n
cell memb
branes.

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• Cholesterrol is a steroid.
• Hydrolysiss of a fat pro
oduces fatty acids and glyycerol. It is carried out byy enzymes caalled lipases,, and acidic or
o
alkaline co
onditions.
• Rancidity of fats occurs either at the
t ester linkkages in triglyycerides or at
a the carbonn–carbon double bonds in
i
unsaturatted triglycerides. Saturated fats are more
m stable than
t unsaturrated fats.

B..4 Carbo
ohydrate
es
Carbohydrat
C tes are oxygeen-rich biomolecules that play a centtral role in metabolic
m reactions of eneergy transferr.

• Carbohydrates contain C and H:O in the same ratio as in water.

w
• Monosacccharides con ntain –OH grooups and either an aldeh
hyde or keton
ne group. Th
hey cyclize in
n solution to
form ring structures, which
w are represented by Haworth projections.
p
• Monosacccharides con
ndense to forrm disaccharrides and pollysaccharides with glycossidic (ether) linkages.
• Monosacccharides are soluble and are used in transport an
nd as energy sources; polysaccharides are insolub
ble
and are used for storaage and strucctural compo
onents.

B..5 Vitam
mins
Vitaminss are organic micronutrieents with dive
erse function
ns and which
h must be ob
btained from
m the diet.

• Vitamins are
a organic micronutrien
m nts; they are synthesized in the body. Vitamin D can
c be madee by the actio
on
of sunligh
ht on the skin
n.
• Vitamins are
a sensitivee to heat. Theeir solubility in water depends on theeir ability to form hydroggen bonds with
w
the waterr.
• Vitamin deficiency disseases are caaused by lackk of a balanced diet. Oveer-processingg of food, poor education
n,
and nutrieent depletion can all con
ntribute to th
his. Solutionss include forttification of staple
s foods,,
supplemeentation, and d education.

B..8 Nucleeic acids

DNA is the genetic material thaat expresses itself by controlling the synthesis
s of proteins by the
t cell.

• The monoomers of nuccleic acids are nucleotidees, composed

d of a pentosse sugar, pho osphoric acid
d, and
nitrogeno
ous base. The
e bases are purines
p (A an
nd G) and pyrrimidines (C,, T, and U).
• DNA is a double
d helix of two polyn
nucleotide sttrands. The ttwo strands are
a held togeether by two
o or three H
bonds bettween the sttacked basess: A=T, C≡G
• The comp
plementary base
b pairing ensures
e thatt the sequence of bases in
i one strandd uniquely deetermines th
he
sequence in the comp
plementary strand.
s This provides
p the basis of DNA
A replication
n.
• DNA has a negative ch o the phosphate groups. It associates with basic histones
harge due to h in ch
hromosomess.
• RNA is a ssingle polynu
ucleotide chaain. It contain
ns the base U in place off T in DNA an
nd ribose in place
p of
deoxyriboose.
• The genettic code is th
he means by which the seequence of bases b in DNA
A is used to determine
d the sequence of
amino aciids in a proteein. It is a trip
plet code and is universaal.

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• Genetically modified food
f refers to
t food produced from organisms thaat have had their
t DNA alttered by
genetic en
ngineering.

B..9 Pigme
ents
B
Biological piggments include a variety of chemical structures with
w diverse functions
f and
which absorb specific waveelengths of ligght.

• Pigments are colouredd compound ds produced by metabolissm. Their colour is due to o highly conjjugated
systems w
with delocalizzed electrons, which abssorb in the viisible region of the spectrum.
• Porphyrin w nitrogen-containingg cyclic ligand
n compoundss are chelatees of metals with ds.
• Chlorophyyll is the prim
mary pigmen nt involved in
n trapping ligght energy in
n photosynth hesis. Its porp
phyrin ring
contains m
magnesium. It undergoess a redox chaange and is reduced
r backk to its origin
nal form by eelectrons fro
om
water. Chlorophyll is more
m sensitivve to changees in temperature in aciddic conditions.
• Hemoglob bin and myoglobin contaain heme gro oups with iron(II) ion, andd act to transsport and sto ore oxygen.
Hemoglob bin is a tetrameric proteiin, which binnds four oxyggen moleculees cooperativvely. Its oxyggen
dissociatioon curve is shifted to thee right (releases oxygen more
m easily) at warmer temperatures and lower
pH/higher concentrattion of CO2. CO C acts as a competitive
c inhibitor forr O2. Fetal heemoglobin haas a higher
affinity fo
or oxygen thaan adult haem moglobin; itss oxygen disssociation currve is shifted d to the left.
• Myoglobin has a higheer affinity for oxygen and
d stores oxyggen. It is mon
nomeric so does
d ow cooperative
not sho
binding.
• Cytochrommes contain iron which undergoes
u reedox change from iron(II) to iron(III). They form the electron
transport chain in aerrobic respirattion and pho
otosynthesis..
• Carotenoiids and anthocyanins actt as accessorry pigments iin photosyntthesis.
• Carotenoiids are lipid soluble
s and can
c be oxidizzed in light-ccatalysed reaactions.
• Anthocyanins are watter soluble an
nd can act ass pH indicato
ors.
• Pigments can be analyysed by thin--layer chrom
matography (TTLC), a form of adsorptio
on chromato
ography. TLC
works on smaller samples than paaper chromattography and is more sensitive.

B..10 Sterreochem
mistry in biomole
b cules
Most biochem
M mical processses are stereeospecific and involve on
nly
m
molecules with a certain configuratioon of chiral carbon atomss.

• Proteins: amino acids are chiral (eexcept glycine) and exist in the L form
m.
• Lipids: unsaturated fats occur mosstly in the ciss form, with relatively low
w melting po
oints. Partial hydrogenattion
of fats con
nverts some of these gro
oups into thee trans positiion, which is associated with
w health problems,
p su
uch
as cardiovvascular dise
ease.
• Carbohydrates: sugarss exist as D or
o L stereoiso
omers; the D form is the most abund dant in nature. Alpha and
d
beta sugaars differ in th
he positions of the –OH groups
g in C1 for glucose and
a C2 for fructose. Starcch and
glycogen are polymerrs of alpha glucose, and cellulose
c is a polymer of beta
b glucosee.
• Vitamins: vitamin A, retinal, undergoes an isom
meric conversion from 11-cis-retinal to all-trans-retinal in thee
visual cycle.

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B..6 Biochemistry and the environm
ment
Our increasing know
wledge of bio
ochemistry hhas led to sevveral environ
nmental
prob
blems, while
e also helpingg to solve oth
hers.

• Xenobiotiics are chemicals found in the environment that are

a not norm mally presentt there. Theyy include
antibiotics and other pharmaceutically active compounds,, pesticides, plastics, etc..
• mulation refers to the build-up of a to
Bioaccum oxin in an orgganism.
• Biomagniffication refers to the incrreasing conccentration off xenobioticss at increasin
ng trophic levvel in food
webs.
• Host–guest chemistryy involves speecifically synthesized mo
olecules that bind to toxin
ns in the envvironment,
forming a supermoleccule with bonnds other thaan covalent.
• Biodegrad
dable substances can be decomposed
d in the natu
ural environm
ment.
• Bioremed
diation includ
des the use of
o enzymes that break do
own pollutan
nts in the envvironment.
• Green Cheemistry seekks to reduce the release into
i the enviironment of hazardous substances.

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ut the Pearson
n Baccalaureatte series pleasse visit
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