INTRODUCTION TO
BIOCHEMISTRY
MUHAMMAD SHARIR BIN ABDUL RAHMAN
1
1.1 The Chemical Elements of Life
1.2 Important Biomolecules
1.3 The Cell as Basic Unit of Life
1.4 Water Molecule
1.5 Ionic and Polar Substances Dissolve in
Water
1.6 pH Scale
1.7 Buffered Solutions Resist Change in pH
2
1.1 Chemical elements of life

Organic chemistry = study of carbon, hydrogen
and their derivatives.

We concentrate on aspect of organic
chemistry that we need to understand what
happen in living cells.
3

Organic chemists study reactions that take
place in laboratory. Biochemists study how
reactions occur in living cells.

Biochemical reactions involve specific chemical
bonds or functional groups (parts of
molecules).
4
General formulas of organic compounds
5
General formulas of functional groups
6
General formulas of linkages in biochemical compounds
Ester & ether linkages are common in fatty acids and lipids.

7
Can chemist make the molecules of life in
the lab?


In 1828, Friedrich Wohler a German scientist performed a
miracle experiment.
He synthesized urea, waste product of animal from
ammonium cyanate, a compound from mineral.
NH4OCN
8
H2NCONH2

Chemical reactions that occur inside cells are the
same kind of reactions that occur in a chemistry lab.

The biggest difference is that almost all reactions
inside cells are catalyzed by enzymes, thus proceed at
very high rates.

It is very useful to distinguish between biochemical
reactions that take place in an organism (in vivo) and
those that occur under laboratory conditions (in
vitro).
9
1.2 Important biomolecules





Most biomolecules contains O2 and N2.
These are among the most electronegative elements.
Others are C, H2, P.
Many of these functional groups are polar.
Their polarity nature plays crucial role in their
reactivity.
10

Biochemistry deals with large molecules referred to
as macromolecules.

Biological macromolecules are usually polymers
created by joining many smaller organic molecules
(monomers) via condensation (removal of the
elements of water).
11
MACROMOLECUL
MONOMERS
ES
12
Protein
Amino acid
Lipid
Fatty acid
Polysaccharides
Monosaccharide
Nucleic acid (DNA & RNA)
Nucleotide
 Each
monomer joined into a macromolecular chain is
termed as residue.
 Certain
carbohydrates consist of repetition of a single
residue.
 Proteins
and nucleic acids consist of different types of
residues which are connected in specific order.
13
Proteins





20 common amino acids incorporated into proteins in all
cells.
Each contain an amino group, a carboxylate group and
side chain group (R).
R is unique to each amino acids.
Peptide bond = bond between carbon atom of 1 amino
acid residue and the nitrogen atom in the next residue.
This amid linkage condense 1 water molecule
14


Many proteins works as enzymes and structural
components of cells.
Sequence of amino acid residues determines the
three-dimensional
structure
(conformational
structure) of proteins.
Structure of mannosebinding lectin
15
Β-sheet
α-helix
Adapted from Weis WI and Drickamer K (1994) Structure, 2:1227-40
Polysaccharides




Carbohydrates (saccharides) primarily composed of
carbon, oxygen and hydrogen.
Simple sugars = Monosaccharides.
Sugar polymers = Polysaccharides.
Structures drawn in:




Fisher projection (open chain and ring form)
Haworth projection (ring form, most common)
Envelop conformation
Example: ribose (C5H10O5)
16


Example: Glucose and cellulose
C-1 of glucose binds to C-4 of another glucose (glycosidic
bond) = cellulose



Monomer = glucose
Polymer = Cellulose, glycogen and starch
Cellulose is the major component of flowering plant
stems &tree trunks.
17
Nucleic Acids




Nucleic acids (polynucleotides) = composed of many
nucleotides.
Plentiful in eukaryotes and prokaryotes.
Nucleotides consists of five-carbon sugar (ribose or
deoxyribose), a heterocyclic nitrogenous base and at least
one phosphate group.
Nitrogenous base of nucleotides = purines and pyrimidines.
18




Purines = adenine (A) and Guanine (G)
Pyrimidines = Cytosine (C), Thymine (T), Uracil (U)
In nucleotide the base is joined to C-1 of sugar and
phosphate group is attached to other sugar carbons
(usually C-5)
Example: Adenosine Triphosphate (ATP)



19
Glycosidic bond (Adenine to ribose)
Phosphoester linkage (C-5 to α phosphoryl)
Phosphoanhydrides (β,ϒ,α phosphoryl group)



20
Polynucleotides = C-3 oxygen
atom of sugar covalently
linked to phosphate group of
one nucleotide (phosphoester
linkage).
Nitrogenous base at C-1.
DNA and RNA (tRNA,
mRNA, rRNA).
Lipids and Membranes



Lipid = diverse class of molecules that are rich in C
and H2 but contains only few O2
Simplest lipid = fatty acids = long chain hydrocarbons
with a caboxylate group at one end.
Fatty acids commonly found as part of larger
molecules called glycerophospholipids.
Glycerophospholipid contains glycerol 3-phosphate and two
fatty acyl group
Other kinds of lipids = steroids and waxes




21
Steroid:ex. Cholestrol
Wax: Beeswax and earwax





22
Lipids have a polar, hydrophilic head that can interact with
aqueous environment and non-polar, hydrophobic tail.
Aqueous environment = hydrophobic tails of such lipids
associate and produce a sheet called lipid bilayer.
Lipid bilayers forms the structural basis of all biological
membranes.
Acts as barriers that impermeable to most water soluble
components.
Flexible because lipid bilayers are stabilized by noncovalent
forces.
23
1.3 Cell basic of life

Every organism is either single or composed of
many cells, except for virus.

A cell can be classified as prokaryotic or
eukaryotic.
24
Prokaryotic Cell




Prokaryotic cells contain genetic information that is
not enclosed in a nucleus membrane (nucleoid
region).
Cytosol has granular appearance because of
ribosome.
They also lack membrane enclosed organelles.
Procakaryotes consist of the Kingdom Monera
(bacteria).
25
26
27
Bacterium, a prokaryote.
Eukaryotic Cell

Genetic information of eukaryotes is enclosed in a
nucleus membrane.

They also have membrane enclosed organelles.

Eukaryotes consist of the kingdom Animalia, Plantae,
Fungi, and Protists (single cell eukaryotes).
28
29
Eukaryotic cell – animal cell
30
Eukaryotic cell – plant cell
Eukaryotic Cell (cont’d)

Three most important organelles




Nucleus: DNA and RNA synthesis.
Chloroplast: Site of photosynthesis (plant cell only).
Mitochondrion: contains enzymes that catalyze important energyyielding reactions (in animal cell only)
Nucleus




31
Surrounded by nuclear envelope.
Has nucleolus, and rich in RNA.
RNA synthesized on a DNA template in nucleolus and transport
to cytoplasm.
Near nuclear membrane has chromatin, aggregate of DNA and
proteins.

Mitochondrion





Endoplasmic Reticulum (ER)

32
Double membrane with inner membrane has many folds called
cristae.
In matrix, oxidation process occur to yield energy for the cell
Mitochondrial DNA located in internal matrix, also has
ribosome in matrix
A theory suggested it comes from absorption of aerobic
bacteria by larger host cells
Rough and smooth RE, ribosomes bound on membrane

Chloroplast
 Photosynthetic apparatus found in grana, membranous body
stacked
 Also has DNA that differ from nucleus and has ribosomes

Golgi apparatus
 Membranous sacs, involves in secretion of proteins
 Proteins are linked to sugar in Golgi apparatus.

Plasma membrane:
 Outer boundary of the cell. A continuous sheet of bilayer
lipid molecule.
 Contain proteins that function as enzymes, receptor for
hormones, molecular pumps and selective channels that
allow entry of certain molecules in and out of cell.
33

Cytosol
 Liquid interface of cells
 Organelles held in places by fine strands (microtubules) of
proteins

Cell wall
 External cell wall other than plasma membrane

Vacuoles
 Sacs that isolate waste that is toxic to plant, occurs as
poison for plant-eaters
34
Lysosomes
 Membrane-bound vesicles that contain hydrolases (catalyze
hydrolytic reactions) & function optimally at pH ~5.
 These enzymes (hydrolases) can catalyze the breakdown of
nucleic acids, proteins, cell wall carbohydrates, and
phospholipids.
 Involve in intracellular digestion (autophagy) & digestion of
material from outside the cell (heterophagy).
 Heterophagy begins with invagination of the plasma membrane,
a process called endocytosis. Example of heterophagy is to
remove bacteria from the body.
35
Peroxisomes or microbodies
 Unlike lysosomes, they do not contain hydrolases.
 An organelle responsible to protect cell from its own
production of toxic hydrogen peroxide.
 Most of catalase in the cell is contained in peroxisomes. This
enzyme catalyzes the conversion of hydrogen peroxide to
water and oxygen.
 Example: white blood cells produce hydrogen peroxide to kill
bacteria. The oxidative enzymes in peroxisomes break down
the hydrogen peroxide into water and oxygen.
36
37
38
VIRUS

Viruses consist of nucleic acid molecule (DNA or RNA)
surrounded by a protein coat.

Viruses are not truly cells because they are unable to carry out
independent metabolic reactions.

They can only propagate after infecting a host cell.

Viruses that infect prokaryotes are usually called bacteriophage
or phage.
39
1.4 Water Molecule

Principle component of most cells.

Electronegativity = the tendency / affinity of atom to
attract electron (e-) to itself in chemical bond.

O and N are highly electronegative compared to C and
H.
40
Polarity
When 2 atoms of same electronegativity create a bond, e- will
be shared equally between the 2 atoms.
41





In O-H bonds in water, oxygen (O) is more
electronegative than hydrogen (H)  electronegativity
difference is large.
So the probability that the bonding e- are closer to O is
higher than to H.
The difference in electronegativity between O and H
give rise to partial negative and positive charge.
δ+ = partial positive, δ- = partial negative
This bond is called polar bond.
42
43





44
In situation where electronegativity difference are small,
sharing of e- in the bond is near to equal. Eg: C-H bond in
CH4
This is called non-polar bond
The bond in a molecule may be polar, but the molecule
itself can be non-polar because of its geometry. Eg: CO2
C=O is polar, but CO2 molecule is linear.
A molecule where its atoms are positioned linearly will
become non-polar.

In CO2 molecule, the attraction of the O for e- in one
bond is cancelled out by the equal and opposite
attraction for the e- by the O on the other side of
molecule.
O=C=O
δ-
δ = délta
45
2δ +
δ-




Water (H2O) is a bent molecule with a bond angle of
104.3 ̊C.
Unlike CO2 ,the e- sharing in H2O is uneven and are not
cancelled out.
Therefore in H2O molecule, the e- are found at O end
rather than the H end.
Bond with positive and negative ends are called dipoles.
46

The radius called Van der Waal radius
Dipole moment
47
1.5 Ionic and polar substance dissolve in
water




Ionic compounds (full charges)(KCl  K+ and Cl- in
water) and polar compounds (partial charges) like
dipoles such as ethanol, C2H5OH and acetone,
(CH3)2C=O are tend to dissolve in water.
This is caused by electrostatic attraction between unlike
charges.
Negative end of water dipole attracts positive ions, or
positive end of other dipole.
Positive end of water dipole attracts negative ion (end) of
other dipole.
48

If aggregation of substance in water happens, its
electrostatic force between unlike charge has lower energy,
so the system is more stable and likely to exist.
49
Ion dipole interaction with water

Dipole-dipole of polar interaction in water
(dipole-dipole interaction)
50
Polar compounds
that easily dissolve
in water includes
alcohols, amines,
carboxylic acids







Attraction between dipoles of these molecules and water
molecules makes them dissolve.
Ionic and polar substance are called hydrophilic = water
loving.
Hydrocarbons (C-H) are non-polar.
No dipole-dipole and ion-dipole interaction in
hydrocarbons.
Less energy between non-polar molecule and water
molecule
Water molecule tends to associate with themselves
This is called hydrophobic = water hating
51


Non-polar interactions called hydrophobic interaction
E.g. fatty acids and cholesterol
52
Hydrogen bonding



Hydrogen bonding = non-covalent interaction of
molecules, and special case of dipole-dipole interaction.
When hydrogen is covalently bonded with (very)
electronegative atom (N or O), it has partial positive
charge.
Partial positive charge can interact with unshared pair of
e- (source of negative charge) on another negative atom.
53
All 3 atoms aligned in straight line, forming hydrogen
bond
 Non-covalently bond
 One type of electroHydrogen bon acceptor
static bond
Hydrogen bon donor
 Weaker than covalent linear
bond (20kJ mol-1)


Linear and non-linear hydrogen bond in water (draw nonlinear hydrogen bond)
54
55
 ~20 kJ mol-1 of heat is released when hydrogen bonded water
molecules form in water under standard conditions.
 Standard conditions: 1 atm pressure, a temperature of 25°C, and a concentration of
1M of reactants and products.
 In other words, +20 kJ of heat energy is required to disrupt
hydrogen bonds between water molecules.
 FYI, energy required to break a covalent O-H bond is ~460 kJ
mol-1, while energy to break a covalent C-H bond is ~410 mol-1 .
 The strength of hydrogen bond is weak, only less than 5% of
the strength of normal covalent bonds.
56


In H 2 O hydrogen bonding forms tetrahedral structure
of molecule, where
one H 2 O is hydrogen bonded to 4 other H 2 O
molecules.
57
Water (H 2 O )
Ammonia (NH3)
Methane (CH4)
Molecular
weight
Melting
point( ̊C)
Boiling point
( ̊C)
18.02
0.0
100.0
17.03
-77.7
-33.4
16.04
-182.5
-161.5
Why can this happen? Explain.
58



Hydrogen bonding also affects water as solvent.
Alcohols, amines, carboxylic acids, esters, aldehydes,
ketones – all form hydrogen bond with water.
The polar solute serves as donor or acceptor of
hydrogen bond.
59