GENERAL
BIOCHEMISTRY
Dr. Dina Abed Bakhotmah
dbakhotmah@kau.edu.sa
With thanks and respect to
Dr. Khadijah Saeed Balamash
Textbook & References
Textbook:
• Voet & Voet: Biochemistry, Wiley & Sons
Inc. New York
References:
• Richard A. Harvey & Denise R. Ferrier :
Biochemistry (Lippincott's Illustrated
Reviews)
Content
General Biochemistry (Bioc 201)
Contents
I-Introduction:
1- Definition
2- Biological Structures
3- Chemical bonds
4- Properties of water
II- Carbohydrates
1- Monosaccharides
2- Disaccharides
3- Polysaccharides
4- Digestion of carbohydrates
III- Amino acids
1- Structures and general properties
2- Peptide bonds
3- Classifications and characteristics
4- Acidic basic properties
IV- Proteins
1- Primary structures
2- Secondary structures
3- Tertiary structures
4- Quaternary structures
V- Lipids and Membranes
1- Lipid classification
2- Properties of lipid aggregates
3- Biological membranes
4- Membrane assembly and protein targeting
5- Lipoproteins
VI- Nucleotides and Nucleosides and Bases
1- The chemical structures of DNA and RNA
VII- Introduction to
1- Enzymes
2- Hormones
3- Vitamins
Exams:
• First exam 15 marks
• Midterm Exam
• Lab 25 marks
• Final Exam 40
20 marks
CHAPTER 1
Introduction:
1- Definition
2- Biological Structures
3- Chemical bonds
4- Properties of water
What is Biochemistry? -1
• Biochemistry is the chemistry of
the living organisms or life.
• Biochemistry deals with:
chemistry, structure,
organization, and function of
living matter.
Principle Areas of Biochemistry
• Structure and function of biological
macromolecules
• Metabolism – anabolic and catabolic
processes.
• Molecular Genetics – How life is
replicated. Regulation of protein
synthesis
Origins of Biochemistry:
Famous Dead Biochemist!
Fallacy #1: Biochemicals can only be produced
by living organisms
•Dead Biochemist #1
•1828 Friedrich
Wohler
Fallacy #2: Complex bioconversion of
chemical substances require living
matter
Dead Biochemists #2
•1897 Eduard Buchner
Glucose + Dead Yeast = Alcohol
Fallacy #2: Complex bioconversion
of chemical substances require
living matter
Dead Biochemists #3
Emil Fischer
•
Cell Theory-1
• Cell is the smallest unit of living
matter. (Don’t confuse this with electrons,
atoms, proteins, DNA, etc.,These are lifeless
molecules)
• Cell is the structural & functional unit of
all organs and/or organisms made up of
thousands of different types of
molecules in highly organized selfassembled structures. .
Cell Theory-2
• All organisms are composed of
one or more types of cells.
• All cells come from preexisting cells by division.
• Spontaneous generation does
not occur.
• Cell is capable of reproduction.
Cell Theory-3
• Cells contains hereditary
information which is passed
from cell to cell during cell
division.
• Most biochemical reactions
(but not all!) take place
within cells
Typical Cells
• Cells come in a variety of
shapes, structures, and
sizes.
• They are usually divided into
two broad groups:
Eukaryotes and Prokaryotes.
Eukaryotic cells
(Eu = true; kary =
nucleus): have a
membranebound
nucleus and a
variety of organelles
and internal
membranes.
Prokaryotic cells
• Prokaryotic cells (Pro =
before) are smaller and
lack much of the internal
compart-mentalization
and complexity of
eukaryotic cells; No
membrane-bound
nucleus or other
organelles.
Viruses
• Viruses do not always
conform to cell theory: one
or more of the basic cell
components is missing.
Inside the host cell, viruses
are living matters.
Sizes and Shapes of Cells
Organization of Life
•
•
•
•
•
•
•
Elements (C, H, O, N)
Simple organic compounds (monomers)
Macromolecules (polymers)
Supramolecular structures (DNA, Lipids)
Organelles
Cells
Tissues (Epithelia, Connective, Muscle, Nerve
Tissue)
• Organs (Heart, skin, kidney, etc.)
• Organisms (Human, bovine, etc)
Chemical Elements of Life
• The cell is a COMPLEX
CHEMICAL FACTORY
containing some of the
same elements found in
the nonliving environment.
• Chemical elements of a living cell are
the same as in the Earth’s crust, but in
different proportions.
• CHNOPS: are the most abundant
elements in cell.
• They account for more than 99% of
atoms in the human body
Chemical Elements of Life
• H, O, N and C have common properties
that are important to the chemistry of
life. They all:
 have relatively low atomic numbers.
capable of forming one, two, three and
four bonds (for H, O, N and C , in
order).
 form the strongest covalent bonds in
general.
TWO TYPES OF COMPOUNDS
• Organic - Contain C, H, and O in
some ratio (usually referred to as
chemicals of life)
–
Carbohydrates, Proteins, Lipids, Nucleic Acids
• Inorganic - usually "support" life - no
specific ratio of C, H, and O
–
Water (H2O), Carbon Dioxide (CO2)
Organic Chemistry
• What makes Carbon Special? Why is
Carbon so different from all the other
elements on the periodic table?
• The answer derives from the ability of
Carbon atoms to bond together to form long
chains and rings.
Organic Chemistry
Organic Chemistry
Carbon can covalently bond with up
to four other atoms.
Carbon can form immensely diverse
compounds, from simple to complex.
Methane with 1
Carbon atom
DNA with tens of Billions
of Carbon atoms
Many Important Biomolecules
are Polymers
• Biopolymers - macromolecules created by
joining many smaller organic molecules
(monomers)
• Condensation reactions join monomers
(H2O is removed in the process)
• Residue - each monomer in a chain
32
Common theme:
Monomers form
polymers through
condensations
Polymers are broken
down through
hydrolysis.
Many Important Biomolecules are Polymers
monomer
polymer
supramolecular
structure
Carbohydrades nucleic acids
lipids
proteins
fatty acid
amino acid
glucose
nucleotide
phospholipid
protein subunit
cellulose
DNA
membrane
protein complex
cell wall
chromosome
There are relatively few species of
monomeric units that occur in each class
of biological macromolecule
• Proteins
– Are all synthesized from the same 20
species of amino acids
 Nucleic acids
 Are made from 8 types of nucleotides
4 each in DNA and RNA
• Polysaccharides
are ~8 commonly occurring types of
sugar in polysaccharides.
1. Where in a eukaryotic cell,
DNA can be found?
A. Nucleus
B. Mitochondrion
C. Vacuole
D. Both (a) and (b)
2-The major elements in a
human are C, H and Si
True
False
3- In a human cell the nucleus
and mitochondria and many
other cell organelles have
membranes surrounding
them.
True
False
4- Discribe the Cell Theory.
1.Cells are the smallest unit of
life
2.All Cells come from previously
existing cells
3.All living things are composed
of cells
5- Name an example of an organ.
Heart
kidney
6- Name several types of tissues
Muscle
Nerve Tissue
Chemical Bonds
COVALENT BONDING
non-polar covalent
And
polar covalent
IONIC BONDING
Chemical Bonds
• Covalent bonds
– Strong
– Hold the atoms in an individual molecule together
• Noncovalent bonds
– Determine the three-dimensional architecture of large
biological molecules and molecular complexes
– Weaker more easily broken
• No one bond is strong, the effect of many weak
bonds functioning together can be very powerful
COVALENT BONDING
SHARING IS CARING!

The outer electron shell of each
atom has a characteristic number of
electrons:
.
.
..
H
. C .
.
. N .
.
..
. P.
.
..
. O .
..
..
. S .
..
These atoms readily form covalent
bonds with other atoms and rarely
exist as isolated entities
As a rule:
• Each type of atom forms a characteristic
number of covalent bonds with other
atoms.
• A hydrogen atom: with one electron in its
other shell, forms only one bond.
• A carbon atom: with four electrons,
generally forms four bonds, as in
methane (CH4):
H
..
H :C: H
..
H
or
• Nitrogen and phosphorus have five
electrons in their outer shells.
– These atoms can form either
• Three covalent bonds, as in ammonia
(NH3)
• Five, as in phosphoric acid (H3PO4)
• Oxygen and Sulphur contain six electrons
in their outermost shells.
– These atoms can forms only two covalent bonds
• In molecular oxygen (O2)
• Hydrogen sulphide (H2S)
O::O
or
• A sulphur atom can
– Form as many as six covalent bonds
• Sulphur trioxide (SO3)
• Sulphuric acid (H2SO4)
• Covalent bonds between different atoms
are generally dipolar:
– Because one of the atoms is usually more
electronegative than the other.
• When a dipolar bond breaks:
– The bonding electrons often stay with the more
electronegative atom, which then becomes a
negatively charged ion, or an anion
– The other part of the molecule becomes a
positively charged ion, or a cation.
Electronegativity decreases as you move down each
column.
Electronegativity increases as you move from left to right.
IONIC BONDS
• Occur when 1 or more electrons are
TRANSFERRED from one atom to another.
• When an atom loses an electron it is a
POSITIVE charge.
• When an atom gains an electron it is a
NEGATIVE charge
• These newly charged atoms are now called
IONS
– Example: NaCl (SALT)
Ionic bonds
• The ionic bonds result from the attraction
of a positive charge for a negative
charge.
• Ionic bond do not have fixed or specific
geometric orientations
– Because the electrostatic field around an ion.
Its attraction for an opposite charge. Is uniform
in all directions.
– Unlike covalent or hydrogen bonds
In some compounds the atoms are so
different in electronegativity:

That the bonding electrons are always found
around the more electronegative atom
– That is, the electrons are never shared.
• Because electrons are not shared,
– The bonds in such compounds cannot be
covalent
• In sodium chloride (NaCl) for example:
– The bonding electron contributed by the sodium
atoms is completely transferred to the chlorine
atoms
– Even in solid crystals of NaCl, the sodium and
chlorine atoms are ionized, so it is more accurate
to write the formula for the compound as Na+ Cl-
The hydrogen bond
• A hydrogen atom normally forms a
covalent bond with only one other atom (D)
at a time.
• A covalently bonded hydrogen atom may
form an additional bond with another atom
(A):
– A hydrogen bond:
• Is a weak association between an
electronegative atom (A) (the
acceptor atom) and a hydrogen atom
covalently bonded to another atom
(D) (the donor atom).
Hydrogen Bonds
• hydrogen bond
donor :to which
hydrogen is covalently
bonded
• hydrogen bond
acceptor : with the
nonbonded electron
pair
 The hydrogen bond in
water is a classic
example:
 A hydrogen atom in
one molecule is
attracted to a pair of
electrons in the outer
shell of an oxygen
atom in an adjacent
water molecule.
Van der Waals Interactions
•
When two atoms approach one
another closely, they create:
– A nonspecific Weak attractive force
that produces a van der Waals
interaction
– Named for Dutch physicist Johannes
Diderik van der Waals (1837-1923),
who first described it.
Van der Waals Interactions
 If
two noncovalently bonded atoms
are close enough together:
– The transient dipole in one atom will
perturb (disturb) the electron cloud of
the other.
– This perturbation generates a
transient dipole in the second atom
– The two dipoles will attract each
other weakly.
Example
d+ H
Cl
d-
A DIPOLE
(it’s polar)
-
e- e e- e- ee- e- ee- - e -e
e e - - e- ee e
d+
e-
Ar
non-polar
INDUCED
DIPOLE
Dipole – Induced Dipole
(weak and short-lived)
d-
Van der Waals Interactions
• All types of molecules, both polar and nonpolar
exhibit van der Waals interactions
– They are responsible for the cohesion (pulling
together) among molecules of nonpolar liquids and
solids:
Van der Waals Interactions
• Attraction decreases rapidly with
– Increasing distance and is effective only when atoms
are quite close to one another.
• If atoms get too close together:
– They become repelled by the negative charges in
their outer electron shells.
• The van der Waals interaction is even weaker
than the hydrogen bond
Properties of Water-1
•
•
•
•
Adhesion
Cohesion
high surface tension
holds heat to regulate temperature (High heat
capacity)
• less dense as a solid than a liquid
PRORERTIES OF WATER-2
• The H2O molecule has a bent geometry
– With an O — H bond distance of 0.958 Å
– An H — O — H bond angle of 104.5°.
PRORERTIES OF WATER-3
• Water molecules Associate through Hydrogen bonds
• The electrostatic attractions between the dipoles of
two water molecules tend to orient them such that
– The O — H bond on one water molecule points toward a lonepair electron cloud on the oxygen atom of the other water
molecule.
• This results in a directional intermolecular
association known as hydrogen bond:
– An interaction that is crucial both to the properties of water
itself and to its role as a biochemical solvent.
PRORERTIES OF WATER-4
• The large electronegativity difference between H and
O confers a 33 % ionic character on the O — H bond
• As water is clearly a highly polar molecule, a
phenomenon with enormous implications for living
system.
• The energy of a hydrogen bond (~ 20 kj. mol-1 in
H2O) is small compared to Covalent bond energies
(for instance, 460 kj. Mol-1 for an O — H covalent
bond).
Properties of Water-5
Water is less dense as a solid! This is
because the hydrogen bonds are stable in
ice – each molecule of water is bound to
four of it’s neighbors.
Water as a solvent
•
Solubility: depends on the ability of a solvent
to interact with a solute more strongly than
solute particles interact with each other.
•
Water is said to be the “universal solvent.”
•
The polar character of water makes it an:
–
Excellent solvent for polar and ionic materials,
which are therefore said to be hydrophilic (Greek:
hydor, water + philos, loving).
AQUEOUS SOLUTION
• Life, as we know it, occurs in aqueous
solution.
• Water is a chemically reactive liquid
with such extraordinary physical
properties.
• The structures of the molecules on
which life is based (proteins, nucleic
acids, lipids, and complex
carbohydrates) Result directly from their
interactions with their aqueous
environment.
In aqueous solutions:
• Simple ions of biological significance, such
as Na+ , K+ , Ca2+ , Mg2+ , and Cl-:
– Do not exist as free, isolated entities.
– Instead, each is surrounded by a stable, tightly
held shell of water molecules
– Primary interaction occurs between the ion and
the oppositely charged end of the water
dipole
• Ions play an important biological role
when they pass through:
– Narrow pores
– Channels
– In membranes
• Ionic movements through
membranes are Essential for the
– Conduction of nerve impulses
– Stimulation of muscle contraction
• Molecules with dipolar bonds
also can attract water molecules,
as can molecules that easily form
hydrogen bonds
– Such polar molecules can dissolve
in water and are said to be
hydrophilic (from the Greek for
“water- loving”).
• Typical chemical groups that
interact well with water are:
–Hydroxyl – OH
–Amino – NH2
–Peptide bond
–Ester bond
Hydrophobic Interactions
• Nonpolar molecules:
– Contain neither ions nor dipolar bonds
– Do not become hydrated. Because they are
insoluble in water, they are said to be
hydrophobic (from the Greek for “waterfearing”).
• The covalent bonds between two carbon
atoms and between carbon and hydrogen
atoms
– Are the most common nonpolar bonds in
biological system.
Hydrophobic Interactions
• Hydrocarbons – molecules made
up only of carbon and hydrogen —
are virtually insoluble in water.
• The force that causes hydrophobic
molecules or nonpolar portions of
molecules to aggregate rather
than to dissolve in water is called
hydrophobic interaction.
Hydrophobic Interactions
• A nonpolar molecule cannot form
hydrogen bonds with water:
– So it distorts the usual water structure
– Forcing the water to make a cage of bonds
around it, but not with it.
• On the other hand, nonpolar molecules bond
together comfortably through van der Waals
interactions
The result is:
– A very powerful tendency for hydrophobic
molecules to bond together and
– Not dissolve in water.
• Small hydrocarbons such as butane
CH3—CH2—CH2—CH3
– Are slightly soluble in water:
• Because they can dissolve without disrupting
the water lattice (net) significantly.
• 1-butanol mixes completely with water in all
proportions
CH3—CH2—CH2—CH2OH
– Thus the replacement of just one hydrogen
atom with the dipolar—OH group allows the
molecule to form hydrogen bonds with water
and greatly increases its solubility.
• Multiple noncovalent bonds can
contribute to the stability of large
biological molecules
• These interactions can also confer
specificity by determining how
molecules will fold or which regions of
different molecules will bind together
• Several different weak bonds and
interactions can bind two protein chains
together.
B. Water as a solvent
•
•
•
Solubility: depends on the ability of a
solvent to interact with a solute more
strongly than solute particles interact with
each other.
Water is said to be the “universal solvent.”
The polar character of water makes it an:
–
Excellent solvent for polar and ionic materials,
which are therefore said to be hydrophilic
(Greek: hydor, water + philos, loving).
• Nonpolar substances are
– Insoluble in water (“oil and water don’t mix”) and
are described as being hydrophobic (Greek:
phobos, fear).
– Soluble in nonpolar solvents such as
• CCl4 or hexane.
• This information is summarized by another
maxim. “like dissolves like.”
1- The formation of large molecules from small
repeating units is accomplished by a(n)
______ reaction.
A.
B.
C.
D.
E.
oxidation
reduction
dehydration
Hydrolysis
decarboxylation
2- Which force is most important in allowing
ammonia, NH3, to dissolve in water?
A.
B.
C.
D.
E.
hydrogen bonding
dipole-induced dipole
ion-dipole
dipole-dipole
ionic
3- Which one of the following species contains
a polar covalent bond?
A. oxygen
B. carbon dioxide
C. sodium chloride
D. magnesium fluoride
E. helium
4- What happens when a covalent bond is
formed?
A. Electrons are transferred from one atom to
another
B. Electrons are shared between two atoms
C. Protons are transferred from one atom to
another
D. Protons are shared between two atoms
5- Water (H2O) has a bent shape, resulting in an
unequal distribution of the electrons. Oxygen, which
is more electronegative than the hydrogens, has a
greater pull on the electrons, giving the oxygen a
partial negative charge and the hydrogens a partial
positive charge. This unequal distribution is called a:
A.
B.
C.
D.
Covalent bond
Tail
Bent geometry
Dipole
6-Which of the following BEST describes the
“bonds” holding liquid water molecules
together?
A. Ionic.
B. Covalent.
C. Adhesion.
D. Hydrogen.