BIOL 307

BIOCHEMISTR
Y
by
Çağdaş D. Son
Outline
 What is Biochemistry
 History of Biochemistry
 Elements in Biomolecules
 Biological Macromolecules
 Organels Cells and Organisms
 Properties of Water
 Weak acids, bases and buffer systems

Lehninger Chapters 1&2

What is Biochemistry
 Biochemistry = Biology + Chemistry
 Explains reactions necessary for Life
 Life :
 able to extract energy from molecules called nutrients
 display the attributes of growth, differentiation, and reproduction
 ability to respond to changes in their environments
 Biochemistry uses the interactions between molecules to
explain Life
 Biochemistry can be organized into three primary areas
WHY SHOULD WE STUDY
BIOCHEMISTRY?
 To understand fundamentals of Life
 How food is digested?
 How is this providing cellular energy?
 How does a brain cell store information?
 Research in biochemistry is providing answers to these and
other important questions.
 To understand medicine, health, nutrition, and the environment
 Design and develop new compounds to improve Life
History of Biochemistry
The Road to Modern Biochemsitry
 Two separate and distinct scientific events have led to our
current state of biochemical knowledge.
1. Structural characteristics of biomolecules through physical
sciences
 Application of basic laws of physics and chemistry to explain the
processes of the living cell. X-ray crystallography to study the
structure of amides and peptides
2. The study of cell organization and function by biologists,
especially microbiologists, cell biologists, physiologists, and
geneticists
The Road to Modern Biochemsitry
 1952 with the announcement by James Watson and Francis
Crick of the double helix structure for DNA combined several
disiplins together.
 Here the application of physics (crystallography), chemistry
(structure and bonding), and biology (storage and transfer of
genetic information) all came together to help solve what was the
most exciting and complex biological problem at that time: the
structure of the genetic material, DNA
The origins of biochemistry
from two perspectives, the physical
and the biological sciences.
The dates of Nobel prizes and of
selected events in the development
of biochemistry are noted in the
scale on the left.

Nobel Prize in Chemi

stry 2018 Is Awarded
to 3 Scientists for
Using Evolution in
Design of Molecules
James Watson
(left)
and Francis Crick
discuss an early
model of the DNA
double helix.
Elements in Biomolecules
 All Living Matter Contains C, H,O, N, P, and S
 Only about 31 (28%) of the more than 100 naturally
occurring chemical elements are essential to
organisms.
 The four most abundant elements in living
organisms, in terms of percentage of total number of
atoms, are hydrogen, oxygen, nitrogen, and
carbon, which together make up more than 99% of
the mass of most cells.
 We do not understand exactly how these elements
were selected by primitive life-forms during the early
stages of evolutionary development.
The biochemist’s periodic table. Elements in red are present in bulk form in living
cells are essential for life. Those in yellow are trace elements that are very likely
essential. Those elements in blue are present in some organisms and may be
essential.
 What Decides Which Elements
 Two posibilities:
1. Random representation of elements in
biomolecules
2. Preference of some elements due to their
charecteristics
 If the first hypothesis is true then we should observe
approximately the same ratios of elements in
biological organizms as we find in the universe.
 What Decides Which Elements
 Two posibilities:
1. Random representation of elements in biomolecules
2. Preference of some elements due to their charecteristics
 If the first hypothesis is true then we should observe
approximately the same ratios of elements in biological
organizms as we find in the universe.
 This is not the case, thus we conclude that elements were
selected according to their abilities to perform certain
structural functions or to provide specific reactivities
Most Abondant in Living Systems
 Carbon forms multiple covalent bonds with other carbon atoms
as well as with other elements such a nitrogen, hydrogen,
oxygen, or sulfur.

 This feature allows the construction of long carbon chains and

rings with the presence of reactive functional groups containing
nitrogen, oxygen, and sulfur as in proteins, nucleic acids, lipids,
and carbohydrates.
Versatility of carbon bonding. Carbon can form covalent single,
double, and triple bonds (in red), particularly with other carbon atoms.
Triple bonds are rare in biomolecules.
 Carbon Skeletons and
Functional Groups
 Covalently linked carbon atoms in biomolecules can
form linear chains, branched chains, and cyclic
structures
 functional groups, which confer specific chemical
properties can be added to these structures
 Most biomolecules are derivatives of hydrocarbons,
with hydrogen atoms replaced by a variety of
functional groups to yield different families of
organic compounds.
Many biomolecules are polyfunctional, containing two or
more different kinds of functional groups,each with its own
chemical characteristics and reactions.

Several common functional groupsin a single biomolecule.

Acetyl-coenzyme A (often abbreviated as acetyl-CoA) is a carrier of acetyl
groups in some enzymatic reactions.
 Cells Contain a Universal Set of
Small Molecules
 Dissolved in the aqueous phase (cytosol) of all cells
is a collection of 100 to 200 different small organic
molecules (Mr ~100 to ~500)

 This
collection of molecules includes the common
amino acids, nucleotides, sugars and their
phosphorylated derivatives, and a number of
mono-, di-, and tricarboxylic acids.
 Cells Contain a Universal Set of
Small Molecules
 Themolecules are polar or charged, water soluble,
and present in micromolar to millimolar
concentrations.

 They are trapped within the cell because the

plasma membrane is impermeable to them—
although specific membrane transporters can
catalyze the movement of some molecules into and
out of the cell or between compartments in
eukaryotic cells.
 Specific Small Molecules
 There are other small biomolecules, specific to certain types of cells or
organisms. For example, vascular plants contain, in addition to the
universal set, small molecules called secondary metabolites, which play a
role specific to plant life.
 These metabolites include compounds that give plants their
characteristic scents, and compounds such as morphine, quinine,
nicotine, and caffeine that are valued for their physiological effects on
humans but used for other purposes by plants.
 The entire collection of small molecules in a given cell has been called that
cell’s metabolome, in parallel with the term “genome”.
Biological Macromolecules
 Macromolecules
 Are the Major Constituents of Cells
 are produced by the polymerization of relatively small
compounds with molecular weights of 500 Da or less.
 The number of polymerized units can range from tens to
millions.
 Synthesis of macromolecules is a major energy-consuming
activity of cells.
 Macromolecules themselves may be further assembled into
supramolecular complexes, forming functional units such as
ribosomes.
Macromolecules
 There are four classes of macromolecules:
1. Polysaccharides
2. Triglycerides
3. Polypeptides
4. Nucleic acids
Macromolecules
 There are four classes of macromolecules:
1. Polysaccharides
2. Triglycerides
3. Polypeptides
4. Nucleic acids
 Polysaccharides
 Carbohydrates have the general formula
[CH2O]n where n is a number between 3 and 6
 Carbohydrates function in energy storage:
 short-term such as sugars
 intermediate-term  ex. starch for plants and glycogen
for animals
 as structural components in cells (cellulose in the cell
walls of plants and many protists), and chitin in the
exoskeleton of insects and other arthropods
 Sugars

 arestructurally the simplest carbohydrates

 They are the structural unit which makes up the other
types of carbohydrates
 Monosaccharides are single sugars
 Important monosaccharides include ribose (C5H10O5),
glucose (C6H12O6), and fructose
Sugars
Polysaccharides
Macromolecules
 There are four classes of macromolecules:
1. Polysaccharides
2. Triglycerides
3. Polypeptides
4. Nucleic acids
 Lipids 
 Are involved mainly with long-term energy storage
 They are generally insoluble in polar substances such as water
 functions of lipids include:
 structural components as in the case of phospholipids that are the
major building block in cell membranes
 "messengers" (hormones) that play roles in communications
within and between cells
 Lipids 
 are composed of three fatty acids (usually) covalently bonded
to a 3-carbon glycerol
 The fatty acids are composed of CH2 units, and are
hydrophobic/not water soluble
 Fatty acids can be saturated (meaning they have as many
hydrogens bonded to their carbons as possible)
 or unsaturated (with one or more double bonds connecting
their carbons, hence fewer hydrogens)
Lipids
Macromolecules
 There are four classes of macromolecules:
1. Polysaccharides
2. Triglycerides
3. Polypeptides
4. Nucleic acids
 Proteins
are very important in biological systems as
control and structural elements
Control functions of proteins are carried out
by enzymes and proteinaceous hormones
Enzymes are chemicals that act as organic
catalysts
Structural proteins function in the cell
membrane, muscle tissue, etc.
 Amino Acids
The building block of any protein is the amino
acid
has an amino end (NH2) and a carboxyl end
(COOH)
In nature there is 20 amino acids commonly
used for protein synthesis
Amino Acids
Macromolecules
 There are four classes of macromolecules:
1. Polysaccharides
2. Triglycerides
3. Polypeptides
4. Nucleic acids
 Nucleic Acids
 are polymers composed of monomer units known
as nucleotides
 There are a very few different types of nucleotides
 The main functions of nucleotides are :
 information storage (DNA),
 protein synthesis (RNA),
 and energy transfers (ATP and NAD)
 consist of a sugar, a nitrogenous base, and a
phosphate
Nucleic Acids
RNA Structure

Phosphodiester bond
Proteins and nucleic
acids are informational
macromolecules: each
protein and each nucleic
acid has a
characteristic
information-rich subunit
sequence.

On the other hand, some

oligosaccharides, with
six or more different
sugars connected in
branched chains, also
carry information; on
the outer surface of
cells they serve as
highly specific points
Organels Cells and Organisms
 Kingdoms of Life
 All living organisms fall into one of three large groups
(kingdoms, or domains)

 Two large groups of prokaryotes can be distinguished on

biochemical grounds: archaebacteria (Greek arche-,
“origin”) and eubacteria (again, from Greek eu, “true”).

 Eukarya, evolved from the same branch that gave rise to

the Archaea; archaebacteria are therefore more closely
related to eukaryotes than to eubacteria.
Kingdoms of Life
Phylogeny of the three domains of life. Phylogenetic relationships are often illustrated
by a “family tree” of this type. The fewer the branch points between any two organisms,
the closer is their evolutionary relationship.
Scientists have long recognized two basic classifications of
organisms:

1. Cells with nuclear envelopes are called eukaryotes (Greek

eu, “true,” and karyon, “nucleus”);
2. those without nuclear envelopes—bacterial cells—are
prokaryotes (Greek pro, “before”).
Eukaryotic cell structure. Schematic illustrations of the
two major types of eukaryotic cell: (a) a representative
animal cell and (b) a representative plant cell. Plant
cells are usually 10 to 100 µm in diameter—larger than
Endoplasmic Reticulum
Material traffic within cells
ER Transfer vesicle Golgi Apparatus
Golgi Apparatus

Arriving from
RER or SER

Moving to plasma membrane

Lysosome in action

1. Foreign substance arrives

and taken in by endocytosis,
2. Isolated in a vesicle,
3. Lysosome is isolated from
the goldi body,
4. Lysosome fuses with the
vesicle,
5. Foreign substance is
digested.
Mitochondria: Power Plant

Adenine

Phosphate Groups

Ribose
Chloroplast
The molecules, cell
components, and cells that
biochemists work with come
in a wide range of sizes.
The dimensions of
biochemical objects studied
in terms of length and the
width or diameter; and the
molecular mass, which is a
measure of quantity of
material in an object, as
the standard, biochemical
unit of molecular mass:
daltons (D) or kilodaltons
(kD, 1000 daltons).
One dalton is equal to the
mass of a hydrogen atom. The
mass of a water molecule is
18 D, and hemoglobin,
64,500D (64,5 kD).
Properties of Water
 Properties
O and 2H atoms forming the water molecule are bond to each
other by polar covalent bonds.
 This unequal sharing of the electrons results in a slightly
positive and a slightly negative side of the molecule.
 water has a great interconnectivity of individual molecules,
which is caused by the individually weak hydrogen bonds
Solutions
 Water has been referred to as the universal solvent
 Living things are composed of atoms and molecules within
aqueous solutions
 Solutions are uniform mixtures of the molecules of two or
more substances.
 The solvent is usually the substance present in the greatest
amount 
Solubility
 The solubility of many molecules is determined by their molecular
structure
 The polar covalently bonded water molecules act to exclude
nonpolar molecules
 Thus organic macromolecules known as lipids that lack polar covalent
bonds will not disolve in water
 The structure of many molecules can greatly influence their
solubility
 Sugars, such as glucose, have many hydroxyl (OH) groups, which
tend to increase the solubility of the molecule.
 Hydrogen Bonding Gives Water Its
Unusual Properties
• Water has a higher melting
point, boiling point, and heat
of vaporization than most other
common solvents.
• These unusual properties are a
consequence of attractions
between adjacent water molecules
that give liquid water great
internal cohesion.
• A look at the electron structure
 Weak interactions, called noncovalent interactions,
bring together whole biomolecules for specific
purposes. Four types of noncovalent interactions are
important in biological systems:
1. Van der Waals forces,
2. ionic bonds,
3. hydrogen bonds,
4. and hydrophobic interactions.
Structure of the water molecule.
Hydrogen bond between two water molecules.
Hydrogen bonding in
ice. In ice, each
water molecule
forms the maximum of
4 hydrogen bonds,
creating a regular
crystal lattice.
By contrast, in
liquid water at room
temperature and
atmospheric pressure,
each water molecule
hydrogen-bonds with
an average
of 3.4 other water
molecules. This
Chemicals are made soluble
in water by noncovalent
interactions.

a)Dipole-dipole
interactions. The carbony
group of an aldehyde,
ketone, or acid can be also
solvated by water.
b)Ion-dipole interactions.
The positively charged
sodium ion is surrounded by
water molecules and the
acetate ion interacts with
the partially positive
hydrogen atoms (dipoles) of
water.
 Water is a polar solvent.
 It readily dissolves most biomolecules, which are generally
charged or polar compounds; compounds that dissolve easily
in water are hydrophilic (Greek, “water-loving”).
 In contrast, nonpolar solvents such as chloroform and benzene
are poor solvents for polar biomolecules but easily dissolve
those that are hydrophobic—nonpolar molecules such as
lipids and waxes.
 Some significant biochemicals have dual properties; have both
nonpolar and ionic characteristics. They are classified as
amphipathic (amphi, on both sides or ends, and philic,
loving).
Because
hydrophobic
molecules have
no polar groups
to interact
water, they
have to be
surrounded by a
boundary of
Liposomes
 Acidic and Basic Conditions
 Water tends to disassociate into H+ and OH- ions
 In this disassociation, the oxygen retains the electrons and only one
of the hydrogens, becoming a negatively charged ion known as
hydroxide.
 Pure water has the same number (or concentration) of H+ as
OH- ions thus is neutral
 Acidic solutions have more H+ ions than OH- ions.
  Basic solutions have the opposite.
 Titration Curves
 Titrationsare often recorded on titration curves,
 the independent variable is the volume of the titrant, while the
dependent variable is the pH of the solution (which changes
depending on the composition of the two solutions).
 The equivalence point is a significant point on the graph (the
point at which all of the starting solution, usually an acid, has
been neutralized by the titrant, usually a base).
A titration curve.
 Almost every biological process is pH dependent;

 Buffers
Are Mixtures of Weak Acids and Their
Conjugate Bases

 Buffersare aqueous systems that tend to resist

changes in pH when small amounts of acid (H+) or
base (OH-) are added.