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 Laying the Ground Work:
 Dynamic Cell, Chemical Foundation, Protein Structure and
Function;
 Dynamic cell growth, division and movement are hallmarks of life and are
essential for the formation of an organism, yet our understanding of the
molecular basis of these processes is far from complete
 The Cell is the fundamental unit of life
• Microscopic examination of any organism reveals that it is composed
of membrane-enclosed structure called cells
• The enclosing membrane is called the cell membrane or the plasma
membrane
• Cells vary enormously in size and shape but
• Even the largest cells would to be much larger to be visible to the
naked eye
•
Within this tiny object thousands of chemical reaction are taking place
- all regulated, all designed to serve specific function
•
Collectively these reactions serve the function of maintaining the
cell and permitting it to replicate when time is right
•
Perhaps the most amazing thing about the living cell is that so
much organized activity takes place in such a small space
•
Following figures show prototypical animal and plant cells along
with some common shapes and sizes of bacteria
Fig 1.7 Nelson and Cox 5th Ed – 2008
•
The evolutionary tree is bisected into a lower prokaryotic domain
and upper eukaryotic domain
•
The term prokaryote and eukaryote refer to the most basic division
between cell types
•
The fundamental difference is that eukaryotic cells contain a
membrane-bounded nucleus, whereas prokaryotes do not
•
The cells of prokaryote usually lack most of the other membranebounded organelles as well
•
Plants, fungi and animals are eukaryotes and bacteria are
prokaryotes
•
The biochemical functions associated with organelles are
frequently present in bacteria, but they are usually located on the
inner plasma membrane
Fig 1.1 Voet
•
Cells are organized in variety of ways in different living forms
•
Prokaryotes of given type produce cells that are very similar in
appearance
•
A bacterial cell replicates by a process in which two identical
daughter cells arise from an identical parent cell
•
Simple eukaryotes can also exist as single non-associating cells
•
Eukaryotes of increasing complexity can contain many cells with
specialized structure and functions
•
For example, humans contain about 1014 cells of more than a 100
different types.
•
Although all cells in multi-cellular organisms have common
constituents and functions – specialized cells types have unique
chemical composition, structure and biochemical reactions –
establish and maintain their specialized functions
•
Such cells arise during embryonic development by the complex
processes of cell proliferation and cell differentiation
• Except germ cells – all cell types contain the same genetic information
– faithfully replicated to daughter cells
• Cell differentiation is a process where by some of this genetic
information is activated in some cells – synthesis of certain proteins
and not other proteins
• Thus specialized cells come to have different complements of enzymes
and metabolic capacities
Fig 1.2 Zubay
Fig 1.14 Voet
 Cells are Composed of Small Molecules, Macromolecules
and Organelles:
•
There are a structural hierarchy in cellular organization
Fig 1.11 Nelson and Cox 5th Ed
P 54, Boyer
Table 2.1 Boyer 3rd Ed
Table 3.1 ?
• Except for water, most of the molecules, found in the cells are Lipids or
macro-molecules, and can be classified into four categories:
 Lipids

•
Carbohydrates
 Proteins and
 Nucleic acids
Each type of macromolecule possesses distinct chemical properties that suit
it for the functions it serves in the cell
Fig 1.6, Boyer 3rd Ed, 2005
Fig 1.3, Zubay
Fig 1.4, Zubay
Fig 1.5, Zubay
Fig 1.6, Zubay
 Macromolecules Fold into Complex Three-Dimensional
Structures:
•
•
The complex folding of bio-macromolecules rarely entails making or breaking
covalent linkages
Rather the folding process is dedicated by:
o Primary structure and
o The way in which different elements of the macromolecule interact with
each other and with water
• The forces that determine folding are non-covalent in character

Water is a Primary Factor in Determining the Type of Structures that
Form:
• Water, as we have seen, is the major component of living systems
• and interacts with many bio-molecules
• Some are water-loving or hydrophilic
• Others are water abhorring or hydrophobic
• and still others are amphiphatic or in between
• What properties of a molecules make it hydrophilic or hydrophobic?
• First, consider the molecular properties of H2O and
• how water interacts with itself?
• An individual water molecules has a significant dipole that is due to
greater electro negativity of the oxygen atom over the hydrogen atom
• This dipole leads to strong interaction between water molecules, in the
form of hydrogen bond
• A hydrogen bond is a non-covalent interaction between polar molecules,
one of which is an unshielded proton



Fig 1.7 Zubay
In solid water or ice, the polar forces hold the individual molecules
together in a regular three-dimensional lattice
Fig 1.8 Zubay
Most of the hydrogen bond present in ice are also present in liquid
water
Hence water is a highly hydrogen-bonded structure, not too
different from ice, but with somewhat less regular structure in
which the individual molecules have greater mobility
P 58 Boyer 1st Ed



The dipolar properties of water molecules affect the interaction
between water and other moles. That dissolve in water
For example, a favorable interaction accounts for the high
solubility of sodium chloride in water
Fig 3.10 Brum
Fig 1.9 Zubay
The kinds of ion-dipole interactions that take place between H2O
and simple ions such as Na+ and Cl- are also important in
interaction between the charged or polar, groups on bio-molecules
and water
• Thus bio-molecules that contain charged residues, H-bond forming
substituents or other kinds of polar groups are hydrophilic
• In the form of small molecules such groups tend to be very soluble in
water
• When attached to biopolymers they determine which parts of the
molecule will be oriented on the exposed surface, where they can
make contact with water
• Apolar groups such as neutral hydrocarbon side chains do not contain
significant dipoles or the capacity for forming hydrogen bonds
• Consequently, they have nothing to gain by interacting with water, as
evidence by their poor solubility in water
• Where such hydrophobic molecules are present in water, the water
forms a rigid clathrate (cage like) structure around them
Fig 1.10 Zubay
Fig 1.11 Zubay
Fig 1.12 Zubay
Fig 1.13 Zubay
• Enormous structural diversity of proteins begins with the amino acid
sequence of polypeptide chains
• Each protein consists of one or more unique polypeptide chains and
• Each of these polypeptide chains is folded into a three dimensional
structure
• This final folded arrangement is called its conformation
• Folded arrangement of proteins can be defined in four levels i.e.
hierarchy of structural organization
Fig 4.14 Zubay
Fig 4.15 Brum
• Most proteins exist in unique conformations exquisitely suited to their
function
• It is the availability of a wide variety of conformations that permits
proteins as a group to perform a broader range of functions than any
other class of biomolecules
Table 4.4 Boyer 2nd Ed / Table 3.4 Boyer 3rd Ed
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