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Chapter 4

CHAPTER 4.docx


Department
Biology
Course Code
BIO206H5
Professor
George S Espie
Chapter
4

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CELL BIOLOGY
CHAPTER 4
Proteins are the building blocks from which cells are assembled
Proteins constitute most of the cell’s dry mass
Proteins provide the cell with shape and structure
Enzymes promote intracellular chemical reactions by providing intricate
molecular surfaces, contoured with particular bumps and crevices that can cradle
or exclude specific molecules
Proteins embedded in the plasma membrane form the channels and bumps that
control the passage of nutrients and other small molecules into and out of the cell
Other proteins carry messages from one cell to another, or act as signal integrators
that relay information from the plasma membrane to the nucleus of individual
cells
Some proteins serve as tiny molecular machines with moving parts (Kinesin
propel organelles through the cytoplasm, others such as helicases pry open DNA
strands)
The multiplicity of functions carried out by proteins arises from the huge number
of different shapes they adopt
THE SHAPE AND STRUCTURE OF PROTEIN
Proteins are by far the most structurally complex and functionally sophisticated
molecules known
The position of each amino acid in the long strings of amino acids that form a
protein determines its three-dimensional shape
The three-dimensional shape is a structure stabilized by noncovalent interactions
between different parts of the molecule
A protein molecule is made from a long chain of these amino acids, each linked to
its neighbor through a covalent peptide bond
Proteins are therefore referred to as polypeptides or polypeptide chains
In each type of protein, the amino acids are present in a unique order called the
amino acid sequence
Each polypeptide chain consists of a backbone that supports the different amino
acid side chains
The polypeptide backbone is made from the repeating sequence of the core atoms
of the amino acids that form the chain
Projecting from this repetitive backbone are any of the 20 different amino acid
side chains
Side chains are the parts of the amino acids that are not involved in forming the
peptide bond
These side chains give each amino acids its unique properties
Some side chains are nonpolar and hydrophobic, while others are negatively or
positively charged, some are chemical reactive
Long polypeptide chains are very flexible; many of the covalent bonds that link
carbon atoms in an extended chain of amino acids allow free rotation of the atoms
they join

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Proteins can fold in huge number of ways; each folded chain is constrained by
many different sets of weak noncovalent bonds that form within proteins. These
bonds involve atoms in the polypeptide backbone as well as atoms in the amino
acid side chains
The noncovalent bonds that help the protein maintain its shape include hydrogen
bonds, electrostatic attractions and van der walls attractions
Individual noncovalent bonds are weaker than covalent bonds, thus it takes many
more noncovalent bonds to hold two regions of a polypeptide chain together
tightly
The stability of each folded shape will therefore be affected by the combined
strength of large numbers of noncovalent bonds
Another weak force also plays a central role in determining the shape of the
protein called hydrophobic interactions.
In an aqueous environment, hydrophobic molecules including the nonpolar side
chains of particular amino acids tend to be forced together to minimize their
disruptive effect on the hydrogen bonded network of the surrounding water
molecules.
An important factor governing the folding of any protein is the distribution of its
polar and nonpolar amino acids
The nonpolar (hydrophobic) side chain tend to cluster in the interior of the folded
protein, tucked away inside the folded protein hydrophobic side chains can avoid
contact with aqueous cystol that surrounds them inside the cell
The polar side chains tend to arrange themselves near the outside of the folded
protein, where they can form hydrogen bonds with water and with other polar
molecules. When the polar amino acids are buried within the protein they are
usually hydrogen-bonded to the polypeptide backbone
Proteins fold into conformation of lowest energy:
oEach type of protein has a particular three-dimensional structure which is
determined by the order of the amino acid in its chain.
oThe final structure or conformation adopted by any polypeptide chain is
determined by energetic considerations: A protein generally folds into the
shape in which the free energy is minimized
oProtein folding has been studied in the lab using highly purified proteins
oA protein can be unfolded or denatured by treatment with solvents that disrupt
the noncovalent interactions holding the folded chain together. This makes
the protein a flexible polypeptide chain that loses its natural structure. When
the denaturing solvent is removed the protein often refolds spontaneously
oAll the information necessary to specify the three-dimensional shape of a
protein is contained in its amino acid sequence
oEach protein folds into a single stable conformation
oThis conformation often changes slightly when the protein interacts with
other molecules in the cell, this change in shape is crucial to the function of
the protein
oWhen proteins fold incorrectly, the sometimes form aggregates that can
damage cells and even whole tissues
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oAggregated proteins underlie a number of neurodegenerative disorders
oPrion diseases are also caused by aggregated proteins. The prion protein can
adopt a misfolded form that is considered infectious because it can convert
properly folded proteins in the infected brain to the abnormal conformation.
This allows the misfolded form to spread rapidly from cell to cell
o Protein folding in s living cell is generally is assisted by special proteins
called molecular chaperones
oMolecular chaperones bind to partly folded chains and help them to fold
along the most energetically favorable pathway
oChaperones prevent newly synthesized protein chains from associating with
wrong partners
oChaperones make the folding process more efficient and reliable
PROTEINS COME IN A WIDE VARIETY OF COMPLICATED SHAPES
Proteins range in size from about 30 amino acids to more than 10000
The majority of proteins are between 50 and 2000 amino acids long
Proteins can be globular or fibrous
They can form filaments, sheets, rings or spheres
Protein sequencing was accomplished by directly analyzing the amino acids in the
purified protein
The only way we can discover the precise folding pattern if any protein is by
experiment, using either X ray crystallography or nuclear magnetic resonance
(NMR) spectroscopy
A protein domain is a conserved part of a given protein sequence and structure
that can evolve, function, and exist independently of the rest of the protein chain.
Most proteins are formed from multiple domains, each folding into a compact
three-dimensional structure
THE a HELIX AND THE B SHEET ARE COMMON FOLDING PATTERNS
The overall conformation of each protein is unique but two regular folding
patterns are often present
The first folding patterns called the alpha helix was found in keratin
The second folding pattern called the Beta sheet was discovered
These two folding patterns are particularly common because they result from
hydrogen bonds that form between the N-H and C=O groups in the polypeptide
backbone
The amino acid side chains are not involved in forming these hydrogen bonds, a
helices and B sheets can be generated by many different amino acid sequences
The protein chain adopts a regular repeating form or motif
HELICES FORM READILY IN BIOLOGICAL STRUCTURES
A helix is a regular structure that resembles a spiral staircase
It is generated simply by placing many similar subunits next to each other, each in
the same strictly repeated relationship to the one before
It is very rare for subunits to join up in a straight line
Depending on the twist of the staircase, a helix is said to be either left-handed or
right-handed
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