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Lecture 5

BIOL 3113 Lecture 5: 5.Proteins


Department
BIOL
Course Code
BIOL 3113
Professor
Barbara S
Lecture
5

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Proteins
Building blocks of cells
Constitute most of the cell’s dry mass
Execute nearly all of cell’s functions
Protein functions:
Enzymes - catalyze covalent bond formation or breakage
Structural proteins - mechanical support in cells and tissues
Transport proteins - carry small molecules or ions
Motor proteins - generate movement in cells and tissues
Storage proteins - store small molecules or ions
Signal proteins - carry signals from cell to cell
Receptor proteins - detect signals and transmit them
Gene regulatory proteins - bind to DNA to switch genes on/off
Special-purpose proteins - highly variable functions
Variety of functions possible because of the huge number of different shapes they adopt
The most structurally complex and functionally sophisticated molecules known
Characteristics:
High molecular weight (10 - 1000 kD), 30-10,000 AA long
Polymers of subunits (monomers) held together by covalent bonds - polypeptides
Subunits attached via a dehydration reaction
Synthesis requires metabolic energy from ATP or GTP
Long polymers are flexible and can fold into three-dimensional configurations
determined primarily by non-covalent bonds
Proteins - Macromolecules composed of one or more flexible chains of amino acids
(polypeptides) held together by peptide bonds
Terminology:
polypeptide = a single chain of amino acids
protein = functional molecule composed of one or more polypeptides
glycoprotein = a protein covalently linked to one or more oligosaccharides
lipoprotein = a protein covalently linked to one or more lipids
Polypeptides have a backbone (formed from repeating sequences of atoms linked by
peptide bonds) and side chains of amino acids (the parts of amino acids not involved in
peptide bond formation)

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Folding
20 different amino acids - each has different chemical property
Three-dimensional conformation of proteins is determined by its amino acid sequence
and interactions between atoms:
*within the same molecule (intramolecular interactions)
*with other molecules (intermolecular interactions) like proteins and phospholipids
*small molecules in the environment (water, inorganic ions, small ligands, etc.)
Most interactions within the same molecule are in the form of weak, non-covalent bonds:
*ionic bonds
*hydrogen bonds
*van der Waals forces
Some interactions are in the form of covalent disulfide bonds (-S-S-)
Each protein normally folds into a single stable conformation
Folding in cells assisted by molecular chaperones (bind to partly folded chains and help
to fold, in crowded cell environment prevent association with other molecules until
folding is complete, recognize products of mutated genes)
Two families of molecular chaperones:
hsp70 - acts early during initial folding of the polypeptide
hsp60 - forms a barrel-like cage into which misfolded proteins are placed and the
folding is corrected
Improper folding - seen in many diseases
Improperly folded proteins can form aggregates and accumulate some storage and
neurodegenerative diseases
Prions - misfolded forms of proteins that can convert properly folded proteins into the
abnormal configuration (PrP in scrapie, BSE, CJD)
Protein structure is complex, comes in a variety of complicated shapes: globular, fibrilar,
can form filaments, sheets, rings, spheres
Several different models have been developed to illustrate the three dimensional
configuration of proteins: backbone, ribbon, wire and space filling
Common Folding Patterns
Although the overall conformational pattern of each protein is unique - two regular
folding patterns are often present in parts of them: helix and sheet
result from hydrogen bonds forming between N-H and C=O groups in the
polypeptide backbone protein chain adopts a regular, repeating form (motif)
amino acid side chains are not involved
Can be illustrated showing all atoms in the polypeptide backbone, backbone
atoms only or cartoon symbols used to represent the helix and the sheet in
ribbon drawings of proteins
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