Biology 1002B Lecture Notes - Lecture 4: Macromolecular Crowding, Asparagine, Glutamine

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18 Apr 2012
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Fundamentals of BiochemistryProtein
(14.1)
The two fields, biochemistry and genetics used to
be completely apart
Molecular biology has ―bridged the gap‖
Now if you are a biochemist, it’s easy to find the
gene that encodes the protein, and if you are a
geneticist it’s easy to take a gene sequence and
synthesize the protein.
Proteins are one of the 4 main biochemical families
o Carbohydrates
o Proteins
o Nucleic acids
o Lipids
Proteins are important-structural and functional molecules of a cell
If you can understand proteins, you understand biology basically
Macromolecules (= big molecules)
Polymers (a category of big molecules, a long chain of nearly
identical smaller molecules joined in a long chain)
Amino Acid
Proteins and peptides are composed of amino acids
Amino acids are monomers = smaller building block molecule
Different: side chains (called R groups), giving different properties
Same: Small organic molecules with both carboxyl (acid) and amino (base) groups (peptide backbone)
3 categories (based on the chemistry of the R group):
o Polar
O or OH in R group
o Charged
Charges
o Non-polar (hydrophobic)
Don’t work well in human bodies because of water
C & H
Pepsin: protein digesting enzyme in the stomach cuts protein at very specific places
Trypsin: Protein digesting enzyme in the small intestine, cuts protein at very specific places
Amino Acid Structure
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Non-polar amino acids hydrophobic effect
Peptide Bonds
Amino acids are linked by peptide bonds
Proteins are more than just chains of amino acids; they have a very
complex 3 dimensional structure
Protein Structure: Primary Structure
Primary structure is the unique sequence of amino acids in a
polypeptide
Protein Structure: Secondary Structure
Is the folding
or coiling of the
polypeptide
(backbone) into a
repeating
configuration
Includes the α helix and the β pleated sheet
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