BIOL 200 Lecture Notes - Leghemoglobin, Hemoglobin, Zinc Finger

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6 Apr 2012
Naveen Sooknanan McGill Fall 2011
Protein structure and function:
DNA is responsible for the transmission of information through transcription and translation in
order to form RNA, and eventually, proteins. Proteins are an important part of the body as they
perform a variety of functions depending on their shape.
Structural proteins determine the shape of a cell
o The provide the structural rigidity of the cell
o They also guide intracellular movements of various molecules and organelles
Enzymes are catalytic proteins which catalyze (speed up) various intercellular and
intracellular reactions
o RNA with 3D structure can also have enzymatic properties
Membrane transport proteins permit the flow of ions small organic molecules through the
plasma membrane
o i.e. oxygen, carbon dioxide, nutrients and waste
Regulatory proteins act as sensors which can control the activities of a cell
o They can do this by regulating the function of other proteins, such as enzymes
Signalling proteins such as hormones or cell-surface receptors can
transmit intracellular signals to the cell exterior
Scaffolding proteins bring other proteins together in order to increase functionality
Motor proteins are responsible for moving cells, organelles and consequently, the
organism as a whole
o They are molecular machines
All of these proteins have 3 generalized functions:
Binding (motor proteins)
Catalyzing (enzymes)
Folding (plasma membrane)
The shape of a protein is very important
It is the unique 3D structure of a protein which determines its function
An alteration in shape caused by a mutation can result in the loss of function or altered
function of the protein
A protein is built from monomers called amino acids. Their
structure is made up of an alpha (α) carbon, a carbonyl group, an
amino group, a hydrogen, and a varying group called an R group,
all attached to the carbon in the following way:
On each amino acid, there is an amino terminus and a
carboxyl terminus
The amino group of one amino acid can form a covalent bond with the carboxyl group of
another amino acid. This bond is called a peptide bond.
There are 20 different R groups creating 20 different amino acids
There are 2 possible isomers for an amino acid: D and L isomers, which are enantiomeric
L isomers make up almost all naturally occurring amino acids
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Naveen Sooknanan McGill Fall 2011
D isomers are rarely found naturally in living organisms although mutations can occur
causing them to become more and more common
D isomers are useful for creating drug resistant bacteria because very few organisms have
enzymes capable of digesting these bacteria which contain artificially synthesized D
isomer amino acids
As stated previously, there exist 20 different amino acids
varying in functional groups. The ones above are
hydrophilic (water loving) and can be subdivided into
further subcategories. Add of these molecules are polar
and water soluble
Lysine, arginine and histidine are all basic amino
acids with positive R groups
Glutamate and aspartate are both acidic amino
acids with negative R groups
Serine, Threonine, Glutamine and Asparagine are all polar amino
acids with no charged R groups
The nonpolar, hydrophobic (water fearing) amino acids are alanine, valine,
isoleucine, leucine, methionine, phenylalanine, tyrosine and tryptophan
These amino acids are water insoluble
There are three special amino acids:
Cysteine contains a sulfhydryl group useful for forming
disulphide bridges, which stabilizes the folding structure of
proteins and is also involved with intra and inter
Glyceine has 2 hydrogens on the alpha carbon. This is useful
in making compact polypeptide chains
Proline has a rigid ring structure which is also useful in compacting
These amino acids arrange themselves in various levels of organization to eventually form
unique 3D structures which are called conformations.
Function is derived from 3D structure and 3D structure is derived from the amino acid
The primary (1°) level of structure is the sequence of amino acids forming the polypeptide chain
Peptides are between 20 and 30 amino acids in length
Polypeptides are 200-500+ amino acids long
Proteins are usually thousands of amino acids in length and have 3D structure
The secondary (2°) level of structure of a protein comes from the interactions between the
carboxyl and amino groups of the individual amino acids which are found on the backbone of the
polypeptide chain
These interactions produce localized folding in certain regions of the polypeptide chain
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