BIO130H1 Chapter Notes -Protein Kinase, Transmembrane Protein, Natural Selection
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Proteins constitute most of a cells dry mass. Not only are they the building blocks, they also
carry out most of the cells functions.
Enzymes promote many of the chemical reactions.
Proteins embedded in the plasma membrane form channels and pumps that control the passage of
small molecules in and out the cell. Other proteins carry messages from one cell to another.
Kinesin: protein that propels organelles through cytoplasm.
Topoisomerase: protein that untangles knotted DNA molecules.
Other specialized proteins act as antibodies, toxins, hormones, antifreeze molecules elastic
fibers, ropes or sources of luminescence.
Protein: a molecule made up of long chains of amino acids, each linked to its neighbor with a
covalent bond. AKA polypeptides.
Each protein has its own unique amino acid sequence.
Polypeptide backbone: the repeating sequence of atoms along the core of the polypeptide chain.
Attached to this repetitive chain are the portions of the amino acids that are NOT involved in
making a peptide bond, that give each amino acid its unique properties.
* figure 3-1 very important.
- Atoms behave almost as if they were hard spheres with a definite radius (their van der Waals
forces). The requirement that no two atoms overlap limits the possible bond angles in a
polypeptide chain. This constraint and other steric interactions severely restrict the possible three
dimensional arrangements of atoms.
Nevertheless a long flexible chain such as the protein can still fold in an enormous number of
The folding of a protein however I'd constrained by many different sets of weak non covalent
bonds that form between one part of the chain and another. These involve atoms in the
polypeptide backbone and amino acids. There are three types of weak bonds: hydrogen bonds,
van der Waals attraction, and electrostatic attraction.
Many weak bonds acting in parallel can hold two regions of a polypeptide chain tightly together.
The (combined strength) of large numbers of no covalent bonds determines the stability of each
there's a fourth weak force that also helps determine the shape of a protein.
Hydrophobic molecules including the non polar side chains of a particular amino acid tend to be
forced together in an aqueous solution environment in order to minimize their disruptive effect
on the hydrogen bonded network of water molecules.
Therefore, an important factor governing the folding of any protein is the distribution of its polar
and nonpolar amino acids.
The nonpolar (hydrophobic) side chains in a protein-belonging to such amino acids as
phenylalanine, leucine, valine, and tryptophan-tend to cluster in the interior of the molecule (just
as hydrophobic oil droplets coalesce in water to form one large droplet).
This enables them to avoid contact with the water that surrounds them inside a cell.
In contrast, polar groups-such as those belonging to Arginine, glutamine, and
histidine-tend to arrange themselves near the outside of the molecule, where they can form
hydrogen bonds with water and with other polar molecules (Figure3-5).
Polar amino acids buried within the protein are usually hydrogen bonded to other polar amino
acids or to the polypeptide backbone.
An amino acid has a carbon, a side chain (R) a carboxyl group a hydrogen and an amino group
_ R is commonly one of the 20 different side chains. At a ph of 7 both amino and carboxyl
groups are ionized.
Optical isomers. The (pie) carbon atom is asymmetric, which allows for two mirror images (or
stereo-) isomers L and D.
Families of amino acids:
- the common amino acid are groups according to whether their side chains are, acidic, basic,
uncharged polar or nonpolar.
These 20 amino acids are given both 3 letter and one letter abbreviations. Ex. Lysine is Lys or K.
R group is: (CH2)4NH3.
Argine is Arg or R, r group is (CH2)3NHC=H2N+NH2. This group is very basic because
positive charges are stabilized by resonance.
Histidine is His, or H, R group: CH2CNH=CHNH=HC. These nitrogen’s have a relatively weak
affinity for an H+ and or only partially positive at a neutral pH.
Pg. 128* and 129 boxes memorize each.
Amino acids are commonly joined by an amide linkage. Called a peptide bond.
Proteins fold into a confirmation of lowest energy.
As a result of all these interactions, most proteins have a particular three dimensional shape
structure which is determined by the order of the amino acids in its chain.
Conformation: folded structure of a polypeptide.
The final conformation is one that minimizes its free energy.
Amino acids sequence contains all the information needed for specifying the three dimensional
shape of a protein.
Each protein normally folds up into a sin gle stable conformation. However the conformation
changes slightly when the protein interacts with other molecules in the cell.
In a living cell proteins called Molecular chaperones often assist in protein folding. Molecular
chaperons bind to partly folded polypeptide chains and help the progress along the most
energetically favorable folding pathway. Fig. 3-5.
In crowded conditions of the cytoplasm, the protein chaperones prevent temporarily exposed
hydrophobic regions from associating with each other to form protein aggregates.
However the final 3 dimensional shape is specified by the amino acid sequence, the chaperones.
Simply make the folding process more reliable.
Proteins come in a variety of shapes and they are generally between 50 to 2000 amino acids
Large proteins usually consist of several distinct protein domains-structural units that fold more
or less independently of each other.
Panel 3-2 (pp. 132-133) presents four different representations of a protein
domain called SH2, which has important functions in eukaryotic cells.
Constructed from a string of 100 amino acids, the structure is displayed as (A) a polypeptide
backbone model, (B) a ribbon model, (C) a wire model that includes the amino acid side chains,
and (D) a space-filling model.