Website for the lecture notes. http://web.mst.edu/~nercal/ teaching/chem361/chem361-lec01/. Introduction. What is biochemistry (BC)? Reasons why BC is exciting Simple compounds that make macromols Molecular models 3 important non-covalent bonds Properties of water.
In the past decade:
Complete genome sequences of many organisms and human beings (human genome has 3 billion base pairs!)
If we were to include the complete sequence of our genome, the chapter would be 500,000 pages!
This is truly a landmark in human history.
Comparisons are made and mechanisms of genetic disorders are discovered!
Bonding arrangement is easier to see
Very simple model
H------> white, C-------> black, N------> blue, O------> red, P----------> yellow, S------> yellow
Skeletal model good for large molecules
Space filling models of carbon, nitrogen oxygen, phosphorus and sulphur atoms.
Space filling models of water, acetate, formamide, glucose and cysteine
A) Covalent Bonds
B) Noncovalent Bonds
H bonds play an important role in biochemistry.
The 2 bonds with hydrogen are directed toward 2 corners of the tetrahedron
the unshared electrons of the 2sp3-hybridized orbitals occupy the 2 remaining corners.
The angle is 105 which is less than the tetrahedral angle (109.5) means “skewed”
Because of this, electrical charge IS NOT UNIFORMLY distributed on water molecule!
Consider amphipathic lipids in water
Lipid molecules disperse in the solution; nonpolar tail of each lipid molecule is surrounded by ordered water molecules
Entropy of the system decreases
System is now in an unfavorable state
Nonpolar portions of the amphipathic molecule aggregate so that fewer water molecules are ordered
The released water molecules will be more random and the entropy increases
All nonpolar groups are sequestered from water, and the released water molecules increase the entropy further
Only polar “head groups” are exposed and make energetically favorable H-bonds
Binding sites in enzymes and receptors are often hydrophobic
Such sites can bind hydrophobic substrates and ligands such as steroid hormones
Many drugs are designed to take advantage of the hydrophobic effect