Review of Basic Concepts
Types of bonds/molecular interaction
Units of measurement
Amount vs concentration
Rate vs amount
pH and the Henderson-Hasselbach
Types of Bonds
(or who shares what with whom)
Covalent vs Ionic
Note that cov
Three Dimensional Structure of
Three dimensional structure is
determined by primary sequence.
Function depends on the structure.
Proteins exist in small number of
Non covalent interactions stabilize the
Biological lipids are water insoluble
Fats and oils store energy.
Phospholipids are major structural elements of the biological
Other lipids play a role as: enzyme cofactors, electron carriers,
hormones, intracellular messengers etc.
Energy of oxidation drives synthesis of ATP.
Occurs in Mitochondria.
Accounts for most of the ATP synthesized by the cell.
Oxidative phosphorylation involves the reduction of O2 to H2O with
Protein Structure II
Molecule bound reversibly to a protein is called a
Ligand can be any molecule including other
Ligand-protein interactions are transient and fast.
Ligand binds at the site on the protein called: th
Enzymes can require no other chemical group for
Some enzymes require additional components
called cofactors or coenzymes.
A coenzyme or cofactor tightly bound to the
enzyme called prosthetic group.
A complete, catalytically
Nucleic Acids I
Based on chemical modification of nucleotides.
Double stranded DNA can be sequenced, if only one
strand is radioactively labeled.
G - (alkali + dimethyl sulfate, then piperdine)
G free energy change
S - Entropy
Large increase in Enrtopy, S, is responsible for dissolving
of salts (NaCl) in water.
When bonds are broken and formed, the
difference between energy extracted from
Catalytic and Regulatory Strategies
(Book has LOTS of detail
Advice: spend most of your time with the information
in the Powerpoint)
Specificity of chymotrypsin
Game of proton shuffle
The catalytic triad
Cleavage activity illustrates cooperation
Lecture 11: Enzymes 2
A few details I Might not have stressed enough :
Turnover = Vmax/E(enzyme cont.)
Catalytic efficiency = K cat/K m. This actually describes the shape of the curve for product
Km where Vmax/2. concentration.
Thermodynamics in Biochemistry
A framework but not the answer to everything
G = H -TS
HOMEOSTASISor what it means to be alive
Homeostasis is NOT equilibrium
(what is the difference?)
Concentration is important!
If you dont h
Lecture 11: Enzymes 2
A few details I might not have stressed enough
Turnover number = Vmax/Eo
Catalytic efficiency = kcat/KM; this actually describes
the shape of the curve for product formation
Inhibitors of Enzymes
Help understand mode
Structure/function in Biochemistry
What was the main tool used in cell biology to distinguish different
organelles, chemicals 75 years ago?
What is different now and how did Biochemistry help solve
some of these questions?
The Hill Plot
3D structure of a protein containing more than a single polypeptide chain
depends on polypeptide interactions
Stereoisomers of amino
The two stereoisomers of alanine, L-, and D- are non
superimposable mirror images (enantomers)
In proteins only L- configuration is found
Cell are able to synthesize L isomers in stereospecific
Transphosphorylation between nucleotides happens in all cell types
Biological Oxidation Reactions
Flow of electrons in oxidation reactions is responsible for all the work
done by living cell.
Electromotive force: emf. Spontaneous flow of e
Reducing sugars (anomeric carbon):
Disaccharides and polysaccharides have a reducing end, free
anomeric carbon (carbon not involved in a glycosidic bond).
Homopolysaccharides-made up from the same subunit.