Biochemistry: Enzyme Inhibition and Antibiotics

Study Notes

Enzyme regulation is crucial as cellular processes continually produce large amounts of an enzyme and products if not regulated
General mechanisms involved in regulation include proteolytic enzymes and zymogens, covalent modification of enzymes, and regulation of enzyme activity by various substances produced within a cell
Allosteric enzymes have quaternary structure, with at least two binding sites: substrate and regulator binding sites, which are distinct from each other

Antibiotics inhibit specific enzymes essential to life processes of bacteria
Two families of antibiotics considered are sulfa drugs and penicillin's
Sulfa drugs exhibit antibiotic activity by competitively inhibiting enzymes responsible for converting PABA to folic acid in bacteria
Folic acid deficiency retards bacterial growth and eventually kills them
Sulfa drugs don't affect humans because we absorb folic acid from our diet

Penicillin's were accidentally discovered by Alexander Fleming in 1928
Several naturally occurring penicillin and numerous synthetic derivatives have been produced
All have structures containing a four-membered Beta-lactam ring fused with a five-membered thiazolidine ring
Penicillin's selectively inhibit transpeptidase by covalent modification of a serine residue
Transpeptidase catalyzes the formation of peptide cross-links between polysaccharide strands in bacterial cell walls

Vitamins are components of coenzymes
Fat-soluble vitamins: A, D, E, and K
Water-soluble vitamins: B vitamins, comprising thiamin (vitamin B1), Riboflavin (vitamin B2), Niacin (vitamin B3), Vitamin B6, Folate (folic acid), Vitamin B12 (cobalamin), Pantothenic acid (vitamin B5), and Biotin
B Vitamins exhibit structural diversity

RNA (ribonucleic acid) is found mainly in the cytoplasm of living cells
DNA (deoxyribonucleic acid) is found mainly in the nucleus of living cells
DNA and RNA are polymers consisting of repeating subunits called nucleotides, which are made of three components: heterocyclic base, sugar, and phosphate
Heterocyclic bases: pyrimidine and purine
Pyrimidine bases: uracil (U), thymine (T), and cytosine (C)
Hydrogen bonds: U hydrogen bonds to A, and G hydrogen bonds to C, forming a set of complementary base pairs

DNA is one of the largest molecules known, containing between 1 and 100 million nucleotide units
Nucleotides in DNA are linked by phosphate groups that connect the 5' carbon of one nucleotide to the 3' carbon of the next
The nucleic acid backbone is a sequence of sugar-phosphate groups, which differ only in the sequence of bases
The base sequence of a DNA strand is always written from the 5' end to the 3' end

The process of DNA replication begins with the unwinding of the nucleic acid strands at a specific point called the replication fork
An RNA primer attaches to the DNA at the point where replication begins
The Okazaki fragments are synthesized by DNA polymerase along the lagging strand as the replication fork moves
The Okazaki fragments are joined by DNA ligase, resulting in two new DNA molecules

PCR is an important laboratory technique that mimics the natural process of replication
A small quantity of target DNA, a buffered solution of DNA polymerase, the cofactor MgCl2, the four nucleotide building blocks, and primers are added to a test tube
The mixture goes through several three-step replication cycles: heat (94-96°C) is used for one to several minutes to unravel DNA into single strands; the primers bind to the DNA strands and serve as starting points for new chain growth; the mixture is cooled, allowing the primers to anneal to the DNA strands

Restriction enzymes, found in a wide variety of bacterial cells, catalyze the cleaving of DNA molecules, except for a few specific types
Restriction enzymes act at sites on DNA called palindromes, where two strands have the same sequence but run in opposite directions
Restriction enzymes are used to break DNA up into fragments of known size and nucleotide sequence, which can then be spliced together with DNA ligases