____________________________________________________________________________________________________

Know more

Web links

 https://en.wikipedia.org/wiki/Enzyme
 https://en.wikipedia.org/wiki/Enzyme_catalysis
 https://en.wikibooks.org/wiki/Structural_Biochemistry/Enzyme_Catal
ytic_Mechanism
 https://www.unifr.ch/biochem/assets/files/schneiter/cours/Voet_Pratt/
Voet_chapt_11.pdf
 https://en.wikipedia.org/wiki/RNA_hydrolysis
 http://biochem.siu.edu/bmb_courses/mbmb451b/lectures/mbmb451b_
enzcat.pdf
 http://faculty.smu.edu/svik/5310/5310lectures/lect14.html
 https://en.wikibooks.org/wiki/Structural_Biochemistry/Enzyme/Metal
_Ion_Catalysis

Chemistry PAPER No. : 16, Bio-organic and bio-physical chemistry

MODULE No. :20, General mechanisms of enzyme action II
____________________________________________________________________________________________________

Suggested reading

The Organic Chemistry of Enzyme-

Catalyzed Reactions
By Richard B.Silverman

Glossary
A
Anomer- An anomer is a special type of epimer. It is one of two stereoisomers of a cyclic
saccharide that differs only in its configuration at the hemiacetal or hemiketal carbon,
also called the anomeric carbon.
C

Chemistry PAPER No. : 16, Bio-organic and bio-physical chemistry

MODULE No. :20, General mechanisms of enzyme action II
____________________________________________________________________________________________________

Catalysis- Catalysis is the increase in the rate of a chemical reaction due to the
participation of an additional substance called a catalyst. With a catalyst, reactions occur
faster and with less energy. Because catalysts are not consumed, they are recycled.
Coenzyme- Coenzymes are organic molecules that are required by certain enzymes to
carry out catalysis. They bind to the active site of the enzyme and participate in catalysis
but are not considered substrates of the reaction.
D
Dielectric constant- The dielectric constant is the ratio of the permittivity of a substance
to the permittivity of free space. It is an expression of the extent to which a material
concentrates electric flux, and is the electrical equivalent of relative magnetic
permeability. As the dielectric constant increases, the electric flux density increases, if all
other factors remain unchanged.
H
Hydrolysis- Hydrolysis is a reaction involving the breaking of a bond in a molecule
using water. The reaction mainly occurs between an ion and water molecules and often
changes the pH of a solution.
M
Metalloenzymes- Metalloenzymes are enzyme proteins containing metal ions (metal
cofactors), which are directly bound to the protein or to enzyme-bound nonprotein
components (prosthetic groups).
Mutarotation- Mutarotation is the change in the optical rotation because of the change in
the equilibrium between two anomers, when the corresponding stereocenters
interconvert. Cyclic sugars show mutarotation as α and β anomeric forms interconvert.
N

P
Phosphodiester bond- The phosphodiester bond is the linkage between the 3' carbon
atom of one sugar molecule and the 5' carbon atom of another, deoxyribose in DNA and
ribose in RNA. Strong covalent bonds form between the phosphate group and two 5-
carbon ring carbohydrates (pentoses) over two ester bonds.
Phosphorylation- Phosphorylation is the addition of a phosphate (PO43−) group to
a protein or other organic molecule. Phosphorylation turns many protein enzymes on and
off, thereby altering their function and activity. Protein phosphorylation is one type of
post-translational modification.
pKa- The pKa of an acid is the pH at which it is exactly half dissociated.
S
Schiff base- A Schiff base, named after Hugo Schiff, is a compound with a functional
group that contains a carbon-nitrogen double bond with the nitrogen atom connected to
an aryl or alkyl group. Schiff bases in a broad sense have the general formula
R1R2C=NR3, where R is an organic side chain. In this definition, Schiff base is
synonymous with azomethine. Some restrict the term to the secondary aldimines

Chemistry PAPER No. : 16, Bio-organic and bio-physical chemistry

MODULE No. :20, General mechanisms of enzyme action II
____________________________________________________________________________________________________

(azomethines where the carbon is connected to a hydrogen atom), thus with the general
formula RCH=NR'. Schiff bases can also be referred to as imines.
T
Transition state- The transition state is the state corresponding to the highest energy
along the reaction coordinate. It has more free energy in comparison to the substrate or
product; thus, it is the least stable state. The specific form of the transition state depends
on the mechanisms of the particular reaction.

Do you know?

GENERAL FUNCTIONS OF METALLOENZYMES

Hemoglobins

A four-subunit molecule, containing a iron atom in each subunit, in which each subunit
binds a single molecule of oxygen. Hemoglobin transports oxygen from the lungs to the
capillaries of the tissue.

Cytochromes

Cytochromes are integral membrane proteins. Cytochromes contain iron which serves to
carry electrons between two segments of the electron-transport chain. The iron is
reversibly oxidizable and serves as the actual electron acceptor for the cytochrome.

Phosphotransferase

The Mg2+ atom serves again in electron transfer.

Alcohol Dehydrogenase

A zinc metalloenzyme with broad specificity. They oxidize a range of aliphatic and
aromatic alcohols to their corresponding aldehydes and ketones using NAD+ as a
coenzyme.

Arginase

The metal atom of Mn2+ is used in electron transfer.

Ferredoxin

An electron transferring proteins involved in one-electron transfer processes.

Cytochrome Oxidase

Chemistry PAPER No. : 16, Bio-organic and bio-physical chemistry

MODULE No. :20, General mechanisms of enzyme action II
____________________________________________________________________________________________________

The copper ions easily accommodate electron removed from a substrate and can just as
easily transfer them to a molecule of oxygen.

Difference between catalyst and enzyme

Enzymes and catalysts both affect the rate of a reaction. In fact, all known enzymes are
catalysts, but not all catalysts are enzymes. The difference between catalysts and enzymes
is that enzymes are largely organic in nature and are bio-catalysts, while non-enzymatic
catalysts can be inorganic compounds. Neither catalysts nor enzymes are consumed in the
reactions they catalyze.

Characteristic Catalyst Enzyme

Function Catalysts are substances Enzymes are proteins that

that increase or decrease the increase rate of chemical
rate of a chemical reaction reactions converting
but remain unchanged. substrate into product.

Molecular weight Low molecular weight High molecular weight

compounds. globular proteins.

Types There are two types of There are two types of

catalysts – positive and enzymes - activation
negative catalysts. enzymes and inhibitory
enzymes.

Nature Catalysts are simple Enzymes are complex

inorganic molecules. proteins.

Chemistry PAPER No. : 16, Bio-organic and bio-physical chemistry

MODULE No. :20, General mechanisms of enzyme action II
____________________________________________________________________________________________________

Alternate terms Inorganic catalyst. Organic catalyst or bio

catalyst.

Reaction rates Typically slower. Several times faster.

Specificity They are not specific and Enzymes are highly specific
therefore end up producing producing large amount of
residues with errors. good residues.

Chemistry PAPER No. : 16, Bio-organic and bio-physical chemistry

MODULE No. :20, General mechanisms of enzyme action II