Transcript Amino acid chains may form helices as parts of the corresponding

Amino acid chains may form helices as parts of the corresponding protein
structure
The amino acid sequence of a protein is the same as its primary structure.
A protein may contain many different types of sub-structures covering local
parts of the overall structure. These local substructures are called secondary
structures and can be reasonably well predicted if the primary structure is
known (which is the case in almost all proteins studied) .
The overall structure of a protein, often containing many different secondary
sub-structures, is called the tertiary structure. It is very complicated to predict
but may, however, be solved by X-ray crystallography in the solid state or by
NMR (nuclear magnetic resonance) spectroscopy (small proteins, typically
below 20 kDa molecular mass), usually in solution.
a)
b)
OH
COO- OH O
HO
OH
-OOC
O
H
HO
OH
OH
HO
c)
G
M
- OOC
O
OH
COO-
O
HO
O
H
OH
HO
An enzyme,
C5-mannuronan
epimerase acting
on alginate (J.
Biol. Chem. 2006
and 2008).
OH
- OOC
H
HO
OH
O
OH
O
O
O
OH
O
OH
G
M
G
- OOC
G
M
R-module
A-module
O
H
O
COO-
O
OH
COO-
O
OH
M
O
Proteins/enzymes have the following very important properties:
•
One particular enzyme can typically bind only one specific compund (the substrate). This can be a
low molecular weight compound (like for example glucose). What it actually binds is determined
by the tertiary structure of the protein. This structure is the result of the amino acid sequence of
the protein, even though one sequence can give rise to more than one structure (boil an egg and
see!).
•
The biggest group of proteins are those that catalyse chemical reactions (they are enzymes), and
each enzyme typically catalyses only one reaction by binding a specific substrate.
•
When a particular reaction has taken place the same enzyme molecule can immediately start over
again and for example carry out 50 catalytic events in a second. Thus, the enzyme is not ”used
up” during catalysis.
•
Enzymes catalyse reactions by lowering the activation energy. Many reactions take place
spontaneously by themselves, but often very slowly. Enzymes increase the reaction rates for
example thousands of times.
•
Enzymes can also catalyse reactions that will not run by themselves, but then energy needs to be
supplied. This is often provided by ATP. One or more phosphate group in ATP is hydrolysed off,
and the energy released is used to catalyse the reaction that would otherwise not run. A typical
example is in fixation of atmospheric nitrogen, which is very energy-demanding.
•
Some enzymes can bind other (specific) compounds than the substrate, like metals, other low
molecular weight organic compounds or other proteins, and this may affect enzyme activity
(regulation)
Enzyme catalysis can be formalized in this simple way:
E+S
ES
EP
E+P
E = Enzyme, S = Substrate, P = Product
For a substrate to be converted to a product it must pass through a transition state,
and this makes the reaction run slowly in the absence of an enzyme. To reach the
transition state ”Free Energy” (ΔG) must be supplied. The enzyme lowers the
energy required to reach the transition state, leading to faster reaction rates.
Activation energy
The kinetics of enzyme reactions (all parameters can vary)
The kinetics of most enzyme-catalysed reactions can be described
mathematically by the = Michaelis–Menten equation:
V0 =
Vmax [S]
Km + [S]
Km is the substrate concentration that leads to V = ½ x Vmax
V = Reaction velocity at Km under the given conditions
Km varies over a wide range among different enzymes
How ATP makes reactions possible, in this case:
Glu + ATP + NH4+
Gln + ADP + Pi
Another way of thinking:
You move electrons around,
as in ordinary light bulbs
Naming of enzymes:
Enzyme names end by ”ase”. The first part of the name reflects what
specific type of reaction the enzyme catalyses. Enzymes belong to
classes called oxidoreductases, transferases, hydrolases, lyases,
isomerases and ligases, depending on what type of reaction they
catalyse. Each enzyme has a more specific name, like alginate lyase (it
belongs to the lyase class, but specifically acts (cleaves bonds) on the
polysaccharide alginate. What is ribonuclease doing?