Samenvatting
Samenvatting celbiologie deel 2 module 2 psychobiologie
- Vak
- Celbiologie
- Instelling
- Universiteit Van Amsterdam (UvA)
Samenvatting celbiologie deel 2 M2.
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Voorbeeld 2 van de 5 pagina's
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Voorbeeld van de inhoud
Module 2 deel 2Hoofdstuk 3
Pag. 134 tot/m 136
Protein function
Each type of protein consists of a precise sequence of amino acids that allows it to fold up into a particular
3D shape. >> precisely engineered moving parts whose mechanical actions are coupled to chemical
events.
All proteins bind to other molecules
A protein molecule’s physical interaction with other molecules determines its biological properties. >> all
proteins stick, or bind to other molecules. Sometimes tight, sometimes weak and short-lived. But always
specific. The substance that is bound to the protein >> ligand for that protein.
Ability of a protein to bind selectively and with high affinity to a ligand depends on the formation of a set of
weak noncovalent bonds plus favorable hydrophobic
interactions. Effective binding only occurs when many of these
bonds form simultaneously >> only possible if the surface
contours of the ligand molecule fit very closely to the protein.
The region of a protein that associates with a ligand >> the
ligand’s binding site >> a cavity in the protein surface formed
by a particular arrange ments of amino acids. Separate regions of the protein surface generally provide
binding sites for different ligands, allowing the proteins activity to be regulated. Other parts of the protein
act as a handle to position the protien in the cell. The atoms buried in the interior of the protein have no
direct contact with the ligand >> form the framework that gives the surface its contours and its chemical and
mechanical properties.
The surface conformation of a protein determines its chemistry
Chemical capabilities of proteins require that the chemical groups on their surface interact in ways that
enhance the chemical reactivity of one or more amino acid side chains >> 2 main categories
The interaction may restrict the access of water molecules to that protein’s ligand-binding sites. >> keeping
a ligand-binding site dry >> increasing that site’s reactivity
The clustering can alter their reactivity >> if protein folding forces together a number of negatively charged
side chains against their mutual repulsion >> affinity for positively charged ion is increased. When amino
acid side chains interact with one another through hydrogen bonds >> unreactive groups can become
reactive, enabling them to be used to make or break selected covalent bonds.
o The surface of each protein molecule has a unique chemical reactivity that depends on which amino
acid side chains are exposed & on their exact orientation relative to one another
Hoofdstuk 3
Pag 138 tot/m 144
The equilibrium constant measures binding strength
Colliding molecules with poorly matching surfaces form few noncovalent
bonds with each other and dissociate as rapidly as they come together.
When many noncovalent bonds form between two colliding molecules,
the association can persist for a very long time. Strong interactions >>
whenever a biological function requires long-time association.
We can measure the strength with which any two molecules bind to
each other. At frequent intervals >> association, but it has a limit. After that, dissociation. From the
concentrations of the molecules, we can calculate a convenient measure of the strength of binding >> the
equilibrium constant (K). The equilibrium constant for a reaction in which two molecules (A and B) bind to
each other to form a complex (AB) has units of liters/mole, and half of the binding sites will be occupied by
ligand when that ligand’s concentration (in moles/liter) reaches a value that is equal to 1/K. This equilibrium
, constant is larger the greater the binding strength, and it is a direct
measure of the free-energy difference between the bound and free
states.
Enzymes are powerful and highly specific catalysts
There are proteins for which ligand binding is only a necessary first step
in their function. >> enzymes. It is the catalysis of organized sets of
chemical reactions by enzymes that creates and maintains the cell,
making life possible.
Enzymes can be grouped into functional classes that perform similar
chemical reactions. Each type of enzyme within such a class is highly specific, catalyzing only a single type
of reaction (table 3-1!).
Substrate binding is the first step in enzyme catalysis
For an enzyme, the binding of each substrate molecule to the protein is
an essential prelude. Basic reaction path: E + S → ES → EP → E + P.
There is a limit to the amount of substrate that a single enzyme
molecule can process in a given time. The rate at which product is
formed eventually reaches a maximum value. >> the enzyme molecule
is saturated with substrate, and the rate of reaction (Vmax) depends
only on how rapidly the enzyme can process the substrate molecule. This maximum rate divided by the
enzyme concentration is called the turnover number (usually about 1000 substrate molecules processed
per second per enzyme molecule).
Other kinetic parameter > Km the concentration of substrate that allows the reaction to proceed at one-half
its maximum rate. Low Km >> the enzyme reaches its maximum catalytic rate at a low concentration of
substrate (tight binding). High Km >> weak binding.
Enzymes speed reactions by selectively stabilizing transition states
Enzymes achieve extremely high rates of chemical reaction:
When two molecules need to react >> the enzyme greatly increases the local concentration of both these
substrate molecules at the catalytic site, holding them in the correct orientation for the reaction that is to
follow.
Substrate molecules must pass through a series of intermediate states of altered
geometry and electron distribution before they form the ultimate products of the
reaction. The free energy required to attain the most unstable intermediate state,
called the transition state, is known as the activation energy for the reaction. >>
Enzymes have a much higher affinity for the transition state of the substrate than
they have for the stable form. Because this tight binding greatly lowers the
energy of the transition state, the enzyme greatly accelerates a particular
reaction by lowering the activation energy that is required
Hoofdstuk 3
Pag 149 t/m 155
The cell regulates the catalytic activities of its enzymes
By their catalytic action, enzymes generate a complex web of metabolic pathways, each composed of
chains of chemical reactions in which the product of one enzyme becomes the substrate of the next. >>
there are many branch points where different enzymes compete for the same substrate. >> elaborate
controls are required to regulate when and how rapidly each reaction occurs.
Regulation occurs at many levels:
The cell controls how many molecules of each enzyme it makes by regulating the expression of the gene
that encodes that enzyme.
The cell also controls enzymatic activities by confining sets of enzymes to particular subcellular
compartments.
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