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Samenvatting molecular biology of the cell
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Samenvatting molecular biology of the cell (pharmacie)
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CHAPTER 2: CELL CHEMISTRY AND BIOSYNTHESISMolecules never have a negative or positive charge; the charge is always 0. But
sometimes the charge within the molecule is not evenly distributed (verdeeld).
Molecules that have a difference in charge are called polar molecules. Molecules in
which the charge in the molecule is completely evenly distributed are called non-polar
molecules.
Four types of noncovalent bonds:
- Electrostatic bonds (also called ionic bonds. An ionic bond forms when two
atoms are held together by the attraction between opposite charges)
- Hydrogen bonds (hydrogen bonds are formed between polar substances. A
hydrogen atom (positively charged) is then bonded to a negatively charged
atom. These can be the following atoms: oxygen, nitrogen or fluorine)
- Van der Waals attractions (the Van der Waals bonds is a weak bond between
molecules, rather than atoms. Between larger molecules, Van der Waals
bonds are greater than between smaller molecules. Thus, the strength of the
bond depends on the size/molecular mass of the molecule)
- Hydrophobic force (the hydrophobic force is the tendency of
nonpolar substances to aggregate in an aqueous solution and
exclude water molecules. Hydrophobes are nonpolar molecules and
usually have a long chain of carbons that do not interact with water
molecules, which maximizes hydrogen bonding between water
molecules and minimizes the area of contact between water and
nonpolar molecules. Hydrophobic Interactions are
important for the folding of proteins. This is important in
keeping a protein stable and biologically active, because
it allows the protein to decrease in surface and reduce
the undesirable (ongewenste) interactions with water)
A covalent bond is an atomic bond, in which atoms share
electrons in order to satisfy the octet rule. Octet rule: tendency
of atoms to prefer 8 electrons in their outer shell. A covalent bond is much stronger
than non-covalent bonds. Covalent bonds are forever, while non-covalent bonds can
be formed and broken.
Acids (zuren) = molecules that release protons when they dissolve in water, thus
forming H3O+ (also called proton donor)
The higher the concentration of H3O+, the more acidic the solution. The H3O+
concentration is usually referred as H+ concentration.
Reaction of an acid: HCl + H2O → Cl- + H3O+
Strong acids lose their protons quickly. A weak acid holds the proton more tightly
when dissolved in water.
,Base = molecules that accept a proton from a water molecule, thus forming OH - (also
called proton acceptor)
The higher the concentration of OH-, the more basic the solution
Reaction of a base: NH2 + H2O --> NH3+ + OH-
Since the reaction of H3O+ with OH- results in 2 H2O, its logical that an increase of
concentration of OH- results in a decrease in concentration in H3O+.
pH = 7 (neutral)
pH > 7 (basic)
pH < 7 (acidic)
The interior of a cell is kept close to neutrality by the presence of buffers: weak acids
and bases that can release or take up protons near pH 7, keeping the environment of
the cell constant.
The carbon compounds made by cells are called organic molecules & all other
molecules, including water, are said to be inorganic molecules.
Cells contain four major families of small organic molecules:
- Sugars
- Fatty acids
- Nucleotides
- Amino acids
The macromolecules in cells are polymers that are constructed by
covalently linking small organic molecules (monomers) into long chains.
Each polymer grows by the addition of a monomer onto the end of a
growing chain in a condensation reaction, in which one molecule of water
is lost with each subunit is added.
Hydrolysis: reverse of the condensation reaction. The polymer is split into
monomers, releasing an H2O molecule.
Fatty acids have a hydrophilic head and a hydrophobic tail. They can
form a phospholipid monolayer, in which the hydrophilic head is in contact
with the water molecules and in which the hydrophobic tail is in contact with
the hydrophobic oil. But they can also form a phospholipid bilayer. They
form a ring in which the hydrophilic heads are facing the water molecules
and the hydrophobic tails are inside, facing each other.
Nucleoside = sugar + base
Nucleotide = sugar + phosphate + base
The phosphate makes a nucleotide negatively charged.
,CHAPTER 3: PROTEINS
Proteins constitute most of a cell’s dry mass (15%). They are not only the cell’s
building blocks; they also execute the majority of the cell’s functions.
A protein molecule is made from a long unbranched chain of amino acids, each
linked together through a covalent peptide bond. Proteins are therefore also known
as polypeptides.
The polypeptide backbone is the core of the polypeptide chain. Attached to it are the
20 different amino acids side chains, those aren’t involved in making a peptide bond.
Some side chains are nonpolar and hydrophobic, negatively/positively charged, easy
to form covalent bonds and so on.
There are four different types of amino acid side chains:
- Basic (bases are proton acceptors, so you can recognize basic side chains by
the positive charge (the hydrogen atom is accepted → + charge))
- Acidic (acids are proton donors, so you can recognize acidic side chains by
the negative charge (the hydrogen atom is donated → - charge))
- Nonpolar (nonpolar = hydrophobic, so these nonpolar side chains contain
mainly C-atoms, but also there can also be a N atom, but this N atom is either
in the polypeptide backbone or in an ring structure, so it is still nonpolar)
- Uncharged polar (polar = hydrophilic, so these polar side chains contain O and
N atoms, but it is uncharged, so it has to be in these forms: = O, -OH, -NH2)
The nonpolar side chains in a protein tend to cluster in the
interior of the molecule. This enables them to avoid
contact with the water that surrounds them inside the cell.
In contrast, polar groups, tend to arrange themselves near
the outside of the molecule, where they can form hydrogen
bonds with the water and the other polar molecules.
The combined strength of non-covalent bonds determines
the folded shape and the stability of a protein.
There are special proteins called molecular chaperones. They assist in protein
folding. Molecular chaperones bind to partly folded polypeptide chains and help them
progress along the most energetically favorable folding way. However, the final three-
dimensional shape of the protein is still specified by its amino acid sequence:
chaperones simply make reaching the folded state more reliable.
Large proteins usually consist of several distinct protein domains – structural units
that fold more or less independently of each other.
, The a helix and the b sheet are 2 regular folding patterns found in almost all proteins,
since it doesn’t require any specific side groups. This is because the folds are cause
by hydrogen-bonds between the N-H and C=O groups of the polypeptide backbone.
The cores of many proteins contain extensive regions of b sheet. They can either
form parallel chains or antiparallel chains. Both type of b sheet produce a very rigid
structure, held together by hydrogen bonds that connect the peptide bonds in
neighboring chains.
An a helix is generated when a single polypeptide chain twists around
on itself to form a rigid cylinder. A hydrogen bond forms between every
fourth peptide bond, linking the C = O of one peptide to the N – H of
another.
In other proteins, a helices wrap around each other to form a particularly
stable structure, known as a coiled-coil. This structure can form when
the two (or sometimes 3/4) a helices have most of their nonpolar
(hydrophobic) side chains on one side, so that they can twist around
each other with these side chains facing inward.
Primary structure = amino acid sequence
Secondary structure = a-helices and b-sheets
Tertiary structure = the full three-dimensional structure
Quaternary structure = complex of more than 1 polypeptide chain
The majority of proteins present in cells do adopt unique and
stable conformations, because of natural selection. A protein with
an unpredictably variable structure and biochemical activity is unlikely to help the
survival of a cell that contains it. Such proteins would therefore have been eliminated
by natural selection through the trial-and-error process that underlies biological
evolution. Proteins are so precisely built that the change of even a few atoms in one
amino acid can sometimes disrupt the structure of the whole molecule so severely
that all function is lost.
Once a protein had evolved that folded up into a stable conformation with useful
properties, its structure could be modified during evolution to enable it to perform new
functions. This process has been greatly accelerated by genetic mechanism that
occasionally duplicate genes, allowing one gene to evolve independently to perform
a new function. As a result, many proteins now can be grouped into protein families,
each family member having an amino acid sequence and a 3-dimensional
conformation that resembles those of other family members.
In general, the structure of the different members of a protein family has been more
highly conserved than the amino acid sequence. In many cases, the amino acid
sequence have diverged so far that we cannot be certain of a family relationship
between two proteins without determining their three-dimensional structures. Many
similar examples show that two proteins with more than 25% identity in their amino
acid sequences usually share the same overall structure. Protein comparisons are
important because related structures often imply related functions.
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