Chapter 2: Basic Principles Flashcards
Molecules of biological interest can be classifi ed into
ions, small molecules and macromolecules
Typical organic small molecules include
ligands of enzymes, substrates and effectors
Ions such as Ca 2+ play a key role in
signalling pathways
Biological
macromolecules are polymers which, by defi nition, consist of covalently linked
monomers
Three main factors determine the three-dimensional structure of a macromolecule
- dihedral torsional angles
- monomer interactions
- macromolecule and solvent
The solvent interactions can be categorised into two types
Solvation
hydrophobic interactions
The interactions between the building blocks of the macromolecule have two interactions types ____ and ____, which can be provided by (3 - H, ele, vn_)
- negative (to avoid atomic clashing)
- positive
- H-bonds - backbone main constitutive force and for residue-specific interactions
- electrostatic - opposite charges between residue side chains
- vdW - weak short-range force between all molecules thus responsible for the complementary surface if two molecules have highly complementary shapes.
The allowable backbone angles provide a framework of
geometric constraints and a balance between attractive interactions and steric tension within the macromolecule.
The structural arrangement of groups of atoms is
conformation
The
angle describing the rotation around a bond between two atoms is called the
dihedral angle
conformational isomerism via interconversion giving individual isomers called
rotamers
How many dihedral angles does a nucleotide bonding situation have
3
the hydroxyl group in the anomeric position gives __ or __ symmetry in case of cyclic sugars in aquaous solution
cis or trans
Chairs conformers have bond angles close to
tetrahedral
Boat conformations for __-membered rings
6
Define primary structure
defi ned by the sequence of the amino acid residues, and is thus naturally dictated by the base sequence of the corresponding gene
Define 2nd structure
defines the localised folding of a polypeptide chain due to hydrogen bonding.
in its most basic form, to three different backbone conformations
Define super-secondary structure
specific combination of particular secondary structure elements giving structural motifs that can render a domain
Define 3rd structure
defines the overall folding of a polypeptide chain of a grouping or domain.
An individual polypeptide chain in an oligomeric protein is referred to as a ___
subunit
The formation of oligomers is driven by ___ complementary between the individual monomers
shape
Domain swapping is a fucntional ____ by oligomerisation
adaptation
Which rwo macroscopic parameters does describe macromolecules?
Spatial extension
molecular mass
We have two ways to describe spatial extension (flexibility)
end-to-end distance
radius of gyration
end-to-end distance is useful for (which types of molecules?)
molecules with regular, mostly linear shape (e.g. rods), such as DNA molecules
What does end-to-end distance describe?
average separation between the two ends of the molecule and depends on the molecular mass as well as the degree of flexibility. Entirely flexible molecules are called random coils and in such cases the end-to-end distance (now called h ) can be calculated by random walk statistics.
Define:
- Radius of gyration
- Hydrodynamic radius
- Geometric radius
- used to estimate the physical extent of a macromolecule. One may visualise Rg for a given macromolecule by a hypothetical hard sphere centred at the centre of gravity of the molecule
- is based on the diffusional properties of the molecule in solution. Therefore, a hard sphere with radius R hydro is indicative of the apparent size of the dynamic solvated particle
- arises from rotation of the protein around its centre of gravity as a rigid body, the radius of gyration refl ects the variable (not necessarily spherical) shape of the molecule.
What happens with DNA in its denatured form?
we get a single-stranded non-native form.
Electrolytes that are weak are partially ____ bases or acids in aqueous solution., and for reagents their ____ ____ is dependent upon their ionization state at the environmental pH.
ionized
biochemical function
the smaller the numerical value of pKa , the
____ the acid meaning its more ___, giving a weaker ___ ___
stronger
ionized
conjugate base
Weak acids will be predominantly be ionised at ___ pH values
high
weak bases will be predominantly be ionised at __ pH
low
Polyprotic weak acids and bases are capable of donating or accepting more than one
____ ion
hydrogen
Describe ionic strength!
govern the effect of counterion atmosphere for proteins due to the presence of charges residue side-chains.
So salt concentrations in a buffer can affect the soluability of proteins (and other charged biolofical species)
by increasing salt conc. –> salting out or salting in
Describe:
- salting out
- salting in
- precipitation of the protein because not enough of waters to hydrate the charged residue side-chains.
- increased solubility because the charged residue side-chains are shielded therefore prevent aggregation
Why is a buffer needed?
for electrolytes to resist change in pH in solution.
For weak electrlytes their ionic status varies with pH so we want to provide a constant environmental conditions during the cource of an experiment
a buffer solution consists of an aqueous mixture of a:
aqueous mixture of a weak acid and its conjugate base
The conjugate base component will neutralise any hydrogen ions generated during an experiment whilst the unionised acid will neutralise any base generated
Buffers are most commonly used in the range 0.02–0.1 M
What does the Henderson–Hasselbalch equation give?
pH estimation of a buffer solution, so idealy we want the pKa of bugger to be equal to pH in solvent. because the conjugate acid and conjugate base molecules are available in equal amounts and can thus neutralise added base or acid
What is buffer capacity?
The ability of a buffer solution to resist a change in pH on the addition of strong acid or alkali.
In practice, Buffer Capacity is largest within the pH range of pH = p K a ± 1.
Amino acids are ___ ____, meaning they can exist as bases and acid at the same time, thus giving cationic species at ___ pH and anionic species at ___ pH. And during a change in pH, Zwitterions (no charge intermediate species) is generated which is the predominantly form of amino acids in solution and crystalline state –> thus giving ___ properties
amphoteric substances
low
high
ionic
Isoionic point: the pH at which ___ predominate in aquesous solution.
and similar too isoelectric point for _____
zwitterions
aminoacids
the isoionic point is the pH at which the protein molecule possesses:
an equal number of positive and negative groups.
the isoelectric point is the pH at which the protein is ____. _____
electrophoretically immobile
It is the pH at which, for example, the protein has minimum solubility. since it is the point at which there is the greatest opportunity for attraction between oppositely charged groups of neighbouring molecules and consequent aggregation and easy precipitation
Below the isoelectric point the ___ and zwitterion will coexist in equilibrium in a ratio determined by the _____ equation
cation
Henderson–Hasselbalch