Chapter 2: Basic Principles

Question 1

Molecules of biological interest can be classifi ed into

Answer 1

ions, small molecules and macromolecules

Question 2

Typical organic small molecules include

Answer 2

ligands of enzymes, substrates and effectors

Question 3

Ions such as Ca 2+ play a key role in

Answer 3

signalling pathways

Question 4

Biological

macromolecules are polymers which, by defi nition, consist of covalently linked

Answer 4

monomers

Question 5

Three main factors determine the three-dimensional structure of a macromolecule

Answer 5

1. dihedral torsional angles
2. monomer interactions
3. macromolecule and solvent

Question 6

The solvent interactions can be categorised into two types

Answer 6

Solvation

hydrophobic interactions

Question 7

The interactions between the building blocks of the macromolecule have two interactions types ____ and ____, which can be provided by (3 - H, ele, vn_)

Answer 7

1. negative (to avoid atomic clashing)
2. positive
3. H-bonds - backbone main constitutive force and for residue-specific interactions
4. electrostatic - opposite charges between residue side chains
5. vdW - weak short-range force between all molecules thus responsible for the complementary surface if two molecules have highly complementary shapes.

Question 8

The allowable backbone angles provide a framework of

Answer 8

geometric constraints and a balance between attractive interactions and steric tension within the macromolecule.

Question 9

The structural arrangement of groups of atoms is

Answer 9

conformation

Question 10

The

angle describing the rotation around a bond between two atoms is called the

Answer 10

dihedral angle

Question 11

conformational isomerism via interconversion giving individual isomers called

Answer 11

rotamers

Question 12

How many dihedral angles does a nucleotide bonding situation have

Answer 12

3

Question 13

the hydroxyl group in the anomeric position gives __ or __ symmetry in case of cyclic sugars in aquaous solution

Answer 13

cis or trans

Question 14

Chairs conformers have bond angles close to

Answer 14

tetrahedral

Question 15

Boat conformations for __-membered rings

Answer 15

6

Question 16

Define primary structure

Answer 16

defi ned by the sequence of the amino acid residues, and is thus naturally dictated by the base sequence of the corresponding gene

Question 17

Define 2nd structure

Answer 17

defines the localised folding of a polypeptide chain due to hydrogen bonding.

in its most basic form, to three different backbone conformations

Question 18

Define super-secondary structure

Answer 18

specific combination of particular secondary structure elements giving structural motifs that can render a domain

Question 19

Define 3rd structure

Answer 19

defines the overall folding of a polypeptide chain of a grouping or domain.

Question 20

An individual polypeptide chain in an oligomeric protein is referred to as a ___

Answer 20

subunit

Question 21

The formation of oligomers is driven by ___ complementary between the individual monomers

Answer 21

shape

Question 22

Domain swapping is a fucntional ____ by oligomerisation

Answer 22

adaptation

Question 23

Which rwo macroscopic parameters does describe macromolecules?

Answer 23

Spatial extension

molecular mass

Question 24

We have two ways to describe spatial extension (flexibility)

Answer 24

end-to-end distance

radius of gyration

Question 25

end-to-end distance is useful for (which types of molecules?)

Answer 25

molecules with regular, mostly linear shape (e.g. rods), such as DNA molecules

Question 26

What does end-to-end distance describe?

Answer 26

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.

Question 27

Define:

1. Radius of gyration
2. Hydrodynamic radius
3. Geometric radius

Answer 27

1. 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
2. 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
3. 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.

Question 28

What happens with DNA in its denatured form?

Answer 28

we get a single-stranded non-native form.

Question 29

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.

Answer 29

ionized

biochemical function

Question 30

the smaller the numerical value of pKa , the

____ the acid meaning its more ___, giving a weaker ___ ___

Answer 30

stronger
ionized
conjugate base

Question 31

Weak acids will be predominantly be ionised at ___ pH values

Answer 31

high

Question 32

weak bases will be predominantly be ionised at __ pH

Answer 32

low

Question 33

Polyprotic weak acids and bases are capable of donating or accepting more than one
____ ion

Answer 33

hydrogen

Question 34

Describe ionic strength!

Answer 34

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

Question 35

Describe:

1. salting out
2. salting in

Answer 35

1. precipitation of the protein because not enough of waters to hydrate the charged residue side-chains.
2. increased solubility because the charged residue side-chains are shielded therefore prevent aggregation

Question 36

Why is a buffer needed?

Answer 36

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

Question 37

a buffer solution consists of an aqueous mixture of a:

Answer 37

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

Question 38

What does the Henderson–Hasselbalch equation give?

Answer 38

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

Question 39

What is buffer capacity?

Answer 39

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.

Question 40

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

Answer 40

amphoteric substances
low
high
ionic

Question 41

Isoionic point: the pH at which ___ predominate in aquesous solution.

and similar too isoelectric point for _____

Answer 41

zwitterions

aminoacids

Question 42

the isoionic point is the pH at which the protein molecule possesses:

Answer 42

an equal number of positive and negative groups.

Question 43

the isoelectric point is the pH at which the protein is ____. _____

Answer 43

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

Question 44

Below the isoelectric point the ___ and zwitterion will coexist in equilibrium in a ratio determined by the _____ equation

Answer 44

cation

Henderson–Hasselbalch