the chemistry of life

what does it mean if all elements found in life have incomplete outer shells?

this means they are unstable — they can react by sharing or donating electrons

• overall, chemical reactions involve ELECTRON TRANSFER

how are covalent bonds formed

by sharing electrons. however it depends on :

• how many ‘spaces’ there are in the outer shell because different elements form DIFFERENT NUMBERS of covalent bonds

what is a double covalent bond?

when atoms share 2 pairs of electrons

• for example, in molecular oxygen, 2 oxygen atoms share 2 pairs of electrons, forming a double covalent bond

what bonds can carbon form?

• single

• double (generates further diversity)

• triple

is rotation of atoms possible with single bonds?

Yes

• a group of atoms can change position relative to one another — CONFORMATION chanes

is bond rotation about a double bond possible?

No

• their atoms remain in a fixed configuration — their relative positions DO NOT change

• their orientation can either be CIS (atoms on opposite sides of double bond) or CIS (atoms on same sides of double bond)

how can carbon form 4 covalent bonds

by sharing 4 electron pairs

is bond rotation about a double bond possible?

No

• their atoms remain in a fixed configuration — their relative positions DO NOT change

• their orientation can either be CIS (atoms on opposite sides of double bond) or CIS (atoms on same sides of double bond)

how is carbon able to form long chains, branched structures or rings

carbon’s ability to form covalent bonds with other carbon atoms

what do carbon skeletons form

• Carbon SKELETONS form the basis of ALL biological macromolecules in the cell

what does alternating double bonds do to the structure of a molecule

• can generate a very strong structure

• the bonding electrons move within the molecule, stabilising the structure by a phenomenon called RESONANCE

what are major biological molecules of the cell built from?

sub-units joined by covalent bonds

• these are strong, and need to be made or broken by enzymes

what are non covalent bonds

bonds (eg H bonds) that form between different parts of a single macromolecule

• allow the correct shapes to form via SELF-ASSEMBLY

• weaker and do not require enzymes

• responsible for assembly of SUPRA-MOLECULAR complexes

why do different atoms attract electrons to different extents

• due to electronegativity

what type of atoms usually have greater electronegativity

larger atoms

• creates charge differences (DIPOLES) in molecules

how are H-bonds formed in water

the weak attraction of partially negative Oxygen of one water molecule with the partially positive Hydrogen atom of the other water molecule forms a HYDROGEN bond

• water molecules will form an extensive hydrogen bonded network

what 2 groups do molecules contain if they are polar and hydrophillic?

hydroxyl (-OH) and amine (-NH) groups

what group do molecules contain if they are non-polar and hydrophobic

Methine (-CH) groups

• this means the molecules cannot dissolve in water, can only be dissolved by fats

what is the hydrophobic effect?

an effect that drives non-polar molecules together, powered by the increase in entropy of water : key to membrane formation and protein folding

• entropy = a measurement of the degree of randomness/disorder

what is an ionic bond

bond formed by elements, allowing them to achieve stable outer shells by donating/receiving electrons

• in aqueous solutions, the ionic bonds dissolve and are WEAKER than covalent bonds (which do not dissolve in water)

how does water dissolve ion crystals

by forming electrostatic interactions between the ion charges and the partial charges on the water’s oxygen and hydrogen atoms,

• forming a HYDRATION SHELL of water molecules around each cation and anion

• when the ions are hydrated it allows them to move in/out of cells

what are van der waals interactions

the generation of a transient (short-lasting), dipole between atoms when electrons are close enough to perturb each other

2 types of van der waals interactions

• attractive force (london dispersion), which depends on the polarisability, dominates at longer distances (typically 0.4-0.7nm)

• repulsive force (steric repulsion) depends on the size of atoms , dominates at short distances

what does molecular complementarity between 2 protein surfaces do

• permit weak interactions that, combined, can form specific, weak to strong, transient to stable interactions

what are salt bridges

electrostatic interactions between charged residues in proteins, important in protein interactions

what does the induced fit binding of one molecule change on the other molecule

• changes conformation of the other molecule, and increases molecular complementarity (eg enzyme-substrate)

how are biological macromolecules assembled

by covalent polymerisation of monomers by dehydration chemistry

lipids

• low solubility in water so dont affect osmotic potential

• hydrophobic

• good for storage

structure of lipids

• fatty acid has carboxylic acid group at one end and long hydrocarbon tail at the other

saturated vs unsaturated bonds between carbons

Saturated = all single bonds

Unsaturated = all double bonds, cant pack as much together, flexible at body temp

what do non photosynthetic cells use for energy generation

oxidation

what do glycoconjugates consist of

• an informational carbohydrate joined to a protein or lipid

• can act as antigens (membrane glycoproteins) and lubricants

what are polysaccharides polymers of

monosaccharides joined via glycosidic bonds

what are monosaccharides

aldehydes or ketones that contain 2 or more hydroxyl groups — these tend to adopt a ring formation in solution

chitin

a modified polysaccharide in exoskeletons and fungi

• a carbohydrate

what are steriosomers

molecules that have the same bonds connecting the same atoms but different relative bond orientations

most carbohydrates and amino acids are chiral — what does this mean?

• they can only exist in 2 isomeric forms which cannot be made to superimpose by rotating or flipping

• this is due to the tetrahedral arrangement formed by carbon and its 4 single covalent bonds

what type of hexose sugars and amino acids does life on earth favour

favours D hexose sugars and L amino acids

why is ATP used by cells top capture, store and transfer energy

• due to the high energy phosphohydride bonds linking the B and Y phosphate :

• energy from ATP hydrolysis can be used to drive energetically unfavourable reactions

• ATP constantly re synthesising as we restore energy from respiration