Nomenclature, isomers and bioinorganic chemistry Flashcards
(45 cards)
What is the role of Fe in organisms?
- FeS redox centres in electron transfer in respiration complexes in mitochondria
- binds oxygen in oxygen carriers and oxidation enzymes (reduction of O2 to H2O/H2O2; reduction of H2O2 to H2O)
- gives colour (red in haemoglobin)
- can change geometry in FeS (tetrachedral) and haemoglobin (octahedral: dome without O2, flat with O2)
- magnetic in some organisms
- normally found chelated in proteins or prosthetic groups.
What is the role of P in organisms?
- Found as a phosphate ion
- phosphorylation of small compounds/enzyme/receptors to activate, deactivate or fix them in cells
- part of the hydrophilic head in phospholipids
- phosphodiester backbone in DNA and RNA
- pyrophosphates store lots of energy (~40-50 kJ/mol) in ATP/ADP (thermodynamically unstable but kinetically stable), which can be transferred
- important buffer and pH marker
- hydroxyapatite in bone matrix and tooth enamel
- always tetrahedral
- N—P bonds in creatine phosphate
What is the role of S in organisms?
- sulphated polysaccharides in connective tissue (dermatan, keratan, chondroitin)
- adenosine phosphosulphate (APS) - how sulphate ions are handled in organisms
- amino acid cysteine (SH): formation of disulphide bridges, nucleophile in enzyme active sites (peptide hydrolysis, intermidiate reaction in phosphorylation), reacts with Fe and Zn
- amino acid methionine (S–CH3): methyl donor (S makes CH3 more reactive), first amino acid in translation of all proteins
- thioesters (high-energy energy thermodynamically unstable bonds), can be hydrolysed easier than normal esters (Coenzyme A)
- ferrodoxins in redox centres in complexes in electron transport chain (1 Fe is supported with 4 cysteines)
- “zinc fingers” regulate transcription (1 Zn is supported with 4 cysteins)
- II oxidation state (amino acids, thioesters), IV oxidation state (sulfonation)
Where disulphide bridges are formed?
Spontaneously in the oxidizing environment (in the endoplasmic reticulum and extracellular space).
All proteins with disulphide bridges are found outside of cells (keratin, immunoglobulins, insulin).
What are isomers?
Molecules with the same formula but with different molecular structures or/and different arrangements of groups in space.
What are the types of isomers?
1) Structural isomers:
- chain isomers
- position isomers
- functional groups isomers
2) Stereoisomers
- conformational isomers (caused just by bond rotations; rotamers/conformers)
- configurational isomers (E/Z and chiral centres)
What determines the differences in melting/boiling points of chain isomers?
Number and types (primary, secondary, tertiary and quaternary) of carbon centres.
The more branching (the bigger number of higher types of carbon centres), the smaller the melting/boiling point.
It is because they are more difficult to pack, so they have less area of contact with each other, so they have weaker intermolecular forces. Less energy is needed to disrupt those forces.
What determines the differences in reactivity of position isomers?
Also number and types (primary, secondary, tertiary) of carbon centres.
Higher types (tertiary, secondary) form more stable carbocations, making them more reactive.
Which bonds can rotate (make conformational isomers)?
Single bonds (tetrahedral, sp3 hybridized).
What are the 2 types of conformational isomers?
1) Staggered - atoms attached to adjacent carbons are far away from each other as possible (“triangle” and “inverted triangle”).
MOST STABLE (less atomic interactions, lowest energy)
2) Eclipsed - atoms attached to adjacent carbons are as close to each other as possible (“triangle” and “triangle”).
LEAST STABLE (more atomic interactions, highest energy)
Use Newman’s projections.
What are 2 subtypes of staggered conformational isomers?
A) Antiperiplanar (most stable ever): the bulkiest groups are as far away from each other as possible (180 degrees).
B) Synclinal/gauche (a bit less stable): the bulkiest groups are closer (60 degrees), it creates some steric strain.
What are 2 subtypes of eclipse conformational isomers?
A) Syn-periplanar (most unstable ever): the bulkiest groups are the closest to each other as possible (0 degrees), it creates severe steric and torsional strain.
B) Anticlinal (unstable): the bulkiest groups are 120 degrees away from each other, it creates significant steric and torsional strain.
What is steric effect?
The repulsion of the orbitals when they are rotated too close to each other to decrease molecular energy.
What is steric hindrance/resistance?
When steric effect prevents the reactions from taking place.
What is Ramachandran plot?
Valid ranges of bond angles in alpha-helixes and beta-sheets based on steric hindrance.
Why cyclohexane is the most common cyclic molecule?
Cyclohexane can arrange itself perfectly into antiperiplanar conformer using tetrahedron bond angles (109.5 degrees) with minimal strain. It makes cyclohexane very stable.
Cyclopentane is also stable and common, but it has two eclipsing bonds.
What are the 4 conformers of cyclohexane?
1) Chair - antiperiplanar - least energy - most stable
2) Half-chair - syn-periplanar - most energy - most unstable
3) Boat - anticlinal - moderate energy - a bit unstable
4) Twist-boat - moderate energy - slightly more stable than boat.
What does happen when cyclohexane interchanges between “left-handed” and “right-handed” chair forms?
Vertical (axial) hydrogens become horizontal (equatorial) and wise-versa.
What happens with preferences for chair forms when there is a bulky substituent (such as CH3)?
In cyclohexane, both chair forms occur 50/50.
But with bulky substituents, the form where the bulky substituent is equatorial occurs more frequently (80%) than axial (20%). It is due to 1,3 steric interactions.
How does Z/E nomenclature work?
1) Draw a line perpendicular to the double bond.
2) Look at the left side and chose the substituent’s closest atom to the double bond in which has the highest atomic number (highest priority).
3) Do the same with right side.
4) If on both sides highest priority groups are on the top/bottom, this is Z isomer.
5) If one highest priority group is on the top and another one the bottom, this is E isomer.
Why E/Z isomers exist?
Because double bonds cannot rotate without breaking pi-bond.
What are chiral centres?
Carbons which are attached to 4 different (asymmetrical) substituents. It creates 2 possible arrangements of substituents in space (S/L and R/D forms), which are mirror images of each other and cannot be superimposed (two enantiomers).
What is prochirality?
Non-chiral substances which can be easily converted to chiral by substituting one of the two same small groups. So, despite being the same, those two groups are non-equivalent.
How does L/D system work?
If the molecule has a similar spatial arrangement as L-glyceraldehyde (reference), it is L. Otherwise, it is D.
