Chemistry for the Biosciences
1. atomic emission spectra: when e- goes to diff E levels (as e- levels are quantised)
then emission of electromagnetic radiation
2. Balmer (atomic emission spectra series): when any level e- goes to level 2
3. Aufbau principle: fill e- with increasing E
4. Pauli exclusion principle: orbitals = 2 e-
5. Hund's rule: partially fill all orbitals before filling them
6. orbitals: s(harp): circle
p(rincipal): hourglass
d(iffuse): four ovals
f(undamental): six
7. as more electron shells, _ orbitals get _: lower orbitals (eg. s & p) get bigger
8. common elements in biology: C, H, O, P, N, S
9. valency: # of valence e- (group 1 = valence of 1)
10. electronegativity: ability for atom to attract e- to itself
- increases as move to the right (F = highest, Fr = least)
- determines type of bond (high = ionic (total transfer), low = covalent (partial
transfer))
11. electronegativity of common elements in bio: H & C = similar
- but diff to N & O (they're more electronegative)
12. when two atoms are tgt: orbitals merge -> single molecular orbit
- form bonding & antibonding orbitals
13. bonding & antibonding: - bonding = low E = favorable, when e- spends most
of time in between two nuclei
- antibonding = high E = unstable, when e- spends most of time outside nucleus
14. dative (coordinate) bond: when covalent bond & both e- fm same atom
15. sigma: single bond
16. pi: double bond
17. sigma & pi: triple bond
18. conjugated system: atoms covalently bonded w/ alternating single & double
bonds
,19. resonance: alt models for molecule as it's unstable
- DON"T swap between models
- represents structure of model as intermediate (combo of other structures)
- important for aromatic compounds
20. benzene: resonance to hexagon with circle in it (more accurate & stable) w/
delocalized e-
21. shape & structure of molecules depend on: - bond lengths
- angles
- rotation
22. as bond # increases (eg. single -> double): bond length decreases
23. bond lengths of covalent bonds: dependent on atomic radii & nature of bonds
(eg. single vs double)
24. VSEPR: - bond angles
- decreased repulsion as increase distance between e-
25. hybridization: atomic orbitals merge -> bonds of equal E
- mixes orbitals of diff E to lower E of bonds in orbitals
- more stable
26. shapes of hybridized: sp3 = tetrahedral
sp2 = trigonal planar
sp = linear
27. repulsion between lone pair / bonding pair in order fm M to L: lone pair &
lone pair
lone pair & bonding
bonding & bonding
- reason why water = 104.5 and ammonia = 106.6
28. pi bonds favorable as: lower E & stabilizes
29. why NH3 -> sp3 hybridization not sp2: bc sp2 = leave behind high E p orbital
- hybridization = lower E = more stable
- remember lone pair
30. rotation around bonds: freely around sigma
restricted around pi (partially or fully)
,31. peptide bond stabilized by: resonance
- has partial double bond -> planar
32. how to check what bond it is: measuring bond length
33. unequal sharing of e- ->: dipoles (partial +/- charges)
- eg. water has permanent dipole = polar solvent
34. examples of what mixes/doesn't mix w/ water: methanol = small & polar so
mix w/ water
octanol = large and unpolar part so can't mix
35. Van der Wells: eg. London Dispersion, dipole - dipole, H-bonds (intermolecular
forces)
36. London Dispersion: transient dipoles fm fluctuations of charge
- can cause neighboring molecules to attract
- greater size = greater dispersion force
37. H-bonds: when H bonds w/ O, N, or F (dipoles form as e- pulled to more electroatom)
- reason why ice less dense than water, high boiling points, DNA & protein bonds
stabilized
38. polarity of functional groups (most to least): amide, acid, alcohol, ketone ~
aldehyde, amine, ester, ether, alkane
39. the more polar something is...: the more soluble it is
40. alkyl group: chain of C & H with single bonds
- connect with other compounds
- CnH2n+1
- alkane missing one H
41. aryl group: functional group w/ aromatic ring
- aromatic ring with R group connected
42. alkanes: C & H, single bonds
- CnH2n+2
43. intermolecular dispersion forces _ as molecule gets larger: increase
44. phospholipids: made of 2 acyl chains (14 C & no double bonds, or 14:0)
- spontaneously create bilayer in water (bc amphiphile)
- dispersion forces sticks tails tgt
, 45. temperature and fluidity of phospholipid bilayer: low temp = gel phase
(hydrocarbons tightly packed)
high temp = fluid, movement allowed
46. length of phospholipid tail and temperature: longer chain = higher melting
point
- therefore need range of lengths to be fluid at diff temp
47. alkenes: unsaturated
- @ least one double bond (C=C)
- CnH2n
- when naming need to say where = is
- cis-trans isomerism (no free rotation due to double bond
48. physical properties of alkanes/kenes/kynes: similar
49. cis trans isomerism: cis = same side of chains (Z)
trans = opposite side (E)
50. phospholipids w/ double bond in chain: lowers melting point
- less closely packed due to "kink", lowers IMFs
51. three types of isomerism: 1) structural (cis trans)
2) enantiomeric (chiral to each other, same molecule structure)
3) enol-keto (alcohol (OH with double bond in molecule) and aldehyde/ketone)
52. structural isomers: diff molecule names, same molecular materials
- diff arrangement
53. enantiomeric: two molecules, same name but chiral
- optical isomers
- amino A = (-) or (b)
- sugars = (+) or (D)
- bend light L = (l/laevorotary), bend light R = (d/dextrorotary)
54. chiral center: 4 diff groups attached to central element
- often C, but can also be N
55. many enzymes are _ selective: chirally
- only one form works
56. Cahn Ingold Prelog (CIP): method to name molecules w/ chiral centers
1. atomic emission spectra: when e- goes to diff E levels (as e- levels are quantised)
then emission of electromagnetic radiation
2. Balmer (atomic emission spectra series): when any level e- goes to level 2
3. Aufbau principle: fill e- with increasing E
4. Pauli exclusion principle: orbitals = 2 e-
5. Hund's rule: partially fill all orbitals before filling them
6. orbitals: s(harp): circle
p(rincipal): hourglass
d(iffuse): four ovals
f(undamental): six
7. as more electron shells, _ orbitals get _: lower orbitals (eg. s & p) get bigger
8. common elements in biology: C, H, O, P, N, S
9. valency: # of valence e- (group 1 = valence of 1)
10. electronegativity: ability for atom to attract e- to itself
- increases as move to the right (F = highest, Fr = least)
- determines type of bond (high = ionic (total transfer), low = covalent (partial
transfer))
11. electronegativity of common elements in bio: H & C = similar
- but diff to N & O (they're more electronegative)
12. when two atoms are tgt: orbitals merge -> single molecular orbit
- form bonding & antibonding orbitals
13. bonding & antibonding: - bonding = low E = favorable, when e- spends most
of time in between two nuclei
- antibonding = high E = unstable, when e- spends most of time outside nucleus
14. dative (coordinate) bond: when covalent bond & both e- fm same atom
15. sigma: single bond
16. pi: double bond
17. sigma & pi: triple bond
18. conjugated system: atoms covalently bonded w/ alternating single & double
bonds
,19. resonance: alt models for molecule as it's unstable
- DON"T swap between models
- represents structure of model as intermediate (combo of other structures)
- important for aromatic compounds
20. benzene: resonance to hexagon with circle in it (more accurate & stable) w/
delocalized e-
21. shape & structure of molecules depend on: - bond lengths
- angles
- rotation
22. as bond # increases (eg. single -> double): bond length decreases
23. bond lengths of covalent bonds: dependent on atomic radii & nature of bonds
(eg. single vs double)
24. VSEPR: - bond angles
- decreased repulsion as increase distance between e-
25. hybridization: atomic orbitals merge -> bonds of equal E
- mixes orbitals of diff E to lower E of bonds in orbitals
- more stable
26. shapes of hybridized: sp3 = tetrahedral
sp2 = trigonal planar
sp = linear
27. repulsion between lone pair / bonding pair in order fm M to L: lone pair &
lone pair
lone pair & bonding
bonding & bonding
- reason why water = 104.5 and ammonia = 106.6
28. pi bonds favorable as: lower E & stabilizes
29. why NH3 -> sp3 hybridization not sp2: bc sp2 = leave behind high E p orbital
- hybridization = lower E = more stable
- remember lone pair
30. rotation around bonds: freely around sigma
restricted around pi (partially or fully)
,31. peptide bond stabilized by: resonance
- has partial double bond -> planar
32. how to check what bond it is: measuring bond length
33. unequal sharing of e- ->: dipoles (partial +/- charges)
- eg. water has permanent dipole = polar solvent
34. examples of what mixes/doesn't mix w/ water: methanol = small & polar so
mix w/ water
octanol = large and unpolar part so can't mix
35. Van der Wells: eg. London Dispersion, dipole - dipole, H-bonds (intermolecular
forces)
36. London Dispersion: transient dipoles fm fluctuations of charge
- can cause neighboring molecules to attract
- greater size = greater dispersion force
37. H-bonds: when H bonds w/ O, N, or F (dipoles form as e- pulled to more electroatom)
- reason why ice less dense than water, high boiling points, DNA & protein bonds
stabilized
38. polarity of functional groups (most to least): amide, acid, alcohol, ketone ~
aldehyde, amine, ester, ether, alkane
39. the more polar something is...: the more soluble it is
40. alkyl group: chain of C & H with single bonds
- connect with other compounds
- CnH2n+1
- alkane missing one H
41. aryl group: functional group w/ aromatic ring
- aromatic ring with R group connected
42. alkanes: C & H, single bonds
- CnH2n+2
43. intermolecular dispersion forces _ as molecule gets larger: increase
44. phospholipids: made of 2 acyl chains (14 C & no double bonds, or 14:0)
- spontaneously create bilayer in water (bc amphiphile)
- dispersion forces sticks tails tgt
, 45. temperature and fluidity of phospholipid bilayer: low temp = gel phase
(hydrocarbons tightly packed)
high temp = fluid, movement allowed
46. length of phospholipid tail and temperature: longer chain = higher melting
point
- therefore need range of lengths to be fluid at diff temp
47. alkenes: unsaturated
- @ least one double bond (C=C)
- CnH2n
- when naming need to say where = is
- cis-trans isomerism (no free rotation due to double bond
48. physical properties of alkanes/kenes/kynes: similar
49. cis trans isomerism: cis = same side of chains (Z)
trans = opposite side (E)
50. phospholipids w/ double bond in chain: lowers melting point
- less closely packed due to "kink", lowers IMFs
51. three types of isomerism: 1) structural (cis trans)
2) enantiomeric (chiral to each other, same molecule structure)
3) enol-keto (alcohol (OH with double bond in molecule) and aldehyde/ketone)
52. structural isomers: diff molecule names, same molecular materials
- diff arrangement
53. enantiomeric: two molecules, same name but chiral
- optical isomers
- amino A = (-) or (b)
- sugars = (+) or (D)
- bend light L = (l/laevorotary), bend light R = (d/dextrorotary)
54. chiral center: 4 diff groups attached to central element
- often C, but can also be N
55. many enzymes are _ selective: chirally
- only one form works
56. Cahn Ingold Prelog (CIP): method to name molecules w/ chiral centers
