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Cellular biology and biochem > Charge and shape in biological reactions > Flashcards

Charge and shape in biological reactions Flashcards

1
Q

What is the nominal mass of an electron?

A

0

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2
Q

Do metal lose or gain electrons to become cations?

A

lose

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3
Q

Why is oxygen electronegative?

A

the electrons shared in the covalent bond are attracted to it pulling the electrons away from the H, polarising the bond

  • O has a partial negative charge
  • each H has a partial positive charge
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4
Q

What is the order of strength interactions from strongest to weakest?

A
  • single covalent
  • cation-anion
  • hydrogen bond
  • pi-cation
  • pi-pi
  • dipole-dipole
  • London dispersion
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5
Q

What types of molecules tend to be hydrophilic?

A

molecules with charge, good H-bonding pot and a low proportion of C atoms

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6
Q

What is an acid?

A

A compound that can lose an H+ ion and become negatively charged in the process

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7
Q

What is a base?

A

A compound that can (reversibly) form covalent bonds with a H+ ion to become positively charged

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8
Q

What types of acid are predominately ionised (negative charge) at physiological PH?

A

Acids with a low pKA (<7.4)

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9
Q

What happens to bases with a high pKA at physiological PH?

A

predominantly ionised

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10
Q

What determines the hydrophobicity/hydrophilicity in an amino acid?

A

The R group

-amides are neutral across physiological PH

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11
Q

What determines the secondary structure of a protein?

A

the shape (conformational preference) of the residues due to their hydrophobicity/hydrophobicity preference, this is maintained by H bonding

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12
Q

What is the secondary structure?

A

Arrangement of the primary structure into defined regions (α helix, beta sheet)

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13
Q

What is the tertiary structure of a protein?

A

Higher folding of the secondary structure maintained by ionic, H bonds and di-sulfide bonds between cysteines

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14
Q

What is the quaternary structure?

A

How chains can together and arrange to from complexes

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15
Q

What is the equation for PH?

A

PH= -log10[H^+]

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16
Q

What is PH 0 equal to?

A

1M HCl

17
Q

What is the concentration of H^+ in pure water?

A

PH of pure water = 7
PH = -log10[H^+] = -log10[10^-7]
therefore [H^+] = 10^-7M

18
Q

Why weak acids usually in equilibrium?

A

Because the energy between reactants and products is very small so it is easy to go forwards and backwards

19
Q

What is Chatelier’s principle?

A

If an equilibrium is disturbed by a change of environment the system will tend to shift its equilibrium position to counteract the effect of the disturbance

20
Q

What is Ka?

A

equilibrium constant

21
Q

What is the equation for KA?

A

Ka= [H+] [A-}
————-
[HA]

22
Q

What is pKA?

A

A logarithmic constant which is proportional to the free energy of the acid-base reaction which tells us how acidic/basic the compound is so can tell us the quantative behaviour of the equilibrium

23
Q

What is the equation for pKA?

A

pKa = -log10(Ka)

24
Q

When does pH =pKa?

A

When [A-] = [HA]

when the compound is 50% ionised

25
Q

What is the Henderson-Hasselbach equation?

A

pH= pKa + log ([A-]/[HA])

26
Q

How do you work out the percentage ionisation of a compound?

A

% compound ionised = 100
————
1 + 10^(charge(pH-pKa)
When the charge for acids = -1
charge for bases = +1

27
Q

What happens when PH =pKa -1 for an acid.

A

Acid will be around 10% disassociated

28
Q

What happened when PH =pKa + 1 for an acid

A

Acid will be around 90% dissociated

29
Q

What happens when PH >pKa +2

A

acid will be more than 99% disassociated

30
Q

What is a deprotonated termed as and why?

A

Conjugate base because it acts as a base, receiving a proton in the reverse reaction

31
Q

What is the Ka for a base?

A

Ka = [H+] [B]
————
[HB+]

32
Q

Can the solvent around a molecule affect pKa?

A

Yes

i.e less exposure to water (shielding) means ionisation is less likely (pKa of acids higher)

33
Q

What is the isoelectric point?

A

When there are multiple pKa values then there can be multiple different states with different charges. When the net charge is 0 it is known as the isoelectric point (the PH when theres no charge)
-equal number of + and - charged groups on the protein so its at its minimum aqueous solubility

34
Q

What moves towards the cathode?

A

positively charged compounds

Cellular biology and biochem (11 decks)

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