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Cellular Biology and Biochemistry > Change and shape in biological reactions > Flashcards

Change and shape in biological reactions Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

How are cations formed?

A

Loss of electrons

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2
Q

How are anions formed?

A

Gain of electrons

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3
Q

What is a hydrogen bond?

A

An attraction between N, O or F and a H on another molecule

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4
Q

What type of bonding is present in liquid water?

A

Covalent bonds: sharing electrons between oxygen and hydrogen
Hydrogen bonds: between adjacent molecules

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5
Q

What kind of environment is water?

A

Polar

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6
Q

What will water easily solubilise?

A

Other polar molecules, regions of molecules or ions

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7
Q

What makes something hydrophilic?

A

Charge
Hydrogen bonding potential
Low proportion of carbon atoms

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8
Q

What makes something hydrophobic

A

No charge

High proportion of carbon atoms

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9
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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10
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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11
Q

What will happen to amino acids with low pKa at physiological pH?

A

They will be negatively charged and anionic

Predominantly ionised

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12
Q

What will happen to amino acids with high pKa at physiological pH?

A

They will be positively charged and cationic

Predominantly ionised

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13
Q

What happens to amides at physiological pH?

A

Amides are neutral at physiological pH

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14
Q

What determines secondary structure?

A

Shape and conformation preference of the residues
Maintained by regular hydrogen bonding pattern
Can be predicted from primary structure

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15
Q

What is tertiary structure?

A

The overall shape of a protein chain

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16
Q

What determines tertiary structure?

A

Bonding interactions:
Ionic & hydrogen
Conformation of residues e.g. proline-induced turns

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17
Q

How does hydrophobicity influence structure?

A

Hydrophobicity residues prefer to be at the centre of the protein away from the water

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18
Q

What is quaternary structure?

A

Chains forming complexes

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19
Q

What determines quaternary structure?

A

Bonding between chains

Hydrophobicity

20
Q

Name three things hydrophobicity determines

A

Structure
Function
Cellular distribution

21
Q

What is pH?

A

Measure of concentration of H+

22
Q

How do we calculate pH?

A

pH = -log10[H+]

23
Q

Why is water polar

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
24
Q

What types of molecules tend to be hydrophilic?

A

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

25
Q

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

A

Acids with a low pKA (<7.4)

26
Q

What determines the hydrophobicity/hydrophilicity in an amino acid?

A

The R group

-amides are neutral across physiological PH

27
Q

Why are 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

28
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

29
Q

What is Ka?

A

equilibrium constant

30
Q

What is the equation for KA?

A

[HA]

31
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

32
Q

What is the equation for pKA?

A

pKa = -log10(Ka)

33
Q

When does pH =pKa?

A

When [A-] = [HA]

when the compound is 50% ionised

34
Q

What is the Henderson-Hasselbach equation?

A

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

35
Q

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

A

1 + 10^(charge(pH-pKa)

When the charge for acids = -1
charge for bases = +1

36
Q

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

A

Acid will be around 10% disassociated

37
Q

What happenes when PH =pKa + 1 for an acid

A

Acid will be around 90% dissociated

38
Q

What happens when PH >pKa +2

A

acid will be more than 99% disassociated

39
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

40
Q

What is the Ka for a base?

A

[HB+]

41
Q

How can the solvent around a molecule affect pKa?

A

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

42
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

43
Q

What moves towards the cathode?

A

positively charged compounds

44
Q

What are the ionisable amino acids?

A

Aspartate
Glutamate
Lysine
Argenine

These amino acids are predmoninantly ionised at phsiological pH meaning there are very hydrophilic

45
Q

Why does pH and pKa matter?

A

Can effect the potential conformation of proteins

Can effect the behaviour of certain moleules

46
Q

What influences pKa?

A

The solvent around a molecule

Accessibility to water influences the side chain ionisation properties

Cellular Biology and Biochemistry (22 decks)

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