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Biochemistry > Amino acids and proteins > Flashcards

Amino acids and proteins Flashcards

1
Q

What is the inside of a cell like?

A

Packed with macromolecules (proteins/RNA/DNA)

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2
Q

Give some roles of proteins.

A
  • enzymatic catalysis e.g. rubisco
  • transport and storage of small molecules
    and ions e.g. myoglobin in muscle and
    ferritin in blood
  • coordinated motion e.g. myosin is a major
    component of muscle, flagella and
    cytoskeleton
  • mechanical support e.g. collagen in high
    tensive strength of skin and bone
  • Immune protection e.g. immunoglobin in
    antibodies to combine with invading
    substances
  • generation and transmission of nerve
    impulses e.g. ACh receptor proteins
    mediate nerve responses to specific
    stimuli
  • control of growth and differentiation e.g.
    hormones and growth factors control gene
    expression
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3
Q

What do polymers of amino acids spontaneously do?

A

Fold into 3D structures.

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4
Q

What do proteins interact with?

A

One another and other biological macromolecules.

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5
Q

Some proteins are rigid and others…

A

flexible

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6
Q

What is the primary structure of a protein?

A

The sequence of amino acids in the polypeptide chain, held by peptide bonds.

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7
Q

What is the secondary structure of a protein?

A

Formed when the chain folds into alpha helices/beta sheets.

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8
Q

What is the tertiary structure of a protein?

A

3D structure of a protein.

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9
Q

What are amino acids?

A

Monomeric unit of a protein.

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9
Q

What is the quaternary structure of a protein?

A

Exhibited by proteins with more than one polypeptide chain.

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9
Q

What groups does the amino acid have?

A

Alpha carbon attached to an R-group, carboxylic acid group and an amino group.

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9
Q

What does the property of an amino acid depend on?

A

The nature of its R-group.

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10
Q

Why is the alpha carbon chiral?

A

It has 4 different substituents.

Substituent = atom/group of atoms occupying place in a molecule.

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11
Q

How do chiral molecules exist?

A

In two different forms (isomers) that are mirror images.

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12
Q

All amino acids except glycine have mirror images.

How do you label each image?

A

L (laevus, left) and D (dexter, right).

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13
Q

Which form (L or D) are amino acids in when they are part of a protein?

A

L form, only in D form in bacterial cell walls.

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14
Q

What is pKa?

A

dissociation constant

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15
Q

What is pH?

A

A measure of the concentration of hydrogen ions in solution.

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16
Q

What is the pH of most bodily fluids?

A

6.5-7.5 = physiological range.

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17
Q

Give the equation for pH.

A

pH = -log10[H+]

so [H+] = 10^-pH

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18
Q

How is H+ released into solution?

A

Acid molecules dissociate.

HA ⇌ H+ + A-

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19
Q

What is the strength of an acid given by?

A

Ka = ([H+][A-])/[HA]

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20
Q

What does the pKa of an acid tell us?

A

The pH at which half the acid present is dissociated.

e.g.
pKa of weak acetic acid = 4.8
pKa of strong hydrochloric acid = -7

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21
Q

Give the equation for pKa.

A

pKa = -log10 Ka

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22
Q

At neutral pH, amino acids in solution exist predominantly as…

A

dipolar ions/zwitterions.

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23
Q

Describe the amino and carboxyl groups of an amino acid in dipolar form.

A

Amino group: protonated (+ve charge) and pKa = 8.0.
Carboxyl group: deprotonated (-ve charge) and pKa = 3.1.

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24
Q

What is the overall charge of an amino acid at pH 0?

A

Positive - both groups protonated.

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25
Q

At pH 12, what is the overall charge of the amino acid?

A

Negative - both groups deprotonated.

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26
Q

Glycine (Gly, G) is hydro…

A

philic.

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27
Q

What is the R group of glycine?
Is it polar?

A

A hydrogen atom.
Non-polar.

28
Q

What does glycine provide for proteins?

A

Provides flexibility to proteins where other side chains would be too bulky.

29
Q

What is the R-group of alanine? How does this affect its size? Is it polar?

A

A methyl (aliphatic) side chain.

Non-polar

Small size.

Aliphatic = organic compounds which carbon atoms form open chains.

30
Q

Alanine (Ala, A) is hydro…

A

phobic.

31
Q

Why is proline (Pro, P) an unusual amino acid?

A

The aliphatic side chain bonds to nitrogen atom of amino group.

32
Q

Proline is hydro…

A

phobic.

33
Q

Is the side chain on proline polar?

A

Non-polar.

34
Q

Why are there tight restraints on the conformation/shape of the protein?

A

Due to the rigidity of the pyrrolidine ring.

35
Q

Where is proline found?

A

In proteins that need to be rigid (collagen and turns of globular proteins).

36
Q

What is the R-group of serine?

A

-CH2-OH

37
Q

What does the hydroxyl functional group mean for the amino acid Ser, S?

A

Polar due to difference in electronegativity between O and H.

Hydrophilic.

Can participate in hydrogen bonding interactions.

38
Q

Where is Serine often found?

A

In the active sites of enzymes because the OH group is reactive (nucleophilic) and can form a covalent bond to the substrate during an enzyme-catalysed reaction.

39
Q

What is the R group on histidine (His, H) and is it polar?

A

Imidazole ring (5 membered aromatic ring).

Polar.

40
Q

Histidine is hydro…

A

philic.

41
Q

Depending on the local environment (protein and solvent), how can histidine be found?

A

Can be neutral or positively charged. Only amino acid with a pKa of side chain of near neutral pH (6.7).

42
Q

Where is histidine found?

A

In the active site of many enzymes because the imidazole ring can bind and release protons during the course of an enzymatic reaction.

43
Q

What is the R-group of cysteine?

A

-CH2SH (thiol functional group).

44
Q

Cysteine (Cys, C) is hydro…

A

phobic.

45
Q

What is pKa of the cysteine side chain? What does this mean?

A

8.4 - often found in active sites because this pKa is close to physiological pH.

46
Q

Is a thiol or hydroxyl group more reactive?

A

Thiol.

47
Q

Cysteine’s side chain is weakly…

A

polar.

48
Q

What is the functional group of phenylalanine (Phe, F)?

A

Benzene.

49
Q

Phenylalanine is hydro…

A

phobic.

50
Q

What is the R group of phenylalanine, tyrosine (Tyr, Y) and tryptophan (Trp, W)? Is it polar?

A

Methylene (CH2) linked to aromatic ring.
Non-polar for phenylalanine and tryptophan but polar for tyrosine.

51
Q

How can phenylalanine, tyrosine and tryptophan help to determine the concentration of proteins in solution?

A

Absorb UV radiation (280nm).

52
Q

What does the hydroxyl group mean on Tyrosine’s phenol side chain?

A

It is less hydrophobic and more reactive.

53
Q

What functional group does tryptophan have?

A

Indole functional group (six membered benzene ring fused to five membered pyrrole ring - 4C, 1N).

54
Q

Tryptophan is hydro…

A

phobic.

55
Q

What do glutamate (Glu, E) and lysine (Lys, K) have in common? What does this mean for them?

A

Charged amino acid side chains. They have highly polar side chains, so can participate in hydrogen bonding and ionic interactions.

56
Q

What is the R-group and functional group of glutamate?
What is the pKa of the functional group?

A

R-group = -CH2-CH2-COO-
Functional group = acidic carboxyl with pKa of 4.1.

57
Q

What is the R-group and functional group of lysine?
What is the pKa of the functional group?

A

R-group = -CH2-CH2-CH2-CH2-NH3+
Functional group = basic amine with pKa of 10.8.

58
Q

Any pKa value higher than pH7 in solution will be…

A

protonated.

59
Q

Any pKa value lower than pH7 in solution will be…

A

deprotonated.

60
Q

Why can cysteine and histidine switch between charges depending on the reaction?

A

Their values for pKa are close to physiological pH.

61
Q

What does a pair of cysteines form when they approach each other in the 3D structure?

A

A covalent bond = disulphide bond.

62
Q

What is special about the disulphide bond?

A

It is the only covalent bond that stabilises the tertiary structure.

63
Q

Write the oxidation-reduction (redox) reaction for the formation of a disulphide bond.

A

2R-SH
⇌
R-S-S-R + 2H+ + 2e-

64
Q

What is a polypeptide?

A

Chains of series of amino acids joined by peptide bonds.

65
Q

Linking 2 amino acids forms a peptide bond and involves a water molecule being…

A

eliminated.

66
Q

What is the name of each amino acid within a polypeptide?

A

A residue.

67
Q

Why do polypeptide chains have different direction?

A

Their ends are different.

68
Q

What do polypeptide chains start with?

A

N-terminal = amino terminal residue.

69
Q

What do polypeptide chains end with?

A

C-terminal = carboxyl terminal residue.

70
Q

Give 2 reasons as to why its important to know the primary structure of a protein.

A
  • Determines the 3D structure of the
    protein so is essential to elucidating
    (making it clear) to the protein’s function.
  • Alterations in sequence can lead to
    abnormal protein function and disease.

Biochemistry (10 decks)

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