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Biomolecules > Lecture 1 and 2 > Flashcards

Lecture 1 and 2 Flashcards

1
Q

What name is given to the central carbon atom in an amino acid?

A

Chiral alpha carbon

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2
Q

Where are NH2 and COOH version of amino acid found?

A

Isolated, powdered amino acids

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3
Q

How many amino acids are found in proteins?

A

20

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4
Q

What other amino acids are found in organisms?

A

Non-protein amino acids

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5
Q

What do amino acids exist of at neutral pH?

A

Dipolar ions called zwitterions

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6
Q

What happens to the amino and carboxyl group when they exist as zwitterions?

A

Amino group is protonated

Carboxyl group is deprotonated

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7
Q

What is pH?

A

A measure of the concentration of H+ free in solution

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8
Q

What molar solution is pure water?

A

55.6M

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9
Q

Why does water dissociate to a small extent?

A

Hydrogen bonds

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10
Q

How to calculate pH?

A

log(H+ concentration)

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11
Q

How to calculate pKa?

A

-logKa

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12
Q

What is pKa a measure of?

A

Acid dissociation constant, the pH at which 1/2 dissociated

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13
Q

A lower pKa means what?

A

A stronger acid

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14
Q

At higher pH’s, amino acids groups are become…

A

Deprotonated

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15
Q

What is the names given to the two types of isomers of amino acids formed due to chiral alpha carbon?

A

L and D

Only L found in proteins

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16
Q

Give to features of glycine

A

R group is a hydrogen atom

Smallest amino acid

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17
Q

Longer aliphatic chains make amino acids more…

A

Hydrophobic

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18
Q

What amino acids have aliphatic R groups?

A

Glycine, Alanine, Valine, Leucine, Isoleucine and methionine

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19
Q

What does methionine contain?

A

A thioester (-S-) group

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20
Q

What does proline have?

A

A cyclic aliphatic R group

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21
Q

Where is proline often found and why?

A

Bends in proteins, because it is more structurally restricted

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22
Q

What are the three aromatic amino acids?

A

Phenylalanine, tyrosine, tryptophan

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23
Q

What do the aromatic amino acids all have?

A

A phenyl group

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24
Q

Are the aromatic amino acids hydrophobic or hydrophilic?

A

Hydrophobic

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25
Q

Tyrosine and tryptophan have some hydrophilic properties due to ….?

A

-OH and -NH- groups respectively

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26
Q

Serine and theronine are hydrophilic because?

A

-OH group

27
Q

Where are serine and threonine usually found?

A

Outside of proteins (hydrophilic)

28
Q

What amino acids contains a reactive thiol group?

A

Cysteine

29
Q

What name is given to a cysteine bonded in a disulfide bond?

A

Cystine

30
Q

Name the three basic amino acids.

A

Lysine, histidine and arginine

31
Q

Lysine and arganine have what charge at neutral pH?

A

Positive

32
Q

What does histidine contain?

A

Imidazole ring

33
Q

What pKa does histidine have? What does this mean?

A

6- it can be charged or uncharged at pH near to neutral

34
Q

Where is histidine often found?

A

Active sites of enzymes where it can bind and release protons

35
Q

Where is histidine an buffer?

A

blood

36
Q

Where does the pKa of histidine change?

A

In Hb

Neighbouring groups affect pKa too

37
Q

Name the two acidic amino acids

A 
Aspartic acid (aspartate)
Glutamic acid (glutamate)
38
Q

What are the uncharged derivatives of aspartate and glutamate called?

A

Asparagine and glutamine

39
Q

How is aspargine and glutamine uncharged?

A

NH2 group replaces O- in carboxyl group

40
Q

Amino acids are linked by

A

Peptide bonds

41
Q

What is the native structure of a protein?

A

The three-dimensional structure of a protein under physiological condisiotns

42
Q

Native conformation tends to be a proteins …. conformation

A

Active conformation

43
Q

What does ribonuclease A do?

A

Hydrolyses RNA

44
Q

Who performed experiments investigating protein folding in the 1950’s?

A

Christian Anfinsen

45
Q

What solutions did Anfinsen use?

A

8M urea or 6M guanidine hydrochloride

46
Q

What happens to proteins in Anfinsens solutions?

A

Denature into random coils

47
Q

What else did Anfinsen use to break disulphide bonds in proteins?

A

Beta-mercaptoethanol

48
Q

What protein did Anfinsen use in his experiment?

A

RNAse

49
Q

What happened when RNAse has the urea and mercaptoethanol removed using dialysis?

A

RNAse spontaneously regained enzyme activity (renatured)

50
Q

What was Anfinsens conclusions?

A

Amino acid sequence of RNAse provides all information required to specify native structure

51
Q

What happened when Anfinsen left urea but removed mercaptoethanol?

A

regained 1% of original activity

52
Q

Why did the RNAse regain 1% activity?

A

1 combination of correct disulphide bonds out of 105 possible

53
Q

What was Anfinsen’s conclusion from his other experiment?

A

Correct disulphide bonds are in a lower free energy state and are more energetically favourable

54
Q

How did RNAse regain it’s activity after being treated with mercaptoethanol?

A

Scrambled the RNAse

55
Q

Is it true that the most thermodynamically stable structure is the native conformation for all proteins?

A

No

56
Q

Who came up with Levinthal’s paradox?

A

Cyrus Levinthal

57
Q

How long would it take a protein containing 100 residues to fold into the correct conformation by random chance?

A

1.6*10^27

58
Q

What name is given to random pathways?

A

Stochastic pathways

59
Q

How do proteins fold into their native structures if not randomly?

A

Via series of intermediates (hydrophobic/philic interactions etc.)

60
Q

Protein folding can be visualized as a

A

funnel

61
Q

What factors determine folding of proteins?

A

Hydrophobic/philic interactions
Interactions between residues
Interaction of backbones

62
Q

How do chaperone proteins help proteins fold correctly?

A

Delay folding

Change environment

63
Q

How does denaturation cause permanant loss of structure?

A

Cell environment
Proteins don’t act in isolation
Form a mesh network of bonds between different chains

Biomolecules (3 decks)

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