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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
Tyrosine and tryptophan have some hydrophilic properties due to ....?
-OH and -NH- groups respectively
26
Serine and theronine are hydrophilic because?
-OH group
27
Where are serine and threonine usually found?
Outside of proteins (hydrophilic)
28
What amino acids contains a reactive thiol group?
Cysteine
29
What name is given to a cysteine bonded in a disulfide bond?
Cystine
30
Name the three basic amino acids.
Lysine, histidine and arginine
31
Lysine and arganine have what charge at neutral pH?
Positive
32
What does histidine contain?
Imidazole ring
33
What pKa does histidine have? What does this mean?
6- it can be charged or uncharged at pH near to neutral
34
Where is histidine often found?
Active sites of enzymes where it can bind and release protons
35
Where is histidine an buffer?
blood
36
Where does the pKa of histidine change?
In Hb | Neighbouring groups affect pKa too
37
Name the two acidic amino acids
``` Aspartic acid (aspartate) Glutamic acid (glutamate) ```
38
What are the uncharged derivatives of aspartate and glutamate called?
Asparagine and glutamine
39
How is aspargine and glutamine uncharged?
NH2 group replaces O- in carboxyl group
40
Amino acids are linked by
Peptide bonds
41
What is the native structure of a protein?
The three-dimensional structure of a protein under physiological condisiotns
42
Native conformation tends to be a proteins .... conformation
Active conformation
43
What does ribonuclease A do?
Hydrolyses RNA
44
Who performed experiments investigating protein folding in the 1950's?
Christian Anfinsen
45
What solutions did Anfinsen use?
8M urea or 6M guanidine hydrochloride
46
What happens to proteins in Anfinsens solutions?
Denature into random coils
47
What else did Anfinsen use to break disulphide bonds in proteins?
Beta-mercaptoethanol
48
What protein did Anfinsen use in his experiment?
RNAse
49
What happened when RNAse has the urea and mercaptoethanol removed using dialysis?
RNAse spontaneously regained enzyme activity (renatured)
50
What was Anfinsens conclusions?
Amino acid sequence of RNAse provides all information required to specify native structure
51
What happened when Anfinsen left urea but removed mercaptoethanol?
regained 1% of original activity
52
Why did the RNAse regain 1% activity?
1 combination of correct disulphide bonds out of 105 possible
53
What was Anfinsen's conclusion from his other experiment?
Correct disulphide bonds are in a lower free energy state and are more energetically favourable
54
How did RNAse regain it's activity after being treated with mercaptoethanol?
Scrambled the RNAse
55
Is it true that the most thermodynamically stable structure is the native conformation for all proteins?
No
56
Who came up with Levinthal's paradox?
Cyrus Levinthal
57
How long would it take a protein containing 100 residues to fold into the correct conformation by random chance?
1.6*10^27
58
What name is given to random pathways?
Stochastic pathways
59
How do proteins fold into their native structures if not randomly?
Via series of intermediates (hydrophobic/philic interactions etc.)
60
Protein folding can be visualized as a
funnel
61
What factors determine folding of proteins?
Hydrophobic/philic interactions Interactions between residues Interaction of backbones
62
How do chaperone proteins help proteins fold correctly?
Delay folding | Change environment
63
How does denaturation cause permanant loss of structure?
Cell environment Proteins don't act in isolation Form a mesh network of bonds between different chains

Biomolecules (3 decks)

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