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Amino Acids Flashcards

1
Q

What functional groups make-up amino acids?

A
  • amino group (-NH2)

- carboxyl group (-COOH)

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2
Q

What are proteinogenic amino acids?

A

20 alpha amino acids that are L isomers (means that they occur in nature)

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3
Q

What is the one amino acid that isn’t chiral (which means it is also the only AA that does not have both a L- and D- form)?

A

glycine

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4
Q

What are the two amino acids that don’t have a (S) absolute configuration at their alpha carbon?

A

cysteine and glycine

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5
Q

Which amino acids have non-polar, non-aromatic side chains?

A
  • LIMPGAV*
  • Leucine (alkyl side chain)
  • Isoleucine (alkyl side chain)
  • Methionine (sulfur atom in side chain)
  • Proline (forms a cyclic AA)
  • Glycine (single H)
  • Alanine (alkyl side chain)
  • Valine (alkyl side chain)
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6
Q

Which amino acids have aromatic side chains?

A
  • TTP*
  • Tyrosine (contains -OH group making it relatively polar)
  • Tryptophan (contains two rings)
  • Phenylalanine (relatively nonpolar)
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7
Q

Which amino acids have polar side chains?

A
  • CATSG*
  • Cysteine (contain a thiol -SH in side chain which is prone to oxidation)
  • Asparagine (amide side chain, nitrogen in amide doesn’t gain or lose protons with changes in pH)
  • Threonine (-OH groups in side chain so highly polar and able to participate in H-bonding)
  • Serine (-OH groups in side chains so highly polar and able to participate in H-bonding)
  • Glutamine (amide side chain, nitrogen in amide doesn’t gain or lose protons with changes in pH)
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8
Q

Which amino acids have negatively charged (acidic) side chains?

A
  • GA*
  • Glutamate (negative charge on side chain at pH of 7.4)
  • Aspartate (negative charge on side chain at pH of 7.4)
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9
Q

Which amino acids have positively charged (basic) side chains?

A
  • LAH*
  • Lysine
  • Arginine (3 nitrogen atoms that delocalizes + charge)
  • Histidine (aromatic ring with 2 nitrogen atoms called imidazole)
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10
Q

What amino acids contain a chiral atom in their side chain?

A
  • Threonine

- Isoleucine

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11
Q

What type of amino acids are found on the surface of a protein?

A
  • amino acids with charged side chains
  • histine, arginine, lysine
  • aspartate, glutamate
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12
Q

What type of amino acids are found inside a protein?

A
  • hydrophobic amino acids

- alanine, isoleucine, leucine, valine, phenylalanine

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13
Q

Why are amino acids considered amphoteric species?

A
  • they have an acidic carboxylic acid group and a basic amino group
  • they can either accept a proton or donate a proton
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14
Q

What happens to ionizable groups at a low pH?

A

protonated (NH3+, COOH)

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15
Q

What happens to ionizable groups at a high pH?

A

deprotonated (NH2, COO-)

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16
Q

What is the pKa?

A

pH at which half the molecules are deprotonated

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17
Q

pH < pKa

A

majority of species is protonated

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18
Q

pH > pKa

A

majority of species is deprotonated

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19
Q

What is the pKa of the amino acid carboxyl group (COOH)?

A

pKa1 = 2

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20
Q

What is the pKa of the amino acid amino group (NH3+)?

A

pKa2 = 9-10ish

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21
Q

How protonated are amino acids in acidic conditions?

A
  • amino group fully protonated (NH3+)

- carboxylic acid protonated (COOH)

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22
Q

How protonated are amino acids in basic conditions?

A
  • amino group deprotonates (NH2)

- carboxylic acid deprotonated (COO-)

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23
Q

What are amino acids like at physiological pH?

A
  • most carboxylic acids are protonated (COOH)

- amino group is deprotonated (NH2)

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24
Q

What occurs when pH is near the pI of the amino acid?

A

the amino acid is a neutral zwitterion – molecule contains charges but is neutral overall

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25
Titration curve is nearly _____ at the pka values of an amino acid
flat
26
Titration curve is nearly _____ at the pI of the amino acid
vertical
27
When does a solution act as a buffer?
when the pH of the solution is approximately equal to teh pKa of the solute
28
What is the pI of amino acids with nonionizable side chains?
- pH at which an amino acid is predominately in zwitterionic form - electronically neutral
29
What are the pI values of amino acids with acidic side chains?
well below 6
30
What are the pI values of amino acids with basic side chains?
well above 6
31
Dipeptides
consist of 2 amino acid residues
32
Tripeptides
consist of 3 amino acid residues
33
Oligopeptides
relatively small peptides with up to 20 amino acid residues
34
Polypeptides
longer peptides with >20 amino acid residues
35
What is a peptide bond?
- join peptide residues - form of an amide bond that forms between the COO- group and the NH3 group of another amino acid - forms the functional group C(O)NH
36
What type of reaction forms peptide bonds?
condensation/dehydration reaction
37
What order are peptides drawn/read from?
N terminus on the left to the C terminus on the right
38
What type of reaction breaks peptide bonds?
hydrolysis using an acid or base catalysis
39
What enzymes in humans catalyze the hydrolysis of peptide bonds?
- hydrolytic enzymes like trypsin and chymotrypsin - both these enzymes function by breaking apart the amide bond by adding a H atom to the amide N and an OH group to the carbonyl carbon
40
Where does the enzyme trypsin cleave a peptide bond?
at the carboxyl end of arginine and lysine
41
Where does the enzyme chymotrypsin cleave a peptide bond?
at the carboxyl end of phenylalanine, tryptophan and/or tyrosine
42
pH=pKa
50% of protonated form, and 50% of deprotonated form
43
Zwitterion has both ___ and ___ species in the same ion
negative and positive
44
What are the ? beta-branched AAs?
- Valine - Isoleucine - Threonine
45
What are beta branched AAs?
AAs that have a branch at the C that is 2C's away from the carbonyl
46
What can be said about beta-branched amino acids?
they are not favored in some secondary structures (i.e. alpha helix)
47
What two amino acids will never be found in alpha helices?
- glycine | - proline
48
Which amino acid introduces a kink in the amino acid chain?
Proline
49
What 3 AAs can be phosphorylated at their R group -OH?
- Serine - Threonine - Tyrosine
50
What two things can be said about Tyrosine?
it is aromatic and nonpolar
51
What two amino acids contain sulfur?
- Cysteine | - Methionine
52
What amino acid can form disulfide bonds under oxidizing conditions?
Cysteine
53
What type of agent is needed to break covalent disulfide bonds? (like the one formed btw two cysteines)
Reducing agent
54
What protein structures are disulfide bonds found in?
- secondary - tertiary - quaternary
55
What is the pKa of Lysine's R-group?
10.5
56
What is the pKa of Arginine's R-group?
12.5
57
What is the pKa of Histidine's R-group?
6
58
Arginine contains a ____ group
guanidinium
59
Histidine contains a ____ group
imidazole
60
Is Histidine aromatic?
yes
61
What is the pKa of Aspartate's (Aspartic Acid) R-group?
4
62
What is the pKa of Glutamate's (Glutamic Acid) R-group?
4
63
Does histidine ionize?
Yes
64
What is a wild-type variant?
normal peptide, no changes
65
What is a T7K variant?
changing the threonine at position 7 in a peptide to lysine
66
What is the pKa of Histidine's side group?
6
67
In an acidic amino acid that is transitioning above it's pKa, its charge goes from __ to ___
neutral to negative [below its pKa of 4 the R group COOH is protonated and neutral, above its pKa the R group COO- is deprotonated and negative]
68
In a basic amino acid that is transitioning above it's pKa, it's charge goes from ___ to ___
positive to neutral [below its pKa the R group NH is protonated with a positive charge, above its pKa the R group N is deprotonated and neutral]
69
What is an Isoelectric Point?
the pH that gives an overall net neutral charge
70
How do you find the isoelectric point of a polypeptide?
average all the pKas of the amino acids in the molecule (make sure to include the N-terminus, 9, and C-terminus, 2, pKas!!!)
71
What is a dipolar molecule?
A molecule that is electrically neutral but still carries a positive and negative charge
72
Proteins are molecules that contain 50 or more amino acid residues, and they can act as excellent buffers because of their:
H-bonding capabilities in forming secondary and tertiary structures

SP MCAT Biochem (16 decks)

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