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MCAT - Biochemistry - Amino Acids > Amino Acids > Flashcards

Amino Acids Flashcards

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1
Q

What are the 2 functional groups of amino acids?

A

Amino group (NH2) and carboxyl group (COOH)

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2
Q

What is a alpha-carbon

A

carbon that bonds the amino and the carboxyl is the same carbon

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3
Q

What are the 4 components of amino acids?

A

Amino group, carboxyl group, hydrogen and a side chain (R-group)

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4
Q

What does the side chain do?

A

Determines the proprieties and the functions of the amino acid

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5
Q

What are called the 20 alpha-amino acids encoded by the human genetic code?

A

Proteinogenic amino acids

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6
Q

What do you call the carbon when the alpha-carbon is in the center?

A

Chiral (stereogenic)

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7
Q

How is the amino acid when the alpha-carbon is chiral?

A

Optically active

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8
Q

What is the only amino acid non optically active?

A

Glycine

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9
Q

How come Glycine isn’t optically active?

A

It has an hydrogen as the side chain, so it’s achiral

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10
Q

What type of amino acids are all chiral amino acids used in eukaryotes?

A

L-Amino acids

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11
Q

How do you draw an L-amino acid in the Fisher projection?

A

The amino group is drawn on the left

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12
Q

What type of configuration has almost all of amino acids in Cahn-ingold-Prelog System

A

(S) absolute configuration

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13
Q

Which amino acid is the exception of the Cahn-Ingold-Prelog System?

A

Cysteine has an (R) absolute configuration

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14
Q

Why cysteine has a (R) absolute configuration?

A

The CH2SH group has priority over the COOH group

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15
Q

What are the amino acids with non-polar, nonaromatic side chains?

A

Glycine, Alamine, Valine, Leucine, Isoleucine, Methionine, Proline

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16
Q

What are the 3 letter and the 1 letter name for Glycine?

A

Gly and G

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17
Q

What are the 3 letter and the 1 letter name for Alamine?

A

Ala, A

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18
Q

What are the 3 letter and the 1 letter name for Valine?

A

Val, V

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19
Q

What are the 3 letter and the 1 letter name for Leucine?

A

Leu, L

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20
Q

What are the 3 letter and the 1 letter name for isoleucine?

A

Ile, I

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21
Q

What are the 3 letter and the 1 letter name for Methionine?

A

Met, M

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22
Q

What are the 3 letter and the 1 letter name for Proline?

A

Pro, P

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23
Q

What are the 3 letter and the 1 letter name for Tryptophan

A

Trp, W

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24
Q

What are the 3 letter and the 1 letter name for Phenylalanine?

A

Phe, F

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25
Q

What are the 3 letter and the 1 letter name for Tyrosine

A

Tyr, Y

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26
Q

What are the 3 letter and the 1 letter name for Serine

A

Ser, S

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27
Q

What are the 3 letter and the 1 letter name for Threonine

A

Thr, T

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28
Q

What are the 3 letter and the 1 letter name for Arginine

A

Arg, R

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29
Q

What are the 3 letter and the 1 letter name for Asparagine

A

Asn, N

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30
Q

What are the 3 letter and the 1 letter name for Aspartic acid

A

Asp, D

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31
Q

What are the 3 letter and the 1 letter name for Glutamic acid

A

Glu, E

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32
Q

What are the 3 letter and the 1 letter name for Cysteine

A

Cys, C

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33
Q

What are the 3 letter and the 1 letter name for Glutamine

A

Gln, Q

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34
Q

What are the 3 letter and the 1 letter name for Histidine

A

His, H

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35
Q

What are the 3 letter and the 1 letter name for Lysine

A

Lys, K

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36
Q

Which amino acid is the smallest?

A

Glycine

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37
Q

Which amino acid is achiral?

A

Glycine

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38
Q

What is the side chain of Glycine?

A

A single H

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39
Q

What are the 2 amino acids with a sulfur atom in their side chain?

A

Methionine and cysteine

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40
Q

Why is methionine relatively non polar?

A

The sulfur atom is attached to a methyl group

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41
Q

What causes the 5 membered chain in Proline?

A

Limit its flexibility and has an effect on its role in secondary structure

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42
Q

What makes Proline unique?

A

The amino nitrogen’s becomes part of the side chain

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43
Q

What are the amino acid with aromatic side chains?

A

Tryptophan, Phenylalanine and Tyrosine

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44
Q

What is the only double ring amino acid?

A

Tryptophan

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45
Q

What is the side chain of Phenylalanine?

A

Benzyl (benzene ring + CH2 group)

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46
Q

How can we compare the Phenylalanine and the Tyrosine polarity?

A

Phenylalanine is less polar (relatively non-polar) and Tyrosine is more polar (relatively polar)

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47
Q

What the difference between Phenylalanine and Tyrosine?

A

Phenylalanine with an OH added

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48
Q

What are the amino acids with polar side chains?

A

Serine, Threonine, Cysteine, Asparagine and Glutamine

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49
Q

What are the two amino acids with polar side chains that has an OH group in their side chain?

A

Serine and Threonine

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50
Q

What the effect of having a OH group making Serine and Threonine highly polar amino acids?

A

They are able to participate in hydrogen bonding

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51
Q

What Asparagine and Glutamine have in common?

A

Both have amide side chains

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52
Q

What is Cysteine side chain?

A

Thiol side chain

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53
Q

What is a thiol side chain?

A

-SH group

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54
Q

Why is the thiol group prone to oxydation?

A

It’s thiol side chain (S-H bond if longer and weaker than O-H bond + the sulfur is more electronegative than the O)

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55
Q

What is the main difference between Asparagine/Glutamine and Aspartate/Glutamate?

A

Aspartate and Glutamate have a carboxylate group (-COO-)

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56
Q

What are the amino acids with a side chain negatively charged (acidic)?

A

Aspartic acid (aspartate) and Glutamic acid (glutamate)

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57
Q

What is aspartate compared to aspartic acid and glutamate compared to glutamic acid?

A

They are the anion (deprotonated aspartic acid or glutamic acid)

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58
Q

What are the amino acids with positively charged (basic) side chains?

A

Arginine, Lysine and Histidine

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59
Q

How many nitrogens are there in Arginine side chain?

A

3

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60
Q

What is Imidazole?

A

The aromatic ring with 2 nitrogens in Histidine

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61
Q

Where are amino acids with long alkyl side chains?

A

In the interior of the protein because it is HYDROPHOBIC

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62
Q

How are amino acids with charged side chains?

A

Hydrophilic

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63
Q

What are the amino acids with long alkyl side chains?

A

Alanine, Isoleucine, Valine, Phenylalanine

64
Q

What are the amino acids with charged side chains?

A

Positively charged Histidine ,Arginine, Lysine, Negatively charged glutamate and aspartate and amides asparagine and glutamine

65
Q

What are the amino acids more in the middle of the protein?

A

Cysteine, Glycine, Leucine, Methionine, Proline, Serine, Threonine, Tryptophan, Tyrosine

66
Q

What is the acid group in the amino acid?

A

Carboxylic group (COOH)

67
Q

What is the basic group in the amino acid?

A

Amino group (NH2)

68
Q

What are amphoteric species?

A

Can either accept or donate a proton depending on the environment pH

69
Q

What does ionizable group do in acidic conditions?

A

Tends to gain protons (protonated)

70
Q

What does ionizable group do in basic conditions?

A

Tends to lose protons (deprotonated)

71
Q

What means the pKa

A

pH where on average half of the molecules are protonated and half are deprotonated

72
Q

Why does amino acids have 2 or more pKa

A

Because at least 2 groups can be protonated/deprotonated

73
Q

What is the average pKa for carboxyl group?

A

2

74
Q

What is the average pKa for amide group?

A

9-10

75
Q

At pH 1, what would be the charge an amino acid?

A

Positively charged (amino group and carboxylic acid group are both protonated. Amino = positively charged. Carboxylic acid = neutral charge)

76
Q

At pH 7.4, what would be the charge of an amino acid?

A

Electrically neutral. Amino protonated (positively charged) and carboxylic deprotonated (negatively charged).

77
Q

How do you call an electrically neutral amino acid?

A

Zwitterions or dipolarions

78
Q

At pH 10.5, what would be the charge of an amino acid?

A

Negatively charged. Amino acid deprotonated (negatively charged) and carboxyl deprotonated (negatively charged).

79
Q

Why would the titration of an amino acid would look like 2 or 3 monoprotic titration curves?

A

If the side chain is charged it will be 3 curves

80
Q

What happens to the titration curve when the pH is close to the pKa

A

The curve flattens

81
Q

What is the pI

A

Isoelectric point (when every molecule is now electrically neutral

82
Q

How do you calculate the pI of an neutral amino acid?

A

(pKa amino group + pKa carboxyl group)/2

83
Q

How do you calculate the pI of an acid amino acid?

A

(pKa R group + pKa carboxyl group)/2

84
Q

How do you calculate the pI of an acid amino acid?

A

(pKa amino group + pKa R group)/2

85
Q

What are peptide made from?

A

Residue (amino acid subunits)

86
Q

How many residue are in a dipeptide?

A

2

87
Q

How many residue are in a oligopeptide?

A

20 or less

88
Q

How many residue are in a polypeptide?

A

More than 20

89
Q

What are peptide bonds?

A

Bonds between an COO- group of aa1 and NH3+ group of aa2

90
Q

Peptide bond formation is made with what reaction?

A

Condensation or déshydratation (results in the removal of a water molecule (H2O)

91
Q

How else can a peptide bond formation be viewed as?

A

Acyl substitution reaction

92
Q

How is a peptide bond formed?

A

The electrophilic carbonyl carbon of aa1 is attacked by the nucleophilic amino group of aa2. The hydroxyl group of the carboxylic group is kicked off

93
Q

What does resonance causes?

A

Rotation of the protein backbone around C-N amide bonds is restricted (not around other bonds that are single bonds) = protein more rigid

94
Q

What is resonance?

A

C-N bond in the amide gets a partial double bond character

95
Q

How do you read a peptide bond?

A

From N-Terminus (amino-terminus) to C-Terminus (carboxy-terminus)

96
Q

What is hydrolysis?

A

Breaking down peptides into amino acids by adding an hydrogen atom to the amide group and a OH group to the carboxyl group

97
Q

What are hydrolytic enzymes?

A

Enzymes that does hydrolysis

98
Q

Hame 2 hydrolytic enzymes

A

Trypsin and Chymotrypsin

99
Q

Where does trypsin acts?

A

At the carboxyl end of arginine and lysine

100
Q

Where does Chymotrypsin acts&

A

At the carboxyl end of phenylalanine, tryptophan and tyrosine

101
Q

What are examples of what a protein can be?

A

Enzymes, hormones, membrane pores and receptors, elements of cell structure

102
Q

What is the primary structure of a protein?

A

Linear arrangement of aa coded in DNA, from N-terminus to C-terminus

103
Q

How are primary structure stabilized?

A

By covalent peptides bonds between adjacent aa

104
Q

How can you find the primary structure of a protein?

A

In a lab while doing sequencing (from the DNA or the protein itself)

105
Q

True or False, the primary structure encodes all the information needed for higher structural levels?

A

True

106
Q

What is the secondary structure?

A

Neighbouring aa (either in alpha-helix or beta-pleated sheet)

107
Q

Secondary structure is created by what?

A

Hydrogen bonding between nearby aa

108
Q

How are secondary structure stabilized?

A

Intramolecular hydrogen bonds between residues

109
Q

What direction goes the alpha-helix formation?

A

Clock-wise around a central axis

110
Q

How are intramolecular hydrogen bonds are matched in alpha-helix?

A

From carbonyl oxygen atom to the amide hydrogen 4 residue down

111
Q

How are the side chains placed in alpha-helices&

A

Pointing away of the helix core

112
Q

What is an example of alpha-helix protein?

A

Keratin

113
Q

What are beta-pleated sheets like?

A

Parallel or antiparallel, chains along side another. Pleated or rippled shape

114
Q

How are the intramolecular hydrogen bonds are matched in beta-pleated sheets?

A

From atoms from adjacent chains

115
Q

How are the side chains orientated in beta-pleated sheets?

A

Above and below the plane of the sheet

116
Q

What is an protein example of beta-pleated sheet?

A

Fibroin

117
Q

What happens if a proline is in a alpha-helix formation?

A

It’s rigid cyclic structure would cause a kink in the peptide chain in the middle of the alpha-helix

118
Q

When could you see a proline in an alpha-helix formation?

A

If it’s in protein that crosses the cell membrane

119
Q

Where would a proline be placed in an alpha-helix formation?

A

At the start

120
Q

Where would you rarely see a proline in a beta-pleated sheet?

A

In the middle

121
Q

Where would you find a proline in a beta-pleated sheet?

A

In the turns between the chains

122
Q

What are the 2 types of proteins?

A

Fibrous and globular

123
Q

What is the shape of a fibrous protein?

A

Sheets or long strands

124
Q

Name an example of fibrous protein

A

Collagen

125
Q

Name an example of globular protein

A

Myoglobin

126
Q

How are tertiary and quaternary structure made?

A

Protein folding

127
Q

What determines the tertiary structure?

A

Hydrophilic and hydrophobic interactions between R-groups of aa.
Hydrogen bonding
Acid-base interactions
Disulfide bonds

128
Q

What is the mechanism of hydrophilic and hydrophobic interactions that causes the protein to fold?

A

The hydrophobic residue wants to be inside of the protein. The hydrophobic residues inside the protein pull hydrophilic bonds such as N-H and C=O inside so they can form electrostatic interactions and hydrogen bonds that’ll stabilize the protein from the inside.

129
Q

Phenylalanine is a highly hydrophobic group, where will it will almost always be in the protein?

A

It will mostly be inside, not on the surface of the protein

130
Q

What are residues at the surface of the protein usually like?

A

Hydrophilic and polar or charged

131
Q

What are salt bridges?

A

Acid-base interactions between aa with charged groups

132
Q

What are disulfide bonds?

A

When 2 cysteine oxidized into 1 cystine

133
Q

What does disulfide bonds do to the protein?

A

Create loops

134
Q

What determines how wavy or curly our hair is?

A

Disulfide bonds

135
Q

What is required to do a disulfide bond?

A

The loss of 2 protons and 2 electrons

136
Q

What is called the intermediate state while the protein in folding?

A

Molten globules

137
Q

What is denaturation?

A

When a protein loses its 3D structure

138
Q

What is a salvation layer?

A

The layer formed around a solute with the solvant

139
Q

What are quaternary structure made from?

A

Protein that contains more than 1 polypeptides chain.

140
Q

What is a quaternary structure?

A

Aggregate of smaller globular particules or subunits

141
Q

What does the quaternary structure represents?

A

The functional form of a protein

142
Q

Does every protein has a quaternary structure?

A

No

143
Q

What are examples of quaternary structure?

A

Hémoglobine and immunoglobulin G

144
Q

What are the similarity between hémoglobine and immunoglobuline G

A

They both have 4 subunits

145
Q

Why would one be in quaternary structure?

A

More stable,
Limits the amount of DNA needed to encode protein complex
Bring catalytic sites closer together
Induce cooperatively or allosteric effets

146
Q

What is the point of bringing catalytic sites closer together?

A

Intermediates from one reaction are directly shuttled to a second reaction

147
Q

What are conjugated proteins?

A

Proteins that gives part of their function ro a covalently attached molecule

148
Q

What are called the group giving the conjugated protein their function

A

Prosthetic group

149
Q

Lipoprotein, glycoprotein, nucleoproteins, what are they?

A

Prosthetic groups made from either lipid, carbohydrate or nucleic acid respectfully

150
Q

Other than giving functionality to a protein, what can a prosthetic group do?

A

Direct protein to be delivered to a certain location

151
Q

Is denaturation reversible?

A

It can be. It is usually irreversible tho

152
Q

What can’t an unfolded protein do?

A

Catalyse reactions

153
Q

What are the 2 main causes of denaturation?

A

Heat and solute

154
Q

How does heat can desaturate a protein?

A

While the Temp is rising, the kinetic energy level is too. Once it’s high enough, it can overcome the hydrophobic-hydrophilic reaction holding the protein together

155
Q

How can solute denaturate a protein?

A

Break disulfide bridges
Overcome hydrogen bonds and other side chains interactions holding alpha-helix and beta-pleated sheets
Solubilize protein

156
Q

What does solubilizing a protein does?

A

Disrupt the non covalent bonds and promote denaturation

157
Q
A

MCAT - Biochemistry - Amino Acids (2 decks)

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