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B. BIO/BIOCHEM MCAT > Amino Acids > Flashcards

Amino Acids Flashcards

1
Q

General properties of amino acids

Functional groups

A

Amino acids have four functional groups attached to the α-carbon
1. Amino group
2. Carboxylic acid group
3. Hydrogen atom
4. R group

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2
Q

General properties of amino acids

α-carbon stereochemistry

A

Stereochemistry of α-carbon in amino acids is L-configuration, as opposed to D-configuration in carbohydrates.

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3
Q

General properties of amino acids

Chirality

A

All amino acids are chiral except glycine.
All chiral amino acids are in (S) configuration except

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4
Q

General properties of amino acids

Acid-base chemistry

A

Amino acids are amphoteric, meaning they can act as either acid or base.

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5
Q

General properties of amino acids

Isoelectric point (pI)

A

At the isoelectric point (pI), amino acids are in zwitterion form, meaning it has opposite charges that cancel out.

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6
Q

General properties of amino acids

Solving for the isoelectric point

A
  • Acidic side chain: average the pKa of the side chain and the carboxylic acid functional group.
  • Basic side chain: average the pKa of the side chain and the amine functional group.
  • Neutral side chain or glycine: average the pKa of carboxylic acid and amino functional groups.
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7
Q

Protein structure

Peptides versus proteins

A

Peptides are chains of amino acids.
Proteins are chains of amino acids folded into a particular 3-dimensional structure.

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8
Q

Protein structure

Primary structure

A

The sequence of amino acids, by convention from the N-terminus to the C-terminus.

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9
Q

Protein structure

Secondary structure

A

The local folding configuration, either α-helices or β-sheets.
Usually stabilized by hydrogen bonds.
The amino acid proline disrupts α-helices due to rigid cyclic structure.

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10
Q

Protein structure

Tertiary structure

A

The three-dimensional shape of a protein.
Stabilized by interactions between functional groups, most notably hydrophobic interactions between side chains.

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11
Q

Protein structure

Quarternary structure

A

The shape between peptides of different subunits in proteins.

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12
Q

Protein bonds

Peptide bonds

A

Formed when the nucleophilic N-terminus (amino group) of one amino acid attacks the electrophilic C-terminus (carboxylic acid group) of another amino acid.

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13
Q

Protein bonds

Disulfide bonds

A

A covalent S-S bond formed between two cysteine molecules.

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14
Q

Protein bonds

Conjugation

A

Some proteins have an additional non-protein molecule attached that is crucial for their function.
Classic example: hemoglobin is attached to heme.

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15
Q

Protein bonds

Denaturation

A

Protein structure unravels due to change in entropy at high temperatures, can render proteins non-functional.
Half of the proteins are denatured at the melting point (Tm).

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16
Q

Protein bonds

Unfolding kinetics

A

Unfolding of proteins is a cooperative process with a sigmoidal binding curve.

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17
Q

Amino acid groups

Basic (+ charge)

A

Arginine (Arg / R)
Lysine (Lys / K)
Histidine (His / H)

Mnemonic: “His Lies Are Basic” = His Lys Arg Basic

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18
Q

Amino acid groups

Acidic (- charge)

A

Glutamate (Glu / E)
Aspartate (Asp / D)

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19
Q

Amino acid groups

Aromatic

A

Tryptophan (Trp / W)
Phenylalanine (Phe / F)
Tyrosine (Tyr / Y)

Note that tyrosine is polar and others are nonpolar

Histidine (His/ H) can be considered aromatic as well

Mnemonic: WiFeY wears aromatic perfumes

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20
Q

Amino acid groups

Nonpolar, non-aromatic

A

Glycine (Gly / G), Leucine (Leu / L), Alanine (Ala / A), Methionine (Met / M), Valine (Val / V), Isoleucine (Ile / I), Proline (Pro / P)

Mnemonic: GLAM VIP

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21
Q

Amino acid groups

Polar

A

Glutamine (Gln / Q), Asparagine (Asn / N), Cysteine (Cys / C), Tyrosine (Tyr / Y), Serine (Ser / S), Threonine (Thr / T)

Mnemonic: QN CYST (“Queen cyst”) is a polarizing ruler.

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22
Q

Amino acid structures - alkyls

A

Glycine
Gly
G

23
Q

Amino acid structures - alkyls

A

Leucine
Leu
L

24
Q

Amino acid structures - alkyls

A

Alanine
Ala
A

25
Q

Amino acid structures - alkyls

A

Valine
Val
V

26
Q

Amino acid structures - alkyls

A

Isoleucine
Ile
I

27
Q

Amino acid structures - alkyls

A

Proline
Pro
P

28
Q

Amino acid structures - alcohols, thiols, amides

A

Serine
Ser
S

29
Q

Amino acid structures - alcohols, thiols, amides

A

Threonine
Thr
T

30
Q

Amino acid structures - alcohols, thiols, amides

A

Methionine
Met
M

31
Q

Amino acid structures - alcohols, thiols, amides

A

Cysteine
Cys
C

32
Q

Amino acid structures - alcohols, thiols, amides

A

Asparagine
Asn
N

33
Q

Amino acid structures - alcohols, thiols, amides

A

Glutamine
Gln
Q

34
Q

Amino acid structures - acids and bases

A

Aspartate
Asp
D

35
Q

Amino acid structures - acids and bases

A

Glutamate
Glu
E

36
Q

Amino acid structures - acids and bases

A

Histidine
His
H

37
Q

Amino acid structures - acids and bases

A

Lysine
Lys
K

38
Q

Amino acid structures - acids and bases

A

Arginine
Arg
R

39
Q

Amino acid structures - aromatics

A

Tryptophan
Trp
W

40
Q

Amino acid structures - aromatics

A

Phenylalanine
Phe
F

41
Q

Amino acid structures - aromatics

A

Tyrosine
Tyr
Y

42
Q

Unique amino acids

Cysteine (Cys / C)

A

Disulfide bonds are formed through oxidation between the thiol groups of cysteine (Cys / C) molecules.
These commonly contribute to the tertiary structure of proteins and can be denatured by reducing agents.

43
Q

Unique amino acids

Proline (Pro / P)

A

Unique because the ring of its R group includes the amino group of the amino acid.
This means the N has bonds to two different C atoms so the N cannot participate in hydrogen bonding.
In protein secondary structure, proline will disrupt α-helices but is useful for inducing turns in β-sheets, both due to its rigid cyclic structure.

44
Q

Unique amino acids

Glycine (Gly / G)

A

Unique for having the smallest R group.
This gives glycine a “floppy” quality meaning that it disrupts α-helices and can induce sharp turns in β-sheets and linker regions.

45
Q

Unique amino acids

Glutamine (Gln / Q)

A

Can simultaneously act as a hydrogen acceptor and donor, meaning it can form a network of hydrogen bonds.
This property stabilizes the β-sheet secondary structure.

46
Q

Unique amino acids

Salt bridges

A

Amino acids that are acids and bases can form salt bridges to stabilize protein tertiary structure.
Acids include aspartate and glutamate. Bases include lysine, arginine, and histidine.
As a result high salt concentration can cause denaturation of proteins.

47
Q

Reactive properties of amino acids

Phosphorylation

A

Addition of a phosphate to an amino acid.
Occurs exclusively to amino acids which are alcohols, specifically serine, threonine, and tyrosine.

48
Q

Reactive properties of amino acids

Nucleophilicity

A

Amino acids containing -SH or -OH groups are good nucleophiles.
These include serine, threonine, tyrosine, and cysteine.
Deprotonation of these groups results in a negative charge that can increase nucleophilicity.

49
Q

Reactive properties of amino acids

Deamidation

A

Amino acids containing amide groups can undergo deamidation, a process which produces ammonia.
These include asparagine (Asn / N) and glutamine (Gln / Q).

50
Q

Reactive properties of amino acids

Ketogenecity

A

Lysine and leucine can be broken down into ketone bodies for energy.

51
Q

Named functional groups

A

Guanidinium
Arginine (Arg / R)

52
Q

Named functional groups

A

Indole
Tryptophan (Trp / W)

53
Q

Named functional groups

A

Imidazole
Histidine (His / H)

54
Q

Summary of amino acids

A

Memorize the three-letter and one-letter codes for all amino acids.

Be able to both recognize and draw out sidechain structures from memory.

Understand the general groupings and properties of amino acids.

Memorization of pKa values is not necessary but have a general idea of the range

B. BIO/BIOCHEM MCAT (29 decks)

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