CH1 | Amino Acids (PT1)

Question 1

What are the monomers or “building blocks” of proteins?

Answer 1

Amino acids (a.a.)

Question 2

What two functional groups are found in all amino acids, which are part of their name’s origin?

Answer 2

An amino group (NH2) and a carboxyl group (COOH).

Question 3

Approximately how many amino acids are found in nature, and how many are standard, proteogenic amino acids found in mammalian proteins?

Answer 3

> 300 in nature; 20 standard and proteogenic.

Question 4

What does “proteogenic” mean in the context of amino acids?

Answer 4

Proteogenic amino acids are those that are incorporated into proteins during translation and are encoded by the genetic code (DNA -> RNA -> amino acids sequence in protein).

Question 5

In the general structure of an amino acid, to which carbon is the R-group (side chain) attached, by convention?

Answer 5

The alpha-carbon (Cα).

Question 6

Which group in the structure of an amino acid defines it’s identity as specific type of amino acid?

Answer 6

The R group.

Question 7

What are the parts that make up an amino acid, chemically?

Answer 7

• Amino group (NH2).
• Alpha carbon (Cα).
• Carboxyl group (COOH).
• R group (side chain).
• Hydrogen.

Question 8

What three components are bonded to the alpha-carbon (Cα) in all 20 of the common amino acids?

Answer 8

An amino group (α-NH2), a carboxyl group (α-COOH), and a hydrogen atom (H)

Question 9

What differs among the 20 common amino acids, and what properties of an amino acid can it affect?

Answer 9

Their side chains (R groups). R groups vary in structure, size, and electric charge. This influences the amino acid’s solubility in water and contributes to a protein’s overall structure.

Question 10

What determines the functional role of an amino acid in a protein?

Answer 10

The nature of its side chain (R).

Question 11

How are amino acids classified?

Answer 11

According to the properties of their side chains (R).

Question 12

At physiologic pH (~7.4), what is the ionization state of the carboxyl and amino groups in an amino acid?

Answer 12

Carboxyl group is dissociated (COO-, negatively charged), and the amino group is protonated (NH3+, positively charged).

Question 13

Give an example of how non-standard amino acids can be part of proteins.

Answer 13

Via post-translational modification of standard amino acid residues, for instance 4-hydroxyproline is generated by the hydroxylation of proline after it’s already been incorporated into certain proteins such as collagen.

Question 14

What is a common non-standard amino acid transformation of proline?

Answer 14

It can be modified into hydroxyproline after translation, through a post-translational modification.

Question 15

What are examples of two free metabolite amino acids?

Answer 15

Ornithine and citrulline.

Question 16

What are ornithine and citrulline part of?

Answer 16

Key intermediates of the urea cycle.

Question 17

What are the 9 non polar hydrophobic amino acids?

Answer 17

Question 18

What are the characteristics of non-polar side chains in terms of binding protons, and participating in hydrogen or ionic bonds?

Answer 18

Non-polar side chains don’t bind or give off protons, nor do they participate in hydrogen or ionic bonds.

Question 19

What terms are used to describe the nature of non-polar side chains?

Answer 19

“Oily” or “lipid-like”.

Question 20

What is the simplest amino acid (a.a) in terms of side chain?

Answer 20

Glycine (its side chain is just a hydrogen atom).

Question 21

Name two branched-chain amino acids with non-polar side chains.

Answer 21

Leucine (Leu), Isoleucine (Ile).

Question 22

How is the side chain of proline unique among amino acids?

Answer 22

It forms a ring structure by bonding with the α-amino group, making proline a secondary amine containing an imino group.

Question 23

Which amino acid with a non-polar side chain contains sulfur?

Answer 23

Methionine (Met)

Question 24

What is the consequence of non-polar side chains being unable to bind/give off protons, nor participate in hydrogen/ionic bonds?

Answer 24

This makes these side chains unable to interact with water, which makes them hydrophobic. They will tend to interact with other hydrophobic groups through Van der Waals interactions.

Question 25

What are the 6 hydrophilic uncharged polar amino acids?

Answer 25

Question 26

What does it mean for an amino acid to be polar and uncharged?

Answer 26

Its side chain (R) has a zero net charge at physiological pH but has a dipole moment, meaning the distribution of electrons is unequal, so it can form hydrogen bonds with water (hydrophilic).

Question 27

Which three amino acids have a polar -OH group in their side chain?

Answer 27

Serine (Ser), Threonine (Thr), Tyrosine (Tyr).

Question 28

Which amino acid has a sulfhydryl group (-SH) in its side chain?

Answer 28

Cysteine (Cys).

Question 29

What is another name for the -SH group found in cysteine?

Answer 29

Thiol group.

Question 30

Which two amino acids have an amide group in their side chain?

Answer 30

Asparagine (Asn), Glutamine (Gln).

Question 31

Why are polar uncharged amino acids hydrophilic, despite having zero net charge?

Answer 31

While their overall charge is zero, the presence of polar groups like -OH, -SH, and amides allows them to form hydrogen bonds with water molecules. This makes polar uncharged amino acids hydrophilic (attracted to water), hence soluble.

Question 32

How do you know polar uncharged amino acids are not also non-polar?

Answer 32

Their side chain contains highly electronegative atoms like oxygen and sulfur which have partial charges, hence they form dipoles.

Question 33

True or false: you can immediately tell polar uncharged amino acids apart from polar charged amino acids, because only polar charged amino acids have a net charge.

Answer 33

True. Because of their having a net charge, polar charged amino acids either bind/give off protons or participate in ionic bonds. In contrast, polar uncharged amino acids do neither.

Question 34

Since Methionine and Cysteine both contain sulfur, what differentiates them from one another in terms of classification?

Answer 34

Methionine has a non-polar side chain and is classified as a non-polar amino acid. In contrast, Cysteine contains a polar, uncharged side chain, due to it containing a highly electronegative S atom.

Question 35

Why are polar uncharged amino acids are neither considered acidic nor basic.

Answer 35

Because they are not charged, this also means they are not proton donors (acidic) nor proton acceptors (basic).

Question 36

What is the name of the functional group in the side chain of cysteine?

Answer 36

Sulfhydryl group (-SH), also known as a thiol group.

Question 37

What is a unique chemical characteristic of the two cysteine -SH groups within proteins?

Answer 37

They can be oxidized and form a dimer called cystine.

Question 38

What is the name of the covalent bond in a cystine molecule, formed between two cysteine residues in proteins?

Answer 38

Disulfide bond or disulfide bridge (-S-S-).

Question 39

What are some defining characteristics of a disulfide bridge, such as its strength and the type of linkage?

Answer 39

A disulfide bridge is a strong, covalent cross-link bond.

Question 40

True or false: it is possible to immediately tell if any two amino acid residues are linked together through a disulfide bond.

Answer 40

True, only two cysteine amino acids side chains contain sulfur (in addition to methionine), thus if a bond between two amino acids involves a S-S linkage, then they must necessarily be cysteine amino acid residues.

Question 41

True or false: If cystine is a constituent of a protein, it is likely it was incorporated via the normal, genetic encoding machinery.

Answer 41

False, since only one cysteine is a standard, proteogenic amino acid, cystine (formed by two cysteines linked together) can not directly be genetically encoded into the protein through the normal translation machinery, from the genetic code (DNA -> RNA -> amino acid). Cystine is generated via a post-translational modification (in other words, two separate cysteines were independently and directly incorporated through the translation machinery into a protein, then the protein itself was post-translationally modified so that the two cysteines become linked together).

Question 42

What is the difference between cysteine and cystine?

Answer 42

Cysteine is one of the 20 standard, proteogenic amino acids with a free sulfhydryl group (-SH) in its side chain. Cystine is formed by the oxidation of the -SH groups of two cysteine residues, creating a disulfide bond (-S-S-).

Question 43

What is this?

Answer 43

The reversible formation of a disulfide bond by the oxidation of two molecules of cysteine.

Question 44

Which three amino acids have aromatic R groups?

Answer 44

Phenylalanine, Tyrosine, Tryptophan

Question 45

What is the aromatic group in phenylalanine?

Answer 45

Phenyl group.

Question 46

What is the aromatic group in tyrosine?

Answer 46

4-hydroxy phenyl group.

Question 47

What is the aromatic group in tryptophan?

Answer 47

Indole ring.

Question 48

Which is a true statement for Tyrosine, and why? A) Tyrosine is less soluble than Phenylalanine because it has a hydroxyl group B) Tyrosine is more soluble than Phenylalanine because it has a hydroxyl group

Answer 48

B is correct. Although both have an aromatic phenyl group which is hydrophobic (insoluble in water), the additional hydroxyl group in tyrosine is polar and can form hydrogen bonds with water, hence it can increase water solubility.

Question 49

What are the two polar charged acidic amino acids?

Answer 49

Question 50

At physiological pH, what is the charge of the side chains of acidic amino acids and what group causes it?

Answer 50

Negative charge, due to the presence of a carboxylate group (COO-).

Question 51

Why are aspartate and glutamate considered acidic amino acids?

Answer 51

Because they are proton donors at physiological pH (in other words, their side chains contain a carboxylic group which readily donates a proton, becoming negatively charged).

Question 52

What is the difference between aspartate and glutamate in terms of their side chain structure?

Answer 52

Glutamate has one extra -CH2 group in its side chain compared to aspartate.

Question 53

Explain this statement: "Aspartate and glutamate are the ionized forms of aspartic acid and glutamic acid, respectively"

Answer 53

It means that at physiological pH, aspartic acid and glutamic acid have donated a proton from their side-chain carboxylic groups (-COOH), thus becoming negatively charged carboxylates (-COO-).

Question 54

True or false: Due to their negatively charged side chains at physiological pH, polar charged (acidic) amino acids are hydrophilic

Answer 54

True. These amino acids can form ionic bonds, including with water, due to the presence of the negative charge in their side chain.

Question 55

What are the three basic amino acids?

Answer 55

Question 56

At physiological pH, what is the charge of the side chains of basic amino acids, and what group causes it?

Answer 56

Positive charge, due to the presence of an NH3+ group.

Question 57

Why are lysine, arginine, and histidine considered basic amino acids?

Answer 57

Because they are proton acceptors at physiological pH (their side chains contain a nitrogen atom that can accept a proton, becoming positively charged).

Question 58

Which amino acid has an imidazole group in its side chain, and what is the chemical formula of this group?

Answer 58

Histidine (His); C3H4N2

Question 59

Which amino acid has a guanidinium group in its side chain, and what is the chemical formula of this group?

Answer 59

Arginine (Arg); (CH6N3+)

Question 60

True or false: Due to their positively charged side chains at physiological pH, polar charged (basic) amino acids are hydrophobic.

Answer 60

False. Polar charged (basic) amino acids are hydrophilic. At physiological pH, the side chains of these amino acids are positively charged. This allows them to interact with other polar, charged molecules through hydrogen or ionic bonds, as well as making them soluble in aqueous solutions (which are also polar and charged).