Amino Acids, Peptides and Protiens Flashcards
1
Q
Amino Acid Properties
A
- Amine Group left
- Carboxylic group on the right
- Both of these functional groups are joined by an alpha carbon
- The alpha carbon has a hydrogen and a unique R group, also known as the side-chain
- The R group is what makes each amino acid distinct
- Carboxylic acids have a low pKa, and the proton will dissociate at physiological pH creating an negatively charged carboxylate
-
Amines have a high pKa, will accept a proton and act as a base at physiological pH and will be positively charged
- Hence, amino acids are often called dipolar ions
2
Q
Fischer Projection
A
- All of the 20 proteinogenic amino acids are L-amino acids
- The reason it is L is because the highest priority group is pointing to the left in a Fischer projection
- 19/20 proteinogenic amino acids are also chiral, except for glycine.
- A chiral centre has four different groups attached
3
Q
How Amino Acids join together
A
- When the nitrogen of the backbone of one amino acid nucleophilically attacks the backbone carbonyl carbon of another amino acid.
- The resulting bond is commonly called a peptide bond, but it is functionally an amide group.
- This happens repeatedly in our body using ribosomes to help place and catalyze the creation of the peptide bond.
4
Q
Amides feature to a peptide bond
A
- The lone pair on the nitrogen in an amide participates in resonance to create a partial double bond between the carbonyl carbon and nitrogen
- This creates structural stability within the protein chain
5
Q
Glycine
A
- Three letter code: Gly
- One letter code: G
- Property: Achiral
- Simpliest and smallest amino acid.
6
Q
Proline
A
- Three-letter code: Pro
- One-letter code: P
- Property: “cis” amino acid
- In proline the sidechain coming off the alpha carbon is attached on the other end to the nitrogen of the backbone
- This creates the “cis” amino acid, which creates kinks when proline is included in the middle of a secondary structural element like an alpha helix
7
Q
Alanine
A
- Three-letter code: Ala
- One-letter code: A
- Property: Hydrophobic
- R Group: Methyl group
- All amino acids EXCEPT glycine have a beta carbon
8
Q
Valine
A
- Three letter code: Val
- One letter code: V
- Property: Hydrophobic
- Adding a “V” of carbons to that beta carbon
9
Q
Leucine
A
- Three-letter code: Leu
- One-letter code: L
- Property: Hydrophobic
- Adding one more methyl group to the chain before it splits into the V
10
Q
Isoleucine
A
- Three-letter code: Ile
- One-letter code: I
- Property: Hydrophobic
- It is an isomer of leusine, so it has the same number of carbons and hydrogens
11
Q
Phenylalaine
A
- Three-letter code: Phe
- One-letter code: F
- Property: Hydrophobic, aromatic
- You start with a methyl group like an alanine and then add a phenyl group.
12
Q
Tyrosine
A
- Three-letter code: Tyr
- One letter code: Y
- Property: aromatic, mildly hydrophobic
- Adding an OH group to phenylalanine
13
Q
Tryptophan
A
- Three-letter code: Trp
- One-letter code: W
- Property: Aromatic, hydrophobic
- Has one of the largest side chains, with a nitrogen attacked to a phenyl group
14
Q
Methionine
A
- Three letter code: Met
- One-letter code: M
- Property: Hydrophobic, start codon
- Found at the beginning of most proteins
- Since it also serves as a signal to indicate that protein synthesis is beginning at this part of the mRNA sequence
- The codon that codes of methionine is AUG, which is also known as the start codon
- This is one of two amino acids with a sulfur in the side chain
- The sulfur is flanked by carbons on either side, which cancels out any polarity conferred by the sulfur, making the side chain mostly hydrophobic
15
Q
Amino Acids with Polar Side Chains
A
- Serine
- Threonine
- Asparagine
- Glutamine
- Cysteine
16
Q
Serine
A
- Three letter code: Ser
- One letter code: S
- Property: Hydrophobic, can be phosphorylated
- An Alanine with an OH group added
17
Q
Threonine
A
- Three-letter code: Thr
- One-letter code: T
- Property: Hydrophobic, can be phosphorylated
- Adding a methyl group to the beta carbon of serine
18
Q
Cysteine
A
- Three-letter code: Cys
- One-letter code: C
- Property: Mildly hydrophilic, covalent disulfide bonds
- The oxygen in the side chain is replaced with the sulfur
- While it is not normally phosphorylated, if you put two cysteine side chains close together in an oxidizing environment, it forms a disulfide bond, which is a covalent link between two sulfur atoms
18
Q
Cysteine
A
- Three-letter code: Cys
- One-letter code: C
- Property: Mildly hydrophilic, covalent disulfide bonds
- The oxygen in the side chain is replaced with the sulfur
- While it is not normally phosphorylated, if you put two cysteine side chains close together in an oxidizing environment, it forms a disulfide bond, which is a covalent link between two sulfur atoms
19
Q
Asparagine
A
- Three letter code: Asn
- One letter code: N
- Property: Hydrophilic
- Has amide as its side chain attached to a beta carbon
- Unlike the amino groups common to all amino acids, the amide nitrogens do not gain or lose protons with chains in pH; they do not become charged.
20
Q
Glutamine
A
- Three-letter code: Gln
- One letter code: Q
- Property: Hydrophilic
- Almost the same as asparagine, but with one more carbon in the side chain before ending with the amide.
21
Q
Negatively Charged (Acid Amino Acids ) Side chains
A
- Aspartic Acid (Aspartate)
- Glutamic Acid (Glutamate)
- At physiological pH, the carboxylic acid in both side chains is deprotonated and negatively charged
- The “ate” ending indicated the deprotonated from of an acid.
22
Q
Aspartic Acid (Aspartate)
A
- Three letter code: Asp
- One-letter code: D
- Property: Negative charge
23
Q
Glutamic Acid (Glutamate)
A
- Three-letter code: Glu
- One letter code: E
- Property: Negative Charge
24
Q
Positively Charged (Basic) Side Chains
A
- Lysine
- Histidine
25
Q
Lysine
A
- Three-letter code: Lys
- One letter code: K
- Property: Positive charge
- Long alkyl chain that is capped with an amine
- At physiological pH, the amine is protonated and positively charged
26
Q
Arginine
A
- Three letter code: Arg
- One letter code: R
- Property: Positive Charge
- Also has a long alkyl chain, but it is capped by an unusual functional group called a guanidino
- One of the nitrogens at physiological pH is protonated and positively charged
27
Q
Histidine
A
- Three letter code: His
- One letter code: H
- Property: Can be positive charged
- The side chain is an imidazole ring, which is aromatic
- One of the nitrogen’s in the imidazole ring has the capability of accepting a proton and becoming positively charged, which is why it is classified along with arginine and lysine as a base.
- However, the pKa of the nitrogen is around 6.5, and so remains neutral and uncharged in physiological conditions since that is below physiological pH