2. Amino Acids and Peptides

Flashcards for reviewing amino acids and peptides lecture.

How many amino acids are used for protein synthesis?

There are 20 amino acids used for protein synthesis.

What are the basic building blocks of peptides and proteins?

Amino acids are the basic building blocks.

Peptides: short polymers of amino acids

Proteins long polymers of Amino Acids

What functional groups are present on the alpha carbon of an amino acid?

Acetic or carboxy group and an amino group on the alpha carbon.

How do amino acids differ from each other?

They differ in their side chains (R groups).

What is a peptide?

A polymer consisting of multiple amino acids.

What type of isomers are asymmetric molecules have?

1. amino acids are chiral around alpha carbon

2. Asymmetric molecules have L and D isomers, which are mirror images of each other.

3. Proteins contains amino acids in L configuration

What configuration are all amino acids present in proteins?

1. Carboxy: loses a proton (deprotonates) at pH > 2

2. Amino: gains a proton (protonates) at pH < 9

At neutral pH, amino acids exist as zwitterions, meaning they have both a positive charge on the amino group and a negative charge on the carboxyl group, resulting in a net charge of zero.

What are zwitterions?

Molecules with two opposite charges.

How are peptide bonds formed?

Formed by covalent linkage of the carboxyl group from one amino acid and the amino group from a second amino acid.

What is the general term for the amide bonds?

Carboxyl-amino linkage.

What is accompanied by the linking of two amino acids (peptide bonds)?

Loss of a water molecule.

What characterizes a specific polypeptide or protein?

Number of amino acids and the specific sequence of these amino acids.

Polypeptide is a zwitterion with what types of charged groups?

N-terminal amino group (positive) and the C-terminal carboxy group (negative).

What are shorter chains called?

oligopeptides

What provide the unique properties of a polypeptide or protein?

Side chains of the amino acids.

What is the sequence of amino acids in leu enkephalin from N-terminal to C-terminal?

1. Pentapeptide (5 amino acids)

2. Oploid peptide modulates pain

3. Sequence: Tyrosine, glycine, glycine, phenylalanine, and leucine.

4. Tyrosine & Phenylalanine: aromatice side chains

5. Glycine: hydrogen side chain

6. Leucine: branched side chain

What would happen if the same amino acids in leu enkephalin were assembled in reverse direction?

It wouldn't have the opioid effect.

What makes amino acids Alpha amino acids?

The amino group is on the carbon adjacent to the carboxyl carbon.

How are amino acids with different side chains divided?

Approximately half are nonpolar, and the other half are polar (either uncharged or charged positively or negatively).

Give an example for the three letter code and one letter abbreviation for amino acids.

Tryptophan is TRP, one letter abbreviation is W.

What are side chain in Glycine and Alanine? Are they polar or nonpolar?

Glycine has a hydrogen, and alanine has a methyl group as its side chain.

Nonpolar

Give examples of non polar amino acids having long hydrocarbon groups.

Valine, leucine, and isoleucine have longer hydrocarbon groups.

What is special about proline's structure?

The side chain forms a ring structure with the nitrogen on the alpha carbon.

Name two amino acids containing sulfur.

Cysteine and methionine.

What is the significance of the sulfhydryl group in cysteine?

The sulfur of cysteine is present as a sulfhydryl group, which can react with other sulfhydryl groups.

Name three amino acids with aromatic rings on their side chains.

Phenylalanine, tyrosine, and tryptophan.

What defines an aromatic ring?

Hydrocarbon ring with alternating single and double bonds.

Are phenylalanine and tryptophan polar or nonpolar?

The side chains of both phenylalanine and tryptophan are non polar and are hydrophobic.

Which amino acids are acidic amino acids?

Aspartate and glutamate whic have additional carboxy group with negative charge

Which amino acids are basic amino acids?

Lysine (2nd amino group) and arginine (3 nitrogens covalently bonded to same carbon) with additional nitrogen groups that have a positive charge

Characteristics of Histidine

1. Non aromatic ring structure with 2 nitrogen and 3 carbon atoms

2. pH slightly below 7 accepts hydrogen ions making it positively charged

3. pKa near 6 which means charged and non charged form is present at neutral pH

4. Found in active site of enzyme

5. Ability to bind and release protons contribute to catalysis

Which amino acids contain hydroxyl groups?

What about Tyrosine?

Serine and threonine.

aromatic and polar

Which amino acids are derived from aspartate and glutamate, having an amino group in amide linkage on the side chain carboxyl group?

Asparagine and glutamine.

• Amino group and amide link on side chain carboxyl group

• highly polar and hydrophilic side chain but can’t ionize at physiological pH

What are the components of leu-enkephalin?

Phenylalanine and tyrosine have large aromatic side chains, one branched chain amino acid leucine, and two small nonpolar glycines.

What is the function of the amino acid side chains.

The side chains determine interactions with other molecules, the overall structure of the molecule, in enzymes determine substrate specificity and are key components of the catalytic mechanism.

How cysteines can form disulfide bonds?

The oxidation of two sulfhydryl groups results in the formation of a disulfide bridge linking two cysteine side chains together.

• Sulfhydryl groups stabilize protein

• removal of 2 hydrogen atoms = removal of 2 electrons and 2 accompanying protons or hydrogen ions

Which small peptide hormone stimulates the kidney to reabsorb water?

Vasopressin

• Contains 9 amino acids with disulfide bridge between 2 cysteine residues

• Net charge of 0 with 1 positive side chain (argenine) and 1 negative side chain (glutamate)

• Model pays close attention to argenine because part of using synthetic peptide analog as a drug for people who don’t synthesize enough hormone

Characteristics of Insulin

• Hormone secreted by beta cells of pancrease to regulate blood sugar

• Two peptide chains are 21 and 30 amino acid long, respectively with different amino acid sequences.

• Chains attached by 2 disulfide bridges

• Chain contains disulfide bridge that forms a loop within the A chain

How many amino acids are needed to synthesize proteins?

20

Characteristics of Tyrosine

• Aromatic Amino Acid'

• Similar to phenylalanine but has hydroxyl group so it’s more polar