Amino Acids, Peptides, Proteins

What are the general features of amino acids?

Central alpha carbon; NH2 (amino) group; Hydrogen atom; COOH (carboxyl) group; Variable group (R)

Optical isomerism: which amino acids show it?

all amino acids except glycine

Why do these amino acids show optical isomerism?

The alpha-carbon atom is asymmetric (chiral center).; L and D stereoisomers.

Which stereoisomers do proteins contain?

Proteins contain exclusively L-amino acids.

What is a zwitterion?

dipolar ion; Molecule with both a (+) and a (-) charge.

What is an amphoteric molecule?

Molecule with both basic (amino) and acidic (carboxyl) group.

What is an amphipathic molecule?

only some amino acids; Molecule with both hydrophobic (nonpolar) and hydrophilic (polar) properties.

What is the isoelectric point (pI)?

the specific pH at which an amino acid has a net charge of zero (0)

How are amino acids classified?

Amino Acids; Hydrophobic (Nonpolar) and Hydrophilic (Polar); Hydrophobic: Aliphatic, Aromatic; Hydrophilic: Charged, Uncharged; Charged: Positively charged, Negatively charged

Which amino acids are hydrophobic (nonpolar) aliphatic?

Glycine; Alanine; Valine; Leucine; Isoleucine; Proline; Methionine

Which amino acids are hydrophobic (nonpolar) aromatic?

Tyrosine; Tryptophan; Phenylalanine

Which amino acids are hydrophilic (polar) uncharged?

Asparagine; Glutamine; Threonine; Serine; Cysteine

Which amino acids are positively charged?

Lysine; Arginine; Histidine

Which amino acids are negatively charged?

Aspartate; Glutamate

Which special amino acid is known as a "helix breaker"?

Proline

Which special amino acid can form a covalent disulfide bond?

Cysteine

How is a polypeptide chain formed?

A polypeptide chain is formed as amino and carboxyl groups on two neighboring amino acids combine and eliminate water.

What type of reaction forms the chain?

Dehydration synthesis reaction

What is the linkage formed called?

The linkage formed is known as a peptide bond.

Chemically, what is a peptide bond?

Chemically, peptide bond is an amide (CONH) bond.

What two ends does a growing chain always have?

No matter how many amino acids are added, the growing chain always has an N or amino- terminus and a C- or carboxy-terminus.

In which direction are amino acid sequences written or read?

Amino acid sequences are always written or read from the N-terminus to the C-terminus.

What are the four levels/orders of protein structure?

Primary (1°) = Order/Sequence of the amino acids; Secondary (2°) = Folding of the polypeptide chain due to hydrogen bonding; Tertiary (3°) = Further folding of the polypeptide secondary structure due to interactions between the amino acid side chains; Quaternary (4°) = Assembly of multiple polypeptide chains (subunits) after attaining tertiary structure

What is the primary structure of proteins?

The polypeptide chain with the amino acids in a specific order/sequence.

What determines the order/sequence of amino acids?

This specific order/sequence of amino acids is determined by the nucleotide sequence on the mRNA, which in turn is determined by the nucleotide sequence on the DNA (Central Dogma of Molecular Biology

What is the secondary structure of proteins?

Folding of the polypeptide chain due to hydrogen bonding

What are the types of beta (β)-sheet?

Flat rectangular sheet; Twisted sheet; β-Barrel

What secondary structures make up proteins?

Proteins are a mix of alpha helices, beta sheets, random coils

What are random coils like?

Random coils are often very flexible regions of the protein.

What is the start of the protein known as?

Start of the protein is known as the N-terminus.

What is the end of the protein known as?

End of the protein is known as the C terminus.

What is the tertiary structure of proteins?

Further folding of the secondary structure (α-helices and β-sheets) due to interactions between the amino acid side chains

What is the quaternary structure of proteins?

The assembly of multiple polypeptide chains (subunits) after attaining tertiary structure.

What are disulfide bonds?

Disulfide bonds are special covalent bonds that can occur between sulfhydryl groups (-SH).

What does folding do for a polypeptide chain/protein?

Folding brings together regions of the polypeptide chain/protein that are needed to perform its biological role.

What forms in an enzyme after folding?

For enzymes, polypeptide/protein forms an active site after folding.

What does the active site form?

The active site forms a pocket for binding the substrate.

What are some amino acid residues at the active site also involved in?

Some of the amino acid residues at the active site are also involved in chemical reactions with the substrate.

What does the Oil Drop Model of Protein Structure illustrate?

hydrophilic groups are exposed to the water environment and that most hydrophobic groups are centrally positioned buried in the core.

In real life, what do many of the hydrophilic groups do?

hydrophilic groups will form hydrogen bonds to the surrounding water molecules.

What do the hydrophilic regions of membrane proteins interact with?

The hydrophilic regions of membrane proteins interact with the aqueous cell interior and exterior.

What do the hydrophobic regions of membrane proteins face?

Their hydrophobic regions face the hydrophobic phospholipids of the membrane.