Macromolecules II: Proteins

What general components make up every amino acid? 

An amino acid (monomer of a protein) is made up of:

- Backbone

• Amino group (N)

• Central (alpha) carbon

• Carboxyl group (C)

- R group (also called sidechain)

Which parts are identical across all 20 amino acids, and which part gives each amino acid its unique chemical identity? (Note: You don't need to memorize the 20 amino acid structures!) 

The backbone (central carbon, amino group, and carboxyl group) is identical across all amino acids. The R group/sidechain is variable between each amino acid, it determines the shape and function of the final protein.

Given a provided structure, how do you evaluate the atoms in a sidechain to classify it and to determine the specific non-covalent interaction(s) it can form?

You identify what functional groups are present in the R group/sidechain of an amino acid as this determines what type of non-covalent interactions it can form.

Identify the four main classes of amino acids and describe their characteristics including the main non-covalent interaction it can form (note: each flashcard answer will contain one class for the next four cards)

Polar uncharged

• R group/sidechain contains polar covalent bonds e.g. O-H, N-H, so it contains electronegative atoms. But the amino acid has no overall charge.

• These amino acids often form hydrogen bonds

Identify the four main classes of amino acids and describe their characteristics including the main non-covalent interaction it can form (note: each flashcard answer will contain one class for the next four cards)

Polar basic ( + charged)

• In an aqueous environment, these amino acids accept a proton and so R group/sidechain carries a full positive charge

• These amino acids often form ionic bonds

Identify the four main classes of amino acids and describe their characteristics including the main non-covalent interaction it can form (note: each flashcard answer will contain one class for the next four cards)

Polar acidic ( - charged)

• In an aqueous environment, these amino acids donate/lose a proton and so R group/sidechain carries a full negative charge

• These amino acids often form ionic bonds

Identify the four main classes of amino acids and describe their characteristics including the main non-covalent interaction it can form (note: each flashcard answer will contain one class for the next four cards)

 

Non-polar

• R group/sidechain has predominately non-polar covalent bonds e.g. C-H bonds

• These amino acids often form hydrophobic interactions (e.g. van der Waals interactions)

• Note: even though tyrosine has a hydroxyl group, it is still considered a non-polar amino acid due to its large non-polar benzene ring

Which amino acid would be most likely to participate in ionic bonds?

Histidine (E). It is a polar basic amino acid which carries a full positive charge. Ionic bonds are non-covalent interactions between a full positive charge and a full negative charge.

Which amino acid would be most likely to participate in “hydrophobic interactions”?

Leucine (B). In its R group/side chain, leucine contains no electronegative atoms and only has non-polar covalent C-H bonds. This makes leucine a non-polar amino acid that can participate in hydrophobic interactions.

Which amino acid would be most likely to participate in hydrogen bonds?

The best answer is asparagine (D), a polar uncharged amino acid. It contains both a hydrogen bond donor (NH₂) and hydrogen bond acceptor (O of the C=O bond) in the R group/sidechain.

Note: serine can also participate in hydrogen bonds because in its R group/sidechain serine contains an -OH group which is a hydrogen bond donor

What specific repeating sequence of atoms makes up the backbone of a polypeptide? Compare and contrast this backbone structure and its variable groups with the structure of a nucleic acid. 

Protein/polypeptide

• Backbone: amino group, central carbon, carboxyl group (repeating sequence)

• Variable group: R group/sidechain

Nucleic acid

• Backbone: phosphate, sugar (repeating sequence)

• Variable group: base  

 

What defines the polarity of a protein, and why do we read protein sequences from N-terminus to C-terminus?

• Amino acids have polarity - there is an amino group on one side of the alpha carbon and a carboxyl group on the other side. The amino acid monomers have polarity and so the resulting protein polymer maintains this polarity (has different ends).

• We read protein sequences from N-terminus (amino end) to C-terminus (carboxyl end) as protein growth occurs in one direction from the N-terminus to C-terminus

What is the primary structure of a protein?

Primary structure is the sequence of amino acids linked by covalent peptide bonds to give an unstructured polypeptide.

A peptide bond is formed between the carboxyl group of one amino acid and the amino group of another amino acid.

Most cytosolic proteins fold in an aqueous environment. How does this environment dictate where nonpolar side chains end up versus where polar/charged side chains end up in a fully folded protein?

• Non-polar amino acids are commonly found in the core of the folded protein due to the hydrophobic effect

• Polar amino acids are commonly found on the surface of the folded protein as the polar side chains can interact with water e.g. through hydrogen bonds

Define secondary structure of a protein.

Secondary structure: regular recurring patterns (e.g. alpha-helices and beta-sheets) formed by hydrogen bonds between backbone atoms

Why is meeting the hydrogen-bonding needs of the backbone so critical when a protein folds?

During protein folding, partial charges are brought into a non-polar environment which is energetically unfavourable and unstable.

Secondary structure enables the hydrogen bonding needs of the backbone atoms (e.g. peptide bond contains hydrogen bond donor and acceptor) to be met, with no partial charges in the hydrophobic core of the protein.

Describe the structure and bonding of alpha-helices (a main type of secondary structure).

Alpha helices appear as twisted cylindrical structures. The hydrogen bonds are formed between backbone atoms of amino acids that are close (4 amino acids away) in the primary structure.

Describe the structure and bonding of beta-sheets (a main type of secondary structure).

Beta-sheets appear as sheet-like structures composed of beta-strands. The hydrogen bonds are formed between backbone atoms of amino acids that can be distant in the primary structure.

Define tertiary structure. What non-covalent interactions stabilize tertiary structure?

• Tertiary structure is the overall 3D conformation (shape) driven by non-covalent interactions and limited covalent bonds.

• Non-covalent interactions that stabilize tertiary structure include: hydrogen bonds, ionic bonds, hydrophobic interactions and van der Waals (see picture) 

Why is it advantageous for higher-level protein structures to be driven primarily by non-covalent interactions rather than requiring dedicated "assembler" enzymes for every folding step?

It is far more efficient, uses less energy and cellular resources and allows for flexibility rather than using a molecular machine with dedicated enzymes to create bonds for every folding step.

What are the levels of protein structure?  What interactions are most important at each level?

What is the difference between a polypeptide and a protein?

Polypeptide: unfolded chain of amino acids linked by peptide bonds (primary structure)

Protein: folded polypeptide chain(s) in its final functional shape (tertiary/quaternary structure)