General Principles

Topic: Amino Acids Peptides Proteins

Proteins are biomolecules made up of one or more amino acid chains (polypeptide chains), and their shape/structure is very important to their function.

There are four levels of protein structure: primary, secondary, tertiary, and quaternary.

The next level of protein structure, secondary structure, refers to local folded structures that form within a polypeptide due to interactions between atoms of the backbone (not R group side chains). The most common types of secondary structures are the α helix and the β pleated sheet. Both types of structures are held in shape by hydrogen bonds, which form between the carbonyl O of one amino acid and the amino H of another.

In an α helix, the carbonyl (C=O) of one amino acid is hydrogen bonded to the amino H (N-H) of an amino acid that is four down the chain. (E.g., the carbonyl of amino acid 1 would form a hydrogen bond to the N-H of amino acid 5.) This pattern of bonding pulls the polypeptide chain into a helical structure that resembles a curled ribbon. The R groups of the amino acids stick outward from the α helix, where they are free to interact.

In a β pleated sheet, two or more segments of a polypeptide chain line up next to each other, forming a sheet-like structure held together by hydrogen bonds. The hydrogen bonds form between carbonyl and amino groups of backbone, while the R groups extend above and below the plane of the sheet. The strands of a β pleated sheet may be parallel, pointing in the same direction (meaning that their N- and C-termini match up), or antiparallel, pointing in opposite directions (meaning that the N-terminus of one strand is positioned next to the C-terminus of the other).

Certain amino acids are more or less likely to be found in α-helices or β pleated sheets. For instance, the amino acid proline is sometimes called a “helix breaker” because its unusual R group (which bonds to the amino group to form a ring) creates a bend in the chain and is not compatible with helix formation. Proline is typically found in bends, unstructured regions between secondary structures. Similarly, amino acids such as tryptophan, tyrosine, and phenylalanine, which have large ring structures in their R groups, are often found in β pleated sheets, perhaps because the β pleated sheet structure provides plenty of space for the side chains.

Many proteins contain both α helices and β pleated sheets, though some contain just one type of secondary structure (or do not form either type).

The overall three-dimensional structure of a polypeptide is called its tertiary structure. The tertiary structure is primarily due to interactions between the R groups of the amino acids that make up the protein.

R group interactions that contribute to tertiary structure include hydrogen bonding, ionic bonding, dipole-dipole interactions, and London dispersion forces – basically, all types of non-covalent bonds. Also important to tertiary structure are hydrophobic interactions, in which amino acids with nonpolar, hydrophobic R groups cluster together on the inside of the protein, leaving hydrophilic amino acids on the outside to interact with surrounding water molecules.

One special type of covalent bond that can contribute to tertiary structure is the disulfide bond. Disulfide bonds are covalent linkages between the sulfur-containing side chains of cysteines, and are much stronger than the other types of bonds that contribute to tertiary structure.

Amino acids all contain the same backbone structure, which has both an acidic (-COOH) and a basic (-NH2) group. Each amino acid also has a functional group attached to the backbone. These functional groups can be positively/negatively charged, neutral, or polar in nature.

By changing the pH of the solution, you can change the charge state of the solute (in this case, the protein). If the pH of the solution is such that a particular molecule (peptide chain or protein) carries no net electric charge, the solute often has minimal solubility and precipitates out of the solution. The pH at which the net charge is neutral is called the isoelectric point. Therefore, the more basic the side chain of an amino acid, the higher the isoelectric point.

 


Practice Questions

 

MCAT Official Prep (AAMC)

Section Bank C/P Section Passage 5 Question 36

Section Bank C/P Section Passage 6 Question 43

Section Bank C/P Section Question 65

Online Flashcards Biochemistry Question 13

Practice Exam 2 B/B Section Passage 3 Question 13

Practice Exam 4 B/B Section Passage 9 Question 49


Key Points

• The simplest level of protein structure, primary structure, is simply the sequence of amino acids in a polypeptide chain.

• Protein secondary structure, refers to local folded structures that form within a polypeptide due to interactions between atoms of the backbone and include α helices and β pleated sheets.

• The overall three-dimensional structure of a polypeptide is called its tertiary structure.

• At a pH equal to a protein’s isoelectric point, a protein will have no net electric charge and will be minimally soluble.


Key Terms

Primary structure: sequence of amino acids in a polypeptide chain.

Secondary structure:  local folded structures that form within a polypeptide due to interactions between atoms of the backbone.

α helix: the carbonyl (C=O) of one amino acid is hydrogen bonded to the amino H (N-H) of an amino acid that is four down the chain, pulling the chain into a helical structure.

β pleated sheet: two or more segments of a polypeptide chain line up next to each other, forming a sheet-like structure held together by hydrogen bonds.

Tertiary structure: overall three-dimensional structure of a polypeptide.

Hydrophobic interactions: amino acids with nonpolar, hydrophobic R groups cluster together on the inside of the protein, leaving hydrophilic amino acids on the outside to interact with surrounding water molecules.

Isoelectric point: pH at which the net charge of a molecule is neutral.



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