Proteins are the major structural and functional molecules of the cell
Lecture 3: Protein structure & function
Independent Studies Outcomes
1. Basic structure of an amino acid and what are the different classes of amino acids.
Amino acids share a similar structure with a central carbon atom attached to an amino group
(-NH2), a carboxyl group (-COOH), and a hydrogen atom. The remaining bond of the central
carbon is to 1 of 20 different side groups represented by the R (the side chain).
Differences in the side groups give the amino acids their individual properties.
- Nonpolar amino acids
- Uncharged polar amino acids
- Negatively charged (acidic) polar amino acids
- Positively charged (basic ) polar amino acids
2. Chemistry of the peptide bond and how it is formed.
A peptide bond is formed by a dehydration synthesis reaction between –NH2group of one
amino acid and the –COOH group of a second.
An amino acid chain always has an –NH2groups at one end, called the N-terminal end, and a
–COOH group at the other end, called the C-terminal end. In cells, amino acids are added only
to the –COOH end of the growing peptide strand.
Amino acids, peptide, polypeptide, protein
The chain or polymer of amino acids formed by sequential peptide bonds is called a peptide.
A polypeptide is usually defined as a peptide greater than 50 amino acids in length.
A protein is one or more polypeptides that are folded into a precise three-dimensional shape.
Only after this occurs is the polypeptide able to function.
The distinction between a polypeptide and a protein: a polypeptide is a string of amino acids; a
protein is a polypeptide that has folded into the specific three-dimensional shape that is
required for most proteins to be functional.
3. The four levels of protein structure.
- Primary structure: the particular and unique sequence of amino acids forming a
- Secondary structure: produced by the twists and turns of the amino acid chain
- Tertiary structure: the folding of the amino acid chain, with its secondary structures into
the overall three-dimensional shape of a protein
- Quaternary structure: the arrangement of polypeptide chains in a protein that is formed
from more than one chain. Example: collagen
All proteins have primary, secondary, and tertiary structures. Each structural level depends upon the
level before it. 4. What bonding arrangements give rise to primary, secondary and tertiary structure.
- Primary structure: covalent bonds link amino acids into chains
- Secondary structure: hydrogen bonds between atoms of the backbone. More precisely,
the hydrogen bonds form between the hydrogen atom attached to the nitrogen of the
backbone and the oxygen attached to one of the carbon atoms of the backbone
- Tertiary structure: the four major interactions between R groups that contribute to tertiary
structure: 1) ionic bonds, 2) hydrogen bonds, 3) hydrophobic interactions, and 4) disulfide
bridge. The tertiary structure of most proteins is flexible, allowing them to undergo limited
alterations in three-dimensional shape known as conformational changes.
5. How are alpha helices and beta sheets formed. Alpha helices: a mo