In this segment, you'll learn about the building blocks of a protein: amino acid

s. As you probably know peptides and proteins are biological polymers, chains of
amino acids bonded together end to end. We will examine the properties of amino
acids that contribute to protein structure. You'll also learn about how protein
s are synthesized from these building blocks. Let's begin by examining the amino
acids. The amino acids our bodies use to make proteins are all alpha amino acid
s, which means that the carboxylic acid group and the amine group are bonded to
the same carbon, that we call the alpha carbon. Alpha amino acids usually exist
as zwitterions meaning the carboxylic acid group loses a hydrogen to become a ca
rboxyl group, and the amine group gains a hydrogen to become an amino group. The
alpha carbon is also attached to a hydrogen called the alpha hydrogen and an at
om or a group of atoms, that we call a side chain. Side chains differentiate the
amino acids from one another.
Let's consider the side chains in detail. Our DNA encodes for 20 different side
chains, thus providing for significant variety in these protein building blocks.
For instance, the side chain is a hydrogen atom in glycine, the smallest of the
amino acids and alcohol and serine and threonine, another amine group in lysine
and so on. We can categorize these amino acids by the chemical properties of th
eir side chains: charged, uncharged, hydrophobic and a few special cases. Some a
mino acids, like lysine or glutamic acid, have charged side chains at physiologi
cal pH. These amino acids can form electrostatic interactions
either with each other, the protein backbone, or with substrates and cofactors.
As you will see in the next segment the chemical properties of the side chain ca
n contribute significantly to the structure of a protein. Other amino acids like
serine or glutamine have uncharged side chains with polar functional groups. Th
ese can also form hydrogen bonds
with each other, the protein backbone, or protein substrates
and cofactors. Most amino acid side chains are neither charged nor polar.
These hydrophobic side chains in amino acids like leucine, isoleucine, methionin
e, or phenylalanine, usually orient themselves to avoid interactions with the wa
ter around the protein forming the core of a protein structure and stabilizing i
t. Then there are the wild cards.
Cysteine has a thiol functional group which can form very strong disulfide linka
ges that influence and stabilize a protein's shape.
Proline's side chain is linked to the amine, so it forces a kink in the protein
backbone whenever it's present. Now that we have discussed the amino acids let's
examine how we string them together into a polypeptide chain. During polypeptid
e synthesis, an amino acid's carboxyl group can bond to another's amino group f
orming an amide bond, also called a peptide bond, and releasing a molecule of wa
ter. The resulting dipeptide still has a free carboxyl group and a free amino gr
oup. This means another amino acid can be added to either side. Theoretically th
e amino acid chain could be extended infinitely, but most proteins are a few hun
dred amino acids long. With the 20 amino acids that our body typically uses, we
can make an incredible number of distinct proteins: 20 to the power of n, where
n is the length of the sequence. That means we could make 3.2 million different
peptides that are only five amino acids long.
The only difference between a peptide and a protein is the length of the chain.
Peptides are short about 40 amino acids or fewer. Anything longer and it's a pro
tein. For a protein of length 100 there are 20 to the 100 or about 10 to the pow
er of 130 theoretically possible different proteins. By comparison there are onl
y 10 to the 24th stars in the entire observable universe. The sequence of a pept
ide or protein is the order in which the amino acids are bonded to each other. F
or example, this is the sequence of insulin, a 51 amino acid polypeptide that he
lps our body
use carbohydrates. It's this sequence, the primary structure, that gives any pro
tein its identity. But the sequence doesn't tell you anything about how the prot
ein looks in three dimensions and it's that three dimensional structure that det
ermines what a protein does and how it does it.