Proteins II: Amino Acids, Polymerization and Peptide Bonds

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  • 0:06 Peptide Bonds and…
  • 0:52 How Peptides are Formed
  • 3:00 Writing Peptides
  • 3:31 Types of Peptides
  • 5:15 Lesson Summary
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Lesson Transcript
Instructor: Meg Desko

Meg has taught college-level science. She holds a Ph.D. in biochemistry.

In this lesson, we'll take a deeper look at amino acids. You'll learn what makes a peptide, and what separates a protein from other kinds of amino acid bonds.

Peptide Bonds and Protein Structure

Examples of amino acid structures
Amino Acids

Think back to a time when you liked to play, and when you liked to take ordinary objects, like paperclips, and turn them into other beautiful things, like necklaces. You did this by taking one paper clip, hooking it up with another one, and then adding another one on the end, and another one, and another one, until you had a long strand of paperclips. Similarly, amino acids, which are the building blocks of proteins, can come together to form different types of peptides and proteins.

Today, we're going to talk about forming those bonds between amino acids, and we'll also talk about the different types of molecules that can be made by making these bonds.

How Peptides are Formed

In our cells, amino acids come together to form peptide bonds at places called ribosomes, which are sort of like a protein-building factory. We won't worry about that right now. What we're really concerned with is how these bonds form between two amino acids. Let's take the two amino acids, glycine and alanine.

The structures of glycine and alanine
Glycine and Alanine

One thing you'll notice is when we show amino acids that we're going to join together, we always show them from the amine side to the carboxylic acid side.

The side with the free amino group is known as the n-terminus of the amino acid. The side with the free carboxylic acid group is known as the c-terminus of the amino acid, or peptide. If glycine on the left and alanine on the right come together, they can form a dipeptide. The way that this happens is that the nitrogen on the amino group of the alanine forms a bond with the carbonyl carbon of the carboxylic acid on the glycine.

The byproduct of this reaction is water, which means that this is a dehydration reaction, or loss of water reaction.

The resulting molecule that's formed is a dipeptide, or peptide consisting of two amino acids. It would also be possible for this dipeptide to come into contact with another amino acid, such as serine. If it came into contact with serine, it is possible that it could form a tripeptide when the nitrogen of the serine amino acid bonded to the carbonyl carbon of the carboxylic acid on the alanine in the dipeptide.

Water would be a byproduct of this dehydration reaction, and we would be left with a tripeptide, consisting of glycine, alanine, and serine. So while it's pretty cool to see a tripeptide in all of its chemical glory, and see all of the bonds that make up these molecules, sometimes, it can be useful to have a shorthand, or have a different way to represent a peptide.

A dipeptide formed from glycine and alanine
Example of a Dipeptide

Writing Peptides

In the case of glycine-alanine dipeptide, we could represent them as two circles that are joined together (almost like they're part of a necklace), with the short names of the amino acids inside - in this case, gly and ala. If we were to add the serine that was part of our tripeptide to this, it would be gly-ala-ser (s-e-r). So you can think of this as a good way to represent a peptide, where the free amino group is on the left-hand side, and the carboxylic acid group is on the right-hand side.

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