Proteins - Online Tutor, Practice Problems & Exam Prep

Proteins, essential biological macromolecules, are polymers made of amino acid monomers, featuring an N-terminal (amino group) and C-terminal (carboxyl group) end. There are 20 amino acids, each with unique R groups that determine their properties. Proteins exhibit four structural levels: primary (amino acid sequence), secondary (alpha helices and beta sheets), tertiary (3D shape), and quaternary (multiple chains). Enzymes, a type of protein, catalyze reactions without being consumed, forming enzyme-substrate complexes. Understanding these concepts is crucial for grasping biochemical processes and the role of proteins in cellular functions.

Proteins

So, proteins are a very heavy topic in biochemistry, and we'll talk a lot of details about proteins later on in our course. Now, in this video, we're going to do a quick recap on proteins. Recall that proteins are one of the four major biological macromolecules that all cells have. Proteins have vast structural and functional roles. We've seen that in our previous biology courses where proteins do so many different things for a cell, and we'll see that in this course too.

Proteins are the polymers of amino acid monomers. All that means is that the monomers of proteins are amino acids. Similar to nucleic acids, proteins have directionality. All that means is that in a chain of a protein, the ends of that protein are chemically different from one another. Proteins have an N-terminal end and a C-terminal end on the opposite end. The 'N' in the N-terminal refers to the presence of a free amino group. Recall that amino groups have a nitrogen atom in them, represented by an 'N'. On the other hand, a C group. The 'C' in C-terminal refers to the carboxyl group.

Let's take a look at our example. Down here, what we'll see is that we have a bunch of amino acid monomers represented by triangles, and these triangles are different colors. These are different amino acids. Through a process, we can link all of these amino acids together in a chain to create a protein polymer. In the next video, we're going to talk about the amino acid itself. What is this monomer and what are the components? So I'll see you guys in that video.

Amino Acids

So now that we've refreshed our memories that amino acids are the monomers of proteins, we can now focus on the structure of the amino acid itself. And recall that each amino acid contains common components as well as a unique R group. Living organisms use a total of 20 different amino acids that can be grouped together based on the properties of their R groups. In our example below, what we see is that this box shows the amino acid components. The ones that are bracketed in red are common to all amino acids, whereas the unique components like the R groups are shown below. The common amino acid components include a central carbon atom, also known as an alpha carbon, shown here in the amino acid structure. It also includes a central hydrogen atom shown above, an amino group on the N-terminal end of the amino acid shown here, and a carboxyl group shown on the opposite end of the amino acid on the C-terminal end, shown here. The shaded portions that I've just highlighted again are common to all amino acids, so the unique parts are shown by the R groups.

Over here, we have a table of the amino acids and their R groups. Notice that I've intentionally made this table kind of small and difficult to read because we're not so interested in the details just yet. We'll talk about all the details of the amino acids in our later videos. For now, I just want you guys to notice that each of the amino acids contains a different R group, and you can see that because the R groups are highlighted in blue and the blue boxes are all different sizes. These amino acids, you can also see, are grouped together based on their properties, and you can see that by the boxes which are grouping amino acids together.

In our next video, we're going to talk about how amino acids come together to create the different levels of protein structure. So I'll see you guys in that video.

Protein Structure & Terms

In this video, we're actually going to do two different things. The first is, we're going to recap the protein levels of structure, and the second, we're going to define several different protein-related terms that tend to confuse students. And so for the first one, recall that proteins can have up to four levels of structure, and they are conveniently called primary, secondary, tertiary, and quaternary levels of structure. And again, in this video, we're just going to do a quick recap, but later on in our course, we're going to dive into a lot more detail for each of these levels of structure. Now, for the second objective, there are several different terms that refer to amino acid chains that vary in length, and so you can have short, intermediate, and longer chains, and these terms include oligopeptide, peptide, polypeptide, and protein. And so in our example below, we'll first consider the protein levels of structure and then we'll define and distinguish between each of these terms.

And so, for the first level of protein structure, recall that it is the primary level of structure. This refers to the types, the quantity, and the order of amino acids from the N-terminal end of a protein to the C-terminal end of a protein. The primary level of protein structure is incredibly relevant because it dictates and influences all the other levels of structure. Now recall that the secondary level of structure is the formation of alpha helices and beta pleated sheets. And so recall that alpha helices are a winding type of structure and beta pleated sheets are a zigzag or a staircase type of structure. Now, the third level of structure is tertiary protein structure, and notice that this includes beta pleated sheets and alpha helices, but it's really referring to the overall three-dimensional shape of that protein. Now, quaternary protein structure refers to a protein that has multiple amino acid chains, and we can see that in this diagram where we have a light-colored gray chain and a darker-colored chain. And these are separate chains that have their own 3D structure and they complex together to form a single protein with multiple subunits. And every protein has primary, secondary, and tertiary levels of structure; however, not all proteins contain quaternary levels of structure.

Now, for our second objective of this video, we're going to define these terms. And so, oligopeptide refers to an amino acid chain that contains between 2-20 amino acids. Peptide refers to amino acid chains that contain less than 50 amino acids. So you can see that there's some overlap between peptide and oligopeptide. Now polypeptide refers to amino acid chains that contain more than 50 amino acids, and proteins can contain from 100 up to several thousands of amino acids. And so, notice there's some overlap between protein and polypeptide. Now, really the main difference between polypeptide and protein is that polypeptide tends to refer to just the chain of amino acids, whereas protein refers to the chain of amino acids, but in its functional form. And so, proteins include the functional form. And so in our next video, we're going to talk about a very specific type of protein and that's the enzyme. So I'll see you guys in that video.

Enzymes

In this video, I'm going to give you guys some quick facts about enzymes. But later on in our course, we'll talk a lot more details about enzymes. Now recall that enzymes are proteins that catalyze chemical reactions or speed up chemical reactions, and they can do so without actually being consumed by the reaction. The reactants of enzymes are called substrates, and the substrates fit perfectly into an enzyme's active site, and then the enzyme converts the substrate into the products. So let's take a look at our example.

And down here what we have are 2 substrates, a red one and a yellow one. And below we have our enzyme, which has an active site, and the substrates fit perfectly into the enzyme's active site to create an enzyme-substrate complex. Then the enzyme induces the reaction and converts the substrates into the product. It does so without being consumed, which means that the enzyme can go back and repeat the reaction on a new set of substrates. Enzymes are incredibly relevant to all life because enzymes pretty much catalyze every cellular reaction and they make those reactions occur at a rate that's sustainable for life.

The last thing I want to leave you with is that the ending "ase" is indicative that it is an enzyme. For example, peptidase ends in "ase" and peptidases are indeed enzymes. We'll be talking about enzymes throughout our entire biochemistry course.

That concludes our lesson on enzymes, and I'll see you in the practice videos.

Which of the following is not a component of an amino acid?

• A. Peptide
• B. α-carbon
• C. Amino group
• D. Carboxyl group

Which level of protein structure corresponds to the formation of α-helices and β-pleated sheets?

• A. Primary
• B. Secondary
• C. Tertiary
• D. Quaternary

Fill in the blanks: Enzymes __________ chemical reactions _________ being consumed by the reaction.

• A. Speed-up ; while
• B. Slow-down ; without
• C. Catalyze ; without
• D. Inhibit ; while

Here’s what students ask on this topic:

What are the four levels of protein structure?

Proteins have four levels of structure: primary, secondary, tertiary, and quaternary. The primary structure is the sequence of amino acids in a polypeptide chain. The secondary structure refers to local folded structures that form within a polypeptide due to interactions between atoms of the backbone, such as alpha helices and beta sheets. The tertiary structure is the overall three-dimensional shape of a single polypeptide chain, stabilized by interactions between R groups. The quaternary structure exists in proteins with multiple polypeptide chains, describing how these subunits are arranged and interact.

What is the difference between a peptide and a polypeptide?

A peptide is a short chain of amino acids, typically containing fewer than 50 amino acids. A polypeptide, on the other hand, is a longer chain of amino acids, usually containing more than 50 amino acids. While both terms refer to chains of amino acids, 'polypeptide' often implies a longer chain that may fold into a functional protein, whereas 'peptide' generally refers to shorter chains that may not have a complex structure.

How do enzymes catalyze chemical reactions?

Enzymes catalyze chemical reactions by lowering the activation energy required for the reaction to proceed. They achieve this by binding to substrates at their active site, forming an enzyme-substrate complex. This complex stabilizes the transition state and reduces the energy needed to convert substrates into products. Enzymes are not consumed in the reaction, allowing them to catalyze multiple rounds of the reaction. This process is crucial for sustaining life, as it accelerates biochemical reactions to rates compatible with cellular functions.

What are the common components of an amino acid?

All amino acids share common components: a central carbon atom (alpha carbon), a hydrogen atom, an amino group (NH₂), and a carboxyl group (COOH). Additionally, each amino acid has a unique side chain, known as the R group, which varies among different amino acids and determines their properties. These components are essential for forming the peptide bonds that link amino acids into polypeptides and ultimately proteins.

What is the significance of the N-terminal and C-terminal in proteins?

The N-terminal and C-terminal refer to the ends of a protein or polypeptide chain. The N-terminal end has a free amino group (NH₂), while the C-terminal end has a free carboxyl group (COOH). These termini are significant because they define the directionality of the protein chain, influencing how the protein folds and functions. The sequence of amino acids from the N-terminal to the C-terminal determines the protein's primary structure, which in turn affects its higher-level structures and biological activity.