Macromolecules

What are Macromolecules?

You know what I'm about to say - time to break down this word...

Macro means large, and you surely know what molecules are by now. So these are large molecules. That sounds an awful lot like a polymer, doesn't it? Well that's no coincidence. We talked about polymers right before this section for a reason. These macromolecules are polymers, each with its own monomers that make it up. The four macromolecules are carbohydrates, lipids, nucleic acids, and proteins.

Carbohydrates

You've definitely heard of these - you might even be trying to avoid them. While it's not healthy to avoid them entirely long term, it is understandable why you might want to cut down on these to try to lose weight.

What is the monomer?

Carbohydrates are made up of monosaccharides. That word means 'one (mono) sugar (saccharide)'. So a carbohydrate is made up of single sugars. We typically refer to carbohydrates as sugars, but not all of them are as sweet as you might be imagining.

What are carbohydrates good for?

Not only do carbohydrates consist of glucose and sucrose, but also many other structures that you might not recognize as sugars because they are not at all sweet. One example of this is cellulose, a carbohydrate that plants synthesize for structural support. Celery, for example, is made primarily up of cellulose and water. But celery is not sweet, despite cellulose being a sugar. In reality, our taste buds cannot taste cellulose because we do not receive much of a benefit from the carbohydrate. We cannot digest the carbohydrate, so it just passes through undigested.

Carbohydrates are also good for short-term energy storage. Plants synthesize glucose via photosynthesis not only to build their bodies up with cellulose (and other polymers), but also so that they can break down the glucose via cellular respiration just like we do.

These are only two uses of carbohydrates for organisms that consume or synthesize them. There are many more, and we will see some as we continue throughout the course. For example, carbohydrates are on the outside of some cells, attached to the membrane, and are used for cell signaling and communication.

Lipids

You may be more familiar with lipids as fats. Lipids, however, are more than that - they can be used for insulation, energy storage, cell membranes, and more.

Lipids

What is the monomer?

For our course, there are two monomers that make up the lipid polymers we will encounter. The monomers are glycerol and fatty acids. They are shown interacting in this image.

Fats or Triglycerides

The image here is a common lipid known as a triglyceride. 'Tri' means three, and you can see that there are 3 fatty acid chains attached to single glycerol (highlighted in red). These are the two monomers of lipids, but lipids don't always look like this on the right. These are the fats that are in your diet.

Phospholipids

Phospholipids, such as the one shown here, are going to be a very important lipid that we will encounter. They are responsible for making up cell membranes. The polar head is hydrophilic (hence, polar) whereas the nonpolar tail is hydrophobic. This is incredibly important, and we will see why in cell membranes.

They are able to keep the insides of the cell inside, and the stuff outside of cells on the outside. But more on that later.

Do not bother memorizing the chemical structure of this molecule - just be able to recognize its general shape.

Sterols

Sterols make up the final type of lipid we will talk about, and it is actually a subgroup of steroids. Sterols are an important part of cell membranes, as they affect the fluidity of the membrane. We will discuss this more when we get to cell membranes, however.

Nucleic Acids

This is the macromolecule that sounds the most intimidating and is one of the most important for the course. However, it really is generally considered to be the easiest of the four to understand in AP Biology.

Nucleic Acid: What is the monomer?

Nucleic acids (the polymer) are made up of nucleotides (the monomer). Any number of nucleotides chained together form a nucleic acid, but the nucleic acids you may be familiar with are generally made up of millions of nucleotides. These two kinds of nucleic acids are DNA and RNA.

Nucleotides have three parts - the phosphate group, the sugar, and the nitrogenous base (in this diagram, the base is adenine(A), but there can also be thymine(T), guanine(G), or cytosine(C)).

DNA

DNA, or deoxyribonucleic acid, is probably the most commonly discussed molecule in your school career so far. It is the recipe for life itself, and that is not stated lightly. There will be a lot of time dedicated to learning about the structure of DNA - the double helix. But, for now, I want you to be familiar with the name and be able to recognize a DNA molecule.

Looking at the image, you can see that DNA is double-stranded. It kind of looks like if you took a ladder and twisted it up quite a bit. That twisted-ladder shape is the double helix.

Each strand is made up of a sugar-phosphate backbone (the blue spine of the strands in the image) and the nitrogenous (the colored part in the middle of the strand). Those are really the same parts as the nucleotides. The sugars and phosphates from the nucleotides are linked together from one nucleotide to those of its neighbor. The nitrogenous base (A, T, C, G) sticks out in the middle, and is really the important part of the molecule.

Those bases are going to be more and more important as we continue on throughout the course, but for now, just know those 4 nucleotides that make up DNA - adenine, thymine, guanine, and cytosine. When they chain together, we can represent their sequence with a chain of their letter. So, if a DNA molecule has a chain of adenine, cytosine, cytosine, adenine, thymine, and guanine (in that order), then we would represent that chain as ACCATG.

RNA

RNA, or ribonucleic acid, sounds very similar to DNA, but there are some key differences. Firstly, the sugar found in the nucleotides are different. Instead of the deoxyribose sugar from DNA (that's where the D comes from), RNA nucleotides contain a ribose sugar (there's the R). You should be familiar with this, but don't need to memorize these sugars.

For us, however, there is a more crucial different here: the nitrogenous bases that can exist within RNA are different from those of DNA. Remember, DNA can be made up of thymine (T), cytosine (C), guanine (G), and adenine (A). RNA, however, cannot contain thymine. Instead, you will see that RNA can contain uracil (U) in addition to the cytosine, guanine, and adenine that the two molecules share.

RNA is also only made up of a single strand, rather than the two strands that make up DNA. It almost looks as if you cut DNA in half down the middle to make RNA.

Proteins

Good, we're back to stuff we think about eating all the time! That's less difficult to spell than nucleic acids at least.

What is the Monomer of Protein? Amino Acids!

Proteins are polymers, just like all of the other macromolecules we discussed. Just like all polymers, they are made up of building blocks, or monomers. In proteins, the monomers that make them up are called amino acids.

Amino acids are made up of three basic parts: the amino group, the carboxyl group (both named for their functional groups), and the R-group (a.k.a. the side chain). Luckily, all amino acids are identical except for the R-group. That means that all amino acids consist of the same amino group and carboxyl group.

The R-group is what makes amino acids unique from one another - it's just like how the nitrogenous base of a nucleotide is what makes it unique compared to another nucleotide.

There are 20 different amino acids, each with a different R-group. You do not need to memorize any of these amino acids or their structures, but we will encounter some quite frequently in coming units.

Functions of Proteins

The molecular tools for most cellular functions

Proteins are composed of one or more polypeptide chains folded and coiled into specific conformations.

Polypeptides are polymers of amino acids.

Cell Functions:

• structural support

• storage (of amino acids)

• transport (hemoglobin)

• signaling (chemical messengers)

• cellular response to chemical stimuli (receptors)

• movement (contractile proteins)

• defense against foreign invaders (antibodies)

• catalysts of biochemical reactions (enzymes)

-Vary in structure, each type has a unique 3-dimensional shape (its conformation) -are commonly made of only 20 amino acid monomers.

Amino acid- building block molecule of a protein; most consist of an asymmetric carbon, which is bonded to:

a. hydrogen atom

b. carboxyl group

c. amino group

d. Variable group ® specific to each amino acid. The physical and chemical properties of the side chain determine the uniqueness of each amino acid.

PROTEIN FOLDING

Protein function depends on its specific conformation

Protein conformation: 3-D shape

Native conformation: functional conformation of a protein under normal biological conditions. * protein to recognize and bind specifically to another molecule (hormone/receptor, enzyme/substrate, and antibody/antigen)

Four Levels of Protein Structure

1. Primary structure

2. Secondary structure

3. Tertiary structure

4. Quaternary structure (2 or more polypeptide chains)

Primary Structure

The unique sequence of amino acids in a protein.

• determined by genes

• slight change can affect protein’s conformation and therefore function

Secondary Structure of Protein:

Regular, repeated coiling and folding of a protein’s polypeptide backbone.

• contributes to overall conformation

• stabilized by hydrogen bonds between peptide linkages in protein backbone (carbonyl and amino groups)

• alpha helix and beta pleated sheets

The Alpha Helix- helical coil- found in fibrous proteins (keratin and collagen)

Beta Pleated Sheet- sheet of antiparallel chains folded into accordion pleats.

Tertiary Structure

3-D structure, now a functional protein!

Irregular contortions of a protein due to bonding between side chain (R groups); third level of complexity. Weak interactions and covalent bonds may both occur.

• Weak interactions hydrogen bonds between polar side chains and ionic bonds between charged side chains.

• Hydrophobic interactions: between nonpolar side chains in the protein’s interior.

• Covalent linkage: disulfide bridges form between cysteine group: strong bond, reinforcing the conformation.

Quaternary Structure

Structure that results from interaction among several polypeptides in a single protein.

• For example: collagen is a fibrous protein composed of 3 helical polypeptides into a triple helix. This is found in animal tissue, and the supercoiled quaternary structure gives collagen its strength.

• Some globular proteins have subunits that fit closely together- Hemoglobin has 2 alpha chains and two beta chains.

AlphaFoldLearn what protein folding is, why it's important and how our AI system AlphaFold is working to solve this grand scientific challenge.

DENATURING OF A PROTEIN

Proteins can become denatured if their normal environment is altered, making the protein lose its native conformation and therefore its biological activity.

Denaturing can occur:

Excessive heat disrupts weak interactions.
pH outside of their optimal range (strong acids and bases..most proteins work best around 7 * Pepsin is an exception it works best at 2
By transfer to an organic solvent- hydrophobic side chains, normally inside the core, move to the outside. Hydrophilic side chains move away from the solvent to the interior.
• Chemical agents that disrupt hydrogen bonding, ionic bonding, and disulfide bridges. • Excessive heat disrupts weak interactions.

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