[AP Biology 1.4] Properties of Biological Macromolecules

Section 1.4 of the AP Biology Curriculum – Properties of Biological Macromolecules – takes a much closer look at the several different kinds of macromolecules. In this section, students learn about the structural components and bonds needed to create nucleic acids, proteins, complex carbohydrates, and lipids.

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ENDURING UNDERSTANDING
SYI-1
Living Systems are organized in a hierarchy of structural levels that interact.

 

LEARNING OBJECTIVE
SYI-1.B
Describe the properties of the monomers and the type of bonds that connect the monomers in biological macromolecules.

 

ESSENTIAL KNOWLEDGE
SYI-1.B.2
Structure and function of polymers are derived from the way their monomers are assembled –

  1. In nucleic acids, biological information is encoded in sequences of nucleotide monomers. Each nucleotide has structural components: a five-carbon sugar (deoxyribose or ribose), a phosphate, and a nitrogenous base (adenine, thymine, guanine, cytosine, or uracil). DNA and RNA differ in structure and function.
  2. In proteins, the specific order of amino acids in a polypeptide (primary structure) determines the overall shape of the protein. Amino acids have directionality, with an amino (NH2) terminus and a carboxyl (COOH) terminus. The R group of an amino acid can be categorized by chemical properties (hydrophobic, hydrophilic, or ionic), and the interactions of these R groups determine structure and function of that region of the protein.
  3. Complex carbohydrates comprise sugar monomers whose structures determine the properties and functions of the molecules.
  4. Lipids are nonpolar macromolecules –
    1. Differences in saturation determine the structure and function of lipids.
    2. Phospholipids contain polar regions that interact with other polar molecules, such as water, and with nonpolar regions that are often hydrophobic.

 

EXCLUSION STATEMENT
The molecular structure of specific lipids is beyond the scope of the AP Exam.

 

1.4 Properties of Biological Macromolecules Overview

This overview covers section 1.4 of the AP Biology Curriculum – Properties of Biological Macromolecules.

Let’s start with arguably the most important biological macromolecule: Nucleic acids. To fully understand how nucleic acids work, we need to look at their structure. First, let’s take a look at the sugar-phosphate backbone of a nucleic acid.

At the center of every nucleic acid is the sugar-phosphate backbone. The phosphate group forms phosphoric acid in water. This phosphate group can bond to the sugar molecule on the next nucleic acid, creating a long chain. No matter how long this sugar-phosphate backbone gets, there will always be a phosphate group exposed on one end and a sugar molecule exposed on the other. Therefore, we call both a single nucleotide and many nucleotides connected together a “nucleic acid.”

The main difference between DNA and RNA lies in the sugar molecule that is used to create the sugar-phosphate backbone. DNA uses deoxyribose, seen here. RNA uses ribose – the same sugar with one extra oxygen atom. This tiny difference creates some of the functional differences between DNA and RNA within cells.

The part of a nucleotide that is most important to carrying information is the nucleotide base. The base attached to this structure is cytosine, one of several bases that can be attached to a nucleotide. Let’s see exactly how these nitrogenous bases work.

There are 5 nitrogenous bases used in nature to create DNA and RNA, which are separated into two groups based on their structure. The purines are based on a double-ring structure, whereas the pyrimidines are based on a single-ring structure. Adenine, Guanine, Thymine, and Cytosine are used to create DNA molecules. Uracil is used in RNA, in place of Thymine.

More importantly, the nitrogenous bases create the double-helix structure of DNA through their ability to form hydrogen bonds. Each purine has a corresponding pyrimidine that it can form hydrogen bonds with. You can remember which nitrogenous bases can form hydrogen bonds using a simple mnemonic device. The tall letters (A + T) can form hydrogen bonds, and the fat letters (C + G) can form hydrogen bonds. This will be very important to remember when we start to learn how DNA is synthesized and how errors in the DNA code are corrected.

DNA stores information through a slightly complex mechanism. DNA is stored in the nucleus as a double helix. This allows it to stay protected from damage. The double-helix also allows for repair proteins to easily find errors. Most errors create a small bump in the DNA, due to the lack of hydrogen bonds between the two strands. To extract the information needed to create new proteins, the exact order of nucleotides must first be copied from DNA into a new RNA molecule within the nucleus. This is called transcription.

RNA is not as stable as DNA, and is more prone to errors. However, RNA molecules can carry the information to where it is needed – like a messenger. This messenger RNA molecule carries the nucleotide sequence out of the nucleus, where a ribosome can attach to it. The ribosome then creates a new protein molecule by matching transfer RNA molecules to every 3-nucleotide sequence, known as a “codon”. This process, called translation, is how the information stored in DNA becomes an actual cellular product and allows the cell to function.

Now that we know how DNA stores the information to build proteins, let’s take a look at proteins themselves. Proteins are simply large strings of amino acids that fold into specific shapes. Each protein serves a different function, made possible by its 3-dimensional shape and the amino acids it is made of.

Amino acids – also called peptides – are bonded together by peptide bonds. These bonds form through a dehydration reaction between a carboxyl group and an amino group on each amino acid. This also ensures that each protein molecule has directionality. One one side is the carboxyl terminus, while the other side of the molecule has an amino terminus. Make sure you understand the difference because questions on the AP test can reference these different sides.

The structures that make each amino acid different are known as R-groups or side-chains. These groups are what gives each amino acid its unique functionality. In fact, though there are 20+ amino acids used in nature, there are only 7 different groups that these molecules can be classified as. While the structure of each amino acid is slightly different, many amino acids bring similar properties to the polypeptides they are a part of.

For instance, several amino acids have charged R-groups. This helps create a hydrophilic portion of the polypeptide that can easily interact with water and other polar molecules. Other amino acids contain sulfur, which is able to form sulfur crosslinks with other sulfur-containing peptides. This can help hold multiple polypeptides together in a large quaternary structure.

The active site is where the protein will actually carry out its function. In order to fit a substrate just right and catalyze a reaction, the active site of the protein must have the right physical and chemical properties. So, not only does the active site need to have the right R-groups exposed, but the protein must also have the right sequence of amino acids to fold into the proper shape.

Likewise, this protein must also have some hydrophobic regions where it needs to bind to the cell membrane. If hydrophilic amino acids were used in place of hydrophobic amino acids, this protein could not stick within the cell membrane and would not be functional. Since proteins serve roles as enzymes, immune responders, receptors, methods of movement, and as structural molecules, there is a nearly infinite number of amino acid arrangements.
Carbohydrates most commonly serve roles as fuel and building materials for a cell. The simplest carbohydrates are hydrocarbon chains of 5 or 6 carbons that often have a ring-like structure. Glucose, for instance, serves as the main fuel molecule for cells. However, as you connect more and more carbohydrate monomers, you can create substances with many different properties.

The exact structure of large polysaccharides helps determine their function. Linear polymers are most often found in structural molecules like cellulose. These fibers – much like the smaller threads in a large rope – can intertwine to create a much stronger material. Some structural carbohydrates even have cross-links between the fibers, adding another layer of strength to a molecule.

By contrast, storage polysaccharides most often have a branched structure. Unlike a linear structure, this allows a cell to store as much energy in as small of a space as possible. Starch molecules – such as amylose found in potatoes – are essentially huge branching structures that fill cells with energy. Humans and animals use the polysaccharide glycogen for a similar purpose. The cell can easily start hydrating the bonds between individual monomers to fill the cell with glucose – which can then be used to power a variety of other reactions.

The last category of macromolecules that we will look at is lipids. There are three types of lipids that are most important to life: fats (triglycerides), phospholipids, and steroids. Some people consider waxes their own category, though they have a structure very similar to triglycerides. Let’s take a look at each of these groups.

Triglycerides are simply fatty acid molecules bound into a larger molecule with glycerol – a three-carbon alcohol. Fatty acids come in two forms: saturated and unsaturated. Palmitic acid is an example of a saturated fatty acid. Every carbon in the chain is bound to at least 2 hydrogens, leaving no room for double bonds between carbon atoms. Structurally, this makes saturated fats very linear. Therefore, you can pack many saturated fatty acids into a very tight space. Because of this structure, saturated fatty acids are usually solid at room temperature because the molecules squeeze tightly together as they lose thermal energy.

By contrast, an unsaturated fatty acid has double bonds between at least 2 carbon atoms in the chain. Double bonds are rigid. This means that lots of fatty acids cannot pack tightly together if they are unsaturated – even if the temperature is not particularly warm. Olive oil is a good example of an unsaturated fatty acid.

To create a triglyceride, three fatty acids bind to a single glycerol molecule. Though lipids are not “true polymers” in the sense that they are linear chains of the same monomers, they are still created through dehydration reactions. The hydroxyl groups on glycerol react with the carboxyl head groups of each fatty acid. A water molecule is lost and an ester bond is formed. There are many triglycerides found in nature, with both saturated and unsaturated fatty acids in their structure. This gives rise to many different types of fat found in different organisms.
Phospholipids are different structurally – compared to triglycerides – and they also serve a much different purpose within organisms. Phospholipids have a hydrophilic head and a hydrophobic tail. When many phospholipids congregate together, the head groups interact with water while the tail groups tend to orient toward each other. This is how the lipid bilayer of all cells is created. Let’s look closer at the structure of a phospholipid.

In the hydrophobic tail are long hydrocarbon chains. The tail sections can contain saturated or unsaturated fatty acids, depending on the organisms. In general, organisms that live in very hot environments tend to have more saturated fatty acids whereas cells that must exist at very low temperatures tend to have more unsaturated fatty acids. Since unsaturated fatty acids tend to remain liquid at low temperatures, this creates a cell membrane that is still fluid and functional in the cold. Each organism must maintain the right balance of fatty acid tails to ensure its cells have functional membranes.

The polar head groups of phospholipids have both phosphate groups and nitrogen – both of which increase the head’s hydrophilic tendencies. This ensures that the molecule’s head is always oriented towards water – whether that is the cytosol of the cell or the external environment.