This section of the AP Biology Curriculum – Structure and Function of Biological Macromolecules – covers the importance of directionality in many large polymers. This section looks at how nucleic acids, polypeptides, and complex carbohydrates are formed and discusses how changes in their structure can drastically affect their function.

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

LEARNING OBJECTIVE
SYI-1.C
Explain how a change in the subunits of a polymer may lead to changes in structure or function of the macromolecule.

ESSENTIAL KNOWLEDGE
SYI-1.C.1
Directionality of the subcomponents influences structure and function of the polymer –

1. Nucleic acids have a linear sequence of nucleotides that have ends, defined by the 3’ hydroxyl and 5’ phosphates of the sugar in the nucleotide. During DNA and RNA synthesis, nucleotides are added to the 3’ end of the growing strand, resulting in the formation of a covalent bond between nucleotides.
2. DNA is structured as an antiparallel double helix, with each strand running in the opposite 5’ to 3’ orientation. Adenine nucleotides pair with thymine nucleotides via two hydrogen bonds. Cytosine nucleotides pair with guanine nucleotides by three hydrogen bonds.
3. Proteins comprise linear chains of amino acids, connected by the formation of covalent bonds at the carboxyl terminus of the growing peptide chain.
4. Proteins have primary structure determined by the sequence order of their constituent amino acids, secondary structure that arises through local folding of the amino acid chain into elements such as alpha-helices and beta-sheets, tertiary structure that is the overall three-dimensional shape of the protein and often minimizes free energy, and quaternary structure that arises from interactions between multiple polypeptide units. The four elements of protein structure determine the function of a protein.
5. Carbohydrates comprise linear chains of sugar monomers connected by covalent bonds. Carbohydrate polymers may be linear or branched.

1.5 Structure and Function of Biological Macromolecules Overview

This section of the AP Biology curriculum takes a closer look at how biological macromolecules are synthesized, and how their structure determines their function. It also discusses the importance of directionality in biological macromolecules, and how this trait allows DNA to store information, create proteins, and keep order within a cell.

Let’s start with nucleic acids. Nucleic acids are directional molecules. This means that they can only be formed one way – with a hydroxyl group exposed on one end and a phosphate group exposed on the other. Each strand of DNA is a separate molecule, and each strand has a hydroxyl group exposed on one end and a phosphate group exposed on the other. We call these ends the 5’ end and the 3’ end. You can remember the difference because hydroxyl groups at the 3’ end are much smaller than the phosphate groups at the 5’ end.

DNA polymerase, the molecule responsible for attaching new nucleotides to a growing sequence, can only function in the 3’ to 5’ direction. When it is time to duplicate the DNA within cells, the two old strands of DNA are separated and DNA polymerase moves in to start adding new nucleotides. DNA polymerase builds a new strand that corresponds to the template by adding new nucleotides that are complementary to the template strand. Multiple DNA polymerase molecules work at the same time, moving in opposite directions on the two template strands.

The double-helix structure of DNA is formed through a relatively simple mechanism – hydrogen bonding. Let’s take a look at how this works. If we consider the complementary nucleotides Adenine and Thymine, we can see that two hydrogen bonds are formed between the nucleotides. Adenine has a slightly positive amino group, which easily forms a hydrogen bond with thymine’s slightly negative oxygen. The nitrogen on adenosine is slightly negative, allowing a hydrogen bond to form with thymines slightly positive nitrogen.

If we look at the complementary relationship between guanine and cytosine, we see a similar relationship. Everywhere that guanine has a slightly positive charge, cytosine has a corresponding negative charge. In this case, 3 hydrogen bonds can be formed. If guanine tried to form hydrogen bonds with thymine, positive charges would meet other positive charges. This would cause the two nucleotides to be repelled, disrupting the structure of the DNA double helix. This is how DNA repair enzymes can easily find and replace nucleotides that are incorrect in the sequence.

Between the sugar-phosphate backbone and these hydrogen bonds, DNA takes on a double-helix structure within the cell. The two strands run antiparallel to each other. In other words, one strand runs in the 3’ to 5’ direction, while the opposite strand runs in the 5’ to 3’ direction. This double helix typically has a major groove and a minor groove as it wraps around itself. This structure protects the nucleotide sequence, and allows DNA to be stored in massive units known as chromosomes.

Similar to the directionality of DNA molecules, proteins are also directional molecules. Each amino acid has a carboxyl group on one end and an amino group on the other end. This directionality makes it possible for ribosomes to create a chain of amino acids. Let’s see how this process works, in detail!

First, the ribosome grabs onto a piece of messenger RNA (mRNA for short). Floating around the ribosome are many loose transfer RNA (tRNA) molecules. These tRNAs have 3 nucleotides exposed, and hold specific amino acids on the opposite end. The tRNAs move into the E site of the ribosome. If the codons in the mRNA molecule form hydrogen bonds with the nucleotides exposed on the tRNA, they can move into the P site. As they transfer from the P site to the A site, a dehydration reaction is encouraged and a new peptide bond is formed.

The new covalent bond is formed between the carboxyl group on the growing peptide chain and the amino group of the new amino acid. This leaves another carboxyl group exposed, allowing another amino acid to be added in the same direction. This is important because it means that amino acids can only be added in one direction. The amino terminus on the first amino acid cannot be added to, meaning that peptides can only be made in the order that the mRNA dictates. This ensures that the DNA code can be perfectly translated into functional protein molecules!

Proteins are very complex molecules, thanks to the 20+ amino acids that can be used to construct them. Each amino acid has a different R-group, which confers both physical and chemical properties to a molecule.

The primary structure of a molecule is simply the order of amino acids within the molecule. This order is dictated by the codons in mRNA, which were transcribed directly from the codon sequence in DNA. Therefore, the primary structure of a protein is determined solely by the order of nucleotides in a DNA molecule.

However, as soon as this primary structure is created, interactions between amino acids in the chain start to create secondary structure. Secondary structure is the simplest level of 3-dimensional structure in a protein. There are several common motifs in secondary structure. The two most common motifs are beta-sheets and alpha-helices. A beta sheet is formed when a protein strand folds back on itself and creates hydrogen bonds. This creates a flat structure, much like a ribbon. By contrast, an alpha-helix is formed when peptides next to each other in the chain form hydrogen bonds, creating a helix structure that creates a rod-like 3D shape.

The tertiary structure of proteins is formed by interactions between different secondary structures. In a typical protein, both alpha-helices and beta-sheets interact to fold the molecule into a specific shape. In general, tertiary structures are formed by hydrogen bonding, polar interactions, and attractions between hydrophobic parts of the molecule. This also means that these interactions can be disrupted when conditions in the cell are not right.

For instance, if the temperature rises or pH is changed, this can lead to denaturation of a protein. The protein will lose its tertiary structure and unfold. Though the primary and secondary structure is unchanged, the protein will not be functional in these conditions. However, if the conditions are changed back (by lowering the temperature or buffering the pH) the protein will renature and become functional once again. This is a major reason why cells and organisms have mechanisms for controlling the physical and chemical conditions within cells.