Biomolecules for the DAT

Learn key DAT concepts related to proteins, protein function, carbohydrates, lipids, and membranes, plus practice questions and answers

Learn everything about biomolecules for the dat

Table of Contents

Part 1: Introduction to Biomolecules

Part 2: Proteins

a) Amino Acids

b) Peptide bonds

c) Protein Structure

Part 3: Non Enzymatic Protein Function

a) Structural Proteins

Part 4: Carbohydrates

a) Monosaccharides

b) Disaccharides

c) Glycogen

Part 5: Lipids and Membranes

a) Insolubility

b) Signaling Lipids

c) Structural Lipids

Part 6: High-yield terms

Part 7: Questions and Answers

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Part 1: Introduction to Biomolecules

Mastering proteins and other biomolecules is crucial for the DAT, but these topics can be complex and require dedicated practice. While this guide introduces these essential concepts, please note that it doesn't cover every detail. Pay close attention to the bolded terms, and be prepared for practice questions at the end.

Now, let's delve into the world of proteins. Do you know which protein is the most abundant in our cells? Surprisingly, it's actin, a nonenzymatic structural protein. This fact highlights the diversity of protein functions. Nonenzymatic proteins are equally vital, contributing to cellular structure and signaling. As you study these proteins, consider creating a chart to help differentiate their roles.

Carbohydrates have been a dietary puzzle for modern humans, with various trends like low-carb diets dominating the scene. However, carbohydrates have played a significant role in human evolution. In this article, we explore the fundamental biochemistry of carbohydrates, providing a solid foundation for understanding their metabolic processes.

In the early 20th century, the primary therapy for controlling pediatric epilepsy wasn't medication but a high-fat, low-carb diet. Fats, or lipids, are relatively simple molecules that serve diverse functions in our bodies, including energy storage and signal transmission. In this guide, we offer a comprehensive understanding of lipids along with practice questions to ensure your success on the DAT.

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Part 2: Proteins

a) Amino Acids

Amino acids serve as the fundamental components of proteins. Understanding the structures of amino acids is a highly rewarding area of study for the DAT.

Each amino acid's structure can be categorized into three distinct regions:

• The amino group, also known as the N-terminus.

• The carboxylic acid group, often referred to as the C-terminus.

• A distinctive identifying side chain, denoted as the R-group.

FIGURE 1: LABELED AMINO ACID

Remember that an amino group is a functional group consisting of NH3+. It resembles ammonium (NH4+), with the distinction that one nitrogen atom is linked to a carbon rather than a hydrogen atom (NH2C instead of NH3). It's important to note that this results in a lone electron pair on the nitrogen atom. Under physiological pH conditions (around pH ~7), this lone electron pair is capable of forming a bond with a hydrogen atom, resulting in a positive charge on the functional group.

On every amino acid, you'll find a carboxylic acid, which is a functional group composed of COOH. At physiological pH (around pH ~7), this carboxylic acid loses a proton, leading to a negative charge on the functional group.

It's worth mentioning that at physiological pH, amino acids exist as zwitterions, containing both positive and negative charges within the same molecule. Most amino acids have a net charge of zero, although exceptions occur when considering the charges on the R-group, or side chain, of the amino acid.

These R-groups, or side chains, can be as simple as a single hydrogen atom or as intricate as an imidazole ring. There are a total of 20 distinct R-groups.

The R-group is linked to the central carbon, known as the alpha carbon. This carbon atom is connected to every component of the amino acid: the amino group (-NH3+), the carboxylic acid portion (-COO-), the R-group, and a hydrogen atom (H).

It's important to note that, among the 20 amino acids, 19 of them have a chiral alpha carbon, meaning it's bonded to four different constituent groups. Glycine is the exception, with its R-group simply being a hydrogen atom. Chirality signifies the molecules' right- or left-handedness, denoted as D- and L- configurations, respectively. In the context of biological molecules, the chirality of amino acids is significant, as only L-configuration (left-handed) amino acids are utilized by the body. D-amino acids are not naturally present in eukaryotic metabolic pathways.

b) Peptide Bonds

Proteins consist of amino acids linked together through peptide bonds. The ribosome catalyzes the formation of these peptide bonds. As the ribosome reads an mRNA strand, it translates the information and appends amino acids to the growing polypeptide chain. The creation of a peptide bond between two amino acids, or between an amino acid and a peptide, serves as an example of a nucleophilic substitution reaction, which is a common reaction type that you should familiarize yourself with for the DAT. This reaction can also be described as a dehydration reaction that produces a water molecule. The reverse reaction is peptide bond hydrolysis. Hydrolysis means breaking (lysis) with water (hydro). So, peptide bonds can be broken by water molecules.

c) Protein Structure

Proteins are composed of many amino acids linked together through peptide bonds. Before discussing structure, it is important to set some nomenclature. Below is a simple representation of a protein composed of n+2 amino acids.

FIGURE 2: A SIMPLE POLYPEPTIDE SEQUENCE.

Take note that the protein structure is represented from left to right, commencing at the N-terminus and concluding at the C-terminus. The N-terminus designates the end of this sequence where the amino group (nitrogen) is exposed, while the C-terminus pertains to the end where the carboxylic acid group (carbon) is exposed. This is the established writing convention for all protein sequences.

Protein structure encompasses four hierarchical levels: primary, secondary, tertiary, and quaternary, all of which are pivotal for the protein's proper functioning. The initial level is the primary structure, which pertains to the linear sequence of amino acids connected by peptide bonds. The primary structure is defined exclusively by the specific amino acids present in it.

Secondary structure arises from hydrogen bonding interactions among atoms comprising the protein's backbone, rather than interactions among the side chains of individual amino acids. It's worth recalling that each amino acid includes:

An N-H group, derived from the amide bond.

A C=O bond, originating from the carboxylic acid.

The secondary structure results from hydrogen bonding interactions between the hydrogen (H) of the N-H group of one amino acid and the carbonyl oxygen (utilizing one of its lone pairs) of another amino acid.

Two primary forms of secondary structure are recognized: alpha helices and beta sheets. The stability of the alpha helix can be attributed to the numerous hydrogen bonds formed when the protein's backbone adopts this specific arrangement. Notably, the R groups of amino acids do not participate in the formation of the hydrogen bonds that create the alpha helix.

FIGURE 3: AN ALPHA HELIX IS AN EXTREMELY STABLE SECONDARY STRUCTURE.

Alpha helices fulfill various roles in diverse proteins. In numerous transmembrane proteins, alpha helices extend through the entire membrane to facilitate the transfer of ions from the exterior to the interior of the protein.

Beta sheets are likewise shaped by hydrogen bonding interactions. However, instead of adopting a helical structure, distinct segments of the amino acid chain align in parallel rows.