Lecture 3: Proteins and Cellular Function PDF

Lecture 3 Proteins and cellular function Learning Outcomes At the end of your study relating to this topic you should be able to: Describe the diversity of protein function and structure Explain the overall makeup of proteins Explain some of the key functions of proteins in the cel...

Lecture 3 Proteins and cellular function Learning Outcomes At the end of your study relating to this topic you should be able to: Describe the diversity of protein function and structure Explain the overall makeup of proteins Explain some of the key functions of proteins in the cell Provide one example of a protein involved in each of: immune defense, digestion and metabolism, DNA and RNA replication, oxygen transport Textbook references: Chapter 1 “Basic molecular themes of life” page 14 – 15, “Proteins” in Biochemistry and Molecular Biology, 6th edition by D. Papachristodoulou, A Snape, W.H. Elliot and D.C. Elliot 5 What are proteins? Amino acids COO- C-terminus NH NH3+ - H - C - COO N-terminus - R Peptide bonds Figure 3-1. The primary structure of a protein. Proteins are large biomolecules, known as macromolecules, consisting of amino acids linked together by covalent peptide bonds, i.e. they are polymers of amino acids. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes. There are 20 different amino acids used to make proteins. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and our physical makeup (making up our muscle, ligaments, tendons, hair, and nails!), and transporting molecules from one location to another. Amino acids Peptide Protein Figure 3-2. Polymerised amino acids fold into a protein. Why study the structure of proteins? As proteins carry out or catalyse almost all of the vitally important processes that keep our bodies alive, it is important that we understand how proteins work, and how they work together. Knowing the structure of a protein is important because the structure of a protein determines its function. Similar to the structure that we call a ‘chair’; it has four legs, a seat and a back rest. We use this ‘chair structure’ to sit on, not to e.g. eat from. Although there are many types of chairs, they all have the same basic structure, and thus have the same function. The same applies to proteins. There are a number of ways in which the structure of a protein can be determined. The most common method is called “protein crystallography” (see box below). Other commonly used methods to determine protein structure include electron cryo-microscopy (which works particularly well for very large proteins), and NMR spectroscopy. 6  Our knowledge of protein structure/architecture has come principally from X-ray crystallography. The protein of interest is isolated and protein crystals are grown. X-rays are shot at the protein crystal and are scattered by the electrons in the protein molecules making up the crystal. The scattered waves recombine to form a diffraction pattern that can be recorded on an X-ray sensitive surface. The pattern depends on the atomic arrangement in the crystal and may be converted mathematically to an electron density map from which the molecular model is built. Improvements in nuclear magnetic resonance spectroscopy (NMR have allowed the structures of small proteins to be determined. Figure 3-3. Schematic of the X-ray crystallography technique (left, Whitford, p.350) and an X-ray diffraction photograph of a glutathione synthetase crystal (right, Campbell and Farrell 7th ed, p.96). 7 Figure 3-4. Examples of actual protein structures. These structures, which have all been experimentally determined, help to illustrate the huge range in size and structure of various proteins found in the human body. Figure adapted from PDB Molecular Machinery poster. Some key functions of proteins in our cells Below are listed some examples of important functions in our bodies where proteins play a vital role. For each of these functions, one example is listed. However, as you will learn throughout this course, each of these important functions is actually mediated by a large number of different proteins each playing their particular role in the overall process. Cell signalling – e.g., insulin Digestion – e.g., trypsin, amylase Metabolism – e.g., hexokinase, alcohol dehydrogenase Oxygen transport – e.g., haemoglobin Immune protection – e.g., antibodies Energetics – e.g., ATP synthase Replication and maintenance – e.g., DNA polymerase, RNA polymerase 8