Bioc 192 Lecture 3 - Introduction To Proteins PDF

BIOC 192 Lecture 3 Introduction to Proteins Diversity of protein structure and function Role of proteins in the cell Professor Kurt Krause Department of Biochemistry Twitter: @otagobiochemist Fa...

BIOC 192 Lecture 3 Introduction to Proteins Diversity of protein structure and function Role of proteins in the cell Professor Kurt Krause Department of Biochemistry Twitter: @otagobiochemist Facebook: Biochemistry.Otago Slide 1  The content and delivery of all resources in this course are subject to copyright and may be used only for the University’s educational purposes. Lecture slides, booklets and learning resources contain material used under copyright licenses for the purposes of teaching. You may access this material for your private study or research but may not make further copies or distribute these materials for any purpose, or in any other form, whether with or without charge. Twitter: @otagobiochemist Facebook: Biochemistry.Otago Slide 2  References for Lecture 3 – Introduction to Proteins are: Lecture Booklet: Part 1 – Proteins, pages 5-8 Textbook References: Chapter 1, “Basic molecular themes of life” pages 14-15, “Proteins”, in your textbook OR Chapter 4, “The Three-Dimensional Structure of Proteins”, page 78, section 4.1 only, in Campbell et al. Twitter: @otagobiochemist Facebook: Biochemistry.Otago Slide 3  Learning Objectives 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 examples of proteins involved in immune defense, digestion and metabolism, DNA and RNA replication, oxygen transport Understand the crowded cellular environment in which proteins function within the cell Slide 2  Why Study Proteins? Proteins are the workhorses of the cell. They are giant molecules that can be described as nanostructures or tiny molecular machines. Recall the fundamental issues faced by a cell to ensure its survival: How does it sense and respond to its environment? How does it obtain the energy it needs? How does it maintain and replicate itself? How does it make and break molecules? Turns out that for most of these questions – proteins are the answer! Slide 3  Why Study Proteins? Some proteins form much of our physical makeup, including muscle, ligaments, tendons, even hair and nails. Other proteins carry out or catalyse almost all of the processes required to sense and respond to the environment, to grow and replicate, to acquire needed energy to fuel all these processes, and to make and break down molecules. That is … to help the cell to live. Proteins are understood now better than ever before. In many cases we know the complete atomic structures of proteins even down to the position of all of their atoms. Slide 4  Getting Started What exactly is a protein? What are proteins made of? How do the pieces fit together? How and why do they form so many complicated shapes? What is the best way to look at these shapes? What are some roles they play in the cell? First steps… Slide 5  Primer on Protein Structure Proteins are non-branching polymers that form macromolecules about 50 - 100 Å in size (1Å = 10-10 m). Each protein is composed of a specific sequence of amino acids joined together by chemical bonds called peptide bonds. Each protein has a distinct unique sequence. There are only 20 different amino acids used to make proteins. But they are arranged in a different order and Ribonuclease A a different length in each different protein. Slide 6  Proteins are Chemicals - just big and very capable People are often comfortable thinking about lots of different molecules, like methane, oxygen or water, but often not so much with proteins. But proteins are actually just molecules, albeit very large! Compare and contrast some common molecules Table salt – NaCl – tasty Table sugar – a glucose-fructose combination called sucrose – also tasty! Proteins – polymer made of up amino acids – sometimes tasty as in “cheese” – mostly protein, sometimes not as in ”hair” – also protein Looking at some examples - table salt, sucrose, haemoglobin Slide 7 Pictures of some common chemicals Sodium Chloride Sucrose Haemoglobin Table salt Table sugar A protein found in red blood cells Molecular Mass 58.4 Molecular Mass 342.3 Molecular Mass 64,458 Slide 8 Why Study the Structure of Proteins? Understanding protein function is a key to understanding the biochemistry of life. To really understand function, you need to know structure. Think of a lock and key, a bicycle, an airplane… Imagine trying to explain how they work without knowing what they look like. By “protein structure” I mean the 3D arrangement of the atoms of a protein. We know more protein structures than ever before. Slide 9  Atomic structure determination of proteins is routinely done now Decades of work have taken place in three areas of science to enable the routine determination of protein structures. Protein crystallography Cryo-electron microscopy NMR spectroscopy More than 25 Nobel prizes have been awarded in these areas. Most research-intensive universities including the University of Otago have research on protein structure. Almost all completed protein structures are publicly available at locations like the Protein Data Bank, aka the PDB Slide 10 Different Ways of Depicting Chemical Structure Skeletal Stryer, Biochemistry,3rd edition Ball and Stick Space-filling ATP Hydrogens are sometimes omitted from these structures for clarity Slide 11 Examples of Actual Protein Structures PDB, Rutgers, 2002 Space-filling structures of proteins Slide 12 Examples of Protein Structure Protein Data Bank, 2002 Slide 13 Cell Signalling - Hormone After a meal, insulin is generated and binds to the insulin receptor to signal cells to take up glucose. Insulin is a hormone. Protein Data Bank, www.rcsb.org, 2002, 2014 Slide 14  Digestion Protein Data Bank, rcsb.org, 2002, 2014 Trypsin Trypsin is an enzyme that breaks down proteins during digestion. Enzymes that breakdown proteins are called proteases Slide 15  HIV Protease Viruses and bacteria make proteins, like proteases too. They use pretty much the same amino acid building blocks as humans. HIV makes a protease that is essential for HIV replication. Here is its structure with and without a bound inhibitor (green). Some HIV drugs target this protease. Slide 16  Digestion Protein Data Bank, rcsb.org, 2002, 2014 Amylase is an enzyme that breaks down starch into sugars. It is found in saliva as well as pancreatic juices. Slide 17  Metabolism Protein Data Bank, rcsb.org, 2002, 2014 Alcohol dehydrogenase is an enzyme that helps to metabolise ethanol. Enzymes catalyse biochemical reactions. Slide 18  Metabolism Protein Data Bank, rcsb.org, 2002, 2014 Hexokinase is an enzyme that adds a phosphate to glucose, after glucose is taken up by the cell. Kinases are enzymes that usually add phosphate to molecules. Two hexokinases are shown here. Slide 19 Oxygen Transport - Metabolism Protein Data Bank, rcsb.org, 2002, 2014 Haemoglobin binds oxygen in the lungs and carries it in the blood to tissues for use in metabolism. Slide 20 Metabolism and Energetics - Membrane Proteins Protein Data Bank, rcsb.org, 2002, 2014 ATP synthase is a remarkable membrane protein that generates ATP for use in cellular functions. Slide 21  Immune Protection Antigens Antigens bind here bind here Protein Data Bank, rcsb.org, 2002, 2014 Antibody Antibodies bind to antigens found on cellular invaders like bacteria and viruses. Antibody binding to antigens can help protect the body from infections. Slide 22 SARS-CoV2 Remember the Spike protein from SARS- Cov2. It can be targeted by protective antibodies Spike Protein Protein Data Bank, 2020 Slide 23 SARS-CoV2 Taka et al, 2020, BioRiv Slide 24  Blocking SARS-CoV2 Therapeutic Antibody fragments Protein Data Bank, 2020 Spike Protein Slide 25  Replication and Maintenance Protein Data Bank, rcsb.org, 2002, 2014 DNA polymerase binds to one strand RNA polymerase creates a single of DNA and adds the complementary strand of RNA that is complementary strand to it to one of the strands of duplex DNA Slide 26 Replication and Maintenance Protein Data Bank, rcsb.org, 2002, 2014 Tiny Molecular Machine RNA polymerase creates a single strand of RNA that is complementary to one of the strands of duplex DNA Slide 27 Yin, W., UT-Austin, 2004 Yin, W., UT-Austin, 2004 Slide 28 Cells as a bag of proteins, lipids and nucleic acids yourgenome.org Simple diagram of eukaryotic cell Slide 29 Slightly more complicated illustration of a cell Cells as a bag of proteins, lipids and nucleic acids Model of packed cellular interior David Goodsell, TIBS, 2013 Benjamin Cummings, Pearson Education, Inc. 2004 Cells are very crowded inside! Ribosomes, enzymes, RNA … Slide 30  Inside of a bacterial cell Cells as a bag of proteins, David Goodsell, TIBS, 2013 lipids and nucleic acids Slide 31 Complex model of a single vesicle inside of a cell Takamori et al, Cell, 2006 Slide 32  Simulation of proteins in a cell In the next three lectures we will learn more about amino acids, elements of protein structure, families of protein structure, protein folding in health and disease But I want to leave you with this creative and insightful dynamic view of proteins and other macromolecules packed in a cell - https://youtu.be/uHeTQLNFTgU Slide 33 Objective-based self-assessment – Lecture 3 1. What are proteins polymers of? 2. How many standard amino acids are there? 3. What is the name of the bond that links amino acids in the polypeptide chain? 4. Does each protein have a unique sequence of amino acids? Explain. 5. Why is it important to know and understand protein structure? 6. What are the main techniques used to determine protein structure? 7. Name a protein that is involved in: DNA replication RNA replication Oxygen transport Immune protection Digestion Metabolism Slide 34