PHGY 170 Module 02: Human Cell Physiology PDF

PHGY 170 oiw HUMAN CELL PHYSIOLOGY MODULE 02 THE NUCLEUS AND ENDOMEMBRANE SYSTEM Please note: This course was designed to be interacted and engaged with using the online modules. This Module Companion Guide is a resource created to complement the online slides. If there is a discrepancy between this guide and the online module, please refer to the module. How can you help protect the integrity and quality of your Queen’s University course? Do not distribute this Module Companion Guide to any students who are not enrolled in PHGY 170 as it is a direct violation of the Academic Integrity Policy of Queen’s University. Students found in violation can face sanctions. For more information, please visit https://www.queensu.ca/academic- calendar/health-sciences/bhsc/. MODULE 02 COMPANION GUIDE PHGY 170 TABLE OF CONTENTS INTRODUCTION..................................................................................................................................................... 6 Video: Introduction to Module 02................................................................................................................... 6 Module 02: Module Learning Outcomes........................................................................................................ 7 Module Assessments........................................................................................................................................ 7 Course Icons...................................................................................................................................................... 8 Module Outline.................................................................................................................................................. 8 SECTION 01: The Nucleus and DNA Packaging.................................................................................................. 9 Introduction toThe Nucleus and DNA Packaging.......................................................................................... 9 The Nucleus....................................................................................................................................................... 9 Function of the Nucleus.................................................................................................................................10 Components of the Nucleus..........................................................................................................................11 DNA Packaging.................................................................................................................................................12 Levels of DNA Packaging................................................................................................................................13 Level 2: Nucleosomes (“Beads on a String”).................................................................................................13 Level 3: Chromatin Fibre................................................................................................................................15 Level 4: Chromatin Looped Domains............................................................................................................15 Level 5: Heterochromatin...............................................................................................................................15 Euchromatin vs Heterochromatin.................................................................................................................16 Video: DNA Packaging.....................................................................................................................................17 Checkpoint Activity Nucleus Structures and Functions..............................................................................18 Checkpoint Activity: DNA Packaging..............................................................................................................18 Section 01: Summary......................................................................................................................................19 SECTION 02: The Endomembrane System.......................................................................................................20 Introduction to The Endomembrane System..............................................................................................20 The Endomembrane System..........................................................................................................................20 Overview of the Endomembrane System.....................................................................................................21 Cargo Transport in the Endomembrane System.........................................................................................23 Video: Introduction to the Endoplasmic Reticulum (ER).............................................................................24 The Endoplasmic Reticulum...........................................................................................................................25 The RER and Ribosomes.............................................................................................................................25 The SER.........................................................................................................................................................26 Vesicle-Mediated Transport...........................................................................................................................27 HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 2 MODULE 02 COMPANION GUIDE PHGY 170 Golgi Networks: Cis, Medial, and Trans.........................................................................................................27 Trans Golgi Network........................................................................................................................................29 Video: Golgi Apparatus Review......................................................................................................................30 Endosomes, Lysosomes, and Peroxisomes.................................................................................................31 Video: Endomembrane System Review........................................................................................................32 Checkpoint Activity: Endomembrane System Organelles..........................................................................34 Checkpoint Question: Modification in the Golgi Apparatus.......................................................................35 Section 02: Summary......................................................................................................................................35 SECTION 03: Protein Modifications and Levels of Protein Folding................................................................37 Introduction to Protein Modifications and Levels of Protein Folding.......................................................37 Targeting Proteins in the Cell.........................................................................................................................37 Protein Transportation into the Endomembrane System..........................................................................38 Translocation Into the ER................................................................................................................................39 Embedding Into the Lipid Membrane...........................................................................................................40 Post-Translational Modifications of Proteins by the ER..............................................................................41 Modifications of Proteins by the ER...............................................................................................................42 The Hierarchy of Protein Structures.............................................................................................................43 Peptide Bond...................................................................................................................................................43 Protein Structure.............................................................................................................................................45 Primary (1°) Protein Structure...................................................................................................................45 Secondary (2°) Protein Structure..............................................................................................................46 Tertiary (3°) Protein Structure...................................................................................................................47 Quaternary (4°) Protein Structure.............................................................................................................48 Domains...........................................................................................................................................................49 Examples of Domains.....................................................................................................................................49 Video: Protein Structures Review..................................................................................................................50 Extra Resources...............................................................................................................................................51 Protein Shape and Function...........................................................................................................................51 How Structure Affects Function.....................................................................................................................52 Types of Protein Changes...............................................................................................................................53 Checkpoint Question: DNA Packaging vs Protein Folding..........................................................................54 Protein Transportation From the ER.............................................................................................................54 Checkpoint Question: Transport From the ER to the Golgi Apparatus.....................................................55 HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 3 MODULE 02 COMPANION GUIDE PHGY 170 Checkpoint Question: Protein Translocation...............................................................................................55 Section 03: Summary......................................................................................................................................56 SECTION 04: Vesicle Trafficking in the Endomembrane System....................................................................57 Introduction to Vesicle Trafficking in the Endomembrane System...........................................................57 Vesicle-Mediated Transport...........................................................................................................................57 1a. Cargo Selection..........................................................................................................................................58 1b. Coat Proteins.............................................................................................................................................59 2. Budding........................................................................................................................................................60 3. Scission.........................................................................................................................................................61 4. Uncoating.....................................................................................................................................................61 5. Transport......................................................................................................................................................62 6 & 7. Tethering and Docking.........................................................................................................................62 8. Fusion...........................................................................................................................................................63 9. Disassembly.................................................................................................................................................64 Checkpoint Question: COPII Coat Protein....................................................................................................64 Checkpoint Question: Vesicle Transportation.............................................................................................64 Checkpoint Activity: Clathrin..........................................................................................................................65 Section 04: Summary......................................................................................................................................65 SECTION 05: Exocytosis and Endocytosis.........................................................................................................66 Introduction to Exocytosis and Endocytosis................................................................................................66 Stages of Exocytosis........................................................................................................................................66 Regulation of Exocytosis in the Cell..............................................................................................................67 Endocytosis: Import of Cargo.........................................................................................................................68 The Endocytic Pathway...................................................................................................................................68 Step 1: Formation of the Endosome.........................................................................................................69 Step 2: The Early Endosome......................................................................................................................70 Step 2: The Early Endosome......................................................................................................................71 Step 3: The Late Endosome.......................................................................................................................72 Step 4: The Lysosome.................................................................................................................................73 Checkpoint Activity: The Exocytic Pathway and Proteins...........................................................................73 Checkpoint Question: Exocytosis in the Human Body................................................................................74 Checkpoint Question: Endocytosis Review..................................................................................................74 Checkpoint Question: Acidity and the Early Endosome.............................................................................75 HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 4 MODULE 02 COMPANION GUIDE PHGY 170 Checkpoint Question: Early to Late Endosome...........................................................................................75 Section 05: Summary......................................................................................................................................75 CONCLUSION.......................................................................................................................................................77 Module Conclusion.........................................................................................................................................77 Module Complete............................................................................................................................................77 Module 02: Credits..........................................................................................................................................77 HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 5 MODULE 02 COMPANION GUIDE PHGY 170 INTRODUCTION Please see the online learning module for the full experience of interactions within this document. VIDEO: INTRODUCTION TO MODULE 0 2 This content was retrieved from Introduction Slide 1 of 5 of the online learning module. Welcome to Module 02 of PHGY 170: Human Cell Physiology! In this module, you will learn about the structure and function of the nucleus and the endomembrane system. The nucleus is one of the most important cellular structures because it contains the genetic material that is responsible for controlling all activities within the cell. The endomembrane system compartmentalizes the cell and is essential for the production and transportation of proteins. Throughout this module you will explore DNA packaging, protein modifications and folding, as well as cellular transportation processes. Watch the video for an introduction to Module 02 from a content specialist. (12:45) Start of Video Transcript: Hello, I am Dr. Cindy Pruss, one of your PHGY 170 content experts. In Module 02, we're exploring the nucleus, and the endomembrane system. You'll begin by learning about the nucleus, and how DNA is packaged inside it. The nucleus is the protector of our DNA and that DNA is transcribed into MRNA to be later translated into proteins in the cytosol and endoplasmic reticulum. You will also be learning about the structures of the endomembrane system, including the endoplasmic reticulum, Golgi Apparatus, endosomes, lysosomes, and peroxisomes. This group of organelles is essential for the production, breakdown, and transportation of proteins and other macromolecules. Next, you will explore how proteins have a hierarchy in folding from the primary sequence of amino acids, to the secondary, tertiary, and quaternary structures and how this folding and other modifications occur in the endoplasmic reticulum and Golgi Apparatus of the cell. Finally, you will delve into the individual steps of vesicle mediated transport and then finish with the processes of endocytosis and exocytosis. Thank you for watching this introduction to Module 02. End of Video Transcript. Page Link: https://player.vimeo.com/video/738390476?h=9b65ce5ea0 HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 6 MODULE 02 COMPANION GUIDE PHGY 170 MODULE 02: MODULE LEARNING OUTCOMES This content was retrieved from Introduction Slide 2 of 5 of the online learning module By the end of Module 02, you will be able to: 1. Describe the structure and function of the various components of the nucleus. 2. Identify and describe the structures and bonds involved in the DNA double helix and in the higher levels of DNA packaging. 3. Describe the structure and function of the different components of the endoplasmic reticulum. 4. Articulate how proteins are folded and modified in the cell and the levels of protein folding. 5. Explain how the endomembrane system and, specifically, how the Golgi apparatus functions. 6. Describe how vesicle-mediated transport works including how cargo is targeted to different cellular locations. MODULE ASSESSMENTS This content was retrieved from Introduction Slide 3 of 5 of the online learning module There are assessments associated with this module. At the end of this module, you will answer questions that will assess your understanding of the learning outcomes for the module. It is recommended that you read these learning outcomes and work to understand them as you progress through the content. For specific details about your module assessments, visit the assessment page in your online learning environment. Learning Outcomes Assignment At the end of this module, you will answer questions that will assess your understanding of the learning outcomes for the module. It is recommended that you read these questions and work on them as you progress through the content. For specific details about this assessment, visit the assessment page in your online learning environment. Discussion Question At the end of this module, you will work in small groups to answer a discussion question relevant to the concepts you learned in this module. These questions are extensions and designed to deepen your understanding of the larger themes in the module and course. For specific details about this assessment, visit the assessment page in your online learning environment. Activities Throughout the Module: HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 7 MODULE 02 COMPANION GUIDE PHGY 170 Note that responses to questions within the learning modules will not be graded unless otherwise specified. These are here to help you gauge your learning. However, your responses to these interactions are recorded in the module and viewable to the instructor(s). COURSE ICONS This content was retrieved from Introduction Slide 4 of 5 of the online learning module As you navigate the course modules, you will come across these course icons. Continue to learn its purpose and function. Audio Clip This icon indicates the presence of an audio clip on the slide from your instructor or other content experts. To play the audio clip, click the play button. Full transcripts and closed captions are available. Reference This icon lives in the sidebar of the slides. Clicking it will reveal the references for content and/or images on the slide. Process This icon lives in the sidebar of the slides. It will appear when there is a process or concept being described over multiple slides. Clicking it will reveal the full process or concept being described. MODULE OUTLINE This content was retrieved from Introduction Slide 5 of 5 of the online learning module Section 01: The Nucleus and D N A Packaging – Refer to page 9 Section 02: The Endomembrane System – Refer to page 20 Section 03: Protein Modifications and Levels of Protein Folding – Refer to page 37 Section 04: Vesicle Trafficking in the Endomembrane System – Refer to page 56 Section 05: Exocytosis and Endocytosis – Refer to page 65 End of Introduction HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 8 MODULE 02 COMPANION GUIDE PHGY 170 SECTION 01: THE NUCLEUS AND D NA PACKAGING INTRODUCTION TOTHE NUCLEUS AND DNA PACKAGING This content was retrieved from Section 01 Slide 1 of 15 of the online learning module In this section, you will learn about the foundational structures and function of the nucleus. You will find out how the genome is carefully organized within the nucleus in a way that allows active genes to be accessible for transcription, and for the chromosomes to be safely packed in the process of cell division. Specifically, you will learn about the five levels of DNA packaging: 1. The DNA double helix 2. Nucleosomes 3. Chromatin fibres 4. Chromatin looped domains 5. Heterochromatin If you stretched out DNA from a single human cell, it would be about two metres long. THE NUCLEUS This content was retrieved from Section 01 Slide 2 of 15 of the online learning module The primary function of the nucleus is to carefully protect the cell’s DNA, which is an essential task since DNA stores all of the information necessary for a cell to survive. Since the nucleus has such an important role in the cell, it is essential that it is protected from other cell processes. Some ways it isolates itself from the rest of the cell include: Having a special double layered membrane, called the nuclear envelope Using very selective nuclear pores Having a unique fluid, called the nucleoplasm Remember, these structures all serve to keep the DNA protected. Without DNA, the cell cannot function. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 9 MODULE 02 COMPANION GUIDE PHGY 170 The nucleus is the leader of the cell. It sends commands to the rest of the cell and stores all of the information (or “laws”) a cell needs to function. These “laws” are stored in the nucleus as DNA. FUNCTION OF THE NUCLEUS This content was retrieved from Section 01 Slide 3 of 15 of the online learning module. To protect the DNA and allow genes to function, the nucleus needs to accomplish three tasks: 1. Allow DNA to be replicated and transcribed into mRNA when needed. 2. Regulate which molecules can access the DNA and separate the DNA from other cell compartments. 3. Keep the DNA organized. DNA is fragile and easily damaged, so any problems with DNA will lead to major problems in the cell and body. To accomplish these tasks, there are five key components of the nucleus that work together to fulfill these tasks while protecting the DNA. These include the nuclear envelope, nuclear pores, the nucleolus, the nucleoplasm and nuclear matrix, and the chromosomes and chromatin. The five components of the nucleus that allow it to perform its key functions. Reference: HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 10 MODULE 02 COMPANION GUIDE PHGY 170 OpenStax. (2021, November 9). Anatomy and Physiology—The Nucleus and DNA Replication. OpenStax CNX. Retrieved March 2022, from: https://cnx.org/contents/9TxHOD3O@12/The-Nucleus-and-DNA- Replication#fig-ch03_03_01 COMPONENTS OF THE NUCLEUS This content was retrieved from Section 01 Slide 4 of 15 of the online learning module These five key components of the nucleus help protect DNA by regulating nucleus access, compartmentalizing DNA, and by keeping DNA organized. Learn more about the function of each structure. Nuclear Envelope The nuclear envelope controls what molecules have access to the nucleus, and separates the D N A from other cell compartments. It is a double membrane structure that encloses the nuclear material. The outer membrane of the nuclear envelope is connected to the endoplasmic reticulum (E R), which is important for making proteins. Chromatin & Chromosomes Strands of DNA are organized and stored in chromatin that make up chromosomes within the nucleus: Chromatin is a complex of DNA and proteins forming highly organized fibres and is located in different defined areas of the nucleus. Some areas will be actively transcribed into mRNA. Chromosomes are highly condensed chromatin found in the nucleus only during cell division. Nucleolus The nucleolus creates ribosomal RNAs (rRNA) and assembles them into the ribosomal subunits used by the cell to translate proteins. The nucleolus is the site of high amounts of rRNA gene transcription, and the DNA that encodes these genes is organized here. Nucleoplasm & Nuclear Matrix HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 11 MODULE 02 COMPANION GUIDE PHGY 170 The nucleoplasm is a viscous, water-based fluid that is enclosed in the nuclear envelope. The main function of the nucleoplasm is to serve as a suspension substance for the nuclear contents. It contains dissolved molecules and ions that are essential for the functions of the nucleus. The nuclear matrix is a network of filaments within the nucleoplasm that helps to organize chromosomes into compartments and provides the scaffold to maintain the shape and structure of the nucleus. Nuclear Pores The nuclear envelope contains pores which regulate molecular traffic in and out of the nucleus. Small molecules like water and oxygen can pass through the membrane freely. Nuclear pore complexes (NPCs) form the gateways in the nuclear pores of the nuclear membrane. These NPCs regulate the movement of large molecules (e.g., proteins and mRNA) into and out of the nucleus. Reference: OpenStax. (2021, November 9). Anatomy and Physiology—The Nucleus and DNA Replication. OpenStax CNX. Retrieved March 2022, from: https://cnx.org/contents/9TxHOD3O@12/The-Nucleus-and-DNA- Replication#fig-ch03_03_01 DNA PACKAGING This content was retrieved from Section 01 Slide 5 of 15 of the online learning module Since cells are only microns in size, it has to carefully package DNA into the nucleus. In doing so, it can adjust its organization to access the genes it needs and tightly package the DNA it does not need. This is one of the main ways the cell is able to protect the DNA, as well as regulate which genes are being transcribed in the nucleus and then later translated in the cytoplasm* of the cell. Definitions*: Cytoplasm: the contents of the cell outside the nucleus that are contained by the plasma membrane. This includes other organelles like the endoplasmic reticulum. Reference: Adapted from Plopper, G., & Ivankovic, D. B. (2020). Principles of Cell Biology (3rd ed., pp. 78). Jones & Bartlett Learning, LLC. Retrieved March 2022, from: http://ebookcentral.proquest.com/lib/queen- ebooks/detail.action?docID=6002586 HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 12 MODULE 02 COMPANION GUIDE PHGY 170 LEVELS OF DNA PACKAGING This content was retrieved from Section 01 Slide 6 of 15 of the online learning module There are five levels of DNA packaging. You have already learned about the first level of DNA packaging, which is the DNA double helix. On the next slides, you will learn about levels 2 through 5 of DNA packaging in more detail. LEVEL 2: NUCLEOSOMES (“BEADS ON A STRING”) This content was retrieved from Section 01 Slide 7 of 15 of the online learning module DNA is wrapped twice around proteins, called histones, which shortens the DNA seven-fold. The DNA- wrapped histones structurally resemble a series of beads on a string and are called nucleosomes. The DNA is the “string” which is then wound onto the individual nucleosomes, which are the “beads.” The nucleosomes are separated by linker-DNA to form the “beads-on-a-string” structure. Continue to learn about the components of a nucleosome. Octamer of Core Histones Eight core histones form one nucleosome in a unit known as an octamer. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 13 MODULE 02 COMPANION GUIDE PHGY 170 Histone H1 Histone H1 is a protein that pins the core DNA to the core particle on the histone octamer. Core DNA Approximately 200 base pairs (bp) of DNA are wrapped around the core histones. This section of DNA is referred to as the core DNA. Linker DNA Linker DNA connects nucleosome “beads” like a string. It is the DNA between core DNA sequences. Process References: Adapted from Plopper, G., & Ivankovic, D. B. (2020). Principles of Cell Biology (3rd ed., pp. 232). Jones & Bartlett Learning, LLC. Retrieved March 2022, from: http://ebookcentral.proquest.com/lib/queen- ebooks/detail.action?docID=6002586 Adapted from Darekk2. (2012). Nucleosome organization. Wikimedia Commons. Retrieved March 2022, from: https://commons.wikimedia.org/w/index.php?curid=21977693 HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 14 MODULE 02 COMPANION GUIDE PHGY 170 LEVEL 3: CHROMATIN FIBRE This content was retrieved from Section 01 Slide 8 of 15 of the online learning module The third level of packaging involves the string of nucleosomes coiled into a spiraling fibre, called a chromatic fibre. This forms a helical structure with a diameter of approximately 30 to 40 nm. This shortens the DNA 42-fold. Reference: Adapted from Plopper, G., & Ivankovic, D. B. (2020). Principles of Cell Biology (3rd ed., pp. 241). Jones & Bartlett Learning, LLC. Retrieved March 2022, from: http://ebookcentral.proquest.com/lib/queen- ebooks/detail.action?docID=6002586 LEVEL 4: CHROMATIN LOOPED DOMAINS This content was retrieved from Section 01 Slide 9 of 15 of the online learning module The 30-40 nm chromatin fibre made of nucleosomes is formed into loops with an average length of 300 nm. This shortens the DNA 750-fold. Reference: Adapted from Plopper, G., & Ivankovic, D. B. (2020). Principles of Cell Biology (3rd ed., pp. 241). Jones & Bartlett Learning, LLC. Retrieved March 2022, from: http://ebookcentral.proquest.com/lib/queen- ebooks/detail.action?docID=6002586 LEVEL 5: HETEROCHROMATIN This content was retrieved from Section 01 Slide 10 of 15 of the online learning module HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 15 MODULE 02 COMPANION GUIDE PHGY 170 In level 5, the folded/twisted looped domains formed by DNA are further compressed and folded into lengths of approximately 700 nm. This heterochromatin is hyper-condensed DNA. It is present in inactive regions of chromosomes (interphase). Heterochromatin is further condensed into entire chromosomes when cells are undergoing mitosis or meiosis (cell division). Reference: Adapted from Plopper, G., & Ivankovic, D. B. (2020). Principles of Cell Biology (3rd ed., pp. 241). Jones & Bartlett Learning, LLC. Retrieved March 2022, from: http://ebookcentral.proquest.com/lib/queen- ebooks/detail.action?docID=6002586 EUCHROMATIN VS HETEROCHROMATIN This content was retrieved from Section 01 Slide 11 of 15 of the online learning module Levels 1 to 4 of DNA packaging are called euchromatin. At these levels, DNA is active, meaning that it can be easily accessed by proteins responsible for: Replicating the chromosomes. Reading a strand of DNA to make RNA. Level 5 of DNA organization is called heterochromatin. At this level, DNA is condensed beyond loop domains and is rendered essentially inactive. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 16 MODULE 02 COMPANION GUIDE PHGY 170 Reference: Adapted from Plopper, G., & Ivankovic, D. B. (2020). Principles of Cell Biology (3rd ed., pp. 241). Jones & Bartlett Learning, LLC. Retrieved March 2022, from: http://ebookcentral.proquest.com/lib/queen- ebooks/detail.action?docID=6002586 VIDEO: DNA PACKAGING This content was retrieved from Section 01 Slide 12 of 15 of the online learning module Now that you have explored the levels of DNA packaging, this video will summarize what you have learned. Watch the video to review the levels of DNA packaging. (1:42) As you watch, focus on the level of magnification needed to analyze each level of DNA packaging. Start of Video Transcript: In this animation we'll see the remarkable way our DNA is tightly packed up to fit into the nucleus of every cell. The process starts with assembly of a nucleosome, which is formed when eight separate histone protein subunits attach to the DNA molecule. The combined tight loop of DNA and protein is the nucleosome. Multiple nucleosomes are coiled together, and these then stack on top of each other. The end result is a fiber of packed nucleosomes known as a chromatin. This fiber, which at this point is condensed to a thickness of thirty nanometers, is then looped and further packaged using other proteins which are not shown here. This remarkable multiple folding allows six feet of DNA to fit into the nucleus of each cell in our body; an object so small that ten thousand nuclei could fit on the tip of a needle. The end result is that the DNA is tightly packed into the familiar structures we can see through a microscope, chromosomes. It is important to realize that chromosomes are not always present. They form only when cells are dividing. At other times as we can see here at the end of cell division, our DNA becomes less highly organized. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 17 MODULE 02 COMPANION GUIDE PHGY 170 End of Video Transcript. Page Link: https://www.youtube.com/embed/gbSIBhFwQ4s?ecver=1 Reference: DNA Learning Center. (2010, March 22). How DNA is Packaged (Advanced). [Video]. Retrieved March, 2022 from: https://www.youtube.com/watch?v=gbSIBhFwQ4s CHECKPOINT ACTIVITY NUCLEUS STRUCTURES AND FUNCTIONS This content was retrieved from Section 01 Slide 13 of 15 of the online learning module Select the term from the drop down menu to match the functions of the nucleus to their components. List of components: Nucleoplasm and Nuclear Matrix, Chromatin, Nuclear Envelope, Nuclear Pores and NPCs, Nucleolus Function Component Contains nuclear nutrients and a network of filaments provides organization to the DNA. An organized form of DNA. Prevents unwanted material from entering nucleus, connects to the ER. Allows large molecules to enter and exit the nucleus. Organizes chromatin for genes that encode rRNA, production site of ribosomes. Feedback: Function Component Contains nuclear nutrients and a network of filaments provides Nucleoplasm and Nuclear Matrix organization to the DNA. An organized form of DNA. Chromatin Prevents unwanted material from entering nucleus, connects to Nuclear Envelope the ER. Allows large molecules to enter and exit the nucleus. Nuclear Pores and NPCs Organizes chromatin for genes that encode rRNA, production Nucleolus site of ribosomes. CHECKPOINT ACTIVITY : DNA PACKAGING This content was retrieved from Section 01 Slide 14 of 15 of the online learning module Select the correct level from the drop down menu to match each description. List of Levels: Level 1: DNA Double Helix, Level 2: Nucleosomes (Beads on a String), Level 3: 30- to 40- nm Chromatin Fibre, Level 4: Chromatin Looped Domains, Level 5: Heterochromatin HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 18 MODULE 02 COMPANION GUIDE PHGY 170 Description Level DNA is wrapped twice around the proteins, called histones, which shortens the DNA 7-fold. Looped domains are compressed and folded, DNA is inaccessible. The 30-40 nm chromatin fibre made of nucleosomes is formed into loops, which shortens DNA 750-fold. DNA in its least packed state. The string of nucleosomes is coiled into a spiraling fibre. Feedback: Description Level DNA is wrapped twice around the proteins, called histones, Level 2: Nucleosomes (Beads which shortens the DNA 7-fold. on a String) Looped domains are compressed and folded, DNA is Level 5: Heterochromatin inaccessible. The 30-40 nm chromatin fibre made of nucleosomes is formed Level 4: Chromatin Looped into loops, which shortens DNA 750-fold. Domains DNA in its least packed state. Level 1: DNA Double Helix The string of nucleosomes is coiled into a spiraling fibre. Level 3: 30- to 40-nm Chromatin Fibre SECTION 01: SUMMARY This content was retrieved from Section 01 Slide 15 of 15 of the online learning module In this section, you learned about the nuclear structures that facilitate the nucleus’ primary functions, which is to protect the cell’s DNA and control the molecules that can access it. These structures include the nuclear envelope, nuclear pores, nucleoplasm and nuclear matrix, the nucleolus, and chromatin and chromosomes. Then you learned there are five levels of DNA packaging: the DNA double helix, nucleosomes (“beads on a string”), chromatin fibre, chromatin looped domains, and heterochromatin. You learned about the utility of each of these structures, and connected the levels of packed DNA to euchromatin and heterochromatin. By successfully protecting the DNA, while providing it a location to be replicated and transcribed, the nucleus works as a command centre of the cell. The nucleus allows DNA to be safely stored and used to produce the RNA that can then be exported and used to generate proteins necessary for the cell to survive. In the next section, you will explore the endoplasmic reticulum and the endomembrane system, and see how they work to follow the “orders” of the nucleus and function. End of Section 01 HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 19 MODULE 02 COMPANION GUIDE PHGY 170 SECTION 02: THE ENDOMEMBRANE SYSTEM INTRODUCTION TO THE ENDOMEMBRANE SYSTEM This content was retrieved from Section 02 Slide 1 of 15 of the online learning module In this section, you will explore each of the structures of the endomembrane system. This will include the rough ER (RER), the smooth ER (SER), and the Golgi apparatus. You will learn about the organelles within these structures and their unique components. You will learn how after mRNA leaves the nucleus, it is transcribed at the rough ER, and how those proteins are further processed and transported to their final location using a cellular system termed the endomembrane system. The endomembrane system. Reference: CNX OpenStax, CC BY 4.0 , via Wikimedia Commons. Retrieved March 2022, from: https://upload.wikimedia.org/wikipedia/commons/4/49/OSC_Microbio_03_04_Endomemb.jpg THE ENDOMEMBRANE SYSTEM This content was retrieved from Section 02 Slide 2 of 15 of the online learning module The endomembrane system is the linked machinery that processes the transport of cargo* throughout the cell. Exocytosis is the process of moving cargo out of the cell using the the exocytic pathway*. Endocytosis is the process of transporting cargo into the cell using the endocytic pathway*. The cell has produced many intracellular membranes, or barriers, to compartmentalize the activities of different organelles, as well as developed a difficult-to-permeate plasma membrane, separating itself from the extracellular space. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 20 MODULE 02 COMPANION GUIDE PHGY 170 Definitions*: Cargo: Throughout this module, proteins, lipids, and other macromolecules that are transported throughout the cell will be referred to as cargo. Exocytic Pathway: The process by which a cell directs the contents of secretory vesicles to the plasma membrane and comprises the endoplasmic reticulum, Golgi apparatus, and exocytic vesicles. Endocytic Pathway: A process by which cells absorb molecules by engulfing them comprising of early and late endosomes and lysosomes. Reference: Plopper, G., & Ivankovic, D. B. (2020). Principles of Cell Biology (3rd ed., pp. 921). Jones & Bartlett Learning, LLC. Retrieved March 2022, from: http://ebookcentral.proquest.com/lib/queen- ebooks/detail.action?docID=6002586 OVERVIEW OF THE ENDOMEMBRANE SYSTEM This content was retrieved from Section 02 Slide 3 of 15 of the online learning module Understanding how the ER is connected to the nucleus and the Golgi apparatus will help you understand the functions of the endomembrane system and the subcellular compartments involved in protein formation. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 21 MODULE 02 COMPANION GUIDE PHGY 170 Review an overview of each structure. Nucleus The nucleus is connected to the ER cisternae* by the outer layer of the nuclear envelope. Some of the nuclear pores connect the nuclear envelope with the ER membranes so molecules can pass through these structures freely. RER The RER is dotted with ribosomes that give it a “rough” appearance. The RER is the site for protein translation and some protein modifications, and the ribosomes are responsible for protein production and translation. SER The SER does not have ribosomes on it and is responsible for lipid processing, carbohydrate metabolism, and can also store calcium. Transport Vesicles Proteins that have been made in the ER are shuttled in transport vesicles to the Golgi apparatus for further modification. These vesicles are also used to deliver cargo between other organelles in the cell. Golgi Apparatus The Golgi apparatus is involved in both protein modification and transport. It acts as the post office of the cell because it labels proteins and other molecules with different signals, similar to bar codes or postal codes, which direct them towards their final destination within the cell. Definition*: Cisternae: One of the interconnected flattened tubules that make up the ER and Golgi apparatus. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 22 MODULE 02 COMPANION GUIDE PHGY 170 CARGO TRANSPORT IN THE ENDOMEMBRANE SYSTEM This content was retrieved from Section 02 Slide 4 of 15 of the online learning module Cellular barriers are important for proper cellular functioning, but they can pose a problem for the transport of cargo throughout the cell. While small molecules can easily move around as well as into and out of the cell, larger molecules require transport systems. The endomembrane system provides a means by which the cell can transport critical larger cargo to various locations within the cell, remove unwanted cargo from within the cell, and obtain necessary cargo from outside of the cell. The next slides will explore the structures of the endomembrane system shown. RER and SER Transport Vesicles Endosomes, Lysosomes, and Peroxisomes HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 23 MODULE 02 COMPANION GUIDE PHGY 170 Golgi Apparatus VIDEO: INTRODUCTION TO THE ENDOPLASMIC RETICULUM ( ER) This content was retrieved from Section 02 Slide 5 of 15 of the online learning module The ER is essential for protein translation. It acts as a highway system, because it carries molecules around the cell. It also acts as a factory warehouse, because it makes proteins, as well as fats, for the cell. The ER synthesizes membrane phospholipids, secreted proteins, and many membrane proteins. These are carried by vesicles to the Golgi apparatus. Watch the video for an introduction to the structures and functions of the ER. (2:02) As you watch, consider how the function of the ER may differ depending on the type of tissue it is located in. Start of Video Transcript: Inside eukaryotic cells, an organelle called the endoplasmic reticulum is responsible for making and packaging proteins and lipids to send around the cell, much like the assembly line in a factory. Many of the lipids that are assembled in the endoplasmic reticulum are used to build plasma membranes for cells. Depending on the type of cell the endoplasmic reticulum is found in, it can have a slightly different function. The types of molecules that are stored and packaged can change in muscle cells that support the skeleton, called skeletal muscle; the endoplasmic reticulum stores calcium ions used when muscles contract. There are two types of endoplasmic reticulum. The rough endoplasmic reticulum appears rough and has ribosomes embedded in it. Ribosomes attached to the rough ER produce proteins that can be quickly packaged by the ER and either used in the cell or exported out of the cell. Rough endoplasmic reticulum is mostly responsible for the final stages of assembling polypeptide chains into proteins and packaging them so that they can be transported throughout the cell or used outside the cell. The smooth endoplasmic reticulum is the portion of the endoplasmic reticulum that does not have any ribosomes embedded in the membrane. The smooth ER is mostly responsible for assembling and packaging lipids to be used by the cell or exported outside of the cell. The endoplasmic reticulum is connected to the nuclear envelope as a part of a system called the endomembrane system. The endomembrane system includes the nuclear envelope, the endoplasmic reticulum, Golgi body, and vesicles. Each of these organelles is important to the creation and transport of HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 24 MODULE 02 COMPANION GUIDE PHGY 170 proteins and lipids. The endomembrane system assembles proteins, modifies them, and encloses them in a plasma membrane to be used inside the cell or transported outside of the cell. End of Video Transcript. Page Link: https://www.youtube.com/embed/eH5k8XYKycs Reference: learnbiologically. (2013, Jan 3). Endoplasmic Reticulum. [Video]. Retrieved March 2022, from: https://youtu.be/eH5k8XYKycs THE ENDOPLASMIC RETICULUM This content was retrieved from Section 02 Slide 6 of 15 of the online learning module The ER is made up of organized flattened disks of membrane called cisternae. The cisternae of the ER are connected to the outer nuclear envelope. There are two functionally distinct sections of the ER, the RER and SER. Continue to learn about the RER and SER. The ER consists of distinct networks of folded membranes called cisternae and can be broken down into two sections: the rough and smooth ER. RER – See pages 25-26 SER – See page 26 THE RER AND RIBOSOMES Subpage of The Endoplasmic Reticulum – RER 1/1 HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 25 MODULE 02 COMPANION GUIDE PHGY 170 The RER has a rough appearance when viewed with electron microscopes. This is because it is studded with ribosomes. Ribosomes assemble at the RER to produce proteins that must go to another organelle. Ribosomes can also be found freely floating in the cytosol*. These ribosomes only produce proteins that stay in the cytosol. The RER is the location for the first step in this system. Recall that ribosomes are a type of enzyme made of rRNA and are composed of two subunits that are the major structures involved in protein translation. Definitions*: Cytosol: the fluid contained by the plasma membrane of the cell. Reference: Adapted from Purves. (2004). Life, the science of biology (7th ed.). Sinauer Associates. THE SER Subpage of The Endoplasmic Reticulum – SER 1/1 The SER does not have ribosomes on it, giving it a smooth appearance when viewed with an electron microscope. The SER has three main functions. Continue to explore each function. Lipid Synthesis The SER synthesizes lipids, such as phospholipids and steroids. Carbohydrate Metabolism HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 26 MODULE 02 COMPANION GUIDE PHGY 170 The SER serves as the location for carbohydrate metabolism. This includes converting glucose-6- phosphate to glucose. Calcium Regulation The SER regulates calcium ion concentration in muscle cells, which is important for muscle contraction. VESICLE -MEDIATED TRANSPORT This content was retrieved from Section 02 Slide 7 of 15 of the online learning module Transport vesicles are used to shuttle materials between organelles in the endomembrane system by way of vesicle-mediated transport. Small vesicles bud off from lipid membranes of organelles or the cell as a whole, with the purpose of transporting cargo, such as soluble or membrane-bound proteins. These vesicles can transport cargo into or out of the cell, or just to a different location within the cell. Once reaching their final destination, they fuse with other lipid membranes to deposit their cargo. Reference: Plopper, G., & Ivankovic, D. B. (2020). Principles of Cell Biology (3rd ed., pp. 923). Jones & Bartlett Learning, LLC. Retrieved March 2022, from: http://ebookcentral.proquest.com/lib/queen- ebooks/detail.action?docID=6002586 GOLGI NETWORKS: CIS, MEDIAL, AND TRANS HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 27 MODULE 02 COMPANION GUIDE PHGY 170 This content was retrieved from Section 02 Slide 8 of 15 of the online learning module Once in the Golgi, vesicles pass from the cis Golgi, through the medial, to the trans Golgi. Continue to learn more about the cis, medial, and trans networks of the Golgi apparatus. Cis Golgi Network The cis Golgi network receives proteins from the ER that have entered the endomembrane pathways. Medial Golgi Network Within the medial Golgi network, sugar groups called oligosaccharides can be added to proteins. Existing oligosaccharides can also be modified. The addition of sugar groups to lipids also occurs in the medial Golgi network. Trans Golgi Network The trans Golgi network performs the final packaging to send materials to different organelles and sorts cargo to specific destinations. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 28 MODULE 02 COMPANION GUIDE PHGY 170 Reference: Adapted from Plopper, G., & Ivankovic, D. B. (2020). Principles of Cell Biology (3rd ed., pp. 929). Jones & Bartlett Learning, LLC. Retrieved March 2022, from: http://ebookcentral.proquest.com/lib/queen- ebooks/detail.action?docID=6002586 TRANS GOLGI NETWORK This content was retrieved from Section 02 Slide 9 of 15 of the online learning module Since the trans Golgi network is the final region of the Golgi before cargo departs the organelle, this structure has several important functions with regard to sorting and packaging. Continue to learn about the trans Golgi network sorting and packing cargo. 1. Other Organelles The cell needs to deliver proteins to the correct organelle for the organelle to function. Depending on the cell type, the different organelles in a cell will need different combinations of proteins. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 29 MODULE 02 COMPANION GUIDE PHGY 170 The trans Golgi network is where the cell packages these products to go to their final location. As such, each cell will have very different requirements for their trans Golgi network. 2. Retrograde Transport Some proteins that have arrived from the ER contain an ER retention signal. Once being processed by the Golgi apparatus, these proteins are packed up with COPI coating proteins* and then recycled back to the ER. This is a common mechanism found in the cell, similar to how proteins in the nucleus return after exporting mRNA to the cytosol. 3. The Lysosome One sugar modification made in the medial Golgi network is the addition of mannose-6-phosphate (M6P). The M6P receptors in the trans Golgi network recognize proteins with M6P tags, and send them to the lysosome, where the cell degrades proteins, DNA, lipids, and sugars. 4. Cargo Transport The transport of vesicles to the outside of the cell is accomplished by exocytosis. Definition*: COPI Coating Proteins: A protein complex that coats transport vesicles bound for the ER from the Golgi apparatus. Reference: Adapted from Plopper, G., & Ivankovic, D. B. (2020). Principles of Cell Biology (3rd ed., pp. 929). Jones & Bartlett Learning, LLC. Retrieved March 2022, from: http://ebookcentral.proquest.com/lib/queen- ebooks/detail.action?docID=6002586 VIDEO: GOLGI APPARATUS REVIEW This content was retrieved from Section 02 Slide 10 of 15 of the online learning module In review, the ER and Golgi collaborate to control protein and phospholipid traffic in cells. Many proteins passing through the Golgi apparatus are post-translationally modified, for example, by adding sugars, phosphate groups, or sulfate groups to amino acids in the proteins. The molecules leave the Golgi apparatus via transport vesicles destined for a variety of intracellular locations. The term exocytosis refers to the transportation of these vesicles to the plasma membrane, which causes the contents of the vesicles to be secreted into the extracellular space. Watch the video to review how the ER and Golgi move cargo throughout the cell. (3:34) Start of Video Transcript: Again, mitochondria- powerhouse. Lysosome is the soldier. Endosome- delivery guy. Rough endoplasmic reticulum: translator. yes. CPU? Yes. Uber? Yes. SER is the doughnut. Golgi (today's topic) is the sorter. It modifies cellular products, sorts them and direct the delivery. Peroxisomes are the gym trainers. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 30 MODULE 02 COMPANION GUIDE PHGY 170 Golgi Apparatus: The distribution center/the sorter, is a group of stacked membrane bound sacs. Stuff goes to the ER (endoplasmic reticulum), then into vesicles, then into Golgi then to their destination. Golgi modifies stuff by adding chemical groups such as phosphate, sulfate, carbohydrates, adding signal sequences. It orders stuff to go into a certain location in the cell, that's why we call it sorter. And it packs stuff into vesicles. How Golgi Works: So here is the nuclear membrane; it has some pores (very cool). Endoplasmic reticulum is here. Here is the Golgi apparatus. First part is called the cis Golgi apparatus and here's the trans-Golgi because it will transport the vesicles upwards, or towards the outside. Here is the vesicle and this vesicle when it goes outside of the cell is called exocytosis. And here is the amazing phospholipid bilayer cell membrane. These vesicles right here are called endoplasmic reticulum vesicles. They get pinched off of the endoplasmic reticulum and they go to the Golgi apparatus. So, it transports them further, and further, and further, keeps detaching and then reattaching these vesicles again, and again, and again until they are transported to the outside. Maybe into the cell or maybe outside of the cell for secretion as an exocytosis. So, three destinations either going outside through exocytosis, okay, or going into lysosomes, or going into cytoplasmic components. So here are the three destinations: number one, vesicles for exocytosis. Number two, the famous lysosomes. And number three, some cytoplasmic components. Golgi apparatus, endoplasmic reticulum, endosomes, and lysosomes work together in harmony. So, this is called endocytosis: getting stuff into the cells called endocytosis. If it's harmful stuff it's it gets destroyed by the lysosome because it has hydrolytic enzymes, as we have discussed in a previous video. So, exocytosis: going out, endocytosis: going in. Golgi helps with the lysosome because it produces the lysosome and helps with exocytosis as well. That's why Golgi is a hero. The cells that are secretory cells, which means they will secrete lots of stuff, they have lots of Golgi apparatuses inside of the, their cells. Form follows function. That's it for today, what do you think about this video? Let me know down below in the comments. Don't forget to subscribe and hit the bell. Follow me on Facebook, Twitter, SoundCloud, Instagram, and don't forget to support this channel on Patreon. Thank you so much for watching. As always be safe, stay happy, and study hard. End of Video Transcript. Page Link: https://www.youtube.com/embed/hQEUFmOPdAs?start=40 Reference: Cain, et al., Discover Biology, Third Edition, W. W. Norton & Co. Animation © 2006 W. W. Norton & Co. and Sumanas, Inc. ENDOSOMES, LYSOSOMES, AND PEROXISOMES This content was retrieved from Section 02 Slide 11 of 15 of the online learning module Endosomes, lysosomes, and peroxisomes are all membrane-bound organelles that handle the sorting and breakdown of proteins and other macromolecules, but have their own distinct roles in these HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 31 MODULE 02 COMPANION GUIDE PHGY 170 processes. These are essential protective processes in the cell for macromolecules that are damaged, dangerous, or no longer working properly and need to be degraded so as to not cause damage. Learn about endosomes, lysosomes, and peroxisomes. Endosomes Endosomes hold content coming into the cell from the extracellular space, through a process called endocytosis. They sort and send cargo to their correct final locations. Lysosomes Lysosomes (involved in waste disposal) break down proteins, lipids, and sugars into their molecular building blocks. Peroxisomes Peroxisomes also break down molecules, specifically those that generate hydrogen peroxide as a byproduct. This way, cells can neutralize hydrogen peroxide as it is produced to prevent cell damage. VIDEO: ENDOMEMBRANE SYSTEM REVIEW HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 32 MODULE 02 COMPANION GUIDE PHGY 170 This content was retrieved from Section 02 Slide 12 of 15 of the online learning module This video provides an overview of how the components of the endomembrane system work together. Watch the video for an overview of the endomembrane system. (6:19) As you watch, pay attention to each component of the endomembrane system and how they collaborate with one another to transport cargo throughout the cell. Start of Video Transcript: What I wanna do in this video is give an overview of the endomembrane system in eukaryotic cells. Endomembrane system. And at a very high level, the endomembrane system is all of the membranes that interact with each other inside of a cell. So what membranes are we talking about? Well, you can start off by talking about the cell membrane itself. And all of these membranes, these have bilayers of phospholipids. Sometimes my brain malfunctions and I call them bilipid layers, but these are bilayers of phospholipids. So, if I were to zoom in right over here, that line, it really is a bilayer of phospholipids, so it would look like this. So, you have your hydrophilic heads pointing outwards, and your hydrophobic tails pointing inwards, and it keeps going. If we think of it from left to right, you have a layer of two, or you have a bilayer, I should say, of phospholipids. That's going to be true of the cellular membrane, that's going to be true of the outer nuclear membrane right over here. We drew this one on the video of the endoplasmic reticulum. And so over here you see these two membranes. You might say, "OK, is this a bilayer?" No, this is actually two bilayers. So, this membrane right over here has a phospholipid bilayer, and this membrane over here also has a phospholipid bilayer. Let me do this in another color. This one that I'm starting to trace in magenta, that's the outer membrane of the nuclear envelope, and it's continuous with the membrane of the endoplasmic reticulum, which I'm starting to highlight right over here. And then the one that I'm highlighting in this purple color, this is the inner membrane of the nuclear envelope, and all of this is part of the endomembrane system. I've already started talking about the endoplasmic reticulum, and we go into some depth on that on the video on the endoplasmic reticulum and the Golgi apparatus, but it's also part of the endomembrane system. And the endoplasmic reticulum in particular can represent up to, or even more than, 50% of the phospholipid membrane associated with the cell. And we've talked about what goes on in the lumen of the endoplasmic reticulum. So, this area right over here… we've talked about what happens there. Proteins can get synthesized. Actually, other molecules, like lipids, can get synthesized there. And then they can go to the smooth ER, and then the place where they exit from the smooth ER, and we saw that in the video on the endoplasmic reticulum, how they can kind of bud out. We call this area, it's often called the transitional ER. So, this area right over here, we would call the transitional endoplasmic reticulum. Transitional ER is this place where these proteins are being budded off, and they're budding off in vesicles. So, this is the transitional ER. And all vesicles are little small compartments that have a membrane around it, that things like a protein can be transported in. And I don't wanna beat a dead horse here, but all of these lines that I'm drawing, even though I drew it as a single line, these are phospholipid bilayers. So, the membrane might be different, the phospholipid bilayers might be different when we go from one piece of the membrane to another, but they all have that same general notion of having this bilayer of phospholipids. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 33 MODULE 02 COMPANION GUIDE PHGY 170 But just as a review, these proteins, they can emerge from the transitional ER, they can make their way to the Golgi apparatus. And we've already talked about how in the Golgi apparatus these proteins can be matured. And when I say being matured, there's a bunch of Golgi enzymes in here, they can do all sorts of things to the proteins: tag them, they can actually add saccharides to them so that they become glycoproteins. They can tag them so they can be used in the cellular membrane, or be used outside of the cellular membrane, or to be used other places in the cell. So, for example, this protein right over here budded off as a vesicle, it makes its way to the Golgi apparatus, the membrane can then merge, and then dump the protein into the Golgi apparatus. From there it can be matured. It might turn into a glycoprotein, who knows what happens to it? And then it could bud off again, and then this protein that's now budded off, it could go to be embedded into the cellular membrane. The protein could be excreted from the cell, or it could go to other parts of the cell. Everything I've just talked about, those aren't the only parts of the endomembrane system. You have things like vacuoles, which are membrane-bound organelles in a cell. In plant cells, a vacuole can be used for storage, it could be used for structure. Vacuoles can get quite large, and they can actually give, kind of the structure of the actual plant. In animal cells, you might have something called a lysosome. And a lysosome is a membrane-bound structure where, essentially, things go to, for the most part, be recycled, or to be torn apart. So maybe something got packaged from someplace. Let me do this in another color. And I drew that vesicle a little bit too big. But maybe this stuff, it needs to be destroyed, so this membrane, it can then merge with that membrane and dump its contents in here, and this has a low pH, and it can actually, kind of, break apart this stuff, and it can digest this stuff, and recycle it into its, I guess you could say, more constituent material. So, all of this is part of the endomembrane system. So once again, I don't think there's an appreciation for how complex and, on a lot of levels, beautiful cells can be. End of Audio Transcript. Page Link: https://www.youtube.com/embed/vC-cEWJxDRY Reference: Khan Academy. (2015, July 23). Endomembrane system | Structure of a cell | Biology | Khan Academy. Retrieved March 2022, from: https://www.youtube.com/watch?v=vC-cEWJxDRY CHECKPOINT ACTIVITY : ENDOMEMBRANE SYSTEM ORGANELLES This content was retrieved from Section 02 Slide 13 of 15 of the online learning module Take a moment to recall the main function(s) of each of the endomembrane system organelles. When you’re ready, click the flashcards to test yourself and reveal each organelle’s function(s). Endoplasmic Reticulum Acts as a highway and warehouse. Involved in protein translation and production of membrane phospholipids. Transport Vesicles HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 34 MODULE 02 COMPANION GUIDE PHGY 170 Transport materials between endomembrane organelles. Endosomes Involved in endocytosis to bring materials into the cell. Golgi Apparatus Acts as a post office. Labels and sorts proteins with signals to direct them towards their final destination. Lysosome Involved in waste disposal and macromolecule breakdown. Peroxisome Involved in breakdown of molecules that generate hydrogen peroxide. Prevents cell damage. CHECKPOINT QUESTION : MODIFICATION IN THE GOLGI APPARATUS This content was retrieved from Section 02 Slide 14 of 15 of the online learning module Answer the question on Golgi apparatus modification to consolidate what you have learned in this section. Question 1 of 1: Where in the Golgi apparatus are oligosaccharides added to proteins and lipids? a) Trans Golgi network b) Medial Golgi network c) Cis Golgi network d) Cisternae of the Golgi apparatus Feedback: Correct response: Oligosaccharides are added to proteins and lipids in the medial Golgi network. SECTION 02: SUMMARY This content was retrieved from Section 02 Slide 15 of 15 of the online learning module In this section, you were provided an overview of the endomembrane system and explored two important components of it in depth: the ER and the Golgi apparatus. The ER has two functionally distinct sections, the RER and SER. The RER contains ribosomes and thus, plays a large role in protein translation. The SER has roles in lipid synthesis, carbohydrate metabolism, and calcium regulation. The Golgi apparatus has three regions, cis, medial, and trans networks. The cis network receives proteins from the ER, the medial network adds sugar groups to proteins, and the trans network HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 35 MODULE 02 COMPANION GUIDE PHGY 170 performs final packaging functions. Proteins are transported in vesicles from the trans Golgi network to various locations in the cell. Finally, you were introduced to endosomes, lysosomes, and peroxisomes and how they handle proteins. End of Section 02 HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 36 MODULE 02 COMPANION GUIDE PHGY 170 SECTION 03: PROTEIN MODIFICATIONS AND LEVELS OF PROTEIN FOLDING INTRODUCTION TO PROTEIN MODIFICATIONS AND LEVELS OF PROTEIN FOLDING This content was retrieved from Section 03 Slide 1 of 22 of the online learning module Once proteins are produced, they must be shuttled to different subcellular areas in order to carry out their intended function. In this section, you will learn how proteins are translocated into the ER and embedded into the ER membrane, as well as the post-translational modifications and folding that take place following this process. You will learn how protein folding is categorized by levels, similar to DNA packaging. This section concludes with a brief introduction to protein transportation from the ER to the Golgi apparatus via vesicles. Before proteins are functional and able to carry out their intended function, they must undergo several modifications post-translation, such as folding. TARGETING PROTEINS IN THE CELL This content was retrieved from Section 03 Slide 2 of 22 of the online learning module To facilitate proteins carrying out their intended function, they need to be transported to various subcellular areas. To accomplish this, unique signal sequences (or lack of a sequence) are used to target proteins to different areas of the cell. Learn about targeting proteins. Proteins Targeted to the Endomembrane System HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 37 MODULE 02 COMPANION GUIDE PHGY 170 Proteins targeted to the ER, Golgi complex, endosomes, lysosomes, the plasma membrane, or other organelles contain target signal sequences or are tagged within the endomembrane system. These proteins eventually end up in various other areas of the cell, as transmembrane proteins*, or in the extracellular space, depending on how they are tagged within the endomembrane system. Proteins Destined for the Cytosol Proteins targeted for the cell’s cytosol lack signal peptides, since free floating ribosomes will translate them in the cytosol. Thus, a target signal sequence is not necessary. Proteins That Need to be Secreted From the Cell Proteins that are to be secreted out of the cell via exocytosis also have distinct signal sequences that are specific for the cargo in the vesicles. These proteins can be produced by cells and are essential for body functions, such as hormones, or proteins that form the extracellular matrix. Definition*: Transmembrane Proteins: Proteins that span a membrane that include the plasma membrane or the membrane of an organelle. PROTEIN TRANSPORTATION INTO THE ENDOMEMBRANE SYSTEM This content was retrieved from Section 03 Slide 3 of 22 of the online learning module You will now learn about the process of a protein moving through the endomembrane system. The first step of getting a protein into the endomembrane system is allowing the protein to get inside the interior of the ER, known as the lumen*. Recall, proteins are often made by ribosomes attached to the RER. The location of protein synthesis on the ribosomes of the RER is important, because it allows them to be transported directly into the endomembrane system following translation, which begins with the RE R. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 38 MODULE 02 COMPANION GUIDE PHGY 170 Proteins translated in ribosomes attached directly to the RER can be translated directly into the lumen. Definition*: Lumen: The lumen is the interior space of a tubular structure, like the space inside the membrane of the ER. TRANSLOCATION INTO THE ER This content was retrieved from Section 03 Slide 4 of 22 of the online learning module Translocation is the process by which proteins go from being translated to being transported into the E R. This process consists of four distinct steps. Continue to learn how proteins are translocated into the ER. Signal Sequence Transport of proteins into the ER begins during translation. This is accomplished by the presence of a signal that is translated as part of the protein, termed the ER signal sequence. SRP Binding This sequence, as it emerges from the ribosome, interacts with a receptor, termed the signal recognition particle (SRP), which binds to the ribosome that is translating the protein. This pauses translation. The binding of GTP simply indicates this is an energy consuming process. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 39 MODULE 02 COMPANION GUIDE PHGY 170 Ribosome Docking During the pause in translation, the ribosome docks onto the ER membrane by the SRP interacting with an SRP receptor and a complex called the translocon. This allows and facilitates the translocation of the growing protein into the ER. Translocation Translation restarts, and once the protein has translocated into the ER, the signal peptide sequence is cleaved off the protein, translation finishes, and the protein folds inside the ER lumen. The finished protein is destined to be soluble and not attached to a membrane. Reference: Adapted from Plopper, G., & Ivankovic, D. B. (2020). Principles of Cell Biology (3rd ed., pp. 376). Jones & Bartlett Learning, LLC. Retrieved March 2022, from: http://ebookcentral.proquest.com/lib/queen- ebooks/detail.action?docID=6002586 EMBEDDING INTO THE LIPID MEMBRANE This content was retrieved from Section 03 Slide 5 of 22 of the online learning module While the previous slide described translocation of soluble proteins into the ER, the process for translocating proteins destined to be embedded in the plasma membrane is a little different. Continue to learn how proteins are translocated into the transmembrane. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 40 MODULE 02 COMPANION GUIDE PHGY 170 Transmembrane Domain The translocon for transmembrane proteins recognizes a signal that is similar to the ER signal sequence, termed the transmembrane signal anchor sequences. This initiates the process for the protein to become embedded in the lipid bilayer. Protein Enters Lipid Bilayer The transmembrane signal sequence becomes embedded in the lipid bilayer and will be the transmembrane domain of the protein once it is a functional mature protein within a membrane. Reference: Adapted from Plopper, G., & Ivankovic, D. B. (2020). Principles of Cell Biology (3rd ed., pp. 376). Jones & Bartlett Learning, LLC. Retrieved March 2022, from: http://ebookcentral.proquest.com/lib/queen- ebooks/detail.action?docID=6002586 POST-TRANSLATIONAL MODIFICATIONS OF PROTEINS BY THE ER This content was retrieved from Section 03 Slide 6 of 22 of the online learning module Once in the lumen of the ER and folded, proteins are often modified in a process termed post- translational modification. Post-translational modification is the covalent modification of the protein after translation. These modifications may include: The addition of proteins, sugars, lipids, and new functional groups like phosphates and methyl groups, which can change the final target location, structure, or function of the protein. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 41 MODULE 02 COMPANION GUIDE PHGY 170 The cleaving (cutting) of the peptide bonds in the protein. The ER signal sequence, typically located at the N-terminus of a protein, is removed. MODIFICATIONS OF PROTEINS BY THE ER This content was retrieved from Section 03 Slide 7 of 22 of the online learning module In addition to post-translational modification, protein folding is facilitated within the ER. Numerous enzymes are involved in this process, but you will learn about two specific enzymes, protein disulphide isomerase (PDI) and a chaperone protein named binding protein (BiP). Learn about two enzymes involved in protein folding. Protein Disulphide Isomerase Folding of a protein is often facilitated by the formation of a disulfide bond between cysteine amino acids. Enzymes called protein disulfide isomerases (PDIs) help form disulfide bonds between the thiol groups in the side chains of cysteines. These disulfide bonds help the protein to fold properly and stabilize it. Binding Protein Another class of protein, termed chaperonins, help fold the polypeptide by binding hydrophobic patches in recently translated proteins. One type of chaperonin is called BiP. BiP brings these patches together to help fold them correctly into the hydrophobic interior of mature proteins. Once buried in the protein folds, BiP can no longer access the hydrophobic patches. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 42 MODULE 02 COMPANION GUIDE PHGY 170 Reference: Adapted from Plopper, G., & Ivankovic, D. B. (2020). Principles of Cell Biology (3rd ed., pp. 383). Jones & Bartlett Learning, LLC. Retrieved March 2022, from: http://ebookcentral.proquest.com/lib/queen- ebooks/detail.action?docID=6002586 THE HIERARCHY OF PROTEIN STRUCTURES This content was retrieved from Section 03 Slide 8 of 22 of the online learning module Now that you have learned how the ER is essential in protein folding and post-translational processing, let’s explore how proteins are constructed from linking amino acids via peptide bonds to fully functional protein complexes. PEPTIDE BOND This content was retrieved from Section 03 Slide 9 of 22 of the online learning module Recall that amino acids are linked together through a peptide bond, and linked amino acids form peptides. Learn about peptide bonds and the amino acids they link together. Formation of Peptide Bonds The carboxyl group of one amino acid reacts with the amino group of the other amino acid. A peptide bond is formed and a molecule of water is released. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 43 MODULE 02 COMPANION GUIDE PHGY 170 The carboxylic acid group of one amino acid and the amino group of a second amino acid undergo a dehydration reaction*. This linkage is the peptide bond. Peptide bonds occur only between these two groups located in the amino acid backbones, not in the R groups of the amino acids. Rotation of Amino Acids Atoms in the peptide bond are in the rigid amide plane. The amino acids can rotate around the peptide bonds that have formed between them. The peptide bond is a rigid plane. Ends of Amino Acid Chains Now that you have reviewed how amino acids are joined, see how these peptide sequences are folded and organized into mature proteins. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 44 MODULE 02 COMPANION GUIDE PHGY 170 In a long chain of amino acids held together by peptide bonds, there will be two distinct ends: one with the amino group free, and one with the carboxylic acid group free. These ends are called the amino terminus (N-terminus) and the carboxy terminus (C-terminus). Definition*: Dehydration Reaction: A reaction where two molecules combine to form one single molecule. A molecule of water is released during the reaction. References: Adapted from Yassine Mrabet. (2007). Peptidformationball. Wikimedia Commons. Retrieved March 2022, from: https://commons.wikimedia.org/wiki/File:Peptidformationball.svg Plopper, G., & Ivankovic, D. B. (2020). Principles of Cell Biology (3rd ed., pp. 278). Jones & Bartlett Learning, LLC. Retrieved March 2022, from: http://ebookcentral.proquest.com/lib/queen- ebooks/detail.action?docID=6002586 PROTEIN STRUCTURE This content was retrieved from Section 03 Slide 10 of 22 of the online learning module Similar to DNA packaging, there is also a hierarchy to protein structure. These levels help scientists to understand how proteins work, because many proteins that perform similar jobs will have similar sequences and shapes – structure relates to function. Learn about each level of protein structure. Primary (1°) – See page 45-46 Secondary (2°) – See page 46-47 Tertiary (3°) – See page 47-48 Quaternary (4°) – See page 48 PRIMARY (1°) PROTEIN STRUCTURE Subpage of Protein Structure – Primary (1°) 1/1 The primary protein structure is the linear peptide sequence. This is simply the linear amino acid sequence. These can be written using the three letter amino acid codes or single letter amino acid codes as shorthand. The convention for amino acid numbering starts at the amino terminal end of the peptide or protein, and concludes at the carboxy terminus. This is sometimes abbreviated N to C. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 45 MODULE 02 COMPANION GUIDE PHGY 170 A sequence of amino acids building from the N towards the C terminus. Reference: Adapted from Plopper, G., & Ivankovic, D. B. (2020). Principles of Cell Biology (3rd ed., pp. 299). Jones & Bartlett Learning, LLC. Retrieved March 2022, from: http://ebookcentral.proquest.com/lib/queen- ebooks/detail.action?docID=6002586 SECONDARY (2°) PROTEIN STRUCTURE Subpage of Protein Structure – Secondary (2°) 1/1 Secondary protein structure are the regions of organization in the peptide sequence. Some examples of common secondary structure motifs are the alpha helix and beta sheets. Learn more about each secondary structure. Alpha Helix The red dashed lines on the left show hydrogen bonds between oxygen and hydrogen in amino acids four amino acids apart. Beta Sheets HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 46 MODULE 02 COMPANION GUIDE PHGY 170 Beta sheets. Note the direction of the peptide bonds. Reference: Adapted from Plopper, G., & Ivankovic, D. B. (2020). Principles of Cell Biology (3rd ed., pp. 299). Jones & Bartlett Learning, LLC. Retrieved March 2022, from: http://ebookcentral.proquest.com/lib/queen- ebooks/detail.action?docID=6002586 TERTIARY (3°) PROTEIN STRUCTURE Subpage of Protein Structure – Tertiary (3°) 1/1 Tertiary structure is the 3D structure of a complete protein. It is defined by the secondary structures and domains of the protein. For a protein to properly fold, other proteins, called molecular chaperones, are necessary. Chaperones ensure that the proteins achieve the correct shape rather than a misfolded one. Note: Disulfide bonds form in the tertiary structure. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 47 MODULE 02 COMPANION GUIDE PHGY 170 Tertiary (3°) protein structure. Reference: Adapted from Plopper, G., & Ivankovic, D. B. (2020). Principles of Cell Biology (3rd ed., pp. 299). Jones & Bartlett Learning, LLC. Retrieved March 2022, from: http://ebookcentral.proquest.com/lib/queen- ebooks/detail.action?docID=6002586 [Source: Figure 3-7, page 299] QUATERNARY (4°) PROTEIN STRUCTURE Subpage of Protein Structure – Quaternary (4°) 1/1 Quaternary structure is when multiple proteins are assembled into a complex. The individual proteins are called subunits of a quaternary structure only if they cannot have a function outside the complex. One classic example is hemoglobin, which has four subunits in a mature unit. Histones are another example, which have eight subunits. Quaternary (4°) protein structure. Note the four distinct subunits within this structure. Reference: HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 48 MODULE 02 COMPANION GUIDE PHGY 170 Adapted from Plopper, G., & Ivankovic, D. B. (2020). Principles of Cell Biology (3rd ed., pp. 299). Jones & Bartlett Learning, LLC. Retrieved March 2022, from: http://ebookcentral.proquest.com/lib/queen- ebooks/detail.action?docID=6002586 DOMAINS This content was retrieved from Section 03 Slide 11 of 22 of the online learning module A domain is the basic building block of a protein structure. Certain protein domains have some clearly defined functions associated with them, like in the case of an enzyme. Such domains often keep performing their original function when they get inserted into different proteins during evolution; a domain is a discrete structural unit that is assumed to fold independently of the rest of the protein and thus has its own function. Learn about the structure of protein domains. Where Do Domains Fit Into Protein Structure? Domains can be composed of 20 or so amino acid residues to up to hundreds of them. They are made up of multiple secondary structure units (alpha helices, beta sheets, etc.). Most proteins are multi-domain, and domains are often conserved between evolutionarily related proteins. EXAMPLES OF DOMAINS This content was retrieved from Section 03 Slide 12 of 22 of the online learning module Some types of protein domains include SH2, zinc fingers, kinase, and transmembrane domains. They are often named alphabetically (e.g., A domain, B domain, etc.) and shown as a cartoon diagram with domains being represented. Explore how ribbon diagrams are used to represent proteins. Ribbon Diagrams Many biochemists will visually simplify complex protein structures with ribbon diagrams. These show the peptide backbone, with arrows indicating the direction of the peptide sequence from N to C. They HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 49 MODULE 02 COMPANION GUIDE PHGY 170 are sometimes shown in a rainbow of colours to show how the protein is folded. Others will colour code secondary structures, domains, or subunits of the protein. Ribbon model of the protein ribonuclease. Reference: Plopper, G., & Ivankovic, D. B. (2020). Principles of Cell Biology (3rd ed., pp. 109). Jones & Bartlett Learning, LLC. Retrieved March 2022, from: http://ebookcentral.proquest.com/lib/queen- ebooks/detail.action?docID=6002586 VIDEO: PROTEIN STRUCTURES REVIEW This content was retrieved from Section 03 Slide 13 of 22 of the online learning module You have now learned about how peptide bonds connect amino acids, and how amino acids can be combined to produce proteins with four structural levels. Watch the video to review these structures. (2:27) Start of Video Transcript: Proteins are single chain polymers made from monomers called amino acids. A condensation reaction forms a peptide = bond and releases water. Each of the twenty amino acids has a unique shape and chemistry. Some are hydrophobic (Ala, Val, Leu, Ile, Phe, Trp, Met, Pro, Asp, Glu, Gly), some are hydrophilic (Ser, The, Cys, Tyr, Asn, Gln, Lys, Arg, His). Some are big and some are small. These 20 amino acids bind in different combinations to form many different proteins. Primary structure is the amino acid sequence. Here we see a protein assembling one amino acid at a time. The side chain size is part of what determines how a protein folds. Secondary structure refers to local sub- structures, such as helices and sheets, held together with hydrogen bonds. Tertiary structure is the globular unit into which the amino acid chain folds. Each unit is held together by disulphide bridges and ionic bonds. Quaternary structure describes the association between subunits. Each subunit is a separate amino acid chain. Hemoglobin has four subunits forming a tetramer. Specific function is due to shape. Here are two examples of different proteins: Ribonuclease A is a monomer. Its function is to turn RNA into smaller pieces. The active site is in this cleft region. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 50 MODULE 02 COMPANION GUIDE PHGY 170 Insulin is another example. It's stored in our bodies as a hexamer but its functional unit is a monomer. End of Video Transcript. Page Link: https://www.youtube.com/embed/Q7dxi4ob2O4 Reference: University of Surrey. (2011, September 9). Protein Structure | University Of Surrey. [Video]. Retrieved March, 2022 from: https://www.youtube.com/watch?v=Q7dxi4ob2O4 EXTRA RESOURCES This content was retrieved from Section 03 Slide 14 of 22 of the online learning module There are many resources that you can access in the interest of expanding your knowledge on the subject of protein folding and structures. For your interest, access some supplementary resources. PDB RCSB Biochemists spend time crystallizing proteins (or just domains of proteins) to determine their structures. The Protein Data Bank (PDB) archive and RCSB are where you can download the coordinates of protein structures. Proteopedia Proteopedia is a great starting point where scientists build information about crystal structures. Page Links: http://www.wwpdb.org/ http://www.rcsb.org/pdb/home/home.do http://proteopedia.org/wiki/index.php/Main_Page PROTEIN SHAPE AND FUNCTION This content was retrieved from Section 03 Slide 15 of 22 of the online learning module Now that you have learned about how proteins are folded into three dimensions, you will need to learn about how shape leads to function. Each protein can have different conformations or shapes, depending on environmental conditions, which alters how they interact with other proteins and how they function. This shape change can occur HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 51 MODULE 02 COMPANION GUIDE PHGY 170 with changes in pH, temperature, and the presence of ions like calcium or magnesium that can alter the folding of proteins. High temperatures or large changes in pH can result in protein denaturation or unfolding. Smaller, more subtle, changes can happen when proteins are modified or bind to other proteins or other chemicals. The structural change a protein undergoes when experiencing changes in pH, temperature, etc. In extremes, the protein may denature or unfold entirely. HOW STRUCTURE AFFECTS FUNCTION This content was retrieved from Section 03 Slide 16 of 22 of the online learning module The structure and function of proteins are directly related. For proteins to function, they must be in the correct shape to properly work. Therefore, a change in the structure or shape of the protein will then change how the protein works. Cells can make changes to proteins by modifying them either short term or long term, depending on how they chemically modify them. One example is a single amino acid change in hemoglobin which leads to sickle cell anemia. The change of a glutamate to valine allows the valine to stick to the oxygen binding site of another hemoglobin. This makes them stick together and not work properly. Compare normal vs sickle cell hemoglobin. Normal HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 52 MODULE 02 COMPANION GUIDE PHGY 170 Sickle Cell Reference: Desforges, J. F., & Wang, M. Y. F. W. (1966). Sickle cell anemia. Medical Clinics of North America, 50(6), 1519–1532. Retrieved March, 2022 from: https://doi.org/10.1016/s0025-7125(16)33102-9 TYPES OF PROTEIN CHANGES This content was retrieved from Section 03 Slide 17 of 22 of the online learning module Cells chemically modify proteins to control their shape and function. The two major types of modifications a cell will make to a protein are covalent and noncovalent modifications. Learn more about these types of modifications. Covalent Modifications Covalent modifications are relatively long lasting. Disulfide bonds and the addition of lipids or sugar structures are examples. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 02 PAGE 53 MODULE 02 COMPANION GUIDE PHGY 170 Adding phosphate groups, methyl groups, or acetyl groups are all methods of changing protein shape. These will activate or inactivate proteins, or change how they can interact with other proteins in the cell. Noncovalent Modifications Noncovalent modifications are relatively short lived. This can include proteins interacting with each other in

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