PHGY 170 Module 01: Introduction to the Cell and Central Dogma PDF

PHGY 170 oiw HUMAN CELL PHYSIOLOGY MODULE 01 INTRODUCTION TO THE CELL AND THE CENTRAL DOGMA 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 01 COMPANION GUIDE PHGY 170 TABLE OF CONTENTS INTRODUCTION..................................................................................................................................................... 7 Video: Introduction to Module 01................................................................................................................... 7 Module Learning Outcomes............................................................................................................................ 8 Module Assessments........................................................................................................................................ 8 Course Icons...................................................................................................................................................... 9 Module Outline.................................................................................................................................................. 9 SECTION 01: Chemical Symbols and Structure Diagrams..............................................................................10 Introduction to The Cell..................................................................................................................................10 The Three Tenets of the Cell Theory.............................................................................................................10 Prokaryotic and Eukaryotic Cells...................................................................................................................10 The Diversity of Cells.......................................................................................................................................11 Question: Red Blood Cells..............................................................................................................................12 Introduction to Organelles.............................................................................................................................12 Video: Eukaryopolis, the City of Animal Cells...............................................................................................12 An Overview of Cellular Structures...............................................................................................................16 Checkpoint Activity: Functions of Cellular Organelles................................................................................17 Section 01: Summary......................................................................................................................................18 Section 02: Molecular Building Blocks of the Cell............................................................................................19 Introduction to: The Molecular Building Blocks of The Cell.......................................................................19 How Water Supports Cells.............................................................................................................................20 Carbon: The Building Block of Important Cellular Molecules....................................................................20 Lipids.................................................................................................................................................................21 Carbohydrates.................................................................................................................................................21 Nucleotides......................................................................................................................................................23 Amino Acids.....................................................................................................................................................24 Amino Acids: R-groups....................................................................................................................................24 Hydrophobic Amino Acids..........................................................................................................................25 Charged Hydrophilic Amino Acids.............................................................................................................26 Polar Amino Acids.......................................................................................................................................26 Aromatic Amino Acids................................................................................................................................27 Peptides and Proteins.....................................................................................................................................28 Checkpoint Question: Carbon Bonds...........................................................................................................29 HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 2 MODULE 01 COMPANION GUIDE PHGY 170 Checkpoint Question: Amphipathic Molecules............................................................................................30 Checkpoint Question: Protein Examples......................................................................................................30 Section 02: Summary......................................................................................................................................30 Section 03: DNA and RNA Structure...................................................................................................................32 Introduction to DNA and RNA Structure.......................................................................................................32 Structure of a Nucleotide...............................................................................................................................32 Five Carbon Sugar.......................................................................................................................................33 Ribose and Deoxyribose............................................................................................................................33 Phosphate Group........................................................................................................................................34 Nitrogenous Bases......................................................................................................................................35 From Nucleotides to DNA...............................................................................................................................36 DNA Structure: Double-Stranded Helix.........................................................................................................37 Video: The Structure of DNA..........................................................................................................................37 Question: The Structure of DNA.....................................................................................................................38 Introduction to RNA.........................................................................................................................................38 How RNA Structurally Differs from DNA.......................................................................................................39 RNA: Functions and Types..............................................................................................................................40 Checkpoint Activity: The Structure and Function of DNA............................................................................42 Checkpoint Activity: DNA Versus RNA............................................................................................................42 Checkpoint Question: The Nucleus and RNA...............................................................................................43 Section 03: Summary......................................................................................................................................43 Section 04: The Central Dogma Part 1 - DNA Replication...............................................................................44 Introduction to The Central Dogma: DNA Replication................................................................................44 Introduction to Genes.....................................................................................................................................44 Structure of a Gene.........................................................................................................................................45 The Central Dogma of Molecular Biology.....................................................................................................46 Stages of DNA Replication..............................................................................................................................48 Stage 1: Initiation of Replication....................................................................................................................48 Stage 2: Elongation of Replication.................................................................................................................49 Stage 2: Elongation of the Leading vs Lagging Strand................................................................................50 Leading Strand............................................................................................................................................51 Lagging Strand.............................................................................................................................................51 Okazaki Fragments..........................................................................................................................................52 HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 3 MODULE 01 COMPANION GUIDE PHGY 170 Ligase............................................................................................................................................................52 Video: Overview of the Replication Fork.......................................................................................................53 Stage 3: Termination of DNA Replication......................................................................................................55 Overhang: Shortening of Chromosomes......................................................................................................55 Telomeres and Telomerase...........................................................................................................................56 Video: Telomerase and Telomeres................................................................................................................56 Checkpoint Activity: DNA Replication Review...............................................................................................57 Video: Summary of DNA Replication............................................................................................................58 Section 04: Summary......................................................................................................................................59 Section 05: The Central Dogma Part 2 - Transcription....................................................................................60 Introduction to Transcription........................................................................................................................60 Stages of Transcription...................................................................................................................................60 Important Proteins in Transcription.............................................................................................................60 Stage 1: Initiation of Transcription................................................................................................................61 Stage 1: The Transcription Complex.............................................................................................................62 Question: The Promoter Region....................................................................................................................63 Stage 2: Elongation of Transcription.............................................................................................................63 Stage 3: Termination of Transcription..........................................................................................................64 Post-Transcriptional RNA Processing............................................................................................................65 RNA Modification: 5’ Methylguanosine Cap.................................................................................................65 RNA Modification: 3’ Polyadenylation...........................................................................................................66 RNA Modification: RNA Splicing.....................................................................................................................67 Video: RNA Splicing.........................................................................................................................................68 RNA Modification: Splicing and AlteRNAtive Splicing..................................................................................68 Question: Mutations at Splicing Sites...........................................................................................................69 Transport through the Nuclear Pore Complex............................................................................................69 Exceptions to the Central Dogma..................................................................................................................70 Review: Replication vs Transcription.............................................................................................................71 Checkpoint Question: DNA Transcription.....................................................................................................71 Checkpoint Question: DNA Post-Transcriptional Modifications................................................................72 Checkpoint Question: Transcription Promoters..........................................................................................72 Checkpoint Question: Transcription Enzymes.............................................................................................72 Section 05: Summary......................................................................................................................................73 HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 4 MODULE 01 COMPANION GUIDE PHGY 170 Section 06: The Central Dogma Part 3 - Translation.......................................................................................74 Introduction to Translation............................................................................................................................74 From Nucleotides to Amino Acids.................................................................................................................74 DNA Sequencing: Speaking in Code..............................................................................................................75 Codons..............................................................................................................................................................76 The Standard Genetic Code...........................................................................................................................77 Codons Variations and Amino Acids.............................................................................................................78 Question: Codon Redundancies....................................................................................................................79 The Components of Translation....................................................................................................................79 Stages of Translation......................................................................................................................................81 Stage 1: Initiation of Translation....................................................................................................................81 Stage 2: Elongation of Translation.................................................................................................................83 Stage 3: Termination of Translation..............................................................................................................84 Checkpoint Question: Errors in DNA Replication.........................................................................................85 Checkpoint Question: Formation of Polypeptides......................................................................................85 Checkpoint Activity: Initiation of Translation...............................................................................................86 Section 06: Summary......................................................................................................................................86 Section 07: Mutations and DNA Repair.............................................................................................................87 Introduction to Mutations and DNA Repair..................................................................................................87 DNA Repair.......................................................................................................................................................87 Video: DNA Repair............................................................................................................................................87 What Happens if DNA is not Repaired?.........................................................................................................88 Mutations.........................................................................................................................................................89 Types of Mutations..........................................................................................................................................90 Point Mutations...........................................................................................................................................90 Insertion.......................................................................................................................................................91 Deletion........................................................................................................................................................91 Large Scale Deletion, Insertion, Recombination.....................................................................................91 Amino Acid Charges and the Genetic Code.................................................................................................92 Checkpoint Question: Codons and Mutations.............................................................................................94 Checkpoint Question: Amino Acid Charges.................................................................................................95 Section 07: Summary......................................................................................................................................95 CONCLUSION.......................................................................................................................................................97 HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 5 MODULE 01 COMPANION GUIDE PHGY 170 Module Conclusion.........................................................................................................................................97 Module 01: Complete!.....................................................................................................................................97 Module 01: Credits..........................................................................................................................................97 HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 6 MODULE 01 COMPANION GUIDE PHGY 170 INTRODUCTION Please see the online learning module for the full experience of interactions within this document. VIDEO: INTRODUCTION TO MODULE 01 This content was retrieved from Introduction Slide 2 of 6 of the online learning module. Welcome to Module 01, Introduction to the Cell and Central Dogma. In this module, you will delve into the main components that make up cells, and how some of them are made. You will begin this module with exploring Cell Theory and the anatomy of a cell, as well as the four key macromolecules integral to a cell’s function. In the second half of this module, you will explore the processes involved in the central dogma: DNA replication, RNA transcription, and protein translation. Watch the video for an introduction to Module 01 from a content specialist. (3:00) Start of Video Transcript: Hi, I am Dr. Cyndi Pruss. Welcome to PHGY 170 Human Cell Physiology. This course has been developed by myself and Dr. Chris Ward and we are here to guide you through the intricate world of the human cell. Let us begin with a quick orientation of the course. Be sure to check out the course timeline and syllabus in your learning management system, and the course announcements from your course instructor for the term. These will explain your assessments, due dates, and course policies. Human Cell Physiology has four main course learning outcomes that you will be working to achieve by successfully completing your course assessments. After completing PHGY 170, students will be able to: 1. Identify and describe basic cellular components to be able to characterize their roles in the structure and function of human cells. 2. Integrate a basic understanding of cellular processes to articulate how human cells interact with their environment. 3. Recognize key principles of human cell function in order to understand the cellular basis of health and disease. 4. Understand how cells, tissues, organs, and systems work together in order to identify and explain the mechanisms through which the body maintains homeostasis. Now that you know what you will learn in the course, I will say goodbye and send you to Module 01 with Dr. Ward. Hi, I am Dr. Chris Ward, and I will introduce you Module 01, where you will explore the cell and the central dogma of molecular biology. In Module 01, we will be introducing you to the key elements and molecules found in cells, and how cells make DNA, RNA, and proteins. Cells are the little wonders of biology that make you, me, and as a matter of fact, every living thing we see around us work in the way that they do. Right now, as you read this, trillions of HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 7 MODULE 01 COMPANION GUIDE PHGY 170 cells are relentlessly laboring away to keep you alive, alert, and your nerve cells in your brain will most certainly not getting bored! Throughout the course of this module, these nerve cells will be continuously breaking and forming new connections. But that’s a good thing because it means you’re learning, and there is a lot to learn, but don’t worry, the cells we see around us didn’t show up overnight, so naturally it will take more than overnight to learn about them. This first module is designed to help you back into the rhythm of things. It will introduce you to the cell in its most basic form. The cell is really a specialized piece of biological machinery, and like all machines, it has different components that allow it to function. In Module 01, you will be introduced to the most important components in a very general way. Later on in the course we will expand upon the complexities, but for now let’s get the simple stuff out of the way. We will begin with water and carbon, and then move onto macromolecules like carbohydrates, lipids, nucleotides and amino acids. You will next learn about the central dogma of molecular biology- how cells replicate DNA, transcribe the genes in DNA to mRNA, and finally how mRNA is translated into protein. Be sure to carefully read the learning outcomes for this module and keep them in mind for your assessments in Physiology 170. Thank you for listening to our introduction of the course and for Module 01. End of Video Transcript. Page link: https://player.vimeo.com/video/738136144 Reference: Chem Academy. (2015, Sept. 22). Chemical Symbols - Explained [Video]. Retrieved October, 2021 from: https://www.youtube.com/watch?v=278r0UaP1Zs MODULE LEARNING OUTCOMES This content was retrieved from Introduction Slide 3 of 6 of the online learning module. By the end of Module 01, you will be able to: 1. Describe the properties of cells in order to explain Cell Theory. 2. Describe the primary role for each of the different cellular organelles in order to explain cellular function. 3. Explain why water and carbon are necessary for supporting life. 4. Compare the differences between the major classes of carbon-based macromolecules. 5. Explain how DNA is synthesized and transcribed to RNA, and how mRNA is modified post- transcriptionally. 6. Explain how RNA is translated into protein. 7. Describe how the cell corrects mutations, and how the different types of mutations impact protein structure and function. MODULE ASSESSMENTS This content was retrieved from Introduction Slide 4 of 6 of the online learning module. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 8 MODULE 01 COMPANION GUIDE PHGY 170 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. Activities Throughout the Module: 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 5 of 6 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 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 Reference(s): This icon lives in the sidebar of the slides. Clicking it will reveal the references for content and/or images on the slide. Process 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 6 of 6 of the online learning module. Section 01: Introduction to the Cell Section 02: Molecular Building Blocks of the Cell Section 03: DNA and RNA Structure Section 04: The Central Dogma Part 1: DNA Replication Section 05: The Central Dogma Part 2: Transcription Section 06: The Central Dogma Part 3: Translation Section 07: Mutations and DNA Repair HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 9 MODULE 01 COMPANION GUIDE PHGY 170 SECTION 01: CHEMICAL SYMBOLS AND STRUCTURE DIAGRAMS INTRODUCTION TO THE CELL This content was retrieved from Section 01 Slide 2 of 11 of the online learning module. How often have you seen a picture of a cell that looks like a simple circular structure with another smaller circular structure inside of it? Cells are not this simple. They are not mainly empty with things floating around in them. Cells are composed of millions of molecules, and accomplish complex tasks. Despite this, nearly all cells are invisible to the naked eye. In this section, you will explore Cell Theory, types and examples of different types of cells, and you will learn why cells are the fundamental units of life. THE THREE TENETS OF THE CELL THEORY This content was retrieved from Section 01 Slide 3 of 11 of the online learning module. Cell theory is the scientific theory that describes the properties of cells. Cells were first discovered in the 17th century. Since then, many scientists have theorized the purpose of cells and their roles as the building blocks of life. Cell theory is the foundation of biology and has three tenets. Continue to learn the three tenets of cell theory. First Tenet All living organisms are composed of one or more cells. Second Tenet The cell is the basic unit of structure and organization in organisms. Third Tenet All cells come from pre-existing cells. PROKARYOTIC AND EUKARYOTIC CELLS This content was retrieved from Section 01 Slide 4 of 11 of the online learning module. All cells share the three basic properties in Cell Theory. Nevertheless, cells can be categorized into one of two groups based on their structure and functions. The two basic types of cells are the simple prokaryotic cell, and the more complex eukaryotic cell. Continue to learn their major differences. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 10 MODULE 01 COMPANION GUIDE PHGY 170 Features Prokaryotes Eukaryotes Nucleus No true nucleus or any Has a nucleus and membrane membrane bound organelles bound organelles Cell Size Smaller cells (~1-5 μm) Large cells (~10-30 μm) Uni- or Multicellular Always unicellular Usually multicellular Cell Division Binary fission Mitosis/Meiosis Reproduction Always asexual Sexual or asexual Examples Bacteria like E. coli Plants and animals THE DIVERSITY OF CELLS This content was retrieved from Section 01 Slide 5 of 11 of the online learning module. Humans are eukaryotic organisms. Although all the cells in the body have the same DNA, they are vastly diverse in structure and function. On this slide, you will review examples of some of the primary cell types found in the human body. Continue to learn about the function of each cell type. Epithelial Cells Epithelial cells form protective barriers in tissues and may be specialized to absorb or secrete specific compounds. Muscle Cells Muscle cells are responsible for movement of the skeleton, heart, and many inteRNAl organs (e.g., stomach). These cells have specialized structures and proteins that allow them to generate motion. Nerve Cells Nerve cells conduct electrical signals throughout the body, control the contraction of muscles, and are responsible for senses including taste, touch, smell, sight, and hearing. Connective Tissue Cells Connective tissue cells create extracellular material that holds cells together in tissue. They may be specialized to absorb or resist exteRNAl forces (e.g., tendons, vertebral discs). Bone Cells Bone cells form the bones of the skeletal system that give strength and support to the body. These cells include osteoclast cells that degrade bone and osteoblast cells that create new bone. Secretory Cells Secretory cells form glands and, as their name implies, secrete substances (e.g., mucous, hormones, enzymes, etc.). Adipose Cells HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 11 MODULE 01 COMPANION GUIDE PHGY 170 Adipose cells are located throughout the body to store fat. This fat is in the form of triglycerides which are released when the body is in a period of fasting. Red Blood Cells Red blood cells are cells formed primarily in the bone marrow and released into the circulation where they move and deliver oxygen throughout the body. They do not have nuclei or mitochondria. They have limited lifespans and must be continuously replaced. QUESTION: RED BLOOD CELLS This content was retrieved from Section 01 Slide 6 of 11 of the online learning module. The previous slide described several different kinds of cells in the body. You learned that eukaryotic cells have a nucleus and organelles like mitochondria, but just learned that red blood cells have neither! Select whether the statement is true or false. 1 of 1: Red blood cells qualify as eukaryotic cells. a) True b) False Feedback: Correct answer: True Specialized cells like red blood cells are formed from a precursor cell, known as a stem cell. These cells can differentiate into many more cell types called blasts, which then become mature cells in the body. Since red blood cells are matured stem cells that have these organelles, they are still considered a eukaryotic cell, even though when they are matured they do not have these organelles. INTRODUCTION TO ORGANELLES This content was retrieved from Section 01 Slide 7 of 11 of the online learning module. As mentioned earlier, eukaryotic cells have many smaller structures contained within them called organelles. Each organelle has its own specific set of functions; this is important for overall cell function because it keeps cell processes organized. It is also important to keep some processes separate from each other to prevent accidental cross reactions. To facilitate this, each organelle is bound in its own membrane within the cell. Organelle membranes are a property found only in eukaryotic cells. VIDEO: EUKARYOPOLIS, THE CITY OF ANIMAL CELLS This content was retrieved from Section 01 Slide 8 of 11 of the online learning module. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 12 MODULE 01 COMPANION GUIDE PHGY 170 The cell is very much like a city. The cell is compartmentalized and the different sub-compartments are responsible for different specialized functions, much like how different parts of a city work together to ensure the city functions successfully as a whole. Watch the video for an introduction to the components of eukaryotic cells using a cell city analogy. (11:35) Note: This video goes into more detail than you need for this module. Details of each organelle will be explained in more detail throughout this course. Start of Video Transcript: This is an animal and this is also an animal an animal animal animal carcass animal animal animal carcass again animal the thing that all of these other things have in common is that they're made out of the same basic building block the animal cell animals are made up of your run-of-the-mill eukaryotic cells and these are called eukaryotic because they have a true kernel in the greek a good nucleus and that contains the DNA and calls the shots for the rest of the cell also containing a bunch of organelles. There's a bunch of different kinds of organelles and they all have very specific functions and all this is surrounded by the cell membrane of course plants are eukaryotic cells too, but they're set up a little bit differently. Of course, they have organelles that allow them to make their own food, which is super nice. We don't have those and also their cell membrane is actually cell wall. It's made of cellulose. It's rigid which is why plants can't dance if you want to know all about plant cells. We did a whole video on it and you could click on it here if it's online yet. It might not be a lot of the stuff in this video is going to apply to all eukaryotic cells which includes plants and fungi and protists now rigid cell walls, that's cool and all but one of the reasons that animals have been so successful is that their flexible membrane in addition to allowing them the ability to dance gives animals the flexibility to create a bunch of different cell types and organ types and tissue types that could never be possible in a plant the cell walls that protect plants and give them structure prevent them from evolving complicated nerve structures and muscle cells that allow animals to be such a powerful force for you know, eating plants animals can move around find shelter in food find things to mate with all that good stuff. In fact the ability to move oneself around using specialized muscle tissue has been 100 trademarked by kingdom animalia. Ah, what about protozoans? Excellent point what about protozoa? They don't have specialized muscle tissue, they move around with cilia and flagella and that kind of thing so way back in 1665 british scientist, robert hook discovered cells with his kind of crude beta version microscope. He called themselves because they looked like bare spartan monks bedrooms with not much going on inside hook was a smart guy and everything, but he could not have been more wrong about what was going on inside of a cell. There is a whole lot going on inside of a eukaryotic cell. It's more like a city than a monk cell. In fact, let's go with that a cell is like a city. It has divine geographical limits a ruling government power plants roads waste treatment plants a police force industry. All the things a booming metropolis needs to run smoothly but this city does not have one of those hippie governments where everybody votes on stuff and talks things out at town hall meetings and crap like that. Nope think fascist. Italy circa 1938 think kim jong- il's i mean kim jong-un's north korea. And you might be getting a closer idea of how eukaryotic cells do there structures cilia being a bunch of tiny little arms that wiggle around in flagella being one long whip-like tail. Some cells have neither sperm cells for instance have flagella and our lungs and throat cells have cilia that push mucus up and out of our lungs silly and flagellar are made out of long protein fibers called HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 13 MODULE 01 COMPANION GUIDE PHGY 170 microtubules and they both have the same basic structure nine pairs of microtubules forming a ring around two central microtubules. This is often called the nine plus two structure. Anyway, that's just so you know, when you're approaching the city watch out for the cilia and flagella, if you make it past the cilia, you will encounter what is called a cell membrane, which is a kind of squishy not rigid plant cell wall, which totally encloses the city in all of its contents. It's also in charge of monitoring what comes in and out of the cell kind of like the fascist border police the cell membrane has selective permeability meaning that it can choose what molecules come in and out of the cells for the most part and i did an entire video on this which you can check out right here. Now the landscape of eukaryopolis important to note is a kind of wet and squishy. It's a bit of a swampland each eukaryotic cell is filled with a solution of water and nutrients called cytoplasm. And inside of this cytoplasm is a scaffolding called the cytoskeleton. It's basically just a bunch of protein strands that reinforce the cell centrosomes are a special part of this reinforcement. They assemble long microtubules out of proteins that act like steel girders that hold all the city's buildings together the cytoplasm provides the infrastructure necessary for all the organelles to do all of their awesome amazing business with the notable exception of the nucleus, which has its own kind of cytoplasm called the nucleoplasm, which is a more luxurious premium environment befitting the cell's beloved leader, but we'll get to that in a minute first. Let's talk about the cells highway system the endoplasmic reticulum or just er are organelles that create a network of membranes that carry stuff around the cell. These membranes are phospholipid bilayers same as in the cell membrane. There are two types of er, there's the rough and the smooth fairly similar but slightly different shapes slightly different functions the rough, er looks all bumpy because it has ribosomes attached to it and the smooth er doesn't so it's a smooth network of tubes. Smoothyrx is a kind of factory warehouse in the cell city, it contains enzymes that help with the creation of important lipids which you'll recall from our talk about biological molecules and phospholipids and steroids that turn out to be sex hormones other enzymes in the smoothie are specialized in detoxifying substance, like noxious stuff derived from drugs and alcohol, which they do by adding a carboxyl group to them making them soluble in water. Finally the smooth, er also stores ions in solutions that the cell may need later on especially sodium ions, which are used for energy and muscle cells. So the smooth er helps make lipids while the rough er helps in the synthesis and packaging of proteins and those proteins are created by another type of organelle the ribosome ribosomes can float freely throughout the cytoplasm or be attached to the nuclear envelope which is where they're spat out from and their job is to assemble amino acids into polypeptides as the ribosome builds an amino acid chain. The chain is pushed into the er, when the protein chain is complete the er pinches it off and sends it to the golgi apparatus and the city that is the cell. The golgi is the post office processing proteins and packaging them up before sending them wherever they need to go calling it an apparatus makes it sound like a bit of complicated machinery, which it kind of is because it's made up of like these stacks of membranous layers that are sometimes called golgi bodies. The golgi bodies can cut up large proteins into smaller hormones and can combine proteins with carbohydrates to make various molecules, like for instance snot the bodies package. These little goodies into sacks called vesicles, which have phospholipid walls just like the main cell membrane then ship them out either to other parts of the cell or outside the cell wall. We learn more about how vesicles do this in the next episode of crash course, the golgi bodies also put the finishing touches on the lysosomes lysosomes are basically the waste treatment plants and recycling centers of the city. These organelles are basically sacs full of enzymes that break down cellular waste and debris from outside of the cell and turn it into simple compounds which are transferred into the cytoplasm as new cell building materials. Now finally, let us talk about the nucleus the beloved leader. The nucleus is a highly specialized. Organelle that lives in its own double membrane high security compound with its body the nucleolus and within the cell the nucleus is in charge in a major way because it stores the cell's D HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 14 MODULE 01 COMPANION GUIDE PHGY 170 NA. It has all the information the cell needs to do its job. So the nucleus makes all the laws for the city orders all the other organelles around telling them how and when to grow what to metabolize what proteins to synthesize how and when to divide the nucleus does all this by using the information blueprinted in its DNA to build proteins that will facilitate a specific job getting done. For instance on january 1st. 2012. Let's say a liver cell needs to help break down an entire bottle of champagne the nucleus in that liver cell would start telling the cell to make alcohol dehydrogenase, which is the enzyme that makes alcohol not alcohol anymore. This protein synthesis business is complicated lucky for you. We will have or may already have an entire video about how it happens. The nucleus holds its precious DNA along with some proteins in a web-like substance called chromatin when it comes time for the cell to split the chromatin gathers into rod-shaped chromosomes, each of which holds DNA molecules different species of animals have different numbers of chromosomes. We humans have 46 fruit flies vape hedgehogs which are adorable but you know less complex than humans have 90. Now the nucleolus which lives inside of the nucleus is the only organelle not enveloped by its own membrane. It's just a gooey splotch of stuff within the nucleus its main job is creating ribosomal RNA or rRNA, which it then combines with some proteins to form the basic units of ribosomes. Once these units are done the nucleolus spits them out of the nuclear envelope where they are fully assembled into ribosomes the nucleus then sends orders in the form of messenger RNA or mRNA to those ribosomes, which are the henchmen that carry out the orders in the rest of the cell how exactly the ribosomes do. This is immensely complex and awesome. So awesome. In fact that we're going to give it the full crash course treatment an entire episode. And now for what is totally objectively speaking, of course the coolest part of the animal cell. It's power plants the mitochondria the smooth oblong organelles where the amazing and super important process of respiration takes place. This is where energy is derived from carbohydrates fats and other fuels and is converted into adenosine triphosphate or ATP, which is like the main currency that drives life and eukaryopolis. You can learn more about ATP and respiration in an episode that we did on that. Now, of course some cells like muscle cells or neuron cells need a lot more power than the average cell in the body. And so those cells have a lot more mitochondria per cell, but maybe the coolest thing about mitochondria is that long ago animal cells didn't have them but they existed as their own sort of bacterial cell and one day one of these things ended up inside of an animal cell probably because the animal cell was trying to eat it but instead of eating it it realized that this thing was really super smart and good at turning food into energy and it just kept it it stayed around and in this day, they sort of act like their own separate organisms. Like they do their own thing within the cell they they replicate themselves. They even contain a small amount of DNA. Now what may be even more awesome if that's possible. Is that mitochondria are in the egg cell when an egg gets fertilized and those mitochondria have DNA, but because mitochondria replicate themselves in a separate fashion, it doesn't get mixed with the DNA of the father. It's just the mother's mitochondrial DNA. That means that your and my mitochondrial DNA is exactly the same as the mitochondrial DNA of our mothers and because this special DNA is isolated in this way scientists can actually track back and back and back and back to a single mitochondrial eve who lived about 200 000 years ago in Africa, all of that complication and mystery and beauty in one of the cells of your body. It's complicated. Yes, but worth understanding review time another somewhat complicated episode of crash course biology. If you want to go back and watch any of the stuff that we talked about it to reinforce it in your brain, if you didn't quite get it, just click on the links and it'll take you back in time to when i was talking about that mere minutes ago. Thank you for watching. If you have questions for us, please ask below in the comments or on twitter or on facebook, and we will do our best to make things more clear for you. We'll see you next time. End of Video Transcript. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 15 MODULE 01 COMPANION GUIDE PHGY 170 Page link: https://www.youtube.com/embed/cj8dDTHGJBY Reference: CrashCourse. (2012, Feb 20). Eukaryopolis - The City of Animal Cells: Crash Course Biology #4 [Video]. Retrieved October, 2021 from: https://www.youtube.com/watch?v=cj8dDTHGJBY AN OVERVIEW OF CELLULAR STRUCTURES This content was retrieved from Section 01 Slide 9 of 11 of the online learning module. Eukaryotic cells require many cellular structures to maintain their life sustaining functions. Continue to review the key cellular structures of the cell. Plasma Membrane The plasma membrane is like the city limit and border police. It is a semi-permeable phospholipid bilayer that keeps all of the cell’s organelles contained and regulates what can come in or leave the cell using specialized proteins. Nucleus The nucleus is the leader of the cell, making the ‘laws’ of Eukaryopolis. The nucleus stores these ‘laws’ as DNA and protects it with specialized structures like a double membrane, nuclear pores, and a unique fluid called nucleoplasm. Mitochondria Mitochondria are the power plants in Eukaryopolis. They produce energy for the cell to use in all of its processes, in the form of ATP; a kind of cellular energy ‘currency.’ The number of mitochondria in a cell depends on its function. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 16 MODULE 01 COMPANION GUIDE PHGY 170 Endoplasmic Reticulum (ER) In Eukaryopolis, the endoplasmic reticulum (ER) acts as a highway system, carrying molecules around the cell, and as a factory warehouse that makes lipids and proteins, and stores ions. Golgi Apparatus The golgi apparatus is the post office of Eukaryopolis that processes and packages proteins, then sends them across the cell. Endosomes, Lysosomes, and Peroxisomes In Eukaryopolis, the cytoskeleton is the steel girdles holding buildings together. Actin, microtubules, and intermediate filaments are structural filaments that use mechanical resistance to stabilize membrane deformations. Myosin, kinesin, and dynein are motor (force) proteins that generate force, or motion. Cytoskeleton Some smaller, membrane-bound organelles contain specific proteins and enzymes. Endosomes are the waste collection vehicles that sort and start breaking things down. Lysosomes are recycling plants that break down proteins, lipids, and nucleic acids. Peroxisomes deal with hazardous waste, such as hydrogen peroxide. CHECKPOINT ACTIVITY: FUNCTIONS OF CELLULAR ORGANELLES This content was retrieved from Section 01 Slide 10 of 11 of the online learning module. Select the correct term from the dropdown menu to match the correct cellular structure with its function List of Cellular Structures: Cytoskeleton, Mitochondrion, Peroxisome, Endosome, Endoplasmic Reticulum (ER) and Golgi Apparatus, Nucleus, Plasma Membrane, Lysosome, Functions: 1. Breaks down molecules that produce hydrogen peroxide. 2. Produces energy for the cell to use. 3. Contains the cell’s genetic material and controls access to it. 4. Sorts and condenses content that arrives from outside the cell. 5. Monitors what can come in and out of the cell and contains organelles. 6. Breaks down waste and debris. 7. Carries molecules around the cell and makes proteins and lipids; processes and packages proteins. 8. Generates motion and stabilizes the cell against deformation. Feedback: 1. Peroxisome 2. Mitochondrion HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 17 MODULE 01 COMPANION GUIDE PHGY 170 3. Nucleus 4. Endosome 5. Plasma Membrane 6. Lysosome 7. Endoplasmic Reticulum (ER) and Golgi Apparatus 8. Cytoskeleton SECTION 01: SUMMARY This content was retrieved from Section 01 Slide 11 of 11 of the online learning module. In this section, you learned about the complexity, variation, and fundamentality of the cell. You explored the three tenets of Cell Theory and the differences between eukaryotic and prokaryotic cells. Then, you were introduced to the primary cell types in the human body and their functions. Finally, you learned about the major cellular structures and organelles essential to the functioning of a eukaryotic cell, in the context of a metaphorical city called Eukaryopolis. Now that you have explored a small sample of different cells that exist just within the human body, you can hopefully get a better idea of the diversity and complexity of this structural unit of biology. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 18 MODULE 01 COMPANION GUIDE PHGY 170 SECTION 02: MOLECULAR BUILDING BLOCKS OF THE CELL INTRODUCTION TO: THE MOLECULAR BUILDING BLOCKS OF THE CELL This content was retrieved from Section 02 Slide 2 of 14 of the online learning module. Water and carbon are the foundational building blocks of cells and are found throughout the entire cell. The organization of water and carbon within a cell is not random. Recall from Module 00 that water is attracted to water - this property is called being hydrophilic*. On the other hand, carbon based molecules are usually large and nonpolar. They tend to be hydrophobic* - they do not dissolve well in water. What’s important to remember is that like dissolves like. This means that hydrophilic molecules are attracted to hydrophilic molecules, but repel hydrophobic molecules, and hydrophobic molecules are attracted to hydrophobic molecules, but repel hydrophilic molecules. For the cell, this means that the nonpolar carbon-based structures are attracted to each other and repel water as much as possible. This is a key aspect that in part, allows a cell to form membranes and subcellular compartmentalization. Formation of phospholipid membranes when mixed in an aqueous environment. Definitions*: Hydrophilic: Means “water-liking.” Hydrophilic molecules are attracted to water. Hydrophobic: Means “water-fearing.” Hydrophobic molecules tend to try and keep away from water. Reference: Biga, L. M., Dawson, S., Harwell, A., Hopkins, R., Kaufmann, J., LeMaster, M., Matern, P., Morrison- Graham, K., Quick, D., & Runyeon, J. (2019). 3.1 the cell membrane. Anatomy Physiology. Retrieved March 4, 2022, from: https://open.oregonstate.education/aandp/chapter/3-1-the-cell-membrane/ HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 19 MODULE 01 COMPANION GUIDE PHGY 170 HOW WATER SUPPORTS CELLS This content was retrieved from Section 02 Slide 3 of 14 of the online learning module. Water is essential for all cell-based life. The two most important properties of water that support cells, and thus life, are its polarity and specific heat capacity. Continue to explore these properties. Polarity The polar properties of water make it an excellent solvent. This facilitates the delivery of nutrients and removal of wastes, and provides an environment that allows cells to exist within a network by facilitating the movement of chemical messengers within and between cells. Specific Heat Capacity The high specific heat capacity of water allows for thermoregulation by acting as a heat sink for the many chemical reactions that occur within cells, as well as the exchange of heat between liquid and air. This is critical for warm-blooded organisms, such as humans, that must regulate their body temperature. CARBON: THE BUILDING BLOCK OF IMPORTANT CELLULAR MOLECULES This content was retrieved from Section 02 Slide 4 of 14 of the online learning module. Recall that cells are mainly composed of water and carbon-based molecules. Carbon is the building block to all life. It is small and can form up to four covalent bonds. This flexibility in bond formation allows it to form a large variety of molecules important to cellular life, such as lipids, carbohydrates, nucleotides, and amino acids. Examples of carbon-based molecules. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 20 MODULE 01 COMPANION GUIDE PHGY 170 Reference: Clark, M. A., Choi, J., & Douglas, M. (2018). Carbon. Retrieved October 2021, from: https://opentextbc.ca/biology2eopenstax/chapter/carbon/ LIPIDS This content was retrieved from Section 02 Slide 5 of 14 of the online learning module. Lipids are the building blocks for oils and fats. They are made of hydrocarbon chains, and are usually quite hydrophobic and are therefore often insoluble in water. However, lipids are commonly amphipathic*. While there are countless examples of lipids being used in the cell, these three examples are some of the most common; they demonstrate the wide variety of lipids’ functions and are important in understanding physiology. You will learn more about lipids and their functions in the cell in Module 03. Continue to explore three of the most common lipids. Cholesterol Cholesterol regulates cell membrane fluidity and is a biological precursor for compounds such as steroid hormones, bile acids, and certain vitamins. Phospholipids Phospholipids are amphipathic lipids that form cell membranes. They have a hydrophilic head and a hydrophobic tail that enables them to form the phospholipid bilayer of cells. Triglycerides Triglycerides are the main component of body fat in animals and are used to store energy. Definition*: Amphipathic: A molecule which is both hydrophilic and hydrophobic in certain sections. CARBOHYDRATES This content was retrieved from Section 02 Slide 6 of 14 of the online learning module. Carbohydrates in the most literal sense, are “hydrated carbon” (i.e., they are composed of carbon and water). Carbohydrates in animal cells can be classified into mono-, di-, oligo-, and polysaccharides. Each of these classes serve a different set of functions. For example, the simple building block of carbohydrates are sugars, which can be built into more complex structures like starches. Continue to learn more about the classes of carbohydrates. Monosaccharides HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 21 MODULE 01 COMPANION GUIDE PHGY 170 Monosaccharides are single carbohydrate molecules containing only carbon, hydrogen, and oxygen. Glucose is an example of a monosaccharide, also referred to as sugar. Disaccharides Disaccharides are two monosaccharides bonded together connected by a glycosidic bond. An example of this is sucrose, which is composed of a glucose connected to a fructose. Table sugar is crystallized sucrose. Oligosaccharides Oligosaccharides are composed of three to ten monosaccharides linked together. Raffinose is an example of a oligosaccharide. Polysaccharides Polysaccharides are much longer chains, are even more complex, and play many important roles in the cell. An example of this is glycogen. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 22 MODULE 01 COMPANION GUIDE PHGY 170 References: NEUROtiker, Public domain, via Wikimedia Commons. Retrieved October 2021, from: https://commons.wikimedia.org/wiki/File:Alpha-D-Glucopyranose.svg Don A. Carlson, CC BY-SA 3.0 , via Wikimedia Commons. Retrieved October 2021, from: https://commons.wikimedia.org/wiki/File:Sucrose- inkscape.svg Paginazero at Italian Wikipedia, Public domain, via Wikimedia Commons. Retrieved October 2021, from: https://commons.wikimedia.org/wiki/File:Raffinosio_struttura.PNG Walty1971, Public domain, via Wikimedia Commons. Retrieved October 2021, from: https://commons.wikimedia.org/wiki/File:Glycogen.jpg NUCLEOTIDES This content was retrieved from Section 02 Slide 7 of 14 of the online learning module. Nucleotides are the building blocks of nucleic acids like deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Recall from Section 01 that DNA governs the activities of a cell. They also form adenosine triphosphate (ATP), the main form of cellular energy used to power reactions within an organism. You will learn more about the structure and function of nucleotides in the next section. The basic molecular structure of a nucleotide. Reference: HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 23 MODULE 01 COMPANION GUIDE PHGY 170 By Hbf878 - Own work, CC0, https://commons.wikimedia.org/w/index.php?curid=74023664. Retrieved October 2021, from: https://en.wikipedia.org/wiki/Nucleotide#/media/File:DAMP_chemical_structure.svg AMINO ACIDS This content was retrieved from Section 02 Slide 8 of 14 of the online learning module. Amino acids are the building blocks of peptides and proteins. The structure of amino acids are consistent; they each have an amino group, a central alpha carbon with an R-group, and a carboxylic acid group. Continue to learn more about the structures in an amino acid. The Carboxylic Acid Group The carboxylic acid group can also exist as a negatively charged carboxylate (-COO-) group. The Amino Group The amino group can also exist as a positively charged -NH3+ group. The R-group The R-group is unique to each amino acid and gives it its distinct molecular characteristics. Reference: Adapted from Plopper, G., & Ivankovic, D. B. (2020). Principles of Cell Biology. Jones & Bartlett Learning, LLC. from: http://ebookcentral.proquest.com/lib/queen-ebooks/detail.action?docID=6002586 AMINO ACIDS: R -GROUPS This content was retrieved from Section 02 Slide 9 of 14 of the online learning module. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 24 MODULE 01 COMPANION GUIDE PHGY 170 The side chains of amino acids contribute significantly to what a protein's structure will be. The 20 most common amino acids are grouped into categories based on the chemical properties of their side chains, called R-groups. Continue to explore the amino acids that belong to each R-group category. Hydrophobic Amino Acids – Refer to pages 25-26 Charged Hydrophilic Amino Acids – Refer to page 26 Polar Amino Acids – Refer to pages 26-27 Aromatic Amino Acids – Refer to page 27-28 Note: You will not be expected to know the chemical structure of the amino acids, only their general properties. HYDROPHOBIC AMINO ACIDS Subpage of Amino Acids: R-groups – Hydrophobic Amino Acids 1/1 Hydrophobic amino acids are also called nonpolar. They can be aliphatic* or aromatic*. These amino acids are normally found in the core of the protein, or interacting with other hydrophobic molecules in a membrane, like fats or lipids. The chemical structure of the side chain of each amino acid will give certain characteristics to a protein. The aliphatic hydrophobic amino acids are glycine, alanine, valine, leucine, isoleucine, methionine, and proline. The aromatic hydrophobic amino acids are phenylalanine, tryptophan. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 25 MODULE 01 COMPANION GUIDE PHGY 170 Hydrophobic amino acids Definitions*: Aliphatic: The R-group consists of carbon chains which can be straight, branched, or non-aromatic rings. Aromatic: The R-group contains an aromatic ring that has double bonds similar to benzene. Reference: Plopper, G., & Ivankovic, D. B. (2020). Principles of Cell Biology (3rd ed.; pp. 94). Jones & Bartlett Learning, LLC. from: http://ebookcentral.proquest.com/lib/queen-ebooks/detail.action?docID=6002586 CHARGED HYDROPHILIC AMINO ACIDS Subpage of Amino Acids: R-groups – Charged Hydrophilic Amino Acids 1/1 These amino acids carry a positive or negative charge, and are therefore hydrophilic. The location of the charge is found on the outside of proteins where they can interact with water. Lysine, arginine, and histidine have positively charged R-groups while aspartic acid and glutamic acid have negatively charged R-groups. Amino acids with positively charged R-groups. Amino acids with negatively charged R-groups. Reference: Plopper, G., & Ivankovic, D. B. (2020). Principles of Cell Biology (3rd ed.; pp. 94). Jones & Bartlett Learning, LLC. from: http://ebookcentral.proquest.com/lib/queen-ebooks/detail.action?docID=6002586 POLAR AMINO ACIDS Subpage of Amino Acids: R-groups – Polar Amino Acids 1/1 HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 26 MODULE 01 COMPANION GUIDE PHGY 170 The polar hydrophilic side chains can form hydrogen bonds that stabilize proteins. These are more common on the outside of a protein. The polar amino acids are serine, threonine, tyrosine, asparagine, glutamine, and cysteine. Continue to learn about the unique features of cysteine. Cysteine has a sulfur-containing thiol that can form a covalent bond called a disulfide bond with another cysteine. These are significant for forming and maintaining three-dimensional protein structure. Reference: Plopper, G., & Ivankovic, D. B. (2020). Principles of Cell Biology (3rd ed.; pp. 94). Jones & Bartlett Learning, LLC. from: http://ebookcentral.proquest.com/lib/queen-ebooks/detail.action?docID=6002586 AROMATIC AMINO ACIDS Subpage of Amino Acids: R-groups – Aromatic Amino Acids 1/1 Aromatic amino acids have ring structures with double bonds that have distinct properties associated with this chemical structure. These are very large amino acids, and the gain or loss of these amino acids can cause deformities in a protein’s structure. Phenylalanine and tryptophan are both nonpolar (hydrophobic), while tyrosine is polar (hydrophilic). Phenylalanine (Phe or F) HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 27 MODULE 01 COMPANION GUIDE PHGY 170 Tryptophan (Trp or W) Tyrosine (Tyr or Y) References: NEUROtiker, Public domain, via Wikimedia Commons. Retrieved October 2021, from: https://commons.wikimedia.org/wiki/File:L-Phenylalanin_-_L-Phenylalanine.svg User:Sergiy O. Bukreyev, CC BY-SA 3.0 , via Wikimedia Commons. Retrieved October 2021, from: https://commons.wikimedia.org/wiki/File:Mol2D.L.Tryptophan.png NEUROtiker, Public domain, via Wikimedia Commons. Retrieved October 2021, from: https://commons.wikimedia.org/wiki/File:L-Tyrosin_-_L-Tyrosine.svg PEPTIDES AND PROTEINS This content was retrieved from Section 02 Slide 10 of 14 of the online learning module When amino acids are connected together by peptide bonds, they form peptides, which have similar naming conventions to carbohydrates. Insulin is an example of a peptide hormone. Proteins are made up of long chains of amino acids, normally more than 20 amino acids. These polypeptides fold into a 3D structure that is required for protein function. There are thousands of different types of proteins in a cell, each accomplishing vastly different tasks. Proteins include enzymes, receptors, structural proteins like keratin, which makes up nails and hair, and hemoglobin, which carries oxygen in red blood cells. Continue to compare a dipeptide with a polypeptide folded into a 3D structure. Dipeptide HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 28 MODULE 01 COMPANION GUIDE PHGY 170 Two amino acids linked together by a peptide bond. 3D Structure of a Protein Proteins form 3D structures, often depicted by ribbon diagrams. Reference: Plopper, G., & Ivankovic, D. B. (2020). Principles of Cell Biology (3rd ed.; pp.302). Jones & Bartlett Learning, LLC. from: http://ebookcentral.proquest.com/lib/queen-ebooks/detail.action?docID=6002586 CHECKPOINT QUESTION: CARBON BONDS This content was retrieved from Section 02 Slide 11 of 14 of the online learning module Answer the question based on what you have learned about carbon. 1 of 3: What is the highest number of bonds carbon can form? a) 4 b) 3 c) 2 HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 29 MODULE 01 COMPANION GUIDE PHGY 170 d) 6 Feedback: Correct answer: a Carbon can form up to four covalent bonds. This flexibility in bond formation allows it to form a large variety of molecules. CHECKPOINT QUESTION: AMPHIPATHIC MOLECULES This content was retrieved from Section 02 Slide 12 of 14 of the online learning module Answer the question based on what you learned about amphipathic molecules. 2 of 3: What does the term amphipathic mean? a) A term that describes the shape of a lipid. b) A molecule that is both hydrophilic and hydrophobic. c) The ability of carbon to form four bonds. d) The property of having a high specific heat capacity. Feedback: Correct answer: b Amphipathic is a term used to describe a molecule that has both hydrophilic and hydrophobic properties. Recall that lipids are commonly amphipathic. CHECKPOINT QUESTION: PROTEIN EXAMPLES This content was retrieved from Section 02 Slide 13 of 14 of the online learning module Answer the question based on what you learned about protein. 3 of 3: Which one of these is not an example of a protein? a) Keratin b) Receptors c) Enzymes d) Cholesterol Feedback: Correct answer: d Transcription factors, receptors, and enzymes are all composed of amino acids linked together by peptide bonds to form a protein. Cholesterol is an example of a lipid. SECTION 02: SUMMARY HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 30 MODULE 01 COMPANION GUIDE PHGY 170 This content was retrieved from Section 02 Slide 14 of 14 of the online learning module In this section, you learned about the importance of water and carbon in cells. You examined two key properties of water that are critical for sustaining life; its polarity and specific heat capacity. You then explored how carbon is the basic building block for lipids, carbohydrates, amino acids, and nucleotides. You learned that the molecular structure of amino acids consist of a carboxyl group, an amino group, and an R-group, and how peptides and proteins are made up of amino acids linked together by peptide bonds. You concluded this section with breaking down amino acid R-groups in four categories, hydrophobic, aromatic, polar, and charged hydrophilic. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 31 MODULE 01 COMPANION GUIDE PHGY 170 SECTION 03: D NA AND R NA STRUCTURE INTRODUCTION TO DNA AND RNA STRUCTURE This content was retrieved from Section 03 Slide 2 of 14 of the online learning module. At the start of this module, you learned that the nucleus of a cell contains deoxyribonucleic acid (DNA). This is the genome* that is unique to each individual, and incredibly important for cell function. Every cell in the body contains the complete genome, including every gene. However, specific cells require different genes* to be turned on and off in order to function properly. For example, a muscle cell will have the genes necessary to make bone turn off. You will explore how the cell packs up unneeded genes later in this course. The other type of nucleic acid is ribonucleic acid (RNA) and it is another critical molecule. RNA functions as a template and makes the machinery required for protein production. Definitions*: Genome: The complete set of genetic material in an organism; all of the DNA in a cell. Gene: A sequence of nucleotides in DNA that determines certain characteristics. STRUCTURE OF A NUCLEOTIDE This content was retrieved from Section 03 Slide 3 of 14 of the online learning module. The basic building blocks of both DNA and RNA are nucleotides. Each nucleotide is made up of three components: a central five carbon sugar attached to a phosphate group and a nitrogenous base. Continue to learn more about each component. As you learn about each, compare the differences in molecular structure between DNA and RNA. Five-Carbon Sugar – Refer to pages 34-35 Phosphate Group – Refer to page 34-35 Nitrogenous Base – See page 35-36 Nucleotides consist of a central five-carbon sugar, a phosphate group, and a nitrogenous base. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 32 MODULE 01 COMPANION GUIDE PHGY 170 Reference: Adapted from Plopper, G., & Ivankovic, D. B. (2020). Principles of Cell Biology (3rd ed.). Jones & Bartlett Learning, LLC. http://ebookcentral.proquest.com/lib/queen-ebooks/detail.action?docID=6002586 FIVE CARBON SUGAR Subpage of Structure of a Nucleotide – Five Carbon Sugar 1/2 Nucleotides contain a central five-carbon sugar, or monosaccharide. Note that in chemistry, the carbons of cyclic sugar rings are numbered, so the carbons are named from 1 to 5. Because of this numbering system, each sugar in a nucleotide will have a 5’ (i.e., five prime) and 3’ (i.e., three prime) end. The 5’ end of the sugar is where the phosphate group is attached in a single nucleotide. The 3’ end is where a phosphate group of a different nucleotide can form a bond. Chemical structure of deoxyribose. Reference: Miranda19983$!, CC BY-SA 4.0 , via Wikimedia Commons. Retrieved October 2021, from https://commons.wikimedia.org/wiki/File:The_difference_between_ribose_and_deoxyribose.png RIBOSE AND DEOXYRIBOSE Subpage of Structure of a Nucleotide – Five Carbon Sugar 2/2 One of the key structural differences between DNA and RNA is at the 2’ carbon. The five-carbon sugar in RNA contains an extra oxygen on the 2’ carbon. DNA on the other hand contains a lone hydrogen at the 2’ carbon and lacks the additional oxygen. Due to this small difference of one oxygen atom, the sugar found in RNA is hence called ribose and the sugar in DNA is called deoxyribose. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 33 MODULE 01 COMPANION GUIDE PHGY 170 Chemical structure of ribose and deoxyribose. Reference: Miranda19983$!, CC BY-SA 4.0 , via Wikimedia Commons. Retrieved October 2021, from https://commons.wikimedia.org/wiki/File:The_difference_between_ribose_and_deoxyribose.png PHOSPHATE GROUP Subpage of Structure of a Nucleotide – Phosphate Group 1/1 Nucleotides normally have one to three phosphates attached to the 5’ carbon. These are high energy bonds and are, in part, why ATP can be used for energy. Phosphates are part of what is called the DNA sugar-phosphate backbone. Phosphates are attached to the 5’ carbon of one sugar and the 3’ carbon of another by a phosphodiester bond*. Note: the attachment of the phosphate at the 5’ and 3’ carbons. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 34 MODULE 01 COMPANION GUIDE PHGY 170 Definition* : Phosphodiester Bond: In DNA, a phosphodiester bond is a covalent bond that joins a phosphate group to the 5’ carbon of one sugar and the 3’ carbon of another sugar. Reference: File:Enlace fosfodiéster.png, File:PhosphodiesterBondDiagram.png: User:G3pro (talk)User:G3pro at en.wikipedia.orgDerivative work: User:Merops (talk)Derivative work: User:Deneapol (talk)Derivative work: User:KES47 (talk)Text tweaks: Incnis Mrsi (talk)Text tweaks: DMacks (talk))Derivative work: User:Miguelferig (talk) with ionizationChem. / graphical improvements: User:Mykhal, CC BY-SA 3.0 , via Wikimedia Commons. Retrieved October 2021, from: https://commons.wikimedia.org/wiki/File:Phosphodiester_Bond_Diagram.svg NITROGENOUS BASES Subpage of Structure of a Nucleotide – Nitrogenous Bases 1/1 Two categories of bases are found in the nucleotides of both DNA and RNA: purines and pyrimidines. These nitrogen-containing compounds are attached to the 1’ carbon of a sugar in a single nucleotide. Continue to learn about purines and pyrimidines. Purines Purines have two rings in their structure. The two purines in DNA are adenine (A) and guanine (G). HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 35 MODULE 01 COMPANION GUIDE PHGY 170 Pyrimidines Pyrimidines have only one ring in their structure. The three pyrimidines are cytosine (C), thymine (T), and uracil (U). Thymine (T) is a pyrimidine that exists only in DNA, and uracil (U) is a pyrimidine that exists only in RNA. Note: The entire genetic code of an organism is stored in strands of DNA that are made up of patterns of these four types of nucleotides. FROM NUCLEOTIDES TO DNA This content was retrieved from Section 03 Slide 4 of 14 of the online learning module. The sugar-phosphate backbone of DNA is held together by phosphodiester bonds. These are added to the 3’ end of the existing strand. The new nucleotide will be connected to the other nucleotide with one phosphate, while its other two phosphates are released, adding the energy needed for this new bond to form. DNA is composed of two strands. Hydrogen bonds between opposite (complementary) bases on each strand form cross-linkages. The purines in one DNA strand will always base-pair with the pyrimidines in the opposing DNA strand. Adenine always pairs with thymine and guanine always pairs with cytosine. This bonding leads to the formation of a double-stranded DNA molecule. Each strand of the DNA is antiparallel to the other, because they run in opposite directions. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 36 MODULE 01 COMPANION GUIDE PHGY 170 DNA strands composed of a sugar phosphate backbone and nitrogenous bases connected by hydrogen bonds to their complementary bases. Reference: Plopper, G., & Ivankovic, D. B. (2020). Principles of Cell Biology (3rd ed.; pp. 70). Jones & Bartlett Learning, LLC. Retrieved February 2022, from: http://ebookcentral.proquest.com/lib/queen- ebooks/detail.action?docID=6002586 DNA STRUCTURE: DOUBLE -STRANDED HELIX This content was retrieved from Section 03 Slide 5 of 14 of the online learning module. The nitrogenous bases of each nucleotide are hydrophobic while the sugar-phosphate backbone is hydrophilic. As a result, when placed in an environment with lots of water (i.e., a cell), the bases stack themselves in the centre while the sugar-phosphate backbone remains outside. In order for the bases to come into contact with as little water as possible, this “ladder” of double- stranded DNA twists to become a spiral staircase, known as a double-stranded helix. VIDEO: THE STRUCTURE OF DNA This content was retrieved from Section 03 Slide 6 of 14 of the online learning module. James Watson and Francis Crick solved the structure of DNA in 1953, using images of DNA from a technique called x-ray crystallography, data which was discovered by Rosalind Franklin and Raymond Gosling. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 37 MODULE 01 COMPANION GUIDE PHGY 170 Watch the video of Watson discussing the base pairing of DNA. (01:41) James Watson Explains DNA Base Pairing Start of Video Transcript: The Cavendish shop was to build with some tin models and that took too long. And you know, finally in desperation. I made some other cardboard. I began moving them around and and one of the other arrangement, you know where I had a big and a small molecule. And so how did you do it somehow you had to form link bonds. So here's a and here's T. And I wanted this hydrogen to point directly at this nitrogen. So I hit something like this. So then I went today with the pair and whether this nitrogen to point to this one like this. Whoa, they look the same you can push we know he could just you know, even if we go up to the ceiling when I'm building a tiny fraction of I'll kill hundreds of million to these base pairs in one mark all fitting into this wonderful symmetry, which we saw, you know, the morning of February 28th 1953. End of Video Transcript. Page link: https://www.youtube.com/embed/PDeaLxoL75M QUESTION: THE STRUCTURE OF DNA This content was retrieved from Section 03 Slide 7 of 14 of the online learning module Answer the question based on what you have learned about the structure of DNA. 1 of 1: How do you think an understanding of hydrogen bonds influenced the discovery of DNA structure? Feedback: Understanding how the bases could pair together to maximize hydrogen bonds (e.g., A with T, C with G) gave Watson and Crick an idea about how wide the structure of DNA could be. INTRODUCTION TO RNA This content was retrieved from Section 03 Slide 8 of 14 of the online learning module RNA is a nucleic acid that is similar to DNA. RNA plays a critical role in the synthesis of proteins, as it relays information stored in the nucleus (in the form of DNA) to the cytoplasm* where all protein is made. You will learn more about this flow of genetic information in the next section. There are many different types of RNA, but the main role of RNA in eukaryotic cells is to carry information that tells the cell what kinds of proteins to make. Definitions*: HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 38 MODULE 01 COMPANION GUIDE PHGY 170 Cytoplasm: the contents of the cell outside the nucleus that are contained by the plasma membrane. HOW RNA STRUCTURALLY DIFFERS FROM DNA This content was retrieved from Section 03 Slide 9 of 14 of the online learning module There are a few major differences between the structural components of RNA and DNA, since their functions in the cell differ substantially. Continue to learn about the structural differences between RNA and DNA. Uracil In RNA, the pyrimidine uracil is used instead of thymine and forms its base pairs with adenine. Ribose The nucleotides in RNA contain ribose rather than deoxyribose. Recall that ribose has an extra oxygen on the 2’ carbon compared to deoxyribose. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 39 MODULE 01 COMPANION GUIDE PHGY 170 Single Strand RNA is single stranded. It does not normally form a double-stranded helix and it is less stable than DNA. Reference: Adapted from Plopper, G., & Ivankovic, D. B. (2020). Principles of Cell Biology (3rd ed.). Jones & Bartlett Learning, LLC. Retrieved February 2022, from: http://ebookcentral.proquest.com/lib/queen- ebooks/detail.action?docID=6002586 RNA: FUNCTIONS AND TYPES This content was retrieved from Section 03 Slide 10 of 14 of the online learning module The main purpose of DNA is to carry and preserve genetic information, whereas the fundamental purpose for RNA is to transport small copies of genes around the cell for a variety of uses. There are three main types of RNA, all of which are involved in the critical process of protein synthesis. Continue to learn about the three types of RNA. Messenger RNA (mRNA) mRNA carries instructions for making proteins in the cell. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 40 MODULE 01 COMPANION GUIDE PHGY 170 Transfer RNA (tRNA) tRNA brings amino acids for protein synthesis during translation. Ribosomal RNA (rRNA) rRNA and ribosomal proteins make up ribosomes, which are in charge of translating RNA into protein. Ribosomes are an example of ribozymes-RNA that has the ability to catalyze chemical reactions. Note: There are other non-coding RNAs that have a wide range of functions that are still being discovered. Short interfering RNA (siRNA) will bind to mRNA and cause it to be degraded. This effectively turns off the expression of a gene. Others help determine mRNA location in the cell, or play a role in gene transcription. Reference: mRNA. Lene Martinsen, STORE NORSKE LEKSIKON. CC BY NC SA 3.0. Retrieved March 2022, from: https://sml.snl.no/mRNA HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 41 MODULE 01 COMPANION GUIDE PHGY 170 CHECKPOINT ACTIVITY: THE STRUCTURE AND FUNCTION OF DNA This content was retrieved from Section 03 Slide 11 of 14 of the online learning module Select the term from the dropdown menu that best fills in the blank to complete each statement. Options: deoxyribonucleotide, phosphate, uracil, hydrogen 1. The fundamental structural unit of DNA is a _________; combinations of these structural units are arranged sequentially to form a linear strand of DNA. 2. Each nucleotide is made up of three parts: a 5-carbon sugar a _______ group, and a nitrogenous base. 3. In DNA there are two purine bases: adenine and guanine as well as two pyrimidine bases: cytosine and thymine which in RNA is replaced by ______. 4. The simplest form of stable DNA in a cell is called a DNA double helix, formed by two strands of DN A oriented antiparallel to one another and held together by ________ bonds between the atoms in the base portion of the deoxyribonucleotides. Feedback: Correct answers: 1. deoxyribonucleotide 2. phosphate 3. uracil 4. hydrogen CHECKPOINT ACTIVITY: DNA VERSUS RNA This content was retrieved from Section 03 Slide 12 of 14 of the online learning module Compare the functions and structure of DNA and RNA. Select whether each phrase describes DNA or RNA. 1. Contains thymine 2. Has ribose sugars 3. Contains uracil 4. Carries and preserves genetic information 5. Normally double-stranded 6. Has deoxyribose sugars 7. Used during protein translation 8. Mostly single-stranded Feedback: Correct answers: 1. DNA HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 42 MODULE 01 COMPANION GUIDE PHGY 170 2. RNA 3. RNA 4. DNA 5. DNA 6. DNA 7. RNA 8. RNA You learned that DNA contains a deoxyribose sugar, is double stranded, and consists of a thymine, adenine, cytosine, or guanine base. The main function of DNA is to carry and preserve genetic information. In contrast, RNA is composed of a ribose sugar, is normally single stranded, and consists of a uracil, adenine, cytosine, or guanine base. RNA is the key messenger during translation. You will learn about translation in Section 05. CHECKPOINT QUESTION : THE NUCLEUS AND RNA This content was retrieved from Section 03 Slide 13 of 14 of the online learning module Answer the question using what you have learned about RNA so far. 1 of 1: What do you think the benefits are to using RNA, for example: mRNA, instead of DNA in cellular processes outside of the nucleus? Feedback: DNA is in full chromosomes and double-stranded, therefore, it is highly protected and more difficult to transport or move to cellular locations. mRNA is easier to move, and easier to break down when it is no longer needed. SECTION 03: SUMMARY This content was retrieved from Section 03 Slide 14 of 14 of the online learning module In this section, you learned about the characteristics of DNA and RNA. This included an overview of nucleotides, deoxyribose and ribose (5-carbon) sugars, phosphate, and nitrogenous bases. It will be important to remember the four bases, adenine, guanine, cytosine, and thymine; their complementary base pairing and antiparallel organization. You then compared and contrasted structural and functional differences between DNA and RNA; this included the replacement of thymine with uracil, double-versus single-stranded, deoxyribose versus ribose sugars, and storing genetic information versus expressing specific genes. Finally, you were given a brief overview of a few important types of RNA: mRNA, tRNA, and rRNA. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 43 MODULE 01 COMPANION GUIDE PHGY 170 SECTION 04: THE CENTRAL DOGMA PART 1 - DN A REPLICATION INTRODUCTION TO THE CENTRAL DOGMA: DNA REPLICATION This content was retrieved from Section 04 Slide 2 of 18 of the online learning module. Now that you have an understanding of the basic structure of DNA and RNA, you will explore their functional significance. DNA is the genetic material that can be inherited by offspring. These seemingly simple strings of nucleotides determine an individual's characteristics (e.g., eye colour, height, nose shape, etc.). You may be wondering how sequences of nucleotides can provide instructions for all these features. This can be explained by the central dogma. The central dogma of molecular biology is a set of principles that explain how DNA contains the instructions for building RNA and subsequent proteins, which are essential for the structure and function of the cell and body. Once you understand the central dogma, you will begin to understand the importance of DNA and why the cell needs to protect it. Without DNA, a cell would have no functional activity. A chromosome being uncoiled into a more accessible or usable structure for gene expression. Click to enlarge. INTRODUCTION TO GENES This content was retrieved from Section 04 Slide 3 of 18 of the online learning module. DNA is divided into functional units known as genes. Genes are small pieces of DNA that contain specific instructions for the synthesis of a functional product, a molecule, needed to perform a job in the cell. This molecule is usually a protein. For instance, let’s take a flower colour gene. This gene would be located somewhere along a chromosome. If you took a closer look at this gene, it would consist of a specific DNA sequence. This HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 44 MODULE 01 COMPANION GUIDE PHGY 170 sequence provides instructions for a specific protein pigment that gives rise to a particular flower colour. Genes are made up of specific DNA sequences that code for specific proteins. Proteins influence phenotype. Typically, genes contain information to make a protein, and this is referred to as coding DNA. In eukaryotes these genes are located on chromosomes and are separated by large spaces of DNA called non-coding DNA. These non-coding regions do not correspond to protein production. Reference: Intro to gene expression (central dogma). (n.d.). Khan Academy. Retrieved February 2022, from: https://www.khanacademy.org/science/ap-biology/gene-expression-and-regulation/translation/a/intro- to-gene-expression-central-dogma STRUCTURE OF A GENE This content was retrieved from Section 04 Slide 4 of 18 of the online learning module. Within a gene, there are several types of nucleotide sequences: exons, introns, and regulatory sequences. These portions of DNA have unique functions. Continue to learn the function of the different DNA sequences found within genes. A gene composed of exons, introns, and regulatory sequences. Exons Exons are the sections of a gene that contain the information that is used to make a protein, called coding sequences, or coding DNA. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 45 MODULE 01 COMPANION GUIDE PHGY 170 Introns Introns are sections of DNA that are not used to make a protein, called non-coding sequences, or non- coding DNA. Regulatory Sequences Regulatory sequences control when a gene is turned on, or used. You will learn more about regulatory sequences in the next section. Note: The important thing to take away is that most of a gene is not actually used to make a protein- only a small amount is. Reference: Plopper, G., & Ivankovic, D. B. (2020). Principles of Cell Biology (3rd ed.; pp. 54). Jones & Bartlett Learning, LLC. Retrieved February 2022, from: http://ebookcentral.proquest.com/lib/queen- ebooks/detail.action?docID=6002586 THE CENTRAL DOGMA OF MOLECULAR BIOLOGY This content was retrieved from Section 04 Slide 5 of 18 of the online learning module. The central dogma explains that there are three key processes that need to occur for information to be converted from DNA to protein: replication, transcription, and translation. These processes describe the flow from DNA, to RNA, to a protein. Continue to learn about the purpose of each process in the central dogma. Replication DNA is replicated (copied) before a cell divides so that both the original cell and the new daughter cells each have complete copies of DNA. The major enzyme involved in this process is DNA polymerase. Transcription Information from a section of DNA is transcribed (copied) into RNA to transport this information out of the nucleus for protein production. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 46 MODULE 01 COMPANION GUIDE PHGY 170 The major enzyme involved in this process is RNA polymerase. Translation The RNA is read and translated from nucleotides to amino acids to produce proteins that perform a specific function in the cell. The major enzyme involved in this process is the ribosome. HUMAN CELL PHYSIOLOGY | PHGY 170 MODULE 01 PAGE 47 MODULE 01 COMPANION GUIDE PHGY 170 Note: You will delve into the details of each of these processes for the remainder of this module. This section focuses on DNA replication. Reference: Laurent, J.P. (n.d.). From Gene to Protein. LGMD2i Research Fund. Retrieved April 2022, from: https://www.lgmd2ifund.org/science-basics/from-gene-to-protein STAGES OF DNA REPLICATION This content was retrieved from Section 04 Slide 6 of 18 of the online learning module. Every cell contains a complete copy of DNA (i.e., genome). Therefore, DNA must be copied in preparatio

PHGY 170 Module 01: Introduction to the Cell and Central Dogma PDF

Document Details

Tags

Related

Summary

Full Transcript

Upgrade to continue