Theme 1: The Structure of the Cell

Biology 1A03 Textbook Link Biology 1A03 MODULE NOTES Theme 1: The Structure of the Cell MODULE 1: The Composition and Structure of Membranes UNIT 1: Cells in our body What cells make up our own body?? continued cell division estimated 10 trillion cells in our body Each cell differs in function: muscle, kidney or neuron cells These are all eukaryotic cells We carry a lot of prokaryotic cells (like bacteria cells) These cells make up 2-3% of our body mass Most are unharmful, so are harmful They are in our teeth, on our skin, in our tract EXAMPLES: Streptococcus salivarius: a normal inhabitant of upper respiratory tract and oral cavity Staphylococcus haemolyticus: Resides on our skin Bacteroides thetaiotaomicron: predominant intestinal bacteria MICROBIOME: Biology 1A03 2 A microbiome is the community of microorganisms that can usually be found living together in any given habitat. UNIT 2: Phospholipids are the building blocks of membranes What is a cell? A membrane bound structure containing macromolecules There are 4 classes of macromolecules 1. Nucleic acids (DNA, RNA) Make up hereditary material of cell and can be found in DNA, chromosome, nucelod Info encoded in DNA is converted into functional products of cell 2. Proteins Make up structural elements of cell and perform metabolic activities 3. Polysaccharides Important structural components and are sources of stored energy 4. Phospholipids Primary component of cell membrane Composed: Glycerol molecule linked to a phosphate and 2 fatty acids (fatty acid tails) CELL MEMBRANE OF A CELL: Biology 1A03 3 made up of lipid macromolecules. Each of these molecules has hydrophobic and hydrophilic properties that allow stacked lipid bilayers to form Cell membranes are VERY thin (5-10nm in thickness) Steroids (cholesterol) are also important part UNIT 3: Organization of cell membranes PHOSPHOLIPIDS SPONTANEOUSLY ADOPT MEMBRANE STRUCTURES: Lipids not only form bilayers but can aggregate and form lipid micelles These structures are important for absorption of fat soluble vitamins and complex lipids in the human body FACTORS THAT AFFECT FLUIDITY OF CELL MEMBRANES: Unsaturated or saturated fatty acids Double bonds in a hydrocarbon tails produce bends on kinks in the chain This has the effect of pushing neighbouring phospholipids further apart and increasing fluidity More double bonds (unsaturated tails) = more fluidity Number of carbons in the fatty acid tails Number of carbons in a hydrocarbon chain varies, typically there are 16 or 18 carbons Longer chains pack together more tightly then the shorter chains, reducing fluidity of membrane Long fatty acid tails = less fluid Biology 1A03 4 temperature Higher temperatures = promotes fluidity Lower temperatures = decrease fluidity Cold adapted organisms tend to have more unsaturated phospholipids in their membrane that help to maintain fluidity the presence or absence of cholesterol A bilipid membrane containing just phospholipids is TOO fluid Cholesterol molecules constrain fluidity of the membrane by packing closely to neighbouring phospholipids At low temperatures, phospholipid bilayers begin to solidify, when this happens cholesterol helps maintain fluidity by keeping the phospholipids apart from one another LIPID RAFT Within membranes, there are domains that demonstrate different degrees of fluidity. Some parts are more fluid that others. The region of lower fluidity is called a LIPID RAFT It can hold macromolecules together in the membrane These rafts gather proteins involved in the same metabolic pathway or a collection of receptors on the surface of the cell Why are these regions LESS fluid? Biology 1A03 5 Region of lipid raft is taller = longer phospholipid hydrocarbon tails = allows for phospholipids to pack together = lowering fluidity = making it possible to hold macromolecules in the raft Higher concentration of cholesterol also decreases fluidity within domain of lipid raft UNIT 4: Movement across cell membranes FLUIDITY OF CELL MEMBRANE ALLOWS FOR TRANSMEMBRANE MOVEMENTS: Changing fluidity alters how much or how quickly a substance will move across a membrane Regions of the membrane high in saturated fatty acids = less permeable = less fluid membrane = substances cannot pass easily Regions of the membrane high in UNsaturated fatty acids = higher permeability = more fluid membrane = substances can pass more easily CELL MEMBRANES ARE SELECTIVELY PERMEABLE Small molecules are ions can cross along a concentration gradient (high to low) Small and non-polar molecules can pass through the phospholipid bilayer quickly Charged and larger polar substances have greater difficulty moving across the membrane. So HOW DO WE GET CHARGED OR LARGER POLAR MOLECULES ACROSS THE CELL MEMBRANE? Proteins embedded in the phospholipid bilayer can facilitate transport across a membrane Biology 1A03 6 Fluid mosiac model UNIT 5: Mechanisms of transport across the cell membrane TYPES OF MOVEMENT ACROSS THE CELL MEMBRANE: PASSIVE DIFFUSION (simple diffusion) from areas of high concentration to low concentration (along a gradient) Involves the movement of: lipid soluble molecules, gases, uncharged polar molecules and some water Process: Molecule comes into contact with crosses the phospholipid bilayer into or out of the cell PASSIVE TRANSPORT (facilitated diffusion) or facilitated diffusion: from areas of high to low concentration (along a gradient) (no energy required) Involved proteins embedded in the membranes Involves the movement of: Ions, hydrophilic molecules Process: Transport proteins provide a hydrophilic core that allows large hydrophilic molecules and most water to move across the cell membrane ACTIVE TRANSPORT Molecules move against a concentration gradient (fueled by energy from the hydrolysis of ATP) OSMOSIS IS THE TRANSPORT OF WATER ACROSS MEMBRANES: Biology 1A03 7 Small amounts of water are able to move across the membrane, but for faster movements we use AQUAPORINS Aquaporins are exclusively permeable to water OSMOSIS IN RED BLOOD CELLS MODULE 2: Organelles and Energy UNIT 1: Eukaryotes and Prokaryotes LIFE AND PHOTOSYNTHESIS BEGAN 4 BILLION YEARS AGO Evolution of these relationships can be observed when we compare prokaryote and eukaryote organisms STRUCTURAL DIFFERENCES IN BOTH TYPES OF CELLS: Both have an external membrane that separates the inside and outside of the cell Eukaryotes cells have a double membrane bound nucleus that serves as an internal compartment to separate the genetic material of the cell or chromosomes SIGNIFICANT CHANGE IN EVOLUTIONARY HISTORY: The transition from prokaryotes that lack a distinct nucleus, and eukaryotes with a true compartmentalized nucleus PROKARYOTES AND EUKARYOTES SHARE A COMMON ANCESTOR Prokaryotic cells have been around for the longest time Eukaryotic cells appeared 2 billion years ago UNIT 2: The evolution of chloroplasts and mitochondria Biology 1A03 8 CHLOROPLASTS MANUFACTURE SUGAR MITOCHONDRIA PRODUCE CHEMICAL ENERGY HOW DID THESE ORGANELLES FORM INSIDE OUR CELLS?? In 1981, Dr. Lynn Margulis proposed that eukaryotic cells originated as communities of interacting entities that are joined together She properd that prokaryotic cells could have been ingested or entered into a host cell. Where overtime the guest prokaryotes and eukaryotes may have developed mutually beneficial interactions Mitochondria and chloroplasts are examples of distinct membrane bound compartments in the cell that may have entered the cell from external origins UNIT 3: Evidence supporting the endosymbiotic theory of organelle evolution CHLOROPLASTS MANUFACTURE SUGAR MITOCHONDRIA PRODUCE CHEMICAL ENERGY HOW DID THESE ORGANELLES FORM INSIDE OUR CELLS?? In 1981, Dr. Lynn Margulis proposed that eukaryotic cells originated as communities of interacting entities that are joined together She properd that prokaryotic cells could have been ingested or entered into a host cell. Where overtime the guest prokaryotes and eukaryotes may have developed mutually beneficial interactions Mitochondria and chloroplasts are examples of distinct membrane bound compartments in the cell that may have entered the cell from external origins Biology 1A03 9 WHY ARE ORGANELLES IMPORTANT? 1. Compartmentalization: All enzymes required for one process are in close proximity (for example: all enzymes in chloroplasts help with photosynthesis) 2. No interfering: Processes that have nothing to do with each other can be kept seperate 3. More efficient: Chemical reactions are more efficient when substrate, enzyme and products are concentrated in an organelle UNIT 4: Cellular Respiration HOW DOES ENERGY FLOW IN BIOLOGICAL SYSTEMS? PLANTS AND ANIMALS STORE POLYSACCHARIDES FOR ENERGY starch -storage in plants 2 types: Unbranched amylose and branched amylopectin glycogen - storage in animals GLUCOSE PROCESSING PRODUCES ATP process is called cellular respiration (4 steps) MODULE 3: Proteins UNIT 1: Proteins, what do they do? How are they made? What do they look like? PROTEINS HAVE VARIOUS FUNCTIONS transport and signaling enzymes movement and structure Biology 1A03 10 defence PROTEINS HAVE VARIOUS STRUCTURE The various proteins in our bodies can have different sizes and shapes Many of these structural differences relate to their FUNCTION For example: TATA-BOX binding protein → interacts with DNA molecules, → is able to do so due to a groove in the protein that allows for this interaction For example: PORIN PROTEINS → important for transport of water (across cell membrane)→ they have a structural hydrophilic pore For example: OTHER SOLUBLE CELLULAR PROTEINS → mostly have globular shapes with hydrophobic interior and a hydrophilic exterior → allows protein to be soluble in aqueous environment of cytosol HOW TO SCIENTISTS REPRESENT PROTEIN STRUCTURES? 2 ways to represent a subunit of the protein INSULIN: 1. Space-filling model This shows the actual relative size and location of each atom (Representing atoms w different colours) CHAT GPT EXPLANATION: What it is: This representation shows the protein as a collection of spheres that represent atoms. Each sphere’s size corresponds to the actual size of an atom’s electron cloud. Biology 1A03 11 Purpose: It gives a realistic view of the protein’s size and shape, and how it might interact with other molecules. It shows the full volume of the protein, emphasizing how tightly packed the atoms are. Best for: Viewing the overall surface and understanding how a protein might fit into other structures or interact with small molecules. 2. Ribbon diagram: Lines represent the backbone of the protein polymer. The broader line represents an organized, reiterated structure called an alpha helix. The thinner line represents a less ordered loop CHAT GPT EXPLANATION: What it is: This simplifies the protein’s structure by representing it with smooth, flowing lines or ribbons that trace the backbone of the protein. Purpose: The ribbon highlights important structural features like alpha-helices and beta-sheets, which are key components of a protein’s 3D structure. Best for: Understanding how the protein folds and the overall organization of its secondary structures, like how helices and sheets are arranged in space. Biology 1A03 12 UNIT 3: An overview of protein synthesis: from DNA to primary protein structures GENETIC INFORMATION CODES FOR PROTEINS Basic principles for proteins synthesis are the same for BOTH eukaryotic and prokaryotic cells. The genetic information for every protein is encoded in the DNA of the cell STEPS: 1. Transcribe that information into RNA, which serves as the template for synthesis of a polypeptide In prokaryotic cell: This is closely linked with translation of the RNA into proteins by ribosomes In eukaryotic cell: Primary RNA transcript is processed to mrna and transported into cytoplasm which is then translated into the protein by ribosomes THE CODE FOR A PROTEIN SEQUENCE IS IN THE NUCLEUS The double membraned nuclear envelope surrounds the nucleus and encloses the genetic material or chromosomes, separating the nuclear contents from the cytoplasm. The nucleus contains a region called the nucleolus This is where ribosomal RNA molecules that are an important components of the ribosomes are transcribed The double membrane of the nuclear envelope has embedded nuclear pore complexes that allows for material to flow into and out of the nucleus Biology 1A03 13 Most ribosomal RNAs are manufactured in the nucleolus They bind to proteins to form the ribosomal subunits These structures are then exported to the cytoplasm The nuclear pore complexes allow the transcribed RNA to exit the nucleus for further processing in the extranuclear regions mrna is also transported through these nuclear pores NUCLEAR PORES ARE NOT ONLY 1 WAY COMPLEXES RIBOSOMES SYNTHESIZE PROTEINS: The cellular machinery that are involved in the synthesis of proteins are called ribosomes 1. Structural component of ribosomes are made in nucleus 2. Then shipped out of the nucleus 3. Then these ribosomes assemble and have lage and small subunit components that both contain RNA molecules and proteins a. Ribosomes are able to remain soluble in the cytoplasm as free ribosomes, or can attach to the endoplasmic reticulum to become bound ribosomes These 2 different types of ribosomes can produce different proteins that will be destined for different parts of the cell or even secretion Biology 1A03 14 MODULE 4: Nucleic Acids Summarized notes on transcript Slides 1-3: Introduction Theme: The focus is on nucleic acids (DNA and RNA). Main Points: The module covers DNA’s role as the hereditary molecule, its structure, location in cells, and the various types of RNA. Slide 4: Macromolecules Overview Main Idea: Nucleic acids (DNA and RNA) are the fourth class of macromolecules alongside lipids, carbohydrates, and proteins. Key Concept: Prokaryotic cells have DNA in the nucleoid and often contain small plasmids, which can transfer genes like antibiotic resistance. Slide 5-6: Chromosomes and DNA Supercoiling Main Idea: Chromosomes are DNA organized with proteins. Eukaryotic cells have linear chromosomes, while prokaryotes have circular ones. Supercoiling: DNA supercoiling compacts long DNA molecules into smaller spaces within cells, preserving the double helix structure. Slide 7: Prokaryotic Genomes Main Idea: Maps of bacterial genomes, like E. coli, help identify the location of genes. Plasmids often carry Biology 1A03 15 additional survival-related genes, such as those for antibiotic resistance. Slides 8-9: Discovering DNA’s Role Main Idea: The lecture transitions to discuss how scientists discovered DNA as the hereditary material, beginning with Frederick Griffith’s experiments. Slides 10-12: Griffith’s Experiment Main Idea: Griffith’s 1928 experiment showed that nonvirulent bacterial strains could transform into virulent ones, suggesting that a hereditary material was being transferred. Slides 13-17: Avery’s Experiment Main Idea: In 1944, Oswald Avery's experiment built on Griffith's by identifying DNA as the molecule responsible for transformation, rather than proteins or RNA. Slides 18-19: Conclusion of Avery’s Findings Main Idea: Without DNA, transformation didn’t occur, confirming that DNA carries hereditary information. Slides 20-22: DNA Structure Discovery Main Idea: Rosalind Franklin’s X-ray diffraction experiments were pivotal in revealing DNA’s helical structure, which Watson and Crick later used to propose the double-helix model. Slides 23-25: Nucleotide Structure Main Idea: DNA consists of nucleotides (phosphate group, sugar, nitrogenous base). Purines (A, G) and pyrimidines (C, T) form base pairs through hydrogen bonds. Biology 1A03 16 Slides 26-28: Chargaff’s Rules and DNA Double Helix Main Idea: Chargaff’s rules show a 1:1 ratio of purines to pyrimidines, which supports the pairing of A with T and C with G in the double helix structure. Slides 29-31: RNA Overview Main Idea: RNA synthesis (transcription) is a process where RNA polymerase copies DNA into RNA. The main types of RNA are messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). Slides 32-34: RNA vs. DNA Main Idea: RNA differs from DNA in that it uses ribose sugar instead of deoxyribose and uracil (U) instead of thymine (T). RNA plays a direct role in protein synthesis. Slides 35-39: Types of RNA Main Idea: mRNA: Carries genetic instructions from DNA to ribosomes for protein synthesis. tRNA: Transfers amino acids to the ribosome during protein synthesis. rRNA: Forms part of the ribosome and plays a role in assembling proteins. Slides 40-43: DNA in Eukaryotic Cells Main Idea: Eukaryotic DNA is found in the nucleus and organized with histones into chromatin. The DNA is compacted through various levels of coiling, especially during cell division. Slide 44: Prokaryotes vs. Eukaryotes Biology 1A03 17 Main Idea: Eukaryotic genomes are larger and more complex than prokaryotic genomes, though both share the same basic nucleotide structure and base-pairing rules. Slide 45: Summary of Module Main Points: DNA stores hereditary information and forms a double helix. RNA plays essential roles in protein synthesis. Both prokaryotic and eukaryotic cells have DNA, though their genomes differ in size and organization. Biology 1A03 18