notes 7

Molecular Biology Chapter 7 Unifying Theories of Biology Theory of Evolution Cell Theory Cell Theory Possible due to microscopy Robert Hooke in 1665 30x magnification Observed cork cells Anton Van Leeuwenhoek 300x Blood and sperm cells By the early 1800s, enough observations had been made to theorize that all living things are made of cells All living things are made of cells Some properties of life are universal The history of life is the history of cell divisions Basic Cell Types Morphologically, 2 types of cells Prokaryote Eukaryote Phylogenetically (evolutionarily, historically), 3 types of cells Bacteria (prokaryote) Archaea (prokaryote) Eukarya (Eukaryote) Prokaryotic Diversity Microbiome 300-500 species in our intestines (mostly large) 10x as many bacterial cells as cells in your body Breast milk contains over 700 species!!!! Thermoacidophiles (Archaea) Live in hot, acidic environments 100+ C, ph of 1 or 2 They make PCR possible Prokaryotes Simplest form of cells, but not simple…. Needed technological advancement in microscopy to understand Vast majority of unicellular Prokaryotic cells are highly organized 3 traits prokaryotes (and all living things) must have: Store information Use information to make functional molecules (proteins) Separate yourself from the environment Information Flow DNA contains information Information is transcribed into RNA as needed Information is translated into functional molecules at the ribosome DNA to RNA to Proteins Prokaryotic structures Chromosome Large DNA molecule with smaller proteins DNA= information, stored in units called genes Proteins= structural support In E.coli, uncompacted, linear chromosome is 1mm long 500x longer than the cell Chromosome is circular DNA is supercoiled Proteins help DNA is found in a region called the nucleoid Roughly 20% of a cell’s volume Bonus DNA!! Small, circular supercoiled DNA Plasmids Contain functional genes Genes probably not required for survival, can carry useful genes i.e. Antibiotic resistance Prokaryotes can swap these with each other, take up from the environment Ribosomes Manufacture proteins Combination of proteins and RNA molecules 10,000s per cell Plasma membrane separates living (inside) from non-living (outside) Inside is different than the outside Selective permeability Concentrations of solutes can be controlled ------------------------------------------------------------------------------------------------------------------------------------------ SIDE NOTE*******Membrane Structure*********SIDE NOTE Fluid mosaic model Phospholipids self- organize into bilayer Polar head= loves water Non-polar tail= hates water NOT held together with covalent bonds!!! Membrane is flexible ------------------------------------------------------------------------------------------------------------------------------------------ Cell wall functions as an “exo-skelleton” Fibrous layer that surrounds the cell Outside of the plasma membrane Structure Protection Osmotic pressure Some bacteria have internal membranes Some chemical reactions occur on membranes Photosynthetic bacteria have extensive layers for photosynthesis More layers= more photosynthesis Flagella “Whips that allow for swimming Roughly 60 body lengths per second at top speed Also found in prokaryotes, but not commonly Organelles (“Little organs”) Membrane bound compartments Storage Sequestering chemical reactions Cytoskeletons (Simple) Protein fibers providing internal structure Eukaryotic Cells Differences from prokaryotic cells Nucleus Much Larger Prokaryotes---1-10 micrometers Eukaryotes---5-100 micrometers Eukaryotes are compartmentalized Organelles Membrane bound structures Advantages Isolation of incompatible chemical reactions Efficiency of chemical reactions Cytoskeleton is much more extensive, found throughout the cell ------------------------------------------------------------------------------------------------------------------------------------------ Side note***********What limits cell size?***********Side note Bacterial cells can be 100x smaller than out cells Cell size notes… How big can a cell get? The amount of required nutrients depends on volume, but…. Cells gain nutrients through their cell membranes How does surface area scale with volume? Calculating cell sizes Surface area= 6 x the length of the side squared Volume= length of the side cubed Nucleus Enclosed by nuclear envelope (membrane) DNA is highly condensed, organized Nucleolus Area where ribosomal RNA is manufactured How does the nucleus hold its shape? Protein filaments (cytoskeleton) act as scaffolding Information storage= inside nucleus Information use= outside nucleus RNA is transcribed, taken to the ribosomes to make proteins Nuclear envelope is continuous with the endoplasmic reticulum (ER) ER is a membrane bound organelle 2 types of ER Rough Endoplasmic Reticulum (Rough ER) “Bumps” are ribosomes Proteins are inserted into the interior (lumen) of the ER Proteins shipped to other parts of the cell via vesicles Smooth Endoplasmic Reticulum (Smooth ER) Lipid processing Synthesizes/ breaks down lipids Builds membranes (phospholipids) Stores Ca++ Golgi apparatus Protein processing Stacked, flattened membrane sacs Cis-side= side facing the nucleus Trans-side= side facing the plasma membrane STEPS>>>>> Cis-side receives vesicles from the rough ER Proteins are deposited into the Golgi’s lumen Proteins are processed inside the Golgi Proteins leave the Golgi via vesicles on the trans-side Free ribosomes Proteins manufactured within the cytosol Not organelles because they are not enclosed by a membrane Peroxisomes Many chemical reactions produce H2O2 Peroxisomes isolate these ractions, break down H2O2 with peroxidase Lysosomes Animals only Interior is roughly pH 5.0 Cytosol is roughly pH 7.2 Roughly 40 different digestive enzymes, can break up proteins, carbohydrates, fats 3 ways materials reach lysosomes Autophagy (Self-eating) Lysosomes recycle other organelles Phagocytosis Plasma membrane engulfs food, forms phagosome Fuses with lysosome for digestion Receptor mediated endocytosis Receptors on the plasma membrane recognize specific food molecules Endosome forms around food molecules H+ is pumped into endosome Digestive enzymes are put into endosome, forming lysosome What happens when they malfunction? Case Study At 6 months, child loses the ability to roll over, sit upright, turn hean in response to mother’s voice At the cellular level, lysosomes are swollen What could be going wrong in the lysosome? Membrane isn’t permeable Not breaking down materials Too much ATP Lack of enzyme Hexoaminidase A Hereditary disorder, HEXA Without hexoaminidase A, fatty acids derivatives called gangliosides are not broken down Gangliosides accumulate on nerve cells Where is there a high concentration of nerve cells in the human body? Vacuoles Plants and fungi In seeds, store proteins In petals, store pigments In leaves, store toxins Can be very large, 80% of the cells volume Commonly store water, ions (K+, Cl-) Semi- autonomous organelles Mitochondria Chloroplasts Specialize in energy conversion, but….. Have their own genomes and ribosomes!! Genome is circular and supercoiled Gene sequences are more similar to existing prokaryotes than they are to eukaryotic nuclei Mitochondria Found in all eukaryotes Cellular respiration Double membraned Cells may have roughly 50 to 1.000,000+ mitochondria Chloroplasts Found in plants and algae Photosynthesis Triple membraned Cell walls Outside the plasma membrane Plants and Fungi Plants= cellulose Fungi= chitin Predominantly large carbohydrates Rigid structure for support, protection Few organisms can digest cellulose Plants can build secondary cell walls out of lignin Wood Cytoskeleton Network of protein fibers that provides: Provides structural support Link the organelles together Shapes Structural stability Organizing organelles within the cell Vesicle pathways Moving the cell through the environment The cytoskeleton is dynamic 3 elements Actin Smallest Filament of actin molecules Can be assembled/disassembled very quickly Maintain cell shapes Move cells (like amoebas) Move organelles around cells Intermediate filaments Fibers made of lots of different proteins We have 70 different ones Maintain cell shapes Anchor the nucleus Not involved in movement Provide resistance to pressure and abrasion keratins Microtubules Largest of the elements Made of alpha and beta- tubulin Dynamic Maintains cell shape Move chromosomes during cell division Form tracks for the vesicles to travel on Variation between cells In multicellular organisms, cells can have specific function STRUCTURE CORRELATES WITH FUNCTION!!!!!! Dynamic cells Cells are not static, they’re always changing Individual phospholipids can move the length of their organelle in roughly 1 minute 10,000,000 ATP cycled/ cell/ second Mitochondria are replaced every 10 days All this activity can make cells difficult to study Moving things around the cell Nuclear transport Nuclear pores Pores are selective Proteins have a specific “tag” in order to be allowed in Roughly 500 molecules more though per second 3-4,000 pores per nucleus Up to 2,000,000 molecules per second Nucleoplasmin Is there a “tag”? If there is a “tag” where would it be? Hypothesis: “Tag” is physically part of the protein on the tail or the core Null hypothesis: there is no tag on the protein itself, or tags don’t really exist How can we test this? Specific 17 amino acid signal/tag/address/zip code that tells the cell to take the nucleoplasmin into the nucleus Is nucleoplasmin floating around the cell until it bumps into the nucleus? Hypothesis” proteins are chauffeured around the cell Prediction: as proteins are made, they move through the cell in an organized fashion Pulse-chase experiment Add a “pulse” of a radioactive tracer Pulse= small amount given for a short time What would be good to label if you want to follow a protein? After the pulse, “chase” with the non-labeled molecules Follow the radioactive proteins over time These labeled proteins all move together in an organized fashion over time Rough ER >>> secretory vesicles >>> secretory ducts Steps….. The ribosomes on the rough ER are outside the lumen. How do the proteins get inside? Must get inside for vesicle formation How do they move from the ER to the Golgi? What happens inside the Golgi? How do finished proteins get to their final destination? Other ways to do pulse-chase Identify steps in biochemical pathway Which compounds are radioactive 5 seconds after the pulse? 10 seconds? 1 minute? Getting into the ER Critical observation When isolated ribosomes (outside a cell) make proteins, they are 20 amino acids longer than the same proteins made by ribosomes inside functioning cells What are those extra 20 amino acids? Once inside the ER, proteins destined for the Golgi are often glycosolated A carbohydrate is attached Glycoprotein Moving from the ER to the Golgi Vesicles bud off from the ER Move to the cis side of the Golgi Fuse with the Golgi and drop their cargo inside How do the vesicles know where to go? They’re tagged, too They can be carried directly, too What happens inside the Golgi? Golgi is dynamic, always being recreated New membrane added at the cis side Membrane lost at the trans side While inside the Golgi, proteins are modified Carbohydrate attached at the ER is removed Different carbohydrates are added Folding is completed How do finished proteins reach their destination? By carrying the right tags Embedded in the Golgi’s membrane are receptors Receptor= protein that recognizes other specific proteins These receptors span the membrane They can recognize molecules both inside and outside the Golgi Example Lysosome-bound proteins have a mannose- 6- phosphate attached to them Receptors from mannose-6-phosphate on the inside of the Golgi’s membrane grab onto these proteins A vesicle forms around the proteins carrying the proteins with the mannose-6- phosphate tags The “outside” part of the receptor recognizes proteins embedded in the lysosome’s membrane When the vesicle and lysosome receptors recognize each other, the vesicle and lysosome fuse, proteins are released inside the lysosome Endomembrane System All these organelles arefunctionally linked together Proteins and vesicles carry tags that direct them to their correct destinations How exactly are the vesicle moving around the cell? Don’t just float around--- they have tracks!!! Cytoskeleton as tracks Motor proteins are the trains Kinesin Use ATP to generate movement and carry vesicles along microtubules