Week 1: Lecture/Reading Notes 1 & 2
Week 1: Lecture/Reading Notes 1 & 2 Bio Sci 152
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Bio Sci 152
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This 21 page Class Notes was uploaded by KelseyH on Sunday September 13, 2015. The Class Notes belongs to Bio Sci 152 at University of Wisconsin - Milwaukee taught by Dr. Daad Saffarini, Dr. Erica Young, Dr. Jane Witten in Fall 2015. Since its upload, it has received 140 views. For similar materials see Foundations of Biological Sciences II in Biological Sciences at University of Wisconsin - Milwaukee.
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Date Created: 09/13/15
iological Sciences M IO SCI 152 9215 Reading covered in these notes 2nd edition 15 363365 402404 1 edition 1395 353354 366367 370 Microbiology Section Lecture 1 Outline Microbiology Introduction 1 Biology Living Organisms a Origin of Life b Formations of the First Organisms i Prokaryotes c Creation of Eukaryotic Cells i Cellular Specialization 1 Formation and Classification of Organisms e Evolutionary Tree of Life 2 Earths Changing Environment a Checkpoint Questions and Answers 3 Eukaryotic Features a Protists b PhagocytosisEndosymbiosis Biology focuses on the study of all living beings also known as organisms All living organisms descend from a shared unicellular ancestor Organisms have multiple attributes in common such as 0 Contain DNA genetic information that makes reproduction possible 0 Show evolutionary changes in their genetic makeup throughout their ancestral lineage 0 Harness energy from their given surroundings 0 Show a structural likeness in their genetic foundation 0 Their genes all use a virtually worldwide code organisms use to create distinct proteins 0 Transform molecules gathered from their surroundings into new and different molecules llPage iological Sciences M IQ S 1152 9215 0 Use the energy obtained from the resources around them to execute biological functions 0 Achieve homeostasis by elaborate internal communications The Formation of the First Organisms Prokarvotes a unicellular organism without a nucleus were the first type of organisms to arise on earth 0 Many prokaryotes early and present existing gather their energy from photosynthesis o Photosvnthesis a chemical process that takes in light energy carbon dioxide H20 and converts it into glucose and oxygen 0 An example of a modern day prokaryote is a microorganism known as cvanobacteria a type of aquatic bacteria blue green algae 0 Photosynthetic prokaryotes that give off energy by completing a chain of reactions that involves oxygen is aerobic metabolism 0 Anaerobic metabolism is releasing energy through a chain reaction that lacks 0 en 0 Much less et cient than the aerobic method 0 The presence of oxygen on earth made it possible for living organisms to migrate from the water on to land 0 Oxygen created a tier of protective ozone that engulfed a majority of the UV rays ZlPage iological Sciences M IQ S 1152 9215 The Creation of Eukaryotic Cells 0 Cells began to evolve bringing rise to specialized membrane encased cubicles with functions The different enclosures are known as organelles o The nucleus is an organelle that contains DNA 0 The cell type that contains a nucleus is called a eukaryote A nucleus and multiple organelles are absent in prokaryotes 0 Organelles derived from endosymbiosis a type of symbiosis where one organism lives inside of another organism o Eukaryotic organelles that support creation by endosymbiosis are the mitochondria and the chloroplasts Mitochondria organelle responsible for respiration and energy release Chloroplasts organelles that carryout the chemical reaction photosynthesis 0 Cellular specialization eukaryotic cells unsuccessful in cell division grew larger from the still attached cells these cells could perform particular functions 0 Cell became more efficient in collecting food and nutrients Formation and Classi cation of Organisms Organisms reproduce by duplicating their entire amount of genetic information or genome 0 There are so many different types shapes and sizes of organisms today because of changes known as mutations in the genome that are inevitable and a necessity for evolution 0 Mutations can cause a change in structural make up biological actions and so on BIPage iological Sciences M IQ S 1152 9215 0 When new species of organisms are identified biologists select a scientific binomial name for the species 0 A binomial name is made up of two bi Latinized words the first word given classifies the genus a species group that hold a common ancestor and the second specifies the species An example of a binomial from page 5 in the book is humans known as Homo sapiens Evolutionary Tree of Life 0 Past knowledge of organisms relationships and DNA sequences lead biologists to pool their data and create a phylogenetic tree a branching diagram showing evolutionary relationships from a common ancestor The tree of life depicts an evolutionary path stemming from All life in general Broad Tree of Life See fig 14 for full view Al Li f e Protists Animals Fungi 0 Biologists broken down life into three categories or domains bacteria archaea and eukarya the latter has three groups protists animals and fungi 4Page iological Sciences M IQ S 1152 9215 Earths Changing Environment Checkpoint Questions and Answers for Chapter 182 2nd edition page 366 1 edition page 355 0 How have volcanic eruptions and meteorite strikes in uenced the course of life s evolution 0 When a volcano erupts it some of the gases that are emitted include water vapor carbon dioxide CO2 sulfur dioxide SO2 hydrogen sulfide hydrochloric acid HCl and carbon monoxide CO and other sulfur gases After these gases are released into the atmosphere sulfurous acid is formed in high quantities which forms a thick high altitude cloud cover This cloud cover blocks out the sun and prevents a considerable amount of sunlight to make it to and thus cools the global temperature on earth this can have catastrophic results such as a mass extinction or growing of icebergs Meteorites commonly strike earth on a yearly basis but if a large enough meteorite collided with earth enough detritus can be released into the atmosphere to spread and cover the earth Once encircling earth the debris will fall and heat the earth hundreds of degrees and cause widespread fires which annihilate droves of species 0 Explain why an occasional major winter blizzard is irrelevant to discussions of global climate warming 0 Winter blizzards don t relate to global climate warming because the earth s climate is constantly going through a long cycle which features a duration of hot climate and a duration of cold During these periods the earth continues to revolve and go through each season as the ozone layer also continues to collect CO2 and grow Climate shifts happen very slowly over thousands and thousands of years An occasional major winter blizzard wouldn t signal or disprove global warming it would just show a very slight temperature shift for a given season SIPage iological Sciences M IQ S 1152 9215 0 Research and explain the di ferent climactic responses to the parasol e ect of major volcanic eruptions and the greenhouse e ect of long term CO2 emissions What is the fundamental di ference in the two e ects o The parasol effect can be thought of as a giant umbrella made of dense cloud and other matter that is suspended in the atmosphere As the sunlight extends down to earth a portion of it bounces off of this umbrella and re ects back up to the atmosphere The greenhouse effect works in the opposite way In the greenhouse effect a layer of greenhouse gases made up mainly of CO2 hover in the atmosphere above the earth s surface As the earth emits energy to be released up into the air a large about is trapped under the ozone layer and stays down on earth raising its overall global temperature 0 How have increases in atmospheric concentrations of O2 a ected the evolution of multicellular organisms o Cyanobacteria were the very first organisms to produce 02 as a waste product when they learned how to involve water for its hydrogen ions in photosynthesis Later when one of their like ancestors converged symbiotically with eukaryotic cells the evolution of photosynthetic plants came to be With an abundance of useable 02 in the atmosphere larger celled organisms could survive and thrive in the environment Earth peaked at its highest 02 level about 250 million years ago at which time giant ying insects and amphibians were able to live their existence in the present time has been made impossible due to the 50 decrease in our 02 levels 0 Eukaryote Features The classification of eukaryotes goes beyond just animals plants and fungi Eukaryotic organisms that fall under the other category are protists 0 Eukaryotes are monophyletic meaning they all derive from a single descendent SIPage iological Sciences M IQ 61152 9215 0 Eukaryotes are more closely related to archaea than bacteria 0 The mitochondria and chloroplasts came from bacterial ancestors Events that were paramount in the creation of the common eukaryotic cell 0 O O O O The creation of a cytoskeletal backbone The creation of a pliable surface membrane The creation of different organelles through endosymbiosis The creation of a nuclear envelope surrounding the genome that contains chromosomes The characteristics of the digestive vacuoles See Fig 201 for the Evolution of the Eukaryotic Cell 2nd edition page 402 15t edition page 389 The evolution of a exible cell surface came from the loss of the cell wall in the early prokaryotes O Losing the ridged wall granted the cell many benefits 0 Being able to grow larger in size 0 Being able to increase the surface area to volume ratio 0 Being able to take in pieces of the surrounding environment via endocytosis Evolution changed the formation and build of a cell this lead to O O A more elaborate cytoskeletal build The creation of internal membranes dotted with ribosomes some also encircles DNA Creating a bound area to hold the cell s DNA The nucleus The creation of agellum The development of digestive vacuoles Cyanobacteria were the organisms that learned use photosynthesis to collect energy and as a result were the ones responsible for introducing oxygen into the environment 7Page iological Sciences M IQ S 1152 9215 0 Phagocytosis the power to consume and dissolve additional cells allowed eukaryotic cells to ingest prokaryotic cells that were able to use 02 o The prokaryotic cells that were absorbed gave rise to organelles through a endosymbiotic relationship SIPage Biological Sciences 11 B10 SCI 152 9415 Reading Covered in These Notes 2nd edition pages 6175 216221 379383 1 edition pages 5664 68 367369 376377 Last Lecture Notes Microbiology Introduction Lecture 2 Outline Cell Structure and Function 1 Cell Structures and Functions a Cells Outer Membrane of Cells c Microscopes i Light Microscopes ii Electron Microscopes 1 Types of Cells i Prokaryote Characteristics ii Eukaryote Characteristics e Cytoskeleton 2 Cell Gene Expression a Prokaryotic Genes i Positive and Negative Regulation ii Viruses 3 Three Domains of Life a Prokaryotic Domain Divide b Prokaryote Relationships Cell Structures and Functions Cells Cell Theory 3 Main Points The facts of life that connect biology 1 Cells are the units of life 2 Cells make up all living things 3 All cells come from cells 1Fage Biological Sciences 11 B10 SCI 152 9415 Cell Theory 2 Concept Points 1 Biology studies life 2 Life is constant and continuous 0 Cells require large surface areatovolume ratio The surface area to volume ratio shrinks as the cell grows in size The cell must change its shape to increase its surface area or the volume will increase at a faster rate Cells form folds in their membranes to increase surface area 0 Volume decides the metabolic rate per unit of time 0 Surface area decides the amount of substances that can pass in and out of the cell membrane Outer Membrane of Cells 0 Cell membrane is a selectively permeable surface that holds all the contents of a cell in and separates the internal and external environments 0 Membrane is made up of a phospholipid bilayer that includes proteins I The phospholipids compose the foundation of the membrane I The proteins are located sporadically in the phospholipids and are responsible for letting molecules in and out Proteins connect the inner an outer environments on either side of the membrane 0 Cell membrane allows the internal environment to communicate with the outside environment 0 The proteins in the membrane give the cell shape and allow other cells to attach to one another 2Page Biological Sciences 11 B10 SCI 152 9415 Microscopes 0 Light microscopes 0 Use lenses and light to create images and 0 Can see 1000 times smaller than the unaided eye 0 Electron microscopes o Utilizes electron beam that use magnets to light up a sample 0 Can see 2 million times smaller than the unaided eye Types of Cells Prokaryotic cells include archaea and bacteria 0 Cells are smaller than eukaryotic cells o Prokarvotes have no nucleus and also lack organelles 0 Size range of these organisms are generally o1 5oum but normally o5 2oum in diameter Prokaryotic Cell Features See g 45 Prokaryotic Cell Components 2nd edition page 64 1 edition page 60 0 Cell membrane surround encases the cell 0 allows material in and out o The genetic material M is located in the nucleoid o C oplasm consist of all the other material in the cell 0 The cytosol is an intra cellular liquid I This is where all metabolic reactions take place 0 The cytoplasm content is constantly moving BIPa Biological Sciences 11 B10 SCI 152 9415 0 Ribosomes are the location of protein production 0 The ribosomes are made up of RNA 0 Size is around 2onm in diameter 0 Flagella long strand like appendages that help cells maneuver through their liquid environments some resemble corkscrews 0 These structures consist of proteins called agellin o Flagellum protrude from the cell membrane or outer membrane of some 0 Motor protein spins in a screw like motion to move the organism Eukaryotic Cell Features See g 47 Eukaryotic Cells 2nd edition page 66 amp 67 1 edition page 62 amp 63 Eukaryotic cells include plants animals and fungi 0 Size range about 10 5oum in diameter 0 Much largg than prokaryotes o Eukagyotes have a nucleus 0 Nucleus is the organelle responsible for holding the cell s M 0 DNA is m up of nucleotides 0 Is the location of transcription where DNA is transcribed into RNA 0 Holds the nucleolus I Where ribosomes form from proteins and RNA 0 Chromosomes long string like structures composed of protein and a single deoxyribonucleic acid DNA reside in the nucleus 0 Two lipid bilavers surround the nucleus and assemble the nuclear envelope 0 Cells have compartmental organelles in their cytoplasm 4Pag Biological Sciences 11 B10 SCI 152 9415 0 Like prokaryotes eukarvotes also have ribosomes 0 Size in eukaryotes is about 25 gonm in diameter o The bulk of a eukaryotic cell is made up of an endomembrane svstem the different membrane enclosed organelles o The interrelated system includes the nuclear envelope endoplasmic reticulum Golgi apparatus and lysosomes o Vesicles membrane encased vacuoles transport substances between the whole endomembrane system 0 The endoplasmic reticulum gER is an array of membranous sacs and tubules o The outer membrane surface of the rough ER RER is studded with ribosomes I RER modifies and synthesizes proteins Proteins being altered move across the membrane to enter the lumen and undergo structural folding and linkage add SEE a When carbohydrates are added it becomes a glvcoprotein o The smooth ER SER has few or no ribosomes studding its membrane surface I The E has four main tasks 1 Chemically modifies molecules makes molecules extra polar 2 In animal cells is the location of glycogen degeneration 3 Location of steroid and lipid synthesis 4 Calcium ion storage 0 The Golgi apparatus GA is a set of attened sacs called cisternae which accumulate forming towers of what looks like plates stacked one on top of the other 5Page Biological Sciences 11 B10 SCI 152 9415 0 Vesicles carrying proteins from the RER merge with the GA membrane and dispense the proteins into the GA lumen I The GA performs multiple tasks Collects packages tags and organizes proteins before sending them to their targeted destination Joins carbs to proteins In plants it is the location where polysaccharides are synthesized o Primarv lvsosomes stem from the GA and hold digestive enzymes ghydrolases and is the location where macromolecules are broken down into monomers by hydrolysis 0 Through phagocvtosis lysosomes receive material from outside of the cell 0 In phagocvtosis an indent in the cell membrane surrounds material from the external environment and engulfs it bringing the material into M in a vesicle called a phagosome o Secondarv lvsosomes are created when a phagosome merges with a primarv lvsosome 0 Cells with the primary purpose of breaking down matter are called phagoc es o All eukaryotes have an organelle called the mitochondria which has its own set of DNA carry their own ribosomes and also have many enzymes o The mitochondria are responsible for cellular respiration by creating ATP from gathered chemical energy PRESENT ONLY IN PLANTS amp ALGAE Q o Plastids various organelles found in plants and algae that are used by photosynthetic eukaryotes Three types of plastids 1 Chloroplasts 2 Chromoplasts 6Page Biological Sciences 11 B10 SCI 152 9415 3 Leucoplasts 1 Chloroplasts are the location where photosynthesis is carried out chloroplasts also store green pigment called chlorophyll a Photosvnthesis is a chemical reaction that converts light energy into chemical energy it uses light energy water and carbon dioxide and produces carbohydrates and oxygen i The light depended reaction in photosynthesis mkes place in the thylakoids membrane compartments inside of the chloroplasts that are shaped like stacks of pancakes 2 Chromoplasts are responsible for the storage of yellow red and orange pigments in fruits and owers 3 Leucoplasts are located in non photosynthetic tissues of plants and serve to store non pigment molecules such as starch lipids proteins o Peroxisomes are organelles that neutralize toxic peroxides like hydrogen peroxide H202 o Peroxisomes also play a part in breaking down amino and fatty acids and have a role in lipid metabolism o Vacuoles are utilized by all eukaryotes but mainly plants and fungi 0 Plant vacuoles have multiple roles I Plants store harmful toxic byproducts in their vacuoles I A central vacuole regulates the cells water concentration and aids in structure I Utilizes pigments in petals and fruits to attract animals to help carryout reproduction through pollination and seed distribution I Vacuoles in plant seeds contain enzymes that hydrolyze seed protein 7Pase Biological Sciences II BIO SCI 152 9415 Cvtoskeleton is a network made up of protein filaments and serves several purposes 0 Supports cell and holds its shape 0 Holds and locks cell organelles and other particles in place inside of the cell 0 Changes the position of organelles and particles in the cell 0 Responsible for cytoplasmic movements called c oplasmic streaming o Communicates with extracellular formations aids in anchoring cell in position 0 Three components in eukaryotic cytoskeleton each have different functions 1 Microfilaments 2 Intermediate filaments 3 Microtubules See g 410 The Cytoskeleton 2nd edition page 74 1 edition page 69 o Micro laments are the thinnest part around znm in diameter of the cytoskeleton and are made of a protein called actin o Microfilaments have two main functions 1 Aids cell and parts of cell in movement 2 Determine and secure shape of cell 0 Actin works with myosin a motor protein in the muscle cells of animals to produce muscle contraction I Any protein that induces movement in a cell is a motor protein 0 Intermediate laments come in a wide variety and consist of a family of related proteins 0 Intermediate filaments are strong stable and about 8 12nm in diameter 0 Intermediate filaments have two structural roles 1 Fasten cell structures in position 2 Withstand stress and tension o Microtubules are the thickest material in the cytoskeleton about 25nm in diameter microtubules are hollow and can be very lengthy SIPage Biological Sciences 11 B10 SCI 152 9415 0 Microtubules have two main functions 1 Assemble sturdy internal skeleton 2 Create framework and together with motor proteins can maneuver structures in the cell 0 Are composed of tubulin dimers or tubulin and B tubulin o Cilia and agella grant maneuverability o Microtubules are present in cilia and agella and internally line these appendages in a 92 array formation I Microtubules provide stiffness help the accessories bend and move Cell Gene Expression Positive and Negative Regulation Gene expression starts at the promoter area of DNA that begins transcription 0 Two regulatory proteins knows as transcription factors control the gene activity repressors and activators o Mgative regulation Repressor attaches to a certain site in on the promoter to inhibit transcription 0 Positive regulation Activator attaches to a certain site in on the promoter to prompt transcription Prokaryotes evolved ways to quickly change gene expression 0 Transcription of certain genes are excited by inducers o The corresponding genes activated by specific inducers are called the inducible genes 9Page Biological Sciences 11 B10 SCI 152 9415 0 Genes that are constantly expressed the majority of the time are called constitutive genes 0 An operon is a group unit of genes with one single promoter 0 Example E coli I Has an inducible lac operon that is needed for the transfer and metabolism of lactose o Operator is a binding site for a repressor protein 0 Example E coli I Lac operon has a DNA sequence located close to the promoter that controls the transcription of lac genes 0 Repressors have different functions for differing operons o Inducible operons are switched off unless the expression is needed 0 Example lac operon o Repressible operons are switched on unless the expression is not needed 0 Example trp operon 0 Any gene that encrypts a protein that is not immediately being used in gene regulation is a structural gene 0 Corenressor is a molecule that inhibits transcription by binding to a repressor forcing its shape to alter and bind to the operator Prokagyotes contain sigma factors proteins that guide the polymerase to particular promoters by binding to RNA polymerase Viruses Viruses use gene regulation to create Virus factories o Viruses fix themselves to a host cell to directly implant their genetic material lolPage Biological Sciences 11 B10 SCI 152 9415 0 New Viruses spawn inside of the host cell I This immediate production of new Viruses is an example of a lytic viral lifecycle 0 Viral cycles can also incorporate a dormant lvsogenic phase Three Domains of Life Prokaryotic Domain Divide Prokaryotic cells vary from eukaryotic cells in a ways 0 Prokaryotic cells don t go through mitosis to divide o Prokaryotes lack the membrane encased organelles that are present in eukaryotes o Prokaryotes arrangement their genetic material differently See table 191 for Domain Differences 2nd edition page 380 1 edition page 368 o Gram stain is a laboratory technique used to analyze bacteria into two groups gram positive and gram negative o Grampositive bacteria absorb Violet dye and look to be blueZpurple o Gramnegative bacteria appear pinered because the Violet stain washes out o Bacteria cellscome in several shapes 0 Cocci oval or spherically shaped o BLilli rod shaped o M spiral corkscrew shape ulPage Biological Sciences 11 B10 SCI 152 o Archaea cell shapes 9415 0 Cocci oval or spherically shaped o BLilli rod shaped o Triangular triangle shaped 0 lm shaped o Flattened or sheet like Prokaryotes Relationships Prokaryotic Domain Difference Table Archaea Cells Bacterial Cells 0 Cell walls are semiridged and protect the organism from the external environment 0 Cell walls lack peptidoglycan they contain o S layerssurface layer proteins 0 Cell Wall contains Peptidoglycan which is composed of disaccharides and amino acids The backbone of the peptidoglycan is derived of N acetylglucosamine NAG and N acetlymuramic acid NAM with a pentapeptide off the NAM o Gramnegative bacteria the inner cell wall is a single layer of peptidoglycan I The peptidoglycan layer is about 2 3nm thick I Outer membrane consists of lipopolysaccharide LPS with proteins and phospholipids I Outer membrane is semi permeable I Periplasm is the region that is between outer membrane and cytoplasmic membrane 0 Grampositive bacteria the cell wall is made up of multiple layers of peptidoglycan 12Page Biological Sciences 11 B10 SCI 152 9415 I The peptidoglycan is about 2o8onm thick I The outer membrane is absent 0 Cell membrane has ether linked lipids 0 Cell membrane contains ester linked lipids o Archaeal agella O Filaments are much thinner than bacterial agella Similar to bacterial agella superficially but not structurally Have no central core like bacterial agella Motion is powered by ATP Flagellar filaments rotate as a single bundle 0 Bacterial agella o Filaments are thicker than that of archaeal agella o Helical screw 0 Flagellum has a hollow core 0 Rotates clockwise and counterclockwise o Flagellar filaments rotate independently 0 Motion is powered by the hydrogen ion gradient 0 Bacterial pili mbriaeplural 0 Long appendage structures made of protein 0 Similar to agella but is thinner and shorter 0 Used to attach bacterium to surfaces or other cells 0 They may be exible or straight 0 Located either at poles of cell or spread over the whole surface Both archaea and bacteria asexuallv reproduce through the process of binary fission budding and fragmentation o Bacteria can asexually reproduce by forming spores 13Fage
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