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HNRS 105: Fundamentals of Biology

by: Alexandra VanBlaricum

HNRS 105: Fundamentals of Biology HNRS 105 H01

Marketplace > Louisiana Tech University > Biology > HNRS 105 H01 > HNRS 105 Fundamentals of Biology
Alexandra VanBlaricum
LA Tech
Honors Fundamentals of Biology
Dr. Jewell

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This study guide is a combination of notes taken from lectures and power points for the test on 1-19-16.
Honors Fundamentals of Biology
Dr. Jewell
Study Guide
Biology, honors
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This 0 page Study Guide was uploaded by Alexandra VanBlaricum on Friday January 15, 2016. The Study Guide belongs to HNRS 105 H01 at Louisiana Tech University taught by Dr. Jewell in Winter 2016. Since its upload, it has received 28 views. For similar materials see Honors Fundamentals of Biology in Biology at Louisiana Tech University.

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Date Created: 01/15/16
I Cell Structure a Historical Background i Robert Hooke observed dead cork cells plants coined the term quotcellquot ii Anton von Leeuwenhoek known as the quotFather of the Microscopequot observed quotanimalculesquot protists sperm bacteria iii Developers of Cell Theory Schleiden Schwann Virchow 1 Modern CellTheory a Every living organism consists of 1 or more cells b The cell is the structural and functional unit of all organisms A cell is the smallest unit of life individually alive even as a part of a multicelled organism c All living cells come from the division of preexisting cells d Cells contain hereditary material which they pass to their offspring during division b Not all cells are alike i Come in many shapes and sizes and perform various functions depending on where they are found c Traits Common to All Cells i Cell or plasma membrane that separates it from the environments serves as a quotgatequot to regulate flow across it contains receptors for cell activity ii DNAcontaining region iii Cytoplasm d Two Types of Cells i Eucaryotic Cells true membranebound nucleus Plants Animals Fungi Protists have a cell membrane cytoplasm ribosomes and DNA 1 De ning Features a Internal membranebound compartments of cytoplasm each with one or more specialized function Organelles i Nucleus control center contains and isolates DNA the stored genetic instructions of each cell de ning organelle of eucaryotic cells 1 Surrounded by membrane nuclear envelope a Double membrane made of two phospholipid bilayers b Controls the passage of molecules between the nucleus and cytoplasm Nucleoplasm uid inside Nucleolus subunits of ribosomes prior to export out of nucleus 4 Reactions for interpreting the genetic instructions of DNA take place here UJN 5 ChromatinChromosomes a Chromatin cell39s total collection of DNA and associated proteins b Chromosomes individual DNA molecule and its associated proteins hereditary information c A cell39s DNA is duplicated and condensed before cell division occurs d DNA code contains instructions for building proteins hereditary instructions e Proteins are speci ed by DNA i Some are stockpiled in cytoplasm ii Some are moved through the cell and are packed in vesicles to be used in cell or exported out iii Proteins are moved through the cell as described above through the cytomembrane system Endoplasmic Reticulum connects nucleus and cytoplasm modi es new polypeptide chains involved in making lipids Tubes and attened sacs Membrane covered pipes Proteins and lipids synthesized here Two types a Rough ER ribosomes attached protein production b Smooth ER no ribosomes attached lipid production Golgi BodiesGolgi Apparatus modify sort and ship proteins lipid synthesis internal use and secretion 1 Resemble stack of pancakes stacked membranous discs 2 Final processing sorting and packaging of proteins and lipids a Transport vesicles delivers proteins from Rough ER to Golgi bodies b As the proteins make their way through the Golgi bodies they WF are processed to complete their structure and identify them for transport to speci c locations in the cell c Proteins are then packaged into transport vesicles which deliver the proteins to their nal destination Nucleus ER and Golgi bodies work together to produce and transport proteins i Nucleus provides instructions for protein production ii Proteins are made in the ER and packaged into vesicles for transport to Golgi bodies iii Proteins receive nal modi cations in Golgi bodies and they are then packaged into vesicles for transport to the site of protein function 3 Edges of sacs in stack break off as vesicles into cytoplasm iv Vesicles transport materials between organelles aid in intracellular digestion 1 Lysosomes contain powerful digestive enzymes break down worn out cell parts or molecules so they can be used to build new cellular structures digest bacteria a Cell39s recycling centers 2 Peroxisomes contain enzymes to break down fatty acids and amino acids a H202 hydrogen peroxide is formed here Then another enzyme breaks down H202 into H20 and 02 v Mitochondria sites of cellular respiration and ATP productions quotpowerhouses of cellquot 1 Transfers energy in carbohydrates to ATP when oxygen is present 2 Composition a 2 membranes i lnner folded cristae ii Outer smooth b Have their own DNA and ribosomes evidence that they at one time may have been independent entities and they may have evolved from ancient bacteria and then were engulfed by some type of primitive eukaryotic cell i Endosymbiosis theory freeliving procaryotic cells engulfed other free living procaryotic cells billions of years ago forming eucaryotic organelles mitochondria and chloroplasts Internal nonmembrane bound structures and other components i Ribosomes sites of protein synthesis 1 Free 2 Attached to membranes ER ii Cytoskeleton 1 Functions a Determines cell shape b Internal organization c Movement Advantages of Compartments Organelles i Many activities can occur at the same time in very limited space ii These structures also allow these reactions to proceed at different times if needed Cytomembrane System components i Endoplasmic Reticulum ii Golgi Bodies iii Vesicles variety Cytoskeleton i Extensive and dynamic internal framework ii Location 1 Between nucleus and cell membrane iii Composition 1 Interconnected systems of bers threads and lattices network protein bers a Microtubules transient b Micro laments permanent iv Functions 1 Cell shapesupport 2 Internal cell organization 3 Basis of cell movement andor locomotion a Flagella long fewer found on 1celled protists sperm cells bacteria Cilia shorter more can cause cell to move surrounding waterparticles to move f Cell Surface Specialization i Cell Wall excluding animal cells rigid structure enclosing cell membrane 1 Location exterior to cell membrane 2 Composition and Related Function a e Pores microscopic allow materials to move to and from cell membrane Wall becomes more rigid as cell matures in order to better protect and support cell i Young plants cellulose polysaccharide made up of glucose molecules is primary cell wall ii Older plants woody lignin secondary wall Between cell walls glue is present to cement adjacent cells together pectin Plasmodesmata channels that cross adjacent cells to connect their cytoplasm Cell surface waxes i Leaf cuticle for waterproo ngreduce water evaporation 2 Specialized Plant Organelles a Plastids i Chloroplasts 1 Function sites of photosynthesis a Capture and conversion of sunlight energy into a useable form 2 Components a b c Double layer outer membrane Fluid interior stroma Thylakoid membrane folded within stroma look liked stacked disks Grana 3 Grana contains chlorophyll green pigment Sunlight is trapped here to form ATP 4 Chloroplasts resemble bacteria more evidence for Endosymbiotic Theory ii Chromoplasts 1 Contain various colored pigments other than green a Carotene orange in root b Xanthophyll yellow in ginkgo leaf iii Amyloplasts 1 Contain no colored pigments 2 Store starch grains 3 Example potato tuber underground stem b Central Vacuole i Takes over 5090 of interior of a mature plant cells As plant grows the CV enlarges ii Functions 1 Storage amino acids sugars ions wastes 2 Cell Enlargement As CV enlargers cell39s outer surface area increases a As cell matures and CV expands cytoplasm is compacted between CV and cell membrane ii Procaryotic Cells no true membranebound nucleus it39s a nucleoid region which resembles a nucleus DNA oats freely in cytoplasm Bacteria and Archaeans 1 Bacteria and Archaeans a Singlecelled organisms with no nucleus b Both groups are very similar Archaeans were once thought to be an unusual group of bacteria i By 1977 it became clear that Archaeans are more closely related to eucaryotes than bacteria so they were given their own separate domain c Smallest and most metabolically diverse forms of life known d lnhabit nearly all of Earth39s environments including most very hostile places Differ in structure and metabolic details Implication is that these cells existed prior to the evolution of cells with a nucleus g Do not have a true nucleus so their DNA is clustered in a nucleoid region which somewhat resembles a nucleus th h Two Domains include i Archaebacteria Archaeans ii Eubacteria True bacteria i Basic Structural Composition i Most have a cell wall exterior to their cell membrane 1 Cell walls are rigid due to peptidoglycan a A polymer made of sugars and amino acids b Allows bacteria to survive in watery environments ii Organelle ribosomes and sometimes chloroplasts iii Genome DNA 1 Found on 1 single looped chromosome 2 Sometimes also on strands plasmids which code for certain traits such as antibiotic resistance iv External Structures 1 Sometimes capsule exterior to cell wall sticky used to attach to surfaces a If bacterium has a capsule it tends to be more virulent 2 Sometimes agella long whiplike structure provides movement not all bacteria are mobile 3 Sometimes pili hollow laments used to attach to surfaces a Neisseria gonorrheae causes STD gonorrhea These bacteria have pili If the pill are removed destroyed infection does not occur Pili are target sites of certain antibiotics for some bacterial infections 2 Have a cell membrane cytoplasm ribosomes and DNA Cytoplasm gelatinous aqueous interior DNA as a molecule of heredity Ribosomes complex of RNA and protein that carry out protein synthesis Composition of Cell Membrane i Flexible yet sturdy structure that forms a boundary between the external environment and the cell39s watery cytoplasm semipermeable only certain substances can cross it freely 1 Prevents many large molecules like glucose and hydrophilic charged substances like sodium ions from crossing a Large or hydrophilic molecules cross the membrane by assistance of transport proteins i Transport proteins Sit in membrane biayer Act as a channel carrier or pump Provide a passageway Can move substance with or against concentration gradient Speci c Facilitated Diffusion large or hydrophilic molecules cross the cell membrane from higher concentration to lower concentration with the help of speci c transport proteins does not require energy 7 Active Transport large or hydrophilic molecules solutes cross the cell membranes from areas of lower concentration to higher concentration with the help of speci c transport proteins and chemical energy to pump molecules against the gradient 2 Allows small uncharged substances to cross via diffusion a Simple diffusion i Natural tendency of dissolved substances to move from an area of higher concentration to one of lower concentration ii No energy required PWN mp1 b ii Bilayer Structure phospholipids amphipathic quot uidquot in consistency 1 Function a Selective barrier to water soluble substances 2 Components a Hydrophilic heads facing surface out toward water b Hydrophobic tails facing inward in away from water 3 Protein molecules embedded within a Components variety of different proteins b Function of various proteins i Transport passive vs active assist speci c ions or molecules across membrane ii Receptors binds to a particular substance outside of the cell iii Recognition identi es a cell as belonging to one s own body self iv Adhesion helps cells stick together in tissues v Enzyme speeds up a speci c reaction membranes provide stable reaction site for them to work in series with other molecules iii Variations in Membrane Compositions 1 Different phospholipids different lengths of fatty acids or their saturation 2 Some proteins are stationary as those that cluster to form rigid pores 3 Some of the phospholipids are not made with fatty acids Archaeans Cell Size i Constraints 1 Limited by surfacetovolume ratio a If the cell gets too large the inward ow of nutrients and the outward ow of wastes across the cell membrane will not be fast enough to keep the cell alive b Affects body plans of multicelled species i Small cells attach end to end to form strandlike algae laments so that each can interact directly with its surroundings ii Almost all cells are too small to see with the naked eyes 1 Need microscopic aids a Light microscopes b Electron microscopes Microscopy i Greater magni cation ii Procaryotes with light microscope iii Metric unit of length to measure procaryotes iv Viruses with light microscope v Instrument used to observe viruses vi Metric unit of length to measure viruses ll Wonder Drug Chapter ExperimentStory a In 1928 Alexander Fleming biologist observed that the fungus Penicilium nototum was capable of killing many kinds of bacteria This led to the discovery of the rst antibiotic as he realized that the fungus on his culture plate was somehow inhibiting the reproduction of bacteria He was the rst to study antibiotics scienti cally and publish his results b How the First Antibiotic Was Discovered i Alexander Fleming rst noticed the bacteriakilling property of Penicilium notatum a mold in September 1928 Looking at a petri dish that contained the uffy white mold he saw that there was a zone around the mold where bacteria did not seem to grow ii Experiments con rmed that the mold was capable of killing many kinds of bacteria including Streptococcus Staphylococcus and Pneumococcus Fleming published his results in 1929 in the British journal of Experimental Pathology He named the antibacterial substance quotpenicillinquot after the fungus producing it Penicilium notatum It was the birth of the rst antibiotic iii Ironically despite its remarkable killing powers penicillin was not immediately recognized as a medical breakthrough when it was rst discovered At the time the idea that an antiseptic agent could kill bacteria without at the same time harming the patient was unheard of so Fleming never considered that penicillin might be taken internally Nor was he a chemist so he lacked the expertise to isolate and purify the active ingredient from the mold While he found that his mold juice made a quotreasonably goodquot topical antiseptic he noted that quotthe trouble of making it seemed not worthwhilequot and largely gave up working on it c Penicillin39s Early Use i In 1938 Ernst Chain a GermanJewish biochemist was working in the pathology department at Oxford University having ed Germany for England in 1933 when the Nazis came to power Both Chain and his supervisor Howard Florey were interested in the biochemistry of antibacterial substances Chain succeeded in isolating and concentrating the active ingredient from the mold ii With the beginning of WWII in 1939 and few other antibacterial medicines available penicillin suddenly became the focus of re search iii At rst it took up to 2000 liters of mold uid to obtain enough pure penicillin to treat one person The breakthrough that allowed it to be produced on a larger scale was a method for growing the mold on corn a crop that the United States had in abundance iv At rst all the penicillin harvested from US production plants came from Fleming39s original strain of Penicilium notatum But researchers continued to look for more potent strains to improve yields Then in 1943 Mary Hunt a researcher discovered a new strain of the mold Penicilium chrysogenum which produced more than 200 times the amount of penicillin as the original strain Production of the drug soared v By the time the Allies invaded France on Dday June 6 1944 they had enough penicillin to treat every soldier that needed it By the following year penicillin was widely available to the general public and for the rst time doctors had a way to treat such deadly illnesses as bacterial pneumonia syphilis and meningitis vi For his pioneering research Alexander Fleming along with Howard Florey and Ernst Chain was awarded a Nobel Prize in 1945 d Penicillin s In uence on Other Antibiotics i Most of the bacterial world falls into one of two categories Grampositive and Gramnegative These names re ect the way bacterial cell walls trap a dye known as Gram stain after its discoverer the Danish scientist Hans Christian Gram Fleming found that while penicillin easily killed Grampositive bacteria like Staphylococcus and Streptococcus it had little effect on Gramnegative bacteria like E coiand Salmonella ii The discovery that penicillin was effective only on Grampositive bacteria led other researchers in the 19405 to look for other antibiotics that could kill Gramnegative bacteria The rst such broadspectrum antibiotic was streptomycin discovered in 1943 by Albert Schatz and Selman Waksman at Rutgers University In addition to killing Gramnegative bacteria streptomycin was the rst effective treatment for the deadly bacterial disease tuberculosis e Antibiotics Today i To those who rst bene ted from its healing powers penicillin seemed like a wonder drug and today antibiotics are some of the most widely prescribed drugs But the overuse and misuse of them has led to antibioticresistance which the Centers for Disease Control and Prevention calls quotone of the world39s most pressing public health problemsquot for more on antibiotic resistant bacteria see Chapter 14 ii Fleming himself warned against this very danger In a 1945 interview in The New York Times he said that improper use of penicillin could lead to the survival and reproduction of virulent strains of bacteria that are resistant to the drug He was right In 1945 when penicillin was rst introduced to the public virtually all strains of Staphylococcus aureus were sensitive to it Today more than 90 of Staphyloccocus aureus strains are resistant to the antibiotic that once conquered this common microbe In 2010 the American College of Physicians estimated that of the more than 133 million courses of antibiotics prescribed in the United States each year as many as 50 are prescribed for colds and other viral infections for which they39re powerless iii Because of the alarming growth in antibioticresistant superbugs drug companies and researchers are trying to develop new antibiotics One strategy they employ is to tweak the chemical structure of existing antibiotics just enough that a bacterium cannot disable it Another approach is to look for antibiotics that target other bacterial weaknesses f Antibiotics i Chemical that can slow or stop the growth of bacteria ii Often naturally produced by living organisms penicillin is produced by Penicilium nototum iii Preferentially kill bacteria without harming human or animal host 1 They target what is unique about bacterial cells bacteria are only organisms with cell wall made of peptidoglycan 2 Target Procaryotic cells eucaryotic cells can resist effects of antibiotics a Penicillin weakens cell wall and bacterial cells ll up with water and burst due to osmosis Diffusion of water across a semipermeable membrane from an area of lowersolute concentration to an area of highersolute concentration Hypotonic vs Hypertonic vs Isotonic 1 Hypotonic cells placed in a lower solute solution take up water and swell 2 Hypertonic cells placed in a higher solute solution lose water and shrivel 3 Isotonic solute concentration is the same as the cell39s cytoplasm no net movement of water into or out of the cell In all cases water moves in a direction that will tend to even out the solute concentrations on each side of the membrane b Bacterial cells are either Grampositive 1 Cell wall with layer of peptidoglycan that retains the Gram stain Gramnegative 1 Cell wall layer of peptidoglycan surrounded by lipid membrane that does not retain the Gram stain a Prevents penicillin from reaching the peptidoglycan underneath c Additional methods of killing bacteria Streptomycin interferes with procaryotic ribosomes procaryotic and eucaryotic cells have ribosomes of different sizes and structures 1 Leaves eucaryotic ribosomes unaffected d Antibiotics can cross procaryotic cell membranes using transport proteins Microorganisms have evolved chemical defenses as a way to protect themselves from other organisms In turn their combatants have evolved countermeasures that give them resistance Bacteria can resist antibiotics using transport proteins as well 1 Pump out antibiotics iv Penicillin 1 Widescale manufacture of penicillin in 19405 a Became new wonder drug of World War H i Millions of soldiers and civilians had died in World War I many from infected wounds With few other antibacterial medicines available penicillin suddenly became the focus of research during World War II In 1941 when Oxford scientists approached the US government and asked for help in growing penicillin on a large scale 1 Used a byproduct of large scale corn processing as a culture in which to grow the fungus to produce penicillin in much greater quantities lll Energy Where it starts photosynthesis Class powerpoint a Living things are based on organic compounds i Two categories 1 Autotrophs selfnourishing a Carbon source carbon dioxide b Energy source i Photosynthetic autotrophs green plants some protists some bacteria harness light energy 2 Heterotrophs feed on autotrophs each other and organic wastes a Dependent on autotrophs for both carbon and energy b Include animals some protists some bacteria fungi b Where is starts i Carbon and energy enter web of life through photosynthesis and in turn are released by the processes of glycolysis and aerobic respiration Sugar produced and released ii Photosynthesis 1 2 stages both occur in chloroplasts but different parts a Light dependent reactions i inner membrane thylakoid membrane system of the chloroplast catch light that eventually makes its way into stroma where next stage occurs ii First stage iii Light conversion into chemical energy stored in form of ATP and coenzyme NADPH the products iv What happens to absorbed energy 1 Photosystems in chloroplasts cluster of 200300 different light absorbing pigments located in the thylakoid a Harvest sunlight Absorbing energy causes electrons to leave photosystems and enter 1 or 2 electron transfer chains in the membrane Flow of electrons through the ETS electron transport system sets up hydrogen ion gradients that drive ATP formation b Type of critter found on determines the number of ETS iv When electrons are activated it sets up hydrogen ion gradient that drives ATP formation pigments absorb energy electrons give up and ATP formed ultimately If 2 ETS Oxygen released 2 things formedATP and co enzyme NADPH formed noncyclic pathway If 1 ETS no coenzyme formed or release of energy just ATP formed cyclic pathway Both have to have electrons transferred c History of cyclic and noncyclic pathways First lifeforms 36 billion years ago procaryotic in nature Cyanobacteria have been performing VI vii viii photosynthesis the last 34 billion iii Since about 2 billion years ago oxygen has begun accumulating in atmosphere because organisms could tolerate it making aerobic respiration possible iv Around 24 billions years ago extinction Many of the obligate anaerobes were eliminated obligated to have absence of oxygen so when oxygen became available they were wiped out v Cyclic 36 bya vi Noncycle 34 bya vii Procaryotes then cyanobacteria then obligate anaerobes temporality eliminated adaptations then eucaryotes plantlike cells and photosynthesis Water molecule split and oxygen is released four things for photosynthesis sunlight water carbon chlorophyll 3 products oxygen sugar glucose water 3 Events 1 Light energy captured by pigments and electrons are given off 2 Molecules of water split ATP adenosine triphosate and coenzyme NADPH formed Oxygen released a A closer look at ATP formation in chloroplasts i Electron flow causes hydrogen ions to accumulate inside the thylakoid portion of chloroplast ii Hydrogen ions ow out of the stroma through channel proteins ATP synthase causes ADP to gain a phosphate to form ATP formation of ATP driven by the ow of hydrogen ions from the thylakoid compartment to the stroma iii Have to have the capability of replacing lost electrons from the beginning Electrons replaced in pigment molecules that rst gave them up so photosynthesis can continue to take place 3 Electrons are replaced in the pigment molecules that rst gave them up b Light independent reactions also CalvinBenson cycle i Semi uid interior stroma of the chloroplast is the site of the second stage of reactions Not dependent on sunlight as that39s already been absorbed Take those raw materials and assemble sugars and other organic molecules doesn39t always have to be glucose and use ATP and NADPH formed above Participants 1 ATP provides energy 2 NADPH provided hydrogen atoms and electrons 3 Atmospheric air which provides carbon and oxygen from carbon dioxide a How do plants capture carbon Carbon dioxide diffuses into leaf as that39s where most of photosynthesis takes place Goes in through stomata Goes across cell membranes of photosynthetic cells and into stroma With the help of the coenzyme Rubisco C02 combines with ribulose bisphosphate RUBP a compound with a backbone of 5 carbon atoms Form unstable 6 carbon intermediate that spits to form 2 molecules of phosphoglycerate PGA 2 to 3 carbon molecules Each PGA receive a phosphate group has phosphate ions added to it which comes in from ATP has 3 phosphates Add hydrogen ions and electrons from NADPH to form phosphoglyceraldehyde PGAL an energized molecules Most PGAL moecues continue in the cycle to x more C02 but 2 PGAL join to form a sugar phosphate which will be modi ed to sucrose starch and cellulose iv Photosynthetic cells convert phosphorylated glucose to sucrose or starch during daylight hours v Transportable sucrose vi Stored starch v Summary 3 things 1 Carbon xed from C02 2 Glucose formed requires ATPfor phosphate and NADPHcoenzyme 3 Enzyme has to be present a RuBP necessary enzyme to capture and x carbon c Process of Glucose Formation i 12H20 6C02 yields 602 C6H1206 6H20 ii Or water carbon dioxide yields oxygen glucose water 2 Nature of light a Most of light that reaches Earth39s surface is in form of visible light electromagnetic spectrumvisibe light portion very small i 380750 nanometers in wavelength b Travels in waves through space i Wavelength distance between crest of one to crest of another or trough to trough 1 Measured in nanometers 2 Wavelengths that are not absorbed are re ected and that re ected light gives each pigment its characteristic color c Packaged in photons which vary in energy as a function of wavelength i Violets are shorter in wavelength but higher in energy Reds are longer in wavelength but lower in energy d Organisms use only a small range of wavelengths for photosynthesis vision and other processes i Most are the ones we see as visible colors e Pigments i Pigment molecules on the thylakoid membranes absorb photons 1 Photosynthetic Pigments a Chlorophyll most common one in plants and also in photosynthetic protists and bacteria i Absorb violet and red light but transmit green re ect b Accessory pigments including other chlorophylls work together with chlorophyll to harvest a wide range of light wavelengths for photosynthesis c Carotenoid absorb violet and blue but transmit yellow orange and red re ect d Phycobilins red and blue pigments found in red algae and cyanobacteria IV Energy Flow and Photosynthesis textbook a Reference to biofuels and using algae to make different fuels discussion about that and how we re overusing our fossil fuels demand will increase over next 25 years and we only have a nite amount so looking for alternative sources i US largest consumer Biofuels are made from living organisms Energy i Capacity to do work ii Have to have energy for life iii Law of Conservation of Energy neither created nor destroyed just changes form iv Chemical energy potential energy stored in bonds v Potential stored vi Kinetic energy of motion vii Energy transfers a lot of time energy is lost in form of heat not really lost because Law of Conservation of Energy viii Energy transformation not super efficient V Chapter 6 How cells release chemical energy dietary energycellular respiration a b c Taking off where photosynthesis took off photosynthesisautotrophs discussing heterotrophs now Making ATP ATP is a chemical is the prime energy carrier i Twoenergy releasing pathways ii Aerobic Respiration Main pathway leading to ATP formation The ef cient way For some critters this is the only way they can generate energy Takes place in mitochondria powerhouse Has to have oxygen available For every 1 molecule of glucose that is broken down through aerobic respiration there will be 36 ATPs in reality 38 but 2 are used in process36 is the gross amount Glucose oxygen yields Carbon dioxide water a Or C6H1206 602 yields 6C02 6H20 Three parts to it sequential a Glycolysis glucose is broken down into intermediate compound known as pyruvate a little bit of ATP formed as well as pyruvate 2 ATPs for 1 molecule of glucose i Endproducts for each glucose moecue degraded 2 pyruvates 2 ATPS 2 NADH ii Have to have 2 NADPH iii Takes places in cytoplasm 1 Enzymes here catalyze several steps in glucose breakdown a Glucose is rst phosphorylated in energyrequiring steps then split to form 2 molecules of PGAL b Enzymes move hydrogen ions and electrons from PGAL to change NAD to NADH later used in electron transport b Krebs Cycle takes over where Glycolysis ended also citric acid cycle Pyruvate broken down into C02 water a little bit of ATP 2 ATPs for 1 molecule of glucose hydrogen ions and electrons i Pyruvate goes into mitochondria One carbon is removed and the 2carbon fragment joins coenzyme A Acetyl CoA then joins oxaoacetate already present from a previous quotturnquot of the cycle ii Hydrogen ions and electrons are transferred to NAD and FAD to become NADH and FADH2 Two molecules of ATP are produced by substratelevel phosphorylation Most of the molecules are recycle to conserve oxaloacetate for continuous processing of acetylCoA 1 Simpler terms hydrogen ions and electrons are combined with other substances that were already there to make NADH and FADH2 respectively iii Bottom line other things formed along the way in order to start the next time the process takes place c Electron Transport Phosphorylation hydrogen ions and the electrons formed during Krebs Cycle will be processed to form more ATPS 32 ATPs for one molecule of glucose Oxygen is nal electron acceptor i NADH and FADH2 give up their electrons to transport enzyme systems embedded in the mitochondrial inner membrane Hydrogen ions are released into the outer compartment of the mitochondria As hydrogen ions ow back into the inner compartment ATP synthases form ATP from ADP and unbound phosphate Oxygen joins with the quotspentquot electrons and H to yield water ii Electrons given up to the system iii Hydrogen ions go into outer compartment of mitochondria 1 Membranes of mitochondria a Outer where this stages takes place b Folded iv Generates most ATP d Not very ef cient only about 40 ef ciency from glucose to ATP About 60 lost to heat e 2 2 32 26 Fermentation Anaerobic Routes 1 Not as ef cient in production of ATP For some this is the only way they can get energy Occurs in cytoplasm never gets to the mitochondria For every 1 molecule of glucose only 2 ATPs are formed UJN a Coenzyme NAD is regenerated as a result of glycolysis i Without NAD glycolysis and ATP production would stop 4 Takes place in absence of oxygen 5 Yeast is an example of fermentation C02 makes it rise 6 2 major fermentation pathways a Alcoholic Fermentation i Cellular enzymes convert pyruvate to acetaldehyde which then accepts electrons from NADH to become ethyl alcohol ii Yeasts this is their means of generating energy 1 Baking industry carbohydrates are broken down in dough by yeasts perform fermentation and C02 is given off as a byproduct of this energygenerating process The gas bubbles cause the dough to rise Alcohol contributes to the odor as the dough rises 2 Alcoholic beverage production wine sugars in juice of grapes are broken down by yeasts by fermentation Ethanol ethyl alcohol is produced as a byproduct b Lactic AcidLactate Fermentation i Pyruvate molecules converted into lactate which is an ionized form of lactic acid ii Certain bacterial organisms are able to ferment yeast is fungal can make milk sour some can be utilized to make certain foods like yogurt and sauerkraut acidophilus milk iii Animal Skeletal Muscles help bones move made up of cells that fuse together and make longs bers bers work differently in how they make ATP two types also has to do with longevity for muscles 1 Red a Whole lot of mitochondria b Aerobic respiration c Red in color because they have much myoglobin which is a protein that stores oxygen for aerobic respiration in these bers 2 White a Don t have a lot of mitochondria b Very limited in aerobic respiration c No myoglobin d Most of their ATP is made by lactate fermentation 4 iv Alternative Energy Sources in Body 1 Carbohydrate breakdown a Excess carb intakes can be stored for later use glycogen in liver and muscle also stored as fat b Free glucose available when low glycogen reserve is tapped into Fibers sustain prolonged activity which is why marathon runners tend to have more of the red bers As these bers don39t support prolonged activity ATP is made quickly by pathway but not for long energy useful for quick strenuous activities sprinters tend to have more of the white bers Why can39t chickens y great distances white muscle bers so can39t endure long distances short bursts of speed quotwhite meatquot is white bers and quotdark meatquot is dark bers c Glycogen makes up about 1 of an average adult39s total energy reserve which is the energy equivalent of about 2 cups of cooked pasta unless you eat regularly you can deplete glycogen stores in less than 12 hours 2 Energy from fats a Excess fats are stored away in cells of adipose tissue Woman typically have more i Adipose tissue connective tissue that specializes in fat storage b Total energy reserve is about 78 body fat most are triglyceridesgycero with 3 fatty acids i Fats triglycerides are digested into 1 Glycerol which enters glycolysis 2 Fatty acids which enter Krebs Cycle c More sustained because slower burning degraded more slowly and yield greater amounts of ATP because they have many more carbon and hydrogen atoms d Low carb diets force body to break down fats into ketones which most of our cells can use for energy instead of glucose This metabolic state starvation can raise the level of LDL bad cholesterol and damage kidneys and liver 3 Energy from proteins a about 21 of total energy reserve b made up of amino acids released by digestion and travel in the blood After amino group is removed the amino acid remnant is fed into the Krebs cycle The amino group becomes ammonia a waste product that the body eliminates in urine i 4 chemical groups 1 Amine NH2aso amino carboxyl hydrogen ion and r group a When the amine group is taken off of the amino acid the rest of the amino acid goes into the Krebs Cycle That amine group is converted into ammonia NH3 which is a waste product as it is not good for our body Taken out through kidneys and passed through body as urine 2 Using proteins as a source of energy could cause buildup of ammonia not sure about this causes muscle damagenot best choice c Broken down and amino acids released and get into bloodstream Vl Textbook powerpoint highlights Dietary Energy and Cellular Respiration a Obesity rate has gone up substantially doubled since the 805 2 big areas that have contributed to it i Biology evolution has taught us to hoard food for the bad times store a lot of excess food as fat ii Culture how we eat and how much we eat b Obese i 20 more fat than recommended for one39s height ii Gender body type and frame size taken into account iii Leads to increased rates of diabetes heart disease and other related illnesses c BMI body mass index i Estimates body fat based on height and weight ii Used by health care professionals to get a rough estimate about whether is a person is at a risk for health problems as a result of their weight iii Doesn39t account for muscle mass gender or frame size d Calories i c Amount of energy required to raise the temperature of 1 g of water by 1 degree Celsius ii Food energy is measured in calories C equal to 1000 calories or 1 kilocalorie iii Storing excess calories 1 Animals a Glycogen muscle and liver cells b Triglycerides fat cells e Food is a source of chemical energy i Contains macromolecules ii Broken down into building blocks or subunits iii Used to make new molecules and as sources of energy Vll DNA structure and replication a Innocence Project i Free people wrongly accused of certain crimes ii Chapter follows story of an individual who was falsely accused and they used this project to try to free him iii DNA can be used to free innocent victims It is a standard procedure in many cases especially criminal In 92 that was not the case because technology hadn39t reached that level But now it s extremely accurate b What is DNA i Hereditary molecule passed down from generation to the next ii Instruction book as to how an individual is made what proteins are to produce iii Found in nucleus of eukaryotic cells in form of chromosomes iv Single DNA molecule wrapped around a protein Histome keep organization of DNA molecule in cell as it gets very very large c Human DNA i One set by father one by mother ii 23 chromosomes 1 23rd chromosomes sex chromosome determines sex a XX female b XY male 2 Karyotype display of micrographs of pairs of chromosomes in metaphase chromosomes line up at equator arranged according to size Centromere is the region of duplicated chromosomes where the two sister chromatids join together 3 Each person has unique DNA except for identical twins 4 Why important to understand structure iii Building Blocks of DNA 1 Nucleotides a Components i Sugar phosphate and nitrogenous base associated with it 1 Sugars can differ DNA has deoxyribose and RNA has ribose ii P04 is phosphate iii Adenine thymine guanine and cytosine are nitrogenous bases associated with DNA d Structure of DNA and organization i Double stranded 2 pairs of nucleotides pair up and twist around each other to form a spiralshaped double helix ii Sugars and phosphates form backbone iii The two strands are held together by hydrogen bondings between the nitrogenous bases of each strand 1 Complementary base pair of strands a A always pairs with T b G always pairs with C 2 The sequence of nitrogenous bases in DNA is unique for each person so as a result of that they can extract the DNA from ourselves to create that individual39s speci c DNA pro le Can visualize their DNA sequence but to do this they need to have many many copies of that portion of the DNA e DNA replication Typically normal process in which cells make an identical copy of DNA molecule When do this have to keep in mind the complementary base pairing rules because the DNA will unwind and have to pick up more nucleotides When ready to replicate the hydrogen bonds are broken and double helix begins to unwind DNA polymerase enzyme that reads the DNA and begins to add complementary nucleotides pairing them up with its complements Semiconservative mechanism the original DNA molecule produces two copies of the original each having a portion of original molecule and a new strand The technique used in lab to try and get a whole lot of these DNA molecules is something known as PCR Polymerase chain reaction replicates DNA and amplify a certain section of that DNA molecule 1 Primers have to be added to this concoction The DNA is often taken from cheek and put in vessel Add primers and enzyme to help guide enzyme to particular section that needs to be copied 2 lnvolves heating processes In each stage each strand begins to separate because of heating Heat makes it go faster and then they cool it back down to allow enzyme to come in and make pairing Heating strand separation cooling DNA replication 3 Allows replication to occur many many times over and over again to where they can get billions of copies from just one sample 4 After this they can begin DNA pro ling a Takes advantage of fact that no two people should have same exact DNA sequencing b Genome one complete set of the genetic instructions encoded by DNA for a given organism c Pro ling determines the entire sequencing of the entire genome but it39s time consuming and expensive So they can take shortcuts by using PCR to amplify only speci c segments of DNA STR short tandem repeats i STRs are sections of the chromosome where the DNA sequencing is repeated The example is using four speci c nucleotides in f a speci c order Sequence was repeated 6 times on maternal and 4 times on paternal 1 In the same places along the chromosome 2 The length varies from person to person When ready to make pro le they collect cells often from cheek and extract DNA Use PCR to amplify STR regions but do it in multiples the more they can do the better it can be usually try to get fteen multiple regions Separate the STRs by using gel electrophoresis make up gels and cut the gels and put those products of PCR and put in gel Put current in this gel and it moves because it is polar The shorter fragments travel the furthest because they are closer to the top They make bands with the fragments Run a uorescent light to make it glow Compare the patterns because everyone has different patterns The original sample of the saliva is made and compare STR bonding patterns Take multiple STRs Each one has a particular name and chromosome location The more STRs tested the more discriminating the test becomes DNA evidence is more reliable than other forms of evidence Bite mark errors can be as high as 91 Hair can only exclude a suspect and not positively identify one However there are identical twins g DNA is hereditary molecule of all living things Found packaged on chromosomes in nucleus 23 pairs of chromosomes one from mother one from father Has linear strands bound together into double helix by complementary pairing of nucleotides Complementary pairing guides DNA replication PCR enables scientists to increase number of copies of DNA sequences Forensic scientists use STRs to construct DNA pro le Vlll Genes to Proteins a Has to do with coding of genes for protein synthesis b Shape of a protein molecule is determined by c There are different levels of complexity As go up scale complexity increases Higher up the more stress on the structure d Animal Genetic Modi cation to Produce Human Proteins i Animals that have been genetically altered are called transgenic organisms 1 Making transgenic organisms a Inject recombinant gene into a fertilized singlecell embryo b That embryo is implanted into the mom and she acts as a surrogate Embryo will grow and gene will be replicated and passed down into every cell i In this example they harvest transgenic milk from goat and purify the protein Isolate the protein from that and able to treat the people that are de cient with that type of protein 2 Isolate gene of interest from human chromosome Insert it into animal embryo Gene must be a hybrid so human protein is expressed in animal a Genetic engineering i Process of assembling new quothybridquot genes ii Novel combinations of regulatory and coding sequences iii Recombinant gene 1 Antithrombin recombinant gene a Regulatory sequence of milk gene b Coding sequencing of antithrombin c Trying to get expression of this protein only in the mammary ceIIs ii PracticaI Application of GMOs genetically modi ed organisms 1 Pharming a Using pharmaceutical aspects in agriculture GMOs b make therapeutic drugs Cost is an issue Makes a lot in short period of time Cheaper but sacri ce is kind of great Antithrombin human protein is being extracted from goat39s39 milk i Antithrombin protein helps prevent blood clots thrombosis Encoded found on chromosome number one Only expressed by cells in the liver Protein is released into the bloodstream ii Some people inherit genetic defect for the production of this protein 1 2 One or both copies of antithrombin gene defective humans have two copies of every gene The sequencing of nucleotides can be identical or only slightly different A different version of the same gene is called an allele a Alleles are alternate versions of the same traits Close but there are differences Different aees can in uence protein functions For antithrombin there is a variation one letter different G instead of C d Also use this in plants 2 Protein a Large macromolecule made up of repeating amino acids b Multifunctional c Encoded as to what39s going to be made is encoded in genes i Gene section of DNA that contains a nucleotide sequence with the instructions to make at least one protein 1 3 Amino Acids When that gene is turned on then that encoded protein can be manufactured Found on chromosomes a Each contains unique set of genes Gene expression synthesis of protein from a gene Organized into two parts a Regulatory sequencing when and how much of the protein that the gene is supposed to make b Coding sequencing associated with actual sequencing of amino acid of the encoded protein a 20 different ones an Have same basic core structure i Amine group hydrogen atom R group and a carboxyl group ii The R group differs with each amino acids Form linear chains As they get larger they start to fold on one another i Form 3D images Determines shape and functionality of a protein Changing an amino acid sequence will also change shape Review transcription and translation and the different RNAs and what they do


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