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HNRS 105: Biology 1, One Week of Notes for Exam 2

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by: Alexandra VanBlaricum

HNRS 105: Biology 1, One Week of Notes for Exam 2 HNRS 105 H01

Marketplace > Louisiana Tech University > Biology > HNRS 105 H01 > HNRS 105 Biology 1 One Week of Notes for Exam 2
Alexandra VanBlaricum
LA Tech

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These notes cover a week's worth of material (1-5-16 and 1-7-16) for the next biology exam on 1-18-16.
Honors Fundamentals of Biology
Dr. Jewell
Class Notes
Biology, honors, Honors Biology
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This 11 page Class Notes was uploaded by Alexandra VanBlaricum on Wednesday January 13, 2016. The Class Notes belongs to HNRS 105 H01 at Louisiana Tech University taught by Dr. Jewell in Winter 2016. Since its upload, it has received 32 views. For similar materials see Honors Fundamentals of Biology in Biology at Louisiana Tech University.


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Date Created: 01/13/16
Louisiana Tech University Winter Quarter 2016 Teacher: Jewell Exam 2: 1 Week Of Notes BIOLOGY ___ Notes 1-5-15 Chapter 3: Cell Structure and Function ● Cell structure ■ Hooke: observed dead cork (plant) cells; coined term cell. Microscopes already developed by this time. Cells looked like there were four walls with nothing in it, but they couldn’t see it at that point. Reminded him of monks living in monastery (living in empty rooms). ■ Leeuwenhoek: dutchman (typically smart, persnicketey, precise). “father of the microscope” (not because first to develop--pair of brothers Janson developed that first-- but because over his career he developed numerous types of microscopes (250-300)). the cells, or critters, he observed he gave the name animalcules (animal like characteristics but smaller than animal cells). Looked at all different kind of cells (protists, sperm, bacteria) and wrote accounts about what he saw which wasn’t done much before that time. As a result of his observations, he began to get a lot of recognition (invitation to present findings to prestigious group called the British Royal Society or Royal Society of London). Very well known. ■ Developers of cell theory: Schleiden (botanist), Schwann (zoologist), Virchow (physiologist) ● Cell theory has several facets ○ All living organisms made up of one or more cells. ○ Cells basic structural unit of life ○ Cells come from preexisting cells ○ Cells contain hereditary information that’s passed down through offspring ○ Traits common to all cells ■ Basic structural and functional unit of life. ■ Cell or plasma membrane: holds contents in structure. gateway (regulates flow of material across). barrier. receptors for cell activity. ■ DNA-containing region: not always a nucleus ■ Cytoplasm ○ Two major types ■ Procaryotic: Bacteria and archaeans. No true membrane-bound nucleus. ■ Eucaryotic: true membrane-bound nucleus (plants, animal, fungi, protists) ○ Composition of Cell Membrane ■ Bi-layered structure made of phosolipids that lends itself to the characteristic of being amphipathic. Hydrophilic and hydrophobic. Directly connects with what can cross membrane. Bi-layer has heads (face surface: hydrophilic) and tails (facing inward: hydrophobic) ● Function of bi-layer: selective barrier to water soluble substances: what may or may not pass. ● protein molecules embedded in bi-layers of different types with different functions ○ Transport: regulate ions and certain molecules going across (passive, active) ○ Receptor sites: binding spots to certain substances ○ Recognition: identifies if something is part of the being or foreign ○ Adhesion: items stick to the surface ○ Enzyme: biggie. catalyze metabolic reactions. ■ Variations in composition: ● Different phospholipids (glycerol and fatty acids attached and phosphate group) as far as the length of the fatty acids attached and sometimes not saturated with hydrogen atoms as much ● Some proteins will be stationary, others not. ● Sometimes the phospholipids do not have fatty acids attached. ○ Cell size constraints ■ Surface volume ratio: limit size. goes back to flow of materials, whether nutrient or waste, that goes across membrane. If too fast cell will die. ■ Body plans of multicelled species: affected by surface-to-volume ratio. some algae organisms are filamentous and their positions have to be such that the filaments connect ○ Cell size: ■ Almost all too small to see with naked eye ● Need microscopic aids: light vs. electron ○ Microscopy: ■ Electron gives greater magnification. ■ Can see procaryotes using light microscope (at least a 1000x). it is difficult ■ Metric unit of length to measure procaryotes: micrometer (1000 micrometers in a millimeter) ■ Can’t see viruses with light microscope: need electron (two types) ● Electron go right through specimen: transmission (TEM). a lot of mag like a million x ● Scanning electron: SEM. electrons are shot through to specimen but don’t go through. bounce around specimen giving 3-D image. more detail, less magnification ■ Metric unit to measure viruses: nanometer (1000 nanometers in a micrometer) ○ Defining Features of Eucaryotic Cells: ■ Major internal cellular components: ● Organelles: internal, membrane-bound compartments of cytoplasm. Each one has one or more specific functions (can overlap) ○ Nucleus: control center, contains and isolates DNA ○ ER (endoplasmic reticulum): connects nucleus, the control center, to the cytoplasm. major function is to modify new polypeptide chains that are formed after protein synthesis. involved in making lips. ○ Golgi bodies (apparatus): capitalized because named after Italian named Golgi. associated with proteins and lipids. make lipids that are used internally and for secretion development. Also associated with proteins as far as modifying and moving them around. Connection between this and ER as far as proteins and lipids. ○ Vesicles: transport materials in between organelles (ER to Golgi bodies). Associated with intracellular digestion (getting rid of worn-out parts) ○ Mitochondria: powerhouse. ATP formed. ● Some structures that are non-membrane bound ○ Ribosomes: sites of protein synthesis. need to be several places. can be free- floating in cytoplasm as well as being attached to ER (Both convenient as they are associated with proteins) ○ Cytoskeleton: depending on what type of cytoskeleton you’re referring dictates the function. related to our skeleton in a way as far as functionality. determines shape of cell. internal organization. movement. ● Advantages of compartments (organelles) ○ A lot going on at same time in small amount of space. This compartmentalization allows a lot to go on at same time at different rates. ● Infographic 3.8, page 56 animal and plant cells ○ Plants have chloroplasts, central vacuole, and cell wall and animals do not. ■ Components of Eucaryotic cells: more in depth ● Nucleus ○ Nucleoid regions: resembles nucleus ○ Fluid on inside (nucleoplasm) ○ Surrounded by membrane ○ Mass of subunits of ribosomes (nucleolus). some exit from nucleus at later point and time. building blocks of ribosomes that make nucleolus up. ○ Chromatin/ Chromosomes ■ Chromatin: total collection of a particular cell’s DNA and associated proteins (not all, just ones associated with DNA) ■ Chromosomes: individual DNA molecules and their associated proteins ■ A cell’s DNA is duplicated and condensed before cell division occurs (has to be condensed because have twice as much material of same size in same amount of space) ■ DNA codes instructions for building proteins (Hereditary info) ● Some stockpiled in cytoplasm ● Some moved through cells and are packaged in vesicles to be used in cell or exported out ● Depends on function of cell. ● Proteins moved through cell to be exported through the cytomembrane system. ○ Cytomembrane system: ■ ER ■ Golgi Bodies ■ Vesicles (variety of them) ● ER: ○ connects nucleus and cytoplasm ○ don’t all look same because some have attached ribosome (rough) and others don’t (Smooth) ○ tubes and flattened sacs ● Golgi Bodies: ○ Stack of pancakes ○ Modify, process, and sort proteins and lipids ○ As time progresses and those lipids/proteins need to be moved, the edges of the Golgi Bodies break off (same as ER) and form packages (vesicles) that contain the proteins/lipids. How they move through cell. ● Vesicles: ○ Lysosomes: contain really powerful digestive enzymes. take out worn out cells and unwanted bacterial organisms (defense mechanisms) ○ Peroxisomes: contain enzymes to break down fatty acids and amino acids (geared more to molecular level). when those enzymes work on those materials, certain bad things are produced ■ H202: hydrogen peroxide. we don’t want that ● Another enzyme has the capability to break down H202 byproduct in water and oxygen: catalase-- breaks it down into H20 and O2. ● Mitochondria ○ Powerhouse of cell ○ To work have to have oxygen present. Transfers energy in carbohydrates to ATP. ○ Composition ■ 2 membranes (think tylenol capsule--elongated, membrane on outside) ● Outer: very smooth, general membrane ● Internally: folded (cristae) to give it more surface area ■ Have their own DNA and ribosomes (more self-sufficient) ● Endosymbiotic Theory: may have evolved from ancient bacteria and were later on engulfed from some primitive eucaryotic cell. If they do have means of producing their own proteins, there may be some validity to this theory. Also chloroplasts. ■ Specialized Plant Organelles: ● Plastids ○ Chloroplasts: ■ Double-layer outer membrane. ■ Inside is fluid (stroma) ● Inside stroma, there is another membrane ○ Thylakoid membrane: folded; looks like it’s made up of discs stacked on tops of one another--grana) ■ Grana contains chlorophyll. Sunlight trapped during photosyntheses (has to get all the way down into the grana). Sunlights trapped to form ATP. ○ In stroma, ATP formed to make sugars. ○ Chromoplasts: ■ Various colored pigments other than green. ● Carotene (pigment): orange in carrot root ● Xanthophyll (pigment): yellow in ginkgo leaf ● Show though when chlorophyll amount goes down (photosynthesis goes way down too so lose leaves because no longer needed as much) ○ Amyloplasts ■ Contain no colored pigments but still need them to store starch grains ● Example: potato tuber (underground stem) ○ Massive amounts of amyloplasts ● Iodine is indicator of starch ● Central Vacuole: CV ○ Size varies according to maturity of plant cell ■ Older the cell the larger the central vacuole ● What made plant cell appear to be empty to Hooke: he couldn’t see any of the material because the CV had pushed it up ● Cytoskeleton: ○ Synonymous to our skeleton. Found between nucleus and cell membrane. ○ Could be made of all different types: fibers, threads, lattices, etc. ■ Forms network of materials ■ Microtubules: transient (not needed all the time so just kind of go away) ■ Microfilaments: permanent ○ Cell shape, organization, movement ■ Movement ● Cilia: shorter, hair-like. move organism from point A to point B or move water around and get nutrients found in water into organisms ● Flagella: longer. fewer associated with particular cell. found on 1-celled protists, sperm cells, bacteria. ● Cell surface specialization: ○ All cells have cell wall except for animal cells. ○ Pores associated with surface to allow for movement across the membrane. ○ Sometimes the walls become very rigid as the cell get older and matures. Young plants that still have like green stems their cell wall is made of cellulose ■ Over time, lignin is laid down as well to make cell wall more rigid (secondary wall); woody ○ Cells stick together to form tissue: glue-like structure to glue one cell to another (pectin) ○ Plasmodesmata: channels to connect adjacent cells ○ Sometimes compounds added to outer part of cells for protection ■ Ex: magnolia leaf: wax to prevent water evaporation to help photosynthesis take place ○ Prokaryotic: ■ Before nucleus. ■ Single-celled. ■ Two domains: ● Archaebacteria ● Eubacteria (true bacteria) ■ Most have a cell wall, external to membrane ■ Have to have at least ribosomes. Don’t have other organelles but have to have ribosomes to make proteins and enzymes ● A few also have chloroplasts to photosynthesize ● Our ribosomes vs. these organisms: not the same. one’s ribosomes have a designation called 70S ribosomes and the other is 80S ○ Target site for certain antibiotics are ribosomes. Will not hurt our ribosomes because it’s for bacterial ribosomes. ● Genome: DNA ○ Not housed in nucleus. ○ Single loop chromosome ■ Can’t get all that info on one chromosome, need plasmids: code for certain traits (ex. antibiotic resistance and tolerance to certain substances--bioremediation, which is using living things to clean up problems in the environment ○ Prokaryotic have to have membrane but not all have to have a cell wall. ■ Some have additional layer known as a capsule. Will be exterior to either the membrane or wall, whichever is there. Protective to that organism. ● If has capsule, its virulence (capability to cause disease) is increased. ● Will also be sticky to help it hook onto a host cell ● Some have flagella, cilia, or no type at all to help move it around. ○ Flagella: not all have to be mobile but some are. Different than other flagella. Long, whip-like structure. Different movements are result of different structure. ○ Pili: hollow filaments. short. pointed ends (usually). radiate out from bacterial organisms. (not all bacteria have it) ■ In Neisseria gonorrhoeae, if pili is removed it cannot attach to urogenital cells and will not cause infection. ● Cell Structure and Function ○ Alexander Fleming: discovered penicillin on accident ■ First antibiotic. RIght hand-side of picture is organism that creates penicillin. grows lot on oranges and cheeses (like acidic things) ■ At first, penicillin was very effective against staphylococcus organisms but now there are groups that are resistant to it ○ Antibiotic: ■ Chemical that can slow or stop the growth of bacteria ■ Often naturally produced by living organisms (not always; some are made synthetically and others semi-synthetically) ■ For example, penicillin is produced by Penicillium notatum. ■ Use target sites ○ Cells (different types pictures) ■ Prokaryotic: lack organelles ● Antibiotics target prokaryotic cells ○ Will sometimes target cell walls: Bacterial cell walls are rigid due to peptidoglycan; this is what makes them up similar to how cellulose makes up plant cell walls (cell walls as target don’t always work due to not all bacteria having them) penicillin targets cell walls. Penicillin will weaken cell wall so that the cell wall is filled up with water. ■ Polymer made of sugars and amino acids ■ Allows bacteria to survive in watery environment ○ Pneumonia can be caused by several different bacteria: ■ Some have cell walls and others don’t. ○ Bacteria cells are either: ■ Gram-positive: cell wall with layer of peptidoglycan that retains Gram stain ■ Gram-negative: cell wall layer of peptidoglycan surrounded by lipid membrane that does not retain the Gram stain. This prevents penicillin from reaching the peptidoglycan underneath. ○ Journal Entry: not due next time but coloring/labeling sheet is ■ Chapter 3: p. 62-65 ● 2, 4, 6, 8, 10, 12, 17, 18, 26, 28 ■ Chapter 5: p. 111-113 ● 1, 12-14, 19, 20 ○ Bring textbook next time. Chapter 5: Energy and Photosynthesis ● Energy: Where it starts- photosynthesis ○ Living things: organic compounds ■ Carbon comes from? ■ Energy come from? ■ These 2 questions bring about two living categories ● Autotrophs: CO2. energy from light. ● Heterotrophs: dependent on autotrophs for both carbon and energy. ○ Where is starts: ■ Carbon and energy enter web of life through photosynthesis. Sugar produced and released. ■ Photosynthesis: ● 2 stages: both associated with chloroplasts, but different parts ○ Light dependent reactions ■ inner membrane (thylakoid). catch light that eventually makes its way into stroma where next stage occurs ■ light conversion made into chemical energy stored in form of ATP and coenzyme NADPH (the products) ■ water molecule split and oxygen is released. ■ four things for photosynthesis: sunlight, water, carbon, chlorophyll ■ 3 products: oxygen, sugar (glucose), water ○ Light independent reactions ■ Take those raw materials and assemble sugars and other organic molecules (doesn’t always have to be glucose) and used ATP formed above and coenzyme to do something ● Nature of light ○ most of light that reaches Earth’s surface is in form of visible light (electromagnetic spectrum--visible light portion very small) ■ 380-750 nanometers in wavelength ○ travels in waves through space ■ Wavelength: distance between crest of one to crest of another (or trough to trough) ● Measured in nanometers ■ packaged in photons and function of wavelength 1-7-15 ● Where Does Photosynthesis Occur ○ 2 stages ■ Light-dependent reactions: associated with thylakoid membrane made up of the grana ● 3 major events: ○ Light energy captured by pigments and electron are given off ○ Water that’s picked up: molecules of water split. ATP (adenosine triphosate) and co- enzyme NADPH formed. Oxygen released. ■ A closer look at ATP formation in chloroplasts: ● The flow of the hydrogen ions formed from thylakoid portion of chloroplast to stroma drives formation of ATP ○ Have to have the capability of replacing lost electrons from the beginning. Electrons replaced in pigment molecules that first gave them up so photosynthesis can continue to take place. ● What happens to absorbed energy ○ Photosystems in chloroplasts: 2-300 different light absorbing pigments depending on type found on thylakoid ■ Type of critter found on determines this. ● Leave photosystems and depending on critter will be one or two electron transport systems in thylakoid membranes. 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 formed--ATP and co-enzyme NADPH formed (noncyclic pathway) ○ If 1 ETS: no co-enzyme formed or release of energy; just ATP formed (cyclic pathway) ○ Both have to have electrons transferred. ■ History of cyclic and non-cyclic pathways: ● lifeforms 3.6 billion years ago that were procaryotic in nature ○ Cyanobacteria could perform photosynthesis (3.4 billion) ○ Since about 2 billion years ago, oxygen has begun accumulating in atmosphere because organisms could tolerate oxygen, making aerobic respiration capable/possible ○ Around 2.4 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) ● Cyclic: 3.6 bya ● Non-cycle: 3.4 bya ○ A closer look at ■ Light-independent reactions: doesn’t have anything to do directly with light; semi- fluid portion of chloroplast called stroma; also referred to as Calvin-Benson cycle ● Carbon dioxide, ATP, oxygen, and NADPH have to be available. ● Takes place in stroma. ● Nothing to do with sunlight as that has already been absorbed ● How do plants capture carbon: ○ Carbon dioxide had to have ability of diffusing into leaf as that’s where most of photosynthesis takes place. Goes in through stomata. Goes across cell membranes of photosynthetic cells and into stroma. That CO2 has to be able to combine with 5- carbon compound to form a 6-carbon compound--enzyme causes this joining (Rubisco) ■ That 6-carbon compound is pretty unstable so doesn't stay as 6-carbon compound very long so splits into 2 3-carbon molecules ● Each has phosphate ions added to it which comes in from ATP (has 3 phosphates). Still trying to fix CO2 and ultimately it happens. Can get glucose, starch, cellulose, etc. can all be formed. ○ Transportable: sucrose ○ Stored: starch ● Summary: 3 things ○ Carbon fixed from CO2 ○ Glucose formed (requires ATP--for phosphate-- and NADPH--coenzyme) ○ Enzyme has to be present ● Energy Flow and Photosynthesis (textbook) ○ 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 finite amount so looking for alternative sources ■ US largest consumer ○ Biofuels are made from living organisms. ○ Energy ■ Capacity to do work ■ Potential and other type ■ Have to have energy for life ■ Law of Conservation of Energy: neither created nor destroyed, just changes form ■ Chemical energy: potential energy stored in bonds ■ Potential: stored ■ Kinetic: energy of motion ■ Energy transfers: a lot of time energy is lost in form of heat (not really lost because Law of Conservation of Energy) ■ Energy transformation not super efficient ○ Journal Entries: ■ Chapter 6: p. 133-135; #5, 7-10, 12-16, 19-22 ● Chapter 6: How cells release chemical energy, dietary energy/cellular respiration ○ Taking off where photosynthesis took off (photosynthesis-autotrophs; discussing heterotrophs now) ○ Making ATP ○ ATP is a chemical is the prime energy carrier ■ Aerobic Respiration ● The efficient 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 process--36 is the gross amount) ● Glucose + oxygen yields Carbon dioxide + water ● Three parts to it: sequential ○ Glycolysis: glucose is broken down into intermediate compound known as pyruvate; a little bit of ATP formed as well as pyruvate (2 ATPs) ■ End-products: 2 pyruvates and 2 ATPS ■ Have to have 2 NADPH ■ Takes places in cytoplasm ○ Krebs Cycle: takes over where Glycolysis ended (also citric acid cycle). Pyruvate broken down into CO2, water, a little bit of ATP, hydrogen ions, and electrons ■ Goes into mitochondria. ■ Hydrogen ions and electrons are combined with other substances that were already there to make NADH and FADH2, respectively ■ Bottom line: other things formed along the way in order to start the next time the process takes place ○ Electron Transport Phosphorylation: hydrogen ions and the electrons formed during Krebs Cycle will be processed to form more ATPS (32). Oxygen is final electron acceptor. (important slide--know where each stage happens) ■ Electrons given up to the system ■ Mitochondria ■ Hydrogen ions go into outer compartment of mitochondria ● Membranes of mitochondria: ○ Outer: where this stages takes place ○ Folded ■ Generates most ATP. ○ Not very efficient; only about 40% efficiency from glucose to ATP. About 60% lost to heat. ○ 2 + 2 + 32 = 26 ■ Fermentation (Anaerobic Routes) ● Not as efficient 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 ● Takes place in absence of oxygen ● Yeast is an example of fermentation. CO2 makes it rise. ● 2 major fermentation pathways ○ Alcoholic Fermentation ○ Lactic Acid Fermentation ■ Pyruvate molecules converted into lactate which is an ionized form of lactic acid. ■ Certain bacterial organisms are able to ferment (yeast is fungal); can make milk sour; some can utilize to make certain foods like yogurt and sauerkraut; acidophilus milk ■ Animal Skeletal Muscles: help bones move. made up of cells that fuse together and make longs fibers. fibers work differently in how they make ATP. two types; also has to do with longevity for muscles ● Red ○ Whole lot of mitochondria ○ Aerobic respiration ○ Protein to help store oxygen ○ Marathon runners tend to have more of the red fibers ● White ○ Don’t have a lot of mitochondria ○ Very limited in aerobic respiration ○ Short sprinters tend to have more of the white fibers ● Why can’t chickens fly great distances: white muscle fibers so can’t endure long distances; short bursts of speed ● “white meat” is white fibers and “dark meat” is dark fibers ○ Alcoholic Fermentation ■ Conversion of pyruvate to acedyl alcohol and eventually down to ethyl alcohol ■ Yeasts ■ Alternative Energy Sources in Body: ● Carbohydrate breakdown ○ Excess carb intakes and is stored for later use (glycogen in liver and muscle; also stored as fat) ○ Free glucose available is low is when glycogen is tapped into ○ Glycogen makes up about 1% of an average adult’s total energy reserve (can deplete stores in 12 hours) ● Fats ○ Adipose tissue is fat tissue. Woman typically have more. ○ Total reserve is about 78% stored in body fat (triglycerides--glycerol with 3 fatty acids) ○ More sustained because slower burning ● Proteins ○ about 21% ○ made up of amino acids ■ 4 chemical groups ● Amine (NH2)--also amino--, carboxyl, hydrogen ion, and r group ○ 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) ● Using proteins as a source of energy could cause build-up of ammonia??? not sure about this. causes muscle damage--not best choice. ○ Broken down and amino acids released and get into bloodstream ● Textbook powerpoint ○ Obesity; rate has gone up substantially (doubled since the 80s). 2 big areas that have contributed to it ■ Biology: evolution has taught us to hoard food for the bad times; store a lot of excess food as fat ■ Culture ○ Obese ■ 20% more fat than recommended for one’s height ■ Increase in diabetes and heart disease and other stuff like that ●


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