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BIOS 1700 & BIOS 1710

by: Makayla Lancaster

BIOS 1700 & BIOS 1710 BIOS 1700

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Makayla Lancaster

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This study guide includes the course material covered in BIOS 1700 and BIOS 1710.
Biological Sciences I
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This 48 page Study Guide was uploaded by Makayla Lancaster on Tuesday August 9, 2016. The Study Guide belongs to BIOS 1700 at Ohio University taught by in Spring 2016. Since its upload, it has received 16 views.


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Date Created: 08/09/16
BIOS 1700/1705 Inside the Cell  The 1 characteristic of life is that it contains cells. Cell Theory:  Pattern component: all organisms consist of cells  Process component: all cells come from preexisting cells 5 Characteristics of Living Things: 1. Contains cells 2. Produce and use energy 3. Process information (genetic and environmental) 4. Replicate 5. Evolve: the change in genetic information in a population over time as a population adapts to its environment. The 3 Domains: 1. Bacteria: prokaryotic 2. Archaea: prokaryotic, live in extreme environments 3. Eukarya: eukaryotic  Plants, animals, fungi, and protists Animal, Plant, and Prokaryotic Cell Structures: Structure Animal cell Plant cell Prokaryotic cell nucleus Yes; a membrane- Yes; a membrane- No; not a bound nucleus bound nucleus membrane-bound nucleus. The chromosomes float in the cytoplasm in a nucleoid. endoplasmic Yes; the rough ER Yes; the rough ER No reticulum houses ribosomes houses ribosomes that synthesize that synthesize proteins that will proteins that will leave the cell. leave the cell. The smooth ER The smooth ER synthesizes lipids. synthesizes lipids. Golgi apparatus Yes Yes No mitochondria Yes; chemical Yes; chemical Most have energy (ATP) is energy (ATP) is chloroplasts. manufactured manufactured here. here. chloroplasts No Yes; light energy is Yes; some that used to create ATP have light available and sugar for them to use do. ribosomes Yes Yes Yes lysosomes Yes; they digest No; they use their No; they use their waste vacuole to digest vacuole to digest waste waste 1 BIOS 1700/1705 peroxisomes Yes; they are Yes No responsible for oxidizing materials via reduction reactions plasma Yes Yes Yes membrane cell wall No Yes Yes vacuole No Yes; it stores Yes; it stores nutrients and ions nutrients and ions cytoskeleton Yes; very complex Yes; very complex Yes; most contain a flagellum Steps of Protein Synthesis & Secretion: 1. Protein is synthesized by a ribosome on the rough ER. An ER signal sequence (a carbohydrate group) is added to the protein if it is destined for secretion through the endomembrane system. This sequence is removed before it leaves the rough ER. 2. The vesicle carrying the protein enters the Golgi on the cis face. 3. The protein is folded into its tertiary or quaternary structure and tagged. This tag directs the protein to a unique vesicle. This vesicle will take it to its destination (e.g. to plasma membrane, to lysosome, to ER) 4. The protein enters a vesicle and leaves the Golgi on the trans face. 5. The vesicle fuses with the plasma membrane by using its tags, and secretes the protein through exocytosis. Kinesin is a motor protein that moves transport vesicles down a microtubule track. Kinesin has a tail, a stalk, and a head. The tail attaches to the vesicle and the head attaches to the microtubule. The head region is composed of two globular proteins that resemble feet. ATP binds to one of these globular proteins and releases energy that is used to facilitate its movement. The movement of kinesin down a microtuble resembles a person walking down a sidewalk. Myosin is a motor protein that works with actin to create muscle movement. Dynein is a motor protein that facilitates the movement of cilia and flagella by “walking” along microtubule doublets. Nuclear Transport: the nucleus is surrounded by a nuclear envelope that has an inner membrane and outer membrane that are composed of phospholipids. Nuclear pore complexes are proteins that are embedded in the envelope that allow ribosomes and mRNA to leave the nucleus and the building blocks of DNA and RNA and enzymes to enter the nucleus. Proteins can enter the nucleus via importins only if they are small or they have a nuclear localization signal (NLS). They are tagged with this signal in the Golgi apparatus. Proteins can leave the nucleus via exportins. Cytoskeleton Components may undergo changes in length when they are active. This observation supports the fact that the cytoskeleton is dynamic. This means that the cytoskeleton adapts and changes. 2 BIOS 1700/1705 A. Actin filaments (microfilaments): two strands composed of actin that are wound in a double helix. The helix has a positive (they grow at this end) and negative end. a. Functions: Maintain cell shape by resisting tension (pull) Move cells via muscle contraction or cell crawling (with the help of myosin) Divide animal cells in two (cytokinesis) Move organelles and cytoplasm (cytoplasmic streaming) B. Intermediate filaments: composed of keratin, vimentin, or lamin fibers wound into thicker cables. The cables are not polar. Examples- keratins, nuclear lamins a. Functions: Maintain cell shape by resisting tension (pull) Anchor nucleus and some other organelles C. Microtubules: composed of α- and β-tubulin dimers that form a hollow tube that is polar. They orginante from centrosomes. Centrosomes contain two bundles of microtubules called centrioles. a. Functions: Maintain cell shape by resisting compression (push) Move cells via flagella or cilia Move chromosomes during cell division (centrioles) Assist formation of cell plate during plant cell division Move organelles Provide tracks for intracellular transport b. Cilia and Flagella: Axoneme contains doublets surrounding two central microtubules. Doublets are composed of two microtubules, and the doublets are connected to each other via a link and to the central microtubules via a spoke. One of the microtubules in the doublet has dynein attached to it. These dynein arms cause the adjacent doublet to slide and this moves the entire structure. Lipids, Membranes, and the First Cells Lipids: 1. Triglycerides: glycerol backbone with 3 fatty-acid tails attached by ester linkages via dehydration reactions. a. Fats: contain a lot of saturated fatty-acid tails and are solids at room temperature. b. Oils: contain a lot of saturated fatty-acid tails and are liquids at room temperature. 2. Steroids: 4-ring structure (3 6-ringed and 1 5-ringed) with an isopropene chain (fatty-acid tail) attached to the 5-ringed and R-group attached to the first 6-ringed. They are amphipathic –the steroid rings and isopropene chain are hydrophobic (nonpolar) and the R-group is hydrophilic (polar). a. Cholesterol b. Sex hormones 3 BIOS 1700/1705 c. Anesthetics 3. Phospholipids: 2 fatty-acid tails and a phosphate group attached to glycerol. A polar or charged group is also attached to the phosphate group. The fatty- acids form 2 tails and the phosphate group and polar or charged group forms a head. They are amphipathic –the fatty-acid tails are hydrophobic (nonpolar) and the head is hydrophilic (polar). Functions of Lipids:  Store energy for later use  Form cell membranes  Act as messengers Phospholipid Bilayer:  Amphipathic: hydrophobic tails and hydrophilic heads o Saturated tails: have only C-H bonds. This causes them to have high melting points and be solid at room temperature. C-H bonds have more free energy than C=C bonds o Unsaturated tails: have kinks because of the double bonds. These kinks cause them to have low melting points. C=C have less free energy than C-H bonds  Selectively permeable: selects what it needs no matter if it can get through or not  Formation is spontaneous and exergonic: micelles and lipid bilayers are much more stable energetically (they have lower potential energy) than individual lipids because their hydrophobic tails can avoid water  Detergents can break the bilayer: they separate the proteins from the phospholipids and form water-soluble complexes around the phospholipids. They are amphipathic, so their hydrophobic tails interact with the hydrophobic tails of the phospholipids. This phenomenon allows them to split the bilayer apart. Factors That Affect Permeability/Fluidity:  Cholesterol content (cholesterol fills spaces and increases hydrophobia) o High= decreased permeability o Low= increased permeability  Degree of fatty-acid tail saturation (kinks provide spaces) o Highly saturated/low unsaturated= decreased permeability o Highly unsaturated/low saturated= increased permeability  Length of fatty-acid tails o Long= decreased permeability o Short= increased permeability  Temperature (increased movement of molecules creates more spaces) o Low= decreased fluidity, decreased permeability o High= increased fluidity, increased permeability Sample situation: A fish that usually lives in a cold environment moves to a tropical environment. What will happen to the composition of the fish’s membrane? In its original habitat, the membrane composition has adapted to cold temperatures. Therefore, the membrane already has adapted features to increase its permeability. These include a low content of cholesterol and a high percentage 4 BIOS 1700/1705 of short, unsaturated and a low percentage of long, saturated fatty-acid tails. The fish’s membrane will need to decrease its permeability in order to adapt to hot temperatures. The membrane will need to gain cholesterol and have a high percentage of long, saturated fatty-acid tails. Membrane Proteins: A. Passive Transport: uses the concentration gradient to move, and not energy a. Diffusion: the movement of molecules from high solute concentration to low solute concentration (small, nonpolar molecules: O , CO2, N ,2lip2ds) b. Osmosis: the diffusion of water from low solute concentration (high water concentration) to high solute concentration (low water concentration). Water moves from hypotonic environments to hypertonic environments. Cell in hypertonic environment (cell is hypotonic) = shrivel Cell in hypotonic environment (cell is hypertonic) = burst c. Facilitated diffusion: the movement of large molecules with the help of proteins that otherwise would not be able to (large, uncharged polar molecules, like glucose, and ions) Channel proteins: selective and carefully controlled  Ion channels move ions across the bilayer when they are moving with their electrochemical gradient (areas of high concentration to low concentration, positive to negative or negative to positive)  Aquaporins allow water to cross 10 X faster than it does without aquaporins.  Gated channels open in response to the binding of a particular molecule or in response to a change in the electrical charge on the outside of the membrane Carrier proteins (transporters): change their shape  GLUT-1 facilitates glucose diffusion, when glucose binds to GLUT-1 it changes its shape to allow glucose through. B. Active Transport: uses energy to move molecules against their concentration gradient. a. Cotransport: a gradient set up by a pump provides the potential energy required to power the movement of a different molecule against its particular gradient.  Na /K -ATPase (sodium-potassium pump): 3 Na leave and 2 K + enter + 1. 3 Na bind to pump 2. 1 phosphate group binds to pump and causes it to change shape. + + 3. This shape change allows the 3 Na to leave and 2 K to bind. 4. The phosphate group leaves the protein and causes it to change shape. 5 BIOS 1700/1705 5. This shape change allows the 2 K to enter and 3 Na to + bind. *Transmembrane proteins in intestinal cells use the Na gradient created by the sodium-potassium pump to bring glucose molecules, along with Na , into the glucose-rich cells. Glucose is moving against its concentration gradient* Carbohydrates Carbohydrates:  Formula: (CH O)2Fon each glycosidic linkage, one molecule of water is taken away. o Triose: C3H6O 3 o Triose + Triose: C6H10 5ne molecule of water is absent in the formula of a disaccharide. o Triose + Triose + Triose: C9H15 7wo molecules of water are absent in the formula of a “tri”saccharide.  Aldose: C=O at 1C  Ketose: C=O at 2C  Most often exist in their ringed form.  Monosaccharides are structurally distinct because they can vary in the placement of the C=O group, the number of Cs, the arrangement of -OH groups, and they can have alternative ring forms.  Monosaccharides polymerize via condensation (dehydration: water is lost) reactions to form polysaccharides. Functions of Carbohydrates:  Provide energy. The α-glycosidic linkages in carbohydrates can be easily hydrolyzed by enzymes (amylases) and glucose is released for energy. The energy released from the breaking of C-H or C-C bonds is the greatest compared to C-O bonds because they hold a lot of free energy (high potential energy because they are nonpolar) o Starch: stored energy in plants  Amylose is not branched because it only contains only α-1,4- glycosidic linkages.  Amylopectin is highly branched because it contains both α-1,4- glycosidic linkages and α-1,6-glycosidic linkages. o Glycogen: stored energy in animals  Provide structural support. The parallel arrangement of the polysaccharides gives them the feature of rigidness. o Cellulose: plants o Chitin: animal exoskeletons and some fungi & algae o Peptidoglycan: bacteria  Identify cells. There are many structurally distinct monosaccharides, and this allows cells to have unique MHC molecules. o MHC: an oligosaccharide attached to a glycoprotein that identifies cells 6 BIOS 1700/1705  Serve as precursors to larger molecules (lipids, proteins, nucleic acids). A carbohydrate contains all of the elements needed to build lipids, proteins, and nucleic acids. These elements are C, H, and O. Every biological macromolecule has these three elements. Proteins Proteins: 25% of our body is protein and 50% of a living cell is protein.  Polymerization is nonspontaneous and endergonic (requires energy) because entropy is decreased and the polymers are much less stable than the individual amino acids. Clinging to a mineral surface allows condensation reactions to take place.  Characteristics of the polypeptide bond: o R-groups are able to interact with each other and with water o There is an amino end (N-terminus) and a carboxyl end (C-terminus). The amino acids are read from the N-terminus to the C-terminus, and proteins are synthesized starts at the N-terminus. o It is flexible because the bonds on each side of the peptide bond can rotate.  Amino acids can be nonpolar, polar, or charged depending on their R-group.  Oligopeptide (peptide)= less than 50 amino acids  Proteins= more than 50 amino acids Functions of Proteins:  Catalysis. The quaternary and tertiary structures that a protein adapts can be specific enough to create an active site for a particular reaction. o Enzymes (trypsin, pepsin, amylase)  Defense o Antibodies and complement proteins  Movement. The structures of motor proteins (α-helices) allow them to “walk” along a supportive structure. o Motor proteins (kinesin, myosin, and dynein)  Signaling o Hormones (glucagon, insulin)  Structure. Proteins can form long fibers. o Keratin gives hair and fingernails structure o Collagen  Transport. The quaternary and tertiary structures that a protein adapts allow it to form unique shapes that can be used to transport molecules across the membrane. o Membrane proteins (aquaporin, channel proteins, carrier proteins) Catalysis speeds up chemical reactions with the help of enzymes. Without catalysis, chemical reactions could not occur fast enough to sustain life. Enzymes: allow two substrates to come together in the active site. They lower the activation energy that is required for the reaction to start, and this allows the reaction to take place at a faster speed. Enzymes can be regulated. Types of Regulation: 7 BIOS 1700/1705 1. Allosteric regulation 2. Competitive inhibition 3. Temperature and pH 4. Concentration of substrate Nucleic Acids Nucleic Acids: polymers of nucleotides. The polymerization is endergonic (requires energy) and nonspontaneous. Three examples of nucleic acids are DNA, RNA, and ATP. Nucleotide Components: 1. Sugar (pentose) a. Deoxyribose in DNA b. Ribose in RNA 2. Phosphate group 3. Nitrogenous base a. Purine: adenine or guanine b. Pyrimidine: cytosine, thymine, or uracil Comparing DNA and RNA DNA RNA Double-stranded Single-stranded Long Short In the nucleus In the cytosol Secondary structure: α-helix Secondary structure: hairpin Not a catalyst Can act as a catalyst (ribozymes) Can replicate Can replicate Contains genetic information Helps in the process of translating genetic information Characteristics of DNA:  The strands are antiparallel o 5’ end contains a phosphate group. o 3’ end contains the sugar and polymerization begins at this end.  The strands form a double-helix in order to be more stable  Purines always pair with pyrimidines (complementation law) and are held together with hydrogen bonds. o Guanine – Cytosine 3 H-bonds o Adenine – Thymine (or Uracil in RNA) 2 H-bonds  DNA has a major groove and a minor groove The Chemical Bases of Life Chemical Evolution Theory  Pattern component: complex carbon-containing substances (biological macromolecules) exist and are required for life.  Process component: early in Earth’s history, simple chemical compounds combined to form more complex carbon-containing substances before the evolution of life. o May have formed in either the atmosphere or deep-sea vents. 8 BIOS 1700/1705 Most Common Elements in Living Things:  Carbon  Hydrogen  Nitrogen  Oxygen  Sodium  Magnesium  Phosphorus  Sulfur  Chlorine Types of Bonds: 1. Covalent: sharing of electrons between two non-metals in a very strong bond. This bond is strong because enzymes are needed to break it. a. Nonpolar covalent –equal sharing of electrons b. Polar covalent –non-equal sharing of electrons. One atom is partially positive and one is partially negative. 2. Ionic: electrons are transferred from the metal to a nonmetal. This bond is weak because most of the bonds can be broken when they dissolve in water. Characteristics of Water: 60-70% of any living organism is water.  Polar molecule: H is partially positive and O is partially negative  Hydrogen bonding: When two water molecules interact the a weak bond will form between the partially positive H and partially negative O. This makes it possible for any charged or polar molecule to dissolve in water.  Cohesive: Water molecules can stick together and this results in high surface tension.  Adhesive: Water can bind to other molecules (plastic, epithelial layers, glass)  Denser as a solid: Ice floats because water expands as it freezes and this causes a crystal lattice to form.  High specific heat capacity: Water can absorb and hold a lot of heat. The First Law of Thermodynamics states that energy is always conserved and it cannot be created or destroyed, it can only be transferred or transformed. The Second Law of Thermodynamics states that entropy always increases and chemical reactions result in products with less ordered and usable energy. Entropy (S): the amount of disorder in a group of molecules.  A spontaneous chemical reaction occurs when the products have less potential energy and higher entropy. These reactions are exergonic (exothermic, no energy is required, energy is released into surrounding environment. This energy can be used to fuel endergonic reactions). Spontaneous Nonspontaneous Exergonic/Exothermic Endergonic/Endothermic Positive ΔS (disorder increases, entropy; Negative ΔS (disorder decreases, S) entropy; S) Negative ΔH (PE decreases) Positive ΔH (PE increases) Negative ΔG (energy is lost) Positive ΔG (energy is gained) Acid-Base Reactions and pH: 9 BIOS 1700/1705 + Acids are proton donors, have a high [H ], and a low pH (<7). + Bases are proton acceptors, have a low [H ], and a high pH (>7). pH=-log[H ] + -4 pH=-log(10 ) pH=4 Buffers are compounds that maintain the homeostasis of pH. H CO <----> HCO + H - + 2 3 3  pH= too high (basic, low [H ]): The blood needs to gain H (lower pH). The equation will move to the right and the concentration of HCO + H will3- + increase. H CO ----> HCO + H - + 2 3 3  pH= just right (neutral): The equation will be at equilibrium. - + H 2O <3---> HCO + H 3  pH= too low (acidic, high [H ]): The blood needs to lose H (increase pH). The equation will move to the left and the concentration of H CO will2 3 increase. H 2O <3--- HCO + H 3 + Cellular Respiration & Fermentation nd The 2 characteristic of life is to be able to produce and use energy. Redox Reactions: Oxidation is a loss of electrons. In cellular respiration, NADH & FADH are oxidized 2 to become NAD & FAD. Glucose is also oxidized and becomes CO . 2 + - Oxidation of NADH: NADH ---> NAD + e + H (H often comes with an electron) - Oxidation of FADH : 2ADH --->2FAD + e + H 2 Combining these oxidations in the presence of O : NADH + FADH + O ---> NAD + + 2 2 2 FAD + H O2 + Reduction is a gain of electrons. In cellular respiration, NAD & FAD are reduced to become NADH & FADH . 2 Reduction of NAD : NAD + e + H ---> NADH Reduction of FAD: FAD + e + H --->2FADH 2 Oxidation & Reduction and Potential Energy: Electrons that are far away from the nucleus have high potential energy. Highly electronegative atoms (O & N ) have 2 2 low potential energy because their electrons are held tightly to the nucleus. Atoms with low electronegativity (C & H) have high potential energy because their electrons are able to be far away from the nucleus. Oxidized molecules have less potential energy compared to their reduced form. This is because an oxidized molecule has electrons that are being pulled away from the nucleus, and therefore the electron is far away from the nucleus. In contrast, a reduced molecule has electrons that are being pulled toward the nucleus. Cellular Respiration: the process of oxidizing glucose to obtain ATP. C 6 O12 O 6---> CO2+ H O + ATP 2 2 10 BIOS 1700/1705 C 6 12:6glucose that comes from food O 2 comes from the air that we breathe CO 2 produced during pyruvate processing and the citric acid cycle H 2: produced during the oxidation of NADH and FADH durin2 the ETC NADH + FADH + O2--->2NAD + FAD + H O 2 ATP: majority is produced during the ETC 1. Glycolysis: Glucose breaks into two molecules of pyruvate through a process with 10 steps and 10 enzymes.  Goes in: glucose, 2ATP, 2NAD +  Comes out: 2pyruvate, 2ATP (produced via substrate-level phosphorylation), 2NADH 2. Pyruvate processing: Pyruvate is converted to acetyl CoA through oxidation.  Goes in: 2pyruvate, 2coenzyme A, 2NAD +  Comes out: 2acetyl CoA, 2NADH, 2CO 2 3. Citric acid cycle: Acetyl CoA gives two of its carbons to citrate (most reduced carboxylic acid) and this starts a sequence of events that produces carboxylic acids that are more oxidized than their precursor, ending with oxaloacetate (the most oxidized carboxylic acid). +  Goes in: 2acetyl CoA, 6NAD , 2FAD  Comes out: 2ATP (produced via substrate-level phosphorylation), 6NADH, 2FADH , 4CO 2 2 4. Electron transport chain (ETC) and chemiosmosis: NADH and FADH are 2 oxidized. The electrons from NADH and FADH are pa2sed through 4 protein complexes embedded in the membrane of cristae in the mitochondria. As these electrons are being transported, the H+ concentration of the intermembrane space is increasing. This creates the proton gradient that ATP synthase will use to synthesize ATP via oxidative phosphorylation.  Goes in: NADH, FADH , O + 2 2  Comes out: NAD , FAD, H O,225ATP Cell-Cell Interactions rd  The 3 characteristic of life is to process information. Extracellular Layers: help determine the cell’s shape and either attaches it to another cell or protects the cell. Plants: primary and secondary cell walls Primary cell wall: composed of pectin and cellulose, and gives the cell structural support Secondary cell wall: unique to each cell type Animals: extracellular matrix (ECM) ECM: composed of collagen and gel-forming polysaccharides Cell-Cell Attachments: 1. Middle lamella: composed of gelatinous pectins that “glue” two adjacent cells together. Common in epithelia tissues- tissues that form external and internal surfaces. 11 BIOS 1700/1705 2. Tight junctions: form tight seals and are dynamic; they can open & close in response to the environment. Common in intestinal and stomach cells, and bladder cells. 3. Desmosomes: proteins within the cell membrane attach to proteins of another cell’s membrane. This is done through selective adhesion and the attachment molecules on the proteins are called cadherins. Cell-Cell Communication (between adjacent cells): 1. Plasmodesmata (plants): direct connections between the cytoplasm of adjacent cells 2. Gap junctions (animals): specialized proteins create channels between cells Cell-Cell Communication (between distant cells): Is done with the help of hormones. Hormones are molecules that carry messages. They are secreted from glands in the endocrine system and travel through the bloodstream. Cells respond to these signals through four steps. 1. Signal reception: a hormone binds to a signal receptor. Signal receptors change their shape after a signal binds to them, and this shape change means that the signal has been received. Lipid-soluble signals have signal receptors in the cytoplasm and lipid-insoluble receptors have signal receptors in the membrane. 2. Signal processing: lipid-soluble signals are able to be processed directly. Lipid-insoluble signals must go through signal transduction because they are unable to enter the cell, and signal amplification before they are processed. a. Signal transduction: converts an extracellular signal to an intracellular signal (a second messenger or a response created by a phosphorylation cascade). This can be done using G proteins or enzyme-linked receptors. a. Via G proteins 1. G protein is off (because it is bound to GDP) and attached to the signal receptor. 2. Signal binds to signal receptor within the membrane. Signal receptor changes shape and this causes the G protein to bind to GTP and split into two parts. 3. One part of the G protein binds to an enzyme. This binding activates the enzyme and the enzyme produces the second messenger. b. Via enzyme-linked receptors (receptor tyrosine kinases, RTKs) 1. Signal binds to RTK 2. RTK changes shape and becomes phosphorylated 3. Proteins form a bridge between RTK and Ras protein. This bridging activates Ras. 4. Ras triggers phosphorylation (and activation) of an intracellular protein 5. Each protein will phosphorylate the next protein until a response is triggered in the cell. This is called a phosphorylation cascade. 12 BIOS 1700/1705 b. Signal amplification: increases the concentration of the signal. This allows the tiny signal to trigger a large response from cells. 3. Signal response: the signal can change which genes are being expressed in the cell or activate or deactivate proteins within the cell. 4. Signal deactivation: signal transduction systems can be shut down quickly and they are sensitive to small changes in the concentration of hormones or the number and activity of signal receptors. a. G proteins are deactivated when their attached GTP is converted to GDP, and when the extracellular signal has stopped. b. Phosphorylation cascades stops when phosphatases dephosphorylate the components of the cascade. When stimulation of RTK ends, phosphatases are able to do this. The Cell Cycle  The 4 thcharacteristic of life is to replicate and reproduce. The Cell Cycle: G -> S -> G -> M 1 2 G 1hase: 7-9 hours  Chromosomes are unreplicated S phase: 6-8 hours  DNA replicates G phase: 4-5 hours 2  Cell gains energy, volume, acquires nutrients, and the organelles replicate. M phase: 3 hours  Nuclear division that is either mitosis or meiosis that is often followed by cytokinesis. Phases of Mitosis: 1. Interphase: DNA replicates 2. Prophase The chromosomes condense and become visible in the nucleus. They have an ‘X’ shape because they are in the form of two sister chromatids. The nuclear membrane disintegrates. The spindle apparatus appears on opposite poles of the cell. The spindle apparatus originates at the centrioles and is composed of microtubules with tubulin subunits. 3. Metaphase The chromosomes line up along the metaphase plate in the middle of the cell. 4. Anaphase The microtubules attach to the kinetochore that is located on the centrosome of the chromosome. Motor proteins on the kinetochore walk along the microtubule toward the minus end. This causes the kinetochore to remove tubulin subunits 13 BIOS 1700/1705 and the microtubule shortens. As the microtubule shortens, the sister chromatids separate and move to opposite sides of the cell. 5. Telophase & Cytokinesis The nuclear envelope re-forms around the chromatids. Cytokinesis often follows telophase.  Animals: a ring of actin filaments forms around the cell and form a cleavage furrow. The cell is pinched apart.  Plants: vesicles that contain the materials needed to build a new cell wall and plasma membrane line up in the middle of the cell and create a cell plate.  Bacteria: do not undergo cytokinesis, but divide through fission. Regulating the Cycle The cell cycle is a process that must occur adequately. If errors occur, cancer can develop. The frequency of the cell cycle is also dependent on the cell type and function. For example, muscle cells and neurons never divide after they mature and are arrested at G 0 phase. In contrast, intestinal cells are constantly dividing. Therefore, the cell cycle contains checkpoints and certain molecules initiate cell division. Mitosis-Promoting Factor (MPF) is a molecule that initiates mitosis. It is composed of cyclin and cyclin-dependent kinase (Cdk). Cdk is a protein kinase that binds to the cyclin subunit. This binding causes Cdk to become phosphorylated at two sites. This phosphorylation makes MPF inactive. During late G 2 phase, enzymes dephosphorylate Cdk and this activates MPF. Cell cycle checkpoints are present to make sure that the cell cycle is following through properly. There are three main checkpoints:  G1checkpoint passed if…(mature cells do not pass this checkpoint because they no longer divide and are arrested at G0)  Cell is big enough  Cell has enough nutrients  Social signals are present (signaling molecules from other cells)  DNA is undamaged  G2checkpoint passed if…  Chromosomes are successfully replicated  DNA is undamaged  MPF is present and activated  Metaphase checkpoint passed if…  Chromosomes are properly attached to the spindle apparatus. If any of these checkpoints are falsely passed, the cell cycle will become deregulated. If cells are able to divide in the absence of social signals, they will form a tumor. If cells continue through the cycle with damaged DNA, many problems result. The cell will no longer be able to properly carry out its functions. Meiosis th  The 4 characteristic of life is to be able to replicate and reproduce. Phases of Meiosis: 14 BIOS 1700/1705 1. Interphase: DNA replicates Meiosis I (reduction) 2. Prophase I  The chromosomes condense and become visible in the nucleus. They have an ‘X’ shape because they are in the form of two sister chromatids.  The nuclear membrane disintegrates.  The spindle apparatus appears on opposite poles of the cell.  The spindle apparatus originates at the centrioles and is composed of microtubules with tubulin subunits.  Non-sister chromatids pair and form a tetrad. The non-sister chromatids within a tetrad cross-over genetic information. 3. Metaphase I  Tetrads line up along the metaphase plate in the middle of the cell. 4. Anaphase I  Homologs separate 5. Telophase I & Cytokinesis  Chromosomes, which are in the form of two sister chromatids (they are still replicated), move to opposite sides of the cell.  The nuclear membrane does not re-form and the cell divides via cytokinesis. Meiosis II (division) 6. Prophase II  The spindle apparatus reappears 7. Metaphase II  The chromosomes line up along the metaphase plate in the middle of the cell. 8. Anaphase II  The sister chromatids separate and move to opposite sides of the cell. 9. Telophase II & Cytokinesis  A nuclear membrane forms around the chromatids (they are unreplicated).  The cell divides via cytokinesis. Meiosis I is considered as a reduction because it reduces the number of genetic material in the daughter cells. The parent cell is diploid (2n) and the two daughter cells become haploid (n). If the parent cell has 2 homologs and the daughter cells will only have 1. This is because the homologs separate during anaphase I. Meiosis II is considered as a division because the haploid (n) daughter cells only divide, they do not have reduced genetic material. This is because the sister chromatids that make up the homolog split during anaphase II. One homolog (X) is genetically equivalent to one chromosome (line). Mistakes in Meiosis:  Nondisjunction occurs when chromosomes do not separate properly during anaphase I or during anaphase II. This results in aneuploidy.  Nondisjunction in anaphase I (homologs separate) 15 BIOS 1700/1705  ½ with trisomy (n+1)  ½ with monosomy (n-1)  Nondisjunction in anaphase II (chromatids separate)  ½ aneuploid (1 with monosomy and 1 with trisomy); ½ normal Comparing Mitosis & Mitosis Meiosis Meiosis What divides Somatic cells (2n) Sex cells (n) Result 2 identical (diploid) 4 genetically unique daughter cells haploid gametes Function Tissue growth and repair, Create gametes that will asexual reproduction for produce genetically unicellular eukaryotes. unique offspring during sexual reproduction. Phases/ Events Both nuclear divisions follow the same series of events: interphase, prophase, metaphase, anaphase, telophase, and cytokinesis. Follows these events During prophase, crossing once. over occurs. Goes through two divisions. First division: reduction (creates two haploid daughter cells) Second division: division (two haploid daughter cells split and create 4 haploid gametes) Regulation Both nuclear divisions are regulated with three main checkpoints. MPF initiates mitosis. Mendel and the Gene th The 4 characteristic is to be able to replicate and reproduce. Heredity is the passing on of traits from generation to generation. Two previous hypotheses attempted to explain the patterns of heredity: 1. Blending inheritance: the traits from the mother and father blend together to create new traits in their offspring (white + black=gray) 2. Inheritance of acquired characteristics: the traits in the mother and father are modified and these modified traits are passed on the their offspring Gregor Mendel performed experiments with pea plants and proved both of these hypotheses wrong. His results were explained by the particulate inheritance hypothesis. This hypothesis claims that traits maintain their integrity from generation to generation. (white + black=white or black) Pure lines consist of genetically identical individuals that were produced through self-fertilization 16 BIOS 1700/1705 Hybrids are produced when two individuals from separate pure lines are crossed through cross-pollination. Monohybrid crosses are used to follow one trait. They involve crossing two individuals from separate pure lines. These individuals are genetically the same with the exception of the trait being studied. The ratio of dominant to recessive phenotypes is always 3:1. Reciprocal crosses are used to determine if the sex of the individual influences the inheritance of a trait. During the first cross, a round male is crossed with a wrinkled female. The reciprocal cross crosses a wrinkled male with a round female. The results of both of the crosses are the same. This means that the sex of an individual does not influence the inheritance of a trait. Dihybrid crosses are used to follow two traits. The appearances of the traits are seen in a 9:3:3:1 ratio. Test crosses are used to determine the genotype of an individual with a dominant phenotype. Their genotype could be Dd or DD. The cross is between a homozygous recessive individual (dd) and an individual with a dominant phenotype (Dd or DD).  dd × Dd = ½ dominant phenotype, ½ recessive phenotype  dd × DD = all dominant phenotype Mendel’s Principles: 1. Principle of Segregation: each gamete contains one allele of each gene. 2. Principle of Independent Assortment: alleles of different gametes don’t stay together when gametes for. Linked genes are an exception to this principle because they always get inherited together. Incomplete dominance occurs when the dominant allele and the recessive allele both show their effects in a new phenotype that is neither the dominant phenotype nor the recessive phenotype. Codominance occurs when the dominant trait is accompanied by some of the recessive trait in the phenotype. The phenotype is a combination of the two alleles. Patterns of Inheritance:  Autosomal recessive traits (appear equally as often in males and females) o Individuals with the trait must be homozygous. o If the parents of an affected offspring are unaffected, they are probably heterozygous for the trait (carriers).  Autosomal dominant traits (appear equally as often in males and females) o Individuals with the trait could be heterozygous or homozygous. o If one parent is heterozygous and the other is homozygous recessive, half of their offspring should show the dominant phenotype. o If both parents are heterozygous, all of their offspring should show the dominant phenotype. o If one parent is heterozygous and the other is homozygous dominant, all of their offspring should show the dominant phenotype.  X-linked recessive traits o Males are much more likely to have the trait o The appearance of the trait skips a generation 17 BIOS 1700/1705 o Half of the sons with carrier mothers will have the trait  X-linked dominant traits o An affected male has all affected daughters but no affected sons (sons get the unaffected X chromosome from their unaffected mother) DNA and the Gene: Synthesis and Repair  The 3 rdcharacteristic of life is to be able to process information. The Hershey-Chase Experiment: 1. Label viruses with P-32 (found only in DNA) or S-35 (found only in protein). The P-32 viruses have labeled DNA and the S-35 viruses have labeled protein. 2. Infect bacteria (E. coli) with the viruses. 3. Agitate cultures to separate empty viral capsids from bacterial cells. 4. Centrifuge solutions. The viral capsids will be in solution and the viral genes will be in the bacterial cells in pellet. The results showed that the radioactive DNA (labeled with P-32) showed up in the bacterial cells. DNA Synthesis (Replication) Three possible replication processes: 1. Semiconservative replication –DNA unzips and one strand acts as a template strand, ½ of the parent molecule is found in the daughter molecule 2. Conservative replication –DNA parent strand clones itself 3. Dispersive replication –DNA breaks into fragments and the fragments are shuffled back together. Process of DNA Replication: 1. Helicase unzips a section of DNA. Single-strand DNA-binding proteins (SSBPs) attach to the strands and prevent them from reattaching. Topoisomerase relieves tension at the replication fork. 2. An RNA primer is added by primase, a type of RNA polymerase. 3. DNA polymerase III begins adding nucleotides to the 3’ end of the RNA primer and creates the leading strand (continuous strand). 4. DNA polymerase III begins adding nucleotides to the 3’ end of the RNA primer on the lagging strand and creates an Okazaki fragment. A gap is created behind the synthesis of the lagging strand because the leading strand is being synthesized in the opposite direction. Therefore, another primer is added by RNA polymerase and DNA polymerase III synthesizes another Okazaki fragment. DNA polymerase I comes back through and removes the RNA primers and DNA ligase joins the Okazaki fragments. 5. At the end of the chromosome, the lagging strand has a gap that is too short to be replicated with a primer. This gap is called the telomere. Telomerase contains its own RNA template and is able to extend the gap long enough for an RNA primer to attach to it. Correcting Mistakes in DNA Replication When DNA polymerase III adds a mismatched base it notices this and corrects it. If DNA polymerase III misses its mistake, mismatched repair occurs. During 18 BIOS 1700/1705 mismatched repair, enzymes surround the mismatched base and excise a section of the DNA that surrounds the mistake and fill in the correct bases. DNA can be damaged by chemical radicals (OH radicals) or ultraviolet light. Nucleotide excision repair fixes damaged bases. 1. Enzymes detect an error that causes an irregularity in the DNA molecule. 2. The enzymes cut out a stretch of DNA that contains the damaged bases. 3. DNA polymerase fills in the gap. 4. DNA ligase links the new and old nucleotide strands. How Genes Work  The 3rdcharacteristic of life is to be able to process information. Genes contain the instructions for making protein. Each individual gene codes for one protein. They are organized with 3-base codes (codons) that are complementary to the mRNA codons that make up the genetic code. Properties of the Genetic Code: 1. It is redundant: most amino acids are coded for by more than one codon 2. It is unambiguous: one individual codon never codes for more than one individual amino acid 3. It is nearly universal: nearly all of the codons specify the same amino acids in all organisms 4. It is conservative: the first two bases in codons that code for the same amino acid are almost always the same (AGU & AGC = serine). This property protects individuals from small, random changes or errors in their DNA. Central Dogma: DNA is transcribed into mRNA and mRNA is translated into a protein. Retroviruses are an exception to this. They use reverse transcriptase to synthesize a strand of DNA from their RNA. This newly synthesized strand of DNA is then used to make more of the virus’s RNA. Mutations: 1. Point mutation: changes a base within a sequence because of an added or deleted base, results in a frameshift. a. Missense mutation: cause changes in the amino acid sequence of a protein b. Silent mutation: does not change an amino acid sequence 2. Chromosome-level mutations a. Aneuploidy: the addition or deletion of a chromosome b. Inversion: a segment of a chromosome breaks, flips, and rejoins the chromosome c. Translocation: a segment of a chromosome breaks off and joins a new chromosome T ranscription, RNA Processing, and T ranslation rd The 3characteristic of life is to be able to process information. 19 BIOS 1700/1705 Process of Transcription: DNA ---> mRNA; RNA polymerization is exergonic, and therefor spontaneous 1. Initiation a. Eukaryotes: basal transcription factors bind to the promoter region of the DNA and RNA polymerase II attaches to the basal transcription factors. b. Bacteria: sigma protein with attached RNA polymerase II binds to the promoter region of the DNA. 2. Elongation: RNA is synthesized in the 5’ ---> 3’ direction 3. Termination a. Bacteria: RNA polymerase II reaches the transcription termination signal. This signal codes for bases that will form a hairpin the RNA. This hairpin shape causes the synthesized RNA to separate from RNA polymerase II. RNA Processing (only in eukaryotes): primary transcript mRNA (pre-mRNA) is synthesized by RNA polymerase II and it must be modified into mature mRNA.  RNA splicing: pre-mRNA contains exons and introns. Exons are expressed in the final mRNA product, and introns are intervening because they do not contain genetic material that codes for amino acids. Small nuclear ribonucleoproteins (snRNPs) take out the introns and the remaining exons join together.  Adding caps and tails: enzymes add a 5’ cap to the 5’ end of mRNA and a poly(A) tail to the 3’ end of mRNA. These caps and tails protect mRNA from degradation and enhance the efficiency of translation Translation: mRNA ---> protein; protein synthesis is catalyzed by RNA 1. Initiation 1) The ribosome binding site sequence on the mRNA binds to its complementary sequence on the small ribosomal subunit. 2) Aminoacyl tRNA (tRNA with amino acid attached) binds to the start codon on mRNA (AUG). 3) The large ribosomal subunit binds to the small subunit. 2. Elongation 1) An aminoacyl tRNA molecule enters the A site of the ribosome. The amino acid at this site forms a peptide bond with the amino acid in the P site of the ribosome. 2) The aminoacyl tRNA molecule at the P site loses its amino acid and moves to the E site, the aminoacyl tRNA in the A site moves to the P site. 3) Another aminoacyl tRNA enters the A site and translation continues. Wobble hypothesis: a correct amino acid can be added to a growing polypeptide chain even if the third base in the mRNA codon is not complementary to the third base in the tRNA anticodon. 3. Termination: when a stop codon on the mRNA (UAG, UGA, or UAA) enters the A site a release factor binds to it. The release factor will remove the 20 BIOS 1700/1705 amino acid from the aminoacyl tRNA at the P site and the polypeptide is released and will be modified. Evolution by Natural Selection th The 5 characteristic of life is to be able to evolve. Theory of Evolution by Natural Selection:  Pattern component: species change through time and are related by common ancestry o Evidence for change through time:  Geological record indicates that the earth is about 4.6 billion years old and life began about 3.4-4.8 billion years ago.  Extinct species exist. This suggests that the collection of species living on Earth has changed through time.  Transitional features have been found.  Vestigial traits are found on species. o Evidence for a common ancestor:  Similar, but distinct, species are found in the same geographic area.  Contemporary populations are undergoing speciation.  Homologies exist Genetic Developmental Structural  Process component: natural selection (as well as genetic drift, gene flow, and mutation) allows for populations to change through time o Natural selection: increases the frequency of the alleles that contribute to reproductive success in a particular environment. Constraints:  Non-adaptive traits: give no benefit to the organism  Genetic constraints: not all aspects of a trait can be optimized and lack of genetic variation does not favor natural selection  Fitness trade-offs: compromises between two traits and this limits evolution  Historical constraints: selection has to work with what it already has o Genetic drift: causes allele frequencies to change randomly o Gene flow: occurs when individuals leave one population and join another. Their alleles are now introduced into the new population. o Mutation Characteristics of Evolution: Evolution occurs in populations; not within an individual. Natural selection sorts existing variants, and does not change them. Acclimatization is not adaptation; acclimatization is seen in individuals and adaptation is seen within a species. o Acclimatization- individual’s phenotype changes in response to changes in the environment and the genotype does not change. 21 BIOS 1700/1705 o Adaptation- allele frequencies within a population change in response to natural selection. Evolution is not goal-directed; it is a random occurring process. Evolution is not progressive; it does not produce “higher” or “lower” organisms across species. Organisms do not act for the good of the species; individuals with self- sacrificing alleles do not survive to reproduce. Animal Form and Function rd  The 3 characteristic of life is to be able to process information. Collagen Fibers Elastic Cells Tissues Reticular Matrix Gel Ground Rubber substance (cartilage) Stoney (bone) Types of Tissues: 1. Connective tissue- cells are loosely arranged in a liquid, jellylike, or solid matrix and it is mostly composed of matrix; connects and binds other types of tissues. a. Loose connective tissue- fibrous proteins in a soft matrix; provides padding (adipose tissue) b. Dense connective tissue- collagen fibers in matrix; connections (muscles, bones, organs) c. Supporting connective tissue- firm, stoney matrix; structural support and protection (bone, cartilage) d. Fluid connective tissue- fluid matrix; transport and protection (blood) 2. Nervous tissue- consists of nerve cells with dendrites, a soma, and long axon; receives, processes, and sends information. 3. Muscle tissue- movement a. Skeletal muscle b. Cardiac muscle c. Smooth muscle 4. Epithelial tissue- layers of closely packed cells; provides protection and controls the transport of water and nutrients (plays a big role in homeostasis). The apical side faces away from other tissues and secretes 22 BIOS 1700/1705 mucus the basolateral side faces the animal’s interior and cements the cells to the basal lamina. Surface Area/Volume and Metabolic Rate: The surface area/volume ratio determines the basal metabolic rate (rate of diffusion of oxygen). In general, small animals have higher BMRs than large animals because their surface area/volume is large. Small animals have more surface area than they have volume and large animals have more volume than they have surface area. Greater surface areas allow for more diffusion, and therefore a larger BMR. Homeostasis: 1. Conformational homeostasis- occurs by conformation to the external environment 2. Regulatory homeostasis- requires a physiological mechanism (uses enzymes) that adjusts the internal state to keep it within tolerable limits.A sensor detects change (cells), an integrator interprets the change (usually the hypothalamus), and an effector restores desired condition (organ or tissues). a. Negative feedback: effectors oppose the change (can never harm an organism)  Thermoregulation (set point: 98.5˚F); conduction, convection, radiation, and evaporation Homeotherms: keep their body temperature constant Heterotherms: tolerate changes in body temperature Endotherms: warms their own tissues with their high BMR Ectotherms: relies on the environment to warm their tissues Endotherms are usually larger than ectotherms. Trade-off: endotherms can be more active, but ectotherms are able to thrive with less food and can use more of their energy to support reproduction.  Blood pressure change (set point: 120/80)  Blood pH change (set point: 7) b. Positive feedback: effectors augment the change (has the potential to harm an organism)  Childbirth  Producing a fever  Blood clotting Animal Nutrition  The 2 nd characteristic of life is to be able to produce and use energy. Four Processes of Obtaining Energy: 1. Ingestion - mouthparts have evolved in response to natural selection. a. Suspension feeders (sponges, tapeworms) b. Deposit feeders (earthworms, sea cucumbers) c. Fluid feeders (mosquitos) d. Mass feeders (majority of animals) 2. Digestion (mechanical & chemical) - breaks down macromolecules with the help of enzymes. Most digestive enzymes are produced in the pancreas and 23 BIOS 1700/1705 released in their inactive forms. The enzyme enterokinase activates the enzymes, but does not do any digesting. The parietal cells in the stomach secrete HCl and pepsinogen (inactive pepsin). Hormones regulate the release of pancreatic enzymes: Secretin is produced by the small intestine when food arrives in the stomach. It neutralizes the acid arriving from the stomach. Cholecystokinin stimulates secretion from the liver and gall bladder. It acts as a hormone in the blood and a neurotransmitter


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