Chapters 1,2,3,4,6 BIOL 1114, 001
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Date Created: 02/14/16
Intro to Zoo (BIO 1114) with Professor Lee CHAPTER 1 The Scientific Study of Life Biology is defined as the scientific study of life The cell is defined as the basic unit of life. Every living organism contains one or more cells Cells use DNA to produce proteins All life forms share 5 characteristics: 1. Organization Atom (all living structures are composted of atoms) Molecule (group of joined atoms) Organelle (membranebound group of molecules) Cell (fundamental unit of life, made up of organelles) Tissue (collection of cells) Organ (consists of multiple tissue types and has a defined/special function) Organ system (a group of organs, either connected physically or chemically, that work together to perform) Organism (living individual) Another level of organization is the organization among the living Population members of the same species occupying the same space at the same time Community all the populations of different species in a place at a time Ecosystem both living and nonliving components of an area Biosphere all parts of the planet that sustain life 2. Energy use Life requires energy During each step of the cycle of life heat is lost Biologists organize organisms in the following categories: Producers (autotrophs) make their own food by extracting energy from nonliving things such as the sun Consumers (heterotrophs) obtain energy by eating other organisms, living or dead Decomposers (heterotrophs) obtain energy by eating dead organisms 3. Maintenance of internal consistency Or HOMEOSTASIS Blood glucose levels are maintained when we intake food When the body’s temperature drops below or rises above the normal temperature, the body uses homeostasis to fix it. Negative feedback: (example) if the temperature goes down, the body brings it back up. Positive feedback: (example) Childbirth or labor the body has contractions over and over until the baby is delivered. Salt levels, nutrients levels, and water levels are all monitored by homeostasis. 4. Reproduction, growth, and development Sexual reproduction sexual reproduction requires two parents and is most successful in a changing environment Asexual reproduction asexual reproduction only requires one parent and is most successful in an unchanging environment 5. Evolution A species adapts to its environment over time to become more successful/to thrive. An example would be a puffer fish. Over time they have become the exact color of their surroundings in order to prey on other things in camouflage or to hide from threats. Natural selection: Process by which organisms with a certain successful trait reproduce and the organisms without that trait do not. THE THREE MAIN BRANCHES ON THE TREE OF LIFE: Domain bacteria (no nucleus) Domain archea (no nucleus and is made up one 1 cell) Domain eukarya (nucleus) Domain bacteria and domain archea are prokaryotes. Pro means before and karyote means nucleus, so that helps explain that those two do not have nuclei. Domain eukarya is a eukaryote. Eu means true and karyote means nucleus, therefore domain eukarya have nuclei. Eukarya: Protista 1 cell of multiple autotrophs/heterotrophs Kingdom Animalia multicellular heterotrophs Kingdom fungi mostly multicellular organisms and heterotrophs (fungi use external digestion) Plantae multicellular autotrophs (use sun energy) The mnemonic levels of organization: Kingdom Phylum Class Order Family Genus Species *Other helpful notes from chapter 1: The endothelial cell can be found in the stomach lining and blood vessels (among other places) Emergent properties properties that arise at each level of biological organization. For example, the bicep muscle is an organ made up of tissue and at this level it begins to serve its function (its function would be whatever the bicep muscle is used to do in daily life). Another example would be a blood vessel.. Before all of the cells came together to make it, it didn’t have a property. Bacteria evolve rapidly In order to write a good hypothesis it must be a possible explanation and it must be testable. Taxonomy scientific study of naming and classifying organisms CHAPTER 2 The Chemistry of Life All life is made up of elements An element (atoms) is basically protons, neutrons, and electrons. Protons have a positive charge, neutrons have a neutral charge, and electrons have a negative charger Protons/neutrons are in the core of each atom Opposite charges attract When looking at the periodic table, the mass # = protons + neutrons Add a neutron, the mass increases Atomic weight= the average mass of all isotopes of that element Isotopes are the same element but with a different number of neutrons For Zoology purposes, know that each atom has a 288 configuration of electrons Hydrogen can hold 2 electrons in its shell Carbon, nitrogen, and oxygen have 2 rings When the outer electron shell is full, the element(atoms) are at maximum stability Everything is also made up of bonds covalent, ionic, and hydrogen bonds Covalent bonds share electrons (strong) Ionic bonds transfer electrons (strongest, but weak in water) Hydrogen bonds have partially positive and partially negative ends, so they are just sticky (weakest) When something is polar, it has both positive and negative ends. Water contains covalent and hydrogen bonds Hydrogen bonds are what hold the double helix of DNA together Electronegativity (how likely an element is to find an electron) helps predict what types of bonds will form. On the periodic table, bottom left elements have low electronegativity and as you go up and to the right on the table it increases. Water is important for all of life Water is both cohesive and adhesive. Cohesive means that water sticks to itself, creating surface tension. Adhesive means that water sticks or climbs other things. Water does not dissolve hydrophobic solutes such as fats, wax, sand, etc. Hydrophobic means “water fearing” Hydrophilic “loves water” Water is a good solvent, it dissolves solutes to create a solution THE pH SCALE: The pH scale is based on the amount of H protons Acids become more acidic when H is added, while bases become more basic. ORGANIC MOLECULES Carbohydrates (sugars) Amino acids (proteins) Nucleic acids (DNA/RNA) Lipids (fats) Mono means one, poly means many. A bunch of monomers make up a polymer. Monomer a single unit of carb, protein, or nucleic acid. NOT LIPID! Carbohydrates A carb polymer is made up of many sugar monomers. Monosaccharides are monomers of carbohydrates Disaccharide is two monomers Polysaccharide is a chain of monomers The following contain carbs: Leaf cellulose Potato starch The liver produces glycogen Amino acids Amino acids are building blocks of proteins Proteins have more variable structures and functions than any others. The function of a protein depends on the shape Their “R” group gives them their personalities All have a core Carbon group R groups are variable 2 monomers ( amino acids) after dehydration synthesis= dipeptide bonds During dehydration synthesis (breaks bonds) an enzyme binds two monomers, releasing water The backward process of the above is called hydrolysis, which creates bonds. The four levels of structure of amino acids are: Alpha helix amino acids are twirled around each other and held together by Hydrogen bonds (secondary structure) Beta sheet a flat structure (secondary) Tertiary structure consist of both alpha helixes and beta sheets Quaternary structure subunits, a mixture of multiple polypeptides Covalent bonds hold amino acids together, but hydrogen bonds make them sticky When hydrogen bonds break, it produces a denatured protein Heat can be used to break both hydrogen and covalent bonds pH also denatures proteins NUCLEIC ACIDS: DNA & RNA DNA RNA BOTH Adenine Adenine Adenine Guanine Guanine Guanine Cytosine Cytosine Cytosine Thymine Uracil Cells contain two types of nucleic acids, deoxyribonucleic acid and ribonucleic acid. LIPIDS (fats): Lipids are composed of long carbon chains Kinks in the chain mean that the fat is not solid Lipids are NOT composed of monomers and polymers They have triglycerides Triglycerides store fat in adipose tissue 3 types of fat include saturated, unsaturated, and trans fat Saturated fat is bad for consumption, but transfat is the WORST Transfat is synthetically made Unsaturated fat is the best fat Sterols are lipid molecules such as cholesterol and testosterone (both hydrophobic) *Extras from chapter 2: Hemoglobin can be found in red blood cells Zoology – Professor Lee Chapters 3 & 4 (touches on 25 and 33) CHAPTER 3- Cells Cells are the smallest unit of life to function alone. The cell membrane is composed of organic molecules - It has a phospholipid bilayer - It has a hydrophobic and hydrophilic regions - It is fluid and dynamic - Phospholipids have a head and a tail, the head is hydrophilic while the tail is hydrophobic. - The membrane acts as a barrier. - The barrier allows hydrophobic things (lipids/non polars) to pass, but it does not allow hydrophilic things (ions, polars) to pass. - Inside the cell membrane: - Transport proteins (is a protein that serves the function of moving other materials within an organism) - Recognition proteins (protein that recognizes and targets specific proteins to the endoplasmic reticulum in eukaryotes and the plasma membrane in prokaryotes) - Cholesterol is also a molecule embedded in proteins ** CHAPTER 4- Energy Two types of energy: Potential energy: chemical energy Kinetic energy: movement (examples would be photons, light, sound, etc) Energy is always lost as heat Energy going IN or OUT: Endergonic (IN): going from a lower energy state to a higher potential energy Exergonic (OUT): going from a higher to a lower energy state Cellulose requires endergonic reactions Thinking moment* What happens when cellulose undergoes an exergonic reaction? (like fire) A: It goes up in flames and releases CO2 and heat. So how do cells harness energy without losing it to heat? A: potential energy metabolism ATP kinetic energy During this process the electron donor donates to the acceptor. After the donation, the donor is considered OXIDIZED and the molecule that accepts the electron is considered REDCUDED. Oxidation- loss of electrons, releases energy Reduction- gain of electrons, requires energy An electron transport chain is a series of membrane proteins that harness energy as it passes. The mitochondria is the power house of the cell and it makes ATP. Energy is mainly stored in the phosphate bond of ATP ATP (adenosine triphosphate) is a nucleotide that temporarily stores energy When the phosphate bond is broken, energy is released *ATP formation is coupled with other exergonic reactions *ATP breakdown is coupled with endergonic reactions - The joining of molecules uses ATP. For example, when monomers become polymers it requires ATP. ATP donates a phosphate that changes the shape of the target molecule. Question time: How does our body control the rate of chemical reactions? - The answer is enzymes (proteins) - Enzymes lower activation energy! - Activation energy: kick start energy, the energy required to actually start the process - An enzyme is a REUSABLE protein, and it binds to a specific substrate. For example, lactase (enzyme) breaks down lactose (it’s a lock and key situation) - The active site of where a substrate joins an enzyme can change shape or be blocked off by an inhibitor - Negative feedback- when a reactions products inhibit the enzyme that catalyzes the reaction. - Positive feedback- the opposite of negative feedback is when a product produces a pathway leading to its own production. - Indirect way of altering enzyme activity: Enzymes are proteins, proteins are genes, and the rate of protein synthesis can be controlled by genes (this will link unit 1 and 2 together) Touching on chapter 25* - Organs promote homeostasis within the body. - Interstitial fluid bathes all body cells from the outside Touching on chapter 33* - Surface area to volume ratio is important. For example, google images of the snowshoe hare vs the jack rabbit or the arctic fox vs the kit fox. Each animal has adapted to its specific environment. - Endotherms- regulate their heat internally (humans are endotherms) - - the hypothalamus controls endotherms body temperature and initiates responses - Ectotherms- move to areas in order to lose or gain heat - Counter current exchange: (used by wolves in cold climates) conserves energy and prevents frostbite. - Vasodilation- expands the diameter of blood vessels (alcohol does this) - Osmoregulation: Is the maintenance of constant water pressure in the fluids of an organism by the control of water and salt concentrations? - Urination regulates salt/water in the body - Marine fish do not really pee, but water leaves their bodies through osmosis. Marine fish drink the salt water. - Freshwater fish do not drink the water, yet they pee more dilute urine. Water enters freshwater fish through osmosis. - Land animals also have strategies to obtain and conserve water. DEFINITIONS TO KNOW FOR CH 3 & 4: Ribosomes- structures that make proteins Cytoplasm- fluid in the cell Adhesion proteins- enable cells to stick to one another Receptor proteins- bind to molecules outside the cell and trigger an internal response Vesicles- transport things within the cell Competitive vs noncompetitive inhibition- competitive means that substrates are competing to bind with the enzyme, while noncompetitive means that the substrate bonded somewhere other than the active site but not intentionally blocking another. Endocytosis- cell engulfs material and brings it into the cell in a vesicle Exocytosis- sends things out of the cell Hypotonic- solution has lower concentration than the interior of the cell Hypertonic- the cell has a higher concentration than the solution around it Isotonic- has equal water Phagocytosis- engulfs BULK matter Metabolism- describes all chemical reactions in a cell Entropy- measure of disorganization Cofactors- enzyme helpers Zoology w/ Dr.Lee CHAPTER 6 CELL MEMBRANE STRUCTURE: The concentration gradient can store potential energy. Cell membranes can form compartments- Endomembrane system is made up of the following: nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, mitochondrial membranes, & cell membrane. INTERMEMBRANE SPACE is where potential energy is stored Another part of the cell membrane structure is the transmembrane proteins. Transmembrane proteins are very selective. The following are transmembrane proteins: carrier proteins, channel proteins, and gated proteins (they all basically move things in and out of the cell) When something enters the cell without a carrier, it is called simple diffusion (a type of passive transport). Things normally want to enter the cell because they are moving down their concentration gradient, which also means they diffuse from high to low concentrations. Passive transports include: simple diffusion, facilitated diffusion, and osmosis (water) Facilitated diffusion is when a protein transports something into the cell Active transport: active transport uses energy (passive does not, passive is powered by the concentration gradients) active requires energy because it moves against the concentration gradient (up the gradient) There are three different types of solutions: isotonic, hypertonic, and hypotonic. Isotonic means that the solution has the same number of solutes as the other solution. Hypertonic means that the solution has a lower concentration than the other, and hypotonic means that the solution has a higher concentration than the other. Active transport includes the following: Sodium-potassium pump (which requires ATP) An active mechanism changes shape in order to drive things through/into the cell. Bulk transport (transports of large things into the cell) is also known as vesicular transport. CELLULAR REPSPIRATION: The three parts of cellular respiration are: - Glycolysis (breaks down glucose) - Krebs Cycle - Electron Transport Chain - Hint: most of the energy transformation occurs in redox reactions - A tip for remembering that oxidation means lost and that reduction means gained (electrons) is OIL RIG. - The electron transport chain: inner membrane, outer membrane, matrix, cristae, DNA, ribosome, and the inter-membrane space holds potential energy. - NADH and FADH come2from the Krebs Cycle and glycolysis. - ATP synthase complex is powered by hydrogen ions - O 2oxygen) is the final electron acceptor during cellular respiration - A basic break down would be: 1. Breathe in oxygen/eat food, 2. Break down polymers into monomers, 3. Feed sugar& O to cells2 and 4. Split glucose into to pyruvate molecules. - GLYCOLYSIS: (does not require oxygen so it is anaerobic) 1. Split into two pyruvate 2. Strip electrons of their energy 3. Make ATP in the process 4. (Now, in the presence of oxygen this happens) passes on 2 pyruvate and two NADH to the mitochondria -KREBS CYCLE: 1. Strips more energy 2. NADH goes on to the electron transport chain (NADH and FADH2 energize transmembrane proteins for active transport) + 3. H increases inter-membrane space 4. Makes ATP (also does not require oxygen) 5. Krebs Cycle passes on 8 NADH and 2 FADH2 to the electron transport chain 6. The ATP synthase harnesses concentration gradient energy to make ATP Electron Transport Chain: - The money maker $$$$ - The last step Overall discussion of cellular respiration: - Transmembrane proteins are on the inner-membrane - Enzymes do the conversions (proteins) - NAD NADH - NAD is limited in the absence of oxygen - NADH gets converted back to NAD creating lactic acid byproducts. - In the presence of oxygen….. Transition step 2 pyruvate Acetly CoAOutput NADH, FADH2, ATP, breathe out CO2. - NADH, FADH2 power + - Energized proteins pump H against the concentration gradient - Chemiosmotic phosphorylation: harnessing the power of the chemical gradient to produce ATP - Conversion rates for our purposes are 1 NADH3 ATP, 1 FADH2 2 ATP - 36= theoretical ATP yield of cellular respiration. - Proteins and fats can enter the cycle at many steps - Proteins enter using beta-oxidation **** Cellular respiration really cannot be explained as well as it should be by these notes, but the best way to learn would be to find google images of the process that has explanation besides each image of the steps. I have reviewed a previous exam and I compiled the following list of things to review/know: Know which types of organic molecules dissolve in water Osmosis Why are single celled organisms limited in size? Which things can pass through the membrane alone, which need a transport protein? Know the isotopes (chemistry) Review polar-covalent bonds Review the molecules and what they look like Enzymes Review case study #2 CELLULAR RESPIRATON
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