Exam 1 Study Guide
Exam 1 Study Guide Life 102
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This 20 page Study Guide was uploaded by Kyra Ferguson on Monday February 8, 2016. The Study Guide belongs to Life 102 at Colorado State University taught by Erik Arthun in Winter 2016. Since its upload, it has received 36 views. For similar materials see Attributes of Living Systems in Life Science at Colorado State University.
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Date Created: 02/08/16
Vocab List Uniformity Macromolecules Diversity Hydrogen bonds Valence Shells DNA Ionic Bond Proteins Covalent Bond Lipids Essential Elements Polysaccharides Protons Mass Conversation Law Neutrons Chemical Equilibrium Electrons Reverse/Reversible Reaction Isotopes Reactants Electro negativity Products Polar covalent bonds Solubility Ionic bonds Solute Properties of Water Solution Cohesion Solvent High surface tension Concentration Specific Heat Molar Heat of vaporization Hydrophobic Density Hydrophilic Surface Area Acid pH formula Base Organic molecule Carbon Carbon Skeleton Isomer (and all types) Side groups Nucleic Acids mRNA Ribosomes Lysosomes Enzyme Polymer Monomer Cytoskeleton Cell Wall Nucleus Nuclear Envelope Endomembrane System Endosymbiont Theory Cytoskeletal fibers Mitochondria Chlorophyll Chloroplast Specialization/Compartmentalization Prokaryote Eukaryote Vacuoles Chapter 1 Biology derived from roots meaning "life" and "the study of" The scientific study of life. Life is everywhere on Earth. Biology studies life in all of its forms and at all levels of organization and time. Biology is broad, multidisciplinary utilizing chemistry, physics, biology, etc. Life as at the same time very uniform and very diverse. Uniformity is exhibited at cellular/molecular level, all organizations consist of cells. Diversity can be used to classify groups "taxonomy". Chapter 2: Chemical Context of Life Element substance that cannot be broken down into other substances by chemical reaction ie., Gold Compound two or more different elements combined in a fixed ratio ie., Sodium Chloride, aka salt There are 25 chemical elements essential for life. 96% of life is comprised of Oxygen, Carbon, Hydrogen, and Nitrogen. The other 4% is comprised of Calcium, Phosphorous, Potassium, Sulfur, Sodium, Chlorine, Magnesium, and trace amounts of another 14 elements. Atom smallest unit of an element, composed of protons, neutrons, and electrons. An atom is mostly empty space. Dalton the weight of a proton or neutron. An electron is considered so light that it weighs practically nothing. Name Weight Charge (Daltons) Proton 1 +1 Neutron 1 0 Electron 0 1 The nucleus of an atom, comprised of protons and neutrons, is so small it is equivalent to an eraser at the center of a football stadium, with the stadium being the rest of the atom. Elements can be written with numbers as a notation to their weight and element number Atomic number of a nucleus is the number of protons in an atom's nucleus. The number of protons there are determines what element it is. Neutron and electron numbers can vary from element to element, but protons cannot change unless it were to become a different element, for example:2 He 4 Atomic mass is the weight of protons and neutrons, for example: He Atoms can undergo changes: 1) Add or lose an electron Ionatom with unpaired proton or electron. An atom that loses an electron becomes positively charged, and an atom that gains an electron becomes negatively charged. 2) Isotopes atoms with different number of neutrons The bottom number is the number of protons (the atomic number) which does not change even as an isotope. Some isotopes are radioactive. Electrons are arranged in shells. Shells are found at different distances to the nucleus. Shells have a maximum number of electrons that can be in it. Shell 1: 2 Shell 2: 8 Shell 3: 10 The outermost shell of an element is called the valence shell. Atoms want full valance shells, so they bond. How atoms get full valence shells: Strategy 1: Donate or accept electrons This makes an ionic bond (name from two ions bonding) Cation (positive charged atom) and anion (negative charged atom) attract Ions can dissolve in water to separate Compounds/molecules have characteristics different from the atoms they are composed of. Strategy 2: Two atoms share their electrons to make a covalent bond H H They share the electrons, but both get to count both electrons as a full valance shell Polar covalent bond electrons not equally shared in a covalent bond due to electronegativity (strength in tugowar over electrons) Polar compounds interact with polar compounds. They attract eachother to make a weak bond called hydrogen bond. A hydrogen bond is very important in things like DNA. Chemical Reactions Molecules react with each other Reactants Products , for example: Na+Cl NaCl Mass conservation law all atoms present in reactants are still present in the products Every chemical reaction is reversible in theory Chemical equilibrium the rate of forward reaction equals the rate of reverse reaction Chapter 3: Properties of Water Water is essential for all life on Earth. Organisms are 7095% water. Water is so fundamental because of 4 properties: 1) Cohesiveness of Water Water molecules have polar covalent bonds, and hydrogen bonds between separate molecules, which are constantly breaking and remaking. The breakage and reformation of bonds makes water "sticky" This means nutrients dissolved in water can be transported even against gravity, such as nutrients in plants travelling from the roots to leaves. Cohesion also means that water has high surface tension measure of how hard it is to stretch/break. 2) Water moderates changes in temperature Water has an unusually high specific high amount of energy required to change 1 gram of water by 1°C Water changes its temperature less than other liquids. When water heats up: hydrogen bonds are broken and heat is absorbed. When water cools down: hydrogen bonds form and heat is released. This is why costal climates are mild and ocean temperatures stay stable. Water also has a high heat of vaporization. As liquid evaporates, its remaining surface cools, called evaporative cooling. Evaporative cooling of water helps stabilize temperatures in organisms and bodies of water. 3) Water expands upon freezing Water is most dense at 4°C, not 0°C. The hydrogen bonds are moving too slow to break, so they separate and creative a lattice, rather than being incredibly dense. This causes frozen water to expand and float. Life can live beneath ice. If ice was too dense and sank, all bodies of water would eventually freeze solid. 4) Water is a polar solvent Hydrophilic substances waterloving substances, high affinity for water NOTE Ions Polar molecules Remember, ions have separate charges, and Hydrophobic substances waterfearing substances, low affinity for water polar compounds nonionic molecules have a shared nonpolar molecules partial charge Most biological reactions occur in water. Important properties of solutions solution concentration o rates of biological reaction depends on concentration of reactants o high concentration causes solutes to bump into each other o solvent dissolves the substance o solute substance that gets dissolved o concentration how much solute is present per volume per solvent (Molar) + pH ranges from 0 to 14, a measurement of the concentration H within a solution. o The dissociation of water molecules produces H 2 OH + H + o pure water is has equal numbers of OH and H o pure water has an [H ] = 10 M, making the pH=7 + o The greater the [H ], the more acidic the solution + Change in pH by 1 unit is a change in [H ] tenfold + Acid any substance that increases [H ] of a solution (low pH number) + Base any substance that reduces the [H ] of a solution (high pH number) Two ways for a base to reduce the [H ] in a solution (increase pH number) 1) Take up H ions NH +3 NH 4+ + + 2) Some OH can interact with H to form water and reduce H + + + + KOH + H K + OH + H K + H 2 Controlling pH is important for cells Biological reactions have optional pH (68) + Buffer minimized changes in [H ] and SOH in solution acidbase pair ie H 2O 3 HCO 3 H + carbonic acid bicarbonate ion changes in H concentration drive reactions Chapter 4: Organic Carbonbased Molecules The dry of matter or organisms consists mainly of organic molecules: proteins, DNA, fats, sugars, acids etc. Advantage of carbon as a building block of a life carbon is a tetravalent it needs 4 electrons to fill its valence shell It can make 4 chemical bonds, and therefore is capable of a 4 way connection Carbon is extremely useful for large, complex, and diverse molecules The shape of a molecule affects its function, and decides its properties. When carbon doublebonds to another carbon, it lies flat. Carbon compounds vary in their: Carbon Skeleton basic architecture, how carbons are joined Side groups “accessories” to the Carbon Skeletons Variations in Carbon Skeleton: 1) Length number carbon atoms in a molecule connected to one another 2) Branching when the shape of the carbon chain is nonlinear, ie does not form a straight line and has carbon that juts out Isomers same atomic composition (number of types of atoms) but different structures) Structural isomers different carbon skeleton structures Geometric isomers molecules that are locked into their spatial positions with respect to one another due to a double bond or a ring structure but can have a variation of side groups Cis isomers a geometric isomer that has the side groups or atoms on the same side of the double bond Trans isomers a geometric isomer that has side groups or atoms on opposite sides of the double bond Enantiomers similar to how left and right hands are a mirror of each other, but cannot be super imposed The shape of ibuprofen, or other molecules, effects the effectiveness of its function 3) Double bonds vary in location, changing location of rigidness 2-Butene vs 1-Butene, name based on double bond carbon 4) Ring structures Accessories (side groups): 1) Hydroxyl groups (polar) OH can form hydrogen bonds with water, helps dissolve organic compounds, polar as a result of spending more time with electronegative oxygen. 2) Carbonyl groups (polar) O Carbon double bonded with oxygen C Ketones within the Carbon Skeleton Aldehyde at the end of the Carbon Skeleton 3)Carboxyl groups (acid) O The combination of hydroxyl and carbonyl, organic acid. Acts as an acid by donating H + C because the covalent bond between O and H is + OH Ie acetic so polar. Found in cells with a charge of 1. 4) Amino groups (base) H Nitrogen attached to two hydrogens. It acts as a + N base by picking up H from surrounding H solution, found in cells with +1 charge. Ie glycine 5) Sulfhydryl groups (binds Two sulfhydryl groups together can form a SH other sulfhydryl) Ie Cysteine strong bond called disulfide bridges. The (amino acid) breakage and reformation of these bridges is used in perms (permanent waves treatment) 6) Phosphate groups (polar, Contributes a negative charge. Found in ATP reactive) (adenosine triphosphate, which has three phosphate groups, which causes a pushing reaction from the phosphates, like a spring) 7) Methyl groups (non Addition of methyl in DNA affects the polar) expression of genes, such as the arrangement of methyl in sex hormones an affect shape and function, such as in estradiol and testosterone Chapter 5: Large Biological Molecules Macromolecules Big molecules, typically succeeding 100,000 Daltons (the weight of a proton or neutron), with the exception of Lipids, which are only 1,000. Most macromolecules are "polymers", meaning they are composed of strings of "monomers". They are linked by covalent bonds. Polymers are created and disassembled through dehydration and hydrolysis. Dehydration removes a water molecule, forming a new bond. This is called (Dehydration) Synthesis Hydrolysis breaks a bond by adding water. This is called (Hydrolysis) Disassembly. The 4 Macromolecules are: Polysaccharides (carbohydrates) Polysaccharides sugars and their polymers, serving as fuel and building material "Poly""saccharides" means "many" "sugars". Carbohydrates are hydrated carbon. Polysaccharides are composed of monosaccharides, most commonly as glucose. Monosaccharides aldoses (ie glyceraldhyde, libose, glucose/galactone (isomers)) ketoses (ie dihydroxacetone, ribulose, fructose) most 5Carbon and 6Carbon sugars form ring structures Disaccharides combination of two Monosaccharides, through dehydration synthesis ie maltose (glucose + glucose) or sucrose (glucose + fructose) Polysaccharides are composed of up to 100,000 units αGlucose ↔βGlucose o 2 forms of glucose that differ in placement of hydroxyl group attached at carbon1 o Starch polymer of αGlucose (stored plant energy). o Cellulose polymer of βGlucose (structure for plants). Functions of polysaccharides: Energy storage (fuel) o Starch in plants and Glycogen in animals Support (structure) o Cellutose in plants and Chitin in animals, insects, and crustaceans Lipids Lipids are not polymers, not as big as other macromolecules, and are hydrophobic Biologically, important lipids include: Fats are "triglycerides", or the combination of glycerol and 3 fatty acids through dehydration synthesis reaction. Fats are hydrophobic because they are nonpolar CH bonds Fats are divided into two groups of saturated and unsaturated fats. Saturated animal fats, solid at room temperature, no double bonds Unsaturated liquid at room temperature, double bonds add kinks which means they can't be packed together tightly enough to solidify Functions of fats are to store energy, protect, and add insulation Phospholipids The class will go more in depth on phospholipids after Exam #1 Structure: hydrophilic head and 2 hydrophobic tails "Phospholipid bilayers" form membrane because the tails hide between heads Steroids Cholesterol and cholesterol derived molecules Characterized by four rings with side groups Hydrophobic molecules Cholesterol keeps cell membranes "fluid" Steroids derived from cholesterol and vertebrate sex hormones (ie testosterone and estrogen) Proteins Proteins the most structurally sophisticated molecules known Structure composed of polymers of amino acids There are 20 different amino acids in proteins, depending on the side group, which can make an amino acid: 1) Nonpolar or polar 2) Uncharged or charged 3) acidic or basic Peptide bonds link individual amino acids through dehydration synthesis Proteins have structure, which determines their function. Levels of protein structure: 1) Primary The "Primary structure" of a protein is a series of amino acids that are peptidebonded to each other, like a "string of pearls". The primary structure is like a piece of yarn it is not actually function as it is, but when folded and coiled, like a sweater, it gains its shape and function. 2) Secondary αhelix or βpleated sheets (coiling and folding) 3) Tertiary second layer of folding and coiling. Some proteins can stop here rather than have another level of structure, but some proteins, like hemoglobin, require further development. 4) Quaternary multiple protein structures combined together The amino acid sequences determines the 3D structure that protein will have under normal cellular conditions. Forces that stabilize tertiary structure: 1) Hydrogen bond 2) Hydrophobic interactions 3) Disulfide Bridges (from back in chapter 4 and sulfhydryl groups) 4) ionic bonds Functions of proteins: Enzymes (act as catalysts, speeding up chemical reactions, like saliva) Antibodies Structural proteins Contractile proteins (muscle contraction) Transport proteins Cell communication Denaturation loss of protein conformation/structure, results in loss of function. It can be irreversible. Causes can be heat, pH, chemical conditions Ie., boiling lake water to kill bacteria Nucleic Acids Polymer of nucleotides sugar, phosphate, and nitrogen base (cystosine, thymine, adenine, guanin, or uracil) 2 types of nucleic acid Deoxyribonucleic acid commonly known as DNA, which provides information for its own replication and directs the synthesis of messenger mRNA Ribonucleic acid RNA, created from DNA strands to serve purposes outside the nucleus DNA Structure Double stranded helix zipped up by hydrogen bonds between bases of adeninethymine or guaninecytosine base pairs DNA strands Complementary (not complimentary) and antiparallel, like a divided highway (written with a 5' on the end that has a Phosphate and a 3' on the end with an OH) Function of DNA: To carry genetic information (genes). The "blueprint of the cell." DNA → RNA → cell RNA Structure similar to DNA structure except it has uracil instead of thymine Functions of RNA: mRNA messenger, brings information to ribosomes rRNA component of ribosomes tRNA transfers, carries individual amino acids to ribosomes Chapter 6: A Tour of the Cell To be classified as alive, a being/cell must: 1) Be able to separate insides from outsides 2) Store information 3) Store energy 4) Create structures 5) Protect self from environment 6) Get rid of waste 7) Reproduce (this is the quality that makes viruses considered notalive) Features that are common to all cells: Plasma membrane, cytosol, chromosomes, ribosomes, Most cells are 1 um 100 um 1 um 1/1,000,000 of a meter However, big animals do not have big cells This is due to total surface area. They get a larger surface area from multiple small cells than one large one. A large surfacetovolume ratio is needed for optimal exchange fo nutrients and gases into and out of the cells. for this same reason, things like intestines and proteins are folded. Organisms are made out of two types of cells: Prokaryotic (prokaryotes) bacteria and archaea lacks a nucleus Instead has "nucleoid", cytoplasm, membrane, and cell wall Prokaryotes are smaller because they are all unicellular. Eukaryotic (eukaryotes) protists, fungi, animals, and plants are all eukaryotic characterized by having DNA in a nucleus that is bounded by a membranous nuclear envelope, membranebound organelles, and cytoplasm in the region between the plasma membrane and nucleus Eukaryotes (plant, animal cells, all have a nucleus) are much larger that prokaryotic because they can be multicellular or unicellular (like a chicken egg) However, big animals do not have big cells This is due to total surface area. They get a larger surface area from multiple small cells than one large one. A large surfacetovolume ratio is needed for optimal exchange fo nutrients and gases into and out of the cells. for this same reason, things like intestines and proteins are folded. Many specialized cells Advantage: division of labor (faster production) Membranes separate compartments have "organelles", similar to organs in a body, carry out specific, specialized functions plant cells: cell wall, plasmodesmata, chloroplast, central vacuole (water sac) Nucleus Present in all Eukaryotes Nuclear envelope double membrane surrounding nucleus Pore complex connects nucleus to cytoplasm Chromosomes DNA, genetic information, bundled up Proteins are made in the ribosomes Instructions to make proteins are in DNA in the nucleus Ribosomes carry out the instructions with the aid of mRNA DNA is like a Social Security card of birth certificate you would make a copy of it for work or documentation because you cannot lose the original Every single organism is related according to evolution, which is why we all have similar structures The Endomembrane System regulates protein traffic and performs metabolic functions o components nuclear envelop endoplasmic reticulum (smooth and rough) golgi apparatus lysosomes vacuoles plasma membrane connects the nuclear membrane with organelles and cytoplasma Endoplasmic Reticulum Rough dotted with ribosomes (reads RNA that leaves the nucleus) Folded large surface area so it can make a lot of proteins in small area Smooth makes lipids (no ribosomes, so it cannot make proteins) Vesicles transports proteins to the golgi apparatus Golgi Apparatus Stacks of flattened membrane sacs Modifies proteins adding sugar groups "glycosylation" adding phosophate groups Functions of added groups "address label" for proper destination, such as outside the cell (like with insulin) alter protein/lipid function Ships proteins off to final destination Plasma membrane secretion (outside the cell) Lysosomes/vacuoles Lysosomes/Vacuoles digestion and breakdown Lysosomes Digestive enzyme vesicles Membrane bound sac with enzyme (protein) Digestion of food particles and damaged organelles It is almost a oneuse enzyme, and needs to be replaced Knows what not to digest because they are kept inactive by acidic pH autophagy "selfeating", such as with liver, eats its own cell or parts would only digest nucleus in apoptosis phagocytosis eating food Vacuole Found in plants Water balloon Comes from golgi apparatus, dissolves things Mostly potassium is dissolved Sturdiness and Storage o The reason plants stand up straight o ions o metabolites o pigments o toxins Nonendomembrane organelles have a membrane but are not part of endomembrane system mitochondria and chloroplasts o they are semi autonomous, meaning they have their own DNA and ribosomes essentially a long, long time ago, eukaryotes engulfed a bacteria (mitochondria), and it stayed within the cell because it was advantageous to the cell, then same thing happened with chloroplast in plant cells this conclusion was made because of the DNA and ribosomes inside them Mitochondria Chemical energy conversion Powerhouse of the cell They have a smooth outer membrane and an inner membrane folded into cristae They have an inner membrane that creates two compartment intermembrane space and mitochondrial matrix Some metabolic steps of cellular respiration are catalyzed in the mitochondria matrix Cristae present a large surface that are for enzymes that synthesize ATP Chloroplast Chloroplasts contain the green pigment chlorophyll as well as enzymes and other molecules that function in photosynthesis Chloroplasts are found in leaves and other green organs in plants and algae Peroxisomes Oxidation Are specialized metabolic compartments bounded by a single membrane Peroxisms produce hydrogen peroxide and convert it to water basically can break down poisons (like alcohol) Other structures in Eukaryotic cells (not organelles): Macromolecular structures No membrane → not organelles o Cytoskeleton network of protein fibers throughout cells 3 components: microtubules, microfilaments, intermediate filaments Functions: support and movement, organizes the cell's structures and activities, anchoring many organelles microtubules thick, straight, hollow fibers of "tubulin" Important in spindle formation Movement (organelle movement and cell mobility, as in flagella) microfilaments thin, solid rods of "actin" temporary structure contraction (as in muscle contraction) cytoplasmic streaiming cell movement Intermediate filaments extremely solid rods of "keratin" permanent structures and cell shape o Extracellular components Connections between cells help coordinate cellular activities Most cells synthesize and secrete materials that are external to the plasma membrane Cell walls of plants Protects plant cells, maintains its shape, and prevents excessive uptake of water cellulose fibers help to support cells made of polysaccharides Extracellular Matrix Made primarily of glycoproteins functions: support, adhesion, movement and signals Cell Junctions neighboring cells in tissues, organs, or organ systems often adhere, interact, and communicate through direct physical contact intercellular junctions facilitate this contact types: o plasmodesmata (plants) cytoplasmic connections between cells o tight junctions (animal) prevent fluid transport across cell layer prevents mixing of contents from 2 compartments like glue o desmosomes (animal) similar to plasmodesmata like a rivet in construction, or staples anchoring junction o gap junctions cytoplasmic connections for molecular transport channel between cells allows things to pass The cells rely on integration of sturctures and organelles in order to function A macrophages ability to destroy bacteria involves the whole cell, coordinating, components, such as the cytoskeleton, lysosomes, and plasma membrane
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