Biology Ch. 1&2 notes
Biology Ch. 1&2 notes
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Introduction to Biology: an overview biology: science of living organisms and life processes, including the study of structure, function, growth, origin, evolution and distribution of organisms biology is an umbrella more specific areas of study: cytology - cells histology - tissue zoology - animals botany - plants limnology – brackish water ecology – the relationship between an organism and its environment pathology - diseases evolutionary biology – changing of an organism over time herpetology - reptiles ornithology - birds ichthyology - fish mammology - mammals vertebrate zoology – animals with backbones invertebrate zoology – animals without backbones taxonomy – classification anatomy - structure of bones morphology – shape/form osteology – bones biochemistry – chemistry of life genetics – heredity microbiology – bacteria entomology – insects animal husbandry – mating/breeding Overview of Life’s Unity (How to Define Life) - life is extremely diverse, yet there are some unifying characters all living organisms share characteristics (unity) of life - all living things have: 1 organization (unity) of life on earth: a hierarchy (molecules cells organs …) - most important is the DNA molecule - each level is based on the level below it and provides the basis for the one above it (simple to complex) emergent properties – inactions between the parts making up the whole subatomic particles - particles that make up an atom (protons, neutrons, and electrons) atom - smallest particle of an element that has the properties of that element (H, Al, Fe, O) molecule - 2 or more joined atoms (H + 2 = water) organic molecules = composed mainly of C organelle - structure within a cell that performs a specific function, cannot survive on its own cell - smallest unit of life unicellular - composed of one living cell - must contain DNA, be able to perform chemical reactions (gather food for E, expel waste…), surrounded by a membrane for protection tissue - group of cells that perform a function together (brain tissue, lung tissue) organ - structure composed of tissues that function together (brain, lung) organ system - two or more organs working together (nervous system) organism - all organ systems functioning together to make up a single living individual multicellular organism – living individual composed of >1 cell species - group of genetically similar organisms (lion) population - members of the same species living together (lion pride) 2 community - populations of different species living together (lion pride, zebra herd) ecosystem or biome - community plus its non-living environment (water, soil, temp…) - terrestrial (land) ecosystem = tropical rain forest, grasslands - aquatic (water) ecosystem = lakes, ponds, coral reef biosphere - earth and its’ living (biotic) & non-living (abiotic) components - in ecosystems, the same nutrients keep cycling through populations, but E flows because it is eventually converted to heat - human populations tend to modify existing ecosystems for its own purpose - biodiversity is being threatened by these changes biodiversity = # and size of populations in a community - estimated as high as 80 million species with only about 2 million identified and named - 24 – 100 species lost daily to human activity extinction – the death of a species or larger classification category extinct in the wild – only found in captivity, no longer in nature metabolism (implying change) - acquire and use materials (nutrients) to obtain E, this E carries out chemical reactions such as growing/reproducing - nutrients from the air, water, soil energy (E) = the ability to do work How do organisms acquire these nutrients? producers (autotrophy - “self-feeder”) – photosynthesis consumers (heterotrophy - “other feeder”) decomposers – breakdown material to be recycled 3 homeostasis (homo = the same; stasis = standing) - maintenance of oelatively constant internal body conditions (pH, temp (37 C), water) - all organisms have a range of tolerance, cells perform chemical reactions in order to maintain internal conditions within these ranges ability to grow and develop ability to reproduce - all living things pass on their DNA, the genetic information within all organisms asexual DNA from one parent, identical offspring bacteria, plants, sponges, …. sexual exchange of DNA, two parents, genetic mix ability to respond to stimuli – with the aid of receptors - light, sound, the presence of prey capacity to evolve - the genetic info. of one organism stays the same over its lifetime; however, variations between parents and offspring allow for the genetic material of a species to change over time An Evolutionary View of Diversity = heritable change in a line of descent over time What causes change: mutations = changes in DNA three basic concepts of evolution: 1. genetic variation exists within a population: - differences in the actual genetic code occur in individuals of the same population 2. inheritance of those differences occurs when parents pass them to their offspring 3. natural selection occurs 4 - allows for the survival and increased reproduction of the individuals with the most favorable genetic variations over time physiological processes (improved digestion) behavior (new way to gather food) shapes (better at hiding from predators) sizes (long legs for running) - evolve to enable an individual to be better suited to its environment this is an adaptation - if the environment changes, the adaptation may no longer be beneficial over a long period of time; this may change the genetic make-up of a population as new adaptations arise difference between acclimation and adaptation: acclimation = a temporary adjustment to an environmental condition = when you reduce the temp. in a fish tank; the fish responds by changing their breathing rates - they are adjusting to a new environment adaptation = an inherited genetic trait passed on from parent to offspring - the result of evolution over a tremendous amount of time is a vast variety of species each with its own set of requirements for living: = interrelationships between predators, prey, parasites = temperature, nutrient & water requirements biodiversity - the diversity of species and the complex interrelationships that surround each of them artificial selection – one form of a trait is favored over another in an artificial environment under contrived, manipulated conditions. (dogs, cats, cows, corn) 5 If So Much Unity, Why So Many Species: Living Things Classified taxonomy (tasso - arrange, classify; nomas – usage, law) - the discipline of identifying and classifying organisms according to certain rules - each species is given a binomial (bis = two; nomen = name) Bison bison (Genus species) or Bison bison Carolus Linnaeus = Father of Taxonomy 1735 - developed the binomial system of naming organisms Categorizing the Diversity of Life - a hierarchy usually categorized by: cell number unicellular vs. multicellular cell type prokaryotic vs. eukaryotic how E is acquired producer vs. consumer Cell types: 1) Prokaryotic “no nucleus”: Domain: Bacteria “true-bacteria” – decomposers of the world = distributed in various environments Archaea - live in extreme environments = hot springs, high salinity, low pH, etc. - unicellular organisms which are structurally similar, metabolically complex - can be autotrophic or heterotrophic or decomposers 2) Eukaryotic “true nucleus”: Domain: Eukarya - mostly multicellular organisms - some unicellular organisms Kingdoms Protista – auto/heterotrophic or decomposers; uni/multicellular (euglena, amoeba, kelp) - protists are currently being split up 6 Fungi - multicellular; heterotrophic or decomposers (molds, mushrooms) Plantia - multicellular; autotrophic (photosynthesis oaks, roses, grasses Animalia - multicellular; ingest their food herbivores = plant eater (zebra, deer) carnivores = meat eaters (lions, wolves) parasites = host eater (tapeworm) decomposers = eat dead things (vultures) insectivores = insect eaters (bats, spiders) omnivores = plant and meat eater (humans) - broken down further into: Phylum, Class, Order, Family, Genus species (or Genus species) The Nature of Biological Inquiry: The Process of Science biology – the scientific study of life science: an organized body of knowledge that attempts to explain natural phenomenon with a collection of facts and theories, a process of discovery, it is self-correcting and solves problems, searches for patterns with observable data, information processing. inductive reasoning – using isolated facts and creative thinking to come up with a possible explanation for your observations; creating a hypothesis deductive reasoning – once the hypothesis is stated, it is a general statement that infers a specific conclusion; information based on previous work Scientific Method - method of asking questions and testing those questions observation: using your senses 7 - gather supporting information (Internet, journals) = previous data hypothesis: generate an explanation for your observation, must be testable experiment: a test for data collection and results to support or reject your hypothesis variables - within an experiment, one variable/ factor must change independent var. – what is changed dependent var. – response to change control – a standard used for comparison against one or more experimental groups (the baseline) replication - repeats the experiment to obtain consistent results - gives “power” to the experiment, able to average results conclusions: explanation of your results in order to inform other people (graphs, publication) theory: general explanation of a natural phenomenon, after much testing; concepts that join together well-supported and related hypotheses - fundamental principles of biology such as: cell theory - all living things are composed of cells biogenesis (bio = life; genesis = first) – life comes from life evolution – all living things have a common ancestor and are adapted to a particular way of life gene – organisms contain coded information that dictates their form, function, and behavior all science is based on a small number of assumptions thoroughly tested and found to be valid: 8 1. all events can be traced to natural causes that can be understood (i.e. supernatural powers are not part of science) 2. laws derived from nature are uniform in space and time and do not change: light, gravity, interactions between atoms, etc. 3. objectivity: science requires all people remain objective during scientific pursuits Read through experiments at the end of the chapter (1.6) to understand the scientist process including terms. 9 Life’s Chemical Basis Introduction: Every process that goes on within plants, animals, fungi, and microbes is a chemical reaction, collectively these reactions describe metabolism. These reactions are biochemical (bio – life, so it’s the chemistry of life). Why is chemistry important in the study of biology? metabolism, biological molecules, energy, radioactive tracers, and medicine – all deal with chemical reactions chemistry = the study of matter and the changes that it undergoes matter = the “stuff” that makes up all material things in the universe - anything that has mass and, therefore, takes up space = solid, liquid, or gas Matter is made up of elements (pure substance) - elements are made up of the same type of atom (i.e. oxygen gas) which can neither be broken down nor converted to other substances by ordinary chemical means - each particular type of atom forms a different element - 92 naturally occurring elements as seen in the PERIDOIC TABLE along with man-made elements – developed by Dmitry Mendeleev - each element is designated a one or two-letter abbreviation of its Arabic, English, or Latin name; this abbreviation is its SYMBOL C – carbon Fe – iron Na – sodium - 25 elements are essential to life o bulk elements = required in large amounts (C, H, O, N) o minerals = essential other than the bulk elements (P, Na, Mg, K, Ca) o trace elements = are required in small amounts Eight important elements make up 99.5% of the mass of living organisms: O-65%, C-18.5%, H-9.5%, N-3.3%, Ca-1.5%, P-1%, K-0.4%, S-0.3% Other biologically important elements are: Na, Cl, Mg, and Fe 1 Start with Atoms Atoms - makes up matter; everything is composed of atoms. Atoms are the basic structural units of matter and are composed of still smaller particles: protons, neutrons and electrons (e’) Structure of Atoms (proposed by John Dalton in the 1800’s): 1) nucleus – a central core composed of the 2 heavy subatomic particles – protons (positive) and neutrons (neutral) 2) energy shells “e’ cloud” – surrounds the nucleus of the atom and contains the electrons (negative); they are 1/2000 the mass of a proton or neutron; they are located a various distances from the nucleus within the E shells - the negative charge of the (electron) e’ exactly equals or balances the positive charge of a proton - atoms vary in size, weight, and how they interact with others The chemical and physical properties of an atom are determined by the # of protons and neutrons in the nucleus, and by the # and arrangement of electrons (e’) in its’ energy (E) shells. Atomic Number - number of protons in a nucleus Ex: Hydrogen (H) #1, Carbon (C) #6, Chlorine (Cl) #17 - this equals the number of e’ in the E shells mass number C – symbol of element atomic number 6 Atoms and their components all have mass. Protons and neutrons are equal in mass while e’ are lighter. Atomic Mass – equal to the weight (mass) of the total # of protons and neutrons in the nucleus of an atom o e’ weigh so little, their weight is not considered Atomic Weight – a measure of the Earth’s gravitational pull on mass Mass vs. Weight - weight is the measure of gravity on mass 2 - different on different planets Measuring mass measures the amount of matter present, the greater the mass the greater the amount of matter. Putting Radioisotopes To Use Isotopes - atoms of the same element that have different numbers of neutrons in the atomic nucleus, but the same numbers of protons o different mass number, same atomic number - most C atoms are carbon-12 (6 protons and 6 neutrons) - some C atoms are carbon-13 (6 protons and 7 neutrons) - some C atoms are carbon-14 (6 protons and 8 neutrons) Some isotopes are radioisotopes and are useful as “labels” or “markers” in studying biological processes because they are unstable and decay over time; as they decay, the type of energy (alpha, beta, or gamma radiation) they give off allows for dating of the atom. - Henri Becquerel (1896) discovered the use of uranium will produce a bright image on a photograph - Marie Curie worked with Becquerel in the study of radioactivity and she named it - Geiger counter are used to detect radiation Low Levels of Radiation - Melvin Calvin used isotopes as tracers to detect the various processes of photosynthesis since radioactive isotopes are similar to the stable isotope - used to take images of organs/tissues = patients drink a tracer and doctors can detect its movement helping to diagnose diseases High Levels of Radiation - harmful effects caused by radiation can led to cancer - Marie Curie and many coworkers developed cancer - radiation can stay in the environment causing years of harm to all organisms - research has led to the use of high radiation in treating cancer What happens When Atom Bonds With Atoms chemical reactions - chemical changes that occur because of the behavior of e’ 3 - # of electrons in each atom of an element determines how that atom will react with other elements Electrons constantly orbit the atomic nucleus. They are always in motion, in 3-D space; thus, it is impossible to tell exactly where an e’ will be, but 90% of the time it is within its orbital. - the first orbital (valence shell – innermost shell)can have up to two e’ - atoms can have >1 orbital, each orbital has its own characteristic shape and orientation. - orbitals make up the E levels around the atomic nucleus called e’ shells - e’ shells are labeled K, L, M, N, O, P, and Q - e’ shell closest to the nucleus have the least E and the furthest has the most E Atoms interact with one another by gaining, losing or sharing e’ from their outer shells. The outermost shell is important in determining how the atom combines with other atoms. If the outer shell is full of e’, the atom is not chemically reactive, it is stable and will not react with other atoms. If the outer shell is not full of the max # of e’, the atom is chemically reactive. All atoms “seek” to be stable by having 8 e’ (or zero e’) in their outer orbital. They can attain this by either sharing/gaining/losing one or more e’ from their outer orbital (octet rule). Bohr’s models - Danish physicist created a model to represent e’ rotations of an atom He H (highly flammable) When atoms share or exchange e’, they are bonded together creating a stable associations of atoms called molecules = 2 or more atoms linked by chemical bonds 4 chemical bond - attractive force linking two or more atoms into a compound compound – molecules that consist of two or more different elements in proportions that never do vary molecules (mass) = the smallest part of a compound that still has the properties of that compound - strength lies in the stability of the atoms when their outer shells are full of e’ - E exist between those bonds which can be given off or absorbed - that E allows an organism to maintain a certain level of cellular organization O 2 Cl 2r I 2 - Halogens (group 7) of the periodic table form diatomic molecules – molecules composed of the same elements chemical reactions - making and breaking of chemical bonds Major Bonds in Biological Molecules TYPES of BONDS: 1) Covalent Bonds = “co” means a shared condition - the bond between two atoms when they share e’ -makes the atoms more stable, by filling outer shells Ex: H has one e’ in its outer shell. If two H are close together, the e’ in one is attracted to the proton in the atomic nucleus of the other. When the two are close enough, the e’ begin to share space, filling the outer shell of each other’s orbital, thus the atoms are covalently bonded together into H 2.is molecule of H gas is very stable. O2- double bonded - O atoms share two pairs (4 e’) N – triple bond – N atoms share three pairs (6 e’) 2 C – four bonds –C atoms share 4 pairs (8 e’) Most biological molecules use covalent bonds. - living and once living are composed of C C has 2 e’ in its inner shell, four e’ in its outer shell, so it can react with up to 4 other atoms. CH g4s forms when C is in close contact with 4 H atoms, 5 filling every atom’s outer shell to become more stable by sharing 8 e’. Others: CO ,2H C2(ethylene gas) In all of the examples provided, the e’ spend equal time orbiting each nucleus. Therefore, the distribution of charges is symmetrical and the bond is called a nonpolar covalent bond. Because of this equal sharing, the molecule is electrically balanced and as a whole is neutral. Nonpolar substances have no attraction for polar substances. Hydrocarbons - molecules that primarily contain H and C. They produce the “pure” covalent bonds (nonpolar). The e’s orbit each atom equally. ----------- Polar Covalent Bonds = a sharing of e’, but one atom holds onto their e’ more tightly which is known as electronegativity Example: N and O when they bond with less electronegative atoms (such as C, H), they share e’s unequally resulting in a polar covalent bond and the e’s shared spend more time orbiting the more electronegative atom. The bond is polar because this results in one side of the molecule being more negative than the other side. Unequal sharing of e’ can produce polar molecules. Ex: H 2 - O has high electronegativity, so the bonding e’ spend much more time around the O atom, than around the weaker H atoms. Consequently, the O end of the molecule is slightly negative, due to the e’ presence. While the H end is slightly positive since H atoms are basically protons. Polar and Nonpolar Interactions: Molecules with nonpolar bonds (e’ shared equally) do not interact with the charges on polar bonds (unequally shared e’). nonpolar substances = fats/oils/hydrocarbon gases (butane) hydrophobic = “water-fearing” polar and ionic substances = water, salt, etc. hydrophilic substance = “water-loving” As a general rule of thumb, like dissolves like. - no interaction between nonpolar and polar/ionic substance 6 The water molecules form a H-bonded "cage" that surrounds the nonpolar hydrocarbons and pushes them together. These water cages bring together dispersed nonpolar molecules into larger groups. - think about oil sheens on the surface of water - think about oil and vinegar - think about substances not dissolved by water ___________________________ 2) Ionic Bonds = attraction of charged atoms (ions) Atoms with outer shells that are not full can become stable by gaining e’ (filling their outermost shells) or by losing e’ (emptying their outermost shell). Ionic bonds form because some atoms hold onto their e’ more tightly = electronegativity (like polar covalent bonds). Ionic bonds form by electrical attractions between ions bearing opposite charges to make compounds. Ex: sodium (Na) has 1 e in its’ outer shell chlorine (Cl) has 7 e in its’ outer shell If Na loses an e’, it becomes stable and if Cl gains one, it becomes stable. - becoming charged ions = atoms that have altered their balance between the # of protons and e’ Since opposites attract, the atoms stay close together into a molecule of NaCl forming crystals of salt. The electrical attraction between oppositely charged ions = an ionic bond. Ionic bonds are weak and easily broken - salt is dissolved in water + 3) Hydrogen Bonds = arises form the attraction between the slight charge on a H atom and a slight charge on a nearby O, N, or Fl atom - + H 2 = the O in one water molecule is attracted to the H of another molecule this results in an H bond O...H - can also occur with H and an electronegative atom (N or O) H bonds form between molecules, covalent bonds form within molecules. They are weak bonds, but can add up when a lot of them occur together. 7 Important in water molecules and in 3-D shapes of big molecules like DNA and proteins. Types of Chemical Bonds How They Are Formed Covalent sharing of pairs of e’s, equal sharing produces nonpolar covalent bonds; unequal sharing produces polar covalent bonds very strong, holds atoms together to form molecules Ionic* attraction of opposite charges, + and – ions = atoms with a charge Hydrogen* sharing of H atom to link molecules to each other; weak and in polar molecules * weaker bonds, allow interactions between individual atoms or molecules van der Waal’s Attractions - brief, weak attraction between nonpolar substances that occur because of the random variations in e’ distribution as they orbit the atoms This creates opposite charges in adjacent molecules and results in a brief weak attraction. These are important in holding together hydrocarbon chains (H and C) that make up biological membranes and help to stabilize DNA molecules and folded 3-D structures of proteins. Water’s Life-Giving Properties Water’s Life Giving Properties Why is water so important to life? - first cells evolved in water 3.5 billion years ago - water covers approximately 75% of the Earth’s surface - living organisms are composed of 70 to 90% water - all life depends on water and its unique properties - water contributes to the Earth’s habitability o its ability to sustain life - life has a limited temperature range and water helps to regulate it 8 Water has a high heat capacity and high specific heat, which allows it to resist temperature changes and absorb heat and solar radiation. temperature – a measure of molecular motion Ex: Living in a coastal zone provides mild winters and summers. Also, hypothermia can result from prolonged exposure to even warm water because the surrounding water can pull the heat from your body. Water has a high heat of vaporization, which allows for evaporative cooling. The heat is absorbed from the environment in contact with the water; thus, cools the area. The more evaporation taking place, the more cooling. Ex: Sweating and cooling machines (mister with a fan) Water has a high heat of fusion, which allows water to freeze more slowly than most other liquids. Most liquids become more dense when they form a solid, but not water. Ice is less dense than water, which allows the ice to float because of the structure of the water molecules and the hydrogen bonds between molecules. What would happen if ice was denser than water? Ponds and lakes would freeze from the bottom up in winter and kill everything in them. Instead ice forms a protective layer at the top of bodies of water, insulating them by reducing heat flow between the water and the colder air above. Water is the solvent of life (universal solvent). Water is a very versatile solvent able to dissolve a wide range of substances such as salts, sugars, and proteins (solutes). - solution – contains dissolved substances Water has the ability to dissociate ionic molecules and dissolve molecule held together by polar covalent bonds. Because of their electrical attraction and capability to dissolve in water, ions and polar molecules are termed hydrophilic “water-loving”. Nonpolar or uncharged molecules are termed hydrophobic “water-fearing” because they do not dissolve in water. Ex: Oil in water, oil will form globules in water. 9 Water is cohesive and adhesive: Cohesive – sticks to itself Adhesive – sticks to other things The making and breaking of H-bonds explain the cohesive strength of water. The cohesive nature of water allows plants to suck water up their roots to their leaves, the site of photosynthesis. The evaporation of water from the leaves acts as a suction drawing more water up from the soil. The column of water moves up as a result of the pull of the molecules at the top. surface tension - the surface tension of water is high, making it difficult to puncture the surface of a water droplet. The water molecules in the surface layer are H-bonded to other water molecules below. Surface tension permits a glass to be over filled past the brim and for water-bugs to walk on water Acids and Bases Acids, Bases, and the pH Scale: + - Water can come apart into equal numbers of H and OH ions in an ionization process. Free H ions in a cell alters the water environment in which reactions take place. + + Acids donate H Bases accept H Acids - substances that give off H ions (High H Concentration), creating + solu-ions with the concentration of H ions exceeding the concentration of OH ions Bases - substances that give off OH ions (Low H+ Concentration), creating - solutions with the concentration of OH ions exceeding the concentration of H ions pH scale Neutral = 7.0 pure water, tears Acids = 0-6 soda, stomach acid, beer, tomatoes Bases = 8-14 Great Salt Lakes, over cleaner, baking soda - each unit on the pH scale represents a ten-fold change in the concentration of H ions. 10 Ex: The difference between water with a pH of 7.0 and cola with a + pH of 3.0 is that the cola contains 10,000 times more H ions than water. Salts and Water: - salts release ions other than H and OH - - salt forms with the interaction of an acid and a base Living organisms survive in a narrow pH range. This is possible due to substances called buffers. Buffers are substances, which can accept or donate H ions to maintain a constant pH . - CO ac2s as a buffer in our bodies - pH variations can cause sever health problems = respiratory acidosis – fall in blood pH resulting in coma = alkalosis – rise in blood pH which can be lethal Molecules of Life (Organic Molecules) – From Structure to Function 2 Types of Molecules: Inorganic molecules: includes carbon dioxide (CO ) and2all molecules without carbon (C). Ex: table salt Organic molecules: molecules with a C-skeleton that can be synthesized and used by living organisms. Ex: DNA, Glucose C can form up to 4 covalent bonds, making complex shapes - chains, rings, branches - versatility of C and the incorporation of functional groups allow for the great diversity of organic molecules. - C in organic molecules could have functional groups attached, which are less stable than the C backbone and participate in chemical reactions. - functional groups determine the characteristics and chemical reactivity of organic molecules Functional groups important in biological molecules: Group Properties Examples Hydrogen dehydration in almost all organic 11 -H + (release of H O by combining molecules 2 with another molecule) hydrolysis H + OH - H 2 (split molecules into parts using H2O) Hydroxyl polar, dehydration and hydrolysis carbos, nucleic acids, OH - alcohols, steroids + - Carboxyl acidic, releases H and becomes amino acids, fatty acids -COOH involved in peptide bonds + + Amino basic, may bond with H and become amino acids, nucleic acids -NH 2 involved in peptide bonds Phosphate acidic, E-carrier in ATP rxn nucleic acids, -H 2O 4 links nucleotides in nucleic acids phospholipids Methyl makes molecules hydrophobic lipids, many other -CH 3 molecules = other examples of functional groups in text Virtually all organic molecules from all forms of life: use the same set of functional groups use the “modular approach” to make large molecules - functional groups can make molecules hydrophilic or hydrophobic Isomers (equal; part, portion) = chemical compounds that have the same molecular formula but different molecular structures How Do Cells Build Organic Compounds? Macromolecules (big molecules) = contain hundreds or thousands of atoms and have a very large molecular weight Ex: human hemoglobin contains more than 6,000 atoms 12 Macromolecules are chains of small, individual units called monomers (one unit) covalently bonded together to form a polymer (many units). The actual bonds between the monomers can differ according to the particular polymer. No animal acquires macromolecules directly from food. Instead, it uses the subcomponents of its’ food to make new macromolecules suited to its’ unique needs (break down then reassembles). Organic molecules are synthesized by combining atom after atom to form small subunits the monomers “one unit” - long chains of monomers polymers “many units” In organisms, there are three types of polymers: polymer monomer polysaccharide (carbohydrate) monosaccharide polypeptide (protein) amino acid nucleic acid nucleotide Lipids are not true polymers because they have no repeating units (monomers), but they are large organic molecules (C based). Metabolism = sum of all chemical reactions that occur within an organism 2 types: a) Anabolism = synthesis (to make), requires E (dehydration/condensation) - polymers form when E is added to the system = endergonic reactions b) Catabolism = break down, releases E (hydrolysis) - polymers break apart releasing E into the system = exergonic reactions - the subunits of large organic molecules are linked together by dehydration synthesis reactions which literally means “to form by the removal of water” (anabolic = requires E) condensation reaction = forming of water - hydrolysis reactions break down polymers into monomers by adding water, the universal solvent (catabolic = releases E) - hydro “water” and lysis “breaking” 13 Other types of reactions: functional-group transfer = one molecule gives up a functional group entirely, and a different molecule immediately accepts it electron transfer = one or more e’ stripped from one molecule are donated to another molecule rearrangement = juggling of internal bonds converts one type of organic compound into another cleavage = a molecule splits into two smaller ones (hydrolysis) - enzymes (protein) are needed for chemical reactions to occur Nearly all organic molecules fall into one of FOUR categories: 1. Carbohydrates 2. Lipids (not a macromolecule) 3. Proteins 4. Nucleic Acids The Most Abundant Ones – Carbohydrates Carbohydrates (CH 2) n - provide quick E to fuel cell/organism and structure General formula: CH O 2arbon, hydrogen and oxygen (1:2:1 ratio) Three carbon sugars: triose Four carbon sugar: tetrose Five carbon sugar: pentose deoxyribose (DNA) ribose (RNA) Six carbon sugar: hexose Types Example Function monosaccharide: glucose E source for cells, sap (one-sugar) fructose sugar in fruit galactose sugar in milk deoxyribose sugar in DNA ribose sugar in RNA Glucose, fructose & galactose are isomers (C 6 O12. 6 - all 6-carbon sugars (hexose) 14 Types Example Function disaccharide: sucrose table sugar (two-sugars) (glucose + fructose) lactose milk sugar (glucose + galatose) maltose seed sugar (glucose + glucose) - 2 monosaccharides linked by dehydration process which results in the removal of 1 H 2 molecules (C H 12)22 11 Types Example Function oligosaccharide: glycoprotein - sugar attached to protein (3-100 sugars) (cell surface marker like with blood) Types Example Function polysaccharide: starch E storage in plants (many-sugars) glycogen E storage in animals (liver/muscles) cellulose structural material in plants (cell wall) not easily digestible abundant on earth chitin structural material in the fungi and exoskeletons of arthropods and crustaceans (shrimp, crabs, crawfish shells) and cell walls of fungi not easily digestible abundant on earth - “many” sugars formed by the monosaccharides (monomers) binding together - chemical formula more difficult to predict because of dehydration (lose of H2O) Greasy, Oily – Must Be Lipids Lipids (C and H = hydrocarbons, O) - all are insoluble in water because of the many nonpolar covalent bonds and 15 the lack of polar groups - defined by solubility vs. structure (like other organic molecules) - close proximity of nonpolar molecules cause a weak attractive force…van der Waals forces 4 main types: A) Fats and Oils: Triglycerides oil, fat E storage in animals, some plants “true fats” (long-term E storage) - composed of glycerol (a sugar alcohol) + 3 long chain fatty acids—nonpolar hydrocarbon tails. fats - solid at room temperature (20 degrees C) = butter, bacon grease, lard oils - liquid at room temperature = corn oil, vegetable oil, olive oil, peanut oil saturated = solid at room temp, C-atoms saturated w/ H atoms, nestled close together and that makes them rigid unsaturated = liquid at room temp, room between atoms - C-atoms are double bonded, so fewer H-atoms giving the lipid flexibility monounsaturated fat - one double bond Ex: olive oil….which research suggests raises good cholesterol, while lowering bad cholesterol. polyunsaturated fat – 2+ double bonds Ex: corn oil, canola oil Diets that limit saturated fats and favor unsaturated fats help to reduce the heart attacks. Animals store fat rather than glycogen for long-term E storage because of the numerous C-H bonds in their fatty acid chains = a rich source of E B) Steroids - signal molecules - ringed C structures that do not resemble the triglycerides, but have lipid properties. 16 cholesterol: - biologically active steroid that is synthesized in the liver - a component part of cell membrane (makes it stable) - starting molecule for the production of testosterone & estrogen - bile salts that help digest fats - as a hormone, they function as chemical messengers - absorbed from milk, butter and animal fat (deposited in artery walls) Some lipids are vitamins Fat soluble vitamins are formed by plants and bacteria. Man typically obtains these vitamins from dietary sources. Vitamin A - formed from B-carotene, found in green and yellow vegetables. role –vision Vitamin D - regulates absorption of Ca from the intestines. role--skeletal development Vitamin D - 2roduced in the skin by the action of U.V. light on cholesterol. Vitamin E - not a single vitamin, but a group of related lipids that protect cells from damaging effects of oxidation-reduction reactions role--anti-oxidant, anti-aging Commercially, used to slow spoilage of some food stuffs. C) Waxes (similar to fats): fatty acid + alcohol plants: waterproof covering on leaves and stems (cuticle) animals: skin and fur maintenance in waterproofing (prevents dirt and microbial infiltration) beehives D) Phospholipids (similar to oils): - Like triglycerides, phospholipids have fatty acids bound to glycerol by ester linkages, however one of the fatty acid chains has been replaced with a P containing compound. Phospholipids form cell/organelle membranes: one end is hydrophilic (polar – head = soluble in water) = glycerol with the P-group 17 one end is hydrophobic (non-polar – tail = insoluble in H2O) = fatty acid - P functional group has a negative charge (polar), so this portion is hydrophilic, attracting water molecules. - the two fatty acid tails are hydrophobic ("water fearing"), so they are pushed together by the water. - the phospholipids forms a bilayer because of the polar & nonpolar regions Proteins – Diversity in Structure and Function Protein (C, H, O, N, S) amino acid chains - held together by peptide bonds (covalent bond) peptide = chain of a few amino acid polypeptide = lots of amino acids in a chain (several chains) Protein Functions Examples structure collagen and elastin in the skin; keratin in hair, horns, and claws or nails, silk from spiders and worms movement actin and myosin in muscle tissue transport hemoglobin to move O in blood membrane transport proteins defense antibodies in the blood stream, venom in snakes hormones insulin and growth hormone catalysts enzymes to speed up reactions without becoming a part of it Proteins are formed by chains of amino acids: amino acids are the monomers and the protein is the polymer amino acids are composed: amino group, carboxyl group, H-atom and a R Group surrounding a C 18 - the R groups differs among amino acids giving each its distinct property -- 20 different amino acids - amino acids link together by a dehydration synthesis reaction, which forms a peptide bond between the carboxyl group of one amino acid and the amino group of another - one amino acids join through covalent bonding to form a peptide bond - two amino acids join together to form a dipeptide - three amino acids join together to form a tripeptide - many amino acids join together to form a polypeptide (polymer/protein) - Frederick Sanger 1953 = developed a method to determine the sequence of amino acids in a polypeptide. A protein may contain more than one polypeptide chain. There is a great range in protein size. Some are only a few amino acids (50 or less), others are composed of thousands. Each protein has its own characteristic amino acid composition, arranged in a particular sequence. Different proteins have different shapes. The shape of the protein determines its function. There are FOUR levels of organization in protein structure: Primary Structure The unique linear sequence of the amino acid chain in a straight chain. Secondary Structure Alpha helix, a spiral (screw) formed by H-bonds between every 4 peptide bond (ex. – keratin). Beta pleated sheet, polypeptide chain folds back on itself and the parallel region are held together by H bonds (silk fibers). Tertiary Structure The folding into a 3-D shape due to disulfide bridges and hydrophobic interactions. Quaternary Structure The joining of two or more polypeptide chains held together by H bonds. The 3-dimensional structure (shape) of a protein will determine its’ function. 19 Certain environmental changes may cause the protein to unravel and lose its structure (3-D shape). If this happens, the protein cannot function and is biologically inactive. Why Is Protein Structure So Important? Protein sequencing is extremely important. One mistake will completely alter the molecule, thus altering its’ function. - hemoglobin – four tightly packed polypeptides (globins) globins folded chains create pockets (heme group) heme large organic molecules with an Fe center - 2 types: alpha and beta- 2 of each are needed to make up hemoglobin - normal sequence in beta glutamate at the sixth amino acid = negative charge, normal function - abnormal sequence in beta valine at the sixth amino acid = no net charge, abnormal function = mutation in DNA - purpose of hemoglobin is to carry O to different parts of the body - an individual who inherits a mutant gene from each parent will have sickle-cell anemia O flow will be disrupted, results in oxygen starved tissue = the shape of the protein effects its’ function change in shape, change in function (denature) Extreme pH, temperature, and salt concentrations can denature (change the shape of a protein). When the protein loses its’ shape, it can no longer function as it was meant to do – denature. This is usually irreversible. Sometimes denaturation is reversible …. Renaturation. - done at the cellular level - amino acid sequences is very important – read about protein related diseases Nucleotides, DNA, and the RNAs Nucleic Acids (C, H, O, N, P) - chains of nucleotides: 5C sugar (pentose) + phosphate + base - nucleotide = monomer 20 Example Function deoxyribonucleic acid (DNA) genetic material “informational molecules” forming genetic code - this information pertains to replication and protein production - two strands of DNA are held together by H-bonds between the bases - the shape is called the double-helix – like a twisted ladder - bases for DNA: adenine, guanine, cytosine, thymine o complementary base pairs for DNA: A - T and G - C Example Function ribonucleic acid (RNA) genetic material of some viruses, transfer DNA into proteins - bases for RNA: A, G, C, uracil (A - U, G - C) - RNA is copied from DNA o RNA takes the genetic code, deciphers it, and uses it - main function is protein synthesis o since DNA can not leave the nucleus, information is transferred to RNA which will let the nucleus to make the proteins - single strand - nucleotides are linked by H-bonds between the 5-C sugar and the P- group Single nucleotides that are important such as cyclic AMP and ATP: Cyclic adenosine monophosphate (cyclic AMP) = a single nucleotide that is produced when a hormone comes in contact with the cell membrane. Cyclic AMP acts as a messenger between the cell membrane and other molecules within the cytoplasm or the nucleus stimulating necessary reactions. Adenosine triphosphate (ATP) = a single nucleotide with two extra P- groups. This molecule carries E. ATP acquires E within the cell where it is produced and releases it during necessary reactions. Other E carrier within the cell (coenzymes): NAD (nicotinamide adenine dinucleotide) and FAD (flavin adenine dinucleotide) both serve as temporary E carriers within the cell. 21
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