Study Guide PDF

What is Life? To be considered life it must possess all 5 of these characteristics. Some nonliving things may have one or more of these characteristics but not all. Life is Organized The Cell is the fundamental unit of life Many cells make up tissue, many tissues make up an organ, many organs system...

What is Life? To be considered life it must possess all 5 of these characteristics. Some nonliving things may have one or more of these characteristics but not all. Life is Organized The Cell is the fundamental unit of life Many cells make up tissue, many tissues make up an organ, many organs systems make up an organism, many organisms make up a population, many different populations living together make up a community. All living and nonliving things living together make up an ecosystem. Emergent properties- characteristics that living organisms gain when they become part of a larger system. The whole is greater than the sum of its parts e.g. one brain cell has certain characteristics but many brain cells working together have additional characteristics such as the ability to form a memory, 2nd e.g. a bee has certain abilities as an individual but as a group a bee hive takes on additional properties, their ability to thermoregulate the hive, structure of the hive and defense of the hive. Life Requires Energy- all living things need energy to remain alive- the compartments in our cells allow areas where chemical reactions can take place Primary producers (autotrophs) make their own food using energy and nutrients from the nonliving environment Ie. plants are primary producers, they produce glucose out of carbon dioxide and water utilizing energy from the sun. Consumers- (heterotrophs) eat other organisms to acquire nutrients they can break down for energy Decomposers- (heterotrophs) obtain nutrients from dead organisms and recycle nutrients to the nonliving environment. Life Maintains Internal Constancy- homeostasis, the internal environment must be maintained within certain parameters to function properly. Temperature, water, pH, are all kept within certain parameters despite what is happening in the external environment. Life Reproduces, Grows, Develops- organisms reproduce asexually, sexually, or both. Asexual reproduction produces identical copies of the parent Sexual reproduction generates genetic diversity by combining and scrambling DNA from 2 parents. Life Evolves evolution- a change in the genetic makeup of a population over multiple generations. natural selection is where environmental conditions select for organisms with inherited traits, adaptations, that increase the chance of survival and reproduction. Evolution through natural selections explains how common ancestry unites all species. We all have a common ancestor and use DNA as a common genetic language. Taxonomy- the science of classification. Scientists classify types of organisms according to evolutionary relationships. Domain- Kingdom- Phylum- Class- Order- Family- Genus - Species (Dear King Phillip Could Only Find Green Socks) As you go down the levels the organisms are more closely related Prokaryote- single cell organism without nuclear membrane or membrane bound organelles Eukaryote- membrane bound nucleus and organelles present in cell. 3 Domains of Life Bacteria- all are prokaryotes, single cellular organisms- some can cause human illness, ie. E.coli contamination can cause food poisoning Archaea- all are prokaryotes and single cellular organisms, many are (extremophiles living in places without oxygen, or extremely hot, salty, or acidic environments, such as in hot springs or hydrothermal vents) many have unique metabolisms such as the ability to create methane (so far no Archaea are known to cause human disease) Eukarya- are all eukaryotic and can be unicellular or multicellular. (if it is multicellular it will be Eukarya domain) Bacteria and Archaea have some similarities- Single celled Prokaryotic Cell membrane Cell wall Ribosomes Circular DNA of main bacterial or archaea genes Small circular plasmids of DNA that could contain antibiotic resistance genes or other genes and can be transmitted by Horizontal gene transfer Bacteria and Archaea reproduce asexually which would be considered vertical gene transfer. Bacteria and Archaea reproduce by binary fission Horizontal gene transfer- where some genetic material (in form of small circular plasmid) is shared with another bacteria. (NOT PARENT-TO-OFFSPRING TRANSMISSION) 1. a DNA plasmid from one can be transferred to a neighboring bacteria or archaea cell sometimes by releasing plasmids into the environment or using a sex pili where the plasmid is injected into another cell. 2. Destroyed bacteria or Archaea can leak DNA into the environment and it is picked up by neighboring cells 3. Viruses can package its own DNA but capture a little bacterial or archae DNA by mistake and transmit it to another bacterial or archaea cell it infects Domains are divided into kingdoms Domain Eukarya has 4 KINGDOMS Protista- unicellular or multicellular, autotroph( makes own energy) or heterotroph (eats other organisms) (ie. algae, amoebas, slime mold) Slime molds in video- could be unicellular and come together into multicellular organism during stress, could also find quickest path to resources. Just as efficient at finding quickest path as Japanese engineers finding best route for the subway. Fungi- most are multicellular (ie. mushrooms) a few unicellular (ie. yeast) heterotrophs that absorb their food (they are considered decomposers) Animalia- multicellular, heterotrophs that ingest their food (ie. worms, tigers, spiders, humans) Plantae- multicellular, autotrophs( makes its own energy) (ie. trees, flowers) The scientific method- a way of using evidence to evaluate ideas about the natural world. A scientist makes Observations, Asks a question, Consult prior knowledge and uses reason to Formulate a Hypothesis- Hypothesis is a tentative explanation for an observation and must be testable. A hypothesis should be able to lead to a prediction. Then the scientist would Design an experiment,and collect data. Analysis- (is to draw conclusions) after collecting and interpreting the data to decide whether the evidence supports or falsifies the hypothesis. Often the most interesting results are those that are unexpected because that forces the scientist to rethink their hypothesis. Peer review- when enough evidence is gathered to support or reject a hypothesis the scientist will write a paper and submit it to a scientific journal which will send the research to other scientists in the field for peer review which ensures the journal articles and science in them are of high quality. Independent variable- variable that is controlled by scientist to determine if it influences the dependent variable (graphed on X axis) Dependent variable- variable that is measured (graphed on Y axis) control variable- any variable held constant for all experiments including control groups Control group often a group receiving no treatment Note: a control group is not the same as a control variable Scientific theory is a comprehensive explanations with overwhelming evidence and predictive properties Science has limitations- results may be misinterpreted Science community may be slow to accept new data and conclusions Science is self correcting overtime because it does remain open to new data and interpretations Basic and Applied Research Basic Research- aims to expand fundamental understanding of life processes without immediate practical applications. Applied Research- focuses on using biological knowledge to solve practical real- world problems Applied biology uses the insights gained from basic biology to create solutions. They go together Chp 2 Chemistry An element is a substance that cannot be broken down by chemical means into other substances. Organic Chemistry- Living things are mostly composed of six elements: Carbon, Hydrogen, Nitrogen,Oxygen, Phosphorus, Sulfur CHNOPS Atoms The atom is the smallest piece of an element that retains the characteristics of the element. An atom is composed of three smaller particles: protons, neutrons, and electrons. Electrons- electrons are negatively charged and weigh close to 0 and found outside the nucleus. They are very small and move very fast and create an electron cloud around the nucleus. Protons are positively charged and weigh 1 amu (atomic mass unit) and found in the nucleus neutrons are neutral in charge and weigh 1 amu(atomic mass unit) and found in the nucleus The number of Protons determines the atomic number and determines what element it is. Carbon has an atomic number of 6 because it has 6 protons and if you took away or added a proton it would not be Carbon anymore Mass number- is the number of protons and neutrons in an atoms nucleus. The mass number of Carbon is 12. 6 neutrons and 6 protons. Isotopes are the same element with different weights and the same charge because they have different numbers of neutrons Atomic weight is the average mass taking into account the different % of isotopes in a sample as well. Ie. 99% of Carbon is C12 and is 12 atomic weight and 1% of Carbon is C13 and C14 so the average atomic weight is 12.012 Ions are the same element with practically the same weights but with different charges because they have different numbers of electrons. Ie. Na+ and Na are both sodium but Na+ has lost an electron so is positively charged. Hydrogen ion(H+) - hydrogen is only atom without a neutron so H+ ion is just a free proton Outer shell of atom # of Electrons in outer shell (valence shell) determine chemical bonding with other atoms Atoms love having their outer shells filled with electrons to be most stable. Shell 1 can hold up to 2 electrons Shell 2 can hold up to 8 electrons Shell 3 can hold up to 8 electrons Carbon has only 4 electrons in outer shell and has 4 binding sites available with other atoms to complete shell noble gas all have a complete outer shell of electrons and are stable and therefore do not interact with any other elements. Types of Chemical Bonds Covalent bond- a strong bond of shared electrons Polar covalent bond-is a bond of shared electrons but the different atoms share the electrons unequally. Causing a partial negative charge on one atom and a partial positive charge on the other. nonpolar covalent bond- is a bond that shares electrons an equal amount between the different atoms. Hydrogen bonds- a weak bond formed when opposite partial charges on adjacent molecules or within a single large molecule attract each other. Hydrogen is always one of the atoms involved and water can break this bond. Ionic bond- one highly electronegative atom completely rips away electron from another atom, resulting in two stable charged ions that opposite charges bond, strong bond but falls apart in water (no electron sharing) Double covalent bonds have 2 sets of shared electrons (4 electrons are being shared between 2 oxygens to fill each oxygens outer shell) Double covalent bonds are stronger than single covalent bonds. Triple covalent bond has 3 sets of shared electrons. e.g. N2 in atmosphere has a triple bond and is not readily available for most organisms to use. It is converted to ammonia by a few soil bacteria and blue green algae in the ocean. Electronegativity- is an element's ability to pull electrons towards it. Elements on the right side of the periodic table (excluding the noble gases) have a higher electronegativity (they want to pull electrons towards them to complete their shell) more than elements on the left side of the periodic table. Hydrogen bonds give water many of its emergent properties 1.Cohesion is the tendency of water molecules to stick to other water molecules. Cohesion between molecules on the surface of liquid water giving it a high surface tension. Ie. water bugs can walk across surface, water holds together when sucked up in a straw 2.Adhesion-Water molecules also form hydrogen bonds with different molecules in its environment, ie. the molecules making up the plant cell wall. -both adhesion to the plant cell walls and cohesion to other water molecules explains how water seems to defy gravity and move up from plant roots to the highest leaf. 3.Water is a solvent Water dissolves hydrophilic (“water-loving”) substances, for example NaCl is pulled apart in water. The polarity of water molecules helps water dissolve most biologically important molecules, since many of them are hydrophilic. Hydrophobic substances (water hating) do not dissolve in water The molecules in lipids, like oil have nonpolar covalent bonds. 4.Water can regulate temperature Hydrogen bonds between water molecules make water resist changes in temperature. 5. Water expands when it freezes- in ice the hydrogen bonds between the water molecules lock into a hexagonal structure, spreading out the molecules and making ice less dense than liquid water, this means ice floats when it freezes Chemical reactions have an optimal pH. Many organisms try to maintain pH close to 7. Different areas of the cell will have different pH depending on the types of reactions occurring there. pH scale shows the number of H+ ions in the solution Acidic solutions have a low pH and a high H+ concentration. HCL (hydrochloric acid) has a pH of 1 An acid contributes H+ to a solution Basic solutions have a high pH and a low H+ concentration. NaOH (sodium hydroxide) has a pH of 14 A Base will absorb H+ from solution Monomers of Organic Macromolecules The monomers of proteins are amino acids. 20 found in living organisms The monomers of nucleic acids (DNA and RNA) are nucleotide Nucleotide bases (AGCT) found in DNA Adenine, Guanine, Cytosine, Thymine Nucleotide bases (AGCU) found in RNA Adenine, Guanine, Cytosine, Uracil The monomers of carbohydrates are simple sugars such as glucose and fructose. dehydration synthesis- used to link monomers into longer polymer chains (dehydration means getting rid of water, synthesis is building something new so dehydration synthesis is getting rid of water to build something new) Hydrolysis is the opposite reaction where water is added to break long polymer chains into monomer subunits (Hydro means water and lysis is to break so hydrolysis means using water to break something) Protein structure can be classified in 4 levels Primary structure- the amino acid sequence in the chain of polypeptides Secondary structure- are the protein folding into a beta sheet or into an alpha helix structure Tertiary structure- what is the overall 3D structure of the complete protein Quaternary structure- not always present but is when multiple complete 3D proteins come together to form a functioning unit. Nucleic acids carry genetic information Nucleic acids include DNA and RNA. The primary structure of each protein in a cell is determined by the nucleic acids. Nitrogenous bases found in DNA and RNA Bases (AGCT) found in DNA Adenine, Guanine, Cytosine, Thymine Bases (AGCU) found in RNA Adenine, Guanine, Cytosine, Uracil