BIOL141 Test 1 Study Guide PDF

Chapter 1: The Science of Biology **Biology**: The study of life **[The 7 Characteristics of life:]** 1. **Cellular organization:** All life consists of 1 or more cell. A cell is the smallest unit of life. Ex: bacteria are single celled organisms; humans are made up of many cells. 2. *...

Chapter 1: The Science of Biology **Biology**: The study of life **[The 7 Characteristics of life:]** 1. **Cellular organization:** All life consists of 1 or more cell. A cell is the smallest unit of life. Ex: bacteria are single celled organisms; humans are made up of many cells. 2. **Ordered complexity:** All living things are highly ordered and complex (show hierarchical organization). For example: Many cells create a tissue, many tissues create an organ, many organs create an organ system, many organ systems make up an organism. a. **Population-** A group of the same species of organism living in the same place and time. Ex: All coyotes in the Sonoran Desert. b. **Species-** All populations of a particular kind of organism. Ex: All coyotes on earth. c. **Community-** All the populations of different species living together in one place. Ex: All coyotes, scorpions, mountain lions, prickly pear, mesquite trees, etc. in Sonoran Desert. d. **Ecosystem-** Populations and their environment (living and non-living). Ex: All coyotes, scorpions, mountain lions, prickly pear, mesquite trees, etc. in Sonoran Desert plus mountains, rivers, streams, buildings. e. **Biosphere-** All ecosystems on the entire planet. 3. **Sensitivity:** A response to a stimulus. Ex: plants growing toward a light, or our pupils dilating when we go into a dark room 4. **Growth, development, and reproduction:** All living things must be able to grow, develop and reproduce (either sexually or asexually) 5. **Energy utilization:** All living things use energy. Producers create their own food for energy (through photosynthesis). Consumers (like humans) must eat food for energy. 6. **Homeostasis:** The process by which a cell or organism maintains an internal equilibrium (constancy). Ex: sweating to cool off or shivering to warm up. Both are used to maintain a constant body temperature 7. **Evolutionary adaptation:** Living things evolve (genetic change in a population over time). **The Scientific Method:** 1. Observation 2. Hypothesis formation 3. Prediction 4. Experimentation 5. Conclusion **Hypothesis:** A possible explanation for an observation - Must be testable - Can be changed and refined over time **Scientific Theory:** Is supported by much experimental evidence. Expresses ideas of which we are most certain. Ex: Theory of gravity or theory of evolution. **Establishing controls:** - **Variable-** A factor that influences the experiment (what we are testing) - In a good experiment you must be sure to only test 1 variable at a time! - **Control group-** Variable of interest is kept constant - Can have positive and/ or negative controls - **Experimental group-** Variable of interest is altered - The experimental group tests your hypothesis **Charles Darwin:** Wrote "On the origin of species by the means of natural selection". - Observed finches in the Galapagos islands and realized that all were similar (related) but each seemed to be perfectly suited for their environment. - Proposed the *mechanism* for evolution- natural selection! Darwin did NOT come up with the idea of evolution. - **Natural selection**: Advantageous traits will be selected for naturally. Organisms with advantageous traits will survive and pass these traits to their offspring. Organisms with less advantageous traits will not survive and pass traits to their offspring. - **Artificial selection**: Advantageous traits are selected for artificially. Ex: Dog breeders choose with male and female to breed together to get a particular physical appearance or personality trait. **Evidence supporting the Theory of Evolution:** - **Fossil Record:** Transitional forms have been found at predicted positions in time - **Earths age:** Earth is very old (4.5 billion years old), allowing time for evolution to take place. - **Mechanism for hereditary:** We now know more about how traits are inherited (Mendelian genetics- covered in chapter 12) - **Comparative Anatomy:** - **Homologous Structures:** Same evolutionary origin but different structure or function. Ex: Human arm vs. Horse hoof. You can see similar bones- evolved from common ancestor- but different structure/ function. - **Analogous Structures:** Same function, but different evolutionary origin. Ex: Bird wing vs. butterfly wing. Both used to fly, but evolved differently, so different bones etc. Name Date Block EVOLUTION Anatomical Evidence for Evolution In our upcoming study of anatomy and development of organisms, we - **Molecular Evidence:** Genomic (DNA) sequencing **Core concepts in Biology: (each will be discussed in more detail in later chapters)** - Life is subject to chemical and physical laws - Structure determines function - Living systems transform energy and matter - Living systems depend on information transactions - Evolution explains unity and diversity of life Chapter 2: The Nature of Molecules and Properties of Water **Chemistry:** The study of Matter **Matter:** Has mass and occupies space All matter is composed of **atoms** **Atoms are composed of:** - **Protons:** Positively charged subatomic particles found in the nucleus (center) of the atom - **Neutrons:** Neutral (not charged) subatomic particles found in the nucleus (center) of the atom - **Electrons:** Negatively charged subatomic particles found in orbitals surrounding the nucleus **The periodic table of elements show all the elements that are used to build all living and nonliving things around us.** - **4 most common elements in living things: Carbon (C), Hydrogen (H), Oxygen (O) and Nitrogen (N).** - Each element represents an atom with a specific number of protons. - For each element ALWAYS ASSUME THE CHARGE IS NEUTRAL UNLESS OTHERWISE STATED! (\# of protons = \# of electrons) - The periodic table of elements give information about each element. - **Atomic \#:** The number of protons - **Atomic mass:** The number of protons + the number of neutrons. (For this course, always round to nearest whole number, so above would be 16). - **Example:** Using the information above about Oxygen, we can say there are 8 protons (atomic \#), 8 electrons (\# protons = \# electrons) and 8 neutrons (atomic mass = 16 = protons + neutrons, 8 protons + 8 neutrons = 16). **Isotopes:** Same number of protons, but different number of neutrons. Ex: Carbon12 has 6 protons, 6 neutrons and 6 electrons, Carbon 13 has 6 protons, 7 neutrons and 6 electrons, Carbon 14 has 6 protons, 8 neutrons and 6 electrons. **Ions:** Same number of protons, but different number of electrons. This gives the atom a charge - **Cation:** The atom lost an electron, leading to a positive charge. Ex: Na^+^, 11 protons and 10 electrons, giving +1 charge. - **Anion:** The atom gained an electron, leading to a negative charge. Ex: Cl^-^, 17 protons and 18 electrons, giving -1 charge. **Where are electrons found?** - Electrons are found in regions called **orbitals** - Orbitals are found at varying distances from the nucleus in **energy levels** - The farther away from the nucleus, the more energy found in that energy level - The energy level farthest from the nucleus is the **valence level** - **Each orbital holds 2 electrons** - **The first energy level holds 1 orbital (2 electrons)** - **The second energy levels holds 4 orbitals (8 electrons)** - **The first energy level must be filled with electrons before starting to fill the second energy level.** - Atoms are stable (happy) when their energy levels are filled with electrons (like shown below)- if the valence energy level is not full, the atom will be unstable and more likely to chemically bond with another atom  **Molecule:** Groups of atoms held together by chemical bonds **Compound:** Molecules containing more than 1 type of element Ex: H~2~O, CO~2~, NaCl **[Chemical bonds:]** **Ionic bonds:** Do NOT share electrons. Formed by the attraction of oppositely charged ions. Ex: NaCl (Na donates an electron to Cl, Na+ and Cl- are attracted to each other) **Covalent bonds:** When atoms share 2 or more electrons (to give each atom a full valence shell) - **Polar covalent bonds:** Unequal sharing of electrons (giving partial + and partial negative charges on molecule) - **Nonpolar covalent bond:** Equal sharing of electrons (giving uncharged molecule) Diagram Description automatically generated **Electronegativity:** An atoms affinity for electrons. How much do they like electrons? More electronegative elements will not share electrons equally with less electronegative elements (creating polar covalent bonds). Elements with similar electronegativities will share electrons equally (creating nonpolar covalent bonds). **Chemical reactions:** The formation or breaking of chemical bonds. Atoms are not created or destroyed here, they are just rearranged. - **Reactants:** The starting molecules or atoms, shown on left side of reaction (in example below CH~4~ and 2O~2~ are the reactants - **Products:** The final molecules or atoms, shown on right side of reaction (in example below CO~2~ and 2H~2~O are the products  - Looking at the above reaction you can see the same number of Carbon, Hydrogen and Oxygen are seen on both sides of the reaction (1 carbon, 4 hydrogen and 4 oxygen). The atoms are not created or destroyed, only rearranged into different molecules. **Oxidation and Reduction reactions** **L-** Loss of **G-** Gain of **E-** Electrons is **E-** Electrons is **O-** Oxidation **R-** Reduction **[Water is a POLAR molecule]** - Oxygen is more electronegative than hydrogen, so oxygen will have a partial negative charge and the hydrogens will have partial positive charges. Water molecules have one oxygen atom covalently bonded to two hydrogen atoms creating areas of different partial charges (see appendix) - The polarity of water, allows for hydrogen bonding - **Hydrogen bonds:** The partial positive charge on a hydrogen atom of 1 water molecule is attracted to the partial negative charge on an oxygen atom of a different water molecule. - The ability of water to form hydrogen bonds gives it many of its great properties! - **Cohesion:** water molecules are attracted to one another (Ex: surface tension) - **Adhesion:** Water molecules are attracted other polar molecules Water is a great solvent! - Water dissolves polar molecules and ions (anything with a charge) - Non-polar molecules are organized by water (they do not dissolve in water) - **Hydrophilic- "water loving molecules"** (polar molecules and ions) - **Hydrophobic- "water fearing molecules"** (nonpolar molecules) \*\*\*This is why oil and water do not mix! Water is polar (hydrophilic) and oil is nonpolar (hydrophobic), so water forces the oil to aggregate together, and stay separated from the water because water molecules only want to be near other polar molecules they can hydrogen bond with. **[Strength of chemical bonds:]** **Strongest-** Covalent bonds (actual sharing of electrons) **Medium-** Ionic bonds (no sharing of electrons, but attraction of full charges on ions) **Weakest-** Hydrogen bonds (attraction of partial charges on different molecules) Chapter 3: The Chemical Building Blocks of Life **Carbon:** The framework of biological molecules - Organic molecules are defined as molecules containing C-H bonds - Carbon can form 4 covalent bonds **Macromolecules are the chemical makeup of all cells. The 4 major macromolecules are:** 1. Carbohydrates 2. Nucleic Acids 3. Proteins 4. Lipids [Carbohydrates, Nucleic Acids and Proteins are polymers. ] **Polymer-** A large molecule made up of repeating subunits **(Monomers)**. Ex: a puzzle is an example of a polymer, with each puzzle piece being an example of a monomer. Monomers will link together (bond together) to form polymers. **Dehydration synthesis reaction:** Formation of polymers from monomers through the removal of water. A + B C + H~2~O **Hydrolysis reaction:** Breakdown on polymers into monomers through the addition of water. C + H~2~O A + B  **[Carbohydrates:]** - Made up of Carbon, Hydrogen and Oxygen- essentially just sugar! - C-H bonds hold a lot of energy! So Carbs are good energy storage molecules. - **Monomer:** Monosaccharide (a single sugar) Ex: Glucose, Fructose - **Polymer:** Polysaccharide (many sugars) Ex: Cellulose, starch, glycogen - **2 monosaccharides can be joined together through dehydration synthesis reactions to form a disaccharide (2 sugars). [ ]**Ex: Sucrose (table sugar) A diagram of a house Description automatically generated with low confidence **[Nucleic Acids:]** - Hereditary, information molecules! - Central dogma of biology: **DNA RNA Protein** - DNA is used as a recipe to produce RNA, which is used as a recipe to produce protein. The specific proteins that are produced give organisms their individuality. - **Monomer:** Nucleotides - **Polymer: DNA** (Deoxyribose nucleic acid) and **RNA** (ribose nucleic acid) - **Nucleotides are made up of:** - **Nitrogenous base:** ATCG in DNA, or AUCG in RNA - **5 carbon sugar:** Deoxyribose in DNA and Ribose in RNA - **Phosphate group** - Nucleotides are held together by **phosphodiester bonds** - DNA is double stranded, RNA is single stranded - 2 strands of DNA are held together by **hydrogen bonds** - In DNA nitrogenous bases on 1 strand of DNA form hydrogen bonds with nitrogenous bases on the second strand of DNA is a particular way - A pairs with T - C pairs with G  **[Proteins:]** - Most diverse group of macromolecules. They are the workers of the cell, they are have many jobs including (but not limited to) - Catalysts - Defense - Transport - Support - **Monomers:** amino acids - Amino acids are held together by **peptide bonds** - **Polymer:** polypeptide (many peptides) - **There are 20 naturally occurring amino acids.** They all have a central carbon, amino group, carboxyl group, hydrogen and a variable R group. The variable R group gives the amino acids its identity. (Some examples are glycine, alanine, histidine) - There are 4 levels of protein structure: - **Primary:** Sequence of amino acids - **Secondary:** Interaction of R groups in the peptide backbone - **Tertiary:** Final 3D shape of protein - **Quaternary:** Not all proteins have a quaternary structure, it is the arrangement of individual chains in a protein with multiple polypeptide chains. Ex: Hemoglobin (4 heme chains) A picture containing white, clock Description automatically generated  - The structure (shape of the protein) determines its function - If a protein becomes unfolded (loses its shape) also called **denaturation** the protein can no longer perform its job. A protein can unfold due to changes in temperature, pH and salt concentrations. - **Chaperone proteins** help other proteins fold properly. **[Lipids:]** - Lipids are NOT true polymers, but are often made up of fatty acids - **The defining characteristic of a lipid is that it is NOT soluble in water.** - **Lipids are HYDROPHOBIC- "water fearing"** - Examples of lipids are fats, oils, waxes and steroids - Fatty acids are hydrocarbon chains (C-H bonds), chains can very in length (number of carbons) - **Saturated fatty acid:** no double bonds between carbon atoms (left below) - **Unsaturated fatty acid:** double bonds between carbon atoms (right below) Calendar Description automatically generated - An important biological lipid are **phospholipids**. They make up cell membranes. They have a phosphate group attached to a fatty acid. - The phosphate group is **polar (hydrophilic)** - The fatty acid is **nonpolar (hydrophobic)** - **The cell membrane is formed by a phospholipid bilayer, where polar phosphate groups point out toward water, nonpolar fatty acids create a barrier in the interior**