Class: Biology I: Molecular and Cells (BIOL 110 – 4 Credits)

Course Description: Serves as the introductory course for Biology and Pre-Allied Health majors and is the prerequisite course for Anatomy and Physiology and Microbiology. It stresses the basic biological principles common to all living things. Evolution and homeostasis serve as central themes for the topics, which include cell structure and function (both physical and chemical), molecular and cellular reproduction and genetics. The laboratory introduces the student to various biological techniques and emphasizes the process of science. 3 lecture hours and 3 laboratory hours per week.

Professor: Encarni Trueba

Semester: Spring 2009

School: CCBC Essex

Textbook used: Biology, 1st Edition by Brooker

• What is an atom and what is an element?
• What are the four most common elements found within living things?
• Relate the charges and relative sizes of protons, neutrons, and electrons. Where is each located within an atom?
• Distinguish between atomic number and the mass number of an element.
• Describe how electrons are arranged within an atom.
• Define electron orbital, electron shell, valence electron and valence shell. Relate electron shells to energy levels.
• To demonstrate that you understand the concept of energy levels (shells):
  - Record the maximum number of electrons held in each of the first three energy levels.
  - Draw diagrams of the following atoms: ¹⁴₇N, ¹⁶₈O, ³²₁₆S. Working outward from the nucleus, you must fill one shell with electrons before adding electrons to the next shell
• What are isotopes?
• Compare and contrast the characteristics of ionic, polar covalent, and non-polar covalent chemical bonds. How does each type of bond form? Be able to recognize examples of compounds with each type of bond. What is a salt and what do salts usually contain? Compare the strength of ionic versus covalent bonds.
• Show how a molecule is hydrophobic or hydrophilic.
• Describe the following characteristics of water: polarity of water molecules, temperature stabilizing effects, cohesion, and solvent properties. Why does water have each characteristic, and how is each important in living systems?
• Describe hydrogen bonds.
• What is pH? What is the pH scale? Be able to state whether a given pH is acidic, basic, or neutral. Relate the proton concentration to the pH scale.
• Compare and contrast the characteristics of acids and bases, and be able to recognize examples of each. What are buffers? Be able to recognize an example of a buffer.

• Describe the general characteristics of organic compounds. Why there are so many different possible types of organic molecules?
• Describe how both hydrolysis and condensation reactions form organic compounds.
• List the four different categories of biological molecules.
• Tell what a carbohydrate is and state two general functions for carbohydrates.
• Construct a table in which to make quick comparisons among the three kinds of carbohydrates - monosaccharides, oligosaccharides, and polysaccharides. Suggestion: Use the following column headings for your table - Kind of Carbohydrate, Description, Examples & Structure, and Functions.
• Monosaccharides. Describe a monosaccharide. Draw a generalized sketch of a five carbon sugar and beside it list two examples. Draw a similar sketch for a six carbon sugar and beside it list three examples.
• Disaccharides. Draw generalized sketches of a sucrose molecule.
• Polysaccharides. Describe a polysaccharide. Draw the generalized structure of the following molecules: cellulose, glycogen and starch. State the function of each molecule.
• Characterize and state the general functions of lipids.
• Fatty Acids (Building Blocks for Triglycerides and Phospholipids). Describe the structure of a fatty acid. Compare unsaturated and saturated fatty acids.
• Compare the structure and function of three kinds of lipids: triglycerides (neutral fats), phospholipids, and sterols.
• State the general functions of proteins in living organisms.
• Amino Acids, "building blocks" for Making Proteins. Describe the structure of an amino acid.
• Describe the primary structure, secondary structure, and tertiary structure of a protein molecule. Describe the quaternary structure found in some proteins.
• Denaturation Results in Structural Changes in Proteins. Describe the causes and the effects of denaturing a protein.
• Describe the characteristics of nucleotides, and state the classifications of nucleotides. Be able to recognize examples of the different classifications of nucleotides. 

• State the three parts of the cell theory.
• Explain why the size of cells is limited, relating your answer to the surface area to volume ratio and maintaining homeostasis.
• Identify the structure and functions of the major components of the prokaryotic cells.
• Identify the structure and functions of the major components of the eukaryotic cells.
• Describe the differences and similarities between prokaryotic and eukaryotic cells.
• Describe the structure and function of the following parts of the eukaryotic cell nucleus: chromosomes versus chromatin, nuclear envelope, and nucleolus.
• Describe the structure, composition and function of the following organelles, and be able to identify them in a picture or model: endoplasmic reticulum, Golgi body, vesicles, and lysosomes. How do these organelles interact with each other?
• Describe the structure, composition and function of the following organelles, and be able to identify them in a picture or model: ribosomes, mitochondria, chloroplasts, and central vacuole.
• Describe the function and composition of lysosomes.
• Explain the structure, composition and functions of the cytoskeleton.
• Describe the location, functions, and composition of the plasma membrane. Describe the location, functions, and composition of a cell wall, glycocalyx and extracelular matrix.
• Describe the differences between plant cells and animal cells. This description should include any structures, organelles, or functions that distinguish plant cells from animal cells.
• Trace the path of proteins synthesized in the rough endoplasmic reticulum as they are subsequently processed, modified, and sorted by the Golgi complex and then transported to specific destinations.
• Explain the main pieces of evidence for the endosymbiotic theory that modern chloroplasts and mitochondria are the remnants of engulfed ancient bacteria, thus giving rise to eukaryotic cells.

• Describe the structure and functions of cell membranes. Explain the fluid mosaic model of cell membranes.
• State the function of the following types of plasma membrane proteins: transport proteins, receptor proteins, recognition proteins, and adhesion proteins.
• Define the terms selectively permeable and concentration gradient. Describe each of the following processes in terms of concentration gradient, what structures are involved, and if energy is required: simple diffusion, passive transport (facilitated diffusion), active transport, endocytosis/exocytosis, pinocytosis, receptor-mediated endocytosis. State the types of substances that can be moved across cell membranes by each process. Give specific examples of active transport in cells.
• Contrast the physical processes of simple diffusion and osmosis with the carrier-mediated physiological processes by which materials are transported across cell membranes.
• What is osmosis? Explain the concept tonicity and describe the three possible tonicity conditions. What would happen to a cell placed in each possible condition?

• Define and give examples of potential energy and kinetic energy.
• Explain the first and second law of thermodynamics and discuss the implications of these laws as they relate to organisms.
• Explain where the energy within cells is physically located. What happens to much of this energy when it is converted from one form to another? Ultimately, where does most energy for life on earth come from?
• Describe the structure of ATP and where the energy, within an ATP molecule, is located. State how ATP is made and broken apart. What are the products of ATP being broken down? What is phosphorylation? Explain how the chemical structure of ATP allows it to transfer a phosphate group. Discuss the central role of ATP in the overall energy metabolism of the cell.
• Describe electron transport systems in terms of where they occur, the structures involved, and their functions. What generally follows the flow of electrons in electron transport systems? Why?
• Relate the transfer of electrons (or hydrogen atoms) to the transfer of energy.
• What are chemical reactions? Describe what it means for a reaction to be reversible, and what it means for a reaction to be at equilibrium. How do the amounts of products or reactants influence the predominant direction of a reaction? Explain the law of conservation of mass and how it relates to chemical reactions.
• Define metabolic pathway and describe the characteristics of a metabolic pathway. Define the roles of the following participants in metabolic pathways: substrates, intermediates, end-products, enzymes, cofactors, and transport proteins. Be able to recognize a given example as a cofactor.
• Describe specific ways enzymes are regulated.
• List and describe the basic features of enzymes.
• Explain how enzymes work by interacting with their substrates. This explanation should define the terms activation energy and active sites accurately. Explain how enzymes are deactivated. This explanation should define competitive inhibition and noncompetitive inhibition accurately. Explain how an enzyme lowers the required energy of activation for a reaction
• Explain the effects that temperature, pH, and salt concentration may have on enzymes.
• Describe the differences between endergonic and exergonic reactions. Which type of reaction is photosynthesis? Which type of reaction is cellular respiration?
• How do animals ultimately use the food they eat for energy? State the organ systems involved, how these organ systems operate together, how substances move from different locations in the body to individual cells, and what cells do in order to extract energy from certain molecules.
• Describe the process of glycolysis. What are starting materials and end-products of glycolysis? What else is necessary for glycolysis to occur? Where does glycolysis occur in cells? How many net ATP molecules are produced per molecule of glucose from glycolysis?
• Describe the process of the Krebs Cycle. What are the preparatory steps just before the Krebs Cycle? What are the starting materials and end-products of the Krebs Cycle? What needs to be input in order for the Krebs Cycle to occur? How many net ATP molecules are produced per molecule of glucose in the Krebs Cycle? Where does the Krebs Cycle occur in cells?
• Describe the process of electron transport phosphorylation. What are the starting materials and end-products of electron transport phosphorylation? What needs to be input in order for electron transport phosphorylation to occur? What role does oxygen play in electron transport phosphorylation? How many net ATP molecules are produced per molecule of glucose in telectron transport phosphorylation? Where does electron transport phosphorylation occur in cells?
• Describe the process of alcoholic fermentation. State the initial steps, the intermediates, and end products of alcoholic fermentation. What types of organisms use alcoholic fermentation? What commercial products are made by alcoholic fermentation?
• Describe the process of lactate fermentation. State the initial steps, the intermediates, and end products of lactate fermentation. What types of organisms use lactate fermentation? What commercial products are made by lactate fermentation? Explain how lactate fermentation relates to high-endurance exercise in humans.
• Explain how fats and proteins can be used as an energy source. State where they are stored, what they are broken down into, and how they can enter aerobic respiration.

• Compare and contrast the following types of organisms: photosynthetic autotrophs, chemosynthetic autotrophs, and heterotrophs. This comparison should include where each type of organism obtains its energy and carbon. Also, able to recognize a specific example of each type of organism.
• Explain why photosynthesis is important in ecosystems. State the materials that photosynthesis uses and what it ultimately produces. What groups of organisms carry out photosynthesis?
• Describe photosynthesis as a redox process.
• Describe the physical properties of light and explain the relationship between a wavelength of light and its energy.
• Describe the two distinct regions of the chloroplast. In which part of the chloroplast does each photosynthesis reaction take place?
• Describe the properties of pigments and their roles in photosynthesis. What specific pigments are found in plants, and what colors of light does each absorb/reflect?
• Describe the physical properties of light. How do these properties relate to our being able to see distinct colors? Interpret Absorbance versus Photosynthetic Activity graphs.
• Explain the steps of the light-dependent reactions of photosynthesis. Describe what occurs at each step; the structures, ions, and molecules involved (if any); and the role of energy in these reactions. Where in the chloroplast do these reactions take place? State the starting materials and the end-products of the light-dependent reactions.
• Explain the steps of the light-independent reactions of photosynthesis. Describe what occurs at each step; the structures, ions, and molecules involved; and the role of energy in these reactions. Where in the chloroplast do these reactions take place? State the starting materials and the end-products of the light-independent reactions.
• Distinguish between the light dependent reactions and carbon fixation reactions of photosynthesis.
• Describe the flow of electrons through photosystems I and II in the noncyclic electron transport pathway.
• Explain how a proton (H+) gradient is established across the thylakoid membrane and how this gradient functions in ATP synthesis.

• Describe the evidences that DNA is the molecule that carries the genetic information.
• Discuss the location, chemical composition, structure and function of DNA.
• Be able to utilize the following terms: primers, nucleotide, adenine, guanine, cytosine, thymine, purine, pyrimidine, sugar-phosphate backbone, phosphodiester linkage, covalent and hydrogen bonds within the DNA molecule. Direction of each of the DNA strands in the double helix.
• Explain how the two strands of DNA are antiparallel.
• Know the contribution of James Watson and Francis Crick.
• Describe the process and results of DNA replication. Include the role of helicase in producing the replication fork. Discuss the roles of primase, DNA polymerase and DNA ligase and how they function on the continuous (leading) strand and the discontinuous (lagging) strand.

• Summarize the early evidence indicating that most genes specify the structure of proteins.
• Outline the flow of genetic information in cells, from DNA to protein.
• Compare the structures of DNA and RNA.
• Explain why the genetic code is said to be redundant and virtually universal, and discuss how these features may reflect its evolutionary history.
• Compare the processes of transcription and DNA replication, identifying both similarities and differences.
• Identify the features of tRNA that are important in decoding genetic information and converting it into “protein language.”
• Explain how the ribosome functions in protein synthesis.
• Diagram the processes of initiation, elongation, and termination in protein synthesis.
• Compare prokaryotic and eukaryotic mRNAs, and explain the functional significance of their structural differences.
• Describe the differences in translation in prokaryotic and eukaryotic cells.

• What is a mutation?
• Name and explain the different classes of mutations that affect the base sequence of DNA, and explain the effects that each has on the protein produced.

• Explain why cells divide.
• Define the following terms in relation to eukaryotic cells: Chromatin, Chromosomes, Genes, Centromere, Centriolos, Spindle fibers, Homologous chromosomes, Chiasma, Nucelosome and Histones.
• Explain how histones are able to pack DNA.
• Describe how a karyotype is prepared and how it is used.
• Name and describe the stages of the cell cycle and the major events that happen in each phase, including Interphase (G1, S, G2) and M Phase (Mitosis (prophase, metaphase, anaphase, telophase) and cytokynesis).
• Name and describe similarities and differences between cytokynesis in animal and plant cells.
• Explain the terms diploid and haploid.
• Indicate the name and major events in each phase of meiosis. Be able to state whether a cell is diploid or haploid at every phase during meiosis.
• Compare and contrast the outcomes of mitosis and meiosis.
• Name and explain two meiotic events that contribute to genetic diversity.
• Indicate the chromosomal similarities and differences between human males and females.
• Advantages and disadvantages of sexual versus asexual reproduction.
• Explain how nondisjunction in meiosis is responsible for chromosome abnormalities such as Down syndrome, Klinefelter syndrome, and Turner syndrome.
• Distinguish among the following structural abnormalities in chromosomes: translocations, deletions, and fragile sites.
• State whether each of the following genetic defects is inherited as an autosomal recessive, autosomal dominant, or X-linked recessive: sickle cell anemia, cystic fibrosis, Huntington’s disease, and hemophilia A.

• Define the terms phenotype, dominant, recessive, allele, locus, homozygous, heterozygous, and genotype.
• Describe Mendel’s principles of segregation and independent assortment.
• Solve genetics problems involving monohybrid, dihybrid, and test crosses.
• Predict the outcomes of genetic crosses.
• Explain Mendel’s principles of segregation and independent assortment based on what we know about genes and chromosomes.
• Define linkage, and relate it to specific events in meiosis. Calculate linkage units
• Show how data from a test cross involving alleles of two loci can be used to distinguish between independent assortment and linkage.
• Discuss the genetic determination of sex and of X-linked genes in mammals.
• Explain some of the ways in which genes may interact to affect the phenotype; discuss how a single gene can affect many features of the organism simultaneously.
• Solve genetics problems involving incomplete dominance, codominance, multiple alleles, epistasis, and polygenes.