BIOL 1406 EXAM 2 REVIEW

BIOL 1406 – Exam 2 Study Guide Note: this guide is designed to help organize your studying for exam 2. It is not a comprehensive list of all topics presented in the chapters. Reading through the chapters, completing the homework, and utilizing the study area on (including self-examinations and practice quizzes) will greatly benefit you as well. Chapter 5 I) Before beginning this chapter, you should be able to: A) Explain the bonding behavior of a carbon atom (see Concept 4.2) B) Identify the important biological functional groups (see Figure 4.9) C) Understand the chemical nature of functional groups (see Figure 4.9) 1) Specifically whether or not a particular group is polar or nonpolar II) Concept 5.1 – Macromolecules are polymers A) Polymers are made up of monomers 1) What type of reaction joins monomers into polymers? Dehydration synthesis or condensation reaction) 2) What type of reaction breaks apart polymers into monomers? 3) These compounds are made up of what type of bonds? 4) Provide examples of weak interactions (hydrogen bonds) that occur between individual macromolecules B) Be able to identify which macromolecules are polar or nonpolar III) Concept 5.2 – Carbohydrates A) What are carbohydrates? What type of bonds link these monomers together? (general name and specific name) B) Define monosaccharide, disaccharide, and polysaccharide 1) Identify the two ways in which monosaccharides are classified C) Polysaccharides 1) Examples and function of storage polysaccharides 2) Examples and functions of structural polysaccharides (a) What is different about the monomers between the two types of polysaccharides? IV) Concept 5.3 – Lipids A) Are lipids macromolecules? Why or why not? B) Fats 1) Describe the structure/characteristics of the components that make up fats (a) Glycerol (b) Fatty acid tail Saturated Unsaturated 2) What is the major function of fats? C) Phospholipids 1) Be able to describe the structure of a phospholipid (a) Polar vs nonpolar regions? 2) How do phospholipids organize in aqueous solutions? Why is this important? D) Steroids 1) Are steroids polar or nonpolar? V) Concept 5.4 – Proteins A) Proteins have many functions, be familiar with them (Figure 5.13) B) Amino acids make up proteins 1) Each amino acid includes what components? 2) Which component determines an amino acid’s physical/chemical characteristics? 3) Be able to identify polar, nonpolar, and charged amino acids (are charged amino acids polar or nonpolar?) C) Amino acids are linked together into polymers in what type of bond? (general name and specific name) D) What determines the function of a protein? E) Identify the four levels of protein structure (Figure 5.18) 1) How are these levels formed? In other words, what types of bonds are found in each level? VI) Concept 5.5 – Nucleic Acids A) What is gene expression? B) What are the components of nucleotides? 1) What parts are found in RNA only? DNA only? Both? 2) Purine vs pyrimidine C) What does it mean when we describe DNA as being directional (5’ 3’)? D) How is DNA formed? 1) What does it mean when we say it is antiparallel? 2) How are the strands held together? Chapter 6 Note: the organelle chart is very useful for this chapter I) Before beginning this chapter, you should be able to: A) Explain the role of emergent properties in biological systems (see Concept 1.1) B) Describe the structure of a phospholipid (see Concept 5.3) C) List the three domains of life and differentiate between prokaryotes and eukaryotes (see Concept 1.2) D) Describe the process of gene expression (see Concept 1.1) II) Concept 6.1 – Microscopy A) Describe the important parameters of a microscope: 1) Magnification 2) Resolution 3) Contrast B) Identify the strengths/weaknesses of the types of microscopy. When would you use one over the other? 1) Light microscopy 2) Electron microscopy (a) Scanning EM (b) Transmission EM C) Figure 6.2 – size range of cells 1) Have a general idea of what sizes we can see with our eyes, with LM, with EM 2) Know relative sizes of cell components, cells, etc. III) Concept 6.2 – Prokaryotic vs. Eukaryotic A) Know the properties of prokaryotic and eukaryotic cells 1) Differences between the two 2) Commonalities between the two B) Be able to identify structures on a prokaryotic cell (Figure 6.5) C) Know the function of the plasma membrane 1) Understand surface to volume ratio – when a cell increases in volume, does its surface area increase proportionally or not? 2) Why is surface area important? D) Identify structure and function of organelles in Eukaryotic cells (Figure 6.8) IV) Concept 6.3 – Eukaryotic genetic information A) Know the structure and function of the nucleus 1) Nuclear envelope 2) Nuclear pores 3) Nuclear lamina 4) Nucleoulus B) Chromosomes are made up of DNA and tightly packed into chromatin C) Know the composition and function of a ribosome 1) Free vs. bound ribosomes V) Concept 6.4 – The Endomembrane system A) Know the 6 members of the endomembrane system B) Endoplasmic reticulum – know its structure 1) Smooth ER (a) Functions (b) Which cells are likely to have extensive Smooth ER? 2) Rough ER (a) Functions (b) How are secretory proteins moved from the ER C) The Golgi apparatus 1) Function 2) Movement of proteins through the Golgi (a) Cisternal maturation model D) Lysosomes 1) Structure and function 2) Phagocytosis vs autophagy (Figure 6.13) E) Vacuoles 1) Structure 2) Function (a) Food vacuole (b) Contractile vacuole (c) Central vacuole F) Figure 6.15 VI) Concept 6.5 – Mitochondria and Chloroplasts A) Know the evolutionary origins 1) Endosymbiont theory – facts that support this theory B) Mitochondria 1) Structure (a) Membranes (b) Cristae (c) Matrix 2) Function C) Chloroplasts 1) Structure (a) Membranes (b) Stroma What is in the stroma? (c) Thylakoids 2) Function D) Peroxisomes 1) Structure 2) Function (a) Why is it important that a peroxisome is compartmentalized from the rest of the cytosol? VII) Concept 6.6 – Cytoskeleton A) What is the cytoskeleton? B) Components of the cytoskeleton and their main functions 1) Microtubules 2) Microfilaments 3) Intermediate filaments VIII)Concept 6.7 – Extracellular components A) Plant cell walls vs. an Extracellular Matrix (Figure 6.28) 1) Structure – common components 2) Function B) Cell Junctions – structure and function (Figure 6.30) (what is in plants, what is in animals?) 1) Plasmodesmata 2) Tight Junctions 3) Desmosomes 4) Gap Junctions Chapter 7 I) Before beginning this chapter, you should be able to: A) Explain hydrophilic and hydrophobic properties of molecules (see Concept 3.2) B) Describe the structure of a phospholipid (see Concept 5.3) C) Describe the structure of prokaryotic and eukaryotic cells (see Concept 6.2 and Figures 6.5 and 6.8) D) Explain the basic idea of potential energy (see Concept 2.2) II) Concept 7.1 – Cellular membranes A) What components are found in a membrane? B) Be able to describe the fluid mosaic model C) What factors influence membrane fluidity? D) Describe both integral and peripheral proteins 1) What are the functions that membrane proteins carry out? III) Concept 7.2 – Selective permeability A) What does selective permeability mean? B) What types of molecules can freely move across the membrane? What types of molecules require help in the form of transport proteins? C) What are the different types of transport proteins and how do they function? 1) What is the differences and similarities between the two types? IV) Concept 7.3 – Passive diffusion A) What is diffusion? 1) Describe a concentration gradient 2) Is energy needed? B) Describe the process of osmosis 1) In a system with two compartments separated by a membrane, be able to: (a) Predict the movement of water across the membrane depending on the environments (b) Know what happens to the concentration of solutes as water moves across a membrane 2) What happens to cells in isotonic, hypertonic, and hypotonic environments? C) Define facilitated diffusion, be able to identify examples of this V) Concept 7.4 – Active diffusion A) Describe the process of active transport B) Describe how the Sodium-Potassium pump works (Figure 7.15) C) Be able to identify differences between passive and active transport (Figure 7.16) D) What is membrane potential? 1) Define an electrochemical gradient and how that can contribute to membrane potential E) What is cotransport? Where is the energy coming from? VI) Concept 7.5 – Bulk Transport A) Define endocytosis vs. exocytosis B) Describe the different types of endocytosis (Figure 7.19) C) Be able to explain how the process of endocytosis can rejuvenate or remodel a membrane Chapter 8 I) Concept 8.1 – Metabolism A) Define metabolism and metabolic pathways 1) What are catabolic pathways? 2) What are anabolic pathways? B) What is energy? 1) Define the 4 types of energy and be able to provide examples of each (a) How is heat related to thermal energy? (b) How is chemical energy related to potential energy? C) Laws of thermodynamics 1) What is a system, what are the surroundings? 2) Define the 1st law of thermodynamics (a) What happens to energy as it is being used? (b) Describe a process that exemplifies the 1st law 3) Define the 2nd law of thermodynamics (a) What is entropy? (b) What is a spontaneous process? Are they always fast? II) Concept 8.2 – Free energy A) Define free energy 1) What components go into calculating free energy? 2) When does free energy get released? (Refer to figure 8.6) (a) What is this called? 3) When does free energy need to be supplied? (a) What is this called? III) Concept 8.3 – ATP A) What are the 3 main kinds of work a cell does? B) What is energy coupling and why is it advantageous? C) What is the structure of ATP? (Figure 8.9) 1) Which bonds are considered “high energy bonds”? (a) What does this actually mean? D) Describe how ATP hydrolysis works to power reactions 1) Chemically, as well as in relation to transport and mechanical work E) How is energy regenerated? IV) Concept 8.4 – Enzymes A) What is an enzyme? What type of macromolecule is it? B) What is activation energy? Describe how it works molecularly 1) What is the most often method of supplying activation energy? 2) Why is this method not appropriate for cells? C) What do enzymes do for a particular reaction? D) Define the following terms as related to enzymes. In addition, be able to draw the catalytic cycle of an enzyme (figure 8.16) 1) Substrate 2) Enzyme Substrate Complex 3) Active Site 4) Induced fit 5) Products E) In what ways can an enzyme lower EA? F) Define how the following conditions affect an enzyme. Discuss what “optimal conditions” means. 1) Temperature 2) pH 3) Cofactors 4) Enzyme inhibitors (a) Competitive Can this effect be overcome? (b) Noncompetitive Can this effect be overcome? V) Concept 8.5 – Regulation A) Why is it important for enzymes to be regulated? B) What is allosteric regulation? C) What is feedback inhibition?