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BIO 281 Exam 2 Study Guide

by: Andrew Notetaker

BIO 281 Exam 2 Study Guide BIO 281

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This study guide covers all of the material from exam 1 and exam 2 that is required to know.
ConceptualApproachBioMajors I
Study Guide
Photosynthesis, Cellular Respiration, Thermodynamics, Proteins
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This 5 page Study Guide was uploaded by Andrew Notetaker on Monday October 10, 2016. The Study Guide belongs to BIO 281 at Arizona State University taught by Wright in Spring 2016. Since its upload, it has received 300 views. For similar materials see ConceptualApproachBioMajors I in Biology at Arizona State University.


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Date Created: 10/10/16
Exam 2 Study Guide Monday, September 12, 2016 3:08 PM Exam 1 Study Guide  Define evolution and apply your basic knowledge of evolution to explain how more complex molecules may have evolved overtime (continuing objective)  Evolution is the thought that organisms become more complex over time based off of previous ancestor and all living things evolved from a common ancestor. More complex molecules may have evolved overtime through mutations in DNA and reactions of molecules to create new more complex molecules.  Explain how and why the composition and properties of atoms… o facilitates chemical bonding,  Review properties of metals, non-metals and valence electrons (ionic bonds and covalent bonds) o impacts the types and properties of chemical bonds that form (describe types of chemical bonds, electronegativity)  Hydrogen bond, ionic bonds, covalent bonds. Hydrogen bonds are formed between a hydrogen atom and another atom, H 2 for example is a hydrogen bond. Ionic bonds are formed between metals and non metals because metals have a low electronegativity and non metals have a high electronegativity. Covalent bonds are formed between two non metals. o influences the structures and properties of more complex molecules (e.g., polarity)  Water is a polar molecule. Polar molecules act this way due to the uneven distribution of electrons. Polar molecules dissolve in water easily because the two molecules (H2O and the other polar molecule) are both polar and can easily form hydrogen bonds and so the molecules are pulled apart.  Predict how and explain why intra and intermolecular forces (including hydrophobicity and bonding) shape the structures of molecules and or their interactions with themselves and other molecules (Not just with DNA, but RNA and proteins!)  Intra and intermolecular forces such as hydrophobicity, hydrophilicity and chemical bonding all contribute to the shape of molecules because hydrophobic molecules tend to stay away from molecules so for example, a protein will fold to prevent its hydrophobic parts from touching water. These folds contribute to the overall shape of the molecule.  Determine the properties/locations of a molecule/structure/amino acid when given information about how said structures interacts with other molecules/water (and vice versa)  Review amino acids and their properties  Describe the structure and basic characteristics of DNA, including the structure of the monomers of DNA (deoxyribonucleotides)  DNA is made up of monomers of nucleic acids, Adenine, Thymine, Cytosine and Guanine  Thymine and Cytosine are pyrimidines and have one ring  Adenine and Guanine are purines and have two rings  Explain if DNA could have been the initial spark of life!  DNA cannot function as a catalyst, but can only store information. RNA is more of a plausible initial spark.  Correctly generate a complementary sequence of DNA, including generating the sequence in the appropriate direction and labeling 3’ and 5’ sides.  Describe the process of DNA replication.  DNA unwinds and RNA primase is added by RNA polymerase. DNA polymerase adds nucleotides successively to the 3' end until it encounters the next RNA primer and a different polymerase removes the primer and DNA ligase connects the two strands together.  Apply your understanding of DNA replication to determine of the Meselson & Stahl hypothesis was supported.  DNA replicates semiconservatively due to the results of the experiment having two different types of DNA consisting of N and N .4  Describe the structure and basic characteristics of RNA, including the structure of the monomers of RNA (ribonucleotides)  RNA is made up of ribonucleic acids. Uracil replaces Thymine. RNA is a single strand of nucleic acids complementary to a template strand of DNA.  Correctly generate a sequence of RNA, including generating the sequence in the appropriate direction and labeling 3’ and 5’ sides  Describe the process of transcription  Activator proteins bind to enhancers, general transcription factors and the mediator complex are all brought into close proximity to RNA polymerase to start transcription. Promoters are the start site of transcription and terminators are the end of transcription.  Explain if RNA could have been the initial spark of life!  RNA both stores information and can serve as a catalyst so therefore it could be the initial spark of life Bio 281 Lecture Page 1  Correctly generate the primary sequence of a protein (next time we’ll add on information as to why mutations in DNA don’t always produce changes in protein structure and function)  Amino acids are the complements to a strand of mRNA  Describe the process of translation Initiation requires a number of proteininitiation factors that bind to the mRNA. In eukaryotes, one group of initiation factors binds to the 5' cap that is added to the mRNA during processing. These recruit the small subunit of the ribosome, other factors bring up tRNA with Met. The complex scans mRNA until it encounters the first AUG triplet. After AUG is encountered, the large ribosomal subunit joins the complex and the initiation factors are released, and the next tRNA joins the ribosome at the A site. A bond connects Met to the tRNA which is then transferred to the amino group, forming a peptide bond. After this the uncharged tRNA shifts to the E site and is released into the cytoplasm. Ribosome movement along mRNA and formation of peptide bonds require energy from proteins called elongation factors. Elongation continues until a stop codon is reached, then a proteinrelease factor binds to the A site of the ribosome. This causes the bond connecting the protein to the tRNA to break, creating the carboxyl terminus and completing the chain. Once finished, the small and large ribosomal units disassociate from the mRNA and each other. In eukaryotes, initiation complex forms at the 5' cap and scans until AUG is encountered. In prokaryotes, there is no 5' cap therefore the initiation complex is formed at one or more internal sequences present in mRNA known as the Shine-Dalgarno sequence. It is followed by an AUG codon eight nucleotides downstream that serves as the initiation.  Apply knowledge of DNA replication, transcription, and or translation to predict how a disruption to any one of these processes will impact replication, transcription and or translation (including protein structure and function) and/or determine how one might alleviate the symptoms of the disruptive event.  Review case studies from recitation (diphtheria causes an impact of protein production which affects transcription eventually)  Describe the monomers of proteins (amino acids) and their basic characteristics, including how two amino acids bond (these are on the slides on your handout)  Proteins form when amino acids bond covalently called peptide bonds. The carboxyl group bonds to the amino group.  Describe / be able to identify the various structures of a protein and explain how and why intra/intermolecular forces (e.g., hydrogen bonding, hydrophobicity, etc.) shape the structure of molecules (specifically proteins) and their interactions with other molecules  Proteins fold based off of their bonding between molecules, amino acids determine the folds which determine function. When fully folded, some proteins contain pockets with positively or negatively charged side chains at just the right positions to trap small molecules; others have surfaces that can bind another protein or a sequence of nucleotides in DNA or RNA; some form rigid rods for structural support; and still others keep their hydrophobic side chains away from water molecules by inserting into the cell membrane.  Predict how and explain why perturbations (e.g., changing amino acids) impacts protein folding and function  Changing amino acids change the structure because different amino acids interact differently with one another. This is concluded because different proteins have different functions which is determined by structure.  Generate and interpret figures, including writing figure legends/captions.  Figure legends describe the content of a chart or graph  Make predictions and interpret experimental evidence to determine if a hypothesis is supported (for example what we did with the Meselson & Stahl Experiment)  Context based What will you be expected to do? Note – These are the learning objectives I use to craft exam questions. So I try to ask questions that explicitly get at these different objectives. ~66 – 75% of the test will cover the following dates: 9/13 – 10/12  (On your own) Describe the monomers of proteins (amino acids) and their basic characteristics, including how two amino acids bond (these are on the slides on your handout) Review amino acid chart, amino acids bond through peptide bonds and through their R-groups. Bio 281 Lecture Page 2  Describe / be able to identify the various structures of a protein and explain how and why intra/intermolecular forces (e.g., hydrogen bonding, hydrophobicity, etc.) shape the structure of molecules (specifically proteins) and their interactions with other molecules Hydrophobic amino acids are typically in the interior of proteins; hydrophilic amino acids are found along the exterior of a protein. These folds contribute to the structure of the protein.  Predict how and explain why perturbations (e.g., changing amino acids) impacts protein folding, stability and function. By changing amino acids, this could possible affect protein folding, rigidity and function, for example if a hydrophilic amino acid was changed to a hydrophobic amino acid, the protein would be folded at this amino acid.  Explain why flexibility is important for activity of enzymes Flexibility affects catalytic activity of an enzyme. The more flexible an enzyme is, the better the activity of the enzyme.  (on your own) Define/describe catabolic, anabolic, energy, kinetic energy, potential energy, chemical energy, ATP, 1st and 2nd law of thermodynamics, exothermic, endothermic, Gibbs free energy, exergonic, endergonic, enthalpy, enzymes, transition state, activation energy Catabolic- The breakdown of molecules which produce energy. Anabolic- The assembly of bigger molecules which requires an input of energy. Energy- The capacity to do work Kinetic energy- The energy of motion Potential energy- Stored energy, which can be a form of potential chemical energy or kinetic energy. Chemical energy- Potential energy stored in the chemical bonds between pairs of atoms ATP- Adenine Tri-phosphate is the energy molecule which drives chemical processes, the main energy product of cellular respiration st 1 law of thermodynamics- Energy is conserved, energy is neither created nor destroyed. nd 2 law of thermodynamics- Energy transformations result in an increase in disorder in the universe, entropy increases, ability to do work decreases. Exothermic- A reaction that releases energy as heat Endothermic- A reaction that absorbs energy as heat Gibbs free energy- The amount of energy available to do work Exergonic- Energy is released from a reaction, - delta G also spontaneous Endergonic- Energy is absorbed from a reaction, positive delta G non spontaneous Bio 281 Lecture Page 3 Endergonic- Energy is absorbed from a reaction, positive delta G non spontaneous Enthalpy- The total amount of energy of a reaction Enzymes- Proteins that decrease the activation energy of a reaction which speeds up a reaction Transition state- The intermediate stage between reactants and products Activation energy- The energy required to reach the transition state.  Apply knowledge of above concepts to determine if and explain why a reaction will occur spontaneously or not. If a reaction has products with less energy than the reactants, the reaction will occur spontaneously.  Apply an understanding of electronegativity and its impact on electron positions to determine the potential energy of reactants and products; Determine if reactants and products increase or decrease entropy. Electronegativity is the tendency of an atom to attract electrons. The greater electronegativity, the lower the potential energy because it takes more energy to break these bonds.  Explain/illustrate how and why enzymes catalyze chemical reactions, including how enzymes impact delta G values and the role of R-groups in facilitating this process. Enzymes lower activation energy which catalyzes reactions, this does not affect the delta G values of reactions. R-groups are the groups which the enzyme bond to.  Describe what energetic coupling is and explain how cells can facilitate non-spontaneous reactions by harnessing the free energy released from spontaneous reactions. Predict if a reaction can occur given information about other reactions that may facilitate it via energetic coupling. Energetic coupling puts non-spontaneous reactions with spontaneous reactions to drive these non-spontaneous reactions.  Apply your understanding of enzymes and thermodynamics to determine simple reaction energetics (i.e. anabolic/catabolic, endergonic/exergonic, entropy, Gibbs Free Energy) Review properties of these reactions and definitions  Make predictions and interpret experimental evidence Review case studies  Trace and explain the flow of energy and matter through cellular respiration AND photosynthesis, including connecting the two processes o Describe the inputs and outputs of the pathways in cellular respiration and photosynthesis o Indicate which outputs contain energy and mass in cellular respiration and photosynthesis o Explain why cellular respiration and photosynthesis illustrates the laws of the conservation of energy and matter Review recitation activities from week 8  For cellular respiration - Describe how ATP synthesis occurs, how the electron transport chain works, how the citric acid cycle works, how glycolysis works Glycolysis Free energy is raised by adding phosphate groups Electron carriers are formed from the raised potential energy from the phosphate groups Two pyruvate and two ATP are produced from substrate level phosphorylation Stage 2: Pyruvate Oxidation Pyruvate is oxidized by giving an electron to NADH, NADH is reduced Stage 3: Krebs cycle Acetyl-CoA forms NADH, FADH and AT2 More NADH and also FADH produc2ion occurs in the TCA cycle and in pyruvate processing. NADH is formed by redox reactions, oxidizing molecules in the TCA and reducing NAD to NADH.+ Free energy released from complete oxidation of a glucose molecule to carbon dioxide Most of the mass lost is in CO 2 In ETC, electrons are transferred via a series of redox reactions from one complex to the next until they are accepted by oxygen (O ). 2ater is formed as a result of O accep2ing electrons. The energy released as a consequence of these redox reactions is used to pump H across the membrane. ATP synthase uses the proton gradient to drive the synthesis of ATP (transform energy).  For cellular respiration - Apply your understanding of cellular respiration to predict how and explain why disturbances impact cellular respiration Review Cyanide case study. If one process shuts down, eventually this will affect all processes.  For photosynthesis – describe how the synthesis of ATP and NADPH occurs, including the roles of the photosynthetic electron transport chain, water, proton gradients, and redox reactions. Describe how the Calvin cycle works, including the roles of CO2, ATP and NADPH. Bio 281 Lecture Page 4 ATP and NADPH. Carbon dioxide is taken by the Calvin cycle to be bound with another carbon molecule, ATP breaks down to provide energy and NADPH is reduced to form NADP + H a three carbon molecule is then exported and the other is used to regenerate the original starting molecules to start the Calvin cycle. Then, in the PETC, water is split to form O and it creates a proton gradient in the thylakoid lumen to power ATP synthase. 2 Bio 281 Lecture Page 5


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