BIO 221 Exam 2 Final Study Guide PDF

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Filled out study guide from exam 2...

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Biology 221 NON-CUMULATIVE Final Exam Study Guide Chapter 13 (Metabolic Diversity): • Phototrophic way of life: • know key terms listed in lecture slides o Photosynthesis: the conversion of light energy to chemical energy ▪ Phototrophs • Most are photoautotrophs o Requires ATP production, CO 2 reduction

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▪ Requires chlorophylls o Photoautotrophy ▪ Oxidation H2O produces O2 ▪ Oxygen not produced (anoxygenic photosynthesis) ▪ Similarities & Differences b/w oxygenic and anoxygenic photosynthesis o Anoxygenic photosynthesis is found in four phyla of Bacteria ▪ Photosynthesis apparatus is embedded in membranes ▪ Electron transport reactions occur in the reaction center of anoxygenic phototrophs o Oxygenic photosynthesis ▪ Oxygenic phototrophs use light to generate ATP and NADPH ▪ The two light reactions are called photosystem I and photosystem II ▪ Importance/general features of photosynthetic pigments (chlorophyll, bacteriochlorophyll, accessory pigments), examples o Chlorophyll ▪ Organisms must produce some form of chlorophyll (or bacteriochlorophyll) to be photosynthetic ▪ Chlorophyll is related to porphyrins ▪ Number of different types of chlorophyll exist ▪ Different chlorophylls have different absorption spectra ▪ Cyanobacteria produce chlorophyll a ▪ Prochlorophytes produce chlorophyll a and b ▪ Anoxygenic phototrophs produce bacteriochlorophylls ▪ Reaction centers participate directly in the conversion of light energy to ATP ▪ Antenna pigments funnel light energy to reaction centers o Carotenoids and phycobilins ▪ Phototrophic organisms have accessory pigments in addition to chlorophyll, including carotenoids and phycobiliproteins ▪ Carotenoids • Always found in phototrophic organisms

Typically yellow, red, brown, or green Energy absorbed by carotenoids can be transferred to a reaction center • Prevent photooxidative damage to cells Phycobiliproteins are main antenna pigments of cyanobacteria and red algae • Form into aggregates within the cell called phycobilisomes • Allow cell to capture more light energy than chlorophyll alone • •

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o Overall features of photoexcitation/electron flow in anoxygenic and oxygenic photosynthesis. Should know what photosystems are involved, how many in each type of photosynthesis, examples of bacteria that do each. ▪ Reducing power for CO 2 fixation comes from reductants present in the environment (i.e., H 2S, Fe2+, or NO2–) • Requires reverse electron transport for NADH production in purple phototrophs • Electrons are transported in the membrane through a series of proteins and cytochromes (Figure 13.12b) ▪ For a purple bacterium to grow autotrophically, the formation of ATP is not enough • Reducing power (NADH) is also necessary • Reduced substances such as H2S are oxidized, and the electrons eventually end up in the "quinone pool" of the photosynthetic membrane

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• Oxygenic photosynthesis • "Z scheme" of photosynthesis (Figure 13.14)

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Photosystem II transfers energy to photosystem I ATP can also be produced by cyclic photophosphorylation

• Calvin cycle, reverse citric acid & hydroxyproprionate pathways: importance of each, what example organisms do each pathway, major products formed, importance of ATP energy/reducing power in these pathways. Don’t need to memorize every step of these cycles. o The Calvin cycle ▪ Named for its discoverer, Melvin Calvin ▪ Fixes CO2 into cellular material for autotrophic growth ▪ Requires NADPH, ATP, ribulose bisphophate carboxylase (RubisCO), and phosphoribulokinase ▪ 6 molecules of CO2 are required to make 1 molecule of glucose

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▪ o Green sulfur bacteria use the reverse citric acid cycle to fix CO2 (Figure 13.19a) o Green nonsulfur bacteria use the hydroxypropionate pathway to fix CO2

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▪ ▪ For the lecture sections on chemolithotrophy, fermentations, anaerobic respirations: know what these are, general strategies employed in each case & terms presented in class. I will NOT ask you to memorize/recite pathways. Emphasis will be placed on understanding general metabolic strategies used (i.e., what is being oxidized/reduced, how is ATP generated and the like). o Chemolithotrophs are organisms that obtain energy from the oxidation of inorganic compounds ▪ Mixotrophs are chemolithotrophs that require organic carbon as a carbon source ▪ Many sources of reduced molecules exist in the environment ▪ The oxidation of different reduced compounds yields varying amounts of energy o Anaerobic H2-oxidizing Bacteria and Archaea are known ▪ Catalyzed by hydrogenase ▪ Calvin cycle and hydrogenase enzymes allow chemolithotrophic growth o Oxidation of Reduced Sulfur Compounds ▪ Many reduced sulfur compounds are used as electron donors ▪ Discovered by Sergei Winogradsky (ayooo like the columns) ▪ H2S, S0, S2O3– are commonly used ▪ One product of sulfur oxidation is H+, which lowers of the pH of its surroundings ▪ Sox system oxidizes reduced sulfur compounds directly to sulfate ▪ Usually aerobic, but some organisms can use nitrate as an electron acceptor ▪ Electrons from reduced sulfur compounds reach the electron transport system • Transported through the chain to O2

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Generates a proton motive force that leads to ATP synthesis by ATPase

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▪ o Honestly better to just refer to the slides for the rest of this. Starts around slide 41 Chapter 7 (Metabolic Regulation & Two-component signaling systems): •

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Different modes of enzyme regulation: allosteric effects, covalent modification (examples covered in class) o Two major levels of regulation in the cell: ▪ One controls the activity of preexisting enzymes • Post-translational regulation • Very rapid process (seconds) ▪ One controls the amount of an enzyme • Regulates level of transcription • Regulates translation • Slower process (minutes) o DNA binding proteins that regulate transcription (i.e., helix-turn-helix, zinc finger) ▪ Most DNA-binding proteins interact with DNA in a sequencespecific manner ▪ Specificity provided by interactions between amino acid side chains and chemical groups on the bases and sugar –phosphate backbone of DNA ▪ Major groove of DNA is the main site of protein binding

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Inverted repeats frequently are binding site for regulatory proteins Homodimeric proteins: proteins composed of two identical polypeptides Protein dimers interact with inverted repeats on DNA ▪ Each of the polypeptides binds to one inverted repeat Several classes of protein domains are critical for proper binding of proteins to DNA ▪ Helix-turn-helix (Figure 7.4) • First helix is the recognition helix • Second helix is the stabilizing helix • Many different DNA-binding proteins from Bacteria contain helix-turn-helix • lac and trp repressors of E. coli Classes of protein domains ▪ Zinc finger • Protein structure that binds a zinc ion • Eukaryotic regulatory proteins use zinc fingers for DNA binding ▪ Leucine zipper • Contains regularly spaced leucine residues • Function is to hold two recognition helices in the correct orientation Multiple outcomes after DNA binding are possible 1. DNA-binding protein may catalyze a specific reaction on the DNA molecule (i.e., transcription by RNA polymerase) 2. The binding event can block transcription (negative regulation) 3. The binding event can activate transcription (positive regulation)

Examples of negative (Arg & Lac operons) and positive (maltose operon) control of transcription, features associated with each o Negative Control ▪ Repression: preventing the synthesis of an enzyme in response to a signal • Enzymes affected by repression make up a small fraction of total proteins • Typically affects anabolic enzymes (e.g., arginine biosynthesis)

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• Induction: production of an enzyme in response to a signal • Typically affects catabolic enzymes (e.g., lac operon) • Enzymes are synthesized only when they are needed o No wasted energy

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▪ o Positive Control ▪ Positive control: regulator protein activates the binding of RNA polymerase to DNA ▪ Maltose catabolism in E. coli • Maltose activator protein cannot bind to DNA unless it first binds maltose ▪ Activator proteins bind specifically to certain DNA sequence • Called activator-binding site, not operator

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Promoters of positively controlled operons only weakly bind RNA polymerase Activator protein helps RNA polymerase recognize promoter • May cause a change in DNA structure • May interact directly with RNA polymerase Activator-binding site may be close to the promoter or be several hundred base pairs away

Genes for maltose are spread out over the chromosome in several operons • Each operon has an activator-binding site • Multiple operons controlled by the same regulatory protein are called a regulon Regulons also exist for negatively controlled systems

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▪ Terms to know: effectors/types, repressor, co-repressor, activator, etc. o Inducer: substance that induces enzyme synthesis o Corepressor: substance that represses enzyme synthesis o Effectors: collective term for inducers and corepressors o Effectors affect transcription indirectly by binding to specific DNAbinding proteins ▪ Corepressor molecules bind to the repressor to allosterically regulate the repressor protein ▪ Allosteric repressor becomes active and binds to region of DNA near promoter called the operator o Global control/examples/features of each: lac operon (catabolite repression). o Global control systems: regulate expression of many different genes simultaneously o Catabolite repression is an example of global control ▪ Synthesis of unrelated catabolic enzymes is repressed if glucose is present in growth medium (Figure 7.13) ▪ lac operon is under control of catabolite repression ▪ Ensures that the "best" carbon and energy source is used first o Diauxic growth: two exponential growth phases

o o Cyclic AMP and CRP ▪ In catabolite repression, transcription is controlled by an activator protein and is a form of positive control (Figure 7.15) ▪ Cyclic AMP receptor protein (CRP) is the activator protein ▪ Cyclic AMP is a key molecule in many metabolic control systems • Derived from a nucleic acid precursor • Is a regulatory nucleotide

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o Two-component signal transduction systems: general features/components of these (i.e., sensor kinase, response regulator). o In prokaryotes, signal transduction typically involves twocomponent regulatory systems. o Include: ▪ a membrane-integrated sensor His kinase protein ▪ a cytoplasmic response regulator protein.

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o The activity of the response regulator depends on its state of phosphorylation. o YOU DON’T NEED TO KNOW details of two-component system regulating bacterial chemotaxis, components involved, importance of phosphorylation & methylation (adaptation).

Chapter 8 (Viruses) and on-line lecture on Coronaviruses: • General characteristics of viruses o Viral genomes ▪ Either DNA or RNA genomes ▪ Some are circular, but most are linear o • Terms: virion, capsid, capsomere, nucleocapsid, naked vs. enveloped viruses. o Virus particle (virion): extracellular form of a virus ▪ Exists outside host and facilitates transmission from one host cell to another ▪ Contains nucleic acid genome surrounded by a protein coat and, in some cases, other layers of material ▪ Some virions contain enzymes critical to infection • Lysozyme o Makes hole in cell wall o Lyses bacterial cell ▪ Nucleic acid polymerases ▪ Neuraminidases • Enzymes that cleave glycosidic bonds • Allows liberation of viruses from cell ▪ o Capsid: the protein shell that surrounds the genome of a virus particle ▪ Composed of a number of protein molecules arranged in a precise and highly repetitive pattern around the nucleic acid o Capsomere: subunit of the capsid ▪ Smallest morphological unit visible with an electron microscope o Nucleocapsid: complete complex of nucleic acid and protein packaged in the virion ▪ Nucleocapsids are constructed in highly symmetric ways • Helical symmetry: rod-shaped viruses (e.g., tobacco mosaic virus) o Length of virus determined by length of nucleic acid o Width of virus determined by size and packaging of protein subunits • Icosahedral symmetry: spherical viruses (e.g., human papillomavirus; Figure 8.4)

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o Most efficient arrangement of subunits in a closed shell o Enveloped virus: virus that contains additional layers around the nucleocapsid • Lipid bilayer with embedded proteins ▪ Envelope makes initial contact with host cell ▪ o Classification of viruses: what this is based on. o Viruses can be classified on the basis of the hosts they infect ▪ Bacterial viruses (bacteriophages) ▪ Archaeal viruses ▪ Animal viruses ▪ Plant viruses ▪ Other viruses o Examples of early, mid, late genes. o Early proteins ▪ Enzyme for the synthesis and glucosylation of the T4 base hydroxymethylcytosine ▪ Enzymes that function in T4 replisome ▪ Proteins that modify host RNA polymerase o Middle proteins ▪ Additional proteins that modify host RNA polymerase o Late proteins ▪ Synthesized later ▪ Include proteins of virus coat ▪ Typically structural components ▪ Synthesized in larger amounts o How viruses are quantified (plaque assay) o Titer: number of infectious units per volume of fluid o Plaque assay: analogous to the bacterial colony; one way to measure virus infectivity (Figure 8.8) ▪ Plaques are clear zones that develop on lawns of host cells • Lawn can be bacterial or tissue culture (Figure 8.9) • Each plaque results from infection by a single virus particle

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o o Plating efficiency is used in quantitative virology ▪ The number of plaque-forming units is almost always lower than direct counts by electron microscopy • Inactive virions • Conditions not appropriate for infectivity o Features/steps of virus replication (associated terms: latent period, eclipse, maturation period) o Phases of viral replication (Figure 8.6) ▪ Attachment (adsorption) of the virus to a susceptible host cell ▪ Entry (penetration) of the virion or its nucleic acid ▪ Synthesis of virus nucleic acid and protein by cell metabolism as redirected by virus ▪ Assembly of capsids and packaging of viral genomes into new virions (maturation) ▪ Release of mature virions from host cell o Virus replication is typically characterized by a one-step growth curve o Latent period: eclipse + maturation o Burst size: number of virions released

o Virus attachment: what factors determines host range/tropism o Attachment of virion to host cell is highly specific

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Requires complementary receptors on the surface of a susceptible host and its infecting virus ▪ Receptors on host cell carry out normal functions for cell (e.g., uptake proteins, cell-to-cell interaction) ▪ Receptors include proteins, carbohydrates, glycoproteins, lipids, lipoproteins, or complexes o The attachment of a virus to its host cell results in changes to both virus and cell surface that facilitate penetration o Permissive cell: host cell that allows the complete replication cycle of a virus to occur o Importance of restriction enzymes in bacterial host cell defense against bacteriophage Bacteriophage: types (virulent/lytic & temperate) and examples (i.e., T4 phage, lambda phage) covered in class. o Virulent mode: viruses lyse host cells after infection o Temperate mode: viruses replicate their genomes in tandem with host genome and without killing host ▪ Virus can also be lytic o Temperate viruses: can undergo a stable genetic relationship within the host ▪ But can also kill cells through lytic cycle o o Bacteriophage lambda ▪ Linear, dsDNA genome ▪ Complementary, single-stranded regions 12 nucleotides long at the 5′ terminus of each strand ▪ Upon penetration, DNA ends base-pair, forming the cos site, and the DNA ligates and forms double-stranded circle ▪ When lambda is lysogenic, its DNA integrates into E. coli chromosome at the lambda attachment site (attλ)

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o Terms: provirus/prophage, lytic, lysogenic, lysogen. o Lysogeny: state where most virus genes are not expressed and virus genome (prophage) is replicated in synchrony with host chromosome o Lysogen: a bacterium containing a prophage o Under certain conditions, lysogenic viruses may revert to the lytic pathway and begin to produce virions

o Lambda phage (temperate): know general features. o When it enters lytic pathway, lambda synthesizes long, linear concatemers of DNA by rolling circle replication Animal viruses: general classification, examples of cytopathic effects (i.e., Slide #61: transformation, latent infections, persistent infections, lysis, & transformation). o Persistent infections: release of virions from host cell does not result in cell lysis ▪ Infected cell remains alive and continues to produce virus o Latent infections: delay between infection by the virus and lytic events o Transformation: conversion of normal cell into tumor cell o Cell fusion: two or more cells become one cell with many nuclei

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