Table S1. 45 significantly up-regulated P. mirabilis HI4320 genes as determined by SAM during iron-limiting microarray a
|
|
|
- Annice Powers
- 6 years ago
- Views:
Transcription
1 Table S1. 45 significantly up-regulated P. mirabilis HI4320 genes as determined by SAM during iron-limiting microarray a PMI no. Gene Description Log 2 fold-change b PMI0029 exbb biopolymer transport protein 7.66 PMI0030 exbd biopolymer transport protein 5.61 PMI0172 putative Dyp-type peroxidase 4.92 PMI0174 putative membrane protein 5.49 PMI0175 putative exported protein 5.66 PMI0176 putative exported protein 8.36 PMI0229 ABC transporter; permease protein (FecCD transport family) 4.81 PMI0231 putative citrate lyase β chain 6.45 PMI0232 putative siderophore biosynthesis protein 6.36 PMI0233 putative TonB-dependent siderophore receptor 6.04 PMI0234 putative decarboxylase 5.30 PMI0235 putative pyridoxal-phosphate dependent enzyme 4.77 PMI0331 putative ABC transporter; substrate-binding protein 6.49 PMI0409 putative TonB-dependent heme receptor 6.22 PMI0413 nrdf ribonucleoside-diphosphate reductase β chain 4.88 PMI0415 nrdi NrdI 4.50 PMI0416 nrdh glutaredoxin-like protein 5.68 PMI0842 putative TonB-dependent receptor 7.20 PMI1026 sitb iron ABC transporter; ATP-binding protein 5.49 PMI1210 PadR-family transcriptional regulator 4.67 PMI1211 hypothetical protein 4.25 PMI1355 tonb TonB 4.18 PMI1413 sufd subunit of cysteine desulferase; activator complex 4.29 PMI1414 sufc putative ATP-dependent transporter 3.79 PMI1416 sufa putative scaffold protein for iron-sulfer cluster assembly 4.65 PMI1424 putative hemin uptake protein 8.52 PMI1425 hmur1 hemin receptor 5.92 PMI1426 hmur2 hemin receptor 7.89 PMI1427 hmus hemin transport protein 6.96 PMI1428 hmut hemin binding periplasmic protein 5.02 PMI1430 hmuv hemin transport system; ATP-binding protein 5.42 PMI1437 putative iron utilization protein 7.38 PMI1447 conserved hypothetical protein 4.83 PMI1548 putative TonB-dependent receptor 5.47 PMI1549 ptrb oligopeptidase B 5.32 PMI1550 TonB-like protein 4.25 PMI1551 putative lipoprotein 6.69 PMI1945 irea putative TonB-dependent ferric siderophore receptor 6.65 PMI2497 putative membrane protein 5.92 PMI2596 putative siderophore TonB-dependent receptor 7.13 PMI2598 conserved hypothetical protein 7.93 PMI2957 putative iron ABC transporter; substrate-binding protein 6.20 PMI2930 glpd/glyd aerobic glycerol-3-phosphate dehydrogenase 4.94 PMI3252 bfd bacterioferritin associated ferredoxin 5.69 PMI3446 putative exported protein 3.74 a One-class unpaired test performed by Significance Analysis of Microarray (SAM). False Discovery Rate=0; all up-regulated genes listed are statistically significant. Genes listed in ascending order by P. mirabilis gene identification number (PMI no.). b Log 2 transformation of fold-change values determined by taking ratio of transcript level of P. mirabilis growth in LB and LB broth treated with 15 µm Desferal averaged across all five microarray experiments.
2 Table S2. 43 significantly down-regulated P. mirabilis HI4320 genes as determined by SAM during iron-limiting microarray a PMI no. Gene Description Log 2 fold-change b PMI0031 hybo hydrogenase-2 small chain precursor 3.46 PMI0033 hybb hydrogenase-2 cytochrome; b subunit 3.25 PMI0034 hybc hydrogenase-2 large subunit 3.18 PMI0035 hybd hydrogenase-2 maturation protease 2.19 PMI0037 hypb hydrogenase nickel incorporation protein 3.08 PMI0038 hybg hydrogenase-2 maturation protein 3.11 PMI0039 hypd hydrogenase formation protein 2.85 PMI0040 hype hydrogenase formation protein 2.73 PMI0041 putative membrane protein 2.36 PMI0042 SirA-like protein 2.34 PMI0134 putative cytoplasmic sulphur reductase 1.99 PMI0648 putative ATP-binding protein 2.08 PMI0657 probable alcohol dehydrogenase 3.94 PMI0874 conserved hypothetical protein 2.25 PMI0882 pept peptidase T 2.47 PMI1007 ftna ferritin 2.98 PMI1082 putative membrane protein 3.30 PMI1176 ABC transporter; ATP-binding protein 1.81 PMI1350 ompw outer membrane protein 2.94 PMI1397 sodb superoxide dismutase [Fe] 3.88 PMI1705 dmsa putative dimethyl sulfoxide reductase; chain A 3.69 PMI1706 dmsb anaerobic dimethyl sulfoxide reductase; chain B 3.88 PMI1740 kata catalase 1.92 PMI1769 conserved hypothetical protein 2.17 PMI1800 conserved hypothetical protein 1.54 PMI1836 conserved hypothetical protein 3.02 PMI1855 fdx 2Fe-2S ferredoxin 1.98 PMI1898 grca autonomous glycyl radical cofactor 2.81 PMI2509 conserved hypothetical protein 3.04 PMI2724 putative regulatory protein 2.18 PMI2725 TetR-family transcriptional regulator 3.11 PMI3442 protease 2.43 PMI3443 putative lipid carrier protein 2.36 PMI3450 nrdg anaerobic ribonucleoside-triphosphate reductase; activating protein 2.07 PMI3451 nrdd anaerobic ribonucleoside-triphosphate reductase 2.86 PMI3582 hybf probable hydrogenase nickel incorporation protein 2.41 PMI3583 hypc putative hydrogenase formation protein 2.25 PMI3585 frdd fumarate reductase subunit D 4.07 PMI3586 frdc fumarate reductase subunit C 4.21 PMI3587 frdb fumarate reductase iron-sulfur protein 3.96 PMI3588 frda fumarate reductase flavoprotein subunit 4.15 PMI3674 probable aminohydrolase 2.93 PMI3675 putative C4-dicarboxylate transporter 3.67
3 Table S3. Oligonucleotides used in this study. Experiment PMI # (Gene) Direction a Primer Name Sequence (5' 3') qpcr 3280 (rpoa) F rpoa GCAAATCTGGCATTGGCCCTGTTA R rpoa TAGGGCGCTCATCTTCTTCCGAAT 0030 (exbd) F exbd ACGATGGCCAGTGTCTTGGATTCT R exbd TCCCGCCTTCCTTAATGAGTCCAT 0842 F 0842 AAGCGTGTTGCATCTCGTGAAACG R 0842 ATACGCTCAATCGCGGGTAAAGGA 1027 (sita) F sita TGCGGTCGTTGTCACTGAAGGTAT R sita ATCCATGCATGTGGGTTTGGGTTG 1425 (hmur1) F hmur1 TCTTATGGTGGTGTGATCGCAGGT R hmur1 TCATCAGCAATACGTATCGGGCCA 2930 (glpd) F glpd ATTGTCATCGGCGGCGGAATAAAC R glpd TGGCTAAGTCTTGAGCTTCCAGCA 3252 (bfd) F bfd CTGTCTGTGTCATGGTGTGAGTGA R bfd TGCCTACAGGTAGGATTTGACGCA 1007 (ftna) F ftna GCGCTTGGTGCGATGATAAAGGAT R ftna CCCTAACAAAGGCATAGCACCTGT 2596 F 2596 GGCCAATCTTCGGCCGATTTCTTT R 2596 ATGCTTCAGCGTGACTACTGGGTT 2597 (nrpx) F nrpx TGATGGCATGGCGGTAGAACAGAT R nrpx CTCCTATTTCTCCTCCGCCAACTT 2598 (nrpy) F nrpy AGCGAACCTCATTGGGAAACTCGT R nrpy TGGCCAGTGCCGGAACCTATATTT 2599 (nrpr) F nrpr ATCCCATGCCAGCGCAATGAATAC R nrpr AGTGCTGATATGGCAAGTACCCGA 2600 (nrps) F nrps TCCTGAAGGTGCATCTCAAGGTGT R nrps TTAAGTACCGCGGCAGCAATTTGG 2601 (nrpu) F nrpu TTCCAAAGGTAGCACTCGTTCTCG R nrpu CCAACAATGGCTGATCGCACAACA 2602 (nrpt) F nrpt AGGCTGCCAAGCTCCTCATATTCA R nrpt CAGCATCACATCCACCAATGGCAA 2603 (nrpa) F nrpa TAAGTCATATTGCCGCACATCGGG R nrpa ACGTCGCAGATTTCCACTGCCATA 2604 (nrpb) F nrpb ACAAGCCCGTCTAAGAATAGCCGA R nrpb TGATGCAAGATCACCACTGCGTTG 2605 (nrpg) F nrpg GCTATCAAGAGTCATGTTACGCGA R nrpg GCGAGAGCAACACAATTATTTGAATG 0229 F 0229 TGAATGCTTGGAAACTGACGGCAC R 0229 TATTGGGCCAACAAATGCTACCGC 0230 F 0230 TTAACGGTCTCACTGCTTCCACGA R 0230 ACCACCTGCTCTGCTCGTTTAGAA 0231 (pbti) F pbti AAGCGTTGCTATACGCAAGAAGCC R pbti AGTTTAGCGCCAAATCCAAGAGCG 0232 (pbta) F pbta TTTATGGCATTGCCCTTGAGGCAC R pbta ATGCCGGGCCAGATATAAGGTTGA 0233 (pbtb) F pbtb TCTCCAGCAAGCGTTCCCAAAGTA R pbtb TGGCGTCACCGCTGATTCATCATA 0234 (pbtc) F pbtc TGGATTGCAGGCCATAGCTGTTTG R pbtc ACCGCAGTTAATCTTGTGGGCAAC 0235 (pbtd) F pbtd TGGCGAGAAATATGGTTGTTGCGG R pbtd ATAGCAGCGATTGCCAACCCAATG 0236 (pbte) F pbte ACGTCACTCTTTACAGCAGTCGCT R pbte CGCCTCATCAATGGCTTCTGTCAT 0237 (pbtf) F pbtf TGGGCAAGATGGTTTGAAGCACAC R pbtf TGCGGTTAATACTGGCGTTGTTGC 0238 (pbtg) F pbtg TTAATACAGTCCGATCCGGCCACA R pbtg ATCAAACGTTCCTTGTTCGCTGCC 0239 (pbth) F pbth GCTCCGTCCTTCAGAAGAAGTCA
4 R pbth GTGTTGTCCATCTTTGGCAACGGA Mutant design pbta::kan pbtaibs AAAAAAGCTTATAATTATCCTTATCATTCTGGATAGTGCGCCCAGATAGGGTG & confirmation pbtaebs1d CAGATTGTACAAATGTGGTGATAACAGATAAGTCTGGATACTTAACTTACCTTTCTTTGT pbtaebs2 TGAACGCAAGTTTCTAATTTCGGTTAATGATCGATAGAGGAAAGTGTCT F CpbtA::kan GAACTTATGGGGATACTGAAAA R CpbtA::kan ATGCCGGGCCAGATATAAGGTTGA nrpr::kan nrpribs AAAAAAGCTTATAATTATCCTTAAGTTACTCATTAGTGCGCCCAGATAGGGTG nrprebs1d CAGATTGTACAAATGTGGTGATAACAGATAAGTCTCATTACTTAACTTACCTTTCTTTGT nrprebs2 TGAACGCAAGTTTCTAATTTCGATTTAACTTCGATAGAGGAAAGTGTCT F CnrpR::kan CTCTTGGTGGTGTTGCTTGCCAAA R CnrpR::kan AATGGCAGAAGAGGAGAGTCTGGT nrprpbta::kan nrpr2050-ibs AAAAAAGCTTATAATTATCCTTAATATACCTATATGTGCGCCCAGATAGGGTG nrpr2596::kan nrpr2050-ebs1d CAGATTGTACAAATGTGGTGATAACAGATAAGTCCTATATTGTAACTTACCTTTCTTTGT nrpr2050-ebs2 TGAACGCAAGTTTCTAATTTCGATTTATATTCGATAGAGGAAAGTGTCT F CnrpR(2050)::kan CTCTTGGTGGTGTTGCTTGCCAAA R CnrpR(2050)::kan AGTGCTGATATGGCAAGTACCCGA nrpr2596::kan 2596IBS AAAAAAGCTTATAATTATCCTTAGATGACTTGAGCGTGCGCCCAGATAGGGTG 2596EBS1d CAGATTGTACAAATGTGGTGATAACAGATAAGTCTTGAGCGCTAACTTACCTTTCTTTGT 2596EBS2 TGAACGCAAGTTTCTAATTTCGATTTCATCTCGATAGAGGAAAGTGTCT F C2596::kan TGTAGCTGCCACAGAACAGCATGA R C2596::kan ATGCTTCAGCGTGACTACTGGGTT RT-PCR F 3' 0228 AAGAGTAATAAAAGCCTCTGCAGA R 5' 0229 GAAACGACGAAGTATCTGTCGCTG F 3' 0229 TGAATGCTTGGAAACTGACGGCAC R 5' 0230 AACCACCTGCTCTGCTCGTTTAGA F 3' 0230 TTATCGCGTTAGCGCCCGTATTGA R 5' 0231 ACCATGCTAGCGCTCTTGGATTTG F 3' 0231 CAAATCCAAGAGCGCTAGCATGGT R 5' 0232 TGGCGGCCATCCATTGATTTAAGG F 3' 0232 ACTGTGATCGGCGAAGAGCTTGAA R 5' 0233 CCGCGCTGACGAAATCAGGAATTA F 3' 0233 TCCTTGCCTCGGTAAGTGTTGACT R 5' 0234 TTGGCGACTTCGACCATGGCATTA F 3' 0234 TGGATTGCAGGCCATAGCTGTTTG R 5' 0235 CCGATTGCAGCAGCGGTAATTGAA F 3' 0235 TTGCACTTGCTATGGCTGATGGTG R 5' 0236 ACAGCTTCTGAGCGACTGCTGTAA F 3' 0236 AACGTCTTCGAGTACCAACACCCT R 5' 0237 ATAGGTGCGATATACACGCCGGTT F 3' 0237 TTGCCTCTATGGTTGGCATTGCAC R 5' 0238 CGCGCTGTACCGGTAATTTGACAT F 3' 0238 TCCAGCAGCTAGCTAAGTGGATAC R 5' 0239 TGTTGTCCATCTTTGGCAACGGAC F 3' 0239 AAGGTAATATTTTCCCTTATAAAA R 5' 0240 TCACGCCATAATACTTCTGCAATA F 3' 2596 AGCCAGTGCTTCCTCCTGTATTGA R 5' 2597 CTCAGGCGTTCAATAAATGGAGACC
5 Fig. S1. Growth of P. mirabilis wild-type and siderophore biosynthesis mutants in LB broth alone and LB broth containing 15 µm Desferal. Growth of P. mirablis HI4320 wild-type, proteobactin synthetase/receptor mutant (pbta::kan), yersiniabactin synthetase mutant (nrpr::kan), yersiniabactin synthetase and proteobactin synthetase/receptor mutant (nrprpbta::kan), yersiniabactin synthetase/receptor mutant (nrpr2596::kan) in LB broth alone (black symbols and lines) and in LB broth containing 15 µm Desferal (red symbols and lines). Fig. S2. Independent infection of yersiniabactin-related synthetase/receptor mutant and wild-type HI4320. Each data point represents the log 10 CFU/g tissue collected from a single animal. The bars represent the median values of the populations. The limit of detection of this assay is CFU/g. A significant difference in colonization was determined using a two-tailed Mann-Whitney test.
TCA Cycle. Voet Biochemistry 3e John Wiley & Sons, Inc.
TCA Cycle Voet Biochemistry 3e Voet Biochemistry 3e The Electron Transport System (ETS) and Oxidative Phosphorylation (OxPhos) We have seen that glycolysis, the linking step, and TCA generate a large number
Table S1. 10μM_rfp_B1 2,074, ohr 10μM_rfp_C2 2,074, ohr
Table S1 Selection without RpoD Insert Start Position Insert End Position Potential Tolerance Gene Candidates 0μM_rfp_A1 2,076,184 -- ohr 0μM_rfp_B1 2,082,864 -- ohr 0μM_rfp_C1 2,076,798 -- ohr 1μM_rfp_A1
Bioinorganic Chemistry
PRINCIPLES OF Bioinorganic Chemistry Stephen J. Lippard MASSACHUSETTS INSTITUTE OF TECHNOLOGY Jeremy M. Berg JOHNS HOPKINS SCHOOL OF MEDICINE f V University Science Books Mill Valley, California Preface
Supplementary Figure 1. The proportion S. aureus CFU of the total CFU (S. aureus + E. faecalis CFU) per host in worms
Supplementary Figure 1. The proportion S. aureus CFU of the total CFU (S. aureus + E. faecalis CFU) per host in worms alive or dead at 24 hours of exposure. Two sample t-test: t = 1.22, df = 10, P= 0.25.
Life 21 - Aerobic respiration Raven & Johnson Chapter 9 (parts)
1 Life 21 - Aerobic respiration Raven & Johnson Chapter 9 (parts) Objectives 1: Describe the overall action of the Krebs cycle in generating ATP, NADH and FADH 2 from acetyl-coa 2: Understand the generation
SUPPLEMENTAL MATERIAL
SUPPLEMENTAL MATERIAL SUPPLEMENTAL RESULTS Microarray analysis of F. tularensis LVS within hepatocytes: As described in Materials and Methods, the global gene expression of LVS organisms grown in FL83B
Characters related to higher starch accumulation in cassava storage roots
Characters related to higher starch accumulation in cassava storage roots You-Zhi Li **1, Jian-Yu Zhao *1, San-Min Wu 1, Xian-Wei Fan 1, Xing-Lu Luo 1 & Bao-Shan Chen **1 1 State Key Laboratory for Conservation
Gene expression profiles of Nitrosomonas europaea, an obligate chemolithotroph. Daniel Arp. Department of Botany and Plant Pathology.
Gene expression profiles of Nitrosomonas europaea, an obligate chemolithotroph. Daniel Arp. Department of Botany and Plant Pathology. Oregon State University, Corvallis OR. 97331 Technical report for product
Table 5. Genes unique to G. thermodenitrificans NG80-2 Gene ID Gene name Gene product COG functional category
Table 5. Genes unique to G. thermodenitrificans NG80-2 GT0030 gt30 Methionine--tRNA ligase/methionyl-trna synthetase COG0143, Translation GT0033 gt33 Unknown GT0106 gt106 Ribosomal protein L3 COG0087,
Biological Process Term Enrichment
Biological Process Term Enrichment cellular protein localization cellular macromolecule localization intracellular protein transport intracellular transport generation of precursor metabolites and energy
Strain or plasmid Relevant characteristics Reference
Table S1. Bacterial strains, and plasmids Strain or plasmid Relevant characteristics Reference M. xanthus strains DK1622 Wild-type M. xanthus 1 AG306 pnbc6::nla6, Kan r 2 AG1151 DK 1622 pkg51::mxan2688
Effect of RyhB Small RNA on Global Iron Use in Escherichia coli
JOURNAL OF BACTERIOLOGY, Oct. 2005, p. 6962 6971 Vol. 187, No. 20 0021-9193/05/$08.00 0 doi:10.1128/jb.187.20.6962 6971.2005 Effect of RyhB Small RNA on Global Iron Use in Escherichia coli Eric Massé,
GO ID GO term Number of members GO: translation 225 GO: nucleosome 50 GO: calcium ion binding 76 GO: structural
GO ID GO term Number of members GO:0006412 translation 225 GO:0000786 nucleosome 50 GO:0005509 calcium ion binding 76 GO:0003735 structural constituent of ribosome 170 GO:0019861 flagellum 23 GO:0005840
A Novel Organotrophic Nitrate-reducing Fe(II)-oxidizing Bacterium. Isolated from a Paddy Soil and Draft Genome Sequencing
Electronic Supplementary Material (ESI) for RSC Advances. This journal is The Royal Society of Chemistry 2017 Supplementary information for A Novel Organotrophic Nitrate-reducing Fe(II)-oxidizing Bacterium
Genomic insights into high exopolysaccharide-producing dairy starter. bacterium Streptococcus thermophilus ASCC 1275
Supplementary information of Genomic insights into high exopolysaccharide-producing dairy starter bacterium Streptococcus thermophilus ASCC 1275 Qinglong Wu, Hein Min Tun, Frederick Chi-Ching Leung, Nagendra
RECONSTRUCTING GENE REGULATORY NETWORKS FROM FUNGAL TRANSCRIPTOMIC DATA USING BAYESIAN NETWORK
RECONSTRUCTING GENE REGULATORY NETWORKS FROM FUNGAL TRANSCRIPTOMIC DATA USING BAYESIAN NETWORK Li Guo Fungal Comparative Genomics Laboratory Department of Biochemistry and Molecular biology University
ΔG o' = ηf ΔΕ o' = (#e ( V mol) ΔΕ acceptor
Reading: Sec. 19.1 Electron-Transfer Reactions in Mitochondria (listed subsections only) 19.1.1 Electrons are Funneled to Universal Electron Acceptors p. 692/709 19.1.2 Electrons Pass through a Series
PHOTOSYNTHESIS: A BRIEF STORY!!!!!
PHOTOSYNTHESIS: A BRIEF STORY!!!!! This is one of the most important biochemical processes in plants and is amongst the most expensive biochemical processes in plant in terms of investment. Photosynthesis
Subsystem: Succinate dehydrogenase
Subsystem: Succinate dehydrogenase Olga Vassieva Fellowship for Interpretation of Genomes The super-macromolecular respiratory complex II (succinate:quinone oxidoreductase) couples the oxidation of succinate
Role of Metal Ions in Microbial Gene. Inorganic Biochemistry: Transport and storage, introduction (Chapter 3, pp ).
Lesson 1 (31 October 2000) Welcome and introduction to class. Overview of syllabus topics. Discuss what we need to know about essential and toxic metal ions in biological systems. Inorganic Biochemistry:
Transmembrane Domains (TMDs) of ABC transporters
Transmembrane Domains (TMDs) of ABC transporters Most ABC transporters contain heterodimeric TMDs (e.g. HisMQ, MalFG) TMDs show only limited sequence homology (high diversity) High degree of conservation
Supplementary Figures
Supplementary Figures Supplementary Figure 1. Growth profiles of E. coli strains used in this study in response to iron availability. Doubling times of WT (K-12 MG1655), Fur-8myc, and fur strains were
Scale in the biological world
Scale in the biological world 2 A cell seen by TEM 3 4 From living cells to atoms 5 Compartmentalisation in the cell: internal membranes and the cytosol 6 The Origin of mitochondria: The endosymbion hypothesis
Energy Metabolism exergonic reaction endergonic reaction Energy of activation
Metabolism Energy Living things require energy to grow and reproduce Most energy used originates from the sun Plants capture 2% of solar energy Some captured energy is lost as metabolic heat All energy
BBS2710 Microbial Physiology. Module 5 - Energy and Metabolism
BBS2710 Microbial Physiology Module 5 - Energy and Metabolism Topics Energy production - an overview Fermentation Aerobic respiration Alternative approaches to respiration Photosynthesis Summary Introduction
Anaerobic Respiration Using a Complete Oxidative TCA Cycle Drives Multicellular Swarming in Proteus mirabilis
RESEARCH ARTICLE Anaerobic Respiration Using a Complete Oxidative TCA Cycle Drives Multicellular Swarming in Proteus mirabilis Christopher J. Alteri, Stephanie D. Himpsl, Michael D. Engstrom, and Harry
MOLECULAR CELL BIOLOGY
1 Lodish Berk Kaiser Krieger scott Bretscher Ploegh Matsudaira MOLECULAR CELL BIOLOGY SEVENTH EDITION CHAPTER 13 Moving Proteins into Membranes and Organelles Copyright 2013 by W. H. Freeman and Company
Table S1: Domain based (meta)genome comparison of selected metagenomes of methanotrophs and genomes of selected methanogens*
ANME-1-s ANME-1-m ANME-2a ANME-2d-h ANME-2d-a AM A M-1 M-2 M-3 H-1 H-2 H-3 H-4 S Table S1: Domain based (meta)genome comparison of selected metagenomes of methanotrophs and genomes of selected methanogens*
NADH dehydrogenase in Corynebacterium glutamicum
NADH dehydrogenase in Corynebacterium glutamicum Nawarat Nantapong 1, Hirohide Toyama, Kazunobu Matsushita Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University ( 1 Present address:
20. Electron Transport and Oxidative Phosphorylation
20. Electron Transport and Oxidative Phosphorylation 20.1 What Role Does Electron Transport Play in Metabolism? Electron transport - Role of oxygen in metabolism as final acceptor of electrons - In inner
Metabolism. Fermentation vs. Respiration. End products of fermentations are waste products and not fully.
Outline: Metabolism Part I: Fermentations Part II: Respiration Part III: Metabolic Diversity Learning objectives are: Learn about respiratory metabolism, ATP generation by respiration linked (oxidative)
number Done by Corrected by Doctor Nafeth Abu Tarboush
number 8 Done by Ali Yaghi Corrected by Mamoon Mohamad Alqtamin Doctor Nafeth Abu Tarboush 0 P a g e Oxidative phosphorylation Oxidative phosphorylation has 3 major aspects: 1. It involves flow of electrons
Electron Transport Chain (Respiratory Chain) - exercise - Vladimíra Kvasnicová
Electron Transport Chain (Respiratory Chain) - exercise - Vladimíra Kvasnicová Respiratory chain (RCH) a) is found in all cells b) is located in a mitochondrion c) includes enzymes integrated in the inner
Lecture #8 9/21/01 Dr. Hirsh
Lecture #8 9/21/01 Dr. Hirsh Types of Energy Kinetic = energy of motion - force x distance Potential = stored energy In bonds, concentration gradients, electrical potential gradients, torsional tension
Courtesy of Elsevier. Used with permission.
Chemistry 5.07 2013 Problem Set 5 Answers Problem 1 Succinate dehydrogenase (SDH) is a heterotetramer enzyme complex that catalyzes the oxidation of succinate to fumarate with concomitant reduction of
Received 25 August 2006/Accepted 5 December 2006
JOURNAL OF BACTERIOLOGY, Mar. 2007, p. 1845 1855 Vol. 189, No. 5 0021-9193/07/$08.00 0 doi:10.1128/jb.01354-06 Copyright 2007, American Society for Microbiology. All Rights Reserved. Nitric Oxide in Chemostat-Cultured
Lecture 12. Metalloproteins - II
Lecture 12 Metalloproteins - II Metalloenzymes Metalloproteins with one labile coordination site around the metal centre are known as metalloenzyme. As with all enzymes, the shape of the active site is
Iron and Fur Regulation in Vibrio cholerae and the Role of Fur in Virulence
INFECTION AND IMMUNITY, Dec. 2005, p. 8167 8178 Vol. 73, No. 12 0019-9567/05/$08.00 0 doi:10.1128/iai.73.12.8167 8178.2005 Copyright 2005, American Society for Microbiology. All Rights Reserved. Iron and
(starvation). Description a. Predicted operon members b. Gene no. a. Relative change in expression (n-fold) mutant vs. wild type.
1 Table S1. Genes whose expression differ in the phyr mutant 8402 and/or in the ecfg mutant 8404 compared with the wild type when grown to the mid-exponential phase (OD600 0.5-0.7) in rich medium (PSY)
CHEM 463: Advanced Inorganic Chemistry Modeling Metalloproteins for Structural Analysis
CHEM 463: Advanced Inorganic Chemistry Modeling Metalloproteins for Structural Analysis Purpose: The purpose of this laboratory is to introduce some of the basic visualization and modeling tools for viewing
BCH 4054 Spring 2001 Chapter 21 Lecture Notes
BCH 4054 Spring 2001 Chapter 21 Lecture Notes 1 Chapter 21 Electron Transport and Oxidative Phosphorylation 2 Overview Oxidation of NADH and CoQH 2 produced in TCA cycle by O 2 is very exergonic. Some
Chapter 6. Ground Rules Of Metabolism
Chapter 6 Ground Rules Of Metabolism Alcohol Dehydrogenase An enzyme Breaks down ethanol and other toxic alcohols Allows humans to drink Metabolism Is the totality of an organism s chemical reactions Arises
Ground Rules of Metabolism CHAPTER 6
Ground Rules of Metabolism CHAPTER 6 Antioxidants You ve heard the term. What s the big deal? Found naturally in many fruits and vegetables Added to many products What do they actually do? Antioxidants
2.1 Atoms, Ions, and Molecules
2.1 Atoms, Ions, and Molecules Living things consist of atoms of different elements. An atom is the smallest basic unit of matter. An element is one type of atom. 6 elements make up 99% of all living things
Advanced Higher Biology. Unit 1- Cells and Proteins 2c) Membrane Proteins
Advanced Higher Biology Unit 1- Cells and Proteins 2c) Membrane Proteins Membrane Structure Phospholipid bilayer Transmembrane protein Integral protein Movement of Molecules Across Membranes Phospholipid
BIOCHEMISTRY. František Vácha. JKU, Linz.
BIOCHEMISTRY František Vácha http://www.prf.jcu.cz/~vacha/ JKU, Linz Recommended reading: D.L. Nelson, M.M. Cox Lehninger Principles of Biochemistry D.J. Voet, J.G. Voet, C.W. Pratt Principles of Biochemistry
Energy and Cellular Metabolism
1 Chapter 4 About This Chapter Energy and Cellular Metabolism 2 Energy in biological systems Chemical reactions Enzymes Metabolism Figure 4.1 Energy transfer in the environment Table 4.1 Properties of
Structure of mitochondria
Structure of mitochondria Subcompartments of mitochondria Outer membrane (OM) Inner membrane (IM) Matrix Intermembrane space (IMS) Cristae membrane Inner boundary membrane Cristae compartment Molecular
CHAPTER 8. An Introduction to Metabolism
CHAPTER 8 An Introduction to Metabolism WHAT YOU NEED TO KNOW: Examples of endergonic and exergonic reactions. The key role of ATP in energy coupling. That enzymes work by lowering the energy of activation.
Transcriptomics reveals a crossmodulatory. riboflavin and iron and outlines responses to riboflavin biosynthesis and uptake in Vibrio cholerae OPEN
www.nature.com/scientificreports Received: 21 November 2017 Accepted: 31 January 2018 Published: xx xx xxxx OPEN Transcriptomics reveals a crossmodulatory effect between riboflavin and iron and outlines
Outline. Metabolism: Energy and Enzymes. Forms of Energy. Chapter 6
Metabolism: Energy and Enzymes Chapter 6 Forms of Energy Outline Laws of Thermodynamics Metabolic Reactions ATP Metabolic Pathways Energy of Activation Enzymes Photosynthesis Cellular Respiration 1 2 Forms
2. In regards to the fluid mosaic model, which of the following is TRUE?
General Biology: Exam I Sample Questions 1. How many electrons are required to fill the valence shell of a neutral atom with an atomic number of 24? a. 0 the atom is inert b. 1 c. 2 d. 4 e. 6 2. In regards
Principles of Cellular Biology
Principles of Cellular Biology آشنایی با مبانی اولیه سلول Biologists are interested in objects ranging in size from small molecules to the tallest trees: Cell Basic building blocks of life Understanding
RNA Synthesis and Processing
RNA Synthesis and Processing Introduction Regulation of gene expression allows cells to adapt to environmental changes and is responsible for the distinct activities of the differentiated cell types that
Transcriptome of Proteus mirabilis in the Murine Urinary Tract: Virulence and Nitrogen Assimilation Gene Expression
INFECTION AND IMMUNITY, July 2011, p. 2619 2631 Vol. 79, No. 7 0019-9567/11/$12.00 doi:10.1128/iai.05152-11 Copyright 2011, American Society for Microbiology. All Rights Reserved. Transcriptome of Proteus
5 Selected samples. 5.1 Organic Radicals in Solution CH 3 H 3 C N O N O. 2,2,6,6-tetramethyl-1-piperidinyloxyl (TEMPO) dimethylnitroxyl radical 5-1
5 Selected samples 5.1 Organic Radicals in Solution 2,2,6,6-tetramethyl-1-piperidinyloxyl (TEMPO) H 3 C H 3 C N O CH 3 CH 3 344 345 346 347 348 349 350 351 dimethylnitroxyl radical H 3 C N O CH 3 340 342
Dps biomineralizing proteins: multifunctional architects of nature
Biochem. J. (2012) 445, 297 311 (Printed in Great Britain) doi:10.1042/bj20120514 297 REVIEW ARTICLE Dps biomineralizing proteins: multifunctional architects of nature Kornelius ZETH 1 Zentrum für Molekulare
Conceptofcolinearity: a continuous sequence of nucleotides in DNA encodes a continuous sequence of amino acids in a protein
Translation Conceptofcolinearity: a continuous sequence of nucleotides in DNA encodes a continuous sequence of amino acids in a protein Para além do fenómeno do wobble, há que considerar Desvios ao código
CHLOROPLASTS, CALVIN CYCLE, PHOTOSYNTHETIC ELECTRON TRANSFER AND PHOTOPHOSPHORYLATION (based on Chapter 19 and 20 of Stryer )
CHLOROPLASTS, CALVIN CYCLE, PHOTOSYNTHETIC ELECTRON TRANSFER AND PHOTOPHOSPHORYLATION (based on Chapter 19 and 20 of Stryer ) Photosynthesis Photosynthesis Light driven transfer of electron across a membrane
CP Biology Unit 5 Cell Energy Study Guide. Electron Carriers Electron Transport Chain Fermentation Glycolysis Krebs cycle Light-Dependent Reactions
Name: KEY CP Biology Unit 5 Cell Energy Study Guide Vocabulary to know: ATP ADP Aerobic Anaerobic ATP Synthases Cellular Respiration Chlorophyll Chloroplast Electron Carriers Electron Transport Chain Fermentation
(Na++ K +)-ATPase in artificial lipid vesicles: influence of the concentration of mono- and divalent cations on the pumping rate
254 Biochimica et Biophysica Acta 862 (1986) 254-264 Elsevier BBA 72961 (Na++ K +)-ATPase in artificial lipid vesicles: influence of the concentration of mono- and divalent cations on the pumping rate
PHOTOSYNTHESIS. Chapter 8
PHOTOSYNTHESIS Chapter 8 ENERGY & LIFE ENERGY The ability to do work. Can be stored in chemical bonds. Cells need energy to do things like active transport, dividing, moving, and producing and storing
Chapter 8 Metabolism: Energy, Enzymes, and Regulation
Chapter 8 Metabolism: Energy, Enzymes, and Regulation Energy: Capacity to do work or cause a particular change. Thus, all physical and chemical processes are the result of the application or movement of
Tuesday 9/6/2018 Mike Mueckler
Tuesday 9/6/2018 Mike Mueckler mmueckler@wustl.edu Intracellular Targeting of Nascent Polypeptides Mitochondria are the Sites of Oxidative ATP Production Sugars Triglycerides Figure 14-10 Molecular Biology
UNIT 6 PART 3 *REGULATION USING OPERONS* Hillis Textbook, CH 11
UNIT 6 PART 3 *REGULATION USING OPERONS* Hillis Textbook, CH 11 REVIEW: Signals that Start and Stop Transcription and Translation BUT, HOW DO CELLS CONTROL WHICH GENES ARE EXPRESSED AND WHEN? First of
Tracking Protein Allostery in Evolution
Tracking Protein Allostery in Evolution Glycogen phosphorylase frees sugars to provide energy GP orthologs diverged 600,000,000 years can respond to transcription controls, metabolite concentrations and
2. Cellular and Molecular Biology
2. Cellular and Molecular Biology 2.1 Cell Structure 2.2 Transport Across Cell Membranes 2.3 Cellular Metabolism 2.4 DNA Replication 2.5 Cell Division 2.6 Biosynthesis 2.1 Cell Structure What is a cell?
Supplementary Information
Supplementary Information The direct role of selenocysteine in [NiFeSe] hydrogenase maturation and catalysis Marta C. Marques a, Cristina Tapia b, Oscar Gutiérrez-Sanz b, Ana Raquel Ramos a, Kimberly L.
Generation of new compounds through unbalanced transcription of landomycin A
Applied Microbiology and Biotechnology Generation of new compounds through unbalanced transcription of landomycin A cluster Maksym Myronovskyi #1, Elke Brötz #1, Birgit Rosenkränzer 1, Niko Manderscheid
Ch 7: Cell Structure and Functions. AP Biology
Ch 7: Cell Structure and Functions AP Biology The Cell Theory 1. All living things are made of cells. 2. New cells come from existing cells. 3. Cells are the basic units of structure and function of living
Chapter 6: Outline-2. Chapter 6: Outline Properties of Enzymes. Introduction. Activation Energy, E act. Activation Energy-2
Chapter 6: Outline- Properties of Enzymes Classification of Enzymes Enzyme inetics Michaelis-Menten inetics Lineweaver-Burke Plots Enzyme Inhibition Catalysis Catalytic Mechanisms Cofactors Chapter 6:
BACTERIAL PHYSIOLOGY SMALL GROUP. Monday, August 25, :00pm. Faculty: Adam Driks, Ph.D. Alan Wolfe, Ph.D.
BACTERIAL PHYSIOLOGY SMALL GROUP Monday, August 25, 2014 1:00pm Faculty: Adam Driks, Ph.D. Alan Wolfe, Ph.D. Learning Goal To understand how bacterial physiology applies to the diagnosis and treatment
Cellular Respiration. The mechanism of creating cellular energy. Thursday, 11 October, 12
Cellular Respiration The mechanism of creating cellular energy What do we know?? What do we know?? Grade 5 - Food --> Energy What do we know?? Grade 5 - Food --> Energy Grade 10 - glu. + O2 --> CO2 + H20
Cellular Transport. 1. Transport to and across the membrane 1a. Transport of small molecules and ions 1b. Transport of proteins
Transport Processes Cellular Transport 1. Transport to and across the membrane 1a. Transport of small molecules and ions 1b. Transport of proteins 2. Vesicular transport 3. Transport through the nuclear
Name Synonym Product C4.3 SMD_ glna SMD_0103 glutamine synthetase glnb SMD_0104 nitrogen regulatory protein P-II - SMD_0155 glyoxalase -
Name Synonym Product C4.3 SMD_0048 - glna SMD_0103 glutamine synthetase glnb SMD_0104 nitrogen regulatory protein P-II - SMD_0155 glyoxalase - SMD_0193 3-dehydroquinate dehydratase acea SMD_0200 Isocitrate
2: CHEMICAL COMPOSITION OF THE BODY
1 2: CHEMICAL COMPOSITION OF THE BODY CHAPTER OVERVIEW This chapter provides an overview of basic chemical principles that are important to understanding human physiological function and ultimately homeostasis.
Photoperiodic effect on protein profiles of potato petiole
Photoperiodic effect on protein profiles of potato petiole Shweta Shah 1, Young Jin-Lee 2, David J. Hannapel 3 and A. Gururaj Rao* 1 1 Department of Biochemistry, Biophysics and Molecular Biology, Iowa
Arabidopsis PPR40 connects abiotic stress responses to mitochondrial electron transport
Ph.D. thesis Arabidopsis PPR40 connects abiotic stress responses to mitochondrial electron transport Zsigmond Laura Supervisor: Dr. Szabados László Arabidopsis Molecular Genetic Group Institute of Plant
Gene and Protein Expression Profiles of Shewanella oneidensis during Anaerobic Growth with Different Electron Acceptors
OMICS A Journal of Integrative Biology Volume 6, Number 1, 2002 Mary Ann Liebert, Inc. Gene and Protein Expression Profiles of Shewanella oneidensis during Anaerobic Growth with Different Electron Acceptors
Global Iron-Dependent Gene Regulation in Escherichia coli:
JBC Papers in Press. Published on May 13, 2003 as Manuscript M303381200 Global Iron-Dependent Gene Regulation in Escherichia coli: A New Mechanism for Iron Homeostasis Jonathan P McHugh 1*, Francisco Rodríguez-Quiñones
Transcriptional Response of Leptospira interrogans to Iron Limitation and Characterization of a PerR Homolog
INFECTION AND IMMUNITY, Nov. 2010, p. 4850 4859 Vol. 78, No. 11 0019-9567/10/$12.00 doi:10.1128/iai.00435-10 Copyright 2010, American Society for Microbiology. All Rights Reserved. Transcriptional Response
Bacillus anthracis. Clostridium botulinum Clostridium perfringens and other, but never Gram-negative microbes
SPORES (endospores) the spore is formed inside the parent vegetative cell hence the name endospores The spore is a dehydrated, multishelled structure that protects and allows the bacteria to exist in suspended
An Introduction to Metabolism
An Introduction to Metabolism I. All of an organism=s chemical reactions taken together is called metabolism. A. Metabolic pathways begin with a specific molecule, which is then altered in a series of
Synthesis and Characterization of a Series of Zinc and Nickel Dithiolate Complexes. Olivia M. Campbell Alfred University
ynthesis and Characterization of a eries of Zinc and ickel Dithiolate Complexes Olivia M. Campbell Alfred University Importance of Zinc Essential cofactor for many enzymes active in digestion and metabolism,
CHARACTERISTICS OF LIFE ORGANIZATION OF LIFE CELL THEORY TIMELINE
CHARACTERISTICS OF LIFE 1. composed of cells either uni/multi 2. reproduce sexual and/or asexual 3. contain DNA in cells 4. grow and develop 5. use material/energy in metabolic reactions 6. respond to
Cells & Cell Organelles. Doing Life s Work
Cells & Cell Organelles Doing Life s Work Types of cells bacteria cells Prokaryote Eukaryotes animal cells plant cells Cell size comparison Animal cell Bacterial cell most bacteria 1-10 microns eukaryotic
Biochimica et Biophysica Acta
Biochimica et Biophysica Acta 1803 (2010) 748 766 Contents lists available at ScienceDirect Biochimica et Biophysica Acta journal homepage: www.elsevier.com/locate/bbamcr Review Biogenesis of membrane
Student Learning Outcomes: Nucleus distinguishes Eukaryotes from Prokaryotes
9 The Nucleus Student Learning Outcomes: Nucleus distinguishes Eukaryotes from Prokaryotes Explain general structures of Nuclear Envelope, Nuclear Lamina, Nuclear Pore Complex Explain movement of proteins
Electron Transport & Oxidative Phosphorylation; Aerobic Respiration
Electron Transport & Oxidative Phosphorylation; Aerobic Respiration The mitochondria is a double membrane structure with and intermembraneous space and a matrix. The bulk of the mito proteins are bound
Chapter Outline. The Living Cell. The Cell Theory. The Nature and Variety of Cells. Cell theory. Observing Cells: The Microscope
Chapter Outline The Living Cell Chapter 21 The Nature and Variety of Cells How Does a Cell Work? Metabolism: Energy and Life Cell Division Great Idea: Life is based on chemistry, and chemistry takes place
Bioinformatics: Network Analysis
Bioinformatics: Network Analysis Flux Balance Analysis and Metabolic Control Analysis COMP 572 (BIOS 572 / BIOE 564) - Fall 2013 Luay Nakhleh, Rice University 1 Flux Balance Analysis (FBA) Flux balance
Living and nonliving matter is composed of atoms.
Chemistry Topics Covered Atomic structure and interactions Properties of Water Biological Molecules: carbohydrates, lipids, nucleic acids, and proteins Central Dogma: DNA à RNA à Protein Protein Structure:
B. Implications for Protein Evolution
One important reason for classifying proteins is simply to make the structures more memorable. The system proposed above can help to do that, especially for those cases which fall into one of the more
Basic Concepts of Enzyme Action. Enzymes. Rate Enhancement 9/17/2015. Stryer Short Course Chapter 6
Basic Concepts of Enzyme Action Stryer Short Course Chapter 6 Enzymes Biocatalysts Active site Substrate and product Catalyzed rate Uncatalyzed rate Rate Enhancement Which is a better catalyst, carbonic
Enzymes and Protein Structure
Enzymes and Protein Structure Last Week PTM s We (Re)Learned About Primary Structure And Tertiary Structure S-Q-D-A-G-M-Q-Q-G-A-D-M-D-Q-V-S-A Secondary Structure Enzymes What are these crazy things called
Lecture 7 Cell Biolog y ٢٢٢ ١
Lecture 7 ١ Mitochondria ٢ Mitochondria Mitochondria are the energy factories of the cells. The energy currency for the work that animals must do is the energy-rich molecule adenosine triphosphate (ATP).
Nature of matter. Chemical bond is a force that joins atoms
Nature of matter Atom the smallest unit of matter that cannot be broken down by chemical means The subatomic particles of an atom consist of protons, neutrons and electrons Element is a pure substance
(kilo ) or heat energy (kilo ) C. Organisms carry out conversions between potential energy and kinetic energy 1. Potential energy is energy;
I. Biological work requires energy A. Energy is the to do work B. Energy is expressed in units of work (kilo ) or heat energy (kilo ) C. Organisms carry out conversions between potential energy and kinetic
CHEMISTRY OF THE HUMAN BODY
CHEMISTRY OF THE HUMAN BODY (Sample Questions) WUCT 2018 The three questions below are meant to give a sense of the kinds of questions that might be asked on the exam in April 2018. The actual exam is
Chem Lecture 10 Lipid, Amino Acid, and Nucleotide Metabolism Part III: Nucleotide Metabolism
Chem 352 - Lecture 10 Lipid, Amino Acid, and Nucleotide Metabolism Part III: Nucleotide Metabolism Lipid Metabolism Chem 352, Lecture 10, Part I: Lipid Metabolism 2 Lipid Metabolism Question: Draw a general