Study Guide Midterm 1 MCBL121 PDF

lOMoARcPSD|5053619 Study guide midterm 1 mcbl121 Introductory Microbiology (University of California Riverside) Scan to open on Studocu Studocu is not sponsored or endorsed by any college or university Downloaded by StudyHelp IO ([email protected]) lOMoARcPSD|5053619 I. 🧬1 History of Mic...

lOMoARcPSD|5053619 Study guide midterm 1 mcbl121 Introductory Microbiology (University of California Riverside) Scan to open on Studocu Studocu is not sponsored or endorsed by any college or university Downloaded by StudyHelp IO ([email protected]) lOMoARcPSD|5053619 I. 🧬1 History of Microbiology A. Historical Background → Microorganism ​= any living organism too small to be seen w/ naked eye ○ Diverse (genetically & metabolically) ○ Microbes can affect food availability ○ Part of humans, animals, & plants ○ Diseases can change history B. Scientists i. Robert Hooke​: invented microscope; described first microbes -- fruiting structures of fungi ii. Antonie van Leeuwenhoek​: observed 1​st ​ single-celled organisms -- bacteria C. Microbes Origin → “Spontaneous Generations” ​= theory that living creatures could arise without parents i. Francesco Redi​: ​meat/flies experiment​: only flies can make more flies; maggots arose when flies lay eggs = this experiment disproved the idea of spontaneous generation for large organisms → “Life force”​ present in matter, including air and oxygen ii. Lazzaro Spallanzani​: sterilized meat broth by boiling failed to grow microbes -didn’t allow air access iii. Louis Pasteur​: disproved “spontaneous generation” via ​Swan-necked flask experiment​: combined sterilization by boiling with access to air & whatever “life force” was in it *liquid remained sterile until microorganisms were introduced from outside D. Microbe Growth *To prove a particular bacterium caused a specific disease, pure culture of microorganisms were needed ● Each colony/spot of bacterial growth represents the progeny of one original cell ● Colonies are ​clonal ​– replicates of the original cell that started the colony Downloaded by StudyHelp IO ([email protected]) lOMoARcPSD|5053619 🧬2 II. ● Isolating bacteria colonies & growth in broth => isolation of clonal (replicates) population in pure culture (one kind of bacteria) ● Angelina & Walther Hesse discovered solid medium using agar allowed for bacterial culture to grow E. Koch’s Postulates i. Robert Koch ○ Germ Theory of Disease​: specific type of microorganism causes a specific disease ○ Methods and principles led to the isolation of pure bacterial cultures (1) Postulate #1: suspect organism should be present in ALL cases of disease & absent from healthy (ALL OR NOTHING) (2) Postulate #2: suspected organism should be grown in PURE CULTURE (3) Postulate #3: cells from pure culture of suspected organism should CAUSE DISEASE in healthy (4) Postulate #4: suspected organism should be REISOLATED (a) Limitations ○ Slow growing pathogens/pathogens may fail postulate ○ Pathogens may not be culturable w/ known techniques ○ Original host is not always available for inoculation (vaccination) (b) Alternatives ○ Animals > humans for studying bacterial pathogens & diseases ○ Related studies linking specific bacteria/bacterial communities w/ disease through molecular biology/immunology ○ Eliminate disease-causing microbe from infected host/prevent exposure to microbe should eliminate/prevent disease Biogenesis, Evolution, & Diversity A. Origins of Life → Stromatolites​ = clear fossilized evidence of bacterial communities i. Before first cell evolution, fundamental conditions were: 1. Essential elements​: To compose organic molecules 2. Continual source of energy​: Mainly nuclear fusion reactions within the sun 3. Temperature range permitting liquid water​: Otherwise metabolic reactions cease B. Prebiotic Soup​: ​hypothetical set of conditions present on Earth ~ 4 billions of years ago ● Small organic molecules arise abiotically from reduced chemical sparked by lightning => complex macromolecules that self-replicates & membrane compartmentalized C. Miller-Urey Experiment ● Stimulated chemical & energy conditions of prehistoric Earth's “water cycle” ● Began with hydrogen, ammonia, methane (atmosphere), water (ocean), condenser (to cool atmosphere to cool like rain), sparks (lightning) => Produced glycine, alanine, some other amino acids and AA derivatives ● Molecules of life can form in different environment w/ different starting chemicals & energy Downloaded by StudyHelp IO ([email protected]) lOMoARcPSD|5053619 🧬3 D. Metabolist Model ● Self-sufficient (thermodynamically favorable) abiotic chemical rxns formed cellular metabolism ● Accumulation of organic molecules => combined to make more complex forms (AA, lipids, etc.) => then catalyzed more organic molecule formation/trigger metabolism = nucleic acids/AA E. RNA ● Precursor to DNA ● In genome of some viruses ● Has catalytic activity ● Synthesizes proteins (in ribosomes) i. Structure ○ RNA bases can base-pair within same molecules (2​°​ structure) ○ Function necessary = base pairing conserved Metabolist Pro - Con - RNA Citric acid cycle (Krebs/TCA) is central to most organic biochemistry Many proteins use metal cofactors (hypothesized to be earliest metabolic catalysts) - Nucleotides are co-factors for many protein enzymes Slow (Iron-Sulfur catalysts) Without replication or informational material, how to reproduce/evolve? - Ribozymes (catalytic RNAs) have not been found to carry out some chemical reactions done by proteins RNAs are unstable - F. Molecular Clock/Evolutionary Chronometer → Molecular Clock​ = time info. contained in macromolecular sequence; ​average rate at which a species' genome accumulates mutations i. Requires alignment of homologous sequence in divergent species/strains to determine genetic relatedness ii. Universal molecule found in all organisms iii. Has conserved functions in all organisms iv. Strictly vertically transferred (generation to generation) v. Can’t be picked up from the environment/different cells vi. Constant substitution rate ​– sequence divergence proportional to time (slow evolving *genes that measure evolutionary time encode transcription & translation Downloaded by StudyHelp IO ([email protected]) lOMoARcPSD|5053619 🧬4 *widely used molecular clock = rRNA (SSU rRNA) -- 16S rRNA (bacteria); 18S rRNA (prokaryotes) ~ 1.5kb G. Translation ● Ribosome-binding site (RBS aka S ​ hine-Dalgarno ​sequence)​ on mRNA allows binding to 30s subunit ● Shine-Dalgarno site is complementary to sequence at the 3​’​ end of the 16sRNA *Ribosomes are in all cells, and machinery is conserved *In prokaryotes, translation is tightly coupled w/ transcription H. Scientist i. Carl Woese​: discovered prokaryotes lived in hot springs/produced methane & analysis of the 16S rRNA => organisms were distinct form of life I. Phylogenetics​: study of evolutionary relationships among biological individuals (species, groups of organisms, genetic sequences) ● computerized/molecular ● 16S rRNA genes are need to sequence bacterial species relationships ● Sequence alignment​: find the most similar sequences & work backwards J. Diversity ● Most biodiversity is microbial (archaea are not bacteria) ○ Similar size, shape ○ Different cell wall and membrane lipid biochemistry ○ Different basic metabolism ○ Ribosomes more similar to eukaryotes ● Microbes are found in all environments with life ● Archaea & bacteria share 16S rRNA sequences in ribosome K. Endosymbiont Theory​: o​rigin of eukaryotic cells from prokaryotic organisms ​(controversial b/c it implies polyphyletic over monophyletic) - Mitochondria WERE bacteria - Chloroplasts WERE cyanobacteria - Infected/eaten by other species - Ended up living together inside i. Eukaryotes ○ Similar to archaeal DNA ○ mitochondria/chloroplast DNA similar to bacteria DNA → Endosymbionts​ = microbes livings symbiotically inside a larger organism *endosymbiotic microbes make essential nutritional contributions to host animals ii. Mitochondria behave like endosymbiotic organisms: ‒ Live inside of another organism ‒ Reproduce independently ‒ Contain their own circular genomes and prokaryotic-like ribosomes (w/ 16S) ‒ Extreme reductive evolution III. *prokaryotic genetic info. changed by mutation/acquisition of genetic material within generations Genomes & acquisition of genetic information A. Genome → Genome​ = entire genetic complement of DNA in a cell i. Organization ○ 490-4,900 kb ○ Bacterial genomes have little non-coding DNA (untranscribed) ○ No introns ○ Fewer repeated sequences ○ More compact genomes Downloaded by StudyHelp IO ([email protected]) lOMoARcPSD|5053619 🧬5 B. Genes → Genes​ = ~1 kilobase pairs in length ○ Structural gene produces functional RNA which encodes protein for translation ○ DNA control sequence regulates expression (transcription) of structural gene - the promoter (does not encode RNA) (i) Functional Units ● Genes can operate independently or tandem w/ operon → Operons​ = polycistronic (many transcribed together on single transcript) *Genes in bacteria are lowercase and italicize *Proteins produced from genes are capitalized *Operons not include many genes can be written together as they appear or described as one operon C. Nucleoid → No membrane separates DNA from cytoplasm → Single Loop of double-stranded DNA (single molecule of DNA) → Attached to cell membrane: DNA origin → Replicates once for each cell division starting from DNA origin i. Organization ○ Forms ~50 Loops of chromosomes called ​domains ○ Each domain = DNA supercoiled and partly compacted by DNA-binding proteins ○ Large circular/linear c’somes ■ Episomes (plasmids)​ – circular extrachromosomal DNA ○ Genome copy # varies D. Mosaic Nature of Genomes → Genomic islands​ = regions of genome w/ signs of horizontal transfer → Homologs​ = genes w/ shared ancestry → Orthologs​ = genes derived from other species → Paralogs​ = genes created by duplication within genome ○ Mutations of single bp is slow, but gained overtime ○ Deletions/insertions ○ Natural selection E. Bacteria & Gene Acquisition → Horizontal Gene Transfer​ = from other species → Vertical Gene Transfer​ = from parent to child ○ Transferred from environment ○ Some beneficial & initiated by bacteria themselves ○ Some harmful & forced on bacterial cells (i) Advantageous Traits ● Antibiotic-resistance genes ● Pathogenicity islands (PAIs) : encode harmful gene pathogen to cause disease ● Genes to produce metabolites *Genes are passed vertically in bacteria F. Gene Transfer Process Downloaded by StudyHelp IO ([email protected]) lOMoARcPSD|5053619 1. Transformation​: DNA taken up from environment (can be induced) ○ Natural transformation (requires competent/artificial manipulation) ■ Uptake competent DNA from environment ■ Use indiscriminate DNA as food ■ Protein complexes @ cell surface take up foreign DNA ■ Use specific DNA to repair damaged genomes ■ Stress can induce competence ■ Acquire new genes through horizontal gene transfer (1) Discovery -- discovered w/ morality experiment w/ mice w/ same bacterium: ● Smooth -- w/ capsule, caused disease ● Rough -- w/o capsule, did not cause disease 🧬6 Rough + heat = smooth bacteria = disease 2. Transduction​: bacteriophage carries infected host DNA from one cell to another cell ○ Bacteriophages: viruses that attack bacteria, but does not harm eukaryote ○ Injects viral DNA into host => replicated viral DNA packed into new particle to be released to infect other cells (1) Generalized transduction​: can transfer any gene from a donor to a recipient cell ● Host genome hydrolyzed & fragments moved into new phage particle (2) Specialized transduction​: can transfer only a few closely linked (adjacent) genes between cells ● Phage integrated into bacterial genome & cuts it out … parts of host genome move with it into phage particle 3. Conjugation​: cell-cell contact (sex pilus) ○ Transfer of DNA from one bacterium to another after cell-to-cell contact; “bacterial sex” iniitatied by pilus protuding from donor cell ■ Pilus encodes genes on fertility plasmid/F factor (makes own transfer machinery) ■ Recipient cell (F-) receives F factor => F+ & ability to transfer DNA *Some bacteria can transfer genes across biological domains (Bacteria & Eukarya) G. Gram-Negative Bacteria ○ CaCl​2​ & low temp. enhances competence making membrane more permeable to DNA ○ Can be driven into competent bacteria cells by heat-shock/electroporation (pulse of high voltage electricity) Downloaded by StudyHelp IO ([email protected]) lOMoARcPSD|5053619 ○ Physiological state of cell: peaks during early log phase growth H. Fate of DNA entering cell ■ Plasmids can coexist & replicate in the cell as extrachromosomal DNA ■ DNA can incorporate into the chromosomal DNA by recombination ■ Most forgein DNA will degrade by restriction endonucleases in recipient cell I. Recombination ​= combination of 2 DNA molecules ; requires specific recombination proteins (Rec), homologous DNA sequence 1. RecBCD protein machine unwinds donor DNA 2. Copies of RecA bind to revealed single strand 3. RecA finds homology to recipient DNA 4. RecA invades recipient & donor to homologous stretch of recipient (cross-over) 5. DNA rearranges, junction is cleaved & any breaks repaired a. Generalized​: requires long stretch of sequence homology (>50bp) b. Site-specific (specific)​: requires little sequence homology but a short 10-20bp sequence recognized by recombination enzyme (recombinase) *DNA restriction & modifiction during exchange (“safe sex”) … involves enzymatic cleavage of alien DNA by restriction endonucleases @ restriction sites & methylation *foreign DNA w/o native DNA methylation pattern is destroyed IV. Genomes & replication A. Bacterial DNA replication ● Nucleoid is replicated via replisome complexes, beginning @ origin of replication ● Replication of cellular DNA in most cases is semiconservative​: e​ach daughter cell receives one parental and one newly synthesized strand B. Replisome ● DNA helicase​: unwinds the two strands of DNA ● SSBs (single-stranded DNA binding proteins)​: keep the single DNA strands apart during DNA synthesis ● Clamp loader & sliding clamps​: recruit DNA polymerase III and tether it to the DNA ● DNA polymerase III​: synthesizes new DNA strands ● DNA primase​: produces RNA primers ○ Primase makes RNA that act as primers (3’-OH group) for DNA polymerase III to synthesize new DNA strands *RNA primers are required for DNA replication *DNA primase = RNA polymerase C. Replication Forks → Leading strand​: steady growth following DNA helicase (5’-3’) → Lagging strand​: okazaki fragments (3’-5’) Downloaded by StudyHelp IO ([email protected]) 🧬7 lOMoARcPSD|5053619 🧬8 *DNA primase moves to new sites as fork moves … DNA polymerase III synthesizes ~1 kb DNA after each RNA primer D. Completion of DNA replication ● RNase H​ removes the RNA primers ● DNA polymerase I​ fills the gaps in the DNA strand ● DNA ligase​ seals the junctions E. Termination of Replication ● Ends @ termination (ter) sites opposite to origin ● Topoisomerase IV​ catalyzes a breaking & rejoining event that passes the c’somes F. Plasmids → Plasmid ​= replicon: depends on chromosomal genes such as DNA polymerase: origin can be stringent/relaxed ○ Extrachromosomal DNA usually circular & varying in size (kb/Mb) ○ Contain genes that benefit host cell i. ii. iii. iv. *Can be moved between cells via transformation or conjugation a. Stringent​: Plasmid replicates only w/ c’some b. Relaxed​: Plasmid replication is independent of chromosomal replication Inheritance ○ High copies of plasmids segregate randomly to daughter cells = inc. chance of daughter cell inheriting some plasmids ○ Plasmids carry benefits (e.g. drug resistance, ability to cause disease) ○ Low copies reduces metabolic demands on cell; inc. fitness of cells making plasmids Segregation - ParMRC system - parC​: sequences on the plasmid that bind to ParR - ParR​: a DNA-binding protein that binds to plasmid - ParM​: an actin-like protein that forms filaments Addiction ○ 2 adjacent genes on plasmid encoding toxin(protein)-antitoxin(RNA) module in plasmids for self-maintenance ○ Pressure on cells to maintain plasmids ○ Cells need to maintain plasmid to have constant source of antitoxin against the plasmid-expressed toxin Replication ○ Bidirectional ○ Unidirectional “rolling circle” 1. Starts at a nick on a single DNA strand 2. Provides 3¢-OH for synthesizing a new strand (plus strand) Downloaded by StudyHelp IO ([email protected]) lOMoARcPSD|5053619 🧬9 V. 3. The old plus strand is released and used as the template to synthesize the new minus strand (no Okazaki fragments) Mutation & DNA repair A. Mutations → Mutant​ = organism of normal species (wild type), but different - containing mutations → Mutations​ = heritable changes in the nucleic acid bases in the genome of organism (RARE!!!) → Spontaneous mutations​ = occurs @ low rate due to absence of agged agent ; error in DNA replication → Induced mutations ​= created by treating w/ mutagens -- mutagenesis i. Types of Mutagens (1) Physical​: radiation or heat ● UV & ionizing radiation cause the formation of toxic oxygen radicals ● Radicals => dimerized thymine ● Distorted DNA structure/can introduce mutations on replication (2) Chemical​: compounds interfere with DNA chemistry – many are carcinogens ● Base analogs: similar structures to natural bases (added during DNA replication … leads to point mustation b/c incorrect pairing) ● DNA-modifying agents - change base’s structure & pairing characteristics (ex: G with A or T instead of C) --- wrong pairing!!! ● Intercalating agents - distort DNA inducing single nucleotide insertion/deletion (3) Biological​: insertion of transposons ii. Types of Mutations: 1. Point mutation​ = change in single base 2. Transition​ = purine → purine/pyrimidine → pyrimidine 3. Transversion​ = purine ↔ pyrimidine 4. Inversion ​= DNA flipped orientation 5. Reversion​ = DNA mutates back to original sequence a. Silent mutation​: does not change the AA sequence b. Missense mutation​: changes the AA sequence to another c. Nonsense mutation​: changes the AA sequence to a stop codon d. Frame-shift mutation​: changes the open-reading frame of the gene B. Ames Test​ = test for mutagen strength ● Used bacterial mutant within hisG gene ● Place on defined medium (w/o his) + chemical w/ unknown mutagen activity ● Mutagen => reversion mutation of hisG back to functional form *More colonies = stronger mutagen C. DNA Repair ■ Hypermutation phenotypes​ = rapid accumulation of mutations Downloaded by StudyHelp IO ([email protected]) lOMoARcPSD|5053619 🧬10 VI. ○ Proofreading​: correction of mismatch by DNA polymerase III during DNA replication ○ Photoreactivation​: Photolyase enzyme binds to a pyrimidine dimer => UV radiation & cleaves the cyclobutane ring 1. Excision Repair ​(most common) i. Cut out duplex DNA & recopy remaining complementary strand (CUT, COPY, PASTE) ii. Enzyme removes damaged nucleotide(s) iii. DNA polymerase copies template to replace cut strand iv. DNA ligase seals backtogerher (a) Nucleotide excision repair ● Recognizes damage that causes distortion in DNA structure ● An endonuclease removes a patch of single-stranded DNA containing damaged bases, including dimers (b) Base-excision repair ● Recognizes and repairs bases that (mostly) do not distort DNA structure ● In general, recognition is at damaged bases, not a distorted DNA helix (c) Methyl mismatch repair ● Recognizes mismatches missed by proofreading ● Use DNA methylation as an indicator for the newer strand – containing the error 2. SOS response *extensive DNA damage = SOS response i. LexA prevents expression of SOS gene (OFF!!!) (a) RecA-ssDNA activates protease/self-break of LexA = genes activated (ON!!!) ii. RecA (single-strand DNA binding protein) inactive LexA when DNA damaged iii. DNA mutase​: error prone DNA polymerase - repair DNA, but make a lot of mutations 3. Double-strand break repair i. Non-homologous end joining (NHEJ) ■ Ku-family protein bind broken ends ■ Ligase to fix break ii. Recombination ■ Requires homology ; RecA mediated; restores replication fork D. Transposons (transposable elements) ​= “jumping genes”; DNA that can hop from 1 place to another (transposition) *large amounts of transposons in living organisms Transcription & Translation A. Transcription ● Copy DNA into RNA (5’ to promoter) ● Gene coding region = protein ● -35 & -10 (Pribnow Box) is where RNA polymerase binds Downloaded by StudyHelp IO ([email protected]) lOMoARcPSD|5053619 🧬11 i. VII. Initiation (1) 𝝈​ factor binds to DNA (2) 𝝈 ​factor attaches to core enzyme in promoter region (3) Core enzyme unwinds DNA @ promoter (open complex) -- allows RNA polymerase to add to leading strand (4) 𝝈 ​factor released ii. Elongation (1) Synthesizes RNA (5’-3’) by adding complementary bases to template strand -- has U instead of T iii. Termination → Rho​ = helicase (unwinds nucleic acids) (a) Rho-dependent 1. Binds mRNA & moves along 2. Catches up to RNA polymerase & kicks off (b) Rho-independent 1. GC (strong) stem loop forms (2° structure) 2. RNA polymerase pauses b/c of GC stem loop is bulky 3. Destabilized @ poly-U site -- UA (weak) 4. mRNA breaks off & DNA polymerase released B. RNA Polymerase​: protein complex uses nucleic acid template to generate RNA polymer → Core enzyme ​= RNA synthesis → Sigma Factors ​= needed for initiation of RNA synthesis; recognizes -10 & -35 promoters ○ 𝝈​70 = “housing keeping” factor; needed for gene homeostasis *Core enzyme + Sigma factor = ​Holoenzyme C. Translation ● RNA to protein ● Ribosome-binding site (RBS aka Shine-Dalgarno: ​complementary to sequence at the 3​’ end of the 16sRNA) on mRNA allows binding to 30s subunit *Transcription & translation = coupled process in ​prokaryotes​: no nucleus → Polysomes ​= multiple ribosomes bind to each mRNA molecule Structure of microbial cell *Most bacteria have: thick complex outer envelope, small genome, & tight cell functions A. Prokaryotes vs. Eukaryotes B. Bacteria Cells i. Surface area vs. volume ○ Large surface / volume (allow for faster growth rate) Downloaded by StudyHelp IO ([email protected]) lOMoARcPSD|5053619 🧬12 ii. iii. iv. v. vi. ○ Faster growth rate = rapid transport rates, excretion of waste, & import of nutrients ○ Large membrane = more active metabolism Shapes 1. Cocci (coccus)​ - spheres 2. Bacilli​ - rods 3. Vibrios​ - bent rods 4. Spirochetes​ - helical → Morphogenesis​ = changes in cell shape → Pleomorphic​ = cells have multiple shapes ■ Changes during growth -- smaller w/ age ■ Nutrients limitation => inc. surface/volume ratio ■ Response to environmental cues ■ Can undergo filamentation during stress Cytoskeleton 1. FtsZ​ : forms “Z-ring” in spherical cells 2. MreB​ : forms coil inside rod shaped cells 3. CreS “crescentin” : forms polymer along inner side of crescent-shaped bacteria Model ➢ Cytoplasm: gel-like membrane inner ➢ Cell membrane: encloses cytoplasm ➢ Cell wall: covers cell membrane ➢ Nucleoid: non-membrane-bound area of cytoplasm that contains looped coil c’somes ➢ External structures: pili/fimbriae or flagella Cell membrane ○ Double layer of phospholipids - lipid bilayer (permeability barrier) ○ Fluid mosaic model - integral proteins embedded in lipid membrane helps w/ transport, making energy, & senses environmental changes → Hapanoids​ = molecules that strengthen lipid membrane Bacterial Cell wall → Sacculus​ = bacteria made of peptidoglycan (murein) ■ Single interlinked molecule w/ sugar chains wrapped in circle around cell & linked by peptides ○ Rigid structure outside of phospholipid membrane ○ Enables bacteria to withstand ​turgor pressure (​force within the cell that pushes the plasma membrane against the cell wall​) due to dissolved solutes in cell → Peptiodo​ = 4 AA linked by peptide Downloaded by StudyHelp IO ([email protected]) lOMoARcPSD|5053619 🧬13 → Glycan = N-acetylmuramic acid (NAM) + N-aceylglucoamine (NAG) disaccharide ○ Can be used to distinguish groups of bacteria C. Gram Stain i. Gram + ​: blue & thick ○ Crosslink peptidoglycan w/ peptide interbridge → Teichoic acid ​= threads through peptidoglycan to strengthen wall → Lipoteichoic acid = links cell wall to cell membrane - maintains cell structure (absence in Gram -) ii. Gram - ​: pink & thin → Crosslink peptidoglycan cross-linking VIII. IX. w/ direct Outer membrane - protection barrier (IN: phospholipid; OUT: LPS) Outer membrane has ​porins​: proteins for transport & ​murein lipoprotein​: link to peptidoglycan Downloaded by StudyHelp IO ([email protected]) lOMoARcPSD|5053619 🧬14 X. → Lipopolysaccharide (LPS) = Lipid A + core polysaccharides (~5 sugars) + O-specific polysaccharide (~200 sugars; protective & stabilizing layer) A. Other outer coverings → Glycocalyx​ = network of polysaccharides from cell surface → Capsule​ = organized glycocalyx; difficult to remove → S-layers = all Archaea & many bacteria; layers of protein/glycoprotein that protect against pH, viral infection, extracellular enzymes Transport & secretion A. Gradients & energy ○ Chemical gradients can store energy ○ When gradient is released … energy can be used to drive cellular processes B. Transport → Transporters = proteins that help polar, charged, & large molecules cross the membrane using a channel i. Passive Transport =​ (follow gradient, no energy) [High] → [Low] 1. Simple Diffusion = small uncharged molecules (O​2 & CO​2​) & weak acids/bases can pass through membrane → Osmosis​ = diffusion of water across membrane 2. Facilitated diffusion ​= specific transporters allow diffusion of substrates across membrane ii. Active Transport =​ (against gradient; requires energy) [Low] → [High] 1. Primary AT​ = direct use of ATP (via ATP hydrolysis & coupling) 2. Secondary AT​ = driven by gradient of another solute (coupled transport) (a) Symporter​: multiple things same way against gradient (b) Antiporter​: multiple things different ways against gradient (c) Uniport​: moves 1 thing across against gradient → ABC Transporters (​A​TP-​B​inding C​assette) - Solute-binding proteins (SBP)​: substrate specific (escort specific substrate to transporter) + solute - ATP-hydrolyzing protein provides energy for final transport via conformational change of transporter 3. Proton-Motive Force = ​promotes movement of protons across membranes downhill the electrochemical potential *energy can have the potential to make & store energy C. Group Translocation “phosphotransferase system” (PTS) = sugar transport 1. Enters cell via facilitated diffusion w/ specific transporter Downloaded by StudyHelp IO ([email protected]) lOMoARcPSD|5053619 🧬15 2. Substrates are modified by phosphorylation => gradient maintained! 3. Use energy from phosphoenolpyruvate (PEP) to attach phosphate to sugar during transportation 4. Maintains glucose gradient to drive entry by modifying glucose to G6P D. Bacterial Secretion System​ = movement of proteins out of cytoplasm ○ Proteins can be moved in unfolded/folded depending on system ○ Usually secreted proteins have signal tag telling secretion machinery to move protein out E. Sec System​ = transport of unfolded proteins requiring ATP hydrolysis to move out ○ Sec-dependent secretion proteins have speci AA sequence @ N-terminus, ​signal peptide ○ Sec-dependent uses sec complex to move signal-peptide containing proteins into periplasm ○ Signal peptide is cleaved by signal ​peptidase​ during secretin F. Cell-cell secretion ● Usually used to inject toxins/harmful molecules (mechanism for competition) ● Large needle-like protein complexes used from secretion ● Injection can be into eukaryotic/bacterial cells i. Type III: inject into euk. cells only ii. Type VI: inject into euk./bac. cells iii. Sec-independent systems Downloaded by StudyHelp IO ([email protected])