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Cell and Molecular Bio Final Notes

by: Karen Notetaker

Cell and Molecular Bio Final Notes BIOL 231

Karen Notetaker
University of Louisiana at Lafayette

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These notes cover the material learned before the final exam.
Cell and Molecular Biology
Patricia Mire-Watson
Biology, Cell, Molecular, final, exam
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This 39 page Bundle was uploaded by Karen Notetaker on Sunday April 17, 2016. The Bundle belongs to BIOL 231 at University of Louisiana at Lafayette taught by Patricia Mire-Watson in Spring 2016. Since its upload, it has received 12 views. For similar materials see Cell and Molecular Biology in Biological Sciences at University of Louisiana at Lafayette.

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Date Created: 04/17/16
Chapter 6 4/19 Sunday, April 28, 2013 7:55 AM Fig. 6-28 Mutations rare due to repair mechanisms Ex. Humans & whales diverged ~50-100 mya; identical seqs at places in genome Fig. 6-19 Replication error: usually point mutations (1bp) Ex. sickle-cell  anemia:  A  to  T  substitution  in  β-globin gene. glutamic acid → valine glutamic acid: charged, acid lost p+ = (-) charge valine: nonpolar DO NOT behave same in H2O environment -hemoglobin long fibrous = low O2 = not globular shape; low O2 to tissues -mutation would be selected against – don’t affect organ to reproduce or is an advantage = malaria malaria: heterozygous 1 alleles = recessive trait homozygous for 2 alleles = sickle cell Fig. 6-13 Repair Mechanisms: 1) Proof Reading: during replication on DNA poly checks bp; if incorrect, replaces nt (usu correct). nt = nucleotide same polymerase Fig. 6-22 2) Mismatch repair: After proof reading, protein complex finds mismatch, deforms helix, excises piece. DNA poly makes new piece Ligase seals gap. poly = polymerase New strand recognized? Before ligase, nicks (gaps) after proofreading & before ligase Fig. 6-20 Mutation in mismatch proteins = accumulate mutations with time Ex. Inherited colon cancer Fig. 6-23 Spontaneous Mutations: Depurination = loss of A or G (missingteeth) Deamination = loss of NH2 fr C; changes to U Deamination = loss of NH2 fr C; changes to U chemically Fig. 6-25 Deaminations: G to A base sub after replication Depurinations: base pair del after replication del = deletion Fig. 6-24 Environmental mutations: UV = links pyrimidine(thymine dimer) Replication/ transcription problems Fig. 6-26 3) Long – term repair enzymes: during  cell’s  life. 3 steps: excision, synthesis,& sealing Fig. 6-27 ds DNA break mutations: radiation, strong oxidizingagents, some metabolites ds= double strand dangerous if happens in middle of gene will not be transcribed into functional gene 4) Nonhomologous end joining: “Quick  &  dirty” Lose some nts useful in noncoding DNA nts = nucleotides nuclease chews off ends ligase seals gap lost some nucleotides exons (coding) – introns (noncoding = doesn’t matter if done here) Fig. 6-29 5) Homologous recombine: more accurate BRCA genes: tumor suppressors, homol recombo proteins breast cancer – inherited active to prevent cell from not normal from producing Nearby, similar chromosomes (chromatids/ homologs) similarto Intact chromosome template to repair broken chromosome Fig. 6-30 Homol recombo during meiosis: homologs cross-over; exchange pieces. Increases genetic diversity Increases genetic diversity Fig. 6-32 MGE (Mobile Genetic Element) mutations DNA transposons (move as DNA). Transposases gene + seqs. cause movement. Some antibiotic resistance genes (bacteria) Fig. 6-33 Transposase enzyme moves transposon: Cut & paste = moved from donor DNA to target DNA replicative = replicated; copy inserted into target DNA Fig. 6-34 Retreotransposons (move as RNA). RNA poly transcribes RNA; reverse transcriptase (RT encoded by MGE) makes DNA copy; DNA copy inserts elsewhere. Most eu. MGEs important in humans Chapter 6 4/22 Sunday, April 28, 20138:09 AM Figure 6.34 • Retro transposons (Move as RNA). ○ One type of MGE • RNA poly transcribes RNA • Reverse Transcription (RT encoded by MGE) makes DNA copy ○ DNA copy inserts elsewhere. Most eukaryote MGE's (Mobile Genetic Element) ▯ Retro- Something going backwards ▯ Reverse transcription □ Make DNA-DNA and RNA-DNA ○ Happens on same/different chromosomes Table 6.2 • Viruses= intercellular MGE's ○ DNA or RNA w/ Protein coat • Retroviruses (ssRNA)only in Eukaryotes, many human diseases Figure 6.36 DNA Virus • Attach to plasma membrane; inserts into genome ○ Host cell replicates Genome/ makes proteins ○ New virus exists • Symptoms- 4m cell lysis ○ Fever, inflammation Figure 6.38 Retrovirus • Intergrase Gene + RT ○ Virus carries reverse transcriptase on the end • RT makes single strand DNA copy than double stranded DNA. Intergrase inserts double stranded DNA into host genome • DNA transcribed into RNA. Some RNA translated into proteins • New Virus exits ○ Can hide out, then later become active ▯ Shingles Figure ? • Evolution despite repair mechanisms ○ Errors escape repair, especially point mutations (nt subs, adds, deletes) ○ "repair" mechanisms ▯ Nonhomologues repair (quick and dirty) □ Mechanism for repairing double-strand breaks in DNA in which the two broken ends are brought together and rejoined without requiring sequence homology. ▯ Homologues recombine during meiosis create genetic diversity ○ MGE's change DNA • Natural selection favors beneficial, tolerates neutral and diminishesdetrimental (drives evolution) Chapter 7 4/22 Sunday, April 28, 2013 8:54 AM Figure 7.1 Central Dogma Expression of Genes • DNA stores genetic info, replicated for daughter cells • Transcription ○ Information flows from DNA-RNA • Translation ○ 4m RNA to protein Figure 7.3c • RNA= ribonucleic acid ○ Linked by Phosphodister bonds ○ U instead of T ○ Backbone ▯ Ribose sugar and phosphates Figure 7.5 • RNA's mainly ss (mRNA) ○ Some double stranded forming 3D shapes ▯ H-bond b/t bps) for function □ tRNA Table 7.1 • mRNA, rRNA, tRNA protein synthesis,miRNA, sRNA other functions ○ Mi-mircro ○ s-small Figure 6.17b- Replication vs. Figure 7-7 Transcription • Similarities 1. DNA helix opens; template 2. Poly: Phosphoester bond formation/NTP hydrolysis(nucleoside triphosphate) i. Provide energy (NTP hydrolysis) 3. New nucleotide added to 3' end of polypeptide 4. New strand antiparallel and complementary i. Base pair matching (A-T/U) (G-C) • Differences Replication Transcription Product DNA RNA # of Templates 2 1 Proteins Helicase, Primase, DNA RNA polymerase (bacteria) polymerase, Clamp polymerase, Clamp Primer RNA w/ primer None "de nova" Fate of New Strand Remains H-bonded to Released from template template Part of DNA involved All Portions (genes) Proofreading Yes No Chapter 9 4/22 Sunday, April 28, 2013 8:29 AM Figure 9-29 • 45% human DNA is MGE. Most retro transposons • 20% LINES (Long INterspersed ElementS) • 12% SINES (Short INterspersed ElementS) (ALU) • 7% retroviral like • 1% DNA transposons • Most mutate; no longer move ○ 7% repeat/ duplicates ○ 30% non-repetitive DNA ○ Genes 20%, but only 1.5% are exons ▯ Exon: Segment of a eukaryotic gene that is transcribed into RNA and expressed; dictates the amino acid sequence of part of a protein. • Sequences on ends, that are mutated aren't recognized by retro transposons so they don't move • Disorder from transposons cause problems ○ Hemophilia • Genes ○ Coding regions- axons ○ Not so much of genes you have, but the way they are expressed Chapter 6 4/24 Sunday, April 28, 2013 8:10 AM Fig. 7-9 3 Steps Transcription: Initiation: RNA poly binds promoter Elongation: Poly synthesizes RNA at start site thru terminator Termination: Poly stops synthesis at stop site, releases DNA & RNA Prok: Sigma factor recognizes promoter, releases during elongation Fig. 7-10 Conserved seqs. in promoter pt. RNA poly forward. Start  site:  RNA  poly  bps  in  5’  to  3’  direction,  uses  3’  to  5’  template. Poly stalls at terminator; transcribes until stop site. TATA box – bact & pro promoters poly to bind →directionality – new strand antiparallel to template read 3-5 in 5-3 direction bottom strand on rt. read through terminator seq. = stalls get terminator in RNA reaches stop & stops Table 7-2 Prok; 1 RNA poly Euk; 3 polys. RNA poly II transcribes most; all protein coding genes (mRNA) 5S RNA = ribosomes RNA poly 2? Fig. 7-12 Euk: General transcription factors (TFs) assistPoly II 1.TFIID binds promoter TATA box w/ TBP 2.Poly II + other TFs bind promoter 3.TFII H opens DNA & phosphorylates polyII tail functions as helicase polyII has a tail kinase = to polyII 4.Conformation change releases polyII from TFs for elongation nucleosidetriphosphates – UTP, ATP, GP, GTP NRG phosphoester bonds Elongation/ termination similarto prok. Euk;  mRNAs  begin  as  immature  (1°)  transcripts;  processed  before  leaving  nucleus 5’  capping splicing 3’  polyadenylation 3’  polyadenylation Processing enzymes on tail of poly II Fig. 7-16a Cap & polyA increase stability of mRNA aid in nuclear export, identify transcript as mRNA some  don’t  have  polyA  tails use to catch polyA tail = polyTs – magnet beads Fig. 7-17 coding seq = compare pro – eu genes = differ Most prok genes = only coding seqs (after promoter) Most euk genes = coding seqs. (exons) interrupted by noncoding seqs. (introns) initial  1°  transcript  formed yes will have both mature only has = coding Fig. 7-19 Splicing by spliceosome(complex). Spliceosome core: snRNPS (snurps); small nuclear RNAs (snRNAs)& proteins. snRNAs recognize intron/exon boundaries; binds & cleave RNA. Removes introns Fig. 7-21 Benefits of Introns: Alt. splicing of mRNA = different proteins from same gene Longer genes more susceptible to mutations = raw material for evolution Chapter 7 4/26 Sunday, April 28, 2013 8:10 AM Figure 7.23 Gene Expression • A: Eukaryotes ○ Exons, code ○ Introns, Non-coding • B: Prokaryotes ○ Splicing gets rid of introns ○ Exons, not all always in RNA ▯ DO not know why some exons stay/some leave, also, do not know why particular ones stay/go • RNA cap at 5' methylated; tail at 3' poly Figure 7.24 Why the language? • Each codon on mRNA= 3 bases ○ GAC ○ Possiblecodons ▯ 4^3 = 64 □ 4=number of bases; 3=3 positions available • 20 amino acids • Degenerate ○ 20aa's; most aa's more than 1 codon • Specific ○ Each codon= 1 aa ○ 61 code for aa's ○ 3 stop codons ▯ UAA ▯ UAG ▯ UGA Figure 7.25 • Codons read 5'-3' during translation. Reading frame by start codon (AUG codes for Met) ○ Methylene Figure 7.28 • tRNA ○ 3-D cloverleaf adaptor ▯ anticodon (complimentary to codon) on one leaf ▯ AA binding site on stem Figure 7.29 • tRNA's charged w/ aa by tRNA synthase ○ Catalyzes bond b/t aa and tRNA/ATP hydrolysis • Specific aa depends on anticodon. Different synthase for each aa • Specific aa depends on anticodon. Different synthase for each aa ○ tRNA can be reused; recharged ▯ Get degraded after X amount of use Figure 7.30 • 400nm • mRNA and charged tRNA meet at ribosomes for translation Figure 7.31 • Ribosomes ○ Marco molecular complex (euk=4200 KD) ▯ ~82 proteins and 4 mRNAs ▯ Lg. and Sm. Subunits together □ Make it functional Figure 7.32 • Four binding sites ○ mRNA site on small subunit ○ 3 sites for tRNAs ▯ A site: aa-tRNA ▯ P site: Polypeptide-tRNA ▯ E site: empty-tRNA exits Figure 7.35 Initiation 1. Small subunit + met-tRNA bind mRNA at start codon 2. Lg. Subunit binds, Met-tRNA in P site 3. Another aa-tRNA binds in A site 4. Peptidyl transfer a. Met-tRNA hydrolysiscoupled to peptide bond formation b/t Met and second aa. Ribosome moves 1 codon (5' to 3' on mRNA) i. Transfer peptide to tRNA Figure 7.33 Elongation 1. Polypep-tRNA in P site, empty tRNA in E site exits, next aa-tRNA binds A site. 2. Peptidal transfer b/t last aa in P site and aa in A site 3. Ribo moves placing polypeptide-tRNA in P site Figure 7.37 Termination • Stop codon in A site; release factor binds,everything releases ○ Ends translation ○ mRNA reused until degraded Table 7.3 • Several antibiotics exploit differences b/t Euk. And Prok. Transcription or translation Figure 7.34 • 23s rRNA of lg. subunitis peptidyl transferase Ribozyme (RNA enzyme) Table 7.4 • Most ribozymes cleave/splice RNA or DNA Chapter 8 4/29 Sunday, May 5, 2013 7:20 AM Figure 8.1 • Differentiation = cells with same genome become different w/in a multicellular organism • Proteome= characteristics/functions • Selective gene expression=specificproteome ○ Neuron ○ Lymphocyte- produce antibodies ○ They have the same genome, but different proteomes Figure 8.2 a and b • Differentiation ○ Alter genome or expression of genome ▯ Is genic material intact, to be able to produce whole new being □ Example one : transfer nucleus from skin cell of adult frog to enucleated; unfertilized egg cell (tadpole) ▯ Clone of the adult □ Example two: Root cells from carrot, one cell develops into embryo and adult sporophyte (plant) ▯ Most plants cell totipotent (produce all other cell types) □ Example Three: Epithelia cell from first cow fused w/ an enucleated unfertilized egg cell of a second cow. All "zygote" divide in vitro, transplant embryo into second cow. Calf is clone of first cow. ▯ Downside, using adults ◊ Telomere on chromosome is shorter, so cells have trouble functioning □ Conclusion ▯ Different cells do not change genome □ Different cells produce "housekeeping" proteins for growth and survival and special proteins to perform particular functions. □ All cells express housekeeping genes but only subset of specialized genes □ Housekeeping proteins: ▯ RNA polymerase, repair/transcription proteins, cytoskeleton proteins, nuclear pore proteins, etc. □ Specialized proteins: ▯ Hemoglobin, antibodies, neurotransmitters, etc. Figure 8.3 • How do cell control which gens get expressed into functional protein? ○ Transcriptional regulation most common, no unnecessary intermediate formed Chapter 8 5/1 Sunday, May 5, 2013 7:20 AM Figure 8.4 • Genes have regulatory DNA sequences (10-10000) recognized by transcription regulators (TRS) ○ Act as switches for transcription ▯ Factors involved in eukaryotic polymerase at promoter ○ Transcription regulator binds in the major groove protein and DNA = H+ bonding ▯ Does not interfere w/ base pairs ○ Specific Transcription regulators for different sets of gens ○ TR in major groove attach non-covalent to sideof bases ▯ ~ 20 interaction= specificity and strength Figure 8.5 • Transcription Regulators DNA binding motifs (Domains) a. Homeodomain: 3 Alpha helices b. Zinc Finger: Alpha Helix + Beta Sheet + Zinc c. Lucien Zipper: 2 Alpha Helices from dimmer straddle DNA i. Dimer = 2 subunits ii. Lucien holds configuration to DNA Figure 8.6 • Bacteria ○ Regulates DNA sequences (operators) in promoters bind TRS (repressors) control suite of genes transcribed as singlemRNA using same promoter (operon) ▯ Ex: Genes for tryptophan synthesis enzymes Figure 8.7 • Repressor activated by Tryptophan in cell a. Trp low: repressor inactive, cannot bind operator; RNA polymerase binds/transcribes operon b. Trp high: Repressor active, binds operator; RNA polymerase can't bind/ operon not transcribed Figure 8.8 • Bacteria: Activator sites (AS) Near promoter bind activator proteins (AP) • AP's assist RNA polymerase binding to "weak" promoters, increase transcription ○ Enhance transcription by assisting RNA polymerase to bind to promoter Figure 8.9 • Cyclic cAMP (CAP) binds to Activator site ○ Lac Operon transcribed unless repressor bound to operator ▯ CAP □ Activator protein, enhance transcription □ Activator protein, enhance transcription □ Lac Operon, expressed by the same ▯ Ex: Bacteria Lac Operon regulated by CAP (activator protein) and repressor ○ Orange- Lac Operon ○ Blue-CAP binding site ○ Green- Repressor/Operator ▯ Controlled by the amount of lactose/glucose present ○ ****Bacteria use Lactose**** ○ Lac genes; proteins for lactose uptake/digestion on ▯ Glucose low/lactose high Figure 8.10 • Euk: Aps bind AS (enhancers) far from gene ○ Mediator interact w/ transcription factors ○ Mediator interacts w/ AP and general transcription factors (DNA loops) ○ Repressors prevent TF and RNA polymerase binding Figure 8.11 • H3 covalently bonded ○ Gene expression; remodeling chromatin histone remoliving complex • AP's recruit histone modifying enzymes and chromosomes remodel complex; increase gene expression • Repressors recruit enzymes to remove histone tags; decrease gene expression Chapter 8 5/3 Sunday, May 5, 2013 7:20 AM Figure 8.17 • Euk: ○ Genes far apart must be coordinated ○ Each gene regulated by combo of TRS (transcription regulators) "deciding" factor proteins ▯ Ex: Glucocorticoid receptor is final TR in TR combo for many genes when hormone present receptor interacts w/ different AP's bound to enhancers ▯ Protein-activator proteins Figure 8.18 • Ex: Myo D (protein) causes skeletal muscle cell differentiation from myoblasts ○ Loss of function ▯ Fibroblast (connective) change to myoblasts, fuse, express muscle specific proteins, when Myo D gene activated ▯ Deciding proteins in differentiation of cells called "master Factors" Figure 8.19 • Embryogenesis: Unequal distribution of master factors can generate different cell types from single cell Figure 8.25 • Ex: EY gene protein ○ Master factors regulate development of whole organs ▯ EY master in flies (and pak 6 inverts) cause eye development. EY gene activation in larval cells of precursor leg makes an eye Figure 8.20 • Differentiated cell (liver hepatocytes) use positive feedback to pass on memory of cell type • Product of gene turns on expression of its own gene Figure 8.22 • Methyl tags added to DNA (cytosine) methyaltransferse ○ Methylate the app. Ones • Methyl tags on DNA silence gens. New DNA methylated after replication in same pattern as pDNA (epigenetic inheritance) Figure 8.26 • Post transcriptional reg ○ RNA interference ▯ RISC (RNA inducing silencing Complex) ▯ SS miRNA proteins □ Hybridize to compl. mRNA--- degradation ▯ Regulate greater than or equal to 1/3 human protein coding genes Comprehensive Study Guide Sunday, April 28, 2013 8:13 AM Chapter One • Cells: ○ Size ▯ 0.5 um(microns) to 100um ▯ Big variation in sizes ○ Shape ▯ They very, from simple to complex □ Dynamic- cells change shape ○ Function ▯ Specialized in multicellularorganisms ▯ Basic unit of life ○ Chemistry ▯ Same fundamental molecules and mechanisms for making those molecules ▯ All cells have a common ancestor • Figure 1.5 ○ All cells have the same DNA ○ Cells w/ identical DNA can have different traits ▯ Gene Expression: the process by which a gene makes its effect on a cell or organism by directing the synthesis of a protein or an RNA molecule with a characteristic activity □ Ex: Cell types in a multicellular organism, same genome, different proteomes! • Microscopes ○ Resolution- How clean/ much detail you can see ○ Light ▯ Discover 17th century by Robert Hooke (dead cells, cork) ▯ First live cells, Leeuwenhoek; protozoa and bacteria ▯ White light bent by glass lenses, resolution limited b/c wavelength of light up to 0.2 um □ (BF, PC, IC, DF, Live cells) ▯ It works bc it illuminates the subject w/ white light, lens bends and light goes through specimen ▯ Good for seeing pigmented or dyed objects ▯ BF- good for natural pigmented (live cells) or dyed objects (dead cells) ▯ PC, IC, DF: Good to do live, non-pigmented organisms ○ Epiiflouorence ▯ Wavelength selected by filters. Dyes absorb on wavelength and emit another color (live cells) ▯ Epi= above or on top ▯ The lightthat illuminates the specimen comes from above. Set two filters put in the path ▯ Good for livecells, if let w/ light on too long will kill cells ▯ Green Fluorescent Protein (GFP) □ Label expressed protein in living cells, originally found in jelly fish (produced naturally) ○ Confocal ▯ Discovered 1960's ▯ Single laser wavelength. Pinhole detects emitted light from specific area (dead cells); Kills live cells quick ▯ Very expensive ○ Electron Microscopes ○ Electron Microscopes ▯ Discovered Mid-20th century ▯ Electromagnetic/ metal coated ▯ Electrons instead of light, electro magnets instead of lens ▯ To produce contrast; the cells have to be coated w/ metal ▯ Used for dead cells ▯ High resolution, still have clear/ detailed image ▯ Two Types □ TEM (Transmission) ▯ This sections (50nm thick), 2D resolution, diamond or glass knife w/ machine to cut □ SEM (Scanning) ▯ Whole specimen, 3D surface, 3-20 nm resolution ▯ High voltage, electron gun; have to use vacuum to keep them in check • Eukaryotes ○ True Nucleus ○ Many membrane bound cells ○ Complex structures ○ Some singlecelled (Protists and yeasts) ○ Most multicellular (Fungi, Plant, animals) ○ Components ▯ Nucleus (fig 1.15) □ Contains DNA, Bound by a nuclear envelope w/ pores, (except during cell division) ▯ Endo membrane system (endo= inside) (figure 1.25) □ Plasma membrane ▯ Outer layer of cell ▯ Semi permeable exchange materials w/ extras cellular fluid; receives signals ◊ Vesicles- used to transport material going in/ out the cell ▯ Endocytosis- going into cell (importing) ▯ Exocytosis- exported material out of cell ▯ ER and Golgi to transport b/t different membranes ▯ Cytoplasm (figure 1-24) □ B/t plasma membrane and nucleus, cytosol (water, molecules, ions, chemical rxns) organelles. ◊ Free ribosomes, cytoskeleton □ Looks like white/ clear in BF microscope ▯ Mitochondrion (figure 1.18) □ Makes ATP, from aerobic (respiration), O2 used; at end oxidation phosphorylation □ Chemiosmosis, how ATP is made □ Contains DNA □ Most cells have many mitochondria □ Inner membrane, folded, called cristae □ 1 um or more in size ▯ Chloroplasts (in plants, figure 1.18) □ Not found in all cells □ Photosynthesis happens □ Similar to mitochondria ▯ Size ▯ Structure □ Has thylakoids, chlorophyll in these membranes, the beginning of photosynthesis □ Contains DNA ▯ EndoplasmicReticulum (ER, figure 1.22) □ Folded up membranes that make up the channels (called lumen) □ If black dots, rough ER Dots-ribosomes ▯ Dots-ribosomes ▯ Function- make proteins □ Smooth ER ▯ Function- transport send/ receive vesicles; making cell membrane components □ Lipids involved in composing all the membranes that make up cells are made by the smooth ER ▯ Ribosomes □ The protein factors ▯ Make cytoplasmic proteins (free) □ Attached to Rough ER, some in cytosol/ cytoplasm □ Large macromolecular; no outer membrane so not organelle □ Secrete proteins that become part of PM, or something else ▯ Golgi (body or apparatus) □ Looks like deflated tires stacked on each other □ Post office of the cell ▯ Deals w/ modifying and packaging the molecules then to be where they need to go in the cell ▯ Receives vesicles from ER or PM and then they fuse w/ Golgi. ▯ Get modified by enzymes, bud off at end then get to other surface or wherever they need to go ▯ Lysosomes □ Break down molecules ▯ Enzymes for intracellular digestion ◊ "suicide sacs", if they were to burst open at the same times, the cell would be digested; will not happen b/c needs low pH to function, around lysosomeusually high pH ▯ Includes things cell takes in from environment ◊ Endocytosis ▯ Vesicle fuse with lysosome, breaks down cellular structure ▯ Peroxisomes □ Look similarto lysosomes,but enzymes are used in rxns to produce H202 (peroxide) □ Need to enclose them b/c they are not healthy for cells b/c they kill bacteria; in body converted to water and other things ▯ Cytoskeleton □ Filaments for motility, shape, internal organization and scaffold □ Most recent discovery (b/c so small) ▯ Around 7 nm smallest (Actin) ▯ 20 nm for largest (microtubules) ▯ Intermediate 14nm □ Actin and Microtubules: Causes cell to change shape, cell to move, or things w/in the cell □ Intermediate ▯ Stable: scaffold and strength ◊ Scaffold: something to hold onto ▯ Do not change shape • Ancestral Cells ○ Prokaryotes came first; simpleless complex ▯ Eukaryotes came from prokaryotes, that at some time became predators □ Mobility, bigger ▯ Bacteria has flagella, but eukaryotes can moves it's self ▯ Endocytosis, cells surround the prey and take in the item w/ pseudopodia ▯ Flexible membrane ▯ Evolved to lose the cell wall to be able to move and be flexible ▯ Evolved to lose the cell wall to be able to move and be flexible ▯ Grew Larger, ability to move (cytoskeleton), nuclear membrane to protect DNA from digested prey ▯ Evidence □ Mitochondria, originated aerobic bacteria, but they benefited mutualistic so became an organelle ▯ Have DNA and Ribosomes Chapter 2 • Chemical proerties of Wather and Bio. Sig. of the properties ○ HYDROGEN BONDS ▯ Because they are polarized, two adjacent H2O molecules can form a linkage known as a hydrogen bond. Hydrogen bonds have only about 1/20 the strength of a covalent bond. ▯ Hydrogen bonds are strongest when the three atoms lie in a straight line ○ WATER ▯ Two atoms connected by a covalent bond may exert different attractions for the electrons of  the  bond.  In  such  cases  the  bond  is  polar,  with  one  end  slightly  negatively  charged  (δ–) and the other slightly positively charged (δ+). ▯ Although a water molecule has an overall neutral charge (having the same number of electrons and protons), the electrons are asymmetrically distributed, making the molecule polar. The oxygen nucleus draws electrons away from the hydrogen nuclei, leaving these nuclei with a small net positive charge. The excess of electron density on the oxygen atom creates weakly negative regions at the other two corners of an imaginary tetrahedron. On these pages we review the chemical properties of water and see how water influences the behavior of biological molecules ○ WATER STRUCTURE ▯ Molecules of water join together transiently in a hydrogen-bonded lattice. ▯ The cohesive nature of water is responsiblefor many of its unusual properties, such as high surface tension, specificheat, and heat of vaporization. ○ HYDROPHILIC MOLECULES ▯ Substances that dissolvereadily in water are termed hydrophilic. They are composed of ions or polar molecules that attract water molecules through electrical charge effects. Water molecules surround each ion or polar molecule on the surface of such a solid and carry it into solution. ▯ Ionic substances such as sodium chloride dissolvebecause water molecules are attracted to the positive (Na+) or negative (Cl–) charge of each ion. ▯ Polar substances such as urea dissolvebecause their molecules form hydrogen bonds with the surrounding water molecules ○ HYDROPHOBIC MOLECULES ▯ Substances that contain a preponderance of nonpolar bonds are usually insolublein water and are termed hydrophobic. Water molecules are not attracted to their molecules and so have little tendency to surround them and carry them into solution. ▯ Hydrocarbons, which contain many C–H bonds, are especially hydrophobic. ○ WATER AS A SOLVENT ▯ Many substances, such as household sugar, dissolvein water. That is, their molecules separate from each other, each becoming surrounded by water molecules. ▯ When a substance dissolvesin a liquid, the mixture is termed a solution. The dissolved substance (in this case sugar) is the solute, and the liquid that does the dissolving(in this case water) is the solvent. Water is an excellent solvent for many substances because of its polar bonds. ○ ACIDS ▯ Substances that release hydrogen ions into solution are called acids. ▯ Substances that release hydrogen ions into solution are called acids. ▯ Many of the acids important in the cell are not completely dissociated, and they are therefore weak acids—for example, the carboxyl group (–COOH), which dissociates to give a hydrogen ion in solution. □ Note that this is a reversible reaction. ▯ pH □ The acidity of a solution is defined by the concentration of hydronium ions it possesses,generally abbreviated as H+. For convenience we use the pH scale, where ○ HYDROGEN ION EXCHANGE ▯ Positively charged hydrogen ions (H+) can spontaneously move from one water molecule to another, thereby creating two ionic species. ▯ Because the process is rapidly reversible, hydrogen ions are continually shuttling between water molecules. Pure water contains a steady-state concentration of hydronium ions and hydroxyl ions (both 10–7 M). ○ BASES ▯ Substances that reduce the number of hydrogen ions in solution are called bases. Some bases, such as ammonia, combine directly with hydrogen ions. ▯ Other bases, such as sodium hydroxide, reduce the number of H+ ions indirectly, by making OH– ions that then combine directly with H+ ions to make H2O. ▯ Many bases found in cells are partially associated with H+ ions and are termed weak bases. This is true of compounds that contain an amino group (–NH2), which has a weak tendency to reversibly accept an H+ ion from water, increasing the quantity of free OH– ions • 4 types of Organic monomers ○ Monosacchairders (sugars) ▯ Compounds with the general formula (CH2O)n, where n is usually 3, 4, 5, or 6. Sugars, and the molecules made from them, are also called carbohydrates because of this simple formula. Glucose, for example, has the formula C6H12O6 ▯ Monosaccharides can be linked by covalent bonds—called glycosidicbonds—to form larger carbohydrates. Two monosaccharides linked together make a disaccharide, such as sucrose, which is composed of a glucose and a fructose unit. Larger sugar polymers range from the oligosaccharides ○ Fatty Acids ▯ A fatty acid molecule, such as palmitic acid (Figure 2–18), has two chemically distinct regions. One is a long hydrocarbon chain, which is hydrophobic and not very reactive chemically. The other is a carboxyl (–COOH) group, which behaves as an acid (carboxylic acid): it is ionized in solution (–COO–), extremely hydrophilic, and chemically reactive. Almost all the fatty acid molecules in a cell are covalently linked to other molecules by their carboxylic acid group (see Panel 2–4, pp. 70–71). Molecules such as fatty acids, which possess both hydrophobic and hydrophilicregions, are termed amphipathic ▯ Saturated: it has no double bonds between its carbon atoms and contains the maximum possiblenumber of hydrogen. Unsaturated tails, with one or more double bonds along their length. The double bonds create kinks in the molecules, interfering with their ability to pack together in a solid mass, and it is the absence or presence of these double bonds that accounts for the difference between hard (saturated) and soft (polyunsaturated) margarine. ▯ Fatty acids are also found in cell membranes, where the tightness of their packing affects the fluidity of the membrane. The many different fatty acids found in cells differ only in the length of their hydrocarbon chains and in the number and position of the carbon– carbon double bonds ○ Amino Acids ▯ Amino acids are a varied class of molecules with one defining property: they all possess a carboxylic acid group and an amino group, both linked to the same carbon atom called the α-carbon (Figure 2–21). Their chemical variety comes from the side chain that is also α-carbon (Figure 2–21). Their chemical variety comes from the side chain that is also attached to the α-carbon. ▯ The covalent linkage between two adjacent amino acids in a protein chain is called a peptide bond; the chain of amino acids is also known as a polypeptide (Figure 2–22). □ Peptide bonds are formed by condensation reactions that linkone amino acid to the next. ▯ Regardless of the specific amino acids from which it is made, the polypeptide always has an amino (NH2) group at one end (its N-terminus) and a carboxyl (COOH) group at its other end (its C-terminus). This gives a protein or polypeptide a definite directionality □ A structural (as opposed to electrical) polarity ○ Nucleotides ▯ The sugar part is pentose, 5 carbons □ If ribose sugar than one more oxygen, dioxy ribose means one less sugar ▯ The nitrogen-containing rings are generally referred to as bases for historical reasons: under acidic conditions they can each bind a H+ (proton) and thereby increase the concentration of OH– ions in aqueous solution. There is a strong family resemblance between the different nucleotide bases. Cytosine (C), thymine (T), and uracil (U) are called pyrimidine's because they all derive from a six-membered pyrimidinering; guanine (G) and adenine (A) are purine compounds, which bear a second, five-membered ring fused to the six-membered ring. Each nucleotide is named after the base it contains ▯ The most fundamental role of nucleotides in the cell is in the storage and retrieval of biological information. Nucleotides serve as building blocks for the construction of nucleic acids—long polymers in which nucleotide subunits are covalently linked by the formation of a Phosphodister bond between the phosphate group attached to the sugar of one nucleotide and a hydroxyl group on the sugar of the next nucleotide • Relationships (figure 2.17) ○ Monomers ▯ Individual building blocks □ Sugars, amino acids, nucleotides ○ Polymers ▯ Repeated monomers linked by covalent bonds □ Globular proteins and RNA ○ Macromolecular Complex ▯ Polymers of same/different types interacting noncovaletnly (form together) □ Ribosome-proteins and RNA molecules stable structures ○ Monomers→Polymers→Macromolecular complex ○ Examples: ▯ Monomers to Polymers □ Condensation rxn (dehydration); one loses OH; other H to release water □ Input of energy ▯ Polymer to Monomer □ Hydrolysis rxn; water splits into OH and H which attack to monomers Chapter 3 • Metabolic pathways (figure 3.1) ○ Connected series of rxn products of 1st reaction are substrates for the next ○ Each reaction catalyzed by different enzyme ▪ Regulated at each stop ○ Types ▯ Catabolic □ Break down foodstuffs into smaller molecules, thereby generating both a useful form of energy for the cell and some of the small molecules that the cell needs as form of energy for the cell and some of the small molecules that the cell needs as building blocks ▯ Anabolic □ Anabolic(biosynthetic), pathways usethe energy harnessed by catabolism to drive the synthesis of the many molecules that form the cell • Why expend energy? ○ Use energy to maintain/generate order ▯ Energy from catabolism of food used to create bonds ▯ Some released (as heat) to create disorder extracellularly ○ Photosynthesis ▯ Directly/indirectly from sun, radiant energy captured in bond of organic molecule. Uses H20 and CO2; releases O2, sugar and heat. Inorganic carbon "fixed" into organic molecule (sugar)j ○ Respiration gradually release energy from sugars/other organic molecules; stores energy in smaller amounts for later use. • Redox Reactions ○ Organic molecules gradually brown down by redox rxns ○ OIL RIG- Oxidation Is Loss (lossof e-, H, or gain of polar bonds usually O); Reduction Is Gain (Gain of e-, H or loss of polar bond) ○ Organic molecules oxidized while other "carrier" molecules reduced • 3 benefits utilizing Enzymes (fig 3.12-3.15) ○ Speed ▯ Decrease activation energy required to start rxn ○ Low affinity ▯ Product released from active site/ binds more substrate ○ High specificity ▯ Active sites specific for only particular substrates • Favorable vs unfavorable ○ Change should be y →x ○ G= Gibbs free energy; potential energy of sub. ○ ∆G= change in free energy when reactants converted to products ▯ ∆G = G (P) - G r ▯ ∆G < 0 favorable; Free energy released/ disorder increased ▯ ∆G > 0 unfavorable ○ Cells must run unfavorable rxns (anabolic) enzymes couple unfavorable to favorable rxns. If net ∆G of couple rxns is - then both run ○ Energy carries temporarily store energy from favorable rxns, transfer energy to run unfavorable rxns Chapter 4 • Functional Proteins ○ Enzyme ▯ Catalyzes covalent bond breakage or formation □ Pepsis ○ Structural Protein ▯ Provide mechanical support to cells/tissues □ Elastin, collagen (Wenis) ○ Transport Protein ▯ Carries small molecules or ions □ Hemoglobin ○ Motor Protein ▯ Generate movement in cells and tissues □ Move the cell itself or things around it; myosin/ skeletal muscle cells □ Move the cell itself or things around it; myosin/ skeletal muscle cells ○ Storage protein ▯ Store small molecules or ions □ Ferritin; stores iron in liver ○ Signal Protein ▯ Carries signals from cell to cell □ Insulin ○ Receptor Proteins ▯ Detect signal and transmits them to the cell response machinery □ Rhodopsin in retina, detects light ○ Gene regulatory Protein ▯ Binds to DNA to switch genes on/off □ Lactose repressor in bacteria silences the genes for the enzymes that degrade the sugar lactose ○ Special- Purpose Protein ▯ Highly Variable □ The antifreeze proteins of Arctic and Antarctic fishes protect their blood against freezing; green fluorescent protein from jellyfish emits a green light • Polypeptide Folding ○ Flexible backbone of alternative Amino group, C-H and a Carboxyl group ○ Side chains (R-group) protrude from backbone ○ R-groups change the polypeptide Figure 4-2 ○ In vitro, spontaneous, thermodynamically stable conformation appears ○ Crowded cytoplasm means proteins need help folding ▯ Chaperones help proteins to fold □ Prevent newly synthesized proteins from associating with wrong partners. □ Makes folding more efficient and reliable ○ General structure of proteins and polypeptide ▯ Polypeptide= AA bonded w/ peptide bonds Figure 4.5 • Denaturing (unfolding)Conditions= 2 degree, 3 degree, 4 degree are weak interactions ○ Easy to cause peptide to change 3-D shape ○ Protein loosing 3-D shape, causes loss of function, and removal of denaturing condition restores function ○ Some conditions ▯ Increase temperatures, increase K ▯ Change pH of environment □ Change [H+] to interfere w/ ionic bonds ▯ Add or remove salts -> adds/ removes ions to solution interferes w/ ionic bonds ○ Reducing agents (uree, DTT, mercaptoethonal) ▯ Breaks disulfidebridge (covalent bond) ▯ Interrupts DS bridges b/t proteins (cysteine) • Prions= proteins that are mutated ○ Mutation allows them to misfold to stable conformation ○ They are infections; Upon contact of other proteins of the same type, they cause it to misfold □ Misfold proteins tend to aggregate, they lose their function ○ Protein aggregates damage cells, tissues resists heat, pH, most reducing agent ▯ From aggregate proteins you can get □ BSE- Bovine Spongiform Encephalitis (Mad Cow) □ CJD- Creutzfeldt Jacob Disease □ CJD- Creutzfeldt Jacob Disease □ Kury □ Alzheimer's □ Huntington's • 2 degree structure ○ Common holding patterns w/ in 3 degree ▯ Alpha Helix ▯ Beta Pleated sheets ▯ Hydrogen bond b/t O and Carboxyl group (amino backbone) □ H-bonds b/t N-H and C=O of backbone (not AA specific) ○ Secondary Structure = 2 degree ▯ The folded sections w/in the tertiary structure □ Types: alpha helix and beta sheets ▯ H-bonds b/t N-H and C=O, backbone (not AA specific) ▯ Alpha helix= spiral shaped, in particular the alpha helix □ H-Bonds  occur  b/t  every  4  amino  acids.    So  it’s  the  amino  group  of  one  amino   acid that H-bonded to the carboxyl group of another AA that is four positions away from it. The more H-Bond, the stronger the structure. ▯ Takes about 20 AA to make it stable Figure 4.32 • 3 ways lower activation energy to start RXN ○ 2 or more Rxns come together- where they react together "comfy sofa" come together and react more easily ○ By changing the arrangement of charges, "electric chair" unlike charges next to each other ○ Dealing with substrate needs to bend in order to go into Rxn to change product. Puts in "traction device" to bend it to how it needs. Figure 4.34 • Feedback Inhibition ○ Definition: ▯ A form of metabolic control in which the end product of a chain of enzymatic reactions reduces the activity of an enzyme early in the pathway. ○ Regulation in cells (metabolic pathways) ○ Negative feedback inhibition-final product of pathway inhibits enzyme catalyzing first reaction ○ Resources not used up ○ Efficient- no inhibitor synthesis ○ Self-regulating; product builds up, enzyme inhibited more ○ Fast: Not changing gene expression to up/down regulate enzyme Figure 4.36 ○ Competitive- inhibitor binds to active site ○ Noncom = inhibitor binds to allosteric site (not active) causes conformational (shape) change to active site ○ Feedback inhibition ▯ Benefit of noncompetitive □ Can attach to enzyme regard less of substrate concentration Figure 4.42 • Allostery Definition ○ Definition ▯ "other shape/ solid" □ Type of Feedback ○ Molecular Motors = allosteric proteins, shape changes by binding/hydrolysisof ATP and release of ADP ▯ Hydrolysis irreversible w/o energy input; motor moves in one direction along cytoskeletal filament ▯ Carry organelles or cause filament to slide Chapter 11 • Fluidity of Lipid Bilayer Figure 11-16 ○ Animal plasma membrane around 20% cholesterol (provides rigidity) ▯ Decreases membrane fluidity (no cell wall), cholesterol small; easily inserts between unsaturated fats tails, 4 rings are rigid ○ Depends on the tails ▯ Temperature ▯ The closer and more packed (more viscous, less fluid) □ Length of tails ▯ Number of double bounds ◊ A shorter chain reduces the tendency to interact w/ one another; increase fluidity ▯ Vary 14-24 carbons □ Most 18-20 ○ When sat/unsated. Equals more fluidity in bilayer • Asymmetry Figure 11-17 ○ Lipid bilayer is asymmetrical ▯ Non-cytosol leaflet has different phospholipidsthan cytosol leaflets (types and concentrations) □ Abundance of phospholipidswith read heads that face extra cellular space; they are dictating phospholipid Colene □ Brown headed ones are myelin ▯ G's stand for sugar, so glycolipids □ Cytosol lipids are higher in phospholipidcylene which are light green ones □ Gray things are cholesterol, equal concentration between the two leaflets □ Proteins are also, asymmetrical in both ▯ Glycolipidsonly extracellular leaflet, except phosphotidyl inositol (sugar); internal signaling in cytosol leaflet. ▯ Proteins asymmetrical distributed for function *Flipase-Cytosol Leaflet *Flopase-Non cytosol leaflet • Functional classes of Membrane proteins 1. Transporters a. Ex. Na+ pump b. Diffusionof specific hydrophilicsubstance or moves substance up concentration gradient. c. Diffusion(passive) moves w/ gradient (more to less) can also be part of active 2. Anchors a. Ex: Integrin b. Links membrane to molecules or complexes on either side b. Links membrane to molecules or complexes on either side i. Intracellular linked to cytoskeleton filaments ii. Extracellular linked to collagen/elastin 3. Receptors a. Ex: platelet-derived growth factor (PDGF) b. Detect signals (ligand) from one side and relay info to molecules on other side i. Allosteric proteins (change shape = function change) ii. Binding to the other side changes the activity of the receptor at the other end. 4. Enzymes a. Ex: Adenylyl Cyclase b. Catalyze or couple specific reactions on one side of membrane i. Catalyze reactions ii. Coupling favorable and unfavorable reactions iii. Specific to substrate based on active site • 4 ways proteins associate w/ lipid bilayer Figure 11-21 1. Trans membrane a. Extends through bilayer exposed on both sides (alpha helix and beta barrels) i. Useful for transporters 2. Mono-layered Association i. Hydrophobic imbedded in one leaflet; hydrophilicstands out 3. Lipid-Linked i. Covalent to lipid, lipid in one leaflet, protein extends from it 4. Protein attached i. Non covalent to another membrane protein 1) To disrupt non covalent bonds you can a) Increase kinetic energy (temp) b) pH c) Salt 2) PA=  Peripheral  Proteins  (salt,  pH,  or  temp  to  extract…  Figure  11-26 • Detergents ○ For lipid linked need to add detergent to extract, BC it has both hydrophilic/hydrophobic sides. Inserts b/t the lipids ▯ Trans membrane, mono layered association and lipid layer □ Equals integral proteins, detergent extractions ○ Detergent (amphipathic); linear CH chains w/ charged (SDS; SO4); or polar region (Triton X: OH) ○ Detergents interact with hydrophobic, hydrophilicor amphipathic substances ○ Detergents break up membranes ○ BC they are small anti-pathogens ○ Insert b/t lipidsand membrane BC proteins are weak (non-covalent bonds) ○ Physical perturbation: increase temp; detergent and lipid proteins form micelles ○ To separate the proteins from lipids ▯ Centrifugation separates micelles by type protein, heavier ▯ Then you can do SDS-PAGE, which separates denatured polypeptides by size. • Carbohydrate layer ○ Definition ▪ A layer of sugar residues, including the polysaccharide portions of proteoglycans and oligosaccharides attached to protein or lipid molecules, on the outer surface of a cell. ○ Helps to protect the cell surface from mechanical and chemical damage. ▪ As the oligosaccharides and polysaccharides in the carbohydrate layer adsorb water, they give the cell a slimy surface. they give the cell a slimy surface. ▪ This coating helps motile cells such as white blood cells to squeeze through narrow spaces, and it prevents blood cells from sticking to one another or to the walls of blood vessels. ○ An important role in cell–cell recognition and adhesion. ○ Serves  as  a  kind  of  distinctive  clothing,  like  a  police  officer’s  uniform,  that  is  characteristic   of cells specialized for a particular function and that is recognized by other cells with which each must interact. Chapter 12 • Electrochemical gradient ○ Definition ▪ Driving force that causes an ion to move across a membrane. Caused by differences in ion concentration and in electrical charge on either side of the membrane. ○ Diffusionof ions depends on electrochemical (EC) gradient=charge and concentration difference across membrane ○ Electrostatic around particle ○ Combine concentration gradient and net charge ○ Synergistic: concentration gradient and net charge pull ion in same direction ▯ Na influx into cytosol ○ Antagonistic: concentration gradient and net charge pull ion in opposite directions ▯ K efflux from cytosol • 3 types of active transporters ○ Coupled transporters-Secondary active transporters ▯ Couple the uphill transport of one solute across the membrane to the downhill transport of another. ▯ Using energy from other substrate going down e-chem gradient (couples favorable to unfavorable) ○ ATP-driven pumps-Primary active transporters ▯ Couple uphill transport to the hydrolysisof ATP ▯ Use ATP hydrolysis to move substances up e-chem gradient ▯ Must also be ATPase as well ○ Light-driven pumps ▯ Which are found mainly in bacterial cells, couple uphill transport to an input of energy from light • Na+-K+ pump (Na+-K+ ATPase, sodium pump) ○ Definition ▯ Transmembrane carrier protein, found in the plasma membrane of most animal cells, that pumps Na+ out of and K+ into the cell, using the energy derived from ATP hydrolysis. Figure 12-9 ○ ATP driven pump (Na+/K+ pump) ▯ 2 substances moving against e-chem gradient ▯ Primary antiporter ○ Na+/K+ pump ▯ Transport Na out and K in, both against e-chem gradient □ Na (larger) ▯ Elec, conc gradient= synergistic(same direction) □ K ▯ Elec, conc gradient= antagonistic (different directions) Figure 12-11 Process: ○ Process: a. From cytosol 3 Na(s) bind to Na/K pump (on cytosolic site) b. ATP hydrolysis,,brings E up 1) Phosphate attaches to pump itself (high E link) c. Pump changes conformation (cytosolic site closes ec site opens) 1) B/c of phosphorylation (causes lack of affinity/fit to Na) d. 2K's bind to new conf. of pump from EC e. Pump loses P (DE phosphorylation) f. Pump changes conf. to original, release K, good to bind Na again (EC site closes, C site opens, site of bind changes shape to orig.) ***Phosphate group is negative; weak non-covalent bonds in protein (pump) depend on dipole presence and disturbed by P (-) presence. Can continue as long as ATP present Figure 12-12, 12-13 ○ 3Na/2K movement benefits all: • 3 out vs. 2 in--> Delta= 1 out, prevents high concentration of solutes • In cell, prevents water moving into cell via osmosis • Animal cell: □ Na/K pump maintains osmotic equilibriumby pumping out more ions that it pumps in • Solutes: (ions, organic mols) are high in cells • Water is relatively low □ Water influx by osmosis would cause cell to swell, burst osmotic pressure balanced by 3Na out/2K in • Plant cells: vacuoles collect water and push against cell walls, stopping water influx(largerpressure) □ Cell wall prevents bursting cells □ rigid→push back cytosol = turgor □ Rely on turgor to provide more rigidity • Protist: contractile vacuoles collect water and discharge water to outside of cell Figure 12-28 ○ Na/K pump also very important for maintaining charge dist. Across membrane ▯ Membrane outside=positive ▯ Membrane inside=negative ▯ Both together = membrane potential ▯ By pumping more + ions out than it take in, it makes outside more positive ▯ Negative molecules insidethe cells □ CL □ Phosphate groups ▯ K leak channels allow some k ions leak out the cell b/c of e-chem gradient. • Two GlucoseTransporters Figure 12-17 ○ Big green thing is a transporter, you can tell b/c things are binding to it ○ Third way potassium pump is helpful ○ Transporter- things can bid to ○ It's moving 2 things in the same direction (symporter) ○ Active transporter ▯ BC it is being moved against the concentration/electrical chemical gradient ▯ Secondary (doesn't use ATP Hydrolysis) □ Gradient of Na, it being transported down it's gradient, so its favorable □ They couple favorable/unfavorable reactions for energy ○ Na + EC grad. Used by secondary transport • Eg. Na+/glucose symport in apical membrane of epithelial Intestinal cells. Active glucose transport from lumen into cytosol coupled with passive Na+ transport. glucose transport from lumen into cytosol coupled with passive Na+ transport. Figure 12.18 ○ Cartoon on intestine, so we can look at epithelial cells ▯ Coupling the transporter of Na/glucose into the epithelial cells □ Showing us a conc. Gradient of glucose on the side □ Low to high □ Sodium is greater in the lumen then in the cell □ As glucose comes in, the Na comes in as well ▯ Active transporter ○ Na/K pump keeps cytosol {Na+} low ○ Basel membrane uniport (only one type molecule): ▯ Passive glucose transport into bloodstream ▯ Moving down it's conc. Gradient ▯ It’s  a  carrier,  BC  it  has  binding  sites ○ Tight Junction (diffusionbarriers) • 3 Ion gated mechanisms ○ 3 stimuli gate ion channels: voltage VG, ligand LG, mechanical stress MG 1. Voltage gated i. When at rest (inside-) outside + ii. Altered by the membrane potential (change in voltage) 2. Ligand gated i. Chemicals that bind to receptors ii. When channel binds the ligands, the proteins changes iii. Can come from the outside or the inside 3. Stress gated i. Opening is controlled by a mechanical force applied to the channel ▯ Inner Ear Hair Cells (in cochlea) Figure 12-26a ◊ In cochlea: Sound into fluid wave, moves basilar membrane, lifts hair cells in organ of Corti. Bundle of stereocillia on hair cell bends when bump against tectorial membrane. ▯ Stereocilla is an Actin filament (the hairs on the basilar membrane Fig 12-26b ◊ MG ion channels at stereocllia tips. Gates tethered to tips links. Pull open gates, cation influx, hair cell signals to auditory nerve ◊ The tip-linked model ▯ MG currents from Sea Anemone Hair Cells ◊ Use hair for vibrations for communication • Action Potenti


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