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Bio midterm 2 review.docx

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University of Waterloo
Dragana Miskovic

Unit 6 Biological membranes  Two types of membrane transporter proteins: carrier and channel  Carrier is like a revolving door, solute attaches to solute binding site, then the protein moves it to wherever it needs to go  Channel is a channel in which ions pass through an aqueous pore from one side to another  They contrast as channels mostly detect size and charge as long as channel open, anything with that size/charge can pass. Carriers require that molecule fit a particular binding site; one molecule at a time can be transported  Membrane proteins are transporters, anchors, receptors and enzymes  Permeability- High to those like O2, CO2, H20 is okay, urea will have trouble just like ions, glycerol can zip right through, if its fatty loving, it will be fine at getting inside (hydrophobic)  Osmoconformers-marine organisms adjust internal salt concentrations to match seawater  Osmoregulators- regulate osmolarity through their bodies that is iso-osmotic with their cytoplasm  Turgor- hyper-osmotic to their environment, water pulled in, presses membrane out to cell wall  All cells have a plasma membrane which encloses its contents  Eukaryotic cells have membrane bound organelles, which means they have a nuclear envelope, and double membranes of mitochondria and chloroplasts, present are the ER, GA, etc  Membranes provide a selectively permeable membrane, transport solutes, respond to external signals (signal transduction), energy transduction- conversion of one form to another, Compartmentalization (eukaryotes), scaffold for biochemical activities  Amphipathic phosphate means its charged, named by its head part  All membrane lipids are amphipathic like cholesterol and galactocerebroside  Membrane fluidity is how easily lipid molecules move within a membrane leaflet  Tight- less fluid Free- higher fluidity  Length of FA’s, shorter carbons allow more fluidity, degree of saturation of FA’s  Cholesterol makes membrane stiffer-less fluid, only in animals, stiffens at high temperatures  High temp- membranes are fluid, move freely  Low temp- tails pack together and membrane gels( solidifies)  Fluid state must be maintained for normal cell function  Maintaining- Change composition, alter phospholipids, desaturate fatty acids, change length of FA chain, adjust amounts of cholesterol (seen in cold resistant plants etc)  Lipid bilayer asymmetrical  Human RBC model organism for plasma membrane- cells inexpensive, present in suspension, no nucleus, no ER, no mitochondria, no lysosomes, very simple!  Asymmetry preserved during membrane transport, sugar groups attached to outward facing membrane  Proteins give membranes their functions, transporter and anchors known as integrin’s  Receptors/enzymes have a sigma molecule bind to them, cascade of reactions  Integral- transmembrane, monolayer, lipid-linked0 Peripheral- protein-linked  Polypeptide chains usually cross as a-helices  Proteins folded into pleated sheets can form pores  Cells can restrict movement of membrane proteins, epithelial cells don’t exist in the body  Membrane protein distribution- Apica, lateral, basal plasma membrane  Transport- need to allow passage of certain substances in/out of cell (gases, ions, etc)  Bilayers tend to block passage of polar (water-soluble) molecules  Can enter through bilayer, across bilayer by proteins acting as carriers or channels, engulfed by cell, avoid passing through membrane  Dissolved solutes in constant random motion, spread out until concentrations even  More solute on right side of membrane, solute cannot cross, water moves across to attempt to equalize concentration  Conc of water equal on both sides, Conc of total solute equal as long as water can cross  Osmosis is the diffusion of water across a semi permeable membrane down a conc gradient  Once equal, no movement, all ions dissolved in fluid  In mammalian RBC- Hypo is swelling, Iso is equal, Hyper is shrinking  In walls- Hypo is turgid, Iso is flaccid, and Plasmolyzed in plants. Lysed is hypo, normal is iso and shriveled is hyper Unit 5 Gene Expression  Goes from DNA replication to RNA synthesis (transcription) to protein synthesis (translation)  Final protein will take on different shapes, which will give us different phenotypes  RNA- OH group, ribose, uracil DNA- just H, deoxyribose, thymine  Many genes code for RNA molecules that are not mRNA, do not code for proteins  RNA involved in regulation of gene transcription, mRNA processing before translation  Translation is that transport of amino acids, and catalyzes the formation of peptide bonds  mRNA- code for protein rRNA- core of ribosome and catalyze protein synthesis, miRNA- regulate gene expression tRNA- serve as adaptors between mRNA and amino acids during protein synthesis, others used in splicing, maintenance  Only one strand of DNA transcribed which is the template strand, other strand is the coding strand, coding DNA strand matches RNA except that RNA has uracil instead of thymine  Phosphodiester bonds form between the RNA and DNA template, H bonds between bases  Exergonic hydrolysis of ATP drives RNA synthesis, energetically unfavourable, thermodynamically possible  DNA transcribed by RNA polymerase, passes through, unravelled, ribonucleoside triphosphate tunnel allows them to pass, we get a newly synthesized RNA transcript, active site needed to catalyze  Core of RNA polymerase where synthesis occurs, sigma factor is a regulatory subunit  Sigma factor recognizes a promoter sequence, two boxes upstream (35 and 10), recognized by sigma proteins  Transcription initiated at sections of DNA called promoters  Typical sequences found at boxes, rest of promoter highly variable, transcription begins when sigma binds to the boxes, orienting the RNA polymerase holoenzyme at the start site  Sigma factor binds to template strand, Spread and break apart, send template strand to active site, Non template strand away from the active site, Divert the DNA, Once it’s on its way, sigma factor will disassociate , Sigma just used to recognize the start of transcription  mRNA molecule, region in gene, Transcription occurs, hair and loop structure formed, stimulates whole complex to fall apart, Secondary structure is what stimulates termination  Template strand depends on gene, promoter always on non-template strand  Transcription in Eukaryotes vs. Prokaryotes  Eukaryotes have transcription in nucleus, Prokaryotes have no nucleus, trans and trans occur at same place, Eukaryotes deal with DNA packaging, wrap around histones, tightly packed  DNA molecules can adapt higher order structure  RNA 1- most rRNA genes, RNA 2- protein coding, miRNA, end up with protein sequence, RNA 3- tRNA, transcription into tRNA molecules  Eukaryotic more complex, TATA box which is 35 bp upstream RNA 2, RNA 1 and RNA 3 interact with different promoters  Require large team of accessory proteins, assemble at promoter  Transcription – r0  Recognizes TATA box, kink and partial unwinding of double helix  mRNA requires processing before being shipped  5 prime cap and poly A tail, only added to mRNA molecules, tail added to end of molecule, small delay  Genes spread out, allows for complex regulation of gene transcription  Introns are what we don’t want, Exon are what we want, so we splice to get what we want  Spliceosomes composed of RNA as well, components that are used to break the bonds  Bonds broken, we get looped lariat which will degrade  RNA splicing involves more work, more opportunity for error, mutations can result in the loss of exons and inclusion of introns  It can create different proteins from same gene, same primary mRNA transcript depending on cell type  Cap and A-tail marked by proteins, group called exon junction complex, only then mRNA will be transported out of the nuclear pore into the cytoplasm  Eukaryotes have transcription in nucleus, translation in cytoplasm  Prokaryotes have the above in the cytoplasm  Genetic code is the relationship between the sequence of nucleotides in DNA/RNA and the sequence of AA’s in protein  64 possible codons, 20 AA’s, methionine and tryptophan specified by more than one codon  Plant mitochondria uses universal code, plants can easily transfer genes to genome  tRNA is the adapter, tRNA plus the amino acid (aminoacyl tRNA synthetase) gives us aminoacyl tRNA  different ATS and tRNA’s for each AA, each tRNA carries a specific AA  CCA sequence at 3’ end is binding site  Site binds ATP and AA, leucine for example bound to AMP, tRNA has activated amino acid, finished aminoacyl tRNA ready for translation  tRNA charged by aminoacyl-tRNA (amino acid to ATP)  Wobble hypothesis by Crick stated as the third position requires a nonstandard base, explains how one tRNA can be paired with more than one codon  Eukaryotic ribosomes made up of a Large sub unit and Small sub unit  Translation begins when anticodon binds to codon in mRNA, ends when AA forms peptide bond with growing chain  A site- acceptor site P site- peptide bond forms that adds amino acid to chain E site- tRNA no longer bound, exit ribosome  tRNA is on A and P site, ejects the A site to ma
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