Alison Stewart 11/12/06 Prokaryotic Cells, Eukaryotic cells and HIV: Structures, Transcription and Transport Section Handout Discussion Week #7

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1 Alison Stewart 11/12/06 Prokaryotic Cells, Eukaryotic cells and HIV: Structures, Transcription and Transport Section Handout Discussion Week #7 Compare and contrast the organization of eukaryotic, prokaryotic and HIV genomes: Human E. coli HIV size 3.3 x 10 9 bp 4.6 X bp Proteins per gene 1 1 or more 1 or more Gene organization random random + operons? Coding sequence Discontinuous Introns/exons Continuous (no introns) Both This is not to memorize, but more to clearly display the differences. You should know that eukaryotic genes have exons/introns, but generally prokaryotes do not. How the HIV genome packs so much information into a tiny genome? 1) overlapping genes e.g. gag and pol 2) genes separated so splicing must occur (we will get to splicing, it basically means cutting and pasting a gene or RNA together from two or more different segments) e.g rev and tat Also HIV does not need to code for everything since it is not self sufficient. HIV genes to know: gag Erin Envelope protein, helps budding env Erin Encodes gp120 and gp41 pol Rob/David Encodes reverse transcriptase, integrase, and protease tat Rob Enhances transcription rev Rob Nuclear export Cellular/Viral particle Structure: Prokaryotic Cell

2 Outside: plasma membrane phospholipid bilayer cell wall - (remember transpeptidase, it helps build the cell wall), keeps shape of cell periplasmic space - small space in between membranes or in this case between cell wall and plasma membrane Inside: NO compartments - (there are LOTS of prokaryotes so this is a generalization) Genetic material is DNA - organized into nucleoid NO MEMBRANE, but has associated nucleoid proteins not naked DNA Eukaryotic Cell Outside: plasma membrane phospholipid bilayer Inside: Compartments- called organelles, they are also surrounded by membranes Genetic material is DNA contained in nucleus, bound up by proteins called histones Other important organelles: (These are the important ones, but not key to memorize unless mentioned in class) Mitochondria - energy generators of the cell - they harness energy from food to make ATP - the chemical that fuels cell activities; surrounded by a double membrane (therefore have periplasmic space!) Endoplasmic Reticulum, (ER) - a maze of interconnected spaces surrounded by a membrane, the site of synthesis of proteins destined for membranes. The ER is contiguous with the nuclear membrane, but this does NOT mean that the the proteins, lipids, etc. in the two membranes are the same. Golgi apparatus - a stack of flattened disks of membrane that receives proteins from the ER, modifies them and directs them to other organelles, the plasma membrane or to the exterior of the cell (carried in secretory vesicles). Lysosomes - sites of degradation of macromolecules (a sort of trash can) Peroxisomes - a contained environment for reactions involving hydrogen peroxide, a highly reactive molecule. Transport in and out of organelles Nucleus has pores so that small molecules and ions can freely cross and diffuse from cytosol, but NOT large proteins or nucleic acids (they must be transported) Other organelles, e.g. ER and mitochondria no pores, must have special transport for ions, small molecules, and proteins

3 Transport of proteins occurs in lipid vesicles within the secretory pathway (more on this later) Virus Outside: structural proteins for HIV gp41 and gp120 are important, they are glycoproteins plasma membrane phospholipid bilayer Inside: Capsid- made of protein, it protects proteins and genome inside until release is appropriate for infection Genetic material for HIV it is RNA, in general viruses can have RNA or DNA genomes, also associated with proteins so it is not naked when injected into a human cell Intracellular Trafficking pertinent to eukaryotes and HIV viral particle maturation Key components of the secretory pathway: ER Golgi Plasma membrane Lysosomes Endosomes come from outside the cell and bud into the cell with outside stuff Targeting: Targeting occurs by signal sequences, these signals are recognized by transport receptors. There is at least one transport receptor for each compartment. Target sequences can be contiguous or not contiguous if the amino acids are close in the folded up tertiary structure. The SNARE pathway is an example of how the target sequence causes proteins to be transported to other compartments. See the image.

4 1) Cargo binds to a cargo receptor that associates with a vesicle-snare 2) A vesicle covered with v-snares finds a compartment with the complementary target-snares. 3) The v-snare binds the t-snare which causes a folding into a bundle of 4 helices that brings the membranes together for fusion. This is analogous, but not the same as the hairpin intermediate formed in HIV entry and fusion. Targeting to ER From the ER proteins go to lysosomes, the golgi and the plasma membrane (remember endosomes come from the outside). As soon as a signal sequence is synthesized the nascent polypeptide can go into the ER, even if the protein is not finished being made. Water soluble and transmembrane proteins can be made in the ER. However, once proteins go in the ER they typically do NOT go back out into the cytosol. They can be put in the plasma membrane or another compartment or outside of the cell. HIV takes advantage of this targeting to get its membrane proteins made and glycosylated. The HIV protein gp160 is a membrane protein that is the precursor of gp120 and gp41. It has an N-terminal sequence that directs it to the ER. Post-translational modifications: Post-translational refers to after a gene (DNA) is transcribed into RNA then translated into a protein made of amino acids, then any subsequent changes are post-translational. Signal sequences targeting to the ER are cleaved in the ER by signal peptidase. Glycosylation, the addition of oligosaccharides is performed. In addition, the ER has proteins that assist in folding properly and the formation of the correct disulfide bonds.

5 The N-terminal signal of gp160 is cleaved, then at least some of its 30 potential N-linked glycosylation sites (which amino acid does this mean!?!) are glycosylated by enzymes and 10 disulfide bonds are formed. Without these changes the protein does not function properly and can aggregate. The Golgi apparatus Vesicles from the ER are targeted to the Golgi by proteins that coat the vesicles. Exactly which proteins when is not key, but here is an image showing that process. In the Golgi there is further glycosylation - addition, modification and removal of sugars to the overall oligosaccharide occurs. The cis-golgi is near the ER and the trans Golgi is across the rest of the Golgi from the ER. As proteins in the Golgi move from the cis to the trans Golgi this is when processing occurs since there are different proteins in the different compartments. The contents of the compartments are overlapping so this is a general trend rather than a strict rule. At the trans-golgi proteins leave and get sorted to different locations, such as to the plasma membrane. In the Golgi gp160 glycosylation is modified, then in the trans-golgi it is cleaved into gp120 and gp41, which are targeted to the plasma membrane and travel via secretory vesicles. To finish the HIV story: Viral assembly and exit from the cell - Gag is a cytoplasmic protein, once it is modified by the addition of a fatty acid tail it goes to the inner leaflet of the membrane. There it attracts the viral genome and is presumed to help deform the plasma membrane and the viral particle buds off with gp41 and gp120 on the outside.

6 What is missing from this picture? Draw it in. Transcription: Prokaryotic transcription: Initiation: Promoters are often at specific locations, -10 and -35 upstream from the transcriptional start site (position +1). Transcriptional start sites are thus dictated by the promoter site. Transcription factors specific sigma factors (s) bind to the -10 and -35 site and recruit RNA polymerase to that location. RNA polymerase catalyzes the polymerization of new RNA strands. Termination: At specific sequences (termination sequences), the newly synthesized RNA will fold onto itself due to self-complementarity. This will create a hairpin structure that will help the newly synthesized RNA push off RNA polymerase from the RNA/DNA hybrid. This is not always how it happens, but the example for you to remember. Eukaryotic transcription: Promoters You can refer to the entire regulatory region (core promoter that has binding site for RNA polymerase complex and also DNA that has binding site(s) for transcription factors) as a promoter. Transcription factors function like the Sigma factor, but instead of one protein being used, many proteins bind and assemble together to perform the same function. They recruit and activate RNA Pol to a specific location (gene). RNA Polymerase performs the same function as bacterial RNA polymerase. mrna transcription uses RNA Pol II.

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