Lec#4: Cellular Level II - Inside The Cell Student Notes PDF

Lec#4: Cellular Level II- Inside The Cell Menu LO1 Section A: Organelles LO2 Section B: Cytoskeleton LO3 Section C: Nucleus...

Lec#4: Cellular Level II- Inside The Cell Menu LO1 Section A: Organelles LO2 Section B: Cytoskeleton LO3 Section C: Nucleus LO4-8 Section D: Protein Synthesis ©Beatriz Castro Copyright © 2024 by Beatriz Castro. All rights reserved. LO1: Identify, describe the structure, and explain the function of each organelle associated with human cells. ORGANELLES- "little organs" within the cell that perform specific functions --suspended in the jelly like cytoplasm. They are either enclosed by membranes or lack a membrane https://www.aatbio.com/catalog/cell-structures-and-organelles  ENDOPLASMIC RETICULUM —system of channels (cisterns) enclosed by membrane Rough ER Lack ribosomes Smooth ER flattened, sac- Lipid synthesis like structures Calcium storage (muscle cell) “Rough” because it has ribosomes on the extensive surface--Site of Protein synthesis and network of modification tubules RIBOSOMES Small granules of proteins and ribosomal RNA. Composed of 2 subunits. They may be free or attached to membranes (like rough ER) They “read” coded genetic messages (messenger RNA) and assemble amino acids into proteins specified by the code. ©Pearson, Inc.  GOLGI APPARATUS It performs further protein processing steps (e.g. glycosylation, proteolytic cleavage)- Based on the modifications and attached tags, the Golgi Golgi vesicle containing digestive apparatus sorts proteins enzymes becomes a lysosome for their final (storing enzymes) destinations within the cell or for secretion outside the cell. Golgi vesicle containing membrane components fuses Golgi vesicle with the plasma mb containing proteins to be secreted becomes a secretory vesicle package and delivery of proteins (exported in vesicles) produced by the ribosomes  LYSOSOMES Membranous sacs of hydrolytic enzymes packaged by the Golgi apparatus. PEROXISOMES —resemble lysosomes but contain different enzymes Membrane-bound sacs housing different enzymes such as oxidases and catalase. Detoxification generate hydrogen peroxide (H₂O₂) which decomposes H₂O₂ into water and oxygen. Other functions include: Lipid Metabolism: breakdown of very long-chain fatty acids through beta-oxidation, & contribute to the synthesis of cholesterol and bile acids Protect the cell from oxidative damage by metabolizing reactive oxygen species (ROS) https://micro.magnet.fsu.edu/cells/lysosomes/lysosomes.html  The ubiquitin proteasome system is responsible for most of 20S associate with additional PROTEASOMES the endogenous proteins degradation in cells (ATP required). protein complexes (“caps”): Located in both nucleus and cytosol 30S Proteasome (the 26S proteasome has only Polyubiquitin chain one19S cap at one end) 20S Proteasome Recycled ubiquitin (the core particle) barrel-like shape 19S Regulatory ligases subunit (cap) Catalytically unfold the condemned active subunit protein and remove the ubiquitin chain before entering the core (protein) Made of proteases-- their proteolytic sites facing the hollow ubiquitylation tag a protein interior cavity through which the for degradation condemned protein travels acts like a "kiss of death" polypeptides are digested to short peptides Fig. https://doi.org/10.1038/sj.leu.2402417 https://www.embopress.org/doi/full/10.1038/s44320-024-00028-7  MITOCHONDRIA The “powerhouse” of the cell -- generate ATP through oxidative phosphorylation Metabolic Roles: Krebs cycle & Fatty Acid Oxidation Contains porins, which allow the passage of ions and small molecules. Inside the matrix: mitochondrial Small, quickly accumulate protons--role DNA (mtDNA) in the establishment of a proton gradient. A gel-like substance enclosed by the inner membrane. Krebs cycle take place here. Infoldings of the inner mb--Provide a large surface area for the e- transport chain & ATP synthase, facilitating efficient ATP production Highly convoluted and folded into cristae, which ↑ surface areal Houses the components of the electron transport chain and ATP synthase https://depositphotos.com/vectors/mitochondria.html  LO2: Discuss the cytoskeleton and its components. The cytoskeleton is a complex, dynamic network of interlinking protein filaments that extends throughout the cell. Specific Filament Types: (Courtesy of Harald Herrmann, University of Heidelberg, Germany. strands of several fibrous proteins (such as keratin) Their function is purely structural. They bear tension, thus maintaining cell shape, and anchor the nucleus and other organelles in place. Crucial role in moving chromosomes during cell division & organelles transport. Form cilia and flagella in certain cells Participates in muscle contraction, cell shape & motility, & cytokinesis during cell division. Form microvilli & pseudopods. https://bio.libretexts.org/Courses/University_of_California_Davis/BIS_2A%3A_Introductory_Biology_(Easlon)/Readings/14%3A_The_Cytoskeleton  Vesicular & Organelle Transport within the cell : Motor Proteins Motor proteins are specialized proteins that convert chemical energy, typically from the hydrolysis of ATP, into mechanical work. This enables them to move along cytoskeletal filaments, transporting cellular cargos. The three primary families of motor proteins are kinesin, myosin, and dynein. cargo thick filament periphery They "walk" along microtubules toward opposite ends through a coordinated series of steps powered by ATP hydrolysis They attach to both cargos and filaments cell nucleus myosin motors, organized into bundles called ‘thick filaments', move along actin filaments in a ‘running' motion. cargo *Cellular cargos are various types of materials and structures within the cell that need to be transported from one location to another (example organelles and vesicles). © 2004 Wiley-VCH.  Centrosome & Centrioles role in organizing the spindle microtubules which moves chromosomes during cell division During cell division, the centrosome duplicates, (9 sets) and move to opposite poles of the cell. serves as the main Connecting fibers microtubule-organizing center (regulates Microtubules organization & growth of microtubules in a cell) cylindrical structures At the core composed of microtubules arranged in pairs and Surrounding the centrioles is a matrix of proteins known as perpendicularly the pericentriolar material. https://nursehub.com/courses/ati-teas-science-review/lessons/describe-cell-structure-function-and-organization/topics/cilia-flagella-and-centrioles/ Encyclopedia of Biological Chemistry (Third Edition), 2021 https://microbenotes.com/centrosome/  LO3: Describe the structure of the nucleus Directs cell activities (the “brain” of the cell) Large protein complexes that span both mb, allowing exchange of molecules (such as RNA double membrane with large pores and proteins) b/w nucleus-cytoplasm. Nuclear envelope Nuclear pores composed of histone Chromatin proteins and DNA strands Nucleus Nucleolus Nucleoplasm Nucleoli (plural) semi-fluid matrix inside the sub-nuclear structure, not mb-bound nucleus It is the site of ribosomal RNA (rRNA) synthesis and ribosome assembly. Cisternae The outer nuclear mb is continuous with the ER  How is DNA efficiently packaged within the microscopic nucleus? DNA wouldn't fit within the nucleus if (3) Nucleosomes further condense by it were left uncoiled coiling into a thread-like structure called (2) Each histone complex with chromatin. its associated DNA segment forms a unit, the nucleosome (4) As the cell prepares to divide (prophase), chromatin condenses even further with the help of additional proteins, forming the visible, rod-shaped structures we call Throughout most of the (1) These positively charged chromosomes. cell's life (interphase), proteins tightly wrap around DNA exists as chromatin the negatively charged DNA within the nucleus molecule. Fig.©Pearson, Inc.  LO4: Explain the concept of genetic code It is the set of instructions contained in a gene that tells a cell how to make a specific protein. It translates the four-letter chemical code of DNA (A, C, G, and T) into the 20-letter code of amino acids, which are the building blocks of proteins. Each three-base sequence (triplet) calls for a particular amino acid to be built into a polypeptide chain. A codon is a sequence of three nucleotides on a strand of DNA or RNA. Each codon is like a three-letter word. The nucleotide sequence of a gene is ultimately translated into an amino acid sequence of the gene’s corresponding protein. https://www.ancestry.com/c/dna-learning-hub/dna-code-codons  LO5: Explain the flow of genetic information from DNA to protein, including transcription, splicing, mRNA modification, and translation (1) Both coding and noncoding regions of DNA are transcribed into mRNA. TRANSCRIPTION: DNA-directed synthesis of RNA (2) RNA splicing: Some regions are removed (introns). Remaining exons are spliced together. (3) The spliced mRNA molecule (red) is prepared for export out of the nucleus through addition of an endcap (sphere) and a polyA tail mRNA leaves nucleus through nuclear pores (4) Once in the cytoplasm, the mRNA can be used to construct a protein (translation). TRANSLATION: Synthesis of polypeptides from © 2010 Nature Education All rights reserved. RNA template  LO6: Briefly indicate how and why mRNA is synthesized. Complementary base pairing matches DNA nucleotide sequence with new mRNA sequence (A-U; G-C) 1.Removal of histones and DNA uncoiling 2.DNA strands separate RNA polymerase binds to a promoter sequence near the beginning of a gene & uses one of the DNA strands (the template strand) to create a complementary RNA molecule. Why is mRNA synthesized? 1. mRNA, being a smaller and single-stranded molecule, can easily travel out of the nucleus and into the cytoplasm where ribosomes reside. 2. DNA is the precious genetic blueprint, and constant unwinding for translation would increase the risk of damage. mRNA acts as a temporary copy that can be "used up" during protein synthesis. 3. Many genes may not need to be translated all the time. Having an mRNA intermediate allows for selective control over which genes are currently being expressed into proteins. 4. Alternative splicing is a process that allows a single gene to produce multiple protein variants by selectively including or excluding specific exons during RNA transcript processing. ©Pearson Inc.  LO7: Explain the roles of tRNA, mRNA, and rRNA in protein synthesis. Translation: “reading” of the mRNA by a functional complex consisting of the ribosome and tRNA molecules + peptide bonding of the aa into the polypeptide chain. Transfer RNA (tRNA): Adapter molecules that ferry amino acids to the ribosome based on the instructions on catalyzes peptide 60S the mRNA. bond formation decodes the genetic message 40S Messenger RNA (mRNA): Carries instructions for polypeptide synthesis from nucleus to ribosomes in the cytoplasm The mRNA has a sequence of nucleotides (A, Ribosomal RNA (rRNA): C, G, U) with triplets called codons, each The major structural components of ribosomes. specifying a particular amino acid (except for Provide a scaffold for the mRNA and tRNA molecules to stop codons signaling the end). interact during translation.  Structure of tRNA A tRNA is a single RNA strand that folds into a complex 3D structure, forming double-stranded regions and loops, Each tRNA molecule has two key regions: ultimately shaping it into an L. complementary triplet of nucleotides The anticodon searches for and binds to its matching codon on the mRNA molecule during translation. _Image modified from "TRNA-Phe yeast," by Yikrazuul (CC BY-SA 3.0). The modified image is licensed under a CC BY-SA 3.0 license._ www.khanacademy.org Image modified from "Translation: Figure 3," by OpenStax College, Biology (CC BY 4.0).  LO8: Summarize the steps involved in translation, including the movement of tRNA molecules through the A, P, and E sites in the large ribosomal subunit The large ribosomal subunit has three tRNA binding sites represented by letters-- As translation progresses, tRNAs move directionally through them: A site → P site → E site P site (Peptidyl site): holds the tRNA that is A site (Aminoacyl site): the entry currently linked to the growing polypeptide chain. point for a new tRNA molecule carrying an amino acid corresponding to the next codon E site (Exit site): the exit point on the mRNA. for the deacylated tRNA (tRNA that has transferred its aa and the start codon no longer carries one). At the start codon, the large ribosomal subunit binds to the initiator tRNA, forming a complete ribosomal complex The initiation complex attaches to the 5’-end of the mRNA transcript and moves towards the start codon (5’ → 3’) https://www.khanacademy.org/science/biology/gene-expression-central-dogma/translation-polypeptides/a/the-stages-of-translation  (2) a second tRNA (4) Once the aa is transferred to (1) The initiator molecule pairs with the the growing chain in the P site, the (6) Next tRNA- tRNA is bound to next codon in the A site tRNA becomes deacylated (no aa) aa is coming the central P site and exits through the E site. (3) The aa in the P site is covalently attached via a peptide bond to the (5) the tRNA carrying the peptide aa in the A site chain moves from A site to the P site Elongation and translocation continue in a repeating cycle until the ribosome reaches a stop codon--do not recruit a tRNA molecule, but instead recruit a release factor that signals for translation to stop. https://ib.bioninja.com.au/translation-ahl/