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Chapter 5

Chapter 5 bio 102

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BIOL 102
Wayne Snedden

Chapter 5: Systems Biology of Cell Organization o Describe the relationship of the macromolecules DNA, RNA, and protein to the terms genome and proteome. DNA gets transcribed into RNA and then RNA gets translated into a protein. An organism’s genome is its complete collection of DNA and from that DNA, specific cells make specialized proteins that perform different functions which make up the proteome. o Understand how the unifying biological principle that structure determines function is particularly important in creation of molecular machines. A protein is considered a machine because it undergoes conformational change to perform a function. Has moving parts and does useful work. In proteins, shape dictates function because if a protein doesn’t have a specific shape to bind to a receptor, then that process will not occur. Molecular machines are vital in promoting cell organization. The cytoskeleton is involved in the organization of the cytosol. Although some molecular machines can assemble spontaneously from their components, the complex interacting machinery of the cell is so complex that it needs existing structure to guide assembly of the new components. Thus we can see why one biological principle is that all cells originate from existing cells o Describe how a eukaryotic cell can be viewed as four interacting systems: the nucleus, cytosol, endomembrane system, and semiautonomous organelles. Nucleus – houses a cell’s DNA and its processes include protection, replication and packaging for cell division. It is also the site of transcription. Cytosol – coordinates a response to the environment, metabolism and motor proteins Endomembrane system – includes the nuclear envelope (surrounds nucleus), rough and smooth ER, golgi body, lysosomes/vacuoles, peroxisome and plasma membrane. Semiautonomous organelles – mitochondria (animals) and chloroplast (plants) which provide energy for the cell. o Create a labelled diagram describing the flow of information from the nucleus, to the cytoplasm, to the environment, to the cytoplasm, and back to the nucleus, and label key structures and molecules. o Name the particular RNA molecules that are intermediates for producing the proteome, and indicate which proteins are important decision makers in producing these RNA molecules. The particular RNA molecules that produce the proteome are mRNA, tRNA and rRNA. They are all created in the nucleus, exit through the nuclear pores and enter the cytoplasm to function in translation. Specific amino acids join together to create a polypeptide and once this is created, the polypeptide must fold into its proper shape and get to the correct part of the cell to become a functional protein. When proteins reach their destination they create the foundation for cell structure, function and organization by providing structural proteins, transport proteins, extracellular proteins, signaling proteins and enzymes. Transcriptional factors – the proteins that help determine which parts of the genome will be selected for transcription. o Justify thinking of the outer leaflet of the cell membrane as an important part of the cell. The outer leaflet is a phospholipid bilayer. The outer leaflet is very important because it is the part of the cell that interacts with the outside environment o List the categories of proteins that are sorted cotranslationally and those that are sorted post- translationally. - Membrane proteins are sorted cotranslationally into the ER and contain a signal recognition particle that is inserted via translation - Proteins needed in the nucleus, peroxisomes, mitochondria, or chloroplasts enter sorting post-translationally • Proteins that stay in the cytosol lack sorting signals • Sorting to nucleus, mitochondria, chloroplasts, and 
peroxisomes (some) occur after the protein is made – Post-translational sorting - For post translational sorting to occur the protein must contain a specific amino acid sequence called a targeting signal that directs that protein to its desired location • Synthesis of other proteins destined for ER, Golgi, lysosome, vacuole, plasma membrane, or secretion halts until the ribosome is bound to the ER 
– Cotranslational sorting o Describe the steps that occur during the cotranslational sorting of proteins to the endoplasmic reticulum. The steps include: 1) Sorting begins in the transcription phase when the ER signal peptide is created and attaches the signal recognition particle (SRP) which pauses transcription (ER signal sequence is where the “postal code” is) 2) The SRP moves the entire complex (mRNA, ribosomes and emerging signal peptide) to the ER membrane 3) The ribosome opens the protein channel and provides passages to the lumen of the ER. SRP releases 4) The growing peptide threads through the channel and eventual the ER signal sequence is cleaved 5) Polypeptide is released into the lumen of the ER o Explain how proteins are moved via vesicles through the endomembrane system. If there is no ER retention, then vesicles transport (Proteins that stay in the ER have ER retention signals in addition to ER signals  this doesn’t so proteins must be transported by vesicles and these vesicles incorporate coat proteins for specificity and incorporate v-snares that indicate for certain cargo  t-snare on targer recognizes v-snare and vesicle fuses with target membrane) - Proteins coming from the lumen of the ER are always encased in vesicles - Protein molecules bind to the cargo receptors which stimulates the binding of a cage-like shell which helps the membrane bud from the vesicle (this handshake will only happen between golgi and the vesicle because of proper recognition between the 2) o Outline the steps of post-translational sorting of proteins to mitochondria or chloroplasts. This is after polypeptide is made  most proteins for mito, chloro and all proteins for peroxisomes are sorted post-translationally  they must have a sorting signal) - Chaperone proteins keep protein unfolded so the mitochondria sorting signal can bind - The protein releases the chaperones and enters the outer and inner membrane via channels - Chaperones bind again in the matrix - The sorting signal is cleaves and the protein is threaded into matrix - Chaperones release and protein folds into tertiary structure. o Describe the proteasome-based process of protein degradation. Explain the purposes of the proteosome system. Contrast the proteosome degradation system with that of the lysosome. - To degrade proteins proteasomes are enzymes that cleave the bonds between amino acids  they are also considered molecular machines - Ubiquitin (most common flag to degrade proteins) recognizes if the protein is necessary or unnecessary and targets unnecessary proteins to the proteasome  also can target misfolded proteins - Proteasomes degrade proteins into small peptides or amino acids and recycle them back into the cytosol - In the cytosol those cleaved amino acids are used to make new proteins - Lysosomes can also degrade materials in the cytosol or degrade proteins that enter the cell in endocytosis o Describe the major events proposed to account for the evolution of the double- membrane organelles: the nucleus, mitochondria, and chloroplasts. - it is said that the mitochondria and chloroplasts are derived from ancient symbiotic relationships (symbiosis occurs when 2 different species live in direct contact with each other and benefit) - Endosymbiosis is when the smaller organism lives inside the larger one - Scientists believe the mitochondria, chloroplasts and nucleus were once their own organism that decided to reside inside a cell and over time that cell evolved to include those organelles  this is why these organelles contain separate membranes and are semi-autonomous o Discuss the evidence for the endosymbiosis theory. From this theory it is proposed that mitochondria are derived from purple bacteria and chloroplasts from cyanobacteria  proof: a. Have a double membrane – outer membrane has eukaryotic orgin and inner membrane has prokaryotic origin b. Have a single loop of DNA c. Reproduce by binary fission d. Have ribosomes but are of prokaryotic origin e. About the same size as prokaryotes o Explain the functional roles of the extracellular matrix in animals. (don’t put too much emphasis in the studying of this and everything else below this) - The ECM in animals serves a similar role to the cell wall in plants it allows certain cells to adhere to the ECM on only one side - It provides support, strength, organization and cell signaling - The tough stuff on animal cells (i.e. shells) are the ECM - The skeleton of animals are composed of the ECM - The attachment of cells to the ECM promotes organization - Cell signaling is how organisms interact with environment and is controlled by the ECM o Describe the structure and function of plant cell walls. - It is a protective layer that forms outside the plasma membrane of the plant cell and is composed of the primary and secondary cell wall (primary  made before) - The main component of the primary cell wall is cellulose and made to grow with the cell - The secondary cell wall is created after the cell has finished growing o Outline the structure and function of anchoring junctions, tight junctions and gap junctions. - Anchoring junctions play a role in anchoring cells to one another or in the extracellular matrix - Tight junctions seal cells together into a tissue that prevents small molecules from leaking through one cell layer to another - Gap junctions allow cells to communicate directly with each other o Describe the structure and function of middle lamella and plasmodesmata - Middle lamella is a call junction in plants and is the first layer to divide  it is also rich in pectin, which is negatively charged carbohydrate polymers - The primary cell wall is made in the middle lamella - Middle lamella forms a hydrated gel with Ca and Mg +2 - Plasmodesmata allow the pa
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