Week 1 - intro to cell signaling

• Bacteria branches are less complicated than eukaryotes as they contain increased biological complexity, forms of signalling, and levels of control.

  
• Cellular signalling can take place in the DNA, RNA, and protein level with the DNA level being the slowest to regulate and the protein level the fastest.

  
• the tertiary and quaternary structures of proteins are most likely going to be the most affected by changes in function due to changes in conformation.

  
• Non-covalent interactions play distinct protein folding rolls within proteins.

  
• Electrostatic and hydrogen bonding interactions drive interactions between dynamic and surface-exposed regions. Van der Waals interactions drive protein folding by creating a hydrophobic core.

  
• cell-signalling events tend to be covalent modifications of proteins altering their folding mechanism.

  
• Protein function is determined by structure

  
• Slight changes in protein structure can have a big impact on protein function.

  
• Many proteins are made up of components called motifs and domains.

  
• Motifs - are regions of the protein (often a few amino acids) that have a defined function but do NOT fold into a structure independently of the rest of the protein. Motifs tend to affect proteins' primary and sometimes secondary structures.

  
• Domains are regions of a protein with a defined function AND can fold into a structure independently of the rest of the protein. domains tend to affect the secondary and tertiary levels of proteins.

  
• Biological membranes are made up of lipid bilayers and proteins. They are often heterogeneous and contain structures like lipid rafts.

  
• Lipid rafts are regions of the membrane distinct from the rest and enriched in cholesterol, some proteins, sphingolipids and saturated lipids.

  
• Adenosine triphosphate (ATP) is the common energy "currency" molecule. This is done through a reversible covalent reaction that allows directionality in pathways.

  
• Chemical equilibrium does not equate to cellular homeostasis.

  
• Chemical equilibrium is a state in which the forward reaction rate equals the backward reaction rate. Think of adding acid to water or buffer. It rapidly moves towards a new balanced pH

  
• Homeostasis is a state in which the internal stability of a system is needed for survival of an organism.

  
• The cell membrane separates the living from the non-living world. Cell pathways have mechanisms that connect the outside signals inside.

  
• the smallest unit of life is called a cell

  
• RNA polymerases can be regulated by transcription factors hindering or enhancing their abilities. These transcription factors can also be regulated themselves

  
• generally there are 2 types of bacteria cells: Gram-positive and Gram-negative.

  
• Gram-negative bacteria is made up of 2 cell membrane layer with the peptidoglycan sandwiched in between. The outermost layer is made up of the outer membrane. It is harder for molecules to pass through when compared to Gram-positive as there are more layers.

  
• Gram-positive bacteria is made up of a thick peptidoglycan layer as its outermost layer. underneath it is a layer of cell membrane. It is easier for molecules to penetrate the cell when compared to Gram-negative bacterias.

  
• eukaryotic cells when compared to bacterias are: larger, more complex, have a nucleus, membrane bound organelles.

  
• The ON and OFF states of molecular machines/enzymes represent different conformation. One is conductive to function, and the other is not.

  
• A kinase is an enzyme that attaches a phosphate group to a protein while a phosphatase removes a phosphate group from a protein

  
• GEF enzymes are responsible for exchanging the GDP of GDP-bound proteins with GTP.

  
• GAP proteins work by removing a phosphate group of the GTP-bound protein via hydrolysis turning the target protein into a GDP-bound protein.

  
• there are 4 main types of cellular signalling methods: Contact dependent, Paracrine (Autocrine), Synaptic, and Endocrine.

  
• Contact-dependent: cell signalling requires the cell to be in close proximity to another cell allowing physical contact for signalling.

  
• Paracrine: cell signalling is done by the release of chemical signals to communicate over short distances between cells. Autocrine signalling is done by the release of chemical signals to communicate within the cell itself.

  
• synaptic: cell signalling that is done between the junction of nerve cells where signal transmission occurs

  
• endocrine: cell signalling that is done by specialized endocrine cells and carried through the circulation to act on target cells at distant body sites

  
• extrinsic signals initiate from the environment outside the cell, usually signals from other cells/tissues to conduct physiological processes.

  
• Intrinsic signals: signals that initiate within the cell itself, such as the release of hormones or the activation of enzymes

  
• Cells have a wide variety of signals: chemical and mechanical.

  
• Basic extrinsic signalling: The process starts off with an extracellular signal molecule that binds to a receptor on the cell's surface. This signal is then propagated to the intracellular signalling proteins that form a cascading event downstream of the system. Effector proteins found downstream are the proteins that cause change in a cellular process.

  
• there are 3 levels of signalling effect: changes to molecules/processes, changes to cell physiology, and changes to tissues/organs.

  
• [3 levels of signalling] Changes to molecules/processes: This is a simple process of making changes towards certain molecules in the body like turning on a gene or metabolic processes like glycolysis.

  
• [3 levels of signalling] changes to cell physiology: these changes can cause the rearrangement of cell cytoskeleton, motility of cell, differentiation, apoptosis and many more.