W1: Intro to Cell Signalling

• from bacteria -> archaea -> eukaryotes, there is increased

  • signalling complexity
  • increased forms of signalling
  • increased levels of control
• in the central dogma of molecular biology,

  • DNA (slow regulation) -> RNA -> protein (fast regulation)

  
• the 4 levels of protein structure is

  • primary (amino acids) -> usually phosphorylated by kinases at this level
  • secondary (alpha helix/beta sheets)
  • tertiary (polypeptide, domains)
  • quaternary (assembled subunits)

  
• kinases add a phosphate group on amino acids that have a hydroxyl on their side chains
• covalent bonds drive changes in proteins in cell signalling and cellular responses while noncovalent interactions drive protein folding within proteins
• noncovalent interactions drive protein folding within proteins

  • H bonds -> proton donor/acceptor
  • electrostatic interactions -> charged residues
  • vanderwaals -> hydrophobic

  
• key concepts in protein structure and function

  • protein structure determines function
  • small changes in structure can have a big impact on function
  • many proteins are made of motifs and domains
• • motifs are regions of a protein that have a defined function but DO NOT fold into a structure independently of the rest of the protein (secondary structure)
  • domains are regions of a protein that have a defined function and DO fold into a structure independently of the rest of the protein (tertiary structure)
• • motifs are regions of a protein that have a defined function but DO NOT fold into a structure independently of the rest of the protein (secondary structure)
• • domains are regions of a protein that have a defined function and DO fold into a structure independently of the rest of the protein (tertiary structure)
• biological membranes are made of lipid bilayers and proteins can reside anchored inside/outside the cell and can be integral/apical to the membrane

  
• biological membranes are usually heterogeneous and contain structures like lipid rafts which are regions of the membrane that are enriched in cholesterol, some proteins, sphingolipids, and saturated lipids

  
• ATP is the common energy currency molecule in the cell and are held together by phosphoanhydride bonds (between phosphate groups)

  
• • chemical equilibrium is the state in which the forward and backward reaction rates are equal
  • homeostasis is the state in which the internal stability of a system is achieved for organismal survival
• • chemical equilibrium is the state in which the forward and backward reaction rates are equal
• • homeostasis is the state in which the internal stability of a system is achieved for organismal survival

  
• a cell is the smallest unit of life which is surrounded by a membrane which separates living and non living matter, the inside of the cell is ordered/structured and receives nutrients/info/energy from the outside world
• basics of gene regulation

  • DNA encodes gene of interest -> RNA polymerase binds operator to stimulate RNA transcription -> inactive repressor (TF) allows this to occur but can add molecule to repressor to bind operator and block RNA pol or vice versa with an activator

  
• the 2 types of bacteria are gram-

  • positive -> 1 membrane and peptidoglycan & techoic acid covering it
  • negative -> 2 membranes with peptidoglycan inbetween and lipopolysaccharides on the outer membrane

  
• • gram negative -> 2 membranes with peptidoglycan inbetween and lipopolysaccharides on the outer membrane

  
• • positive -> 1 membrane and peptidoglycan & techoic acid covering it

  
• a eukaryotic cell has 1 membrane but a vast distance and concentration barrier in terms of cell signalling, has membrane bound organelles like nucleus, nuclear envelope, ER, lysosome, peroxisome, golgi apparatus, mitochondria, PM

  
• molecular machines/enzymes can be quickly turned on/off by changing conformations, this can control

  • enzymatic activity
  • protein/ligand interactions
  • protein/DNA interactions
  • protein localization

  *this is QUICKLY done at the protein/translational level rather than transcriptional

  
• the 2 types of signalling are

  • covalent modification (phosphorylation)
  • ligand binding (GTP binding protein)

  
• signalling by covalent modification is achieved by kinases that catalyze the cleavage of phosphoanhydride bond of ATP to phosphorylate other molecules which cause a change, phosphatase can remove the phosphate

  
• signalling by ligand binding is achieved by the GTPase system

  • protein is off when GDP bound -> GEF exchanges GDP with GTP -> protein is on when GTP bound -> GAP hydrolyzes GTP into GDP and protein is off again

  *protein is bound to different ligands (GTP/GDP), never modified, NOT COVALENT MODIFICATION

  
• the 4 types of cell signalling are

  • contact dependent/juxtacrine -> physical contact between 2 or more cells
  • paracrine -> cell transmits signal which diffuses through extracellular space and binds to nearby cells (or itself, autocrine)
  • synaptic -> nerve cells transmitting signals
  • endocrine -> cell transmits signal which travels through bloodstream to all cells that have the receptor for the signal

  
• 2 types of signal origins are

  • extrinsic -> signal from the environment, different cell, or tissue which usually signals for a cellular response part of larger physiological process OR population dynamics
  • intrinsic -> signal from within the cell itself, this can signal metabolic flux, nutrient availability, damage

  
• cell signals can be chemical (small molecules, peptides, proteins, lipids, glycans, ions) and mechanical (force)

  
• the basic architecture of chemical extrinsic signalling is

  • extracellular signal molecule
  • receptor protein
  • intracellular signalling proteins
  • effector proteins -> have actual effect/cause change of cellular process
  • response/lack thereof -> like TF, turning an enzyme on/off, etc.

  *the signal is usually a small chemical molecule, can be toxic/beneficial, can alert/warn the cell

  
• the impact of cellular signalling can have tiered outcome levels

  • changes to molecules/processes
  • changes to cell physiology
  • changes to tissues/organs (multicellular)

  
• level 1: changes to molecules/processes

  • turning on a single gene
  • localize a protein

  
• level 2: changes to overall cell physiology

  • cell can be given signals to survive, grow/divide, differentiate, or die, rearrange cytoskeleton

  
• level 3: changes to tissues/whole-body physiology

  *changes in molecules and cellular outcomes add up to impact the morphology of tissues

  • ex: angiogenesis, signal -> low oxygen
  • level 1: triggers signals to change transcription
  • level 2: newly made proteins lead to hormone secretion (VEGF)
  • level 3: VEGF changes properties of endothelial cells (formation of blood vessels)

  
• types of cell surface receptors for extrinsic signals can be

  • ion couple receptors
  • G protein coupled receptors
  • enzyme linked receptors

  
• ion coupled receptors for extrinsic signals

  • ligand/ion binds to receptor
  • conformation change

  
• G protein coupled receptors (GPCR) for extrinsic signals

  • ligand binds to GPCR
  • conformation change
  • G protein cascade activated

  
• enzyme linked receptors for extrinsic signals

  • ligand binds to receptor
  • conformation change of receptor which activates enzyme activity (ie kinase)

  
• fast responses to signals come from altering protein function as the target of effector molecules because the protein is already made and the only step is to change the protein itself

  
• slow/regulated responses to signals come from altering TF to regulate things at the gene level like RNA transcription because these take longer to accomplish