PCB 3023 Cell Biology Summer 2024 PDF

PCB 3023 Cell Biology Summer 2024 1 Why Do We Study Cells? Bacteria, protozoa, seaweed, fungi, plants, animals— – all consist of one or more cells – organisms are “alive” because cells are “alive” Because cells are the basic unit of “life” – we study cells to understand life Viruses are not cells 2...

PCB 3023 Cell Biology Summer 2024 1 Why Do We Study Cells? Bacteria, protozoa, seaweed, fungi, plants, animals— – all consist of one or more cells – organisms are “alive” because cells are “alive” Because cells are the basic unit of “life” – we study cells to understand life Viruses are not cells 2 Cells are “Alive” But the molecules that make up cells are not How do non-living molecules make living structures? –studying cells allows us to see this remarkable transition: Cells take up matter and energy from their surroundings –and combine these to make copies of themselves –nothing less than a cell can do this To accomplish this, all cells synthesize and utilize –molecular –molecular –molecular –molecular 3 switches machines catalysts (enzymes) structures Course Objective Molecular machines, switches and enzymes, held in place by molecular structures, organize and control all biological processes – regardless of scale same basic set of properties for all beings In this course we will examine these subcellular structures – how do they work? – why has evolution selected the forms that exist? – how do they combine to form “living” structures? 4 Strategy for Learning Review basic biochemistry – especially the energetics of molecular behaviors Examine fundamental processes to see how switches and machines organize fundamental processes Emphasis will be on understanding WHY certain molecular structures and related mechanisms have evolved to perform specific tasks 5 Lectures PowerPoint outlines—mostly for me Read as much as possible with comprehension before coming to lecture Reading assignments vs. reading slides Read syllabus 6 Assessment Four unit exams – – – – – – in-person only 50 questions, 100 points, 75 minutes multiple choice, true/false, fill in blank, short answer concepts and mechanisms very little memorization closed book, no notes i>clicker extra credit 7 i>clicker Bring i>clicker transmitter to every lecture 1 point for answering – even if all wrong 1 additional point if correct – max points per question = 2 No voting for absentee friends...this is cheating 8 Missed Assignments i>clicker extra credit—no makeups Missed Exam – one cumulative makeup during final week of semester for any missed exam – only available for approved reasons – documentation required and checked – in-person in Boca testing center 9 How to do Well in This Course Focus on learning the material – not on doing well on the exams Attend every lecture Keep up SLIDES ARE A GUIDE TO WHAT TO FOCUS ON THE TEXTBOOK Read and study textbook Do not waste time memorizing slides Form study groups Ask questions Office hours—instructor and/or TA 10 Most Cells are Procaryotic All Procaryotes are Unicellular 11 Procaryotic Cells Procaryote (procaryotic)—as old as “life” – includes the eubacteria and the archaea – “simple” genome – single circular DNA molecule drifts within cytosol – all are unicellular no true multicellular forms – all have cell wall, none have organelles – extremely diverse – most cells are procaryotic 12 ~ 4 – 6 x 1030 cells, ??species Some Cells are Eucaryotic Eucaryote (eucaryotic)—evolutionarily young – multiple DNA molecules contained within a nucleus leads to other important differences – “complex” genome – network of internal membranes organelles – unicellular and multicellular forms – cell wall only in plants – limited diversity 13 ~ 1018 cells, 107 species Most Eucaryotes Are Unicellular 14 Some Eucaryotes Are Multicellular plants and fungi—10 – 20 cell types 15 Some Eucaryotes Are Multicellular animals—100 – 200 cell types 16 Eucaryotic Characteristics Nuclear envelope allowed genome to increase – larger genome = more proteins = more machines, more switches, more structures – cell got larger – cytoskeleton evolved – cell wall was lost (reacquired in plants) Not all of larger genome codes for protein – much of the eucaryotic genome is non-coding – many of these regions function in regulation Controlled and selective expression of genes – allows development of multi-cellular organisms 17 Phagocytosis Led to Evolution by Symbiosis Mitochondria and Chloroplasts: – originated as free-living bacteria which were engulfed via phagocytosis possess their own genome replicate by fission surrounded by double membrane 18 Procaryotic and Eucaryotic Procaryotic – all unicellular – single DNA molecule – – – – – – – – 19 circular no nucleus simple genome no organelles all have cell wall evolutionarily ancient huge number of species tremendous diversity > 99% of all cells 100 trillion (?) in human body Eucaryotic – uni- and multi-cellular – multiple DNA molecules – – – – – – – – linear within a nucleus complex genome internal organelles only plants have cell wall evolutionarily young few species limited diversity < 1 % of all cells 50 – 100 trillion in human body Universal Features of All Cells 20 All Cells Use DNA All cells store their hereditary information in deoxyribonucleic acid (DNA) – long polymer of nucleotides – nucleotides consists of sugar-phosphate “backbone” nitrogenous “base” attached to sugar 21 All Cells Replicate Their DNA The way in which new DNA is synthesized ensures that the new molecules are identical to the old The parent strand of DNA serves as a template – “daughter” strand is complementary to template Each new DNA molecule – one “old” template strand – one new “complementary” daughter strand – DNA replication is therefore “semi-conservative” 22 Cellular DNA is Double Stranded The way in which new DNA molecules are synthesized creates a double stranded molecule – eucaryotic—linear – procaryotic—circular existing “template” strand new “daughter” strand 23 All Cells Transcribe DNA Into RNA Portion of single-stranded DNA (genes) serves as template for synthesis of an RNA molecule (transcript) All cells transcribe mRNA, tRNA, rRNA Eucaryotes also transcribe – pre-mRNA, siRNA, snoRNA, snRNA, plus others 24 RNA—Another Kind of Nucleic Acid Ribose sugar instead of deoxyribose T instead of U in DNA – RNA bases are A, G, C, U – DNA bases are A, G, C, T Most important difference— RNA molecules are usually single-stranded – fold onto itself into unique 3-D shapes – less stable than DNA 25 All Cells Regulate Transcription Procaryotes—limited control Eucaryotes—extensive control 26 All Cells Synthesize Proteins Using mRNA as a Template Combination of proteins defines organism – enzymes – machines and switches – structural proteins All cells also assemble ribonucleoproteins – combination of proteins and RNA molecules – function as machines and / or switches ribosomes (all cells) telomerase, spliceosome (eucaryotes only) 27 All Cells Require “Free Energy” Conditions within cells are kept constant – but far from chemical equilibrium Cells require large amounts of energy to maintain this homeostatic disequilibrium 28 All Cells Have a Plasma Membrane Selective barrier – retain nutrients and synthesized products in – exclude waste products Structural “scaffold” – attachment for proteins and other molecules Cell Wall – most bacteria and plant cells – very few animal cells – plasma membrane--all cells 29 Cells Need “Fixed” Nitrogen and Carbon C and N are common – but common forms (CO2 and N2) are very stable – not very “accessible” Phototrophs “fix” carbon – pry it off the very stable CO2 – make it readily available (in the form of CH2O) Several species of bacteria synthesize an enzyme that catalyzes the conversion of N2 to ammonia – also lightning, geothermal events 30 Life Can Be Pretty Simple Mechanisms of molecular and cell biology seem numerous and complex Many processes were originally “optional” equipment – many have now become “standard” – evolution Mycoplasma genitalium – accomplishes everything required for “life” – with just 477 proteins 31 Cell Chemistry 32 Cells are Made of Molecules A molecule consists of one or more atoms bonded together Atom: equal # protons & neutrons bundled together into a nucleus (-) charged electrons orbit the nucleus – same #: neutral – more: anion (-) – fewer: cation (+) 33 Hydrogen is unique— only atom without a neutron Electron Shells Electrons occupy discreet spaces around the nucleus called shells Each shell can hold a specific maximum number of electrons Shells closest to the nucleus must fill first 34 Unfilled Electron Shells The outermost shells of many atoms are only partially “filled” Atoms with unfilled outer shells are inherently less stable than atoms with filled outer shells 35 Increasing Stability Atoms with unfilled outer shells try to reduce instability – by finding ways to fill their outermost shell Interacting with another atom is one way to get closer to a full outer shell 2 important interactions – covalent bonds – ionic bonds 36 Covalent Bonds Two atoms with nearly filled outer shells may share an outer shell electron – a covalent bond forms – a molecule is formed Covalent bonds are relatively strong and relatively stable 37 Covalent Bonds Covalent bonds can be “single” – single bonds can rotate – single bonds are flexible Covalent bonds can be “double” – double bonds are shorter, stronger, and less flexible Triple bonds exist but are uncommon in cells – nitrogen gas N2 – acetylene C2H2 38 Covalent Bonds Are Not All Equal The “strength” of a bond is the difference in energy between the free atoms – and the energy of the molecule they form Therefore, different covalent bonds have different strengths – stronger bonds are more stable, possess less energy – e.g., CO2, H2O Weaker covalent bonds are less stable – possess more energy – molecules with weaker covalent bonds can be a form of stored energy – e.g., CH2O 39 Electron Sharing is Often Not Equal Different atoms attract electrons to different degrees—electronegativity When atoms with different electronegativities form a covalent bond— – the result is an unequal distribution of electrical charge across the molecule—a polar molecule is formed Polar molecules are very important in biological systems 40 Polar Covalent Bonds If the polar difference is small, then attractions can develop between atoms on two different polar molecules Most important—hydrogen bond – electrostatic attraction between electropositive hydrogen atom on one polar molecule and an electronegative atom on another Individually weak, but many such bonds together can be strong 41 If the Polar Difference is Large... The molecules behave as acids or bases Acids give up the H+ in their polar bond to a base In aqueous environments (i.e. the cell) the “base” that picks up this H+ is often H2O, resulting in H3O+ The stronger the acid, the more likely its Hδ+ will exist mostly as part of a hydronium ion 42 Acids and Bases But in the cell, water can also act as the acid – giving up it’s polar Hδ+ to a base – which will also often be water As a result, H+ are often being tossed back and forth, so there is an abundance of H+ in the cell at any point in time – this is extremely important to the chemistry of the cell H+ H+ 43 Another Way to Fill Outer Shells One atom with nearly filled outer shell may transfer electron(s) to another atom that also has a nearly filled outer shell Each atom now becomes a charged ion – one cation (+) and one anion (-) 44 Another Way to Fill Outer Shells The opposite charges attract each other – an ionic bond forms – an ionic compound is formed – a salt is formed 45 Ionic Bonds Ionic bonds are a type of electrostatic attraction – same type of attractive force as hydrogen bond – but much stronger due to full rather than δ charge – very strong and pliable 46 Ionic Bonds Ionic bonds can be very strong But there’s a “catch” – – – – – 47 polar liquids (solvents) dissolve ionic bonds water is a very polar solvent cells are 70% water most salts in cells are in their ionic form except in spaces where water is excluded Other Interactions Hydrophobic interactions – tendency for nonpolar molecules (or nonpolar regions of very large molecules) to associate together and avoid water van der Waals attractions – attraction between the fluctuating electron clouds of two polar molecules – individually very weak but significant in numbers van der Waals radii – minimum distance allowed between two atoms – determined by dimensions of electron clouds 48 Summary of Interactions Covalent bonds—relatively strong and stable – but not all covalent bonds are the same Electrostatic interactions – ionic bonds—strong only in nonpolar environments – interactions between polar molecules—weak hydrogen bond—common interaction between polar molecules involving H atom – van der Waals attractions—weak Hydrophobic interactions—weak van der Waals radii—defines distances and other spatial positioning 49 “Complementary” Molecules 1) molecules with high degree of “fit” between 3dimensional shapes (i.e. van der Waals dimensions) 2) alignment of many numerous weak, noncovalent interactions which bring regions together and hold the molecules together note the two-way arrow— very important !! 50 Biological Molecules 51 The Most Important Biological Molecule Water has many unique properties – all life has developed around these properties – all life forms require water Water constitutes ~ 70% of the weight of every kind of cell 52 Biological Molecules In order to be useful to cells, biological molecules must possess special properties – most atoms are not part of biological molecules Mostly H,C,N,O Less common but still important: – Na, Mg, P, S, Cl, K, Ca Especially important (though not most abundant) is C 53 Cells are Made From Carbon Other than water – every molecule in the cell contains carbon Carbon has 4 missing electrons in its outermost shell – can form covalent bonds with 2, 3, or 4 other atoms – some of these carbon molecules are small – many are enormous polymers – organic molecules 54 Cells are Chemical Factories Most reactions within cells involve just four small organic molecules : – – – – 55 amino acids sugars nucleotides lipids Two Primary Reactions in Cells 1) Catabolic—large, high energy organic molecules are broken down 56 Two Primary Reactions in Cells 1) Catabolic—large, high energy organic molecules are broken down – energy is released – smaller molecules are produced 57 Two Primary Reactions in Cells 1) Catabolic—large, high energy organic molecules are broken down – energy is released – smaller molecules are produced 2) Anabolic—the small molecules are then built into different larger molecules – using some of the energy released when the larger ones were broken down Catabolism + anabolism = metabolism 58 – millions of reactions per second Biochemical Reactions Same principles as any other reaction – one or more reactants – yielding one or more products Two basic types – Energetically Favorable: product bonds possess less energy than reactants, energy is released “spontaneous” or “exothermic” reactions – Energetically Unfavorable: product bonds possess more energy than reactants, energy is required “endothermic” 59 Biochemical Reactions Energy “possessed” is the difference between the free energy of the covalently bonded molecule as it currently exists – and the free energy of the lower energy molecule that results from further breakdown Ionic bonds, hydrogen bonds, van der Waals forces, hydrophobic interactions – do not = stored energy 60 Covalent Bonds and Energy In the presence of O2 – most energetically stable state of C is CO2 – most energetically stable state of H is H2O Many organisms can use energy (sunlight, chemical) to break CO2 and H2O into free, high energy, unstable atoms (C, H and O) – these organisms then allow them to go back down to their lowest energy state – but not all the way, and not all at once – they “stop” the process at the level of CH2O 61 Photosynthesis photon energy + CO2 + H2O (stable)  unfavorable reaction  free C, O, and H (unstable)  favorable reaction  CH2O + O2 + heat energy (intermediate stability) CH2O is less stable than CO2 + H2O – but more stable than C, O and H Importantly, CH2O possesses chemical energy 62 – an amount equal to the difference in energy level between CH2O, and the lowest state possible for these atoms, which is CO2 + H2O – and also holds C in a more “accessible” form CH2O Two important things to think of when you think of CH2O – it possesses chemical energy – it is a source of “usable” C Some processes will make use of just the energy aspect – some processes will make use of just the carbon – and some processes will make use of both 63 Gibbs Free Energy G ΔG: Quantitative measure of the net change in free energy between reactants and products neg ΔG: products end up with less energy than the reactants – energy is lost – catabolism, disassembly of larger molecules neg ΔG reactions are favorable – i.e. “spontaneous” – spontaneous does not mean unpredictable 64 Gibbs Free Energy G pos ΔG : – products end up with more energy than the reactants – energy must be put into the reaction pos ΔG reactions are unfavorable – anabolism, synthesis of larger molecules 65 Reduction and Oxidation The chemical energy in a molecule is actually “possessed” by the electrons participating in the covalent bonds – when energy is lost, electrons are lost – when energy is gained, electrons are gained Reduction: a gain of electrons – reduced atom has a more (-) charge, or a more reduced electrical charge Oxidation: a loss of electrons – oxidized atom is left with a more (+) charge Reduction and oxidation must go together – redox reactions 66 Electrons Two important things to think of when you think of electrons – they represent a unit of energy – they represent a unit of negative charge Not all electrons have the same energy – electrons in more stable molecules possess less energy than electrons in less stable molecules – all electrons, however, have the same charge Some processes use just the energy – some processes use just the charge property – some processes use both 67 Second Law of Thermodynamics States that “in the universe, or in an isolated system, disorder is always increasing” Entropy – – a measure of how “disordered” a system is Elements within a system always work towards arrangements that provide the highest entropy possible for the situation – lowest energy state – highest stability 68 Rates of Reactions If allowed, all molecules will react – until they result in products with the absolute lowest possible energy state These are favorable reactions – release energy – produce less and less organized products – increase entropy of the system through increased disorder and release of heat 69 Rates of Reactions Favorable or unfavorable pos ΔG or neg ΔG Large reaction or small reaction Says nothing about the rate at which a reaction proceeds 70 Rates of Reactions Consider the decay of a wooden desk – this is a favorable reaction – why does it take so long? Molecules must contact each other in precisely the proper orientation – and with sufficient force – to overcome unstable intermediates One bond at a time 71 Activation Energy The amount of heat energy required to produce enough random thermal motion to accomplish this is the Activation Energy – the energy required to put atoms in just the right orientation for the reaction to proceed – and with enough force to pass through unstable intermediate stages 72 Changing the Rate of a Reaction Is it possible to change the rate of a reaction? YES!—touch a lighted match to the desk Increase rate of random molecular movement Reaction thermodynamics are exactly the same with or without the fire Only difference is the rate at which the reaction proceeds 73 Controlling the “Burn” Cellular processes force oxidation to proceed in small steps Stepwise progression allows harvest of a little bit of the released energy – about 5% Control and organization accomplished by protein enzymes 74 Enzymes Do not increase the rate of random thermal motion Enzymes lower the activation energy – “grab” two or more reactants – bring them into proper orientation – stabilize the unstable intermediates The reaction occurs “on demand” – in a controlled, multi-step process 75 Enzymes Loss of energy as heat is reduced – some energy (about 5%) is captured and stored – used later to form different covalent bonds elsewhere ΔG, Δentropy remain the same – but activation energy has changed 76 Unfavorable Reactions pos ΔG – require input of energy Result in products with higher energy Result in products that are more organized than the reactants – less disordered 77 Enzymes In unfavorable biological reactions, enzymes perform two functions: 1) lower activation energy – same as for a favorable reaction 2) also couple the unfavorable reaction – to a separate, favorable reaction 78 79 Activated Carrier Molecule used by enzymes to couple unfavorable reactions to favorable ones High energy bond at one end Complex surface across remainder of molecule ATP most common and widely used activated carrier Other important carriers—NADH, NADPH, Acetyl CoA, GTP 80 Control of Biosynthesis Anabolism and catabolism are highly coordinated and integrated processes – amazingly complex, surprisingly stable Proteins control this smooth-running chemical factory – machines – switches – enzymes 81