PDF Biology Past Paper - Introduction to Cells

Variation in Life forms Fungi Viruses Animals Plants Features of Living Organisms Adaptation Order/Organization Control/Regulation Obtain/Use Energy Growth Reproduction & Heredity Responsiveness Molecular Processes Adaptation Order/Organization Responsiveness Control/Regulation Obtain/Use Ener...

Variation in Life forms Fungi Viruses Animals Plants Features of Living Organisms Adaptation Order/Organization Control/Regulation Obtain/Use Energy Growth Reproduction & Heredity Responsiveness Molecular Processes Adaptation Order/Organization Responsiveness Control/Regulation Obtain/Use Energy Growth Reproduction & Heredity REPLICATION METABOLISM Self-Replication - as the defining feature of life? Animals Plants Bacteria ORGANISMAL LEVEL Self-Replication - as the defining feature of life? Animals Plants Bacteria ORGANISMAL LEVEL ???? Viruses Computer code/virus Robots/AI Self-Replication - as the defining feature of life? Animals Plants  Bacteria ORGANISMAL LEVEL DNA Proteins ??? MOLECULAR LEVEL Self-Replication - as the defining feature of life? Animals Plants Bacteria ORGANISMAL LEVEL DNA Proteins ??? MOLECULAR LEVEL Self-Replication - as the defining feature of life? Genes/DNA as “replicators”, Organisms as “vehicles”, Human/Animal behavior promotes replication Self-Replication - as the defining feature of life? Self-Replication - as the defining feature of life? The Cell - the molecular machine which allows Self-Replication? The Cell - the molecular machine which allows Energy Generation Energy Generation - the molecular process which allows Self-Replication The Cell - the molecular machine which allows Energy Generation Energy Generation - the molecular process which allows Self-Replication How did all this come together & WHEN The Origin of Life aka THE BIGGEST RIDDLE OF THEM ALL https://www.rte.ie/player/series/earth/10002724-00-0000?epguid=AQ10002725-01-0002  Theories on The Origin of Life Life Continuously “Arises” (from Non-Living Things) “Spontaneous Generation” Life Continuously “Evolves” (from Living Things) “Darwinian Evolution” Theories on The Origin of Life Life Continuously “Arises” (from Non-Living Things) “Spontaneous Generation” OBSERVATION VERSUS Life Continuously “Evolves” (from Living Things) “Darwinian Evolution” EXPERIMENTATION Theories on The Origin of Life ABIOGENESIS: Non-Living Things BIOGENESIS: Living Things -> -> Living Things Non Continuously/Spontaneously Occurring Continuously Occurring Living Things Theories on The Origin of Life ABIOGENESIS: Non-Living Things BIOGENESIS: Living Things -> EXCEPT ABIOGENESIS: Non-Living Things -> Living Things Not Continuously/Spontaneously Occurring Continuously Occurring (The Tree of Life) Living Things -> Living Things It had to start somewhere..../some-when Theories on The Origin of Life ABIOGENESIS: Non-Living Things BIOGENESIS: Living Things -> EXCEPT PANSPERMIA: -> Living Things Not Continuously/Spontaneously Occurring Continuously Occurring (The Tree of Life) Living Things Extra-Terrestrial -Living Things -> https://astrobiology.nasa.gov/news/in-search-of- panspermia/ Terrestrial Living Things The Origin of Life “Timeline” INNOVATION/DRIVEN BY GEOLOGICAL CHANGES/EVENTS CHEMICAL CHANGES/EVENTS BIOLOGICAL CHANGES/EVENTS Early Earth 4.54 BYA Temperature - Reducing (no O2) - Other Gases – Water? - PRESENT DAY 3.8 BYA The First Rain Fossil Record indicates liquid water between 4.2- 3.8 BYA Consistent with cooling of atmosphere The First Rain Terrestrial Source (H2 interacting with magma) Fossil Record indicates liquid water between 4.2- 3.8 BYA Consistent with cooling of atmosphere Extra-Terrestrial Source (Asteroids) Fossil Record indicates liquid water between 4.2- 3.8 BYA Consistent with cooling of atmosphere Water (H20) – is key solvent for biological life; - Cohesion of water molecules - Moderate temperature - Allow Floating - Aqueous solutions/Solvent (aka MEDIUM for Life) Other substances dissolve in it Some substances repel it & form “BARRIERS’ Extra-Terrestrial Source (Asteroids) The First Rain Terrestrial Source (H2 interacting with magma) Key to opposing Thermodynamics [Ch3 Campbell] Prebiotic Conditions Can Give Rise to Biotic Molecules - Experiment Miller Experiment (Fig 4.2, Campbell) - Simulated early-earth (prebiotic) conditions, atmosphere [gases], liquid water, temperature & energy, (closed conditions) - Took Samples for analysis => KEY READOUT – the presence of Amino Acids (precursors of proteins), also detected purines & pyrimidines (nucleic acids) 1953; Link between DNA & Amino Acids emerges Miller Experiment Highlight measured Amino Acids (Precursors of Proteins) Watson, Crick & Franklin Molecular Structure of DNA Instructions for Proteins Updated Hypothesis? Refining the Experiment Patel et al Experiment - More accurately simulated prebiotic conditions (gases, UV light) READOUT; measured 3 key ingredient for Cells (Cells in a blender -> Nucleotides, Amino Acids But also LIPIDS (separation from environment) Key to opposing Thermodynamics Not Just DNA; What Came Before THE RNA WORLD Idea The RNA world: RNA can act as an informational polymer but also an enzyme to promote Self Replication In more unstable prebiotic conditions, RNA was superior biological polymer => DNA evolved, more stable & became protected as Cells evolved EVIDENCE: - RNA viruses, mRNA? (It can be the sole source of genetic information) - Ribozymes, The Ribosome (It can be the catalyst for metabolic reactions) The First Evidence of Cellular Life Stromatolites Living Fossil Record of earliest forms of oceanic life Aquatic (ocean-living) progenitors of Cyanobacteria - Likely preceeded by simpler life which used C02 & other gases to make CH4 (Methane) Cyanobacteria make Food/Early Biomolecules & O2 from H20 & CO2 (Early photosynthesis) Production of O2 transformed the planet & evolution of life BIOLOGICAL CHANGES/EVENTS The Origin of Life “Timeline” INNOVATION/DRIVEN BY GEOLOGICAL CHANGES/EVENTS CHEMICAL CHANGES/EVENTS After the First Cells & Photosynthesis; => Endosymbiosis Key Steps Early photosynthetic bacteria (Cyanobacteria) Early Aerobic bacteria, can use oxygen Division of Labor & primitive nucleus forming* 1st STEP in Endosymbiosis; Aerobic bacteria enters primitive eukaroytic cell 2nd STEP in Endosymbiosis Endosymbiotic relationship with photosynthetic bacteria established Last Common Ancestor of Animals split from Plants before 2nd Step (Evidence – we lack Chloroplasts & evolved our bodies around obtaining Food) * After the First Cells & Photosynthesis; => Endosymbiosis After Endosymbiosis; => Multi-cellularity Obtaining Food & Reproduction drove evolution; - Amoeba (single cell eukaryotic ‘animal’) - Slime Mould (Dictosytelium) – sexual reproduction - Sea Sponge (Hydra) - cell specialization [prey] Recap Lecture 1 (Previous): Module/Course overview What is Biology What is Life The Origin of Life FURTHER READING CAMPBELL BIOLOGY - Essential Biology Textbook - Ch's 1, 3-4 The Selfish Gene – Richard Dawkins The Vital Question – Nick Lane Notes on Blackboard https://www.scientificamerican.com/article/the -search-for-extraterrestrial- life-as-we- dont-know-it/ BBC's EARTH (with Chris Packham?) - RTE Player Contact: [email protected], Twitter; @Fredtwee & Good Luck BYU11101 – From Molecules to Cells (2022-2023). Section 1 Origins-Diversity-Cellular: Cellular Basis of Life Lecture 2; Cellular Organization Dr Frederick Sheedy School of Biochemistry & Immunology Cells come in all shapes & sizes Bacterial Cell Animal Cell Fungal Cell Neurons Muscle Cell Plant Cell TISSUES Cells are made of Bio-molecules ELEMENTS: C Carbon –based lifeforms, Carbon backbone of all molecules (hydrocarbons = organic chemistry) H Hydrogen - bonding, part of water O -Oxygen - is life N Nitrogen - nitrogenous bases & amine group P Phosphorous – energy carrier & backbone of DNA S Sulfur – disulphide bonds H20; WATER – solvent for life Cells are made of Bio-molecules HYDROPHILIC Water Loving Dissolve/Mix in water ELEMENTS: C Carbon –based lifeforms, Carbon backbone of all molecules (hydrocarbons = organic chemistry) H Hydrogen - bonding, part of water O -Oxygen - is life N Nitrogen - nitrogenous bases & amine group P Phosphorous – energy carrier & backbone of DNA S Sulfur – disulphide bonds H20; WATER – solvent for life HYDROPHOBIC (or Hydrophobicity) Water-hating Will not mix with water Cells are made of Bio-molecules Nucleic Acids Proteins -- DNA genetic material The Selfish Gene RNA - messenger Lipids Give structure Provide barriers - Products of genes - Catalysts to promote replication Carbohydrates - - - Provide energy for growth & replication - Give structure Cells are made of Bio-molecules Nucleic Acids Proteins -- DNA genetic material The Selfish Gene RNA - messenger Lipids Give structure Provide barriers - Products of genes - Catalysts to promote replication Carbohydrates - - - Provide energy for growth & replication - Give structure Cellular Life What is life? The capacity for GROWTH & SELF-REPLICATION Processes: Biomolecules: What is life? The capacity for Processes: Biomolecules: GROWTH METABOLISM MAINTAIN ORDER RESPOND TO STIMULI & SELF-REPLICATION INHERITANCE OF GENETIC MATERIAL Cellular Life What is life? The capacity for Processes: Biomolecules: GROWTH METABOLISM MAINTAIN ORDER RESPOND TO STIMULI PROTEINS CARBOHYDRATES LIPIDS & SELF-REPLICATION INHERITANCE OF GENETIC MATERIAL NUCLEIC ACIDS – DNA/RNA Cellular Life What is life? The capacity for Processes: GROWTH METABOLISM MAINTAIN ORDER RESPOND TO STIMULI PROTEINS CARBOHYDRATES LIPIDS EVOLUTION Biomolecules: Alterations: & SELF-REPLICATION INHERITANCE OF GENETIC MATERIAL NUCLEIC ACIDS – DNA/RNA Cellular Life VARIATION IN LIFE-FORMS The Central Dogma of Molecular Biology Biomolecules: DNA Processes: Function: Genetic material Self-replicating molecule “Selfish Gene” instructions for cellular life Temporary copy of DNA Expresses the instructions for life ”Messenger” Catalysts for Cellular Life (Metabolism) Effectors RNA PROTEINS THE TRANSMISSION OF GENETIC INFORMATION The Central Dogma of Molecular Biology Biomolecules: DNA Processes: Replication of DNA Transcription of DNA Function: Genetic material Self-replicating molecule “Selfish Gene” instructions for cellular life Temporary copy of DNA Expresses the instructions for life ”Messenger” Catalysts for Cellular Life (Metabolism) Effectors RNA PROTEINS Translation of RNA THE TRANSMISSION OF GENETIC INFORMATION The Central Dogma of Molecular Biology Biomolecules: DNA Processes: Replication of DNA Transcription of DNA Metabolism Growth Response to Stimuli RNA PROTEINS Translation of RNA THE CATALYTIC EVENTS SUPPORTING THE TRANSMISSION OF GENETIC INFORMATION THE TRANSMISSION OF GENETIC INFORMATION The Central Dogma of Molecular Biology Biomolecules: DNA Processes: Replication of DNA Transcription of DNA Metabolism Growth Response to Stimuli RNA PROTEINS Translation of RNA TRANSMISSION OF GENETIC INFORMATION & PROCESSES TO SUPPORT THIS ARE FACILITATED BY CELL STRUCTURE THE CATALYTIC EVENTS SUPPORTING THE TRANSMISSION OF GENETIC INFORMATION THE TRANSMISSION OF GENETIC INFORMATION Common features of Cells NUCLEAR REGION contains genetic material (DNA) Allows DNA Replication & DNA Transcription (DNA + RNA + PROTEIN) PLASMA MEMBRANE separates cell from outside maintains order allows transport (LIPID + PROTEIN) CYTOPLASM Contains multiple organelles & sites of catalytic action to support metabolic activities required for growth & replication Human skin cell Imaged by Light Microscopy Low resolution Need to decipher contents Light powered Frog pigment cell Imaged by Fluorescent Confocal Microscopy High resolution Labelling of contents Laser-powered Hierarchy to Cell Structure NUCLEUS ‘Administrative capital of the cell Contains, Protects, decides & sends out the instructions for cell behavior DNA -> RNA * Evolution of a nucleus (Internal membranes) was first step to Compartmentalization of cells to diversify & specialize functions NUCLEAR REGION genetic information in cytoplasm NUCLEUS Genetic information (DNA) contained within nuclear membrane separated from cytoplasm The Tree of Life PROKARYOTES no true/before nucleus (NUCLEOID) EUKARYOTES true nucleus The Tree of Life - 3 Domain System Bacteria Domain formerly known as “Eubacteria” ARCHAEA no true nucleus More closely related to Eukaryotes than Prokaryotes based on “phylogenetic sequencing” of rRNA Modifying the 3 Domain System (Eu)-Bacteria no true nucleus Fatty acids + ester linkages rRNA Archaea no true nucleus Fatty acids + ether linkages rRNA – distant from eubacteria EUKARYA True nucleus Membrane bound organelles rRNA Bacteria + Archaea = PROKARYOTES Modifying the 3 Domain System ASGARD ARCHAE (Eu)-Bacteria no true nucleus Fatty acids + ester linkages rRNA Archaea no true nucleus Fatty acids + ether linkages rRNA – distant from eubacteria EUKARYA True nucleus Membrane bound organelles rRNA Bacteria + Archaea = PROKARYOTES 2 Groups 7 Kingdoms Photosynthetic uni/multi-cellular non-plants eg – some algae unicellular eukaryotic microbes eg – some Amobea Prokaryotes Versus Eukaryotes PROKARYOTES no true nucleus Nuclear region called “Nucleoid” no membrane separating it No membrane-bound organelles – metabolism in cytoplasm Cell Wall gives structure & rigidity Smaller cells 1-5 μM EUKARYOTES true nucleus DNA Within nucleus, nucleolus region Membrane-enclosed Contain organelles (eg-Mitochondria) & internal membranes;“Division of labor” No Cell Wall – more fluidic shape Larger cells 10-50 μM Note on Cell Size (Surface Area:Volume Ratio) Calculate the surface area to volume ratio for each. A. B. C. Smaller cells working together overcomes Surface Area:Volume problem For the following Eukaryotic organisms, suggest ways in which they have overcome the surface area : volume ratio problem - Fungal hyphae - Eukaryotic muscle tissue - Plant cell Recap Lecture 2 (Recap): Biomolecules (Intro) Information Flow in Biology General Cell Structure The Tree of (Cellular) Life Pro Versus Eukaryotic Cells BYU11101 – From Molecules to Cells. Section 1 Origins-Diversity-Cellular: Cellular Basis of Life Lecture 3; The Nucleus Dr Frederick Sheedy School of Biochemistry & Immunology Prokaryotes Versus Eukaryotes?? Prokaryotes Versus Eukaryotes?? Prokaryotes Versus Eukaryotes?? The Nucleus/Nuclear Region Nucleus (DAPI), Cytoplasm (Actin stain) The Nucleus: CHROMOSOMES # contains DNA packaged with proteins called chromatin #Only visible in replicating cells NUCLEOLUS* area rich in ribosomal RNA *obvious under microscope NUCLEAR ENVELOPE Two phospholipid bi-layer’s form the Nuclear Membrane Studded with Nuclear Pores Allows transport of RNA out & signals inward... The Nuclear Envelope Nuclear Envelope: (2 bi-layers) Outer membrane Inner Membrane Nuclear pore Surface of nuclear envelope (TEM – Transmission Electron Microscopy) Pore complexes (TEM) Pores, lined with a structure called a pore complex, regulate the entry and exit of molecules from the nucleus The nuclear side of the envelope is lined by the nuclear lamina, which is composed of proteins and maintains the shape of the nucleus THE DOUBLE HELIX: 2 strands of ‘complementary’ DNA => dsDNA helix sugar-phosphate backbone DNA DOUBLE HELIX STRUCTURE ALLOWS: - DNA REPLICATION – whole genome unwinding & copying chromosomes - DNA TRANSCRIPTION – regulated unwinding of specific genetic sequences/genes, creation of “RNA” copy Hydrogen-bonded base pairs Nuclear Proteins in Eukaryotes HISTONE PROTEIN DNA NUCLEOSOMES CHROMATIN CHROMOSOMES DNA, Chromosomes -> The Genome THE GENOME IS THE BOOK OF LIFE DNA bases – Letters DNA strands – Sentences Genes – “Dialog/Action Words” Chromosomes – 1 Chapter, contains many genes “dialog” & sentences that give these context “Regulatory DNA” Our Genome - BOOK Blueprint for Life YEAR 2000 – MAJOR DEVELOPMENTS BioFlix: Tour of an Animal Cell Play from 1:27→ 2:10 mark, “Enter the nucleus & DNA packaging”. Reading the DNA - Transcription Template: DNA (Gene) Catalyst: RNA polymerase (protein enzyme) RNA nucleotides Product: messenger RNA (mRNA) RNA SUGAR COMPONENT – Ribose “R in RNA” URACIL as base Unstable, short-lived single strand DNA SUGAR COMPONENT – Deoxyribose “D in DNA” Thymine as base Stable Structure double stranded Reading the DNA - Transcription Template: DNA (Gene) Catalyst: RNA polymerase (protein enzyme) RNA nucleotides Product: messenger RNA (mRNA) The Fate of RNA.. mRNA “Translated” into proteins Exported from Nucleus To sites of PROTEIN SYNTHESIS - RIBOSOMES The Fate of RNA.. mRNA “Translated” into proteins Exported from Nucleus To sites of PROTEIN SYNTHESIS - RIBOSOMES amino acid attached to tRNA molecule rRNA ribosomal RNA Forms a complex with proteins – RIBOSOME tRNAs transfer RNAs RNA species that links up with AMINO ACIDS -> PROTEINS Site of protein synthesis Found in Ribosomes Template: mRNA (Nucleotides) Lost in Translation ? Catalyst: RIBOSOME (protein & RNA complex) rRNA + tRNA Product: Protein (Amino Acids) The Ribosome Ribosomes: Found in pro & eu-karyotes Central in flow of genetic information Translate mRNA into PROTEINS Complex of rRNA, proteins, tRNA & mRNA Found free in cytoplasm Or associated with Endoplasmic Reticulum (ER) – membrane network from nucleus into cell 0.25 μm Free ribosomes in cytosol Endoplasmic reticulum (ER) Ribosomes bound to ER TEM showing ER and ribosomes BioFlix: Tour of an Animal Cell Play from 2:10 → 2:42 mark, “RNA->Protein”. Proteins are Key Cellular Effectors Bacteria => LIFE Fungi Viruses Animals Plants Recap Lecture 3 (Recap): Pro Versus Eukaryotic Cells Nucleus/Nuclear Region DNA & The Genome RNA & Ribosomes BYU11101 – From Molecules to Cells. Section 1 Origins-Diversity-Cellular: Cellular Basis of Life Lecture 4; Beyond the Nucleus Dr Frederick Sheedy School of Biochemistry & Immunology Recap NUCLEUS DNA resides mRNA made CYTOPLASM (Ribosome) mRNA translated into PROTEIN Beyond the Nucleus CYTOPLASM: Area defined by nuclear membrane & plasma membrane Consists of CYTOSOL + membrane- bound ORGANELLES Cytosol Intracellular fluid inside the cell (transparent) Mainly water, ions, biomolecules/metabolites & proteins Concentration Gradients of Biomolecules - metabolism Protein Complexes (Inflammasomes/Apoptosomes/Centrosomes) – cell signalling/division -Free Ribsomes CYTOSKELETON proteins - Shape, Structure & Motility Cytoskeleton ACTIN FILAMENTS: Aka Microfilaments, “Actin” polymers, Cellular growth as actin filaments polymerizes & depolymerizes at opposite ends “Myosin” binds & “moves” along INTERMEDIATE FILAMENTS: Larger filament structures, Various proteins – cell-type specific, Eg – “Keratin” in epithelia Anchor organelles & organize 3-D shape MICROTUBULES: Hollow cylinder structure, “Tubulin” polymers, Involved in cellular organization & Centrosome Where do the proteins go? - The Endomembrane System The Endomembrane System The endomembrane system consists of – Nuclear envelope – Endoplasmic reticulum – Golgi apparatus – Lysosomes – Vacuoles – Plasma membrane These components are either continuous or connected via transfer by vesicles The endomembrane system is a complex and dynamic player in the cell’s compartmental organization The Endoplasmic Reticulum Endoplasmic Reticulum Membrane network from nucleus into cell Consists of folds – Cisternae Rough ER – studded with Ribosomes, sites of protein synthesis & modification (glycoproteins) Smooth ER – no Ribosomes, important in Lipid synthesis & detoxification Lipid + Protein Synthesis -> Membrane Factory The Endoplasmic Reticulum Endoplasmic Reticulum Membrane network from nucleus into cell Consists of folds – Cisternae Rough ER – studded with Ribosomes, sites of protein synthesis & modification (glycoproteins) Smooth ER – no Ribosomes, important in Lipid synthesis & detoxification Q - Where does it lead? It doesn’t reach plasma membrane directly Vesicles bud off – (membrane bound) & transport contents around & out of cell [Sorting & Packaging Function] Intracellular Transport Golgi Apparatus: Directs/Sorts traffic inside the cell Smooth ER – traffics lipid (steroid hormones/membrane) to GOLGI Rough ER Vesicles – delivers protein cargo to GOLGI New membrane-bound organelles/Vesicles bud off GOLGI Go to... ENDO-LYSOSOME – for recycling PLASMA MEMBRANE –for Transport Functions The Golgi Apparatus Golgi Vessel/Apparatus Membrane network within cytoplasm Generally 4-8 folds/sacs-Cisternae (ER-derived) Cis face – nuclear “receiving” side Trans face – plasma membrane “shipping” side Directs & sorts trafficking of proteins within & out of the cell via the PLASMA MEMBRANE Cellular Transport - Out ENDOCYTOSIS SECRETION Aka Exocytosis Cellular Transport - In ENDOCYTOSIS Cellular Transport - In The Lysosome Membrane bound compartment within the cell Highly acidic Contains degradative (hydrolytic) enzymes (work at acidic pH) – made in rER, bud off & acidify -> LYSOSOME Cargo delivered to LYSOSOME => DEGRADATION Integrates Transport Network from ER/Golgi (Vesicles) & Endosomes (incoming cargo from external environment or cytoplasm) Important in response to external cargo eg-food/pathogens (PHAGOCYTOSIS) Important in recycling old organelles within cytoplasm (AUTOPHAGY) Lysosome Peroxisome (b) Autophagy Mitochondrion Vesicle Digestion The Lysosome Digestive enzymes Plasma membrane Food vacuole (a) Phagocytosis Membrane bound compartment within the cell Highly acidic Contains degradative (hydrolytic) enzymes (work at acidic pH) – made in rER, bud off & acidify -> LYSOSOME Cargo delivered to LYSOSOME => DEGRADATION Integrates Transport Network from ER/Golgi (Vesicles) & Endosomes (incoming cargo from external environment or cytoplasm) Important in response to external cargo eg-food/pathogens (PHAGOCYTOSIS) Important in recycling old organelles within cytoplasm (AUTOPHAGY) Lysosome Digestion Animation: Lysosome Formation © 2018 Pearson Education Ltd. Video: Phagocytosis in Action © 2018 Pearson Education Ltd. The Plasma Membrane WE HAVE REACHED OUR FINAL DESTINATION FOR TODAY Common features of Cells NUCLEAR REGION PLASMA MEMBRANE separates cell from outside maintains order allows transport (LIPID + PROTEIN) CYTOPLASM The Plasma Membrane KEEP WHITE WALKERS INVADERS OUT MAINTAIN ORDER WITHIN The Plasma Membrane - separates cell from outside environment - maintain order & organization Q – How do you chemically achieve this?? PROBLEM: Cytoplasm – mainly water, Proteins Hydrophilic environment (Water soluble) Some nucleic acids (RNA) Need something that won’t mix with these to provide separation The Plasma Membrane - separates cell from outside environment - maintain order & organization Q – How do you chemically achieve this?? PROBLEM: Cytoplasm – mainly water, Proteins Some nucleic acids (RNA) Hydrophilic enviroment (Water soluble) Need something that won’t mix with these to provide separation (NON-POLAR) (Hydrophobic) Lipids provide the “solution” LIPIDS: a diverse group of biochemicals contain carbon-hydrogen chains/rings confers rigid structure INSOLUBLE in Water “Hydrophobic” “Non-Polar” aka Water-hating Common feature is (in)solubility, not structure Lipids provide the “solution” LIPIDS: a diverse group of biochemicals contain carbon-hydrogen chains/rings confers rigid structure INSOLUBLE in Water “Hydrophobic” “Non-Polar” aka Water-hating Common feature is (in)solubility, not structure Lipids can have hydrophobic & hydrophilic portions (amphipathic) Ideal for use in membranes The Phospho-lipid bi-layer PHOSPHO-LIPID: amphipathic lipid species – contains hydrophobic and hydrophilic portions PHOSPHATE HEAD – water soluble/hydrophilic/polar 2 FATTY ACID (C/H chain) tails – hydrophobic/non-polar, insoluble eg – phosphatidylcholine Q – What happens when phospholipids get together ??? The Phospho-lipid bi-layer BI-LAYER: Flat-sheet containing 2 layers of phospholipids Hydrophobic tails attracted to each other Exposes the Hydrophilic Heads to the external and internal water soluble environments Hydrophobic tails provide separation Hydrophilic Heads allow mixing with the environment Plasma membrane terminus for eukaryotes, Prokaryotes have more "layers" PROKARYOTES no true nucleus Nuclear region called “Nucleoid” no membrane separating it No membrane-bound organelles – metabolism in cytoplasm Cell Wall gives structure & rigidity EUKARYOTES true nucleus DNA Within nucleus, nucleolus region Membrane-enclosed Contain organelles (eg - Mitochondria) & internal membranes; “Division of labor” No universal Cell Wall – more fluidic shape *Exception; plants/fungi Smaller cells 1-5 μM Larger cells 10-50 μM Bacterial Cell Wall Provides extra support Contains many lipid, lipoprotein, carbohydrate/sugar species Some bacteria have second “plasma membrane” outside their cell wall Allows more specificity/selectivity Cell Wall & Membrane components often associated with immunogenicity and pathogenicity Targeted by antibiotics Some structures derived – flagella/pillae involved with movement or attachment to substrates Some bacteria possess polysaccharide CAPSULE outside cell wall or develop tougher structures for survival (SPORES) Bacterial kingdom divided into 2 Groups based on Cell Wall Structure & how they stain under biochemical assays (Gram stain) Gram Negative Vs Gram Positive GRAM NEGATIVE Contain outer membrane with lots of lipids/lipoprotein & transport proteins Thin cell wall of peptidoglycan (stain negative) GRAM POSITIVE No outer membrane Major Peptidoglycan (carbohydrate polymer) cell wall (Stain positive – retain counterstain) Contains periplasmic space Smaller periplasmic space Animal Vs Plant Cells PLANT CELLS Have a thick cellulose cell wall (carbohydrate polymer) Confers stability & protection Survive high osmotic pressure Plant Cell Wall PLANT CELLS Neighboring cell walls exist side by side Each has a 3-layer structure - Plasma membrane (inside) - 3 layers of cellulose “primary wall” - Outer “middle lamella”, forms the division/border with neighboring cell Prokaryotes Versus Eukaryotes PROKARYOTES no true nucleus Nuclear region called “Nucleoid” no membrane separating it No membrane-bound organelles – metabolism in cytoplasm Cell Wall gives structure & rigidity Smaller cells 1-5 μM EUKARYOTES true nucleus DNA Within nucleus, nucleolus region Membrane-enclosed Contain organelles (eg-Mitochondria) & internal membranes;“Division of labor” No Cell Wall – more fluidic shape Larger cells 10-50 μM Prokaryotes Versus Eukaryotes MITOCHONDRIA All free-living eukaryotes Double membrane system (similar to prokaryotic cells) Inner membrane – folds “Cristae” Own DNA & Ribosomes in “Mitochondrial matrix” Allows cellular respiration, Breakdown of Glucose (cytoplasm) & other intermediates (matrix) to generate energy via oxidative phosphorylation (cristae - req O2) CHLOROPLASTS Plants & Algae only Double membrane system (similar to prokaryotic cells) Contain “Chlorophyll” chemical in internal membrane network “Thylakoids” Own DNA & Ribosomes in “Stroma” Allows Photosynthesis, Captures light energy, fuel enzymatic formation of Glucose (req CO2/H20), generates O2 Prokaryotes Versus Eukaryotes Endoplasmic Nucleus reticulum Nuclear envelope earliest step in eukaryotic cell evolution Engulfing of oxygen- using nonphotosynthetic prokaryote, which becomes a mitochondrion Ancestor of eukaryotic cells (host cell) Engulfing of photosynthetic prokaryote Mitochondrion Mitochondrion Chloroplast At least one cell Nonphotosynthetic eukaryote Photosynthetic eukaryote Cellular Compartmentalization Fig X.xx Campbell Biology & Integrated Assignment Worksheet Recap Lecture 4 The Cytoplasm, Cytosol & Cytoskeleton The Transmembrane Network - Endoplasmic Reticulum/The Golgi Lysosomes & Recycling The Plasma Membrane Cell Walls Organelles with prokaryotic origin & metabolic function BYU11101 – From Molecules to Cells. Section 1 Origins-Diversity-Cellular: Cellular Basis of Life Lecture 5; Cell Division Dr Frederick Sheedy School of Biochemistry & Immunology Cell Division – facilitating Self-Replication Levels of “Replication” Replication & Duplication of DNA Types of Cell Division Mitosis Cytoplasmic Events in Replication Stages of Cell Division & Regulation Special Forms of Cell Division (Meiosis) Levels of Replication The Cell – the Molecular Machine for Self-Replication? Replication of DNA DNA  Cellular Growth, Expansion & Division PROTEINS LIPIDS THE DOUBLE HELIX: 2 strands of ‘complementary’ DNA => dsDNA helix sugar-phosphate backbone Replication of DNA DOUBLE HELIX STRUCTURE ALLOWS: - DNA REPLICATION – whole genome unwinding & copying chromosomes - DNA TRANSCRIPTION – regulated unwinding of specific genetic sequences/genes, creation of “RNA” copy Hydrogen-bonded base pairs DNA Replication -> Chromosome Organization DNA HISTONE PROTEIN NUCLEOSOMES CHROMATIN CHROMOSOMES DNA Replication -> Chromosome Organization DNA HISTONE PROTEIN Only appears like this after “DNA REPLICATION” NUCLEOSOMES CHROMATIN SISTER CHROMATIDS VIDEO illustrating CHROMSOMAL DUPLICATION PLAY FROM 0:20 sec to 1:00 min mark... 2 Centromere – anchors chromatids Replication of DNA DNA Chromosomal Duplication 1 Chromosomes Chromosomal DNA molecules Centromere Chromosome arm Chromosome duplication 3 Sister chromatids Separation of sister chromatids DNA Replication – 1 side of the story... Replication of DNA DNA  Cellular Growth, Expansion & Division PROTEINS LIPIDS Nuclear & Cytoplasmic Events allow Seperation Types of Cell Division - DNA REPLICATION – central to ‘all’ Cell Division - Different Cells have different STRUCTURES - DNA is organized very differently in different CELLS - => Different Types of Cell Division Bacterial chromosome No nucleus 1 “bacterial chromosome” Kinetochore microtubule Intact nuclear envelope Kinetochore microtubule Fragments of nuclear envelope (a) Bacteria (c) Diatoms and some yeasts (b) Dinoflagellates (d) Most eukaryotes Chromosomes Duplicates by replication Cell divides around this “BINARY FISSION” Microtubules Intact nuclear envelope Types of Cell Division - DNA REPLICATION – central to Cell Division - Different Cells have different STRUCTURES - DNA is organized very differently in different CELLS - => Different Types of Cell Division Bacterial chromosome Kinetochore microtubule chromosome Intact nuclear envelope (c) Diatoms and some yeasts (a) Bacteria Chromosomes Kinetochore microtubule Microtubules Nuclear envelope remains Bacterial Kinetochore microtubule Intact nuclear envelope (a) Bacteria (c) Diatoms and some yeasts “BINARY FISSION” Chromosomes Have nuclei & chromosome (s) (b) Dinoflagellates (d) Most eukaryotes (b) Dinoflagellates envelope nuclear separate envelope Microtubules Intact nuclear envelope Cell Walls Kinetochore microtubule intact Intact nuclearChromosomes duplicates & Fragments of nuclear envelope Fragments of (d) Most eukaryotes “BINARY FISSION/BUDDING” Types of Cell Division - DNA REPLICATION – central to Cell Division - Different Cells have different STRUCTURES - DNA is organized very differently in different CELLS - => Different Types of Cell Division (a) Bacteria Chromosomes duplicates & Bacterial chromosome Bacterial chromosome Have nuclei Kinetochore microtubule Kinetochore microtubule Intact nuclear envelope (c) Diatoms and some yeasts “BINARY FISSION” Chromosomes (a) Bacteria (a) Bacteria Nuclear envelope re-forms (b) Dinoflagellates (b) Dinoflagellates (d) Most eukaryotes (b) Dinoflagellates (d) Most eukaryotes envelope envelope Microtubules Chromosomes Microtubules Intact nuclear envelope Intact nuclear envelope Kinetochore Kinetochore microtubule Fragments of nuclear envelope Bacterial & multiple chromosomes chromosome  No Cell Walls Kinetochore Intact nuclear Nuclear envelope dissolves (c) Diatoms and some yeasts separate Intact nuclear envelope Cell divides around this “BINARY FISSION/BUDDING” microtubule envelope Chromosomes (c) Diatoms and some yeasts microtubule “MITOSIS” Microtubules Kinetochore microtubule Fragments of nuclear Intact nuclear Fragments of nuclear envelope (d) Most eukaryotes Types of Cell Division - DNA REPLICATION – central to Cell Division - Different Cells have different STRUCTURES - DNA is organized very differently in different CELLS - => Different Types of Cell Division Bacterial chromosome Bacterial chromosome Have nuclei Kinetochore microtubule Kinetochore microtubule Intact nuclear envelope (c) Diatoms and some yeasts “BUDDING” Kinetochore microtubule Fragments of nuclear envelope “BINARY FISSION” Chromosomes (a) Bacteria Bacterial & multiple chromosomes (a) Bacteria Chromosomes duplicates & chromosome No Cell Walls Kinetochore Intact nuclear Nuclear envelope dissolves (c) Diatoms and some yeasts separate Intact nuclear envelope Cell divides around this microtubule envelope  Chromosomes (c) Diatoms and some yeasts (a) Bacteria Nuclear envelope re-forms Microtubules Chromosomes Microtubules Intact nuclear envelope Intact nuclear envelope Kinetochore microtubule “MITOSIS” Microtubules Kinetochore microtubule Fragments of (b) Dinoflagellates (b) Dinoflagellates (d) Most eukaryotes (b) Dinoflagellates (d) Most eukaryotes envelope envelope nuclear Intact nuclear Fragments of nuclear envelope PROTEINS LIPIDS (d) Most eukaryotes Mitosis Form of Cell Division in most eukaryotes: - DNA Replication – duplication & separation of the chromosome(s) - Cytokinesis – cytoplasmic events required to separate chromosomes & divide the cytoplasm - 1 cell gives rise to - 2 daughter cells with identical genetic complement - “preserves the continuity of life” Cytoplasmic Events - Cytokinesis - Separation of the sister chromatids -> daughter chromosomes - Division of the cytoplasm - Nuclear envelope (membranes) dissolve & reform - Movement of daughter chromosomes away from each other (& fidelity therein) - Formation of new plasma membrane -> 2 daughter cells Mitosis – The Mitotic Spindle - PROTEIN NETWORK: - Microtubule proteins– chromosomes move along - “CENTROSOME” PROTEIN COMPLEX – acts as anchor/nexus - Must be “POLARITY” – to result in 2 cells with equal chromosomal content... Mitosis – CENTROSOME - Animal Cells - aka MTOC – Micro-Tubule Organizing Center - PROTEIN COMPLEX – basic protein unit “CENTRIOLE” - Normally 1 per cell - Before Cell Division (after DNA Rep/Chromosomal Duplication) => CENTROSOME DUPLICATION must also occur => 2 centrosomes per cell, allows division of Cytoplasm into 2 Mitosis – Spindle Formation Aster Centrosome Spindle microtubules - Microtubule proteins form from the CENTROSOME & extend into cytoplasm - More “Tubulin” protein subunits added on -> Expansion of the Microtubules - Short Microtubules – “Aster” - Longer Microtubules – “Spindle Microtubules” - TARGETS: Kinetochore proteins on the Chromosomal CENTROMERE Video: Spindle Formation During Mitosis © 2018 Pearson Education Ltd. Mitosis – Spindle Formation - Microtubules which bind a chromosome-> Kinetochore Microtubules - ASTERS @ 1 end & Microtubules at kinetochore -> PUSH/PULL - Places tortion/stress on sister chromatids/chromosomes Mitosis – Separation - Enzyme assisted “Separase” – breaks down connections btw sister chromatids - Sister Chromatids migrate away - Moving along kinetochore microtubules – toward centriole, - Move along the network - Kinetochores M/T shorten – depolymerization, Chromatids move on as they do... Cytokinesis – Division of Cytoplasm - Role of Spindle Microtubules regulating Division of Cytoplasm: - Opposing Centrosomes give “Polarity” - Short “Aster” microtubules give push in opposite direction – away from centre - Before separation, “Non-kinetochore microtubules” play important role; - > Elongating the cytoplasm by extending in opposing directions Cytokinesis – “Cleavage” - Cleavage – division of cytoplasm - Division without growth, type of cleavage common in developing embryo - Formation of “Cleavage Furrow” - From which new membrane forms -> separating daughter cells Cytokinesis – “Cleavage” Cleavage furrow Contractile ring of microfilaments Daughter cells - “Microfilament proteins” important here (actin & myosin) – - After separation & migration of chromosomes - New microfilament bundles form along center - ”Push” to counteract pull of Spindle.... - Invagination of membrane “Cleavage” Cytokinesis – “Cleavage” - “Microfilament proteins” important here (actin & myosin) – - After separation & migration of chromosomes - New microfilament bundles form along center - ”Push” to counteract pull of Spindle.... - Invagination of membrane “Cleavage” Stages of Mitosis - Frequency of mitosis is tightly regulated - & varies from cell-type/tissue/organism - Linked with Growth & Metabolism - Need new nucleotides for DNA Replication - New organelles, nutrients, increased cytoplasm, lipids... - Arranged into CELL CYCLE Stages of Mitosis - Frequency of mitosis is tightly regulated - & varies from cell-type/organism - Linked with Growth & Metabolism - Need nucleotides from DNA Replication - New organelles, nutrients, increased cytoplasm, lipids... - Arranged into CELL CYCLE M Mitosis – referred to as the M-phase in cell cycle - Non Mitotic phase of cell – INTERPHASE - Divided into different parts: - G1 -S - G2 G1 S (DNA synthesis) G2 Cell Cycle Stages of Cell Division (M-phase) - Cell Division involves – segregation of replicated chromosomes & Cytokinesis events - That need to be aligned - Temporal regulation - Divide mitosis into Phases -P - (P) -M -A -T  Stages of Cell Division (M-phase) - Cell Division involves – segregation of replicated chromosomes & Cytokinesis events - That need to be aligned - Temporal regulation - Divide mitosis into Phases - Prophase - Pro-Metaphase - Metaphase - Anaphase - Telophase Stages of Cell Division (M-phase) Interphase - Preparatory events Growth NUCLEUS: DNA Replication CYTOPLASM: Centrosome duplication G2 of Interphase Prophase Prom Centrosomes (with centriole pairs) Chromosomes (duplicated, uncondensed) Early mitotic spindle Fragments Aster Centromere envelope of nuclear Nucleolus Nuclear envelope Plasma membrane Two sister chromatids of one chromosome Kinetocho Stages of Cell Division (M-phase) Prophase - NUCLEUS: Prophase Prometaphase Nonkinetochore microtubules G2 of Interphase Sister Chenrtoromsomaetisds appear Chromosomes (with centriole (duplicated, Early mitotic spindle Fragments pairs) uncondensed) of nuclear Aster Centromere envelope CYTOPLASM: Early Spindle formation Nucleolus Plasma Nuclear membrane envelope Two sister chromatids Kinetochore of one chromosome Kinetochore microtubules 10 μm Stages of Cell Division (M-phase) Pro-meta-phase - NUCLEUS: Prometaphase hase Prophase Membrane dissolves Chromosomes (duplicated, Early mitotic Aster Fragments Nonkinetochore microtubules (Fragments remain) of nuclear uncondensed) spindle Centromere envelope CYTOPLASM: Microtubules extend Attachment to Kinetochore Plasma membrane e Two sister chromatids of one chromosome Kinetochore Kinetochore microtubules 10 μm p rp Stages of Cell Division (M-phase) Metaphase - “NUCLEUS”: Attached chromosomes align on “Metaphase Plate” CYTOPLASM: Extension of Spindle forms symmetry & plate formation Metaphase Metaphase plate Anaphase Telopha Cleavage furrow Daughter chromosomes Spindle Centrosome at one spindle pole Nuclear envelop forming s e  Stages of Cell Division (M-phase) Anaphase - “NUCLEUS”: Anaphase Separation of sister chromatids CYTOPLASM: De-polymerization of Microtubules & Migration of Chromatids Metaphase Telophase and Cytokinesis Metaphase plate Cleavage furrow Nucleolus forming Spindle Nuclear envelope forming Daughter chromosomes Centrosome at one spindle pole 10 μm e “NUCLEUS”: taphase Cleavage furrow Stages of Cell Division (M-phase) Telophase - Reformation of nuclear Nucleolus forming m CYTOPLASM: Cytokinesis & Cleavage Dissolution of Spindle Daughter chromosomes entrosome at ne spindle pole e m p la brane (from remnants te Anaphase Telophase and Cytokinesis of old envelope) Nuclear envelope forming 10 μm s e Co  Stages of Cell Division (M-phase) Telophase - During G1 phase: Correct chromosome number 1 centrosomes e “NUCLEUS”: S-phase: Double chromosome (chromatids) G2-phase: 2 centrosomes Reformation of nuclear Nucleolus forming taphase Cleavage furrow m CYTOPLASM: Cytokinesis & Cleavage Dissolution of Spindle Daughter chromosomes entrosome at ne spindle pole e m p la brane (from remnants te Anaphase Telophase and Cytokinesis of old envelope) Nuclear envelope forming Post-Mitosis (÷2) Each daughter cell: - Correct chromosome number - 1 centrosome 10 μm s e Co VIDEO illustrating STAGES OF MITOSIS PLAY FROM 1:00 min to 3:00 min mark... Regulation of the Cell Cycle - Frequency of mitosis is tightly regulated - & varies from cell-type/organism - Linked with Growth & Metabolism - Need nucleotides from DNA Replication - New organelles, nutrients, increased cytoplasm, lipids... - Arranged into CELL CYCLE M Mitosis – referred to as the M-phase in cell cycle  Regulation of the Cell Cycle G1 checkpoint M checkpoint G1 G2 M Control system S G2 checkpoint - Important to ensure enough metabolites available - SIGNALS in external (& internal) environment control this – Growth Factors - Too much PROLIFERATION – dangerous -> CANCER - Sometimes, a cell must die -> APOPTOSIS, “Programmed Cell Death” Regulation of the Cell Cycle G1 checkpoint Before DNA Replication Most important IF NO PROGRESSION SIGNAL -> Cell Cyle Arrest G0 phase G1 G2 M Control system S - Has the cell sufficient nutrients to allow DNA Replication & Cell Division M checkpoint G2 checkpoint Regulation of the Cell Cycle G1 checkpoint G1 G2 M Control system S M checkpoint - Pre-mitosis check DNA replication ok ? G2 checkpoint - - DNA damage 2 centrosomes? Regulation of the Cell Cycle G1 checkpoint After Anaphase; To check for correct separation of chromosomes, Preserve fidelity of DNA M checkpoint Control system S G1 M G2 G2 checkpoint require a surface for division Escape from Cell Cycle Control Density-dependent inhibition: cells form a single layer Density-dependent inhibition: cells divide to fill a gap and then stop 20 μm (a) Normal mammalian cells (b) Cancer cells Cells will continue to grow if supplied with enough nutrients But reach tipping point – too many cells on monolayer -> Growth Inhibition (G1 checkpoint) Cancer Cells escape these checks & grow in unlimited manner (on top of each other) -> Masses aka Tumors 20 μm Functions of Cell Division a) PropagationofLife b) Growth&embryonic development or organisms c) Repairs&Renewalafter tissue damage (a)Asexualreproduction (b) Growth and development (c) Tissue renewal Functions of Cell Division a) PropagationofLife b) Growth&embryonic development or organisms c) Repairs&Renewalafter tissue damage (a)Asexualreproduction d) SexualReproduction? - Variation in DNA allows evolution (c) Tissue renewal (b) Growth and development A special type of cell division that produces gametes – sperm & egg cells Halves the genetic complement (chromosome content) In diploids (2 copies of each chromosome) => 1 copy of each chromosome (& linked genes) BASIS FOR INHERITANCE 2 divisions; 1 cell -> 4 daughters 1 REPLICATION with 2 SEPARATIONs In Round 1, pairs of chromosomes separate In Round 2, sister chromatids Interphase Pair of homologous chromosomes in diploid parent cell Pair of duplicated homologous chromosomes Sister chromatids Chromosomes duplicate Diploid cell with duplicated chromosomes Meiosis Meiosis I 1 separate (like mitosis) Haploid cells with unduplicated chromosomes Meiosis II Homologous chromosomes separate Haploid cells with duplicated chromosomes 2 Sister chromatids separate Basis for genetic variation: Before pairs of chromosomes separate, CROSSOVER occurs - exchange of DNA “HOMOLOGOUS RECOMBINATION” => Mutation Division of chromosomes separates traits also – basis for genetics & inheritance Random fertilization -> variation also Prophase I of meiosis Pair of homologs Chiasma Centromere TEM Anaphase I Anaphase II Daughter cells Nonsister chromatids held together during synapsis 1 Synapsis and crossing over 2 Movement to the metaphase I plate 3 Breakdown of proteins holding sister chromatid arms together Meiosis Recombinant chromosomes Recap Lecture 5 DNA Replication & Chromosomal Duplication Types of Cell Division Mitosis Cytoplasmic Events in Replication Stages of Cell Division & Regulation Special Forms of Cell Division (Meiosis) FURTHER READING - CAMPBELL BIOLOGY Essential Biology Textbook - Ch 11/12 Notes on Blackboard