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endomembrane system Semi-autonomous organelles Protein sorting to organelles Systems biology of cells Cell Biology & Cell Theory Cell biology: The study of individual cells and their interactions. Cell Theory (Schleiden & Schwann, with contributions from Virchow): All living organisms are composed of one or more cells. Cells are the smallest units of life. New cells arise only from pre-existing cells through division (e.g., binary fission). Origins of Life: Four Overlapping Stages Stage 1: Formation of Organic Molecules Primitive Earth conditions favored spontaneous organic molecule formation. Hypotheses on the origin of organic molecules: Reducing Atmosphere Hypothesis: Earth's early atmosphere (rich in water vapor) facilitated molecule formation. Stanley Miller’s experiment simulated early conditions, producing amino acids and sugars. Extraterrestrial Hypothesis: Organic carbon (amino acids, nucleic acid bases) may have come from meteorites. Debate exists over survival after intense heating. Deep-Sea Vent Hypothesis: Molecules formed in the temperature gradient between hot vent water & cold ocean water. Supported by experimental evidence. Alkaline hydrothermal vents may have created pH gradients that allowed organic molecule formation. Stage 2: Formation of Polymers Early belief: Prebiotic synthesis of polymers was unlikely in aqueous solutions (water competes with polymerization). Experimental evidence: Clay surfaces facilitated the formation of nucleic acid polymers and polysaccharides. Stage 3: Formation of Boundaries Protobionts: Aggregates of prebiotically produced molecules enclosed by membranes. Characteristics of a protobiont: Boundary separating the internal & external environments. Polymers with information (e.g., genetic material, metabolic instructions). Catalytic functions (enzymatic activities). Self-replication. Liposomes: Vesicles surrounded by lipid bilayers. Can enclose RNA and divide. Stage 4: RNA World Hypothesis RNA was likely the first macromolecule in protobionts due to its ability to: Store information. Self-replicate. Catalyze reactions (ribozymes). Chemical Selection & Evolution: RNA mutations allowed faster replication & self-sufficient nucleotide synthesis. Eventually, RNA world was replaced by the DNA-RNA-protein world due to: DNA providing more stable information storage. Proteins offering greater catalytic efficiency and specialized functions. Microscopy Microscopy Parameters Resolution: Ability to distinguish two adjacent objects. Contrast: Difference between structures (enhanced by special dyes). Magnification: Ratio of image size to actual size. Types of Microscopes Light Microscope: Uses light; resolution = 0.2 micrometers. Electron Microscope: Uses electron beams; resolution = 2 nanometers (100x better than light microscopes). Light Microscopy Subtypes Bright Field: Standard; light passes directly through. Phase Contrast: Amplifies differences in light phase shifts. Differential Interference Contrast (DIC): Enhances contrast for internal structures. Electron Microscopy Subtypes Transmission Electron Microscopy (TEM): Thin slices stained with heavy metals. Some electrons scatter while others pass through to create an image. Scanning Electron Microscopy (SEM): Heavy metal-coated sample. Electron beam scans the surface, producing 3D images. Cell Structure & Function Determined by matter, energy, organization, and information. Genome: The complete set of genetic material. Prokaryotic vs. Eukaryotic Cells Feature Prokaryotic Cells Eukaryotic Cells Nucleus ❌ Absent ✅ Present Membrane-bound organelles ❌ None ✅ Yes Size Small (1-10 µm) Large (10-100 µm) Examples Bacteria, Archaea Plants, Animals, Fungi, Protists Prokaryotic Cell Structure Plasma Membrane: Lipid bilayer barrier. Cytoplasm: Internal fluid. Nucleoid Region: DNA storage (no nucleus). Ribosomes: Protein synthesis. Cell Wall: (Some) Provides structure & protection. Glycocalyx: Protection & hydration. Flagella: Movement. Pili: Attachment. Eukaryotic Cell Structure Nucleus: Contains DNA & controls cell functions. Organelles: Rough ER: Protein synthesis & sorting. Smooth ER: Lipid synthesis, detoxification. Golgi Apparatus: Protein modification & sorting. Mitochondria: ATP production (Powerhouse of the Cell™). Lysosomes: Digestive enzymes for breakdown & recycling. Peroxisomes: Breakdown of harmful substances. Cytoskeleton: Provides structure (microtubules, actin filaments, intermediate filaments). Plasma Membrane: Regulates transport & signaling. Endomembrane System Includes: Nucleus, ER, Golgi apparatus, lysosomes, vacuoles, and plasma membrane. Nuclear Envelope: Double membrane structure. Nuclear pores allow molecule transport. Golgi Apparatus: Modifies & sorts proteins/lipids. Packages proteins into vesicles for secretion (exocytosis). Lysosomes: Contain acid hydrolases for macromolecule breakdown. Perform autophagy (organelle recycling). Semi-Autonomous Organelles Mitochondria Function: ATP production (cellular respiration). Structure: Outer & inner membrane (inner folds = cristae for increased surface area). Mitochondrial matrix houses metabolic enzymes. Chloroplasts (Plants & Algae) Function: Photosynthesis (light energy → chemical energy). Structure: Outer & inner membrane. Thylakoid membrane (site of photosynthesis). Contains chlorophyll. Endosymbiosis Theory Mitochondria & chloroplasts evolved from free-living bacteria that were engulfed by an ancestral eukaryotic cell. Protein Sorting & Cell Organization Co-translational sorting: Proteins destined for ER, Golgi, lysosomes, vacuoles, or secretion. Post-translational sorting: Proteins sent to nucleus, mitochondria, chloroplasts, peroxisomes. Systems Biology Studies how cellular components interact to form a functional system
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Lysosomes, Vacuoles
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vacuole
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vacuoles/vesicles
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vacuole
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The Endoplasmic Reticulum (Er) Plays A Key Role In The Modification Osince The Rough Er Helps Modify Proteins That Will Be Secreted From The Cell, Cells Whose Job Is To Secrete Large Amounts Of Enzymes Or Other Proteins, Such As Liver Cells, Have Lots Of Rough Er. Smooth Er The Smooth Endoplasmic Reticulum (Smooth Er) Is Continuous With The Rough Er But Has Few Or No Ribosomes On Its Cytoplasmic Surface. Functions Of The Smooth Er Include: Synthesis Of Carbohydrates, Lipids, And Steroid Hormones Detoxification Of Medications And Poisons Storage Of Calcium Ions In Muscle Cells, A Special Type Of Smooth Er Called The Sarcoplasmic Reticulum Is Responsible For Storage Of Calcium Ions Which Are Needed To Trigger The Coordinated Contractions Of Muscle Fibers. There Are Also Tiny "Smooth" Patches Of Er Found Within The Rough Er. These Patches Serve As Exit Sites For Vesicles Budding Off From The Rough Er And Are Called Transitional Er . The Golgi Apparatus When Vesicles Bud Off From The Er, Where Do They Go? Before Reaching Their Final Destination, The Lipids And Proteins In The Transport Vesicles Need To Be Sorted, Packaged, And Tagged So That They Wind Up In The Right Place. This Sorting, Tagging, Packaging, And Distribution Takes Place In The Golgi Apparatus (Golgi Body), An Organelle Made Up Of Flattened Discs Of Membrane. Micrograph Of The Golgi Apparatus Showing A Series Of Flattened Membrane Discs In Cross-Section _image Credit: "The Endomembrane System And Proteins: Figure 3" By Openstax College, Biology (Cc By 3.0), Modification Of Work By Lousia Howard_ The Receiving Side Of The Golgi Apparatus Is Called The Cis Face And The Opposite Side Is Called The Trans Face. Transport Vesicles From The Er Travel To The Cis Face, Fuse With It, And Empty Their Contents Into The Lumen Of The Golgi Apparatus. As Proteins And Lipids Travel Through The Golgi, They Undergo Further Modifications. Short Chains Of Sugar Molecules Might Be Added Or Removed, Or Phosphate Groups Attached As Tags. Carbohydrate Processing Is Shown In The Diagram As The Gain And Loss Of Branches On The Purple Carbohydrate Group Attached To The Protein. Image Showing Transport Of A Membrane Protein From The Rough Er Through The Golgi To The Plasma Membrane. The Protein Is Initially Modified By The Addition Of Branching Carbohydrate Chains In The Rough Er; These Chains Are Then Trimmed Back And Replaced With Other Branching Chains In The Golgi Apparatus. The Protein, With Its Final Set Of Carbohydrate Chains, Is Then Transported To The Plasma Membrane In A Transport Vesicle. The Vesicle Fuses With The Plasma Membrane, Its Lipids And Protein Cargo Becoming Part Of The Plasma Membrane. _image Modified From "The Endomembrane System And Proteins: Figure 1" By Openstax College, Biology (Cc By 3.0), Modification Of Work By Magnus Manske_ Finally, The Modified Proteins Are Sorted (Based On Markers Such As Amino Acid Sequences And Chemical Tags) And Packaged Into Vesicles That Bud From The Trans Face Of The Golgi. Some Of These Vesicles Deliver Their Contents To Other Parts Of The Cell Where They Will Be Used, Such As The Lysosome Or Vacuole. Others Fuse With The Plasma Membrane, Delivering Membrane-Anchored Proteins That Function There And Releasing Secreted Proteins Outside The Cell. Cells That Secrete Many Proteins—Such As Salivary Gland Cells That Secrete Digestive Enzymes, Or Cells Of The Immune System That Secrete Antibodies—Have Many Golgi Stacks. In Plant Cells, The Golgi Apparatus Also Makes Polysaccharides (Long-Chain Carbohydrates), Some Of Which Are Incorporated Into The Cell Wall. Lysosomes The Lysosome Is An Organelle That Contains Digestive Enzymes And Acts As The Organelle-Recycling Facility Of An Animal Cell. It Breaks Down Old And Unnecessary Structures So Their Molecules Can Be Reused. Lysosomes Are Part Of The Endomembrane System, And Some Vesicles That Leave The Golgi Are Bound For The Lysosome. Lysosomes Can Also Digest Foreign Particles That Are Brought Into The Cell From Outside. As An Example, Let'S Consider A Class Of White Blood Cells Called Macrophages, Which Are Part Of The Human Immune System. In A Process Known As Phagocytosis, A Section Of The Macrophage’S Plasma Membrane Invaginates—Folds Inward—To Engulf A Pathogen, As Shown Below. Diagram Of Phagocytosis, In Which The Phagosome Generated By Engulfment Of A Particle Fuses With A Lysosome, Allowing Digestion Of The Particle. _image Credit: Modified From "The Endomembrane System And Proteins: Figure 4" By Openstax College, Biology (Cc By 3.0)_ The Invaginated Section, With The Pathogen Inside, Pinches Off From The Plasma Membrane To Form A Structure Called A Phagosome. The Phagosome Then Fuses With A Lysosome, Forming A Combined Compartment Where Digestive Enzymes Destroy The Pathogen. Vacuoles Plants Cells Are Unique Because They Have A Lysosome-Like Organelle Called The Vacuole. The Large Central Vacuole Stores Water And Wastes, Isolates Hazardous Materials, And Has Enzymes That Can Break Down Macromolecules And Cellular Components, Like Those Of A Lysosome. Plant Vacuoles Also Function In Water Balance And May Be Used To Store Compounds Such As Toxins And Pigments (Colored Particles). Lysosomes Vs. Peroxisomes One Point That Can Be Confusing Is The Difference Between Lysosomes And Peroxisomes. Both Types Of Organelles Are Involved In Breaking Down Molecules And Neutralizing Hazards To The Cell. Also, Both Usually Show Up As Small, Round Blobs In Diagrams. However, The Peroxisome Is A Different Organelle With Its Own Unique Properties And Role In The Cell. It Houses Enzymes Involved In Oxidation Reactions, Which Produce Hydrogen Peroxide ( ) As A By-Product. The Enzymes Break Down Fatty Acids And Amino Acids, And They Also Detoxify Some Substances That Enter The Body. For Example, Alcohol Is Detoxified By Peroxisomes Found In Liver Cells. Importantly, Peroxisomes—Unlike Lysosomes—Are Not Part Of The Endomembrane System. That Means They Don'T Receive Vesicles From The Golgi Apparatus. You Can Learn More About How Proteins Are Shipped To The Peroxisome In The Article On Protein Targeting.F Proteins And The Synthesis Of Lipids. It Consists Of A Network Of Membranous Tubules And Flattened Sacs. The Discs And Tubules Of The Er Are Hollow, And The Space Inside Is Called The Lumen. Rough Er The Rough Endoplasmic Reticulum (Rough Er) Gets Its Name From The Bumpy Ribosomes Attached To Its Cytoplasmic Surface. As These Ribosomes Make Proteins, They Feed The Newly Forming Protein Chains Into The Lumen. Some Are Transferred Fully Into The Er And Float Inside, While Others Are Anchored In The Membrane. Inside The Er, The Proteins Fold And Undergo Modifications, Such As The Addition Of Carbohydrate Side Chains. These Modified Proteins Will Be Incorporated Into Cellular Membranes—The Membrane Of The Er Or Those Of Other Organelles—Or Secreted From The Cell. If The Modified Proteins Are Not Destined To Stay In The Er, They Will Be Packaged Into Vesicles, Or Small Spheres Of Membrane That Are Used For Transport, And Shipped To The Golgi Apparatus. The Rough Er Also Makes Phospholipids For Other Cellular Membranes, Which Are Transported When The Vesicle Forms.
Updated 284d ago
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1.3 Macro Intro Breaking a bond = hydrolysis Build/make a bond = remove water, dehydration synthesis 1.4 Macros Nucleic Acids DNA and RNA Made from nucleotides A, T, C, G, U Proteins Amino acids Polypeptide To make it into a protein you need to fold and modify Carbs Monosaccharides Ex. glucose Polysaccharides Ex. starch, cellulose, glycogen, chitin Lipids nonpolar Ex. phospholipids Saturated (butter) vs unsaturated (oil) 1.5 Macros structure + function Uses covalent bonds between nucleotides Main structure want it to be covalent bond so its strong Bases use hydrogen bonds DNA is antiparallel, equally spaced read in opposite directions Protein Primary - Amino acids Secondary - Pleats and coils (hydrogen bonding) Tertiary - Interactions between the R-groups (unique shapes) Quaternary - 2 or more chains (any bond) Carbs Chains of sugars using covalent bonds 1.6 Nucleic Acids DNA Deoxyribose sugar T Double stranded RNA Ribose sugar U Single stranded Common Both use nucleotides A, G, C U2 Cells Organelles Ribosomes = protein synthesis Found on rough ER or free Show common ancestry Endoplasmic Reticulum Rough = ribosomes Smooth = makes lipids, detox Golgi complex Protein trafficking Packaging and transport of proteins mitochondria Site of cellular respiration, ATP production Double membrane Own DNA circular DNA Chloroplast Site of photosynthesis Own circular DNA Lysosome Hydrolytic enzymes Apoptosis Vacuole Large in plants Small in animal cells 2.3 Cell Size Small cells Inc surface area to volume ratio More efficient Better for transportation, elimination of waste, heat, exchanges, etc 2.4 Plasma Membrane Small and nonpolar can pass through easily (oxygen and carbon dioxide) 2.5 Membrane Permeability Selectively permeable Transport proteins needed for larger polar molecules Cell wall - plants, fungi, and prokaryotes Provides extra support and protection 2.6 Transport Passive transport (high to low) Does Not require any energy Diffusion Osmosis Facilitated diffusion (uses proteins) Active transport (low to high) Require energy Exocytosis Moving things in or out Endocytosis 2.7 Facilitated diffusion Uses integral proteins Ex. aquaporins, ion channels, neurons Proteins also used for active transport 3.6 Cellular Respiration Glycolysis Within the cytoplasm Evidence of common ancestry because all organisms go through glycolysis Glucose to 2 pyruvates Energy investment phase and energy payoff phase Get pyruvate, ATP, and NADH Fermentation (ONLY IF NO OXYGEN) To reset everything Takes NADH and turns it back to NAD+ to keep running glycolysis Grooming Phase Modify and turn it into Acetyl CoA Kreb Cycle With in the matrix Making electron carriers (NADH and FADH2) Inner mitochondrial membrane Where the electron transport chain takes place 3.7 Fitness Max offspring Variation can increase fitness Unit 4 Cell Communications 4.1 Signal Transduction Pathway Autocrine (signal yourself) Paracrine (next to you) Endocrine (far from you) 4.2 Signal Transduction Pathway intro Reception → transduction → response Reception: ligand attacks to the receptor The process by which a cell detects a signal in the environment. Ex. ligand binds to G protein which activates Transduction: phosphorylation cascade and amplifies signal The process of activating a series of proteins inside the cell from the cell membrane. Response: The change in behavior that occurs in the cell as a result of the signal. Second messenger - first is ligand, second messenger is for amplification (cAMP - each can have their own phosphorylation cascades) 4.3 STP Responses Turn gene off/on Apoptosis Cell growth start/stop 4.4 changes to STP Mutations (respond too much or too little to the signal molecule attacking) Chemical can release that can interfere with your STP resulting with death 4,5 Feedback Respond to changes (homeostasis) Negative (reverse change) Positive (increasing the change) 4.6 / 4.7 Cell Cycle/ Regulation G1 - growth G1 checkpoint (determine if you go to S phase or to G0 non dividing state) S - DNA replication G2 - organelle replication and growth G2 checkpoint - make sure the cell is ready for division M phase - Mitosis PMAT Prophase - nucleus disappears Metaphase - lined up at the equator Anaphase - replicated chromosomes are split Telophase - move to opposite ends M-phase checkpoint - checks to make sure division is correct Cytokinesis - final split into 2 Cyclin increases during S and peaks at M Cdk binds with cyclin to produce mpf Level of cyclins lets cell know where it’s supposed to be Tells your cell you are at your full maturity ready to produce Unit 5 Heredity 5.1 / 5.2 Meiosis Increases genetic variation Crossing over (Prophase 1) Reduction division haploid (half the amount of genetic information) Random fertilization Nondisjunction (meiosis 1 all 4 cells are irregular / meiosis 2 half the cells are irregular) Independent Assortment Increases genetic diversity 5.3 Mendelian Genetics A = dominant allele a = recessive allele Genotype - combination of letters (AA, Aa, aa) Phenotype = looks Law of Segregation - Aa → A / a Law of Independent Assortment (Aa Bb → AB, Ab, aB, ab) Sex Linked Located on a sex chromosome Usually X Sex linked recessive is more common in males because they only have one X Sex linked dominant both can inherit easily Incomplete dominance - blending Codominance - both alleles expressed 5.5 Environmental Effects Ex. weather, pH of soil 5.6 Chromosomal Inheritance Mutation → inherited Some have no effect, negative effect, neutral effect, 6.1 Gene Expression and Regulation 6.1 DNA Double stranded Deoxyribose T RNA Ribose Single stranded U 6.2 Replication (S-Phase) 5’ → 3’ Ligase - binds the new bases together Helicase - unwinds the DNA DNA poly - put down the new bases Primase - makes primer Topoisomerase - stops DNA from getting overwind Leading - able to all go in one go Lagging - many primers and okazaki fragments 6.3 Transcription and Processing Nucleus RNA poly makes primary transcript (pre mRNA) from DNA Template strand is the one the DNA is using to build Non template strand one not being used RNA processing Introns are removed Exons are put together Add cap and tail for protection Alternative splicing 6.4 Translation Ribosome Reverse Transcriptase retroviruses Ex. HIV RNA genomes use reverse transcriptase to make DNA from RNA 6.5 Regulation of Gene Expression Signal to unpack the gene Transcribed (transcription factors differ by cells and allows different gens to turn on) RNA editing Translation Polypeptide folding All need to go correctly or else the gene wont be expressed Acetylation of histones - adding acetyl group causes the DNA to be more loose making it easier to read Methylation of histones - adding methyl groups to the DNA causes it to be tighter and harder to read Enhancers - enhances transcription and causes it to occur more often Activators - dont bind to RNA poly it binds to the enhancer Depends of which genes and stage of development Epigenetics - one gene controls another gene Inducible Operon - usually off Repressor is bound to operon and lactose inactivates Repressible Operon - usually on Repressor is usually inactive, trp activates repressor 6.6 Gene Expression and Cell Specialization Promoter region (TATA box) alerts RNA poly that its a promoter region and where to attach Negative regulation - blocks promoter so RNA poly cant attach small RNA - can turn certain genes off 6.7 Mutations Increase normal gene function Decrease normal gene function Can lead to new phenotypes Cancer can be due to overproduction of growth factors, hyperactive proteins (requires many mutations Can have positive, negative, or no effect Causes of mutation Exposures Random Errors in DNA replication Increase or decrease in chromosome number Prokaryotes Transformation - pick up random DNA Transduction - virus accidentally is filled with bacterial DNA Conjunction - mating bridge/sex pilus 6.8 Biotechnology Electrophoresis - separates DNA by charge and size PCR - artificial DNA replication, increases amount of DNA sample Transformation - you make the bacteria take up a gene you're interested in Unit 7 7.1 Natural Selection natural / selective pressures decide survival Reproductive fitness (max out your kids) 7.2 Natural Selection Acts on phenotypes which can affect genotype Preferring brown fur over white decreases white fur allele frequency Environmental changes → selective pressures 7.3 Artificial Selection Humans select (ex. Dogs, livestock, etc) Convergent evolution - not closely related but because of similar environments you look alike Divergent - had a recent common ancestor but you started becoming separate Niche partitioning - choosing separate niches so you dont have to compete with others 7.4 Population Genetics Mutation - variety and evolution Genetic drift - random event that alters the gene pool Bottleneck effect - an event causes a large part of the population to die off and the remaining left repopulate with a different gene pool Founder effect - the og are there but some leave/get separated 7.5 Hardy Weinburg Large population No natural selection Random mating No mutation No gene flow P+q = 1 p2 + 2pq +q2 = 1 (AA) + (Aa) + (aa) = 1 7.6 Evidence of Evolution Fossils DNA (molecular homologies) Anatomy Vestigial structure (things we dont need anymore) (evidence of common ancestry) Biogeography (species are found all around the world)(kangaroos, genetic code, glycolysis) 7.7 Common Ancestry All Eukaryotes Membrane bound organelles Linear DNA and chromosomes Genes with introns 7.8 Continuing Evolution Genomic changes over time Continuous changes in fossils Evolution of antibiotic resistance Disease evolution 7.9 Phylogeny / Cladistics Phylogeny = included time Cladograms = just traits Shared characters Derived characters Molecular (DNA, proteins, amino acids) are more accurate than characteristics Parsimony - the one with the fewer events on it, the frewer you have the more likely it is 7.10 Speciesation Pre-zygotic Mechanical - parts dont match Gametic - egg doesnt match Geographical - dont live in the same place Temporal - ready to mate at different times Behavioral - specific type of mating display is not there Post-zygotic Hybrid sterility - the hybrid made is healthy but they cannot have children (mule) Hybrid breakdowns - the hybirds are okay but after a generation or two they cannot produce anymore Hybrid inviability - hybrid is produced but cannot survive long enough to reproduce Sympatric New species arrises in the original location Gradualism - slow steady evolution Allopstric Separation leads to speciation Punctuated - long periods of evolution with no change then rapid change 7.11 Extinction Can be natural or human caused If something goes extinct it can open up opprotunities for other species 7.12 Variation Genetic diversity Diversity of the ecosystem = inc biodiversity Less likey to be 7.13 Origins of Life on Earth No oxygen on earth 4.6 billion No ozone layer Tons of UV radiation High ocean levels Vooacanic eruptions RNA was the first genetic material DNA is dependant of RNA in
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vacuole
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