Iron oxide nanoparticles can be dispersed in an organic solvent ( toluene ). Upon its evaporation, they may self-assemble (left and right panels) into micron-sized  mesocrystals  (center) or multilayers (right). Each dot in the left image is a traditional "atomic" crystal shown in the image above. Scale bars: 100 nm (left), 25 μm (center), 50 nm (right). [ 1 ]


AFM  imaging of self-assembly of 2-aminoterephthalic acid molecules on (104)-oriented  calcite . [ 3 ]


The  DNA  structure at left ( schematic  shown) will self-assemble into the structure visualized by  atomic force microscopy  at right.


The yeast cohesin complex consists of specialized proteins, including Scc1. [ 10 ]


Network diagram with feedback loops to generate switch-like activation of anaphase. [ 12 ]


Figure 4: Potential network diagram involving securin and separase to generate switch-like activation of anaphase


An overview of methods for single-cell epigenomic sequencing. Each method is labelled on the bottom row. Arrows are coloured by method, showing the flow from starting material to sequence data. Adapted from  [ 1 ]


One method for single cell DNA methylation sequencing [ 4 ]


Comparison of single cell DNA methylation sequencing methods in terms of coverage as at 2015 on  Mus musculus


Two methods for single-cell ATAC-seq [ 8 ]


This single cell shows the process of the  central dogma of molecular biology , which are all steps researchers are interested to quantify (DNA, RNA, and Protein).


An example of single cell analysis. Here, imaging software is used track individual cells as they migrate over time. [ 2 ]


Models of SMC and cohesin structure


Structure of SMC dimer


Figure 1 . This image illustrates the basic cellular structure of a solenocyte cluster extending off of a side branch of protonephridium (A and B). The solenocyte cell body is circular in nature and resides at the top of each tubule, while the flagella pass through the length of the intracellular tubule lumen.


Figure 2.  The transmission electron micrograph (TEM) depicts the 9+2 array of microtubules of two eukaryotic flagella in cross-sections (upper panel).


Figure 3.  This diagram outlines the fundamental anatomy of the lancelet, also called amphioxus ( Branchiostoma ).


A simplified scheme describing the suggested sequence of sperm guidance events in mammals (Michael Eisenbach, Weizmann Institute of Science, 2009)


Formation of a temperature gradient in the rabbit's oviduct at ovulation by a temperature drop at the sperm storage site. The scheme is not drawn to scale, and objects are magnified disproportionally for demonstration purposes.


General structures of sphingolipids


Metabolic pathways of various forms of sphingolipids.  Sphingolipidoses  are labeled at corresponding stages that are deficient.


Pluripotent, embryonic stem cells originate as inner cell mass (ICM) cells within a blastocyst. These stem cells can become any tissue in the body, excluding a placenta. Only cells from an earlier stage of the embryo, known as the  morula , are totipotent, able to become all tissues in the body and the extraembryonic placenta.


Human  embryonic  stem cells   A: Stem cell colonies that are not yet differentiated.   B:  Nerve  cells, an example of a  cell type  after differentiation.


Human mesenchymal stem cells


Stem cell division and differentiation A: stem cell; B: progenitor cell; C: differentiated cell; 1: symmetric stem cell division; 2: asymmetric stem cell division; 3: progenitor division; 4: terminal differentiation


Diseases and conditions where stem cell treatment is being investigated


Stress granule dynamics


Graphs of surface area,  A  against volume,  V  of the Platonic solids and a sphere, showing that the surface area decreases for rounder shapes, and the surface-area-to-volume ratio decreases with increasing volume. Their intercepts with the dashed lines show that when the volume increases 8 (2³) times, the surface area increases 4 (2²) times.


Plot of the surface-area:volume ratio (SA:V) for a 3-dimensional ball, showing the ratio decline inversely as the radius of the ball increases.


Cells  lining the  small intestine  increase the surface area over which they can absorb nutrients with a carpet of tuftlike  microvilli .


CHO cells in suspension


SH-SY5Y cells adhered to a surface


Orbital laboratory shaker.


Syncytium caused by  HSV-1  infection in  Vero cells


Structure of a teichoic acid repeat unit from  Micrococcaceae


Structure of the lipoteichoic acid polymer


DNA microarray  used to analyze the expression of human (left) and mouse genes.


TNP BINDING


Effect of different solutions on  red blood cells


Micrographs of osmotic pressure on red blood cells


A red blood cell in a hypertonic solution, causing water to move out of the cell.


A red blood cell in a hypotonic solution, causing water to move into the cell.


Depiction of a red blood cell in an isotonic solution.


Figure shows the  Drosophila melanogaster  TTFL and their general interactions between the main players. In this case we can see how CLK and CYC are the positive regulators (yellow and green) and PER and TIM are the negative (red and blue) regulators that each play a role in the circadian clock.


Figure shows the mammalian TTFL and the general interactions between the main players. This shows how PER and CRY both are negative regulators (red arrows) for BMAL1 and CLOCK, since they cause inhibition of BMAL1 and CLOCK by preventing transcription. BMAL1 and CLOCK (green arrows) are positive regulators since they encourage the transcription, and later the translation of PER and CRY.


Overview of the  Neurospora  TTFL and the general interactions between the regulators. In this case WC-1 and WC-2 (red) are seen as the positive elements where they come together to encourage transcription of FRQ. FRQ (green) is the negative regulator which after translation, comes back as negative feedback.


Figure shows the TTFL of plants ( Arabidopsis ). This shows how the different regulators function and how this still qualifies to be a TTFL because of the feedback loops that occur.


CryoTEM image of  GroEL  suspended in  amorphous ice  at  50 000 × magnification


Overview of two-hybrid assay, checking for interactions between two proteins, called here  Bait  and  Prey .   A . The  Gal4  transcription factor gene produces a two-domain protein ( BD  and  AD ) essential for transcription of the reporter gene ( LacZ ).   B , C . Two fusion proteins are prepared:  Gal4BD+Bait  and  Gal4AD+Prey . Neither of them are usually sufficient to initiate transcription (of the reporter gene) alone.   D . When both fusion proteins are produced  and  the Bait part of the first fusion protein interacts with the Prey part of the second, transcription of the reporter gene occurs.


Overview of three-hybrid assay.


Currently identified secretion systems


This plated viability assay measures various yeast viability though a method called "frogging". The research is completed through drop-inoculation techniques. Research has since been conducted on "tadpoling", which is a variation of "frogging" that is completed by keeping the test cells diluted in liquid throughout their examination. [ 1 ]


Flow cytometry  using  7-Aminoactinomycin D  (7-AAD), wherein a lower signal indicates viable cells. Therefore, this case shows good viability (viability of the cells in flow cytometry should be around 95% but not less than 90%. [ 8 ] ).


Victimless leather, photo from TC&A webpage  [1]


Immunofluorescence staining pattern of vimentin antibodies. Produced by incubating vimentin primary antibodies and FITC labelled secondary antibodies with HEp-20-10 cells.


Immunofluorescence staining of   HeLa Cells  with antibody to reveal vimentin containing intermediate filaments in green and antibody to  LAMP1  to reveal lysosomes in red. Nuclear DNA is seen in blue. Antibodies and image courtesy   EnCor Biotechnology Inc .


Pioneers of voltage-sensitive dyes: A. Grinvald, L.B. Cohen, K. Kamino, B.M. Salzberg, W.N. Ross; Tokyo, 2000


Structure of xylan in hardwood. [ 1 ]


Plant cell wall is composed of cellulose, hemicellulose, pectin and glycoproteins. [ 2 ]  Hemicelluloses (a heterogeneous group of polysaccharides) cross-link glycans interlocking the cellulose fibers and form a mesh like structure to deposit other polysaccharides.


Optical microscope image of barley straw xylan single crystals mounted in Nephrax (reproduced from Yundt 1949).


Throughout the past decade in the field of tissue engineering, novel cell sources, engineering materials, and tissue architecture techniques have provided engineering tissues that better restore, maintain, improve, or replace biological tissues.


Micro-mass cultures of C3H-10T1/2 cells at varied oxygen tensions stained with  Alcian blue


Regenerating a human ear using a scaffold


Stained cells in culture


Mouse   embryonic  stem cells


This animation of a rotating  carbon nanotube  shows its 3D structure. Carbon nanotubes are among the numerous candidates for tissue engineering scaffolds since they are  biocompatible , resistant to  biodegradation  and can be functionalized with  biomolecules . However, the possibility of toxicity with non-biodegradable nano-materials is not fully understood. [ 36 ]


Tissue engineered vascular graft


Tissue engineered heart valve


Bioreactor for cultivation of vascular grafts


Different models of 3D printing tissue and organs


A 3D bioprinter


Such steak-like meat could mitigate issues of  environmental impact of meat production  and  animal welfare .


Schematic illustrating cell microencapsulation


Microphotographs of the  alginate - chitosan  (AC) microcapsules


Illustration of the APA microcapsule integrity and morphological changes during simulated GI transit. (a) Pre-stomach transit. (b) Post-stomach transit (60 minutes). (c) Post-stomach (60 minutes) and intestinal (10-hour) transit. Microcapsule size: (a) 608 ± 36 μm (b) 544 ± 40 μm (c) 725 ± 55 μm. From Martoni et al. (2007).


Classic DPN mechanism: Molecular ink diffusing from a nanoscale tip to a surface through a water meniscus.


Liquid ink deposition mechanism


Cantilever biosensor functionalized with 4 different proteins


SEM image of DPN fabricated gold metastructure arrays.


Gold on silicon metastructure fabricated with top-down DPN methods


Streptavidin  (4 nm thickness) deposited using microcontact printing


An example of a Gastruloid formed from Brachyury::GFP mouse ESCs, treated with a pulse of the Wnt/β-Catenin agonist CHIR99021 between 48 and 72h and imaged by wide-field fluorescence microscopy at 120h. Notice the polarised expression of Brachyury::GFP (Bra) at the elongating tip of the Gastruloid. Image from van den Brink  et al.  (2014), used with CC-BY licence.


A captive  axolotl  ( Ambystoma mexicanum )


The  eastern newt  ( Notophthalmus viridescens )


Orthopedic implants to repair fractures to the radius and ulna. Note the visible break in the ulna. (right forearm)


A  coronary stent  — in this case a  drug-eluting stent  — is another common item implanted in humans.


AMS 800 and ZSI 375 artificial urinary sphincters


Complications can arise from implant failure. Internal rupturing of a breast implant can lead to bacterial infection, for example.


Macromolecular crowding in the  cytosol  of cells alters the properties of  macromolecules  such as  proteins  and  nucleic acids . [ 1 ]


The volume of accessible solvent (red) for two molecules of widely different sizes (black circles) at high concentrations of  macromolecules  (grey circles). Reducing the available volume increases the  effective concentration  of macromolecules.


Optical image of an array (left) and SEM image of the tip (right)


Microfabrication sequence


In vitro single cell injection using NFP


Donated organ prepared for kidney transplant.


An example of a 3D Bioprinter that can be used for organ printing.


Schematic illustration of the layers in normal oral mucosa. 1:  Stratum basale 2:  Stratum spinosum 3:  Stratum granulosum 4:  Stratum corneum


Total  artificial heart  developed at  ETH Zurich


A CELLINK 3D Bioprinter


Schematic drawing of a lung-on-a-chip. The membrane in the middle can be stretched by vacuum in the two side chambers.


Schematic of a liver-chip [ 65 ]


Proposed positioning of the Liver-Chip within a typical pharma  preclinical workflow [ 65 ]


Potential financial impact of improved preclinical testing with liver-chips according to one study [ 65 ]


Intestinal organoid grown from Lgr5+ stem cells


An intestinal organoid (Minigut) grows up in 7 days. The scale bars are 200 μm.


A scanning electron microscopy (SEM) image highlighting the complex collagenous microarchitecture underlying the luminal surface of OFM.


Risk assessment procedure


Quality considerations for medicinal products and examples for possible characteristics that need to be documented and characterized.


A colony of human embryonic stem cells


A diagram of a human tooth. Stem cells are located in the pulp in the center. [ 41 ]


A typical free-radical polymerization showing the formation of a poly( N -isopropyl acrylamide) hydrogel.


Polymer chains may be crosslinked in the presence of water to form a hydrogel. Water occupies voids in the network, giving the hydrogel its characteristic surface properties


An example of a dangling chain self healing hydrogel network. The carboxylic acid tail groups react with one another to crosslink the backbone carbon chain of the self healing hydrogel. In addition, the hydrophilic functional groups ensure the network readily absorbs water.


Seeding cells into scaffold ready for tissue engineering use and implantation


Decellularized tricuspid biological heart valve


Multi-nucleated  Foreign body giant cell  (FBGC) from the fusion of macrophages


Diagram of the opened heart viewed from the front, displaying the complex anatomical geometry of valves


1: Microfilaments 2: Phospholipid Bilayer 3: Integrin 4: Proteoglycan 5: Fibronectin 6: Collagen 7: Elastin


A diagram of the formation of an atherosclerotic plaque. Note the blue vascular smooth muscle cells, which migrate from the tunica media into the tunica intima, where the stiff plaque is forming.


Three-dimensional schematic of the interstitium, a fluid-filled space supported by a network of collagen


Scheme to show the possible self-assembled structures of typical peptide amphiphiles.


Figure 19.1: Overview of the extracellular matrix.


Figure 19.2: Schematic of integrin structure. The protein spans the plasma membrane and is an extracellular domain that can bind other matrix proteins.


Figure 19.3: Summary of cell adhesion mechanisms.


Figure 18.2: Spatial organization of the three types of fibers. Microfilaments thicken the cortex around the cell’s inner edge. Intermediate filaments have no role in cell movement. Their function is purely structural. They help the cell resist compression, provide a track along which vesicles move through the cell, and pull replicated chromosomes to opposite ends of a dividing cell.


Figure 18.3: Microfilaments are comprised of two globular protein intertwined strands, which we call actin. For this reason, we also call microfilaments actin filaments.


Figure 18.4: Several strands of fibrous proteins that are wound together comprise intermediate filaments.


Figure 18.1: Summary of the three major types of structural filaments.


Figure 18.5: Microtubules are hollow. Their walls consist of thirteen polymerized dimers of α-tubulin and β-tubulin. The left image shows the tube’s molecular structure.


Figure 18.6: This transmission electron micrograph of two flagella shows the microtubules’ 9 + 2 array: nine microtubule doublets surround a single microtubule doublet.


Figure 18.7: Comparison of the three different motor proteins.


Figure 18.8: Summary of the roles and movement of the motor proteins along various cytoskeletal elements.


Figure 17.1: EM of the nucleus and nucleolus.


Figure 17.2: Interaction of the endomembrane systems.


Figure 17.3: Unfolded protein response in the RER.


Figure 17.4: General process of phagocytosis. In phagocytosis, the cell membrane surrounds the particle and engulfs it.


Figure 17.5: Receptor-mediated endocytosis; LDL receptor is a classic example of this process.


Figure 17.6: Exocytosis: vesicles containing substances fuse with the plasma membrane. The contents then release to the cell’s exterior.


Figure 16.1: Schematic of the cell membrane. Plasma membranes range from 5 to 10 nm in thickness.


Figure 16.2: Structure of a phospholipid.


Figure 16.3: Important membrane lipids.


Figure 16.4: Diffusion across the plasma membrane.


Figure 16.5: Illustration of osmosis. In the diagram, the solute cannot pass through the selectively permeable membrane, but the water can.


Figure 16.6: Comparison of red blood cell morphology in isotonic, hypertonic, and hypotonic solutions.


Figure 16.7: Protein channel.


Figure 16.8: Carrier proteins. This aptly named protein binds a substance and thus triggers a change of its own shape, moving the bound molecule from the cell’s outside to its interior.


Figure 16.9: Electrochemical gradients.


Figure 16.10: Different types of carrier proteins for active transport.


Figure 16.11: Primary active transport.


Figure 15.1: Summary of types of cell signaling.


Figure 15.3: Common G-protein-coupled receptor signaling cascade.


Figure 15.4: Signaling cascade initiated by DAG and IP3.


Figure 15.2: Examples of steroid hormones.


Figure 15.5: Receptor tyrosine kinase signaling.


Figure 15.6: Comparison of intrinsic and extrinsic apoptosis pathways.


Figure 15.7: Neurotransmission by acetylcholine.


Figure 15.9: Summary of the action potential as it relates to change in ion concentration across the membrane.


Figure 15.8: Summary of the action potential to membrane potential.


Figure 14.1: Punnett square illustrating allelic distribution of recessive traits.


Figure 14.2: Allelic distributions in dominant traits.


Figure 14.3: Graphic representation of penetrance and expressivity.


Figure 14.4: Mitochondrial inheritance pattern.


Figure 14.5: Trinucleotide repeat expansion characteristic of Huntington’s disease.


Figure 14.6: Relationship between centimorgans and recombination frequency.


Figure 14.7: Schematic of GWAS.


Figure 13.1: Representative karyotype illustrating twenty-two pairs of autosomes and one pair of sex chromosomes.


Figure 13.2: Basics of chromosome structure.


Figure 13.3: Summary of meiotic and mitotic cell divisions.


Figure 13.4: Comparison of nondisjunction in meiosis I versus meiosis II.


Figure 13.5: Mosaicism resulting in cells with differing genetics across the body.


Figure 13.6: Genetic basis of Prader-Willi syndrome (PWS) and Angelman syndrome (AS). UPD: Uniparental disomy; Square: imprinting on the maternal allele.


Figure 13.7: Example of a chromosome inversion and translocation.


Figure 13.8: Basic process for DNA extraction.


Figure 13.9: Male karyotype with G-banding patterns.


Figure 13.10: Schematic of Sanger sequencing technique.


Figure 13.11: Overview of polymerase chain reaction.


Figure 13.12: Schematic of southern blotting technique.


Figure 12.1: Example of transcriptional complex involving two separate genes.


Figure 12.2: Modification of DNA and histones can alter DNA accessibility and therefore transcription.


Figure 12.3: Five common modes of alternative splicing.


Figure 12.4: Regulation of translational initiation.


Figure 12.5: RNA-Binding proteins can increase stability of the transcript.


Figure 12.6: Proteasome-mediated degradation.


Figure 12.7: Overview of the cell cycle.


Figure 12.8: Summary of the mitotic phase.


Figure 12.9: Summary of cell cycle checkpoints and the role of CDK inhibitors in halting cell cycle progress.


Figure 12.10: Overview of meiosis.


Figure 11.2: Schematic view of a eukaryotic gene structure.


Figure 11.3: Transcription initiation.


Figure 11.4: Overview of mRNA processing involving the removal of introns (splicing) and the addition of a 5’ cap and 3’ tail.


Figure 11.5: Summary of mRNA splicing.


Figure 11.1: Colinearity of DNA and RNA.


Figure 11.8: Summary of translational elongation.


Figure 11.6: Genetic code; each codons is three nucleotides corresponding to a specific amino acid. The code is degenerate, meaning several codes are present for the same amino acid and the codes for similar amino acids are clustered.


Figure 11.7: Summary of translational initiation. eIF4 recruits the small ribosomal subunit and other initiation factors to the mRNA. The charge Met-tRNA also binds the complex, and the large ribosomal subunit is recruited to the initiation complex. Once the large ribosomal subunit binds, the initiation factors can be released, and translation can proceed to elongation of the polypeptide chain.


Figure 10.3: General structure and hydrogen bonding pattern of DNA.


Figure 10.4: Organizational structure of DNA illustrating condensation and supercoiling into chromosomes.


Figure 10.1: Basic structure of nucleotides including the sugar (ribose or deoxyribose), base (pyrimidine or purine), and phosphate groups.


Figure 10.2: Structure of pyrimidine and purine bases.


Figure 10.5: Comparison on three types of repair: (A) proofreading, (B) mismatch, and (C) nucleotide excision repair.


Figure 10.6: Summary of base excision repair. This is a similar process to NER but requires a glycosylase.


Figure 10.8: Summary of telomerase activity to fill the overhang on the lagging strand.


Figure 10.7: Summary of DNA replication.


Figure 9.2: Fructose metabolism and reaction by aldolase B. Deficiencies in aldolase B can result in hereditary fructose intolerance, while deficiencies in frutokinase can result in essential fructosuria.


Figure 9.1: Convergence of fructose and glucose metabolism.


Figure 9.3: Galactose metabolism; glucose 6-phosphate is converted to glucose 1-phosphate, which enters the pathway.


Figure 9.4: Comparison of classical and nonclassical galatosemia.


Figure 9.5: Overview of ethanol metabolism. The pathway spans the cytosol and the mitochondria, and NADH is produced in both steps of the pathway.


Figure 9.7: Clinical consequences of alcoholism.


Figure 9.6: Overview of alcohol metabolism.


Figure 9.8: Ethanol detoxification by MEOS.


Figure 8.1: Metabolism of phenylalanine requires BH4 and also produces tyrosine. Deficiencies in cofactor or phenylalanine hydroxylase can result in phenylketonuria.


Figure 8.2: Tyrosine can be produced from phenylalanine metabolism and is required for the production of melanin and the catecholamines. Deficiencies can occur at several different locations in the pathway and result in albinism, alkaptonuria, or tyrosinemia.


Figure 8.3: Metabolism of tryptophan to melatonin.


Figure 8.4: Glutamate metabolism as it interfaces with nitrogen transport and synthesis of GABA.


Figure 8.6: Metabolism of methionine. Remethylation and transsulfuration of homocysteine are illustrated. Cofactor or enzymatic deficiencies can result in an elevation of homocysteine.


Figure 8.5: Metabolism of branched-chain amino acids. Deficiencies in branched-chain keto acid dehydrogenase (BCKAD) can result in the presentation of maple syrup urine disease.


Figure 7.1: Overview of the pentose phosphate pathway and its interface with glycolysis.


Figure 7.2: Pentose phosphate pathway and its connection to glycolysis and glutathione synthesis.


Figure 7.3: NADPH in the red blood cell as a means of reducing glutathione.


Figure 7.4: Basic structure of nucleotides.


Figure 7.5: Overview of purine and pyrimidine bases.


Figure 7.6: Synthesis of PRPP and regulation of PRPP synthetase.


Figure 7.7: Overview of purine synthesis. The reaction catalyzed by GPAT is the regulatory enzyme of the pathway.


Figure 7.9: Breakdown of nucleotides.


Figure 7.10: Nucleotide base salvage. Reaction catalyzed by HGPRT is clinically relevant as deficiencies can cause accumulation of uric acid.


Figure 7.12: Overview of pyrimidine synthesis. The reaction catalyzed by carbamoyl phosphate synthetase I is the regulatory enzyme of the pathway.


Figure 7.13: Interaction of thymidylate synthesis with the folate cycle. SHMT: serine hydroxymethyltransferase; DHFR: dihydrofolate reductase.


Figure 7.8: Purine synthesis and regulation of glutamine: phosphoribosylpyrophosphate amidotransferase.


Figure 7.11: Nucleotide specific pathways for base salvage.


Figure 6.2: Cholesterol synthetic pathway.


Figure 6.3: Regulatory step catalyzed by HMG-CoA reductase.


Figure 6.4: Regulation of cholesterol synthesis.


Figure 6.5: Esterification of cholesterol by LCAT.


Figure 6.1: Structure of cholesterol.


Figure 6.6: Overview of lipoprotein size and structure.


Figure 6.7: Transport of dietary lipids via chylomicrons.


Figure 6.8: Transport of TAGs from de novo synthesis using VLDL.


Figure 6.9: Comparison of the role of chylomicrons and VLDLs in lipid transport.


Figure 6.11: Uptake of LDL and regulation of cholesterol synthesis.


Figure 6.10: Interaction of chylomicrons and VLDL with HDL in circulation.


Figure 5.1: Glucose production by glycogenolysis and gluconeogenesis.


Figure 5.2: Comparison of glycolysis and gluconeogenesis.


Figure 5.11: Overview of ketone body formation.


Figure 5.3: Locations of amino acid and lactate entering gluconeogenesis as substrates for the pathway.


Figure 5.4: Glycerol as a substrate for gluconeogenesis; after phosphorylation to glycerol 3-phosphate it can be converted to DHAP, which can enter directly into glycolysis.


Figure 4.1: Summary of glycolysis. The three regulated steps of the process will be the focus, and those are catalyzed by the enzymes glucokinase/hexokinase, phosphofructokinase 1 (PFK1), and pyruvate kinase. All other steps in glycolysis are reversible (as indicated by the arrows) and are also used in gluconeogenesis.


Figure 5.6: Hepatic glycogenolysis by epinephrine.


Figure 5.7: Skeletal muscle glycogenolysis.


Figure 5.5: Reaction catalyzed by pyruvate carboxylase; this allows the bypass of the irreversible step catalyzed by pyruvate kinase.


Figure 5.9: Overview of LCFA transport into the mitochondria and β-oxidation.


Figure 5.10: Regulation of β-oxidation.


Figure 5.8: Process of lipolysis.


Figure 5.14: Movement of ammonia from peripheral tissues to the liver.


Figure 5.16: Key regulatory step in the urea cycle. CPS1 is activated by N-acetylglutamate.


Figure 5.12: Transamination reaction.


Figure 5.13: Reactions catalyzed by glutamate dehydrogenase, glutaminase, and glutamine synthetase.


Figure 5.15: Overview of the urea cycle; the pathway spans both the mitochondria and cytosol.


Figure 5.17: Entry of the second nitrogen into the urea cycle; aspartate donates the second nitrogen for the synthesis of urea.


Figure 4.2: Regulatory step committed by hexo or glucokinase. The first regulatory step in glycolysis is the phosphorylation of glucose by hexo or glucokinase. The reverse reaction, which is part of gluconeogensis, is catalyzed by glucose 6-phosphatase.


Figure 4.3: Comparison of glucokinase and hexokinase kinetics.


Figure 4.4: Regulation of glucokinase by glucokinase regulatory protein.


Figure 4.5: Regulation of PFK1 by fructose 2,6-bisphosphate generated by PFK2.


Figure 4.6: Regulation of pyruvate kinase phosphorylation and fructose 1,6-bisphosphate.


Figure 4.7: Glycerol 3-phosphate shuttle.


Figure 4.8: Malate-aspartate shuttle.


Figure 4.9: Regulation of the pyruvate dehydrogenase complex (PDC).


Figure 4.10: Overview of the TCA cycle.


Figure 4.11: Substrates produced by the TCA cycle.


Figure 4.12: Anaplerotic reactions of the TCA cycle.


Figure 4.13: Regulation of the TCA cycle.


Figure 4.14: Overview of the electron transport chain (ETC).


Figure 4.15: Citrate shuttle reaction moves citrate from the mitochondria to the cytosol for fatty acid synthesis.


Figure 4.16: Fatty acid synthesis is an iterative process that begins with the transfer of an acetyl moiety from acetyl-CoA to fatty acid synthase; following this activation, carbons are added to the growing chain in the form of malonyl-CoA.


Figure 4.17: Regulatory reaction of fatty acid synthesis. The synthesis of malonyl-CoA by acetyl-CoA carboxylase is highly regulated within the cytosol.


Figure 4.18: Glycogen synthesis.


Figure 3.1: Overview of the fed state.


Figure 3.2: Overview of fasted state metabolism.


Figure 2.1: Heme degradation.


Figure 2.2: Reaction catalyzed by lactate dehydrogenase.


Figure 2.3: Mechanism of action of vitamin A.


Figure 2.4: Vitamin K stimulates the maturation of clotting factors.


Figure 1.2: Chart of amino acids.


Figure 1.1: Basic structure of amino acids and ionization.


Figure 1.3: Basics of enzyme kinetics.


Figure 1.4: Graphical representation of the Michaelis–Menten equation.


Figure 1.6: Competitive vs. noncompetitive inhibition.


Figure 1.7(a): Allosteric enzyme regulation.


Figure 1.7(b): Allosteric enzyme regulation.


Figure 1.5: Lineweaver–Burk plot to illustrate Km and Vmax.


1: Microfilaments 2: Phospholipid Bilayer 3: Integrin 4: Proteoglycan 5: Fibronectin 6: Collagen 7: Elastin


The Golgin  GMAP210  has functional regions at both ends.


The ALPS of GMAP210 binds to curved, but not flat, lipid layers


GRASP domain alignment of  GRASP55  and the GRASP homologue of  Cryptococcus neoformans


Microinjection of antibodies to GRASP65 prevents normal Golgi stack formation.


Three-dimensional schematic of the interstitium, a fluid-filled space supported by a network of collagen


ATP synthesis as seen from the perspective of the matrix. Conditions produced by the relationships between the catabolic pathways (citric acid cycle and oxidative phosphorylation) and structural makeup (lipid bilayer and electron transport chain) of matrix facilitate ATP synthesis.


Micrograph of thin cross-section of  Chlamydomonas  axoneme


A simplified model of intraflagellar transport.


Basic cellular compartments


Eukaryotic motile cilium


Illustration depicting motile cilia on  respiratory epithelium .


Tracheal  respiratory epithelium showing cilia and much smaller  microvilli  on non-ciliated cells in  scanning electron micrograph .


Scanning electron micrograph  of nodal cilia on a  mouse  embryo


Multiple exophers produced by a mechanosensory neuron in  C. elegans


Lysosomes digest material. Step one shows material entering a food vacuole through the plasma membrane, a process known as endocytosis. In step two a lysosome with an active hydrolytic enzyme comes into the pictures as the food vacuole moves away from the plasma membrane. Step three consists of the lysosome fusing with the food vacuole and hydrolytic enzymes entering the food vacuole. In the final step, step four, hydrolytic enzymes digest the food particles. [ 5 ]


TEM views of various vesicular compartments. Lysosomes are denoted by "Ly". They are dyed dark due to their acidity; in the center of the top image, a Golgi Apparatus can be seen, distal from the cell membrane relative to the lysosome .


The lysosome is shown in purple, as an endpoint in endocytotic sorting. AP2 is necessary for vesicle formation, whereas the mannose-6-receptor is necessary for sorting hydrolase into the lysosome's lumen.


Schematic drawing of  Cafeteria roenbergensis  ( Heterokonta :  Bicosoecida ) with two unequal (heterokont) flagella: an anterior straminipilous (with tubular tripartite mastigonemes) and a posterior smooth


A chrysomonad ( Heterokonta :  Chrysophyceae ) under  TEM , with a smooth flagellum (1) and a long flagellum covered with mastigonemes (3)


Two cryptomonads ( Cryptophyceae ) under  SEM . Mastigonemes not visible.


Muscle fibre organisation


A diagram of the structure of a myofibril (consisting of many  myofilaments  in parallel, and  sarcomeres  in series)


Sliding filament model  of  muscle contraction


Model of the retromer heteropentameric complex ( VPS26  in green;  VPS35  in orange, and  VPS29  in red). The retromer forms a polymeric network arc on the outside (cytoplasmic side) of the endosome tubule. Inside the tubule, the cargo receptor  SORL1 , forms its own network and binds protein cargo for trafficking. SORL1 connects to retromer on the outside via a transmembrane helix and a short C-terminal tail that binds VPS26. Model built based on structural data by Brett Collins and Yu Kitago.


Ribbon diagram of the retromer heterotrimeric complex comprising the proteins VPS26 (green), VPS35 (orange) and VPS29 (red). On the endosomal membrane, this heterotrimer forms an arch-shaped dimer via interaction of two VPS35 molecules (see next image). [ 11 ]


CryoET structure of retromer heterotrimer dimer on the tubular endosome membrane in surface rendering. VPS26 is in green, VPS35 in orange, and VPS29 in red. The heterotrimer forms a characteristic dimeric arch. The grey SNX protein aids in tubulation and retromer membrane binding. [ 11 ]


Longitudinal section of the  pelagophyte   Plocamiomonas psychrophila  under  transmission electron microscopy  showing system II fibre or rhizoplast (r) positioned at the base of the  basal bodies  and continuing parallel to the  nucleus  (N). The mature (mf) and immature (if)  flagella  are also visible.


The cytosol is a crowded solution of many different types of molecules that occupy up to 30% of the cytoplasmic volume. [ 1 ]


Intracellular fluid content in humans


Carboxysomes  are protein-enclosed  bacterial microcompartments  within the cytosol. On the left is an  electron microscope  image of carboxysomes, and on the right a model of their structure.


Shown is a micrograph of an amoeba; the darker pink nucleus is central to the eukaryotic cell, with the majority of the rest of the cell's body belonging to the endoplasm. Though not visible, the ectoplasm resides directly internal to the plasma membrane.


This is a perikaryon of a nerve cell, displayed here because of the obvious cytoplasmic granules. The granules, which appear almost black due to their high electron density, take up a large portion of the endoplasm. They are suspended in cytosol - the fluid component of the cytoplasm.


This image displays the 3 main processes of cell respiration - the pathway from which the cell obtains energy in the form of ATP. These processes include glycolysis, the citric acid cycle, and the electron transport chain.


Glowing dinoflagellate bloom


The cytoskeleton consists of (a) microtubules, (b) microfilaments, and (c) intermediate filaments. [ 1 ]


Cross section diagram through the cilium, showing the “9 + 2” arrangement of microtubules


F-actin  distribution in the cell cortex as shown by  rhodamine   phalloidin  staining of  HeLa  cells that constitutively express  Histone H2B - GFP  to mark  chromosomes .  F-actin  is thus red, while  Histone H2B  is displayed in green. The left-hand cell is in  mitosis , as demonstrated by  chromosome  condensation, while the right-hand cell is in  interphase  (as determined by intact  cell nucleus ) in a suspended state. In both cases,  F-actin  is enriched around the cell periphery. Scale bar: 10 micrometers.


Forebrain  neuronal culture after 40 days of differentiation from  induced human pluripotent stem cells . iPSCs from a patient with  familial Alzheimer's disease , a mutation in the  PSEN1  gene. TUJ-1-positive cells express a marker (β3-tubulin) of mature neurons (red).  GABA-positive cells  (green). Cell nuclei are stained with DAPI (blue).


Motifs and domains in Cordon-bleu protein.


Working model of Cobl-induced actin nucleation. [ 5 ] [ 20 ]


In humans, the DMD gene is located on the short (p) arm of the  X chromosome  between positions 21.2 and 21.1


This electron micrograph shows exaggerated filopodia with club-like shape induced by formin mDia2 in cultured cells. These filopodia are filled with bundled  actin filaments  which were born in and converged from the  lamellipodial network .


Structure of intermediate filament


Keratin  intermediate filaments (stained red) around  epithelial cells


Vimentin  fibers in  fibroblasts


Intracellular transport between the  Golgi apparatus  and the  endoplasmic reticulum


How SNARE proteins play a role in intracellular transport


A cytoplasmic dynein motor bound to a microtubule.


A kinesin molecule bound to a microtubule.


How microtubules play a role in intracellular transport


Microscopy of keratin filaments inside cells


The  horns  of the  impala  are made of keratin covering a core of  bone .


The neutral–basic keratins are encoded on chromosome 12 (12q13.13).


The acidic keratins are encoded on chromosome 17 (17q21.2).


Protein sequence alignment of human keratin 1, 2A, 3,4, 5, 6A, 7, and 8 (KRT1 – KRT8). Only the first rod domain is shown above. Alignment was created using  Clustal Omega .


Keratin (high molecular weight) in  bile duct  cell and oval cells of  horse   liver .


A human toe nail that fell off after a small trauma. Three small punctures were made on it, while it was still attached.


Figure 1. Lamellipodia are thin-like projections on the leading edge of a cell (Image A). It is a feature of motile cells such as endothelial cells, neurons, and immune cells. The lamellipodia on the leading edge of the cell (green arrows) contain ATP- bound actin and the lamella on the "spike" end of the cell contain ADP-bound actin (red arrow). This allows for a "treadmilling" action to occur when the cell is signaled to move (Image B).  [ 3 ]


Microtubule and tubulin metrics [ 1 ]


Microtubules are one of the cytoskeletal filament systems in eukaryotic cells. The microtubule cytoskeleton is involved in the transport of material within cells, carried out by motor proteins that move on the surface of the microtubule.


Cartoon representation of the structure of α(yellow)/β(red)-tubulin heterodimer, GTP and GDP. [ 11 ]


Components of the  eukaryotic  cytoskeleton.  Actin filaments  are shown in red,  microtubules  are in green, and the  nuclei  are in blue. The cytoskeleton provides the cell with an inner framework and enables it to move and change shape.


Image of a fibroblast cell containing fluorescently labeled actin (red) and microtubules (green).


A 3D diagram of a centriole. Each circle represents one microtubule. In total there are 27 microtubules organized into 9 bundles of 3.


This diagram depicts the organization of a typical mitotic spindle found in animal cells.  Shown here are the three main types of microtubules during mitosis and how they are oriented in the cell and the mitotic spindle.


Microtubule arrangement in a  9+2 axoneme  of  bronchiolar  cilia


Rat brain cells grown in  tissue culture  and stained, in green, with an antibody to neurofilament subunit NF-L, which reveals a large neuron. The culture was stained in red for α-internexin, which in this culture is found in neuronal stem cells surrounding the large neuron.


A formalin fixed and paraffin embedded section of human  cerebellum  stained with an antibody to neurofilament light, NF-L revealed with a brown dye, cell nuclei are revealed with a blue dye. Nuclear rich region at left is granular layer, region at right is molecular layer. The antibody binds processes of basket cells, parallel fiber axons, the perikarya of  Purkinje  cells and various other axons.


Antibody   stain  against neurofilament (green) and  Ki 67  (red) in a mouse  embryo  12.5 days after  fertilization . The cells expressing neurofilaments are in the  dorsal root ganglia  shown in green while  proliferating cells  are in the  ventricular zone  in the  neural tube  and colored red.


Micrograph  of  white matter  (bottom of image) and the  anterior horn of the spinal cord  showing  motor neurons  with  central chromatolysis . Neurofilament  immunostain .


Elements of the  Caulobacter crescentus  cytoskeleton. The prokaryotic cytoskeletal elements are matched with their eukaryotic homologue and hypothesized cellular function. [ 1 ]


schematic domain structure of septin polypeptide chain


a) schematic of septin molecule with GTP binding domain to one side and the N and C termini of the polypeptide chain to the other  b) schematic of septin heterohexameric complex (of human septins), where different septins bind to each other via their GTP binding domains or via the N and C termini. Note the symmetry of the complex   c) schematic how septin complexes could align to form septin filaments


Septins in  Saccharomyces cerevisiae   (fluorescent micrograph)  • Green: septins ( AgSEP7- GFP )  • Red: cell outline ( phase contrast )  • Scale bar: 10 μm


Septins in  Ashbya gossypii   (fluorescent micrograph) • Green: septins ( AgSEP7- GFP )  • Red: cell outline ( phase contrast )  • Inlay: 3D reconstruction of a discontinuous septin ring  • Scale bars: 10 μm


A schematic diagram of spectrin and other cytoskeletal molecules


Localization of alpha-II spectrin in green under the plasma membrane of rat neurons in tissue culture as shown with  confocal microscopy  and  immunofluorescence . The nuclei of the cells is revealed in blue by the DNA dye  DAPI .


Transmission electron micrograph  depicting tonofilaments, labeled tf, running longitudinally within the dorsal epidermal cells of the  girdle  of a  chiton


Immunofluorescence staining pattern of vimentin antibodies. Produced by incubating vimentin primary antibodies and FITC labelled secondary antibodies with HEp-20-10 cells.


Immunofluorescence staining of   HeLa Cells  with antibody to reveal vimentin containing intermediate filaments in green and antibody to  LAMP1  to reveal lysosomes in red. Nuclear DNA is seen in blue. Antibodies and image courtesy   EnCor Biotechnology Inc .


Principal interactions of structural proteins at cadherin-based adherens junction. Actin filaments are associated with adherens junctions in addition to several other actin-binding proteins such as  vinculin . The head domain of vinculin associates to E-cadherin via α-, β - and γ -catenins. The tail domain of vinculin binds to membrane lipids and to actin filaments.


Amyloplasts in a potato cell


A diagram showing the different types of plastid


Diagram of a  voltage-gated ion channel , showing the three states: closed, open, and inactivated. Ball and chain inactivation can only happen if the channel is open.


Diagram of a  voltage-gated sodium channel , showing the important residues for inactivation in red. The domain structure (I – IV) is further subdivided into segments (S1 – 6). The S4 segment is the voltage sensor, which moves out during  depolarisation  of the  cell membrane . This frees up the  alanine  and  asparagine  residues with which the IFMT residues in the ball domain bind to. Adapted from Goldin, 2003. [ 13 ]


During  apoptosis , blebbing is the first phase (left) of cell disassembly. [ 1 ]


Chemical structure of blebbistatin [ 17 ]


Nuclei of mouse cells (blue) containing Cajal bodies (green) visualized by fusion of p80/Coilin protein to GFP


Electron micrographs showing alpha-carboxysomes from the chemoautotrophic bacterium  Halothiobacillus neapolitanus : (A) arranged within the cell, and (B) intact upon isolation. Scale bars indicate 100 nm. [ 1 ]


Model for the structure of the carboxysome. RuBisCO and carbonic anhydrase are arranged in an enzymatic core (organized by various core proteins) and encapsulated by a protein shell.


Electron micrograph of (A) alpha-carboxysomes in  Halothiobacillus neapolitanus  and (B) beta-carboxysomes in  Synechococcus elongatus  PCC 7942, indicated by arrows. Scale bars 200 nm.


Structure of a typical  prokaryotic  cell


Structure of a typical animal cell


Structure of a typical  plant cell


Detailed diagram of lipid bilayer of cell membrane


A fluorescent image of an endothelial cell. Nuclei are stained blue,  mitochondria  are stained red, and microfilaments are stained green.


Deoxyribonucleic acid  (DNA)


Human cancer cells, specifically  HeLa cells , with DNA stained blue. The central and rightmost cell are in  interphase , so their DNA is diffuse and the entire nuclei are labelled. The cell on the left is going through  mitosis  and its chromosomes have condensed.


Diagram of the  endomembrane system


Prokaryotes  divide by  binary fission , while  eukaryotes  divide by  mitosis  or  meiosis .


Staining of a  Caenorhabditis elegans  highlights the nuclei of its cells.


Stromatolites  are left behind by  cyanobacteria , also called blue-green algae. They are among the oldest fossils of life on Earth. This one-billion-year-old fossil is from  Glacier National Park  in the United States.


In the theory of  symbiogenesis , a merger of an  archaean  and an aerobic bacterium created the eukaryotes, with aerobic  mitochondria , some 2.2 billion years ago. A second merger, 1.6 billion years ago, added  chloroplasts , creating the green plants. [ 31 ]


Robert Hooke's drawing of cells in  cork , 1665


Cartoon of the dividing epithelium cell surrounded by epithelium tissue. Spindle apparatus rotates inside the cell. The rotation is a result of astral microtubules pulling towards tri-cellular-junctions (TCJ), signaling centers localized at the regions where three cells meet.


Some examples of cell junctions


This image shows a desmosome junction between cells of the epidermal layer of the skin.


The cartoon of epithelium cells connected by tricellular junctions at the regions where three cells meet.


Illustration of a  eukaryotic  cell membrane


Comparison of a  eukaryotic  vs. a  prokaryotic  cell membrane


Examples of the major membrane phospholipids and glycolipids:  phosphatidylcholine  (PtdCho),  phosphatidylethanolamine  (PtdEtn),  phosphatidylinositol  (PtdIns),  phosphatidylserine  (PtdSer).


A detailed diagram of the cell membrane


Illustration depicting cellular diffusion


Diagram of the arrangement of amphipathic lipid molecules to form a  lipid bilayer . The yellow  polar  head groups separate the grey hydrophobic tails from the aqueous cytosolic and extracellular environments.


Alpha intercalated cell


Diagram of the cell membrane's structures


HeLa cells  stained for  nuclear DNA  with the blue  fluorescent   Hoechst dye . The central and rightmost cells are in  interphase , thus their entire nuclei are labeled. On the left, a cell is going through  mitosis  and its DNA has condensed.


A mouse  fibroblast  nucleus in which  DNA  is stained blue. The distinct chromosome territories of chromosome 2 (red) and chromosome 9 (green) are stained with  fluorescent in situ hybridization .


Diagram of the nucleus showing the  ribosome -studded  outer nuclear membrane ,  nuclear pores ,  DNA  (complexed as  chromatin ), and the  nucleolus .


A cross section of a  nuclear pore  on the surface of the  nuclear envelope  (1). Other diagram labels show (2) the outer ring, (3) spokes, (4) basket, and (5) filaments.


An  electron micrograph  of a cell nucleus, showing the darkly stained  nucleolus


Cajal body


A generic  transcription factory  during transcription, highlighting the possibility of transcribing more than one gene at a time. The diagram includes 8 RNA polymerases however the number can vary depending on cell type. The image also includes transcription factors and a porous, protein core.


Macromolecules , such as  RNA  and  proteins , are  actively transported  across the nuclear membrane in a process called the  Ran - GTP  nuclear transport cycle.


An image of a  newt   lung  cell  stained  with  fluorescent   dyes  during  metaphase . The  mitotic spindle  can be seen, stained green, attached to the two sets of  chromosomes , stained light blue. All chromosomes but one are already at the metaphase plate.


Human red blood cells, like those of other mammals, lack nuclei. This occurs as a normal part of the cells' development.


Oldest known depiction of cells and their nuclei by  Antonie van Leeuwenhoek , 1719


Drawing of a  Chironomus   salivary gland  cell published by  Walther Flemming  in 1882. The nucleus contains  polytene chromosomes .


An illustration of  podocytes , which surround the  glomerular capillaries  with their cell bodies, primary processes and interdigitating  foot processes .


Filopodia and lamellipodia in two fluorescently-labeled  growth cones .


3D Structured illumination microscopy (SIM)  enables visualisation of the glomerular filtration barrier, using multiplex  immunofluorescence  staining for markers for podocytes ( synaptopodin ,  nephrin ),  endothelial cells  ( EHD3 ), and the  glomerular basement membrane  ( agrin ).


Confocal microscopy  can reveal changes in the processes of  Müller cells , in the  retina , shown here in the  rat . On the left,  GFAP  expression is predominant in the  inner retinal layers .        localized to the innermost  layers of the retina ; on the right GFAP-positive fibers show a thickening in Müller cell processes indicating  gliosis .


Vasoactive modulators, released from astrocytic endfeet, act on smooth muscle cells in arterioles, and pericytes in capillaries to regulate the  vascular tone .


Glomerular podocytes possess a diverse array of  surface-expressed proteins  that contribute to the selective filtration of solutes across the glomerular barrier, thereby maintaining fluid homeostasis within the body.


This  SEM  image illustrates the communication between osteocytes (Ocy) and transcortical vessels (TCV) via their endfeet (yellow arrows) to facilitate mitochondrial transfer.


Ramified microglia in a rat  cortex  before  traumatic brain injury .


Amoeboid microglia after traumatic brain injury.


Effacement of foot processes (FP) of podocytes is evident in this  scanning electron microscopy  (SEM) image, enhanced with false coloring for improved visualization.


The 154 kb chloroplast DNA map of a model flowering plant ( Arabidopsis thaliana : Brassicaceae) showing genes and inverted repeats.


Chloroplast DNA replication via multiple D loop mechanisms. Adapted from Krishnan NM, Rao BJ's paper "A comparative approach to elucidate chloroplast genome replication."


Over time, base changes in the DNA sequence can arise from deamination mutations. When adenine is deaminated, it becomes hypoxanthine, which can pair with cytosine. During replication, the cytosine will pair with guanine, causing an A → G base change.


A circular chromosome, showing DNA replication proceeding bidirectionally, with two replication forks generated at the "origin". Each half of the chromosome replicated by one replication fork is called a "replichore". (Graphic computer art by Daniel Yuen)


Bidirectional replication in a circular chromosome.


oriC  motifs in bacteria


Most circular bacterial chromosomes are replicated bidirectionally, starting at one point of origin and replicating in two directions away from the origin. This results in semiconservative replication, in which each new identical DNA molecule contains one template strand from the original molecule, shown as the solid lines, and one new strand, shown as the dotted lines.


Figure 1: Methods of dynamin-dependent and independent clathrin-independent endocytosis.


Figure 2: Clathrin-independent endocytic processes uses (a) FEME, (b) CLIC/GEEC, and (c) CL-Lect hypothesis


Cystolith from leaf of  Ficus elastica


Drawing of a cystolith from leaf of  Ficus elastica


Proteins in different  cellular compartments  and structures  tagged  with  green fluorescent protein


Illustration of the plasmodesmata structure spanning the cell wall (CW). The desmotubule (DM) is shown as a continuation of the endoplasmic reticulum (ER), with various membrane proteins linking it to the plasma membrane (PM).


Figure1. Illustrates the movement of a diplosome in the early stages of mitosis as described in  Diplosome in Mitosis .


The different types of endocytosis


Schematic drawing illustrating clathrin-mediated (left) and clathrin-independent endocytosis (right) of  synaptic vesicle   membranes


From left to right: Phagocytosis, Pinocytosis, Receptor-mediated endocytosis.


Detail of the endomembrane system and its components


Diagram of the nucleus with the nuclear envelope shown as the orange portion


1   Nucleus     2   Nuclear pore     3  Rough endoplasmic reticulum (RER)     4  Smooth endoplasmic reticulum (SER)     5   Ribosome  on the rough ER     6   Proteins  that are transported     7  Transport  vesicle     8   Golgi apparatus     9  Cis face of the Golgi apparatus     10  Trans face of the Golgi apparatus     11  Cisternae of the Golgi apparatus


By using  electron microscope , ribosomes ("particles") on the  rough endoplasmic reticulum  can be observed


Micrograph of Golgi apparatus, visible as a stack of semicircular black rings near the bottom. Numerous circular vesicles can be seen in proximity to the organelle.


Detailed illustration of the plasma membrane. Including the structure of a  phospholipid .


Summary of ESCRT machinery and accessory proteins. [ 3 ] [ 6 ]


Trafficking of membrane bound proteins to the lysosome using ESCRT machinery.  Membrane bound proteins are taken into the cell via endocytosis. Ubiquitin tags on the protein are recognized by ESCRT machinery and recruited to the endosome. Multivesicular bodies are formed, which then fuse with the lysosome where these proteins are degraded. Adapted from. [ 1 ]


Recruitment of ESCRT Complexes to the Midbody.  Cep-55 binds MKLP1. Cep-55 recruits ESCRT-I and ALIX. ESCRT-I and ALIX recruit ESCRT-III. ESCRT-III forms spiral around membrane neck between daughter cells leading to constriction and cleavage. Adapted from. [ 22 ]


Retroviral budding of HIV.  A) Accumulation of viral proteins under the cell membrane causes the virus to protrude outward. B) A constriction is formed by the ESCRT complexes at the base of membrane protrusion causing formation of a virus containing vesicle. C) The bud pinches off leaving a free extracellular virion.  (Photo provided by Dr. Matthew Gonda (Wikimedia Commons: Nov. 1998), National Cancer Institute Image ID: 2382)


Fluid mosaic model of a  cell membrane


The Frye-Edidin experiment showed that when two cells are fused the proteins of both diffuse around the membrane and mingle rather than being locked to their area of the membrane.


S.cerevisiae  septins Septin ring-like structures (in green) can pinch cell membranes and split them into subdomains.


Connexon pairing across membranes bridges the gap between two cells and between vesicles to membranes. [ 20 ]


Light microscope images do not allow us to see connexons or innexons themselves but do let us see the fluorescing dye injected into one cell moving into neighboring cells when gap junctions are known to be present. [ 38 ]


Cell pannexin tree with white squares having communication proteins yet to be discovered


Effects of perinexal width on ephaptic coupling, for G gap = 0 nS


Eye lens showing arrangement of fiber cells with photos of gap junction plaques from different regions


Beta cell  with insulin granules, which are the dark black spots surrounded by a white area called a halo.


Starch granules in potato cells.


Assembly and disassembly of stress granules.


Cartoon of the dividing epithelium cell surrounded by epithelium tissue. Spindle apparatus rotates inside the cell. The rotation is a result of astral microtubules pulling towards tri-cellular-junctions (TCJ), signaling centers localized at the regions where three cells meet.


In  histopathology , pathologic homogenization is seen as a loss of variations, such as of  collagen  in  lichen sclerosus  (pictured).


Nostoc  with hormogonia


Micrographia cells [ 1 ]  in 1665.   But I couldn't find with my microscope, breath or any other way I have tried, a passage out of one cell into another, yet I cannot conclude, that there aren't any passages that exist that the plant juices must pass through .


Cell signalling


4 types of cell junction simplified


Epithelium TCJ


Cell pannexin tree


Fungal hypha


Plasmodesma allowing the symplast pathway


Tubular bridges for bronchial epithelial cell migration and communication


Complete neuron cell diagram


Nervous systems of sponges (porifera) and placozoans


Ctenophore neural systems.


Paristatoid wasp on caterpillar


Simplified structure of a mitochondrion


Electron transport chain and intermembrane space of a mitochondrion


Apoptotic components released from the intermembrane space of a mitochondrion


Simplified structure of a chloroplast


Simplified structure of a eukaryotic cell nucleus


A microscope picture of a cell's invadopodium.


Red arrows indicate secreted lamellar bodies, and green arrows indicate lamellar bodies in the cytoplasm. Scale bar = 200 nm.


A  High resolution 3D live-cell fluorescence image of a tunneling nanotube (TNT) (white arrow) connecting two primary mesothelial cells. Scale bar: 20 μm. B  Depiction of a TNT (black arrow) between two cells with scanning electron microscopy. Scale bar: 10 μm. C  Fluorescently labeled F-actin (white arrow) present in TNTs between individual HPMCs. Scale bar: 20 μm. D  Scanning electron microscope image of a potential TNT precursor (black arrowhead). Insert shows a fluorescence microscopic image of filopodia-like protrusions (white arrowhead) approaching a neighboring cell. Scale bar: 2 μm. [ 1 ]


3D live-cell microscopy of immunofluorescent rat PC12 cells demonstrating tunneling nanotubes. From one of the first published papers to describe the phenomenon in 2004.  [ 7 ]


Mitochondrial network (green) in two human cells ( HeLa cells )


Mitochondria, mammalian lung - TEM (2)


Ciliates are unicellular eukaryotes that display nuclear dimorphism involving a macronucleus and a micronucleus.


Tetrahymena  provide an example of a cell that displays nuclear dimorphism. It includes a micronucleus and macronucleus, and it has been very helpful in various research.


The location of NORs and the nucleolar cycle in human cells.


Silver-stained nucleolus organizer region (arrow) at the tip of a chromosome of the Gecko  Lepidodactylus lugubris


The DJ forms a perinucleolar anchor for rDNA repeats.


The  protoplasmic  material of the nucleus including the  nucleolus  labelled as nucleoplasm.


Polish - German   botanist  and namer of nucleoplasm,  Eduard Strasburger .


An example of the  sodium-potassium pump , a  P-type ATPase , which controls the ionic gradient across the  cell membrane  and the  nuclear envelope  as well as the ionic makeup of the nucleoplasm through the selective pumping of  sodium  and  potassium   ions .


Histology of a null cell adenoma


(A) Electron micrograph of  Halothiobacillus neapolitanus  cells, arrows highlight  carboxysomes . (B) Image of intact carboxysomes isolated from  H. neapolitanus . Scale bars are 100 nm. [ 23 ]


Structure of  Candidatus  Brocadia anammoxidans , showing an  anammoxosome  and intracytoplasmic membrane


An overlay of a fluorescence micrograph (green) onto a DIC image of a HeLa cell expressing a Yellow fluorescent Protein fusion of Paraspeckle Protein 1 (PSP1): 1. cytoplasm; 2. nucleus; 3. nucleolus; 4. paraspeckles


West et al. (2016) [ 7 ]  suggest that the NEAT1  is folded and bound to  paraspeckle core proteins to first form units, which are bridged together by FUS proteins to form the ordered paraspeckle sphere. [ 8 ]


Phragmosome formation in a highly vacuolated plant cell. From top to bottom: 1) Interphase cell with large central vacuole. 2) Cytoplasmic strands starting to penetrate vacuole. 3) Nucleus migration into center and formation of the phragmosome. 4) Phragmosome formation completed and formation of preprophase band marking future cell division plane.


The structure of a primary plasmodesma. CW= cell wall , CA= callose , PM= plasma membrane , ER= endoplasmic reticulum , DM=desmotubule, Red circles= actin , Purple circles and spokes=other unidentified proteins [ 1 ]


Tobacco mosaic virus movement protein 30 localizes to plasmodesmata


Sketch of a longitudinal ultrathin section through a typical motile bacterium bearing a flagellum and surrounding polar organelle at one end of the cell.


Amoeba proteus  extending lobose pseudopodia


The forms of pseudopodia, from left: polypodial and lobose; monopodial and lobose; filose; conical; reticulose; tapering actinopods; non-tapering actinopods


Jessica Polka 's electron micrograph of negatively stained purified type 51 R bodies in their extended (low pH) state


Schematic illustration of the supramolecular architecture of the major classes of prokaryotic cell envelopes containing surface (S) layers. S-layers in archaea with glycoprotein lattices as exclusive wall component are composed either of mushroom-like subunits with pillar-like, hydrophobic trans-membrane domains (a), or lipid-modified glycoprotein subunits (b). Individual S-layers can be composed of glycoproteins possessing both types of membrane anchoring mechanisms. Few archaea possess a rigid wall layer (e.g. pseudomurein in methanogenic organisms) as intermediate layer between the plasma membrane and the S-layer (c). In Gram-positive bacteria (d) the S-layer (glyco)proteins are bound to the rigid peptidoglycan-containing layer via secondary cell wall polymers. In Gram-negative bacteria (e) the S-layer is closely associated with the lipopolysaccharide of the outer membrane. Figure and figure legend were copied from Sleytr  et al.  2014, [ 2 ]  which is available under a  Creative Commons Attribution 3.0 International (CC BY 3.0) licence   .


Muscle contraction based on  sliding filament theory


Molecular model of the Sarcomere in the A-band. Organization of the central region of the A-band (C-zone). The thin filaments (actin in green, tropomyosin in pink) and the thick filaments (myosins in the OFF state are depicted in shades of blue, titin in red) are densely packed within the sarcomere. The myosin-binding protein C (yellow) connects thick and thin filaments. Artistic representation based on publicly available models  [ 4 ] .


Cardiac sarcomere structure


Plant cell overview, showing secondary cell wall.


Sepate junction in developing trachea in  Drosophila


Micrograph  showing condensed  chromosomes  in  blue ,  kinetochores  in  pink , and  microtubules  in  green  during  metaphase  of  mitosis


This diagram depicts the organization of a typical mitotic spindle found in animal cells. Chromosomes are attached to  kinetochore   microtubules  via a multiprotein complex called the kinetochore. Polar microtubules interdigitate at the spindle midzone and push the spindle poles apart via  motor proteins .  Astral microtubules  anchor the spindle poles to the  cell membrane . Microtubule polymerization is nucleated at the  microtubule organizing center .


In the centrosome-mediated "search and capture" model (left), microtubules nucleated from centrosomes contact chromosomes by chance and become stabilized at kinetochores to form the spindle. In the chromatin-mediated "self-organization" model (right), microtubules are nucleated around the vicinity of mitotic chromatin and organized into a bipolar array by motor proteins.


Cartoon of the dividing epithelium cell surrounded by epithelium tissue. Spindle apparatus rotates inside the cell. The rotation is a result of astral microtubules pulling towards tri-cellular-junctions (TCJ), signaling centers localized at the regions where three cells meet.


Depiction of the transmembrane proteins that make up tight junctions: occludin, claudins, and JAM proteins.


TEM  of rat kidney tissue shows a protein dense tight junction (three dark lines) at ~55,000x magnification.


Occludin interacting with GEF-H1/Lfc, which then activates RHOA, a regulator of cell differentiation and motility.


The ultrastructure of a single  bacterial cell  ( Bacillus subtilis ). The scale bar is 200  nm .


Plant cell structure


Animal cell structure


The  anthocyanin -storing vacuoles of  Rhoeo spathacea , a  spiderwort , in cells that have plasmolyzed


An overview of the trafficking of some adaptor protein (AP) complexes.


Adaptor Protein complexes and COPI-F subcomplex. [ 1 ]


Adaptor Protein, COPI and TSET complexes.


More trafficking pathways. Note, the colors are not the same as in the lead figure


A rendering of a COPII tube.


The early evolution of adaptor protein complexes


The evolution of TSET, COPI and APs from the Last Eukaryotic Common Ancestor


Production of a clathrin coated vesicle


Electron microscope image of a coated vesicle. EM series showing the budding of these kind of vesicles can be seen  [ 8 ]  and  [ 9 ]


A small portion of an accessory protein binds specifically to part of AP-2 complex


Protein phosphorylation allows specific interactions with a clathrin adaptor protein complex


Immunofluorescence coloration of actin (green) and the focal adhesion protein vinculin (red) in a fibroblast. Focal adhesions are visible as red dots at the end of the green bundles.


Image of a fluorescently-labeled growth cone extending from an axon  F-actin  (red)  microtubules  (green).


Two fluorescently-labeled growth cones. The growth cone (green) on the left is an example of a “filopodial” growth cone, while the one on the right is a “lamellipodial” growth cone.  Typically, growth cones have both structures, but with varying sizes and numbers of each.


Model of growth cone-mediated axon guidance. From left to right, this model describes how the cytoskeleton responds and reorganizes to grow towards a positive stimulus (+) detected by receptors in the growth cone or away from a negative stimulus (-).


Actin cytoskeleton of  mouse   embryo   fibroblasts , stained with  Fluorescein isothiocyanate - phalloidin


The outer red layer in this diagram is the capsule, which is distinct from the cell envelope. This bacterium is  gram-positive , as its cell envelope comprises a single  cell membrane  (orange) and a thick  peptidoglycan -containing cell wall (purple).


A bacterial capsule has a semi-rigid border that follows the contour of the cell. The capsule excludes India Ink when dyed. A slime layer is a non-rigid matrix that is easily deformed and is not able to exclude India Ink. Biofilms are composed of many cells and their outer barriers. The primary functions of both capsules and slime layers are for protection and adhesion.


Structure of gram-negative cell envelope


An illustration depicting diversity in the architecture of protein secretion systems found in  diderm bacteria [ 1 ]


T1SS schematic


T2SS schematic


T3SS schematic


T4SS schematic


T5SS schematic


ESX-5: type VII secretion system, Mycobacterium xenopi


Type IX secretion system schematic diagram [ 38 ]


Schematic of the chlorosome (rod hypothesis) [ 1 ]


Halobacterial Gas Vesicles. (A)  Halobacterium salinarum  colonies on a solid medium. Pink, opaque colonies from gas vesicle-containing cells; a red, transparent colony from gas vesicle-deficient cells. (B) Cryo-transmission electron micrograph of cells in 3 M NaCl plus 81 mM MgSO 4 . The image has the low signal-to-noise ratio due to the high concentration of NaCl. (C) Cryo-transmission electron micrograph of a focused ion beam-thinned cell in 3 M NaCl plus 81 mM MgSO 4 . The periodicity of the gas vesicle is clearly discerned. (A) Adapted from Pfeifer (2015), (B, C) from Bollschweiler et al. (2017), with permission from the publisher.


Gas vesicles imaged with transmission electron microscopy. (A) Wild-type cells. (B) Pressurized wild-type cells. (C) Mutant cells deleted for the gas vesicle gene clusters. (D) Gas vesicles with different widths. (A~D) Adapted from Ramsay et al. (2011), with permission from the publisher.


Gas vesicle formation and morphology. (A) and (B) Transmission electron micrographs of gas vesicles in Halobacterium salinarum. Spindle-shaped gas vesicles in (A). Isolated cylinder-shaped gas vesicles in (B). (C) Morphogenesis of gas vesicles from a bicone to a spindle- or cylinder-shaped gas vesicle. (D) Groups of gas vesicles. They form clusters during the early stage of gas vesicle formation, and fill the cells later. (E) Detailed diagram of a gas vesicle. A gas nanocompartment enclosed with a gas-permeable shell. (A~D) Adapted from Pfeifer (2012) and (E) from Shapiro et al. (2014), with permission from the publisher.


The Hammer Experiment


Mesosomes form in bacterial cells prepared for  electron microscopy  by chemical fixation, but not by freeze-fracture fixation. [ 1 ]


Formation of the  Escherichia coli  nucleoid   A.  An illustration of an open conformation of the circular genome of  Escherichia coli . Arrows represent bi-directional DNA replication. The genetic position of the origin of bi-directional DNA replication ( oriC ) and the site of chromosome decatenation ( dif ) in the replication termination region ( ter ) are marked. Colors represent specific segments of DNA as discussed in C.  B.  An illustration of a random coil form adopted by the pure circular DNA of  Escherichia coli  at thermal equilibrium without supercoils and additional stabilizing factors. [ 4 ] [ 5 ]   C.  A cartoon of the chromosome of a newly born  Escherichia coli  cell. The genomic DNA is not only condensed by 1000-fold compared to its pure random coil form but is also spatially organized.  oriC  and  dif  are localized in the mid-cell, and specific regions of the DNA indicated by colors in A organize into spatially distinct domains.


Nucleoid at ≥1 kb scale. DNA organization by nucleoid-associated proteins.   DNA is depicted as a grey straight or curved line and the nucleoid-associated proteins are depicted as blue spheres.


Genome-wide occupancy of nucleoid-associated proteins of  E. coli .   A circular layout of the  E. coli  genome depicting genome-wide occupancy of NAPs Fis, H-NS, HU, and IHF in growth and stationary phases in  E. coli . Histogram plots of the genome occupancy of NAPs as determined by chromatin-immunoprecipitation coupled with DNA sequencing (ChIP-seq) are shown outside the circular genome. The bin size of the histograms is 300 bp. Figure prepared in circos/0.69-6 using the ChIP-Seq data from. [ 46 ] [ 50 ]


DNA supercoiling   A.  A linear double-stranded DNA becomes a topologically constrained molecule if the two ends are covalently joined, forming a circle. Rules of DNA topology are explained using such a molecule (ccc-DNA) in which a numerical parameter called the linking number (Lk) defines the topology. Lk is a mathematical sum of two geometric parameters, twist (Tw) and writhe (Wr). A twist is the crossing of two strands, and writhe is coiling of the DNA double helix on its axis that requires bending. Lk is always an integer and remains invariant no matter how much the two strands are deformed. It can only be changed by introducing a break in one or both DNA strands by DNA metabolic enzymes called topoisomerases.  B.  A torsional strain created by a change in Lk of a relaxed, topologically constrained DNA manifests in the form of DNA supercoiling. A decrease in Lk (Lk<Lk 0 ) induces negative supercoiling whereas an increase in Lk (Lk>Lk 0 ) induces positive supercoiling. Only negative supercoiling is depicted here. For example, if a cut is introduced into a ccc-DNA and four turns are removed before rejoining the two strands, the DNA becomes negatively supercoiled with a decrease in the number of twists or writhe or both. Writhe can adopt two types of geometric structures called plectoneme and toroid. Plectonemes are characterized by the interwinding of the DNA double helix and an apical loop, whereas spiraling of DNA double helix around an axis forms toroids.


Basic units of genomic organization in bacteria and eukaryotes   Genomic DNA, depicted as a grey line, is negatively supercoiled in both bacteria and eukaryotes. However, the negatively supercoiled DNA is organized in the plectonemic form in bacteria, whereas it is organized in the toroidal form in eukaryotes. Nucleoid associated proteins (NAPs), shown as colored spheres, restrain half of the plectonemic supercoils, whereas almost all of the toroidal supercoils are induced as well as restrained by nucleosomes (colored orange), formed by wrapping of DNA around histones.


Twin supercoiling domain model for transcription-induced supercoiling   A.  An example of topologically constrained DNA. A grey bar represents a topological constraint, e.g. a protein or a membrane anchor.  B.  Accommodation of RNA polymerase for transcription initiation results in the opening of the DNA double helix.  C.  An elongating RNA polymerase complex cannot rotate around the helical axis of DNA. Therefore, removal of helical turns by RNA polymerase causes overwinding of the topologically constrained DNA ahead and underwinding of the DNA behind, generating positively and negatively supercoiled DNA, respectively. Supercoiling can manifest as either change in the numbers of twists as shown in C or plectonemic writhe as shown in D.


The chromosomal DNA within the nucleoid is segregated into independent supercoiled topological domains   A.  An illustration of a single topological domain of a supercoiled DNA. A single double-stranded cut anywhere would be sufficient to relax the supercoiling tension of the entire domain.  B.  An illustration of multiple topological domains in a supercoiled DNA molecule. A presence of supercoiling-diffusion barriers segregates a supercoiled DNA molecule into multiple topological domains. Hypothetical supercoiling diffusion barriers are represented as green spheres. As a result, a single double-stranded cut will only relax one topological domain and not the others. Plectonemic supercoils of DNA within the  E. coli  nucleoid are organized into several topological domains, but only four domains with a different number of supercoils are shown for simplicity.


Nucleoid is spatially organized into chromosomal interactions domains (CIDs) and macrodomains   A.  Chromosome conformation capture (3C) methods probe 3D genome organization by quantifying physical interactions between genomic loci that are nearby in 3D-space but may be far away in the linear genome. A genome is cross-linked with formaldehyde to preserve physical contacts between genomic loci. Subsequently, the genome is digested with a restriction enzyme. In the next step, a DNA ligation is carried out under diluted DNA concentrations to favor intra-molecular ligation (between cross-linked fragments that are brought into physical proximity by 3D genome organization). A frequency of ligation events between distant DNA sites reflects a physical interaction. In the 3C method, ligation junctions are detected by the semi-quantitative PCR amplification in which amplification efficiency is a rough estimate of pairwise physical contact between genomic regions of interests and its frequency. The 3C method probes a physical interaction between two specific regions identified a priori, whereas its Hi-C version detects physical interactions between all possible pairs of genomic regions simultaneously. In the Hi-C method, digested ends are filled in with a biotinylated adaptor before ligation. Ligated fragments are sheared and then enriched by a biotin-pull down. Ligation junctions are then detected and quantified by the paired-end next-generation sequencing methods.  B.  Hi-C data are typically represented in the form of a two-dimensional matrix in which the x-axis and y-axis represent the genomic coordinates. The genome is usually divided into bins of a fixed size, e.g., 5-kb. The size of bins essentially defines the contact resolution. Each entry in the matrix, m ij , represents the number of chimeric sequencing reads mapped to genomic loci in bins i and j. A quantification of the reads (represented as a heatmap) denotes the relative frequency of contacts between genomic loci of bins i and j. A prominent feature of the heatmap is a diagonal line that appears due to more frequent physical interaction between loci that are very close to each other in the linear genome. The intensity further from the diagonal line represents the relative frequency of physical interaction between loci that are far away from each other in the linear genome. Triangles of high-intensity along the diagonal line represent highly self-interacting chromosomal interaction domains (CIDs) that are separated by a boundary region that consists of a smaller number of interactions.  C.  In many bacterial species including  E. coli , it appears that supercoiled topological domains organize as CIDs. Plectonemic supercoiling promotes a high level of interaction among genomic loci within a CID, and a plectoneme-free region (PFR), created due to high transcription activity, acts as a CID boundary. Nucleoid-associated proteins, depicted as closed circles, stabilize the supercoiling-mediated interactions. The actively transcribing RNA polymerase (depicted as a green sphere) in the PFR blocks dissipation of supercoiling between the two domains thus acts as a supercoiling diffusion barrier. The size of the CIDs ranges between 30 and 400 kb. Several triangles (CIDs) merge to form a bigger triangle that represents a macrodomain. In other words, CIDs of a macrodomain physically interact with each other more frequently than with CIDs of a neighboring macrodomain or with genomic loci outside of that macrodomain. A macrodomain may comprise several CIDs. For simplicity, a macrodomain comprising only two CIDs is shown.


Genome-wide occupancy of MatP and MukB of  E. coli   A circular layout of the  E. coli  genome depicting genome-wide occupancy of MatP and MukB in  E. coli . The innermost circle depicts the  E. coli  genome. The regions of the genome which organize as spatial domains(macrodomains) in the nucleoid are indicated as colored bands. Histogram plots of genome occupancy for MatP and MukB as determined by chromatin-immunoprecipitation coupled with DNA sequencing (ChIP-seq) are shown in outside circles. The bin size of the histograms is 300 bp. The figure was prepared in circos/0.69-6 using the processed ChIP-Seq data from. [ 155 ]


Models for DNA organization by MatP and MukBEF   A.  A  matS -bridging model for DNA organization in the Ter macrodomain by MatP. MatP recognizes a 13-bp signature DNA sequence called  matS  that is present exclusively in the Ter macrodomain. There are 23  matS  sites separated by one another by an average of 35-kb. MatP binds to a  matS  site as a dimer, and the tetramerization of the DNA-bound dimers bridges  matS  sites forming large DNA loops.  B.  The architecture of the  E. coli  MukBEF complex. The complex is formed by protein-protein interactions between MukB (blue), MukF (dark orange) and MukE (light orange). MukB, which belongs to the family of structural maintenance of chromosomes (SMCs) proteins, forms a dimer (monomers are shown by dark and light blue colors) consisting of an ATPase head domain and a 100 nm long intramolecular coiled-coil with a hinge region in the middle. Because of the flexibility of the hinge region, MukB adopts a characteristic V-shape of the SMC family. MukF also tends to exist as a dimer because of the strong dimerization affinity between monomers. [ 157 ] [ 158 ]  The C-terminal domain of MukF can interact with the head domain of MukB while its central domain can interact with MukE. Two molecules of MukE and one molecule of MukF associate with each other independent of MukB to form a trimeric complex (MukE 2 F). Since MukF tends to exist in a dimeric form, the dimerization of MukF results in an elongated hexameric complex (MukE 2 F) 2 . [ 159 ]  In the absence of ATP, the (MukE 2 F) 2  complex binds to the MukB head domains through the C-terminal domain of MukF to form a symmetric MukBEF complex (shown on the left). The stoichiometry of the symmetric complex is B 2 (E 2 F) 2 . The ATP binding between the MukB head domains forces the detachment of one MukF molecule and two MukE molecules. [ 132 ] [ 159 ]  As a result, an asymmetric MukBEF complex of the stoichiometry B 2 (E 2 F) 1  is formed. Since MukF readily dimerizes, the MukF dimerization can potentially join two ATP-bound asymmetric molecules resulting in the formation of a dimer of dimers with the stoichiometry of B 4 (E 2 F) 2  (shown on the right). The stoichiometry of the MukBEF complex  in vivo  is estimated to be B 4 (E 2 F) 2  suggesting that a dimer of dimers is the functional unit  in vivo . [ 160 ]   C.  A model for loop extrusion by a MukBEF dimer of dimers. A dimer of dimer loads onto DNA (depicted as a grey line) through DNA binding domains of MukB. MukB has been shown to bind DNA via its hinge region and the top region of its head domain. [ 48 ] [ 161 ]  The translocation of the complex away from its loading site then extrudes DNA loops. The loops are extruded in a rock-climbing manner by the coordinated opening and closing of the MukBEF ring through the MukB head disengagement that occurs due to coordinated ATP hydrolysis in the two dimers. [ 160 ]  Dark and light blue circles represent ATP binding and hydrolysis events respectively. MukE is not shown in the complex for simplicity.


Nucleoid as a helical ellipsoid with longitudinal high-density DNA regions   A.  A cartoon of  E. coli  cell with a curved nucleoid (dark grey). A curved centroids path, denoted by red and green dots, emphasizes the curved shape of the nucleoid [ 13 ]   B.  Cross-sectioning of the  E. coli  nucleoid visualized by HU-mCherry. Fluorescence intensity is taken as a proxy for DNA density and is represented by blue to red in increasing order. [ 14 ]


This caption is not  succinct .  Please  improve this article  if you can.   ( July 2017 )  Transmission electron micrograph of outer membrane vesicles (OMV) (size 80–90 nm, dia) released by human pathogen  Salmonella  3,10:r:- in chicken ileum,  in vivo . OMVs were proposed to be 'blown off' from large bacterial periplasmic protrusions, called  periplasmic organelles  (PO) with the help of 'bubble tube'-like assembly of about four  type III secretion  injectisomal  rivet complexes  (riveting bacterial outer and cell membrane to allow pockets of periplasm to expand into POs). This allows  membrane vesicle trafficking  of OMVs from gram negative bacteria to dock on host epithelial cell membrane (microvilli), proposed to translocate signal molecules from pathogen to host cells at the  host–pathogen interface .


Monoderm bacteria have a thin periplasm between the cell wall and the plasma membrane [ 2 ]


Gram-negative  (diderm)  cell wall


Figure demonstrating modulation of RcsF signaling by changes in the periplasmic intermembrane distance [ 17 ]


Schematic drawing of bacterial conjugation.  1-  Donor cell produces pilus.  2-  Pilus attaches to recipient cell, brings the two cells together.  3-  The mobile plasmid is nicked and a single strand of DNA is then transferred to the recipient cell.  4-  Both cells recircularize their plasmids, synthesize second strands, and reproduce pili; both cells are now viable donors.


Escherichia coli  undergoing  conjugation . Bacteria produce long extracellular appendages called sex pili, which connect two neighbouring cells and serve as a physical conduit for transfer of DNA. Adapted from  [ 4 ]


Proposed conjugation mechanisms between donor and recipient cells in archaea (left) and bacteria (right). The schematic shows how ssDNA substrates are generated by the HerA-NurA machinery in the donor archaeal cells and by the plasmid-encoded relaxosome in bacteria. The figure is reproduced from  [ 8 ]


Escherichia coli .


Type IV Pilus Twitching Motility   1.  Pre-PilA is made in the cytoplasm and moves into the inner membrane.  2.  Pre-PilA is inserted into the inner membrane.   3.  PilD, a  peptidase , removes a leader sequence, thus making the Pre-PilA shorter and into PilA, the main building-block protein of Pili.   4.  PilF, a  NTP -Binding protein that provides energy for Type IV Pili Assembly.   5.  The secretin protein, PilQ, found on the outer membrane of the cell is necessary for the development/extension of the pilus. PilC is the first proteins to form the pilus and are responsible for overall attachment of the pilus.   6.  Once the Type IV Pilus attaches or interacts with what it needs to, it begins to retract. This occurs with the PilT beginning to degrade the last parts of the PilA in the pilus. The mechanism of PilT is very similar to PilF.   7.  Degradation of the pilus into the components to be utilized and synthesized into PilA again. [ 13 ]


Type IVa pilus machine architectural model


This figure depicts fimbriae adhesion. In this process the fimbriae of a bacterial cell (right) adhere to specific proteins, called receptors, found on the outer membrane of a host cell (left). They do this by a specific interaction between the receptors of the host cell and the perfectly matched adhesions found on the bacteria's fimbriae. This process of bacteria adhering to a host cell can result in the colonization of that host cell as more and more bacteria collect around it, and is integral to the continued survival of the bacteria, enabling them to infect tissues and entire organs.  [ 25 ]


Diagram of a bacterium showing chromosomal DNA and plasmids (Not to scale)


There are two types of plasmid integration into a host bacteria: Non-integrating plasmids replicate as with the top instance, whereas  episomes , the lower example, can integrate into the host  chromosome .


Overview of bacterial conjugation


Electron micrograph  of a DNA fiber bundle, presumably of a single bacterial chromosome loop


Electron micrograph of a bacterial DNA plasmid (chromosome fragment)


A schematic representation of the  pBR322  plasmid, one of the first plasmids to be used widely as a  cloning vector .  Shown on the plasmid diagram are the genes encoded ( amp  and  tet  for  ampicillin  and  tetracycline  resistance respectively), its origin of replication ( ori ), and various  restriction sites  (indicated in blue).


Insulin


The structure of the Ti plasmid


The  repABC gene  cassette of Ti plasmids in Agrobacteria, with a schematic of their gene product and activities


The composition of the  vir  region of octopine-type Ti plasmids


3D structure of the human apoptosome-CARD complex. blue: apoptosome platform; magenta: CARD disk [ 1 ]


Pseudo atomic structure of the human apoptosome  (Yuan et al. 2010, Structure of an apoptosome-procaspase-9 CARD complex [ 1 ]


Rendering of apoptosome showing clear central-hub


Human, fruit fly, & nematode apoptosomes


Electron micrographs of  Sulfolobus acidocaldarius  MW001 during normal growth.  Indication of archaella (black arrows) and pili (white arrows). Negative staining with uranyl acetate.


2015 model of the crenarchaeal archaellum. [ 16 ]


The structure of the Bacterial Microcompartment shell.  The first structure of a BMC shell, determined by X-ray crystallography and cryo-electron microscopy, [ 1 ]  contains representatives of each of the shell protein types:  BMC-P, BMC-H and BMC-T, in both its trimer  (upper right) and dimer of trimer (lower right), forms. [Image: Todd Yeates]


Generalized function schematic for experimentally characterized BMCs. (A) Carboxysome. (B) Metabolosome. Reactions in gray are peripheral reactions to the core BMC chemistry. BMC shell protein oligomers are depicted on the left: blue, BMC-H; cyan, BMC-T; yellow, BMC-P. 3-PGA, 3-phosphoglycerate, and RuBP, ribulose 1,5-bisphosphate. [ 25 ]


Electron micrographs showing alpha-carboxysomes from the chemoautotrophic bacterium  Halothiobacillus neapolitanus : (A) arranged within the cell, and (B) intact upon isolation. Scale bars indicate 100 nm. [ 54 ]


Electron micrograph of Synechococcus elongatus PCC 7942 cell showing the carboxysomes as polyhedral dark structures. Scale bar indicates 500 nm.


Electron micrograph of Escherichia coli cell expressing the PDU BMC genes (left), and purified PDU BMCs from the same strain (right).


Schematic of the eukaryotic flagellum. 1-axoneme, 2-cell membrane, 3-IFT ( Intraflagellar transport ), 4-Basal body, 5-Cross section of flagellum, 6-Triplets of microtubules of basal body.


Longitudinal section through the flagella area in  Chlamydomonas reinhardtii . In the cell apex is the basal body that is the anchoring site for a flagellum. Basal bodies originate from and have a substructure similar to that of centrioles, with nine peripheral microtubule triplets (see structure at bottom center of image).


Formation and examples of membraneless organelles


Starch granules of corn


Glycogen granules in Spermiogenesis in Pleurogenidae (Digenea)


Micelle caseine


Lens epithelium containing crystallin. Hand-book of physiology (1892)


Stress granule  dynamics


Formation and examples of  nuclear bodies


Biomolecular partitioning


Diagram of the plant cell, with the cell wall in green.


Cell wall in multicellular plants – its different layers and their placement with respect to protoplasm (highly diagrammatic)


Molecular structure of the primary cell wall in plants


Photomicrograph of onion root cells, showing the centrifugal development of new cell walls (phragmoplast)


Chemical structure of a unit from a  chitin  polymer chain


Scanning electron   micrographs  of  diatoms  showing the external appearance of the cell wall


Illustration of a typical  gram-positive bacterium . The cell envelope comprises a  plasma membrane , seen here in light brown, and a thick  peptidoglycan -containing cell wall (the purple layer). No  outer lipid membrane  is present, as would be the case in  gram-negative bacteria . The red layer, known as the  capsule , is distinct from the cell envelope.


A schematic overview of the pap chaperone-usher system showing all subunits and their organisation. PapD is the chaperone; PapC is the usher; PapA and the remaining subunits form the fimbria itself


PAP pilin major protein, PapA homo13mer, top view, E.Coli.


EVOS Imaging depicting a single celled organism with distinctive cilia


Cilia Structure


This illustration shows where the cisternae can be found on the Golgi apparatus. As well as the location of the cis and trans Golgi network.


Complex oil bodies of  Plagiochila asplenioides


Distinct blue complex oil bodies of  Calypogeia azurea.


Radula complanata  laminal cells, bearing 1-2 large tinted oil-bodies.


Marchantia polymorpha  antheridiophore with dark ocelli.


Protist  Paramecium aurelia  with contractile vacuoles


A  Dictyostelium discoideum  (slime mold) cell exhibiting a prominent contractile vacuole on its left side


Transmission electron micrograph of a thin section of the surface of the ciliate  Paramecium  putrinum , showing the alveoli (red arrows) under the cell surface


Diagram of a  ciliate


Diagram of  T. gondii  structure with dense granules


Electron micrograph of endosomes in human  HeLa cells . Early endosomes (E - labeled for EGFR, 5 minutes after internalisation, and transferrin), late endosomes/MVBs (M) and lysosomes (L) are visible. Bar, 500 nm.


Diagram of the pathways that intersect endosomes in the endocytic pathway of animal cells. Examples of molecules that follow some of the pathways are shown, including receptors for EGF, transferrin, and lysosomal hydrolases. Recycling endosomes, and compartments and pathways found in more specialized cells, are not shown.


The ERGIC lies between the rough endoplasmic reticulum (RER) and Golgi on the secretory pathway


Different types of  plastid


Schematic representation of a  Euglena  cell with red eyespot (9)


Schematic representation of a  Chlamydomonas  cell with chloroplast eyespot (4)


Prokaryotic  (bacterial and archaeal) flagella run in a rotary movement, while eukaryotic flagella run in a bending movement. The prokaryotic flagellum uses a  rotary motor , and the eukaryotic flagellum uses a complex sliding filament system. Eukaryotic flagella are ATP-driven, while prokaryotic flagella can be ATP-driven (Archaea) or proton-driven (Bacteria). [ 11 ]


Bacterial flagellar motor assembly: Shown here is the C-ring at the base with FliG in red, FliM in yellow, and FliN in shades of purple; the MS-ring in blue; the MotAB in brown; the LP-ring in pink; and the rod in gray. [ 25 ]


Eukaryotic flagella. 1–axoneme, 2–cell membrane, 3–IFT (IntraFlagellar Transport), 4–Basal body, 5–Cross section of flagella, 6–Triplets of microtubules of basal body


Cross section of an  axoneme


Longitudinal section through the flagella area in  Chlamydomonas reinhardtii . In the cell apex is the basal body that is the anchoring site for a flagellum. Basal bodies originate from and have a substructure similar to that of centrioles, with nine peripheral microtubule triplets (see structure at bottom center of image).


The "9+2" structure is visible in this cross-section micrograph of an axoneme.


Beating pattern of eukaryotic "flagellum" and "cillum", a traditional distinction before the structures of the two are known.


Glycosomes in the trypanosomatid


By taking advantage of the pores in the membrane of the glycosome, a drug can enter the organelle and be used to kill the trypanosoma brucei


Diagram of a single "stack" of Golgi


3D rendering of Golgi apparatus


The Golgi apparatus (salmon pink) in context of the secretory pathway


Diagram of secretory process from endoplasmic reticulum (orange) to Golgi apparatus (magenta). 1.  Nuclear membrane ; 2.  Nuclear pore ; 3. Rough endoplasmic reticulum (RER); 4. Smooth endoplasmic reticulum (SER); 5.  Ribosome  attached to RER; 6.  Macromolecules ; 7. Transport vesicles; 8. Golgi apparatus; 9.  Cis  face of Golgi apparatus; 10.  Trans  face of Golgi apparatus; 11. Cisternae of the Golgi apparatus.


Activity in a  Spironucleus salmonicida  hydrogenosome:  pyruvate  (PYR) is turned into  carbon dioxide  (CO 2 ) and  acetate  while producing  molecular hydrogen  (H 2 ) and converting  ADP  into  ATP


Abb.1: Model of ATP-synthesis in hydrogenosomes.


Eukaryote cells sort misfolded proteins into two quality control compartments: JUNQ and IPOD, based on their ubiquitination state.


Eukaryote cells sort misfolded proteins, based on their ubiquitination state, into two quality control compartments:  1. JUNQ (green), which is tethered to the  nucleus  (orange) 2. IPOD(green), which is tethered to the  vacuole  (black shadow)


A JUNQ inclusion viewed by a ubiquitinated VHL protein(green), is tethered to the  nucleus  (orange).


An IPOD inclusion viewed by a non-ubiquitinated VHL protein(red), tethered to the  vacuole  (green).


Image of kinetochores in pink


Kinetochore structure and components in vertebrate cells. Based on Maiato  et al.  (2004). [ 9 ]


Fluorescence microscopy micrographs, showing the endogenous human protein  Mad1  (one of the spindle checkpoint components) in green, along the different phases in mitosis;  CENP-B , in red, is a centromeric marker, and  DAPI  (in blue) stains DNA


Chromosomes attach to the  mitotic spindle  through sister kinetochores, in a bipolar orientation


Scheme showing cell cycle progression between prometaphase and anaphase. (Chromosomes are in blue and kinetochores in light yellow).


Metaphase cells with low CENP-E levels by  RNAi , showing  chromosomes unaligned at the metaphase plate (arrows). These chromosomes are labeled with  antibodies  against the mitotic checkpoint proteins Mad1/Mad2. Hec1 and CENP-B label the centromeric region (the kinetochore), and DAPI is a specific stain for DNA.


Scheme showing different anchoring configurations between chromosomes and the mitotic spindle. [ 55 ]


Electron micrograph of normal kinetoplast (K) of  Trypanosoma brucei


Figure 8. Illustration of the location of the antipodal protein complex relative to kinetoplast disk (above) and the migration of minicircle to these complexes for replication (below).


Figure 9. Illustration of kinetoplast rotation during minicircle replication.


Kinetoplast (K) divides first and then the nucleus (N) in dividing  T. brucei


Leucoplasts, specifically,  amyloplasts


Magnetite magnetosomes in Gammaproteobacteria strain SS-5. (A) Chain of highly elongated magnetosomes. (B) Part of a magnetosome chain. (C) The magnetosome in the lower right in (B), viewed along the

 [
 1

 1
 ¯

 0
 ]

 {\displaystyle \scriptstyle [1{\overline {1}}0]}

  direction, with its Fourier transform in the lower right. [ 1 ]


Formation of Magnetosome chain. [ 8 ]


Lab Growth of magnetite crystals under controlled conditions to simulate growth within the magnetosome. [ 10 ]


TEM Images of the progressive collapse of the magnetosome chain structures in cells. [ 11 ]


Bacterial Conjugation. Note that the sex  pilus  is a structure on the F +  cell whereas the mating bridge (not labeled) is the connection between the two bacteria.


Transmission electron micrograph of red blood cell infected with  P. falciparum . Maurer's clefts are marked with arrows. Scale bar is 500 nm.


Images from original description of Maurer's clefts in 1902. Images show red blood cells infected with  Plasmodium falciparum  stained with alkaline methylene blue.


Fish and frog melanophores are cells that can change colour by dispersing or aggregating pigment-containing melanosomes.


Microbody structure - a peroxisome


Micronuclei visible in boxes


B, C . Micronuclei in peripheral blood erythrocytes of penguins  Pygoscelis papua.


A middle stage midbody stained with tubulin


Illustration of exons and introns in pre-mRNA. The mature mRNA is formed by splicing.


A comparison between major and minor splicing mechanisms


U1 and U11 can be folded similarly


Black arrow: the nitroplast inside  B. bigelowii  (motile phase)


Nucleolus contained within the  cell nucleus


Electron micrograph of part of a  HeLa  cell. The image is a screen capture from  this movie , which shows a Z-stack of the cell.


A  light micrograph  of an ocelloid-containing dinoflagellate. The  nucleus  is marked  n , the ocelloid is indicated with a double arrowhead, and a posterior cell extension is indicated with an arrow; scale bar = 10 μm. [ 1 ]


A micrograph of a single ocelloid; scale bar = 5 μm. [ 1 ]


A  negative staining   transmission electron micrograph  of an ocelloid (white box), indicating the hyalosome (H) and retinal body (R), as well as a portion of the piston (Ps). Scale bar = 10 μm. [ 5 ]


Comparison between the structures of the ocelloid (1) and the  vertebrate  eye (2). Components are indicated as the hyalosome (H), retinal body/retina (R), and  crystallin  lens (C). [ 5 ]


diagram of situation of the fungal organelle parenthesome in the cell


Basic structure of a peroxisome


Peroxisome in rat neonatal cardiomyocyte


The process of phagocytosis showing phagolysosome formation. Lysosome(shown in green) fuses with phagosome to form a phagolysosome.


Amino acid transport and phagolysosome resolution in three stages: (A) Inside the phagolysosome, hydrolases break down proteins into amino acids, represented by pink and blue dots. Amino acid transporters, such as LAAT-1 (shown in pink) and SLC-36.1 (shown in blue), export these different amino acids from the phagolysosome lumen into the cytosol.  (B) The exported amino acids activate mTOR (depicted in green). This activation leads to ARL-8-mediated tubulation. ARL-8 (shown in red) likely interacts with motor proteins and microtubules (represented in orange) to facilitate this process.(C) The tubulation process results in the formation of phagolysosomal vesicles. This cycle repeats until the phagolysosome is fully resolved.