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5.4: Summary- Organelles - Biology


Learning Outcomes

  • Describe the basic composition of cytoplasm
  • Describe the structure and function of the nucleus and nuclear membrane
  • Describe the structure, function, and components of the endomembrane system
  • Describe the structure and function of ribosomes
  • Describe the structure and function of mitochondria
  • Describe the structure and functions of vesicles
  • Describe the structure and function of peroxisomes
  • Demonstrate familiarity with various components of the cytoskeleton
  • Describe the structure and functions of flagella and cilia
  • Explain the structure and function of cell membranes
  • Identify key organelles present only in plant cells, including chloroplasts and vacuoles
  • Identify key organelles present only in animal cells, including centrosomes and lysosomes

Table 1 provides the components of prokaryotic and eukaryotic cells and their respective functions.

Table 1. Components of Prokaryotic and Eukaryotic Cells and Their Functions
Cell ComponentFunctionPresent in Prokaryotes?Present in Animal Cells?Present in Plant Cells?
Plasma membraneSeparates cell from external environment; controls passage of organic molecules, ions, water, oxygen, and wastes into and out of the cellYesYesYes
CytoplasmProvides structure to cell; site of many metabolic reactions; medium in which organelles are foundYesYesYes
NucleoidLocation of DNAYesNoNo
NucleusCell organelle that houses DNA and directs synthesis of ribosomes and proteinsNoYesYes
RibosomesProtein synthesisYesYesYes
MitochondriaATP production/cellular respirationNoYesYes
PeroxisomesOxidizes and breaks down fatty acids and amino acids, and detoxifies poisonsNoYesYes
Vesicles and vacuolesStorage and transport; digestive function in plant cellsNoYesYes
CentrosomeUnspecified role in cell division in animal cells; source of microtubules in animal cellsNoYesNo
LysosomesDigestion of macromolecules; recycling of worn-out organellesNoYesNo
Cell wallProtection, structural support and maintenance of cell shapeYes, primarily peptidoglycan in bacteria but not ArchaeaNoYes, primarily cellulose
ChloroplastsPhotosynthesisNoNoYes
Endoplasmic reticulumModifies proteins and synthesizes lipidsNoYesYes
Golgi apparatusModifies, sorts, tags, packages, and distributes lipids and proteinsNoYesYes
CytoskeletonMaintains cell’s shape, secures organelles in specific positions, allows cytoplasm and vesicles to move within the cell, and enables unicellular organisms to move independentlyYesYesYes
FlagellaCellular locomotionSomeSomeNo, except for some plant sperm.
CiliaCellular locomotion, movement of particles along extracellular surface of plasma membrane, and filtrationNoSomeNo

Like a prokaryotic cell, a eukaryotic cell has a plasma membrane, cytoplasm, and ribosomes, but a eukaryotic cell is typically larger than a prokaryotic cell, has a true nucleus (meaning its DNA is surrounded by a membrane), and has other membrane-bound organelles that allow for compartmentalization of functions. The plasma membrane is a phospholipid bilayer embedded with proteins. The nucleolus within the nucleus is the site for ribosome assembly. Ribosomes are found in the cytoplasm or are attached to the cytoplasmic side of the plasma membrane or endoplasmic reticulum. They perform protein synthesis. Mitochondria perform cellular respiration and produce ATP. Peroxisomes break down fatty acids, amino acids, and some toxins. Vesicles and vacuoles are storage and transport compartments. In plant cells, vacuoles also help break down macromolecules.

Animal cells also have a centrosome and lysosomes. The centrosome has two bodies, the centrioles, with an unknown role in cell division. Lysosomes are the digestive organelles of animal cells.

Plant cells have a cell wall, chloroplasts, and a central vacuole. The plant cell wall, whose primary component is cellulose, protects the cell, provides structural support, and gives shape to the cell. Photosynthesis takes place in chloroplasts. The central vacuole expands, enlarging the cell without the need to produce more cytoplasm.

The endomembrane system includes the nuclear envelope, the endoplasmic reticulum, Golgi apparatus, lysosomes, vesicles, as well as the plasma membrane. These cellular components work together to modify, package, tag, and transport membrane lipids and proteins.

The cytoskeleton has three different types of protein elements. Microfilaments provide rigidity and shape to the cell, and facilitate cellular movements. Intermediate filaments bear tension and anchor the nucleus and other organelles in place. Microtubules help the cell resist compression, serve as tracks for motor proteins that move vesicles through the cell, and pull replicated chromosomes to opposite ends of a dividing cell. They are also the structural elements of centrioles, flagella, and cilia.

Animal cells communicate through their extracellular matrices and are connected to each other by tight junctions, desmosomes, and gap junctions. Plant cells are connected and communicate with each other by plasmodesmata.

Practice Question

In the context of cell biology, what do we mean by form follows function? What are at least two examples of this concept?

[practice-area rows=”4″][/practice-area]
[reveal-answer q=”596885″]Show Answer[/reveal-answer]
[hidden-answer a=”596885″]“Form follows function” refers to the idea that the function of a body part dictates the form of that body part. As an example, organisms like birds or fish that fly or swim quickly through the air or water have streamlined bodies that reduce drag. At the level of the cell, in tissues involved in secretory functions, such as the salivary glands, the cells have abundant Golgi.[/hidden-answer]


5.4: Summary- Organelles - Biology

All cells, whether they are prokaryotic or eukaryotic, have some common features. These common features are:

DNA, the genetic material contained in one or more chromosomes and located in a nonmembrane bound nucleoid region in prokaryotes and a membrane-bound nucleus in eukaryotes

Plasma membrane, a phospholipid bilayer with proteins that separates the cell from the surrounding environment and functions as a selective barrier for the import and export of materials

Cytoplasm, the rest of the material of the cell within the plasma membrane, excluding the nucleoid region or nucleus, that consists of a fluid portion called the cytosol and the organelles and other particulates suspended in it

1. The genetic material (DNA) is localized to a region called the nucleoid which has no surrounding membrane.

2. The cell contains large numbers of ribosomes that are used for protein synthesis.

3. At the periphery of the cell is the plasma membrane. In some prokaryotes the plasma membrane folds in to form structures called mesosomes, the function of which is not clearly understood.

4. Outside the plasma membrane of most prokaryotes is a fairly rigid wall which gives the organism its shape. The walls of bacteria consist of peptidoglycans. Sometimes there is also an outer capsule. Note that the cell wall of prokaryotes differs chemically from the eukaryotic cell wall of plant cells and of protists.


Organelles

Much of what you will need to know applies to the structure of eukaryotic cells. They are characterised by having membrane-bound organelles.

Cytosol and Endoplasmic Reticulum (ER)

Cytoplasm refers to the jelly-like material with organelles in it.

If the organelles were removed, the soluble part that would be left is called the cytosol. It consists mainly of water with dissolved substances such as amino acids in it.

Also present in the cytosol are larger proteins and enzymes used in reactions within the cell. Running through the cytosol is endoplasmic reticulum (ER), a system of flattened cavities lined by a thin membrane. It is the site of the synthesis of many substances in the cell and so provides a compartmentalised area in which this takes place. The cavities also function as a transporting system whereby substances can move through them from one part of the cell to another.

There are 2 types of ER - rough (RER) and smooth (SER). SER obviously looks as though it has a smooth surface. It is where lipids and steroids are made so you would expect there to be a lot of SER in liver cells where lipid is metabolised.

RER looks rough on the surface because it is studded with very small organelles called ribosomes. Ribosomes are made of RNA and protein and are the site of protein synthesis (see DNA and Genetic Code).

There may be free ribosomes in the cytoplasm as well, which also are the site of protein synthesis. The proteins (which include enzymes) that are synthesised then move into the cavities of the RER to be transported.

Golgi apparatus

The Golgi apparatus is a series of flattened layers of plate-like membranes.

The proteins that are made by the RER for export from the cell are pinched off at the end of the cavity of the RER, so that a layer of membrane surrounds them. The whole structure is called a vesicle. This vesicle will move through the cytosol and fuse with the membrane of the Golgi apparatus.

In the cavity of the Golgi apparatus, the vessel proteins are modified for export - for example, by having a carbohydrate added to the protein. At the end of a Golgi cavity, the secretory product is pinched off so that the vesicle containing the substance can move through the cytosol to the cell surface membrane.

The vesicle will fuse with this membrane and so release the secretory product. If the vesicle contains digestive enzymes, it is called a lysosome. Lysosomes may be used inside the cell during endocytosis, or to break-down old, redundant organelles.

Mitochondria

A typical cell may contain 1,000 mitochondria, though some will contain many more. Generally, they are sausage-shaped organelles whose walls consist of 2 membranes.

The inner membrane is folded inwards to form projections called cristae. Inside this is the matrix.

Most of the reactions for aerobic respiration take place in the mitochondria so it is an incredibly important organelle.

During respiration, ATP is produced, which is used to provide energy for the cells' reactions. Most of the ATP is produced on the inner mitochondrial membrane.It is highly folded so there is maximum surface area available.

Cell wall and chloroplasts

These are only found in plant cells.

Chloroplasts will be discussed in photosynthesis - but, like the mitochondria - they have an envelope of two membranes making up the outer "wall".

They have pairs of membranes called thylakoids arranged in stacks, each stack being called a granum. Connecting different grana together are inter-granal thylakoids. Surrounding the internal membranes, inside the envelope is the stroma.

The reactions of photosynthesis take place in the membranes and stroma of the chloroplast.

The cell wall is rigid and made of cellulose fibres running through a mixture of other polysaccharides (more complex sugars) such as pectins and hemicelluloses.

The sticky middle lamella that holds next-door cells together is made of calcium pectate and magnesium pectate.

In young cells, the cellulose fibrils of the primary cell wall run parallel to each other. In older cells, a secondary cell wall may be laid down where the fibres are all parallel to each other, but at a different angle to those of the primary cell wall.

The cell wall is fully permeable unless a substance called lignin is deposited in the cellulose layers. Lignin makes the cell wall very strong and resistant to strain but it also makes it impermeable. If all the gaps between the fibres are filled in, the wall becomes completely impermeable and the cell will die.

Nucleus

The nucleus is separated from the surrounding cytoplasm by the double membrane around it, the nuclear envelope. This regulates the flow of substances into and out of the nucleus.

At some points around the nucleus, the 2 membranes fuse to create nuclear pores - these are channels through which substances can move. The outer of the 2 membranes is continuous with the ER.

Within the nuclear envelope is the nucleoplasm. In this are suspended thread-like chromosomes (for chromosome structure see DNA and Genetic Code).

Another structure within the nucleus is the nucleolus. The RNA, which will be made into ribosomes, is synthesised in the nucleolus.

Other organelles

Vacuole: a fluid-filled space in the cytoplasm surrounded by a membrane called the tonoplast. It contains a solution of sugars and salts called the cell sap.

Microtubules: hollow rod-like structures with walls of tubulin protein. They provide the structural support of cells and can aid transport through the cell.

Microfilaments: rod-like structures made of contractile protein. Again, like microtubules, provide support and aid movement.

Centrioles: a pair of short hollow cylinders, usually found near the nucleus of an animal cell. They are involved in the formation of spindle fibres used in mitosis (see Reproduction and Cell Cycle Learn-it).

Cilia: hollow tubes extending outside some cells. They move fluid, which is outside the cell - for example, ciliated cells lining the respiratory tract move mucus, away from the lungs.

Flagella: similar to cilia, though longer. Used in the movement of the whole cell. The only structure like this in humans is the tails of the sperm.

Investigating the function of cell organelles

To obtain reliable information about the activity of an organelle, it is necessary to isolate it and test it individually.

First the cells are broken open or cell fractionation occurs to produce a homogenate or suspension. This is done using a blender with the cells in an isotonic, cold solution. Because the solution is isotonic, the organelles neither gain, or loose water by osmosis and as it is cold, the action of enzymes, which might damage the organelles, is prevented.

Differential centrifugation of the suspension is then carried out. A tube containing the suspension is spun in a centrifuge at a speed, which causes the heaviest organelles to be thrown to the bottom, forming a sediment. The other lighter organelles remain floating in the clear supernatant fluid above the sediment.

The sediment may be removed and the activity of the heaviest organelles such as the nucleus, determined. The supernatant may then be spun at a faster speed so that lighter organelles like the mitochondria sediment out.


Sperm Are Highly Adapted for Delivering Their DNA to an Egg

Typical sperm are “stripped-down” cells, equipped with a strong flagellum to propel them through an aqueous medium but unencumbered by cytoplasmic organelles such as ribosomes, endoplasmic reticulum, or Golgi apparatus, which are unnecessary for the task of delivering the DNA to the egg. Sperm, however, contain many mitochondria strategically placed where they can most efficiently power the flagellum. Sperm usually consist of two morphologically and functionally distinct regions enclosed by a single plasma membrane: the tail, which propels the sperm to the egg and helps it to burrow through the egg coat, and the head, which contains a condensed haploid nucleus (Figure 20-25). The DNA in the nucleus is extremely tightly packed, so that its volume is minimized for transport, and transcription is shut down. The chromosomes of many sperm have dispensed with the histones of somatic cells and are packed instead with simple, highly positively charged proteins called protamines.

Figure 20-25

A human sperm. It is shown in longitudinal section.

In the head of most animal sperm, closely apposed to the anterior end of the nuclear envelope, is a specialized secretory vesicle called the acrosomal vesicle (see Figure 20-25). This vesicle contains hydrolytic enzymes that may help the sperm to penetrate the egg's outer coat. When a sperm contacts an egg, the contents of the vesicle are released by exocytosis in the so-called acrosome reaction in some sperm, this reaction also exposes or releases specific proteins that help bind the sperm tightly to the egg coat.

The motile tail of a sperm is a long flagellum, whose central axoneme emanates from a basal body situated just posterior to the nucleus. As described in Chapter 16, the axoneme consists of two central singlet microtubules surrounded by nine evenly spaced microtubule doublets. The flagellum of some sperm (including those of mammals) differs from other flagella in that the usual 9 + 2 pattern of the axoneme is further surrounded by nine outer dense fibers (Figure 20-26). These dense fibers are stiff and noncontractile, and it is not known what role they have in the active bending of the flagellum, which is caused by the sliding of adjacent microtubule doublets past one another. Flagellar movement is driven by dynein motor proteins, which use the energy of ATP hydrolysis to slide the microtubules, as discussed in Chapter 16. The ATP is generated by highly specialized mitochondria in the anterior part of the sperm tail (called the midpiece), where the ATP is needed (see Figures 20-25 and 20-26).

Figure 20-26

Drawing of the midpiece of a mammalian sperm as seen in cross section in an electron microscope. The core of the flagellum is composed of an axoneme surrounded by nine dense fibers. The axoneme consists of two singlet microtubules surrounded by nine microtubule (more. )


What Are the Parts of the Cell?

Have you ever wondered what the inside of a cell looks like? If you think about the rooms in our homes, the inside of any animal or plant cell has many similar room-like structures called organelles. Each organelle is a place where specific jobs are done.

Plant and animal cells have many of the same organelles. But in some cases, the organelles in cells are different. For example, in plant cells, there are more types of organelles than are found in animal cells. And fungal cells have organelles not found in any other cell type. Below are some names and descriptions of organelles commonly found in certain cells. There is also an interactive cell viewer and game that can be used to learn about the parts of animal, plant, fungal, and bacterial cells. Archaea cells are very similar to bacterial cells, so have not been included separately.

Plasma membrane - The membrane enclosing a cell is made up of two lipid layers called a "bilipid" membrane. The lipids that are present in the plasma membrane are called "phospholipids."

These lipid layers are made up of a number of fatty acid building blocks. The fatty acid that makes up this membrane has two different parts to it- a small water loving head- hydrophilic head. Hydro stands for water and philic means liking or loving. The other part of this fatty acid is a long water-repelling or water hating tail.

This tail is hydrophobic- Hydro stands for water and phobic means fear. The plasma membrane is arranged in such a way so that the tails face each other on the inside and the heads face towards the outside of the membrane.
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Channels/pores- A channel in the cell's plasma membrane. This channel is made up of certain proteins that control the movement of molecules, including food and water, into the cell.
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Cell wall and plasmodesmata - In addition to cell membranes, plants have cell walls. Cell walls provide protection and support for plants. In land plants, the cell wall is mostly made of cellulose.

Unlike cell membranes, materials cannot get through cell walls. This would be a problem for plant cells if not for special openings called plasmodesmata.

These openings are used to communicate and transport materials between plant cells because the cell membranes are able to touch and therefore exchange needed materials.
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Cell wall septum and pores - Fungal cells have both cell membranes and cell walls, like plant cells. Cell walls provide protection and support. Fungal cell walls are largely made of chitin, which is the same substance in insect exoskeletons.

Because materials cannot get through cell walls, fungal cells have special openings called pores. Materials can be moved between fungal cells through the pores.

Some fungal cells also have a septum (plural is septa) that are special internal walls between cells that are found in long tube-shaped strings or strands called hyphae.


MATERIALS AND METHODS

Yeast strain construction

Standard methods were used throughout. All strains used in this study were congenic w303 (MATa his3-11,15 trp1-1 leu2-3 ura3-1 ade2-1). All anchor genes were cloned from the genome directly and tagged with PhyB (aa 1–908) and mCherry at the N-terminus with a 15-aa linker (EFDSAGSAGSAGGSS) between the PhyB and mCherry and a 10-aa linker (SAGSAGKASG) between mCherry and anchor gene. Endogenous GAL80 and CLB2 were tagged with mCitrine and PIF at the C-terminus with an 11-aa linker (AAAGDGAGLIN) between GAL80/CLB2 and mCitrine. CLB1 was deleted by using the KanMX2 fragment. Endogenous SPC42 was tagged with GFP at the C-terminus with an 11-aa linker (AAAGDGAGLIN). All strains were characterized by sequencing PCR products.

Time-lapse microscopy

Cells growing exponentially in synthetic liquid medium were seeded onto thin 1.5–2% agarose slabs of the same medium. For titration and spatial control experiments, cells were seeded onto concanavalin A–coated well plates with 0.17-µm coverglass bottoms. Multiple different positions were followed simultaneously. For most experiments, stacks of nine images were acquired every 3 min at 30°C, with 30-ms exposure for green channel and 50 ms for red channel. For reversibility experiments, only one image was acquired for each time point. For light control experiments, PCB was added to cells 2 h before imaging with a final concentration of 27 μM (stock, 5.4 mM in dimethyl sulfoxide). PCB was purified according to Toettcher et al. (2011b) or purchased from ChemPep (Wellington, FL). Because room light activates the system, cells were kept in the dark once PCB was added.

For most experiments, fluorescence and phase microscopies were performed in the University of California, San Francisco (UCSF), Nikon Imaging Center using a TE2000U inverted microscope (Nikon, Melville, NY) with Yokogawa CSU22 spinning-disk confocal illumination (Solamere Technology Group, Salt Lake City, UT) and a Cascade II CCD Camera (Photometrics, Tucson, AX). Images were acquired using Micromanager software (http://micromanager.org/) and analyzed using ImageJ (National Institutes of Health, Bethesda, MD) with the SpotTracker2D plug-in (http://bigwww.epfl.ch/sage/soft/spottracker/gasser.html). Potential toxicity of PCB and fluorescence illumination was evaluated in control experiments (Supplemental Figure S1).

Titration and spatial control experiments were performed on a Nikon Eclipse Ti inverted microscope using a 100× PlanApo total internal reflection fluorescence, 1.49 numerical aperture objective, a xenon arc-lamp (Sutter Instrument, Novato, CA), and an Evolve electron-multiplying charge-coupled device camera (Photometrics). For these experiments, the microscope, dichroic positions, filters, shutters, and camera were controlled using the open-source Micromanager software package with additional custom Matlab code (Toettcher et al., 2011a). Epifluorescence images were computationally denoised in collaboration with John Sedat (UCSF), using an algorithm built into the Priism image analysis package (Kervrann and Boulanger, 2006).

For fully activating and inactivating light control experiments, we used one 650- and one 750-nm light-emitting diode (LED Lightspeed Technologies, Campbell, CA), which are directly attached on the microscope condenser. For the titration and spatial control experiments, we used one 650-nm LED and two 750-nm LEDs (Lightspeed Technologies). Light intensity was controlled by changing the applied voltage (0–5 V). Voltage was controlled using custom Matlab code by connecting the LEDs to the analogue outputs of a DT9812 board (Data Translation, Marlboro, MA). For spatial control, user-defined patterns of LED light were projected on the sample using a custom dual-input digital micromirror device (DMD Andor, Belfast, United Kingdom). Pixels on this device can be in two states, ON or OFF ON pixels are illuminated with both 650- and 750-nm light, and OFF pixels are illuminated by the second 750-nm light source with a constant voltage. Sample exposure to DMD light was controlled using a 620-nm short-pass filter (Chroma Technology, Brattleboro, VT). In addition, we used a 625-nm sputtered short-pass emission filter (Chroma) to block DMD light from reaching the camera during imaging, allowing us to keep the 620-nm short-pass filter in place (and thus continue exposing the sample to 650- and 750-nm light) while images were collected.

Image analyses

Image segmentation and fluorescence quantification were performed using custom Matlab software and ImageJ with Image5D plug-in. Maximum-intensity projections of z-stacks were reported for most experiments, except for plasma membrane images. For the plasma membrane, the middle plane was used.

For assaying the concentration increase/decrease measurements as the system is turned ON and OFF (Figure 5, C and D), PhyB library strains were mixed wild-type cells that do not contain fluorescence labeling. Nonfluorescent cells were used to subtract cell autofluorescence, and the anchor images were used to define the desired position. Average fluorescence intensity per pixel was used to calculate the decrease/increase. Typically, 50–100 cells were used for each anchor strain.


The health of a cell requires proper functioning, regulation, and quality control of its organelles, the membrane-enclosed compartments inside the cell that carry out its essential biochemical tasks. Aging commonly perturbs organelle homeostasis, causing problems to cellular health that can spur the initiation and progression of degenerative diseases and related pathologies. Here, we discuss emerging evidence indicating that age-related defects in organelle homeostasis stem in part from dysfunction of the autophagy-lysosome system, a pivotal player in cellular quality control and damage clearance. We also highlight natural examples from biology where enhanced activity of the autophagy-lysosome system might be harnessed to erase age-related organelle damage, raising potential implications for cellular rejuvenation.

In eukaryotic cells, molecular waste and damaged materials can be delivered to lysosomes for enzymatic degradation via autophagy [1]. During this process, autophagic vesicles, termed autophagosomes, form around select cargo, then subsequently fuse with the lysosome to allow for targeted degradation. Though autophagosomes were first observed by electron microscopy in the mid-1950s [2], it was not until nearly 40 years later that the first autophagy genes were identified in yeast [3–5]. Since then, breakthroughs in live-cell imaging have enabled sophisticated, real-time imaging of the autophagic process in several eukaryotic species, including animals [6,7]. In addition, an expanding pharmacological toolkit of molecules that modify autophagic activity in vivo (Table 1) has facilitated manipulation of this system in live organisms and raised exciting therapeutic prospects.

A defining feature of the autophagy-lysosome system is its unique ability to recalibrate cellular homeostasis in response to a cell’s needs. If a cell is under intrinsic or extrinsic stress, activation of autophagy can help to erase molecular damage and to recycle material needed to support basic biological functions [1]. When these mechanisms fail, the stress can amplify, leading to an irreparable collapse in cellular homeostasis. Notably, aging is accompanied by several molecular signs of stress. As cells get older, genetic instability increases, proteins cluster into non-functional aggregates, and organelles, the cellular mini-factories that execute distinct signaling and metabolic functions, become damaged and inefficient [8]. Is this age-related collapse in cellular health and homeostasis linked to defects in autophagy?

Remarkably, researchers have found that an early-age decrease in lysosome and autophagic activity may be an initiating “domino” in age-related cellular deterioration [9,10]. Consistent with this model, modifying autophagic activity has profound effects on the aging process experimental inhibition of lysosomal and/or autophagic factors accelerates aging in various organisms [11–14], whereas interventions that boost autophagic activity delay the appearance of cellular signs of aging and extend lifespan [15–17]. Even human centenarians [18], like long-lived mutant animals [19], have been reported to display exceptionally high levels of autophagic activity. These and other findings highlight the autophagy-lysosome system as an emerging nexus in the control of aging and longevity (Figure 1). Still, molecular details of this regulation remain obscure.

Figure 1. Changes to autophagy of cellular organelles during the aging process. Lysosomes in young, healthy cells (on the left) are acidic and effectively degrade cellular waste, including organelles when necessary. This maintains robust homeostasis, which supports proper functioning not only of a cell but of a whole organism. However, in an old cell (on the right), lysosome dysfunction jeopardizes autophagic turnover, causing a build-up of damaged organelles along with protein aggregates this leads to several age-related disease pathologies and brings about changes to organismal physiology. Re-establishing the correct dynamics of organelle turnover at lysosomes in old cells might provide one entry point to trigger a rejuvenation of cellular health and homeostasis. AP, autophagosome.

For one, how is different autophagic cargo handled in aging cells, and do changes to cargo turnover directly contribute to the aging process? Many studies have investigated how defective autophagy impedes protein-aggregate clearance in old cells [20]. This is an important line of research, given that impaired protein homeostasis (‘proteostasis’) is characteristic of many age-related diseases, including Alzheimer’s [21]. Yet, defective organelles are also common to age-related diseases [22–24], and their turnover is likewise sensitive to lysosome dysfunction [1,25]. To date, surprisingly little is known about the dynamics and control of organelle turnover in aging cells. Clarifying the regulation of organelle-specific autophagy during aging could provide novel clues on the biological basis of age-related disease, and might also hint at therapies for fighting the aging process.

Perhaps the most information is currently known regarding the age-related regulation of mitochondria, the energetic hubs of a cell. With age, mitochondrial function and homeostasis break down. Several proteins involved in oxidative phosphorylation and fatty-acid metabolism, two key cellular processes that occur at mitochondria, have been reported to decrease in abundance in old animals [26–28]. These molecular alterations, combined with other age-induced changes to mitochondrial protein levels and stoichiometry [29], are thought to impair mitochondrial activity and destabilize cellular bioenergetics and metabolism. As a consequence of this dysfunction, fragmented, oxidatively-damaged mitochondria are commonly seen in old cells of diverse eukaryotic species, ranging from yeasts to mammals [8,9,30–32]. Though healthy cells can effectively eliminate dysfunctional mitochondrial fragments by mitochondrial autophagy, or ‘mitophagy’ [33], mitochondrial-clearance mechanisms show signs of failure in old age [34,35]. This disrupts the balance between mitochondrial biogenesis and degradation, causing an age-dependent increase in damaged mitochondria that further exacerbates cell stress [34]. Mitophagy defects can predispose humans to degenerative disease indeed, dysfunction of mitophagy factors, including Parkin and PINK1, is commonly seen in Parkinson’s disease patients [36,37]. Thus, impaired turnover of damaged organelles is at least partly to blame for some of the classic aging pathologies commonly seen in the clinic.

Importantly, impaired turnover with age does not appear to be limited to mitochondria. In cells, lysosomes are responsible for degrading additional types of organelles, including portions of the endoplasmic reticulum (ER), peroxisomes, and even other lysosomes. Like mitochondrial damage, ER stress accumulates in old cells [38]. Strikingly, genetic inhibition of ER-phagy causes progeric phenotypes and shortened lifespan in mice [39], hinting that ER turnover might be required to slow the pace of aging. Additionally, peroxisomes and lysosomes have been reported to increase in abundance in late age in some species and cell types [40,41]. In fact, uncleared lysosomes generate a non-degradable, autofluorescent ‘age pigment’, which has been used as a visual readout for biological age in multiple systems [42–44]. It will be important to clarify how directly these age-related changes in organelle number reflect impairment of the autophagy-lysosome system, and whether these changes bring about physiological effects on metabolic functioning in old animals.

While the general trend is that organelle turnover appears to decline with advanced age due to autophagy-lysosome dysfunction (Figure 1), this may not be true of all organelles, or for all stages of the aging process. For example, pieces of the nucleus are degraded at lysosomes in aging worms, even in the healthiest of individuals [45]. How nuclear autophagy (‘nucleophagy’) regulates organismal physiology, particularly during aging, is unclear, but it may be protective, as suggested in mouse models of laminopathies [46]. It remains to be seen whether other organelles likewise undergo regulated, active turnover in aging animals. Some organelles may even be degraded in early aging but start to accumulate later once lysosomes become dysfunctional. Understanding the dynamics and timing of organelle turnover at different stages of aging could reveal complexities that affect aging rate and/or stochasticity among different individuals in a population.

If organelle damage is generally characteristic of very old age, could harnessing organelle-specific autophagy help an old cell to regain its vitality and youthfulness? Germ (reproductive) cells provide a unique opportunity to study cellular rejuvenation, because age is naturally reset across generations. We and others have shown that cellular damage, including defective mitochondria, can be rapidly reversed as oocytes prepare for fertilization [47,48]. Removal of dysfunctional molecules and organelles is also seen during gametogenesis in single-celled yeast [49]. These findings imply that damage-clearance mechanisms may function centrally to the biological mechanisms of transgenerational rejuvenation. In support of this interpretation, lysosomes are activated in maturing oocytes prior to fertilization [47], and, once active, they could conceivably clear various forms of cellular damage, including dysfunctional organelles, to reset cellular health and homeostasis across generations. Though the specific cargo received by oocyte lysosomes awaits full description, identification of natural mechanisms that renew organelle health in the immortal germ-cell lineage could point the way to new strategies to counteract organelle damage in old somatic cells.

Lysosome induction has been reported to also occur during stem-cell activation and differentiation [50–52]. In these contexts, as in oocyte maturation, lysosome activation is linked to a developmental rewiring of cellular metabolism. Though, again, much attention has been paid to the role of lysosome activity in stem-cell proteostasis, there is recent evidence that organelle-specific autophagy plays a fundamental role in stem-cell and regenerative biology [53–57]. For one, impaired mitophagy leads to muscle stem-cell quiescence in old mice, and re-establishing autophagic flux is sufficient for old muscle stem cells to exit quiescence and regain stemness [58]. Importantly, defective mitophagy appears to cause oxidative stress and stem-cell depletion in other cell types as well [59,60]. These findings hint that mitochondrial turnover might be a pivotal determinant of regenerative capacity.

Notably, mitophagy also appears important in the generation of induced pluripotent stem cells (iPSCs) [57,61]. A number of rejuvenating events, including telomere re-lengthening and organelle renewal, have been associated with iPSC generation from differentiated cells [62–64]. Inhibiting mitochondrial fission, one of the early steps in mitophagy induction [33,65], prevents the conversion of fibroblasts to iPSCs [61]. Thus, it is exciting to speculate that organelle-specific autophagy may be integrated with other rejuvenating events involved in iPSC reprogramming, and that enhancing these activities might provide an entry point to improve the efficiency of this process.

Beyond mitophagy, other forms of organelle-specific autophagy are only beginning to be studied in the context of cellular regeneration and rejuvenation. Interestingly, elevated ER stress has been linked to iPSC death [66], and significant ER remodeling occurs as part of iPSC reprogramming [67]. In principle, ER quality control mechanisms, including ER-phagy, could aid regenerative capacity, particularly in old animals where persistent ER stress abounds [38]. As a compelling corollary, the ER has been shown to undergo dramatic rearrangements coincident with oocyte maturation and lysosome activation in the C. elegans germline [68]. How the ER and lysosomes are functionally and/or mechanically linked to support cellular rejuvenation is an important open question moving forward, as is the involvement of other organelle-turnover events in cellular-rejuvenation mechanisms.

In summary, dynamic changes to the landscape of the cell occur during aging, and several of these age-related changes can be traced to alterations in organelle homeostasis and turnover (Figure 1). Harnessing the natural rejuvenating capacities of the autophagy-lysosome system provides one possible means to reverse age-related organelle damage and re-establish a more youthful cellular environment (Figure 1). In fact, pharmacological tools that boost lysosome function (Table 1) are currently being tested as potential anti-aging therapies in old animals and humans [69,70]. Looking forward, it seems likely that growing knowledge on the mechanistic principles that govern organelle turnover at lysosomes, and the specific parts of these systems that fail with old age, will open new doors for aging-biology researchers in the quest to promote healthy aging, particularly at a cellular level.


Structure of Cell Nucleus

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The cell nucleus consists of a nuclear membrane (nuclear envelope), nucleoplasm, nucleolus and chromosomes. Nucleoplasm, also known as karyoplasm, is the matrix present inside the nucleus. Let’s discuss in brief about the several parts of a cell nucleus.

Nuclear Membrane

The nuclear membrane is a double-layered structure that encloses the contents of the nucleus. The outer layer of the membrane is connected to the endoplasmic reticulum. A fluid-filled space or perinuclear space is present between the two layers of a nuclear membrane.

The nucleus communicates with the remaining of the cell or the cytoplasm through several openings called nuclear pores. Such nuclear pores are the sites for exchange of large molecules (proteins and RNA) between the nucleus and cytoplasm.

Chromosomes

Chromosomes are present in the form of strings of DNA and histones (protein molecules) called chromatin. The chromatin is further classified into heterochromatin and euchromatin based on the functions. The former type is a highly condensed, transcriptionally inactive form, mostly present adjacent to the nuclear membrane. On the other hand, euchromatin is a delicate, less condensed organization of chromatin, which is found abundantly in a transcribing cell.

Nucleolus

The nucleolus (plural nucleoli) is a dense, spherical-shaped structure present inside the nucleus. Some of the eukaryotic organisms have nucleus that contains up to four nucleoli. The nucleolus plays an indirect role in protein synthesis by producing ribosomes. These ribosomes are cell organelles made up of RNA and proteins they are transported to the cytoplasm, which are then attached to the endoplasmic reticulum.

Ribosomes are the protein-producing organelles of a cell. Nucleolus disappears when a cell undergoes division and is reformed after the completion of cell division.


What Are the Three Organelles Involved in Protein Synthesis?

There are four organelles that are involved in protein synthesis. These include the nucleus, ribosomes, the rough endoplasmic reticulum and the Golgi apparatus, or the Golgi complex. All four work together to synthesize, package and process proteins.

Protein synthesis begins with DNA. The DNA in an organism creates the RNA that then codes for and synthesizes the proteins. DNA is found in the cell’s nucleus and makes the RNA in the nucleus as well. The RNA then exits the nucleus and is translated by the cell’s organelles into amino acids. These small subunits are then put together in the ribosomes that are attached to the membrane of the rough endoplasmic reticulum. Then, the proteins exit the ribosomes and exit the rough endoplasmic reticulum to enter the Golgi apparatus. The Golgi apparatus packages the proteins and sends them out of the cell.


Cell Fractionation [back to top]

This means separating different parts and organelles of a cell, so that they can be studied in detail. All the processes of cell metabolism (such as respiration or photosynthesis) have been studied in this way. The most common method of fractionating cells is to use differential centrifugation:

1. Cut tissue (e.g. liver, heart, leaf, etc) in ice-cold isotonic buffer. Cold to stop enzyme reactions, isotonic to stop osmosis, and buffer to stop pH changes.

2. Grind tissue in a blender to break open cells.

3. Filter. This removes insoluble tissue (e.g. fat, connective tissue, plant cell walls, etc). This filtrate is not called a cell-free extract, and is capable of carrying out most of the normal cell reactions.

4. Centrifuge filtrate at low speed

5. Centrifuge supernatant at medium speed

6. Centrifuge supernatant at high speed

7. Centrifuge supernatant at very high speed

8. Supernatant is now organelle-free cytoplasm

A more sophisticated separation can be performed by density gradient centrifugation. In this, the cell-free extract is centrifuged in a dense solution (such as sucrose or caesium chloride). The fractions don't pellet, but instead separate out into layers with the densest fractions near the bottom of the tube. The desired layer can then be pipetted off. This is the technique used in the Meselson-Stahl experiment (module 2) and it is also used to separate the two types of ribosomes. The terms 70S and 80S refer to their positions in a density gradient


Watch the video: 11. Η Αντιγραφή του DNA. Δράση DNA πολυμεράσης 1 2ο κεφ. - Βιολογία Γ λυκείου. (January 2022).