Organelles

Question	Answer
What is phagocytosis?	The endocytosis of large particles, such as microorganisms or cellular debris, by phagosomes, which are ~>250nm in diameter. This mainly occurs in specialised phagocytic cells such as macrophages.
How do chloroplasts divide?	By binary fission, like bacteria - this supports the endobiotic theory of endocytosis of a photosynthetic bacterium into a eukaryotic cell.
Outline phagocytosis.	Phagocytic cells such as B lymphocytes, macrophages and neutrophils detect invading organisms using antibodies on their cell surface and this binding results in pseudopods being extended to engulf the bacterium and fuse at the ends to form a phagosome. This phagosome then fuses with a lysosome and the bacterium is digested.
Why is it important for the thylakoid membranes to be very fluid as a result of their high concentration of unsaturated fatty acids?	The photosystems are contained in the thylakoid membranes and these use cofactors which must be able to move between the photosystems as they exist separately - photosystem II is located in the granal stacks of thylakoids while photosystem I is found in the lumen of the unstacked/stromal thylakoid regions.
Why do thylakoid membranes adhere to form granal stacks?	Because photosystem II is found here and has a high tendency to donate electrons, resulting in forces that cause the membranes to adhere and form stacks.
What is pinocytosis generally carried out by?	Clathrin-coated pits and vesicles of the plasma membrane.
What is chlorophyll?	A pigment consisting of a flat, porphyrin ring, similar to that in haemoglobin, with alternating double and single bonds which allow it to absorb blue (~400nm) and red (~700nm) wavelengths and reflect green light. Mg2+ is the central ion and the hydrocarbon tail dissolves easily in lipids which allows chlorophyll to embed in membranes.
Name a more efficient process than pinocytosis and outline why it is more efficient.	Receptor-mediated endocytosis is more efficient than pinocytosis because it specifically binds to macromolecules in the extracellular matrix and endocytoses them, resulting in a higher concentration of substrate with a lower overall intake of extracellular fluid.
Name 3 substances endocytosed by a receptor-mediated mechanism.	LDL-cholesterol complexes, iron, and vitamin B12.
What is an endosome?	Late endosomes (aggregates of early endosomes) consist of a complex set of connected membrane tubes and larger vesicles. The endosome compartment is kept acidic by an ATP-driven H+ pump in the endosomal membrane which serves to dissociate the receptors from their substrates, along with the small number of lysosomal enzymes present. Endosomes are the site of the beginning of macromolecular digestion.
What are lysosomes?	Membranous sacs of hydrolytic enzymes that carry out the controlled intracellular digestion of both extracellular materials and senescent organelles. They contain ~40 types of hydrolytic enzymes including proteases, lipases and those that degrade nucleic acids and oligosaccharides. The enzymes act optimally at ~pH5 so their damage is limited if they escape into the more neutral cytosol.
How do lysosomal proteins avoid digestion by proteases?	They are highly glycosylated to avoid contact between the protein and the enzyme.
What is autophagy?	The process in which autophagosomes form around senescent organelles, or those that the cell uses for energy during starvation, and these bind to lysosomes so that digestive enzymes can break them down into their components.
List some processes that mitochrondria are involved in.	Metabolism, production of ATP, control of apoptosis, Ca2+ movements (as energy required) and the production of heat in endotherms.
Why can mitochrondria synthesis their own proteins?	Because they contain their own DNA, RNA and ribosomes.
Describe the structure of a mitochondrion.	Mitochondria consist of an outer membrane and an inner membrane folded into convolutions called cristae. The matrix (specialised cytosol) inside the inner membrane contains ribosomes, granules, ATP synthase particles and more. Mitochondria are ~1.5um in length, a similar size and shape to bacteria.
Why is the composition of the intramembranous space of the mitochondria similar to the cytosol?	Because the outer membrane contains porins, channels which are permeable to all molecules of 5000 Daltons or less, including small proteins.
What is the inner mitochondrial membrane impermeable to?	The passage of ions and small molecules, except by means of membrane transport proteins - this makes it highly specialised.
Where does electron transport and proton pumping occur?	The inner mitochondrial membrane, which has a large concentration of ATP synthase as a result, as well as other proteins required for oxidative phosphorylation.
Where are high concentrations of mitochondria found?	In skeletal and cardiac muscle cells, wrapped around muscle fibres, in sperm flagellae, and in kidney and liver cells.
What stain can be used to differentiate mitochondria?	Altman's Acid Fuchsin stain colours mitochondria, nucleoli and erythrocytes red - this is slightly difficult to differentiate (so can be compared with a contrasting slide) but mitochondria cannot be differentiated without a stain as they are too small.
Can the nucleus be resolved by light microscopy? Which is the best stain to use in a metaphase spread?	The nucleus is a prominent organelle, ~10um in diameter, and can be resolved using light microscopy. Hoechst staining is best for identifying DNA in metaphase spreads as it stains DNA a bright blue.
What is heterochromatin?	Tightly packed chromatin, located peripherally within the nucleolus in the nucleoplasm, which is less expressed as a result of its conformation.
What is euchromatin?	Less tightly packed chromatin, located centrally within the nucleolus in the nucleoplasm, and actively expressed due to its conformation.
What is chromatin?	Chromatin is the collective term for nuclear DNA bound to histones and nonhistone chromosomal proteins. This may also be referred to as the epigenome.
Why is the nucleolus extremely electron dense?	Because it is packed with proteins and nucleic acids.
What is the perinuclear space?	The space between the inner and outer nuclear membranes that is continuous with the lumen of the endoplasmic reticulum.
What sized molecules can passively diffuse through nuclear pore complexes?	Small molecules, <50 kDa (1 Dalton = weight of 1 H molecule).
What signals for a molecule (e.g. mRNAs, RNA polymerase etc) to be removed from or retained in the nucleus?	A nuclear localisation signal or 'tag', a series of amino acids that interacts with nuclear pore complex to facilitate transport in molecules that should be able to leave the nucleus. This is not present in molecules which should be retained.
What is a chromosome territory?	Even when not in a formation such as lining up during cell division, chromosomes exist in regular locations in the nucleus as uncondensed chromatin.
What is a lampbrush chromosome?	A giant DNA complex with mRNA 'synthesising off' it like villi. These occur in amphibian eggs so that rapid protein synthesis and development can occur to avoid predators after birth.
What are lamin proteins?	Structural proteins on the inside of the nuclear membrane.
What are the 3 components of the nucleus, named after their staining density in electron microscopy?	A lightly staining granular component, a fibrillar component and a densely staining fibrillar component. All 3 are involved in RNA processing.
What is the main function of the nucleolus?	The nucleolus forms around rRNA genes and so rRNA transcription and processing is its main function. The granular component of the nucleolus is the main site of rRNA processing.
What are casal bodies?	Coiled bodies mainly composed of the protein coilin which are the sites of factors involved in rRNA biogenesis and pre-mRNA processing, amongst other functions.
What are ribosomes?	Macromolecular complexes of rRNA and proteins that mediate the process of mRNA translation.
What determines how often a protein is translated and demonstrates how active a gene is?	The efficiency of the recruitment of ribosomal subunits to a sequence of mRNA for translation.
In Svedberg units, what size is a prokaryotic ribosome and what sizes are its subunits?	The whole ribosome is 70S, and its large and small subunits are 50S and 30S respectively.
What are Svedberg units and why can't they be added together?	Svedberg units refer to the relative rate of sedimentation of a molecule in centrifugation, which is affected by its shape as well as its mass, and these cannot be added together because they are relative.
What size, in Svedberg units, are eukaryotic ribosomes and their subunits?	Eukaryotic ribosomes are 80S in total, and their large and small subunits are 60S and 40S respectively.
List some conformations that RNA may be visible as.	Single stranded, double stranded, bulges and stem loops.
How can one break a ribosome down into its subunits?	Add EDTA to the suspension to remove the Mg2+ ions which help RNA to form its secondary structure.
In which cells is there a regulated exocytosis pathway?	Cells that are specialised for secretion.
What are chloroplasts?	Organelles present in photosynthetic organisms which contain light capturing pigments such as chlorophyll and enzymes and cofactors for photosynthesis, which are present in the thylakoid membrane systems.
Why does exocytosis not increase the size of the plasma membrane and deplete organelle membranes?	Because it occurs in equilibrium with endocytosis.
How does the trans Golgi network differentiate between secretory and constitutive proteins?	The trans Golgi network has an acidic pH and a high concentration of Ca2+ ions in its lumen which causes secretory proteins to aggregate, but not constitutive proteins. These aggregated proteins are then pinched off into secretory vesicles which have a higher concentration than vesicles of constitutive proteins and which wait for an extracellular signal before fusing with the plasma membrane.
Give examples of what may be secreted from secretory vesicles.	Hormones such as insulin, mucus, or digestive enzymes such as pepsin.
How big are chloroplasts?	~10um in diameter. Always larger than mitochondria.
Give examples of extracellular signals that may cause vesicles to fuse with the plasma membrane and release their contents into the cell exterior.	Low blood sugar, hormone-receptor interaction, sympathetic nervous stimulation.
What is continuous exocytosis significant in?	Sections of proteins to the plasma membrane, extracellular matrix and beyond, and plasma membrane growth before cell division.
What are the 3 membrane systems of the chloroplast?	The outer, inner and thylakoid membranes.
What is endocytosis?	Cellular internalisation of fluid along with large and small molecules.
What happens to endocytic material?	It is delivered by endosomes to lysosomes where it is digested and the metabolites produced are transferred into the cytosol where they can be used.
What is pinocytosis?	The endocytosis of fluid and molecules by vesicles less than 150nm in diameter. This occurs in all eukaryotic cells.
Where does the formation of disulphide bonds occur and why are they important?	Oxidation of cysteine side chains to form disulphide bonds occurs in the endoplasmic reticulum. Disulphide bonds stabilise the protein for interaction with pH and enzymes outside of the cell, and it could not happen in the reducing environment of the cytosol.
Glycosylation occurs in the ER lumen by enzymes not present in the cytostol. List some functions of the covalent attachment of short oligosaccharides to proteins.	Protecting the protein from degradation, acting as a transport signal to guide a protein to the appropriate organelle, or in cell recognition.
What is the basic process of glycosylation before the modification of the oligosaccharides in the ER and Golgi bodies to diversify them?	The pre-formed, branched oligosaccharide of 14 sugars is originally attached to a dolichol lipid in the ER membrane. As the polypeptide undergoes translocation into the ER lumen, oligosaccharide protein transferase recognises a short sequence near asparagine on the polypeptide chain and attaches the oligosaccharide on to an NH2 group of an asparagine side chain in one enzymatic step.
What are chaperone proteins?	Chaperone proteins retain misfolded proteins or multimeric proteins in which other chains are missing, until enzymes re-fold or attach chains in order to produce a functioning protein. If they are not, they are degraded. Consequently, they are involved in quality control.
What is the unfolded protein response and how may apoptosis occur?	The unfolded protein response is a vast transcriptional protein program which produces more endoplasmic reticulum as a result of the accumulation of misfolded proteins when the system of ER and chaperone proteins is overwhelmed by vigorous protein synthesis. If even this cannot restore proper protein folding and processing and stop misfolded proteins from accumulating, the unfolded protein response can direct the cell to undergo apoptosis.
What is the Golgi apparatus and where is it located?	The Golgi apparatus is a collection of ~3-20 flattened membrane-enclosed sacs (cisternae) piled like stacks of plates. It is located near the nucleus and, in animal cells, often near the centrosome. Each stack has a cis, or entry, face adjacent to the endoplasmic reticulum and a trans, or exit, face pointing towards the plasma membrane.
How do soluble proteins and membrane travel through the Golgi cisternae?	By transport vesicles that bud from one cisternae to the next.
How are proteins/membrane segments modified in the correct sequence?	The enzymes that modify the proteins/membrane segments are present in the Golgi cisternae in the correct order of their activity from the cis to trans direction to ensure this.
Which two protein components are involved in guiding the ER signal sequence to the ER membrane, and how does this work?	A signal recognition particle (SRP) present in the cytosol and its receptor on the membrane of the ER are involved. The SRP binds to the signal sequence when it is exposed on the ribosome, and this initially slows down protein synthesis until the polypeptide has reached the ER membrane. Once the polypeptide has reached the ER membrane, the SRP joins with its receptor and is discarded and recycled. Polypeptide synthesis is resumed through a translocation channel and into the ER lumen.
Which terminus is the signal sequence usually located at?	The N-(amino) terminus of the polypeptide.
What are the two functions of a signal sequence?	To direct the polypeptide to the endoplasmic reticulum and to bind to a complementary area of the translocation channel and cause it to open.
What causes the translocation of a polypeptide across the endoplasmic reticulum membrane to stop?	A signal peptidase cleaves off the signal sequence at some stage during translocation and the signal sequence is rapidly degraded. Transmembrane proteins do not fully enter the lumen but water-soluble proteins are signalled to have fully entered the lumen by their C-terminus.
How does a simple transmembrane protein stop translocation fully through the ER membrane?	It contains a stop transfer sequence further into the polypeptide sequence after the N-terminus. This drifts laterally out of the translocation channel and becomes embedded in the membrane, forming an alpha-helix. The closing of the translocation channel signals the signal peptidase to cleave the N-terminus.
What are the two major vesicular transport pathways between membrane-enclosed compartments?	A major outward secretory pathway, in which polypeptide synthesis begins on the ER membrane, they enter the ER which leads through the Golgi apparatus to the cell membrane or to lysosomes, and a major inward endocytic pathway, responsible for ingestion and degradation of extracellular molecules through endosomes to lysosomes.
Why are there different types of transport vesicle?	To ensure that the appropriate proteins are carried to the appropriate destination, to ensure that the destination is not confused with another organelle, and to ensure that the organelle maintains its own identity based on its membrane proteins (because of budding and fusing). It maintains specialisation.
What are cargo receptors and coat proteins?	Cargo receptors are transmembranous proteins on the membranes of structures of the secretory or endocytic pathways, for example the Golgi apparatus. They recognise transport signals on secretory molecules and bind to them. The extramembranous part of the cargo protein has an adaptin coat protein attached to it and a clathrin (or another coat protein) attaches to the adaptin/cargo protein complex and begins to form a pit that buds off. As the pit enlarges, a small GTP-binding molecule called dynamin constricts the neck of the deeply invaginated pit and separates the vesicle.
What are Rab proteins?	A protein family that exist on the surface of vesicles to identify its origin and cargo to the appropriate destination.
How does docking of a vesicle occur?	A tethering protein on the surface of a target will recognise Rab proteins on a vesicle and these will interact. After this interaction, vesicular snare proteins and complementary target snare proteins will interact more intimately and dock the vesicle.
How does fusion of a vesicle to a target occur?	After pairing, the vesicular and target snare proteins wrap around each other and act like a winch that draws the two membranes into close proximity. A fusion complex is formed at the fusion site and consists of specialised proteins which lower the energy barrier involved in displacing the water of the cytosol between the two membranes - the membranes must be within 1.5nm of each other so that their lipids can intermix and their membranes fuse. Fusion adds the vesicle membrane to the organelle membrane as well as delivering the contents of the vesicle into the interior of the organelle.
In eukaryotic cells, what is the endoplasmic reticulum continuous with?	The outer nuclear membrane.
What is the function of the rough endoplasmic reticulum?	Protein and membrane synthesis.
What is the function of the smooth endoplasmic reticulum?	The smooth endoplasmic reticulum is scantily present in most eukaryotic cells and possesses no ribosomes so does not perform protein synthesis. Its functions vary from generalised lipid synthesis to specialised steroid hormone synthesis in the adrenal gland cells.
What is the function of the Golgi apparatus?	The Golgi apparatus receives proteins and lipids from the rough and smooth endoplasmic reticulum and modifies them (e.g. adds sugars to form glycolipids), before packaging them into vesicles for dispatch to other destinations in or out of the cell.
What governs transport in a cell?	Transport is guided by the cytoskeleton. Motor proteins use energy from ATP hydrolysis to propel organelles and vesicles along the filaments.
Which proteins are not synthesised by cytoplasmic ribosomes?	Several mitochondrial or chloroplast proteins that are synthesised by the organellar ribosomes.
What do the cytosolic and membrane-bound ribosomes each tend to synthesise?	Free/cytosolic ribosomes tend to be involved in the synthesis of proteins for the nucleus, mitochondria, chloroplasts and peroxisomes. Membrane-bound ribosomes, such as those in the endoplasmic reticulum, tend to be involved in the synthesis of proteins for plasma membranes, secretory vesicles and endosomes.
What is a sorting signal?	An amino acid sequence on a protein which directs it to the organelle by which it is required. This is often, but not always, removed from the finished protein once it has been sorted.
In which structures do proteins usually unfold, rather than remaining globular, in order to pass through?	The translocators of the endoplasmic reticulum, mitochondria and chloroplasts. Nuclear pores allow the protein to just move through without changing its conformation.
What are the two types of protein transferred from the cytosol to the endoplasmic reticulum?	Water-soluble proteins, which are destined either for secretion by exocytosis or for the lumen of an organelle, and prospective transmembrane proteins, which are only partially translocated across the ER membrane and may remain there or be destined for another organelle or the plasma membrane.
What is the need for the separate rough region of the endoplasmic reticulum?	The proteins synthesised by the rough endoplasmic reticulum, primarily those which will be incorporated into the plasma membrane, begin to be threaded across the ER membrane before the polypeptide chain has been fully synthesised so the ribosomes must be attached to the ER for continued synthesis.

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