Chapter 3: A tour of the cell Flashcards
What is the difference between Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy (TEM)?
- SEM uses the application of a metallic layer onto a sample which deflects the electron beam onto the detector and is used to study the external cell surface.
-TEM passes the electron bean through a thin sample and can be used to study internal cell structure.
What are the most common reagents used for protein and lipid fixing in TEM?
Protein fixing: Glutaraldehyde
Lipid fixing: Osmium tetroxide
Why are heavy metals used for sample staining in TEM?
Heavy metals preferentially bind to specific molecules and increase the contrast of images by preventing electrons passing through due to their large size (causing darker areas)
What are the two most common reagents used for sample staining in TEM and what do these elements bind to?
- Uranium: Nucleic acids and proteins
-Lead: Lipids
What piece of equipment is used to cut ultrathin EM sections?
Ultramicrotome
What is the approximate thickness of a sample suitable for TEM?
How does this compare to the thickness on EM samples?
- approx. 70 nm thick
-Much smaller than the 5-50 µm samples used in EM.
What does the electron beam hit and what occurs to make the visible image in TEM?
The electron beam hits a fluorescent screen that emits visible light on impact.
Why is the interior of an electron microscope a vaccuum?
To prevent scattering of the electron beam on impact with air molecules.
What controls the direction of the electron beam in an electron microscope?
Magnets
What is Immunoelectron microscopy?
The use of immunolabelling to localise specific molecules to particular organelles using an electron microscope.
What is cell fractionation?
A technique using disruption and ultracentrifugation of a cell/s to separate its components
When cells are disrupted (i.e. before centrifugation) what is formed?
A cell homogenate
In centrifugation, what does the rate of settlement depend on?
- Particle size, shape and density
- Liquid density
- Rotational speed of centrifuge
What is the name for the particles that have collected together at the bottom of a tube during centrifugation?
A pellet
Describe the process of differential sedimentation.
Centrifugation taking place at increasingly higher speeds to separate particles according to their size and density. Each pellet is removed from the supernatant (remaining suspension) before the next speed increase.
Describe density gradient centrifugation
A cell lysate is laid upon a pre-prepared density gradient sucrose solution. Movement through the density gradient optimises separation into bands and can be removed as fractions with a pipette or pierced hole.
How does the nucleoid of a prokaryote appear under an electron microscope - light or dark?
Light
What shape does the DNA molecule form in a prokaryote?
Circular
What is the function of glycogen granules within prokaryotic cells?
Energy storage
What does a gram-negative bacteria have that a gram-positive bacteria does not?
Periplasmic space separating the inner and outer membrane
In bacteria, what is the cell wall composed of?
Peptidoglycan (polymer of sugars linked by amino acids)
What is the difference between gram-positive and gram-negative bacteria?
Gram positive
- thick layer of peptidoglycan at surface
Gran-negative
- Thinner layer of peptidoglycan within the periplasmic space (separates inner and outer membrane)
How can Gram stain be used to distinguish and how?
Gram stain can be used to distinguish between gram-positive and gram-negative bacteria.
Gram stain is absorbed and held by gram-positive bacteria’s thick peptidoglycan layer
Gram stain is not absorbed and held by gram-negative bacteria’s thin peptidoglycan layer
After staining the gram stain is dissolved to dissolve cell membranes and decolourise the cell. Gram positive bacteria will present as purple.
What do the capsules that some bacteria possess protect them from?
Desiccation and phagocytosis by other cells
What is the purpose of a bacterium’s cell wall?
- Support
-Shape
-Prevents expansion from water absorption
Peripheral proteins and Integral membrane proteins interact with what part of the phospholipid bilayer?
Peripheral proteins - hydrophilic heads
Integral membrane proteins - hydrophobic tails
Out of Plant, Animal, Protist, and Fungal cells - which have cell walls?
Plant cells DO
Fungal cells DO
Animal cells DO NOT
Protist cells SOMETIMES DO
What does the cell membrane of eukaryotic cells contain?
Phospholipid bilayer
Proteins and glycoproteins
Cholesterol
What types of proteins and glycoproteins are related to the cell surface and what are their functions?
Transporters and channels - selective movement of ions, nutrients, and other molecules across the membrane
Receptors - Responding to molecular changes in the extracellular environment
Recognition molecules - Promote adhesion between adjacent tissue cells
Intracellular proteins - Attached to cytoplasmic surface (includes cytoskeleton with structural roles)
What are the three protein assemblies that form the cytoskeleton of a eukaryotic cell and what are their constituents?
Microfilaments (actin filaments) - Actin
Intermediate filaments - Several different constituents
Microtubules - α and β Tubulin
What are the approximate diameters of Microfilaments, Microtubules, and intermediate filaments?
Microfilaments - 6 nm
Microtubules - 25 nm
Intermediate filaments - 8 - 10 nm
What is the structure of microfilaments?
Long helical chains of actin linked together in networks or bundles
What is the structure of microtubules?
Hollow tubes made up of (usually) 13 parallel filaments of tubulin assemblies
What is the structure of Intermediate filaments?
Rope-like structures of approximately 8 protofilaments wound around eachother
Where are each of the cytoskeleton filaments most prominent within a eukaryotic cell?
- Microfilaments | In the cell cortex, within microvilli, the leading edge of moving cells
- Microtubules | Radiating from the centrosome (itself near the nucleus)
- Intermediate filaments | All over (links to adjacent cells and extracellular membrane)
What is the function of microfilaments and how does their abilities facilitate this?
Their ability to quickly disassemble and reassemble makes it successful as a tool for cell motility.
What are the functions of microtubules?
- Cell shape maintenance
- Intracellular movement
- Reorganisation of chromosomes during cell division
- Role in distribution of organelles
- Components of cilia and flagella
Are microtubules stable or unstable? What can change this?
Extremely unstable.
Stabilised when it attaches to a membrane, organelle, or capping protein.
Intermediate filaments have what functions?
- Provide mechanical strength to cells and tissues (they are strong)
- Link adjacent cells and extracellular matrix
What occurs within the nucleus within a cell?
DNA replication
Transcription of DNA into RNA
Ribosomal assembly
What regulates the nuclear structure (Cell nucleus)?
What do the components link to?
Nuclear Lamina (network of a type of intermediate filament - lamins)
They link to the nuclear membrane and the chromatin
What are the components of the eukaryotic cell nucleus?
- Nuclear envelope
-Nuclear pores
- Nuclear pore complex (complex protein arrangements)
- Nucleolus
- Genetic material
What is the approximate size of nuclear pores and what do they allow?
Approx. 9 nm
Allow free movement of water molecules
What is DNA wound round?
Histones (proteins)
What is the difference between heterochromatin and euchromatin, where they are found within the nucleus, and how they appear on EM?
- Heterochromatin is tightly packed DNA, has fewer genes, more prominent near the nuclear envelope, and appears dark on EM.
-Euchromatin is loosely packed DNA, has more genes, found more central in the nucleus, appears pale on EM.
Why is some DNA packed more densely or loosely within a cellular nucleus?
As part of gene expression. Less densely packed DNA is able to be accessed by enzymes involved in transcription.
What occurs within the nucleolus? Describe the process.
- Ribosomal assembly
- Sections of chromosomes with required genes loop into the nucleolus and the ribosomal RNA molecules are transcribed from the DNA. They are then packed together with ribosomal proteins that are imported in from the cytosol to form the ribosomal sub units and overall ribosome.
What would a large or multiple nucleolus within a cell indicate?
That the cell’s function requires high levels of protein synthesis.
What are ribosomes?
rRNA and protein complexes that are responsible for protein synthesis from mRNA
Name the subunits of a eukaryotic ribosome.
Large subunit (60s) and small subunit (40s)
(80s)
What are the subunits of a prokaryotic subunit?
Large subunit (50s) and small subunit (30s)
(70s)
What are the components of a ribosome?
Protein complexes and rRNA
Where are ribosomes formed within a eukaryotic cell?
Within the nucleolus
What is a polysome/polyribosome?
A group of several ribosomes attached through their connection to an mRNA molecule.
What are the two types of ribosomes found within a cell?
-Free ribosomes: found within the cytosol
-Membrane-bound ribosomes: embedded in the membrane of the rough endoplasmic reticulum
What are the destined locations for proteins formed by free ribosomes?
-Cytosol
-Nucleus interior
-Mitochondria
-Chloroplasts
-Peroxisomes
What are the destined locations for proteins formed by membrane-bound ribosomes?
-Lysosomes
-Membranes
-Secreted
What is the signal sequence of a protein?
A short amino acid sequence that acts as an address, targeting the protein for transport to the correct location.
Most proteins will be sorted and targeted based on the intended location; when would you expect the proteins to just be released by the ribosome?
When they are proteins that will form the cytoskeleton.
What shapes/structures are seen formed by the endoplasmic reticulum?
Tubes and sacs
What is the function of the rough endoplasmic reticulum (RER)?
-Protein synthesis
-Protein folding
-Protein modification (N-type glycosylation)
-Protein packaging
What is the function of the smooth endoplasmic reticulum?
-Lipid synthesis (fatty acids, phospholipids, cholesterol)
-Detoxification/biotransformation (CY450 enzyme)
-Glucose 6-P metabolism
-Calcium storage
What is the main structural difference between the rough endoplasmic reticulum and the smooth endoplasmic reticulum?
The RER has membrane-bound ribosomes whilst the SER has none.
How are vesicles transported within a cell?
-Diffusion for short distances
-Motor proteins using the cytoskeleton for long distances
What is the function of the Golgi apparatus?
-Protein modification (N-type and O-type glycosylation; phosphorylation)
-Packaging of proteins and lipids for transport lysosomes, cell membrane, secretion
What are the two faces of the Golgi apparatus?
-Cis face which receives incoming vesicles
-Trans face which releases vesicles
Describe the structure of the Golgi apparatus
A stack of flat, smooth, slightly curved, membranous sacs (cisternae)
Where does the Golgi apparatus receive incoming vesicles from?
The endoplasmic reticulum
What is the difference between ‘constitutive secretion’ and ‘regulated secretion’?
Constitutive secretion - Small amounts constantly secreted
Regulated secretion - Secretion on demand of specific signals
Define ‘exocytosis’
The process of a vesicle fusing with the cell membrane to which it has been transported, and the subsequent release of material out of the cell
What are the functions of a lysosome?
- Digestion of large molecules brought into the cell through endocytosis
-Autophagy (has a role in cell growth, death, and infection)
What is contained within a lysosome?
Digestive enzymes
How does the pH of lysosomes compare to that of the cell’s cytosol?
How is this difference maintained?
The cytosol of a cell has a pH of 7.2
The inside of a lysosome has a more acidic environment with a pH of 5
Maintained by hydrogen pumps within the lysosomal membrane which pumps hydrogen ions inside the lysosome
How do lysosomes show on EM?
Pale/electron lucent
Where are lysosomal proteins synthesised?
The rough endoplasmic reticulum
How do peroxisomes present on EM?
Dark/electron-dense
Where are peroxisomal proteins synthesised?
Free/cytosolic ribosomes
Where are you more likely to find lysosomes - plant or animal cells?
Animal cells
-Common in animal cells, rare in plant cells
Describe the process of lysosomes digesting large molecules brought in to the cell through endocytosis.
The large molecules are brought in through endocytosis, forming membrane-bound endosomes which then can fuse with lysosomes, merging, and allowing the relevant digestive enzymes to reach the large molecules and subsequently break them down.
How do lysosomes carry out autophagy of an organelle?
First, a membrane will form around the old/damaged organelle which will then fuse with the lysosome, and the lysosomal enzymes will break down all parts.
What is the function of peroxisomes?
What is the byproduct of this and what happens to it?
Breakdown of fatty acids
This also forms hydrogen peroxide which can be broken down by the peroxisomes catalases into water and oxygen
What is larger, a peroxisome or a lysosome?
A lysosome is usually larger being 0.5-1.0 µm across whilst a peroxisome is 0.2 – 1.0 µm in diameter
Are peroxisomes electron-dense or electron-lucent when using electron microscopy?
Peroxisomes are electron dense and show up dark in EM
Where are peroxisomal proteins synthesised?
Cytosolic ribosomes
What is the term to describe the inside of a mitochondria (within the inner membrane)?
The mitochondrial matrix
What do mitochondria have that massively increases the membranous surface area?
Cristae
What is the average diameter and length of a mitochondria?
Diameter: 0.5 – 1.0 µm
Length: 2 - 8 µm
What organelle has the ability to divide, fuse, and move?
Mitochondria
What is the term to describe the space between the inner and outer membrane of a mitochondrion?
The intermembrane space
What is the function of the mitochondria?
ATP synthesis
Mitochondria contain their own DNA separate from the nuclear DNA. Where is this inherited from?
The mother of the individual.
Which organelle has its own ribosomes?
Mitochondria
What is the average diameter and length of a chloroplast?
Diameter: 2-4 µm
Length: 5-10 µm
What are the three membrane systems present in a chloroplast?
Outer membrane
Inner membrane
Lamellae
Desrcibe the structure of the lamellae of chloroplasts
Thylakoid membranes form flattened sacs (thylakoids) than contain the thylakoid lumen. The sacs are stacked into grana that are all linked by stroma lamellae which forms a continuous compartment.
The thylakoid membrane and stroma lamellae both contain embedded chlorophylls and other light-absorbing pigments.
What do chloroplasts contain their own of?
- DNA
-Ribosomes
What are the functions of chloroplasts?
-Photosynthesis
-Some protein synthesis
-Chemical reactions
What type of cells are vacuoles prominent in?
Plant cells
Do vacuoles have a higher or lower pH than the surrounding cell cytosol?
Vacuoles have a lower pH than the cytosol of a cell
What is the function of vacuoles?
- Storage of water, ions, and small organic molecules
- Structural support (shape, rigidity)
- Breakdown of large molecules (contains digestive enzymes)
What is the tonoplast and what is it’s function?
The Tonoplast is the membrane of the vacuole.
- Controls passage of molecules that cannot freely move across membrane with the use of specialist transporters
What molecules can freely move across the vacuolar membrane?
Water molecules
What is aptptosis?
Programmed cell death
How is the growth of new organelles connected to nuclear division?
It is not - they are independent.
Calcium regulation is carried out by which organelles and what is it’s importance?
- Endoplasmic reticulum
-Mitochondria
-Essential for cell signalling
What is the Extracellular matrix?
An organised network that is a hydrated mixture of glycosaminoglycans (GAGs) and proteoglycans, with embedded proteins (Especially fibrous ones).
What is the function of the extracellular matrix?
- Interaction between cells and extracellular fluid (information to cells)
-Cell properties
-Maintains tissue structure
-Cell behaviour
What is the name of the cells responsible for the majority of secretion of extracellular matrix components?
Fibroblasts
What are proteoglycans?
Heavily glycosated proteins composed of glycosaminoglycans (GAGs) and attached proteins.
What is the most abundant fibrous protein present in the extracellular matrix?
Collagen
What are integrins?
Receptors within cell membranes that link the extracellular matrix and the actin cytoskeleton of the cell.
Name the two types of anchoring junctions of cells and what do they do?
Desmosomes - Link adjacent cells
Hemidesmosomes - Link cell to extracellular matrix
What are tight junctions?
What are they essential for maintaning?
Junctions between cells that link them closely, forming a barrier that prevents the mocement of molecules and ions through the gaps between cells, and prevent movement of integral proteins of the cell membrane.
The polarity of a cell.
What are the functions of a gap junction and how do they carry this out?
Intracellular communication
Allows movement of moleciles and electrical signals between adjacent cells
What is an Adherens junction?
A type of cell junction that links adjacent cells by their actin skeletons via transmembrane proteins (cadherins) and intracellular proteins that link the cadherins to the cytoskeletons.
What do adherens junctions form in cells that form an epithelial sheet?
Belt like arrangements around them.
What are the cells of animal tissues held together by?
Extracellular matrix and cell junctions
