Basic components of living systems (microscopy, cell structure) Flashcards
How does a compound light microscope work?
A light microscope has two lenses:
• The objective lens - this produces a magnified image
• The eyepiece lens - the magnified image created by the objective lens is magnified by the lens
‣ This configuration allows for much higher magnification and reduced chromatic aberration (blurriness) than an average light microscope
‣ Illumination is usually provided by a light underneath the sample
What ways can you prepare a sample slide?
- Dry mount = specimen viewed whole or cut into thin slices (sectioning), e.g. hair, pollen, dust, insect parts
- Wet mount = specimen suspended in a liquid (e.g. water, immersion oil), and the cover slip is placed on from an angle, e.g. aquatic samples
- Squash slides = wet mount prepared first, then a lens tissue is used to press down the cover slip, e.g. good for soft samples like root tips
- Smear slides = edge of the slide is used to smear the sample and covered with a cover slip, e.g. blood samples
What is the cytosol of a cell and other cell structures?
Cytosol is the aqueous interior and is often transparent
What is gram stain technique?
- This is used to separate bacteria into two different groups: gram-positive and gram-negative. Crystal violet is applied to a bacteria specimen, then iodine, which fixes the dye. The slide the specimen is on is washed with alcohol. If the bacteria is gram-positive, it will retain the dye, appearing blue/purple
‣ A counterstain (safranin dye) is used, making the gram-negative bacteria appear red
‣ Gram-positive bacteria are susceptible to penicillin, inhibiting the formation of cell walls. Gram-negative bacteria have thinner cell walls which aren’t susceptible to penicillin
What is acid-fast technique?
- This is used to differentiate species of mycobacterium from other bacteria
- A lipid solvent carries carbolfuchsin dye onto the cells being studied
- The cells are then washed with a dilute acid-alcohol solution
- Mycobacterium are not affected by the acid-alcohol solution and retain the carbolfuchsin dye, which is bright red
- Other bacteria lose the stain and are exposed to a methylene blue stain
Which stages do pre-prepared slides go through in production?
- Fixing - chemicals like formaldehyde are used to preserve specimens in a near-natural state as possible
- Sectioning - specimens are dehydrated with alcohols and then placed in a mould with wax or resin to form a hard block. This can be sliced thinly with a knife called a microtome
- Staining - specimens are often treated with multiple stains to show different structures
- Mounting - the specimens are then secured to a microscope slide and a cover slip placed on top
What rules do you have to follow to produce a good scientific drawing?
- Include a title
- State magnification
- Use a sharp pencil for drawings and labels
- Use white, unlined paper
- Use as much of the paper as possible for the drawing
- Draw smooth, continuous lines
- Do not shade
- Draw clearly defined structures
- Ensure proportions are correct
- Label lines should not cross and should not have arrow heads
- Label lines should be parallel to the top of the page and drawn with a ruler
What is magnification?
Magnification is how many times larger an image is than the actual size of the object being viewed
What is resolution?
- Resolution is the ability to see individual objects as separate entities
- The resolution of a microscope determines the amount of detail that can be seen - the higher the resolution the more details are visible
- Its limited by the diffraction on light as it passes through samples (and lenses)
- Resolution can be increased by suing beams of electrons which have a wavelength thousands times shorter than light - reduces diffraction, meaning structures can be seen separately with minimal blurriness
How would you calculate magnification?
Magnification = size of image/actual size of object
‣ In a formula triangle, size of image goes at the top
What is a graticule eyepiece?
This piece of equipment (a glass disc) is used to calibrate microscopes. Its marked with a fine scale of 1-100
What is a stage micrometer?
- A microscope slide with a very fine accurate scale in micrometers (μm) engraved on it
- The scale marked on the micrometer slide is usually 100 divisions = 1mm, so 1 division = 10μm
How would you calibrate a lens?
e.g. x4 objective lens
• Put the stage micrometer in place and the eyepiece graticule in the eyepiece
• Get the scale on the micrometer slide in clear focus
• Align the micrometer scale with the scale in the eyepiece. Take a reading from the two scales, then use this information to calculate the calibration factor for the x4 objective lens
What is electron microscopy? What kind of image is produced?
- In electron microscopy, a beam of electrons with a wavelength of less than 1nm is used to illuminate the specimen
- More detail of cell ultrastructure can be seen because electrons have a much smaller wavelength than light waves
- They can produce magnifications of up to x500,000 and still have clear resolution
Advantages and disadvantages to electron microscopy?
- Expensive to buy and operate
- Large and needs to be installed
- Complex sample preparation
- Sample preparation often distorts material
- Vacuum is required
- Black and white images produced (but can be coloured digitally)
- Over x500,000 magnification
- Low resolving powers
- Specimens are dead
What is an artefact?
Structures that are produced due to the preparation process, e.g. air bubbles
What are the two different types of electron microscopes?
- Transmission electron microscope (TEM) - a beam of electrons is transmitted through a specimen and focused to produce an image. This has a resolving power of 0.5nm
- Scanning electron microscope (SEM) - a beam of electrons is sent across the surface of a specimen and the reflected electrons are collected. This has a resolving power of 3-10nm and can produce 3D images
Advantages and disadvantages to light microscopy?
- Inexpensive to buy and operate
- Small and portable
- Simple sample preparation
- Sample preparation does not usually lead to distortion
- Vacuum is not required
- Natural colour pf sample is seen (or stains are used)
- Up to 2000x magnification
- Resolving power is 200nm - this is much higher compared to electron microscopes
- Specimens can be viewed living or dead
What is laser scanning confocal microscopy?
- A laser scanning confocal microscope moves a single spot of focuses light across a specimen (point illumination). It uses a laser to get higher intensities, improving illumination
- This causes fluorescence from the components labelled with a ‘dye’
- The emitted light from the specimen is filtered through a pinhole aperture
- Only light radiated from very close to the focal plane (the distance that gives the sharpest focus) is detected
- Produces a 2D image, however a 3D image could also be produced by creating images at different focal planes
- Currently used in science in the diagnosis of diseases of the eye and is being developed for use in endoscopic procedures
How can fluorescent tags be used?
- By using antibodies with fluorescent tags, specific features can be targeted and therefore studied by confocal microscopy with much more precision than when using staining and light microscopy
- The dye is sourced from jellyfish (𝘈𝘦𝘲𝘶𝘰𝘳𝘦𝘢 𝘷𝘪𝘤𝘵𝘰𝘳𝘪𝘢): green fluorescent protein (GTP) - this emits a bright green light when illuminated by ultraviolet light
What are prokaryotes?
Prokaryotes are single-celled organisms with a simple structure of just a single undivided internal area called the cytoplasm (composed of cytosol, which is made up of water, salts and organic molecules)
What are eukaryotes?
- Eukaryotic cells make up multicellular organisms like animals, plants and fungi
- They have a much more complicated internal structure, containing a membrane-bound nucleus (nucleoplasm) and cytoplasm, which contains many membrane-bound cellular components
What is metabolism?
Metabolism is a term that is used to describe all chemical reactions involved in maintaining the living state of the cells and the organism. Metabolism can be conveniently divided into two categories:
• Catabolism - the breakdown of molecules to obtain energy
• Anabolism - the synthesis (building up) of all compounds needed by the cells
Function of membranes
They’re selectively permeable and control the movement of substances into and out of the cell and organelles
Name all features/components found in eukaryotes (12)
- Cell-surface membrane/plasma membrane
- Cytoplasm (cytosol)
- Vesicle/secretory vesicle
- Ribosome
- Centriole
- Rough endoplasmic reticulum (RER)
- Smooth endoplasmic reticulum (SER)
- Cytoskeleton (microfilaments, microtubules and intermediate fibres)
- Mitochondria
- Nucleolus
- Nucleus (nuclear envelope, nuclear pores)
- Golgi apparatus
Function of the nucleus (DNA)
- The nucleus contains coded genetic information in the form of DNA molecules, which direct the synthesis of proteins required by the cell, meaning the DNA controls the metabolic activities of the cells
- DNA is contained within a double membrane called the nuclear envelope. This contains pores that allow molecules to move into and out of the nucleus
- DNA is too big to leave (to the site of protein synthesis in the cytoplasm) via the pores and so is transcribed into smaller RNA molecules
- DNA associates with proteins called histones to form a complex called chromatin, which coils and condenses to form chromosomes
Function of the nucleolus
- This is an area within the nucleus and is responsible for producing ribosomes
- It is composed of proteins and RNA
Function of mitochondria
- Mitochondria are the site of cellular respiration, where the energy is stored in the bonds of complex, organic molecules and is made available for the cell to use by the production of the molecule ATP
- More active cells will contain more mitochondria than less active cells
- They have a double membrane. The inner membrane is highly folded to form structures called cristae and the fluid interior is called the matrix. The membrane containing the cristae contains the enzymes used in aerobic respiration
- Mitochondria contain a small amount of their own DNA - mitochondrial DNA or (mt)DNA - and can produce their own enzymes and reproduce themselves
Function of vesicles
- These are membranous sacs that have storage and transport roles
- They consist of a single membrane with fluid inside
- They are used to transport materials inside the cell
- e.g. lysosomes - contain hydrolytic enzymes and are responsible for breaking down waste material in cells, including old organelles (play a role in the immune system, as they break down pathogens ingested by phagocytic cells)
What is apoptosis?
Programmed cell death
What is the cytoskeleton?
- A network of fibres necessary for the shape and stability of a cell (and also mechanical strength)
- Organelles are held in place by the cytoskeleton and it controls cell movement and the movement of organelles within cell
Components of the cytoskeleton
- Microfilaments - contractile fibres formed from the protein actin, responsible for cell movement and cell contraction during cytokinesis
- Microtubules - globular tubulin proteins polymerise to form tubes that are used to form a scaffold-like structure that determines the shape of the cell
- Intermediate fibres - these fibres give mechanical strength to cells and help maintain their integrity
What are centrioles?
- These are a component of the cytoskeleton (present in most eukaryotic cells with the exception of flowering plants and most fungi)
- Composed of microtubules
- Two associated centrioles form the centrosome, which is involved in the assembly and organisation of the spindle fibres during cell division
- In organisms with flagella and cilia, centrioles are thought to play a role in the positioning of these structures
What are flagella and cilia?
- Whip-like and hair-like respectively, these are extension that protrude from some cell types, with flagella being longer than cilia, but cilia being in greater number
- Flagella are used mainly for movement, but can be used as a sensory organelle, detecting chemical changes in the cell’s environment
- Cilia can be either mobile or stationary. If mobile, they beat in a rhythmic fashion, creating a current which causes fluids or objects next to the cell to move (e.g. keeps air passageways clean). If stationary, they have an important function in sensory organs (e.g. the nose)
- Have a 9+2 arrangement
What is secretion?
Transport out of the cell
What is the endoplasmic reticulum?
- A network of membranes enclosing flattened sacs called cisternae. It is connected to the outer membrane of the nucleus
What is the smooth endoplasmic reticulum?
A type of endoplasmic reticulum that is responsible for lipid and carbohydrate synthesis, and storage
What is rough endoplasmic reticulum?
- A type of endoplasmic reticulum that has ribosomes bound to the surface and is responsible for the synthesis and transport of proteins
- Secretory cells, which release more hormones or enzymes, have more RER than cells that do not release proteins
What are ribosomes?
- These are constructed of RNA molecules made in the nucleolus of the cell and are the site of protein synthesis
- They can be free-floating in the cytoplasm or attached to endoplasmic reticulum, forming RER
- They aren’t surrounded by a membrane
- Mitochondria and chloroplasts also contain ribosomes, as do prokaryotic cells
- Eukaryotic ribosomes are designated 80S
- Involved in the formation of more complex proteins (in eukaryotes)
What is the Golgi apparatus?
- Its role is to modify proteins and ‘package’ them into vesicles. These may be secretory vesicles, if the proteins are destined to leave the cell, or lysosomes, which stay in the cell
- It is a compact structure formed of cisternae (similar in structure to smooth ER) and does not contain ribosomes
Steps of protein production
- Proteins are synthesised on the ribosomes bound to the endoplasmic reticulum
- They then pass into its cisternae and are packaged into transport vesicles
- Vesicles containing the newly synthesised proteins move towards the Golgi apparatus via the transport function of the cytoskeleton
- The vesicles fuse with the cis face of the Golgi apparatus and the proteins enter. The proteins are structurally modified before leaving the Golgi apparatus in vesicles from its trans face
- Secretory vesicles carry proteins that are to be released from the cell. The vesicles move towards and fuse with the cell-surface membrane, releasing their contents by exocytosis. Some vesicles form lysosomes - these contain enzymes for use in the cell
What features does a plant cell have?
- Cell wall
- Cell-surface membrane/plasma membrane
- Chloroplasts
- Cytoplasm
- Vacuole (containing cell sap)
- Nucleus
What are plant cell walls made out of? What is its function?
- Cellulose, a complex carbohydrate
- They are freely permeable, so substances needed in the cell can pass into the cell (endocytosis) through the cell wall and excreted out of it (exocytosis)
- It provides shape
- The contents of the cell press against it, making it rigid, which helps give structure
- It can also act as a defence mechanism in protecting the contents of the cell to invading pathogens
What are vacuoles?
- Exclusive to plants (if they appear in animals, they are small and not permanent), these are membrane-lined sacs in the cytoplasm containing cell sap
- They are important in the maintenance of turgor, so that the contents of the cell push against the cell wall, making it rigid
- Its membrane is called a tonoplast and is selectively permeable
What are chloroplasts?
- These are the organelles responsible for photosynthesis in plant cells
- They contain a pigment called chlorophyll
- Found in the green parts of a plant, so the leaves and stems
- They have a double membrane (similar to mitochondria in animal cells)
- The fluid enclosed in chloroplasts is called the stroma
- They have an internal network of membranes, which form flattened sacs called thylakoids. Several of these are arranged in a stack - this is called a granum (plural - grana). Grana are joined by membranes called lamellae and contain chlorophyll, where the light-dependent reactions occur during photosynthesis
- Starch produced by photosynthesis is present as starch grains
- Similar to mitochondria, they also contain their own DNA and ribosomes, and are therefore allowed to make their own proteins
When did prokaryotes first appear (extremophiles)?
- Around 3.5 billion years ago, when the surface of the Earth was a very hostile environment
- Scientists believe that these early cells were adapted to living in extremes of salinity, pH and temperature
- These extremophiles still exist today, for example, they can be found in hydrothermal vents and salt lakes
- They are usually in the domain Archaea
What is DNA like in prokaryotes?
- Fundamentally the same as in eukaryotes, however is packaged differently, as they generally only have one molecule of DNA (a chromosome), which is supercoiled to make it compact
- The genes on the chromosome are often grouped into operons, meaning a number of genes are switched on or off at the same time
What are ribosomes like in prokaryotes?
- They’re much smaller than the ones in eukaryotes, and their relative size is determine by the rate at which they settle, or form in sediment, or solution
- Prokaryotic ribosomes are designated 70S
- Necessary for protein synthesis
What are prokaryotic cell walls made of?
Peptidoglycan, also known as murein, is a complex polymer formed from amino acids and sugars
What are flagella like in prokaryotes?
- In prokaryotes, flagella are much thinner and do not follow the 9+2 arrangement
- The energy to rotate the filament that forms the flagellum is supplied from the process of chemiosmosis, not from ATP as in eukaryotic cells
- Its attached to the cell membrane of a bacterium by the basal body and rotated by molecular motor
‣ The basal body attaches the filament comprising the flagellum to the cell-surface membrane of the bacterium. A molecular motor causes the hook to rotate giving the filament a whip like movement, which propels the cell
When did the first eukaryotic cells appear?
About 1.5 billion years ago
How is DNA in eukaryotic cells stored?
- The DNA is present within the nucleus and exists as multiple chromosomes, which are supercoiled, and each one wraps around a number of proteins called histones, forming a complex for efficient packaging
- This complex is called chromatin, which coils and condenses to form chromosomes
Which kingdoms have organisms composed of eukaryotic cells?
Plant, animal, fungi and protoctista
‣ Many are multicellular
Do prokaryotes have circular or linear DNA?
Circular
Do eukaryotes have circular or linear DNA?
Linear
What is the name of the extra chromosomal DNA in prokaryotes?
Circular DNA called plasmids
What are fungi cell walls made of?
Chitin
How do prokaryotes reproduce?
By binary fission
How do eukaryotes reproduce?
By asexual or sexual reproduction
