Chapter 2 Basic components of living systems Flashcards
Unit conversions
M –> MM –> um –> Nm. ×1000 for each forwards arrow
Magnification formula =
Image size/ actual size
Important points
- careful with units - need to be the same to cancel out
- try to avoid cm - stick to M, mm, um, nm
- choose appropriate decimal places/ significant figures
Scale bars
- length of scale bar measured = image size of scale bar
- Actual size = written
Magnification definition?
The number of times bigger an image is than the actual size of an object
Resolution definition
- the level of detail in an image
- the smallest distance 2 points can be apart, and still be resolved as separate points
Light microscope: max resolution & magnification
Max resolution: 200nm
Max Magnification: ×1500
Electron microscope: max mag & resol
Maz resolution is 0.5nm
Max mag is 500,000 - 3,000,000
What limits resolution?
Wavelength of energy used:
- Light energy: 400nm wavelength (average)
- Electron beam = 1nm
What is the defraction limit?
Resolution = 0.5 × wavelength
Uses of stains in microscopy?
- to increase contrast of an image
- making specific parts of the cell stand out
Fluorescent stains
- Commonly used with confocal microscopy, often combined with antibodies
- antibodies bind with specific molecules in the cell and stains emit light
Differential staining?
The use of 2 OR MORE STAINS AT ONCE
- Useful to identify cell types e.g Gram staining identifies 2 different types of bacteria - Gram positive + Gram negative
Prokaryotic
Pro - before
Prokaryotic - before nucleus
Eu-karyotic
True nucleus
Eukaryotic organisms are in these kingdoms:
Animalia
Plantae
Fungi
Protoctista
ALL in domain EUKARYA
Prokaryotic kingdom
Prokaryotae
2 domains:
- bacteria, archae
What is naked DNA
No histone
How can genetic material transfer across bacteria
The pilus (1 is pili)
What shape are bacterial chromosomes
Circular
Invagination definition
Infolding of membrane to increase SA
The human eye can distinguish objects about ??? apart
The human eye can distingush objects about 0.1mm apart - about the size of a human egg cell
Light microscopes how they work
- light is sent from a light source through a specimen, the image of which is magnified by glass lenses
Advantages of light microscopes
- cheap
- easy to use
- used to study living cells
Disadvantages of light microscopes
Light microscopes use visible light to create an image -> so resolution is limited to 200nm and magnification to ×2000
Laser scanning microscopes
- use a high power beam of light to create an image
- the laser passes over each single point ij the specimen and CREATES AN IMAGE over time
- 3D image
- more expensive than light microscopes have a high resolution
Electron microscopes
- Instead of beam of light like in traditional microscopes, electron microscopes use a beam of electrons to study specimens
Why are electron microscopes higher resolution?
Electrons have a higher wavelength and so can be used to create higher resolution images (micrographs)
What is a micrograph
A micrograph is a digital image taken through a microscope to show a magnified image of an object
2 types of em: SEM &TEM
- in both types a beam of electrons is focused by a magnet towards a specimen
- specimens must also be stained or coated with a metal and placed in a vaccum
- this preparation means electron microscopy can only be used to study dead specimens
SEM
- The electron beam hits the specimen and is scattered into a detector
- this means the microscope image can be 3D because the different orientations where electrons land are scattering in various directions
- 3d but low magnification and resolution
TEM
The electron beam travels through the specimen to a detector below
This allows for a higher resolution and magnification than SEM but a 2D image
SEM Vs TEM
Electron beam ✅
3D 〰️ 2D
MAX MAG - 200,000 〰️ 2,000,000
Max resolution- 20nm 〰️ 0.1nm
sample preparation - dry mount
solid specimens are viewed whole or cut into very thin pieces with a sharp blade - this is called sectioning
- the sample is then placed on the centre of the slide, and cover slip placed over
sample preparation -wet mount
specimens are suspended in a liquid such as water or an immersion oil. A cover slip is placed on from an angle
sample prep - squash slides
wet mount 1st prepared, then lense tissue is used to gently press down the cover slip. depending on the material, potential damage to a cover slip may be avoided by squashing the sample between 2 microscope slides
- good tech for soft samples
sample prep for smear slides
the edge of a slide is used to smear the sample, creating a thin even coating on another slide
-e.g used for blood sample
what is the cytosol?
aqueous interior of cells
differential staining can?
distinguish between 2 types of organisms that would otherwise be hard to identify
gram stain technique is used to?
seperate bacteria into 2 groups - Gram-positive and Gramnegative bacteria
acid fast technique is used for?
to differentiate species of Mycobacterium from other bacteria
4 stages of slide production?
- Fixing
- Sectioning
- Staining
- Mounting
what is fixing (stage 1)
- chemicals like formaldehyde are used to preserve specimens in as near natural state as poss
what is sectioning (stage 2)
- specimens are dehydrated with alcohols and then placed in a mould with wax or resin to form a hard block. This can then be sliced thinly with a knife called a MICROTOME
what is staining (stage 3)
- Specimens are often treated with multiple stains to show difv structures
what is mounting (stage 4)
- the specimens are then secured to a microscope slide and a cover slip placed on top
stains- risk management
many of the stains used in the preperation of slides are toxic or irritant. A risk assessment must be carried out before any practical work is started
magnification definition?
it’s how many times larger the image is than the actual size of the object being viewed
what allows the user to adjust the mag?
interchangeable objective lenses on a compound light microscope
resolution definition?
the ability to see individual objects as seperate entities
diffraction definition?
is the tendency of light waves to spread as they pass close to physical structures such as those present in the specimens being studied
why can detail be lost?
the structures present in the specimens are very close to each other and the light reflected from individual structures can overlap due to diffraction.
- this means the structures are no longer seen as separate entities and detail is lost
resolution can be increased by…
using beams of electrons which have a wavelength thousands of times shorter than light. Electron beams are still diffracted but the shorter wavelength means that the individual beams can be much closer before they overlap. so, smaller objects which are closer together can be seen separately without diffraction blurring the image
MAGNIFICATION EQUATION?
Image size/ Actual size
note: need to be same units
why does every lense and every microscope have to be calibrated individually?
the true mag of the diff lenses of a microscope can vary slightly from teh stated mag, so every microscope and lesne has to be calibrated individually using eyepiece graticule and a slide micrometer
electron microscopes -?
- very expensive
- can only be used inside a carefully controlled environment in a dedicated space
- specimens can be damaged by the electron beam and bc the preperation process is very complex, there is a problem with artefacts
why is the inside of an electron microscope a vaccum?
to ensure that the electron beams travel in a straight line
which microscope requires dead samples?
electron, light can use both living and dead samples
colour images ?
for light, natural colour of sample is seen (or stains are used), electron black and white images are produced (but can be coloured digitally)
light mi are small and portable, but electron mi are _____ and ___ __ ____________
large, need to be installed
light mi, sample prep does not usually lead to
distortion, but for electron - sample prep often distorts material
the human eye can distinguish objects about ______ apart
0.1mm
light microscope vs. laser scanning
- both light beam
- 2D vs 3D
- both x1500
- 200nm vs 160 nm
- both living
why don’t we always stain?
some structures naturally modify light as it passes thru
how stains work?
by collecting around paticular types of molecules
when is staining done?
when we want to see individual structures that we wouldnt normally be able to see
organelles and the production and secretion of protiens
- Proteins are synthesised on the ribsomes bound to the ER
- they then enter into the cisternae and are packaged into transport vesicles
- vesicles containing the newly synthesised protiens 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 the trans face
- secretory vesicles carry the proteins that are to be released from then cell. the vesicles move towards and fuse with the cell surafce membrane releasing their conetnts
- by exocytois, some vesicles form lysosomes- these contain enzymes for us in the cell
a microtubule is made of…
A tube of tubulin protein subunits
diameter: 25nm
function of the microtubule?
- form eukaryotic cilia and flagella (9 + 2 arrangement of microtubules)
- form tracks for the movement of vesicles
- form spindle fibres which cause the movement of chromosomes in cell divison
a microfilament is made of?
helical strands of ACTIN subunits
7nm diameter
function of microfilaments
- cause cell movement and changes in cell shape
- cytokenisis
- lengthen and shorten - TREADMILLING
an intemediate filament is made of?
many different types of protien (e.g. keratin) in a variety of deformable filaments
8-10 nm
intermediate filaments function?
form a scaffold inside the cell providing mechanical strength
what is a scale bar?
line representing a distance
length of scale bar measured?
image size of scale bar
actual size ?
written
what is a cell?
the basic unit of all living things
prokaryotes are…
single celled organisms with a simple structure of just a simple structure of just a single undivided internal area called cytoplasm
eukaryotes are…
they make up ulticellular organisms like animals, plants, fungi. they have a much more complicated internal structure contaning a membrane bound nucleus (nucleoplasm) and a cytoplasm - which contains many membrane bound cellular components
ultrastructure of eukaryotes - mitochondria
- production of molecule ATP
- site of final stages of cellular respiration
- double membrane
- inner membrane is highly folded into structures called cristae and fluid interior is called matrix
- membranes forming cristae contain enzymes used in resp
ultrastructure of eukaryotes - vesicles
- membranous sacs that have storage and transport roles
- consist of a single membrane with fluid inside
- used to transport materials inside the cell
ultrastructure of eukaryotes - lysosomes
- specialised forms of vesicles that contain hydrolytic enzymes
- responsible for breaking down waste materials, including old orgnelles
- break down pathogens ingested by phagocytic cells
- role in programmed cell death
ultrastructure of eukaryotes - flagella
- extension that protrudes from some cell types
- longer than cilia
- used to enable cell motility
- in some cells, are used as a sensory organelle detecting chemical changes in the cells environment
ultrastructure of eukaryotes - cilia
- extension that protrudes from some cell types
- can be mobile or stationary
- stationary cilia are present on the surface of many cells and have an important function in sensory organs
- mobile cilia beat in a rhythmic manner, creating a current and cause fluids/ objects adjacent to the cell to move
- each cilium contains 2 central microtubules surrounded by 9 pairs of microtubules arranged like a wheel
what causes ciilia to move in a beating motion?
pairs of parallel microtubules side over each other causing cilia to move in a beating motion
ultrastructure of eukaryotes - golgi apparatus ?
- similar structure to smooth ER
- compact structure formed of cisternae and does not contain ribosomes
- role in modifying proteins and ‘packaging’ them into vesicles
- these may be secretoty vesicles that are if protiens destined to leave cells, or lysomes which stayb
ultrastructure of eukaryotes - centrioles?
- component of the cytoskeleton
- present in most eukaryotic cells- exception of flowering plants and most fungi
- composed of microtubules
- 2 centrioles form the centrosome involved in the assembly and organisation of spindle fibres during cell division
ultrastructure of eukaryotes - cytoskeleton?
- present throughout cytoplasm of ALL eukaryotes
- network of fibres necessary for shape and stability of a cell
- holds organelles in place and controls cell movement and the movement of organelles within cells
- 3 components - microfilaments, microtubules, intermediate fibres
ultrastructure of eukaryotes - ribosomes?
- can be free floating in the cytoplasm or attached to the rough ER
- not surrounded by a membrane
- constructed of RNA molecules made in the nucleolus
- site of protein synthesis
ultrastructure of eukaryotes - microtubules?
- globular tubulin proteins polymerise to form tubes that re used to form a scaffold like structure that determines the shape of a cell
- they also act as tracks for the movement of organelles including vesicles, around the cell
- they compose spindle fibres which have a role in the physical segregation of chromosomes
ultrastructure of eukaryotes - membrane ?
- structures that separate contents of cells from their environment
- also separate diff areas within cells from each other and the cytosol
- some organelles are divided further by internal membranes
- all have same basic structure
ultrastructure of eukaryotes - Nucleus?
- contains coded genetic info in the form of DNA molecules
- DNA directs the synthesis of all proteins required by the cell
- the DNA controls the metabolic activities of the cell = many of the proteins = enzymes required for metabolism
ultrastructure of eukaryotes - nuclear pores?
DNA is too large to leave the nucleus to teh site of protein synthesis in cytoplasm so it is transcribed in smaller RNA molecules which are exported via nuclear pores
ultrastructure of eukaryotes - nuclear envelope?
- double membrane
- contains nucleus to protect it from damage in the cytoplasm
- contains nuclear pores that allow molecules that move in and out of the nucleus
ultrastructure of eukaryotes - SER ?
- The ER is a network of membranes enclosing a flattened sacs called cisternae. Connected to the outer membrane of nucleus
- responsible for lipid and carbohydrate synthesis and storage
- Cisternae more tubular then RER
ultrastructure of eukaryotes - the RER?
- has ribosomes bound to the surface and is responsible for the synthesis and transport of protiens
- secretory cells (release hormones/ enzymes) have more than cells that do not release proteins
- closest to nucleus
ultrastructure of eukaryotes - microfilaments ?
- contractile fibres formed from the protein acetin
- responsible for cell movement and contraction during cytokinesis
what is cytokinesis?
the process in which the cytoplasm of a single eukaryotic cell is divided to form 2 daughter cells
ultrastructure of eukaryotes - intermediate fibres?
they give mechanical strength to cells and help maintain their integrity
additional features of plant cells: cellulose cell wall?
- freely permeable so substances can pass in/out of cell
- plant cells are rigid structure- contents of cell press against cell wall making it rigid
- also acts as a defense mechanism protecting against pathogens
- all plants have
additional features of plant cells - chloroplasts?
- responsible for photosynthesis
- double membrane structure like mitochondria
- fluid enclosed in chloroplasts called stroma
- also contain DNA and ribosomes so can make own protein
- internal membranes provide the large SA needed for the enzymes, proteins, pigment molecules necessary for photosynthesis
additional features of plant cells- vacuoles?
- membrane lined sacs in cytoplasm containing cell sap
- maintenance of turgor
- acts as a temporary store of energy
what is a tonoplast?
membrane of a vacuole in a plant cell
what is an organelle?
component of a cell with a specific function
what is the nucleoplasm?
the cytoplasm inside the nucleus
the cytoplasm is an ….
aqueous solution
intermediate filaments?
are usually found surrounding the nucleus and hold it in place
- can also extend outside of the cell - allows cells to stick together and communicate with each other
microtubules ___ _______ around the cell using _____
moving organelles, motor protiens
endocytosis definition
uptake things into the cell
exocytosis definition
when substances are released out of the cell
what are centrioles?
bundles of microtubules that lie perpendicular to each other
centrioles and microtubules are also important for for the formation of ___ and ___
cilia and undulipodia
what is a undulipodia>?
a single long protrusion of microtubules
lysosomes are?
vesicles filled with digestive enzymes that are formed by the golgi
digesting materials outside of cells?
some cells secrete digestive enzymes from the lysosomes, such as cells in the stomach
the empirical formula for lipids?
CnH2n minus 2 O(^little 2)
can vesicles enter AND exit cells?
yes
apoptosis/ autolysis definition?
breaking down cells to kill them and recycle their contents
what is cisternae?
fluid filled cavities
like mitochondria, chloroplasts also contain?
smaller ribosomes than tehr est of the cell
amyloplasts ?
starch filled oraganelles (plants)
