A2.

2 Cell structure
1. Cells - basic structural unit of all living organisms
Whether living organisms were composed of
An endlessly divisible fluid
Indivisible subunits
-> invention of the microscope -> organisms are made of cells
Cell : smallest unit of self-sustaining life
Unicellular organisms : only have one cell
Multicellular organisms : have more than one cell
2. Microscopy skills
Skill 1 : making temporary mounts
1. Put the cells / tissue onto a microscope slide in a drop of water
2. Lower a cover slip onto the sample carefully
To avoid creating air bubbles
3. Ensure there's only a thin sample on the slide
By squeezing out any excess fluid
Skill 2 : staining
Colourless / white structures in cells - very hard to see unless stained
Stain : pigment that binds to specific chemicals
Ex. Methylene blue binds to DNA -> useful for revealing nuclei in cells
Usually added to cells / tissues on the microscope slide, before the cover slip is added
Skill 3 : measuring sizes using and eyepiece graticule
Graticule : graduated scale that is placed inside the eyepiece of a microscope
Used like a ruler
-> measure lengths of structures seen with the microscope
Must be calibrated for each objective lens
-> eyepiece units converted into micrometres
Example
Cell diameter of 12 graticule units
Calibration :
1 graticule unit = 1.5 µ
m

Actual diameter = 12 x 1.5 µ = 18 µ

m m

Skill 4 : focusing with course and fine adjustments

Focusing knobs : change distance bw specimen & objective lens -> focus
1. Start with the specimen & lens as far as possible
2. While looking down the microscope
Use coarse focusing knob to move the specimen
 Use objective lens closer together until the specimen comes into focus
3. The fine focusing knob
Used to get the sharpest possible focus
Used to focus on a particular level in the specimen
Skill 5 : taking photographs
Microscopes used for research usually have an inbuilt camera that can take
photomicrographs of images
High quality photos can be taken with any microscope
Hold camera lens of a smartphone close to eyepiece
Maybe necessary to adjust brightness of lighting & the focus to produce best possible
photo
Skill 6 : calculating actual size and magnification
Magnification =
Calculating the magnification of an image (drawing / diagram / photomicrograph)
1. Choose an obvious length (ex. max diameter of a cell) -> measur it in the image
2. Measure same length on the actual specimen
3. If different units used for two measurements -> convert (1 mm = 1 000 µ )
m

4. Calc magnification using the equation ( length on image

)
Example
length on actual specimen

Thickness of the leaf in the electron micrograph = 32 mm = 32 000 µ

m

Actual thickness of the leaf = 80 µ

m

Magnification of micrograph = 32 000 ÷ 80 = 400

Calculating the actual size of a specimen
1. Rearrange the equation
Actual size =
size of image

2. Calc actual size

magnif ication

Example
Diameter of a nucleus in a drawing = 12 mm
Magnification of the drawing = 1 000
×

Actual diameter of nucleus = 12 ÷ 1 000 = 0.012 mm = 12 µ m

Skill 7 : adding a scale bar

Scale bars : allow sizes of structures in images to be deduced
1. Rearrange the equation
Size of image = actual size magnification
×

Length of scale bar = length it indicates magnification

×

2. Decide what length of scale bar is appropriate (e.g. 10 µ ) m

3. magnification to obtain the length of scale bar

×

÷ 1 000 to convert µ to
m mm

3. Microscopy developments
17th century
Microscopes first invented
 Led to the discovery of cells
19th century
Improved light microscopes
Discovery of bacteria, chromosomes, mitosis, meiosis, gametes & fertilization
Many developments in microscopy have since been made
1. Fluorescent stains & immunofluorescence
Fluorescence : absorbance of light & re-emission at a longer wavelength
Fluorescent stains : used in microscopy for over 100 yrs
Fluorescence microscopes : have been developed with intense single wavelength light
sources
Such as high-power LEDs or lasers
Light re-emitted by stained sample -> generate bright images
Immunofluorescence : development of fluorescent staining
1. Antibodies (that bind to a specific chemical in the cell) are produced
2. A fluorescence marker linked to antibodies
3. Images produced of cells treated with antibodies
4. Show cell structure overlain with bright colour of the fluorescent marker
Where the specific chemical occurs in the cell
Multicoloured fluorescent images can be produced, using multiple types of antibodies
with fluorescent markers of different colours
2. Electron microscopes
Magnification with microscope - until a point beyond which the image can no longer be
↑

focused sharply
Resolution of the microscope exceeded
Resolution : the ability of a microscope to show two close objs separately in the image
Better resolution -> higher magnification -> more smaller structures can be seen than light
microscopes
Allow scientists to investigate detailed cell structures (ultrastructure)
Microscope Resolution Magnification
Light 0.25 µ m 500 ×

Electron 0.25 nm 500 000

×

3. Freeze-fracture electron microscopy

Used to produce images of surfaces within cells
1. A sample plunged into liquefied propane at -190˚C -> rapidly freezes
2. A steel blade used to fracture frozen sample
3. The fracture goes through the weakest points of the cells
The weakest point usually the middle of membranes - bw two layers of phospholipid
Freeze-fracture process gives unique image of this part
4. A vapour of platinum / carbon fired onto the fracture surface
 At an angle of about 35˚ -> form coating
5. This creates replica of the fracture surface
6. The replica removed from the frozen sample
7. Examined using an electron microscope
It's 2 nm thick on avg
But thickness varies because of the angle the coating is applied
Gives the impression of a 3D image with shadowing
4. Cryogenic electron microscopy
Used for researching structure of proteins
1. A thin layer of a protein solution applied to a grid
2. Flash-frozen with liquid ethane at -183˚C
To create smooth vitreous ice
To prevent formation of water crystals
3. The grid placed in an electron microscope
4. Detectors record patterns of electrons transmitted by individual protein molecules
5. Computer algorithms used to produce 3D image of the protein molecules
6. Cryo-EM can give resolutions of 0.12 nm -> so individual atoms in a protein can be located
Analyses proteins at the instant in time when the water around them froze
-> allows scientists to research proteins that change from one form to another, as
they carry out their function
4. Cellular structures found in all living organisms
All typical cells have
DNA as genetic material
Needed for producing mRNA by transcripiton -> proteins can be synthesized
**Cytoplasm composed mainly from water
Contains enzymes (catalyse many chemical reactions)
Plasma membrane composed of lipids
controls the movement of substances in / out of the cell
Allows different chemical conditions to be maintained inside the cell from those
outside
Such as pH
5. Structure of prokaryote cells
Ex. Bacteria
No nucleus
DNA in the cytoplasm
Usually a single chromosome, circular & naked
Not associated with proteins
Cell bounded by both cell wall & plasma membrane
Principal component of cell wall = peptidoglycan
 Cytoplasm has a high protein content
Mostly enzymes
-> appear dark in electron micrographs
<-> usually paler in cytoplasm region holding DNA
Many ribosomes
70S (S = Svedberg measure how fast something sediments when centrifuged)
6. Structure of eukaryote cells
Usually a nucleus & many other organelles
Organelle : discrete structure adapted to perform one or more vital function within a cell
Organelles classified - according to # of membranes
0 : 80S ribosomes, microtubules, microfilaments
1 : Rough ER, smooth ER, Golgi apparatus, lysosomes, vesicles, vacuoles
2 : Nucleus, mitochondria, chloroplasts
Membrane-bound organelles divide cytoplasm of eukaryotic cells into smaller compartment
<-> prokaryotic cells : the whole cell = single compartment
7. Life processes in unicellular organisms
Unicellular organisms : consist only one cell - carry out all functions of life
Ex. Amoeba
Metabolism
Produces enzymes
-> catalyse chemical reactions in the cytoplasm
Nutrition
Feeds on smaller organisms
engulfed by endocytosis -> digested in vesicles
Growth
Assimilating digested foods -> in size & dry mass
↑

Excretion
Metabolic waste products diffuse out of the cell
Ex. CO from respiration
Homeostasis
2

Regulates internal conditions

Ex. Expelling excess water using contractile vacuoles
Movement
Ameboid movement
From one side of the cell = draws cytoplasm
From another side = uses it to extend the cell
Response
Reacts to stimuli
Ex. Moving towards higher conc of peptides released by bacteria
 Reproduction
Asexually using mitosis
Sexually using meiosis & gametes
8. Comparing eukaryotic cell structure among animals,
fungi and plants
Cell walls
Tough layers outside plasma membrane
Main component
In plant - cellulose
In fungal - chitin
Animal cells - no cell walls
Allows to take in food by endocytosis
But vulnerable to burst if too much water enters by osmosis
Vacuoles
Single-membrane sacs of fluid in cytoplasm
Often a large permanent vacuole in cells of fungi & plants
Used for storage of substances
Used for pressurizing the cell
2 types of small temporary vacuole occur in some animal cells ( in plant, fungal cells)
×

Contractile vacuoles : expel excess water by exocytosis

Food vacuoles : digest food / pathogens taken in by endocytosis
Plastids
A family of double-membraned organelles
Plant cells have varied types
Chloroplasts (for photosynthesis)
Amyloplasts (to store starch)
× in animal, plant cells
Centrioles
Organelles composed of a 9 + 2 arrangement of microtubules
Used in animal cells
During mitosis & meiosis - organize assembly of a spindle of microtubules
Cilia & flagella
Whip-like structures
Inside : a 9 + 2 arrangement of microtubules
Outside : plasma membrane
Protrude from cell & generate movement by beating action
Some types of animal cell have many cilia
Small & move fluids adjacent to the cell
Male gametes (sperm) in animals have a single flagellum (tail)
Much longer than cilia
 Cause the sperm to move
Plant & fungus cells - cilia
×

Some plants (including ferns & mosses)

Have motile male gametes with a flagellum
<-> conifers, flowering plants & almost all fungi do not
Animals Fungi Plants
Cell wall x o o
Vacuoles small large large
Plastids x x o
Centrioles o x x
Cilia some x x
Flagella some some some

9. Atypical cell structure in eukaryotes

Some cells are anucleate (no nucleus)
Can't transcribe DNA to make mRNA
-> can't synthesize proteins
Red blood cells (in mammals)
No nucleus -> more space for haemoglobin
Without source of proteins for repair or other functions -> limited lifespan
4 months at most
Phloem sieve tube elements (in plants)
Subunits of the tubes that transport sugar-containing sap
Initially have a nucleus -> break down -> sap flow more easily
Supplied with proteins by adjacent companion cells
Which have a nucleus & rough ER
Some cells are multinucleate (many nuclei)
Can produce more mRNA
-> can produce more protein
Skeletal muscle
Made up of muscle fibres
Each fibre enclosed inside a plasma membrane like a cell
300 or more mm long (much larger) & contains hundreds of nuclei
Aseptate fungi
Consist of thread-like structures called hyphae
Hyphae not divided up (into subunits containing a single nucleus)
Long undivided sections of hypha
Contain many nuclei
10. Examining cells and their structures in light and electron
micrographs
1. Is a cell prokaryotic or eukaryotic?
If a cell is part of a multicellular tissue, must be form of eukaryote
Bc prokaryotes = unicellular / simple chains of cells
Prokaryotic cells
Nucleoid region visible in the cytoplasm
Cytoplasm without membrane-bound organelles
Eukaryotic cells
Nucleus (or chromosomes if the cell is dividing)
Mitochondria / other membrane-bound organelles
2. **Is it a plant or animal cell?
Differences in structure
Not all eukaryotes are plants / animals
Plant cells
Cell wall always present
Large permanent vacuole often present
Chloroplasts / other plastids present
Animal cells
Cell wall never present
Only small & temporary vacuoles
Cilia present in some animal cells
11. Creating drawings from electron micrographs
Sharp pencil, labelled structures, (+ annotate drawings with functions)
Boundaries of the cell
Plasma membrane - single unbroken line
If there's cell wall - double line (far thicker than cell membrane), hatching can be used to
indicate that the wall is solid
In a healthy plant cell / bacterium
Plasma membrane pushed up against the cell wall by turgor pressure
Animal cells
Don't have cell wall -> plasma membrane can change shape
With invagination & protrusions
Some have microvilli
Many finger-like protrusions -> SA for absorption
↑

Gene storage in cells

Nucleus of a eukaryotic cell
Has double membrane with pores in it
Unbroken pencil line - double back at the pores
Interior has distictive grainy appearance
 Much of it is lighter euchromatin, with patches of darker heterochromatin often
around the edge
Heterochromatin : parts of chromosomes - have remained condensed after
mitosis
During mitosis, chromosomes all become densely stained heterochromatin
-> nuclear membrane breaks down -> releasing chromosomes into cytoplasm
Nucleoid of a prokaryotic cell = region of less dense staining in the centre of the cell
**Single-membraned organelles
Large permanent sap vacuole of plant & fungus cells - appears white / very pale in
electron micrographs
Single membranes of vacuoles, vesicles, endoplasmic reticulum & Golgi apparatus - single
line
Golgi apparatus : stack of flattened membrane-bound sacs
Usually curved with vesicles at the ends
Endoplasmic reticulum : network of membrane-bound spaces
Smooth endoplasmic reticulum mostly tubular
Rough endoplasmic reticulum are lamellar (sheet-like)
Ribosomes appear as densely stained granules with a diameter 2~3 thick of a cell
×

membranes
Free ribosomes - float in the cytoplasm
Rough ER has ribosomes attached to its outer surface
Double-membraned organelles
Chloroplast
Is an extensive network of thylakoids inside
Thylakoids : single-membraned spaces
Most disc-shaped
Most arranged in stacks (grana)
Grains of starch & droplets of oil sometimes visible
Mitochondrion
Inner membrane of the mitochondrion infolded -> SA ↑

Appear darker than surrounding cytoplasm

Due to proteins in the fluid inside them (stain densely in electron micrographs)
12. AHL_Endosymbiosis
Evidence suggests that all eukaryotes
Evolved from a unicellular ancestor that had a nucleus
Reproduced both sexually (by meiosis & fertilization), and asexually (by mitosis)
Common ancestor respired anaerobically -> then ingested an aerobically respiring bacterium
Bacterium remained alive inside a vacuole in the cytoplasm
Giving the common ancestor a supply of ATP produced efficiently by aerobic respiration
Bacterium provided with food
Allowing it to grow & divide
 & passed on to daughter cells when the host cell divided
= endosymbiosis
Bc the organisms live together (symbiosis)
With one inside the other (endo)
= mutualistic relationship
Bc both benefit
-> relationship continued when the host cell divided
As long as both daughter cells contained at least one aerobic bacterium
Bacteria continue to grow, divide, pass on genes & evolve inside the host cells
Gradually over many generations, the relationship became so close
Neither the host cell nor the bacteria inside it could survive without the other
& the bacteria evolved into the mitochondria -> now occurring in all typical eukaryotic cells
Some eukaryotes also ingested photosynthetic bacteria
-> developed into the chloroplasts of plants and eukaryotic algae
Summary
1. Anaerobic eukaryote ancestor engulfs an anaerobic bacterium
2. Anaerobic eukaryote ancestor evolves into aerobic eukaryote with mitochondria
3. Aerobic eukaryote ancestor engulfs a photosynthetic bacterium
4. Heterotrophic aerobic ancestor evolves into a photosynthetic eukaryote
= endosymbiotic theory
Evidence = structure of mitochondria & chloroplasts
Have a loop of naked DNA, as in bacteria
DNA contains genes -> transcribed into RNA
Have 70S ribosomes & make some of their own proteins
Suggests they were once independent cells
Size of ribosome same as bacteria
Reproduce by splitting in two, as in bacteria
Double membraned
Expected if a bacterium with its own plasma membrane was ingested in a vacuole
formed by endocytosis
Originally would have been a bacterial cell wall bw two membranes
<-> no function -> lost by evolution
13. Cell differentiation
In a multicellular organism
By developing along different pathways
Despite all having the same genome
By differences in gene expression bw cells
Housekeeping genes = expressed in all living cells
As they're required for basic functions
Such as respiration
Other genes only expressed in some cells
 As they cause the development of specialized structures
Such as genes for synthesis of haemoglobin -> only expressed during
development of RBCs
Chemical signals in a cell's environment
Determine which genes are expressed -> how cell differentiates
A group of cells receive the same signal -> a tissue develops
-> develop same structure & carry out same function
Cells in a tissue interact with each other (except in blood)
-> use membrane proteins for cell-to-cell adhesion
-> maintain integrity of the tissue
Advantage
Form can match function more specifically
-> usually perform function better
14. Multiple evolutions of multicellularity
All plants & animals = multicellular
Multicellularity evolved independently
More than once in the origins of plants
& at least once in animals
Many fungi & eukaryotic algae = multicellular
Advantage
Longer lifespan
Bc death of one cell doesn't prevent continued survival of an individual
Larger body size
Useful in animals that are predators
Useful in plants that compete for light
Cell differentiation
Each cell carries out its function more effectively
More complex body forms can develop
NOS) Theories
The statement that living organisms are made of cells = ex of a theory
Features of theories in science Cell theory
- Theories are based on observed patterns / on - Robert Hooke & later microscopists observed
hypothesis that have been tested cells in all organisms that they examined
- Theories are general explanations that can be - According to cell theory, all organisms are
applied widely composed of cells
- Predictions can be generated from theories - Prediction : a newly discovered organism will
by deduction consist of one or more cells
Features of theories in science Cell theory
- When predictions are tested, a theory is - Cell theory has been repeatedly
either corroborated, or shown to be false and corroborated, through some atypical structures
so rejected have been found

NOS) Observations
Observers = scientists
Qualitative : a drawing of the structure of a cell
Quantitative : a measurement of the diameter of the cell
Instruments required (ex. microscope)