Drawing diagrams

p3 fig 1.3, fig 1.4

p4 fig 1.5
p10 fig 1.11, 1.12
p12 fig (1.14)
p14 1.17

Why cells?
Thought of as bag where chemistry life occurs
Partially separated from environment outside cell – thin membrane- (effective barrier) allows
controlled trafficking/ exchange of materials across -in both directions between cell and
environment -> partially permeable
if freely permeable life couldn’t exist -chemicals of cell mixing with surrounding chemicals by
diffusion

Cell biology (study of cell) and microscopy

2 different types of microscope used. Both use form of radiation to create image of specimen-

 Light microscope- light as radiation source

 Electron microscope- electrons
Cytology- examining with microscopes of prepared material
a generalised cell shows all the structures that are typically found in a cell.

Animal and plant cells have features in common

Cell surface membrane Surrounds each cell. Very thin. Also called
plasma membrane
Nucleus Large structure stains intensely – very
conspicuous (visible). Many cell contents are
colourless
Chromatin Inside nucleus. Deeply staining. Mass of
loosely coiled threads. Collects to form
separate chromosomes during nuclear
division. Contains DNA (deoxyribonucleic
acid) molecule with instructions that control
activity of cell
Nucleolus (Variable no. of nucleoli, 1-5 Loops of DNA from several chromosomes.
common in mammals) Deeply staining
Cytoplasm Aqueous/watery material (vary fluid to jelly
like) between nucleus and cell surface

Mitochondria (sing. Mitochondrion)
Golgi apparatus/body/complex
membrane. Small structures in it – small
organs (organelles– a 2functionally or
structurally distinct part of cell. Sometime
have own membrane to separate activity
and cytoplasm -compartmentalisation)
Carry out aerobic respiration. Most
numerously seen with light microscope. Can
move about, change shape and divide.
Part of complex internal sorting and
distribution system

Each organelle has own function- division of labour sharing of work between diff specialised
organelles

Differences between plant and animal cells

Plant Animal
Larger Often smaller (cell size varies largely)
Centriole- small structure (under light
microscope) close to nucleus
Outside c-s-membrane surrounded by Cell wall
giving cell definite shape. Rigid as contains fibres
of cellulose (a polysaccharide) strengthen the
wall- prevents burst when water enters by
osmosis- allows large pressure build. May have
extra cellulose or lignin (hard material) for extra
strength. Freely permeable- allow free movement
of molecules and ions through c-s-membrane.
Plant cells linked with cytoplasm strands -
plasmodesmata (sing. Plasmodesma). Pass
through pore-like structures in walls
Large permanent, central vacuole. Many function May have small ones which are
i.e. Help regulate osmotic properties of cell (flow temporary e.g. phagocytic vacuoles
of water in & out), pigment-colour flower
petals/veg parts e.g. red beetroot pigment. Etc.
Its membrane-tonoplast, controls exchange with
cytoplasm. Vacuole fluid is solution of: -
pigments, enzymes
sugars, mineral salts
organic compounds (e.g. some water products)
oxygen, CO2
Chloroplasts -found in green parts of plants
mainly leaves. Relatively large (easily seen with l-
microscope, & also tiny ‘grains’ inside) grana sing.
granum, parts of chloroplast containing
chlorophyll (green pigment absorbs light during
photosynthesis)
Cell wall and membrane:

 cell wall relatively thick and physically strong

cell membrane very thin
 Cell walls freely permeable
cell membranes partially permeable
 ALL cells have c-s-membrane

Units of measurement
Fraction of a metre Unit Symbol
One thousandth millimetre mm
1/1000
0.001
10-3
One millionth micrometre µm
1/1 000 000
0.000 001
10-6
One thousand millionth nanometre nm
1/1 000 000 000
0.000 000 001
10-9
Smallest structure visible by human eye 50-100µm in diameter
Body contains about 60 million million cells vary in size of 5 -40µm
Mitochondria average diameter of 1 µm
Ribosomes about 25nm in diameter

Microscopy
Magnification- the number of times larger an image is than the real size of the object
Magnification = Observed size of image
actual size
I
M A

Eyepiece graticule- transparent scale with 100 divisions that’s placed in the microscope eyepiece at
the same time as the object being measured
to know actual size the graticule is calibrated using a miniature transparent ruler called a stage
micrometre scale. Placed on microscope stage and focused pg. 7 jones
A photograph taken with a light microscope- a photomicrograph
a photograph taken with an electron microscope- an electron micrograph
Resolution- the ability to distinguish between 2 objects very close together. Higher resolution =
clearer =greater detail seen. If 2 points can’t be resolved they will be seen as 1 point
Max resolution of l-microscope -200nm (if 2 objects closer than 200nm cannot be distinguished as
separate). With a microscope magnification up to the limit of resolution reveals further detail but
any further magnification increases size and blurring
The electromagnetic spectrum
Resolution is linked with nature of light. Light travels in waves. Length of waves of visible light
varies from (shortest visible wavelength) 400nm (violet) to 700nm (red light) – human eye can
distinguish. In brain the differences are changed to colour differences. (So brain invented colour).
The whole range of different wavelengths is the electromagnetic spectrum. Visible light is one part
of the spectrum.
Longer waves =lower frequency.
All waves travel at same speed so shorter waves pass at higher frequency.
There’s no limit to length of waves. Wavelength change with energy. Greater energy = shorter
wavelength.
To effect, specimen should interfere with light waves. Limit of resolution is about ½ the wavelength
of the radiation used. (If object is smaller than ½ the wavelength it can’t be seen separate from
nearby objects. E.g. best resolution obtained on visible light microscope is 200nm. Ribosomes are
25nm so can never be seen on this.

The electron microscope

Ultraviolet and X- ray microscopes have been built with little success because of difficulty in
focusing X-rays. Better to use electrons (negatively charged particles that orbit nucleus of an atom).
When a metal becomes very hot, some electrons gain so much energy and escape from orbit. Free
electrons behave like electromagnetic radiation.
Electrons are suitable because
 Have extremely short wavelength.
 Negatively charged (can be focused easily using electromagnets. Magnet used to alter path
of beam like glass lens bend light)
TEMs and SEMs
2 types of electron microscope
 Transmission electron microscope (TEM)
Original. Beam of electrons passed through the specimen before viewed. Only electrons
transmitted (pass through) are seen. Allows to see thin and thus see inside cell
 Scanning electron microscope (SEM)
Beam scans surface of structures and only reflected beams are observed. Advantage is
surface structure is seen, great depth of field is obtained so much is in focus, 3D
appearances. Disadvantage is it can’t achieve same resolution as TEM. SEM resolution 3nm -
20nm

Viewing specimens with electron microscope

Electron beams can’t be seen so it’s projected onto fluorescent screen. Areas hit by electrons shine
bright, give black and white picture. Stains that improve contrast of biological specimens for
electron microscopy contain heavy metal atoms, which stop passage of electron. Results in X-ray
like photo. More densely stained parts appear blacker. ‘False-colour’ images made by colouring the
black and white on computer.
 Electron beam, specimen and fluorescent screen must be in vacuum. If electrons collide
with air molecules they scatter (no sharp picture).
 Water boils at rtp in vacuum- all specimens must be dehydrated- only dead material can be
examined.
The detailed structure of a cell by the electron microscope is its ultrastructure.
E.g. ultrastructure of animal cell as with TEM

Ultrastructure of an Animal cell

Structures and functions of organelles
Compartmentalisation and division of labour in cells is more obvious with electron microscope

Nucleus
 Largest cell organelle
 Surrounded by 2 membranes - nuclear envelope containing nuclear pores. Outer continues
with endoplasmic reticulum, ER
 Nuclear pores(small pores) allow exchange with cytoplasm
e.g. RNA and ribosomes for protein synthesis
ATP (adenosine triphosphate)
some hormones e.g. thyroid hormone T3
  Within, loosely coiled chromosomes –chromatin (except during nuclear division)
 Chromosomes contain DNA organised into functional units- genes- controlling activity of cell
and inheritance – thus nucleus controls cell activity
 Nucleolus makes ribosomes using the info in its own DNA
 When cell is dividing, nucleus divides first so each new cell has its own

Endoplasmic reticulum and ribosomes

 ER- a continuation/extensive system of (the outer nuclear envelop) membrane running
through the cytoplasm, forming fattened compartments called sacs. Processes take place in
them separate form cytoplasm. Sacs interconnect forming complete system (reticulum).
 2 types of ER
o Smooth ER - lacks ribosomes, has different function.
Makes lipids and steroids, such as cholesterol
and reproductive hormones oestrogen and testosterone.
o Rough ER –covered in many ribosomes
 Ribosomes (tiny organelles). Seen as black dots.
At high magnification seen to consist 2 subunits; a large and small subunit.
 Made of RNA (ribonucleic acid) and protein
 The site of protein synthesis.
Protein made by ribosomes on rough ER enter the sacs and move through them. Proteins
are modified in some way on their journey.
 Can be free in cytoplasm or on rough ER
 Diameter 25nm
 Small sacs called vesicles can break/bud off from ER, join to form Golgi body. They form part
of the secretory pathway because the proteins can be exported from the cell via the Golgi
vesicles.
 Size measured in ‘S units’ - how fast they sediment in a centrifuge
70S- smaller-about 20nm- mitochondria, chloroplasts (and bacteria)
80S –slightly larger about 25nm- cytoplasmic

Golgi body/ Golgi apparatus/ Golgi complex

http://www.sumanasinc.com/webcontent/animations/content/vesiclebudding.html
 stack of flattened/saucer shaped sacs
 More than one may be present in a cell.
 The stack is constantly formed at one end, from vesicles which break/bud off from the ER.
Then, breaks/bud off at the other end to form Golgi vesicles which may form secretory
vesicles whose contents can be released at the cell surface by exocytosis. The stack together
with the vesicles is the Golgi apparatus/Golgi complex.
 It collects, processes and sorts molecules (particularly proteins from rough ER), to transport
in Golgi vesicles to other parts of cell or out of the cell (secretion)
 processes in the Golgi body
o addition of sugars to proteins to make glycoproteins (molecules)
o removal of the first amino acid, methionine, from newly formed proteins to make a
functioning protein
 In plants, enzymes in the Golgi body convert sugars into cell wall components. Golgi vesicles
are also used to make lysosomes.
Lysosomes
o Spherical sacs
o Surrounding single membrane
o No internal structure
o diameter 0.1– 0.5 μm
o contain digestive (hydrolytic) enzymes –separate from rest of cell to prevent damage
o responsible for breakdown/digestion of unwanted structures e.g.
 old organelles
 whole cells e.g. mammary glands after lactation
 in white blood cells, to digest bacteria (endocytosis)
o enzymes sometimes released outside cell e.g. replacing cartilage with bone in development
o Sperm heads contain a lysosome, the acrosome, to digest a path to the ovum

Mitochondria
Sing. Mitochondrion
Diameter about 1 μm. Various shapes often sausage
Responsible for aerobic respiration. Number varies. Cells with a high demand for energy,
e.g. liver and muscle cells, contain large numbers. Liver cell may contain as many as 2000
mitochondria. Regular exercise causes muscles make more.
2 membranes (envelope) intermembrane space between them. Inner folded forming finger-
like cristae projecting into the (matrix) interior solution. Outer contains transport protein
porin that forms wide aqueous channels -allows easy access of small, water-soluble
molecules from cytoplasm into the intermembrane.
Replicate themselves independently (cell division) by dividing into 2.
Inner more selective barrier. Controls ions and molecules entering the matrix
Mitochondrial ribosomes are seen as dark orange dots in the mitochondrial matrix
Function
o Aerobic respiration
o Synthesis of lipids
During respiration, reactions take place which release energy from energy rich molecules
e.g. sugars and fat. Most energy is transferred to molecules of ATP(the energy carrying
molecule on living cells)
Respiration reactions occur in the matrix and cristae.
Matrix contains enzymes in solution e.g. of the Krebs cycle (supply hydrogen and electrons
for reactions in the cristae). Flow of electrons along precisely placed electron carriers in the
membranes of cristae provides power to generate ATP molecules. Folded cristae increases
surface area increasing efficiency of respiration. Once made, ATP (small and soluble) leaves
mitochondria spreads to all parts of the cell where energy is needed. Energy is released by
breaking the molecule down to (adenosine diphosphate) - hydrolysis reaction. ADP can be
recycled into a mitochondrion for conversion back to ATP during aerobic respiration.
The endosymbiont theory
Mitochondria and chloroplasts (and bacteria) have smaller ribosomes than in cytoplasm
Cytoplasmic ribosomes are 80S
The others 70S
 Bacteria have small, circular DNA molecules, (like in mitochondria and chloroplasts) later
proved they’re, ancient bacteria which now live in larger animal and plant cells
(endosymbiont theory) but can no longer live independently. Endo (inside) symbiont
(organisms that live in mutually beneficial relationships with another organisms).
DNA and ribosomes of mitochondria and chloroplasts are still active and responsible for
coding and synthesis of certain vital proteins.

Cell surface membrane

 Thin- 7nm
 Partially permeable- controls exchange with environment
 At high (×100 000) magnification 3 layers are seen (a trilaminar appearance) 2 dark outer
lines(heavily stained) and a narrow pale interior

Microvilli
• Sing. Microvillus
• Finger like extensions of cs-membrane
• Typical of certain epithelial cells (cells covering surfaces of structures)
• Increase the surface area useful e.g.
o absorption in gut
o reabsorption in the proximal convoluted tubules (kidney)

[Microtubules and microtubule organising centres (MTOCs)]

 long rigid hollow tubes in cytoplasm
 (Microtubules) made of tubulin (a protein with 2 forms)
α-tubulin (alpha-tubulin) and β-tubulin (beta-tubulin). The α- and β-tubulin molecule
combine -> dimers (double molecules). Dimers join end to end ->long protofilaments
(polymerisation). 13 line up alongside each other in a ring to form a cylinder with a hollow
centre (microtubule)

 Diameter 25nm
 Mechanical function is support
 Together with actin and intermediate filaments they make up the cytoskeleton (essential
structural component helps determine cell shape.
 Secretory vesicles, other organelles and cell components can be moved along the outside
surfaces of microtubules, forming an intracellular transport system
 Membrane bound organelles are held in place by the cytoskeleton
  In nuclear division, the spindle used for separating chromatids or chromosomes is made of
microtubules, and microtubules form part of the structure of centrioles
 Assembly of microtubules from tubulin molecules is controlled by locations called MTOCs
and their simple construction, means microtubules can be formed/broken down very easily
at MTOCs

[Centrioles and centrosomes]

I. Outside the nucleus are 2 centrioles (500nm long hollow cylinder. Ring of 9 triplets of
short microtubules) lying at right angles in the centrosome (the region)
II. 2 seen on electron microscope, 1 seen on light)

III.
Centrioles in transverse and longitudinal section.
The left is TS Showing 9 triplets.

IV. Centrioles believed to act as MTOCs for the assembly of the microtubules that make up the
spindle during nuclear division. Actually done by the centrosome, but does not involve the
centrioles
V. Centrioles found at the bases of cilia and flagella (known as basal bodies) act as MTOCs.
VI. Microtubules extending from basal bodies into the cilia and flagella are essential for the beating
movements of these organelles

Ultrastructure of a plant cell

Plant cells have no centrosomes/centrioles and microvilli.
These are only found in plant cells

Cell wall
Large central Vacuole
Chloroplasts

 Have elongated shape. Diameter 3-10μm

 2 membranes –chloroplast envelope
 Replicate independently
 Function - carry out photosynthesis
1. 1st (light dependent stage) light absorption by photosynthetic pigments (green
chlorophyll),
2. Splitting water into H and O. H is fuel that’s oxidised to provide energy
3. Energy used to manufacture ATP from ADP (requiring electron transport in
membranes –like mitochondria) Chloroplasts have a complex system of membranes.
4. Membrane system has thylakoids (fluid filled sacs). In places, form fat disk like
structures stacking up forming grana (grains)
5. These membranes contain photosynthetic pigments and electron carriers (needed
for this stage). Membranes and whole chloroplasts can change orientation for max
light.
6. 2nd (light independent stage) use energy and reducing power generated to convert
CO2 into sugars- requires the Calvin cycle (enzyme controlled reactions in the
stroma(matrix)
7. Sugars may be stored as starch grains in the stroma
 Lipid droplets in the stroma (black spheres) are lipid reserves for making membrane or from
membrane breakdown in chloroplasts.
 Have their own protein synthesising machinery (70Sribosomes/circular DNA strand)
 chloroplasts originated as endosymbiotic bacteria- photosynthetic blue-green bacteria

Two fundamentally different types of cell

Fungi and bacteria are different from animals and plants cells. 2 different cells

Prokaryote cells Eukaryote cells

A group of organisms that lack a cell An organism whose cells contain complex
nucleus and other membrane bound structures enclosed within membranes
organelles
 Nucleus lack nuclei (pro-before; karyote- (you carry)(eu –true). 1 or more nucleoli and
nucleus) DNA which is linear and bound to proteins to
form chromatin. Include animals, plants,
fungi, protoctists (most unicellular
eukaryotes).
Diameter/ 0.5 -5μm. 1 000-10 000 times Up to 40μm.
Size smaller volume than eukaryotes
Structure Simpler Complex, believed to evolve from
prokaryotes 1500 million years after
prokaryotes 1st appeared.
DNA Circular. Lies free in cytoplasm Not circular. Enclosed in nucleus
Naked Associated with protein. Form chromosomes
ribosomes 70S 80S
ER none Yes, may be rough
Cell Few!!- no separate compartments Many!!-extensive compartmentalisation and
organelles (membrane bound) unless infolding division of labour
of cs-membrane • some bounded by single membrane
i.e. lysosomes, Golgi body, vacuoles
• 2 membranes i.e. nucleus,
mitochondrion, chloroplast
• None i.e. ribosomes, centrioles,
microtubules
Cell wall Present with murein- a Sometimes e.g. plants( with cellulose or
peptidoglycan (polysaccharide + lignin) and fungi with chitin (a nitrogen-
amino acids) containing polysaccharide similar to
cellulose)

Comparison
Structures always present
a) cell wall containing murein
b) cs-membrane
c) cytoplasm
d) circular DNA/chromosomes
e) ribosomes
Additional (sometimes)
a) flagellum for locomotion
b) capsule (additional protection)
c) infolding cs-membrane (forms photosynthetic membrane/carry out nitrogen fixation)
d) plasmid(small circle of DNA, may be several)
e) pili attaches to other cells/surfaces (involved in sexual reproduction)
Viruses
 pass through the finest filters
 50× smaller than bacteria-> 20-300 nm
 boundary between living and non-living
 Unlike prokaryotes and eukaryotes, have no cell structure -not surrounded by a membrane,
contain cytoplasm etc.
 Simpler structure of
o A self-replicating of DNA or RNA molecules (acts as its genetic code)
o a protective coat of protein molecules
 its capsid (protein coat) is made of capsomere (separate protein molecules)
 Parasitic- only reproduce by infecting/taking over host living cells. Virus DNA/RNA takes
over protein synthesis machinery to make new virus particles