OCR A LEVEL BIOLOGY - YEAR 1 - MODULE 2 -
SUMMARY NOTES
2.1.1 Microscopes
Transmission electron microscope (TEM)
-Dehydrated and stained with metallic salts as chemically fixed
-Electrons pass through specimen
-2D black and white image (greyscale)
Optical microscopes
-Cheap
-Easy to use
-Portable
-Study whole living organisms
-Limited resolution
-Image seen = Pictomicrograph
Electron microscopes
Beam fast travelling electrons fired from cathode focused by
magnets onto screen or photographic plate, expensive and highly skilled
to use
Scanning electron microscope (SEM)
-Secondary electrons bounce of specimen and focused on screen
-3D image, can add false colour
-Dead specimens as in vacuum
Laser scanning microscope (confocal microscope)
-Scan object point by point and pixels assembled by computer to produce
image
-High resolution and contrast
-Depth selectivity
-Study living specimens and cells
2.1.2 Slides and photomicrographs
Magnification = image size / actual size
Using scale bars: Magnification = image size (measured)/ actual size
(written)
Mm -> µm x1000
µm -> nm x1000
,Optical microscopes view
-living organism (amoeba)
-smears (blood human cheek cells)
-thin sections of tissue
Stains are coloured chemicals bind to molecules in on specimens
Differential staining -> stains bind to specific cell structures so easily
identified and provides contrast stand out clear
Preparing permanently fixed slide
1.Dehydrated to remove water
2.embedded in way to prevent distortion
3.thin slices sections preserved in chemicals
4.mount
Observing unstained specimens
Some use light interference for clear image
Some use dark background so illuminated specimen shows up - iris
diaphragm
Methylene blue all purpose stain
Eosin cytoplasm
Iodine in potassium iodide cellulose yellow starch blue black
Acetic orcein DNA and chromosomes dark red
Sudan red lipids
2.1.3 Measuring objects seen with a light microscope
Graticules are transparent with small ruler etched on it
As viewed eyepiece graticule scale superimposed on specimens and
dimensions can be measured in eyepiece units epu
Graticule has to be calibrated for each objective lens
Eyepiece graticule is arbitrary so represents different lengths and different
magnifications
Stage micrometre on stage
Graticule in eyepiece
Stage micrometre set measurement
Total magnification = magnifying power eyepiece lens x magnifying power
objective lens
Stage micrometre calibrates eyepiece graticule
Stage micrometre is a microscopic ruler etched on special slide placed on
stage
,2.1.4 The ultrastructure of eukaryotic cells
nucleus
structure: surrounded by double membrane contains chromatin (the
genetic material - DNA wound around histone protein)
function: controls cells activities, stores genome, transmits genetic
information, provide instructions for protein synthesis
nuclear envelope
structure: double membrane with pores
function: separates nucleus contents from rest of cell, pores allow large
substances to leave or enter nucleus (mRNA or steroid hormones), inner
and outer regions fuse to allow dissolved substances through
nucleolus
structure: no membrane, contains RNA
function: where ribosomes are made
mitochondria
structure: spherical, rod shaped, branched, surrounded by 2 membranes
with fluid filled space between them, inner membrane folded into cristae
and is fluid filled matrix
function: site ATP production during aerobic respiration, self replicating
so more made if energy need increases, abundant in cells where much
metabolic activity occurs, own DNA
vacuole
structure: membrane called tonoplast, contains fluid
function: plants have large permanent vacuole filled with water and
solutes to maintain stability, makes cell turgid
rough endoplasmic reticulum
structure: system membranes with fluid filled cavities (cisternae),
continuous from nuclear membrane, coated with ribosomes
function: intracellular transport system, cisternae from channels provide
large SA for proteins
chloroplast
structure: double membrane, inner continuous stacks of flattened
membrane sacs (thylakoids) contain chlorophyll, each stack thylakoid is a
granum, fluid filled matrix is the stroma, contain loops own DNA and
starch grains
function: photosynthesis, stage 1 - light energy trapped by chlorophyll
make ATP in grana and water split to supply H ions, stage 2 - H reduces
co2 using energy from ATP to make carbohydrates in stroma, abundant in
leaf cells
, smooth endoplasmic reticulum
structure: system membranes with fluid filled cavities (cisternae) but no
ribosomes
function: lipid metabolism, synthesis, transportation
Golgi apparatus
structure: stack membrane bound flattened sacs, secretory vesicles
bring materials to and from Golgi apparatus, have membrane cisternae
function: modify and package proteins, vesicles pinched off and stored in
cell or moved to plasma membrane
cilia and undulipodia
structure: protrusions from cell, contain microtubules, formed from
centrioles
function: beat and move mucus, most cells have one cilium and acts as
antenna containing receptors to detect signals about immediate
environment, only human cell to have undulipodia is spermatozoon
enables it to move - sperm tail
lysosomes
structure: small bags formed from Golgi apparatus surrounded by single
membrane, contain hydrolytic enzymes - lysozymes - abundant in
phagocytic cells
function: keep enzymes separate from rest of cell, engulf old cell
organelles and foreign matter, digest them and return digested
components to cell for reuse
2.1.5 Other features eukaryotic cells
ribosomes
structure: small spherical, made of ribosomal RNA, made in nucleolus as
two separate subunits, pass through nuclear envelope and combine in
cytoplasm, some remain free, some attach to ER, no membrane
function: bound to extension of RER mainly for synthesising proteins that
are exported, those that are free are primary site assembly of proteins
used in cell
centrioles
structure: two bundles of microtubules at right angles to each other,
microtubules made of tubulin protein subunits form a cylinder
function: before cell divides, spindle forms, chromosomes attach to
middle of spindle and motor proteins walk along tubulin threads pulling
chromosome to opposite ends of cell, involved in formation cilia and
undulipodia, before cilia forms centrioles multiply and line up beneath cell
surface membrane then microtubules sprout outwards from centriole
cytoskeleton
SUMMARY NOTES
2.1.1 Microscopes
Transmission electron microscope (TEM)
-Dehydrated and stained with metallic salts as chemically fixed
-Electrons pass through specimen
-2D black and white image (greyscale)
Optical microscopes
-Cheap
-Easy to use
-Portable
-Study whole living organisms
-Limited resolution
-Image seen = Pictomicrograph
Electron microscopes
Beam fast travelling electrons fired from cathode focused by
magnets onto screen or photographic plate, expensive and highly skilled
to use
Scanning electron microscope (SEM)
-Secondary electrons bounce of specimen and focused on screen
-3D image, can add false colour
-Dead specimens as in vacuum
Laser scanning microscope (confocal microscope)
-Scan object point by point and pixels assembled by computer to produce
image
-High resolution and contrast
-Depth selectivity
-Study living specimens and cells
2.1.2 Slides and photomicrographs
Magnification = image size / actual size
Using scale bars: Magnification = image size (measured)/ actual size
(written)
Mm -> µm x1000
µm -> nm x1000
,Optical microscopes view
-living organism (amoeba)
-smears (blood human cheek cells)
-thin sections of tissue
Stains are coloured chemicals bind to molecules in on specimens
Differential staining -> stains bind to specific cell structures so easily
identified and provides contrast stand out clear
Preparing permanently fixed slide
1.Dehydrated to remove water
2.embedded in way to prevent distortion
3.thin slices sections preserved in chemicals
4.mount
Observing unstained specimens
Some use light interference for clear image
Some use dark background so illuminated specimen shows up - iris
diaphragm
Methylene blue all purpose stain
Eosin cytoplasm
Iodine in potassium iodide cellulose yellow starch blue black
Acetic orcein DNA and chromosomes dark red
Sudan red lipids
2.1.3 Measuring objects seen with a light microscope
Graticules are transparent with small ruler etched on it
As viewed eyepiece graticule scale superimposed on specimens and
dimensions can be measured in eyepiece units epu
Graticule has to be calibrated for each objective lens
Eyepiece graticule is arbitrary so represents different lengths and different
magnifications
Stage micrometre on stage
Graticule in eyepiece
Stage micrometre set measurement
Total magnification = magnifying power eyepiece lens x magnifying power
objective lens
Stage micrometre calibrates eyepiece graticule
Stage micrometre is a microscopic ruler etched on special slide placed on
stage
,2.1.4 The ultrastructure of eukaryotic cells
nucleus
structure: surrounded by double membrane contains chromatin (the
genetic material - DNA wound around histone protein)
function: controls cells activities, stores genome, transmits genetic
information, provide instructions for protein synthesis
nuclear envelope
structure: double membrane with pores
function: separates nucleus contents from rest of cell, pores allow large
substances to leave or enter nucleus (mRNA or steroid hormones), inner
and outer regions fuse to allow dissolved substances through
nucleolus
structure: no membrane, contains RNA
function: where ribosomes are made
mitochondria
structure: spherical, rod shaped, branched, surrounded by 2 membranes
with fluid filled space between them, inner membrane folded into cristae
and is fluid filled matrix
function: site ATP production during aerobic respiration, self replicating
so more made if energy need increases, abundant in cells where much
metabolic activity occurs, own DNA
vacuole
structure: membrane called tonoplast, contains fluid
function: plants have large permanent vacuole filled with water and
solutes to maintain stability, makes cell turgid
rough endoplasmic reticulum
structure: system membranes with fluid filled cavities (cisternae),
continuous from nuclear membrane, coated with ribosomes
function: intracellular transport system, cisternae from channels provide
large SA for proteins
chloroplast
structure: double membrane, inner continuous stacks of flattened
membrane sacs (thylakoids) contain chlorophyll, each stack thylakoid is a
granum, fluid filled matrix is the stroma, contain loops own DNA and
starch grains
function: photosynthesis, stage 1 - light energy trapped by chlorophyll
make ATP in grana and water split to supply H ions, stage 2 - H reduces
co2 using energy from ATP to make carbohydrates in stroma, abundant in
leaf cells
, smooth endoplasmic reticulum
structure: system membranes with fluid filled cavities (cisternae) but no
ribosomes
function: lipid metabolism, synthesis, transportation
Golgi apparatus
structure: stack membrane bound flattened sacs, secretory vesicles
bring materials to and from Golgi apparatus, have membrane cisternae
function: modify and package proteins, vesicles pinched off and stored in
cell or moved to plasma membrane
cilia and undulipodia
structure: protrusions from cell, contain microtubules, formed from
centrioles
function: beat and move mucus, most cells have one cilium and acts as
antenna containing receptors to detect signals about immediate
environment, only human cell to have undulipodia is spermatozoon
enables it to move - sperm tail
lysosomes
structure: small bags formed from Golgi apparatus surrounded by single
membrane, contain hydrolytic enzymes - lysozymes - abundant in
phagocytic cells
function: keep enzymes separate from rest of cell, engulf old cell
organelles and foreign matter, digest them and return digested
components to cell for reuse
2.1.5 Other features eukaryotic cells
ribosomes
structure: small spherical, made of ribosomal RNA, made in nucleolus as
two separate subunits, pass through nuclear envelope and combine in
cytoplasm, some remain free, some attach to ER, no membrane
function: bound to extension of RER mainly for synthesising proteins that
are exported, those that are free are primary site assembly of proteins
used in cell
centrioles
structure: two bundles of microtubules at right angles to each other,
microtubules made of tubulin protein subunits form a cylinder
function: before cell divides, spindle forms, chromosomes attach to
middle of spindle and motor proteins walk along tubulin threads pulling
chromosome to opposite ends of cell, involved in formation cilia and
undulipodia, before cilia forms centrioles multiply and line up beneath cell
surface membrane then microtubules sprout outwards from centriole
cytoskeleton
