AS BIOLOGY

UNIT 2

Chapter 3A

Light Microscope

● Are used for specimens larger than 200 nm so resolution is upto 200 nm
● Up to 2000 mag
● Useful for looking at whole cells, small plant and animal organisms, and tissues within organs such
as in leaves or skin
● Specimen is placed on the stage and this is illuminated from beneath using the reflection of
sunlight or by a built-in light source; light is directed through a thin layer of the material. This
light is focused through several lenses so that an image is visible through the eyepiece. The
magnifying power of the microscope can be increased by rotating the higher power objective lens
into place
● 2 types of lenses - an eyepiece lens which often has a magnification of x10 and a series of, usually
3, objective lenses, each with a different magnification
● Objective lens produces magnified inverted image and eyepiece lens focuses the image at the eye
● Total magnification = magnification of objective lens x mag of eyepiece lens
● Usually specimens are dead but living organisms can also be analyzed
● Dead specimens are stained , specially preserved and sectioned
● Staining makes it easier to identify types of / parts of cells
● Cheap , light , portable
● Preservation and staining tissue may produce artifacts
● Limit powers of resolution and magnification power

Artifacts - things observed in scientific investigation that aren't naturally present and occur as a result of
the preparation/investigation (they are things that are easy to mistake as part of tissue but are not part of
the living tissue , as a result of preserving and staining)

Electron microscope
● are used for specimens larger than 0.5 nm so resolution is upto 0.5 nm
● Up to 500,000 mag
● useful for looking at organelles, viruses, and DNA, as well as looking at whole cells in more detail
● Uses a beam of electrons to form an image
● Electrons are scattered by the specimen , behave in the same way as lightwaves but with a smaller
wavelength
● Electromagnetic lenses will focus the electron beams to form the image
● As the wavelength gets smaller , resolving power increases
● 1000 times better resolving power that light and has huge powers of magnification
 ● Specimens must be in a vacuum because air would scatter the electrons and produce blurred image
, so are always dead- Impossible to look at living material
● requires the specimen to be dead so this can provide a snapshot in time of what is occurring in a
cell, e.g. DNA can be seen replicating and chromosome position within the stages of mitosis are
visible
● Preparation is complex ; chemical preservation , freeze drying , freeze fracturing , dehydration ,
embedding , sectioning , mounting on metal grid
● Stained to improve scattering of electrons - using heavy metal ions ; lead , uranium
● Staining produces at image with more contrast , clearer, easier to interpret
● Image displayed on computer screen
● Two types ; transmission electron micrograph which gives 2D images and scanning electron
micrograph that gives 3D images but has lower magnification
● Specimen undergo severe treatment that can result in artifacts
● Preparing is very skilled work
● Instrument is large and needs to be kept at certain temp n pressure with an internal vacuum

Transmission Electron Microscopes

● TEMs use electromagnets to focus a beam of electrons which is transmitted through a thin
specimen
● Denser parts of the specimen absorb more electrons; these denser parts appear darker on the final
image, producing contrast between different parts of the object being observed
● The internal structures within cells, or even within organelles can be seen as a 2D image
● The resolution of these images is very high

Scanning Electron Microscopes

● SEMs scan a beam of electrons across a specimen which bounces off the surface of the specimen
and the electrons are detected, forming an image
● This means SEMs can produce 3D images that show the surface of specimens
● Since they scan the outside surface it means that the specimen viewed does not have to be thin
● The images they form are of a lower resolution than TEMs

This is how SEM microscope pictures look like. In TEM

we can clearly see organelles in the nucleus as well and it is not 3D.

Actual size = image size/magnification

Resolution
Resolution, or resolving power, is the ability to distinguish between two separate points
● If two separate points cannot be resolved, they will be observed as one point and the image will be
unclear
● The resolution of a microscope limits the magnification that it is capable of; there is no point in
magnifying an image at low resolution as this will just result in a big blur
● The resolution of a light microscope is limited by the wavelength of light; the wavelength of light
is too long to allow for high resolution
● Electron microscopes have a much higher resolution, and therefore magnification, than a light
microscope as electrons have a much smaller wavelength than visible light

Staining
Specimens to be viewed under a microscope sometimes need to be stained, as cell structures may be
transparent or difficult to distinguish
● Most of the colors seen in images taken using a light microscope are the result of added stains
● The type of stain used is dependent on what type of specimen is being prepared/ what the
researcher wants to observe
● Different molecules absorb different dyes
● Specimens or sections are sometimes stained with multiple dyes to ensure that several different
tissues within the specimen show up; this is known as differential staining
● Some common stains include HMAITP
○ Hematoxylin - Stains plant and animal cell nuclei purple, brown or blue
○ Methylene blue- Stains animal cell nuclei blue
○ Acetocarmine- Stains chromosomes in dividing nuclei of plant and animal cells dark red
○ Iodine- Stains starch-containing material in plant cells blue-black
○ Toluidine blue - Stains tissues that contain DNA and RNA blue
○ Phloroglucinol- Stains lignin found in plant cells red/pink

Eukaryotic cells
Eukaryota, whose members are known as eukaryotes, is a diverse domain of organisms whose cells have a
nucleus. All animals, plants, fungi, and many unicellular organisms, are eukaryotes.

The typical animal cell

 ● Cell surface membrane surrounds the cell. Inside is the cytoplasm and nucleus - together known as
protoplasm.
● Cytoplasm contains the components that perform the functions of the cell
● Nucleus contains information needed to produce chemical substances that the cell is made from
● Ultrastructure of the cell are the structures that can only be seen using the microscope

Membrane
● Membranes inside the cell localize enzymes in reaction pathways and keep biological molecules
separate
● Microvilli are folded regions of the cell surface membrane that increase cell surface area for
absorption, e.g. in the small intestine
● All cells are surrounded by a cell surface membrane which controls the exchange of materials
between the internal cell environment and the external environment
● Partially permeable, meaning that some substances can pass through the membrane while others
cannot
● Cell membrane is formed from a phospholipid bilayer
● Many organelles inside cells are surrounded by cell membrane
● Can also be referred to as the plasma membrane

Nucleus
● Surrounded by a double nuclear membrane with holes or pores
● Chemical substances can pass in and out through nuclear pores ; important channels for allowing
mRNA and ribosomes to travel out of the nucleus, as well as allowing enzymes, e.g. DNA
polymerases, and signaling molecules to travel in . Alow to control events in the cytoplasm
● The nucleus contains chromatin, the material from which chromosomes are made
○ Chromosomes are made of sections of linear DNA tightly wound around proteins called
histones
● The nuclear membrane / nuclear envelope serves to separate the chromosomes from the cell's
cytoplasm and other contents. An array of pores in the nuclear membrane permits the selective
passage of certain materials, such as nucleic acids DNA RNA and proteins, between the nucleus
and cytoplasm
● When the cell is not actively dividing , DNA is bonded to the protein to form chromatin
● In the nucleus is at least one nucleolus - an extra dense area of almost pure DNA and protein. It is
the site of production of ribosomes and it may play a part in the control of cell growth and
division. Usually, at least one or more darkly stained regions of the nucleolus can be observed
under a microscope.
Mitochondria
● The site of aerobic respiration within eukaryotic cells - will oxidize respiratory molecules in
cellular respiration and produce ATP that is used to drive other functions of the cell
● Cells that need less energy have less mitochondria and cells with energy demanding functions have
many
● Have an outer and inner membrane - are surrounded by a double-membrane with the inner
membrane folded to form structures called cristae which gives a large surface area and is
surrounded by a fluid matrix that contains enzymes needed for aerobic respiration, producing ATP
● This internal arrangement provides more space for metabolizing more proteins and therefore they
are able to create more energy at one time
● Are just visible with a light microscope
● Contain their own genetic material - small circular pieces of DNA, known as mitochondrial DNA,
and ribosomes are also found in the matrix- these are needed for replication of mitochondria before
cell division

Centrioles

● Before cell division, the centrosome duplicates and then, as division begins, the two centrosomes
move to opposite ends of the cell.
 ● Centrioles are made of hollow fibers knows as microtubules ; filaments of protein that can be used
to move substances around inside a cell, as well as to support the shape of a cell from the inside
● In each cell there is a pair of centrioles near the nucleus
● Each centriole has a bundle of 9 sets of tubules
● Two centrioles at right angles to each other form a centrosome which organizes the spindle fibers
during cell division
● When a cell divides , the centrioles pull apart to produce a spindle of microtubules that are
involved in the movement of chromosomes.
● Centrioles are not found in plants and fungi

80s and 70s ribosomes

● Made from ribosomal RNA and protein
● Can be found as free organelles in the cytoplasm of all cells or as part of the rough endoplasmic
reticulum in eukaryotic cells
● Are the site of translation
● Consist of a large and small subunit
● Main type is 80s ribosomes, when they are broken into 2 units , they are made up of 40s small
subunits and 60s large subunits. RNA to protein ratio is 1:1
● 70s ribosomes exist in the mitochondria and chloroplasts. Are usually found in prokaryotic cells.
Consist of 30s ss, 50s ls with ratio 2:1
○ These are reproduced in mitochondria and chloroplasts in cell division and this provides
evidence for the endosymbiotic theory
● S stands for Svedberg which is a unit used to measure how quickly particles settle in a centrifuge
Lysosomes
● Lysosomes are specialist forms of vesicles which contain hydrolytic enzymes(a mix of digestive
enzymes) which fuse 1.together 2.with a membrane bound vacuole that contains food or 3. an
organelle
● They are dark spherical bodies in the cytoplasm
○ Main role is to break down waste materials such as worn-out organelles,
○ Lysosomes are used extensively by cells of the immune system and in programmed cell
death ; when a cell is old and needs to be removed / has a mutation/is under stress, then the
lysosomes may rupture and release enzymes to destroy the contents of the cell - this
programmed cell death is known as apoptosis.
○ They break down food taken into protoctista cells( like amoeba ) into simple chemical
substances that can be used
○ The enzymes then break down the contents from 2/3 into molecules to be reused.
○ Lysozyme may fuse with the outer cell membrane to release enzymes outside the cell to
destroy bacteria or for digestion

Endoplasmic Reticulum
● 3D network of cavities surrounded by membranes and spread through the cytoplasm
● Some cavities are sac like , some are tubular
● The network is a large part of the transport system within a cell
● Site of synthesis of important chemical substances
Rough ER
● Outside of the ER is covered in granules which are 80s ribosomes - this is known as rough ER
● The function of ribosomes is to make proteins. The RER has a large surface area for their synthesis
and it stores and transports the proteins within the cell after they have been made.
● Cells that secrete materials have large amount of RER

Smooth ER
● Not all ER are covered with ribosomes
● The ser is involved in synthesis and transport of carbohydrates , steroids and lipids

The amount and the type of ER in a cell give an idea of their functions

Golgi apparatus

● Made up of stacks of parallel, flattened membrane pockets formed by vesicles from the ER fusing
together
● Proteins are brought in vesicles from the RER ,the vesicles fuse with the membrane sacs of the
golgi apparatus and the protein enters and is modified as they travel through the GA, preparing
them for secretion. The GA aligns the areas of the protein needed to be on the outside of the cell
membrane so when they arrive at the membrane , they are inserted facing in the correct
direction.The modified proteins then leave the Golgi apparatus in vesicles
● It seems to be involved in producing materials for plant and fungal cell walls and insect cuticles
● Enzymes may also be transported through the GA and then in vesicles to the cell membrane where
they will fuse with the membrane to release extracellular digestive enzymes.
● The inner areas are rich in enzymes that modify proteins in different ways. This is where most
enzymes or membrane proteins are converted into the final product
 ● In outer areas, there are lots of unfinished protein products but not many of the enzymes that make
them

Production and secretion of proteins

In cells, many organelles are involved in the production and secretion of proteins:
● Nucleus -Transcription of the DNA code occurs here
● Ribosomes- Free ribosomes and those on the RER produce proteins in the process of translation
● Rough endoplasmic reticulum (RER)
● Golgi apparatus
● Cell surface membrane- Proteins formed within the cell are secreted here
1. Ribosomes on the RER produce proteins that can be secreted out of the cell or become attached to
the cell surface membrane
2. Proteins that have been passed into the lumen of the rough endoplasmic reticulum are folded and
processed here
3. Note that free ribosomes found within the cytoplasm make proteins that stay within the cytoplasm
rather than being moved to another organelle or being exported from the cell
4. Processed proteins from the RER are transported to the Golgi apparatus in vesicles which fuse with
the Golgi apparatus, releasing the proteins into the Golgi which modifies the proteins, preparing
them for secretion
5. Proteins that go through the Golgi apparatus are usually Exported, e.g. extracellular enzymes, Put
into vesicles and called lysosomes, e.g. hydrolytic enzymes , Delivered to other membrane-bound
organelles
6. The modified proteins then leave the Golgi apparatus in vesicles
Prokaryotic Cells - single-celled organisms belonging to the domains Bacteria and Archaea. Prokaryotic
cells are much smaller than eukaryotic cells, have no nucleus, and lack organelles. All prokaryotic cells
are encased by a cell wall. Many also have a capsule or slime layer made of polysaccharide. bacteria ,
cyanobacteria , archaebacteria.

The structure of bacteria

Cell wall
● All bacteria have a cell wall
● Contents of the cell are usually hypertonic to the medium around them so water moves in by
osmosis - cell wall prevents swelling and bursting
● maintains the shape as well as supports and protects the cell contents
● Cell wall made of peptidoglycan (polysaccharides and amino acids) and a form of peptidoglycan
called murein
● Some have a capsule or slime layer made from starch , gelatin, protein - protects the bacteria from
phagocytosis by WBC, covers the cell markers making it harder to be identified by immune system
and so easier for bacteria to cause disease eg. tuberculosis , meningitis and pneumonia . it also
helps to protect bacteria from drying out

Peptidoglycan - is a polysaccharide, it is a rigid envelope surrounding the membrane of most bacterial

species

Pilli
● Thread like protein projections from the surface
● Used for attachment to a host cell
● Used for sexual reproduction
● Ms says - pili allow bacteria to adhere (to surfaces)
● Make bacteria more vulnerable to infections as bacteriophage use them as an entry point to the cell
○ Bacteriophages, also known as phages, are viruses that infect and replicate only in bacterial
cells.

Flagella
● Bacteria move themselves using flagella
● Made of many stranded helix of the protein flagellin
● Flagellum move bacteria by rapid rotations

Cell surface membrane

● Similar in structure and function of eukaryotes
● No mitochondria so the membrane is the site of respiratory enzymes
● Cell membrane contains folds known as mesosomes- allows aerobic respiration, dna replication ,
cell wall formation to take place
Nucleoid and plasmids
● The genetic material consists of a circular strand of DNA which isn't in a nucleus
● DNA is folded and coiled to fit into the bacteria
● Area where it is held is the nucleotide which occupies half of the cytoplasm
● Smaller circles of DNA are the plasmids which code for particular aspects of the phenotype
● Can reproduce themselves by being transferred from one bacteria to another in the form of sexual
reproduction using pili

Ribosomes
● The only organelle in bacteria
● These are 70s ribosomes
● Involved in protein synthesis

What is present in animal cells but not in plant cells ?

Only cilia, glycogen (granules, flagella
Along with lysosomes and centrioles
Gram staining
● All bacteria cells have peptidoglycan but two types - this can be seen by gram staining
● Diff types of disease causing bacteria are vulnerable to diff antibiotics so the type of cell wall they
have can affect how vulnerable they are
● Before staining , bacteria are often colorless
Gram positive bacteria
● Cell wall has a thick layer of peptidoglycan made up of chemical substances like teichoic acid
● The crystal purple complex of the gram stain is trapped in the layer , resisting decolouring when
bacteria is dehydrated using alcohol
● Bacteria do not pick up red counterstain , appearing purple under light microscope
Gram negative bacteria
● Thin layer of peptidoglycan in cell wall
● Outer membrane made of lipopolysaccharides which dissolves when bacteria is dehydrated
● The dissolving makes the lippo layer and the crystal purple complex washed out
● Peptidoglycan takes up the red counterstain and so cells appear red in light microscope
Apart from gram staining there are other ways to classify bacteria
Shapes
● Spherical - cocci
● Rod shaped - bacilli
● Twisted - spirilla
● Comma shaped - vibrio
Respiratory requirements
● Obligate aerobes - need oxygen
● Facultative anaerobes - use oxygen if available , manage without it
● Obligate anaerobes - only respire in absence of oxygen , it can kill it
Cell theory includes three main ideas
● -All living organisms are made up of one or more cells
● -Cells are the basic functional unit in living organisms
● -New cells are produced from pre-existing cells

Cells can become specialized for specific functions

● Epithelial cells in the small intestine are specialized to absorb food efficiently
● Red blood cells are specialized to transport oxygen
● Xylem cells in plants are specialized to allow the transport of water around a plant

Specialized cells of the same type can group together to form tissues
A tissue is a group of cells that work together to perform a particular function
● Four main tissues - muscle , connective , elastic , epithelial , nervous
● Muscle cells group together to form muscle tissue, the function of which is to contract in order to
move parts of the body

Epithelial tissues
● Epithelial cells group together to form epithelial tissue tTissues that line the surfaces inside and
outside the body and protect cells below it
● Sit tightly together and form a smooth surface
● All cells originate from the basement membrane
● Squamous epithelium - lining the surface of BV and the alveoli
● Ciliated epithelium- lines the respiratory passage and oviducts ; often contain goblet cells secreting
mucus
● Compound epithelium - found in areas that are constantly scratched/abraded like the skin.
Thickness of tissue protects what's beneath and new cells continue to grow from basement
membrane
● The function in the small intestine, is to absorb food
Connective tissue
● Main supporting tissue for the body
● Bone , cartilage , packing tissue
● Supports and protects some organs

Leaf tissues - mesophyll , vascular , epithelial tissues

Different tissues can group together to form organs

An organ is a group of tissues working together to perform a particular function
● Different tissues; cardiac muscle tissue, blood vessel tissues and connective tissue, group together
to form the heart, enabling it to function to pump blood around the body
● Tissues including palisade mesophyll, spongy mesophyll, and vascular tissue, group together in
plants to form leaves, enabling them to perform photosynthesis effectively

Different organs work together to form organ systems

An organ system is a group of organs working together to perform a particular function
● The heart and blood vessels work together to form the circulatory system, the job of which is to
allow blood to circulate around the body
● The stomach, pancreas, small intestine, and large intestine work together to form the digestive
system, the job of which is to digest food and absorb nutrients

Imp difference is that organ has many functions whereas a tissue has {one / fewer}
Chapter 3B
Key Terms
● Nucleosomes repeatedly fold in on themselves to tighten and condense the packaged DNA to form
chromosomes
● Karyotype- special display showing all the chromosomes of a cell
● Cell cycle controlling- cell cycle is controlled by chemical signals that are brought about at
checkpoints between each phase within the cycle. The signals are controlled by the chemical
substances which are proteins called cyclins. They will build up and attach to enzymes called
cyclin dependant kinases to form the Cyclin - CDK complex
● Chiasmata
● Contractile fibers - cytokinesis in animal cells
● Gonad - sex organ that produces the gametes
● Flowers - ovaries and ovule , anther and pollen
● Animals - ovaries and oocyte/ova and testes and spermatozoa
● Gametogenesis
○ In animals gametes form directly from meiosis , in flowers meiosis forms microspores and
megaspores that develop into gametes
● Microgametes- are the pollen grain with tube nucleus and generative nucleus
● Mega Gamete- are the egg cell with 2 polar nuclei and female gamete
● Zona pellucida
● Sperm has condensed chromosomes , acrosome , mitochondria , tail and
○ Microtubules - in the sperm will produce whip like movements of the tail keeping the
sperm in suspension and helping it swim to the ovum
● Egg cell - follicle cells , zona pellucida , food reserves , cytoplasm with mitochondria , cell
membrane
● Polyspermy
● Cortical reaction
● Double fertilization
● Endosperm triploid nucleus

Calculating the mitotic index - an

example
P = Prophase, where the cell Prepares to
divides

M = Metaphase, where the chromosomes align along the Middle

A = Anaphase, where the chromosomes move Away from each other

T = Telophase, where Two nuclei reform

Mitosis important for

Growth of multicellular organisms

● The two daughter cells produced are genetically identical (clones) and have the same number of
chromosomes as the parent cell which enables unicellular zygotes (as the zygote divides by
mitosis) to grow into multicellular organisms
● Growth may occur across the whole body of the organism or be confined to certain regions, such
as in the meristems (growing points) of plants

Replacement of cells & repair of tissues

● Damaged tissues can be repaired
● Cells are constantly dying they need to be continually replaced by genetically identical cells
● In humans cell replacement occurs rapidly in the skin and the lining of the gut
● Some animals can regenerate body parts, for example, zebrafish can regenerate fins and axolotls
regenerate legs and their tail amongst other parts

Asexual reproduction
 ● Asexual reproduction is the production of new individuals of a species by a single parent organism
– the offspring are genetically identical to the parent
● For unicellular organisms such as Amoeba, cell division results in the reproduction of a genetically
identical offspring
● For multicellular organisms new individuals grow from the parent organism (by cell division) and
then detach (‘bud off’) from the parent in different ways eg.runners from strawberries

Meiosis is important to produce genetic variation from

Independent assortment
● Independent assortment is the production of different combinations of alleles in daughter cells due
to the random alignment of homologous pairs along the equator during metaphase I of meiosis I
● The different combinations of chromosomes in daughter cells generate an increase in the genetic
variation
● In meiosis I, homologous chromosomes pair up and are pulled towards the equator of the spindle;
the way the pairs are arranged is completely random
● The combination of alleles that end up in each daughter cell depends on how the pairs of
homologous chromosomes were lined up

idea that the (pairs of) homologous chromosomes

randomly line up along the equator (of the cell) ;
(resulting in) { different / new } combinations of
{ chromatids / chromosomes } ;
(resulting in) { different / new } combinations of
alleles in the { gametes / eq } ;

Crossing Over
● Crossing over is the process by which non-sister chromatids exchange alleles because enzymes
will cut and join bits of maternal and paternal chromatids together
● During prophase I of meiosis I homologous chromosomes pair up and are in very close
proximity to each other
● The paired homologous chromosomes are known as bivalents
● The non-sister chromatids can cross over and get entangled
● These crossing points where the chromatids break are called chiasmata
● The entanglement places stress on the DNA molecules so a section of chromatid from one
chromosome may break and rejoin with the chromatid from the other chromosome
● This swapping of alleles can result in a new combination of alleles on the two chromosomes

Chapter 3C
● Gene linkage
● Polygenic inheritance
 graph of polygenic inheritance shows normal distribution

● Dihybrid cross
● Unexpected ratios from the test cross
● Continuous variation - features which show a huge range of values , polygenic and affected by
environmental factors eg.weight
● Discontinuous variation - small range of fixed values , inherited on one or small number of genes,
either present or not present eg. blood group

Studies
● Twin studies used to measure diff in environmental and genetic factors with ordinary siblings as
control group
● Studying continuous variation eg. height
○ It is a polygenic feature affected by genes and environment
○ Genes affect height like - male or female , growth hormone production , length of bone in
the legs , rate of bone growth
○ Environment affects height like - balanced diet with calcium for bone growth and protein
○ Deprivation of environmental factors means can't reach genetic height potential
○ Another environmental factors from MS is a factor which would reduce energy available
for growth like living in cold climate and using energy for body temperature regulation

Controlling gene expression

Pre translation control

Transcription factors - promoter sequences ( alters transcription by interacting with RNA polymerase )
and enhancer sequences (regulate activity by changing structure of chromatin making it less open or more
open to RNA polymerase )

RNA splicing - pre mRNA modified through processes removing introns and some exons, spliceosomes
join exons in different ways through RNA splicing - one gene forming diff variety of proteins and
variations of phenotypes

Post translation control

Modification of proteins after they have been synthesized

Dna methylation
● Addition of methyl group where cytosine occurs next to a guanine in the DNA chain
● Methyl group added by dna methyltransferase enzyme
● Group changes the arrangement of the DNA molecule , preventing transcription from taking place
- silencing a gene of a sequence of genes
 ● Can also modify the structure of histones - has epigenetic effect in more than one way
● Important in X chromosome inactivation
● DNA demethylation is removal of methyl group to enable genes to become active so they can be
transcribed
● Both are associated with diseases including cancers

Histone modification
● Can be modified in a number of ways to affect transcription of dna and gene expression
● Histones make up the chromosomes and so determine structure of chromatin - when chromatin is
supercoiled and dense, genes cant be copied to make proteins- known as heterochromatin
● Active chromatin is loosely held and uncoiled , genes are available for transcription so new
proteins can be made
● Histone acetylation - an acetyl group is added to one of the lysines in the histone structure
● Adding the group will open up the structure ,activating the chromatin , allowing genes to be
transcribed
● Removing the group will produce heterochromatin again
● Histone methylation- methyl group is added to the lysine in the histone , depending on the position
of the lysine , methylation causes inactivation of dna or activation of a region
○ Linked to the silencing of a gene or whole chromosomes
○ Plays a role in silcencing of one of the X chromosomes in every cell in female mammals

Non coding RNA

● Affects transcription of dna and modifies the products of transcription
● Genes and whole chromosomes can be silenced
● In female mammals one of the X chromosomes in every cell is deactivated by random
○ Due to the presence of a non coding rna called X inactive specific transcript produce by the
active Xist gene on the inactive chromosome
○ Xist coats one of the X chromosomes , deactivating it
○ Chromosome supercoils , condenses forming the stable inactive Barr body
● This is done to balance the gene products in males and females
● Another role for ncrna is in chromatin modification where it act on histones , making areas of
DNA available /unavailable for transcription

Specialization by gene modifications and controlling gene expression

1. Chemical stimulus eg.demethylation or transcription factors
2. Certain genes switched on or activated
3. Mrna produced from these genes
4. Translation forming a protein
5. Permanent modification of cell - specialized for its functions

Stem cells
A stem cell is a cell that can divide by mitosis an unlimited number of times and each new cell has the
potential to remain a stem cell or to develop into a specialized cell by a process known as differentiation
This ability of stem cells to differentiate into more specialized cell types is known as potency. There are
three main types of potency: totipotency , pluripotency , multipotency

Totipotency
● totipotent stem cells are embryonic stem cells
● can differentiate into any cell type found in an embryo, as well as extra-embryonic cells (the cells
that make up the placenta and umbilical cord)
● exist for a limited time in early mammalian embryos
● The zygote formed when a sperm cell fertilizes an egg cell is totipotent

Pluripotency
● pluripotent stem cells are embryonic stem cells that can differentiate into any cell type found in an
embryo but are not able to differentiate into cells forming the placenta and umbilical cord

Multipotency
● multipotent stem cells are adult stem cells that have lost some of the potency associated with
embryonic stem cells and are no longer pluripotent
● Stem cells are also found in some adult tissues but they are much less potent than embryonic stem
cells (i.e. they can only specialize into certain types of cells)

Totipotent - pluripotent- somatic adult stem cells and fully differentiated mature cells

● First stage of embryonic development is called cleavage

● Cleavage involves a special kind of mitosis where cell divide repeatedly without the interphase
● The earliest embryonic cells up to the 16-cell stage of human embryo development (around the
fourth day after fertilization) are also totipotent
● By around the 4th day after fertilization , they become a solid ball of 10-30 cells known as a
morula , the cells are all totipotent
● Within another day , the fifth day after fertilization, the embryonic cells have divided further and
formed a structure known as a blastocyst, which has an outer layer of cells and an inner mass of
cells
● By the time the blastocysts is formed , the cells in the inner layer have lost some of their ability to
differentiate and are no longer totipotent - they are known as pluripotent embryonic stem cells and
have become pluripotent as a result of some genes being permanently switched off
● The outer layer of cells will later form the placenta

Usually mark scheme is looking for this answer:

● Gene expression is controlled by switching on and off transcription of genes using transcription
factors / epigenetic factors
● During the process of differentiation , some parts of chromosomes undergo supercoiling to prevent
some genes being transcribed , other chromosome areas uncoil and open up for transcription so
new proteins are made
● Some genes activated , some genes silenced - the combination of the particular genes that are
activated or silenced results in different characteristics of fully differentiated mature cells
 ● Initially, the totipotent cells in the embryo are unspecialised but during development, totipotent
cells begin to translate only part of their DNA, which results in cell specialization
● There are no totipotent cells present in the later stages of development as cells lose their ability to
differentiate into any cell type

Explain why the cells in the morula are genetically identical.

• they are all (genetically identical due to being) derived
from the zygote (cell) (1)

• {DNA/ chromosomes} are replicated (in interphase / in

semi-conservative replication) (1)
• (therefore) each cell receives one identical copy of each
{strand of DNA / chromosome} (1)

Umbilical cord stem cells

● Blood draining from placenta and umbilical cord is a rich source of pluripotent stem cells
● If the blood is stored and frozen , stem cells can be available to the individual throughout life
● It is expensive and needs storage space and there is less evidence that this blood can successfully
treat someone

Adult stem cells / somatic stem cells

● Remain as undifferentiated cells found among normal differentiated cells in tissues/ organs
● Will differentiate when needed to produce a cell
○ White bone marrow has stem cells that form WBC
● Very small number of these cells in tissues
● Difficult to extract
● Form a limited range of differentiated cells- multipotent
● Difficult to grow in lab

Use of Stem Cells in Medicine

As stem cells have the ability to differentiate into other specialized cell types, they are very valuable in
medical research and treatments as they have the potential to replace damaged tissues and cells (that result
from certain diseases)

● many stem cell therapies already exist, including the treatment for leukemia (bone marrow cancer),
in which the existing stem cells in the bone marrow are killed, before being replaced using a bone
marrow stem cell transplant, which will eventually replace all the bone marrow cells - Bone
marrow stem cells can form different types of blood cells
● Other stem cell therapies are being researched, including therapies that replace damaged nerve
tissue to treat spinal cord injuries and therapies that replace damaged heart tissue to treat heart
disease and tissue damage caused by heart attacks

Therapeutic cloning
Experimental technique hoped to use in the future to produce large quantities of healthy tissue
● Technique used to produce embryonic stem cells from an adult cell donor
● Removing the nucleus from one normal body cell of a patient and transferring into a human ovum
with the original nucleus removed
● Mild electric shock used to fuse the nucleus with new cell and trigger development
● Newly formed cells develop , divide,produce a collection of identical cells with same genetic info
as the patient
● Stem cells are harvested and cultured in a suitable environment to differentiate into the required
tissue
● The cells transferred to patient where they do their job without ricks of rejection of immune system
● Adult stem cell nucleus must be modified before adding to empty ovum otherwise cultured stem
cells would carry the genetic mutation causing the problem in the first place

Induced pluripotent stem cells

Adult cells that have been reprogrammed by introduction of new genes to become pluripotent again
● They are pluripotent so can be turned into most cell types by manipulating transcription and
epigenetic factors
● Come from the individual patient so no issues of rejection
● Appear to be similar to human embryonic stem cells
● Overcomes ethical issue of using embryonic stem cells

● Making them differentiate into tissue that is needed is difficult

● Shows a tendency to become cancerous very quickly - genes used to make cell pluripotent is
associated with cancer development

There are two sources of human stem cells for use in medicine and research:

Use of embryonic stem cells

● Due to their ability to differentiate into almost any cell type, embryonic stem cells have huge
potential in the therapeutic treatment of many diseases
● For many countries the use of embryonic stem cells is banned, even for research
● In other countries the use of embryonic stem cells is allowed for research but is very tightly
regulated
● Embryonic stem cells can be totipotent if taken in the first 3-4 days after fertilization or pluripotent
if taken on day 5
● The embryos used for research are often the waste (fertilized) embryos from in vitro fertilization
(IVF) treatment - means these embryos have the potential to develop into human beings- why
many people have ethical objections to using them in research or medicine

Use of adult stem cells

● Adult stem cells can divide (by mitosis) an unlimited number of times but they are only able to
produce a limited range of cell types
● A small number of adult stem cells are found in certain tissues within the body such as: Bone
marrow - used to produce different types of blood cell , Brain - used to produce different types of
neural and glial cells
 ● These small numbers of stem cells remain to produce new cells for the essential processes of
growth, cell replacement and tissue repair
● Research is being carried out the introduction of adult stem cells into damaged tissue to treat
diseases (e.g. leukaemia) and injuries (e.g. skin burns)
● The use of adult stem cells is less controversial than embryonic stem cells because the donor is
able to give permission
● However, if adult stem cells are being donated from one person to another they need to be a close
match in terms of blood type and other body antigens otherwise, there is a chance that the cells
used are rejected by the patient's immune system (the cells in the stem cell transplant are
recognised as being foreign and are attacked by the patient's immune system)
● Ideally, the patient's own adult stem cells are used to treat them, as there is a much lower chance of
rejection

Treating diseases

Parkinsons
● Age related brain disorder
● Nerve cells in brain that produce dopamine stop working , dopamine levels fall and people develop
uncotrobbale tremors in hands and body , body becomes rigid , can't move normally at all
● Scientists hope that stem cell transplants can allow them to replace lost brain cells and restore
dopamine production

Type 1 diabetes
● Glucose sensitive insulin secreting cells from islets of langerhans in pancreas are destroyed ,
insulin not produced and blood glucose concentration is uncontroleed
● Stem cell therapy can give the people working pancreas cells again , restoring insulin production
and blood glucose control
Organs
There is a desperate need for organs that don't cause rejection problems and the hope is that pluripotent
stem cells will be able to provide the huge supply of organs needed for transplantation globally

Evaluating the use of stem cells in medicine

● Medical therapies are a breakthrough for cures to diseases that millions of people suffer from
● The use of stem cells that are collected from embryos created via IVF is ethically questionable as
this results in a viable embryo (an embryo that could become a fetus if implanted in a uterus) being
destroyed
● The disadvantage of only using adult stem cells is that, unlike embryonic stem cells, they are
unable to differentiate into all of the specialized cell types (some of which may be required to treat
certain diseases)
● society has to use all the available scientific knowledge to make decisions about the use of stem
cells (especially embryonic stem cells) in medical therapies, considering all the arguments for and
against their use

● Official regulatory authorities are required to help society make these decisions. They do this by
comparing the benefits and ethical issues of stem cell research and making decisions on the extent
to which stem cells can be used. These regulatory authorities carry out the following tasks:
1. Reviewing proposals for scientific research that uses stem cells and deciding if this research should
be allowed to go ahead
2. Licensing and monitoring of research centers that are involved in stem cell research
3. Providing guidelines for stem cell researchers to ensure they are working to the same high
standards
4. Monitoring developments in scientific research into stem cell therapies
5. Providing governments with correct, up-to-date advice and information on stem cell research,
which in turn helps society to understand how stem cells are being used and why this work is
important

Give two reasons why there are regulatory authorities relating to

human embryo research
1. idea of need to { monitor research / ensure research
is necessary } ;
2. to issue licenses (for stem cell research) ;
3. to monitor sources of stem cells ;
4. ensure that only early stage embryos are used as sources
of stem
cells ;
5. to prevent unethical use of stem cells ;
Chapter 4
Flagellum for motility and mobility
Capsule to prevent dehydration

Index of diversity - does not measure genetic diversity , it measures the different types (such as
species) there are in a dataset (a community)

Seed Banks - MS answers

PROS
Take up less space / smaller so more can be stored
Idea of greater genetic { diversity / variation } if large numbers of seed are stored
Can be stored for a long time /reference to dormancy
Idea of different species of plant being stored in {same/similar} conditions
Idea of not requiring maintenance in the same way as growing plants
Reference to economic advantage / reduced cost

CONS
Are not of interest to public
Cannot spread awareness/ raise funds easily

Collection
Seeds are collected from a large number of individual plants to ensure a high genetic diversity.
.Seeds are X-rayed to check for fully formed embryos so that only viable seeds are stored.
.Seeds are dried to prolong viability/survival, and stored at -20°C to stop enzyme activity and prevent
germination and decomposition.
.Seeds are periodically germinated to make new seeds, replace dead and decaying seeds and check for
viability.

Conditions
Low temperatures and dry atmosphere
-reduce { enzyme activity / metabolic processes / respiration / eq } in seed
-seed less likely to germinate / seed kept dormant
-reduce { enzyme activity / growth / eq } of { bacteria / fungi / micro-organisms / eq }
-decreases rate of decomposition

Genetic diversity
1. idea of seed harvested from different plants of the
same species ;
2. idea of seed collected from plants growing in different
{ locations / countries / eq } ;
3. idea of { variety of alleles / large gene pool } ;

Zoos
Prevent extinction.
.Maintains breeding populations when habitats are lost.
.Breeding programmes increase numbers so endangered animals can be introduced back into the wild.
.Zoos are used for research to gain a better understanding for conservation.
.Zoos raise awareness to educate the public on endangered species.

Captive Breeding and Genetic Diversity

1. idea that 18 individuals is a small population / small gene pool / low genetic diversity / may have been
closely related / eq ;
2. captive breeding will increase population ;
3. studbooks /records kept of breeding programme / eq ;
4. (zoos) select mates ;
5. inter-zoo exchange of animals for breeding / eq ;
6. idea of the need to prevent inbreeding ;
7. idea of avoiding genetic drift ;
8. use of { IVF / AI / use of surrogates } ;
9. process for measuring genetic diversity described, e.g. DNA profiling / eq ;

Explain why seeds are dried and then stored in a temperature-controlled environment.
1. so that germination will not take place ;
2. so that fungi do not grow / eq ;
3. to reduce enzyme activity ;
4. so that seeds will remain viable / eq ;

Suggest why seed germination is tested at regular intervals.

1. to check seed viability / eq ;
2. to grow plants to collect more seeds / to find out if
more seeds need to be collected ;