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Phylogenetics Is The Study of Evolutionary Relationships Among Biological Entities
Phylogenetics Is The Study of Evolutionary Relationships Among Biological Entities
Phylogeny: The study of the history of the evolution of a species or group, especially in reference to lines
of descent and relationships among broad groups of organism
Phylogenetics is the study of evolutionary relationships among biological entities
Nucleus No No Yes
Membrane-bound No No Yes
organelles
Mitochondria
● Surrounded by inner and outer membranes. Inner membrane folded to make cristae which is
surrounded by a fluid matrix
● contain their own genetic material; to replicate themselves during cell division
● Function: Releases energy from food in the form of ATP using Oxygen in a series of biochemical
reactions → aerobic respiration
● More found in cells requiring more energy, i.e; muscle cells
Centrioles
● Two found in each cell. Each a bundle of nine tubules.
● Function: Pull apart to form a spindle of microtubules in mitosis
Cytoskeleton
Dynamic, 3D, web-like structure made of microfilaments (protein fibres) and microtubules (protein
tubes)
Function: gives cytoplasm structure and keeps organelles in place
Vacuoles
Mostly found in plant cells. Formed and lost as needed in some animal cells. i.e; white blood cells
Gametogenesis: (meiosis)
Meiosis is a process where a single cell divides twice to produce four cells (sex cells or gametes) containing
the haploid number of chromosomes.
It consists of two stages;
➔ Meiosis l
◆ Same process as mitosis; two diploid cells produced
◆ Crossing over occurs during prophase (during synapsis); homologous chromosomes1 wind
around each other at the chiasmata and sections of each chromosome switch places;
genetic information is shared between the two → genetic variation even between siblings
◆ independent assortment occurs as a result of the alignment of homologs during metaphase
I, determining which maternal and paternal chromosomes assort to each daughter cell. Each
pair of alleles separates independently of every other pair of unlinked alleles leading to a
new combination of chromosomes.
➔ Meiosis ll
◆ Same process as mitosis (prophase, metaphase, anaphase, telophase) but DNA is not
replicated
◆ Only one of the four cells produced becomes an ovum; the others are polar bodies
Spermatogenesis (in testes) → spermatids → differentiate into mature sperm within about two months.
*occurs from onset of puberty throughout a man’s lifetime.
1 Carry the same genes but not necessarily the same alleles
Fertilisation:
Animals
1. Sperm move through the female
reproductive tract and the
acrosome region matures
2. Sperm cluster around ovum
(secondary oocyte)
3. Heads of sperms touch surface of
ovum → acrosome reaction2
4. One sperm3 eventually wriggles
through the weakened barriers
and touches the surface
membrane of the secondary
oocyte
5. The oocyte undergoes second
meiotic division to provide a
haploid egg nucleus
6. A tough fertilisation membrane is formed to prevent polyspermy following the cortical reaction
7. The head of the sperm enters the oocyte and the tail is left behind; the male and female
chromosomes fuse and a diploid4 zygote is produced
Plants
1. If the molecules on the surface of the pollen grain and the stigma recognise each other as being
from a different plant5 from the same species the pollen grain begins to grow or germinate
2. Pollen tube grows through stigma into the hollow style
3. Nucleus of pollen tube divides to form two male nuclei and the tip of the tube eventually passes
through the micropyle of the ovule *growth of pollen tube is very fast due to rapid elongation of
cell
4. Two male nuclei pass into the ovule
5. Double fertilisation occurs → one male nucleus fuses with the nuclei of the two polar bodies to
form the triploid endosperm nucleus and the other fuses with the egg cell to form the diploid
zygote
Stem cells
Stem cells are undifferentiated cells (Totipotent, Pluripotent, or multipotent) which have the potential to
differentiate and give rise to different specialised cells such as muscle cells. These cells are present in some
organs where they will divide to replace and replenish damaged tissue.
2 Enzymes are released from the acrosome which digest the follicle cells and the zona pellucida as the sperm
approach the egg
3 One sperm alone does not produce sufficient enzymes to penetrate the protective layers around the ovum; reason
for large number of sperm released in ejaculation
4 Containing two complete sets of chromosomes one from each parent
5 For more variation
Pluripotent: Can give rise to any type of specialised cell other than placental cells. i.e; embryonic
stem cells, taken from the blastocyst
Multipotent: Can give rise to more than one type of specialised cell- more limited than pluripotent
stem cells. i.e; adult stem cells
Uses of stem cells:
The main two types of stem cells are embryonic cells, which are derived from the blactocyst (a ball
of cells which developes 3-5 days after fertilisation) produced under IVF or fetal tissue, and adult
stem cells which are taken from adult tissues such as the bone marrow.
Due to their unique regenerative abilities (They are capable of continuous cell division and
technically have no hayflick limit), stem cells can be used to treat several diseases including type 1
diabetes- where they can be induced to become insulin producing beta cells.
Problems with using stem cells from donors:
➔ You need to find a suitable match which can be difficult
➔ Risk of rejection
➔ Risk of transmission of disease
➔ The recipient would have to take immunosuppressant drugs to prevent their body from rejecting
the stem cells making them vulnerable to opportunistic diseases
➔ Can cause cancer to develop
Stem cell ethics:
❖ Is it okay to create and destroy life for scientific purposes? Sometimes extra embryos from IVF are
used, they would be thrown away anyway
❖ Is it okay to ‘alter’ humans?
❖ What if stem cell therapy heralds damaging effects on humans in the future?
❖ Embryos should have the same human rights as a fully grown adult
❖ Stem cell research offers the hope of curing millions of hopeless people suffering from illnesses like
Parkinson’s and Alzheimer’s
❖ Use of adult stem cells is ethically less sensitive
Cell differentiation/differential gene expression
● external/internal stimulus (i.e; hormones, chemicals) triggers diff. Genes to be activated
● Diff. sections of dna are transcribed; active mRNA produced + translated into proteins
● Proteins are made→ control cell processes and determine cell structure and function
Genetic variation
❖ Alleles are alternative forms of the same gene that occupy the same location (gene locus)
A phenotype is the result of an interaction between genotype and the environment (e.g. animal hair
colour, human height, monoamine oxidase A (MAOA) and cancers). For example, about 400 genes
contribute to human height, however, environmental factors which determine a child’s nutrition and
overall health also affect it. The data on the relative contributions of genes and environment is often
difficult to interpret.
Gene locus
A locus (plural loci), in genetics, is the specific location or position of a gene, DNA sequence, on a
chromosome.
Phenotype and gene interactions
Some phenotypes are affected by many genes at different loci (polygenic inheritance) as well as the
environment (e.g. height) and this can give rise to phenotypes that show continuous variation.
Polygenic inheritance occurs when one visible characteristic (phenotype) is controlled by two or
more genes at different loci. Often the genes are large in quantity but small in effect. Examples of
human polygenic inheritance are height, skin color, eye color and weight. These characteristics do
not seem to follow mendelian rules in their inheritance patterns.
When there are large numbers of genes involved, it becomes hard to distinguish the effect of each
individual gene
Nucleus No No Yes
Membrane-bound No No Yes
organelles
Initially, scientists used morphology, or the physical appearance of organisms to identify the degree of
similarity or difference between them and in turn, grouping them into species, genus and so on. A species
is a group of closely related organisms which can interbreed to produce fertile offspring.
Some organisms may look similar while they are actually very different. The new science of
molecular phylogeny uses the analysis of the structures of many different chemicals 6 and genes to identify
how closely related organisms are and in turn back up or even disprove the relationships based on
morphology. This is done with the evidence from DNA profiling and analysis of the sequence of bases in
DNA and RNA as well as amino acid sequences.
The theory that there are three domains; two prokaryotes (Archea and bacteria) and the
eukaryotes developed as a result of analysis of ribosomes, enzymes and chemicals such as DNA and RNA
under molecular phylogeny. The three-domain system, remains a source of debate and uncertainty,
however, as some scientists argue that archaea are not more closely linked to eukarya and that the
evolution of organisms would be better represented by a complex web of life rather than a simple tree.
9 10-100,000 cellulose molecules (straight chains) joined by hydrogen bonds make up microfibrils.
Cambium: a layer of unspecialised cells between xylem and phloem.
Plant fibres and starch are renewable resources unlike oil which is limited and becomes increasingly
expensive. They are also biodegradable and are of better quality in some cases 10. Plant resources can be
carbon neutral; they take in carbon as they grow and release it as they are burnt or used. Thus, these
contribute to sustainability.
cotton:
Short, single fibres found around cotton seeds are spun to form long, continuous threads with are then
woven together to make fabrics.
Wood:
A composite material made of lignified cellulose fibres embedded in hemicelluloses 11. Wood has a very
high tensile strength at is quite flexible making it suitable for weight-bearing in buildings, making furniture
and making boats.
To make paper:
10 For instance, clothing made from cotton are more absorbent and therefore more comfortable to wear than those
made from synthetic fibres
11 Polysaccharides found in cell walls which are less complicated in structure than cellulose.
➔ Soak in a strong alkali such as caustic soda
➔ Pulp consisting of cellulose and lignified cellulose left in water
➔ Thin layers of pulp pressed onto frames
➔ Layers of pulp dry to form paper
Biodiversity
The variety of organisms present in a given habitat
➔ Species richness: The number of species present in a habitat in a given time.
➔ Species evenness: How close in numbers each species in an environment is.
➔ Genetic diversity (within a species): The variety of alleles in a gene pool of a species; the more
genetic variation the better bc. Higher chances of survival
Endemism
The ecological state of a species being unique to a defined geographic area (in the wild) where they are not
found anywhere else.
Concept of Niche
A niche is the specific role or function of an organism in its habitat which is a result of its physical,
anatomical, and physiological adaptations.
Adaptations:
➔ Behavioral; The ways an organism acts
◆ I.e.: bird calls, migration
➔ Physiological: processes that take place inside an organism’s body
◆ I.e.: Making venom, secreting slime
➔ Anatomical: Structural features of an organism
◆ I.e.: long beaks, sharp claws
Natural selection:
The differential survival and reproduction of individuals due to differences in phenotype.
This is a type of directional selection which shows a change from one phenotypic property to a new one
more advantageous in the circumstances.
*This often begins with geographical isolation which changes the selection pressures on a species
1. There are genetic differences13 between organisms within the same species which results in
different phenotypic traits.
2. Some traits are favourable; they make organisms fitter as these adaptations make them better
suited to their environments14
3. Many favourable traits are heritable, meaning they can be passed onto offspring
4. The fitter15 animals are more likely to survive and pass16 on their advantageous phenotypic traits to
their offspring
Mechanisms of evolutionary change:
★ Natural selection: *cannot operate unless there is genetic variation
★ Genetic drift: *Cannot operate unless there is genetic variation - The chance disappearance of
individuals who die or do not reproduce
★ Mutation; a source of genetic variation
★ Migration; As genetically different organisms join a population; their alleles become more frequent
in that population
Charles Darwin Identified this as a key mechanism of evolution, the change in heritable traits of a
population over time. Under the idea of the survival of the fittest, organisms 17 with favourable traits are
most likely to reproduce and pass on the alleles that code for these traits as they give them an advantage
in a particular niche. Over generations, the alleles that mark their variation become more frequent and
eventually whole populations change. This can also lead to speciation whereby new and distinct species
are formed in the course of evolution.
Conservation refers to the maintainance and protection of a living and changing environment in order to
maintain biodiversity.
Animal species at risk of extinction can be saved in different ways:
❖ Regions can be established as national parks or protected areas to prevent the further destruction
of habitats by human activity
❖ Zoos can use captive breeding programmes.
➢ Individuals of a species are bred in zoos and parks *stud books and DNA profiles are kept
➢ Genetic diversity is maintained as sperm can be swapped with other zoos (for artificial
insemination)
❖ Reintroduction programmes:
➢ Captive-bred animals can be reintroduced to their natural habitats in the wild to restore the
original populations
➢ Reintroduction is most successful in national parks or other protected areas. The Californian
condors have been saved in this way.
Problems with captive breeding and reintroduction:
*Core practical; tensile strength, plant mineral deficiencies, antimicrobial properties of plants
18 I.e., they may not know how to interact with other animals
19 Between -20 and -40 degrees celsius