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Biology – Cellular Control, Biotechnology, Environments,
Responding to the Environment

Module 1 – Cellular Control/Genetics
   1) HOW DNA CODES FOR PROTEINS

A gene is a length of DNA that codes for one or more polypeptides. In the human
genome, there are about 25,000 genes. Each gene occupies a locus on the
chromosome.

The sequence of nucleotide bases on a gene provides a genetic code, instructions
for the construction of a polypeptide. It has a number of characteristics:

   -   It is a triplet code, i.e. a sequence of three nucleotide bases codes for an
       amino acid. The number of different triplet sequences is 64.
   -   It is a degenerate code, i.e. all amino acids except methionine have more
       than one code.
   -   Some codes do not code for an amino acid, but indicate “stop” – the end of
       the polypeptide chain.
   -   It is widespread but not universal. All triplet codes may not code for the same
       amino acids in all organisms.

Transcription

A messenger RNA molecule is made. For this, one strand of the length of DNA is
used as a template. There are free DNA nucleotides in the nucleoplasm and free
RNA nucleotides in the nucleolus.

   -   A gene to be transcribed unwinds and unzips. To do this, the length of DNA
       that makes up the gene dips into the nucleolus. Hydrogen bonds between the
       complementary base pairs break.
   -   Activated RNA nucleotides bind, through hydrogen bonding, to their exposed
       complementary bases. This is catalysed by the enzyme RNA polymerase.
   -   The two extra phosphoryl groups are released. This releases energy for
       bonding adjacent nucleotides.
   -   The mRNA produces in complementary to the nucleotide base sequence on
       the template strand of the DNA and is therefore a copy of the base sequence
       on the coding strand of the length of DNA.
   -   The mRNA is released from the DNA and passes out of the nucleus, through
       a nuclear pore in the nuclear envelope, to a ribosome.
2) TRANSLATION

Translation is the second stage of protein synthesis, when the amino acids are
assembled into a polypeptide. The sequence of amino acids is dictated by the
sequence of codons on the mRNA.

Transfer RNA

Another form of RNA, transfer RNA, is made in the nucleus. They are lengths of
RNA that fold into hairpin shapes and have three exposed bases at one end where a
particular amino acid can bind. At the other end of the molecule are three unpaired
nucleotide bases, known as an anticodon. Each anticodon can bind temporarily with
its complementary codon.

Assembly

   1) A molecule of mRNA binds to a ribosome. Two codons are attached to a
      small subunit of the ribosome. The first exposed mRNA codon is always AUG.
      Using ATP energy and an enzyme, a tRNA with methionine and the anticodon
      UAC forms hydrogen bonds with this codon.
   2) A second tRNA, bearing a different amino acid, binds to the second exposed
      codon with its complementary anticodon.
   3) A peptide bond forms between the two adjacent amino acids. An enzyme,
      present in the small ribosomal unit, catalyses the reaction.
   4) The ribosome now moves along the mRNA, reading the next codon. A third
      tRNA brings another amino acid, and a peptide bond forms between it and the
      dipeptide. The first tRNA leaves and is able to collect and bring another of its
      amino acids.
   5) The polypeptide chain grows until a stop codon is reached. There are no
      corresponding tRNAs for these three codons (UAA, UAC and UGA), so the
      polypeptide chain is now complete.

   3) MUTATIONS – 1

A mutation is a change in the amount of, or arrangement of, the genetic material in a
cell. It is a random change to the genetic material, due to a change in the DNA (base
deletion, addition or substitution; inversion or repeat of a triplet), or by chromosome
mutation, involving a change to the structure of a chromosome (deletion, inversion or
translocation). Mutations can also occur during semi-conservative replication of
DNA. Certain substances, like tar from tobacco, UV light, X-rays and gamma rays,
can cause mutations.
There are two main classes of DNA mutations:

   -   Point mutations, where one base replaces another. These are also known
       as substitution mutations.
   -   Insertion/Deletion mutations, where one or more nucleotide pairs are
       inserted or deleted from a length of DNA. This causes a frameshift.

Many genetic diseases are the result of DNA mutations:

   -   In 70% of cystic fibrosis cases, the mutation is the deletion of a triplet of base
       pairs, deleting an amino acid from the sequence of 1480 amino acids in the
       normal polypeptide.
   -   Sickle-cell anaemia is the result of a point mutation on codon 6 of the gene for
       the beta-polypeptide chain of haemoglobin. It causes the amino acid valine to
       be inserted at this position of the polypeptide chain in place of glutamic acid.
   -   Growth-promoting genes are called proto-oncogenes, which, by a point
       mutation, can be turned into oncogenes. While proto-oncogenes can be
       switched off, oncogenes cannot be, so oncogenes result in unregulated cell
       division, leading to a tumour.
   -   Huntington disease results from an expanded triple nucleotide repeat – a
       stutter. The normal gene for Huntington protein has repeating CAG
       sequences. If they expand above a threshold number, the protein is altered
       sufficiently enough to cause Huntington disease.

   4) MUTATIONS – 2

If a gene is altered by a change to its base sequence, it becomes another version of
the same gene. It is an allele of the gene. It may produce no change to the
organism’s phenotype if:

   -   The mutation is in a non-coding region of the DNA.
   -   It is a silent mutation: although the base sequence has changed, it still
       codes for the same amino acid, so the protein is unchanged.

Mutations that have neutral effects are mutations that change the genotype and
phenotype of the organism, but the changed characteristic gives no particular
advantage or disadvantage to the organism.

   5) THE LAC OPERON

The bacterium E. coli can synthesise about 3000 different polypeptides. However,
there is great variation in the numbers of different polypeptides within the cell. There
may be 10,000 molecules of ribosomal polypeptides in each cell and just 10
molecules of some of the regulatory proteins.

Enzymes involved in basic cellular functions are synthesised at a fairly constant rate.
Inducible enzymes are synthesised at varying rates, according to the cell’s
circumstances. Bacteria adapt to their environments by producing enzymes to
metabolise certain nutrients only when those nutrients are present. For example, E.
coli metabolises glucose, but it can also use lactose as a respiratory substrate.

The lac operon is a section of DNA within the bacterium’s DNA. It consists of a
number of parts:

Structural genes: One gene codes for the enzyme beta-galactosidase but another
gene codes for the enzyme lactose permease.

The operator region: A length of DNA next to the structural genes. It can switch the
structural genes on and off.

The promoter region: A length of DNA to which the enzyme RNA polymerase binds
to begin the transcription of the structural genes.

How the lac operon works when lactose is absent:

   1) The regulator gene is expressed and the repressor protein is synthesised.
      The repressor protein can bind to both lactose and the operator region.
   2) The repressor protein binds to the operator region, which also means it covers
      some of the promoter region. Because of this, RNA polymerase cannot attach
      as it normally does.
   3) The structural genes cannot be transcribed into mRNA.
   4) Without mRNA these genes cannot be translated and the enzymes cannot be
      synthesised.

How the lac operon works when lactose is present:

   1) Lactose (inducer) molecules bind to the other site on the repressor protein.
      This causes molecules of the repressor protein to change shape so that its
      other binding site cannot now bind to the operator region.
   2) This leaves the promoter region unblocked, so RNA polymerase can bind to it
      and initiate the transcription of mRNA for the genes that code for beta-
      galactosidase and lactose permease.
   3) The operator-repressor-inducer system acts as a molecular switch. It allows
      transcription and subsequent translation of the structural genes into the lac
      enzymes.
6) GENES AND BODY PLANS

Drosophila Development

When the eggs are laid a series of mitotic divisions is triggered, at a rate of one
every 6-10 minutes.

   -   At first, no new cell membranes form, and a multinucleate syncytium is
       formed.
   -   After the 8th division, the 256 nuclei migrate to the outer part and by the 11 th
       division the nuclei form an outer layer around a central, yolk-filled core.
   -   The division rate slows, and the nuclear genes switch from replicating to
       transcribing.
   -   The plasma membrane invaginates around the 6000 nuclei, and the resulting
       cells form a single outer layer.
   -   After another 2-3 hours, the embryo divides into a series of segments. These
       correspond to the organism’s organisation or body plan.
   -   Three segments merge to form the head, three to form the thorax and 8 to
       form the abdomen.

Genetic Control

   - Some genes determine the embryo’s polarity. Polarity refers to which end is
     anterior and which end is posterior.
   - Other genes, called segmentation genes, specify the polarity of each
     segment.
   - Homeotic selector genes specify the identity of each segment and direct the
     development of individual body segments. These are the master genes in the
     control network of regulatory genes. There are two gene families:-
    - The complex that regulates development of thorax and abdomen sections.
      - The complex that regulates development of head and thorax sections.

Homeobox genes control the development of the body plan of an organism,
including the polarity and positioning of organs. There are homeobox genes in the
genomes of segmented animals from segmented worms to vertebrates. The
homeobox genes each contain a sequence of around 180 base pairs, producing
polypeptides of about 60 amino acids. Some of these polypeptides are transcription
factors and bind to DNA upstream to prevent or allow the expression of other genes.

Homeobox genes are arranged in clusters known as Hox clusters:

   -   Nematodes have one Hox cluster.
   -   Drosphila has two Hox clusters.
   -   Vertebrates have four clusters, of 9 – 11 genes, located on separate
       chromosomes.
7) APOPTOSIS

Apoptosis is programmed cell death that occurs in multicellular organisms. Cells
should undergo around 50 mitotic divisions (the Hayflick constant) and then undergo
a series of biochemical events that leads to orderly cell death. This is contrasting to
cell necrosis, a damaging cell death that occurs after trauma and releases hydrolytic
enzymes.

   -   Enzymes break down the cell cytoskeleton.
   -   The cytoplasm becomes dense, with organelles tightly packed.
   -   The cell surface membrane changes and small bits called blebs form.
   -   Chromatin condenses and the nuclear envelope breaks. DNA breaks into
       fragments.
   -   The cell breaks into vesicles that are taken up by phagocytosis. The cellular
       debris is disposed of and does not damage any other cells or tissues.

The process is controlled by a diverse range of cell signals, some of which come
from inside the cells and some from outside. The signals include cytokines made by
cells of the immune system, hormones, growth factors and nitric oxide. Nitric oxide
can induce apoptosis by making the inner mitochondrial membrane more permeable
to hydrogen ions and dissipating the proton gradient. Proteins are released into the
cytosol. These proteins bind to apoptosis inhibitor proteins and allow the process to
take place.

One signal that can cause a cell to undergo apoptosis is a cytokine called TNF. It
binds to a receptor on the plasma membrane which has a “death domain” on the
cytoplasmic side. When TNF is bound, the death domain can bind to the death
domain of a different protein called FADD, which has a “death effector domain.”
When FADD binds to the death domain of the receptor, it activates an enzyme called
caspase that initiates the process of apoptosis.

Apoptosis and Development

Apoptosis is an integral part of tissue development. There is extensive division and
expansion of a particular cell type followed by pruning through programmed cell
death. The excess cells shrink, fragment and are phagocytosed so that the
components are reused and no harmful hydrolytic enzymes are released into the
surrounding tissue.

Apoptosis is tightly regulated during development, and different tissues use different
signals for inducing it. It weeds out ineffective or harmful T-lymphocytes during the
development of the immune system. During limb development, apoptosis causes the
digits (fingers and toes) to separate from each other.
If the rates of apoptosis and mitosis are not balanced:

   -   Not enough apoptosis leads to the formation of tumours.
   -   Too much leads to cell loss and degeneration.

   8) MEIOSIS

It is important to remember the significance of having homologous pairs of
chromosomes in the nucleus of a cell.

All living organisms can reproduce. In eukaryotes, asexual reproduction can be
achieved by mitosis, and in prokaryotes, binary fission. The offspring produced
through asexual reproduction are produced to be genetically identical; however,
variation occurs through random mutation.

In sexual reproduction, the offspring are genetically different from each other and
from the parents. Each parent produces special reproductive cells, known as
gametes. Gametes (one from each parent; in the case of humans a sperm cell and
an egg cell) fuse together at fertilisation to produce a zygote.

When two gametes fuse together to make one cell, the cell produced must have a
diploid number of chromosomes in its nucleus. Therefore, the gametes must have a
haploid number of chromosomes; this ensures that, after fertilisation, the original
chromosome number is restored. Because of this, meiosis is the type of nuclear
division where the chromosome number is halved.

Meiosis consists of two divisions, meiosis I and meiosis II, and each division has 4
stages: prophase, anaphase, metaphase and telophase. Before meiosis I,
interphase occurs, and the DNA replicates.

Meiosis I

Prophase I

   -   The chromatin condenses and undergoes supercoiling so that the
       chromosomes shorten and thicken.
   -   The chromosomes come together in their homologous pairs to form a
       bivalent. Each member of the pair has the same genes at the same loci, and
       consists of one maternal and one paternal chromosome.
   -   The non-sister chromatids wrap around each other and attach at points called
       chiasmata.
   -   They may swap sections of chromatids with one another in a process called
       crossing over.
   -   The nucleolus disappears and the nuclear envelope disintegrates.
   -   A spindle made of microtubules forms.
-   Prophase I can last for days, months or even years, depending on the species
       and on the type of gamete (male or female) being formed.

Metaphase I

   -   Bivalents line up across the equator of the spindle, attached to spindle fibres
       at the centromeres. The chiasmata are still present.
   -   The bivalents are arranged randomly (random assortment) with each
       member of a homologous pair facing opposite poles.
   -   This allows the chromosomes to independently segregate when they are
       pulled apart in anaphase I.

Anaphase I

   -   The homologous chromosomes in each bivalent are pulled by the spindle
       fibres to opposite poles.
   -   The centromeres do not divide.
   -   The chiasmata separate and lengths of chromatid that have been crossed
       over remain with the chromatid to which they have become newly attached.

Telophase I

   -   In most animal cells two new nuclear envelopes form – one around each set
       of chromosomes at each pole – and the cell divides by cytokinesis. There is a
       brief interphase and the chromosomes uncoil.
   -   In most plants, the cell goes straight from anaphase I into meiosis II.

Meiosis II

Prophase II

   -   If the nuclear envelope has reformed, then it breaks down again.
   -   The nucleolus disappears and the chromosomes condense, and the spindles
       form again.

Metaphase II

   -   The chromosomes arrange themselves on the equator of the spindle, and
       they are attached the spindle fibres at the centromere.
   -   The chromatids of each chromosome are randomly assorted (arranged).

Anaphase II

   -   The centromeres divide and the chromatids are pulled to opposite poles by
       the spindle fibres. The chromatids randomly segregate.
Telophase II

   -   Nuclear envelopes reform around the haploid daughter nuclei.
   -   In animals, the two cells now divide to give four haploid cells.
   -   In plants, a tetrad of four haploid cells is formed.

   9) GENETIC CROSSES

Two alleles:          G – white skin              g – green skin

Parent phenotype:        green                          green

Parent genotype:           gg                             gg

Gametes:                 (g)(g)                          (g)(g)

Offspring genotype:                     gg

Offspring phenotype:                   green

Homozygous individuals are said to be “true breeding” or “pure breeding” because
they can only pass on one particular allele for a particular gene. The same would be
true if the individuals were homozygous dominant rather than homozygous
recessive.

If an individual’s phenotype is white skinned, we do not know whether their genotype
is homozygous (GG) or heterozygous (Gg). To found out, we would have to carry out
test crosses.

   10) CODOMINANCE

Codominance occurs when both alleles for a particular gene contribute to the
phenotype. Neither allele is dominant over the other and the overall phenotype is
due to a mixed effect of two alleles.

The alleles are defined by superscript letters in the gene, i.e. red colour is C^R and
white colour is C^W.

Parent phenotype:       red flowers                   white flowers
Parent genotype:         C^RC^R                         C^WC^W
Gametes:                (C^R)(C^R)                     (C^W)(C^W)

Offspring genotype:                     C^RC^W
Offspring phenotype:                   pink flowers
11) THE CHI-SQUARED TEST

The chi-squared test tests the null hypothesis through statistical analysis. The null
hypothesis is a useful starting point in examining the results of a scientific
investigation. It is based on the assumption that “there is no (statistically) significant
different between the observed and expected numbers, and any difference is due to
chance.”

The formula for calculating a value of     :




Example

The numbers of resulting offspring for each observed phenotype of Drosophila were
counted:

Straight wing, grey body – 113
Straight wing, ebony body – 30
Curled wing, grey body – 29
Curled wing, ebony body – 115

Phenotype      Straight/grey   Straight/ebony    Curled/grey       Curled/Ebony
O              113             30                29                115
E ratio        1               1                 1                 1
E              71.75           71.75             71.75             71.75
O-E            41.25           -41.75            -42.75            43.25
(O-E)^2        1701.5625       1743.0625         1827.5625         1870.5625
(O-E)^2/E      23.71515679     24.29355401       25.471255436      26.07055749

   = 99.55 (to 2 s.f.)

A degrees of freedom of 3 should be used, as there are four classes.

By looking up the critical value in a table, we know that it is 7.82.

Since the chi-squared value is greater than 7.82, we know that there is a very low
probability that the difference in the observed results compared to the expected
results occurred by chance. This means that independent assortment of these gene
loci is unlikely to have occurred.
12) SEX LINKAGE

Parent’s sex:                  Female                             Males
Parent’s chromosomes:           XX                                 XY
Gametes:                       (X)(X)                            (X)(Y)

Offspring chromosomes:               XX                  XY
Offspring sex:                     Female                Male

The sex chromosomes X and Y also carry genes. However, the X and Y
chromosomes are not a true pair because part of the Y chromosome is missing. This
means that some alleles present on the X chromosome are not present on the Y
chromosome. Therefore, males sometimes only possess one allele for a particular
gene locus.

Such alleles are sex linked:




The “yellow” gene has only one allele in males, as it is only present on the X
chromosome and not the Y. The “red” gene, however, will act in the same way as
any other gene, with the dominant allele being expressed over the recessive.

The allele that causes red-green colour blindness is sex linked. The genotype of this
male with red-green colour blindness is r-. This is often written as X^rY, indicating a
sex-linked condition.

Example

r = red-green colour blindness                R = normal vision

Parent genotype:    X^rY X^RY       X^rX^r            X^RX^R         X^rX^R
Gametes:         (X^r)(Y) (X^R)(Y) (X^r)(X^r)       (X^R)(X^R)      (X^r)(X^R)

Offspring genotype:         X^rY           X^RY       X^RX^r         X^RX^R
Offspring phenotype:     colour blind      normal     normal         normal
Offspring sex:              male            male      female          female

The offspring with colour-blindness must be male.
13) DIHYBRID CROSSES

A dihybrid cross involves studying the inheritance of two genes (2 loci) at the same
time.

Genotype: TtGg                                Genotype: HhFF
Gametes: (TG)(Tg)(tG)(tg)                     Gametes: (HF)(HF)(hF)(hF)

   14) EPISTASIS

Epistasis is the interaction between two genes where one locus (epistatic gene)
masks or suppresses the expression of the gene at the other locus (hypostatic
gene).

The epistatic gene and hypostatic gene may work in a complementary fashion (work
with each other) or may work in an antagonistic fashion (work against each other).

Complementary Fashion

Two genes that code for enzymes in a sequential metabolic reaction are examples of
complementary alleles, e.g. melanin is a brown pigment made indirectly from an
amino acid phenylalanine via another amino acid called tyrosine.

Phenylalanine             E1       Tyrosine         E2         Melanin

Production of melanin required the consequential action of enzymes E1 and E2
coded for by genes A and B respectively. The dominant alleles are needed to
express active enzymes. Without either active enzyme, the phenotype is ALBINO
(WHITE) rather than brown.

AABB – not albino aABB – not albino           AAbB – not albino      aaBB – albino
aabB – albino aabb – albino

Antagonistic Fashion

Genes may work against each other in two ways, dominant epistasis and
recessive epistasis.

Dominant epistasis is where the expression of a dominant allele at one locus
masks the expression of alleles at a different locus.

           H - hairy                                     E – masks
                                                         H

                                                      E – does not mask H
           h - hairless


HHEE – hairless         HhEE – hairless HHEe – hairless HhEe – hairless
hhEE – hairless        HHee – hairy Hhee – hairy hhee – hairless hhEe – hairless
Recessive epistasis is where the expression of a dominant allele at the epistatic
locus is needed for the expression of alleles at the hypostatic locus. Therefore, a
homozygous recessive individual for the epistatic gene results in no expression of
the hypostatic gene.


         P - purple                              A – white
                                                 ifrecessive

                                                     a
         p - pink



AABB – purple AABb – purple AAbb – pink AaBB – purple AaBb – purple
Aabb – pink aaBB – white aaBb – white aabb – white

   15) VARIATION

Variation in biology is the presence of differences between individuals. It results in
different phenotypes for the individuals. Variation occurs between members of the
same species as well as between members of different species. Even identical twins
can show slight phenotypic variation from one another.

Discontinuous Variation – there are discrete categories for the phenotype. These
are qualitative phenotypes. It may be caused by the inheritance of different alleles of
one gene only (monogenic). For example, cystic fibrosis is caused by the inheritance
of a mutated allele of a single gene. Discontinuous variation may also be caused by
inheritance of a few genes which interact with each other in an epistatic manner.

In discontinuous variation, different alleles for the same gene will have large effects
on a phenotype. Different loci will have quite different effects on the phenotype.
Dominant, recessive and codominant patterns of inheritance are examples of
discontinuous variation.

Continuous Variation – there are a range of phenotypes with a minimum and
maximum value and many intermediate values in between. These are quantitative
phenotypes. Continuous variation is caused by the inheritance of two or more genes.
Each gene has a small additive effect on the overall phenotype of the organism.
Different alleles at the same locus have a small effect on the phenotype. A large
number of genes may affect the phenotype (POLYGENIC).

Variation is also caused by environmental influence, e.g. nutrition, UV, radiation, etc.
16) POPULATION GENETICS

Population genetics involves determining the frequency of alleles in whole
populations rather than in individuals. A whole population is likely to possess more
different alleles than an individual. Population geneticists study the genetic structure
of whole populations.

The set of genetic information carried by a whole population is referred to as the
gene pool. Population geneticists measure the frequency of different alleles in the
gene pool.

When alleles show codominance, this is quite easy to do as the number of
heterozygous phenotypes is the same as the number of heterozygous genotypes.

In a population of snapdragons, 30 are red, 49 are pink and 10 are white. The
frequency of each allele is easy to measure in this population of plants:

Red alleles – 109
White alleles – 69

However, the situation is more complicated with dominant and recessive alleles and
the Hardy-Weinberg principle must be used:

The frequency of the dominant allele is assigned letter “P” and the frequency of the
recessive allele “Q.”

In a cross between two heterozygotes the offspring are produced in the following
ratio and the frequency of each genotype is described using P and Q as follows:

1 homozygous dominant (p^2)
2 heterozygous (2pq)
1 homozygous recessive (q^2)

The frequency of genotypes adds to one: p^2 + 2pq + q^2
The frequency of alleles also adds to one: p + q = 1

If the frequency of the homozygous recessive genotype is known, then the
frequencies of p and q can be calculated.

e.g. phenylkatenuria is caused by a recessive allele. It occurs in 1 in 10,000 live
births:

q^2 = 0.0001
q = 0.01
p = 0.99

p^2 + 2pq + q^2 = 1
2pq = 0.0198
17) GENES AND ENVIRONMET – EVOLUTION

A selection pressure is an environmental factor that confers greater chances of
survival to reproductive age on some members of the population. If a selection
pressure maintains a phenotype, it is known as stabilising selection. If the
environment changes and the phenotype begins to become more/less prevalent, this
is known as directional selection and acts as an evolutionary force leading to
evolutionary change.

Any change to the frequency of alleles in a population is referred to as genetic drift.
Genetic drift is more likely to happen in smaller populations of organisms.
Populations can become smaller by a variety of isolating mechanisms:

   -   Geographical (ecological), where subpopulations are separated by barriers
       such as rivers, seas, mountain ranges, etc. This can lead to alopatric
       speciation.
   -   Seasonal (temporal), where barriers such as climate change throughout the
       year separate populations.
   -   Reproductive barriers, where individuals can no longer physically mate due to
       incompatible genitals, breeding seasons or courtship behaviours.

In each different subpopulation, different alleles may increase or decrease, maybe
eventually leading to a new species, i.e. that can no longer breed at all. This process
is called speciation.

Genetic drift is more likely to occur in smaller populations because allele frequencies
can change in a more dramatic fashion. However, in a large population, only small
changes in allele frequency would be expected. However, this may not be the case if
evolutionary forces caused directional selection.

In extreme cases, genetic drift can cause elimination of an allele from a population.
This will remove variation and could reduce the chances of survival in a new
environment. It could therefore contribute to the extinction of a species. Genetic drift
can also lead to the formation of a new species.

   18) WHAT IS A SPECIES?

Biological Species Concept – “a group of similar organisms that can interbreed to
produce fertile offspring and is reproductively isolated from other such groups.” This
is used for classification but presents problems for organisms that do not reproduce
sexually, i.e. binary fission in bacteria.

Phylogenetic Species Concept – “organisms that have similar morphology
(anatomy), physiology, embryology (stages of development) and behaviour; and also
occupy the same ecological niche.” The phylogentic approach us based upon
analysis of differences or similarities between the DNA of different organisms.

A particular base sequence of an organism is called its haplotype, which can be
compared between organisms.
A divergence can be calculated as:




The least divergent organisms are put into a group called a clade, and a cladogram
shows evolutionary relationships between groups, i.e. phylogeny.

The cladistic approach uses:

   -   Evolutionary relationships rather than structural similarity
   -   Quantitative analyses requiring computer programs.
   -   Relies on DNA (and RNA) sequencing.

If often confirms Linnaean classification, but sometimes leads to organisms being
reclassified, as was the case for the 3-domain system of classification.

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  • 1. Biology – Cellular Control, Biotechnology, Environments, Responding to the Environment Module 1 – Cellular Control/Genetics 1) HOW DNA CODES FOR PROTEINS A gene is a length of DNA that codes for one or more polypeptides. In the human genome, there are about 25,000 genes. Each gene occupies a locus on the chromosome. The sequence of nucleotide bases on a gene provides a genetic code, instructions for the construction of a polypeptide. It has a number of characteristics: - It is a triplet code, i.e. a sequence of three nucleotide bases codes for an amino acid. The number of different triplet sequences is 64. - It is a degenerate code, i.e. all amino acids except methionine have more than one code. - Some codes do not code for an amino acid, but indicate “stop” – the end of the polypeptide chain. - It is widespread but not universal. All triplet codes may not code for the same amino acids in all organisms. Transcription A messenger RNA molecule is made. For this, one strand of the length of DNA is used as a template. There are free DNA nucleotides in the nucleoplasm and free RNA nucleotides in the nucleolus. - A gene to be transcribed unwinds and unzips. To do this, the length of DNA that makes up the gene dips into the nucleolus. Hydrogen bonds between the complementary base pairs break. - Activated RNA nucleotides bind, through hydrogen bonding, to their exposed complementary bases. This is catalysed by the enzyme RNA polymerase. - The two extra phosphoryl groups are released. This releases energy for bonding adjacent nucleotides. - The mRNA produces in complementary to the nucleotide base sequence on the template strand of the DNA and is therefore a copy of the base sequence on the coding strand of the length of DNA. - The mRNA is released from the DNA and passes out of the nucleus, through a nuclear pore in the nuclear envelope, to a ribosome.
  • 2. 2) TRANSLATION Translation is the second stage of protein synthesis, when the amino acids are assembled into a polypeptide. The sequence of amino acids is dictated by the sequence of codons on the mRNA. Transfer RNA Another form of RNA, transfer RNA, is made in the nucleus. They are lengths of RNA that fold into hairpin shapes and have three exposed bases at one end where a particular amino acid can bind. At the other end of the molecule are three unpaired nucleotide bases, known as an anticodon. Each anticodon can bind temporarily with its complementary codon. Assembly 1) A molecule of mRNA binds to a ribosome. Two codons are attached to a small subunit of the ribosome. The first exposed mRNA codon is always AUG. Using ATP energy and an enzyme, a tRNA with methionine and the anticodon UAC forms hydrogen bonds with this codon. 2) A second tRNA, bearing a different amino acid, binds to the second exposed codon with its complementary anticodon. 3) A peptide bond forms between the two adjacent amino acids. An enzyme, present in the small ribosomal unit, catalyses the reaction. 4) The ribosome now moves along the mRNA, reading the next codon. A third tRNA brings another amino acid, and a peptide bond forms between it and the dipeptide. The first tRNA leaves and is able to collect and bring another of its amino acids. 5) The polypeptide chain grows until a stop codon is reached. There are no corresponding tRNAs for these three codons (UAA, UAC and UGA), so the polypeptide chain is now complete. 3) MUTATIONS – 1 A mutation is a change in the amount of, or arrangement of, the genetic material in a cell. It is a random change to the genetic material, due to a change in the DNA (base deletion, addition or substitution; inversion or repeat of a triplet), or by chromosome mutation, involving a change to the structure of a chromosome (deletion, inversion or translocation). Mutations can also occur during semi-conservative replication of DNA. Certain substances, like tar from tobacco, UV light, X-rays and gamma rays, can cause mutations.
  • 3. There are two main classes of DNA mutations: - Point mutations, where one base replaces another. These are also known as substitution mutations. - Insertion/Deletion mutations, where one or more nucleotide pairs are inserted or deleted from a length of DNA. This causes a frameshift. Many genetic diseases are the result of DNA mutations: - In 70% of cystic fibrosis cases, the mutation is the deletion of a triplet of base pairs, deleting an amino acid from the sequence of 1480 amino acids in the normal polypeptide. - Sickle-cell anaemia is the result of a point mutation on codon 6 of the gene for the beta-polypeptide chain of haemoglobin. It causes the amino acid valine to be inserted at this position of the polypeptide chain in place of glutamic acid. - Growth-promoting genes are called proto-oncogenes, which, by a point mutation, can be turned into oncogenes. While proto-oncogenes can be switched off, oncogenes cannot be, so oncogenes result in unregulated cell division, leading to a tumour. - Huntington disease results from an expanded triple nucleotide repeat – a stutter. The normal gene for Huntington protein has repeating CAG sequences. If they expand above a threshold number, the protein is altered sufficiently enough to cause Huntington disease. 4) MUTATIONS – 2 If a gene is altered by a change to its base sequence, it becomes another version of the same gene. It is an allele of the gene. It may produce no change to the organism’s phenotype if: - The mutation is in a non-coding region of the DNA. - It is a silent mutation: although the base sequence has changed, it still codes for the same amino acid, so the protein is unchanged. Mutations that have neutral effects are mutations that change the genotype and phenotype of the organism, but the changed characteristic gives no particular advantage or disadvantage to the organism. 5) THE LAC OPERON The bacterium E. coli can synthesise about 3000 different polypeptides. However, there is great variation in the numbers of different polypeptides within the cell. There may be 10,000 molecules of ribosomal polypeptides in each cell and just 10 molecules of some of the regulatory proteins. Enzymes involved in basic cellular functions are synthesised at a fairly constant rate. Inducible enzymes are synthesised at varying rates, according to the cell’s
  • 4. circumstances. Bacteria adapt to their environments by producing enzymes to metabolise certain nutrients only when those nutrients are present. For example, E. coli metabolises glucose, but it can also use lactose as a respiratory substrate. The lac operon is a section of DNA within the bacterium’s DNA. It consists of a number of parts: Structural genes: One gene codes for the enzyme beta-galactosidase but another gene codes for the enzyme lactose permease. The operator region: A length of DNA next to the structural genes. It can switch the structural genes on and off. The promoter region: A length of DNA to which the enzyme RNA polymerase binds to begin the transcription of the structural genes. How the lac operon works when lactose is absent: 1) The regulator gene is expressed and the repressor protein is synthesised. The repressor protein can bind to both lactose and the operator region. 2) The repressor protein binds to the operator region, which also means it covers some of the promoter region. Because of this, RNA polymerase cannot attach as it normally does. 3) The structural genes cannot be transcribed into mRNA. 4) Without mRNA these genes cannot be translated and the enzymes cannot be synthesised. How the lac operon works when lactose is present: 1) Lactose (inducer) molecules bind to the other site on the repressor protein. This causes molecules of the repressor protein to change shape so that its other binding site cannot now bind to the operator region. 2) This leaves the promoter region unblocked, so RNA polymerase can bind to it and initiate the transcription of mRNA for the genes that code for beta- galactosidase and lactose permease. 3) The operator-repressor-inducer system acts as a molecular switch. It allows transcription and subsequent translation of the structural genes into the lac enzymes.
  • 5. 6) GENES AND BODY PLANS Drosophila Development When the eggs are laid a series of mitotic divisions is triggered, at a rate of one every 6-10 minutes. - At first, no new cell membranes form, and a multinucleate syncytium is formed. - After the 8th division, the 256 nuclei migrate to the outer part and by the 11 th division the nuclei form an outer layer around a central, yolk-filled core. - The division rate slows, and the nuclear genes switch from replicating to transcribing. - The plasma membrane invaginates around the 6000 nuclei, and the resulting cells form a single outer layer. - After another 2-3 hours, the embryo divides into a series of segments. These correspond to the organism’s organisation or body plan. - Three segments merge to form the head, three to form the thorax and 8 to form the abdomen. Genetic Control - Some genes determine the embryo’s polarity. Polarity refers to which end is anterior and which end is posterior. - Other genes, called segmentation genes, specify the polarity of each segment. - Homeotic selector genes specify the identity of each segment and direct the development of individual body segments. These are the master genes in the control network of regulatory genes. There are two gene families:- - The complex that regulates development of thorax and abdomen sections. - The complex that regulates development of head and thorax sections. Homeobox genes control the development of the body plan of an organism, including the polarity and positioning of organs. There are homeobox genes in the genomes of segmented animals from segmented worms to vertebrates. The homeobox genes each contain a sequence of around 180 base pairs, producing polypeptides of about 60 amino acids. Some of these polypeptides are transcription factors and bind to DNA upstream to prevent or allow the expression of other genes. Homeobox genes are arranged in clusters known as Hox clusters: - Nematodes have one Hox cluster. - Drosphila has two Hox clusters. - Vertebrates have four clusters, of 9 – 11 genes, located on separate chromosomes.
  • 6. 7) APOPTOSIS Apoptosis is programmed cell death that occurs in multicellular organisms. Cells should undergo around 50 mitotic divisions (the Hayflick constant) and then undergo a series of biochemical events that leads to orderly cell death. This is contrasting to cell necrosis, a damaging cell death that occurs after trauma and releases hydrolytic enzymes. - Enzymes break down the cell cytoskeleton. - The cytoplasm becomes dense, with organelles tightly packed. - The cell surface membrane changes and small bits called blebs form. - Chromatin condenses and the nuclear envelope breaks. DNA breaks into fragments. - The cell breaks into vesicles that are taken up by phagocytosis. The cellular debris is disposed of and does not damage any other cells or tissues. The process is controlled by a diverse range of cell signals, some of which come from inside the cells and some from outside. The signals include cytokines made by cells of the immune system, hormones, growth factors and nitric oxide. Nitric oxide can induce apoptosis by making the inner mitochondrial membrane more permeable to hydrogen ions and dissipating the proton gradient. Proteins are released into the cytosol. These proteins bind to apoptosis inhibitor proteins and allow the process to take place. One signal that can cause a cell to undergo apoptosis is a cytokine called TNF. It binds to a receptor on the plasma membrane which has a “death domain” on the cytoplasmic side. When TNF is bound, the death domain can bind to the death domain of a different protein called FADD, which has a “death effector domain.” When FADD binds to the death domain of the receptor, it activates an enzyme called caspase that initiates the process of apoptosis. Apoptosis and Development Apoptosis is an integral part of tissue development. There is extensive division and expansion of a particular cell type followed by pruning through programmed cell death. The excess cells shrink, fragment and are phagocytosed so that the components are reused and no harmful hydrolytic enzymes are released into the surrounding tissue. Apoptosis is tightly regulated during development, and different tissues use different signals for inducing it. It weeds out ineffective or harmful T-lymphocytes during the development of the immune system. During limb development, apoptosis causes the digits (fingers and toes) to separate from each other.
  • 7. If the rates of apoptosis and mitosis are not balanced: - Not enough apoptosis leads to the formation of tumours. - Too much leads to cell loss and degeneration. 8) MEIOSIS It is important to remember the significance of having homologous pairs of chromosomes in the nucleus of a cell. All living organisms can reproduce. In eukaryotes, asexual reproduction can be achieved by mitosis, and in prokaryotes, binary fission. The offspring produced through asexual reproduction are produced to be genetically identical; however, variation occurs through random mutation. In sexual reproduction, the offspring are genetically different from each other and from the parents. Each parent produces special reproductive cells, known as gametes. Gametes (one from each parent; in the case of humans a sperm cell and an egg cell) fuse together at fertilisation to produce a zygote. When two gametes fuse together to make one cell, the cell produced must have a diploid number of chromosomes in its nucleus. Therefore, the gametes must have a haploid number of chromosomes; this ensures that, after fertilisation, the original chromosome number is restored. Because of this, meiosis is the type of nuclear division where the chromosome number is halved. Meiosis consists of two divisions, meiosis I and meiosis II, and each division has 4 stages: prophase, anaphase, metaphase and telophase. Before meiosis I, interphase occurs, and the DNA replicates. Meiosis I Prophase I - The chromatin condenses and undergoes supercoiling so that the chromosomes shorten and thicken. - The chromosomes come together in their homologous pairs to form a bivalent. Each member of the pair has the same genes at the same loci, and consists of one maternal and one paternal chromosome. - The non-sister chromatids wrap around each other and attach at points called chiasmata. - They may swap sections of chromatids with one another in a process called crossing over. - The nucleolus disappears and the nuclear envelope disintegrates. - A spindle made of microtubules forms.
  • 8. - Prophase I can last for days, months or even years, depending on the species and on the type of gamete (male or female) being formed. Metaphase I - Bivalents line up across the equator of the spindle, attached to spindle fibres at the centromeres. The chiasmata are still present. - The bivalents are arranged randomly (random assortment) with each member of a homologous pair facing opposite poles. - This allows the chromosomes to independently segregate when they are pulled apart in anaphase I. Anaphase I - The homologous chromosomes in each bivalent are pulled by the spindle fibres to opposite poles. - The centromeres do not divide. - The chiasmata separate and lengths of chromatid that have been crossed over remain with the chromatid to which they have become newly attached. Telophase I - In most animal cells two new nuclear envelopes form – one around each set of chromosomes at each pole – and the cell divides by cytokinesis. There is a brief interphase and the chromosomes uncoil. - In most plants, the cell goes straight from anaphase I into meiosis II. Meiosis II Prophase II - If the nuclear envelope has reformed, then it breaks down again. - The nucleolus disappears and the chromosomes condense, and the spindles form again. Metaphase II - The chromosomes arrange themselves on the equator of the spindle, and they are attached the spindle fibres at the centromere. - The chromatids of each chromosome are randomly assorted (arranged). Anaphase II - The centromeres divide and the chromatids are pulled to opposite poles by the spindle fibres. The chromatids randomly segregate.
  • 9. Telophase II - Nuclear envelopes reform around the haploid daughter nuclei. - In animals, the two cells now divide to give four haploid cells. - In plants, a tetrad of four haploid cells is formed. 9) GENETIC CROSSES Two alleles: G – white skin g – green skin Parent phenotype: green green Parent genotype: gg gg Gametes: (g)(g) (g)(g) Offspring genotype: gg Offspring phenotype: green Homozygous individuals are said to be “true breeding” or “pure breeding” because they can only pass on one particular allele for a particular gene. The same would be true if the individuals were homozygous dominant rather than homozygous recessive. If an individual’s phenotype is white skinned, we do not know whether their genotype is homozygous (GG) or heterozygous (Gg). To found out, we would have to carry out test crosses. 10) CODOMINANCE Codominance occurs when both alleles for a particular gene contribute to the phenotype. Neither allele is dominant over the other and the overall phenotype is due to a mixed effect of two alleles. The alleles are defined by superscript letters in the gene, i.e. red colour is C^R and white colour is C^W. Parent phenotype: red flowers white flowers Parent genotype: C^RC^R C^WC^W Gametes: (C^R)(C^R) (C^W)(C^W) Offspring genotype: C^RC^W Offspring phenotype: pink flowers
  • 10. 11) THE CHI-SQUARED TEST The chi-squared test tests the null hypothesis through statistical analysis. The null hypothesis is a useful starting point in examining the results of a scientific investigation. It is based on the assumption that “there is no (statistically) significant different between the observed and expected numbers, and any difference is due to chance.” The formula for calculating a value of : Example The numbers of resulting offspring for each observed phenotype of Drosophila were counted: Straight wing, grey body – 113 Straight wing, ebony body – 30 Curled wing, grey body – 29 Curled wing, ebony body – 115 Phenotype Straight/grey Straight/ebony Curled/grey Curled/Ebony O 113 30 29 115 E ratio 1 1 1 1 E 71.75 71.75 71.75 71.75 O-E 41.25 -41.75 -42.75 43.25 (O-E)^2 1701.5625 1743.0625 1827.5625 1870.5625 (O-E)^2/E 23.71515679 24.29355401 25.471255436 26.07055749 = 99.55 (to 2 s.f.) A degrees of freedom of 3 should be used, as there are four classes. By looking up the critical value in a table, we know that it is 7.82. Since the chi-squared value is greater than 7.82, we know that there is a very low probability that the difference in the observed results compared to the expected results occurred by chance. This means that independent assortment of these gene loci is unlikely to have occurred.
  • 11. 12) SEX LINKAGE Parent’s sex: Female Males Parent’s chromosomes: XX XY Gametes: (X)(X) (X)(Y) Offspring chromosomes: XX XY Offspring sex: Female Male The sex chromosomes X and Y also carry genes. However, the X and Y chromosomes are not a true pair because part of the Y chromosome is missing. This means that some alleles present on the X chromosome are not present on the Y chromosome. Therefore, males sometimes only possess one allele for a particular gene locus. Such alleles are sex linked: The “yellow” gene has only one allele in males, as it is only present on the X chromosome and not the Y. The “red” gene, however, will act in the same way as any other gene, with the dominant allele being expressed over the recessive. The allele that causes red-green colour blindness is sex linked. The genotype of this male with red-green colour blindness is r-. This is often written as X^rY, indicating a sex-linked condition. Example r = red-green colour blindness R = normal vision Parent genotype: X^rY X^RY X^rX^r X^RX^R X^rX^R Gametes: (X^r)(Y) (X^R)(Y) (X^r)(X^r) (X^R)(X^R) (X^r)(X^R) Offspring genotype: X^rY X^RY X^RX^r X^RX^R Offspring phenotype: colour blind normal normal normal Offspring sex: male male female female The offspring with colour-blindness must be male.
  • 12. 13) DIHYBRID CROSSES A dihybrid cross involves studying the inheritance of two genes (2 loci) at the same time. Genotype: TtGg Genotype: HhFF Gametes: (TG)(Tg)(tG)(tg) Gametes: (HF)(HF)(hF)(hF) 14) EPISTASIS Epistasis is the interaction between two genes where one locus (epistatic gene) masks or suppresses the expression of the gene at the other locus (hypostatic gene). The epistatic gene and hypostatic gene may work in a complementary fashion (work with each other) or may work in an antagonistic fashion (work against each other). Complementary Fashion Two genes that code for enzymes in a sequential metabolic reaction are examples of complementary alleles, e.g. melanin is a brown pigment made indirectly from an amino acid phenylalanine via another amino acid called tyrosine. Phenylalanine E1 Tyrosine E2 Melanin Production of melanin required the consequential action of enzymes E1 and E2 coded for by genes A and B respectively. The dominant alleles are needed to express active enzymes. Without either active enzyme, the phenotype is ALBINO (WHITE) rather than brown. AABB – not albino aABB – not albino AAbB – not albino aaBB – albino aabB – albino aabb – albino Antagonistic Fashion Genes may work against each other in two ways, dominant epistasis and recessive epistasis. Dominant epistasis is where the expression of a dominant allele at one locus masks the expression of alleles at a different locus. H - hairy E – masks H E – does not mask H h - hairless HHEE – hairless HhEE – hairless HHEe – hairless HhEe – hairless hhEE – hairless HHee – hairy Hhee – hairy hhee – hairless hhEe – hairless
  • 13. Recessive epistasis is where the expression of a dominant allele at the epistatic locus is needed for the expression of alleles at the hypostatic locus. Therefore, a homozygous recessive individual for the epistatic gene results in no expression of the hypostatic gene. P - purple A – white ifrecessive a p - pink AABB – purple AABb – purple AAbb – pink AaBB – purple AaBb – purple Aabb – pink aaBB – white aaBb – white aabb – white 15) VARIATION Variation in biology is the presence of differences between individuals. It results in different phenotypes for the individuals. Variation occurs between members of the same species as well as between members of different species. Even identical twins can show slight phenotypic variation from one another. Discontinuous Variation – there are discrete categories for the phenotype. These are qualitative phenotypes. It may be caused by the inheritance of different alleles of one gene only (monogenic). For example, cystic fibrosis is caused by the inheritance of a mutated allele of a single gene. Discontinuous variation may also be caused by inheritance of a few genes which interact with each other in an epistatic manner. In discontinuous variation, different alleles for the same gene will have large effects on a phenotype. Different loci will have quite different effects on the phenotype. Dominant, recessive and codominant patterns of inheritance are examples of discontinuous variation. Continuous Variation – there are a range of phenotypes with a minimum and maximum value and many intermediate values in between. These are quantitative phenotypes. Continuous variation is caused by the inheritance of two or more genes. Each gene has a small additive effect on the overall phenotype of the organism. Different alleles at the same locus have a small effect on the phenotype. A large number of genes may affect the phenotype (POLYGENIC). Variation is also caused by environmental influence, e.g. nutrition, UV, radiation, etc.
  • 14. 16) POPULATION GENETICS Population genetics involves determining the frequency of alleles in whole populations rather than in individuals. A whole population is likely to possess more different alleles than an individual. Population geneticists study the genetic structure of whole populations. The set of genetic information carried by a whole population is referred to as the gene pool. Population geneticists measure the frequency of different alleles in the gene pool. When alleles show codominance, this is quite easy to do as the number of heterozygous phenotypes is the same as the number of heterozygous genotypes. In a population of snapdragons, 30 are red, 49 are pink and 10 are white. The frequency of each allele is easy to measure in this population of plants: Red alleles – 109 White alleles – 69 However, the situation is more complicated with dominant and recessive alleles and the Hardy-Weinberg principle must be used: The frequency of the dominant allele is assigned letter “P” and the frequency of the recessive allele “Q.” In a cross between two heterozygotes the offspring are produced in the following ratio and the frequency of each genotype is described using P and Q as follows: 1 homozygous dominant (p^2) 2 heterozygous (2pq) 1 homozygous recessive (q^2) The frequency of genotypes adds to one: p^2 + 2pq + q^2 The frequency of alleles also adds to one: p + q = 1 If the frequency of the homozygous recessive genotype is known, then the frequencies of p and q can be calculated. e.g. phenylkatenuria is caused by a recessive allele. It occurs in 1 in 10,000 live births: q^2 = 0.0001 q = 0.01 p = 0.99 p^2 + 2pq + q^2 = 1 2pq = 0.0198
  • 15. 17) GENES AND ENVIRONMET – EVOLUTION A selection pressure is an environmental factor that confers greater chances of survival to reproductive age on some members of the population. If a selection pressure maintains a phenotype, it is known as stabilising selection. If the environment changes and the phenotype begins to become more/less prevalent, this is known as directional selection and acts as an evolutionary force leading to evolutionary change. Any change to the frequency of alleles in a population is referred to as genetic drift. Genetic drift is more likely to happen in smaller populations of organisms. Populations can become smaller by a variety of isolating mechanisms: - Geographical (ecological), where subpopulations are separated by barriers such as rivers, seas, mountain ranges, etc. This can lead to alopatric speciation. - Seasonal (temporal), where barriers such as climate change throughout the year separate populations. - Reproductive barriers, where individuals can no longer physically mate due to incompatible genitals, breeding seasons or courtship behaviours. In each different subpopulation, different alleles may increase or decrease, maybe eventually leading to a new species, i.e. that can no longer breed at all. This process is called speciation. Genetic drift is more likely to occur in smaller populations because allele frequencies can change in a more dramatic fashion. However, in a large population, only small changes in allele frequency would be expected. However, this may not be the case if evolutionary forces caused directional selection. In extreme cases, genetic drift can cause elimination of an allele from a population. This will remove variation and could reduce the chances of survival in a new environment. It could therefore contribute to the extinction of a species. Genetic drift can also lead to the formation of a new species. 18) WHAT IS A SPECIES? Biological Species Concept – “a group of similar organisms that can interbreed to produce fertile offspring and is reproductively isolated from other such groups.” This is used for classification but presents problems for organisms that do not reproduce sexually, i.e. binary fission in bacteria. Phylogenetic Species Concept – “organisms that have similar morphology (anatomy), physiology, embryology (stages of development) and behaviour; and also occupy the same ecological niche.” The phylogentic approach us based upon analysis of differences or similarities between the DNA of different organisms. A particular base sequence of an organism is called its haplotype, which can be compared between organisms.
  • 16. A divergence can be calculated as: The least divergent organisms are put into a group called a clade, and a cladogram shows evolutionary relationships between groups, i.e. phylogeny. The cladistic approach uses: - Evolutionary relationships rather than structural similarity - Quantitative analyses requiring computer programs. - Relies on DNA (and RNA) sequencing. If often confirms Linnaean classification, but sometimes leads to organisms being reclassified, as was the case for the 3-domain system of classification.