biology module 4 classification and evolution

taxonomy

practice of biological classification

name the taxonomic ranks from highest to lowest

1. domain

2. kingdom

3. phylum

4. class

5. order

6. family

7. genus

8. species

what is a species

• a group of organisms that are able to reproduce to produce fertile offspring

what are binomials

scientific names given to individuals species, consists of the organisms genus and species name in Latin

what are the three domains of life

• Bacteria (prokaryotes)

• Archaea (prokaryotes)

• Eukarya (eukaryotes)

archaea

• Organisms within this domain are sometimes referred to as the extremophile prokaryotes, as archaea were first discovered living in extreme environments (although not all archaea do)

• Archael cells have no nucleus (and so are prokaryotic)

• They were initially classified as bacteria until several unique properties were discovered that separated them from known bacteria, including:

  • Unique lipids being found in the membranes of their cells

  • No peptidoglycan in their cell walls

  • Ribosomal structure (particularly that of the small subunit) are more similar to the eukaryotic ribosome than that of the bacteria

bacteria

• These are organisms that have prokaryotic cells which contain no nucleus

• They vary in size over a wide range: the smallest are bigger than the largest known-viruses and the largest are smaller than the smallest known single-celled eukaryotes

• Bacterial cells divide by binary fission

eukarya

• Organisms that have eukaryotic cells with nuclei and membrane-bound organelles are placed in this domain

• They vary massively in size from single-celled organisms that are only several micrometres across, to large multicellular organisms many-metres in size, such as blue whales

• Eukaryotic cells divide by mitosis

• Eukaryotes can reproduce sexually or asexually

differing membrane lipids in bacteria and archaea

• The membrane lipids found in the cells of Archaea organisms are completely unique

• They are not found in any bacterial or eukaryotic cells

• The membrane lipids of Archaea consist of branched hydrocarbon chains bonded to glycerol by ether linkages

• The membrane lipids of Bacteria consist of unbranched hydrocarbon chains bonded to glycerol by ester linkages

differing ribosomal RNA in bacteria and archaea

• Both Archaea and Bacteria possess 70S ribosomes

• The 70S ribosomes in Archaea possess a smaller subunit that is more similar to the subunit found in Eukaryotic ribosomes than subunits in Bacterial ribosomes

  • The base sequences of ribosomal RNA in Archaea show more similarity to the rRNA of Eukarya than Bacteria

  • The primary structure of ribosome proteins in Archaea show more similarity to the ribosome proteins in Eukarya than Bacteria

composition of cell walls in bacteria and archaea

• Organisms from the Bacteria domain have cells that always possess cell walls with peptidoglycan

• Organisms from the Archaea domain also have cells that always possess cell walls, however these do not contain peptidoglycan

name the five kingdoms

• Prokaryota

• Protoctista

• Fungi

• Plantae

• Animalia

prokaryota

• This kingdom includes bacteria and blue-green bacteria

• The main features of all organisms within Prokaryota include:

  • Most are unicellular (some can be found as filaments of cells or groupings of similar cells known as colonies)

  • Their cells have cell walls (not made of cellulose) and cytoplasm but no nucleus or mitochondria

  • They vary in size over a wide range: the smallest are bigger than the largest known viruses and the largest are smaller than the smallest known single-celled eukaryotes

  • Their cells divide by binary fission

• Blue-green bacteria and some bacteria are autotrophic (they are photosynthetic)

• Many bacteria are heterotrophic (feeding by decomposing living or dead organic materials)

protoctista

• All Protoctista are eukaryotic, and this broad group of cellular life encompasses all eukaryotic cells that do not belong to the other three eukaryotic kingdoms

• Members of this kingdom show great diversity in all aspects of life including structure, life cycle, feeding and trophic levels and well as modes of locomotion

• Protoctists can exist as single-celled organisms or as a group of similar cells

• A group of Protoctista known as protozoa possess cells similar to animal cells

  • Their cells have no cell wall

• Another group of Protoctista known as algae possess cells similar to plant cells

  • Their cells have cellulose cell walls and chloroplasts

fungi

• All fungi are eukaryotic cells

• The cells of fungi:

  • Possess non-cellulose cell walls (often made of the polysaccharide chitin)

  • Don’t have cilia

• Fungi are heterotrophs:

  • They use organic compounds made by other organisms as their source of energy and molecules for metabolism

  • They obtain this energy and carbon by digesting dead/decaying matter extracellularly or from being parasites on living organisms

• Fungi reproduce using spores that disperse onto the ground nearby

• Fungi have a simple body form:

  • They can be unicellular (like the common baker’s yeast Saccharomyces cerevisiae

  • Some consist of long threads called hyphae that grow from the main fungus body and form a network of filaments called the mycelium

  • Larger fungi possess fruiting bodies that release large numbers of spores (this is how many fungi reproduce)

plantae

• Plants are multicellular eukaryotic organisms

• Plant cells:

  • All have cell walls composed of cellulose

  • Possess large (and usually permanent) vacuoles that provide structural support

  • Are able to differentiate into specialized cells to form tissues and organs

  • Possess chloroplasts that enable photosynthesis (not all plant cells have chloroplasts)

  • Can sometimes have flagella

• They are autotrophs

  • This means they can synthesize their organic compounds and molecules for energy use and building biomass from inorganic compounds

• Plants have complex body forms

  • They have branching systems above and below the ground

animalia

• Animals are also multicellular eukaryotic organisms

• Animal cells:

  • Are able to differentiate into many different specialised cell types that can form tissues and organs

  • Have small temporary vacuoles (for example, lysosomes)

  • Have no cell walls

  • Sometimes have cilia

• They are heterotrophs and have a wide range of feeding mechanisms

• Communication within their complex body forms takes place through a nervous system and chemical signalling

molecular evidence for the theory of evolution by natural selection

• DNA found in the nucleus of cells can be sequenced and used to provide evidence of evolutionary relationships between species and how the genetic code of species has changed as they have evolved

• The differences between the nucleotide sequences in the analogous genes of different species can provide a lot of information:

  • The more similar the sequence the more closely related the species are

  • Two groups of organisms with very similar DNA will have separated into separate species more recently than two groups with less similarity in their DNA sequences

• As a result, DNA sequence analysis and comparison can be used to create phylogenetic trees that show the evolutionary relationships between specie

fossil evidence for the theory of evolution by natural selection

• Fossils are preserved remains of organisms or other features left by organisms, such as footprints, burrows and faeces

  • We can tell from fossils that environments (and the organisms living in these environments) have changed significantly over millions of years

  • Fossils, as well as the rocks they are found in, can be dated, allowing us to accurately put fossil organisms into a sequence from oldest to youngest (i.e to see how the organisms changed through evolutionary time)

  • Fossils also allow us to show similarities between extinct species (i.e. how related they are) and even between now-extinct, ancestral species and present-day species

what is variation

• The term variation refers to the differences between living organisms

• Variation can be:

  • between different species or within a single species

  • continuous or discontinuous

  • caused be genetic and/or environmental factors

interspecific variation

• Interspecific variation is that which exists between individuals of different species

• Interspecific variation can be useful for classifying organisms into species groups

  • Different species may show clear phenotypic variation that can help differentiate them

  • Some species have such similar phenotypes that they can be very difficult to distinguish, meaning that genetic variation must be used for classification

intraspecific variation

• Intraspecific variation is that which exists between individuals of the same species

  • These differences are smaller than those found between individuals of different species

discontinuous variation

• Discontinuous variation refers to differences that fall into discrete and distinguishable categories with no intermediates

  • E.g. there are four possible ABO blood groups in humans; a person can only have one of them

• Discontinuous variation can be represented using a bar chart with bars that are clearly distinct from each other

continuous variation

• Continuous variation refers to differences that show a range of values and can fall anywhere between two extremes

  • E.g. body mass and height are measured on a continuous scale

• Continuous variation can be represented on a histogram with bars that touch each other, and will often show a characteristic bell-shaped curve

causes of discontinuous variation

• Different genes have different effects on the phenotype

• Different alleles at a single gene locus have a large effect on the phenotype

• Remember diploid organisms will inherit two alleles of each gene, these alleles can be the same or different

causes of continuous variation at the genetic level

• Different alleles at a single locus have a small effect on the phenotype

• Different genes can have the same effect on the phenotype and these add together to have an additive effect

• If a large number of genes have a combined effect on the phenotype they are known as polygenes

environmental factors for continuous variation

• An accident may lead to scarring on the body

• Eating too much and not leading an active lifestyle will cause weight gain

• Being raised in a certain country will cause you to speak a certain language with a certain accent

formula for standard deviation

what is a t-test used for

can be used to compare the means of two sets of data and determine whether they are significantly different or not

• The formula for the t-test will be provided in the exam, but formulae for how to calculate the number of degrees of freedom is not provided in the exam and must be learnt

step 1 of t-test

Calculate the mean for each data set

step 2 t-test

Calculate the standard deviation for each set of data, s₁ = standard deviation of sample 1 and s₂ = standard deviation of sample 2

step 3 t-test

Square the standard deviation and divide by n (the number of observations) in each sample, for both samples:

step 4 t test

Add the values from step 3 together and take the square root:

step 5 t test

Divide the difference between the two means (see step 1) with the value calculated in step 4 to get the t value:

step 6 t test

Calculate the degrees of freedom (v) for the whole data set (remember the formulae for this will not be given in the exam):

step 7 t test

Look at a table that relates t values to the probability that the differences between data sets is due to chance to find where the t value for the degrees of freedom (v) calculated lies

step 8 t test

The greater the t value calculated (for any degree of freedom), the lower the probability of chance causing any significant difference between the two sample means

• Identify where the t value calculated lies with respect to the confidence levels provided

what does the critical value of the t test tell us

• If the t value is greater than the critical value (obtained from the table at a probability level of 0.05) then any difference between the means of the two data sets is said to be statistically significant

  • There is a less than 5 % probability that any difference is due to chance

  • The null hypothesis can be rejected

• If the t value is less than the critical value (obtained from the table at a probability level of 0.05) then there is no significant difference between the means of the two data sets

  • The probability that any difference is due to chance is higher than 5 %

  • The null hypothesis is accepted

what is spearmans rank correlation

• Spearman’s rank correlation determines whether there is correlation between variables that don’t show a normal distribution

steps of spearmans rank correlation

• Step 1: Create a scatter graph and identify possible linear correlation

• Step 2: State a null hypothesis

• Step 3: Use the following equation to work out Spearman’s rank correlation coefficient r

  

  • Where:

    • r_s = spearman’s rank coefficient

    • D = difference in rank

    • n = number of samples

• Step 4: Refer to a table that relates critical values of r_s to levels of probability

• If the value calculated for Spearman’s rank is greater than the critical value for the number of samples in the data ( n ) at the 0.05 probability level (p),  then the null hypothesis can be rejected, meaning there is a correlation between two variables

3 types of adaptation

• anatomical

  • Physical features of an organism

  • E.g. the white fur of a polar bear provides camouflage in the snow so it has less chance of being detected by prey

• physiological

  • Biological processes within an organism

  • E.g. mosquitos produce chemicals that stoa host's blood from clotting when they bite so that they can feed more easily

• behavioural

  • The way an organism behaves

  • E.g. reptiles bask in the sun to absorb heat

convergent evolution

• Organisms from different taxonomic groups may show similar adaptations even though they do not share a recent common ancestor

• Shared adaptations between unrelated organisms arise due to convergent evolution

• Convergent evolution occurs by natural selection as follows:

  • two species live in different parts of the world with similar environments

  • the species deal with the same selection pressures

  • the same characteristics are advantageous in the two environments, so individuals with these characteristics are more likely to survive and reproduce

  • over time the advantageous characteristics become widespread in both populations

genetic variation

• Organisms of the same species have very similar genomes, but two individuals (even twins) will have differences between their DNA base sequences

• These differences in DNA base sequences between individual organisms within a species population are called genetic variation

• Genetic variation is transferred from one generation to the next and results in genetic diversity within a species

what are the two ways in which a bacterium inherits resistance to an antibiotic

• Vertical transmission

• Horizontal transmission

vertical transmission

• Bacteria reproduce asexually by binary fission (the DNA of the bacterial chromosome is replicated and the bacterial cell divides in two, with each daughter cell receiving a copy of the chromosome)

• Bacteria reproduce like this very rapidly (on average, every 20 minutes)

• If one bacterium contains a mutant gene that gives it antibiotic resistance, all of its descendants (millions of which can be produced in a matter of hours) will also have the antibiotic resistance

• This form of transmission enables antibiotic resistance to spread within a bacterial population

horizontal transmission

• Plasmids (the small rings of DNA present in bacterial cells) often contain antibiotic-resistant genes

• These plasmids are frequently transferred between bacteria (even from one species to another)

• This occurs during conjugation (when a thin tube forms between two bacteria to allow the exchange of DNA) – DNA from the bacterial chromosome can also be transferred in this way

• In this way, a bacterium containing a mutant gene that gives it antibiotic resistance could pass this gene on to other bacteria (even those from a different species). This is how ‘superbugs’ with multiple resistance have developed (e.g. methicillin-resistant Staphylococcus aureus – MRSA)

• This form of transmission enables antibiotic resistance to spread within or between bacterial populations