Chapter 14- Classification Flashcards

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1
Q

Who introduced the idea of classification

A

English scientist John Ray surveyed many plant species and gave them short descriptive Latin names.

Carl Linnaeus standardised the binomial system for naming species. He gave every species two names (like a first and surname). The first name reflected the way in which he classified the species and the second often gave some information about it. This is often done to avoid confusion between other species. Ex: the Apodemus sylvaticus which translates to ‘not house, wood’ because this species is often confused between house mouses ‘Mus musculus’.

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2
Q

What are subspecies

A

When species are subdivided into subspecies. In this case, a third name is given.

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3
Q

What does the first name show

A

The genus (or generic name). This indicates a rank higher than species in the classification system. Species that show too many similarities and are closely related are classified together in the same genus.

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4
Q

What does the second name show

A

This is the specific epithet. However, the name of the species is both words (the genus and the epithet). The epithet refers to the one species within the genus.

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5
Q

How do you abbreviate the name of a species

A

The first letter of the genus followed by the epithet.

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6
Q

Why is the Genus name not unique

A

A genus name cannot be used for more than one animal genus just like how a specific genus name cannot be used for more than plant genus.
However, the same genus name can be used for one animal genus and one plant genus.
Ex: Pieris brassicae a cabbage white butterfly
Plant known as Japanese andromeda is Pieris japonica.

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7
Q

Are epithets unique

A

No, some specific epithets are used for many species.

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8
Q

Which international organisations are responsible for devising codes that regulate the naming of organisms

A

International Code of Zoological Nomenclature for animals

International Code of Nomenclature for Algae, Fungi and Plants

International Code for Nomenclature of Bacteria

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9
Q

Who are taxonomists

A

They are biologists who specialise in describing, naming and classifying living and extinct organisms.

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10
Q

Definition of Taxonomy

A

This is the study of classification and the way in which features are used to distinguish between different species and to group them together.

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11
Q

Definition of classification

A

This is the organisation of living and extinct organisms into groups that are arranged in a hierarchy.

Some classifications are natural, in that they attempt to show relationships between species based on a study of many features.
Others are artificial and are done for a specific purpose.

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12
Q

What is a hierarchical classification system

A

This is where large groups were continually subdivided down to the level of the species.

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13
Q

The hierarchical classification- taxonomic ranks (taxons)

A
Species
Genus
Family
Order
Class
Phylum
Kingdom
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14
Q

What are the five kingdoms

A
Prokaryota
Protoctista
Fungi
Plantae
Animalia
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15
Q

Prokaryota kingdom

A

Includes the bacteria and blue-green bacteria
Most prokaryotic cells exist as single cells, filaments of cells or groupings of similar cells known as colonies.
Prokaryotic cells are about 1 micrometre in diameter.
They make up 90% of the ocean’s biomass
Live in a variety of habitats, including extreme conditions of heat, pH and salinity that kills eukaryotes.

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16
Q

Autotrophic prokaryotes

A

Blue-green bacteria and some bacteria are photosynthetic and fix carbon dioxide and produce oxygen in the same way that green plants do

Autotrophic means when light is used to produce food

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17
Q

Heterotrophic prokaryotic cells

A

Decomposers on organic material, both living and dead.

A heterotroph is an organism that cannot manufacture its own food by carbon fixation and therefore derives its intake of nutrition from other sources of organic carbon, mainly plant or animal matter.
These are generally the secondary or tertiary consumers.

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18
Q

Examples of heterotrophics

A

Some parasites:
Neisseria meningitidis
Mycobacterium tuberculosis
Cause diseases in human

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19
Q

Why are prokaryotic cells important

A

They are important in recycling elements such as nitrogen, phosphorus and sulphur. Some live in anaerobic conditions and produce methane (CH4) as a waste.
Some prokaryotic cells can fix nitrogen gas (dinitrogen- N2) to form ammonia from which they can synthesise many nitrogenous compounds. Others can make use of other inorganic substances in place of oxygen in respiration.

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20
Q

How does cell division occur in prokaryotic cells

A

Prokaryotes do not have linear chromosomes like eukaryotes and they do not divide by mitosis.
Their DNA replicates in the same way as in eukaryotes but there is no nuclear envelope to break down and there is no separation of chromosomes so there is no anaphase
Cell division occurs by binary fission, which is a form os asexual reproduction.
The transfer of genetic material from one individual to another happens when bacteria join together and exchange DNA.
Plasmids are also exchanged between bacteria, even between bacteria from different species.
Due to this, bacteria can gain new genes such as those for antibiotic resistance.

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21
Q

How were mitochondria and chloroplasts formed

A

From bacteria that invaded or were taken in by eukaryotic cells than a billion years ago.
Hence the similarities between bacteria and these organelles

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22
Q

Kingdom Protoctista

A

Protozoans (‘simple animals’) such as algae (ex: seaweeds)
Any eukaryote that is not a fungus, plant or animal is classified as a protoctist.
Many such as Paramecium are single celled; some are filamentous and some, such as Pediastrum duplex, are groups of similar protoctists known as colonies.

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23
Q

Seaweed?

A

Most complex multicellular protoctist
Their bodies are not differentiated into organs such as roots, leaves and stems but different areas of the body are specialised for attachment, photosynthesis and sexual reproduction.

Many organisms in this kingdom are more closely related to organisms from other kingdoms than they are to each other. Some might argue that algae (ex: seaweed) is more closely related to the plant kingdom

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24
Q

Where are protoctists found

A

In many different natural and artificial environments
Algae are important photosynthetic organisms in aquatic ecosystems. Ciliates are important in sewage-treatment works, where they feed on bacteria, keeping their numbers in check. Some, such as Plasmodium, which causes malaria, are important human and animal pathogens.

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25
Q

Kingdom Fungi- what are they and why can they be useful?

A

All fungi are heterotrophic, obtaining energy and carbon from dead and decaying matter or by feeding as parasites.
Fungi are just as important as decomposers aiding the recycling of carbon (as CO2) and mineral elements such as nitrogen. None of the fungi can photosynthesise.

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26
Q

Why is fungi bad

A

A few species of fungi are parasitic to animals, but mostly are parasitic to plants. Therefore they are economically damaging pathogens for crop plants.

27
Q

What is yeast composed of

A

They are single-celled, but most are composed of microscopic threads or hyphae that grow over or through their food source.
Each hypha has a cylindrical shape which in some species is subdivided into separate cells. Hyphae secrete enzymes onto their food source. Complex compounds such as cellulose, starch and proteins are digested externally and the soluble products absorbed. The hyphae form a fungal body known as mycelium. When grown on agar in Petri dishes, these mycelia are circular.

28
Q

How do fungi find food source

A

Fungi exhaust their food sources and need to find new ones. They do this by producing millions of spores, a few of which may land on a suitable substrate.

29
Q

What releases spores

A

Fruiting bodies of mushrooms, puffballs, toadstools and bracket fungi.
The fruiting bodies are formed from very compact hyphae.

30
Q

Examples of fungi

A

Honey fungi Armillaria gallica and A. ostoyae

The largest and oldest fungi

31
Q

How does fungi reproduce

A

Reproduce asexually and sexually
Yeast reproduce asexually by budding and alse reproduce sexually by producing haploid cells of different mating strains that fuse together

32
Q

Kingdom Plantae

A

Multicellular photosynthetic organisms
Have complex bodies that are often highly branched, both above and below ground.
Compared to animals, plants have fewer specialised cells and fewer types tissues. However, biochemically, plants are diverse and are able to carry out a wider range of metabolic reactions than animals. (Ex: photosynthesis and respiration). They can also synthesise many substances from simple raw materials- CO2, water and ions such as nitrate, sulphate and phosphate.

33
Q

How are plants dispersed

A

Almost all plants are immobile, because their bodies spread out to cover a wide area. To spread and to avoid competition, they all have means of dispersal. All have a haploid stage that alternates with a diploid stage in their life cycle. In the seed plants, the haploid phase is reduced.

34
Q

How do plants show movement

A

Plants show limited movement. The Venus fly trap is a carnivorous plant that has modified leaves that can snap shut rapidly to trap insects. The leaves then secrete enzymes that digest the insects. All plants release spores that help to spread the species. The spores of seed plants such as conifers and flowering plants are pollen grains that carry male gametes in sexual reproduction.

Plants dominate most ecosystems such as woodlands and grasslands.

35
Q

Kingdom Animalia

A

Multicellular organisms that are all heterotrophic with many ways of obtaining their food. Bodies are usually compact with a wide range of tissues that form complex organs. Organs work together in organs systems.

36
Q

What is the nervous system

A

It consists of a net of nerve cells. It consists of a brain with huge numbers of nerve cells and even larger numbers of interconnections between them.

37
Q

Diversity in animal kingdom

A

Great diversity of forms within animal kingdom.
Usually divided in two groups: vertebrates and invertebrates. However, they are not taxonomic ranks. The vertebrates classes (fish, amphibian, birds, reptiles and mammals) are all classified into the phylum Chordata, which also includes some invertebrate species. The fundamental feature that animals int he phylum Chordata share is a notochord- a stiffening rod that supports the body during early development and is replaced by a backbone.
Invertebrates do not have chordates and therefore do not develop bone (no backbone). Tunicates are an example.
Invertebrates are classified into 30 phyla and represent great diversity.

38
Q

What are corals

A

These are heterotrophs that partner with autotrophic organisms
A basis of a very diverse ecosystem

39
Q

What are the three domains

A

Some Prokaryotes were discovered in extreme environments, for example in hot springs, salt lakes etc.
These extremophiles were found to share features with both bacteria and eukaryotes.
Features such as rRNA, aspects of protein synthesis and the structure of cell membranes and flagella indicated that these extremophiles had eukaryote and bacterial features.

40
Q

What did Carl Woese do in 1990

A

introduced domain as a new taxonomic rank above the rank of kingdom, giving greater weight to molecular biology than to other features.
The extremophiles were classified in a separate domain, the Archaea, which is at the same taxonomic rank as Bacteria and Eukarya.

41
Q

Phylogeny

A

Natural classification systems aim to group organisms according to features that they share. Generally, these groupings reflect the ways in which organisms have evolved. Closely related species are grouped together in the same genus because they share many features in common. However, some of the features they share may be adaptations to the same type of environment or the way of life.

42
Q

What is homology

A

Natural classification systems are based on homology. Features that are homologous are shared by organisms because they have been inherited from a common ancestor.
The more recent two species have shared a common ancestor, the more homologies they share, and the more similar these homologies are.

43
Q

Definition of phylogeny

A

The evolutionary history of any particular taxon.

44
Q

How were organisms classified in the past

A

Limited to external appearance, the internal structure, some details of cell and tissue structure, and patterns of development from zygote to adult.

45
Q

What is important to note while distinguishing organisms

A

Distinguish features that are similar because of common descent and features that are the result of convergent evolution.

46
Q

Using antibodies

A

Variable regions of antibodies have a specific shape that is complimentary to their respective antigens.

47
Q

How can an antigen be tested in different animals

A

Antibodies to a specific antigen can be produced by injecting an animal with that antigen. After a week or so, blood is taken from the animal and prepared as an anti-serum by removing all the cells and adding an agent to stop it from clotting.
The anti-serum contains antibodies from different clones of plasma cells. This can then be used to test the blood of other species to see whether the same antigen is present.

48
Q

How is the antibody experiment carried out

A

Some blood is spun in a centrifuge to remove the red and white blood cells and it is treated to prevent it clotting. A small sample of the plasma is injected into a mouse or a rabbit. Several days later a sample of blood is taken from the rabbit and treated in a similar way. This anti-serum is mixed with human blood in a test tube. The rabbit antibodies attaches to the human antigens and precipitate. This process is repeated with blood plasma samples taken from other species. The degree of precipitation is compared with that between rabbit antibodies and human blood plasma.

49
Q

What is protein sequencing

A

An alternate method to identify similarities and differences between proteins is to sequence the amino acids.
Cytochrome c is found in many organisms, where it plays a key role in respiration. In eukaryotes, it is found in the inner membranes of mitochondria. This protein is a single polypeptide of about 100 amino acids wrapped around a haem group, in a similar way to globins to haemoglobin. Relationships among proteins are discovered by aligning the primary sequences from a number of species; this involves comparing the sequences amino acid by amino acid and looking for similarities and differences.

50
Q

How do you read these amino acid sequences

A

Need to know the one-letter code for amino acids.

51
Q

What happens to the data collected from the investigations

A

Data from investigations on the structures of proteins such as cytochrome c and haemoglobin are used to draw tree diagrams. The lengths of the branches in the tree are drawn proportional to the number of differences in the primary sequence of cytochrome c. The trees clearly display the three main kingdoms of eukaryotes: fungi, animals and plants.
These trees tend to agree closely with those constructed by biologists using traditional methods of studying morphology and anatomy. They provide independent evidence of common descent.

52
Q

What happens when you heat DNA and then cool it

A

The hydrogen bonds between the bases break when heated, thus causing the strands to separate.
When cooled, the attraction between the nucleotides will make the nucleotides to form hydrogen bonds again.

53
Q

How does DNA hybridisation work

A

Scientists cut the DNA of the two species into small segments, heat it to a temperature of about 90 degrees, separate the strands and mix the two species together. The new types od DNA bond together, but the match between the two strands is not perfect, there are more genetic differences between the species. These bonds can be broken with little heat.
Closer match- requires more heat to separate.

54
Q

What is DNA sequencing

A

The sequence of amino acids in proteins such as cytochrome c and haemoglobin is determined by the sequence of bases in the genes that code for these proteins. Easier to sequence DNA than to sequence proteins.
Data is much more detailed thanks to degenerate nature of the genetic code. This has largely replaced protein sequence data in providing useful information for taxonomy. Protein sequences have been derived from DNA data rather than the other way around. Comparing the DNA sequences of different species really gets to the fundamentals of classification and finding common ancestry.

55
Q

Advantage of DNA sequencing

A

Amino acid sequence can be exactly the same in different species, but because the genetic code is a degenerate code this may obscure the fact that the nucleotide sequences for these proteins are different.

56
Q

What are silent mutuations

A

Changes to base pairs that result in the same amino acid due to degeneracy.

57
Q

What is neutral mutations

A

Those that change the amino acid but not the type of R group and have no functional importance.

58
Q

Which are the significant mutuations

A

The ones that have a functional change and spreads through the population- eventually becoming a ‘fixed’ genome.
Therefore comparing gene sequences of different species gives much more information than comparing protein sequences.

59
Q

How do the genomes across life on Earth show

A

The gene that codes for rRNA changes slowly. These genes have therefore proved useful in sorting out relationships between the higher taxa such as domains, kingdoms and phyla. More rapidly changing genes help in showing relationship in recent speciation events and also between isolated populations of the same species, as has been done with groups of humans such as the indigenous human populations of the Americans.

60
Q

How is the mitochondria involved in DNA sequencing

A

DNA sequencing have been done with genes from the DNA in mitochondria, such as the DNA that codes for RNA that becomes part of the ribosomes in mitochondria. In eukaryotes, much of the DNA in the nucleus does not code for proteins.
These regions of DNA have a variety of other functions or none that we yet know about. These regions of DNA are relatively free to vary without changing nay protein such as enzyme or a receptor.

61
Q

How are non-coding sequences useful

A

Mitochondrial DNA does not have these non-coding sequences, so making it easier to align sequences from different organisms.
DNA is more stable than protein. Greater stability means that toxnomists can sequence DNA from extinct organisms such as mammoths.
Sequencing DNA has helped to work out the phylogenetic relationships between mammoths and elephants.

The most useful genes for further analysis are the so called ‘housekeeping’ genes that code for proteins that are required for fundamental features organisms have.

62
Q

Purpose of DNA sequencing

A

Provides the means to identify species by isolating and testing their DNA.

63
Q

Databases

A

Researchers deposit their results in these databases, and the information is freely available to all.
Allows researchers to compare their results with sequences already available in databases.