topic 3 Flashcards
3.1
classification?
Why is a classification system needed?
Classification is the process of naming and organising organisms into groups based on their characteristics.
- provides a catalogue of past + present species
- An internationally recognised way of referring to particular organisms = allows scientists around the world to work together
- use classification to look at evolutionary patterns + makes ancestral relationships clear
What’s Taxonomy?
origins of taxonomy?
Taxonomy is the science of describing, classifying and naming living organisms.
-Carl Linnaeus used physical features (morphology) to group organisms
-devised a hierarchical structure for classification - still used today
-naming organisms using Binomial system.
-split all life into taxonomic groups = 2 kingdoms - animal + plant
-split them further to phylum and then species
- technology + DNA analysis = realised there was 2 distinct groups (eukaryote / prokaryote)
=new taxonomic group added above kingdom - Domain
=3 Domain system introduced
(Archaea, Eubacteria, Eukaryota)
3 Domains (largest taxonomic groups)
- Bacteria
contains 1 kingdom:
Eubacteria - true bacteria
- Archaea
contains 1 kingdom:
archaebacteria - ancient bacteria that can withstand extreme conditions/environments.
- Eukaryota
contains 4 kingdoms:
- Protista
- Fungi
- Plant
- Animal
The 3 domains?
Evidence for the 3 Domains?
3 Domains: Archaea, Bacteria, Eukaryota.
Evidence:
- Differences in sequences of nucleotides in Cell’s ribosomal RNA
- Cell membrane lipid structure
- Sensitivity to antibiotic + toxins
The binomial system?
originally used by Linnaeus, but now universally among biologists.
every organism given 2 names : genus name and species name. [ Homo sapiens]
-must use italics
-genus name UPPER CASE LETTER and species lower case
-after first use, its abbreviated/shortened to initial of genus and then the species name. [H. sapiens]
What are the levels of classification?
Domain (Drunk/Dead)
Kingdom (King)
Phylum (Phillip)
Class (Came)
Order (Over)
Family (For)
Genus (Goat)
Species (Stew)
The Eukaryota Kingdoms
- Plantae
- Autotrophs : make own food through photosynthesis using chlorophyll in chloroplast
- have cellulose cell wall
- Animalia
- Heterotrophs: eat others for food
- no cell wall
- capable of whole body movement
- Fungi
- Live of dead organisms using extracellular digestion
- Chitin cell wall
- reproduce by spores
- Protista
- strange set of microscopic organisms that can have features of the other kingdoms.
Sexual dimorphism?
Molecular phylogeny?
Species?
Sexual dimorphism: when there’s a big difference in the appearance of the male + female of a species.
Molecular Phylogeny: The analysis of genetic material of organisms to establish their evolutionary relationships.
Species - group of organisms with similar characteristics that can interbreed to produce fertile offspring.
Problems with this definition of species?
- sometimes they can be geographically separated + cannot interbreed…Despite being same species
- Plants often interbreed with different species and produce fertile offspring
- sometimes fertile hybrid offspring are produced
- many organisms cannot reproduce sexually
- Fossil organisms cannot reproduce sexually + lack DNA
Improvements to the definition of species?
Groups of organism with similar characteristics that are all POTENTIALLY capable of breeding to produce fertile offspring.
Problems with identifying NEW species
- is it just new in the area?
- has it been previously identified but thought to be extinct?
- is it completely new species or just a variation of a current species?
- some species look very different but are acc the same
There are many different methods of defining a species.
- Morphological species model?
limitation?
based solely on the morphology/ appearance of the organism.
-Sexual dimorphism may make different genders of the same species look very different (peacocks)
-appearance if organism can be affected by different things such as environment/ predators as some change appearance to escape predators
- Biological / reproductive concept?
limitation?
a group of organisms with similar characteristics than interbreed to produce fertile offspring.
- Not all organisms in a species can attempt to interbreed to produce fertile offspring as they may be geographically isolated.
- earlier limitations on species definition
Ecological species model?
limitation?
Based on the ecological niche (role they play in their environment) occupied by an organism.
-Niche definition vary + many species occupy more than 1 niche
Mate-recognition species model?
limitation?
Based on unique fertilisation systems - including mating behaviour.
-Many species will mate with or cross-pollinate with other species - but are never the less different species
Genetics species model?
limitation?
Based on DNA evidence
-Time consuming and expensive to collect data and study them -historically
-need to decide how much genetic differences make 2 organism different species?
Evolutionary species model?
limitation?
Based on shared evolutionary relationships between species
-Not always a clear evolutionary pathways for a particular organism = not always easy to apply
What is DNA sequencing?
DNA profiling?
Why are they useful?
DNA sequencing - process where the base sequences of all or part of the genome of organisms are worked out. [it leads to DNA profiling]
DNA profiling - process where the non-coding areas of DNA are analysed to identify patterns.
These patterns are unique to individuals, but similarities of patterns can be used to identify relationships between individuals and species even.
What is bioinformatics?
why is it useful?
Bioinformatics - the development of the software + computing tools needed to organise and analyse the large amount of biological data (that wouldn’t be possible to be done by humans as there’s too much data).
Allows us to make sense and use the many information generated by DNA sequencing and profiling to identify species and the relationships between them.
Examples of when DNA profiling was used
[don’t need to know]
-external conditions result in major differences in appearance = red deer in one area looked very different to another area (much longer + broader) = thought different species = DNA evidence showed they’re same.
- A plant disease thought to be caused by a single fungus = DNA evidence showed that there was at least 6 different species of this fungi pathogen which had same effect on crops.
-Caviar tin - DNA profiling found that 25% of tins contained eggs of other species that weren’t caviar.
-DNA analysis used in ethics of marketplace - DNA analysis found horse meat in European beef, chicken, pork products.
DNA barcodes?
[don’t need to know]
large group of scientists (IBOL - International Barcode of Life Project + others) developing DNA barcoding as a global standard of species identification.
Involves looking at short genetic sequences from a part of the genome common to particular groups of organisms. Fast and cheap ad numbers of species barcoded increasing all the time.
Important that every specimen used to produce the definitive bar codes is preserved for reference.
Will not replace taxonomy - support it.
Makes it easier to identify plants with no flowers/fruit, immature animals.
Quick identification of invasive species eg makes it easier to deal with threat.
Gel Electrophoresis?
A way of separating DNA / RNA fragments / proteins / amino acids according to their size and charge.
- Chemicals to be compared placed in gel medium in pH buffer solution, with the known DNA / RNA.
- The DNA molecules being identified are cut into fragments by restriction enzymes at specific sites.
- The DNA fragments added to a gel with dye which binds to the fragments + makes them fluorescence under UV light. fragments are inserted into a well at the end of a piece of agar gel.
- Electric current passed through apparatus and DNA fragments move towards the positive anode as their negative charge on the phosphate group in DNA attracts.
- Fragments move at different rates depending on mass and charge. The smaller mass / shorter pieces of DNA fragments move faster through gel matrix and therefore further from the wells than the larger fragments
- plate is placed under UV light after. The DNA fluoresces and shows up clearly so pattern of different bands can be identified
(Probes are single-stranded DNA sequences that are complementary to the regions of interest)
How does the scientific community evaluate and validate data and theories?
- Peer review - data sent to experts in their field so they read and review to check the validity of it. If its valid enough, data will be published in scientific journals.
- Scientific conferences - scientists working in same field get together to discuss ideas and analyse and challenge the validity of results that are being presented.
[also allows exchange of ideas/data/techniques between scientists around the world] - peer reviewed scientific journals
For many years biologist divided organisms into 2 large domains (eukaryotes or prokaryotes).
The theory was that eukaryotes had evolved from prokaryotes billions of yrs ago - how?
- cell engulfed prokaryotic organism capable of
A. aerobic respiration + B. photosynthetic organism. - They’re not digested by chance, A. allowed for efficient respiration so cells grow and reproduce more and B. provided cell with food through photosynthesis giving cell adv to grow and reproduce more.
- become permanent features in cell and copies are made and passed to daughter cells in reproduction.
A. as mitochondria B. as chloroplast
But then new theory about 3 domains not 2?
-looked at internal structures of prokaryotes + eukaryotes and compared + used bioinformatics to process the data generated.
-2 prokaryote domains: Archaea + Bacteria
-Eukaryotes
-All probably had a common ancestor
-some evident suggest that Archaea are more closely related to eukaryotes than bacteria.