A3.1

Question 1

Taxonomy

Morphology?

Answer 1

• The physical appearance or structure of something.
• Large noticable features, but also small cellular structures like whether a cell has a nucleus or not.

Question 2

Taxonomy

Taxon?

Answer 2

• A category or group that something belongs to.
• Can be large or small, and organisms can belong to multiple.

Question 3

Taxonomy

Binomial Nomenclature?

“Two names”

Answer 3

• Refers to the way of assigning scientific names based on taxonomic identification.
• First name is an organism’s genus which is shares with other species (capitalized), and it’s second is its species name, which is unique to it (italisized).

Question 4

Taxonomy

Linnea’s First Classification System

Answer 4

• Carolus Linnaes was struggling to identity plants. While travelling he came up with the idea of categorizing organisms based on their physical features.
• Also came up with the idea of using latin and Greek scientific names.

Question 5

Taxonomy

The Biological Species Concept

Answer 5

• Linnaeus ussed the term species for his smallest taxon (the most similar group of organisms). But his classification was morphological, based on shared physical features.
• Now, species is defined by groups of individuals that can successfully create fertile offspring.

Question 6

Taxonomy

Chromosome Number & Species Indentification

Answer 6

• Members of the same species should have the same diploid chromosome number.
• Species as a gentically similar group, the largest scale of genetic similarity.
• Same chromosome number enables successful reproduction and prevents it with other species with different chromosome numbers.

Question 7

Taxonomy

Karyotypes vs Karyograms

Answer 7

• A karyogram is a specific term that refers to the picture of chromosomes that’s created. Shows the chromosomes of an individual arranged in order.
• The Karyotype is the information that’s provided by the karyogram. This describes the number and appearance of a person’s chromosomes.
• Karyograms provide the karyotype.

Question 8

Taxonomy

The process in creating a karyogram

Answer 8

• Cells from the organisms need to be collected
• The cells are grown in a culture (to multiply) and then stained and prepared on a slide
• Cells that are in metaphase can be seen under the ligh and a photograph is taken.
• The chromosomes in the photo then need to be cut out and organized with their homologous partner (based on size, banding pattern & centromere position).
• These are then placed in order of size to create the final presentation used.

Question 9

Chromosomes and Genomes

Satellite DNA?

Answer 9

• Short term repeating sequences of non-coding DNA
• Generally found in non-coding regions of the chromosome - the centromere and telomers
• The short sequences provide effective ‘structural’ DNA that builds important parts of the chromosomes but doesn’t code for proteins.

Question 10

Chromosomes and Genomes

Telomeres?

Answer 10

• The ends of the chromosomes, and are made up on non-coding DNA that isn’t required for protein synthesis
• In this way, the coding DNA is protected by not being exposed
• Moreover, because DNA polymerases can only replicate in one direction, the last primers at each end can’t be replaced, and a small number of bases aren’t copied each round of division.

Question 11

Chromosomes and Genomes

Bioninformatics

Answer 11

• A research field that uses both computer science and technology to help us understand biological processes
• Most useful in genomics, with the strorage & organization of genetic information in data bases

Question 12

Chromosomes and Genomes

Phylogenetics?

Answer 12

• The process of comparing whole genome sequences between different species to see how closely related organisms are to one another.
• Allows us to better classify organsisms and create cladograms to show evolutionary relationships

Question 13

Chromosomes and Genomes

Whole Genome Sequencing?

Answer 13

• Determines the order of the bases in an organism’s genome - across all of their DNA.
• Done using ‘next-generation sequencing’ that is faster and efficient.
• Uses chemical markers and softward that tracks the bases at each position in the DNA.

Question 14

Chromosomes and Genomes

Evidence for Chromosome 2 Origins

Gorillas, Chimps and Humans

Answer 14

• Both gorillas and chimps have diploid chromosome number of 48, while humans have 46.
• Hence, the theory is that the two smaller chromosomes in the primates merged into one
• Human chromosome 2 is thought to be a combo of their chromosomes 12 and 13 based on:

1. Size and banding patterns
2. Centromere position
3. Presence of satellite DNA normally found in telomeres in the chromosome arm.

Question 15

Chromosomes and Genomes

Role of Human Genome Project

Answer 15

• In 1990 it was initiated to sequence all bases in human genes
• Now the key has been to determine what proteins the genes code for

Question 16

Chromosomes and Genomes

Genome Diversity Between vs Within Species

Answer 16

• Organsisms within the same species share most of their genome in common but variations that provide phenotypic diversity is due to single nucleotide polymorphisms where single bases changes (in an otherwise identical genome).
• This causes alleles that result in different protein expression
• The variation between species is much larger & diverse - some species share similarlity while others share less, depending on their evolutionary relatedness

Question 17

Chromosomes and Genomes

Advantages for Mitochondrial DNA for Species Differences

A tool used to compare organisms (as they have tons of DNA)

Answer 17

Advantages include:
1. Less intraspecies variation without crossing over due to maternal inheritance
2. Fewer genes so comparasions are more efficient
3. The genes code for ascpects of cellular resp. which is a common process across all eukaryotes, so more conserved sequence.

Question 18

Chromosomes and Genomes

Relationships between Genome Size and Organisms Complexity.

Answer 18

• There exists a general trend that genome size is larger in more complex organisms. (Not perfect!)

Question 19

Chromosomes and Genomes

Currenct and Future uses of Whole Genome Sequencing

Answer 19

• Currently, WGS plays a role in diagnositics and agriculture. They play a role in phylogenetics or comparing species to determine evolutionary relationships.
• Future uses could include use in gene therapy for diseases and alternative biofuels. Also the potential for the expansion of personalized medicine.

Question 20

Dichotomous Keys and DNA Barcoding

DNA Barcode?

Answer 20

• DNA sequences stored in a data base are given a barcode identification number (BIN) that can be used to access and compare info about that species.
• The DNA barcode is generally a short sequence of DNA that is unique to that species & therefore can be used to indentify it.

Question 21

Dichotomous Keys and DNA Barcoding

Environmental DNA?

Answer 21

• A collection of DNA that can be extracted from an environmental sample (like water/soil)
• It contains DNA of many different organisms like shredded hair, dead cells, leaf or plant parts etc.
• The DNA from the sample is extracted and separated into unique sequences and then amplified by PCR (polymerases) to identifiy the species that it comes from.

Question 22

Dichotomous Keys and DNA Barcoding

Indicator Species

Also called “Bioindicators”

Answer 22

• Organisms that are very sensitive to certain types of pollution.
• Their appearance in an environment affirms low pollution leveles
• Their disappearence suggests high levels of pollution or poor water/ ecosystem health

Question 23

Dichotomous Keys and DNA Barcoding

Parthenogensis?

Extremely rare

Answer 23

• A unique form of quasi asexual reproduction whereby female organisms repdouce without a male partner
• Done by fusion of haploid egg nucleus with the polar body that is also haploid

Question 24

Dichotomous Keys and DNA Barcoding

Vegetative Propagation?

Answer 24

• Commonly used specific form of asexual reproduction in plants
• Part of the plant can be removed (cutting) and placed in soil and it grows into a new plant that is identical to the parent plant.
• This is a form of uneven asexual reproduction that occurs in eukaryotes.

Question 25

# Dichotomous Keys and DNA Barcoding Horizontal Gene Transfer?

Answer 25

* DNA is generally passed down from parents to offspring via Vertical Gene Transfer. * If however individuals of the **same generation transfer DNA between 'adult' organisms without producing new offspring**, this is Horizontal Gene Transfer. * They **share DNA and transfer plasmids between each other** * Increases genetic diversity in otherwise asexually reproducing organisms.

Question 26

# Dichotomous Keys and DNA Barcoding Complications to Biological Species Concept

Answer 26

* When organisms reproduce asexually, the concept of species becomes more difficult. * Additionally, horizontal gene tranfer complicates it - as **DNA is shared not by reproduction**.

Question 27

# Dichotomous Keys and DNA Barcoding Using a Dichotomous Key

Answer 27

* Start at the **first section of the key** and read the **two descriptions**. * Work out **which description matches the physical features of the organisms** * The answer tells you what next set of questions to move to. * This uses morphology to classify and not DNA.

Question 28

# Dichotomous Keys and DNA Barcoding DNA Libraries for Organisms Identification

Answer 28

* Using DNA sequencing, **millions of DNA barcodes** of known species are stored in DNA libraries. * Often these barcodes include **mitochondrial or ribosomal RNA**. * When an unidentified organisms is found, **DNA can be sequenced from those same regions** and can be entered into a DNA library which will search for matches. * **Matches will be reported** and when the percent matched is high, **the correct identification** of the organisms has likely been found.

Question 29

# Dichotomous Keys and DNA Barcoding Determining Biodiversity with eDNA | Environmental DNA

Answer 29

* After collecting eDNA, **different strands of DNA** can be amplified and identified. * The **no. different species present in an eDNA sample** is an indication of the **biodiversity of the area**.

Question 30

# Dichotomous Keys and DNA Barcoding Bioindicators Present in eDNA

Answer 30

* eDNA can be used to look for **specific species** * Easier than trying to identify all organisms, as it instead utilizes indicator species that by themsleves provide info about the health of the ecosystem. * eDNA is specifically tested for **known bioindicators to determine pollution levels** and the **biotic health** of the ecosystem.

Question 31

# Dichotomous Keys and DNA Barcoding Limitations of using eDNA

Answer 31

* Only says the **present or not** and gives no indication of **population size or each species** * It can't indicate if an organism is **dead or alive** * Chemicals in the environment can **degrade the eDNA** as can **high UV exposure** or **temperature extremes**