evolution I and II

Question 1

Why do we see fluctuations in the severity of the influenza virus?

Answer 1

• Due to the way the influenza virus replicates.
Influenza virus can exchange genetic material through a process called reassortment.

• There are 2 proteins that are present in the virus:
• H-haemagglutinin (virus binds to cell)- responsible for the cell binding to the cell. It will confer specificity to the virus, what kind of cells can it infect and what species of cell it can infect.
• N-neuraminidase (virus released from cell) – how readily is that virus able to be shed by the infected cell. Changes to this protein will affect how efficiently a virus can spread from cell to cell and how quickly it can infect its host.
• Different flu strains infecting the same cell can swap parts of their genetic material and produce different combinations of the H and N proteins with slightly different properties that are then able to affect the efficiency with which the virus can spread and how harmful the virus is. The speed at which the virus spreads within the body can determine how harmful it will be.

Question 2

What is evolution

Answer 2

• Accumulated, heritable changes (changes to the genetic material, either the RNA or DNA) within a population, over generations, giving rise to new species
• New species arise from earlier species.
• Evolution is an observable fact. The process by which it has most likely occurred, natural selection, is a theory.

Question 3

describe one way that changes can arise in the genotype

Answer 3

mistakes during DNA or RNA replication:

little mistakes : small duplications, small insertions, small deletions, base substitutions

big mistakes :
large DNA duplications, chromosome rearrangements, large deletions, viral substitution and insertion of transposable elemnts

Question 4

how can we represent phylogenetic relationships?

Answer 4

• since new species arise from earlier species, they must share relationships.
• All organisms are derived from a single and very distant but common ancestor
• We can represent phylogenetic relationships with phylogenetic trees and phylogenetic trees can be based on molecular data or morphological data.

Question 5

what is systematics

Answer 5

• Systematics deals with classifying living things which has two components:
o Taxonomy: naming of groups of organisms ( taxa)
o Classification: arranging taxa into an ordered hierarchical system

Question 6

what is phylogeny

Answer 6

• Phylogeny – the process of systematics allows the determination of ancestral relationships of organisms and their evolutionary history.

Question 7

describe another reason as to why changes in the genotype arise

Answer 7

• Underlying all genetic change is mutation/recombination of genetic material.
• Recombination can occur due to genetic reassortment such as in viruses or through sexual reproduction.
• Natural selection: organisms better adapted to environment survive to produce more offspring. Survival of the fittest.
• Genetic drift: variation in relative frequency of different genotypes in small populations due to chance. Usually occurs in small and isolated populations.
• Gene flow : transfer of alleles (genes) from one population to another.
• Applied selection : plant or animal breeding. Antibiotic, drug, pesticide resistance.

Question 8

give an example of how we were able to observe evolution

Answer 8

• 12 colonies of E coli from a single clone.
• Each 12 colonies were put into a single flask.
• Every day for 31 years, the colonies were subculture every day .
• Freeze culture samples every 500 generations (75 days).
• Over 73 000 generations have been observed ( until covid )
• Observation: differences between cultures have emerged over the years
• Genetic analysis of ancestors is now possible including the frozen samples.
• The experiment was set up so that the bacteria were growing in a medium with low amounts of glucose but high levels of citrate which they can’t efficiently use in the presence of oxygen.
• So tested for the ability to grow in nitrate in the presence of oxygen
• The ability to use citrate in oxygen evolved after about 30,000 generations in one group in particular
• E. coli cant usually use citrate in oxygen .

Question 9

How was E.coli able to utilise citrate?

Answer 9

The citrate gene is regulated by the citrate promotor. This is normally turned off in the presence of oxygen. It sits in the E.coli gnome next to RNK, which is controlled by the RNK promotor and is turned on in the presence of oxygen.
In the ancestral bacteria, the citrate gene and the RNK promotor were duplicated in tandem. It was inserted into the same region of the genome. The citrate promotor which is controlling the citrate gene is turned off in the presence of oxygen. But the RNK promotor has now been placed next to the duplicated citrate gene. Its normally on in the presence of oxygen so the duplicated citrate gene is also turned on in the presence of oxygen. This allows the bacteria to start growing in the presence of citrate.
Genetic change driven by gene duplication

Question 10

what is meant by the redundancy of the genetic code?

Answer 10

• In many cases, the 3rd base of each codon is redundant, so changes at this position don’t affect the phenotype- changes at this position between organisms suggest greater evolutionary distance. So the genetic code is redundant.

Question 11

describe sickle cell anaemia and why is it common in tropical regions?

Answer 11

• Mutation in the beta-globin gene
• Glu6Val- the glutamic acid residue at position 6 has been mutated to valine.
• Due to single base substitution.
• Mutant Hb molecules: aggregate and form crystals when deoxygenated and form cells with characteristic sickle shape. These cannot pass through smaller blood vessels.
• Autosomal recessive and causes early death
• Correlates with regions of endemic malaria
• Heterozygotes (carriers) have improved malaria survival rates: lower parasitaemia and fewer severe complications from malarial infections.
• Even though it’s a harmful mutation, it confers heterozygote advantage.

Question 12

the mutation that causes sickle cell anaemia is also called ?

Answer 12

a heterozygote advantage

Question 13

phylogentic relations can be inferred from what?

Answer 13

both morphological and molecular analyses.

Question 14

define homology

Answer 14

• Homology: two structures from a common ancestral version
• e.g. tetrapod limbs
• Because these structures are derived from a common ancestor, they form by a common mechanism

Question 15

define analogy

Answer 15

• Analogy: no common ancestor – similar structures produced by selection to meet similar function (convergent evolution)
• e.g. insect wing & bird wing
• Although different developmental mechanisms, some molecular components may be the same

Question 16

what have all modern tetrapod limbs evolved from?

Answer 16

later remodelling of the elements. the basic pattern is conserved through all tetrapods : a single element called a stylopod, a paired element called a zeugopod, and the autopod which is equivalent to the hands/digits.

• so all tetrapod limbs have evolved from the same basic form.

Question 17

describe how the tetrapod limbs of humans bats and horses are homologues but with great diversification.

Answer 17

• In the human arm, there is the humerus proximal element, there is a paired element: radius and ulna and metacarpals called the autopod.

• In the bat, the structure has been modified greatly, but contains the same underlying features. It has a single element most proximal -humerus. The radius and the ulnar are close together because they don’t need to twist in the same way that human forearms do.
• The metacarpals have been elongated to provide the structures over which the skin is then stretched to form the wing.

• In the horse, the humerus is present. The radius and ulna, although they were initially formed as paired elements, have become fused to form a combined ulna and radius. The metacarpals have also been fused or lost, so that is one metacarpal structure.

Question 18

what is molecular analogy

Answer 18

• Also known as molecular convergence. Formation of proteins from genes that are different but the proteins share a common function.

Question 19

give an example of molecular analogy

Answer 19

crystallins ( lens proteins found in the eye)
• There are three main types of crystallins in the lens – alpha, betta gamma family
• Alpha crystallins are related to HSPs ( heatshock proteins)
• So have been recruited to a lens function
• Beta/gamma crystallins are homologous
• But many other different lens proteins exist in different species in addition to the alpha, betta, gamma crystillins.
• These tend to be enzymes/have enzymatic activity
• in addition to being soluble, stable, transparent & refractive (shared property of alpha, betta , gamma)
- they used a different kind of soluable proteins to perform the functions of the crystals.
• Modification of a regulatory region allows expression in lens as well as other tissues

Question 20

what is meant by molecular homology and how is it determined?

Answer 20

• Similarity due to descent at a molecular level.

• Molecular homology determined from amino acid or nucleic acid sequence
o Homologs will have risen from a duplication of the ancestral gene.
o Two genes from same organism (by duplication) – paralogs
o Two genes from different organisms (common ancestor) – orthologs

Question 21

How does gene duplication drive evolution?

Answer 21

o Gene/regulatory region duplication allows the ancestral activity to be maintained
o Duplicated genes can take on other functions, the original gene that was present can carry on performing its original function.
 Complementary functions (redundancy)
 Non-overlapping functions (novel) – duplicated gene.

Question 22

what causes drosophila antennapedia ?

Answer 22

mutation in the HOX gene

Question 23

what are HOX genes

Answer 23

Hox genes are developmentally important transcription factors.
• Hox genes, represents a family of transcription factors and transcription factors bind DNA in a sequence-specific fashion and regulate the expression of adjacent/nearby genes.
• Hox genes Confer positional identity along the Anterior-Posterior (cranio-caudal) axis. So hox genes regulate the identity of tissue.
• Each hox gene is represented along the same chromosome along the cluster. They are all homologs of one another

Question 24

describe what would happen if there are mutations in antennapedia gene in drosophila

Answer 24

• The thoracic segments, T1,T2,T3 are where the antennapedia gene is normally expressed an
• Function: to tell those segments to have thoracic features and be throacic. Its where the legs of the adult drosophila fly would grow. The mutations in the gene antennapedia are not a disruption of the gene but causes the antennapedia gene to be mis expressed in the head region. This is called homeotic transformation. It directs those appendages that would normally form the antennae to form legs instead.

Question 25

how are the different hox genes expressed?

Answer 25

• Different hox genes are expressed in a head to tail pattern which mirrors the organisation of the hox genes on the chromosome.

Question 26

which process allows for diversification

Answer 26

• Gene duplication allows for diversification

Question 27

define homologues

Answer 27

• Homologues are related by descent from a common ancestor

Question 28

define paralogues and orthologoues

Answer 28

• Paralogues are homologues within the same species (eg Mouse Hox a1, a2, a3, a4 etc. are paralogues)
• Orthologues are homologues between species. (eg the fruit fly Antennapedia gene is the orthologue of mouse Hox a6, b6, c6)

Question 29

what do hox genes along the drosophila cluster represent ?

Answer 29

paralogues

Question 30

how have hox genes evolved i inverterbrates ?

Answer 30

• An ancestral hox gene (able to regulate the expression of other genes )will have emerged and duplicated.
• The pair has been duplicated again and again. – organisation observed in invertebrates seen in drosophila .

Question 31

how have hox genes evolved in vertebrates ?

Answer 31

• The cluster has been further duplicated so that the first duplication would provide with 2 clusters.
• The duplication occurs again, so that vertebrates have 4 hox genes clusters numbered A, B, C , D. the hox gene numbers range from 1- 13.
• There have been some individual losses of hox genes within specific clusters, but the fundamental organisation along the chromosome has not changed.
• In vertebrates, genes towards the left hand would be expressed towards the head/anterior end of the embryo, genes towards the right-hand side, would be expressed towards tail end/posterior end of the embryo.

Question 32

what occurs when useful functional domains emergy?

Answer 32

• Once useful functional domains emerge, they get used and reused in organisms : useful for building complexity.

Question 33

give an example of a useful functional domain

Answer 33

In hox genes, the homeodomain is what contacts the DNA.
• Another characteristic of HOX genes, the homeodomain protein region, characterises those specifically as HOX genes.
• PAX GENES : also share homeodomain, but it is joined with another domain : paired domain. This modifies the characteristics of the transcription factors.

The original homeodomain has been joined by other domains that modify that the transcriptional activity.

Question 34

what is the hypothesis for the origins of life

Answer 34

• The RNA World hypothesis
• Early life is thought to have been based on self-replicating, self-catalyzing RNA molecules
• Catalytic RNAs (ribozymes) are present in organisms from bacteria to humans
• The RNA world evolved into a DNA genome/protein enzyme world
• DNA more stable than RNA, greater range/robustness of protein enzymes

Question 35

how can we calculate how old the earth is ?

Answer 35

• Indication on how old the earth is by radioactive dating or radiometric dating.
• Naturally occurring radioisotopes can be used to date rocks and fossils.
• The half-lives range from relatively period of time to a relatively long time ( billions of years)
• Radioactive isotopes can decay to give a characteristic daughter isotope. this characteristic can be used for more accurate radiometric dating.

Question 36

what does radiometric dating measure, and what are radioisotopes used for ?

Answer 36

the ratio of parent/daughter nuclides.

radioisotopes can be used to date rocks and fossils

Question 37

how are we able to measure the relative rations of the parent and daughter atoms?

Answer 37

In igneous rocks, once it forms, it forms an impervious barrier. There is an exponential decay of the parent nucleotide, there is also an exponential increase in the same proportions of its corresponding daughter atom. Each time a parent decays It gives rise to one daughter atom.
When the molten rock forms, it’s a closed and solid system, so nothing can enter, and nothing can escape. This means we can measure the relative rations of the parent and daughter atoms. This gives us an accurate estimation of the age of that material

Question 38

list the requirements for radiometric dating

Answer 38

• The rate of radioactive decay is constant
• Not affected by temperature, pressure, chemicals, electrical or magnetic fields
• Parent and daughter nuclides cannot leave or enter material after it is formed
• No intrusion of other, later rock
• No contamination
• Measuring fossils: fossils form from sedimentary rock – could have a different age to the fossil. So fossils are dated by looking at layers of previously molten rock on either sides of the bands of the sedimentary rock

Question 39

describe the evolution of the cell

Answer 39

• The earliest cells are prokaryotic
• pro (before), karyon (nucleus)
• Surrounding of DNA/protein by phospholipids gave rise to the Emergence of bacterial/archaeal cells
• All three domains (archaea, eukaryotes, prokaryotes) of life share a common origin therefore they share characteristics.
• One characteristic all 3 domains share is the genetic code.
• Each of the three domains have got unique characteristics of their own.

Question 40

describe the evolution of the eukaryotic cell

Answer 40

• Assumed that the eukaryotic cell is formed from earlier prokaryotic cells. It is thought that eukaryotes have acquired organelles by endosymbiosis of organisms :
• Ancestral host that is prokaryotes has either engulfed or merged with another bacterium .
• Merged with aerobic bacterium which has evolved to form eukaryotic mitochondria
• Merged with cyanobacterium which has evolved to form chloroplasts if plant.

Question 41

which process generated organelles and the nucleus ?

Answer 41

endosymbiosis

Question 42

what is the evidence for the endosymbiotic evolution of eukaryotic cells ?

Answer 42

• Mitochondria have their own circular genome which replicates independently of nuclear DNA
• New mitochondria are produced by fission of existing mitochondria, like prokaryotic binary fission
• All mitochondrial genomes share similarity with the Typhus bacterium Rickettsia prowazekii
• Rickettsiales are obligate, intracellular parasites or symbionts of eukaryotes
• By using a phylogentic tree, it is found that all mitochondrial DNA similar to typhus bacterium DNA, and chloroplast genomes resemble cyanobacterial DNA.

Question 43

what are plastid genomes and where are their ‘lost’ genes?

Answer 43

• Plastid genomes encode proteins necessary for plastid function
• Loss of genes compared to ancestral form
• “Lost” genes are still found to be present in nuclear genome

Question 44

what are the 4 basic processes of multicellularity ?

Answer 44

• Spatial organization
• Change in form
• Growth
• Differentiation

Question 45

describe the fossil record

Answer 45

• Most evidence for evolution of complex life within the fossil record.
• The fossil record is incomplete.
• Older rock lies below more recent rock
• Rock and organic material can be dated by measuring the decay of naturally occurring radioactive isotopes
• Fossils usually form in sedimentary rock
• Fossil dates can be bracketed by the age of surrounding igneous rock ( formed from molten rock.

Question 46

how does the fossil record provide evidence for evolution. and what does it allow

Answer 46

• The order and age of organisms can be determined. Within the fossil record, the first life form is unicellular, prokaryote, later eukaryotic cells.
• Evolutionary record shows us we see progressively more complex life forms.
• Also shows that if there is an ancestral form that diverges, we might expect to see transition reforms. Some forms of animals that are part way between two different organisms that we see today.
• We find fossilised organisms that are no longer alive. Intermediate fossils are found (like archeopteryx)

Question 47

compare the formation of eyes in vertebrates to arthropods

Answer 47

• Morphological comparison suggests that eyes have evolved over 40 times.
• All vertebrate eyes form in the same way : the photoreceptors have cilia and are derived from neural tissue. The neural tissue will fold to form the retina. it is covered by epidermal cells, and those epidermal cells will differentiate to form the lens.
• In arthropods, the retina is derived from epidermal cells and they have microvillar photoreceptor cells.

Question 48

the evolution of the eye is an example of

Answer 48

convergent evolution

Question 49

what does the diversity of the eye suggest ?

Answer 49

• The diversity of eyes suggests that they have evolved several times independently (convergent evolution)
• This is further proven by the fact that Crystallins in different taxa are not related

Question 50

eyes are different, but what are some common features ?

Answer 50

• ALL eukaryotes use a homologous family of proteins, opsins, to detect light
• Opsins are G-protein coupled receptors that convert light to nerve impulses
• Eukaryotic opsins share sequence homology and have diverged to detect different wavelengths of light
• (Prokaryotes also have GPCR opsins, but with a different molecular origin – convergent evolution. They don’t share the same sequence similarity as the eukaryotic opsins.)

Question 51

what is the eyeless gene orthologous to ?

Answer 51

Pax6 in humans

Question 52

what does the ectopic expression of the eyeless gene in drosophila lead to?

Answer 52

• Eyeless gene is orthologous to Pax6 in humans (mutation in pax 6 gene in humans causes aniridia – lack of iris) and mouse (smalleye)
• Ectopic expression of eyeless in drosophila leads to ectopic eyes. This means if you take the eyeless gene and express it ectopically in places in the drosophila embryo where it wouldn’t normally be expressed, it gives rise to ectopic eyes. Tissues that are now being forced to express pax 6 will make eye tissue instead of the tissue it normally would have made.

Question 53

what will happen if the mouse pax6 gene is put into the drosophila embryo

Answer 53

• Mouse pax6 gene – put it into the drosophila embryo, and it will cause eyes to form where the pax6 gene is being expressed. So ectopic eyeless or mouse pax6 can induce ectopic eyes

Question 54

which gene in involved in eye development throughout the animal kingdom

Answer 54

pax6

Question 55

is pax6 gene a master gene ?

Answer 55

no

o A master gene is a gene solely responsible for determining the formation of a particular tissue, other genes can also induce ectopic eyes
o Animals without eyes have Pax6
o Pax6 is present in and required for other tissues.
o Therefore, pax6 expression does NOT always lead to eye formation
o More likely that pax 6 organises a gene network required for eye formation.

Question 56

why can eyeloss occur during evolution. give an example

Answer 56

• Some animals have evolved from surface-dwelling forms to underground forms.
• Eye loss is a common feature in such animals
• Example L the Mexican, blind cavefish. The surface-dwelling ancestor has eyes and is pigmented, the derived cave-dwelling form has no eyes
• Cave fisheyes begin to form, but degenerate.

Question 57

why do cavefish eyes degenerate ?

Answer 57

o The lens is essential for the development of other parts of the eye (iris, pupil, cornea, photoreceptors)
o Cavefish lens is smaller and undergoes apoptosis.
o Small apoptotic lens caused by earlier reduction of Pax6 expression and subsequent changes to signalling molecules.

Question 58

what will crossbreeding different strains of mutations responsible for eyeloss result in ?

Answer 58

• Cross breeding of different strains can result in offspring with better developed eyes and vision. This is because the mutations in the different populations that have given rise to loss of vision have occurred in different pathways and so by crossing the two
different mutations, the functioning pathway can compensate.

Question 59

when are morphological differences established ?

Answer 59

during development

Question 60

when do selective pressures act ?

Answer 60

on the adult form

Question 61

how do can we trace human origins ?

Answer 61

• Evidence from the fossil record and from molecular analysis of ancient DNA and modern-day humans.

Question 62

describe the replication of the mitochondria

Answer 62

• Mitochondria are maternally inherited.
• The mitochondrial genome replicates independently of the nuclear genome and does not undergo recombination. Changes over time in the mitochondrial genome are due to the rates of mutation and subject to any evolutionary pressure that takes out harmful mutations.

Question 63

does the Y chromosome undergo recombination ?

Answer 63

no , the male y chromosome does not have a homologous female chromosome to recombine with

Question 64

why do we use the DNA of mitochondria and the Y chromosome to determine how distant the relation is with ancestral organisms.

Answer 64

• Changes in sequence of the mtDNA and the Y chromosome are due to random mutations over time. NOT DUE TO RECOMBINATION. This means the similarity in DNA of mitochondria and Y chromosome with ancestral organisms can be used to determine how distant the relation is.
• Analysis of mtDNA and Y chromosome sequence shows maternal and paternal origin.

Question 65

• Why has neanderthal DNA persisted in homo sapiens ?

Answer 65

evidence that neanderthal genes we tend to keep are involved in immune functions

Question 66

are humans still evolving ?

Answer 66

The main drivers of evolution are mistakes in DNA replication and recombination. Both of which are still occurring, so humans have not stopped evolving.

Question 67

describe in detail an example of recent human evolution

Answer 67

• Different populations have adapted to hypoxia in different ways.
• Such as populations in east Africa live at high altitudes, where there is less oxygen, so have evolved ways adapting to low oxygen environments. Those individuals will produce more Hb than other humans living in lower altitudes. Increased HB- able to carry more oxygen in their blood
• Himalayan regions – populations also have adapted to high altitude by regulating a transcription factor HIF1 (hypoxia inducible factor 1) . A transcription factor that is turned on in low oxygen conditions. It regulates the production of a hormone called erythropoietin, and the production of rbcs.
• In south America, some populations are able to live at high altitudes by making more haemoglobin however the mutation that leads to their increased haemoglobin production is different to the increased haemoglobin production mutation in east Africa. The second population has a different regulation of the same HIF1 transcription factor, a different mutation causing the same outcome as the population in the Andes.

Question 68

what are phylogenetic trees ?

Answer 68

• phylogenetic relationships can be represented using phylogenetic trees
• the phylogenetic tree of life illustrates that all bacteria, archae, and eucaryota are derived from a distant common ancestor called LUCA
• a phylogentic tree can also be based on morphological criteria

Question 69

what is the cambrian explosion ?

Answer 69

the rapid appearance and disappearance of complex organisms in the fossil record – 525 mil years ago

Question 70

what is genetic drift ?

Answer 70

variation in relative frequency of genotypes in small populations due to chance

Question 71

how do populations evolve ?

Answer 71

changes in gene frequency brought about by random genetic drift, gene flow and natural selection

Question 72

what is a gene flow ?

Answer 72

→ transfer of alleles from one population to another

Question 73

what is applied selection?

Answer 73

→ plants or animal breeding

→ antibiotics, drug, pesticide resistance

Question 74

how do populations evolve ?

Answer 74

→ changes in gene frequency brought about by random genetic drift, gene flow and natural selection

Question 75

what is speciation ?

Answer 75

→ gradual evolution of reproductive isolation amongst populations