1
Q
define genes vs alleles
A
Gene:
- sequence of nucleotides that code for a particular characteristic or trait
(DNA codes for proteins which determine our traits)
e.g. eye colour
Allele:
- slight variation in the sequence of a gene
- results in different forms of the trait
e.g. blue, brown eyes
2
Q
define genotype vs phenotype
A
genotype:
- combination of alleles
phenotype:
- observable traits
- determine by genotype AND environment
3
Q
What is a gene pool?
A
- sum of alleles in a population that can be passed on to the next generation
- change over time
e.g. there are 16 pigs in a population. the gene pool has 32 alleles
4
Q
allele frequency
A
- proportion of a relative allele in a population
= (no. of specific allele) / (total no. of alleles in gene pool)
- expressed as percetage or decimal
- if frequency = 1, all organisms are homozygous for that allele
5
Q
factors that affect allele frequency
A
- environmental selection pressure (e.g. predators)
- movement of species (e.g. gene flow, genetic drift?)
- birth/death
- mutations
6
Q
What are mutations? effect
A
- change in DNA that is unpredictable and random
- most have no effect, some result in phenotypic change
- source of new alleles, contribute to change in allele frequency
7
Q
Sources of mutations
A
- DNA replication - occur spontaneously
- Mutagens
- factors that induce mutation
- increase the risk of mutations, but mutations are still random
e,g. radiation, chemicals, pathogens
8
Q
Effects of mutations
A
- neutral- no effect on survival (e.g. colour blindness, dimples)
- beneficial- increase liklihood of survival (e.g. bacteria develop antibiotic resistance)
- harmful- decrease liklihood of survival (e.g. cystic fibrosis)
(most mutations are detected and repaired by enzymes in mitosis)
9
Q
location of mutation:
A
somatic mutations:
- occur in body cells (diploid)
- only affect that individual
germline mutations
- affect gametes (haploid)
- heritable
- may bring a new allele into gene pool, affecting allele frequencies
10
Q
types of mutations:
A
- Point mutations
- change at nucleotide level
- one or handful of bases affected - Block mutations
- change at gene level
- whole genes are deleted or duplicated - aneuploidy
- change at chromosomal level
- extra or missing chromosome
11
Q
Point mutations: substitutions
A
- one nucleotide is replaced by another
e.g. normal: TTC- AAG - lys
silent point mutations:
- no effect on amino acid
e.g. TTT-AAA- Lys
nonsense:
- results in stop codon
e.g. ATC- UAG- stop
missense:
- result in different amino acid
- conservative: conserves function
- non conservative: does not function
e.g. TCC- AGG- Arg
12
Q
Point frameshift mutations:
A
- one or two nucleotides are added or removed, alterning every codon in sequence from that point
- cause a shift in the reading frame, resulting in an incorrect reading of codons
- can have significant effect on polypeptide- for every codon altered, different amino acid
- results in loss of function of the protein, as the polyeptide would be completely different
if 3 nucleotdies- not a frameshift, but a 3 nucleotide pair deletion
13
Q
Block mutations: what, how formed, types
A
- affect large sections of the chromosome, usually multiple genes
- usually occur during meiosis in eukaryotic cells
- effects are serious, even lethal
- duplication of a part of a chromosome
- deletion of part of a chromosome
- inversion: segment of chromosome is removed and replaced in reverse order
- translocation: segments are exchanged between non-homologous chromosomes
14
Q
chromosomal abnormalities
A
- genomes lose or gain a chromosome or sets of chromosomes
aneuploidy:
- abnormal number of a particular chromosome
- extra or missing chromosome
polyploidy:
- more than 2 full sets of chromosomes
- entire genome is replicated so that instead of 2 chromosomes in each set, there may be 3
- caused by errors in meiosis- results in diploid gametes
- if one of these gametes is fertilised, zygote will have more than the usual 2 sets of chromosomes
- in humans, polyploidy zygotes do not survive
- common in plants (they survive via asexual reproduction, may improve plant traits)
- possible in fish and amphibians (may lead to advantageous traits or organisms being sterile)
15
Q
What is gene flow?
A
- movement of individuals and their genetic material between populations
Through:
- immigration (movement into a population)
- emigration (movement out of a population)
16
Q
What is genetic drift?
A
- random changes in allele frequencies over many generations due to chance events
- affect smaller populations more because random chance has a bigger impact when there are fewer individuals, may cause alleles to disappear completely
- leads to reduced genetic diversity
two examples that lead to genetic drift:
bottle neck effect
founder effect
17
Q
Genetic drift- Bottleneck effect:
A
- major reduction in population size due to chance / a catastrophe
- individuals suvive by chance
- reduces genetic diversity
e.g. reduction could be due to: - natural disaster
- human activity (deforestation, poaching)
- new disease
- can CAUSE genetic drift (the event itself is a bottleneck, but may cause change in allele frequencies)
- by chance, the new population may not be representative of original one
18
Q
genetic drift- founder effect:
A
- chance event that affects allele frequencies in a population
- small group, called founder population, breaks away from original population to form a new colony
- brings a random sample of alleles from original population
- small population size means new colony will by chance have:
- reduced genetic variation (alleles that are not present in founder group may be lost)
- unrepresentative of original population
(due to small sample size and low genetic diversity, more subject to genetic drift)
19
Q
Selective pressure: definition and examples
A
- external agents that affect an individual’s ability to survive in their environment
- Physical agents: climate change, food shortages, shelter availability
- Biological agents: infectious disease, predation, competition, sexual selection
- Chemical agents: pollutants in soil, pollutants in water, drugs (e.g. antibiotics)
20
Q
How do bacteria genetically change?
A
- mutate
- exchange genetic material with other bacteria of the same or different species (one typo is conjugation- cell to cell contact where a plasmid containing antibiotics resistant gene is transferred)
21
Q
antibiotics: selection pressure
A
- widespread use of broad spectrum antibiotics is a selection pressure- drives evolution of stronger, more resistant bacteria
- Variation in resistance due to mutations
- antibiotics acts as a selection pressure- bacteria with resistance have selective advantage. They are more likley to survive, reproduce and pass favourable alleles onto offspring.
- Over time, the allele frequency for resistance increases.
- bacteria can transfer antibiotic genes to other bacteria via plasmids (conjugation)
22
Q
Consequences of genetic changes in bacteria / what mechanisms allow them to be resistant:
A
- prevent drugs from adhering to their surface
- decrease the permeability of plasma membrane to drug
- actively pump out drug
- use enzymes that destroy action of drug
23
Q
process of natural selection? short answer response
A
V- variation
- initial variation in the population’s gene pool
- created by heritable mutations
- mention phenotypes
E- environment
e.g. the island environment contains shorter grass
S- selection pressure
- create a selective advantage for particular phenotypes (NOT alleles)
I- inheritance
- organisms with these phenotypes are more likely to survive, reproduce and pass on the alleles to offspring
G- generations
- over generations, the frequency of the alleles coding for ______ increases
- organisms with favourable phenotype: selected for
- individuals w/o favourable phenotype: selected against
24
Q
Artificial selection:
A
- There is variation in population’s gene pool (traits must be heritable)
- humans select individuals with the desirable trait and only allow these individuals to breed and pass on the desirable alleles to offspring
- overtime, the allele frequency of alleles that lead to desired phenotype increases
an example is: selective breeding
- only organisms with desired phenotype or known carriers are chosen to reproduce
25
compare genetic drift and natural selection
natural selection:
1. acts on individuals (favours individuals with particular phenotypes)
- effects are seen in populations over time
2. not random
genetic drift:
1. acts on populations
2. random
26
What is a species?
- group of living, similar, organisms that can mate and prorduce fertile offspring
27
process of speciation / short answer questions
V- initial variation: some have...others have....
I- isolation
- geographic (allopatric)
- not separated by geographic barrier (sympatric)
S- exposed to different selection pressures, one has...., other has....
M- mutations accumulate
C/A- changes in allele frequency occur as individuals with favourable phenotype are more likely to survive (...was favoured in ...habitat)
N- new species has formed (populations cannot breed to produce viable, fertile offspring)
28
types of speciation: allopatric
allopatric:
- geographical isolation
- population with initial variation is divided by a physical barrier, becoming geographically isolated
- no gene flow between populations, genetically diverge (i.e. via mutations)
- over many generations, subjected to different environmental selection pressures, so different phenotypes are selected for by natural selection or genetic drift
- if populations cannot produce fertile offspring, they are reproductively isolated
e.g. Galapagos finches- charles darwin
- finches geographically isolated (due to water between islands)
- founders flew to different islands with different environements
- exposed to different selection pressures (food sources)
- different beak sizes and shapes are selected for to assist them eating different foods (fruits, seeds, insects)
- ancestral finch diversified rapidly to occupy different niches of galapagos islands (start with one and radiate out- adaptive radiation)
29
types of speciation: sympatric
sympatric:
- not geographical isolation
- reproductive isolation that prevents interbreeding (temporal, behaviorual)
- population divided by a barrier other than geographical isolation. There is reduced gene flow between populations.
- over many generations, they genetically diverge
- isolated populations respond differently to environmental selection pressures, leading to different phenotypes being selected for by natural selection or genetic drift
- if they can no longer reproduce fertile offspring when brought together, they are reproductively isolated. They are now two different gene pools and species
e.g. Lord Howe Island
- different species of Howea palm trees diverged from same ancestral species
- initial variation in soil preference altered flowering time so they flower and pollinate at different times of the year, preventing cross pollination and gene flow (temporal isolation)
- now, they grow in different soils:
- Volcanic (high in nutrients from mycorrhizal fungi)
- Calcareous (low in nutrients no mycorrhizal fungi)
- soil provided different selection pressures
30
What is a fossil and types:
- evidence of life from the past
mold: impression of living things left in a rock (organism decomposes beneath sediment)
cast: mold filled with minerals and sediments
mineralised / petrified: minerals replace the organic material (bones) of an organism
trace: geological record of organism's activities (footprints, burrows)
31
Fossil formation:
- very rare occurrence
1. organism is rapidly buried by sediment in low oxygen environment, or in colder environments (snow/ice)
2. soft tissue decomposes, leaving behind bone or shell
3. layers of sediment form above organism, increasing compression.
- reduces destruction by predators, weathering or bacteria
4. chemical changes occur
- hard parts (bone) becomes porous
- this allows minerals from surrounding sediment to seep in and replace them to form the fossil
5. as successive layers of sediment build up, sediment is hardened into rock by heat and pressure, preserving evidence of life inside
(must be left undisturbed for a long time)
6. eventually, rock above may erode, exposing fossil
32
Extinction and mass extinction
- loss of a species or group of species
occurs for various reasons e.g.
- species fail to adapt to environmental changes
- species compete for limited resources
- following a mass extinction, period of adaptive radiation (rapid evolution of many diverse species from a single ancestor) usually occurs
- this happens as mass extinction leaves many unoccupied niches and may reduce selection pressures
- increases biodiversity
- shift in the dominant life form
33
what are transitional fossils?
- display both traits from its ancestor (primitive traits) and descendents (derived traits)
- dated to have existed before earliest descendent and after latest ancestor
34
Why is the fossil record biased?
- some organisms appear at a higher frequency
this is because:
- hard body parts (teeth, bones, exoskeletons) are more likely to be preserved than soft body parts (skin, organs)
- favours organisms that live in areas of high sediment accumulation (e.g. near water)
this limts evidence of past life
35
geological scale
- volcanic earth (lifeless)
- first prokaryotic cells- oxygen free environment
- photosynthetic bacteria
- aerobic microbes (oxygen-using)
- then unicellular eukaryotes
- multicellular eukaryotes
- vertebrates?
- insects
- land plants
- amphibians
- ferns
- mammals
-flowering plants
36
law of superposition
In a sequence of undisturbed sedimentary rock layers, the oldest layers are at the bottom, and the youngest are at the top.
37
conditions in evironment that make fossilisation possible
- low oxygen levels (reduces decomposition / not suitable environment for decomposers and scavengers)
- cold environment (reduces decomposition)
- areas of more sediment / rapid burial (reduces decomposition and hides them from scavengers)
- highly mineralised water
- lack of scavengers or decomposers
- hard body parts
- constant humidity and temperature
- no wind, sunlight
38
What is fossil succession?
The principle that sedimentary rock layers contain fossilised organisms in a definite sequence.
- even when rocks look different, the sequence of fossils is always the same
- allows scientists to correlate rock layers from different locations
- index fossils, which existed during known specific time periods, provide evidence for the relative age
39
Why is dating fossils important?
- gives us a time scale of evolution
40
Relative dating
- compares position of a index fossil of a known age to the position of ROCK LAYERS
- age of a fossil or surrounding rock is estimated relative to the known age of a sample
First method: principle of superposition
- each new layer of sediment is desposited on top of existing layers
- the deeper the layer, the older it is
relative dating can be difficult when rock has eroded, buckled, moved or been reburied, as it alters original sequence of strata (layers of sedimentary rock or soil)
2nd method: stratigraphy / index fossils
- matching sedimentary rock layers in one location with those in another
- same level does not equal same age, rather they look at the type of rock, fossils in it
- often done using index fossils
41
What are index fossils? What principle do they rely on?
To be a good index fossil:
- found widespread (mutliple locations)
- many fossils must be found in a single rock layer to have large enough sample size)
- organism existed for only a short time during Earth's history (meaning they are NOT found in many rock layers)
- has a known (absolute) age
- has distinguishable features (unique enough)
- used to date strata:
rely on the principle of fossil succession- certain fossils always occur in a specific order, so you can match that layer with layers in different locations
42
Absolute dating: when is it unreliable, main example, what does it measure
- provides more precise estimate of fossil age
- thre actual age of a rock or fossil
- unreliable if there are very low levels of radioisotope (imprecise), or if fossils are too old or young for the radioisotopes to be present in sample (once ratio is basically constant, it could exist for millions of years)
one example is: radiometric dating which uses isotope decay
- uses naturally occuring radioactive isotopes in the minerals that make up fossils and rocks
43
What are isotopes and radioisotopes?
- isotopes: atoms of the same element (same no. protons) with different no. neutrons
- some isotopes are stable, others are unstable
- unstable isotopes are radioisotopes
radioisotopes:
- unstable parent isotope spontaneously breaks down into a more stable daughter isotope at a known rate
- the process of breaking down is radioactive decay
e.g. carbon 14 (unstable) breaks down into nitrogen 14 (stable)
44
What is half life?
- time it takes for half of the parent isotope to decay into the daughter isotope
45
Isotype systems- absolute dating
Carbon-14 / Nitrogen-14
- measure ratio of carbon 14 to carbon 12 (and compared to ratio in atmosphere today (or more accurately at the time the organism was alive)
- sample must organic to contain carbon
- scientists know the rate of decay
- once ratio becomes stable, carbon dating becomes less accurate
- calculates from 1000 to 50 000 years
Potassium 40 / Argon 40
- measure amount of isotope in surrounding rock, compare to daughter isotope and use half life
- potassium 40 is found in volcanic rock
- as volcanic rock cools, potassium 40 decays into argon 40
- slower decay (half life is 1.3 billion years)
- for older than 60 000 years
- dates the volcanic rock layers, not the fossil
- widely used as most rock contains potassium
Uranium 235 - Lead 207
- half life: 700 million years
- dates uranium containing materials (shells, corals)
- dates rock layers only
- not as widely used (since uranium is harder to find)
- dates from 1 million to 4.5 billion years
Uranium 238- Lead 206
- half life: 4.5 billion years (everything else same)
- measure ratio of parent to daughter isotope
- determine number of half lives that have passed
46
What is structural morphology?
- analysis of structural similarities and differences
47
Structural morphology: homologous structures
- structure within group of species that has a similar structure but different functions according to needs of the organism
- indicates common ancestor
- more similar homologous structure is: more closely related species are AND the more recently they shared a common ancestor
e.g. pentadactyl limb
ancestor species had 5 digit appendage
as it evolved, exposed to different environmental selection pressures, resulting in the different forms seen in descendent species
48
What is an analogous structure?
- same function but look different (not on course)
- due to similar selection pressures
- do NOT indicate common ancestry / relatedness
e.g. bird and insect wings
49
Vestigial structures
- structure in an organism that is no longer functional, but served a purpose in a common ancestor
e.g. whale has pelvis /femur bone from mammalian ancestor
50
Patterns of evolution: divergent evolution
- common ancestor evolves into more than one different species
- due to exposure to different selection pressures and accumulation of mutations (basically speciation)
- homologous and vestigial structures evidence of divergent evolution / speciation over time
51
Patterns of evolution: Convergent evolution
- two NOT closely related species evolve structures with similar functions (via natural selection) when exposed to similar selection pressures
- if the most recent common ancestor did not have that trait, then the two lineages have evolved it INDEPENDENTLY
(may still share a common ancestor BUT it's about whether the trait evolved independently)
e.g. shark fin, penguin wing, dolphin flipper
52
Molecular homology:
- useful when species have no structural similarities
relies on molecular clock hypothesis:
- measuring number of differences in DNA or amino acid sequences between organisms indicates how closely related they are
- DNA and protein sequences evolve at a relatively constant rate over time (within a species or among species??)
2 principles of molecular clock:
- the more similar a DNA or amino acid sequence, the less time has passed (between divergence), the more recently they shared a common ancestor
- the more difference they are, the more time has passed for changes to accumulate, common ancestor is further back
53
amino acid sequences: molecular homology
- analyse amino acid sequences in proteins that are common between the species
- does not reveal all DNA differences (because of degeneracy of genetic code-- does not reveal silent muations)
- differences in amino acids change more slowly than in DNA
54
DNA sequences: molecular homology
- more accurate than amino acid sequences
- the best DNA region to analyse depends on which organism and how far back they diverged (but generally the best is mtDNA)
1. Mitochondrial DNA: passed from mother to offspring in sexually reproducing organisms
2. nuclear DNA: inherited from all ancestors
3. chloroplast DNA
55
advantages of mtDNA
high mutations rate of NON-coding regions (coding regions mutate at a slow rate)
- higher than coding region of nuclear DNA
- can observe differences between closely related species or different populations of same species
- change over a short period of time
mutates at a known/predictable rate compared to nuclear DNA:
- can determine precise time of divergence
no recombination:
- differences are only due to mutations
only passed down from mother to offspring:
- this makes it easier to trace unbroken lineages
mutations are not repaired
- higher mutation rate
- permanent and can be studied
- takes longer to degrade than nuclear DNA
many copies of mtDNA in each cell:
- provides larger sample size to analyse
56
phylogenetic trees: what are they, how do you read them?
- represents an evolutionary hypothesis
how to read:
- longer branch- more genetic divergence (more genetic differences)
- root= hypothesised common ancestor of all taxa in tree
- node= most recent common ancestor of descendent species, represent speciation event
- lack of a node= exact divergence time is unknown
- branch does not reach end of tree: species is extinct
- horizontal line between branches: genetic material passed between species after divergence (interbreeding)
57
advantages of nuclear DNA
- evidence of both paternal and maternal lineages
- bigger amounts of DNA can be sequenced (more bases)
- provides evidence of interbreeding
- lower mutation rate
- presence of introns- can reveal more inherited mutations
- mtDNA does not provide evidence of interbreeding
(this means if a neanderthal male interbred with a Homo Sapiens, then you would only be able to see in nuclear DNA, not mtDNA)
Biology 3/4
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