evidence for evolution Flashcards
genome
the complete set of genetic material in a cell; an organism’s complete set of DNA
DNA cloning
- researchers “clone” – make many copies of – a DNA fragment of interest, such as a gene
- involves inserting a target gene into a circular DNA molecule called a plasmid
PCR acronym
polymerase chain reaction
PCR function
small quantities of DNA to be replicated from a sample (amplified) → producing testable amounts to use in analysis techniques
what does development of PCR enable?
small quantities of DNA to be replicated from a sample → producing testable amounts to use in analysis techniques
- mimics the natural process of DNA replication that occurs prior to cell division
PCR steps
- denaturing
- annealing
- extension
how many times are the steps of PCR repeated?
sequence repeated 20-30 times in a process called thermocycling
thermocycling
process of repeated heating and cooling
how long does it take to produce a billion copies of DNA through PCR
2-3 hours
denaturing
- During natural DNA replication, the enzyme helicase separates the two strands of DNA (allows each strand to be copied)
- PCR uses heat to achieve same function
what temperature does denaturing occur at and why
- Temps of 94-96C used to break hydrogen bonds holding the two strands together
- Separates strands without disrupting each individual strand
annealing
- Allows short strands of DNA called primers to bind to the single DNA strands
- Primers not random sections of DNA → they’re complementary to either end of the section of DNA to be copied
what temperature does annealing occur at
Temperature is decreased to 50-60C
another name for extension
elongation
extension/elongation
- Mimics the process of DNA replication
- Enzyme DNA polymerase is used to join new, complementary nucleotides to the sections originating with the primers
- This extends the nucleotide chain → creates new strands of DNA
- Not the full length of original DNA – starts @ primer not @ end of DNA
- Eventually, majority of DNA strands are the length of DNA b/w location of the primers
- DNA polymerase attaches to double-stranded DNA
- Primers act as starting point → initiate DNA replication
what temperature does extension occur at?
temp increased to 72 degrees
all PCR applications now use heat stable DNA polymerase, what is this polymerase called?
Taq polymerase
where is taq polymerase taken from?
taken from a bacterial enzyme
why is taq polymerase more useful?
- Doesn’t denature when heated
- Allowed the procedure to be simplified and automated → sample can be alternately heated and cooled
how is PCR useful in the study of human evolution?
as it:
- provides testable amounts of DNA from very little
- eg. fossils – usually found in minute quantities
what other than the study of human evolution is PCR useful for?
- DNA profiling – comparing an individuals DNA to a library of DNA from known individuals
- early detection of infectious disease – foreign DNA from viruses/bacteria
- eg. COVID
- medical diagnostics
- forensic analysis
restriction enzymes
- Enzymes that cuts strands of DNA at specific sequence of nucleotides
what happens when restriction enzymes are added to DNA?
- When they are added to DNA → cuts strands into different lengths depending on base sequence of the specific DNA sample
- Length of pieces can be analysed and compared with other DNA samples
gel electrophoresis
- fragments of DNA are pulled through a gel matrix by an electric current by separating DNA fragments according to size
- pulls the negatively charged DNA through the gel from negative to positive electrode
- Technique that uses the banding patterns of DNA fragments as a means of identification; unique to every individual
banding pattern
individuals DNA profile or DNA fingerprint
process
- DNA fragments are placed in a gel
- Weak electric field is applied to the gel
- Electric field pulls the DNA fragments to one end of the gel/fragments move from the negative end (anode) to positive end (positive electrode)
- Fragments move @ diff. rates depending on size
which size fragments move the fastest in gel electrophoresis
Smallest fragments move faster
how are the fragments for different species separated?
in unique patterns
filling the wells
- the wells where the DNA is placed are simply depression in the gel
- DNA will rather move through the gel than diffuse through the solution
- DNA needs to be accurately placed in the wells using a micropipette (these reduce chances of cross contamination as they have disposable tips)
DNA ladder
- Often run at the same time as the samples
- Ladder contains segments of DNA with known lengths
- Results from unknown sample are compared to the ladder to determine the length of the DNA strands in the sample
what stains can be used for visualising DNA in gel electrophoresis
- ethidium bromide
- methylene blue
visualising DNA by using ethidium bromide
- As DNA moves through gel it picks up some of the chemical
- When run is completed, UV light is shone over gel and the DNA fluoresce
visualising DNA by using methylene blue
- Dye that binds to DNA
- When the gel is soaked in the dye, areas containing DNA stain a deeper blue → visible to naked eye
DNA sequencing purpose
Determining of the precise order of nucleotides in a sample of DNA
specific method used in DNA sequencing
Sanger sequencing
DNA (sanger) sequencing process
- The region of DNA to be sequenced is identified and cut (using bacterial enzymes)
- PCR amplifies the sample and creates dye labelled fragments.
- DNA sections are separated using gel electrophoresis (or other chromatography methods)
- Bands form which represent different sizes of DNA
what is used to sequence the DNA sample
computer software
uses for DNA sequencing (medicine)
- Used to identify mutations
- Compare DNA from different organisms
- Useful in identifying inherited disorders (sickle-cell anaemia, cystic fibrosis and cancer) and maternity/paternity tests
- Fertility
- Identify disease causing mutations based on family history
- Family planning
uses for DNA sequencing (science)
- Used by scientists to compare species in order to track evolutionary changes
uses for DNA sequencing (agriculture)
mapping and sequencing genomes of microorganisms making them useful for crops and food plants
uses for DNA sequencing (forensics)
to help identify individuals because each individual has a different genetic sequence
principles for ethical considerations with genetic information
- autonomy
- confidentiality
- equity
- privacy
autonomy
- Respect for the right to be self-determining; choose whether or not to be tested and if tested, to know and share the info
- Right of an individual to decide their own future, independent of genetic info
confidentiality
- Use of genetic info treated sensitively
- Accessed only by those who are authorised to access it
equity
The right to fair and equal treatment regardless of genetic info
privacy
- The right to be left alone
- Make decisions regarding genetic testing and the resulting information, independent of others
comparative studies
- genomics DNA
- genomics mtDNA
- proteins
- bioinformatics
- comparative genomics
- embryology
- homologous structures
- vestigial structures
genomics DNA
- DNA is universal; sequence of organic bases b/w species varies
- New genes gained by mutation
- Lost by natural selection or genetic drift
- Species that are more closely related → more sim.
- Non-coding sequences of bases in DNA (junk DNA) show more similarities with more closely related species → evolved from common ancestor
ERV acronym
endogenous retroviruses
what are endogenous retroviruses?
apparently non-functional DNA, a viral sequence that has become part of an organism’s genome
mitochondria
organelles in the cell where the aerobic phase of respiration occurs to release energy for use by the cell
what is mtDNA
Some DNA is located here (most in the nucleus) = mitochondrial DNA
In the form of small circular molecules (unlike strands of DNA in the nucleus)
- 5-10 molecules in each mitochondrion
how many genes in mitochrondrial DNA
37 genes = all essential for normal functioning
why is most cells containing large numbers of mitochondria an advantage?
- Lot easier to find and extract than DNA in the nucleus
- Smaller samples can be used
inheritance mtDNA
- Mitochondrial DNA only comes from egg
- Inherit nuclear DNA from sperm and egg
- Inherit mitochondrial DNA from egg (mum)
- Mitochondria in sperm destroyed at fertilisation
evidence from mtDNA
- mtDNA has higher rate of mutation
- Human mtDNA slowly diverging from mtDNA of our original female ancestors
- Scientists use the similarity b/w mtDNA of any two individuals to provide an estimate of the closeness of their relationship through their maternal ancestors
identical mtDNA meaning
closely related eg. Siblings
different mtDNA meaning
last common ancestor lived long ago
use of mtDNA as evidence
- Comparing individuals within a species and for species that are closely related
- Allowed scientists to track the ancestry of many species back for generations
- Demonstrate evolutionary relationships b/w humans and closely related species
why is mtDNA an important tool in mapping relationships between species?
- This analysis allows scientists to verify evidence of evolution gained from other sources
- Eg. Examination of mtDNA has shown than the last common ancestor of modern humans and Neanderthals lived around 600 000
- Greater the diversity in mtDNA, the less closely related the species are
proteins
- Consist of long chains of particular amino acids linked together in a precise sequences determined by DNA
- Differences in the DNA sequence give rise to different amino acid sequencing
- All made from 20 types of amino acids
how can degree of similarity be established using proteins
By comparing type and sequence of amino acids in similar proteins from different species, modern biochemical techniques enable the sequence of amino acids in a protein to be determined
amino acid sequences: Animals species
- Animals of the same species have identical amino acid sequences in their proteins
- Those from different species have different amino acids/arranged in different order
evidence from proteins for evolution
- The degree of difference b/w proteins enables an estimate to be made of the amount of evolution that has taken place since two species developed from a common ancestor
- The longer the period of time, the greater the number of amino acids that are different
example of proteins as evidence for evolution
- Alpha and beta chains of haemoglobin are identical in humans and chimpanzees
- Same protein sequence in gorillas differ by one amino acid
- In gibbons = 3 amino acid differences
- Supports evolutionary relationships with primates
how to easily compare amino acid chains?
scientists adopted system where by one letter is used to represent a particular AA, done for a no. of ubiquitous proteins
Ubiquitous proteins
proteins that appear in all species
ubiquitous proteins purpose
- Perform basic essential tasks that all organisms require for life
- Found in all organisms
- Completely independent of an organisms specific function/environment in which it lives (proteins carry out the same functions no matter where they are found
example of ubiquitous protein
cytochrome C:
- This protein performs essential step in the production of cellular energy
- Changed very little over millions of years of evolution
- Contains 104 AA
- Regardless of species – 37 of these have been found at the same positions in every sequences cytochrome C molecule
- Suggests that these proteins have descended from an ancestral cytochrome C molecule found in primitive microbe that existed 2000MYA
how to compare cytochrome C sequences
they need to be aligned so that the max no. of positions containing the same AA can be determined
more similarity between two cytochrome C means
the more recently they’ve evolved from a common ancestor
what areas does bioinformatics combine and why?
all areas of biological science with computer science, engineering, statistics and applied mathematics to help understand biological processes
Use of computers to describe the molecular components of living things
- Uses biochemical analysis to gain info about DNA and proteins; computer software to store and analyse it
- Useful in assisting evolutionary biologists to trace the evolution of a large number of organisms → measuring changes in their DNA (rather than through physical observations)
- The more similar the genes of two species → the close their evolutionary relationship
- Recent research → compare entire genomes
evidence from bioinformatics
- The greater the degree of similarities in specific genes, the closer the evolutionary relationships b/w two species
- Combines computer science, stats, maths, engineering → analyse biological data
- Techniques such as images used to extract results from large amounts of raw data obtained by biochemical testing
- Testing highlights the amount of similarity b/w the species
comparative biochemistry
- Studies evolutionary relationships between species
- Looks at similarities/differences of the neurotransmitters between species to establish relatedness
embryology function/role
- Compares the early stages of development of organisms
- Structures not present in adults can be seen in the embryo
- More similar the structures are for longer in the embryonic stage → more closely placed together on a phylogenetic tree
embryology’s use in providing evidence for evolution
Used in conjunction with evidence collected from other sources
example of embryology as evidence for evolution
Embryo’s of humans and chickens have slits and arches in their neck
- Similar to gill slits and arches in fish → but don’t develop into gills = common ancestor
homologous structures function/role
- Compares anatomical structure from different species
- similar physical features in organisms that share a common ancestor, but the features serve completely different functions.
example: homologous structures as evidence for evolution
- pentadactyl limb (a limb with five digits such as a human hand or foot which are found in many amphibia, reptiles, birds and animals)
- Common to all vertebrates except fish
- Structure has been modified to perform distinct functions in different organisms
- Bats and birds → use for flight
- Primates → forms a hand used to grasp things
- Anthropoids (human-like primates) show anatomical resemblances (arrangement of muscles in legs)
vestigial structures function/role
- Homologous structures that have a benefit/normal function in some species
- More shared features → more closely placed together on phylogenetic trees
- Structures that have changed during evolution → no longer fulfil original function
- Common in vertebrate species
vestigial structures examples
- Nictitating membrane: changes in habitat and eye physiology may have rendered the tissue unnecessary
- Appendix
- Coccyx
- Body hair
- Wisdom teeth
vestigial structures use in evidence for evolution
- Changing environmental conditions → organs no longer essential to survival → reduced to vestigial remnants
- Natural selection reduced organs to non-functional remnant’s → waste of organisms energy/resources to maintain useless structures (no selection pressure to maintain)
fossilisation and fossil discovery steps
- death and decay of the soft parts of the organism
- deposition of sand and silt layers to cover the organism
- permineralisation, where mineral deposits form the internal casts of the organism
- erosion and exposure of the organism to the surface
Fossil
any preserved trace left by an organism that lived long ago
examples of fossils
- Part of an organism: Bones, shells or teeth
- Include footprints, burrows, faeces or plant/animal impressions
- Human ancestors: usually bones, teeth or footprints
how are fossils used by scientists
- determine exactly what extinct species were like
- rocks and fossils of other plants and animals help build a picture of the past
- diet, climate, what other organisms existed @ the time
- build up a sequence of evolution of plant or animal
chance that plant or animal will be fossilised
small chance
what usually happens to dead organisms?
dead organisms are decayed by microorganisms → no trace of existence left
when do parts of organisms may become fossilised
when:
- buried by drifting sand
- mud deposited by rivers, volcanic ash
- if buried rapidly → conditions may not be suitable for decomposers → decomposition slowed
two soils that can have an effect on fossil formation
- wet acidic soils
- alkaline soils
effect of wet acidic soils
- minerals in the bone are dissolved → no fossilisation
- contains no oxygen → complete preservation of the soft tissues and bones may occur
effect of alkaline soils
- produce best fossils → minerals in bones are not dissolved
- new minerals (lime, iron oxide) are deposited in pores of bone → replacing organic matter → bone becomes petrified (turned into rock)
location of fossils
- human ancestors → edges of ancient lakes and river systems, in caves or volcanically active areas
- organism can be buried rapidly, preventing decomposition
- lakes and rivers build up sediments when flooding occurs or water slows rapidly
- caves are in limestone (made up of calcium carbonate)
- may be deposited around dead organisms OR cave roof or walls may collapse → covering bodies of animals
- unusual to be preserved near volcanic eruptions (heat from volcanic material destroys organism)
two ways of fossil discovery
- can be found by chance
- excavation or ‘dig’
fossil discovery can be found by chance
- uncovered at surface of ground by erosion
- ‘fossil fragments’
fossil discovery by excavation or ‘dig’
- areas marked out in sections
- soil removed and sieved
- artefacts often found near fossils
artefacts
objects deliberately made by humans
artefacts examples
Stone tools, beads, carvings, charcoal from cooking fires and cave paintings
DATING FOSSILS
determining age of the material (fossils or artefacts) = dating
knowledge of age is crucial
crucial in finding out sequence of changes that have resulted in present-day humans
dating provides
- absolute dates
- relative dates
absolute dates
actual date of specimen in years
relative dates
comparison of fossils to tell us whether one sample is older or younger than another
two ways of absolute dating
using
- potassium argon
- carbon 14
what is Potassium argon dating based upon
based on the decay of radioactive potassium to form calcium and argon
potassium is a mixture of which 3 isotopes
- Potassium-39
- Potassium-40
- Potassium-41
which potassium isotope is a radioactive isotope and what does it form
- Potassium-40 is a radioactive isotope and decays to form calcium-40 and argon-40
- Occurs slowly but constantly
how is potassium argon used to calculate age of rock
Determining amount of potassium-40 and argon-40 in a rock sample → allows age of rock to be calculated
As rock ages → proportion of potassium-40 decreases while argon-40 increases
limited usefulness of potassium argon dating
- Not all rock types suitable for this method
- Can only date rocks older than 100,000 to 200,00 years
- Half life of potassium-40 = 1250 billion years (1.25 x 109 years)
- Takes 1250 billion years for half of the potassium-40 to decay
requirements to use potassium argon dating
- Suitable rock of same age as fossil must be available
- Age of rock is determined → age of fossil inferred
- Eg. Rocks produced in volcanic eruptions bury bones
what is carbon dating based upon
Based on the decay of radioactive isotope of carbon-14 → nitrogen
Role of Carbon-14 in environment
- produced in the atmosphere
- ratio of one carbon-14 atom to every million million (102) atoms of stable carbon-12 isotope
- plants absorb atmospheric carbon dioxide and incorporate carbon-14 through photosynthesis
why do organisms have carbon 14
animals and ppl eat plants → taken in carbon-14 → becomes part of tissue → death occurs → carbon-14 already in tissues → continues to decay at fixed rate
carbon 14 ratio + half-life
- ratio of one carbon-14 atom to every million million (102) atoms of stable carbon-12 isotope
- declines to over time
- 0.5 in 1012 (half) after 5730 years = half life
- 5730 40 years
what happens after measuring the amount of radiation liberated by a sample
ratio of carbon-14 to carbon-12 can be estimated →age of sample calculated
Methods for carbon 14 dating
- Normal = Requires 3g of organic material
- Accelerator mass spectrometry radiocarbon dating = used to date sample as small as 100 micrograms (0.0001 grams)
- Involves breaking up the sample into it’s constituent (essential) atoms → no. of atoms of each isotope of carbon can be counted
- Become possible to date cave paintings using sample of pigment
Limitations for carbon 14 dating
- Cannot be used to date back more than 60 000 years
- Material to be dated must contain organic compounds (from living things than contain carbon)
- Once assumed ratio of carbon-14 to carbon-12 was constant in atmosphere → it’s not; it varies!
Contributions of carbon 14 dating
- Great to date fossils and artefacts of more recent origin
- Both methods = give anthropologists a number of ways of determining the actual age of ancient material
Relative dating
Determines whether it is older or younger than another sample OR the rock/soil in which it is found
Stratigraphy
Study of layers/strata
two ways that stratigraphy can be useful in dating fossil material
- Principle of superposition
- Correlation of rock strata
Principle of superposition
- Assumes that in layers of sedimentary rock, the layers at the top are younger than those beneath them
- Any fossils found in top layers will be younger than material found lower down
issues with the principle of superposition
- Sequence of rock layers may be distorted by Earth’s crust
- Fossils/artefacts could be buried by animals after deposition of sediment
- Correlation of rock strata
- Matching layers of rock from different areas
- Done by examining rock itself, and the fossils it contains
- Rocks that contain the same fossils = same age
- Index fossils = great value as widely distributed; present on Earth for limited time → makes dating strata more precise
- Fossilised pollen grains → info about amount of vegetation existing at the time deposit was laid down
Four conditions for fossil formation
- Quick burial of material
- Presence of hard body parts
- Absence of decay organisms
- Long period of stability – organism needs to be left undisturbed
why are there Gaps in fossil record
organisms not been preserved
why have only a small proportion of fossils that exist have been discovered
- Some buried too deep or inaccessible
- Not recognised as fossils and destroyed due to agriculture or industry
why is carbon and potassium argon Dating is problematic
- Carbon dating = carbon must be present; only dates back 60,000 years
- Potassium argon = relies on suitable material eg. Volcanic lava to be present
it is _________ to find fossil of entire organism or whole skeleton of organism (especially humans)
unusual
The greater the degree of similiarity of the genome, the…
the closer the evolutionary relationship b/w two species
All species of organisms have DNA, sequences of bases varies due to
- New genes gained by mutation
- Lost by natural selection or genetic drift
Comparative genomics
a field of research that compares the genome sequences of different species
- By comparing the sequence of the human genome with genomes of other organisms → researchers able to identify regions of similarity and difference
comparative genomics provides effective means of:
- Studying evolutionary changes among organisms
- Helping to identify genes that are preserved among species
- Identify genes that give each organism unique characteristics
genomic features
DNA sequence, genes, gene order, regulatory sequences and other genomic structural landmarks or biomarkers
what is comparative genomics used for?
- Used to reveal the diversity of gene composition in different evolutionary lineages
- Research may result in the rearrangement of the way we view some of the evolutionary relationships b/w primates
