DNA, Biotechnology, Evolutionary Mechanisms and Evidence for Evolution

What are the stages of the PCR procedure?

1. Denaturation: (94°C - 96°C) reaction mixture is heated to break down the hydrogen bonds connecting the complementary base pairs of the double-stranded DNA template, seperating it into two single strands

2. Annealing: (50°C - 65°C) the temperature is lowered to allow DNA primers to bind (anneal) via hydrogen bonding to specific complementary sequences on the single-stranded DNA target region

3. Extension: (72°C) the mixture is heated to the optimal working termperatre for Taq polymerase. The enzyme synthesises new complementary DNA strands by starting at the primers and adding free nucleotides in the 5’ to 3’ direction

What is PCR?

An in vitro labratory technique used to rapidly amplify specific sequences of DNA, generating millions of copies from a minute initial sample.

What does PCR stand for?

Polymerase chain reaction

What are the essential components required for PCR?

• DNA template (contains target gene to be copied)

• Primers (short, single-stranded DNA sequences desinged to bind to complementary sequences)

• Taq polymerase (builds new strands of DNA, doesn’t break down → handles heat)

• dNTPs (free Deoxyribonucleotide Triphosphates → building blocks for DNA strand synthesis)

• miniPCR (automated machine → rapidly raises and lowers temperatures precisely)

What method of absolute dating is used for fossils over 1.5 million years old? Why?

Potassium-Argon Dating.

Radiocarbon dating cannot be used as for its effective limit is approximately 50,000 to 60,000 years. At over 1.5 million years old, all Carbon-14 would have decayed. Potassium-Argon dating measures radioactive decay in volcanic ash or rock layers enclosing the fossil, which covers the millions-of-years timescale.

What are the attributes and principles underlying Potassium-Argon Dating?

Radioactive isotope Potassium-40 decays into Argon-40 gas at a known rate (half life of K ~1.25 billion years.

Heating volcanic rock releases trapped argon gas, allowing scientists to measure the ratio of Potassium-40 to Argon-40 to calculate the age of the rock layer surrounding the fossil.

What method of absolute dating is used for fossils around 50,000-60,000 years old? Why?

Radiocarbon (Carbon-14) Dating.

Operational timeframe for measuring radioactive decay directly from organic remains like bone or charcoal.

What are the attributes and principles underlying Radiocarbon (Carbon-14) Dating?

Living organisms absord both Carbon-12 and radioactive Carbon-14 in a constant ratio. Upon death, Carbon-14 intake stops, and Carbon-14 steadily decays into Nitrogen-14 with a half life of ~5,730 years.

Measuring the ratio of remaining Carbon-14 to stable Carbon-12 in organic tissue determines how long ago the organism died.

What factors contribute to distinct species on remote islands?

• Geographic isolation: oceanic distance forms physical barrier preventing gene flow between island populations and mainland populations, allowing mutations and divergent allele frequencies to become fixed within the group

• Founder effect: original small group of colonisers carries a restricted and unrepresentative sample of the mainland populations total genetic variation, atlering starting allele frequencies

• Natural selection: isolated island enviroments feature distinct climatic conditions, different food sources, new habitats, and an absence of specific predators compared to the mainland. Individuals possessing favourable genetic variations better suited to the unique island selection pressures survive, reproduce, and pass on the advantageous alleles to offspring

• Genetic drift: random, non-directional change in allele frequency that occurs by chance (e.g. disease outbreaks, upredictable death of individuals). Particularly significant in small populations.

• Speciation: accumulated genetic variations (mutation, selection, and genetic drift) over time lead to reproductive isolation, preventing island organisms from interbreeding with original mainland populations

How does PCR, microbial enzymes, and gel electrophoresis support evolution?

• PCR amplifies minute or degraded ancient DNA samples extracted from fossils, producing sufficient quantities for comparative analysis

• Microbial enzymes (restriction enzymes) recognise and cut DNA at specific nucleotide sequences into distinct fragment lengths for comparison across species

• Gel Electrophoresis uses an electric current to separate cut DNA fragments through an agarose gel matrix based on size and charge, generating visible DNA band profiles

Comparing DNA banding profiles allows scientists to measure degree of genetic similarity; shared banding patterns demonstrate shared evolutionary ancestry.

Outline the biochemical evidence supporting the notion that groups of species share a relatively recent common ancestor.

• comparative genomics: genome sequences of different species are compared, allowing researchers to identify regions of similarity and difference.

• Shared endogenous retroviruses (ERVs), which are viral DNA sequences inherited in genomes, at the same chromosome locations in different species indicate a recent common ancestor.

• Because mitochondrial DNA (mtDNA) is inherited only from the mother and accumulates mutations over time, species with more similar mtDNA share a more recent maternal common ancestor.

• Similar amino acid sequences in proteins indicate that species share a common ancestor, with more similar protein sequences suggesting a more recent common ancestor.

• Bioinformatics compares DNA and whole genomes between species, with greater genetic similarity indicating a more recent common ancestor.

Outline anatomical evidence that supports that collections of species share a recent common ancestor

• Homologous Structures: Organs or skeletal elements in different species that share a fundamental structural layout despite performing different functions. Similar underlying anatomical layouts indicate that organisms inherited the feature from a shared common ancestor and adapted it to different ecological niches over time.

• Vestigial Organs: Structures that have lost their original function over time (e.g., the human wisdom teeth), demonstrating descent with modification from ancestors in which the structure was functional.

• Comparative Embryology: Structural similarities present during early stages of embryonic development among different vertebrates point to common ancestral genes (e.g. neck slits, arches in vertebrate)

What enviromental conditions are required for preservation of fossils?

• Rapid burial (swift coverage by sediment, volcanic ask, or mud protects remains from scavangers and physical weathering) (often found by ancient lakes, rivers, volcanically active areas)

• Low oxygen enviroments (deprives aerobic decomposers of oxygen, halting decomposition (bacteria, fungi))

• Mineral-Rich, Alkaline soil (prevent bone minerals from dissolving; dissolved minerals replace organic material over time)

• Presence of hard body parts (highly mineralised structures such as bones, teeth, enamel resist decay significantly better than soft tissues)

• No oxygen enviroment such as in the case of peat, can completely preserve the soft tissues and bones of an animal

What are the challenges in constructing a comprehensive fossil record?

• rarity of preservation (very few organisms die in enviroments conductive to fossilisation)

• destruction of geological processes (plate tectonics, erosion, rock folding routinely crush or erode fossil-bearing strata

• soft-bodied organisms (lacking rigid skeletons rarely leave fossil traces, biasing the record toward hard-bodied species

• inaccessible discoveries (fossils buried deep/underwater)

• incomplete skeletons (most fossils are fragments, rather than complete whole skeletons)

What is relative dating? What is absolute dating?

Relative: Determines the chronological order of past events, rock layers, or fossils as older or younger than one another, without providing an exact numerical age.

Absolute: Assigns an actual numerical age in years to a fossil, indicating how long ago it existed.

How precise is relative dating? How precise is absolute dating?

Relative: Comparative/qualitative; provides a sequence of events without exact dates.

Absolute: Quantitative; provides a specific age range

What are the limitations of Absolute Dating?

Limited by the sample material, half-life range, and contaimination risks.

What are the limitations of Relative Dating?

Strata can be disrupted or inverted by faulting, folding, or erosion.

What is the methodology of Absolute Dating?

Relies on measuring radioactive decay rates of unstable isotopes with known half-lives.

What is the methodology of Relative Dating?

Relies on geological principles such the superposition—lower sedimentary strara are older than upper layers.

What is an example of Absolute Dating?

Potassium-Argon dating measures radioactive decay in volcanic ash or rock layers enclosing the fossil, which covers the millions-of-years timescale.

Radiocarbon dating measures the ratio of remaining Carbon-14 to stable Carbon-12 in organic tissue determines how long ago the organism died.

What is an example of Relative Dating?

Stratigraphy uses the position and correlation of rock layers to determine the relative age of fossils, with deeper layers generally containing older fossils than those above them.

Describe how the examination of mtDNA can substantiate the theory of evolution illustrate the interrelationship between Homo neanderthalensis and present-day humans

• mtDNA is inherited exclusively through the maternal line without crossing over or genetic recombination, making it ideal for tracking maternal lineages (only passes from mothers to offspring, no paternal influence)

• Mutations in non-coding regions of mtDNA accumulate at a relatively stable, predictable rate over generations

• By comparing the number of base pair differences in mtDNA between Homo neanderthalnesis and Homo sapiens, scientists can caluclate how long ago the two groups shared a common ancestor

• Analyses reveal that Neaderthal mtDNA falls outside the range of modern human mtDNA variation, proving they were a distinct hominin lineage that diverged from a common ancestor roughly 500,000 to 600,000 years ago

Describe the various types of mutations

Gene Mutations:

• Substitution → one nucleotide is replaced by another

• Insertion → an extra nucleotide is added

• Deletion → a nucleotide is removed

Chromosomal Mutations:

• Duplication → a section of chromosome occurs twice

• Deletion → a section of a chromosome is removed (a piece of DNA is removed)

• Inversion → a section of the chromosome breaks off and joins back in, but the wrong way around

• Translocation → part of a chromosome breaks off and is joined to the wrong chromosome

• non-disjunctional → chromosomes fail to separate during meiosis, producing gametes with too many or too few chromosomes

Somatic Mutations:

• occur in body cells

• affect only the individual (not inherited to offspring)

• passed to daughter cells during mitosis

• often associated with cancers

Germline Mutations:

• occur in reproductive cells (gametes)

• can be passed to future generations

• may cause inherited genetic disorders

Identify the causes of mutations and describe how they can occur

Mutations are permanent changes in DNA that create new alleles. They can cause new traits to appear that were not inherited from either parent. While some mutations are harmful, others are neutral or even beneficial.

Spontaneous Mutations:

Occur naturally due to random errors during-

• DNA replication before cell division

• Mitosis

• Meiosis

Many of these errors are repaired by DNA repair mechanisms, but some remain and are passed on when cells divide.

Induced Mutations:

Caused by mutagens (mutagenic agents), which increase the mutation rate. They Damage DNA, causing changes in base sequence.

• chemical mutagens (e.g. mustard gas, formaldehyde, sulfur dioxide)

• physical mutagens

  • UV light

  • X-rays

  • Gamma rays

  • Cosmic rays

  • Radioactive waste

• biological mutagens (certain viruses that intergrate their genetic material into host DNA)

How has mutations in jaw muscle and brain size in hominins illustrated the importance of mutations to evolve?

• Mutations are the ultimate source of new alleles, creating genetic variation upon which natural selection acts

• In hominin evolution, a specific frameshift/inactivation mutation led to a dramatic reduction in temporalis jaw muscle fiber size and overall bite force

• smaller jaw muscles eliminated the need for massive cranial crets (saggital crests) and heavy brow ridges previously needed for muscle attachement

• reduction in jaw structure removed mechanical constraints on the skull, allowing the braincase to expand in response to selection for higher congnitive capability and tool manufacture

• these benefitcial mutations were inherited by offspring and become more common (natural selection)

• over many generations the accumulation of mutations and their selection resulted in the characteristic Homo feature of smaller jaws, reduced prognathism, larger brains

Describe the features that indicate a hominin is bipedal

Bipedalism:

• the formaen magnum is situated centerally beneath the skull, balancing the head vertically over an upright spine, reducing muscle effort needed to hold the head upright

• short and broad (bowl-shaped) pelvic bone, supporting abdominal organs during upright posture and providing attachement points for gluteal muscles

• femurs slant inward toward the knees, bringing the feet beneath the center of gravity during single-foot stance

• an arched foot, has both longitudinal and transverse arches that acts as springs, absorbing shock during impact and transferring energy forward during toe-off

• non-opposable big toe designed for efficient weight transfer and push-off during striding gait

Describe the features that indicate a hominin was arboreal

• finger and toe bones distintively curved, providing a power grip suited for climbing trees

• shoulders positioned higher and angled upward, enabling easy movement and suspension in tree branches

• upper limbs remain long relative to legs compared to modern humans, aiding arboreal locomotion

• a ribcage structure that flares at the top allows for greater mobility of the shoulder girdle during climbing and brachiating movements

Explain the relationship between bipedalism, increasing cranial capacity and tool use seen in the hominin group. 

• adopting an obligate bidepdal stance freed the upper limbs from locomotion, enabling hands to manipulate objects with percision

• shorter, straight fingers and an opposable thumb enable fine motor control and percision grips

• increased manual dexterity led to the development of early tool cultures (e.g. Oldowan pebble tools by Homo habilis)

• tool use enabled hominins to skin, tenderise, and cut meat outside the mouth, as well as access energy-dense bone marrow

• processing food externally reduced selection pressure for massive jaw muscles, sagittal crests, and large molars, leadings to smaller, less prognathic jaws

• smaller jaw muscle attachments relieved physical constraints on the skull, allowing room for brain expansion

• the shift to a high protein, energy-dense meat diet supplied the high metabolic energy needed to grow and maintain a larger brain, increasing cranial capacity

• higher cranial capacity enabled greater cognitive ability, resulting in more sophisticated tool cultures, which further enhanced foraging success and cognitive development (Oldowan → Acheulean → Mousterian)