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BIOL 1010 notes for all quizzes and tests, Study notes of Biology

Rensselaer Polytechnic Institute (RPI)Biology

Prof. Jeremy Farrell

Evolution Quiz Evolution Test Genetics and Medicine Quiz Genetics and Medicine Test Ecology Quiz Ecology Test BIOL 1010 Jeremy Farrell

Typology: Study notes

2024/2025

Uploaded on 05/03/2025

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EVOLUTION QUIZ

Seven properties of life:

1. Order

2. Reproduction

3. Growth and development

4. Energy processing

5. Response to the environment

6. Regulation

7. Evolution

Clay was important for the emergence of life because clay particles are a

suitable surface for the formation of polymers from monomers, self-

replicating nucleic acid

Solar nebula: cloud of stardust w gravity collapsed into a rotating disc, in center,

temperature rose, and sun was born, gases like hydrogen and helium swept to

far reaches of disc, heavier elements went closer to sun.

Dust grew into pebbles and rocks which grew larger and collided breaking apart,

other times rocks stuck together and became bigger and increased gravity holding

them together shaping into small round planets which started growing bigger and

bigger until they collided and formed the 4 planets closest to sun: Mercury, Venus,

Mars, and Earth.

Earth: 4.5b yrs ago: fiery ball of rock covered in lava, rocks haven’t survived

100m miles from earth: asteroid belt trillions of asteroids, rocks left from planet

building sometimes knocked out of orbit and come here (meteors)

Meteorites are a window into the past and tell us about the conditions of

planets where they were formed and Earth’s beginnings.

All meteorites are 4.5 or 5b yrs old

Iron catastrophe: (global migration of elements), light elements floated to top

i.e. oxygen hydrogen… iron sunk to core creating a molten core in motion 2

times size of moon

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EVOLUTION QUIZ

Seven properties of life:

Order
Reproduction
Growth and development
Energy processing
Response to the environment
Regulation
Evolution Clay was important for the emergence of life because clay particles are a suitable surface for the formation of polymers from monomers, self- replicating nucleic acid Solar nebula: cloud of stardust w gravity collapsed into a rotating disc, in center, temperature rose, and sun was born, gases like hydrogen and helium swept to far reaches of disc, heavier elements went closer to sun. Dust grew into pebbles and rocks which grew larger and collided breaking apart, other times rocks stuck together and became bigger and increased gravity holding them together shaping into small round planets which started growing bigger and bigger until they collided and formed the 4 planets closest to sun: Mercury, Venus, Mars, and Earth. Earth: 4.5b yrs ago: fiery ball of rock covered in lava, rocks haven’t survived 100m miles from earth: asteroid belt trillions of asteroids, rocks left from planet building sometimes knocked out of orbit and come here (meteors) Meteorites are a window into the past and tell us about the conditions of planets where they were formed and Earth’s beginnings. All meteorites are 4.5 or 5b yrs old Iron catastrophe: (global migration of elements), light elements floated to top i.e. oxygen hydrogen… iron sunk to core creating a molten core in motion 2 times size of moon

Geographic north pole is in fixed position but magnetic is constantly in motion (it’s moved 125m off Canadian coast and is speeding up..40km/yr)

Iron created electrical current making earth a giant magnet with north and south poles Magnetic field is necessary because magnetic particles bombard earth (solar flares from sun) hurdle through space = solar wind if solar wind reaches planet strip away atmosphere but magnetic shield deflects these particles BC meteor: carbon rich meteorite, 90 other elements identified 6 stages:

Black (earth formed): earth formed from: meteorites, rocks and dust earth was molten lava then cooled covering earth with first rock: basalt (black) (nothing survived from this stage)
Gray (new minerals formed): original meteorites that formed earth had only 250 minerals->4k Heat and pressures = new minerals Granite = Foundation of continents (No plants or animals)
Blue (oceans formed): earth cooled enough for liquid water; first ocean formed Water = great solvent-> molecules floated and interacted Zircon crystals (4.3b y ago) = tell us there was water then because they could only have formed in presence of water Stromalites (3.5b y ago) = oldest fossil life on earth, provide evidence of ancient microbial life and early photosynthesis Maybe signal of life 3.8b y ago
Red (rise of oxygen): atmosphere was rich in nitrogen and co2 but not free oxygen Microbes conducted photosynthesis-> oxygen Banded iron formations: Oceans were filled w iron which rusted with oxygen, making it sink (O2 reacting with iron, causing it to rust out of the oceans about 2.4 BYA.)

Proteins were thought to be the only molecules capable of catalysis until 1982 Ribozymes: RNA that can catalyze, some are called RNA replicases which can catalyze their own synthesis RNA World hypothesis: RNA used by early life forms and replication preceded proteins and DNA then DNA evolved (RNA acted as both an information carrier and a catalyst for biochemical reactions.) (A current leading hypothesis about the first system of inheritance in the earliest lifeforms involved: self-replicating RNA molecules with ribozyme activity) DNA: double stranded helix made of 4 building blocks (nucleotides) RNA: single stranded helix made of nucleotides (DNA and RNA diff sugar comp) Can:

Switch genes on and off
Defend cells against attackers
Alter other biomolecules
Store genetic information They function by folding into shapes which determine function in cell, too many possible shapes so it is hard to find custom usages like cancer RNA can do what DNA and proteins do RNA nucleotides can permeate fatty acid membranes Fatty acids carry the RNA along into membrane 2010 created mycoplasma membrane and put genome inside with watermark Lipid bilayer:
Natural bilayers made of phospholipid bilayers
Hydrophilic head and 2 hydrophobic tails
H2o spontaneously dorm 2-layered sheet w tails pointing to center
all cell membranes are made of it and so are nucleus and sub-cellular structure surrounding it
fatty acid->phospholipid->micelles->sheets->vesicle

Protocells: (Australia)

structures formed from aggregation of abiotic components like lipids
enclosed by a membrane
can grow and divide
has 2 or more RNA replicases that can make copies of each other
Vesicle Membrane grows through addition of fatty acids from micelle collisions causing elongation and instability, dividing into two daughter protocells
Replication-> osmotic gradient
When membrane stretches, grabs fatty acids from membranes of cells w lower RNA replication rates (lower osmotic gradients)
Cells w higher RNA synthesis take over Plant discovery: Fermi’s Paradox: asks why, given the vast number of potentially habitable planets, we have not yet observed signs of advanced extraterrestrial civilizations. Kepler space telescope (2009-2018):

Kepler-22- first exoplanet orbit star’s habitable zone… may have liquid water, closest possible sister planet-2.4* size earth, 290-day year, discovered by transit method: star will dim planet passes in front of it TESS: Transiting Exoplanet Survey Satellite (2018): SPOC decodes data through 5-step process, watches and keeps track of light of star James Webb Space telescope (2021)

Comets may have delivered water and organic compounds to Earth.
The panspermia hypothesis: life originated in space and spread via comets, asteroids, and space dust.
Scientists have observed comet dust around a star 60 light-years away, hinting at the possibility of life spreading in the cosmos.
Ganymede, one of Jupiter’s icy moons, has a vast subsurface ocean.
Its thick ice sheet blocks sunlight, but hydrothermal vents at the ocean floor could support life.

Viruses:

viruses aren’t living because they cannot reproduce on their own, don’t have to find food or metabolize, rely on host for survival
Viruses are very pretty; they have very high symmetry and certain number of axis
simpler than other living things, able to be created through the purified components. Protein and Nucleic Acid.
can evolve, use host cells to survive and replicate, can have DNA or RNA Simplest known bacteria: carsonella ruddi (182 genes) not from virus differentiation: Earth separated into layers  The Hadean Eon: 4.5 to 3.8 Billion Years Ago. The first early stage of the earth. -> led to possibility of protocells  The Archean Eon: 3.8 to 2.5 Billion Years Ago. There were oceans, banks and rivers during this time. Around 3.5 billion years ago stromatolites formed. 2.8 billion years ago bacteria were able to evolve and be able to use photosynthesis, releasing oxygen. (prokaryotic-most likely bacteria domain)-> archaea (prokaryotic)  anaerobic bacterial photosynthesis (3.2) -> aerobic  Aquifex living fossil. Cyclic photosynthesis  The Great Oxidation Event: 2.8 Billion Years Ago. Oxygen caused a catastrophic event for some organisms while it caused others to thrive.  2.7 BYA beginning of more complex life  Snowball Earths: 2.4 Billion Years Ago to 650 Million Years Ago: There was mass glaciation that happened multiple times
The orbit around the Earth was unstable and while the Earth is far away and tilted away from the sun the Earth cools heavily.
Cyanobacteria create oxygen which disrupts the environment: Oxygen Crisis upsets greenhouse effect and methane… freezes the earth, volcanoes punched through ice maintaining life pumping out co2 and

helping greenhouse effect, fixing snowball earth (Photosynthesis exchanged atmospheric CO2 for O2, and O2 reacted with methane resulting in depletion of the greenhouse gases.) Edicarian fauna: most ancient complex organisms 600-500 MYA by 540 most extinct (not archaea)

Cambrian explosion: proliferation of species possible causes:
1. Oxygen levels increased <-> snowball earth (too long before) o reached deep sea 600MYA, continued to rise allowing larger species, Erosion, calcium, silicon
2. Mineral availability due to post glaciar erosion to make shells but were made from many materials (calcium)
3. Evolutionary innovation Feedback cycle of innovation between predators and prey evolving quickly to survive
4. Emergence of vision
5. Recovery from mass extinction (possibly) Darwin’s dilemma: couldn’t find fossils of Cambrian animals Cambrian explosion fossils in burgess shale 100 different phyla compared to 30 now, hard shelled in beginning (contain fossils exhibiting all modern body plans of animals): characterized by the rapid diversification of multicellular oceanic life (Phanerozoic eon)
The Phanerozoic Eon: 542 Million Years Ago: Extensive forests covered the earth and enabled an even greater influence on life. Three major domains of the living world:

Bacteria (all are prokaryotes): do not reproduce sexually (hard to apply species)

Lack nuclei
Single celled
Before archaea

Archaea: often found in extreme habitats such as low acidity and high temperature

 During photosynthesis, plants take in water, carbon dioxide and solar energy to produce carbohydrates in the chloroplast, (thylakoid membrane.)  No oxygen because there was no source... is highly reactive  Oxygenic or non-cyclic photosynthesis led to slow increase of o2 in atmosphere  Detect oxygen by presence of iron and sulfur oxidized compounds (seen in fossil deposits)  Og .000001% then reached 15% and reacted w iron to form iron oxides  Layers of iron oxide deposited bottom of oceans 2 BYA  Aerobic respiration became the dominant form of metabolism (req. for emergence of eukaryotes) amongst bacteria, (eukaryotes are much more complex than prokaryotes and require greater amounts of energy for their metabolism)  Anaerobes retreated to marginal environments Order: prokaryotes, photosynthesis, eukaryotes, colonization of land by plants and fungi  Chromosome: circular DNA  Synthesizes ATP through photosynthesis Chloroplast and mitochondria arose through endosymbiosis:  Ribosomes similar and synthesize its own proteins  Grows, divides, and duplicates own DNA  Eukaryotic cell without chloroplasts cannot make chloroplasts nor mitochondria Both prokaryotes and eukaryotes:  Enclosed by membrane  Store hereditary info in DNA  Replicate DNA same way  Use RNA to transcribe DNA

 Translate RNA into protein via tRNA and ribosomes  Use proteins as catalysts  Use ATP for free energy

sequence(phenotype)) DNA sequences are random! Reduced allele variation results in an increased chance of extinction. Phenotypic consequences:

Stabilizing selection: extremes aren’t favored, average sizes, colors etc are more probable to live.
Directional selection: environmental factors can shift this to be darker or lighter etc.
Disruptive selection: both ends are favored not intermediate-> causes dimorphism Darwin from England to Galapagos Dr Rosemary and peter grant studied the same island in 1975 marked all birds: they find 13-14 species of finches each with different beaks, for different tasks, they tracked the birds and found a shift in beak width, there was a drought which affected the population as well, the biggest beaks survived (directional selection)  From careful analysis DNA, none of them are more close to a bird on land than each other, so there was only 1 times birds got there from a single common ancestor  The island is called Daphne Major  They would net the bird's weight, size, and beak size. And even labeled them with tags. Two possibilities for finches:

All types came from mainland
One species left mainland and then divided into many

Coevolution: two populations evolve in response to selection pressures that individuals from the 2 populations place on each other
Moths: prey (evolved ear detect sonar know if bat is coming), bats: predators (better ears to hear them move, no use of sonar)

Newt contains poison to kill 20,000 mice, snakes prey get poison resistant, newts get even more poisonous Predators typically learn to associate bright colors with undesirable prey, not desirable prey Some species go extinct, and the animals stay the way they were when they lived because nothing triggers the evolution process again. ghost of predator’s past: hypothesis that describes how prey animals retain a fear of predators even when there is no immediate danger because there used to be a predator who went extinct i.e. moa
Sexual selection: (physical and behavioral) Darwin didn’t understand why peacocks had tails, very environmentally expensive, blue footed bobbies, and butterflies, just in males i.e. antlers Difference between males and females= males competed to reproduce and females choose who to reproduce with, this is because reproduction is mostly done by females (they spend more time and energy in the process)… (interestingly was difficult to prove because women were seen as less in that time)-

this all led to the development of males beautiful aspects and extravagant features which are indicators of good genes

Genetic drift: change in a gene pool due to chance Reduced variation = inbreeding which leads to lower survivorship Bottlenecking: portion of pop is randomly eliminated resulting in a pop that represents those who happen to have survived Founder effect: genetics of pop reflect initial members, not the main pop If maintaining this speed means bearing fewer offspring, given enough time-

species will slow down Speciation: Carl Linnaeus: created binomial nomenclature:

Big branches removed, created space for niche animals to come and grow (late Cretaceous) Fossil records are inconsistent Homologous:

Similar structure
Differing function
Common ancestor Analogous:
Differing structure
Similar function
Not from common ancestor Beta hemoglobin: protein that is useful for comparing the lineage of species. TIMELINE:
85 MYA------ Earliest common ancestor
80-75 MYA-- Evolution of early primates
65 MYA-------Extinction of dinosaurs
65-45 MYA---Adaptive radiation of primates
47 MY---------Ida fossil discovered: the possible missing link between primate/hominid evolution.
30 MYA-------Early primates leading to Old World species Shared through primates:
Grasping Hand:  Grip branches  Grip objects/prey more powerfully  Grasp objects/prey more precisely  Fashion & use tools
Binocular Vision

 Depth perception  Excellent focus  Advantages when living in trees  But limits field of view (not large)

Large Brain  Sensory input, e.g. acute visual system  Motor output  Social interactions  Learning, memory, info gathering
Parental Care and Sociality Human relatives: The earliest primates were arboreal and small in size. According to the fossil record, the genus Homo first arose in East Africa The main categories of evidence that scientists use to study evolution are: evidence from the past (fossils), similarities between living organisms (anatomy and DNA), and the geographical distribution of species.

Australopitheicus afarensis (Lucy 3.2 MYA one of the first: adult female 11-12y.o., stood upright (known because pelvis, knee, and ankle found) (bipedalism: freed two limbs to grip and use tools: The first distinctly hominin trait to appear in the fossil record)
Homo Habilis: handyman (2.1-1.5 MYA), ate meat-> encephalization (growth of brain, temporal lobes grew disproportionate), first to cook (found=tools)
Homo erectus: (2MYA – 143 TYA), first fossils found outside Africa, first to make sea voyag
Homo sapiens neanderthalensis (200 TYA- 40 TYA), separate species interbreeding with, had genes to speak (found=instruments and jewelry)
Homo floresiensis (100 TYA – 60 TYA): hobbit

Humans came out of Africa in two waves
Neanderthals and modern humans interbred

GENETICS QUIZ

DNA (Deoxyribonucleaic Acid):

Molecule= atoms stuck together
in shape of long spiraling ladder (double helix held by hydrogen bonds between complementary base pairs)
blueprint for living things (carries gene info)
tells amino acids how to shape to form protein
4 different kinds of chemicals in it
coils up in nucleus
codons: allow code to be translated into amino acids 4 codons = 4 amino acids = 12 nucleotides
Copies to divide cells
Generates genetic variation by altering gene info
in a chromosome inside nucleus
nucleotides = (deoxyribose sugars with phosphate) alternating down sides of ladder
nitrogenous bases on insides
deoxyribonucleotides = monomers when linked together make DNA polymer (.34nm between nucleotide and next)
helix makes one turn (3.4 nm) = 10 bases in a row
2 nm girth
Strands are anti-parallel Amino acids:
in cytoplasm
building blocks of life
20 kinds
can attach to each other to produce proteins
used to construct specific proteins within ribosomes Proteins:
shaped amino acids
shape determines function

Amino acids -> proteins -> living cells -> tissues -> organs - > living creatures RNA: Partial copies of DNA, missing half travels form nucleus to ribosome Ribosomes:

RNA +protein
protein building machines
read three letters at a time
take amino acids around them and shape them into proteins following the code February 1953: Watson and Crick reveal double helix 1962: Watson, Crick, and Wilkins win Nobel Rosalind Franklin:
Her X-ray diffraction images were critical in elucidating the structure of DNA.
PhD in chem, studied coal structure and bettered gas masks WW
1951 king’s college used Xray to study DNA structure in wet crystals
1952 took Photo 51: clearest image of DNA at the time using Xray diffraction took 100 hrs to get and calculations to analyze took a yr, she submitted the research
Maurice Wilkins stole pic and brought to Watson and Crick which analyzed and used to identify DNA model, submitted own research (Double Helix) Replication:
Results in 2 DNA molecules, each with one new strand and one original
Helicase: rotating motor that unwinds DNA into leasing and lagging strands
single strand binding proteins (SSBs): secure naked single stranded DNA templates
RNA synthesized from DNA template
Enzyme primase: adds an RNA primer at origin of replication (to one strand of DNA)
Opposite polarity of the 2 DNA chains

BIOL 1010 notes for all quizzes and tests, Study notes of Biology

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EVOLUTION QUIZ

GENETICS QUIZ