BIOL 215 midterm flash cards

Ecology vs evolutionary biology

Ecologists study factors affecting distribution, abundance, and function of organisms in their environment. Evolutionary biologists describe/reconstruct and try to understand changes in characteristics of lineages over time.

How are ecology and evolution connected?

Ecology affects evolution (e.g., pollution selects for dark moths) and evolution affects ecology (e.g., predators in an ecosystem change it).

Phytoplankton and iron

Phytoplankton produce organic C and release O2. When iron in the environment increases, more phytoplankton flourish, so more O2 is produced.

When did the solar system originate?

~4.6 billion years ago

When did the first catalytic molecules appear?

~3.7 billion years ago

When did the earliest prokaryotic cells appear?

~3.5 billion years ago

Big Bang theory

Origin of the universe ~10-15 bya. Quarks/elementary particles formed, then made protons/neutrons, then atoms (H and He).

How did the first stars form?

Gas expansion pieces of H and He coalesced and formed protostars, which became massive and dense and heated up from pressure and heat.

What did nuclear fusion in stars create?

New atoms; formed all elements up to Fe (iron).

What happens when a star runs out of fuel?

It collapses and explodes as a supernova.

How did the solar system form?

A supernova created our solar nebula; the sun formed by condensation of elements; planets formed around the sun via gravity.

Unique conditions of early Earth that allowed life

Sun energy, stable climate, liquid water, iron core (magnetic shield from solar/cosmic radiation), wide array of elements, ozone layer (only came once life evolved).

Early formation of Earth

Initially molten, made of Fe, Mg, Si, O. Moon rock samples date back ~4.5 bya. Intense meteorite bombardment kept it hot.

Oldest rocks on Earth

~4.28 bya

When did Earth's crust form?

~4.2-4.1 bya

How do igneous rocks form?

Magma cools, forming minerals (e.g., granite contains crystals of different elements).

How do sedimentary rocks form?

Igneous rocks get weathered and eroded into sediment; wind/water carry it to flat surfaces; organisms get trapped (potential fossils); lithification turns sediment into sedimentary rock.

Metamorphic rocks

Igneous/sedimentary rocks that are heated/compacted, which can destroy fossils (harder to date).

Isotopic dating

Method to find the ages of rocks using radioactive decay.

Why use zircon for dating?

Zircon (ZrSiO4) forms a crystal lattice; impurities get in as U-238, which decays to Pb-206 and stays trapped in the crystal. The ratio of Pb to U gives the age.

Half-life of U-238

~4.47 billion years

Radiometric age equation

Age = (T1/2 / ln 2) x ln(1 + P/D), where P = parent and D = daughter isotope.

Why can't isotopic dating be used directly on sedimentary rock?

Sedimentary rock forms differently (from pieces of older rocks).

How do we date sedimentary rock?

Use relative position (layers). Layers are interspersed with volcanic ash containing zircons, so you can date the layers before and after the fossil-containing layers.

Earth's 1st atmosphere

Composed of H and He.

Earth's 2nd atmosphere

Formed by bodies hitting Earth with other gases plus volcanic outgassing.

Characteristics of the 2nd (early) atmosphere

100-1000x more CO2 than today; N2, H2O, trace H2, H2S, NH3, CH4. These gases are reducing (today's gases oxidize). No free O2, so organic molecules wouldn't be broken down.

Earth's 3rd atmosphere

Decrease in CO2 because oceans dissolved CO2 forming carbonic acid and formed carbonate with Si in rocks. Biological processes led to the rise in N2 and O2.

Chemical weathering

Rocks dissolved because of acids; this caused solutes to enter the sea, making salty water.

When did oceans begin to form?

Once Earth cooled below 100C (~3.5 bya)

Evidence for early liquid water

Zircons with a high ratio of O-18/O-16 can only form with water (~4.4 bya).

Biomarkers (evidence of life)

Molecules (steroids, lipids, pigments); organic C deposits; chemical changes indicating biological reactions (isotope signatures).

Isotope signature of life

C-12 and C-13 are stable isotopes. Enzymes prefer lighter C-12, so products become enriched in C-12 (C-13 depleted).

Oldest biomarker evidence (metamorphic rock)

~3.8 bya: specks of carbon (carbonaceous inclusions) with a C-12/C-13 ratio much higher than found naturally.

Fossil evidence of life from 3.5 bya

Stromatolites (rock structures formed through biological activity).

Strongest evidence of early life

~3.4 bya with microfossils and isotopic analysis (lots of C-12).

Miller-Urey experiment (1953)

Used gases thought to compose Earth's early atmosphere, with lightning (sparks) and condensers. Within a week 17/20 amino acids, all purines/pyrimidines, and other organic compounds formed. Shows organic molecules can form abiotically.

Panspermia theory

Organic chemicals were brought from space.

Murchison meteorite

Found to contain many carbon compounds and amino acids; very similar to Miller-Urey results.

ALH84001

Meteorite from Mars with some evidence of microorganisms: high concentration of compounds, possible fossils on the surface, and crystalline magnetite (Fe3O4) identical to biologically-produced magnetite. Critics are skeptical.

Spectroscopy in space shows

Presence of CH4 (methane) and other carbon compounds in space.

RNA world: the chicken-and-egg problem

All life is based on DNA genes + protein enzymes. You need proteins to make DNA but need DNA to make proteins. Possibly the first macromolecule did both.

RNA world hypothesis

Before life, RNA had the ability to self-replicate and catalyze chemical reactions.

Why RNA first, then DNA?

RNA may have begun coding for proteins. One of those enzymes might have been reverse transcriptase, turning RNA into DNA. DNA holds info better and is more stable because it has 2 strands.

Why RNA and not DNA as the first catalyst?

No natural single-stranded DNA; DNAzymes are far less reactive. DNA's sugar has only a proton (not the hydroxyl of ribose); the 2' OH can H-bond and do acid-base reactions, which is important for catalytic activity.

Origin of RNA polymers: clay model (Crepe model)

Clay has net (+) charges and nucleotides have (-). Some nucleotides bind to the clay surface and line up. Some catalytic reactions (sunlight) in contact with the clay formed polymers.

What do modern ribozymes suggest?

Some modern RNAs have enzymatic properties (ribozymes). Protein synthesis on ribosomes could be evidence for a remnant of the RNA world.

Compartmentalization: why a membrane?

Needed a membrane to enclose genetic material.

Building blocks of protocell membranes

Lipids that are amphipathic (phospholipids).

How could micelles become vesicles?

Micelles could fuse to form vesicles at high enough concentration; stick together to make a sheet that curves into a vesicle. When the closed vesicle contains some nucleic acid, you have a nucleic acid cellular structure (first type of protocell).

Requirements of life

Liquid water, energy source, elements for biomolecules.

Why do organisms need energy?

To drive synthesis of biomolecules (allows molecules to be built up), and needed for mobility (acquisition of resources) and reproduction.

2 main types of energy used by life

1) Light energy (EMR 400-700 nm), used by phototrophs, which leads to chemical energy. 2) Chemical energy (chemotrophs).

Chemoorganotrophs

Use preformed organic compounds and break C-C bonds, capturing that energy to synthesize ATP.

Chemolithotrophs

Use inorganic molecules' chemical bond energy. Example: tube worms at the bottom of the sea where tectonic plates make highly reduced substrate which bacteria use for energy.

Why is energy important to organisms?

It affects the rate at which organisms can grow and the structure of organisms in the environment. The rate of energy intake is limited by external factors (shortage of food, food quality) and internal factors (digestion, enzyme catalysis).

Consequence of limited energy intake

Organisms cannot maximize all life functions; they allocate some to growth, some to defense, some to reproduction (trade-offs).

Photosynthesis-irradiance curve

Photosynthetic rate rises with photon flux density, then saturates.

Elements used by organisms

N, P, S, C, etc. are used for cellular constituents and in biochemical reactions, for structure and catalysis (e.g., cellulose (C) = cell wall).

How many elements do organisms require?

28 elements, with the bulk being CHOPNS.

Essential element

One needed at least once during an organism's life cycle.

Autotroph vs heterotroph

Autotroph: can use inorganic C (CO2) - plants, archaea, bacteria, phytoplankton. Heterotroph: uses organic C (carbohydrates, proteins, and fats).

Photoautotroph

Light energy + inorganic carbon (CO2).

Chemoorganoheterotroph

Gets energy from organic chemicals and carbon from organic molecules (what we are).

Elements in tissue vs environment

Most elements are more concentrated in tissue than externally, so organisms must concentrate and extract elements from the environment. Availability changes in location and through time.

Acclimation to element availability (example)

Grass (Sorghastrum nutans) decreases its root/shoot ratio as availability of N in soil increases.

Early Earth ~4 bya atmosphere

H2, CO2, N2, S gases: anaerobic (no O2) and hot. Used to hypothesize what the earliest life was like.

2 hypotheses for first life's metabolism

1) A chemolithoautotroph obtained both energy and C inorganically (e.g., H2 + 2Fe(III) -> 2Fe(II) + 2H+). 2) Older theory: a heterotroph that used matter synthesized abiotically.

Problem with the heterotroph-first hypothesis

Abiotically produced organic matter was too dilute. Proposed solution: organic matter absorbs to clay.

Other early life characteristics

Anaerobic, hyperthermophilic (like heat), halophilic (like salt); still prokaryotes.

Evidence for chemolithoautotrophy first

All extant organisms near the origin of the phylogenetic tree are hyperthermophiles found in hot springs (like early Earth conditions). They use H2 as an energy source. Massive amounts of magnetite during the Archaean era.

After the first life: new species

Exploited other energy sources; some used products from metabolism of other organisms as substrate. Pockets of organisms layered on top of each other.

Why did photosynthesis evolve?

Organisms developed pigments able to capture light energy. Makes sense because geochemical energy was depleted because of evolution of species (low amount of energy led organisms to specialize).

Earliest photosynthesis

Based on S, not O2. Eventually organisms used H2O because it was so abundant, so O2 was created.

Great Oxidation Event timing

Atmosphere became oxic ~2.45 bya. Took 250 million to 1 billion years to suffice because O2 reacted with other reduced substances (e.g., Fe). Around this time ~1-2% O2 in the atmosphere.

Consequences of O2 production

Much more efficient metabolic pathways (aerobic processes); ocean chemistry changed (sulfate SO4 2- collects and new metabolisms used H2S as substrate); allowed for an ozone layer that blocked UV rays from the sun; poisoned anaerobic organisms, so they either died or went to refuge habitats with low O2.

How did aerobes deal with O2?

Aerobic organisms need to detoxify compounds that come as a result of O2 metabolism (like how we breathe out CO2); required enzymes like peroxidase to break these down.

Why might O2 have driven eukaryote evolution?

Thought that O2 produced eukaryotes because organisms required more complex systems to live.

Evidence for earliest eukaryotes

Prior to ~2 bya it is only bacteria and archaea. Chemical markers (steranes) are only produced by eukaryote membranes; found ~2.7 bya.

Prokaryote features

No nucleus, organelles, or microtubules; synthesize protein on 70S ribosomes; divide by binary fission; outer membrane composed of peptidoglycan.

Eukaryote features

10-1000x larger; very complex (compartments, cytoskeleton, mitochondria); can endocytose, cell divide, cell movement; 80S ribosomes (S = size); replicate through mitosis.

Endosymbiosis theory

Mitochondria and chloroplasts were once free-living bacteria that were engulfed by an archaeon and evolved because of symbiosis.

Origin of mitochondria vs chloroplasts

Mitochondria from Proteobacteria; chloroplasts from Cyanobacteria.

Genes for protein in eukaryotes

Represent the genes in the nucleus and the ones that code for energy metabolism and lipid synthesis are bacterial (from the endosymbiont).

Lokiarchaeota

Group of Archaea identified in deep sea vents; had many genes we associate with eukaryotes (e.g., microfilaments, molecular machinery of eukaryotes). Hadn't been seen by microscope until a 2020 study found Prometheoarchaeum syntrophicum, which is said to be related to the ancestral Archaea that gave rise to eukaryotes. Very morphologically complex.

Secondary endosymbiosis

In 2 groups of protists we can see the remnant of the nucleus of the symbiont that was engulfed. Ancestral Cryptomonad said to have engulfed a eukaryote cell. In chloroplast we can see the nucleomorph (the nucleus of the endosymbiont). Some genes from nucleomorph went to host. 4 membranes: 2 membranes of cyanobacteria and host, 2nd endosymbiont, and outer membrane of host.

Why was classification by morphology a problem?

Lack of morphological features in microbes. Proposed using DNA to classify.

Why is rRNA/DNA good for classification?

Captures ancestral info, so you can compare traits that have been passed down; low copying error so slow changes; large molecule so can study many genes.

The 3 domains of life

Bacteria, Archaea, Eukarya (by looking at rRNA genes). Previously we only thought of Prokaryotes and Eukaryotes.

LUCA

We think all organisms have 1 common ancestor (Last Universal Common Ancestor); some parts, like lipids and core metabolism, are shared. Hard to believe all these complex functions developed more than once. Most recent evidence suggests only 2 domains: eukarya came from Archaea (Bacteria and Archaea, with Eukarya arising from within Archaea).

Horizontal gene transfer (HGT)

Genes not necessarily transferred through parents but across species. Examples: endosymbiont gene transfer when host engulfs endosymbiont; plasmids carrying foreign genes to hosts; viruses.

Eukarya diversity (5 groups)

Historically plants, animals, fungi, and protists (not a natural group). Protists are very diverse evolutionarily, so eukaryotes were split into groups: Plantae (Archaeplastida), Excavates, Rhizaria, Chromalveolates, and Unikonts.

Excavates

Diverse group with no common morphological feature except a feeding groove. Unicellular; some don't have mitochondria because they used to have them but they got lost; many are parasites; all flagellated and don't need O2.

Chromalveolates

Composed of 3 other groups; all photosynthetic organisms here have secondary endosymbiosis (plastids from secondary endosymbiosis).

Dinoflagellates

Very important photosynthetic organisms. Some are important symbionts of reef-building corals; many of these release poisonous blooms.

Diatoms

Responsible for ~25% of global primary production; look like petri dishes.

Oomycetes

Important agricultural pests; responsible for potato blight and mildew of grapes; reason behind the Irish potato famine.

Rhizaria

United only by molecular data (no morphological features). Most are heterotrophs feeding on protists and bacteria; produce pseudopodia used in feeding; critical consumers in the ocean.

Plantae (Archaeplastida)

Red/green algae, land plants, and chloroplasts. All chloroplasts have primary endosymbionts. Several pigments; unicellular/multicellular.

Chlorophytes (Chlamydomonas)

Model organism for evolution, molecular and physical studies. Within chlorophytes, cells get larger in size and more specialized; the most advanced have features with higher plants (distinct reproductive features).