EEMB 3: Midterm 1 Flashcards

How is life’s chemistry tied to water?

• Life first evolved from water

• All organisms require water

• Cells consist of about 75% water

Covalent Bonds

when two atoms (each with an unpaired electron in its outer shell) share a pair of electrons

Two or more atoms held together by covalent bonds form a…

molecule

How does water’s atoms with different electronegativity result in a polar covalent bond?

• oxygen attracts shared electrons more strongly than hydrogen

• shared electrons spend more time near oxygen

• oxygen atom has slightly negative charge and hydrogen atoms have slightly positive charge

How do hydrogen bonds form between water molecules?

• each hydrogen atom of water molecule can form a hydrogen bond with a nearby partially negative oxygen atom of another water molecule

• negative (oxygen) pole of water molecule can form hydrogen bonds to two hydrogen atoms

• Each H₂O molecule can hydrogen-bond to as many as four partners

Why do hydrogen bonds matter?

• They give water its high boiling point, surface tension, and ability to dissolve many substances

• Stabilize DNA base pairs (A-T and G-C)

• Help proteins fold into their functional shapes

Cohesion

attraction between molecules of same substance

High Surface Tension

one of the results of cohesion due to hydrogen bonding, which is the measure of how difficult it is to stretch of break the surface of a liquid (water molecules are hydrogen bonded to one another and to water below but not the air above)

Adhesion

clinging of one substance to another. Adhesion of water by hydrogen bonds to molecules of cell walls helps counter the downward pull of gravity. (Example: water droplets on pine needles or leaves, plant roots absorbing water)

Specific Heat Capacity

the ability of water to absorb or release large amounts of heat with minimal change in temperature. This moderates temperature fluctuations in bodes of water, the atmosphere, and living organisms.

How does water have high heat capacity?

Because heat energy is used to break down and reform hydrogen bonds, water temperature does not increase much

High Heat of Vaporization

a considerable energy required to break down hydrogen bonds in water and turn liquid water into vapor. Evaporative cooling removes heat from the body.

How are water molecules arranged in frozen water?

Hydrogen bonding arranges water molecules into crystalline lattice, keeping them slightly further apart, and therefore, less dense

How are water molecules arranged in liquid water?

Water molecules move about freely, allowing them to be closer to one another

Solution

liquid consisting of uniform mixture of two or more substance

Solvent

dissolving agent (water is the solvent of life!)

Solute

the substance that is dissolved

Aqueous Solution

water is the solvent

How does Mars show evidence of life?

• ancient rivers, lakes, and groundwater systems

• chemical ingredients needed for life (carbon, hydrogen, nitrogen, oxygen, phosphorus, sulfur)

• past environments were warmer and wetter

• preserved sedimentary rocks ideal for trapping biosignatures

Chemical and physical processes could produce simple cells through these four stages:

1. abiotic synthesis of small organic molecules

2. joining small molecules into macromolecules

3. packaging molecules into protocells

4. origin of self-replicating molecules

Protocells

• droplets with membranes that maintain internal chemistry different from their environment

• self-organized, endogenously ordered, spherical collection of lipids produced as rudimentary precursor to cells during origin of life

How long ago did Earth form?

4.6 billion years ago

What prevented sea formation before 4 billion years ago?

collisions with rocks and ice vaporized water

What did the early atmosphere have?

little oxygen, but lots of water vapor plus compounds from volcanic eruptions like nitrogen and its oxides, carbon dioxide, methane, ammonia, and hydrogen

In the 1920s, what did Oparin and Haldane hypothesize?

the early atmosphere was reducing environment (electron removing)

Where did the first organic compounds come from?

volcanoes

In reanalysis of Miller’s results, amino acids did what?

formed under conditions simulating volcanic eruption

Organic compounds could have been produced in…

deep-sea hypothermal vents. Hot water and minerals gush through these vents from beneath Earth’s surface and into the ocean

BUT organic compounds would be unstable in extreme heat released by…

“black smoker” vents. Alkaline vents release water with high pH (9-11) and warm water which would have made more suitable for origin of life.

Meteorites

could also have been a source of organic molecules wince they contain amino acids, lipids, simple sugars and nitrogenous bases

How do RNA polymers form?

they form spontaneously when solution of monomers dripped onto hot sand, clay, or rock. These could have acted as weak catalysts on early Earth.

Adding montmorillonite (mineral clay common on early Earth) does what?

increases rate of vesicle formation. Organic molecules attached to this can be absorbed through vesicle membrane

First genetic material was…

RNA (not DNA). RNA has the central role in protein synthesis and RNA molecules (ribozymes) were found to catalyze different reactions.

• make complementary copies of short stretches of RNA from nucleotides

How could have protocells formed on early Earth?

from vesicles that grew, split, and passed RNA to “daughters”

Natural selection could act on protocells…

making more successful forms over generations.

• RNA could have provided the template for assembly of DNA nucleotides

Trace fossils

footprints and burrows that show ancient behavior

Strata

layers of sedimentary rock layers

Why are fossils an incomplete chronicle of evolution?

• Few organisms preserved as fossils

• Many fossils destroyed by geologic processes

• Only fraction of fossils have yet been discovered

Radiometric dating

to determine age of fossils based on decay of radioactive isotopes

• radioactive “parent” isotope decays to “daughter” isotope at characteristic rate

Half-life

each isotope has a time required for 50% of parent isotope to decay

Mammals originated gradually from what?

group of tetrapods called synapsids

What kind of teeth do tetrapods have?

undifferentiated, single-pointed teeth

• heterodont dentition (multiple tooth types)

• incisors for tearing

• canines for piercing

• pre-molars for shearing and crushing

• molars for grinding and processing

Eon (largest division of geologic time)

• spans hundreds of millions-billions of years

• only four eons exist: Headean, Arghean, Proterozoic, Phanerozoic

Era: subdivision of eon

• shorter than eons but still very long (tens-hundreds of millions of years)

• Three eras: Paleozoic, Mesozoic, Cenozoic

Stromatolites

layered rocks that form when prokaryotes bind thin films of sediment together

• 3.5 billion years ago

• prokaryotes’ sole inhabitants for more than 1.5 billion years

What were the first eukaryotes like?

• single-celled protist-like organisms

• possessed nucleus

• formed through endosymbiosis

• lived in oxygen-increasing oceans

• ancestor to all modern eukaryotes

Endosymbiosis

prokaryotic cell engulfed small cell that would evolve into mitochondrion

• small engulfed cell: endosymbiont: lives within host cell

All eukaryotic cells have…

mitochondria. not all plastids tho

Serial endosymbiosis

hypothesis that mitochondria evolved before plastids through sequence of endosymbiotic events

Larter, more diverse multicellular organisms appeared in fossil record from…

600 million years ago

• included algae, soft-bodied animals, and some unknown taxa

Cambrian explosion

many animal phyla appear suddenly in fossils of Cambrian period (535-525 million years ago)

What types of adaptations for reproduction on land were seen in plants?

wax coating on leaves and vascular system for internal transport (420 million years ago)

Plants and fungi likely colonized land together and formed what type of relationship?

mutualistic

Plate tectonics

• Earth’s surface is covered by a series of crustal plates

• Ocean floors are constantly moving; spreading in center and sinking at edges and being regenerated

• Convection currents beneath plates assist movement

• Heat from mantle drives these currents

Continental drift

movements in mantle cause plates to gradually shift

• can drift apart, collide (mountains), or slide past each other (earthquakes)

Pangea

supercontinent about 250 million years ago that altered many habitats

• ocean basins deeper

• most shallow-water habitat destroyed

• interior of continent colder and drier

• major changes in climate when continent shifts towards or away from the equator

Mass extinction

occurs when large numbers of species rapidly become extinct worldwide

How many mass extinctions have been documented in fossil record in the past 500 million years?

five (more than half of all marine species became extinct in each event)

Adaptive radiation

rapid period of evolutionary change; many species arise and adapt to different ecological niches. can occur in response to:

• opening of niches following mass extinctions

• evolution of novel characteristics that enable exploitation of new resources or habitats

• colonization of new regions with few or weak competitors

After extinction of terrestrial dinosaurs…

mammals underwent adaptive radiation.

Several adaptive radiations occurred in response to evolution of major innovations:

• rise of photosynthetic prokaryotes

• evolution of large predators in Cambrian explosion

• colonization of land by plants, insects, and tetrapods

Regional adaptive radiations

• Hawaiian islands formed from volcanic eruptions

• populated slowly by stray organisms from mainland

• multiple invasions followed by speciation events as organisms adapted to diverse habitats

• thousands of species unique to the islands

Three phenomena that may trigger adaptive radiations

• mass extinction events

• colonization events

• evolutionary innovations

What is the benefit of using carbon in radioisotope dating?

• found in all living things

• can predict half-life and rate of decay

• widely distributed

Phylogeny

evolutionary history of an organism compared to other organisms

Systematics

focused on classifying organisms and determining evolutionary relationships

Taxonomy

organization and classification of organisms

Binomial nomenclature

formal system of naming species

• each species name formed out of Latin and has two parts

• first part identifies genus and second part distinguishes species within genus (always capitalize genus and italicize both)

Placement of groups within Linnaean system of classification…

• does not always reflect revolutionary relationships

• systematists propose that classification be based only on evolutionary relationships

• in this system, only groups that include common ancestor and all its descendants would be named

Rooted

branch points of tree represent most recent common ancestor of all taxa on tree

Basal Taxon

lineage that diverges from all other members of its group early in history

Phylogenetic tree

represents hypothesis about evolutionary relationships

Branch point

divergence of two evolutionary lineages from common ancestor

Sister taxa

groups that share common ancestor not shared by any other group

Phylogenetic trees show…

• patterns of descent, NOT phenotypic similarity

• do NOT indicate when species evolved or how much change occurred in a lineage

• should NOT be assumed that taxon evolved from taxon next to it

Phenotypic and genetic similarities due to shared ancestry are called…

homologies

Homology

similarity due to shared ancestry

Analogy

similarity due to convergent evolution

Superficial similarities evolve in unrelated species through…

convergent evolution in response to natural selection to similar environmental conditions

In some trees, branch length reflects…

number of genetic changes occurring in each lineage

Maximum parsimony

assumes that most likely tree is one that requires fewest evolutionary events

Maximum likelihood

identifies tree most likely to produce a given set of DNA probably tells us about how DNA changes over time (simpler one)

Phylogenetic bracketing

predicts which features shared by two groups will be present in ancestor and all its descendants

Gene duplication

occurs when gene copied producing two version; original gene and duplicate (paralog). Once duplicated, two copies are free to evolve independently

Orthologous gene

homology result of speciation event and occurs between genes found in different species

Paralogous gene

homology results from gene duplication and occurs between gene copies within species

Lineages that diverged long ago often share many…

orthologous genes

Molecular clocks

approach for measuring absolute time of evolutionary change based on observation that some genes and other regions of genome appear to evolve at constant rates

• measure time by counting number of nucleotide substitutions over fixed periods of time

• split from common ancestor for orthologous genes

• gene duplication for paralogous genes

Three-domain system

Bacteria, Archaea, and Eukarya

• bacteria includes most of known prokaryotes

• archaea consists of diverse prokaryotes that inhabit wide variety of environments

• eukarya consists of single-celled and multicellular organisms that have cells containing true nuclei

Horizontal gene transfer

movement of genes from one genome to another, can occur by exchange of transposable elements and plasmids, viral infection, and possibly fusion of organisms

Prokaryotes

single-celled organisms that make up domains Bacteria and Archaea

• adapted to diverse and extreme environments

• most abundant organisms on Earth

• small size and reproduction

• mutations

• rapid evolution

• diverse adaptions

• first organisms to in habit early

• variety of shapes

Cell wall

maintains shape, protects cells, and prevents from bursting in hypotonic environment since most prokaryotes will lose water and experience plasmolysis in such environments (salt used as preservative because water slows reproduction of food-spoiling prokaryotes)

Peptidoglycan

most bacterial cell walls contain this network of sugar polymers cross-linked by polypeptides

Gram stain

scientists use this to classify bacteria by cell wall composition

Gram-positive bacteria

simpler walls with larger amounts of peptidoglycan

Walls of gram-negative bacteria

less peptidoglycan and more complex with outer membrane that contains lipopolysaccharides

Capsule

many prokaryotes have this sticky layer of polysaccharide or protein surrounding the cell. Called capsule if well-defined

Slime layer

not well organized.

• both types enable adherence to substrate or other individuals, prevent dehydration, and protects cell from host’s immune system

Fimbriae

hairlike appendages that allow them to stick to their substrate or other individuals in colony

Pili

longer than fimbriae and function to pull cells together enabling DNA exchange