BIO 1114 Final

HOX Genes: What are they?

Genes that control where, when, and how other genes are expressed.

HOX Genes: Why are they important?

- Makes proteins that signal, activate, mark or otherwise communicate with other genes and their products- Crucial for body plan/development (sets up anterior-posterior and dorsal-ventral axis)

HOX Genes: What kind of responses do they generate in organisms?

- Example: telling cells of a fly where to start building wings- Can lead to homeotic mutations which cause loss-of-function or gain-of-function - Loss-of-function ex: development of second leg pair into antennae - Gain-of-function ex: results in legs where antenna should be (antennapedia)

Gene Families: How do they come about?

Clusters of genes similar in structure and sequence

Gene Families: How does natural selection operate through the formation of gene families?

* Selection acts independently on each gene
* Evo-devo looks at ARRIVAL of the fittest

Gene Families: Gene duplication role

Gene duplications are the most important source of new genes

What happened in the Hadean?

* No fossil record- Differentiation of Earth into crust, mantle, and core- Origin of atmosphere via volcanic outgassing (little O2)- Condensation of water to form freshwater lakes, streams, etc
* Origin of continental crust

What happened in the Archaen?

* Origin of life- Early organisms had methane, SO4, H2S, and produced CO2 and alcohol as byproduct- Photosynthetic organisms appear
* Atmosphere converted to oxygen environment

What happened in Cambrian?

* Relatively sudden appearance of diverse animal forms in fossil record
* All "major" phyla were present by the end

Why did the Cambrian happen?

* Intrinsic explanation: something in animals changed, like HOX and HOX-like genes were duplicated in bilaterians
* Extrinsic explanation: ancient atmosphere had insufficient O2 to allow evolution of active lifestyles

Abiogenesis

Life originated from abiotic precursors already existing on Earth

Miller-Urey Experiment

Synthesized organic compounds from inorganic precursors (water, methane, ammonia, hydrogen) and produced 20+ amino acids and proved evidence for abiogenesis

Panspermia

Earth is constantly bombarded with material from interstellar space consisting of organic compounds which may have provided building blocks of life (ex: Murchison meteorite had amino acids)

Key features of prokaryotes/eukaryotes

Eukaryotes have a DNA containing nucleus and can be single-celled or multicellular while prokaryotes (bacteria and archaea) do not have a nucleus and are unicellular

What did early life look like?

* Consisted of prokaryotes (at least 3.6 billion years old)- Fossil stromatolites
* Early photosynthetic prokaryotes produced oxygen atmosphere

Key characteristics of protists

* Extremely diverse- Only share one characteristic: eukaryotic- Do not belong in any other kingdom
* Range from unicellular to multicellular (algae)

5 phyla of fungi

1. Chytrids
2. Zygomycetes
3. Glomeromycetes
4. Ascomycetes
5. Basidiomycetes

Chytrids

* Water and soil
* Produce swimming pores
* Fungicide used in lakes, killing frogs
* Parasitic

Zygomycetes

* Rots produce, grows fast
* Ruins food

Glomeromycetes

* 90% of plants have these on roots
* Mycorrhizae: mutualistic with plants, helps plant absorb nutrients and fungus gets carbohydrates from plant

Ascomycetes

* Morels, truffles, bread molds, yeast -
* Economically important: yeast, bread, wine, beer -
* Gastronomically important: edible mushrooms like morels, truffles, cheese molds -
* Medically important: source for penicillin

Basidiomycetes

toadstools

Key characteristics of fungi

* Absorptive heterotrophs: digestive enzymes secreted into surroundings, fungus then absorbs digested products -
* Most are decomposers, some are parasitic or symbiotic -
* Body is a network of thin filaments (hyphae)

How does a fungus live (mostly)?

Warm, moist, dead matter

Feeds off of dead matter

Lichen

* Relationship between fungus and photosynthesizer - Important in making soil -
* Can live in extreme conditions -
* Provides protected environment and minerals for autotrophs while autotrophs supply carbohydrates

Key characteristics of land plants

1. Apical meristems (causes root/shoot to grow and increase in length)
2. Alternation of generations
3. Tough, resistant spores from sporangia
4. Special organs for production of gametes

Alternation of generations

1. sporophyte produces haploid spores by meiosis
2. Spores germinate and divide by mitosis and develop into multicellular, haploid gametophytes
3. Gametophytes produce unicellular haploid gametes by mitosis
4. 2 gametes unite during fertilization to form a diploid zygote
5. Zygote divides by mitosis and develops into multicellular, diploid sporophyte

Ploidy levels of different cell types

Haploid: 1 copy of each chromosomes, gametes

Diploid

2 copies of each chromosome, somatic cells, plant cells

Plant phylogeny

(left to right) nonvascular plants, vascular seedless plants, gymnosperm, angiosperm

Nonvascular plants

* No vascular tissue or roots -
* Simplest & most primitive -
* Dependent on water for reproduction -
* Small -
* Water and nutrients move by diffusion -
* Mosses

Seedless vascular plants

* First to evolve xylem & phoelem -
* Use spores for reproduction (wind dispersal)

Gymnosperm

* Produces seeds
* Uses seeds for dispersal
* "naked seeds"
* Conifers
* Don't need water to reproduce
* Don't produce flowers or fruit

Angiosperm: why are they so diverse?

Utilize methods to attract pollinators and prevent selfing

What do flowers do for the plants?

Reproduction: have reproductive structures that attract pollinators and develop fruit

Parts of flower

* 4 whorls
* 2 are sterile (sepal and petal)
* 2 are fertile (stamen & carpel)

Animal phylogenic tree

Four key distinctions that divide the animals

1. True tissues (Eumetazoa) vs None (Parazoa)
2. Radiata vs Bilateria (Symmetry)
3. Blastopore Fate (deuterostome vs protostome)
4. Protostome Development (lophotrochozoa vs ecdysozoa)

Porifera

* No tissues, no symmetry
* Sponges

Cnidaria

* Radial symmetry, diploblastic -
* Cnidocytes: stinging cells -
* Jellyfish, coral, sea anemones

Mollusca

* Bilateral symmetry, triploblastic -
* Protostome: lophotrochozoans -
* Gastropoda: snails, conch -
* Bivalvia: clams, oysters, scallops -
* Cephalopoda: squids, octopus

Annelida

* Segmented -
* Bilateral symmetry, triploblastic -
* Protostome: lophotrochozoans -
* Polychaeta, Oligochaeta (earthworms), Hirudinea (leeches)

Platyhelminthes

* Bilateral symmetry, triploblastic -
* Protostome: lophotrochozoans -
* Flatworms (tapeworms, flukes)

Nematoda

* Bilateral, triploblastic -
* Protostome: ecdysozoa (cuticle) -
* Molts as it grows -
* Roundworms
* Tardigrada: "water bears"

Arthropoda

* Most diverse -
* Bilateral symmetry, triploblastic -
* Protostome: ecdysozoa - I
* nsects, Milli/Centipedes, arachnids, crustaceans

Echinodermata

* Bilateral symmetry, triploblastic -
* Deuterostomes -
* Sea urchins, starfish, sand dollar

Chordata

* Bilateral symmetry,
* triploblastic -
* Deuterostome -
* Tunicates, vertebrates

What is ecology?

The study of interactions of organisms with their environment

Different fields of ecology?

* Individual -
* Population -
* Community -
* Ecosystem (biotic and abiotic)

Types of symbiosis

* Parasitism -
* Mutualism -
* Commensalism -
* Predator-prey -
* Competition

Parasitism

One species benefits but the other is harmed

Mutualism

Beneficial to both species involved

Commensalism

One species benefits and the other is neither benefitted nor harmed

Predator-Prey

* Warning colors -
* Cryptic coloring "camouflage" -
* Mimicry

Batesian:

"sheep in wolf's clothing"; the mimic isn't poisonous or dangerous

Mullerian:

two or more species have warning coloration that is similar

Competition

Individuals fight for the same resources lowering fitness of both parties

What is coevolution?

* Interactions between species are strong -
* Selection and evolution across species boundaries -
* Selection is driven by the interaction between species

Why do we see coevolution occur?

* Mutualism -
* Escalating "arms race" between predator and prey -
* Co-speciation (host/parasite interaction)

To be coevolution, the relationship must be the ____ ____ ____ and there must be _____ in the response

primary selective force; reciprocity

What is needed for coevolution to happen?

Succession: gradual change in species composition over time

Primary: no soil exists

Secondary: community has been damaged but soil remains

How can we test for coevolution?

Compare fitness of the species with/during the relationship and fitness of the species without the relationship

HOX genes

* These are genes that control where, when, and how other genes are expressed.
* ________ ____________ make proteins that signal, activate, mark, or otherwise communicate with other genes and their products.

colinear

HOX genes are _________ on chromosomes, meaning that they are activated in the order the body is developed.

developmental anatomy

HOX genes can be turned off or on to achieve different ____________ ___________.

The more complex an organism is, then the more HOX genes it will have. (T/F)

True

When did life first arise?

3.8 billion years ago

1944 was the first time we recognized bacteria's resistance to penicillin. When and how do you think penicillin resistance ACTUALLY occurred for the first time?

After the mass production of penicillin and it's increased use

After the first person was treated with penicillin

After the first mold manifested anti-bacterial properties

Hard to say; they could have been resistant before molds even manifested anti-bacterial properties

eukaryotic

Protists are alike in that all are

Which of the following characteristics could be considered the least important in defining evolutionary relationships and tremendous speciation in plants?

The ability to photosynthesize

Complete the following: The ________ sporophyte undergoes __________ to produce __________ spores. These develop into __________ gametophytes that undergo __________ to produce ___________ gametes.

diploid, meiosis, haploid; haploid, mitosis, haploid

Which of the following is true of moss?

Moss produce sperm that swim at random in a thin film of water in search of a coveted egg hidden within an archegonium

Your roommate requests that you make her some vegetable juice with your new fancy juice maker. Which of the following is a vegetable, not a fruit?

Spinach

Does spinach make fruits?

Yes

Which of the following is not a feature common to most animals?

asexual reproduction

Which of the following organism is most likely to be a diploblast?

jellyfish

Which of the following is thought to be the most closely related to the common animal ancestor?

protist cells

Process by which two DIFFERENT species evolve in response to changes in each other

Coevolution

When considering predator-prey interactions, in which of the following situations is the strongest co-evolutionary relationship predicted?

When the predator specializes on a prey species and the prey species has primarily one predator

Choose the answer most correct: In a series of isolated populations of garter snakes what would you expect about their resistance to newts' toxins if you know that in some locations newts are either present or not and that their toxicity varies:

Resistance would be variable but will show a geographic pattern

Other names for HOX genes....

Master genes, homeotic genes, developmental regulatory genes

Natural selection can easily act on HOX genes (T/F)

FALSE

Changes in HOX genes will, in many cases, be.....

deleterious

How are HOX genes expressed?

Anterior (head) - Posterior (toes) and Dorsal (back) - Ventral (stomach) axes

Mutations in HOX genes can result in...

major structural changes in the body plan of an organism pretty quickly

The most important source of new genes. This is also how gene families are created

Gene duplication

Gene families

clusters of genes similar in structure and sequence (and often similar in the product they produce. An example would be proteins or HOX genes.

Consequences of gene duplication

\-"New" copy may not have same functional constraints as ancestral copy

\-Mutations may accumulate in new (daughter) copy with fewer consequences

\-Mutations may allow daughter to perform new functions

When we're born the hemoglobin gene is "turned off" since it costs too much to produce and a "cheap gene" is turned on (a gene that is easy to make in a cost effective perspective)

Fetuses in early development don't have lungs and are unable to bring oxygen into their bloodstream, so we produce a hemoglobin that is extremely good at binding oxygen until we develop lungs and are born. What happens to this the hemoglobin gene since it is no longer needed prior to birth (since we are born into an oxygen-rich environment)?

The Hadean

* The first time period -
* No life existed at this time -
* The planet was formed

The Archean

* Origin of life -
* Formation of land masses and continents

What organisms existed in the Archean era?

Prokaryotic bacteria-like organism (basically a capsule of genetic material) and photosynthetic organisms.

During the Archean era, which organisms gave us our oxygenated atmosphere?

Photosynethic organisms

Archaea (the organism)

group of organism-very bacteria like

Known as extremophiles (live in very extreme environments)

Cyanobacteria

* Photosynthesizing organisms. -
* Primary organisms responsible for oxygenated environment -
* Grow in mats (connect together), and mats build up and get thicker -
* snot like

The Proterozoic

* Origin of eukaryotes/emergence of eukaryotic cells -
* Extreme diversification of multicellular organisms and green algeae

"How did we go from prokaryotes to eukaryotes?"

Serial Endosymbiosis Theory

Hypotheses of Serial Endosymbiosis (2)

* Smaller bacterium infects a larger cell and established a symbiotic relationship (parasitism) -
* Larger cell attempted to consume the smaller cell and resulted in a relationship that benefits both of them (consumption)

Evidence of Serial Endosymbiosis

circular genomes in chloroplasts, mitochondria, and bacteria as seen in prokaryotes, and mitochondria have cell membranes very similar to prokaryotes

When did progression toward multicellularity occur?

In the Proterozoic