BIO 1114 SMOCK QUIZ 3

Evidence of Evolution: Homology

Homology:

• Similarity that exists in species descended from common ancestor

Homology can be recognized and studied at three interacting levels:

• Genetic

• Developmental

• Structural

Evidence of Evolution: Genetic Homology

Genetic homology:

• Similarity in DNA nucleotide sequences, RNA nucleotide sequences, or amino acid sequences

Cytochrome C: a protein used in Electron Transport Chain

Evidence of Evolution: Developmental Homology

Developmental homology:

• Similarity in developmental structures or processes

• Example:

  • Early chick, human, and cat embryos have tails and structures called pharyngeal pouches:

    • Product of similar development processes inherited from common ancestor

Evidence: Comparative Anatomy

• Similarities in patterns of embryonic development suggest shared ancestry

• Organisms with very different ways of life often share common anatomical structures due to descendance from common ancestors

Evidence of Evolution: Structural Homology

Structural homology:

• Similarity in adult morphology

• For example, most vertebrates have a common structural plan in the limb bones

Vestigial traits: evolution is not perfection

Evolution’s Internal Consistency

• Multiple data sets support idea that species have descended, with modification, from a common ancestor

• Internal consistency:

  • Observation that data from independent sources agree in supporting predictions made by a theory

• Evidence for the evolution of cetaceans—whales and dolphins—illustrates idea of internal consistency:

  • The fossil record: cetaceans are identified by unique ear bones

  • Phylogeny of the fossil cetaceans:

    • Indicates a gradual transition between terrestrial and aquatic forms

Evolution’s Internal Consistency Continued

• Relative dating and absolute dating both support order of species indicated in phylogeny

• Phylogeny of living whales and dolphins:

  • Estimated from similarities and differences in DNA sequences

  • Indicate that hippos are closest relative to cetaceans

Vestigial hip and hindlimb bones are found in some adult whales and dolphin embryos

Domains of Life

• Bacteria, Archaea, and Eukarya are the three largest branches on the tree of life.

• All bacteria and archaea are prokaryotic and unicellular, and they help form the microbiome.

Fundamental differences between bacteria and archaea:

• Bacteria have cell walls made of peptidoglycan.

• Archaea have unique phospholipids in the cell membranes.

• Bacteria and archaea have different ribosome and RNA polymerase structures.

• Archaea are more closely related to Eukarya than to Bacteria.

Biological Impact of Bacteria

• Ancient, diverse, abundant, and ubiquitous lineages:

  • Oldest fossils are of 3.5-billion-year-old bacteria:

    • Eukaryotes not in fossil record until 1.75 BY later

  • 10,000 species named and described, but hundreds of thousands likely exist:

    • ~1000 microbes in human large intestine

    • ~700 microbes in human mouth

Bacteria and archaea are amazingly abundant

• A mere teaspoon of soil contains billions of microbial cells.

• A liter of seawater contains a community of microbes equivalent to that of a large human city.

• Microbes living under the ocean may make up to 10% of the world’s total living biomass.

• They are found in every possible environment.

• They are very diverse, and we are still discovering entire new phyla.

Some are extremophiles

• Extremophiles live in unusual environments.

  • there are bacteria that live at a pH less than 1.0, at temperatures of 0°C under the ice, and in water 5–10 times saltier than seawater.

  • Studying extremophiles may help us understand the origin of life, since life probably evolved in a high-temperature, anoxic environment.

• Astrobiologists use extremophiles as model organisms in the search for extraterrestrial life.

• Extremophiles are useful in certain commercial and research applications.

A genetic engineering challenge is to produce quantities of a desired protein

• In DNA cloning a human gene that produces an important protein is isolated.

  • insulin

• It is then inserted into a bacterial plasmid.

• As the bacteria multiply, large amounts of the gene, and thus the protein, are produced.

Pathogenic bacteria

• Come from several different lineages in the domain Bacteria.

• Pathogens tend to affect tissues at entry points into the body.

The germ theory of disease

Based on Koch’s postulates (four criteria that had to be met to demonstrate that a specific microbe causes a certain disease).

• infectious diseases are caused by microbes (microscopic organisms).

• Infectious diseases are spread in three main ways:

  • From person to person

  • From bites of insects or animals

  • From ingesting contaminated food or water, or environmental exposure

The germ theory’s immediate impact was in improving sanitation, greatly reducing mortality due to infectious disease.

How have Bacteria and Archaeans diversified?

Genetic variation through gene transfer

1. Transformation—when bacteria or viruses naturally take up DNA from the environment

2. Transduction—when viruses pick up DNA from one prokaryotic cell and transfer it to another cell

3. Conjugation—when genetic information is transferred by direct cell-to-cell contact

Ways to identify bacteria

Size, shape, and motility

Ways to identify bacteria: Cell wall composition

• Gram-positive bacteria have a cell wall with abundant peptidoglycan, which stains dark purple when exposed to a Gram stain.

• Gram-negative bacteria have a cell wall with a thin layer of peptidoglycan 
surrounded by a phospholipid bilayer. They stain light pink.

• Gram stain analysis can predict sensitivity to certain drugs.

Ways to identify bacteria: Metabolic diversity

• Bacteria and archaea are astonishingly diverse in the ways they acquire energy to make ATP and the carbon compounds they can use as building blocks.

• There are three ways to acquire energy to produce ATP:

  • Phototrophs use light energy to energize electrons, producing ATP by photophosphorylation (light reactions of photosynthesis).

  • Chemoorganotrophs oxidize organic molecules with high potential energy, such as sugars (cellular respiration, fermentation).

  • Chemolithotrophs oxidize inorganic molecules with high potential energy, such as ammonia or methane (usually via cellular respiration).

• There are two ways to acquire carbon :

  • Autotrophs use carbon dioxide or methane to build their own carbon-containing compounds.

  • Heterotrophs acquire carbon-containing compounds from other organisms.

• Overall, there are six major “feeding strategies” (the six possible combinations of three methods of acquiring energy and two methods of acquiring carbon).

  • Plants, animals, fungi, and other eukaryotes use only two strategies.

  • Bacteria and archaea use all six.

• Basic chemistry required for photosynthesis, cellular respiration, and fermentation originated in these lineages

• Evolution of variations on each of these processes allowed prokaryotes to diversify into millions of species that occupy diverse habitats

Ecological Diversity and Global Impacts

• Bacteria and archaea produce extremely sophisticated enzymes :

  • As a result, they can live in extreme environments and use toxic compounds as food

• The complex chemistry and abundance of bacteria and archaea make them potent forces for global change

• Bacteria and archaea have altered the chemical composition of the oceans, the atmosphere, and terrestrial environments for billions of years.

The Oxygen Revolution

• No free molecular oxygen existed for first 2.3 billion years of Earth’s history

• Cyanobacteria:

  • lineage of photosynthetic bacteria

  • first to perform oxygenic photosynthesis

  • were responsible for changing Earth’s atmosphere to one with a high concentration of oxygen

Nitrogen Fixation and the N-cycle

• All organisms require nitrogen (N) to synthesize proteins and nucleic acids

• Molecular nitrogen (N2) is abundant in atmosphere

  • Plants cannot use molecular nitrogen (N2) directly

    • Plant growth is often limited by the availability of nitrogen

  • Must obtain N from ammonia (NH3) or nitrate (NO3-)

• Nitrogen fixation—certain bacteria and archaea are the only organisms capable of converting N2 to NH3:

  • Nitrogen-fixing bacteria live in close association with plants (e.g., in root structures called nodules)

Ecological Diversity and Global Impacts

• Other bacteria and archaea convert ammonia to nitrates and nitrites, resulting in a complex nitrogen cycle.

• Nitrogen-fixing legumes can be used to restore N levels in badly degraded soils

Nitrate Pollution

• Widespread use of NH3 fertilizers causes pollution:

  • When NH3 is added to soil, much of it is used by bacteria as food

  • These bacteria then release nitrite or nitrate as waste products

• Nitrates cause pollution in aquatic environments:

  • In an aquatic ecosystem, nitrates can decrease oxygen content, causing anaerobic “dead zones” to develop

Fungi are the master traders and recyclers in terrestrial ecosystems

• Some fungi release nutrients from dead plants and animals into the soil; others obtain nutrients and then transfer them directly to living plants and animals.

• Because they recycle key elements such as carbon, nitrogen, and phosphorus and because they transfer key nutrients to plants and animals, fungi profoundly influence ecosystem productivity and biodiversity.

• In terms of nutrient cycling, fungi make the world go around.

Economic and Ecological Impacts

• ~300 species of fungi cause human illness:

  • This incidence is low compared to other organisms

• Their major destructive impact is on our food supply :

  • Rusts, smuts, mildews, wilts, and blights cause billions of dollars of crop losses each year

  • Saprophytic fungi are responsible for losses due to spoilage

• Fungi have many positive impacts:

  • They are the source for many antibiotics (ex. Penicillin)

  • Mushrooms are eaten in many cultures

  • Yeast (Saccharomyces cerevisiae) is used to make bread, cheese, soy sauce, beer, wine, and other foods

  • Fungal enzymes improve characteristics of foods such as fruit juice, candy, and meat

Saprophytic Fungi Accelerate the Carbon Cycle on Land

• Saprophytes are fungi that digest dead plant material

• Fungi help cycle carbons through terrestrial systems

• The carbon cycle on land has two basic components:

  • Fixation of carbon by land plants

  • Release of C O2 from cellular respiration

• For many carbon atoms, saprophytic fungi connect the two components

Analyzing Morphological Traits

• Fungi have very simple bodies

• Two growth forms exist:

  • Single-celled forms—yeasts

  • Multicellular, filamentous forms—mycelia (singular: mycelium)

• Some species adopt both forms

All mycelia are dynamic

• They constantly grow in the direction of food sources and die back in areas where food is running out

• The body shape of a fungus can change almost continuously throughout its life

The Nature of Hyphae

• Hyphae—the long, narrow filaments of mycelium

• Because mycelia are made of branching networks of very thin hyphae:

  • Fungi have the highest surface-area-to- volume ratio of all multicellular organisms

  • Nutrient absorption is extremely efficient

  • Prone to drying out:

    • Thus most abundant in moist environments

    • Reproductive spores are resistant to drying out

    • Spores can endure dry periods and then germinate

What Adaptations Make Fungi Such Effective Decomposers?

• Given enough time, fungi can turn even the hardest, most massive trees into soft soils

• Large surface area of a mycelium makes nutrient absorption exceptionally efficient

• Saprophytic fungi can grow toward the dead tissues that supply their food

Fungi must digest their food before they can absorb it

• Fungi thus perform extracellular digestion:

  • Digestion that takes place outside the organism

  • Simple compounds resulting from enzymatic action are absorbed by hyphae

  • The two most abundant organic molecules on Earth are digested by fungi:

    • Lignin—in plant secondary cell walls

    • Cellulose—in plant primary and secondary cell walls

Fungi are much more closely related to animals than to land plants

• Fungal infections in humans are more difficult to treat than bacterial infections:

• Recent shared ancestry results in similar cellular and molecular structures

• Drugs that disrupt fungal physiology are likely to damage humans

• Key traits linking animals and fungi:

  • D N A sequence data

  • Both animals and fungi synthesize chitin

  • Flagella in chytrid spores and gametes are similar to animal flagella

  • Animals and fungi store glucose as the polysaccharide glycogen

Fundamental features of eukaryotes

• The nuclear envelope is a synapomorphy that defines the domain Eukarya.

• Most eukaryotic cells are larger than prokaryotes, have many organelles, and have an extensive system of structural proteins called the cytoskeleton.

• Multicellularity has evolved multiple times in eukaryotes.

• Eukaryotes reproduce either asexually via mitosis or sexually via meiosis.

• Protists are all the eukaryotes that are not fungi, green plants, or animals.

  • a collection of lineages which surrounded by water most of the time. 

Three important evolutionary innovations in protists

• evolution of the nuclear envelope/membrane

• origin of the mitochondrion

• origin of chloroplasts

Origin of the Nuclear Envelope

• The evolution of the nuclear envelope was advantageous because it separated transcription and translation.

  • in bacteria and archaea, transcription and translation occur together

  • in eukaryotes RNA transcripts are processed inside the nucleus but translated outside the nucleus

• With a simple nuclear envelope in place, alternative splicing and other forms of RNA processing could occur.

• This important morphological innovation gave the early eukaryotes a novel way to control gene expression.

The endosymbiotic theory

• Lynn Margulis proposed in the 1970s that mitochondria evolved from an aerobic bacterium that was engulfed by an anaerobic eukaryotic cell

• Mutually beneficial symbiosis:

  • The host supplied the bacterium with protection and carbon compounds

  • the bacterium produced much more ATP than the host could produce on its own.

Many lines of evidence support Endosymbiotic Theory

• Mitochondria are similar in size to alpha-proteobacteria. They:

  • divide independently of the host cell, and by fission, as bacteria do.

  • have their own ribosomes (similar to bacterial ribosomes) and synthesize their own proteins.

  • have double membranes, as would be expected if they were engulfed by another cell.

  • have their own chromosomes, which are circular and similar to bacterial chromosomes.

• The most conclusive evidence is that mitochondrial genes are very closely related to the genes from alpha-proteobacteria

Endosymbiosis and the origin of the chloroplasts

• All photosynthetic protists have chloroplasts.

• None of the basic machinery required for photosynthesis evolved in eukaryotes.

  • they likely “captured” it via endosymbiosis

• The eukaryotic chloroplast may have originated when a protist engulfed a cyanobacterium.

• Once inside the protist,

  • the photosynthetic bacterium provided its eukaryotic host with oxygen and glucose

  • the host provided the bacterium protection and access to light

Which eukaryote originally obtained a photosynthetic organelle?

• Because all species in the Plantae have chloroplasts with two membranes, biologists infer that the original, or primary, endosymbiosis occurred in these species’ common ancestor.

• That ancestor eventually gave rise to all subgroups in the Plantae lineage—the glaucophyte algae, red algae, and green plants (green algae and land plants).

Evidence for endosymbiosis and the origin of the chloroplasts

• Chloroplasts have the same list of bacteria-like characteristics presented earlier for mitochondria.

• They contain circular DNA containing genes extremely similar to genes found in various species of cyanobacteria.

• Some algae have a photosynthetic organelle with an outer layer containing the same peptidoglycan found in cyanobacteria.

• There are many examples of endosymbiotic cyanobacteria living inside cells of protists or animals today.

Secondary Endosymbiosis Leads to Organelles with Four Membranes

• In Excavata, Rhizaria, Alveolata, and Stramenopila, the chloroplast is surrounded by more than two membranes—usually four.

• Researchers hypothesize that the ancestors of these groups acquired their chloroplasts by ingesting photosynthetic protists that already had chloroplasts.

  • Secondary endosymbiosis: occurs when an organism engulfs a photosynthetic eukaryotic cell and retains the chloroplasts as intracellular symbionts.

Similarities Between Green Algae and Land Plants

• Of the green algal groups, three most similar to land plants:

  • Based on DNA sequence analysis:

    • Zygnematophyceae (conjugating algae)

    • Coleochaetophyceae (coleochaetes)

    • Charophyceae (stoneworts)

  • Largely multicellular and live in freshwater:

    • Hypothesis: Land plants evolved from green algae that lived in freshwater habitats

How Do Biologists Study Green Algae and Land Plants?

To understand diversification:

1. Compare morphological traits

2. Analyze the fossil record

3. Estimate phylogenetic trees

Plants: Life on Land

• The first-known green algae lived between 700 and 725 million years ago (mya), when oxygen levels began to rise.

• Green algae (protists) live surrounded by water

  • water, minerals

  • Support

  • reproduction

Plants: Life on Land (475 mya)

• Land plants are monophyletic :

  • There was only one successful transition from freshwater environments to land

• To adapt to life on land, plants evolved features that allow them to

  • resist drying out (absorb and retain water)

  • absorb nutrients

  • stand upright without outside support

  • reproduction not dependent on water