Biology Midterm #1

Deuterostomes

("mouth second"): anus arises from the blastopore, mouth arises later. dorsal nervous system internal skeleton

Prokaryotes

- outnumber eukaryotes - all unicellular, but can form colonies -most commonly divide by binary fission - no nucleus or nuclear membrane -typically no membrane enclosed organelles -don't have separate chromosomes, 1 circular chromosome -many form symbiotic relationships with eukaryotes -not a clade

Gram-negative Bacteria

- stain pink to red - Notice the presence of TWO (vs. only one) cell membranes - an inner and outer membrane. A thin layer of peptidoglycan lies between the two layers, resulting in a pink stain.

What are the key features of mammals?

1) Sweat glands 2) Mammary glands 3) Hair 4) Four-chambered heart

What are three major ways of classifying animals based on embryonic development?

1. Diploblasts - two germ layers 2. Triploblasts - three germ layers 3. Sponges - no defined germ layers

Consider the sexual lifecycle of the Ascomycota (sac fungi). Place the of the life cycle in the correct sequence

1. Fusion of hyphae from 2 different mating types 2. Plasmogamy (cytoplasmic fusion) 3. Karogamy (nucleic fusion) 4. Meiosis 5. Spore germination

What are the unique traits of animals that differentiate them from other organisms?

1. Gene sequences - specifically hox genes; these genes are found only in animals 2. Morphological synapomorphies: 2a) Gap junctions 2b) A common set of extra-cellular molecules (including collagen) Note that animal cells does not contain cell walls but contain extracellular matrix which is mostly composed of collagen.

What are the reasons for huge success of arthropods on earth?

1. Jointed appendages 2. Segmentation 3. Rigid exoskeleton for support (mobility) and protection

What are the two examples of mutualists fungi?

1. Mycorrhizae - Association between fungi and plant roots 2. Lichens - Association between fungi and photosynthetic microorganisms

What is the function of exoskeleton in insects?

1. Provides support for walking on land 2. Prevents drying out.

What are the four types of fungi

1. Saprobic 2. Parasitic 3. Pathogenic 4. Mutualists

Morphological synamorphies shared by animal cells

1. unique junctions between cells (allow for communication and transport between cells) 2. a common set of extracellular molecules. including collagen and proteoglycan 3. Similar ribosomal RNAs 4. Similarities in genes that control development

Lichens

= associations between fungi and photosynthetic microorganisms. • Fungi can partner with photosynthetic microorganisms that are NOT plants, typically green alga. Often observed on surfaces like rocks or tree branches. Lichens are sensitive to air pollution. For humans, this makes them good indicators ("passive monitors") of pollution levels. Certain components such as sulfur dioxide appear quite toxic to the lichens

Mammals

A Subgroup of Amniotes In nearly all mammals, the amniote egg shell was lost, and functions of the extraembryonic membranes were expanded to allow the embryo to grow inside the mother. Sweat glands Mammary glands Hair Four-chambered heart that completely separates oxygenated from deoxygenated blood

Which features do cyanobacteria share in common with diatoms?

A cell wall (diatoms have silica cell wall) (peptidoglycan for cyanobacteria) Start by recognizing that diatoms are eukaryotes and cyanobacteria are prokaryotes. Remember that organelles, including mitochondria and chloroplasts, are a feature of eukaryotes but not prokaryotes. The same is true for a complex cytoskeleton - we talked about its role in cell movement and chromosome alignment.

Polyphyletic

A group composed of a collection of organisms in which the most recent common ancestor of all the included organisms is not included, usually because the common ancestor lacks the characteristics of the group. Polyphyletic taxa are considered "unnatural", and usually are reclassified once they are discovered to be polyphyletic. Examples : marine mammals, bipedal mammals, flying vertebrates, trees, algae, etc

Monophyletic

A group composed of a collection of organisms, including the most recent common ancestor of all those organisms and all the descendants of that most recent common ancestor. A monophyletic taxon is also called a clade. Examples : Mammalia, Aves (birds), angiosperms, insects, etc.

Paraphyletic

A group composed of a collection of organisms, including the most recent common ancestor of all those organisms. Unlike a monophyletic group, a paraphyletic taxon does not include all the descendants of the most recent common ancestor. Examples : Traditionally defined Dinosauria, fish, gymnosperms, invertebrates, protists, etc.

eukaryotes

A monophyletic group A sister clade to the archaea Structurally very diverse • Eukaryotes include plants, animals, fungi and protists • Plantsàflowers • Animalsàhumans • Fungiàmushrooms • Protistsàalgae

What characteristics would you look for in a newly discovered prokaryote that would characterize it as Archaea rather than Bacteria?

Absence of membrane-bound organelles and absence of peptidoglycan in cell walls.

Triploblastic (not diploblastic) animals can have one of three general body cavity types:

Acoelomate Pseudocoelomate Coelomate

chordates

All chordates have these derived structures at some stage in their life (often during early development): 1. Dorsal hollow nerve cord 2. Dorsal supporting rod called the notochord Tail that extends beyond the anus

Baker's yeast is an example of an yeast. But, this also belongs to which type of fungi?

Ascomycota (sac)

simplest phylogenetic tree that contains diploblasts, triploblasts, and sponges

BEWARE: diploblasts are paraphyletic

primary endosymbiosis

Direct engulfment of a photosynthetic cyanobacterium by an ancestral eukaryote. (primary and secondary endosymbiosis are differentiated based on what is being engulfed) Choroplasts were not engulfed, bacteria were engulfed and formed plastids

Developmental Pattern differences in animals

During early development, distinct layers of cells called germ layers form in the embryo that give rise to adult tissues. We can distinguish three main animal groups. Diploblasts: two germ layers: endoderm and ectoderm Triploblasts: three germ layers: endoderm, mesoderm, ectoderm- further divided into protostomes and deuterostomes Sponges: no defined germ layers

major groups of deuterostomes

Echinoderms, Hemichordates and Chordates

What Kinds of Genes Frequently Undergo LGT?

Genes that provide beneficial adaptations are much more likely to be retained by a new organism following LGT. Common example: antibiotic resistance genes. These are often carried on bacterial plasmids, which are easily replicated & exchanged.

What is an unique feature of dikaryotic fungi?

Having a dikaryotic state i.e., n+n state

LGT Can Obscure Evolutionary Relationship Patterns

If we construct a phylogenetic tree by comparing the DNA sequence of just a single gene between different species, the resulting "gene tree" might not match the organismal tree if the gene under consideration underwent lateral transfer.

Dikarya

Include the Ascomycota and Basidiomycota Both groups can reproduce sexually, and they have a so-called dikaryon stage in their sexual life cycles

Key Events in the Origin of Eukaryotic Cells

Increased compartmentalization Origin of a flexible cell surface • Origin of a complex cytoskeleton Origin of a nuclear envelope Appearance of digestive vacuoles Acquisition of certain organelles by endosymbiosis

Secondary endosymbiosis

Indirect engulfment of a chloroplast due to engulfment of a eukaryotic cell that already contained a chloroplast.

How Can We Distinguish Major Animal Groups?

Major distinctions include: Differences in early embryonic development Body symmetry Body cavity structure Segmentation & nervous system

karyogamy results in diploid cells

Once both nuclei fuse, diploid (2n) zygotes are produced. Fusion of the two nuclei is called karyogamy and coincides with fertilization.

Adaptations because of loss of rigid cell wall

Plasma membrane can fold inward to facilitate endocytosis & formation of organelles Allows for increased surface area and cell size More surface area allowed for more nutrients to enter and exit

Advantages of compartmentalization

Separation/isolation of chemical reactions or substances in different organelles. Specialization of regions of the cell for specific purposes.

lateral gene transfer

Sometimes, prokaryote species exchange genetic material with other prokaryotes & eukaryotes. This complicates study of relatedness. Shown below is the "lateral" or "horizontal" transfer of a gene (Gene x) between Species C & D. Species C still retains a copy of the gene. Lateral = between species. -LGT by plasmids or virus or uptake of DNA by transformation

key features of body plan

Symmetry Body cavity structure Segmentation External appendages

ecdysozoans

The cuticle of ecdysozoans must be shed or molted repeatedly during growth and replaced with a newer larger one.

dikaryotic stage

The multicellular, haploid structures that result from spore germination can be either (+) or (-) mating type. In the dikarya, hyphae of opposite mating types fuse to produce cells that contain the unfused nuclei of both mating types. This is the dikaryotic stage, a unique feature of dikarya. When hyphae of two mating types fuse, only their cytoplasm fuses initially (plasmogamy), but the nuclei remain unfused for an extended period of time.

plasmids in bacteria

There are many different types of plasmids, and bacteria can differ in the number and types of bacteria that they carry. Lateral gene transfer will cause bacteria from different species to share the same plasmids, but it is dependent on the physical transfer of plasmids or other pieces of DNA. For instance, only bacteria who receive a particular antibiotic resistance gene on a given plasmid will become resistant to the particular antibiotic, while others will remain sensitive.

Are mammals amniotes?

Yes. Mammals are sub-group of amniotes. In nearly all mammals, amniote egg shell was lost and functions of the extra-embyronic membranes were expanded to allow the embryo to grow inside the mother.

cephalization

a concentration of sensory organs and nerve tissues at the front (anterior) end, or head

What feature of early eukaryotes most directly facilitated the process of endosymbiosis?

a flexible cell surface and cytoskeleton

aminotes

a large subgroup of vertebrates well adapted to life in terrestrial habitats. Include reptiles, birds & mammals. Many adaptations led to their success on land, including the amniote egg. Egg shells in some species prevent water loss but allow gas exchange, and store food for the embryo. Extraembryonic membranes protect embryo from drying out.

fungi mutualists

a relationship that benefits both partners Mycorrhizae Lichens

protostomes

a subdivision of triploblastic animals ("mouth first"): mouth arises from blastopore, anus forms later. ventral nervous system external skeleton (if present)

vertebrates

a subgroup of the chordates. In vertebrates, the notochord is replaced during early development by a jointed, dorsal vertebral column (backbone). Internal skeleton provides support for muscles, which are controlled by a nervous system. Very diversified group.

What is amniotic egg?

amniotic egg The type of egg produced by reptiles, birds, and prototherian (egg-laying) mammals (amniotes), in which the embryo develops inside an amnion. The shell of the egg is either calcium-based or leathery. Amnion: A membrane that encloses the embryo of reptiles, birds, and mammals within the amniotic cavity. This cavity is filled with amniotic fluid, in which the embryo is protected from desiccation and from external pressure Note: Fishes and amphibians must lay their eggs in water and therefore cannot live far from water. But thanks to the amniotic egg, reptiles can lay their eggs nearly anywhere on dry land.

protist

any eukaryote that is NOT a plant, animal or fungus. It does not describe a formal taxonomic group, but rather is a convenience term.

Radial symmetry

any plane through a main (central) body axis gives rise to two similar halves.

Mycorrhizae

associations between fungi and plant roots. Many vascular plants depend on these associations. • Benefit to plant: Root hairs able to absorb more water and minerals (esp. phosphorous) due to extensive branching. • Benefit to fungus: Obtain nutrients such as sugars & amino acids from plant.

Types of symmetry

assymetrical radial symmetry bilateral symmetry

bilateral symmetry

can be divided into similar halves along only one plane through anterior-posterior midline. Animals with bilateral symmetry typically show: well-developed central nervous systems. cephalization:the concentration of sense organs, nervous control, etc., at the anterior end of the body, forming a head and brain, both during evolution and in the course of an embryo's development.

Exoskeletons of arthropods evolved from which structures?

cuticles

Bacteria

distinguished by shape, growth environment, cell wall structure (gram stain), metabolic pathways, and genes nearly all bacteria contain peptidoglycan-cross-linked polymer- in cell wall bacterial biolfilms

arthropods

ecdysozoans have thick cuticles that function as exoskeletons. The exoskeleton contains chitin and provides support for walking on land, and also prevents drying out. species with thin cuticles are restricted to moist environments paired appendages jointed appendages segmentation rigid exoskeleton for support and protection with muscles attached to inside insects= largest group or athropods

triplobastic embryo

ectoderm forms outer parts of the body such as skin, hair, eyes, mammary glands and the spinal cord. endoderm creates major organs such as the liver, pancreas, lungs and thyroid. mesoderm grows into skeletal muscles, bones, connective tissues and the heart and forms the kidneys and the dermis of the skin.

Where else is chitin found other than in fungi cell walls?

exoskeletons of arthropods

segmentation

facilitates specialization of body regions. Also allows animal to alter body shape and control movements precisely. Success of the arthropods was largely based on changes in a segmented body plan.

coelomate

includes humans

saprobic fungi

obtain nutrients from non-living organic matter (e.g. dead plants). Some are called molds. Saprobes are major decomposers on earth and critical to earth's carbon recycling.

dinoflagellates

protist mostly marine (oceans & freshwater); major photosynthesizers. ○ They are important primary producers, providing food for many species and much of the atmospheric oxygen. Major part of phytoplankton. ○ Most have two flagella some cause red tide

Gram-positive Bacteria

stain blue to purple - . The cell wall contains a single thick layer of peptidoglycan, which causes a purple Gram stain.

Ascomycota

• Ascomycota include many multicellular members; a very diverse group that also includes many lichens. • Baker's yeast (Saccharomyces cerevisiae) is a single-celled member of this group.

Identify the three main lineages that comprise the opisthokont group on the tree of life

• Early in eukaryote evolution came the separation of bikonts and opisthokonts. • Bikonts gave rise to green plants and major protozoan groups, whereas opisthokonts are the common ancestors of fungi, animals, and choanozoans. • The Opisthokonta group contains protists (both free-floating and colonial) with one flagellum at some stage in their life history.

• Recognize the shared derived traits (synapomorphies) that distinguish the fungi.

• Fungi Are Most Closely Related To Animals & Choanoflagellates • Fungi are a clade • Absorptive heterotrophy Chitin in cell walls • dikaryotic condition is a synapomorphy of sac fungi and club fungi

Explain how endosymbiosis contributed to the evolution of eukaryotes.

• Mitochondria & plastids (and peroxisomes) were derived from bacterial lineages through endosymbiosis. Entire bacteria were engulfed by eukaryotes and evolved into mitochondria and plastids • Original function of mitochondria might have been to detoxify the O2 being produced by cyanobacteria. • Plastids enabled photosynthesis - engulfed bacteria eventually modified into organelles that aided in harvesting energy (from light), providing enzymes to breakdown things like cellulose, breaking down toxins Mitochondria originated from proteobacteria Chloroplasts originated from cyanobacteria

mycelium

• Most fungi are multicellular. The body of a multicellular fungus is called a mycelium. • The mycelium consists of many tube-like filaments called hyphae, which are used to absorb nutrients. • The mycelia of many fungi live underground, and can cover very large areas. • Mushrooms are spore-producing fruiting structures that grow above ground. The mycelial mass is often much larger than the mushroom.

Basidiomycota

• Some club fungi are saprobic and are important in the carbon cycle. • They also include some of the most economically damaging plant pathogens. • The fruiting structures include many mushrooms and also puffballs. This is where the spores are released.

Define what a protist is, and describe and recognize the unique features of particular protists that were discussed in lecture, including their influence on earth's ecosystems and humankind.

• The term protist is used to describe any eukaryote that is NOT a plant, animal or fungus. It does not describe a formal taxonomic group, but is a convenience term • Plankton- free-floating aquatic organisms • Phytoplankton- photosynthetic plankton • Autotroph- Get their carbon atoms entirely from inorganic matter (such as CO2) • Heterotrophs- Require organic compounds made by other organisms as their source of carbon • ALVEOLATES- are unicellular and have sacs called alveoli just below their plasma membranes • Plasmodium, a group of apicomplexans, are the causative agent of malaria. ○ Malaria is an infectious disease transmitted by mosquitoes that are infected by the protists; the mosquitoes transfer it to humans • Dinoflagellates produced toxins that killed shellfish, resulting in huge losses for the shellfish industry • Living Diatoms store oil as an energy reserve and to keep afloat. Over millions of years, diatoms have died and sunk to the ocean floor, ultimately becoming petroleum and natural gas. Their remains are a fossil fuel

Absorptive heterotrophy

• fungi secrete enzymes into their immediate environment to break down nutrients, and subsequently absorb digested nutrients back into their cells.

Where do virus's fit in the tree of life?

• not cellular • Viruses infect both eukaryotic and prokaryotic cells. • There is no defined viral clade • A common way to group viruses is based on their genome structure. Major distinctions are RNA vs. DNA genomes, as well as double-stranded vs. single-stranded genomes. (CONTAIN SOME SORT OF NUCLEIC ACID) • Viruses such as HIV (diagrammed below) are enclosed by a membrane and have surface proteins that enable the virus particles to bind and infect specific host cells. The viral membrane is often derived from the host cell by "budding."

diatoms

•protist Diatoms deposit silicon in their cells walls, which gives them their characteristically intricate appearance. ○ Soil composed of diatom skeletons = diatomaceous earth. ○ Diatoms are major photosynthetic producers in coastal waters and in fresh waters. ○ they perform 1/5th of all photosynthetic carbon fixation on earth, roughly the same as all of earth's rainforests combined ○ Tubular hairs on the longer of their two flagella remains are fossil fuel

parasitic fungi

○ Some fungi are parasites. For instance, they invade plant leaves in order to absorb nutrients. Hyphae are well suited to absorbing nutrients from living plants

pathogenic fungi

○ Some fungi are pathogenic, meaning they cause diseases. A fungal infection is called a mycosis. ○ Athlete's foot ○ Most people with AIDS die of fungal diseases Most of the important plant pathogens are fungi anti-fungal creams target specific cholesterol in fungi

Archaea

Archaea have ether fatty acid linkage

yeast

• Sometimes, fungi are found to be single-celled (unicellular). Single-celled fungi are called yeasts. • "Yeast" refers to a lifestyle, NOT a clade. Some fungal species have both uni- and multicellular life stages.

Briefly explain what evidence supports a close phylogenetic relatedness between choanoflagellates & animals.

• The common ancestor of animals was probably a colonial flagellated protist, similar to existing colonial choanoflagellates and sponges. • Cells in the colony began to specialize for different functions. Coordination among groups of cells eventually led to larger, more complex animals. • Similarities between colonies of choanoflagellate protists and sponge choanocytes supports a close evolutionary link between choanoflagellates and animals

septa

• The hyphae of some mycelia are subdivided into smaller compartments by crosswalls (aka septa). Organelles can still move between compartments, however.

How can discrepancies between gene trees and organismal trees be minimized in the presence of LGT

• Use more than one gene to construct gene trees. (genes will be retained if they are helpful) • Analyze genes that are less likely to be retained by an organism even if the gene is transferred ("stable core genes" that are optimized to a particular species)

Chitin in cell walls

• a (modified) polysaccharide polymer that forms a main component of fungal cell walls and adds structure & rigidity. Chitin itself is NOT unique to fungi, but its presence in cell walls is.

biofilms

• cells bind to a solid surface and secrete a sticky polysaccharide matrix that traps other cells. • Can form on any surface, including contact lenses, artificial joint replacements, metal pipes, etc.