BIOL 371 MIDTERM 1

BIOL 371 Midterm 1 UofC

THEME 1

What is an organism (2)?

The living world can be organized hierarchically - organism is one level in this hierarchy

An organism can consist of a single cell or multiple cells

Define the domains of life

The major divisions of the living world are defined by cell characteristics (morphologically look similar, which is why it comes down to a cellular basis)

What are the 3 domains of life?

Bacteria, Archaea, Eukarya

Lateral transfer was an important route for ___

The acquisition of evolutionary novelties

Major Characteristics of a Eukaryote (7)

1) Cytoskeleton

2) Endomembrane system

3) Primary genome of multiple linear chromosomes

4) 80s ribosomes

5) Mitochondria

6) Plastids (in algae/plants)

7) Sexual reproduction

• Provides diversity through gametes & fusion of gametes

Cytoskeleton Importance (3)

Protein fiber networks support plasma membrane and organelles within cytoplasm

Allows movement of organelles within the cell and maintenance of their spatial relationships

Allows cell to control its shape, and move

Components of Cytoskeleton (7)

*Purple interconnections are intermediate filament

Continuation of Cytoskeleton Importance

Enables eukaryote cell to engulf food particles (phagocytosis)

Microtubule (Composition & Function)

Hollow tube formed from tubulin dimers

• Thirteen tubulin dimers side by side in a microtubule

• Two types of tubulin dimers: α-tubules & β-tubules

• Polar: α-tubules (-) compose one end and grow slowly & β-tubules (+) compose the other end and grow quickly

Organize the position of organelles, direct intracellular transport, & support the shape of the cell by resisting compression

• Molecules (like vesicles) grab them and move on them like railway tracks

Intermediate Filament (Composition & Function)

An intermediate filament is a strong fiber composed of intermediate filament proteins

Build cable networks connecting the cells of epithelial sheets, and provide mechanical strength (resist tension) that allows the cell to maintain its shape

Microfilament (Composition & Function)

A double helix of actin monomers

Important in movement (site for myosin to grab onto and move), and intracellular transport

What are the cytoskeletal elements that allow cells to move or create currents? (2)

Cilia & Flagella

Cilia & Flagella (Composition, Function, & Examples)

Composition (same for both): Ring of microtubules wrapped in a membrane

Function (Flagella): Whip back and forth to propel a cell through liquid (propeller like motion)

Example:

• Sperm Cells - Swim by movement of the flagellum

Function (Cilia): Wave back & forth (like rowers)

Example:

• Cilia of a Paramecium - Coordinated beating of the cilia that cover the paramecium moves the cell through its environment

• Cilia in human airways - Cilia on the epithelial cells of the airway propel mucus containing debris out of the lungs

Eukaryote Endomembrane System (2)

Definition + 5 Major Components

Collective term for nuclear envelope, lysosomes, Golgi apparatus, vacuoles, endoplasmic reticulum

Definition: Series of flattened sacs and tubes formed of lipid bilayer membranes, directly interconnected or connected by moving vesicles

General Function of the Eukaryote Endomembrane System

To compartmentalize the interior of the cell to greatly increase available surface area for synthesis

• This is done by isolating incompatible biochemical processes, and transferring products between these compartments

Structure of Eukaryote (3) vs. Prokaryote Genome (2)

Prokaryote genome is a single loop of DNA

• Good for rapid replication, but gene regulation must be simple (everything is on the same structure)

Eukaryote genome divided between a number of linear chromosomes

• Allows for complex gene regulation

• Allows cell differentiation and the production of different tissue types

• Chromosome replication can take place in parallel

Mitochondria & Chloroplasts (2 + Definitions)

Neither of these is found in prokaryote cells, although there are prokaryotes that engage in oxidative phosphorylation and photosynthesis

Both greatly increase surface area available for these processes when compared to prokaryotes

• Folded up areas in a small volume

Mitochondria: Site of oxidative phosphorylation in eukaryote cells

Chloroplasts: Site of photosynthesis in eukaryote cells

Sexual Reproduction (2)

The fusion of two haploid gametes from two parents to form a new individual genetically different from either parent (vertical transmission)

Generates genetic diversity through independent assortment and recombination

Evidence For The Endosymbiotic Origins of Mitochondria & Plastids (6)

• Circular DNA

• Independent Fission: Remove mitochondria or plastids from a eukaryotic cell and it cannot produce new ones

• Size (1-10µm: bacteria sized)

• Double membrane

• Certain proteins specific to bacteria cell membrane are also in mito/chloro membranes

• 70s ribosomes

Primary Endosymbiotic Hypothesis (Part 1 & 2)

Heterotrophic eukaryotes evolved through union of ancestral archaean with aerobic α-proteobacterium, which became mitochondrion

Autotrophic eukaryotes evolved from heterotrophic eukaryotes through union with photosynthetic cyanobacterium, which became chloroplasts

The acquisition of mitochondria and plastids by primary endosymbiosis is a form of __

Lateral transfer

The two alternative scenarios for evolution of the final form of heterotrophic eukaryote cells:

Hypothesis 1) Ancestral archaean first evolved endomembrane system, then entered symbiosis with α-proteobacterium, which became mitochondrion

Hypothesis 2) Primary Endosymbiotic Theory Part 1

An All-At-Once Model (5)

• The endosymbiotic event that produced the mitochondria also produced the endomembrane system

• Archaea can’t engage in phagocytosis (cell wall)

• Outgrowth of archaean cell wall around adjacent symbiotic α-proteobacterium enclose them - they became mitochondria

• Archaean cell membrane becomes endomembrane system

• Alternatively, endomembrane system could arise from mitochondria vacuoles

Prokaryote ___ transferred to eukaryote ___

Genes

Nucleus

Secondary Endosymbiosis

Major eukaryote taxa arose as a result of symbiosis of heterotrophic eukaryote cell with an autotrophic eukaryotic cell

• 3 Independent occurences

• This process allowed photosynthesis to appear in lineages that did not initially possess primary chloroplasts

Cell Sizes

Cells are small - most have diameters in the 1-100µm range)

• Eukaryotic cells are generally much larger than prokaryotic cells

Surface Area/Volume Relationships - Cells

Cube-Square Relationship: Surface area & volume of a solid do not increase linearly with an increase in linear dimensions

• Surface area is proportional to (length)_²

• Volume is proportional to (length)³

• Surface area is proportional to (volume)^2/3

Define Constraining Relationship

Exchange across membranes around or within a cell is by diffusion or active transport (both only work effectively over very short distances & rates are dependent on surface area)

Critical limiting relationship in biology (this is why cells are small)

Cube-Square Relationship

The rates at which all materials enter and exit the cell are a function of its ___

Surface Area

The rate at which gasses and nutrients are used and wastes produced are a function of the cell’s ___

Volume

Small cells exchange materials ___ with their environment than large ones

More effectively

• To big of a cell will choke on it’s own waste and die

Endomembrane systems and increased internal surface areas of chloroplasts & mitochondria involve ___, allowing ___

Elaborate folding of extensive membranes

More scope for membrane-associated processes

• Allows eukaryotic cells to produce more energy & have greater synthetic scope (they can be bigger and more energetic than prokaryotic cells)

• This happens because more function of the ETC on the membrane allowing more energy overall to be produced (and more area for photosynthesis for chloroplasts)

Types of Multicellularity (2)

1) Simple Multicellularity

2) Complex Multicellularity

Simple Multicellularity (3)

Cell adhesion, cell-cell communication (less), structurally simple, no bulk flow

Most cells are in direct contact with the environment

Made up of multiple similar cells that are connected by adhesive molecules

Define Bulk Flow

Movement of fluids or gasses through channels, rather than cell-to-cell

Complex Multicellularity

Cells adhere, communicate, differentiate, and specialize (formation of tissues)

Origins of Multicellular Life (3 Theories)

1) Symbiotic Theory

• Separate species came together to form a multicellular organism

2) Syncytial Theory (e.g placenta)

• A single unicellular organism, with multiple nuclei, could have developed internal membrane partitions around each of its nuclei, and then specialized to form a new cell

3) Colonial Theory

• Multiple cells from the same unicellular species came together and specialized to become a multicellular organism

Reason For The Evolution of Multicellularity (3)

Cyanobacteria (The Great Oxygenation Event)

Rise in environmental oxygen levels due to photosynthesis advantage

• Gave selective advantage to possession of mitochondria and aerobic respiration, which permitted multicellularity (excess energy)

The Rise of Multicellularity (2)

Simple multicellularity appears at the end of the Great Oxygenation Event

Complex multicellularity appears with subsequent rise in environmental O2 levels

Origins of Multicellularity: Colonial Theory (5)

Most evolutionary models begin with flagellated unicellular organisms

• Choanoflagellates in the case of animals

Required that cells be able to adhere to one another

Required that cells divide up tasks, specialize

Required that cells learn to communicate with one another

• Affect one another’s behaviour, influence one another’s development, coordinate complex actions

Why Multicellularity? (3)

Unicellular organisms must carry out all functions of metabolism, homeostasis, reproduction, repair etc., with the resources of a single cell

Single isolated cells must deal directly with their environment

Unicellular organisms can’t get very big (cube-square relationship keeps cells small)

Selective Advantages of Multicellularity

Division of labour and economy of scale

• Bunch of cells in an environment means more effective (turned into large colonies to avoid predation & stayed large)

Increased size

• Avoid predation/eat larger things

• Exploit new environments (reach upwards)

• Storage

• Increased feeding mechanisms/opportunities

• Protected internal environment that can be regulated (reduces work needed in order to maintain homeostasis)

• Cells can specialize since internal environment is regulated (less expenditure of energy in order to maintain internal environment means leftover energy)

• New metabolic functions (bigger size means easier to retain heat - body temperature)

• Enhanced motility (self-actuated movement - expend energy to move yourself and structures to do such)

• Increased traction in wind/current (smaller organisms carried away by wind and/or water)

• Share information with other cells (more cells that make up the body means more elaborate communication between them - neural networks, cells for hormone secretion, etc.,)

Consequences of Multicellularity

Complexity

• Predator/prey and host/parasite interactions

• Increased opportunity for diversity in form/function & niches

Challenges of Multicellularity

Intercellular communication (cells must be able to communicate with one another)

• Diffusion

• Gap junctions/plasmodesmata

• Bulk flow

• Nerves

• Signalling molecules

Cell Adhesion (cells in a multicellular body must stick together)

Cube-Square Relationship

• Volume increases as a function of the cube of the linear dimensions with increasing size

• Surface area increases as a function of the square of the linear dimensions with increasing size

• As an organism gets larger, its surface area becomes smaller relative to its volume (or mass)

• Exchange takes place across surfaces

• Must create solutions to allow exchange and rapid transport

Structure & Support

• Physical laws set absolute limits on animal size & performance

• Morphology reflects accommodation with these limits, i.e. terrestrial animals can get only so big, aquatic animals require streamlining, small animals lose heat to the environment quickly, etc.,

• Challenges vary over animal body size range and habitat

Animals, Size, & Physics

Size range of animals is about 12 orders of magnitude

Surface Area/Volume Relationships: Metabolic Rate & BMR

Metabolic rate in mammals is measured by organism O2 consumption

O2 consumption increases with body size

• Resting elephant consumes more O2 in any given interval than resting mouse (200,000x mass difference)

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Basal Metabolic Rate (BMR) (rate at which body uses energy at rest) much lower for elephant than for the mouse

• The elephant has proportionally much less surface area for dissipation of heat than rabbit

• With greater body size, mass-specific metabolic rate must decrease

Adaptations For Increasing Surface Area (3)

1) Gas Exchange

• Gills bear lamellae, composed of flattened epithelial cells highly folded to pack greater surface area into small volume

2) Nutrient Absorption

• Villi of small intestine epithelial cells increase surface area for absorption, within a small volume

3) Filtration

• Body’s combined capillary beds provide extremely large cumulative surface area for exchange between blood & tissues

Challenges of Being Multicellular - Continuation

Homeostasis

• Defend cells against hostile environment

• Maintain stable internal environment for internal cells

E.g. The water content of a multicellular organism can be divided into two major compartments:

1) Intracellular Fluid (60%)

• The intracellular fluid compartment is all of the body’s water found within cells (liquid portion of cytoplasm)

2) Extracellular Fluid (40%)

• All of the body’s water not found within cell plasma membranes (Forms cells’ immediate environment: interstitial fluid, plasma, bone & dense connective tissue)

There is a lot of exchange (gasses, nutrients, waste, etc.,) between intracellular fluid & extracellular fluid, and so composition and volume of extracellular fluid must be kept stable to minimize the amount of work cells must do to maintain their own individual homeostasis

Reproduction & Growth

• The multicellular body must be able to produce new multicellular bodies

• Sex, fertilization, development, & growth

• Development & differentiation require complex & flexible control systems

Reproduction & Growth (Unicellular vs. Multicellular)

Unicellular

• Fission or mitosis (quick & easy)

Multicellular

• Fusion of gametes followed by growth & differentiation

Cell Adhesion/Cell Junctions (3)

Cells in multicellular bodies must be attached to one another or to an acellular matrix

1) Tight Junctions

• Penetrate cell membranes of adjacent cells, fix cells in place, prevent movement of liquids between cells

2) Anchoring Junctions

• Adjacent cells link to each other and intermediate filaments or microfilaments of cytoskeleton

• Provide a physical connection between cells of the body by reinforcing their cell-cell adhesion through direct association with cytoskeletal components of both cells

3) Gap Junctions

• Form channels between adjacent cells; penetrating cell membranes

• Signalling molecules & water can be passed directly from cell to cell; cells can thus communicate with one another

Tissues (3)

Group of similar cells & extracellular substances working together to carry out specific function for the organism as a whole

Requires that cells attach to one another & communicate with one another

Both plants & animals are organized at the tissue level

Tissues in Animals (2)

In triploblasts, four types of tissues, arising from three embryonic germ layers

The organs of multicellular organisms are composed of basic tissue types, specialized in structure & functions to carry out different tasks for the organism as a whole

Extracellular Matrix & Cells

Characteristic of animals

Basic matrix is acellular, penetrated by network of collagen fibres

• Varies greatly among different organisms and types of connective tissues

Collagen & Connective Tissues

Collagen is an extracellular fibrous protein found in connective tissues

• Unique to animals

• Collagen is the primary structural protein within connective tissues, providing strength, flexibility, and resilience

THEME 2: ANIMALS

Define Clades

Group of organisms with a unique common ancestor and sharing synapomorphies (shared derived characters/homologies)

• Can be more or less inclusive

Clade: Opisthokonts (Composed of (3))

1) Choanoflagellates

2) Animals

3) Fungi

Define Opisthokonts (3)

Opisthios - Single, posterior

Kontos - Flagellum

• Opisthokonts are characterized by the single, posterior flagellum and flattened cristae in mitochondria (but variable)

Choanoflagellates: Characteristics (3)

1) Unicellular opisthokont eukaryotes

2) Sessile

3) Reproduce asexually

What is the closest clade to animalia among opisthokonts?

Choanoflagellates

“Collar” around flagellum in choanoflagellates consists of ___

Contractile microfibrils

Define filter feeding in choanoflagellates

Currents set up by flagellar action carry food particles into collar, trapped and carried down to cell

What is the theory for the origins of animals (opisthokonts)?

Ancestral animal was descended from a colonial choanoflagellate

Animals: Characteristics (9)

1) Multicellular eukaryote

2) Chemoheterotrophic

3) Extracellular digestion

4) Cell membranes contact adjacent cell membranes (no cell walls)

5) Motile (self-directed movement)

6) Oxidative phosphorylation to supply ATP

7) Sense and respond to the environment rapidly

8) Sexual reproduction featuring eggs and sperm (single cells)

9) Diploid stage is dominant (usually), haploid is short-lived

4 diagnostic characteristics only found in animals

1) Develop from a blastula and undergo gastrulation

2) Cell membranes contain cholesterol

3) Certain extracellular matrix molecules (e.g. the proteoglycan collagen)

4) Certain cell-cell membrane junctions

• Tight/septate junctions

• Anchoring junctions

• Gap junctions

Archaeplastida: Plants (Characteristics (5))

1) Multicellular eukaryotes

2) Photoautotrophic (mostly)

• Fix inorganic carbon using light energy

3) Cell walls

• Cell membranes are not in contact

4) Sessile

5) Alternation of generations life cycle

• Haploid (gametophyte) stage alternates with diploid (sporophyte) stage

• Both are prominent/multicellular

Cell Structures in Plant Cells (3)

1) Cell wall

• Maintains cell shape

• Protects cell

2) Large vacuole

• Part of endomembrane system

• Produces turgor against cell wall

3) Chloroplast

• Fixation of inorganic carbon

Plants can “move” in 4 ways

1) Grow (up/down/laterally)

2) Phototropic

3) Move in response to physical stimuli

4) Disperse by pollen/seeds

Necessary correlates of requiring motility (can move themselves) (8)

1) Muscle

2) Well developed senses & cephalization (concentrated sensory and neural organs in an anterior head - looking forward)

3) Nervous system

4) Digestive system

5) Excretory system

6) Skeletal system

7) Locomotory organs

8) High metabolic rate (requires bulk flow & gas exchange systems)

___ is the science of classification of the living world

Systematics

Define Shared Derived Characters (Homology) (3)

• Character (morphological, behavioral, molecular) found in all members of a group of species, that is derived from a character found in the common ancestor of that group of species

• How useful homologies are in determining phylogeny depends upon how widely they are shared

• We must be careful to avoid using characters that are similar in different organisms, but were not derived from a common ancestor (convergent evolution)

The likeliest phylogeny is the one requiring the ___ in a character

least amount of proposed evolutionary change

In cladistic classification, we want to identify ___

monophyletic taxa (clades)

Ediacaran Fauna

• 635-541 MYA

• Uncertain affinities (some may have been identified as animals because cholesterol has been isolated from their fossils

Cambrian Explosion

Burgess Shale Fauna: 525 - 515 MYA

• First diverse fauna of large complex multicellular animals

• First recognizable representatives of most modern animal phyla

• First fauna with eyes & jaws

• First fauna with largely bilaterian component

Homeotic Genes (4)

Genes specifying the development of specific structures at particular locations during embryogenesis

• Responsible for symmetry, anterio-posterior, and dorso-ventral axes

• Appear to be strongly conserved among animalia

• Hox genes are a special class of homeotic genes

Changes in ___ and ___ may have enabled rapid diversification of body forms

Homeotic genes

Gene regulation

Cambrian explosion represents ___ in animalia

evolutionary radiation

• Rapid increase (high rate of speciation) in the diversity of one clade

Animal Classification: Phyla

An animal phylum is a major monophyletic group originally distinguished by a unique basic body plan

Define The 3 Major Symmetries of Animal Classification

Asymmetric: No major axis of symmetry (e.g. sponges)

Radial Symmetry: Body can be cut into identical pie segments; no right/left, anterior/posterior (e.g. jellyfish sea anemones, starfish, sea urchins)

Bilateral Symmetry: Body has mirror-image; left-right symmetry

Define The 2 Major Developmental Patterns of Animal Classification

Diploblastic: Two embryonic tissue layers, endoderm & ectoderm

Triploblastic: Three embryonic tissue layers, endoderm, mesoderm, & ectoderm

Define The 3 Major Body Cavities (coelom) of Bilateria

Acoelomate: No cavity enclosing the gut

Pseudocoelomate: Cavity enclosing the gut lined with mesoderm on outer side

Coelomate: Gut suspended in cavity lined with mesoderm on both sides

Two Divisions of Bilaterians

1) Protostomes

2) Deuterostomes

• Both triploblastic

Protostomes (3)

1) Spiral cleavage

2) Schizocoely

• Type of coelom formation that occurs during embryonic development, where the coelom forms by the splitting of the mesodermal tissue

3) Mouth derived from blastopore

Deuterostomes (3)

1) Radial cleavage

2) Enterocoely

• Mesoderm is formed in a developing embryo in which the coelom forms from pouches pinched off of the digestive tract

3) Anus derived from blastopore

Another morphological character used in animal classification is ___

Body segmentation

Metameric Segmentation

• Repeating

• Occurs in both protostomes & deuterostomes (chordates, arthropods, annelids)

• Dorsoventral orientation of central nervous system & the main elements of circulatory system

__ & ___ are now the primary source of information about phylogenies

DNA

Proteins

Phylum Ctenophora: The Comb Jellies (3)

• Diploblastic - biradial symmetry

• Sister group to all other animals (possibly)

• “Combs” are rows of fused cilia that are used in locomotion

Phylum Porifera (Sponges) (5)

• Assymetrical

• Parazoans (no true tissues) neither diploblasts or triploblasts

• Sessile as adults

• Choanocytes (very similar to choanoflagellates) coordinated flagellar action produces inward water currents

• Suspension Feeders: Choanocytes filter food particles out of water

Phylum Cnidaria (3)

• Radial symmetry (diploblastic)

• Jellyfish, sea anemones, coral hydra

• Life cycles generally incorporate both polyp & medusa stages

Polyp & Medusa Stages

Sessile formations are called polyps, whilst swimming forms are referred to as medusa. The difference between polyp and medusa is that polyp is a fixed, cylindrical structure that symbolizes the asexual stage. Medusa is a free-swimming, umbrella-like structure representing the sexual stage.

Cnidocytes & Nematocysts (2) + Definitions

• Shared derived character of Cnidaria

• Used to capture prey

Cnidocytes: Specialized cells that contain the stinging organelles located on the tentacles and other parts of cnidarians. Activated by touch or chemical signals, and when triggered release nematocysts to deliver a sting.

Nematocysts: Stinging organelles within cnidocytes that upon activation eject rapidly, penetrating the target and often releasing toxins to immobilize or harm the prey or predator.

Colonial Cnidarians (2)

• Species within the phylum cnidaria that live in colonies, where individual organisms (polyps) are physically connected and function together as a single entity

1) Siphonophores

• Colonial cnidarians composed of several different types of individuals, modified for different functions

2) Corals

• Colonial cnidarians that build calcareous or proteinaceous skeletons

Protostomes are divided into: (2)

1) Lophotrochozoans

• Some phyla have a “trochophore” larva (a type of free-swimming, planktonic larval stage with bands of cilia)

• Some phyla have a lophophore feeding structure (a crown of ciliated tentacles around the mouth, used for feeding)

2) Ecdysozoans

• Growth is through ecdysis of the cuticle or exoskeleton (acellular - secreted by epidermal cells)

Ecdysis: Moulting/shedding of the cuticle/exoskeleton

Lophotrochozoans: Phylum Platyhelminthes (3)

• Acoelomate (no cavity between the body wall and gut)

• Parasites and predators

• Gut has only one opening (acts as both mouth & anus)

Example: Flatworm

Lophotrochozoans: Phylum Mollusca (5)

• 100,000 species

• 1mm to over 18m

• Body organized into foot, mantle, visceral mass

• Unsegmented (but some evidence of earlier segmentation)

• Considerable morphological variation among major groups

Lophotrochozoans: Phylum Annelida (2)

• Metameric Segmentation

• Coelomate