Biol221 - Organismal Biology

Introduction to Organismal Biology (BIOL221) - Dr. S.G. Saupe; Biology Department, College of St. Benedict/St. John's University, Collegeville, MN 56321; ssaupe@csbsju.edu; http://www.employees.csbsju.edu/ssaupe/

Top Five Lists

General: The following lists represent the key topics for each of the major units that we covered during the semester. These lists are essentially typed directly for the lists that you turned in to me. In a few cases, I revised them slightly. Note - these lists should provide a good summary of some important topics that we covered during the semester. However, there may be some topics not included.

Surface/Volume Ratios (Trang)

Be able to define surface area (outside, skin), volume (interior, guts), and surface-to-volume ratio (proportion of outside to the inside (=SA/V)
Surface area increases by the square of the linear dimension while volume increases by the cube. Therefore, as something gets bigger its S/V decreases.
Exchange with the environment occurs through SA, and therefore it must be appropriate for an organism�s volume and needs.
S/V ratios are an important factor in the evolution of organismal/cell shape and S/V also sets a limit on scaling/size
S/V ratios also determine metabolic rates.
Surface area is the amount of an object that is directly exposed to the environment. The unit for surface area is expressed in squared units.
Volume is a rough measure of the size of a structure and the amount of space it occupies. The unit volume is expressed in cubic units.
The surface-to-volume ratio refers to the amount of �skin� compared to the amount of �guts.� To calculate, take the surface area divides by the volume.
To get larger, an organism can either increase the size of its cells or increase the number of its cells.
Gut shape and length are a function of S/V ratios.

Plant Form & Function (Reema)

Plants have three main vegetative organs � leaves, stems, roots (Roots, stems and leaves. (Roots: taproot, lateral roots, adventitious roots, root hairs; Stems: nodes, internodes, axillary bud, apical bud, apical dominance; Leaves: leaf, blade, petiole)
Three main types of cells and their characteristics (parenchyma -- can divide, and perform synthesis and storage; collenchyma-- uneven walls, support the young and growing parts of a plant; sclerenchyma (fibers and sclerids)-- thick walls for supporting mature parts of the plant that will no longer grow.
Four major tissue types � meristematic, vascular, dermal, ground.
Meristems can be primary or secondary, and include apical meristems, pericycle, cork cambium, and vascular cambium; primary vs. secondary growth
The characteristics of a plant are: photosynthetic autotrophs, walls of cellulose, immobile, multi-cellular, eukaryotic.
Zone of cell division, zone of elongation, zone of differentiation.
Analysis of a twig-- Apical bud, bud scale, axillary buds, leaf scar, bud scar, node, inernode, last year's growth, etc. Be able to recognize these and use them to estimate how old it is.

Animal Form & Function (Caitlin)

Animal form & function is a product of evolution
Form & function involves evolutionary �trade-offs� � constraints on adaptations
Homeostais � maintenance of relatively constant steady state
Correlation between form and function
Hierarchy of organization of cells to form tissue, organ, and organ systems stuck together by gap junctions, anchoring junctions and tight junctions.
Four kinds of animal tissues: (a) epithelial tissue - covers the body and lines organs, cavities in the body, for lubrication, secretion, diffusion, absorption, transport, protection, support; (b) connective tissue - binds and supports other tissues and includes cartilage, tendons, ligaments, blood, bone, adipose tissue; (c) Muscle tissue � for movements, three types (Skeletal- voluntary, fibers, striated, long cylindrical cells, Cardiac- involuntary, fused at ends, striated, Smooth- involuntary, tapered, spindle shaped, in blood vessel walls, stomach, bladder); (d) nervous tissue - transit signals and sense stimuli, consists of neurons
Homeostasis: maintain internal conditions relative to external conditions such as regulating blood pH, body temperature, blood glucose, and stomach acidity
Control systems: ways to maintain �set point� through a signal, sensor, integrator, effecter, and response to bring about either positive or negative feedback for the system.

Thermoregulation (Taylor & Taylor)

Thermoregulation - maintaining internal temperature within a tolerable range
Heat exchange occurs by conduction, convection, radiation, evaporation
Countercurrent Exchange - flow of adjacent fluids in opposing directions that maximizes transfer rates of heat or solutes.
Circulatory Adaptions include vasodilation (increase in diameter of blood vessels near the body surface) and vasoconstriction - reduces blood flow and heat transfer
The hypothalamus is the sensor for thermoregulation, which is located in the brain. The hypothalamus functions as a thermostat which responds to body temperatures outside of a normal range by activating mechanisms that promote heat loss or gain.
Cooling mechanisms � sweat, blood vessels in skin dilate; warming mechanisms � blood vessels in skin constrict diverting blood from skin to deeper tissues, shivering
Endotherms (regulators) & ectotherms (conformers).

Animal Nutrition & Digestion (Sarah)

Animals are heterotrophs and they have different methods of getting their food: suspension feeders, fluid feeders, and bulk feeders (humans)
The general sequence of nutrition processing is: ingestion--> digestion-->absorption-->elimination
Structure and function of the digestive tract (=Square dude)
4. Food moves through the gut via peristalsis. There is a high pressure behind the bolus, a low pressure in front of the bolus, and a rhythmic contraction to push the bolus along. (golf ball in hose!)
Digestive enzymes � know location and functions of main ones (proteases, lipases, nucleases, amylases)
Compare and contrast nutrient types on plants and animals (complexity, type, concentration in environment, localization) Or, why did animals develop a digestive tract?
Note functioning of stomach, small intestine, large intestine

Plant Nutrition (Mac)

Macronutrients; carbon, hydrogen oxygen (major 3), nitrogen, potassium, phosphorus, calcium, magnesium, sulfur. Micronutrients; iron, chorine, zinc, manganese, molybdenum, boron, copper, manganese, nickel. (CHOPKNS caf� Mighty good, Closing. Mob Coming with Machines)
Nitrogen Cycle: Ammonification - organic nitrogen via bacteria to ammonium. Nitrogen fixation - N2 via lightening/bacteria to ammonium. Nitrification - Ammonium via bacteria to nitrates. Denitrification - nitrates via bacteria to N2
Fertilizer: N-P-K (nitrogen, phosphorus, potassium). Phosphorus outlawed in MN
Mycorrhizae: symbiotic fungi. Endo - penetrates root, ecto - coats root
Other ways : holo-parasite; hemi-parasite; epiphytes; mycotroph; carnivorous plants.

Gas Exchange (Meghan)

Know the equation that relates photosynthesis and respiration
Know the difference between bulk flow and diffusion
What is Fick�s law?
Compare and contrast positive and negative pressure breathing
What are the components of the hemoglobin and relate to the Bohr effect.
Partial pressure

Circulation (Molly & Keshia)

Heart chambers and circuits have increased evolutionarily
Comparison of the closed and open circulatory systems
SA & AV nodes provide electrical activation for heart function & cardiac cycle
Route of blood flow in mammals Vessel physiological composition, set-up flow, characteristics
Relationship of pressure and blood flow; flow rate is inversely related to diameter; force of walls=blood flow*resistance; Artery > veins; Systole < diastole
Form & function of the circulatory system (e.g., parts of heart & function)
Functions of animal circulatory systems include: Transferring nutrients, Maintaining fluid balance and pH, Removes waste, Immune defense, Heat distribution, Homeostasis

Plant Transport (Alyssa, Ben)

Water potential refers to the energy state of water and determines the rate and direction of water movement
Route of movement of water from the soil to the stele; water can cross the cortex through the symplast or apoplast, but minerals move through the apoplast then across the selective membranes of the endodermal cells.
Mechanism of phloem transport
Bulk flow (cohesion-tension) hypothesis explains water transport to the leaves
Stomata control water loss from the leaf
Root pressure - created by endodermis not allowing apoplastic entry to stele
Phloem transport sugar
Short distance transport occurs by diffusion or active transport and long-distance transport by bulk flow.
Water and minerals absorbed by roots are transported by xylem
Transpiration
Sugars transported from leaves to site of use (source to sink)

Hormones (Alex)

hormones active in low concentration
hormones have a target remote from site of synthesis/release
some hormones enter the target cell and bind to receptors directly to change gene expression, others bind to receptors and use secondary messengers to convey the message to the gene being transcribed/translated
general response scheme: hormones � receptor � amplification � ranscription/translation/etc � response
requirements (four) to identify a hormone
GA and flowering in corn cockle
Steroid Hormone action (Lipid Soluble) vs. Water Soluble Hormone action
General chemical structures of a hormone

Neurons (Jon & Laura)

Parts of a neuron: dendrites � short, highly branched, receive signal and carry it toward cell body; axons � long, carry signal away from cell body, terminal branches; cell body � large section, contains the nucleus and other goodies; myelin � lipid coating derived from membrane of Schwann cells, acts as a kind of insulation; Nodes of Ranvier � gaps between Schwann cells; synaptic terminal � end of the axon, junction with another neuron or effector
3 types of neursons: sensory, interneuron, and motor neurons and how they differ
Membrane/resting potential and the role of sodium / potassium pump
Gated channels and pumps
Phases of an action potential - depolarization, the rising phase, peak, falling phase, undershoot, and resting potential Resting, Depolarization, Repolarization, Undershoot
Know how neurons communicate with each other via electrical current flowing through a chemical synapse, involving neurotransmitters that bind to post- synaptic receptors
Electrical vs Chemical Signaling

Vertebrate Nervous System (Jimmy)

Nervous systems consist of circuits of neurons and supporting cells
Central nervous system = Brain and Spinal Cord; Peripheral nervous system=cranial nerves, ganglia outside CNS, and spinal nerves
Cerebrospinal fluid - fills the ventricles and the central canal
Grey matter vs. white matter
The vertebrate brain is regionally specialized into forebrain, midbrain, and hindbrain
Brainstem consists of pons and the medulla
Cerebellum - coordinates movements and balance

Immunology

Animals have three lines of defense against invaders (barriers/moats � the first line, innate, acquired).
There are three types of leukocytes involved in wound response/healing (mast cells � release histamine, macrophages � phagocytes, signal other immune cells; neutrophils � phagocytic, release oxidizers
When tissue damage occurs, platelets, mast cells, and phagocytes respond and work together to heal the tissue
The major histocompatibility complex (MHC) consists of a group of genes that code for marker proteins on all nucleated cells (MHCI) and immune system cells (MHCII).
Antibodies are a result of acquired immunity that recognize one specific antigen and eliminate invaders by binding to it and: neutralizing it directly or targeting it for elimination by the complement system (proteins) or phagocytes
Lymphocytes are an organism�s final line of defense and include antibody producing cells (B cells) and T cells.
Humoral response - circulation of free antibodies; destroys free (not inside a cell) pathogens; extracellular. Named because it is associated with the "humors" (blood);
Cell-mediated immunity - destroys cells containing intracellular pathogens (and transplanted tissues, cancer cells)

Sensory Systems (Jordan, Dan)

Basic scheme of sensory system response (receptor, transduction, amplification, transmission, integration, response)
Structure and function of the ear (the basic pathway that sound travels through the ear and into the brain)
Structure and function of the eye
Receptor types � Photoreceptors, Chemoreceptors, Thermoreceptors, Mechanoreceptors, Nocireceptors

Muscles (Kelsey)

Muscle types (smooth, skeletal, cardiac)
Muscle structure (fibers, myofibrils, sarcomeres, sarcoplasmic reticulum, t tubules)
Muscle function (actin, myosin, troponin, tropomyosin, Ach, t-tubules, sarcoplasmic reticulum, calcium
How an action potential allows for release of acetylcholine which in turn helps calcium in its role for muscle contraction.
The three energy sources for muscle contraction- ATP, creatine phosphate, and glycogen
Three types of muscle cells- Skeletal (voluntary movement), Smooth (involuntary movement), and Cardiac (involuntary contractions- found in heart)

Sensory Systems in Plants (Jenny, Kolby)

GA stimulates aleurone layer to undergo transcription & translation to produce amylase that breaks down starch into simple sugars. ABA, on the other hand, inhibits amylase production.
Little seeds commonly have light-triggered germination. Red light triggers seed germination while far-red light inhibits germination. If a seed is treated first with red light and then with far-red light, the seed will not germinate. However, if the seed is treated with far-red light and then with red light, the seed will germinate.
Phytochrome is the light receptor in plants. It can exist in the red from (Pr) and the far-red form (Pfr). Pr is converted into Pfr when exposed to red light and Pfr is converted into Pr when exposed to far-red light.
Etiolation is the term used for plant morphological adaptations for growing in darkness. Characteristics of a plant growing in the dark are as follows: no chlorophyll (they are white), elongated internodes, unexpanded leaves, and an apical hook. Theses features are nature's way of conserving energy.
Gravitropism � plant response to gravity; mMechanism for gravitropism (signal � receptor � transducing mechanism � response). Gravity acts as the stimulus. Statoliths, a type of amyloplast located in the root cap, are the receptors of this stimulus. The statoliths sink in the columella cells in response to gravity which causes auxin to migrate. High auxin concentrations in the stem activate growth, while high concentrations of auxin in the root inhibits growth. When cells elongate on only one side, they bend. Roots bend down while stems bend up.

Kidney & Osmoregulation (Kayli, Nick)

Sodium/potassium pump
Form & function of the kidney (Headphones dude, filtration dude, Bowman�s capsule)
Osmoregulation and why it�s important
Function of a nephron � (a) filtration - fluid is forced across epithelium, any molecules (except very large) will move across membrane (nonselective); product = filtrate; (b) secretion - selective process of dumping extra materials into filtrate (into nephron) via passive and active transport; (c) Reabsorption � reclaiming materials from filtrate (nephron to interstitial fluid)
Kidney Regulation. Low blood pressure - renin converts angiotensinogenin to angiotensin which increases thirst, increases water intake and raises blood pressure. High blood pressure - atrial stretch receptors cause atrial naturietic hormone to cause kidney to decrease sodium reabsorption which decreases water reabsorption, then blood volume and finally blood pressure

Reproduction � General (Katie)

Asexually vs. sexual reproduction
Asexual reproduction can happen through budding, parthenogenesis, or fragmentation/fission and produces clones of the parent
Sexual reproduction is advantageous because it creates individuals with different genes than the parents, aka genetic diversity
The basic sexual lifestyle begins with an adult (2n) then meiosis which produces gametes (n) which are fertilized to produce a zygote (2n) which develops into a embryo and later an adult
There are exceptions to both asexual and sexual methods of reproduction (or in Steve's words, "kinky sex")

Plant Reproduction (Maggie & Amanda)

Floral structure and function (parts of flower and their function)
double fertilization
sexual vs. asexual reproduction
seed structure & function
pollination � anther to ovary & the steps involved
Fruit -- derived from ovary; the function of fruit is seed dispersal.
alternation of generations (gametophytes, female & male; sporophytes)
The female gametophyte develops from one of the four megaspores produced in the ovule by meiosis. The male gametophyte, a 2-nucleate pollen grain, is produced when a microspore in the anther undergoes mitosis.
The pollen tube follows a gradient of calcium ions, or GABA, to deliver the sperm to the ovule, where it can fertilize the egg.

Animal Reproduction (Katie, Sarah)

sexual life cycle including meiosis & fertilization
form & function of the female reproductive system (ovaries, oviduct, uterus, vagina, vulva, mammary glands)
female reproductive (menstrual) cycle (The hypothalamus releases GnRH to stimulate the pituitary gland to release FSH and LH. These hormones move to the ovary where it stimulates the growth of a follicle to produce estrogen. Progesterone spikes and stimulates large production of LH. LH starts ovulation in which the follicle collapses and becomes corpus luteum. Progesterone shuts off hypothalamus to wait for fertilization. If no pregnancy, corpus luteum disintegrates, hypothalamus turns on, and FSH and LH production starts� cycle repeats.
form & function of the male reproductive system (Seminal vesicles contain the food necessary for sperm while the prostate produces a fluid to reduce the pH of the vagina. Bulbourethral gland makes fluid to lubricate penis and urethra, and the vas deferens holds the sperm while it matures and then the epididymis is a holding tank for the sperm for maturation. This ultimately produces semen which contains the sperm to fertilize the egg)
Contraceptive methods (e.g., NFP, barrier methods, hormonal methods, vaccine)
Human Gametogenesis: Spermatogenesis and Oogenesis
Fertilization will not happen if there is defective sperm or there�s a hostile environment in the vagina. The female reproductive system attacks some of the sperm and sometimes the not so smart sperm swim up the wrong oviduct and try to fertilize a nonexistent egg. Other sperms get stuck in the oviduct and there isn�t any mucin to propel and help the sperm swim upstream.
Natural family planning is one way to plan pregnancy. This is done by counting days, checking cervical mucus, measuring basal body temperature
Barrier methods prevent the sperm from entering the uterus/cervix. These include the condom, diaphragm, sponge, and suppository. All of these methods can be used with spermicide to kill any wayward sperm. Oral contraceptives are also effective for the women. The �pill� along with Norplant and Depo-Provera also work by adding hormones to your body to alter the release of other hormones to prevent pregnancy. Douche is used to clean the vagina of sperm, but is very ineffective. Sterilization, tubal ligation and vasectomy, is a permanent type of contraceptive that in women can�t be reversed, but in men can sometimes be reversed. Plan B and Ru486 are morning after pills that cause a women to shed the uterine lining, menstruate, and therefore prevent pregnancy. Withdrawal is a poor choice too because it is ineffective and, besides, some semen still leaks out before ejaculation.
The follicular phase occurs from Day 1 of a women�s cycle to day 14, give or take, and the luteal phase happens from day 14 of a women�s cycle to day 28, give or take depending on the women�s natural cycle length. Day 1 is the first day of bleeding and day 14 is when ovulation begins, which is indicated by a spike in basal body temperate. If a women gets pregnant a hormone call HCG will be present and is detected by home pregnancy tests.