Lab Ex 6:  6.1: image, another

                 6.4: M =                  108        88  74    64                         26
                        C =                  108 106               64       56               26
                       W =      134             106               64       56
                        X =      134                          74    64 62                     26
                        Y = 138           108                                56     32       26
                        Z =             110              88     72     62                 28 

Who is the father?

Lab Ex 7
The genetic code is written as:  either  DNA > amino acid,  or  mRNA > amino acid
Note that:  DNA:  ATG (start) > methionine;  & mRNA:  AUG (start) > methionine, etc.

But the mRNA is the complement of DNA,
So it must be the non-coding side of DNA that is transcribed (complemented) into mRNA

Lab Ex: DNA        TATAAA ATG   "coding" starts at ATG
DNA complement  ATATTT TAC    "non-coding" but complements the mRNA
mRNA                                            AUG   start codon methionine
Protein selected                      met 

Protein folding & wiki

A. Ex 2.1 Enzymatic Breakdown of Collagen, Collagenase
Bromelin/Bromelain is several enzymes, extracted from pineapples, that hydrolyse proteins, including collagen - a fibrous protein in the extracellular matrix of many animal tissues (so bromelin is used as a meat tenderizer).  Pineapples are bromeliads - thus was the extract named.  Bromelin also has anti-inflammatory properties & is used to treat arthritis, this may not be related to the fact that it is a protease.

B. Experiments with Membranes
6.1 Lipid solubility of cell membranes:  Membranes are mostly phospholipid bilayers plus proteins.  Being lipid they are more soluble in more non-polar solvents.  If beetroot cells are placed in a set of alcohol solvents, the more the solvent is non-polar the quicker it will dissolve the plasma membrane, and let the red color leave the cells. 
6.2 Osmosis: Because cells cannot prevent water from crossing the plasma membrane they act as osmometers: if placed in a more salty solution than themselves they loose water & shrink (the salt outside sucks), but if placed in a less salty solution than themselves they gain water and swell.  Plant cells contain a large vacuole isosmotic (same osmolarity) with the cytoplasm.
6.3 Pinocytosis: A few living cells gain water by ingesting it in a container (vacuole).  Amoeba can put a dye in water.  If the dye enters the amoeba it must have "drunk" it, as the molecule is too large to enter by diffusion.  Requires live amoeba.

(Ch 4)
Ex 2.2 Mitochondria, & Cell Organelles: their size does not matter, only their appearance in different cells

• Paramecium (unicellular):  image, draw, & label organelles here, images
  
• Euglena (unicellular):  image,  draw, & label organelles here. images
  
• Spyrogira (unicellular, but cells are like beads):  images, scroll to #5, draw cell & spiral chloroplast, euglena & spirogyra
  
• Onion Root Tip: draw a cell & label cell wall & chromosomes,  images,  image,
  
Trachea:  images, draw cell with nucleus & cilia, & goblet cell (GC) filled with mucus (no cilia) & scroll to first image 

• Mitochondria: Skip as done in Ex 2.2 in onion, mitochondria (tiny, NOT green), chloroplasts, leucoplast, plant cell details,
  
• Dicot Leaf x.s:  draw cell with chloroplasts & vacuole (in palisade cell layer in leaf the chloroplasts lie just inside each cell)
  

New Healthy Food Pyramid, Old Unhealthy Food Pyramid

E. coli..bioindicator (see water purification).  Salinas valley is at risk as farming is industrial: land never rests & pesticides are used at all stages of the plant life cycle.  Workers must wear protective clothing: Salinas valley, workers, another, artichoke, Steinbeck

Least Favorite Places:
Dirty or smelly place (motel, campground, city, farm, industrial site, water treatment plant) 20, Gary 10, boring store (in tow: father or boyfriend - just say no) 8, restaurant (food) or job in fast food 8, overcrowded place includes cities & states 7, another state (boring or ?) 5, specific stores 6, hospital 2, desert, Mammoth Cave, Pine Lake, 6 Flags, polluted lake, jail, previous college, apartment, Iraq, Caribbean island.  So: many different choices, most include human activites being inadequately monitored?
Most Favorite Places:
Local beach or improved natural area, includes parks 25, distant developed natural area like Yellowstone 18, big city 8, another country 8, theme park 5, small town 5, library, elem. school, baseball field, night sky, skyscraper.  Mall 0!, wilderness 0.  Safe natural areas won but maybe lecture influenced result?  I was expecting more unatural choices!  FL State Parks..springs..

Ex: Pond Watch: 
print & print 91 & 92..color photos..key...Riverwatch...IN data..water quality edu..resource.
This exercise is intended to complement last week's exercise, 15.4, in which you learned to use some aspects of water chemistry & clarity to decide if a lake is eutrophic.  A eutrophic lake has too many plant nutrients & too much biomass whose decomposition causes lack of oxygen.  These conditions also determine who can live in the lake.  All in the following Riverwatch table are benthic (bottom)-living organisms, so some are in the laval stage. 
Data are for 8 AM, 10 AM, 1 PM labs: I collected water, weeds & bottom muck at three different shoreline locations:

Group 1: need most O2	Group 2	Group 3	Group 4: need least O2
stonefly: 1,5,3	damselfly: 1,3,1	midges: 4,1,3	left hand snail: 0,0,1
mayfly: 2,4,1	dragonfly: 6,1,2	blackfly: 2,0,3	worms: 6,1,7
caddisfly: 1,0,3	sowbug: 1,0,0	planaria: 2,0,3	blood midge: 1,0,3
dobsonfly: 0,0,3	scud: 1,2,3	leech: 0,0,2	rat-tail maggot: 3,0,0
riffle beetle: 4,3,1	cranefly: 0,0,5
water penny: 9,17,9	clam/mussel: 0,3,3
right hand snail,0,0,2	crayfish: none

Also found were many organisms listed in this pond key, because the key includes all organisms, not just those living on the bottom.   Their pollution tolerance is not on the key (but probably on the www): backswimmer, water boatman, 23 water mites, 13 springtails, 13 tadpoles, hydra, water strider, water flea, 5 cyclops or copepod, 5 mosquito larvae or pupae, pouch snail, 2 threadworms, shrimps, giant water bug, phantom midge larva, diving beetle larva, midge larva soldierfly larva

The pond provides habitat for all four groups of organisms, even quite close together.  Perhaps microhabitats are the explanation - when I sampled I mixed pond layers & adjacent areas - (wiki-habitat, restoration, fragmentation, creation).

Ex.15.5
Bioaccumulation/magnification..tuna biomagnify 100,000 x (five trophic levels)..humans..lesson..farmed fish..

Ex 15.4 Compare two lakes: for Eutrophication
these have the data (see table below & lab book) that you need:
MN; Ice (no Chlor.), Shagawa, Grindstone (no Chlor.), Independence (no Chlor.), Minnetonka (no Chlor.)
NY: Otisco, Onondaga very built up, George (no Chlor.),
NV: Mead: ONLY use Las Vegas Bay as it has shallow depth data, but a river flows through Mead, does this matter?,                
WA: Washington, Sammamish

For each (2) lake, click real time data, select weekly, & HTML. 
For two days: one mid-July, one mid-August, as high chances of eutrophication, record the information in the table:
Record at surface, isf available, & @ depths of about 5 m., ~10 m., & ~15 m.:
Date & temperature, Chlorophyll ug/L, Turbidity NTU, & dissolved Oxygen in both mg/L & % saturation
Describe each lake/environment & discuss the data - as your laboratory book requests

Lake / depth	July: temp. & depth	Chlor. ug/L & Turb NTU	dO mg/L & % sat.............	August: temp, Chlor., Turb., dO., & % sat...................
Name: 0 - surface 5 m. depth 10 m. 15 m.
Name: 0 surface 5 m. depth 10 m. 15 m.

Ex 14.1
Several students asked if wolves ate beaver?,  grass regrows quickly but aspen more slowly, the PM lab wolves kept one elk alive, what to do with an elk which survives and reproduces but is then killed - the baby should survive?,
14.4 please do it (grades not tabulated): on wall near lab are nw IN posters: Ice Age Mammals & Ecosystems

Ex 15.1
p 169: folded sheet is 0.2 mm
p 171: Table 2: Population Size = No,  r = (b - d) / 1000 
p 172: r = (b - d + m) / 1000

Only follow the populations of two countries over ten years, and for the remaining parts of the exercise.

p 173: r (act) = r (intr) (K - N) / K, & you can make extra columns in Table 8: for K-N and for Popn. Change = r (act) * No
p 174: N1 = No + change, change = r (act) * No         (* means multiplied by, No is N subscript o)

In the logistic growth part, part C: it would be clearer to continue following the two countries but place a limit on their population, and see what happens to the growth rate as the limit is approached (scroll for a calculator)

Ex. 1
Four conditions are needed: no wash, water wash (not in the lab book), soap wash & antiseptic soap wash.  But the lab book sets up the experiment in a good way: each student swab one hand, then wash hands, then swab again.  That people vary in the amount of bacteria on their hands matter less.  In looking at plates, sometimes impossible to decide # of colonies, as they have grown together.

No wash: 249,35,39,25,,7//22,210,13,196,11,100//35,125, 20,17,354,4:      mean 86.0, s.d. 102      95% c.i.: 86.0 +/- 199
Water:     176 12 10 99 36 19 25 114 27 21 9 205 32 126 17 264 11 18:     mean 67.8, s.d.  76.0     95% c.i.: 67.8 +/- 149
Soap:        86 45 320 9 169 25 31 66 124 192 188 52 6 23 3 1 15:              mean 79.7, s.d.  87.3     95% c.i.: 79.7 +/- 171
Antiseptic: 23 90 0 104 5 177 8 30 21 17 129 300 20 84 19 53 15 98:         mean 66.3, s.d.  74.7      95% c.i.: 66.3 +/- 146

95% confidence intervals: scroll "To calculate a 95% confidence interval for a normal distribution: mean 70 & s.d. 10: multiply 10 by critcal number 1.96 (= 19.6). Then subtract 19.6 from 70 for lower limit, i.e. 50.4, & add 19.6 to 70 for upper limit, i.e. 89.6.  So c.i. is 50.4 to 89.6, i.e. 95% of the items that contributed towards this normal distribution lie in the region 50.4 to 89.6."