Thursday, January 24, 2008
Cell organization, and viewing cells
Cells need mobility, sustainability, most cell sizes and shapes reflect their functions, and this is necessary for their homeostasis.
Ways of seeing:
Phase contrast takes advantage of variations in density within cells. the density variations alter certain regions of the cytoplasm to refract and bend light.
Conventional light microscopy doesn't allow assessment of live cells.
But can be very accurate and effective, especially with high quality slides.
Fluorescent microscopy utilizes location of molecules in cells. Fluorescent stains are molecules which absorb light energy at a particular wavelength and release some of that as a different wavelength.
Electron microscopes use electron beams, similar to how conventional microscopes use light. Where conventional microscopes use glass lenses, the electron microscope will utilize condenser lenses.
TEM- transmission electron microscopy
SEM- scanning electron microscopy
for TEM the specimen is suspended in plastic, which allows for extraordinarily thin slides, photographic plates.
for SEM the specimen is coated in gold or some other metallic substance, and is viewed as a solid.
Ways of seeing:
Phase contrast takes advantage of variations in density within cells. the density variations alter certain regions of the cytoplasm to refract and bend light.
Conventional light microscopy doesn't allow assessment of live cells.
But can be very accurate and effective, especially with high quality slides.
Fluorescent microscopy utilizes location of molecules in cells. Fluorescent stains are molecules which absorb light energy at a particular wavelength and release some of that as a different wavelength.
Electron microscopes use electron beams, similar to how conventional microscopes use light. Where conventional microscopes use glass lenses, the electron microscope will utilize condenser lenses.
TEM- transmission electron microscopy
SEM- scanning electron microscopy
for TEM the specimen is suspended in plastic, which allows for extraordinarily thin slides, photographic plates.
for SEM the specimen is coated in gold or some other metallic substance, and is viewed as a solid.
I'll karyote on homeostasis and organization further
Cell organization v. homeostasis
-cell homeostasis is where there is appropriate internal environment. The plasma membrane forms a cytoplasmic compartment, which maintains homeostasis by allowing cells to exchange materials with their environment. Organelles are internal structures which carry out specific functions which are often highly complex.
Electron microscopes have superior resolving power, which is often helpful in understanding the anatomy of cells.
Prokaryotes - have plasma membrane, little internal organization, usually cell wall, ribosomes, may have a propeller like flagella.
Eukaryotes- membrane enclosed nucleus, and a variety of organelles.
Three key functions of cell membranes :
Proteins- hugely important in cell membranes.
-cell homeostasis is where there is appropriate internal environment. The plasma membrane forms a cytoplasmic compartment, which maintains homeostasis by allowing cells to exchange materials with their environment. Organelles are internal structures which carry out specific functions which are often highly complex.
Electron microscopes have superior resolving power, which is often helpful in understanding the anatomy of cells.
Prokaryotes - have plasma membrane, little internal organization, usually cell wall, ribosomes, may have a propeller like flagella.
Eukaryotes- membrane enclosed nucleus, and a variety of organelles.
Three key functions of cell membranes :
- divide cells into compartments with specialized activities, in small areas of cytoplasm
- energy storage and conversion (electron transport chains, concentration gradients)
- concentration of molecules
Proteins- hugely important in cell membranes.
Wednesday, January 23, 2008
Pharma-ethics
This is an opinion piece, and should be evaluated as such, If you do not agree that is within your right, and I encourage any questions or comments you feel inclined to pose.
There have always been serious considerations necessary when working with pharmaceuticals and science. There are as many ethical questions as there are strategic/factual ones. When is a drug or treatment safe enough for human use, how do you conduct tests to determine that, and who should receive treatment. Because of the complex nature of the human body, it is necessary that many large-scale trials occur after tedious pre-trial testing. Even after well conducted research scientists cannot have enough confidence to know that there will be no adverse results. They cannot fully anticipate long term effects a drug will have, or how all people, especially pregnant women, young children, and elderly will respond. Prior to the age of consumer safety (for the interests of this post I will claim modern standards and practices were pioneered as late as Nadar's campaign against unsafe Chevrolet's) there were few limitations on what drugs, "patent medicines" and purported miracle cures could be distributed. Many of these drugs contained narcotic or addictive substances, or toxins. These drugs were often reckless and harmful, and in some cases, pure profiteering.
The trials, have three phases prior to a drug being ready for human use, and are intended to reduce the possibility of negative effects, like birth defects. These are generally accepted as a necessity in ethical treatment. The question in the opening paragraph, of who should receive treatment, and how, is mixed in with many religious and social themes. An example of this, would be how the majority of political leaders in the United States would see condemning Euthanasia as important, where many other places would not. Asking when terminal patients should be allowed to try experimental treatment is more than a matter of denying or permitting 'treatment.' There is a misconception about the nature of experimental trials, they are generally not intended to treat patients, instead, they are meant to see first and foremost if it is safe, and the nature of side effects if there are any. Later it is determinedd if the drugs are effective, along with this is the constant struggle with money, and profiteering like what happened with the patent medicines. Because of the necessary trial phase, drug development takes a lot of time and resources, and for this reason, people considering the ethical milieu of drug treatment must consider the interest companies have in skipping the research and selling experimental medicines, ad a buyer beware status. Companies might be tempted to do this, and this would be bad, because eliminating the interest and reward for long term research, combined with the low success even for drugs in Phase 2 trials, may result in stagnation of medical research.
After watching things like "Lorenzo's Oil" and looking at similar cases, I worry what will become of ethical cases like that. I am familiar to some extent with the policies of the Bush Administration and its policies with Bioethics. I look to the Presidents' bioethics Committee, which basically is a dog show, judging whose medical science is most westernized, and conservative. They found, for example, that the Netherlands was not acting in the interests of its citizens. At most the actions of this committee will reflect on policies allowed or disallowed in our country. They use their findings as evidence to support policies here, and because of our ethnocentrism, I worry it will limit legitimate science.
There have always been serious considerations necessary when working with pharmaceuticals and science. There are as many ethical questions as there are strategic/factual ones. When is a drug or treatment safe enough for human use, how do you conduct tests to determine that, and who should receive treatment. Because of the complex nature of the human body, it is necessary that many large-scale trials occur after tedious pre-trial testing. Even after well conducted research scientists cannot have enough confidence to know that there will be no adverse results. They cannot fully anticipate long term effects a drug will have, or how all people, especially pregnant women, young children, and elderly will respond. Prior to the age of consumer safety (for the interests of this post I will claim modern standards and practices were pioneered as late as Nadar's campaign against unsafe Chevrolet's) there were few limitations on what drugs, "patent medicines" and purported miracle cures could be distributed. Many of these drugs contained narcotic or addictive substances, or toxins. These drugs were often reckless and harmful, and in some cases, pure profiteering.
The trials, have three phases prior to a drug being ready for human use, and are intended to reduce the possibility of negative effects, like birth defects. These are generally accepted as a necessity in ethical treatment. The question in the opening paragraph, of who should receive treatment, and how, is mixed in with many religious and social themes. An example of this, would be how the majority of political leaders in the United States would see condemning Euthanasia as important, where many other places would not. Asking when terminal patients should be allowed to try experimental treatment is more than a matter of denying or permitting 'treatment.' There is a misconception about the nature of experimental trials, they are generally not intended to treat patients, instead, they are meant to see first and foremost if it is safe, and the nature of side effects if there are any. Later it is determinedd if the drugs are effective, along with this is the constant struggle with money, and profiteering like what happened with the patent medicines. Because of the necessary trial phase, drug development takes a lot of time and resources, and for this reason, people considering the ethical milieu of drug treatment must consider the interest companies have in skipping the research and selling experimental medicines, ad a buyer beware status. Companies might be tempted to do this, and this would be bad, because eliminating the interest and reward for long term research, combined with the low success even for drugs in Phase 2 trials, may result in stagnation of medical research.
After watching things like "Lorenzo's Oil" and looking at similar cases, I worry what will become of ethical cases like that. I am familiar to some extent with the policies of the Bush Administration and its policies with Bioethics. I look to the Presidents' bioethics Committee, which basically is a dog show, judging whose medical science is most westernized, and conservative. They found, for example, that the Netherlands was not acting in the interests of its citizens. At most the actions of this committee will reflect on policies allowed or disallowed in our country. They use their findings as evidence to support policies here, and because of our ethnocentrism, I worry it will limit legitimate science.
Tuesday, January 22, 2008
some living descriptions
Protista-
- unicellular eukaryotes, some multicelled forms
- cell sturcture simple to very complex
- some heterotrophs- protozoans
- some autotrophs- algae
- asexual repro, some both sexual, asexual
- motile, non-motile, sizes- most microscopic but some may be 100m in length
- cell walls
- ex. paramecium, amoeba, euglena, diatoms, volvox, dinoflagellates, plasmodium, trypanosomes.
- multicellular Eukaryotic
- chitin cell walls, hyphae for cell forms, Yeasts are ovoid cells
- heterotrophs (saphrophytes, parasites, mutualistic)
- many species show both sexual and asexual
- organisms range from microscopic to many meters in length
- Ex. morels, corn smut, yeasts, bread mold, mildews
- Plantae-multicellular Eukaryotes
- cellulose cell walls
- photosynthetic autotrophs
- sexual repro
- alternation of generations
- sporophyte
- gamophyte
- can be marine, freshwater, terrestrial etc
- starch as stored glucose
- chloroplasts
- vascular have xylem and phloem
- avascular ex: mosses liver worts
- Chlorophyll A.
- Multicellular Eukaryotes
- no cell wall
- heterotrophs
- typically motile
- zygotes formed
- glycogen
- invertebrates/vertebrates
three domains - detailed description
| Bacteria (eubacteria) | Archaea | Eukarya |
| Most bacteria (formerly monerans) | Methanogens | Protista |
| | Thermophiles | Fungi |
| | Halophiles | Animalia |
| | | Plantae |
|
| Eubacteria Bacteria | Archaea | Eukarya |
| Nuclear envelope | Absent | Absent | Present |
| Membrane bound organelles | Absent | Absent | Present |
| Peptidoglycan in cell wall | Present | Absent | Absent |
| Membrane Lipids | Unbranched Carbons | Some branched | Unbranched |
| RNA Polymerase (enzyme that reads DNA) | One Kind | Several | Several |
| Initiator amino acid for protein synthesis | Formyl methionine | Methionine | Methionine |
| Introns (non-coding genes) | Rare | Present | Present |
| Response to streptomycin, Chloramphenicol | Growth inhibited | Growth not inhibited | Growth not inhibited |
| Histones with DNA | Absent | Present | Present |
| Circular chromosome | Present | Present | Absent |
| Ability to grow at temps >100° C | NO | Some species | No |
Scientific Measure, Conversions
Basic Quantities
Length-meter (m)
Mass- gram (g)
Volume-Liter (L)
Time-second (s)
Temperature- degrees Kelvin (K)
Amount of Substance- Mole (mol)
Heat Energy- joule (J)
Electric Current- ampere (A)
Luminous intensity- candela (cd) Energy-joules (J) calories (c)
Prefixes
tera- T 10^12
giga- G 10^0
mega- M 10^6
kilo- k 10^3
hecto- h 10^2
deka- da 10^1
deci- d 10^-1
centi- c 10^-2
milli- m 10^-3
micro- μ 10^-6
nano- n 10^9
pico- p 10-12
femto- f 10^-15
atto- a 10^-18
Metric-English
1.00 in = 2.54 cm
1.00 kg= 2.20 lb
1.00 lb= 454 g
1.00 L= 1.06 qt
1cm3; (1cc)= 1 mL
1 fluid ounce = 29.6 mL (cc)
K= C+ 273
C= 5/9 (F-32)
F= 9/5 C+ 32
Kelvin and Celsius have 100 degrees between freezing and boiling, where Fahrenheit has 180.
the freezing and boiling points in degrees for
Kelvin 273, 373
Celsius 0, 100
Fahrenheit 32, 212
Example Problems
1)an epithelial cell has a diameter of 63.5 microns (μ)
a) express the diameter in meters
63.5 μ or 63.5x10^-6 meter = 10^1
the epithelial cell is 6.35x10^-5 m
b) in Angstroms (Å)
63.5 μ or 63.5x10^-6 to Å 10^-10
=63500
Note: when going from a larger unit to a smaller unit, the number must increase, and when going from a smaller unit to a larger unit the number must decrease.
Connect to Biostudies
Viruses are very small, and so they are generally visualized with the use of electron microscopy. The most sensible unit for viral particles is nm. This is equal to 10^-9 meters or 100 micron (μ).
Bacterial cells are typically measured in microns(μ) and visualized using light microscopy with oil immersion, of 1000X or greater.
Animal and plant cells are typically measured in microns and observed using conventional light microscopy (~40-400X). Some cells are large enough (like eggs) to be seen with the naked eye.
Liquid volume example.
1) Adult male has total blood volume of 5.15 L
a) express this volume in mL
5.15L= 5150 mL
b) 5.15L= 51.5 dL
Length-meter (m)
Mass- gram (g)
Volume-Liter (L)
Time-second (s)
Temperature- degrees Kelvin (K)
Amount of Substance- Mole (mol)
Heat Energy- joule (J)
Electric Current- ampere (A)
Luminous intensity- candela (cd) Energy-joules (J) calories (c)
Prefixes
tera- T 10^12
giga- G 10^0
mega- M 10^6
kilo- k 10^3
hecto- h 10^2
deka- da 10^1
deci- d 10^-1
centi- c 10^-2
milli- m 10^-3
micro- μ 10^-6
nano- n 10^9
pico- p 10-12
femto- f 10^-15
atto- a 10^-18
Metric-English
1.00 in = 2.54 cm
1.00 kg= 2.20 lb
1.00 lb= 454 g
1.00 L= 1.06 qt
1cm3; (1cc)= 1 mL
1 fluid ounce = 29.6 mL (cc)
K= C+ 273
C= 5/9 (F-32)
F= 9/5 C+ 32
Kelvin and Celsius have 100 degrees between freezing and boiling, where Fahrenheit has 180.
the freezing and boiling points in degrees for
Kelvin 273, 373
Celsius 0, 100
Fahrenheit 32, 212
Example Problems
1)an epithelial cell has a diameter of 63.5 microns (μ)
a) express the diameter in meters
63.5 μ or 63.5x10^-6 meter = 10^1
the epithelial cell is 6.35x10^-5 m
b) in Angstroms (Å)
63.5 μ or 63.5x10^-6 to Å 10^-10
=63500
Note: when going from a larger unit to a smaller unit, the number must increase, and when going from a smaller unit to a larger unit the number must decrease.
Connect to Biostudies
Viruses are very small, and so they are generally visualized with the use of electron microscopy. The most sensible unit for viral particles is nm. This is equal to 10^-9 meters or 100 micron (μ).
Bacterial cells are typically measured in microns(μ) and visualized using light microscopy with oil immersion, of 1000X or greater.
Animal and plant cells are typically measured in microns and observed using conventional light microscopy (~40-400X). Some cells are large enough (like eggs) to be seen with the naked eye.
Liquid volume example.
1) Adult male has total blood volume of 5.15 L
a) express this volume in mL
5.15L= 5150 mL
b) 5.15L= 51.5 dL
Unifying themes in Biology
this will be built on heavily as posting progresses. These unifying ideas should help to make it so that the interconnectivity of biology is clearer, so while learning, questions like "what is this all for/why is it important?" can be answered.
1. Emergent Properties - all life forms show hierarchy of organization extending from organic molecules to the ecosystem.
2. Cells- cell theory states that cells are the basic unit of life, of which all living things are composed, and that all cells are derived from preexisting cells. Two main cell types are Eukaryotic (Fungi, Plants, Animals and Protists) and Prokaryotic (Eubacteria, Archaebacteria)
3. Heritable Information- DNA codes for the continuity of life, the basic genetic code lies in the nucleotide sequence of the DNA. These nucleotides (arranged as genes) dictate the specific proteins of a given species.
4. Form and Function- are complimentary at every level of biological organization. Life's structures are the bases for life's functions. If you don't understand something's function, analyze its form, and vis versa.
5. All life forms are dependent upon interactions with their abiotic and biotic components. Organisms are open systems exchanging energy and nutrients with their environment. Nutrients cycle, energy flows. Ex, energy from the sun goes to producers to consumers and dissipates as heat. Life depends on energy sources.
6. Regulation- all functional aspects of life's chemistry must be regulated to maintain homeostasis. Feedback mechanisms are often integrated into the organism.
7. Unity and Diversity- diversity in the varying forms of life (three domains- Eukarya, Archaea, Eubacteria). Unity is found in many shared biochemical processes, such as, a common genetic code, or the basic chemistry of cell respiration.
8.Genetic change through time- Evolution, brought on by mutation and natural selection account for much of the unity and diversity in life.
9. Science includes observation based discovery and the testing of hypotheses through experimentation. Data analysis includes statistical studies to validate hypothesis. Statistical analysis, T-Score, and other calculations.
10. Science, Technology and society- many technologies are based upon scientific discovery and a desire to solve a problem.
1. Emergent Properties - all life forms show hierarchy of organization extending from organic molecules to the ecosystem.
2. Cells- cell theory states that cells are the basic unit of life, of which all living things are composed, and that all cells are derived from preexisting cells. Two main cell types are Eukaryotic (Fungi, Plants, Animals and Protists) and Prokaryotic (Eubacteria, Archaebacteria)
3. Heritable Information- DNA codes for the continuity of life, the basic genetic code lies in the nucleotide sequence of the DNA. These nucleotides (arranged as genes) dictate the specific proteins of a given species.
4. Form and Function- are complimentary at every level of biological organization. Life's structures are the bases for life's functions. If you don't understand something's function, analyze its form, and vis versa.
5. All life forms are dependent upon interactions with their abiotic and biotic components. Organisms are open systems exchanging energy and nutrients with their environment. Nutrients cycle, energy flows. Ex, energy from the sun goes to producers to consumers and dissipates as heat. Life depends on energy sources.
6. Regulation- all functional aspects of life's chemistry must be regulated to maintain homeostasis. Feedback mechanisms are often integrated into the organism.
7. Unity and Diversity- diversity in the varying forms of life (three domains- Eukarya, Archaea, Eubacteria). Unity is found in many shared biochemical processes, such as, a common genetic code, or the basic chemistry of cell respiration.
8.Genetic change through time- Evolution, brought on by mutation and natural selection account for much of the unity and diversity in life.
9. Science includes observation based discovery and the testing of hypotheses through experimentation. Data analysis includes statistical studies to validate hypothesis. Statistical analysis, T-Score, and other calculations.
10. Science, Technology and society- many technologies are based upon scientific discovery and a desire to solve a problem.
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