Feb. 2, 2008
REVIEW for EXAM #1
From LAB -BIOETHICAL PRINCIPLES: be able to apply
A. AUTONOMY
- individual choice/freedom;autonomy of action should not be subjected
to controlling constraint by others
B. NON-MALEFICENCE: Above all, do no
harm; the first medical principle
C. BENEFICENCE -relationship to
others not just self; oft cited as the 2nd medical principle - 1. Basic version: help others only if
they want help
- 2. Strong version=PATERNALISM:
higher authority enforces its idea of good
D. JUSTICE -equal or fair
treatment, equal rights, equal goods:
- 1. Egalitarian -equal goods
- 2. Libertarian -equal
rights/freedoms
UNIVERSAL FEATURES of LIFE [don't
need to memorize this, just
use as organizational themes]
I. SELF-MAINTAINING -ability to convert disorder to a
specific self-order
Maintenance Systems==>Digestion & Nutrition, Circulation, Respiration,
Excretion
II. SELF-REGULATING -ability to compensate for
variable/disruptive environment, etc.="Higher" Regulatory
Systems==>Nervous, Endocrine, Immune
III. SELF-SUPPORTING
AND MOVING
==>Musculoskeletal systems
IV. SELF-REPRODUCING -as a species; ==>Reproductive
Systems
V. EVOLVING over
generations -product
of, subject to Natural Selection
WHY needed? There are optimal
states for many things such as water
content, temperature, etc.
HOW to keep at optimum? 1. Negative Feedback System!
a) -May be unreferenced, where some state/process is disturbed, which directly triggers a compensating
process which opposes the disturbance (not
very accurate control); OR:
b) -May be referenced, with specific sensor/receptor to measure the state/process, an integrator to compare to a set point, and a specific effector to oppose the disturbance (more accurate). This is the main
model we will use. ->see
DIAGRAMS from lecture/text for examples of
Room Thermostat and Body Temperature
NOTE: -NEGATIVE
term refers to a system that OPPOSES the disturbance, whether up or down
-VARIATIONS:
a)
Antagonistic or DUAL control: TWO
effectors that have opposite corrective effects (e.g., furnace,
air-conditioner) [or 1 effector that can be boosted or inhibited (e.g. heart
can be slowed or sped up)]
b) -effectors may be behaviors, e.g., seeking warm spots; hunger + eating, etc.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - -
B.
REGULATED CHANGE
-not
everything has a constant optimum
WHY? Many types of change are
useful: growth, puberty, fight-or-flight, cycles, new situations ‰
HOW? 2 different
mechanisms:
1. RESET System: changes the
set point of a negative feedback system.
- a) temporary emergencies: e.g., fever; stress
- b) cyclical "clocks": e.g., sleep/wake
cycle [brain •s clock lowers your body
temperature set point about 1 »C at night, lowers metabolism]
2. POSITIVE FEEDBACK System -one
which accentuates a change rather than reducing it. Sometimes
this is not adaptive but a dangerous malfunction -SEE FEEDBACK LAB for example.
BUT sometimes it can be useful for desired rapid changes: e.g., nerve impulses, blood clotting, ovulation. Know basic
diagram.
1. DELAY
PROBLEM: Over and/or Undercompensations!
Delay problems
are INHERENT in a simple feedback system because 1) the system must be
disturbed before it can act, and 2) they are not infinitely fast; there are
always delays in getting a signal from the disturbed state to an effector's
response. See FEEDBACK LAB -if delays are too long and/or
disturbance too fast, the system will oscillate (over and under-compensation)
unacceptably
EXAMPLE(s): body temperature during exercise over-and
undercompensated due to delays in sweating control if exercise is started or stopped too abruptly
- What to do about delays?
Sometimes nothing. But
sometimes evolution has produced solutions. There is one main way this can happen:
ANTICIPATION system -one which activates a feedback system before the
disturbance changes a regulated state; may use a sensor to measure the oncoming disturbance rather than the state itself. May be innate physiology or
learned behaviors. Examples
-see lecture; anticipating the sweating-delay problem through slow warm-up and
cool-down exercise, or unconsciously with fight-or-flight reaction!
2.
NEW-SITUATION PROBLEM: existing
feedback system may not work well at high altitude, with new diet or activity
regime, etc.
Solution
= ACCLIMATIZATION or
"ADAPTATION" system: change capacity
or capability of feedback component.
Example
(i) -buy a bigger air conditioner if the climate is getting too hot for your
old one. In the body: training in the desert may lead to increased sweating
capacity over time (army experiment)
Example (ii) -High
altitude and EPO: how this hormone
is made by kidney, what it does; BIOETHICAL issues including beneficent use and justice
issues of athletic abuse of EPO!
LAST POINT: feedbacks abound in
complex systems! See READING. Is an "emergent" non-linear property
of parts working together via i) feedback within the system and ii) interactions with other systems
Principles of EVOLUTION
A. 2 LEVELS
of EXPLANATION in Biology: see lecture & reading examples
1. "Proximate" = mechanistic function "as is"; how does it work , what is it made of analysis
2. "Evolutionary" = historical/selective reason; why did it end up this way
analysis
B.
Essentials of Evolution with Natural Selection
--1. REPRODUCTION:
Members of a species reproduce, usually
more than needed to replace parents;
--2. VARIATION: Offspring have (semi)random differences in genes due to a) sex and b) mutations and c) Other
Genome changes (some newly discovered)
--3. "SURVIVAL OF THE FITTEST" ensues:
in the long run, those with "better" genes will leave more
successful offspring, so the
"better" genes eventually dominate the species
Never-ending process (no final or
ultimate "fit" state): Species change, diverge over generations since
environments (which include other species that are also evolving) change over
millenia, so this is a never-ending process!
DETAILS:
STEP 2 -SEMI-RANDOM VARIATION is Not predictive, cannot anticipate future needs
a) Sex: i) crossing-over: new combinations of parental
chromosomes in sperm and egg; plus ii) fertilization combines male, female
chromosomes
b) Mutations: alterations in codes of existing genes
&
Other Genome changes -more later! Pseudogenes, gene
shuffling, duplications, etc.
STEP 3 -SURVIVAL OF THE FITTEST
How? "Consumption, Competition, Cooperation" -fittest
genetic combinations lead to more viable offspring by i) better ability to eat,
avoid diseases andbeing eaten; ii) outdoing rivals and/or iii) cooperating with
other individuals or species in useful ways.
IMPLICATIONS/OUTCOMES
OF NATURAL SELECTION
-1) OVER time, may
produce exquisite ADAPTATIONS: e.g.,
kidney as a filter better than any human-made filters
-2) IMPERFECTIONS due to Historical constraints and
Slowness -often evolution is slow relative to one or a few
generations, and usually builds on pre-existing features, resulting in:
- -- a) Vestigial features: once-useful
adaptations become useless or harmful, usually because environments or other
adaptations changed and evolution has not caught up or cannot modify. E.g.,
human appendix, gill pouches in embryo, etc. -see Useless Body Parts article
- -- b) Compromises: useful adaptations with flaws; e.g. human spine
--3) Creates GENETIC DIVERSITY: diversity is inherent to life, changes each generation, and provides the raw
material for natural selection; there is no "perfect/ideal Platonic
human" (or any other organism) towards which evolution is aiming!
AND - - -> Species and
populations (subgroups of single species) with higher genetic diversity tend to
survive better.
EXAMPLES: incest taboos; Irish potato
famine;
C. EVIDENCE
for Evolution: see also text
1. Fossils
2. Biogeography
3. Observed
natural selection: e.g.,new plant species in historic times; new disease bacteria,
viruses and antibiotic resistances evolving right now
4. Comparative
Biochemistry & Genetics:
e.g., compare chimp to human DNA
5. Comparative
Embryology, Anatomy & Physiology: homologies
e.g., arm bones of vertebrates all have the same basic parts as we do
- -- illogical
features showing historical contraints give some of the strongest
evidence -see earlier
HIERARCHY OF BIOLOGY
I. ATOMS & MOLECULES
A. ELEMENTS:
building blocks of the universe
Atoms =
protons (& neutrons) in nucleus (+ charge), electrons in "orbits"
(negative-charge);
-Outer electrons usually responsible for
bonds, reactions, interactions
-Crucial property for life=electron affinities: strength of attraction for electrons!
-Most important elements= C, H, O, N, P,
S; also many others at lower amounts
B.
MOLECULES (atoms
join) & COMPOUNDS (molecules with different atoms joined)
-BONDS:
1. COVALENT (STRONG) BONDS
[=atoms SHARE electrons]:
-Single bond is one shared pair, symbolized by -; can also be double = &
triple = bonds
-Different
elements form different numbers of bonds: Key EXAMPLES: water, oxygen, etc.
-Electron
affinities yield 2 crucial types of molecules:
a)
NON-POLAR molecules: Equal affinities,so equal share; EXAMPLE: Methane, fats, oxygen!
b)
POLAR -unequal share:
EXAMPLE: water!!
2.
IONIC bond: One gives up electron to
other; then stay joined by opposite charges attracting; e.g., Na+Cl-
3. HYDROGEN bonds -polar molecules with hydrogen bind to other polar or
charged molecules: weak but crucial; especially water: keeps water liquid at normal temperatures, and water can dissolve salts such as NaCl by this attraction property!
C. Hydrophobic
or Non-polar
interaction:
Non-polar
compounds forced out of water as water molecules, unable to bind to non-polar
molecules, attract other water molecules. So non-polar compounds are squeezed
out of the way into a separate layer -"oil and water do not mix".
D.
INORGANIC Ions and Molecules:
|
1. Inorganic ions: electrolytes, acids dissolved in
water, etc. (many others not shown here): a) Na+, plus b) Cl-
dominate extracellularly; c) K+ dominates in cells; others
later d) H+ -determines ACIDITY |
2.
Inorganic molecules:
many not shown. E.g., a) Water: H2O or H-O-H b) O2 or O=O: c) CO2 or O=C=O |
E. ORGANIC compounds: have C and H, plus
usually other atoms.
4 categories of basic types of
small unit molecules to macromolecules:
1. CARBOHYDRATES: made of C, H, O:
|
a) Monosaccharide sugars such as GLUCOSE=C6H12O6 USES: i) energy ii) make larger
molecules - -> |
b)
Disaccharides such as SUCROSE
=glucose+fructose USES: mainly for energy |
c)
Polysaccharides such as GLYCOGEN in
liver, muscle, etc =large chains
of Glucose USE -energy storage |
2. AMINO ACIDS (AAs) & PROTEINS: C, H, O and N in specific array;
|
a) AAs: -20 different AAs with unique
properties according to "R" or side groups USES: i) energy; ii) neurotransmitters iii) join in chains to form
proteins |
b) PROTEINS -specific folded linear chains of AAs: AA sequence yields specific 3-D shape due to attractions and repulsions among various R (side) groups . Most
active cell functions due to proteins
with specific binding sites; each
type of protein attracts & binds one specific type molecule due to bonds:
lock
& key model: SEE
LECTURE; this is a KEY CONCEPT |
PROTEIN USES: Don't memorize
i) major cell/tissue/organ STRUCTURES
ii) ENZYMES: catalyze specific REACTIONS
[note: enzymes usually have names with -ase suffix]
iii) TRANSPORTERS and other MEMBRANE proteins -—move
molecules around
iv) REGULATORS -control other proteins or genes
3. LIPIDS: dominated by non-polar C-H bonds (hydrophobic!)
|
a) Fatty acids etc. single long C-H
chains [with acid group] Uses: energy,
making larger molecules |
b) Fats Triglyceride
type = main animal storage: 3 long C-H chains linked together (with a glycerol;
a sugar) Use: energy
storage |
c)
Phospholipids 2 long C-H
chains, a sugar, and polar group
|