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AJ Warzecha
Mrs. Huntemann
AP Biology D
13 December 2013
Immune System and Biochemistry Unit
Chapter 31 - Immunology: Animal Defense Systems
1.) A person can survive an infection through the reaction of their immune system inside the
body and this system can further prevent infection by memorizing the sickness to effectively
destroy it when it if it isn't prevented from entering the body through physical barriers.
2.) Self and nonself refers to the identification method that the immune system uses to
differentiate between the host's cells and an incoming infection through triggers using marker
molecules.
3.) A person that uses antibacterial soap can leave themselves more vulnerable to more
pathogens through two pathways. One, the bacteria that is already living on their body could
mutate to become resistant to the specific treatment they are using and spread rapidly or two,
their secondary line of defense of the immune system using identifying antibodies loses the
opportunity to identify and remember the specific signatures of each of the foreign bacteria that
is destroyed outside the body.
4.) This picturing is showing an autoimmune response of a white blood cell using phagocytosis
to destroy a foreign yeast cell that gained entry into the body through a failed physical barrier of
the immune system.
5.) Lysozymes and defencins are signal molecules that attach themselves to different types of
foreign material or bacteria that enter the body. The marked bacteria or object is then surrounded
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by more agents of the innate immune system such as T cells and white blood cells to eliminate
the threat.
6.) Natural killer cells are used to create a blanket defense against a large number of disease and
bacteria by not needing to recognize a specific antigen like the T cells do.
7.) First the bacteria enters the wound bypassing the physical barrier of skin that was destroyed
by the knife. Next, the blood coming from the wound begins to clot and inflammation occurs as
another preventative measure against further infection. Then the innate immunosystem sends
unspecified cells to destroy the incoming bacteria with the adaptive imunnosystem sending
specialized cells if the foreign agent is previously known. If the area becomes infected the body
must quickly adapt to isolate the foreign materials and begin to fight back the infection using
specialized cells. However, if it appears to be using special medicine might need to be used to
prevent further damage to your body depending on a doctor's advice.
8.) "A key event is the exposure or presentation of the antigen to the immune system." This
quote explains that a vital step in the process of further infection prevention is the adaptive
immune system's response to a new virus/bacteria by memorizing the chemical makeup and
warning signs for a future infection and thereby stopping it from commencing the next time
around.
9.) It is an effective evolutionary tool because over time the system will get better at identifying
threats, however it is a double edged swords also. The pressure from the system pushes antigens
to mutate more rapidly to avoid being thwarted continuously by the adaptive immune system.
Also, this system can be passed on from generation to generation through the mother's fluids in
the embryo. As nutrients are passed along certain antigens might also be passed, and there, in the
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animal's mother, a immune system can primitively be developed to recognize different antigens
without lethal exposure to deadly diseases.
10.)
An antibody is created through the binding of an antigen with a TH cell to from plasma cells that
can synthesize and secrete specific antibodies. Through four polypeptide chains(two heavy and
two light), a variable region controls the antibodies specific immunoglobulin and a constant
region on the heavy chain to determine its class of the 5 immunoglobulins which differ in
function.
11.) The survival of successful of a B cell to create different antibodies that have been mutated is
like natural selection because the unuseful antibodies' maker dies out through like of resources
sent. This can be seen as a way to weed out the least successful B cells, which in turn, increases
the host's overall health.
12.) Cancer occurs more frequently in individuals that are immunosuppressed because the
weakened immune system is at a much higher risk for opportunistic infections and viruses that
can essentially hijack a host cell to create an instance of cancer through rapid reproduction that
would have normally been halted by a healthy immune system.
13.) Memory cells sustain an immunity to a pathogen by continuously excreting certain
antibodies that can stop a specific strain of bacteria or virus, so if that person does become
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infected again, the illness is suppressed before any real harm can be done if all things go right
and the learned virus/bacteria has not mutated.
14.) Vaccines work by infecting the body with an extremely weak counterpart of a known strain
of bacteria which is then destroyed and learned by the adaptive immune system through memory
cells that prevent further infection by that specific strain through an early recognition and
suppression.
15.) You can still get the flu after a flu shot because the shot you received could be for only one
particular strain of the virus that your body will now recognize and there are many other
divergences because of mutation in the flu that your body will still not recognize until an
infection occurs.
16.) A cell mediated response directly and only attacks that specific cell with the chemical
marking while a non-specific response might be less effective but a blanket attack to keep out
infections.
17.) Doctors are no longer using antibiotics like they used to because they have learned that these
bacterial agents have been put under a high selective pressure and because of that natural
evolution has increased the number of individuals within that population that are resistant to that
treatment. Nowadays, doctors more often use a rolling type of prescription where a different
antibiotic is rotated over a period of time to decrease the chance that a mutation will arise in the
population that is resistant to the several antibiotics used.
18.) An autoimmune disease is a condition that creates an abnormal functioning immune system
that can no longer differentiate between self and nonself effectively destroying a host's body
from the inside making them further susceptible to infection. They could form from an outside
virus and lateral passing of DNA from the virus into a now infected host cell.
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Mini Research Project:
1.) To defeat the mumps virus, I first had to eat one member of the invading virus through
phagocytosis where then the attacking cell sprouted antigens, which I could finally move to a T
cell and fuse the two together to begin the development of memory B cells that could lock onto
the specific virus and eradicate them with antibodies.
2.) I preformed research on AIDS virus.
3.) The reason the HIV virus is so successful is because it targets the immune system cells, so
ironically, sending more white blood cells to control the virus results in a weakened immune
system with a surplus in host cells for the virus.
4.) The swine flu has so many health officials scared because the virus is highly contagious and
deadly in humans, but mostly because the virus is susceptible in pigs through three separate
species strains. The avian, human, and pig strains all can gather in the pig body allowing huge
amounts of lateral gene transfer to take place essentially increasing deadly or infectious mutation
chance three-fold.
5.) The swine flu vaccine could be developed quickly because it has a relatively low mutation
rate and is unlike HIV because it does not directly attack the immune system, which in turn
allows a vaccine to be developed and memorized by B cells.
6.) I do not think a vaccine is possible for HIV because the development of the virus has made it
effective at attacking and weakening the immune system, so a memory vaccine based on the
adaptive immune system would only end up strengthening the already mutated stronger virus
through natural selection in the body. However, I do think that medical pills and treatments can
be bettered to create a overall better life for the infected patient or prevent further infection of the
population.
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7.) AIDS from the perspective of the virus is genius; it developed a counterattack to our highly
developed immune system allowing it to live on indefinitely without medical interference.
However, from the human standpoint, it puts a selective pressure on the human immune system
to develop an alternative way to stop infection once inside the body besides the adaptive immune
system.
Autoimmune Diseases:
Graves is an autoimmune disorder that results in over activity of the thyroid gland. It is
caused by a malfunction in the endocrine system controlling metabolism. The disorder tells the
body to enter hyperthyroidism and is most common in women over 20. Some of the systems are
anxiety, breast enlargement, double vision, eye irritation and tearing, sweating, insomnia, tremor,
weight loss, and muscle weakness. The treatment to cure the disorder stems from a control of the
thyroid gland. Medicine called beta-blockers are often used to treat symptoms of anxiety,
sweating, and high heart rate until hyperthyroidism is controlled. Popular treatments are
antithyriod medication, radioactive iodine, and surgery. The latter two require replacement
thyroid hormone medication for the rest of your life. Eye problem symptoms usually leave once
the hyperthyroidism is controlled.
Chapter 2 - Life, Chemistry, and Energy
1.) The search for water is important in the search for life because all current life uses water as a
means to obtain energy and the majority of the organisms on the planet are made mostly of
water.
2.) The electrons are the most important part of the atom when it comes to a chemical reaction
because the outermost valence electrons are the part of the atom that does the interacting while
the protons and neutrons in the nucleus do not come into contact with other atoms directly. Also,
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the number of electrons in an atom can create a positive or negative charge that will attract the
atom to other atoms of the opposite charge, which can also be affected if the atom does not have
the magic number of "8" valence electrons or a full shell.
3.) The octet rule is a rule that implies all atoms want to have 8 outermost electrons or a full shell
to be happy. This rule is important because it influences chemical reactions between atoms and
molecules to get to that ideal 8.
4.) Ionic bonding - Often between a metal and a nonmetal, a metal gives up an electron to a
nonmetal to satisfy an octet.
Covalent bonding - Electrons are shared between to atoms to satisfy an octet.
Polar covalent bonding - A covalent bond that the sharing is not equal creating partial charges on
the poles of the molecule for example water.
5.) Water has high surface tension, the ability to dissolve many other substances, and a high
tolerance to heat which all stem from its polar covalent bonding making it polar and causing it to
form many hydrogen bonds.
6.) Hydrophobic molecules do not like to be interacting with water and so they move to areas
where they have the least amount of contact with the polar H20 whereas hydrophilic molecules
like to have the most amount of contact with the surrounding water because of their polar
tendencies to interact with water.
7.) Dehydration synthesis is the process that by taking out H20 from two separate molecules that
will combine the two original molecules together. A great example is the dehydration synthesis
that creates saturated and unsaturated fats.
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8.) Sugars are like Legos because they can link to each other and branch off of each other either
linearly or diagonally through the many hexagon shaped sugars. For example cellulose and
starch use their distinct sugars as block to the branching of other sugars, like Legos.
9.) Cellulose branches off linearly and starch can branch off in many more directions, however
each sugar acts as a building block to the branching of another. Starch therefore gives off more
energy as the contact with dissolving acids is greater while cellulose takes longer to digest and
forms strong structures like the plant cell walls.
10.) The difference between saturated and unsaturated fatty acid is that the saturated is full of
hydrogen bonded to all the carbons while unsaturated has a double bonded carbon that creates a
kink in the normally linear molecule branch. This creates the side effect that the saturated fat,
because they are more condensed, to contain more inherent energy for the body's metabolism to
use. Also, saturated fats are solid and room temperature whereas the less dense unsaturated fats
are a liquid.
11.) The first law of thermodynamics states that no matter is lost in a chemical reaction, however
the second law states that even though no matter is lost there are two energy types that stem as
the sum of the reaction as usable(free) energy and unusable energy. This means that even though
there essentially is no loss of material during the metabolic process, some energy cannot be used
by the body after the reaction making foods differ in the amount of energy the body can
physically use after the metabolism digests them.
Chapter 3 - Nucleic Acids, Proteins, and Enzymes
Biomolecules:
Polymer
Monomer
Role in living things
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Carbohydrates
Monosaccharide
(polysaccharides)
[N(CH2O)n]
Short-term energy, structural
building materials, "tags" to
recognize molecules
Proteins (polypeptide) Amino acids
Structural materials, enzyme
catalysts, antibodies, cell
signaling
Lipid/fat
Glycerol or fatty acids
(triglyceride)
(fats, oils, steroids, waxes)
Cell membrane, storing
concentrated energy, regulating
hormones
DNA
Nucleotides (purine/pyrmadine
Cellular information database
base, phosphate group, and pentose
(Catalytic ability in RNA)
sugar)
1.) The six main elements of biomolecules are carbon, hydrogen, oxygen, phosphorous, nitrogen,
and sulfur.
2.)
C- carbon
H- hydrogen
N- nitrogen
O- oxygen
P- phosphorous
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S- sulfur
3.) I think oxygen is the most important of these elements because the simple concentration of it
in our atmosphere has dictated whether life can survive through mass extinctions and species
radiation.
4.) Biomolecules are mainly held together by covalent bonds between atoms.
Functional Group Structure Where found
Special properties
Hydroxyl
-Polar
Alcohols
-Capable of Hydrogen bonds
Carbonyl
Aldehydes
-Strongly polar
Ketone
-Hydrogen bond acceptor
Carboxyl
Carboxylic acids
-Capable of Hydrogen bonds
Amino
Amines
-Polar
-Capable of Hydrogen bonds
Sulfhydryl
Thiols
-Disulfide bonds
Phosphate
Organic phosphates (nucleotides) -Capable of Hydrogen bonds
Carbohydrates:
1.) A carbohydrate is a large biomolecule in the format N(CH2O)n that stores energy: sugars,
starches, and cellulose. (Monosaccharides, disaccharides, and polysaccharides)
2.) Carbohydrates play the role of storing energy in living things and release energy when they
are broken down.
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3.) A monosaccharide is the simplest building block of a single sugar such as fructose where
polysaccharides are long chains of many monosaccharide such as cellulose.
4.) Five and six carbon sugars usually form a ring structure because of the distinct sharing of
electrons that result in a specific angle, which ends up coming around in a ring because the angle
that the molecules bond together at remains fairly constant in a sugar with a specific number of
carbons.
# of Carbons Category name Relevant examples
3
Triose
Glyceraldehydes
4
Tetrose
D-erhythose, D-threose
5
Pentose
Ribose
6
Hexose
Galactose, fructose, glucose
Polysaccharide Origin
Role in living things
Disaccharides
Formed by combining two
Short-term energy
Lactose
monomers in a dehydration reaction
Maltose
Sucrose
Glycogen
Animal tissue
Storage form of glucose in animals and
steady blood pressure.
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Starch
Plants
Storage form of glucose in plants
Chitin
Bugs
Strong building structure for an
exoskeleton (like cellulose but for
animals)
Fats/Lipids:
1.) Fats and lipids play the role of long-term energy storage in living things and the essential
ability to form cell membranes through phospholipids bilayers.
2.) A fatty acid is a triglyceride chain that is a major source of energy in animals.
3.) An essential part of a fatty acid is the carboxyl group holding the glyceride chain together.
4.) A triglyceride is a molecule derived from glycerol and acts as a major storage of energy
through chemical reactions in the body.
5.) Cholesterol is made by the body as a storage form of energy and it is highly useful in the
mobility of cell membranes which dictate the coming and leaving of substances into and out of
cells.
6.) A phospholipid is a chain of lipids that hydrophilic on phosphate end and hydrophobic on the
fatty acid chain which can be combined in a bilayer to make the cell membrane.
Nucleic Acids:
1.) Living things use nucleic acids in DNA and several forms of RNA as messenger RNA,
transferal RNA, and ribosomal RNA which are involved in protein synthesis.
2.) The most important type of DNA to life is B DNA because of its 5'-3' strands that pair to the
opposite 3'-5' and allow an easy splitting of the pyrine/pyrmadine groups by a polymerase.
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Functional Groups Review:
Concept/description
Facts(underline most important)
Explanation
CHNOPS
6 most important molecules in
Carbon, hydrogen, nitrogen,
organic chemistry
oxygen, phosphorus, sulfur
Valence and Covalent
Octet rule, Sharing of electrons,
Every atom wants to have 8
Bonding
determined by (outer)valence shell
electrons in their valence shell
Organic Molecules
Hydrocarbons(Methane), double and Simplest organic molecule only
Isomers
triple bonds(dioxygen gas)
containing carbon and hydrogen
Variation, types: structural,
The same molecules can be put
enatiomers, geometric
together hundreds of different
ways
Polarity
Unequal sharing
Covalent sharing isn't always
equal creating poles that are
slightly positive or negative
Functional Groups
6 most important groups
Hydroxyl, Carbonyl, Carboxyl,
Amino, Sulfhydryl, Phosphate
Quiz
1. D
4. E
7. E
2. D
5. D
8. D
3. B
6. B
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Biomolecules Review:
Biomolecule
Facts(underline most important)
Explanation
Carbohydrates (CH2O)n, used for short-term energy, -This is the general formula for most
monosaccharide
carbohydrate molecules
-Monosaccharide is the monomer of
carbs
Proteins
Enzymes, Structural materials,
-Act as catalysts to speed up chemical
specific binding, specific carriers,
reactions
signaling, amino acids, Peptide bonds -Dehydration reactions can create
peptide bonds creating a long chain of
amino acids(polypeptide-protein)
Lipids
Nucleic Acids
Formation, sugars, structural
-(CH2O)n
material, short-term energy, "tags"
-Glucose, fructose, lactose, glycogen
DNA and RNA, structure: purine or
-DNA is the information data base,
pyrmadine, pentose sugar, phosphate
RNA carries data and translates it
Quiz
1. B
6. A
11. C
16. B
2. E
7. B
12. E
17. E
3. B
8. B
13. C
4. C
9. E
14. A
5. E
10. A
15. E