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Priya Sorab
AP Bio Study Guide
Note: This does not cover everything for the AP Exam but does highlight many
important topics.
I.
Intro to Biology
The chemistry behind it
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A.
1.
Chemical Elements and Compounds
The study of Earth’s ozone layer
Several scientists study the ozone layer of the earth and how it affects life on the
planet.
There are several specialists.
Biologists are scientists who specialize in the study of life.
Matter consists of chemical elements in pure form and in combinations called
compounds.
Organisms are made of matter, anything that takes up space and has mass (not
weight).
Mass exists in many form and is present in everything, such as rocks and glass.
Some Greek philosophers believed the four elements were only air, water, fire and
earth, pure substances.
An element is a substance that cannot be broken down to other substances by
chemical reactions-there are currently 92 occurring elements such as gold, copper,
and oxygen.
A compound is a substance consisting of two or more elements in a fixed ratio.
Table salt is sodium chloride-NaCI. Chlorine and sodium are in a 1:1 ratio.
Life requires about 25 chemical elements
25 of the natural elements are essential, like carbon, oxygen, hydrogen and
nitrogen. They make up 96% of living matter.
Phosporus, sulfur, calcium and potassium account for the remaining 4%.
Trace elements are elements required by an organism in only small quantities.
Some, like iron, are needed by all forms of life.
Iodine is only needed in vertebrates to produce iodine.
Atoms and Molecules
Atomic structure determines the behavior of an element-subatomic particles
The properties of chemical elements and compounds are due to the structure of
atoms.
2. Each element has a certain kind of atom, the smallest unit of matter tha still
retains the properties of an element.
3. They are so small that a million of them stretch across the period printed at the
end of a sentence.
4. The atom is the smallest unit possible, and is composed of subatomic particles
called neutrons, protons and electrons.
5. The neutrons (neutral charge) and protons (positive charge) are packed together to
form the atomic nucleus, the dense core at the center of an atom.
6. Electrons and protons have opposite charges, electrons are negatively charged.
7. The neutron and proton are almost identical in mass.
8. The Dalton is a unit of measurement for atoms and subatomic particles, in honor of
scientist John Dalton who developed the atomic theory.
B. Atomic Number and Atomic Weight
1. Atoms differ in the number of subatomic particles.
2. All atoms have the same number of protons if they are from the same element.
3. The atomic number refers to the number of protons unique to one element and is
written as a subscript to the left of the symbol of the element.
4. The atom, unless otherwise indicated, is neutral in electrical charge.
5. The mass number is the sum of protons and neutrons in the nucleus of an atom.
6. Superscript to the left of the symbol of the element.
7. Almost all of an atom’s mass is in its nucleus-electrons do not contribute very much
to the mass.
8. The atomic weight is the total mass of an atom.
C. Isotopes
1. All atoms of an element have the same number of protons but can differ in the
number of neutrons.
2. Different atomic forms are called isotopes and an element occurs as a mixture of
isotopes.
3. The element carbon has three isotopes, all of which have six protons but differ in
neutrons.
4. Radioactive isotopes have useful applications in biology. Tracers follow atoms
through metabolism and use the radioactive atoms as diagnostic tools in medicine.
5. Kidney disorders are diagnosed by injecting small doses of substances with
radioactive isotopes into blood and measuring the amount of tracer in urine.
6. Radiation from decaying isotopes is dangerous and damages cellular molecules. Ex:
fallout from nuclear incidents.
D. Energy Levels of Electrons
1. When two atoms approach each other during a chemical reaction, their atoms do
not come close enough to interact.
2. Only electrons are involved in chemical reactions.
3. Energy is defined as the ability to do work, potential energy is the energy matter
stored because of position or location.
4. Ex: Water in a reservoir on a hill.
5. Electrons of an atom have potential energy because they are close to the nucleus
and attracted to the nucleus.
6. The further the electron from the nucleus, the greater the potential energy.
7. Energy levels/electron shells are the different states of potential energy for
electrons in an atom.
8. The first shell is closest to the nucleus and electrons here have the lowest energy.
9. An electron can change its shell by absorbing or losing energy equal to the
different potential energy between the two shells.
E. Electron Orbitals
1. The three-dimensional space where an electron is found 90% of the time is called
an orbital.
2. At most two electrons can be in the same orbital, the first shell has a single orbital
and can accommodate two electrons.
3. There is called the 1s orbital.
4. The second shell can hold eight electrons, two in each of four orbitals and is called
2s orbital. It has a greater diameter than 1s.
F. Electron Configuration and Chemical Properties
1. The chemical behavior of an atom is determined b its electron configuration, the
distribution of electrons in the atom’s electron shells.
2. The simplest atom is hydrogen.
3. The elements in the periodic table are arranged in three rows, or periods,
depending on the sequential addition of electrons to orbitals in the first three
electron shells.
4. The valence electrons are outer electrons, those in the outermost shell. The
valence shell is the outermost shell holding these electrons.
5. An atom with a completed valence shell doesn’t react readily with other atoms.
This is a noble gas.
6. Helium, neon and argon have full valence shells. The rest are chemically reactive
because of unfilled valence shells.
7. Atoms with the same number of electrons in their valence shells exhibit similar
chemical behavior-fluorine (f) and chlorine (CI) have seven valence electrons and
combine with sodium to form compounds.
G. Atoms combine by chemical bonding to form molecules.
1. Atoms with incomplete valence shells interact with other atoms so that each
partner completes it valence shells.
2. Atoms share or transfer valence electrons.
3. Chemical bonds are bonds that hold together atoms. The strongest types are
covalent and ionic bonds.
H. Covalent Bonds
1. Covalent bond=the sharing of a pair of valence electrons by two atoms.
2. When two hydrogen bonds approach each other, they come close enough for 1s
orbitals to overlap and share electrons so that they each have two electrons.
3. A molecule is two or more atoms held together by covalent bonds.
4. A structural formula is a notation which represents both atoms and bonding.
5. A molecular formula indicates that the molecule consists of a certain number of
atoms of an element.
6. Hydrogen has six electrons in the second electron shell and needs two more
electrons to complete the valence shell. Two oxygen atoms form a molecule by
sharing two pairs of valence electrons.
7. A double covalent bond holds them together.
8. The bonding capacity of an atom is called its valence and equals the number of
unpaired electrons in the valence shell.
9. Valence of hydrogen=1, oxygen=2, nitrogen=3, carbon=4.
10. Phosporus can have a valence of 3 but in important molecules it has 5, forming
three single bonds and one double bond.
11. Molecules of H2 and O2 are pure elements. H20 makes water. It is a compound.
Methane is also a compound.
12. Electronegativity is the attraction of an atom for the electrons of a covalent bond.
13. The more electronegative an atom is, the more strongly it pulls shared electrons
toward itself.
14. A nonpolar covalent bond is a bond where two atoms’ fight for electrons is a
standoff resulting in equal electronegativity.
15. A polar covalent bond is a bond where the electrons aren’t shared equally.
16. In a water molecule, the bonds between Oxygen and Hydrogen are polar because
oxygen is very electronegative and pulls electrons stronger than hydrogen does.
I. The Use of Radioactive Tracers in Biology
1. Radioactive isotopes are among the most versatile tools in biological research.
2. Organisms process radioactive and stable isotopes of the same element in the same
way.
3. Radioactive isotopes are used to label certain chemical substances to follow a
metabolic process.
4. Cells are grown in a medium with the ingredients to make DBA. Thymidine is
labeled with 3H.
5. Cells are grown at different temperatures and then eventually killed once the
samples are taken out and DNA is saved.
6. The papers with DNA are placed in vials with scintillation fluid to emit light
whenever radiation cites certain chemicals.
7. The frequency of flashes is measured in counts per minute. The higher this is, the
more DNA the cells have made.
8. When the counts are plotted against the temperatures at which the cells were
growth scientists find out that the temperature affects the rate of DNA
synthesis.
9. In autoradiography, scientists locate radioactively labeled DNA when thick cell
slices are placed on glass slides in the dark covered by photographic emulsion.
10. Radiation from the radioactive tracer in ant new DNA exposes this and creates a
pattern of black dots.
J. Ionic Bonds
1. Two atoms can be very unequal and the more electronegative atom steals an
electron away from its partner.
2. An atom of sodium encounters an atom of chlorine, the sodium has eleven electrons
in one valence electron in the third electron shell.
3. Chlorine has seventeen electrons, seven in the valence shell. When the atoms
meet, the valence electron of sodium is transferred to the chlorine atom.
4. An ion is a charged atom or molecule.
5. If the charge is positive it is called a cation. If it is negative, it is an anion.
6. An ionic bond is a bond in which cations and anions attract each other.
7. Ionic compounds are called salts and are found as crystals, and are cations and
anions bonded by electrical attraction and arranged in a 3-D lattice.
8. A salt crystal doesn’t consist of the same molecules a covalent compound does.
9. Ion also applies to entire molecules with electrical charge. Environment affects
the strength of ionic bonds.
10. In a dry salt crystal, the bonds are so strong that it takes a hammer and chisel to
break enough of them to crack the crystal.
11. If placed in water, the salt dissolves as the attractions between ions decrease.
K. Weak chemical bonds play important roles in the chemistry of life.
1. Covalent bonds link atoms to form the molecules of a cell, but the properties of
life also play a role.
2. When two molecules in the cell contact, they temporarily use chemical bonds that
are weaker than covalent bonds and this lets contact be brief, the molecules
briefly interact and separate.
3. The importance of weak bonding can be seem in chemical signaling in the brain.
One cell signals another by releasing molecules that use weak bonds to dock onto
receptor molecules of a receiving cell.
4. The bonds last long enough only to trigger a momentary response. If this failed to
happen, there would be diseases.
5. The ionic bond is weak in the presence of water. The hydrogen bond is also weak
but crucial to life.
L. Hydrogen Bonds/Van der Walls Interactions
1. A hydrogen bond occurs when a hydrogen atom covalently bonded to one
electronegative atom is also attracted to another electronegative atom.
2. In living cells, the electronegative partners are in oxygen or nitrogen atoms.
3. Hydrogen bonding between water and ammonia: if the ammonia molecule, an
electronegative nitrogen atom has a small amount of negative charge, is close to a
water molecule, a weak attraction occurs, causing a hydrogen bond.
4. Because electrons are in constant motion they are not always symmetrically
distributed in the molecule and can accumulate.
5. There are called van der Walls interactions, and are weak and only occur when
atoms and molecules are very close together.
6. These form not just between molecules but also between regions of one large
molecule like a protein.
M. A molecule’s biological function is related to its shape.
1. A molecule made of two atoms like hydrogen and oxygen is always linear but
molecules with over two atoms have complicated shapes determine by the positions
of atoms’ orbitals.
2. When an atom forms covalent bonds, its orbitals rearrange.
3. For atoms with valence electrons in both s and p orbitals the single s and three p
orbitals hybridize to form four new orbitals.
4. In the water molecue, the two hybrid orbitals are shared with hydrogen atoms and
form a molecule shaped like a V.
5. The methane molecule has the shape of a tetrahedrom because its four hybrid
orbitals are shared.
6. The nucleus of the carbon atom is at the center and has four covalent bonds going
to the hydrogen nuclei at the corners.
7. Molecular shape is crucial in biology and determines how most molecules of life
recognize and respond to each other.
8. In the brain-cell signaling, the molecules released have a unique shape.
9. Molecules with shape similar to the brain’s signal molecules can affect the mood
and pain perceptions of the brain.
N. Chemical Reactions Make and Break Chemical Bonds
1. The making and breaking of chemical bonds leading to changes in the composition
of matter are called chemical reaction-ex: reaction between hydrogen and oxygen
to form water.
2. This reaction breaks the covalent bonds of hydrogen and oxygen, forms the new
bonds of H20.
3. In chemical reactions an arrow indicates the conversion of starting materials,
reactants, to products, the final product.
4. The coefficients indicate the number of molecules involved.
5. The chemical shorthand that summarizes the process of photosynthesis is:
6CO2+6H2o=C6H12O6+602
6. Photosynthesis happens with carbon dioxide, and water absorbed from the soil.
7. The sunlight powers conversion of these ingredients to glucose, used as fuel for
the plants.
8. Some chemical reactions go to completion and all reactants are converted to
products.
9. Most reactions are reversible and the products of the forward reaction become to
reactants.
10. Hydrogen and nitrogen molecules can combine to form ammonia which can in turn
regenerate: 2H2+N2=2 NH3
11. A factor affecting the rate of reaction is the concentration of reactants, the
higher it is, the more molecules collide and react.
12. This is also true for products.
13. Once the forward and reverse reactions occur at the same rate, the
concentrations stop changing.
14. Chemical Equilibrium=the point at which reactions offset each other exactly.
15. This does not mean that the reactants and products are equal in concentration,
they have just stabilized.
I.
Introduction
A. Water
1. Scientists study new planets and look for water on them.
2. All organisms are made of mostly water and live in environments with water.
3. Water is the biological medium on Earth.
B. The Role of Water on Earth
1. Life on Earth began and evolved in water.
2.
3.
4.
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6.
II.
Modern life is tied to water.
Most cells are surrounded in water and are 70-90% water.
¾ of Earth is in water.
Most is liquid but water is also present as ice and vapor.
Water is present in all three states of matter, solid, liquid and gas.
The Effects of Water’s Polarity
A. The Polarity of water molecules results in hydrogen bonding.
1. The water molecule is simple, it has two hydrogen atoms joined to the oxygen atom
by single covalent bonds.
2. Oxygen is more electronegative than hydrogen and the electrons of the polar
bonds spend more time closer to the oxygen atom.
3. The oxygen region of the molecule has a slightly negative charge and the hydrogen
parts have a positive charge.
4. The water molecule is shaped like a V.
5. It is a polar molecule-a molecule where opposite ends have opposite charges.
6. The properties of water come from the attractions among polar molecules, which is
electrical.
7. The molecules are held together by a hydrogen bond.
8. Each water molecule can form hydrogen bond with up to four other molecules.
B. Organisms depend on the cohesion of water molecules
1. Water molecules stick together because of hydrogen bonding, when water is liquid,
these bonds are fragile.
2. They form, break and re-form very fast. Each bond only lasts a few trillionths of a
second.
3. Cohesion-a phenomenon in which hydrogen bonds hold together a substance.
4. Cohesion due to hydrogen bonding lets water transport itself to plants against
gravity.
5. When water reaches the leaves through vessels that extend upwards, it
evaporates and is replaced from the vessels in the veins of a leaf. The new water
is pulled upwards
6. Adhesion=the clinging of one substance to another, also plays a role.
7. Surface tension, a measure of how difficult it is to stretch or break the surface of
a liquid, relates to cohesion. Water has a higher surface tension than most other
liquids.
8. Ex: Water stands above the rim in a filled glass. Also, the surface tension lets us
skip rocks in a pond. Some animals can stand, walk or run on water.
C. Water moderates temperatures on Earth.
1. Water stabilizes air temperatures by absorbing heat from the air and released
stores heat to air that is cooler.
2. Water is a heat bank and can absorb or release heat with only a slight change in its
own temperature.
D. Heat and Temperature
1. Kinetic energy=the energy of motion. Anything that moves has it.
2. Atoms and molecules have kinetic energy because they always move.
3. Heat is the measure of the total quantity of kinetic energy due to molecular motion
in a body of matter.
4. Temperature measures the intensity of heat due to the average kinetic energy of
the molecules.
5. When the average speed of molecules increases, a rise in temperature is present
as well. However, heat isn’t the same as temperature.
6. When two objects of different temperature are brought together heat goes from
the warmer to the cooler body until the two are the same.
7. Molecules in the cooler object speed up.
8. The Celsuis Scale indicates temperature-Water freezes at 0oC and boils at 1000C.
9. The calorie, or cal, is the amount of energy it takes to raise the temperature of 1 g
water by 1 0C.
10. The calorie is also the amount of heat that 1 g of water releases when it cools by
the same amount.
11. A kilocalorie or kcal, 1000 cal, is the quantity of heat required to raise the
temperature of 1 kg of water by 10C.
12. The joule is also a measurement of energy, .239 cal.
E. Water’s High Specific Heat
1. The ability of water to stabilize temperature depends on it’s high specific heat.
2. The specific heat of a substance is defined as the amount of heat that must be
absorbed or lost for 1 g of that substance to change its temperature by 10C.
3. The water’s specific heat is known already, it is 1.
4. The specific heat of water is 1 calorie per gram per degree Celsuis, 1 cal/g/0g.
5. Water has an unusually high specific heat. Ethyl alcohol is only 0.6 cal.
6. The high specific heat of water makes water change its temperature less when it
absorbs or loses heat.
7. Water’s high specific heat can be traced. Heat is absorbed to break hydrogen
bond and is released when hydrogen bonds form.
8. A calorie of heat causes a small change in the temperature of water because a lot
of the heat energy disrupts hydrogen bonds before the water molecules begin to
move faster.
9. A large body of water can absorb and store a lot of heat from the sun in the
daytime and releases it in the night.
10. The high specific heat of water stabilizes ocean temperatures.
F. Evaporative Cooling
1. Molecules of a liquid stay together because they are attracted to each other.
2. Molecules moving fast enough to overcome these attractions leave the liquid state
and become a gas.
3. The transformation from a liquid to a gas is vaporization or evaporation.
4. Heat of vaporization is the quantity of heat a liquid must absorb for 1 g of it to be
converted from the liquid to the gaseous state.
5. Compared with other liquids water has a high heat of vaporization, to evaporate a
gram of water at room temperature, 580 cal of heat are needed.
6. Water’s high heat of vaporization is its emergent property caused by hydrogen
bonds, and these must break before the molecules leave the liquid.
7. Water’s high heat of vaporization means it absorbs solar heat, making the climate
milder.
8. Evaporative cooling is when the surface of the liquid that remains behind cools
down. It occurs because the hottest molecules are most likely to heave as gas.
9. Evaporative cooling of water gives stability to the temperatures of lakes and
ponds.
10. Evaporation of water from the leaves keeps the leaves’ tissues from becoming too
warm in the sunlight.
11. The evaporation of sweat dissipates body heat and prevents overheating.
G. Oceans and lakes Don’t Freeze Solid Because Ice Floats.
1. Water is less dense as a solid than as a liquid, this makes ice float.
2. Water begins to freeze when its molecules decrease in movement and break their
hydrogen bonds.
3. The temperature reaches 00C and water becomes locked into a crystalline lattice
and each molecule is bonded to at most four partners.
4. Hydrogen bonds keep the molecules far enough apart to make ice 10% less dense
than liquid water.
5. When ice absorbs enough heat for the temperature to rise, the ice melts.
6. Water reaches its highest density at 40C and expands as the molecules move
faster.
7. If ice sank, all ponds, lakes and oceans would freeze solid.
8. In reality, in winter, only the top layer of a lake freezes and the rest doesn’t
freeze because of insulation from floating ice.
H. Water is the solvent of life.
1. A sugar cube placed in water will dissolve, and the liquid is a mix of sugar and
water.
2. A solution is a liquid that is completely a homogeneous mixture of two or more
substances.
3. The dissolving agent of a solution is the solvent.
4. The substance that is dissolved is the solute.
5. A solution where water is the solvent is an aqueous solution.
6. Water is the best solvent. It is due to its polarity.
7. If sodium chloride is placed in water, the ions are exposed to the solvent.
8. The ions and water molecules have affinity, and the oxygen regions of the water
molecules are negatively charged. They cling to the sodium cations.
9. The hydrogen regions of the water molecules are positively charged and cling to
the anions.
10. Water separates the sodium and chloride. It dissolves all the ions, and the what is
left is a solution of sodium and chloride mixed with the solvent, water.
11. A compound does not need to be ionic to dissolve in water. Polar compounds are
soluble in water too.
12. Sugar is water-soluble because water molecules cover the polar sugar molecules.
I. Hydrophilic and Hydrophobic substances
1. Any substance that has affinity with water is hydrophilic. This knowledge is
important especially when dealing with cells.
2. This is true even if the substance will not dissolve in water because the molecules
are too large. An example is cotton, which has large cellulose molecules.
3. Water sticks to the cellulose fibers.
4. Substances that do not have an affinity with water are hydrophobic and are not
ionic and are nonpolar.
5. Ex: vegetable oil, does not mix well with water or watery substances.
6. This is due to nonpolar bonds.
J. Solute Concentration in Aqueous Solutions
1. A mole or mol is used in measurement of molecules and is equal to the molecular
weight of a substance in units of grams.
2. A carbon atom weighs 12 daltons. A hydrogen atom weights one Dalton.
3. Molecular weight is the sum of the weights of all the atoms in the molecule. The
molecular weight of sucrose is 342 daltons.
4. It is better to measure in moles because the mole of one substance has the same
number of molecules as a mole of any other substance. Substances can be
combined in fixed ratios of molecules.
5. To obtain the concentration of one liter of solution made of one mol of sucrose,
dissolved in water, scientists weigh out 342 grams of sucrose and add water while
stirring until the sugar is dissolved.
6. Enough water would be added to bring the total volume to 1 L and then there would
be a one molar solution of sucrose.
7. Molarity is the number of moles of solute per liter of solution, the unit of
concentration most often used by biologists for aqueous solutions.
III. Dissociation of water molecules
A. Hydrogen Molecules
1. Sometimes a hydrogen atom shared between two water molecules shifts from one
molecule to the other, and it loses its electron.
2. The transferred atom is actually a hydrogen ion, a proton-so it is positively
charged.
3. The water molecule that lost the proton is a hydroxide ion. It has a charge of -1.
4. The proton binds fully to the other water molecule, and this results in a hydronium
ion, H3O+.
5. This reaches dynamic equilibrium when the water dissociates at the same rate that
it is re-formed from H+ and OH-. The water molecules are highly concentrated at
this point.
6. The dissociation of water is reversible and rare, but it is important. Hydrogen and
hydroxide are reactive and if their concentrations change, the cell’s proteins and
other molecules also change.
7. The concentrations of H+ and OH- are equal in water but adding an acid or base
disrupts the balance.
8. The pH scale describes how acidic or basic a solution is.
B. Organisms are sensitive to changes in pH. Acids and Bases1. An acid is a substance that increases the H+ concentration of a solution.
2. The extra source of H+ in a solution results in more of it than OH-. This is an
acidic solution.
3. A base reduces the hydrogen ion concentration in a solution.
4. Some bases reduce H+ concentration by dissociating to form hydroxide ions.
5. One of these bases is sodium hydroxide and water dissociates into its ions.
6. Some bases reduce H+ concentration by accepting hydrogen ions. Ammonia is a
base if its valence shell attracts a hydrogen ion from the solution. This causes an
ammonium ion (NH4+). Formula (Page 44):
7. The base reduces the H+ concentration and solutions with more OH- are called
basic solutions.
8. HCI and NaOH dissociate fully if water mixes with them. Hydrochloric acid is a
strong acid and sodium hydroxide is a strong base.
9. They dissociate fully.
10. Ammonia is a weak base.
11. Carbonic acid is a weak acid because it accepts hydrogen ions again.
12. The equilibrium favors the reaction in the left direction. When carbonic acid is
added to water just 1% of the molecules are dissociated at any time.
C. The pH Scale
1. The product of the H+ and OH- is always 10-14M. This is written as[H+] [OH-]=10-14M2
2. The brackets mean molar concentration for the substance in them.
3. In a neutral solution [H+]=10-7 and [OH-]=10-7.
4. If there is enough acid, [H+] becomes 10-5 and [OH-] declines by an amount of
about 10-9M (10-5X10-9=10-14)
5. An acid adds hydrogen ions to a solution and removes hydroxide ions.
6. A base has the opposite effect of an acid.
7. If enough of a base is added to raise OH- concentration to 10-4M, the H+
concentration goes to 10-10.
8. The pH scale isfrom 0 to 14 and measures solution concentrations, which can differ
by a factor of 100 trillion or more.
9. The pH scale compresses the range of H+ and OH- concentrations by using
logarithms.
10. pH declines as the H+ concentration goes up. The pH scale implies both H+ and OHconcentrations.
11. The pH of a neutral solution is seven and this is the midpoint of the scale.
Anything less is acidic, anything more is basic.
12. Biological fluids are between pH of 6-8, but some exceptions are present, such as
the digestive juice of the human stomach. It is highly acidic and at pH 2.
13. Each pH unit is equal to a tenfold difference in H+ and OH- concentrations.
D. Buffers
1. The internal pH of living cells is about 7 but a change in this can be harmful
because it would change chemical processes.
2. Biological fluids resist changes in their pH when acids or bases are introduced,
because of buffers, substances that minimize changes in the concentrations of H+
and OH- in a solution.
3. Ex: in human blood, the pH is about 7.4 and a human cannot survive for over a few
minutes if the blood pH goes to 7 or rises to 7.8.
4. A buffer takes and stores hydrogen ions from the solution when there are too
many and adds them to the solution when they are needed.
5. Buffers are weak acids or bases that reversibly combine with hydrogen ions.
6. Human blood is an example of a buffer.
7. The chemical equilibrium between carbonic acid and bicarbonate is a pH regulator.
8. If the hydrogen concentration in blood falls, more carbonic acid dissociates and
there are more hydrogen ions.
9. When the hydrogen ion concentration in blood goes up, the bicarbonate ion is a
base and takes away the excess ions.
10. Many buffers are acid-pairs.
E. Acid precipitation threatens the fitness of the environment
1. Contamination of water is serious.
2. Pure rain has a pH of 5.6 and is slightly acidic.
3. Acid precipitation is rain, snow or fog more acidic than 5.6.
4. Acid precipitation is caused by sulfur oxides and nitrogen oxides in the air, they
react with compounds in the air to acids in acid rain.
5. The compounds are from burning fossil fuels.
6. Electrical power plants that burn coal produce more pollutants than any other
single source.
7. Winds carry the pollutants away.
8. In the spring, as snow melts, the surface melts and drains down, and the acid does
into lakes and streams.
9. Meltwater has a pH of at least 3. This hurts fish that are young and fertile.
10. Strong acidity changes biological molecules and prevents them from carrying out
chemical processes.
11. Acid precipitation’s effects are controversial. Research has proven that it affects
solubility of soil minerals and washes away mineral ions that help soil and plants.
12. Other minerals reach toxic concentrations when their solubility goes up.
13. Sulfur dioxide emissions have gone down and with this acid rain decreases as well.
Organic Chemistry:
The importance of Carbon
I.
A.
1.
2.
3.
Introduction
Most chemicals are based on carbon.
It can form different, large molecules.
The cell has carbon-based compounds.
4. Proteins, DNA, carbohydrates, and other molecules are made of carbon atoms
bonded to each other and to atoms of other elements.
5. Examples are Hydrogen, oxygen, nitrogen, sulfur, and phosphorus.
B. Organic Chemistry is the study of carbon compounds
1. Organic chemistry is the study of carbon compounds.
2. Organic compounds come from all kinds of molecules.
3. The percentages of the major elements of life are uniform.
4. Organic chemistry originated in attempts to purify and improve the yield of
products and chemists learned to make simple compounds in the laboratory by
combining elements under the right conditions.
5. The Swedish chemist Jons Jakob Berzelius made the distinction between organic
compounds and inorganic compounds (in the nonliving world).
6. Chemists began to chip away at the foundation of vitalism when they synthesized
organic compounds.
7. In 1828 Friedrich Wohler tried to make inorganic salt by mixing solutions of
ammonium and cyanate. This led to urea, a compound in urine of animals.
8. The cyanate was from animal blood.
9. Hermann Kolbe made the organic compound of acetic acid from inorganic
substances from pure elements.
10. Vitalism went down after more decades of synthesis of organic compounds. In
1953, Stanley Miller established a relationship between carbon compounds and
evolution.
11. Organic chemistry was defined as the study of carbon compounds regardless of
their origin.
C. Carbon atoms are the most versatile building blocks of molecules
1. The key to chemical characteristics of an atom is the configuration of electrons
which determines the kinds and number of bonds an atom will form with other
atoms.
2. Carbon has six electrons, two in the first shell and four in the second shell.
3. It doesn’t often lose or gain electrons.
4. A carbon atom completes its valence shell by sharing electrons with other atoms in
four covalent bonds.
5. When a carbon atom forms single covalent bonds the arrangement of its four
hybrid orbitals makes the bonds angle towards the corners of an imaginary
tetrahedron.
6. Carbon can bond with several other elements.
7. The structural formula for CO2 is o=c=o.
8. Each bond represents a pair of shared electrons.
9. Carbon dioxide is a simple molecule and it is considered inorganic even though it
has carbon.
10. Urea is also a simple molecule and the structural formula is (page 50):
11. Each atom has the required number of covalent bonds, and one carbon atom is in
both single and double bonds.
D. Variation in carbon skeletons contributes to the diversity of organic molecules.
1. Carbon chains form the skeletons of most organic molecules.
2. The skeletons are different in length.
3. Some have single bonds and others have double bonds.
4. All these carbon skeletons are hydrocarbons, organic molecules made of only
carbon and hydrogen.
5. Hydrogen atoms are attached to the carbon skeletons whenever electrons are
available for covalent bonding.
6. Hydrocarbons are major petroleum components.
7. They are not in living organisms, but many of a cell’s organic molecules have regions
made of only carbon and hydrogen.
8. Fats have long hydrocarbon tails attached to them.
E. Isomers
1. Isomers are compounds that have the same molecular formula but different
structures and properties.
2. Structural isomers are isomers that have different atomic covalent arrangements.
3. The number of possible isomers increases as carbon skeletons grow larger.
4. Geometric isomers all have the same covalent partnerships but are different in
spatial arrangements.
5. They are due to the inflexibility of double bonds.
6. Enantiomers are molecules that are mirror images of each other. The four groups
of atoms are arranged in space around the asymmetric carbon in two different
ways.
7. They are important in the pharmaceutical industry but it is important to remember
that two enantiomers may have different functions.
8. Thaliomide, produced for pregnant women in the 1960’s, had one enantiomer to be a
sedative but the other one causing birth defects.
9. Scientists want to synthesize drugs in isomeric form.
II. Functional Groups
A. Functional Groups also contribute to the molecular diversity of life.
1. The components of organic molecules that are involved in chemical reactions are
called functional groups.
2. They are attachments that replace one or more of the hydrogens bonded to the
carbon skeleton of the hydrocarbon.
3. Each functional group acts differently between organic molecules based on the
number and arrangement of the groups.
4. Both estrone and testosterone are steroids, because they are organic molecules
with a common carbon skeleton as four used rings.
5. They are different only when certain functional groups are present.
6. The six functional groups most important in the chemistry of life: hydroxyl,
carbonyl, amino, sulfhdryl, and phosphate groups. They are hydrophilic.
B. Hydroxyl Group
1. The hydroxyl group is a hydrogen atom bonded to an oxygen atom which is bonded
to the carbon skeleton of the organic molecule.
2. Alcohol is organic compounds containing hydroxyl groups.
3. The hydroxyl group, in a structural formula, is abbreviated by leaving the covalent
bond between the oxygen and hydrogen out.
4. The group is polar because of the electronegative oxygen atom attracting
electrons. Water molecules are attracted to the group, and dissolve organic
compounds with the groups.
C. The Carbonyl Group
1. The carbonyl group is a carbon atom joined to an oxygen atom by a double bond.
2. If the group is on the end if a carbon skeleton is called an aldehyde. Otherwise it
is a ketone.
3. The simplest ketone is acetone with three carbons.
4. Acetone has different properties.
D. The carboxyl group
1. The carboxyl group is an oxygen atom double-bonded to a carbon atom also bonded
to a hydroxyl atom.
2. Carboxylic acids are compounds with carboxyl groups.
3. Acetic acid has two carbons and gives vinegar a sour taste.
4. A carboxyl group has hydrogen ions and the covalent bond between oxygen and
hydrogen is so polar, the hydrogen dissociates from the molecule as an ion.
5. If the double bonded oxygen and hydroxyl group attached to separate carbons,
there would be less tendency for the –OH group to dissociate because the second
oxygen would be further away.
E. The Amino Group
1. The amino group has a nitrogen atom bonded to two hydrogen atoms and the carbon
skeleton.
2. Amines are organic compounds with this functional group, an example is glycine.
3. Glycine also has a carboxyl group and is an amine and carboxylic acid.
4. It belongs to a group called amino acids, which can also be bases.
F. The Sulfhydryl Group
1. Sulfur is right below oxygen in the periodic table and has six valence electrons,
forms two covalent bonds.
2. This group is the sulfhydryl group and has a sulfur atom bonded to a hydrogen
atom.
3. Organic compounds with sulfhydryls are called thiols.
G. The Phosphate Group
1. Phosphate is an anion formed when an inorganic acid, phosphoric acid, dissociates.
2. It loses hydrogen ions and is negative in charge.
3. These are phosphate groups and organic compounds with them have a phosphate ion
covalently attached by one of its oxygen atoms to the carbon skeleton.
4. Phospate groups transfer energy between organic molecules.
H. The chemical elements of life, a review
1. Living matter is made of carbon, hydrogen, oxygen and nitroten with some sulfur
and phosphorus.
2. These elements form strong covalent bonds.
3. Carbon’s chemical behavior makes it be used as a building block.
4. It forms four covalent bonds, links into molecular skeletons and joins other
elements.
Biochemistry:
A. The living cell
1. The living cell is a chemical industry and thousands of chemical reactions occur in
it.
2. Sugars and amino acids are changed and converted.
3. Molecules are made into polymers.
4. Cellular respiration drives the cells by taking out energy in sugars.
5. Cells use this energy to perform tasks.
I.
Metabolism, energy and life
A. The chemistry of life is organized into metabolic pathways.
1. Metabolism is the totality of an organism’s chemical processes.
2. It is an emergent property of life.
3. Metabolism manages the material and energy resources of the cell.
4. Some pathways release energy by catabolic pathways, they break down complex
molecules into simpler compounds.
5. Anabolic pathways consume energy to build complicated molecules from simpler
ones.
6. An example is the synthesis of a protein from amino acids.
7. Bioenergetics is the study of how organisms manage their energy resources.
B. Organisms transform energy
1. Energy is the capacity to do work and move matter against opposing forces.
2. Kinetic energy is the energy of motion, found in any moving objects.
3. Heat and thermal energy are kinetic energy that result from the random movement
of molecules.
4. Stored energy/potential energy is energy matter possesses because of its location.
5. An example is water on a dam, due to its altitude.
6. Stored energy is converted to kinetic energy as the object begins to move
7. Chemical energy can be disturbed when chemical reactions rearrange the atoms in
molecules so potential energy becomes kinetic energy.
8. This also happens when the hydrocarbons of gasoline react explosively with oxygen
and release energy to push pistons.
9. Cellular respiration unleashes energy stored in sugar.
C. The energy transformations of life are subject to two laws of thermodynamics
1. Thermodynamics is the study of energy transformations that occur in a collection
of matter.
2. Scientists use the word system to denote matter under study.
3. The rest is called surroundings.
4. A closed system is isolated from its surroundings, in an open system, energy is
transferred between the system and surroundings.
5. Organisms are open system because they absorb energy.
6. The first law of thermodynamics states that the energy of the universe is
constant.
7. Energy can be transferred or transformed but not created or lost.
8. Ex: light converts to chemical energy, and the plant is the energy transformer.
9. The second law of thermodynamics states that every energy transfer makes the
universe more disordered.
10. Entropy is a measure of disorder.
11. Every energy transfer increases entropy.
12. Increased entropy is present in the physical disintegration of a system’s organized
structure.
13. In most energy transformations ordered forms of energy are converted to heat.
14. 25% of the chemical energy in the fuel tank of a car is used for the car motion and
the rest is lost as heat.
15. In machines and organisms, most energy is converted to heat. All chemical energy
a child uses to climb a slide is made into heat.
16. Energy is conserved because heat is a form of energy-in its most random state.
17. By combining the laws, the quantity of energy in the universe is the same, but the
quality differs.
18. Heat is the lowest grade of energy.
19. An organism takes in organized forms of matter and energy from surroundings, and
replaces them with less ordered forms.
20. An animal gets starch and proteins and releases carbon dioxide and water.
21. Organisms are open systems and exchange energy and materials with their
surroundings.
22. Complex organisms evolved from simple ancestors.
23. The entropy of a system can decrease as long as that of the universe increases.
D. Organisms live at the expense of free energy
1. A spontaneous process is the change that can occur without outside help.
2. The downhill flow of water can be used to turn a turbine.
3. When a spontaneous process happens, the stability of the system goes up.
4. A system of charged particles is not very stable because opposite charges aren’t
apart.
E. Free Energy: A Criterion for Spontaneous Change
1. Free energy is the portion of a system’s energy that can perform work when
temperature is uniform throughout the system.
2. It is called free energy because it is available for work.
3. The system’s quantity of free energy is symbolized by the letter “G”. The two
components of this are the total energy (H) and entropy (S).
4. Free Energy Formula: G=H-TS
5. T is absolute temperature.
6. Not all the energy in a system is available for work; the entropy is subtracted from
the total energy in finding the capacity of the system to do work.
7. Systems that are rich in energy like stretched spring are unstable, and so are
highly ordered systems like complex molecules.
8. Systems that change spontaneously to a more stable state have high energy and/or
low entropy.
9. In any spontaneous process, the free energy of a system goes down.
10. Formula for the change in free energy:
11. For a process to occur spontaneously the system gives up energy or order.
12. The greater the decrease in free energy, the higher the maximum amount of work
the process can perform.
F. Free Energy and Equilibrium
1. There is a relationship between free energy and equilibrium, including chemical
equilibrium.
2. Most chemical reactions are reversible.
3. The reaction is at chemical equilibrium, and as the reaction goes towards this point,
the free energy of the reactants and products decreases.
4. Free energy goes up when a reaction is pushed away from equilibrium.
5. A chemical reaction or physical process at equilibrium performs no work.
6. Movement away from equilibrium is not spontaneous and can happen with the help
of an outside energy source.
G. Free Energy and Metabolism
1. Based on their free energy changes chemical reactions are either exergonic or
endergonic.
2. An exergonic reaction proceeds with a net release of free energy.
3. The chemical mixture loses free energy. The exergonic reactions occur
spontaneously.
4. An endergonic reaction absorbs free energy from its surroundings.
5. These reactions are not spontaneous.
6. The chemical reactions of metabolism are reversible and would reach equilibrium if
occurring in a test tube.
7. Metabolic disequilibrium is one of the defining features of life.
8. Some of the reversible reactions of respiration are pulled in one direction and out
of the way of equilibrium.
9. The product of one reaction should not accumulate but should become a reactant in
the next step.
10. The sequence of reactions is due to the free-energy difference between glucose at
the uphill of respiration and carbon dioxide and water at the downhill.
11. A key strategy of bioenergetics is energy coupling, the use of an exergonic process
to drive an endergonic one.
H. ATP powers cellular work by coupling exergonic reactions to endergonic ones.
1. A cell does mechanical work (like the beating of cilia), transport work, the pumping
of substances across membranes, and chemical work, the pushing of endergonic
reactions that would not occur spontaneously.
2. The source of energy is ATP.
I. The structure and hydrolysis of ATP
1. ATP, or adenosine triphospate, is related to one type of nucleotide found in nucleic
acids.
2. ATP has the nitrogenous base of adenine bonded to ribose.
3. In RNA, one phosphate group is attached to the ribose.
4. Adenoside triphospate has a chain of three phosphate groups attached to the
ribose.
5. The bonds between the phosphate groups of ATP’s tail can be broken by hydrolysis.
6. When the terminal phosphate bond is broken a molecule of inorganic phospate
leaves the ATP and makes it adenosine diphospate, ADP.
7. When a reaction occurs in the cell, and not in the test tube, the G is about -13
kcal/mole.
8. The hydrolysis of phosphate bonds of ATP releases energy and they are called
high-energy phosphate bonds.
9. These are not very strong bonds, and are weak when compared to other bonds in
organic molecules.
10. When a system changes in the direction of stability, the change is exergonic.
11. The release of energy during ATP hydrolysis is because of the chemical change to a
more stable condition.
12. In the ATP molecule, all three groups are negatively charged.
13. The like charges repel each other and this makes the region of the ATP molecule
instable.
J. How ATP Performs work
1. ATP is hydrolyzed in a test tube and the free energy hets up the surrounding
water.
2. In the cell, this is dangerous.
3. The cell uses enzymes to send the energy to endergonic processes by transferring
an ATP phosphate group to another molecule.
4. Phosphorylated intermediate is more reactive than the original molecule.
5. All cellular work depends on the energizing of other molecules by transferring
phosphate groups.
K. The Regeneration of ATP
1. ATP is a renewable source and can be renewed by adding a phosphate to ADP.
2. The ATP cycle moves at a fast pace.
3. The working muscle cell recycles all its ATP once each minute.
4. The regeneration of ATP from ADP is endergonic. Formula (Page 91):
5. Catabolic/exergonic pathways, like cellular respiration, provide energy for the
endergonic process of making ATP.
II. Enzymes
A. The actions of an enzyme
1. An enzyme regulates metabolic reactions.
2. If the enzyme sucrose is added to the solution of sucrose, all of it is hydrolyzed
within seconds.
B. Enzymes speed up metabolic reactions by lowering energy barriers
1. Enzymes are catalytic proteins.
2. A catalyst is a chemical agent that changes the rate of a reaction without being
consumed by the reaction.
3. Every chemical reaction involves breaking bonds and forming bonds.
4. The hydrolysis of sucrose involves breaking the bond between glucose and fructose
and then forming new bonds with hydrogen and hydroxyl groups.
5. The reactant molecules must absorb energy from the surroundings to break the
bonds.
6. Breaking the bonds releases energy.
7. Free energy of activation/activation energy is the initial amount of energy needed
to start a reaction and break bonds in the reactant molecules.
8. If the reaction is exergonic, the activation energy is repaid by the formation of
new bonds and more energy being released.
9. Reactant bonds break only when the molecules have enough energy to become
unstable.
10. The activation energy is represented by uphill portions of a reaction graph.
11. At the top, the reactants are in the unstable transition state and the reaction
occurs here.
12. As the molecules settle into new bonding arrangements, energy is related.
13. The barrier of activation energy is needed in life.
14. Proteins and DNA have a lot of free energy and can decompose spontaneously.
15. These molecules only exist at certain temperature.
16. An enzyme speeds the reaction by lowering the activation energy barrier.
17. An enzyme cannot make an exergonic reaction endergonic.
C. Enzymes are substrate-specific
1. A substrate is the reactant an enzyme acts on.
2. The enzyme binds to its substrate and the catalytic action of the enzyme converts
the substrate to the product of the reaction.
3. Formula (Page 92):
4. As sucrose breaks sucrose into its monosaccharides, glucose and fructose, the
following goes on:Formula: (Page 92):
5. An enzyme distinguishes the substrate from closely related compounds so each
type of enzyme catalyzes a particular reaction.
6. Only the restricted region of the enzyme bonds to the substrate-called active site.
7. The active site is formed by a few of the amino acids of the enzyme.
8. The specificity of an enzyme is based on a compatible fit between the shape of its
active site and the shape of the substrate.
9. Induced fit-As the substrate enters the active site, it makes the enzyme change
shape so the active site fits around the substrate.
D. The active sit is an enzyme’s catalytic center
1. In an enzymatic reaction, the substrate binds to the active site and forms an
enzyme-substrate complex and the substrate is held in the active site by weak
interactions.
2. Side chains of the amino acids catalyze the conversion of the substrate to the
product.
3. Once the product departs the enzyme can take another substrate molecule.
4. Some enzymes are faster than others.
5. Enzymes use several mechanisms to lower activation energy and spread up a
reaction.
6. In reactions with over two or more reactants, the active site is a template for the
substrates to come together.
7. The enzyme stresses the substrate molecules and stretches or bends chemical
bonds.
8. The active site can also be a microenviroment that is conductive to a particular
type of reaction.
9. If the active sites’ amino acid has acidic side chains the active site has low pH.
10. Also, the active site directly participates in chemical reaction. There might be
temporary covalent bonding between the substrate and a side chain.
11. The rate that an enzyme converts substrate to product is a function of the initial
concentration of substrate-the higher it is, the more they access the active sites.
12. There is a limit to the speed of the reaction.
13. The concentration of substrate can be so high that all enzyme molecules have busy
active sites.
E. A cell’s physical and chemical environment affects enzyme activity
1. The activity of an enzyme is affected by the environment.
F. Effects of Temperature and pH
1. The velocity of an enzymatic reaction increases with higher temperature because
substrates collide with active sites a lot when the temperature is higher.
2. Beyond a certain temperature, the speed drops.
3. Thermal agitation of the enzyme molecule disrupts hydrogen bonds, ionic bonds and
other interactions that stabilize the conformation.
4. Each enzyme has a temperature where the reaction rate is fastest.
5. Each enzyme also as a pH at which it is most active, between 6 and 8 for most.
6. Pepsin works best at pH2-there are exceptions.
G. Cofactors
1. Cofactors are nonprotein helpers required by enzymes for catalytic activity.
2. They may be bound tightly to the active site, permanently or temporarily.
3. A coenzyme is a cofactor that is an organic molecule.
4. Example-vitamins
H. Enzyme Inhibitors
1. Some chemicals selectively inhibit actions of certain enzymes, this is not reversible
if there is a covalent bond present.
2. Competitive inhibitors are inhibitors that compete for admission into the active
site, and reduce productivity of the enzymes.
3. They block the substrate from entering the active site. This is reversible, the
concentration of substrate should increase.
4. Noncompetitive inhibitors do not directly complete with substrate.
5. They bind to other parts of the enzyme and cause the molecule to change its shape
making the active site unreceptive.
6. Poisons absorbed from the environment can act by inhibiting enzymes,
7. Selective inhibition and enzyme activation by molecules are needed in metabolism
control.
III. The control of metabolism
A. Intro
1. Chemical chaos would happen if all of a cell’s metabolism pathways were opened at
the same time.
2. A cell regulates it metabolic pathways by controlling when and where its enzymes
are active.
B. Metabolic control often depends on allosteric regulation.
1. Some regulatory molecules bind to an allosteric site, a specific receptor site on a
part of the enzyme molecule remote from the active site.
C. Allosteric Regulation
1. Most enzymes allosterically regulated are made from two or more polypeptide
chains.
2. Each subunit has its own active site and the allosteric site is where the active sites
are connected.
3. The complex is between two conformational states, one is catalytically active and
the other isn’t active.
4. An activator binds to an allosteric site to stabilize the conformation with a
functional active site.
5. The binding of an activator to an allosteric site stabilizes the conformation with a
functional active site.
6. The areas of contact between the subunits connect so that the shape change in
one subunit is transferred to the others.
7. Allosteric regulators attach to an enzyme with weak bonds.
8. The activity of the enzyme changes due to different regulator concentrations.
9. The inhibitor and activator can be similar enough to complete for the same
allosteric site.
10. Some enzymes of catabolic pathways have allosteric sites that fit AMP and ATP.
11. These enzymes are inhibited by ATP and activated by AMP.
12. If ATP production fails, AMP accumulates and activates its enzymes.
D. Feedback Inhibition
1. Feedback inhibition is the switching off of a metabolic pathway by its end product.
2. The end product is the enzyme inhibitor.
3. Some cells use this pathway to synthesize amino acid isoleucine.
4. This is the end product and slows down its own synthesis.
5. It allosterically inhibits the enzyme for the first step of the pathway.
E. Cooperativity
1. Substrate molecules can stimulate the catalytic powers of an enzyme.
2. The binding of a substrate to an enzyme induces a favorable change in the shape of
the active site.
3. If an enzyme has multiple subunits, the interaction triggers the same change in all
other subunits.
4. Cooperativity amplifies the response of enzymes to substrates.
5. One substrate molecule primes the enzyme to accept additional substrate
molecules.
F. The localization of enzymes within a cell helps order metabolism.
1. Structures inside a cell help bring order to metabolic pathways, sometimes, a team
of enzymes for several steps of a metabolic pathway is assembled together.
2. The arrangement controls the reaction sequence.
3. Some enzyme and enzyme complexes have fixed locations in the cell as structural
components and others are in solutions in specific membranes.
G. A review
1. Life is organized in a hierarchy of structural levels.
2. New properties emerge per level.
3. The behavior of water results from interactions of water molecules.
4. Organic molecules are assembled into giant ones and a macromolecule doesn’t
behave like a bunch of monomers.
Genetics:
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Character=any heritable feature
Variant of a character=trait
True breeding=two parents of the same genotype have offspring of the same
genotype (and only the same genotype)
Law of segregation: The two alleles (alternative versions of a gene) go into
different gametes
Ex: If the character is flower color, alleles could be pink and white
For each character in the gene (like flower color), the organism gets one allele
from the father, one from the mother. The dominant allele is what is expressed in
the phenotype. In this case, the recessive allele is carried on, but is not
expressed.
Suppose I mated two cats, one is black and one is gray. Black is dominant. The
genotypes of the parents are: (black cat) Aa and (gray cat) aa. The black cat
passes on either the “A” allele or “a” allele to the offspring. The gray cat can only
pass on the “a” allele. The offspring can be Aa (black) or aa (gray)
Note that, the black cat could pass on either the A or the a allele. The two alleles
could not both go to the same gamete. The fact that they separate illustrates the
law of segregation
The gray cat is homozygous; the alleles are identical. If the black cat was AA,
then it would also be homozygous. Since its alleles are different (A and a) it is
heterozygous. The dominant allele carries over to the phenotype in this case.
Phenotype-the appearance
We can always find the genotype of an organism with a testcross, crossing a
recessive homozygote with the organism of unknown genotype. For example,
suppose I had a black cat but I didn’t know if its genotype was AA or Aa. I must
cross it with a gray cat (aa). IF the black cat’s genotype is Aa, one offspring is
black but three are gray. But if the black cat is AA, then all the offspring are
black.
But remember that in this case we only tracked ONE trait. In a dihybrid cross,
two characters differ. It is important to know the law of independent assortment
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(the segregating of one pair of alleles does not affect the separation of the other
pair)
Suppose I am crossing a blue bird and a red bird where blue is dominant (D), red is
recessive (d). I am also tracking the gene for having spots, where S is dominant
(has spots) and s is recessive (no spots). Both parents are DdSs (genotype). Any
one gamete can get either the D allele or the d allele but the segregation of the S
and s alleles is not affected by the segregation of D and d.
In the case above the alleles end up being (per parent) DS, Ds, dS and ds.
DS
Ds
dS
Ds
DS
DDSS
DDSs
DdSS
DDSs
Ds
DDSs
DDss
DdSs
DDss
dS
DdSS
DdSs
ddSS
DdSs
Ds
DdSs
Ddss
ddSs
ddss
Sometimes there may be incomplete dominance. The heterozygotes have an
appearance intermediate between the two homozygotes (recessive and dominant)
Ex: I cross red flowers and white flowers, the heterozygotes are pink
In codominance, both alleles show up. Ex: MN blood group
Genes may exist in several forms. Multiple alleles may occur. Example: a person’s
blood can be group A, B, AB, or O (neither A nor B)
Pleitotropy=when a gene can affect an organism in many ways. Ex: Sickle cell
disease alleles cause many symptoms
Epistasis=when one gene changes the phenotype expressed by another gene
Ex: A cat has stripes but another gene codes for there to be no color at all on the
cat, therefore the stripes fail to appear
Some traits are controlled by several pairs of genes. For example, skin tone is
controlled by many genes. The more dominant alleles there are, the darker a
person is, and the more recessive alleles there are, the lighter (aabbcc).
DNA replication
-The DNA polymerase is what adds nucleotides to the existing strand, elongating
it.
-Remember, adenine pairs with thymine, guanine with cytosine. In RNA, replace
thymine with uracil.
-This template rule is used when DNA polymerase decides which nucleotide to add
based on this rule
-At the replication fork the helicase tears apart the two strands in the double
helix of DNA
-Single Stranded Binding Protein keeps the DNA strands apart.
-Remember, DNA polymerase can only add nucleotides to an existing polynucleotide
chain...
-RNA primase starts of synthesis by making an RNA primer. It is about 10
nucleotides in length
-the DNA polymerase begins to elongate off this (adding new nucleotides)
-In the LEADING STRAND (5' to 3') elongation is simple. After the nucleotide
chain is complete, the DNA polymerase replaces hte RNA primer with DNA
-In the LAGGING strand, 3' to 5', DNA elongation occurs in short fragments
called Okazaki Fragments. DNA ligase later joins these to make one chain.
REPAIR
-Mismatch repair: if the wrong base is added then DNA Polymerase fixes it during
replication
-Excision Repair: If there is a malfunctioning part in the DNA chain then nuclease
cuts it out and DNA polymerase and DNA ligase replace it with the correct
nucleotides.
-At the end of the 5' end of a DNA strand, there is a telomere-with a short DNA
sequence repeating itself-aded by telomerase
-the RNA in telomerase lets it support the telomere
-Telomeres are not located in somatic cells.
Proteins:
The first step is transcription.
1.
The DNA has a promoter region, which determines which strand is used as
the template and where transcription starts. The RNA polymerase binds to the
promoter in prokaryotes, but in eukaryotes proteins called transcription factors
bind to the TATA box in the promoter, and the RNA polymerase binds to those,
creating a transcription initiation complex.
2.
RNA polymerase pries apart the two strands of DNA, only one of them is
used as a template strand for transcription. RNA polymerase plays the role that
helicase plays in DNA replication.
*The transcription unit-how much of the DNA will be transcribed-is marked by
nucleotide sequences on the DNA.
1.
RNA polymerase untwists the DNA and transcribes it (adding matching RNA
nucleotides and connecting them) as it goes, the DNA double helix then twists back
together and the pre-mRNA peels off. The rules for base pairing between DNA
and pre-mRNA: Adenine-Uracil, Thymine-Adenine, Guanine-Cytosine, CytosineGuanine.
2.
Then, a terminator sequence is transcribed onto the pre-mRNA.
Transcription stops immediately in prokaryotes, and the pre-mRNA is released. But
it goes on for 10-35 nucleotides downstream in eukaryotes, and the pre-mRNA is
then cut off from the RNA polymerase.
3.
A 5’ cap, or modified guanine, is added to the 5’ end of the pre-mRNA and a
poly(A) tail, or 30-200 Adenines, are added to the 3’ end. Both prevent the premRNA from degrading and the ribosome later attaches to the 5’ end.
4.
RNA splicing occurs-while only 1200 nucleotides are needed, there are about
8,000. Noncoding regions (introns) are in between coding regions (exons). snRNP’s
(small nuclear ribnonucleoproteins) that have RNA in them combine with additional
proteins to form spliceosomes. They recognize sequences at the ends of introns
and cut them off. But depending on which areas are treated as introns, one gene
can produce different proteins. Introns also allow for crossing over and genetic
recombination, shuffling exons. Exons also code for domains of a protein, so
shuffling exons leads to diverse domains.
Translation:
1.
tRNA (transfer RNA) is needed for translation. Aminoacyl-tRNA synthetase,
an enzyme, covalently bonds the right tRNA with the right amino acid.
2.
After tRNA picks up an amino acid from the cytoplasm, the ribosomal
subunits (each made of protein and rRNA), and the mRNA, arrive at the cytoplasm.
3.
4.
5.
6.
tRNA has an anticodon at the the other end of it, which is really the opposite of
the mRNA codon it must bond to so that it can deposit the amino acid.
Using the energy of GTP as well as protein helpers called initiation factors,
the mRNA and ribosomal subunits join. The tRNA carrying MET bonds to the
AUG/START codon in mRNA.
The steps above were initiation of translation. In elongation’s first step,
codon recognition, the mRNA binds to the anticodon of the tRNA in the ribosome’s
A site. GTP is used here. Then, in the second step, peptide formation, the
polypeptide chain on the tRNA in the P site moves over to the amino acid in the A
site and bonds with it. In translocation, the tRNA carrying the entire polypeptide
chain-now in the A site, moves to the P site. The tRNA that was previously in the P
site moves to the E site and exits.
In termination, a stop codon in mRNA reaches the A site and bonds with a
release factor. Instead of another amino acid, a molecule of water bonds to the
polypeptide chain and it is released.
The polypeptide chain may go through posttranslational modifications, and it
may be cut, or sugars, lipids or phosphate groups may be added to it.
More molecular genetics…
1. Viral life cycles:
Phages reproduce with lytic or lysogenic cycles. In a lytic cycle, the bacteria that
has created the phages lyses (breaks open) to let them out and each phage can go
on to infect more cells. A virulent virus only reproduces this way. In a lysogenic
cycle, the virus enters the cell but because it’s a temperate virus, it can take a
lysogenic or lytic path. In a lysogenic path, the DNA Of the phage gets
incorporated on the chromosome of the bacteria-as a prophage-and one gene in it
tells the others to be quiet; however, a few are expressed, so each carrier may
produce toxins. After some time, due to a trigger, the virus may exit the
chromosome and enter the cell, it now becomes active and leads to the cell lysing.
In animals, each virus may have a viral envelope made of glycoproteins. These
glycoproteins bind to the cell’s surface and fuse with the plasma membrane; the
capsid and virus now enter. Enzymes take away the capsid and it takes over the
cell. New glycoproteins are synthesized by the membrane and as viruses leave the
cell they wrap themselves in the new membrane. The cell isn’t killed.
2. Bacterial genetic recombination
a.
Conjugation: Genetic material is transferred between two bacteria. This is due
to the F plasmid which codes for sex pilli. The “male” has a plasmid with genes that
allow for sex pilli; it transfers the plasmid to the “female”. But if the plasmid isn’t
b.
c.
3.
4.
on the chromosome then only the F plasmid is transferred. But if the F plasmid of
the male is on his chromosome then along with it some genetic material from the
chromosome goes to the female as well.
Transformation: A live, nonpathogenic cell takes up some DNA that gives a cell a
cell coat that protects the bacteria from any enzymes in the host cell. The new
allele becomes a part of the chromosome and replaces the previous allele. In some
bacteria certain proteins only allow this to happen between closely related species.
Transduction: This is the transfer of genetic material by a phage. In general
transduction, when a virus is being made, it gets the host cell’s DNA and not its
own; so it has no function. It injects this host cell DNA into another bacteria. In
specialized transduction, the prophage on the chromosome (in a lysogenic cycle)
leaves but carries some of the chromosome with it, and the cell it reaches get this
new DNA.
HIV-Reverse Transcriptase
Retroviruses have reverse transcriptase; an enzyme that goes RNA-DNA. It
elongates DNA from RNA, and this DNA then becomes a provirus on the
chromosome. RNA polymerase transcribes mRNA from it; some of this becomes
new protein for the protein coat of the virus. The genome of HIV enters the host
cell because the virus fuses with the plasma membrane of the host cell. The capsid
is removed, then reverse transcriptase catalyzes DNA from the RNA. The DNA
becomes a provirus and is then transcribed into mRNA, leading to production of a
virus. Capsids arrange around the genome.
Operons:
Genes with related functions are grouped on the same promoter region. When the
bacteria must make trypoptan, the enzymes are synthesized due to the operator
being on. The operator is on the promoter and controls the access of RNA
polymerase to the genes. The operator, promoter and genes (that code for
enzymes needed in metabolic pathways) are called the operon.
Trp is a corepressor, it cooperates with the repressor protein and helps switch off
the operon. This happens when trypoptan is present and need not be synthesized.
The lac can be switched off by an allosteric repressor protein if it binds to the
operator Lac is active by itself and the lac operon is switched off. Allolactose is
the inducer that inactives the repressor.
Gene to protein synthesis is very complicated, and there are several steps in
it. There are several ways that mistakes in this process can lead to evolution. In
1909, it was discovered that the function of a gene is to catalyze the production of
an enzyme. Organisms that are defective in a gene lack an enzyme, and this means
that they are blocked at different steps in their metabolic pathways that
synthesize certain nutrients. This could lead to evolution in bacteria. Wild-type
Neurospora can survive only on a minimal medium because it synthesizes its other
nutrients from the medium. However, mutants that are defective in certain genes
lack an enzyme, so somewhere in the metabolic pathway where the medium should
be synthesized, synthesis is blocked. Evolution can play two major roles in this
case. If the defect were to multiply and spread to several other bacteria, it could
eventually make up a large portion of the population. Natural selection could wipe
out all the mutants that need more than the minimal medium. On the other hand,
supposing that the environment does provide additional nutrients, then a new class
of mutants could evolve and live, and a large portion of the population might require
additional nutrients. An ineffective gene can be passed down through generations,
meaning many organisms have an ineffective enzyme.
During the transcription part of protein synthesis, introns, or noncoding
sequences in the pre-mRNA, are cleaved off in eukaryotic mRNA transcripts.
However, depending on which parts are treated as introns and which are treated as
exons, two different proteins may arise from the same gene. Alternative splicing
does occur. This can be observed in the fruit fly. Introns also increase the chance
of crossing over between exons. Homologous chromosomes may exchange single
exons. Each exon codes for a domain, or a part of the protein. This means that
any combination of exons in a protein is possible, and through repeated
recombinations, a new protein with new functions could be made. In addition, after
translation, posttranslational modifications may alter a protein significantly.
Enzymes can take away certain amino acids, or attach sugars, lipids and phosphate
groups. These changes to proteins lead to changes in an organism. Lastly,
mutations can greatly change an organism or a population. Point mutations that
occur in gametes can be passed on to future generations. A certain mutation may
make a gene ineffective; and in turn, an enzyme is not made-so a reaction is not
catalyzed. This could mean an additional nutrient is needed for mutant
Neurospora. Silent base-pair mutations do not affect the organism; the codon may
change but the amino acid remains the same. However, if an amino acid is changed,
protein activity change as well. Sometimes, it may improve the protein and give it
an even better function-the exon is changed. However, if a nonsense mutation
occurs (a premature stop codon) the polypeptide will be much shorter. If any of
these mutations do take place in germ line cells, then they can be passed on to
future descendants and multiply. The phenotype may be changed. In the case of
an insertion or a deletion, the reading frame changes-a frameshift mutation
occurs. Therefore, the codons change and so do the amino acids. If the mutation
is near the beginning of the gene, the protein may possibly not function. On the
evolutionary scale, if several organisms inherit this trait, then natural selection
may wipe out a large portion of the population. If the trait is not too harmful, it
may be passed on to future generations as well. In addition, DNA itself can
suffer from mutagens-the mutations are caused by errors during DNA replication
or repair. If the mutations have been caused due to errors in DNA replication,
then it means that the original DNA is faulty, and any mRNA that is transcribed
from it, and then made into a protein, will be faulty as well. The mutation can be
spread in this manner.
More chemistry:
Glycolysis
Animals use cellular respiration (with oxygen) or fermentation (without oxygen) to
break down fuel. When glucose is broken down energy is given off, this later helps
the chemiosmotic gradient. In respiration redox reactions oxidize (take electrons
away) from glucose and reduce (add electrons) to NAD+ and FADH+ but electrons
are juts stored here, no energy is lost. Electrons only lose energy in the electron
transport chain. As they go closer to the electronegative oxygen they give up
potential energy. Dehydrogenase strips hydrogen off the fuel; therefore, anything
with hydrogen-like glucose-is good fuel. In glycolysis, carbon is split into two
sugars. They are then oxidized and NADH is made. The remaining molecules are
called pyruvate. 2 molecules of ATP were used to phosphorylate the glucose but
the yield is 4-substrate level phosphorylation created 4 ATP molecules, so the net
is 2. 2 NADH have been created too. Then, the pyruvate is made ready for the
Krebs Cycle; it enters the mitochondrion if there is oxygen attracting it. The
carboxyl of the pyruvate is given off as carbon dioxide. The pyruvate is then
oxidized, creating NADH and a coenzyme A is added to make it reactive. The
Acetyl CoA combines with oxoacetate to make citric acid. The substrate loses
carbon dioxide twice in the process and it is oxidized each time so two NADH are
made. At one point electrons go to FADH2 but it contributes electrons to the
chain at a lower energy level. Also, substrate level phosphorylation does occur
because a phosphate group combines with ATP. The NADH and FADH2 (later in the
chain) carry the electrons over to the electron transport chain, which is a group of
proteins in the inner membrane/cystea, each with a prosthetic group, like iron,
which helps transfer electrons to the next protein. First, electrons go to the
flavoprotein, then to the iron-sulfur protein, then to the Q lipid. They then go to
cytochromes, with heme groups that help transfer electrons. The last protein
sends the electrons to oxygen and this forms water. However, no ATP is made.
Electrons are just passed along and they release energy at each point. Along with
the electrons, protons might be transported and some proteins take them. Others
send them into the surrounding solution. The energy lost by the electrons is used
to pump protons into the cell. This can only happen through the enzyme that makes
ATP, ATP synthase; nothing else is permeable to hydrogen ions. This is
chemiosmosis. The ions diffuse back out but as they do this there is a protonmotive force. They cause a rod inside the synthase to rotate and this changes the
shape of the knob, and activates sites where ADP and phosphate groups join and
make ATP. The most ATP is made this way. Fermentation leads to ATP without
oxygen being involved. This is anaerobic respiration. In alcohol fermentation,
pyruvate turns into ethanol and it has lost carbon dioxide. However, NADH gives
off its electrons to acetaldehyde. In lactic acid fermentation, NADH reduces
pyruvate into lactate and no carbon dioxide is given off. Fungi use lactic acid
fermentation, and so do human cells. Sugar catabolism is faster than oxygen’s
diffusion into cells. Therefore the cell uses fermentation, the lactate can be
toxic if in excess but the blood carries it away. Lactate is later made into
pyruvate again. Both fermentation and respiration make ATP but cellular
respiration, because it uses oxygen, makes more ATP with oxidative
phosphorylation (using the electron transport chain). In fermentation, an organic
molecule like pyruvate accepts electrons but in respiration NADH and FADH2 store
them. The energy in pyruvate can be used because there is oxygen attracting it
into the mitochondrion. Facultative anaerobes use fermentation or respiration to
make all the ATP they need to survive. Muscle cells are an example because
pyruvate leads to either acetyl CoA (if there is oxygen present), or if there is no
oxygen/no Krebs Cycle, pyruvate accepts electrons. Many organisms, even ancient
prokaryotes, used glycolysis. Some simple organisms make ATP from substrate
level phosphorylation only. But the end products of respiration and fermentation
are not just ATP, some energy is lost as heat. Also carbon skeletons are needed
for synthesis of nutrients. Sometimes organic monomers from digestion can be
used, like amino acids but sometimes compounds formed by glycolysis are sent into
anabolic pathways and cells synthesize nutrients they need from them. Glucose can
be made from pyruvate and acetyl CoA can be broken into fatty acids. If a cell
needs more ATP it speeds up respiration but if it needs less, then it slows down
respiration. Phosphofructokinase is an enzyme in glycolysis that commits the
enzyme to the process
Plants
I.
Photosynthesis
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Plants get energy through photosynthesis: 6CO2+6H2O+light→C6H12O6 + 6O2
In plants, there are pigments that absorb light energy. The pigments absorb
different wavelengths of light energy, this is the reason there are two different
photosystems in plants.
In noncyclic photophosphorylation, ATP is made from ADP and a phosphate group.
Light enters photosystem II and excites electrons. When electrons are excited,
they move to a higher energy state.
In photosystem II, light of wavelength 680 nm is absorbed.
The electrons, which are now excited, go to the primary electron acceptor and
from there to an electron transport chain. Proteins pass on the electrons here.
With each step, the electrons lose energy that they have previously absorbed.
This energy is used to make ATP
Know that the usage of this energy to make ATP is called photophosphorylation
because light energy caused it
The electron then goes to photosystem 700 and reaches a primary electron
acceptor there
The electron then goes to a second transport chain. NADP+ reductase places the
electron in NADP+ and stores it here.
Cyclic electron flow only uses photosystem I and not photosystem II.
After this step the Calvin cycle happens. Carbon fixation occurs (CO2 is
incorporated and attached to RuBP by the enzyme rubisco).
Each molecule is split into two pieces, each of which is called 3-phosphoglycerate.
Each of these tiny molecules get another phosphate group, and then NADPH, which
received an electron pair earlier, donates the electrons. The molecule is now called
G3P
The Calvin cycle takes five molecules of G3P and reduces it to three molecules of
RuBP (uses ATP to do so).
Photosynthesis in plants is possible because of chloroplasts. There is an
outermembrane (phospholipids), intermembrane space, inner membrane, and
stroma. The stroma is where the Calvin cycle happens. There are also stacks of
thylakoids (where the protein complexes are). Chloroplasts are where
chemiosmosis happens. H+ ions create a gradient in the thylakoids and as these
flow (through ATP synthase channel proteins) into the stroma, energy is released
and used to make ATP.
Photorespiration is the fixation of oxygen along with carbon dioxide. This reduces
plant efficiency and also, products formed from oxygen are not useful.
Peroxisomes inside the chloroplast break down unnecessary products of
photorespiration.
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II.
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CAM plants do photosynthesis during the day, when their stomata are closed,
therefore reducing loss of water. They absorb water in the night.
Structure
The three levels of transport in plants are cells absorbing water, short distance
(lateral) transport of minerals and long distance transport of sap. Plant cells all
have plasma membranes; they are selectively permeable.
But solutes can cross a membrane with a transport protein. These are specific;
they either bind to the solute and take it across the membrane or they provide
selective channels (gated channels open by stimuli) to let the specific solute pass
through. There is some active transport too. The proton pump does this; it
hydrolyzes ATP and the energy is used to pump hydrogen ions out of the cell.
The outside becomes positive and the inside negative; this charge is the membrane
potential. It allows for positively charged Potassium (K) ions to diffuse into the
cell down their electrochemical gradient-both the charge and concentrations favor
this. However, there can also be active transport. As hydrogen ions come back
into the cell negatively charged nitrate ions bind to it and come in too, this is
cotransport. Proton pumps play a role in chemiosmosis.
Plants gain water by osmosis; this is the passive transport (down a concentration
gradient) of water across a membrane. The water goes from a hypotonic (less
solute) to hypertonic (more solute) solution. Both physical pressure and
concentration combined cause the water potential; water flows from higher to
lower water potential.
Anything with solute in it has a negative water potential and attracts water.
However, adding physical pressure increases the water potential. Physical pressure
makes water escape from an exit, and applying pressure to a solution can stop it
from taking in water. Water flows from higher to lower water potential; pressure
makes it higher, so water is less likely to flow there.
If a cell is in a solution that is hypotonic and the cell has more solute, water rushes
in and creates turgor-the plant cell goes up against its wall. This makes it firm and
healthy. But if the solution is more concentrated with solute, water flows out of
the cell and it plasmozlyes or shrinks.
Water comes in and out through small selective channels called aquaporins. They
facilitate diffusion or passive transport.
A plant cell has three major compartments. The protoplast is the part without the
cell wall. The three compartments are the cell wall, cytosol and the vacuole; its
membrane, the tonoplast, regulates passage of items between the vacuole and
cytosol. Plasmodesmata make up the symplast; the continous cytosols between
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cells, and walls are chared in the apoplast but vacuoles are not shared. These are
used for transport. Lateral transport is short-distance transport.
Items can either move out of one cell and into the other, this means crossing each
plasma membrane. They can also use the symplast (entering the cell just once) or
the apoplast (using the walls, never needs to enter the cell). Long distance
transport happens by bulk flow. This happens due to tension in the xylem and
hydrostatic pressure in the phloem. Water and minerals must first be absorbed
into the roots; the roots have root hairs and special fungi called hyphae that mingle
with the roots to form mycorrhizae to increase the surface area of absorption.
The soil solution binds to the hair, gets absorbed by the epidermis and travels into
the cortex.
The cells of the epidermis take up some of the minerals right here. They go from
the walls, or apoplast, to the cytosol or symplast. They then reach the
endothermis and the minerals of the symplast simply continue on through the
plasmodesmata.
Those in the apoplast are stopped by the Casparian strip and must cross the plasma
membrane of the endothermic. So, all the minerals collect in the symplast. They
must then reach the xylem but the cells of the xylem lack protoplasts; everything
is part of the cell wall, so they go to the apoplast. This transferring of minerals to
the apoplast happens by diffusion and active transport. Xylem sap actually flows
upwards through the tissues of the plant. This is due to transpiration (loss of
water vapor).
Some of it is by root pressure; the minerals from the cortex are locked into the
stele, creating a negative water potential and attracting water. This water creates
hydrostatic pressure that pushes up the minerals. This pressure leads to guttation;
water drops can be seen on plants in the morning because more water enters the
plants than is transpired. The escape valves for water are hydathodes. But this is
not responsible for most transport; transpiration pull causes it too.
Stomata are spores on the leaf and the air in them is saturated with water vapor.
Water can leave through evaporation from here.
Also, negative pressure can happen in the leaf. The water evaporates and the film
of water that is left goes into the cell walls’ pores to adhere to the wall. The
water is cohesive so it resists an increase in its surface area. The adhesion and
surface tension make the water form a film called a meniscus.
The water causes negative pressure and this drives water from the xylem to the
surface. Water comes to the mesophyll through the cytosol (symplastic) and walls
(apoplastic). Water pushes and pulls up due to cohesion; it tends to stick
together. Water adheres to cell walls to fight gravity. This all creates tension in
the xylem and pushes the walls of the pipe inwards.
 When cavitation occurs, water vapor forms in xylem and this breaks the pull.
Transpiration stream can go around the water vapor. Guard cells control
transpiration by limiting the size of the stomata.
 Stomata can increase the internal surface area of a leaf. This increases exposure
to carbon dioxide. The surface area for evaporation also increases. The
transpiration to photosynthesis ratio tells how efficient a plant uses water in
regards to absorbing carbon dioxide. Transpiration helps transport minerals to the
leaves and also cools the leaf down.
 The stomata have guard cells that control their diameter by changing shape. When
guard cells are watered, they become turgid and swell and when cells lose water,
they lose diameter and close space between them. Turgor pressure on the guard
cells open and close stomata. Stomata open when guard cells have potassium from
other cells and the water potential turns negative and this attracts water creating
turgor. If potassium leaves the guard cells, water is lost and the stomata closes.
The entrance of potassium is all passive transport; it is due to active transport of
hydrogen ions out of the cell as potassium comes in.
 Stomata open in the day and close at night so that they do not lose water when it
is too dark to synthesize sugar. Light tells guard cells to become turgid; a bluelight receptor in a guard cell is activated and this activates proton pumps which
leads to the pumping of potassium into the cell. Light also drives photosynthesis in
the guard cells and opens stomata. Stomata also open when more carbon dioxide is
needed and are controlled by circadian ryhtms over 24 hours.
 However, if the plant is losing too much water, the stomata will close. Abscisic
acid tells guard cells to close stomata. This can all cause less photosynthesis but
also less wilting. Xerophytes have adaptations to reduce transpiration; their leaves
are thick and surface area of evaporation is reduced. Also ice plants take in
carbon dioxide by CAM in the night and photosynthesize (with closed stomata) in
the day.
 Plants use photosynthesis to generate energy for themselves. Plants are
autotrophs, they do depend on the outside environment but do not decompose
other organisms. They just need carbon dioxide, water and light-they are
photoautotrophs.
 Heteroautotrophs decompose other organisms. Photosynthesis takes part on the
chloroplast; it can be anywhere in the plant but is most concentrated in the
mesophyll cells of a leaf.
III. Structure and Photosynthesis
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Chlorophyll is the green pigment that absorbs light energy; oxygen leaves and
carbon dioxide enters through the stomata or stoma. 12 molecules of water enter
the cycle and six are re-made, a carbohydrate is also made. The first part of
photosynthesis is the light reactions part; it takes place in the thylakoid
membrane. Light drives the transfer of electrons from water to NADP+ to make it
NADPH which stores electrons. Water is split and oxygen is given off. The light
reactions also add a phosphate group to ATP-this is photophosphorylation; it makes
ATP. Light must be absorbed for photosynthesis; light travels in waves of
electromagnetic energy.
The distance between the crests of the waves is called wavelength and different
wavelengths code for different colors. The shorter the wavelength is, the
stronger (more energy) each photon, or particle of light, is. The most important
light is visible light, from 380 to 750 mm, and it can be detected as different
colors or wavelengths. Pigments absorb visible light-chlorophyll most often
absorbs red and blue-but transmit or reflect the colors that we see; they are not
the same as what was absorbed.
A spectrophotometer measures the ability of a pigment to absorb different
wavelengths and this ability is shown on a graph called the absorption spectrum.
The ability of each pigment to absorb colors is determined by the photons:
depending on the strength, each photon can excite the electron of a molecule of
pigment to a certain orbital level. Each pigment has a set orbital level the
electrons can excite to and the difference of (regular level) and (excited level)
must be the same as the energy of the photon. An action spectrum shows how
good each color (wavelength) is with photosynthesis by measuring the amount of
oxygen released.
Absorption spectra sometimes underestimate how powerful each wavelength is
because both chlorophyll a and b transmit the energy of a pigment but only
chlorophyll a can connect it to photosynthesis. Chlorophyll b is almost identical to
chlorophyll a but chlorophyll a is blue-green and b is yellow-green; it transmits its
energy to chlorophyll a. There are also carotenoids, they are hydrocarbons that
are yellow or orange.
They absorb but then get rid of excessive energy which may harm the chlorophyll.
The color absorbed does disappear; but the energy is used to excite an electron to
a higher orbital level. It drops back, and this releases heat as well as possibly light
and a photon is given off in the process. If the excited chlorophyll is in a thylakoid
membrane then it goes through the photosystem. The photosystem has chlorophyll
a and b as well as carotenoids and transmits the energy of a photon. Both
chlorophyll a and b transmit them to the chlorophyll a in the reaction center; the
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IV.
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first reaction occurs here. The primary electron acceptor is also in the reaction
center. It captures the electron before it falls back to its regular level.
The membrane has photosystem I and photosystem II, they both have identical
chlorophyll a molecules with different absorption spectra but the color being
absorbed is the same, red.
The xylem sap flows to the phloem and this transports the products of
photosynthesis around the plant. This is translocation. The phloem is an aqueous
solution and has a lot of sugar and amino acids as well. Phloem sap moves by bulk
flow, it loads and causes high solute concentrations in the sieve tube and the water
potential lowers. Then water flows into the tube as well.
Hydrostatic pressure develops and the pressure only goes down when transpiration
makes water evaporate. The sugar source in the plant is where sugar is made from
photosynthesis; this is the chloroplast. A sugar sink is where sugar is consumed or
stored. Phloem supplies these sugar sinks. Solutes can be transported along with
sugar to sugar sinks. A sugar sink gets its sugar from sources near it, like a
growing shoot tip and roots.
Sugar from the mesophyll goes itno the sieve-tube to go to sugar sinks.
Sometimes, apoplastic and symplastic pathways are used. The sugar moves out of
the cell walls and into other cells. Transfer cells are cells that increase their
surface area because of numerous branches in their walls. Sieve-tube members
store sugar and phloem loads more there; this is active transport, done by proton
pumps that use the energy of a gradient.
Plant Hormones
Auxin helps elongate, or lengthen, developing plant cells. It increases H+
concentration which then loosens cellulose fibers. In turn, water enters the cell
and it becomes larger
Auxin is made at the tips of shoots and roots.
Gibberellins promote cell growth. They are made in seeds and are transported to
other parts of the plant. Sudden, rapid growth may occur due to this hormone.
Abscisic Acid, ABA, inhibits growth. It causes scales and dormancy.
Cytokinins stimulate cell division. They cause lateral growth and therefore weaken
the influence of apical dominance. They delay aging. They are found in active
tissues and act in collaboratin with auxin. However-it may work against auxin in
some situations. Auxin goes down the shoot and encourages lengthening of a plant.
Cytokinins entering a shoot encourage lateral growth.
Ethylene causes fruit to ripen.
Senescence in plants is defined as a progression of irreversible change that leads
to death. Xylem vessels and work cells die.
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VI.
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Fruit ripening occurs when cell walls degrade, and the amount of chlorophyll
decreases. The presence of ethylene hastens this process.
Tropism
Tropism=growth response that causes the plant to curve
Phototropism=response to light; may result from auxin. The shoot tip is where
photoreception occurs and this triggers growth towards light.
Gravitropism=response to gravity. Roots curve downwards, shoots curve upwards.
Plants orient themselves based on statoliths, plastids that migrate to the low parts
of cells.
Thigmotropism=growth in response to touch
Plants may also grow due to turgor pressure.
Photoperiodism=when plants respond to changes in photoperiod, or daylight and
night. It is influenced by phytochrome, a protein that absorbs light. The two
types of phytochrome are Pr and Pfr.
Pfr is the active form of the protein and resets the circadian rhythm clock. It
accumulates in the day time. Pr accumulates at night because only sunlight converts
it to PFr. These proteins are equal in the daytime.
Long-day plants flower when there is more daylight. Short day plants flower when
there is less daylight. When the photoperiod is right, a hormone called florigen
travels to shoot tips and flowering occurs.
Plant Nutrition
Plants need water but also nutrients, otherwise, a limiting nutrient can be a loss of
primary productivity (new vegetation grown, or biomass, decreases)
Water mostly contributes in the zone of elongation
Organic material in plants=mostly carbon
Plants need nitrogen; those without it have few amino acids and are protein
deficient
They obtain it as NH4 or NO3, some is it in the rain and some is in the soil (soil is
formed by weathering down of rocks, loam=fertile soil, humus=bacteria decompose
dead material into soil and release nutrients into it)
Some is in the rain
The rest is made by nitrogen fixation. First, roots send out specific flavenoids
that are absorbed by specific bacteriods. The flavenoids trigger the nod genes in
the bacteriodes that generate Nod Factors; these Nod factors go to the plants
and act as growth factors that tell the Nodulin genes to make nodes.
The nodes host nitrogen fixing bacteria and give them carbohydrates (This is an
evolutionary tactic as well as mutualism) in return for the bacteria fixing nitrogen
and making it NH4, the NH4 is released and some is absorbed, the rest is
converted to NO3, absorbed by plants then made back into NH4
Plants increase surface area of absorption by mycorhizae (also controlled by
nodulin genes); ectomycorhizae form a mantle over the root and form dense
networks to absorb and endomycorhizae are thin but extent into the roots. These
are fungi that help absorb; they get carbs from the plant in return (mutualism
again, and evolutionary tactic)
Parasitism-bacteria like Mistletoe absorb xylem sap from plants
Commensalism-the seedless vascular epiphyte lives on plants but doesn’t harm
them, it doesn’t take their nutrients
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Some body systems:
Immune:
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The components of blood
Blood is made up of plasma, the liquid that carries the components, as well as
formed elements, which are red blood cells, white blood cells and platelets
Erythrocytes are red blood cells. They have hemoglobin on them and carry oxygen
and carbon dioxide. They do not have nuclei and have a lifespan of only 80 to 120
days.
Leukocytes are white blood cells. They protect the body from infections and can
move around the body to kill pathogens.
One type of leukocyte is a neutrophil, which engulfs pathogens. It releases
enzymes in the process.
Another type of leukocyte is an eosinophil, which attacks any pathogens labeled
with antibodies.
The smallest neutrophil is a lymphocyte, which can be either a B cell or a T cell. B
cells form in the bone marrow and respond to antigens. Each B cell has a special
antibody on it. When a B cell runs into an antigen that binds to its antibody, the B
cell multiplies. The two types of B cells are plasma cells (release antibodies) and
memory cells (keep their antibodies).
T cells end up producing cytotoxic T cells that kill foreign cells, and Helper T cells,
which stimulate the development of B cells.
Monocytes move around the body and engulf pathogens.
Platelets are parts of large cells, when there is a cut, they coagulate to form a
platelet plug and prevent excessive blood loss.
II.
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Blood Type
The four blood types are A, B, AB and O. Each is characterized by a type of
antigen on the blood molecules. Molecules characterized as Type A blood have A
antigens and anti-B antibodies.
 Molecules that are Type B blood have B antigens and anti-A antibodies.
 Molecules that are AB blood have no antibodies but both Antigen A and Antigen B.
 Type O blood has no antigens
 During blood transfusions, those with AB Blood can accept blood from anyone. But
those with type O blood can only accept blood from other Type O people.
 It is important to note that Type O blood can be given to people with type A or
type B blood as well.
III. Composition of Blood
 Most of it is water
 Blood also includes solutes such as electrolytes that maintain osmotic pressure
 It also has organic nutrients used for ATP production.
 Blood also has plasma proteins. Albumins help maintain osmotic pressure
 Globulins transport ions.
 Fibrinogen, when converted to fibrin, helps in the clotting process
 Blood also contains enzymes.
 The Kidney
 Vertebrate kidneys obtain blood from the renal artery and the blood leaves
through the renal vein. The kidney has two regions-the renal cortex and renal
medulla. The cortex has the cortical nephrons and the medulla has the
juxtamedullary nephrons. The nephron has a long exrectory tubules and capillaries
that make up the golmerulus; together these form the Bowman’s Capsule. Blood
pressure sends water and other solvents to capillaries, where the solvents dissolve
in the film and then diffuse into the tubules where they are less concentrated-the
concentration gradient drives them. The filtrate then goes to the proximal tubule;
extra toxins are secreted into the filtrate and good solutes are reabsorbed into
the blood. The secretion and reabsorption are both based on the epithelium of the
proximal tubule; substances must dissolve in it and then diffuse across it. Salt and
water are both reabsorbed; salt dissolves in the cells of the epithelium and then
diffuses back into the blood in the capillaries. Water follows the salt by osmosis
because the blood with the salt is now hypertonic to the water. Then, the filtrate
goes to the descending part of the loop of Henle. This is more evident in the renal
medulla than in the renal cortex. Water is reabsorbed but in the loop of Henle,
the epithelium is a permeable membrane only to water; the cells do not serve as
permeable membranes to salt. The area surrounding the loop of Henle is
hypertonic, or hyperosmotic, to the filtrate on the inside. Each nephron has an
afferent arteriole and the capillaries leave the glomerulus and make the efferent
arteriole. This arteriole then diverges into the peritubular capillaries which form
the vasa recta-this actually exchanges materials with the loop of Henle through
the fluids that surround both. In the descending part of the loop of Henle, water
is lost and the salt in the loop is greater. But in the ascending loop of Henle, the
cells are permeable to salt but not water. Therefore, the salt is lost. The fluid in
the medulla gets this salt and gains osmolarity. It is hypertonic. The filtrate now
moves to the distal tubule, it sends potassium into the filtrate and salt out using
special gated ion channels that are in its cell membranes. From the distal tubule,
the filtrate returns to the medulla. The epithelium of the collective duct is
permeable to water but not to salt, and the fluid outside of it is hyperosmotic to
the water inside it. Therefore, water is lost through a concentration gradient. At
the bottom of the duct, the epithelium is permeable to urea, so the urea that was
previously concentrated now diffuses out into the interstitial fluid because it does
not contain a lot of urea and it must balance quantities. All the processes that
took place to process the filtrate were due to diffusion of solutes across
membranes and osmosis; water moved across the membranes just to counter the
flow of solutes all in one direction at any given time. The urine is very diluted
because it has lost a lot of urea before being excreted. Several hormones regulate
osmoregulation. Anti-diuretic hormone is made in the hypothalamus and targets
the tubules and kidneys, forcing them to be more permeable to water so that more
water is conserved. The juxtaglomerular apparatus gives the glomerulus blood; this
blood in turn is filtered and loses its fluid through the membrane formed by the
podoctyes and capillaries. When the blood pressure is low, there will not be enough
filtration. The enzyme rennin will initiate the making of anguintensin II, a peptide
that increases blood pressure and blood volume. It also leads to the production of
aldosterone, which makes the distal tubes absorb more salt and water. ADH only
acts when osmolarity changes, not when volume of liquid changes. But the RAAS
pathway acts when water and salt must be reabsorbed to increase the volume of
blood. Increasing the reabsorption of water and salt leads to more fluid being
retained and this means more blood is present because the fluid mixes with the
blood. However, RAAS is opposed by the atrial natriuretic factor; when the blood
pressure is high ANF is released by atria walls and it stops the release of rennin
from the JGA and this stops RAAS. The passage of any item in the excretory
system happens through the walls of a membrane such as those of a capillary or
other blood vessel. Water diffuses through osmosis; the fact that many
membranes in the kidney are permeable to water means that it can be retained and
not sent away in the filtrate. So the excretory system works to preserve the
water balance; this is done due to membranes. If membranes in the tubules were
not permeable to water it wouldn’t ever be reabsorbed. Also, membranes let the
bad solutes diffuse across them into the tubules and good solutes diffuse back
based on concentration gradients as well as active transport, this keeps the body
clean.
Muscles:
I.
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II.
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What is an action potential?
First, know how neurons are organized: sensory neurons communicate information,
touch neurons that connect with other neurons, and then motor neurons convey the
impulses to effector cells.
When the impulse is given to the effector cell, a reflex occurs (this could be a
muscle movement).
All cells have a membrane potential (voltage across a plasma membrane). Such cells
are excitable.
Sometimes stimuli trigger depolarization of the membrane, the electrical gradient
is decreased. This could happen if positive ions flow into the membrane.
An action potential will be triggered. It happens because of voltage-gated ion
channels that open and close based on membrane potential.
When depolarization first occurs, the activation gate opens and lets the ions in, to
depolarize the membrane even more. The more ions enter, the more depolarization
happens. This is when the action potential actually occurs
Action potentials travel along axons by themselves. It is generated as ions flow
across membranes.
Muscle Contraction
When the action potential reaches the synaptic end bulb, calcium ions diffuse
through the voltage gated channels mentioned above
The calcium ion presence makes the vesicles migrate to the cell membrane and fuse
with it.
The neurotransmitter acetycholine is released by the vesicles; it binds to specific
receptors on the sarcolemma
Motor end plate is depolarized
The sodium ion then enters and creates an action potential
The potential travels through the tubules on the sarcolemma
As the potential travels, calcium ions are released into the sarcoplasm. They bind
to troponin and move tropomyosin, exposing sites on actin
ATP binds to myosin and separates into ADP and a phosphate group.
The myosin and actin form a cross bridge
The actin is pulled inwards
Then a new ATP binds to myosin, ending contraction
The stimulus stops and there is no more acetycholine (diffuses away)
Calcium ions are actively transported out of the sarcolemma.
The calcium ions, in turn, expose binding sites on actin
Myosin binds to actin
Myosin loses its ADP and P
Myosin heads change shape and drag actin into the middle of the sarcomere,
shortening it
 Contraction only stops when a new ATP binds to myosin and the cross bridges break
III. Skeletal Muscle Organization
 The epimysium surrounds the entire muscle
 The perimysium surrounds a fascicle (bundle of fibers or muscle cells)
 Around each cell is the endomysium
 In each muscle cell there is a sarcolemma (the cell membrane), sarcoplasm
(cytoplasm), and sarcoplasmic reticulum (stores calcium ions, is the endoplasmic
reticulum).
 The sarcoplasmic reticulum has Transverse tubules on it, these conduct stimuli and
tie together reticuli
 If there is an action potential it travels down the sarcolemma, into T tubules, and
into the sarcoplasmic reticulum
IV. Other info
 If your muscles are burning they are suffering from fatigue
 If they do not work they suffer hypotrophy, if they do a lot of work they
strengthen (hypertrophy)
 Bursa=fluid filled sac protecting muscles from bones and tendons
 Faccia=sheath protecting muscles from pathogens
 Cramps occur because muscles are contracting
 In isometric contraction the muscle wont change length
 In isotonic contraction the muscle will change length but in concentric, it shortens,
in eccentric, it lengthens
 Nervous System
The nervous system is made of neurons, which are large cells. They
participate in cell communication. Neurons make up nerves; neurons send messages
through communication pathways either electrically or chemically. Neurons have
large cell bodies with processes called dendrite and axons; axons are very long and
conduct messages to dendrites of other cells or neurons. They are surrounded by
Schwann cells that form the myelin sheath; the membranes of these cells are very
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important. They are made of lipids and lipids do not conduct electricity well; as a
result, electrical currents cannot enter the axons and interfere negatively with
signaling. This is where the permeability of the membranes is important. The end
of an axon is the synaptic terminal and it sends other cells messages, either
directly in an electrical synapse (place where the two cell meet) or through
neurotransmitters in a chemical synapse. Sensory neurons are the cells that get
information about outside conditions and they convey it to the interneurons and
motor neurons in the central nervous system-the brain or spinal cord. Motor cells
send impulses to effector cells in the body that conduct movement. Interneurons
also receive messages to stop or start movement elsewhere in the body, for
example. Neurons are arranged in circuits. A ganglion is a set of nerve cell bodies
and a ganglion in the brain is called a nuclei; this lets the nervous system conduct
movement and thought without utilizing the entire brain. Glia are the supporting
cells and they may serve as astrocytes, which force capillaries in the brain to bond
tightly together. This forms the brain-blood barrier and stops other substances
from entering the brain. Schwann cells surrounding the axons have plasma
membranes that protect the axons from electrical current. When action potentials
must jump from cell to cell, they base themselves on transport proteins in the
Schwann cells. Neurons have impulses, which are electrical signals across plasma
membranes. These are based on membrane potentials; which are is the voltage
across the plasma membrane. The resting membrane potential is -70mV but in
depolarization goes to +35 mV. In hyperpolarization the gradient is increased,
more potassium moves out of the cell than is needed and there is no stimulation.
Normally-the inside of the cell is negative and the outside is positive; the charge
between them is the membrane potential. The plasma membrane is selectively
permeable; its pores are so small it only lets through certain materials. In addition
the passage of ions is regulated by transport proteins. Inside the cell there is
more Potassium K+ than there is sodium Na+ because there is more sodium
surrounding the cell. Specific channels allow each ion to cross the membrane. Due
to diffusion, Potassium should diffuse out of the cell and when it does this, it takes
the positive charge with it and eventually the electrical gradient brings it back to
balance out the positive and negative charges. This is passive transport; no work is
done. The concentration gradient is the potential energy driving the force. The
membrane is not very permeable to Sodium but some channels to allow sodium to
pass through the membrane. There is less sodium inside the cell than outside so
the concentration gradient favors the diffusion of sodium into the cell. This would
make the cell more positively charged on the inside. Some cells are called
excitable cells because they can change their membrane potential. When resting,
these cells are said to be in resting potential. Ions enter the cells through gated
ion channels, which are channels made of transport proteins because the core of
the membrane stops ions from passing through. The channel opens due to external
stimuli. The sodium-potassium pump uses ATP to send the sodium out of the cell
and potassium into the cell. It restores the original concentrations. Depending on
the stimulus, there is either a hyperpolarization-increasing the membrane potential
or the difference in charges-or a depolarization, reducing the electrical gradient.
In this case, sodium must flow into the cell to make the inside of it turn more
positive. This voltage is called a graded potential because it changes by the
stimuli’s actions. Sodium continues to enter the cell through the gated ion channels
in depolarization; this is due to the concentration gradient as well as the electrical
gradient-the sodium and the positive charge are lacked in the cytoplasm and
therefore travel there. Then, no more stimuli can be added at the threshold
potential. The action potential is reached, where more and more sodium enters the
cell. Voltage gated ion channels are opened up by the difference in electrical
gradient, allowing for more sodium to come in, until the insides of the cell is
positive and the outside is negative. This is because the activation channel for
sodium is open and so is the inactivation channel; the inactivation channel must
close. But it slowly closes, meanwhile potassium channels slowly open and allow for
potassium to flow out-this leads to depolarization because the potassium, as it
flows by its concentration gradient to where it is less concentrated, is also flowing
by its electrical gradient to the now-negatively charged exterior of the cell. This
balances out the charges. After the action potential impulse is over, the
inactivation channel of the sodium closes, preventing it from starting an action
potential again-this is the refractory period. However, the action potential impulse
travels from region to region of each neuron on the axon. This sends messages to
the brain. The presynaptic cell uses its axons to send the impulse to the
posystynpatic cell’s dendrites right away through an electrical synapse where the
two cells just join. But more common is the chemical synapse-the cells aren’t
coupled, so the impulse is made into neurotransmitters which are sent over to the
postsynaptic cell. They bind to channels here, the neurotransmitters only reach
the new cell because calcium ions bind to the neuron and makes the vesicles fuse
with the membrane of the presynaptic cell and release the neurotransmitters
through endocytosis. The neurotransmitter is often destroyed in the new cell
before it can convey much information. The action potential actually conveys
signals through neurons. The sodium potassium pump also sends signals to the
brain. The nerves regulate the heartbeat-one set of nerves speeds it, the other
set slows it, and this regulates the adrenaline rush. The nervous system regulates
the body because anything experienced by the five senses is sensed by the sensory
nerves; they conduct messages to the interneurons and motor neurons and from
there to the effector cells, making the body react. For example the hypothalamus
has a thermostat that regulates body temperature. Nerve cells sense a change in
body temperatures and warm receptors signal the nerves in the hypothalamus if
the temperature increases; cold receptors tell the hypothalamus if the
temperature decreases. This leads to the inhibition or activation of mechanisms
like vasoconstriction or vasodilation to regulate heat.