ap bio big study guide

7/30/2019 AP Bio Big Study Guide

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Priya Sorab

AP Bio Study Guide

Note: This does not covereverything for the AP Exam but does highlight many important topics.

I. Intro to Biology

The chemistry behind it

I. Chemical Elements and Compounds

A. The study of Earths ozone layer

1. Several scientists study the ozone layer of the earth and how it affects life on the planet.

2. There are several specialists.

3. Biologists are scientists who specialize in the study of life.

B. Matter consists of chemical elements in pure form and in combinations called compounds.

1. Organisms are made of matter, anything that takes up space and has mass (not weight).

2. Mass exists in many form and is present in everything, such as rocks and glass.

3. Some Greek philosophers believed the four elements were only air, water, fire and earth, pure substances.

4. 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.

5. A compound is a substance consisting of two or more elements in a fixed ratio.

6. Table salt is sodium chloride-NaCI. Chlorine and sodium are in a 1:1 ratio.

C. Life requires about 25 chemical elements

1. 25 of the natural elements are essential, like carbon, oxygen, hydrogen and nitrogen. They make up 96% of living matter.

2. Phosporus, sulfur, calcium and potassium account for the remaining 4%.

3. Trace elements are elements required by an organism in only small quantities.

4. Some, like iron, are needed by all forms of life.

5. Iodine is only needed in vertebrates to produce iodine.

II. Atoms and Molecules

A. Atomic structure determines the behavior of an element-subatomic particles

1. 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.


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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 atoms 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 inurine.

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


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1. The chemical behavior of an atom is determined b its electron configuration, the distribution of electrons in the atoms 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 doesnt 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 arent 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.


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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 chlorineatom.

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 doesnt 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 weakbonds 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.


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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 molecules 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 determineby 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 brains 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.


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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. Modern life is tied to water.

3. Most cells are surrounded in water and are 70-90% water.

4. of Earth is in water.

5. Most is liquid but water is also present as ice and vapor.

6. Water is present in all three states of matter, solid, liquid and gas.

II. The Effects of Waters 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 newwater 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.


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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 isnt 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. Waters High Specific Heat

1. The ability of water to stabilize temperature depends on its 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 waters 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. Waters 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. Waters high heat of vaporization is its emergent property caused by hydrogen bonds, and these must break before the molecules leave the liquid.

7. Waters 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 toheave as gas.

9. Evaporative cooling of water gives stability to the temperatures of lakes and ponds.


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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 Dont 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 doesnt 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


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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

cells 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 Bases-

1. 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.


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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 OH- concentrations.

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.


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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 precipitations 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:

I. The importance of Carbon

A. Introduction

1. Most chemicals are based on carbon.

2. It can form different, large molecules.

3. 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 carboncompounds 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


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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 doesnt 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 cells 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 intwo different ways.

7. They are important in the pharmaceutical industry but it is important to remember that two enantiomers may have different functions.


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8. Thaliomide, produced for pregnant women in the 1960s, 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


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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. Carbons 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 organisms 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.


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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 systems 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.


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4. A system of charged particles is not very stable because opposite charges arent apart.

E. Free Energy: A Criterion for Spontaneous Change

1. Free energy is the portion of a systems 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 systems 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.


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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 ATPs 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.


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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 hydroxylgroups.

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 enzymes 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.


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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 accessthe 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 cells 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.


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III. The control of metabolism

A. Intro

1. Chemical chaos would happen if all of a cells 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 isnt 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.


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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 doesnt behave like a bunch of monomers.

Genetics:

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 didnt know if its genotype was AA or Aa. I must cross it with a gray cat (aa). IF the black catsgenotype 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 (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


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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 persons 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

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.


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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, Cytosine-Guanine.

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 pre-mRNA 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). snRNPs (small nuclear ribnonucleoproteins) that have RNA in them combine with additional proteins to formspliceosomes. 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. 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 thatit can deposit the amino acid.

3. 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.

4. The steps above were initiation of translation. In elongations first step, codon recognition, the mRNA binds to the anticodon of the

tRNA in the ribosomes 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.

5. In termination, a stop codon in mRNA reaches the A site and bonds with a release factor. Instead of another amino acid, a molecule ofwater bonds to the polypeptide chain and it is released.

6. 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

its 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 ofthe 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 cells surface and fuse with the plasmamembrane; 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 isnt 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 isnt 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.


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b. Transformation: A live, nonpathogenic cell takes up some DNA that gives a cel l 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.

c. Transduction: This is the transfer of genetic material by a phage. In general transduction, when a virus is being made, it gets the host cells 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.

3. 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 reversetranscriptase 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.

4. 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-typeNeurospora 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 wherethe 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 overbetween 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. Inaddition, 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 geneineffective; 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 aninsertion 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 transcribedfrom 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 (addelectrons) 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 themitochondrion if there is oxygen attracting it. The carboxyl of the pyruvate is given off as carbon dioxide. The pyruvate is then oxidized,


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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 theflavoprotein, 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 thatmakes ATP, ATP synthase; nothing else is permeable to hydrogen ions. This is chemiosmosis. The ions diffuse back out but as they do thisthere is a proton-motive 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 oxygens diffusion into cells. Therefore the cell uses fermentation, thelactate 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 nooxygen/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

Plants get energy through photosynthesis: 6CO2+6H2O+lightC6H12O6 + 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


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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.

CAM plants do photosynthesis during the day, when their stomata are closed, therefore reducing loss of water. They absorb water in the night.

II. 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 activetransport. 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; waterflows 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 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 happensdue 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 wi

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