Chapter 2: Chemistry

The emphasis on detail is different between an AP biology course and a regular high school biology course.

You can get a more thorough understanding of biology with the understanding of biological processes at the molecular level.
AP examiners want to know if you have this kind of understanding.
A brief review of chemistry and the characteristics of major groups of biological molecule is what you should start with.

The AP exam won't ask you to draw structures or distinguish differences between molecule because chemistry deepens your understanding of biology.

You only need to be able to distinguish between groups of the same type of molecule.

Outside the nucleus, negatively charged electrons are arranged.

Chemical bonds between atoms are formed by their electrons.

When the electronegativities of the atoms are different, one atom has a stronger pull on the electrons than the other.

The atom that gains electrons has a negative charge, while the atom that loses electrons has a positive charge.
The positive and negative ion are attracted to each other.
The bond formed in a molecule of NaCl is an ionic bond.

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When the two atoms sharing electrons are the same, the electronegativities are the same.

This kind of bond has different electronegativities and an equal distribution of electrons.

The positive pole is created by the weaker pull on the electrons in the area around the atom.
electrons are shared between the oxygen atom and each hydrogen atom in a molecule of water Oxygen exerts a stronger pull on shared electrons than does each hydrogen atom.
The negative pole is near the oxygen atom and the positive pole is near the hydrogen atom.

Imagine a continuum based on the differences of electronegativities when you think of chemical bonds.

There are no differences in the electronegativities of the atoms on the left end.

Nonpolar bonds form when electrons are shared equally.

When there are large differences in electronegativities, the right end represents bonds that form.
ionic bonds form when electrons are transferred from one atom to another.

The poles of the polar water molecule interact with the ionic substances and separate them into ion substances.

Substances with polar covalent bonds are similar to those with no bonds at all.

It is often referred to as a universal solvent because it has so many different kinds of molecule in it.

The degree to which a substance changes temperature is called specific heat.

Water has a high specific heat, changing temperature very slowly with changes in its heat content.
You have to add a large amount of energy to warm water or remove a large amount of energy to cool it.
Vaporative cooling is when a large amount of heat is taken with sweat and you are cooled.
The water temperature remains constant when it changes physical states from solid to liquid to gas.
The absorbed energy can only be used to break the hydrogen bonds in the water.
The energy released in the reverse reactions reestablishes the hydrogen bonds.

Molecules can periodically approach one another if hydrogen bonds are weak.

In the solid state of water, the weak hydrogen bonds between water molecule become rigid and form a crystal that keeps the molecule separated and less dense than its liquid form.
If ice did not float, it would sink and remain frozen.
The survival of organisms at the bottom of bodies of water would be affected by this.

A water surface that is firm enough to allow many insects to walk upon it without sinking is created by the strong cohesion between water molecule.

If you wet your finger, you can pick up a straight pin by touching it because the water on your finger sticks to both your skin and the pin.

Some people wet their fingers to help them.

Four of carbon's electrons can be used to form bonds with other atoms.

You will always see four lines connecting a carbon atom to other atoms, each line representing a pair of shared electrons.

A complex molecule can be formed by stringing carbon atoms together in a straight line or by connecting carbons together to form rings.
Nitrogen, oxygen, and other atoms add to the carbon molecule.

The molecule's acidity or polarity is given by each functional group.

The following sections discuss four important classes of organic molecule.

The AP exam doesn't require you to know their formulas.
You should be aware of the general characteristics that distinguish one group from another.

There is a single sugar molecule in this picture.

Changes in the position of certain atoms can change the chemistry of a molecule.

A water molecule is lost during the joining process.

The formula is C12H22O11 when the two sugars link to form sucrose.

A polysaccharide consists of repeating units of a monosaccharide.

It has a different pattern of branching than starch.

The bonds in starch can easily be broken down by humans and other animals, but only subtle changes in the structure of the molecule can lead to dramatic chemical changes.

Lipids are a class of substances that are almost insoluble in water, but are highly soluble in nonpolar substances, like ether or chloroform.

The carboxyl group at one end of the chain is what makes up the Fatty Acids.

The number of carbons and the placement of single and double bonds between the carbons affect the structure of the Fatty Acids.

The bend at the bond is caused by the double bond in the acid.

As a result, saturated fatty acids pack together more tightly, have higher melting temperatures, and are usually solid at room temperature.

You can remember this by thinking that each carbon is saturated with hydrogen.

The two "tails" of the phospholipid are not polar and are non-hygenic.

Phospholipids are often found in sandwich-like formations, with the hydrophobic tails grouped together on the inside of the sandwich and the hydrophilic heads facing the outside.

The structural foundation of cell membranes is provided by formations of phospholipids.

Steroids include cholesterol and hormones such as testosterone and estrogen.

The functions of the proteins can be grouped.

The structures of the proteins are similar.

One H2O molecule is released during the formation of each peptide bond, similar to the formation of carbohydrate polymers.

There is a central carbon bond between the carboxyl group and the hydrogen atom.

The fourth bond of the central carbon is shown with the letter R, which means an atom or group of atoms that varies from one type to another.
The R is a hydrogen atom.
R is CH2OH for serine.
Sulfur and a carbon ring can be found in R for other amino acids.
The side chain is called the R group.

The molecule is made up ofNH2 at one end andCOOH at the other.

The R group is specific to each amino acid.
The R group can make the amino acid acidic or basic.
Dramatic differences in protein function can be caused by the differences in structure.

The primary structure for the antidiuretic hormone can be written with three letters.

There are factors that contribute to the tertiary structure.

The bridge helps maintain the folds of the chain.

Four peptide chains are held together by hydrogen bonding and interactions among R groups.

The genetic information of a cell can be found in the deoxyribonucleic acid.

The genetic instructions to ribonucleic acid are passed on to the cell.

Pyrimidines are single-ring nitrogen bases and purines are double-ring bases.

The first letter of each of the four bases is often used to represent the respective nucleotide.

A single-stranded DNA molecule is formed when the phosphate group of one nucleotide joins to the sugar of another.

Two strands of DNA are joined by weak hydrogen bonds between the bases to form a double-stranded DNA.
A double helix is formed when DNA is bonded in this way.

The strands of the helix are oriented in opposite directions.

ribose is the sugar in the nucleotides that make an RNA molecule.

It is not possible to find the thymine nucleotide in RNA.

It is replaced with uracil.

uracil pairs with adenine when the bases are in the same place.

The double helix in DNA is caused by single-stranded RNA.

The AP exam only requires you to know the general structure of a nucleotide, the names of the nucleotides, and the differences between DNA and pyrimidines.

A catalyst is a substance that causes a reaction but does not cause a chemical change.

The catalyst can be used over and over again.

Concentration of the reactants and end products is what determines the net direction of the reaction.

The rate at which C and D are formed in the forward direction is the same as the rate at which A and B are formed in the reverse direction.

The breakdown of the amylose is accomplished by the amylase.

They are specific to the substrates.

The b-glycosidic linkage can't be broken by the amylase because it can't break the a-glycosidic linkage.

As a result of a reaction, the enzyme is unchanged.

It can do its function many times.

There is a reaction in both directions.

By keeping the product concentration low, the net direction of the reaction can be driven in the forward direction.

The efficiency is affected by temperature and pH.

The temperature of the human body is close to the optimal temperature for most human enzymes.
The pepsin, which digests proteins in the stomach, becomes active only at a low pH.

There is an active site with which the reactants readily interact because of the shape.

The interaction of the reactants and the enzyme causes the enzyme to change shape.
The new position is favorable to the reaction.

The product is released once the reaction is complete.

Coenzymes are components of vitamins.

Adenine is an adenine nucleotide with two additional groups.

One way to regulate a reaction is by regulating itsidase.

It is possible to permanently change the structure of the enzyme by modifying an amino acid.

The effects of other inhibitors can be reversed by ionic or hydrogen bonds.

The mimic prevents the enzyme from catalyzing the substrate.

The shape of the enzyme is altered by the inhibitor.

There are many toxins and antibiotics that are noncompetitive.

This can happen in enzymes that have two or more of the same quaternary structure, each with its own active site.

A common example of this process is hemoglobin, whose binding capacity increases after the first oxygen binding to an active site.

A review of the material presented in this chapter is provided by the questions that follow.

They can be used to evaluate how well you understand the concepts.
AP multiple-choice questions are often more general, covering a broad range of concepts.
The two practice exams in this book are for these types of questions.

Four possible answers or sentence completions are followed by each of the following questions or statements.

The one best answer or sentence is what you choose.

Products E and L are usually consumed by other reactions.

Product B's net rate of production would decrease.

Product C's net rate of production would decrease.

Product D's net rate of production would decrease.

Product J's net rate of production would decrease.

Product D's rate of production would increase.

Product E's rate of production would increase.

Product J's rate of production would increase.

The rate of production would decrease.

Two curves describe the potential energy of substances during a chemical reaction.

Curve B could be showing the influence of an animal.

The amount of energy in the reactants is more than the amount in the products.

The energy of the reaction could be given by X + Y + Z.

Themolecule that is being described is indicated for each question.

The questions that follow are typical of an entire AP exam question or just that part of a question that is related to this chapter.

There are two types of questions on the AP exam.

It takes about 20 minutes to answer a long free-response question.
Sometimes they offer you a choice of questions to answer.
6 minutes is the time it takes to answer a short free-response question.
diagrams can be used to supplement your answers, but a diagram alone is not adequate.

When cooked, the white solid surrounding the egg's yolk is a clear liquid.

Explain why cooking causes this change.

Most of the cells are made of water.

Explain why the specific heat of water is important to a cell in one or two sentences.

Explain the significance of the ends during the assembly of a double-helix DNA molecule.

The table below shows the rate of a reaction with and without an enzyme.

Explain the significance of temperature and the presence of anidase on the rate of a reaction in three to four sentences.

Phospholipids are made up of two fatty acids and one phosphate group.

The rate of production of E would decrease as a result.

Product D's rate of production decreases as it accumulates.
The reverse reaction, of D to C, increases at the same time.
As C increases, the rate of production of J increases.
The rate of production of D would equal the rate of the reverse reaction and the equilibrium between C and D would be zero.

Less and less quantities of C would be converted to products D and J.

The rate of production of D, J, E, K, and L would decrease.
The reverse reaction of C to B and then to A would increase as quantities of C increased.

The rate of production of products D, E, J, K, and L would be zero if A, B, and C were in chemical equilibrium.

There is a single molecule of Glucose.

They are made from repeating units of glucose.

It's a mixture of acids and sugars.

Curve A shows how the activation energy would be lowered if there was an animal present.

The products have less energy than the reactants.
This kind of reaction is called an exergonic reaction.
It would be an endergonic reaction if the products had more energy than the reactants.

There is a ring structure.

Amylose is found in plants.

There are five polypeptide acids in this.

This is a fat.

There is one saturated and one monounsaturated fat in thislipid.

Long hydrocarbon chains are nonpolar.

There is a polar molecule.

A substance that ionizes in water becomes hydrophilic.

There is a polypeptide.

There are two types of sugars: monosaccharide and polysaccharide.

A three-dimensional structure is lost when a protein is heated above a critical temperature.

When the secondary, tertiary, and quaternary structures of aProtein break down, as they will when excessively heated, the structure of theProtein is permanently destroyed.

Water has a high specific heat capacity and it takes it a long time to change its temperature.

The internal temperature of the cell is not changed by the activities of the cell that release or absorb energy.

A double-helix DNA molecule has two single-strands.

The two strands have to be arranged in opposite directions.

There are more reactions because the molecule is moving faster at higher temperatures.

The coming together of the reactants is a catalyst.
The effect of the enzyme is eliminated because the high temperature denaturizes it and the reaction rate falls back to the rate that occurs without it.

There are two types of Enzymes.

The bonds between the chains of amino acids are bonds ofpeptides.

There is a central carbon atom that is bonded to an amino group, a carboxyl group, and a hydrogen atom.

A fourth bond is made with a group of atoms.
A variable group can be a single hydrogen atom or a group of many atoms.
The individual amino acids interact with one another, giving the protein special spatial and functional characteristics.

The unique attributes of the enzyme allow it to make specific reactions.

Four features of theprotein's structure are used to derive its characteristics.
The kind and arrangement of the amino acids is described by the primary structure.
A secondary structure is formed from hydrogen bonding.
The threedimensional shape of a helix is the secondary structure.
A tertiary structure is created by further interactions between amino acids.
The interactions include hydrogen bonding and ionic bonding between R groups, the "hiding" of R groups into the interior of the protein, and a disulfide bridge between two cysteine amino acids.
The shape of the enzymes is a result of all of the interactions.

The function of an enzyme is to speed up a reaction.

The model describes how enzymes work.
In this model, there are specific active sites within the enzyme.
In order to reduce the amount of activation energy required for a bond to form between the substrate molecule and the active sites, the enzyme changes shape.
Bonding proceeds at a faster rate with less energy required.

A cofactor is required to make a reaction.

Cofactors include coenzymes and metal ion.

There are a number of ways that enzymes are regulated.

Allosteric effectors are substances that bind to the enzyme and make it work.
Sometimes an allosteric inhibitor is a product of a series of reactions.
This is a feedback example.
Allosteric effectors bind to special sites.
In competitive inhibition, the active site is competing with the substrate molecule.

The activity of the enzyme is stopped.

Some drugs and toxins are examples.
Environmental factors play a role in the activity of enzymes.
The temperatures and pH of the organisms are the best.
When the pH is low, the stomach'sidases are not active.

You may be able to shorten your answer to allow you time to answer other questions.

On the other hand, if you had time, you could give examples of some specific enzymes or coenzymes, which you'll learn about in subsequent chapters.