Roberto Nieves AP Bio P.

Chapter 2 (questions from chap 2 got erased in transfer from school Microsoft word to home but all the answer are still here) 1. An element is only made of one type of matter whereas a compound is made up of two or more types of elements. 2. Nitrogen, Oxygen, Hydrogen, and Carbon a. Neutrons are neutral subatomic particles with neutral charges and protons have positive charges of +1. They are both found in the nucleus. b. Atomic number refers to the number of protons whereas mass number is the sum of protons and neutrons. c. Mass number is the mass of a particular isotope of an element; atomic weight is the average mass number of an element when accounting for all isotopes and their natural abundance. Two isotopes of an element are similar in that they have the same number of protons but they have a different number of neutrons. Covalent bonds share electrons; ionic bonds utilize the attraction between oppositely charged ions. If the electrons are shared equally, then the bond is nonpolar. If the electrons aren t shared equally, then the bond is polar. Strong covalent bonds are necessary to link atoms to form a cell s molecules. Weak bonds are also necessary for the emergence of the properties of life, such as hydrogen bonds and how they allow insects to walk and live on water. Hydrogen bonds result from the attraction between the partial positive charge on the hydrogen atom of water and the partial negative charge of another electronegative atoms, usually nitrogen or oxygen. Van der Waals interactions are a result of atoms and molecules being in extremely close proximity to each other. The shape of a molecule is important because biological molecules are designed to fit specific shapes and make reactions. Endorphins, which are signaling molecules, bind to specific receptors to make specific reactions. Chemical equilibrium is when the forward and reverse reactions occur at the same rate, and the relative concentrations of products and reactants stop changing.

Chapter 3 The Properties of Water 1. With the use of a diagram or diagrams, explain why water molecules are:

a. polar They are polar because opposite ends of a molecule have opposite charges. The hydrogen is slightly positive of one molecule and the oxygen is slightly negative of the molecule, thus the attraction is electrical. b. capable of hydrogen bonding with four neighboring water molecules 1. Define cohesion and adhesion. Explain how water s cohesion and adhesion contribute to the movement of water from the roots to the leaves of a tree.

Cohesion is when the hydrogen bonds hold a substance together . Cohesion due to hydrogen bonding contributes to the transport of water and dissolved nutrients against gravity in plants. Adhesion is the clinging of one substance to another; it helps overcome the force of gravity and pull it upward. 3. Explain the following observations by referring to the properties of water:
y

Coastal areas have milder climates than adjacent inland areas. Water has a high specific heat, which means that it temperatures in water are maintained at a stable level, meaning the climate by the water is stabilized as well. Ocean temperatures fluctuate much less than air temperatures on land.

Water has a high specific heat, so it rarely fluctuates greatly. Water resists change more than air, because it has a higher specific heat.
y

Insects like water striders can walk on the surface of a pond without breaking the surface.

The high surface tension of water, resulting from the collective strength of its hydrogen bonds allows the water strider to walk on the pond without breaking its surface.
y

If you slightly overfill a water glass, the water will form a convex surface above the top of the glass.

Cohesion makes the water stick together, thus the water won't overflow from the top of the glass.
y

If you place a paper towel so that it touches spilled water, the towel will draw in the water.

This is due to adhesion, since water clings to other substances.

Ice floats on water.

Ice is less dense than water and it expands when it freezes, its molecules are not packed in as close as in water.
y

Humans sweat and dogs pant to cool themselves on hot days.

Evaporative cooling means that only the hottest molecules, with the greatest kinetic energy, leave and the cooler water remains on our bodies, in the form of sweat. 4. Distinguish among a solute, a solvent, and a solution. A solute is the substance that is dissolved and the solvent is what dissolves the substance. A mixture of a solute and a solvent make a solution. 5. Distinguish between hydrophobic and hydrophilic substances. Hydrophobic substances repel water while hydrophilic substances have a affinity for water, thus hydrophilic substances will mix with water while hydrophobic substances won't. The Dissociation of Water Molecules 1. Define acid, base, and pH.

Acid is a substance that increases the hydrogen concentration of a solution. A base reduces the hydrogen concentration of a solution. The pH is the negative logarithm for hydrogen ions. 1. Explain how acids and bases may directly or indirectly alter the hydrogen ion concentration of a solution.

Acid is a substance that increases the hydrogen concentration of a solution. A base reduces the hydrogen concentration of a solution. Chapter 4 The Importance of Carbon 1. Explain how carbon s electron configuration accounts for its ability to form large, complex, and diverse organic molecules.

Carbon has 4 valence electrons is a shell that tends to hold 8. Thus, carbon rarely gains or loses electrons to form ionic bonds, since it would have to gain or donate 4 electrons to form those bonds. Thus carbon usually completes its shell by sharing valence electrons with other molecules. Carbon's tetravalence allows it to make large, complex molecules.

1. Describe the basic structure of a hydrocarbon and explain why these molecules are hydrophobic.

Covalent bonds between hydrogen atoms and carbon atoms are nonpolar thus, they are hydrophobic. Hydrocarbon are organic molecules consisting of only carbon and hydrogen. Carbon chains form the skeletons of most organic molecules. 1. Distinguish among the three types of isomers: structural, geometric, and enantiomer.

A structural isomer differs in the covalent arrangement of its atoms. Geometric isomers differ in spatial arrangements. Enantiomers are molecules that are the mirror images of each other. Functional Groups 1. Name the major functional groups found in organic molecules. Describe the basic structure of each functional group and outline the chemical properties of the organic molecules in which they occur.

Hydroxyl group is when a hydrogen atoms is bonded to an oxygen atom which is then bonded to the carbon skeleton of the organic molecule. Organic compounds containing hydroxyl groups are called alcohols and their names end in ol. Carbonyl group consists of a carbon atom joined to an oxygen atom by a double bond. The organic compound is called aldehyde, when the carbonyl group is towards the end of the skeleton and the ketone is when the carbonyl group is in the middle. Carboxyl group is when an oxygen is double bonded to a carbon atom that is also bonded to a hydroxyl group. Compounds containing carboxyl groups are known as carboxylic acids or organic acids. Amino group consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton. The organic compound within this group is the amine. The sulfhydryl group, sulfur bonds with hydrogen. Organic compounds containing sulfhydryls are thiols. Phosphate is an anion formed by disocciation of an inorganic acid called phosphoric acid. The loss of hydrogen ions by dissociation leaves the phosphate with a negative charge. The organic compounds are called phosphate groups.

10. Polypeptides are polymers that make up proteins. 1. Distinguish between monomers and polymers.

Monomers are the small building blocks of polymers. Polymers are long molecules consisting of many similar or identical monomers. 1. Explain what happens in condensation and hydrolysis reactions.

Condensation reactions occur when two monomers covalently bind by losing a water molecule. Hydrolysis reactions disassemble polymers to monomers by breaking bonds by adding a water molecule. Carbohydrates Serve as Fuel and Building Material 1. Distinguish among monosaccharides, disaccharides, and polysaccharides.

Monosaccharides are single (simple) sugars. Disaccharides are double sugars, created by two monosaccharides joined via condensation reactions. Carbohydrates that are macromolecules are polysaccharides; they are composed of many simple sugars. 1. Describe the formation of a glycosidic linkage.

Glycosidic linkages are covalent bonds formed between two monosaccharides by a dehydration reaction. 1. Distinguish between the glycosidic linkages found in starch and cellulose. Explain why the difference is biologically important.

Starch uses alpha rings whereas cellulose uses beta rings. These differing types of linkages give both types different shapes; starch is used for storage and cellulose is used for structure. Lipids Are a Diverse Group of Hydrophobic Molecules 1. Describe the building-block molecules, structure, and biological importance of fats, phospholipids, and steroids.

Lipids do not consist of polymers. They are all hydrophobic. Fats are made of three fatty acid molecules and one glycerol molecule. They serve as long-term energy storage and insulation. Phospholipids are made of two fatty acid molecules, one glycerol molecule, and a phosphate group molecule. The self-assembled bilayer structure of phospholipids allows the hydrophilic head to shield the hydrophobic tail from water. Steroids are lipids characterized by a carbon skeleton consisting of four fused rings. Many hormones are

steroids produced from cholesterol. Cholesterol is the steroid from which other steroids are synthesized. 1. Identify an ester linkage and describe how it is formed.

Ester linkage is a bond between a hydroxyl group and a carboxyl group. Three fatty acids link to one glycerol molecule to make a triglyceride, or a fat. 1. Distinguish between saturated and unsaturated fats.

Saturated fats have no double bonds and as such are saturated with hydrogen. Unsaturated fats have double bonds and are not saturated with hydrogen. 1. Name the principal energy storage molecules of plants and animals.

Plants store energy in starch and animals store energy in fats. Proteins Have Many Structures and Many Functions 1. Distinguish between a protein and a polypeptide.

A protein is a polymer made up of polypeptides, which are polymers of amino acids. 1. Explain how a peptide bond forms between two amino acids.

When two amino acids are next to each other, an enzyme can join the amino acid by means of a dehydration reaction, which is a peptide bond. 1. List and describe the four major components of an amino acid. Explain how amino acids may be grouped according to the physical and chemical properties of the R group.

The carboxyl group, the R-group , the amino group and the hydrogen atom all make up the amino acid. The R-group, the side chain, differs with the amino acid. The chemical and physical properties of the side chain determine the characterisitcs of a particular amino acid. A R -group can be acidic, basic or hydrophilic, thus its properties will vary based on these characteristics. 1. Explain what determines protein conformation and why it is important.

Protein conformation is determined by the amino acid sequence of a polypeptide. This is important because a protein's specific conformation determines its function. 1. Explain how the primary structure of a protein is determined.

The primary structure of a protein is determined by its unique sequence of amino acids. 1. Name two types of secondary protein structure. Explain the role of hydrogen bonds in maintaining secondary structure.

Two types of secondary protein structure are the alpha helix and the beta pleated sheet. The coils and folds in the secondary protein structure are the result of the hydrogen bonds at regular intervals along the polypeptide backbone. Hydrogen bonds are in generally weak but when repeated continuously over a long region of a polypeptides chain, they can support a particular shape for a certain part of the protein. 1. Explain how weak interactions and disulfide bridges contribute to tertiary protein structure.

Weak interactions, such as van der Waals attractions and hydrogen bonding ,help maintain a protein's specific shape. Disulfide bridges a strong covalent bonds that further reinforce a protein's shape. 1. List four conditions under which proteins may be denatured.

Ph, temperature, salt concentration or other aspects of its environment are altered , a protein may unravel and lose its native conformation. Nucleic Acids Store and Transmit Hereditary Information 1. List the major components of a nucleotide, and describe how these monomers are linked to form a nucleic acid.

An organic molecule called a nitrogenous base, a pentose and a phosphate group. These nucelotides are joined by covalent bonds called phosphodiester linkages between phosphate of one nucleotide and the sugar of the next. 1. Briefly describe the three-dimensional structure of DNA.

Double helic- two polynucleotides that spiral around an imaginary axis 20. Distinguish between: a. pyrimidine and purine a. Pyrimidines have six membered rings of carbon and nitrogen atoms. They include cytosine, thymine, and uracil. Purines are larger, with a six-membered ring fused to a five-membered ring. They include adenine and guanine. b. nucleotide and nucleoside Nucleosides are the portions of nucleotides without the phosphate group. i. ribose and deoxyribose

Deoxyribose lacks an oxygen atom in the second carbon in its ring. Hence the name. i. 5 end and 3 end of a nucleotide ii. The 5 end is where the phosphate group is and the 3 end is where the hydroxyl group is.

Chapter 8 Metabolism, Energy, and Life 1. Explain the role of catabolic and anabolic pathways in cellular metabolism.

Catabolic pathways in cellular metabolism , release energy by breaking down complex molecules to simpler compounds. Anabolic processes, on the other hand, consume energy to build complicated molecules from smaller ones. 1. Distinguish between kinetic and potential energy.

Kinetic energy is the energy of motion while potential energy is the energy that matter possesses because its location or structure. 1. Explain why an organism is considered an open system.

An organism is considered an open system because it transfers energy constantly. 1. Explain the first and second laws of thermodynamics in your own words.

The first law of thermodynamics states that energy cannot be created or destroyed. The second law of thermodynamics states that energy is always inefficient; it is lost in the form of heat. 1. Distinguish between exergonic and endergonic reactions in terms of free energy change.

Exergonic reactions release energy, thus the delta G is negative. Endergonic reactions absorb energy thus the delta G is positive. 1. Explain why metabolic disequilibrium is one of the defining features of life.

Chemical systems at equilibrium have a delta G of zero and can do no work so if a cell has reached equilibrium, it's dead. 1. List the three main kinds of cellular work. Explain in general terms how cells obtain the energy to do cellular work.

The three main kinds of cellular work are mechanical work, transport work, and chemical work. Mechanical work refers to the beating of cilia, the contraction of muscle cells, and the movement of chromosomes during cellular reproduction. Transport work describes the pumping of substances across membranes against the direction of spontaneous movement. Chemical work is the pushing of endergonic reactions, which would not occur spontaneously, such as the synthesis of polymers from monomers. Cells obtain energy to do work by ATP. 1. Describe the structure of ATP and identify the major class of macromolecules to which ATP belongs.

ATP has the nitrogenous base of adenine bonded to ribose , as in a adenine nucleotide of RNA. But in adenosine triphosphate , the ribose has three phosphate groups attached to it. 1. Explain how ATP performs cellular work.

ATP performs cellular work by hydrolyzing and releasing free energy. The hydrolysis yields inorganic phosphate and ADP. With the help of certain enzymes, cells are able to couple endergonic processes by transferring a phosphate group from ATP to some other molecule. The recipient is thus said to be phosphorylated. Enzymes Are Catalytic Proteins

1. Describe the function of enzymes in biological systems.

Enzymes are catalysts, they speed up the metabolic reaction by lowering energy barriers. 11. Explain why an investment of activation energy is necessary to initiate a spontaneous reaction. Energy is needed to break bonds in the reactant molecules, thus the activation energy is necessary to initiate a spontaneous reaction. 1. Explain how enzyme structure determines enzyme specificity.

Enzyme structures have certain fits that can only be satisfied by specific substrates. As such, only certain substrates can fit into certain enzymes. 1. Explain the induced-fit model of enzyme function.

When the substrate enters its active site, it makes the enzyme to change its shape so that the active sight fits snugly around the substrate. This induced fit brings chemical groups of the active sight into positions that enhance their ability to catalyze the chemical reaction. 1. Describe the mechanisms by which enzymes lower activation energy.

The mechanism makes the reaction require less heat and energy, thus it speeds the reaction up. 1. Explain how substrate concentration affects the rate of an enzyme-catalyzed reaction.

As the concentration of substrate increases, the rate of reaction increases until the point of saturation occurs. At this point, adding more substrate does not do anything. 1. Explain how temperature, pH, cofactors, and enzyme inhibitors can affect enzyme activity.

As temperature rises, a protein s (enzyme) molecular structure will become more and more unstable until denaturation occurs. Just as enzymes have an optimal temperature, they also have an optimal pH value. The optimal values for most enzymes usually are between 6-8, but there are exceptions. Cofactors are molecules that will fit into the active site of an enzyme and help perform catalytic activity. Enzyme inhibitors attach to enzymes in order to prevent certain processes.

The Control of Metabolism 1. Explain how metabolic pathways are regulated.

Regulatory molecules change an enzyme's shape and function by binding to an allosteric site, a specific receptor site on some part of the enzyme molecule remote from the active sight, 1. Explain how the location of enzymes in a cell may help order metabolism The arrangement controls the sequence of reactions, as the product from the first enzyme becomes substrate for the adjacent enzyme in the complex, until the endpoint is released.