biology - arvicbabol 10 biological... · biology douglas wilkin, ph.d. niamh gray-wilson say thanks...

Biology

Douglas Wilkin, Ph.D.Niamh Gray-Wilson

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Printed: August 15, 2016

AUTHORSDouglas Wilkin, Ph.D.Niamh Gray-Wilson

CONTRIBUTORJean Brainard, Ph.D.

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Contents www.ck12.org

Contents

1 Cell 11.1 The Cell Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21.2 Cells - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41.3 Discovery of Cells - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61.4 Cell Size and Shape - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101.5 Common Parts of Cells - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151.6 Cell Structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171.7 Two Types of Cells - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201.8 The Nucleus - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 251.9 The Mitochondria - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281.10 Ribosomes - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 321.11 Endoplasmic Reticulum - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 351.12 The Golgi Apparatus - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 381.13 Vesicles and Vacuoles - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 411.14 Other Structures of Cells - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 451.15 Plant Cells - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 491.16 The Cytoplasm and Cytoskeleton - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . 541.17 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

2 Cell Cycle 582.1 Cell Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 592.2 Mitosis - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 632.3 Genetic Variation - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 692.4 Meiosis - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 732.5 Significance of Mitosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 802.6 Significance of Meiosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 812.7 Genetic Disorders - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 822.8 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89

3 Transport Mechanisms 903.1 The Cell Membrane: A Semi-Permeable Barrier . . . . . . . . . . . . . . . . . . . . . . . . . . 913.2 Cell Transport - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 943.3 Diffusion - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 973.4 Facilitated Diffusion - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1003.5 Osmosis - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1033.6 Active Transport - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1073.7 Exocytosis and Endocytosis - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1103.8 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114

4 Biological Molecules 1154.1 Biological Molecules (organic compounds) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1164.2 Carbohydrates - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127

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4.3 Lipids - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1314.4 Proteins - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1354.5 Enzymes and Metabolism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1404.6 Nucleic Acids - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1444.7 Chemical Reactions - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1494.8 Solutions - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1524.9 How Enzymes Speed Up the Chemical Reactions . . . . . . . . . . . . . . . . . . . . . . . . . 1574.10 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159

5 Energy Transformation 1605.1 Energy Transformation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1615.2 Energy Carrying Molecules - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1655.3 Autotrophs vs. Heterotrophs - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1705.4 Photosynthesis - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1755.5 The Photosynthesis Reaction - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1795.6 The Chloroplast - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1855.7 The Light Reactions - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1905.8 The Calvin Cycle - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1955.9 Chemosynthesis - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2015.10 Cellular Respiration - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2035.11 Cellular Respiration Overview - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2065.12 Glycolysis - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2155.13 The Mitochondria in Cellular Respiration - Advanced . . . . . . . . . . . . . . . . . . . . . . . 2225.14 The Krebs Cycle - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2245.15 The Electron Transport Chain - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2305.16 Anaerobic Respiration - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2345.17 Lactic Acid Fermentation - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2375.18 Alcoholic Fermentation - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2415.19 Aerobic vs. Anaerobic Respiration - Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . 2455.20 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249

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4.5. Enzymes and Metabolism www.ck12.org

4.5 Enzymes and Metabolism

• Explain the importance of enzymes to living organisms.

FIGURE 4.20

Metabolism

Metabolism is the name given to the collection of, the lump sum of, chemical reactions performed by an organismto survive.

The study of metabolism is divided into two broad categories, or types, of metabolic reactions:

(1) Anabolism: These are reactions that synthesize, or build up molecules/materials from simpler ingredients/reactants.Most anabolic reactions are endergonic, the name given to reactions that require cells to expend energy to build morecomplex molecules from simpler ones. Endergonic reactions are not considered as spontaneous reactions, energymust be inputted for the reaction to proceed. These types of reactions are indicated with a positive number for "energygoing in" (+G). A common anabolic pathway is the synthesis of starch/polymers from smaller sugar/monomers.

(2) Cataboism: These are reactions that breakdown, break apart, complex molecules/materials into simpler molecules-usually releasing energy to complete these reactions. These reactions are exergonic reactions, the name given toreactions that break down molecules and release energy in the process. This category of reactions generate energy,and are indicated with a negative number for "energy being released" (-G).

Enzymes are catalysts for chemical reactions- enzymes control and catalyze (i.e accelerate) , biochemical reactionsof an organism. A catalyst is a substance that causes a chemical reaction to happen more quickly.

Anotherwords: ENZYMES make an organism’s METABOLIC reactions go faster, speed up.

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What is a biological catalyst?

This super fast train can obviously reach great speeds. And there’s a lot of technology that helps this train go fast.Speaking of helping things go fast brings us to enzymes. Life could not exist without enzymes. Essentially, enzymesare biological catalysts that speed up biochemical reactions.

Enzymes

Enzymes and Biochemical Reactions

Most chemical reactions within organisms would be impossible under the conditions in cells. For example, thebody temperature of most organisms is too low for reactions to occur quickly enough to carry out life processes.Reactants may also be present in such low concentrations that it is unlikely they will meet and collide. Therefore,the rate of most biochemical reactions must be increased by a catalyst. A catalyst is a chemical that speeds upchemical reactions. In organisms, catalysts are called enzymes. Essentially, enzymes are biological catalysts.

How do enzymes speed up biochemical reactions so dramatically? Like all catalysts, enzymes work by loweringthe activation energy of chemical reactions. Activation energy is the energy needed to start a chemical reaction.This is illustrated in Figure below . The biochemical reaction shown in the figure requires about three times asmuch activation energy without the enzyme as it does with the enzyme.

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FIGURE 4.21

Enzymes are extremely efficient in speeding up reactions. They can catalyze up to several million reactions persecond. As a result, the difference in rates of biochemical reactions with and without enzymes may be enormous.A typical biochemical reaction might take hours or even days to occur under normal cellular conditions without anenzyme, but less than a second with an enzyme.

Cellular processes consist of many chemical reactions that must occur quickly in order for the cell to functionproperly. Enzymes catalyze most of the chemical reactions that occur in a cell. A substrate is the molecule ormolecules on which the enzyme acts. In the urease catalyzed reaction, urea is the substrate. The Figure belowdiagrams a typical enzymatic reaction.

FIGURE 4.22

Enzymes, an overview of these proteins, can be viewed at http://www.youtube.com/watch?v=E90D4BmaVJM&feature=related (9:43).

MEDIAClick image to the left or use the URL below.URL: https://www.ck12.org/flx/render/embeddedobject/203

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As you view Enzymes, focus on these concepts:

1. the role of enzymes in nature,2. other uses of enzymes.

Importance of Enzymes

Enzymes are involved in most of the chemical reactions that take place in organisms. About 4,000 such reactionsare known to be catalyzed by enzymes, but the number may be even higher.

In animals, an important function of enzymes is to help digest food. Digestive enzymes speed up reactions thatbreak down large molecules of carbohydrates, proteins, and fats into smaller molecules the body can use. Withoutdigestive enzymes, animals would not be able to break down food molecules quickly enough to provide the energyand nutrients they need to survive.

Summary

• Enzymes are biological catalysts. They speed up biochemical reactions.• Enzymes are involved in most of the chemical reactions that take place in organisms.

Practice

Use this resource to answer the questions that follow.

• http://www.hippocampus.org/Biology ! Biology for AP* ! Search: Enzymes as Catalysts

1. What are enzymes?2. What are substrates? What is the enzyme-substrate complex?3. How do enzymes work?4. What happens to the enzyme during a reaction?

Review

1. What are enzymes?

2. Explain why organisms need enzymes to survive.

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4.6. Nucleic Acids - Advanced www.ck12.org

4.6 Nucleic Acids - Advanced

• Describe the structure and function of nucleic acids.• Name the components of a nucleotide.• Compare DNA to RNA.• Describe the structure and function of ATP.

You may have heard that "it’s in your DNA." What does that mean?

Nucleic acids. Essentially the "instructions" or "blueprints" of life. Deoxyribonucleic acid, or DNA, is the uniqueblueprints to make the proteins that give you your traits. Half of these blueprints come from your mother, and halffrom your father. And they come in different combinations every time. In fact, every couple - every man and womanthat has every lived - together has over 64,000,000,000,000 combinations of their chromosomes, which is where theDNA is found. Therefore, every person that has ever lived - except for identical twins - has his or her own uniqueset of blueprints - or instructions - or DNA.

Nucleic Acids

Nucleic acids are organic compounds that contain carbon, hydrogen, oxygen, nitrogen, and phosphorus. They aremade of smaller units called nucleotides. Nucleic acids are named for the nucleus of the cell, where some of themare found. Nucleic acids are found not only in all living cells but also in viruses. Types of nucleic acids includedeoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

Structure of Nucleic Acids

A nucleic acid consists of one chain (in RNA) or two chains (in DNA) of nucleotides held together by chemicalbonds. Each individual nucleotide unit consists of three parts:

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• a base (containing nitrogen)• a sugar (ribose in RNA, deoxyribose in DNA)• a phosphate group (containing phosphorus)

The sugar of one nucleotide binds to the phosphate group of the next nucleotide. Alternating sugars and phosphategroups form the backbone of a nucleotide chain, as shown in Figure 4.23. The bases, which are bound to the sugars,protrude from the backbone of the chain. In DNA, pairs of bases-one from each of two nucleotides-form the middlesection of the molecule.

FIGURE 4.23Part of a Nucleic Acid (DNA). This smallsection of a nucleic acid shows how phos-phate groups and sugars alternate to formthe backbone of a nucleotide chain. Thebases that jut out to the side from thebackbone are adenine, thymine, cytosine,and guanine. Hydrogen bonds betweencomplementary bases, such as betweenadenine and thymine, hold the two chainsof nucleotides together.


RNA consists of a single chain of nucleotides, and DNA consists of two chains of nucleotides. Bonds form betweenthe bases on the two chains of DNA and hold the chains together (Figure 4.23). There are four different types ofbases in a nucleic acid molecule: cytosine (C), adenine (A), guanine (G), and either thymine (T) (in DNA) or uracil(U) (in RNA). Each type of base bonds with just one other type of base. Cytosine and guanine always bond together,and adenine and thymine (or uracil) always bond with one another. The pairs of bases that bond together are calledcomplementary bases.

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The binding of complementary bases allows DNA molecules to take their well-known shape, called a double helix.Figure 4.24 shows how two chains of nucleotides form a DNA double helix. A simplified double helix is illustratedin Figure 4.25. It shows more clearly how the two chains are intertwined. The double helix shape forms naturallyand is very strong. Being intertwined, the two chains are difficult to break apart. This is important given thefundamental role of DNA in all living organisms.

FIGURE 4.24DNA Molecule. Hydrogen bonds betweencomplementary bases help form the dou-ble helix of a DNA molecule. The lettersA, T, G, and C stand for the bases ade-nine, thymine, guanine, and cytosine. Thesequence of these four bases in DNA is acode that carries instructions for makingproteins. Shown is a representation ofhow the double helix folds into a chro-mosome. In this double-stranded nucleicacid, complementary bases (A and T, Cand G) form hydrogen bonds that holdthe two nucleotide chains together in theshape of a double helix. Notice thatA always bonds with T and C alwaysbonds with G. The hydrogen bonds helpmaintain the double helix shape of themolecule.

FIGURE 4.25Simple Model of DNA. In this simplemodel of DNA, each line represents anucleotide chain. The double helix shapeforms when the two chains wrap aroundthe same axis.


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Role of Nucleic Acids

The order of bases in nucleic acids is highly significant. The bases are like the letters of a four-letter alphabet. These"letters" can be combined to form "words." Groups of three bases form words of the genetic code. Each code word,called a codon, stands for a different amino acid. A series of many codons spells out the sequence of amino acidsin a polypeptide or protein (Figure 4.26). In short, nucleic acids contain the information needed for cells to makeproteins. This information is passed from a body cell to its daughter cells when the cell divides. It is also passedfrom parents to their offspring when organisms reproduce.

How RNA codes for Proteins

FIGURE 4.26The letters G, U, C, and A stand for thebases in RNA, specifically mRNA or mes-senger RNA. Each group of three basesmakes up a codon, and each codon rep-resents one amino acid (represented hereby a single letter, such as V (valine), H(histidine), or L (leucine)). A string ofcodons specifies the sequence of aminoacids in a protein.

DNA and RNA have different functions relating to the genetic code and proteins. Like a set of blueprints, DNAcontains the genetic instructions for the correct sequence of amino acids in proteins. RNA uses the information inDNA to assemble the amino acids and make the proteins. More about the genetic code and the role of nucleic acidswill be discussed in Concept Molecular Biology (Advanced).

Adenosine Triphosphate

Adenosine Triphosphate (ATP), or Adenosine-5’-triphosphate, is another important nucleic acid. ATP is describedas the "energy currency" of the cell or the "molecular unit of currency." One molecule of ATP contains threephosphate groups, and it is produced by ATP synthase from inorganic phosphate and adenosine diphosphate (ADP)or adenosine monophosphate (AMP). The structure of ATP consists of the purine base adenine, attached to the1’ carbon atom of the pentose sugar ribose. Three phosphate groups are attached at the 5’ carbon atom of thepentose sugar. It is the removal of these phosphate groups that convert ATP to ADP (adenosine diphosphate) and toAMP (adenosine monophosphate). ATP is produced during cellular respiration, and will be further discussed in theCellular Respiration (Advanced) concepts.

ATP is used as a substrate in signal transduction pathways by kinases that phosphorylate proteins and lipids, aswell as by adenylate cyclase, which uses ATP to produce the second messenger molecule cyclic AMP (cAMP). Theratio between ATP and AMP determines the amount of available energy. This regulates the metabolic pathwaysthat produce and consume ATP. Apart from its roles in energy metabolism and signaling, ATP is also incorporatedinto DNA and RNA by polymerases during both DNA replication and transcription. When ATP is used in DNAsynthesis, the ribose sugar is first converted to deoxyribose by ribonucleotide reductase.

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FIGURE 4.27ATP. The ATP molecule clearly shows thethree phosphate groups.

Summary

• Nucleic acids are organic compounds that consist of carbon, hydrogen, oxygen, nitrogen, and phosphorus.• DNA, RNA and ATP are important nucleic acids.• DNA and RNA are made up of repeating units called nucleotides. They contain genetic instructions for

proteins, help synthesize proteins, and pass genetic instructions on to daughter cells and offspring.

Review

1. What is a nucleic acid?2. Identify the three parts of a nucleotide.3. What is the structure of DNA?4. Bases in nucleic acids are represented by the letters A, G, C, and T (or U). How are the bases in nucleic acids

like the letters of an alphabet?5. Describe the role and structure of ATP.

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4.7 Chemical Reactions - Advanced

• Describe what happens in a chemical reaction, and identify types of chemical reactions.

Understanding chemistry is essential to fully understand biology. Why?

A general understanding of chemistry is necessary to understand biology. Essentially, our cells are just thousands ofchemicals — made of elements like carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur — in just the rightcombinations. And these chemicals combine through chemical reactions.

What Are Chemical Reactions?

A chemical compound may be very different from the substances that combine to form it. For example, the elementchlorine (Cl) is a poisonous gas, but when it combines with sodium (Na) to form sodium chloride (NaCl), it is nolonger toxic. You may even eat it on your food. Sodium chloride is just table salt. What process changes a toxicchemical like chlorine into a much different substance like table salt?

A chemical reaction is a process that changes some chemical substances into other chemical substances. Thesubstances that start a chemical reaction are called reactants. The substances that form as a result of a chemicalreaction are called products. During the reaction, the reactants are used up to create the products. For example,when methane burns in oxygen, it releases carbon dioxide and water. In this reaction, the reactants are methane(CH4) and oxygen (O2), and the products are carbon dioxide (CO2) and water (H2O).

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Chemical Equations

A chemical reaction can be represented by a chemical equation. Using the same example, the burning of methanegas can be represented by the equation:

CH4 + 2 O2 ! CO2 + 2 H2O.

The arrow in a chemical equation separates the reactants from the products and shows the direction in which thereaction occurs. If the reaction could also occur in the opposite direction, then two arrows, one pointing in eachdirection, or one arrow pointing in both directions, would be used. On each side of the arrow, a mixture of chemicalsis indicated by the chemical symbols joined by a plus sign (+). The numbers preceding some of the chemical symbols(such as 2 O2) indicate how many molecules of the chemicals are involved in the reaction. (If there is no number infront of a chemical symbol, it means that just one molecule is involved.)

In a chemical reaction, the quantity of each element does not change. There is the same amount of each element atthe end of the reaction as there was at the beginning. This is reflected in the chemical equation for the reaction. Theequation should be balanced. In a balanced equation, the same number of atoms of a given element appear on eachside of the arrow. For example, in the equation above, there are four hydrogen atoms on each side of the arrow.

Types of Chemical Reactions

In general, a chemical reaction involves the breaking and forming of chemical bonds. In the methane reaction above,bonds are broken in methane and oxygen, and bonds are formed in carbon dioxide and water. A reaction like this, inwhich a compound or element burns in oxygen, is called a combustion reaction. This is just one of many possibletypes of chemical reactions. Other types of chemical reactions include synthesis, decomposition, and substitutionreactions.

• A synthesis reaction occurs when two or more chemical elements or compounds unite to form a more complexproduct. For example, nitrogen (N2) and hydrogen (H2) unite to form ammonia (NH3):

N2 + 3 H2 ! 2 NH3.

• A decomposition reaction occurs when a compound is broken down into smaller compounds or elements.For example, water (H2O) breaks down into hydrogen (H2) and oxygen (O2):

2 H2O ! 2 H2 + O2.

• A substitution reaction occurs when one element replaces another element in a compound. For example,sodium (Na+) replaces hydrogen (H) in hydrochloric acid (HCl), producing sodium chloride (NaCl) andhydrogen gas (H2):

2 Na+ + 2 HCl ! 2 NaCl + H2.

Redox Reactions

Reduction-oxidation reactions, or redox reactions include all chemical reactions in which atoms have their oxidationstate changed. This can be either a simple redox process, such as the oxidation of carbon into carbon dioxide or thereduction of carbon by hydrogen into methane, or a complex process such as the oxidation of glucose through aseries of complex electron transfer processes during cellular respiration. Oxidation is the loss of electrons or anincrease in oxidation state by a molecule, atom, or ion. Reduction is the gain of electrons or a decrease in oxidationstate by a molecule, atom, or ion.

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Redox Reactions in Biology

Many important biological processes involve redox reactions, which frequently store and release energy. Forexample, photosynthesis involves the reduction of carbon dioxide into glucose and the oxidation of water intooxygen. This process stores the energy of sunlight in the bonds of sugars. The reverse reaction, cellular respiration,converts the energy in glucose into ATP. Cellular respiration involves the oxidation of glucose to carbon dioxide andthe reduction of oxygen gas to water. This process depends on the reduction of NAD+ to the electron carrier NADH,and the reverse oxidation of NADH to NAD+. The reduction of NAD+ leads to the formation of a proton (H+)gradient, which drives the synthesis of ATP. NADH (nicotinamide adenine dinucleotide) and NADPH (Nicotinamideadenine dinucleotide phosphate) are electron carriers in biological systems. The term redox state is often used todescribe the balance between NAD+/NADH and NADP+/NADPH (Nicotinamide adenine dinucleotide phosphate).


Summary

• A chemical reaction is a process that changes some chemical substances into others. It involves breaking andforming chemical bonds.

• Types of chemical reactions include synthesis reactions and decomposition reactions.

Review

1. Identify the roles of reactants and products in a chemical reaction.2. Describe each type of chemical reaction.3. What is wrong with the following chemical equation? How could you fix it? CH4 + O2 ! CO2 + 2H2O4. What type of reaction is represented by the following chemical equation? Explain your answer. 2Na + 2HCl

! 2NaCl + H2

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4.8. Solutions - Advanced www.ck12.org

4.8 Solutions - Advanced

• Define solution, and describe water’s role as a solvent.• State how water is used to define acids and bases.• Identify the pH ranges of acids and bases.• Describe a neutralization reaction.• Give examples of acids and bases in organisms.

Acids and bases. Why are these important in biology?

It comes back to a number of biological and biochemical processes. For example, some enzymes work best atspecific pH levels of acids. Other biochemical reactions need a relatively neutral environment to function properly.Take your stomach, a very acidic environment. The enzyme pepsin that works best in that acidic environment couldnot work in your mouth. What would your food taste like if your mouth was also a very acidic environment? Otherbiochemical reactions need a relatively neutral environment to function properly.

Solutions

Water is one of the most common ingredients in solutions. A solution is a homogeneous mixture composed of twoor more substances. In a solution, one substance is dissolved in another substance, forming a mixture that has thesame proportion of substances throughout. The dissolved substance in a solution is called the solute. The substancein which it is dissolved is called the solvent. An example of a solution in which water is the solvent is salt water. Inthis solution, a solid—sodium chloride—is the solute. In addition to a solid dissolved in a liquid, solutions can alsoform with solutes and solvents in other states of matter. Examples are given in Table 4.4.

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TABLE 4.4: Solutions and Three States of Matter

Gas Liquid SolidGas Oxygen and other gases in

nitrogen (air)Liquid Carbon dioxide in water

(carbonated water)Ethanol (an alcohol) inwater

Sodium chloride in water(salt water)

Solid Hydrogen gas in metals Mercury in silver andother metals (dental fill-ings)

Iron in carbon (steel)

The ability of a solute to dissolve in a particular solvent is called solubility. Many chemical substances are soluble inwater. In fact, so many substances are soluble in water that water is called the universal solvent. Water is a stronglypolar solvent, and polar solvents are better at dissolving polar solutes. Many organic compounds and other importantbiochemicals are polar, so they dissolve well in water. On the other hand, strongly polar solvents like water cannotdissolve strongly nonpolar solutes like oil. Did you ever try to mix oil and water? Even after being well shaken, thetwo substances quickly separate into distinct layers.

Acids and Bases

Water is the solvent in solutions called acids and bases. To understand acids and bases, it is important to know moreabout pure water, in which nothing is dissolved. In pure water (such as distilled water), a tiny fraction of watermolecules naturally breaks down, or dissociates, to form ions. An ion is an electrically charged atom or molecule.The dissociation of pure water into ions is represented by the chemical equation:

2 H2O ! H3O+ + OH�.

The products of this reaction are a hydronium ion (H3O+) and a hydroxide ion (OH�). The hydroxide ion isnegatively charged. It forms when a water molecule donates, or gives up, a positively charged hydrogen ion. Thehydronium ion, modeled in Figure 4.28, is positively charged. It forms when a water molecule accepts a positivelycharged hydrogen ion (H+).

Acidity and pH

Acidity refers to the hydronium ion concentration of a solution. It is measured by pH. In pure water, the hydroniumion concentration is very low. Only about one in ten million water molecules naturally dissociates to form ahydronium ion in pure water. This gives water a pH of 7. The hydronium ions in pure water are also balancedby hydroxide ions, so pure water is neutral (neither an acid nor a base).

Because pure water is neutral, any other solution with the same hydronium ion concentration and pH is alsoconsidered to be neutral. If a solution has a higher concentration of hydronium ions and lower pH than pure water,it is called an acid. If a solution has a lower concentration of hydronium ions and higher pH than pure water, it iscalled a base. Several acids and bases and their pH values are identified on the pH scale, which ranges from 0 to 14,in Figure 4.29.

The pH scale is a negative logarithmic scale. Because the scale is negative, as the ion concentration increases, thepH value decreases. In other words, the more acidic the solution, the lower the pH value. Because the scale islogarithmic, each one-point change in pH reflects a ten-fold change in the hydronium ion concentration and acidity.For example, a solution with a pH of 6 is ten times as acidic as pure water with a pH of 7.

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FIGURE 4.28A hydronium ion has the chemical formulaH3O+. The plus sign (+) indicates that theion is positively charged. How does thismolecule differ from a water molecule?

Acids

An acid can be defined as a hydrogen ion donor. The hydrogen ions bond with water molecules, leading to a higherconcentration of hydronium ions than in pure water. For example, when hydrochloric acid (HCl) dissolves in purewater, it donates hydrogen ions (H+) to water molecules, forming hydronium ions (H3O+) and chloride ions (Cl�).This is represented by the chemical equation:

HCl + H2O ! Cl� + H3O+.

Strong acids can be harmful to organisms and damaging to materials. Acids have a sour taste and may sting or burnthe skin. Testing solutions with litmus paper is an easy way to identify acids. Acids turn blue litmus paper red.

Bases

A base can be defined as a hydrogen ion acceptor. It accepts hydrogen ions from hydronium ions, leading to a lowerconcentration of hydronium ions than in pure water. For example, when the base ammonia (NH3) dissolves in purewater, it accepts hydrogen ions (H+) from hydronium ions (H3O+) to form ammonium ions (NH4

+) and hydroxideions (OH�). This is represented by the chemical equation:

NH3 + H2O ! NH4+ + OH�.

Like strong acids, strong bases can be harmful to organisms and damaging to materials. Bases have a bitter taste andfeel slimy to the touch. They can also burn the skin. Bases, like acids, can be identified with litmus paper. Basesturn red litmus paper blue.

Neutralization

What do you think would happen if you mixed an acid and a base? If you think the acid and base would “cancel eachother out,” you are right. When an acid and base react, they form a neutral solution of water and a salt (a molecule

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FIGURE 4.29Acidity and the pH Scale. Water has apH of 7, so this is the point of neutralityon the pH scale. Acids have a pH lessthan 7, and bases have a pH greaterthan 7. Approximate pHs of examples aredepicted.

composed of a positive and negative ion). This type of reaction is called a neutralization reaction. For example,when the base sodium hydroxide (NaOH) and hydrochloric acid (HCl) react, they form a neutral solution of waterand the salt sodium chloride (NaCl). This reaction is represented by the chemical equation:

NaOH + HCl ! NaCl + H2O.

In this reaction, hydroxide ions (OH�) from the base combine with hydrogen ions (H+) from the acid to form water.The other ions in the solution (Na+) and (Cl�) combine to form sodium chloride.

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Acids and Bases in Organisms

Enzymes are needed to speed up biochemical reactions. Most enzymes require a specific range of pH in order to dotheir job. For example, the enzyme pepsin, which helps break down proteins in the human stomach, requires a veryacidic environment in order to function. Strong acid is secreted into the stomach, allowing pepsin to work. Once thecontents of the stomach enter the small intestine, where most digestion occurs, the acid must be neutralized. This isbecause enzymes that work in the small intestine need a basic environment. An organ near the small intestine, calledthe pancreas, secretes bicarbonate ions (HCO3

�) into the small intestine to neutralize the stomach acid.

Bicarbonate ions play an important role in neutralizing acids throughout the body. Bicarbonate ions are especiallyimportant for protecting tissues of the central nervous system from changes in pH. The central nervous systemincludes the brain, which is the body’s control center. If pH deviates too far from normal, the central nervous systemcannot function properly. This can have a drastic effect on the rest of the body.


Summary

• A solution is a homogeneous mixture in which a solute dissolves in a solvent. Water is a very common solvent,especially in organisms.

• The ion concentration of neutral, pure water gives water a pH of 7 and sets the standard for defining acids andbases. Acids have a pH lower than 7, and bases have a pH higher than 7.

Review

1. What is pH?2. Define solution, and give an example of a solution.3. What is the pH of a neutral solution? Why?4. What type of reaction is represented by this chemical equation: KOH + HCl ! KCl + H2O? Defend your

answer.5. What is pepsin and give an example of how the body neutralizes its environment?

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4.9 How Enzymes Speed Up the Chemical Re-actions

Enzyme Function

Do cells have one enzyme with lots of functions, or many enzymes, each with just one function?

Enzymes. Magical proteins necessary for life. So how do enzymes work? How do they catalyze just one specificbiochemical reaction? In a puzzle, only two pieces will fit together properly. Understanding that is one of the mainsteps in understanding how enzymes work.

How do enzymes speed up biochemical reactions so dramatically? Like all catalysts, enzymes work by loweringthe activation energy of chemical reactions. Activation energy is the energy needed to start a chemical reaction.This is illustrated in Figure 4.30. The biochemical reaction shown in the figure requires about three times as muchactivation energy without the enzyme as it does with the enzyme.

As you view Enzyme Animation, focus on this concept:

1. how enzymes function.

Enzymes generally lower activation energy by reducing the energy needed for reactants to come together and react.For example:

• Enzymes bring reactants together so they don’t have to expend energy moving about until they collide atrandom. Enzymes bind both reactant molecules (called the substrate), tightly and specifically, at a site on theenzyme molecule called the active site.

• By binding reactants at the active site, enzymes also position reactants correctly, so they do not have toovercome intermolecular forces that would otherwise push them apart. This allows the molecules to interactwith less energy.

• Enzymes may also allow reactions to occur by different pathways that have lower activation energy.

Enzyme Animation

This animation of how enzymes work is a basic rundown of enzyme functions and illustrates what enzymes do.

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4.9. How Enzymes Speed Up the Chemical Reactions www.ck12.org

FIGURE 4.30The reaction represented by this graphis a combustion reaction involving the re-actants glucose (C6H12O6) and oxygen(O2). The products of the reaction arecarbon dioxide (CO2) and water (H2O).Energy is also released during the reac-tion. The enzyme speeds up the reactionby lowering the activation energy neededfor the reaction to start. Compare theactivation energy with and without the en-zyme.


Watch the video at: https://www.youtube.com/watch?v=CZD5xsOKres

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4.10 References

1. Mariana Ruiz Villarreal (LadyofHats), modified by CK-12 Foundation. . Public Domain2. Caroline Davis. . CC BY 2.03. User:Booyabazooka/Wikimedia Commons. http://commons.wikimedia.org/wiki/File:Saccharose.svg . Pub-

lic Domain4. Mariana Ruiz Villarreal (LadyofHats) for the CK-12 Foundation. CK-12 Foundation . CC BY-NC 3.05. Seeds: Lebensmittelfotos; Olives: Steve Jurvetson; Nuts: Petr Kratochvil. Seeds: http://pixabay.com/en

/barley-grain-cereals-whole-wheat-74247/; Olives: http://www.flickr.com/photos/jurvetson/454873761/; Nuts: http://www.publicdomainpictures.net/view-image.php?image=424&picture=nuts . Seeds: Public Domain;Olives: CC BY 2.0; Nuts: Public Domain

6. Wolfgang Schaefer (User:WS62/Wikimedia Commons). http://commons.wikimedia.org/wiki/File:Fat_triglyceride_shorthand_formula.PNG . Public Domain

7. User:YassineMrabet/Wikimedia Commons. http://commons.wikimedia.org/wiki/File:AminoAcidball.svg .Public Domain

8. Courtesy of the National Human Genome Research Institute. http://commons.wikimedia.org/wiki/File:Protein_primary_structure.svg . Public Domain

9. Hana Zavadska, based on image from the National Human Genome Research Institute. CK-12 Foundation .CC BY-NC 3.0

10. Image copyright ynse, 2014. http://www.shutterstock.com . Used under license from Shutterstock.com11. Marianna Ruiz Villarreal (LadyofHats) for the CK-12 Foundation. CK-12 Foundation . CC BY-NC 3.012. Marianna Ruiz Villarreal (LadyofHats) for the CK-12 Foundation. CK-12 Foundation . CC BY-NC 3.013. User:Honeymane/Wikimedia Commons and User:LucasVB/Wikimedia Commons. http://commons.wikim

edia.org/wiki/File:Double_Helix.png . Public Domain14. Madeleine Price Ball (User:Madprime/Wikimedia Commons), modified by CK-12 Foundation. http://commo

ns.wikimedia.org/wiki/File:Genetic_code.svg . Public Domain15. User:NEUROtiker/Wikimedia Commons. http://commons.wikimedia.org/wiki/File:Adenosintriphosphat_proto

niert.svg . Public Domain16. User:Bensacoount/Wikipedia. http://commons.wikimedia.org/wiki/File:Hydronium.png . Public Domain17. Hana Zavadska and Marianna Ruiz Villarreal (LadyofHats). CK-12 Foundation . CC BY-NC 3.018. Hana Zavadska. How enzyme changes activation energy .

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