How RNA codes for Proteins
Figure 2.16
The letters G, U, C, and A stand for the bases in RNA. Each group of three bases makes up a code word, and each code word represents one amino acid (represented here by a single letter, such as V, H, or L). A string of code words specifies the sequence of amino acids in a protein.
DNA and RNA have different functions relating to the genetic code and proteins. Like a set of blueprints, DNA contains the genetic instructions for the correct sequence of amino acids in proteins. RNA uses the information in DNA to assemble the amino acids and make the proteins. You will read more about the genetic code and the role of nucleic acids in protein synthesis in Chapter 8.
Lesson Summary
Carbon’s exceptional ability to form bonds with other elements and with itself allows it to form a huge number of large, complex molecules called organic molecules. These molecules make up organisms and carry out life processes.
Carbohydrates are organic molecules that consist of carbon, hydrogen, and oxygen. They are made up of repeating units called saccharides. They provide cells with energy, store energy, and form structural tissues.
Lipids are organic compounds that consist of carbon, hydrogen, and oxygen. They are made up of fatty acids and other compounds. They provide cells with energy, store energy, and help form cell membranes.
Proteins are organic compounds that consist of carbon, hydrogen, oxygen, nitrogen, and, in some cases, sulfur. They are made up of repeating units called amino acids. They provide cells with energy, form tissues, speed up chemical reactions throughout the body, and perform many other cellular functions.
Nucleic acids are organic compounds that consist of carbon, hydrogen, oxygen, nitrogen, and phosphorus. They 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 Questions
State the function of monosaccharides, such as glucose and fructose.
Why do molecules of saturated and unsaturated fatty acids have different shapes?
What determines the primary structure of a protein?
Identify the three parts of a nucleotide.
What type of organic compound is represented by the formula CH3(CH2)4COOH? How do you know?
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.
Why is carbon essential to all known life on Earth?
Compare and contrast simple sugars and complex carbohydrates.
State two functions of proteins, and explain how the functions depend on the ability of proteins to bind other molecules to them.
Further Reading / Supplemental Links
B.G. Davis and A.J. Fairbanks, Carbohydrate Chemistry. Oxford University Press, 2002.
Michael I. Gurr, John L. Harwood, and Keith N. Frayn, Lipid Biochemistry: An Introduction. Wiley, 2005.
James D. Watson, The Double Helix: A Personal Account of the Discovery of DNA. Touchstone, 2001.
David Whitford, Proteins: Structure and Functions. Wiley, 2005.
http://en.wikipedia.org
Vocabulary
amino acid
Small organic molecule that is a building block of proteins.
carbohydrate
Type of organic compound that consists of one or more smaller units called monosaccharides.
cholesterol
Type of steroid that is an important part of cell membranes and plays other vital roles.
complementary bases
Nucleic acid bases that form bonds with each other and help hold together two nucleotide chains.
complex carbohydrate
Another term for a polysaccharide.
deoxyribonucleic acid (DNA)
Double-stranded nucleic acid that contains the genetic instructions for proteins.
disaccharide
Small carbohydrate, such as sucrose, that consists of two monosaccharides.
double helix
Normal shape of a DNA molecule in which two chains of nucleotides are intertwined.
essential amino acids
Amino acids that the human body needs but cannot make and must consume in food.
essential fatty acids
Fatty acids that the human body needs but cannot make and must consume in food.
fatty acid
Organic compound found in lipids that has the general formula CH3(CH2)nCOOH.
functional group
Small group of elements within an organic compound that determines the nature and function of the organic compound.
lipid
Type of organic compound that consists of one or more fatty acids with or without additional molecules.
monosaccharide
Small carbohydrate, such as glucose, with the general formula (CH2O)n.
nucleic acid
Type of organic compound that consists of smaller units called nucleotides.
nucleotide
Small organic molecule that is a building block of nucleic acids.
peptide
Short chain of amino acids.
phospholipid
Type of lipid that is a major component of cell membranes.
polypeptide
Long chain of amino acids.
polysaccharide
Large carbohydrate that consists of more than two monosaccharides.
protein
Type of organic compound that consists of smaller units called amino acids.
ribonucleic acid (RNA)
Single-stranded nucleic acid that uses information contained in DNA to assemble amino acids and make proteins.
saturated fatty acid
Type of fatty acid in which all the carbon atoms are bonded to as many hydrogen atoms as possible.
simple sugar
Another term for a monosaccharide or disaccharide.
steroid
Type of lipid that has several functions, such as forming cell membranes and acting as sex hormones.
trans fatty acid
Artificial, unsaturated fatty acid that has properties similar to saturated fatty acids.
triglyceride
Type of lipid that is the main form of stored energy in animals.
unsaturated fatty acid
Type of fatty acid in which some carbon atoms are not bonded to as many hydrogen atoms as possible.
Points to Consider
Organisms are made up of thousands of very large, complex molecules called organic molecules. These molecules consist of repeating units of smaller molecules, such as amino acids or nucleotides.
How do organic molecules form?
How do smaller molecules join together to form larger molecules?
What chemical processes are involved?
Chemical Reactions
Lesson Objectives
Describe what happens in a chemical reaction, and identify types of chemical reactions.
Explain the role of energy in chemical reactions, and define activation energy.
State factors that affect the rate of chemical reactions.
Explain the importance of enzymes in organisms, and describe how enzymes work.
Introduction
A chemical compound may be very different from the substances that combine to form it. For example, the element chlorine (Cl) is a poisonous gas, but when it combines with sodium (Na) to form sodium chloride (NaCl), it is no longer toxic. You may even eat it on your food. Sodium chloride is just table salt. What process changes a toxic chemical like chlorine into a much different substance like table salt?
What are Chemical Reactions?
A chemical reaction is a process that changes some chemical substances into other chemical substances. The substances that start a chemical reaction are called reactants. The substances that form as a result of a chemical reaction are called products. During the reaction, th
e 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).
Chemical Equations
A chemical reaction can be represented by a chemical equation. Using the same example, the burning of methane gas 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 the reaction occurs. If the reaction could also occur in the opposite direction, then two arrows, one pointing in each direction, would be used. On each side of the arrow, a mixture of chemicals is 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 in front 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 at the end of the reaction as there was at the beginning. This is reflected in the chemical equation for the reaction. The equation should be balanced. In a balanced equation, the same number of atoms of a given element appear on each side 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, in which a compound or element burns in oxygen, is called a combustion reaction. This is just one of many possible types of chemical reactions. Other types of chemical reactions include synthesis, decomposition, and substitution reactions.
A synthesis reaction occurs when two or more chemical elements or compounds unite to form a more complex product. 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) and hydrogen gas (H2):
2 Na+ + 2 HCl → 2 NaCl + H2.
Chemical Reactions and Energy
Some chemical reactions consume energy, whereas other chemical reactions release energy. Each of the energy changes that occur during a reaction are graphed in Figure below. In the reaction on the left, energy is released. In the reaction on the right, energy is consumed.
Figure 2.17
The reaction on the left releases energy. The reaction on the right consumes energy.
Exothermic Reactions
Chemical reactions that release energy are called exothermic reactions. An example is the combustion of methane described at the beginning of this lesson. In organisms, exothermic reactions are called catabolic reactions. Catabolic reactions break down molecules into smaller units. An example is the breakdown of glucose molecules for energy. Exothermic reactions can be represented by the general chemical equation:
Reactants → Products + Heat.
Endothermic Reactions
Chemical reactions that consume energy are called endothermic reactions. An example is the synthesis of ammonia, described above. In organisms, endothermic reactions are called anabolic reactions. Anabolic reactions construct molecules from smaller units. An example is the synthesis of proteins from amino acids. Endothermic reactions can be represented by the general chemical equation:
Reactants + Heat → Products.
Activation Energy
Regardless of whether reactions are exothermic or endothermic, they all need energy to get started. This energy is called activation energy. Activation energy is like the push you need to start moving down a slide. The push gives you enough energy to start moving. Once you start, you keep moving without being pushed again. The concept of activation energy is illustrated in Figure below.
Figure 2.18
To start this reaction, a certain amount of energy is required, called the activation energy. How much activation energy is required depends on the nature of the reaction and the conditions under which the reaction takes place.
Why do reactions need energy to get started? In order for reactions to occur, three things must happen, and they all require energy:
Reactant molecules must collide. To collide, they must move, so they need kinetic energy.
Unless reactant molecules are positioned correctly, intermolecular forces may push them apart. To overcome these forces and move together requires more energy.
If reactant molecules collide and move together, there must be enough energy left for them to react.
Rates of Chemical Reactions
The rates at which chemical reactions take place in organisms are very important. Chemical reactions in organisms are involved in processes ranging from the contraction of muscles to the digestion of food. For example, when you wave goodbye, it requires repeated contractions of muscles in your arm over a period of a couple of seconds. A huge number of reactions must take place in that time, so each reaction cannot take longer than a few milliseconds. If the reactions took much longer, you might not finish waving until sometime next year.
Factors that help reactant molecules collide and react speed up chemical reactions. These factors include the concentration of reactants and the temperature at which the reactions occur.
Reactions are usually faster at higher concentrations of reactants. The more reactant molecules there are in a given space, the more likely they are to collide and react.
Reactions are usually faster at higher temperatures. Reactant molecules at higher temperatures have more energy to move, collide, and react.
Enzymes and Biochemical Reactions
Most chemical reactions within organisms would be impossible under the conditions in cells. For example, the body 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 up chemical reactions. In organisms, catalysts are called enzymes.
Like other catalysts, enzymes are not reactants in the reactions they control. They help the reactants interact but are not used up in the reactions. Instead, they may be used over and over again. Unlike other catalysts, enzymes are usually highly specific for particular chemical reactions. They generally catalyze only one or a few types of reactions.
Enzymes are extremely efficient in speeding up reactions. They can catalyze up to several million reactions per second. 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 an enzyme but less than a second with the enzyme. For an animation of a reaction in the presence or absence of an enzyme, see http://www.stolaf.edu/people/giannini/flashanimat/enzymes/prox-orien.swf.
How Enzymes Work
How do enzymes speed up biochemical reactions so dramatically? Like all catalysts, enzymes work by lowering the activation energy of chemical reactions. This is illustrated in Figure below. The biochemical reaction shown in the figure requires about three times as much activation energy without the enzyme as it does with the enzyme. An animation of this process can be viewed at http://www.stolaf.edu/people/giannini/flashanimat/enzymes/transition%20state.swf.
Figure 2.19
The reaction represented by this graph is a combustio
n reaction involving the reactants glucose (CHO) and oxygen (O). The products of the reaction are carbon dioxide (CO) and water (HO). Energy is also released during the reaction. The enzyme speeds up the reaction by lowering the activation energy needed for the reaction to start. Compare the activation energy with and without the enzyme.
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 at random. Enzymes bind both reactant molecules (called substrate), tightly and specifically, at a site on the enzyme molecule called the active site (Figure below).
By binding reactants at the active site, enzymes also position reactants correctly, so they do not have to overcome intermolecular forces that would otherwise push them apart. This allows the molecules to interact with less energy.
Enzymes may also allow reactions to occur by different pathways that have lower activation energy.
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