Metabolism

Metabolism refers to all chemical reactions that take place in an organism. These reactions (1) extract energy from nutrient biomolecules (such as proteins, carbohydrates, and lipids) and (2) either synthesize or break down molecules. Metabolism is often divided into catabolism, reactions that release energy through the breakdown of large biomolecules, and anabolism, energy-utilizing reactions that result in the synthesis of large biomolecules. Anabolic and catabolic reactions take place simultaneously in cells throughout the body, so that at any given moment, some biomolecules are being synthesized while others are being broken down.

The energy released from or stored in the chemical bonds of biomolecules during metabolism is commonly measured in kilocalories (kcal). A kilocalorie is the amount of energy needed to raise the temperature of 1 liter of water by 1 degree Celsius. One kilocalorie is the same as a Calorie, with a capital C, used for quantifying the energy content of food. One kilocalorie is also equal to 1000 calories (small c).

Much of the energy released during catabolism is trapped in the high-energy phosphate bonds of ATP or in the high-energy electrons of NADH, FADH2, or NADPH. Anabolic reactions then transfer energy from these temporary carriers to the covalent bonds of biomolecules.

Metabolism is a network of highly coordinated chemical reactions in which the activities taking place in a cell at any given moment are matched to the needs of the cell. Each step in a metabolic pathway is a different enzymatic reaction, and the reactions of a pathway proceed in sequence. Substrate A is changed into product B, which then becomes the substrate for the next reaction in the pathway. B is changed into C, and so forth:

A B C D

We call the molecules of the pathway intermediates because the products of one reaction become the substrates for the next. You will sometimes hear metabolic pathways called intermediary metabolism. Certain intermediates, called key intermediates, participate in more than one pathway and act as the branch points for channeling substrate in one direction or another. Glucose, for instance, is a key intermediate in several metabolic pathways.

In many ways, a group of metabolic pathways is similar to a detailed road map (Fig. 4.8). Just as a map shows a network of roads that connect various cities and towns, you can think of metabolism as a network of chemical reactions connecting various intermediate products. Each city or town is a different chemical intermediate. One-way roads are irreversible reactions, and big cities with roads to several destinations are key intermediates. Just as there may be more than one way to get from one place to another, there can be several pathways between any given pair of chemical intermediates.

FIG. 4.8 Metabolic pathways resemble a road map

Cells Regulate Their Metabolic Pathways

How do cells regulate the flow of molecules through their metabolic pathways? They do so in five basic ways:

  1. By controlling enzyme concentrations

  2. By producing modulators that change reaction rates

  3. By using two different enzymes to catalyze reversible reactions

  4. By compartmentalizing enzymes within intracellular organelles

  5. By maintaining an optimum ratio of ATP to ADP

We discussed the effects of changing enzyme concentration in the discussion of protein-binding reactions: as enzyme concentration increases, the reaction rate increases [here]. The sections that follow examine the remaining four items on the list.

Enzyme Modulation

Modulators, which alter the activity of a protein, were introduced in the discussion of protein binding [here]. For enzymes, the production of modulators is frequently controlled by hormones and other signals coming from outside the cell. This type of outside regulation is a key element in the integrated control of the body’s metabolism following a meal or during periods of fasting between meals.

In addition, some metabolic pathways have their own built-in form of modulation, called feedback inhibition. In this form of modulation, the end product of a pathway, shown as Z in Figure 4.9, acts as an inhibitory modulator of the pathway. As the pathway proceeds and Z accumulates, the enzyme catalyzing the conversion of A to B is inhibited. Inhibition of the enzyme slows down production of Z until the cell can use it up. Once the levels of Z fall, feedback inhibition on enzyme 1 is removed and the pathway starts to run again. Because Z is the end product of the pathway, this type of feedback inhibition is sometimes called end-product inhibition.

FIG. 4.9 Feedback inhibition

Reversible Reactions

Cells can use reversible reactions to regulate the rate and direction of metabolism. If a single enzyme can catalyze the reaction in either direction, the reaction will go to a state of equilibrium, as determined by the law of mass action (Fig. 4.10a). Such a reaction, therefore, cannot be closely regulated except by modulators and by controlling the amount of enzyme.

FIG. 4.10 Enzymes control reversibility of metabolic reactions

Figure Question: What is the difference between a kinase and a phosphatase? (Hint: See TBL. 4.4.)

However, if a reversible reaction requires two different enzymes, one for the forward reaction and one for the reverse reaction, the cell can regulate the reaction more closely (Fig. 4.10b). If no enzyme for the reverse reaction is present in the cell, the reaction is irreversible (Fig. 4.10c).

Compartmentalizing Enzymes in the Cell

Many enzymes of metabolism are isolated in specific subcellular compartments. Some, like the enzymes of carbohydrate metabolism, are dissolved in the cytosol, whereas others are isolated within specific organelles. Mitochondria, endoplasmic reticulum, Golgi apparatus, and lysosomes all contain enzymes that are not found in the cytosol. This separation of enzymes means that the pathways controlled by the enzymes are also separated. That allows the cell to control metabolism by regulating the movement of substrate from one cellular compartment to another. The isolation of enzymes within organelles is an important example of structural and functional compartmentation [here].

Ratio of ATP to ADP

The energy status of the cell is one final mechanism that can influence metabolic pathways. Through complex regulation, the ratio of ATP to ADP in the cell determines whether pathways that result in ATP synthesis are turned on or off. When ATP levels are high, production of ATP decreases. When ATP levels are low, the cell sends substrates through pathways that result in more ATP synthesis. In the next section, we look further into the role of ATP in cellular metabolism.

ATP Transfers Energy between Reactions

The usefulness of metabolic pathways as suppliers of energy is often measured in terms of the net amount of ATP the pathways can yield. ATP is a nucleotide containing three phosphate groups [here]. One of the three phosphate groups is attached to ADP by a covalent bond in an energy-requiring reaction. Energy is stored in this high-energy phosphate bond and then released when the bond is broken during removal of the phosphate group. This relationship is shown by the following reaction:

ADP + P i  + energy   ADP ~ P(=ATP)

The squiggle ~ indicates a high-energy bond, and Pi is the abbreviation for an inorganic phosphate group. Estimates of the amount of free energy released when a high-energy phosphate bond is broken range from 7 to 12 kcal per mole of ATP.

ATP is more important as a carrier of energy than as an energy-storage molecule. For one thing, cells can contain only a limited amount of ATP. A resting adult human needs 40 kg (88 pounds!) of ATP to supply the energy required to support one day’s worth of metabolic activity, far more than our cells could store. Instead, the body acquires most of its daily energy requirement from the chemical bonds of complex biomolecules. Metabolic reactions transfer that chemical bond energy to the high-energy bonds of ATP, or in a few cases, to the high-energy bonds of the related nucleotide guanosine triphosphate, GTP.

The metabolic pathways that yield the most ATP molecules are those that require oxygen—the aerobic, or oxidative, pathways. Anaerobic {an-, without + aer, air} pathways, which are those that can proceed without oxygen, also produce ATP molecules but in much smaller quantities. The lower ATP yield of anaerobic pathways means that most animals (including humans) are unable to survive for extended periods on anaerobic metabolism alone. In the next section, we consider how biomolecules are metabolized to transfer energy to ATP.

Concept Check

  1. Name five ways in which cells regulate the movement of substrates through metabolic pathways.

  2. In which part of an ATP molecule is energy trapped and stored? In which part of a NADH molecule is energy stored?

  3. What is the difference between aerobic and anaerobic pathways?

Catabolic Pathways Produce ATP

Figure 4.11 summarizes the catabolic pathways that extract energy from biomolecules and transfer it to ATP. Aerobic production of ATP from glucose commonly follows two pathways: glycolysis {glyco-, sweet + lysis, dissolve} and the citric acid cycle (also known as the tricarboxylic acid cycle). The citric acid cycle was first described by Hans A. Krebs, so it is sometimes called the Krebs cycle. Because Dr. Krebs described other metabolic cycles, we will avoid confusion by using the term citric acid cycle.

Carbohydrates enter glycolysis in the form of glucose (top of Fig. 4.11). Lipids are broken down into glycerol and fatty acids [here], which enter the pathway at different points: glycerol feeds into glycolysis, and fatty acids are metabolized to acetyl CoA. Proteins are broken down into amino acids, which also enter at various points. Carbons from glycolysis and other nutrients enter the citric acid cycle, which makes a never-ending circle. At each turn, the cycle adds carbons and produces ATP, high-energy electrons, and carbon dioxide.

Both glycolysis and the citric acid cycle produce small amounts of ATP directly, but their most important contribution to ATP synthesis is trapping energy in electrons carried by NADH and FADH2. These compounds transfer the electrons to the electron transport system (ETS) in the mitochondria. The electron transport system, in turn, uses energy from those electrons to make the high-energy phosphate bond of ATP. At various points, the process produces carbon dioxide and water. Cells can use the water, but carbon dioxide is a waste product and must be removed from the body.

Because glucose is the only molecule that follows both pathways in their entirety, in this chapter, we look at only glucose catabolism.

We will examine protein and lipid catabolism and synthetic pathways for lipids and glucose when we look at the fate of the nutrients we eat [Chapter 22].

The aerobic pathways for ATP production are a good example of compartmentation within cells. The enzymes of glycolysis are located in the cytosol, and the enzymes of the citric acid cycle are in the mitochondria. Within mitochondria, concentration of H+ in the intermembrane compartment stores the energy needed to make the high-energy bond of ATP.

Concept Check

  1. Match each component on the left to the molecule(s) it is part of:

    • (a) amino acids

    • (b) fatty acids

    • (c) glycerol

    • (d) glucose

    1. carbohydrates

    2. lipids

    3. polysaccharides

    4. proteins

    5. triglycerides

  2. Do endergonic reactions release energy or trap it in the products?

One Glucose Molecule Can Yield 30–32 ATP

Recall from Figure 4.11 that the aerobic metabolism of one glucose molecule produces carbon dioxide, water, and 30–32 ATP. Let’s review the role of glycolysis and the citric acid cycle in that ATP production.

In glycolysis (Fig. 4.12), metabolism of one glucose molecule C6H12O6 has a net yield of two 3-carbon pyruvate molecules, 2 ATPs, and high-energy electrons carried on 2 NADH:

Glucose + 2 NAD +  + 2 ADP + P i 2  Pyruvate + 2 ATP + 2 NADH + 2 H +  + 2 H 2 O

In the next phase, the conversion of pyruvate to acetyl CoA produces one NADH (Fig. 4.13). Carbons from one acetyl CoA going through the citric acid cycle trap energy in 3 NADH molecules, 1 FADH2 and 1 ATP. These steps happen twice for each glucose, giving a total yield of 8 NADH, 2 FADH2, and 2 ATP for the pyruvate-citric acid cycle phase of glucose metabolism.

In the final step, high-energy electrons of NADH and FADH2 passing along the proteins of the electron transport system use their energy to concentrate H+ in the intermembrane compartment of the mitochondria (Fig. 4.14). When the H+ move down their concentration gradient through a channel in the ATP synthase, the energy released is transferred to the high-energy phosphate bond of ATP. On average, the NADH and FADH2 from one glucose produce 26–28 ATPs.

When we tally the maximum potential energy yield for the catabolism of one glucose molecule through aerobic pathways, the total comes to 30–32 ATP (Fig. 4.15). These numbers are the potential maximum because often the mitochondria do not work up to capacity. There are various reasons for this, including the fact that a certain number of H+ ions leak from the intermembrane space back into the mitochondrial matrix without producing an ATP.

FIG. 4.15 Energy yields from catabolism of one glucose molecule

Figure Questions

  1. How many NADH enter the electron transport system when glucose is metabolized to lactate?

  2. Some amino acids can be converted to pyruvate. If one amino acid becomes one pyruvate, what is the ATP yield from aerobic metabolism of that amino acid?

A second source of variability in the number of ATP produced per glucose comes from the two cytosolic NADH molecules produced during glycolysis. These NADH molecules are unable to enter mitochondria and must transfer their electrons through membrane carriers. Inside a mitochondrion, some of these electrons go to FADH2, which has a potential average yield of only 1.5 ATP rather than the 2.5 ATP made by mitochondrial NADH. If cytosolic electrons go to mitochondrial NADH instead, they produce two additional ATP molecules.

Anaerobic Metabolism Makes 2 ATP

The metabolism of glucose just described assumes that the cells have adequate oxygen to keep the electron transport system functioning. But what happens to a cell whose oxygen supply cannot keep pace with its ATP demand, such as often happens during strenuous exercise? In that case, the metabolism of glucose shifts from aerobic to anaerobic metabolism, starting at pyruvate (Fig. 4.16).

FIG. 4.16 Aerobic and anaerobic metabolism

In anaerobic glucose metabolism, pyruvate is converted to lactate instead of being transported into the mitochondria:

Pyruvate is a branch point for metabolic pathways, like a hub city on a road map. Depending on a cell’s needs and oxygen content, pyruvate can be shuttled into the citric acid cycle or diverted into lactate production until oxygen supply improves.

The conversion of pyruvate to lactate changes one NADH back to NAD+ when a hydrogen atom and an electron are transferred to the lactate molecule. As a result, the net energy yield for the anaerobic metabolism of one glucose molecule is 2 ATP and 0 NADH (Fig. 4.15a), a very puny yield when compared to the 30–32 ATP/glucose that result from aerobic metabolism (Fig.  4.15b). The low efficiency of anaerobic metabolism severely limits its usefulness in most vertebrate cells, whose metabolic energy demand is greater than anaerobic metabolism can provide. Some cells, such as exercising muscle cells, can tolerate anaerobic metabolism for a limited period of time. Eventually, however, they must shift back to aerobic metabolism. [Aerobic and anaerobic metabolism in muscle are discussed further in Chapters 12 and 25.]

Concept Check

  1. How is the separation of mitochondria into two compartments essential to ATP synthesis?

  2. Lactate dehydrogenase acts on lactate by (adding or removing?) a(n)       and a(n)      . This process is called (oxidation or reduction?).

  3. Describe two differences between aerobic and anaerobic metabolism of glucose.

Proteins Are the Key to Cell Function

As you have seen, proteins are the molecules that run a cell from day to day. Protein enzymes control the synthesis and breakdown of carbohydrates, lipids, structural proteins, and signal molecules. Protein transporters and pores in the cell membrane and in organelle membranes regulate the movement of molecules into and out of compartments. Other proteins form the structural skeleton of cells and tissues. In these and other ways, protein synthesis is critical to cell function.

The power of proteins arises from their tremendous variability and specificity. Protein synthesis using 20 amino acids can be compared to creating a language with an alphabet of 20 letters. The “words” vary in length from three letters to hundreds of letters, spelling out the structure of thousands of different proteins with different functions. A change in one amino acid during protein synthesis can alter the protein’s function, just as changing one letter turns the word “foot” into “food.”

The classic example of an amino acid change causing a problem is sickle cell disease. In this inherited condition, when the amino acid valine replaces one glutamic acid in the protein chain, the change alters the shape of hemoglobin. As a result, red blood cells containing the abnormal hemoglobin take on a crescent (sickle) shape, which causes them to get tangled up and block small blood vessels.

The Protein “Alphabet”

One of the mysteries of biology until the 1960s was the question of how only four nitrogenous bases in the DNA molecule—adenine (A), guanine (G), cytosine (C), and thymine (T)—could code for more than 20 different amino acids. If each base controlled the synthesis of one amino acid, a cell could make only four different amino acids. If pairs of bases represented different amino acids, the cell could make 42 or 16 different amino acids. Because we have 20 amino acids, this is still not satisfactory. If triplets of bases were the codes for different molecules, however, DNA could create 43 or 64 different amino acids. These triplets, called codons, are indeed the way information is encoded in DNA and RNA. Figure 4.17 shows the genetic code as it appears in one form of RNA. Remember that RNA substitutes the base uracil (U) for the DNA base thymine [p. 35].

FIG. 4.17 The genetic code as it appears in the codons of mRNA

Of the 64 possible triplet combinations, one DNA codon (TAC) acts as the initiator or “start codon” that signifies the beginning of a coding sequence. Three codons serve as terminator or “stop codons” that show where the sequence ends. The remaining 60 triplets all code for amino acids. Methionine and tryptophan have only one codon each, but the other amino acids have between two and six different codons each. Thus, like letters spelling words, the DNA base sequence determines the amino acid sequence of proteins.

Unlocking DNA’s Code

How does a cell know which of the thousands of bases present in its DNA sequence to use in making a protein? It turns out that the information a cell needs to make a particular protein is contained in a segment of DNA known as a gene. What exactly is a gene? The definition keeps changing, but for this text we will say that a gene is a region of DNA that contains the information needed to make a functional piece of RNA, which in turn can make a protein.

Figure 4.18 shows the five major steps from gene to RNA to functional protein. First, a section of DNA containing a gene must be activated so that its code can be read . Genes that are continuously being read and converted to RNA messages are said to be constitutively active. Usually these genes code for proteins that are essential to ongoing cell functions. Other genes are regulated—that is, their activity can be turned on (induced) or turned off (repressed) by regulatory proteins.

BioFlix: Protein Synthesis

Once a gene is activated, the DNA base sequence of the gene is used to create a piece of RNA in the process known as transcription {trans, over + scribe, to write} (Fig. 4.18 ). Human cells have three major forms of RNA: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). Messenger RNA is processed in the nucleus after it is made . It may either undergo alternative splicing (discussed shortly) before leaving the nucleus or be “silenced” and destroyed by enzymes through RNA interference. Processed mRNA leaves the nucleus and enters the cytosol. There it works with tRNA and rRNA to direct translation, the assembly of amino acids into a protein chain .

Newly synthesized proteins are then subject to posttranslational modification (Fig. 4.18 ). They fold into complex shapes, may be split by enzymes into smaller peptides, or have various chemical groups added to them. The remainder of this chapter looks at transcription, RNA processing, translation, and posttranslational modification in more detail.

DNA Guides the Synthesis of RNA

The first steps in protein synthesis are compartmentalized within the nucleus because DNA is a very large molecule that cannot pass through the nuclear envelope. Transcription uses DNA as a template to create a small single strand of RNA that can leave the nucleus (Fig. 4.19). The synthesis of RNA from the double-stranded DNA template requires an enzyme known as RNA polymerase, plus magnesium or manganese ions and energy in the form of high-energy phosphate bonds:

FIG. 4.19 Transcription

A promoter region that precedes the gene must be activated before transcription can begin. Regulatory-protein transcription factors bind to DNA and activate the promoter. The active promoter tells the RNA polymerase where to bind to the DNA (Fig.  4.19 ). The polymerase moves along the DNA molecule and “unwinds” the double strand by breaking the hydrogen bonds between paired bases . One strand of DNA, called the template strand, serves as the guide for RNA synthesis . The promoter region is not transcribed into RNA.

During transcription, each base in the DNA template strand pairs with the complementary RNA base (G-C, C-G, T-A, A-U). This pairing of complementary bases is similar to the process by which a double strand of DNA forms [see Appendix C for a review of DNA synthesis]. For example, a DNA segment containing the base sequence AGTAC is transcribed into the RNA sequence UCAUG.

As the RNA bases bind to the DNA template strand, they also bond with one another to create a single strand of RNA. During transcription, bases are linked at an average rate of 40 per second. In humans, the largest RNAs may contain as many as 5000 bases, and their transcription may take more than a minute—a long time for a cellular process. When RNA polymerase reaches the stop codon, it stops adding bases to the growing RNA strand and releases the strand (Fig. 4.19 ).

Concept Check

  1. Use the genetic code in Figure 4.17 to write the DNA codons that correspond to the three mRNA stop codons.

  2. What does the name RNA polymerase tell you about the function of this enzyme?

Alternative Splicing Creates Multiple Proteins from One DNA Sequence

The next step in the process of protein synthesis is mRNA processing, which takes two forms (Fig. 4.18 ). In RNA interference, newly synthesized mRNA is inactivated or destroyed before it can be translated into proteins (see the Emerging Concepts box). In alternative splicing, enzymes clip segments out of the middle or off the ends of the mRNA strand. Other enzymes then splice the remaining pieces of the strand back together.

Alternative splicing is necessary because a gene contains both segments that encode proteins (exons) and noncoding segments called introns (Fig. 4.20). That means the mRNA initially made from the gene’s DNA contains noncoding segments that must be removed before the mRNA leaves the nucleus. The result of alternative splicing is a smaller piece of mRNA that now contains only the coding sequence for a specific protein.

FIG. 4.20 mRNA processing

One advantage of alternative splicing is that it allows a single base sequence on DNA to code for more than one protein. The designation of segments as coding or noncoding is not fixed for a given gene. Segments of mRNA that are removed one time can be left in the next time, producing a finished mRNA with a different sequence. The closely related forms of a single enzyme known as isozymes are probably made by alternative splicing of a single gene.

After mRNA has been processed, it exits the nucleus through nuclear pores and goes to ribosomes in the cytosol. There mRNA directs the construction of protein.

Concept Check

  1. Explain in one or two sentences the relationship of mRNA, nitrogenous bases, introns, exons, mRNA processing, and proteins.

mRNA Translation Links Amino Acids

Protein synthesis requires cooperation and coordination among all three types of RNA: mRNA, rRNA, and tRNA. Upon arrival in the cytosol, processed mRNA binds to ribosomes, which are small particles of protein and several types of rRNA [p. 35]. Each ribosome has two subunits, one large and one small, that come together when protein synthesis begins (Fig. 4.21 ). The small ribosomal subunit binds the mRNA, then adds the large subunit so that the mRNA is sandwiched in the middle. Now the ribosome-mRNA complex is ready to begin translation.

FIG. 4.21 Translation

During translation, the mRNA codons are matched to the proper amino acid. This matching is done with the assistance of a tRNA molecule (Fig. 4.21 ). One region of each tRNA contains a three-base sequence called an anticodon that is complementary to an mRNA codon. A different region of the tRNA molecule binds to a specific amino acid.

As translation begins, the anticodons of tRNAs carrying amino acids attach to the complementary codons of ribosomal mRNA. For example, a tRNA with anticodon sequence UUU carries the amino acid lysine. The UUU anticodon pairs with an AAA codon, one of two codons for lysine, on mRNA. The pairing between mRNA and tRNA puts newly arrived amino acids into the correct orientation to link to the growing peptide chain.

Dehydration synthesis links amino acids by creating a peptide bond between the amino group (-NH2) of the newly arrived amino acid and the carboxyl end (-COOH) of the peptide chain [here]. Once this happens, mRNA releases the “empty” tRNA. The tRNA can then attach to another amino acid molecule with the aid of a cytosolic enzyme and ATP.

When the last amino acid has been joined to the newly synthesized peptide chain, the termination stage has been reached (Fig. 4.21 ). The mRNA, the peptide, and the ribosomal subunits separate. The ribosomes are ready for a new round of protein synthesis, but the mRNA is broken down by enzymes known as ribonucleases. Some forms of mRNA are broken down quite rapidly, while others may linger in the cytosol and be translated many times.

Protein Sorting Directs Proteins to Their Destination

One of the amazing aspects of protein synthesis is the way specific proteins go from the ribosomes directly to where they are needed in the cell, a process called protein sorting. Many newly made proteins carry a sorting signal, an address label that tells the cell where the protein should go. Some proteins that are synthesized on cytosolic ribosomes do not have sorting signals. Without a “delivery tag,” they remain in the cytosol when they are released from the ribosome [Fig. 3.7, here].

The sorting signal is a special segment of amino acids known as a signal sequence. The signal sequence tag directs the protein to the proper organelle, such as the mitochondria or peroxisomes, and allows it to be transported through the organelle membrane. Peptides synthesized on ribosomes attached to the rough endoplasmic reticulum have a signal sequence directs them through the membrane of the rough ER and into the lumen of this organelle. Once a protein enters the ER lumen, enzymes remove the signal sequence.

Proteins Undergo Posttranslational Modification

The amino acid sequence that comes off a ribosome is the primary structure of a newly synthesized protein [here], but not the final form. The newly made protein can now form different types of covalent and noncovalent bonds, a process known as posttranslational modification. Cleavage of the amino acid chain, attachment of molecules or groups, and cross-linkages are three general types of posttranslational modification. More than 100 different types of posttranslational modification have been described so far.

In some common forms of posttranslational modification, the amino acid chain can:

  1. fold into various three-dimensional shapes. Protein folding creates the tertiary structure of the protein.

  2. create cross-links between different regions of its amino acid chain

  3. be cleaved (split) into fragments

  4. add other molecules or groups

  5. assemble with other amino acid chains into a polymeric (many-part) protein. Assembly of proteins into polymers creates the quaternary structure of the protein.

Protein Folding

Peptides released from ribosomes are free to take on their final three-dimensional shape. Each peptide first forms its secondary structure, which may be an a-helix or a b-strand [here]. The molecule then folds into its final shape when hydrogen bonds, covalent bonds, and ionic bonds form between amino acids in the chain. Studies show that some protein folding takes place spontaneously, but it is often facilitated by helper proteins called molecular chaperones.

The three-dimensional shape of proteins is often essential for proper function. Misfolded proteins, along with other proteins the cell wishes to destroy, are tagged with a protein called ubiquitin and sent to proteasomes, cylindrical cytoplasmic enzyme complexes that break down proteins.

Cross-Linkage

Some protein folding is held in place by relatively weak hydrogen bonds and ionic bonds. However, other proteins form strong covalent bonds between different parts of the amino acid chain. These bonds are often disulfide bonds (S–S) between two cysteine amino acids, which contain sulfur atoms. For example, the three chains of the digestive enzyme chymotrypsin are held together by disulfide bonds.

Cleavage

Some biologically active proteins, such as enzymes and hormones, are synthesized initially as inactive molecules that must have segments removed before they become active. The enzyme chymotrypsin must have two small peptide fragments removed before it can catalyze a reaction [Fig. 2.12a here]. Posttranslational processing also activates some peptide hormones.

Addition of Other Molecules or Groups

Proteins can be modified by the addition of sugars (glycosylation) to create glycoproteins, or by combination with lipids to make lipoproteins [here]. The two most common chemical groups added to proteins are phosphate groups, PO 4 2 and methyl groups, -CH3. (Addition of a methyl group is called methylation.)

Assembly into Polymeric Proteins

Many complex proteins have a quaternary structure with multiple subunits, in which protein chains assemble into dimers, trimers, or tetramers. One example is the enzyme lactate dehydrogenase (described on p. 99). Another example is the hemoglobin molecule, with four protein chains [Fig. 2.3].

Concept Check

  1. What is the removal of a phosphate group called?

  2. List three general types of posttranslational modification of proteins.

  3. Is hemoglobin a monomer, dimer, trimer, or tetramer?

The many ways that proteins can be modified after synthesis add to the complexity of the human body. We must know not only the sequence of a protein but also how it is processed, where the protein occurs in or outside the cell, and what it does. Scientists working on the Human Genome Project initially predicted that our DNA would code for about 30,000 proteins, but they were not taking into account alternative splicing or posttranslational modifications. Scientists working on the Human Proteomics Initiative are now predicting that we will find more than a million different proteins. The magnitude of this project means that it will continue for many years into the future.