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BIOCHEMISTRY
In one semester: The coverage you want. The relevance your students need.Biochemistry: The Molecular Basis of Life is a one-semester text focusing on the essential biochemical principles that underpin the modern life sciences. The sixth edition:
• Offers deeper coverage of the chemistry of reactions, while emphasizing the relationship between biochemistry and human biology
• Places biochemical principles into the context of the physiology of the cell and biomedical applications
• Applies biochemical principles to the fields of health, nutrition, agriculture, engineering, and others
• Equips students with a complete view of the living state
• Strikes the perfect balance of biology and chemistry coverage
2
Handout on the U.S. Bureau of Labor Statistics web site offers an unbiased assessment of future employment prospects.) No matter the economic conditions when students graduate, employment opportunities are always better for those who have undergraduate research experience. Devel-oping of a network of connections beginning with professors and expanding into the student’s field or interests (e.g., by attending science career fairs or professional society conferences) also increases employment opportunities. Further-more, writing, data analysis, problem solving, and communication are skills that employers always value highly. For students not interested in research careers, there are opportunities in science journalism, education, and software en-gineering. Other examples of alternate careers where a life science degree will be an asset in-clude public policy (e.g., public health risk as-sessment and health product regulation), law (e.g., lawyers for pharmaceutical and biotech companies), and marketing and sales (e.g., drugs and medical devices).
Why study biochemistry? For students em-barking on careers in the life sciences, the
answer should be obvious: biochemistry, the sci-entific discipline concerned with chemical pro-cesses within living organisms, is the bedrock upon which all of the modern life sciences are built. During the past two decades the influence of biochemistry and the allied field of molecular biol-ogy has increased exponentially. Life sciences as diverse as agronomy (the science of soil manage-ment and crop production), forensics, marine bi-ology, plant biology, and ecology are now being explored with powerful biotechnological tools. As a result, there is now a vast array of career oppor-tunities in federal or state government agencies and industry (e.g., pharmaceutical, biotechnology, and agribusiness companies) for recent gradu-ates with life science degrees. Examples of such fields include biomedical and clinical research, forensic analysis, plant or animal genetics, envi-ronmental protection, and wildlife biology.
Economic conditions often dictate life science career choices. (The Occupational Outlook
Why Study Biochemistry?
OverviewFROM MODEST BEGINNINGS IN THE LATE NINETEENTH CENTURY, THE
SCIENCE OF BIOCHEMISTRY HAS PROVIDED INCREASINGLY MORE
sophisticated intellectual and laboratory tools for the investigation of living
processes. Today, in the early years of the twenty-first century, we find our-
selves in the midst of a previously unimagined biotechnological revolution. Life
sciences as diverse as medicine, agriculture, and forensics have generated
immense amounts of information. The capacity to understand and appreciate
the significance of this phenomenon begins with a thorough knowledge of bio-
chemical principles. This chapter provides an overview of these principles. The
chapters that follow focus on the structure and functions of the most important
biomolecules and the major biochemical processes that sustain the living state.
T his textbook is designed to provide an introduction to the basic principles of biochemistry. The opening chapter provides an overview of the major components of living organisms and the processes that sustain the living
state. After a brief description of the nature of the living state, an introduction to the structures and functions of the major biomolecules is provided. This ma-terial is followed by an overview of the most important biochemical processes.
01-McKee-Chap01.indd 2 27/02/15 3:18 pm
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General and Organic Chemistry Review Primer P-11
Ascertaining a molecule’s three-dimensional shape begins with a correct Lewis dot structure. The molecule’s geometry is then determined based on the number of bonding and nonbonding electrons on the central atom (Figure 4). If there are two electron pairs, the molecule has a linear shape. Carbon dioxide (CO2), for example, is a linear molecule with two electron groups. Its bond angle is 180o. Formaldehyde (H2C5O), with three electron groups, has trigonal planar geometry with bond angles of 120o. Molecules with a central atom with four pairs of electrons have a tetrahedral shape. Methane (CH4), with its four carbon-hydrogen bonds, has bond angles of 109.5o. If one of the four electron groups in a tetrahed-ron is a lone pair, the molecular shape is trigonal pyramidal. Because of the strong repulsion of the lone pair, bond angles are less than 109.5o. For example, the lone pair in NH3 forces the NH bonding electron pairs closer together with bond angles of 107.3o.
Three-dimensional shape also affects molecular polarity. In polar covalent bonds there is an unequal sharing of electrons because the atoms have different electronegativities. This separation of charge is called a dipole. Although a polar molecule always contains polar bonds, some molecules with polar bonds are nonpolar. Molecular polarity requires an asymmetric distribution of polar bonds. For example, CO2 contains two C—O dipole bonds. Carbon dioxide is a non-polar molecule because of its linear shape (i.e., its bond dipoles are symmetrical and cancel each other out). Water, which also has two polar bonds (two O—H
Linear Trigonal planar
180° 120°
Bent (V shaped)Trigonal pyramidalTetrahedral
109.5°
FIGURE 4Common Molecular Geometrics
These structures illustrate the spatial orientations of electron groups. Note that unpaired electrons are indicated by an enlarged representation of an orbital.
What is the Lewis electron dot formula for formaldehyde (H2C=O)?
SOLUTIONThe valence electrons for hydrogen, carbon, and oxygen are 2 (1 for each atom), 4, and 6, respectively, for a total of 12 electrons. Single bonds between the ele-ments account for 6 electrons, leaving 6 electrons unaccounted for. Group the remaining 6 electrons around the most electronegative atom (oxygen) until a total of 8 electrons (bonding and nonbonding) is reached. Using one pair of these electrons to form a double bond between carbon and oxygen completes the carbon octet. The final Lewis structure is given below.
OC
H
H
WORKED PROBLEM 2
McKee_Primer.indd 11 14/05/15 2:24 AM
FIGURE 4Common Molecular Geometrics
These structures illustrate the spatial orientations of electron groups. Note that unpaired electrons are indicated by an enlarged representation of an orbital.
General and Organic Chemistry Review Primer P-13
In the methane molecule (Figure 6), each of the four sp3 hybrid orbitals overlaps with the 1s orbital of hydrogen to form a sigma bond. A sigma bond (s), which is formed by the overlapping by the outermost orbitals of two atoms, is the strongest type of covalent bond.
sp3
sp3sp3
sp3
H
HH
H
Each of the two carbon atoms in the molecule ethene (H2C5CH2) is bonded to three atoms in trigonal planar geometry. Carbon’s 2s orbital mixes with two of the three available 2p orbitals to form three sp2 orbitals.
1s2 2sp2 2sp2 2sp2 2p
Two of the three sp2 orbitals of each carbon atom overlap the orbital of a hydro-gen atom, forming a total of four s bonds. The third sp2 orbital of the two carbon atoms overlap to form a carbon-carbon s bond. The p orbitals, one on each carbon, overlap to form a pi (p) bond (Figure 7). A double bond in molecules such as ethene consists of a s bond and a p bond.
πH
CH
H
H
π H
(c)
C C
(b)(a)σ bondH
H
C
H
H
120°
120°
120°
C
CH
H
H
σ
Acetylene (C2H2) is a molecule with a triple bond with each carbon bonded to two other atoms in a linear geometry. Carbon’s 2s orbital
1s2 sp sp 2p 2p
mixes with one 2p orbital to form 2 sp hybrid orbitals. Each carbon also possesses two unhybridized 2p orbitals. Acetylene has a triple bond consisting of one s bond and two p bonds. The carbon-carbon s bond is formed by the overlap of an
FIGURE 6Structure of Methane
Methane (CH4) has a tetrahedral geometry with four s bonds formed by the overlap of four sp3 orbitals of carbon with four 1s orbitals of hydrogen atoms.
FIGURE 7Ethene Structure
(a) Each carbon atom in ethane (also known as ethylene) has three sp2 orbitals with bond angles of 120 ,̊ which have a trigonal planar geometry. (b) Two of the sp2 orbitals of each carbon (green) overlap with an s orbital of hydrogen (red) forming a total of 4 s bonds. The remaining two sp2 orbitals, one from each carbon, overlap to form a carbon-carbon s bond. (c) Two p orbitals (blue), one from each carbon atom, overlap to form a π bond.
McKee_Primer.indd 13 14/05/15 2:25 AM
New to This Edition
A NEW CHEMISTRY PRIMERThis helpful in-text resource reviews foundational general chemistry and organic chemistry topics, getting students up to speed so that they can master the biochemical concepts to come
DEEPER CHEMISTRYExpanded chemical explanation and
emphasis on the chemistry of reactions
280 CHAPTER EIGHT Carbohydrate Metabolism
9. Dehydration of glycerate-2-phosphate. Enolase catalyzes the dehydra-tion of glycerate-2-phosphate to form PEP:
The terminal phosphoryl group of ADP acting as a nucleophile attacks the phosphorus of the phosphoanhydride of glycerate-1,3-bisphosphate to yield glycerate-3-phosphate. Reaction 7 is an example of a substrate-level phosphorylation. Because the synthesis of ATP is endergonic, it requires an energy source. In substrate-level phosphorylations, ATP is produced by the transfer of a phosphoryl group from a substrate with a high phos-phoryl transfer potential (glycerate-1,3-bisphosphate) (refer to Table 4.1) to produce a compound with a lower transfer potential (ATP) and therefore DG , 0. Because two molecules of glycerate-1,3-bisphosphate are formed for every glucose molecule, this reaction produces two ATP molecules, and the investment of phosphate bond energy is recovered. ATP synthesis later in the pathway represents a net gain.
8. The interconversion of glycerate-3-phosphate and glycerate-2- phosphate. Glycerate-3-phosphate has a low phosphoryl group transfer potential. As such, it is a poor candidate for further ATP synthesis (DG89 for ATP synthesis is –30.5 kJ/mol). Cells convert glycerate-3-phosphate with its energy-poor phosphate ester to phosphoenolpyruvate (PEP), which has an exceptionally high phosphoryl group transfer potential. (The standard free energies of hydrolysis of glycerate-3- phosphate and PEP are 212.6 and 261.9 kJ/mol, respectively.) In the first step in this conversion (reac-tion 8), phosphoglycerate mutase catalyzes the conversion of a C-3 phos-phorylated compound to a C-2 phosphorylated compound through a two-step addition/elimination cycle.
+ +
Phosphoglyceratekinase
Mg2+
Glycerate-3-phosphate
HOC
CH2 P O−
O
O−
O
C O−
O
H
Glycerate-1,3-bisphosphate
HOC
CH2 P O−
O
O−
O
C P O−
O
O−
O
O
HADP ATP
7. Phosphoryl group transfer. In this reaction ATP is synthesized as phos-phoglycerate kinase catalyzes the transfer of the high-energy phosphoryl group of glycerate-1,3-bisphosphate to ADP:
H2O Pi
Pi
Phosphoglyceratemutase
HOC
CH2 P O−
O
+
O−
O
Glycerate-3-phosphate
C O−
O
H
HO
C
CH2
P O−
O
O−
O
Glycerate-2-phosphate
C O−
O
H
C
CH2 P O−
O
O−
O
C O−
O
H P O−
O
O−
O
Phosphoglyceratemutase
Glycerate-2,3-bisphosphate
08-McKee-Chap08.indd 280 14/05/15 3:05 am
Pyrophosphate
+
ATPHO HO
CH2O
CH
OPO
O
−O
PO
O
−O
P−− O
O
−O
OPO
O
−O
P− −O
O
−O
OP
O
−O
CHR
Fatty Acid
2CH2C
O
O
CHR
Fatty Acid - AMP
AMP
2CHCoASH
S CoA
2 C
O
O
CHR 2CH2 C
O
NH2
N
NN
N
HO HO
2O
NH2
N
NN
N
FIGURE 1.14Activation of a Fatty Acid
Before a fatty acid can be degraded to yield energy or used in the synthesis of a triacylglycerol, it must first be activated. In the first step the carboxylate ion attacks a phosphate of ATP to form a fatty acyl-AMP intermediate and pyrophosphate (PPi). In the second step the fatty acyl-AMP is attacked by the thiol group of coenzyme A (CoASH) to form the thioester fatty acyl-SCoA and AMP. The rapid hydrolysis of PPi to form two phosphates (Pi) drives the reaction forward.
1.3 Is the Living Cell a Chemical Factory? 15
hydroxyl oxygen on carbon 6 of the sugar molecule is the nucleophile and phos-phorus is the electrophile. Adenosine diphosphate is the leaving group.
ELIMINATION REACTIONS In elimination reactions a double bond is formed when atoms in a molecule are removed.
CC
A
H
H
H
B
H
+ A BCC HH
H H
−++
The removal of H2O from biomolecules containing alcohol functional groups is a commonly encountered reaction. A prominent example is the dehydration of 2-phosphoglycerate, a reaction in glycolysis, which is a biochemical pathway in carbohydrate metabolism (Figure 1.17). As illustrated on pp. P-33–P-34, this reaction occurs via an E1cB mechanism. Other products of elimination reactions include ammonia (NH3), amines (RNH2), and alcohols (ROH).
01-McKee-Chap01.indd 15 14/05/15 2:38 am
716 CHAPTER EIGHTEEN Genetic Information
is incorporated into a ribonucleoprotein complex called RISC. The other miRNA strand (the passenger strand) is degraded. A RISC protein called argonaute posi-tions the miRNA so it can bind the target mRNA, thereby inactivating it.
MiRNA-mediated gene silencing utilizes components of RNA interference, a process originally believed to be limited to protection against viruses and transposons. Cells use double-stranded si-RNAs to recognize and then degrade target mRNAs. siRNAs are the products of dicer-induced cleavage of larger RNA molecules (e.g., a viral RNA genome). Once the guide siRNA is incorpo-rated into RISC (Figure 18.54), it binds to its complementary sequence on the target mRNA. Because the sequences match exactly, slicer (an enzymatic activ-ity in a domain of argonaute) cleaves the mRNA into pieces.
RNA TRANSPORT mRNA transport out of the nucleus, a highly regulated process, occurs in three phases: processing reactions, docking and passage through NPC (p. 55), and release into the cytoplasm. In the first phase pre-mRNA molecules are simultaneously processed into mRNAs and packaged into ribonucleoprotein complexes (mRNPs). mRNP proteins (e.g., cap binding protein, EJCs, and poly(A)-binding protein) recruit export factors that allow NPC targeting. The capping and splicing proteins allow binding to TREX, an export protein complex. Once mRNPs are linked via a TREX subunit to Nxf1-Nxt1, a heterodimer nuclear export receptor, they move through the NPC. When an mRNP complex reaches the cytoplasm, the release of export proteins triggers the remodeling of the complex that in turn directs transport to its final destination where translation will occur.
TRANSLATIONAL CONTROL Eukaryotic cells can respond to various stimuli (e.g., heat shock, viral infections, and cell cycle phase changes) by selectively altering protein synthesis. The covalent modification of several translation factors (nonribosomal proteins that assist in the translation process) has been observed to alter the overall protein synthesis rate and/or enhance the translation of specific mRNAs. For example, when cellular iron levels are low, a repressor protein binds to mRNAs coding for the iron storage protein ferritin. When iron levels rise sufficiently the binding of iron to the repressor protein triggers a conformational change that causes it to dissociate from mRNA. The ferrritin mRNA can then be translated.
SIGNAL TRANSDUCTION AND GENE EXPRESSION All cells respond to signals from their environment in part by altering gene expression patterns.
Gene
RNAP II
pri-miRNA
pre-miRNA
Microprocessor
Transport intocytoplasm
Dicer
miRNA
ViraldsRNA
Dicer
siRNA
RISC
mRNA
FIGURE 18.54mi-RNA and si-RNA Processing
In posttranscriptional gene silencing, the primary transcript of a miRNA gene, pri-miRNA, is processed by microprocessor, a protein complex containing pasha and drosha, and dicer to form miRNA. The miRNA guide strand is then incorporated into the RISC ribonucleoprotein complex where it binds a complementary sequence in the 39 UTR of its target mRNA. Because these two sequences are not perfectly complementary, the mRNA is silenced, but not degraded. In RNA interference, a foreign dsRNA is cleaved by dicer to yield the ds-RNA molecule siRNA. Once the guide strand of the siRNA has been positioned within the RISC, it binds to its complementary sequence on the viral mRNA. Because these two sequences are perfectly complementary, the slicer activity of the RISC proceeds to cleave the mRNA into pieces.
18-McKee-Chap18.indd 716 14/05/15 3:32 AM
UPDATED CONTENTNew discussions of RNA interference, epigenetics, metabolic regulation, and proteostasis
19.3 THE PROTEOSTASIS NETWORKWithin the highly crowded and dynamic interior of living cells, millions of pro-teins perform a vast array of functions such as DNA replication and transcrip-tion, cell signal transduction, immune responses, cell cycle control, and molecular transport. Life depends on the proper function of proteins, which in turn requires that these linear macromolecules fold into their “native states” yet retain some degree of conformational flexibility. As a result, many proteins, especially those that are composed of 100 or more amino acids or are completely or even partially unstructured, are marginally stable and therefore prone to misfolding. Misfolded or partially folded proteins often have exposed hydrophobic patches that may interact with other molecules to form amorphous aggregates. In addition, some misfolded molecules may rearrange to form the b-strands of amyloid fibrillar aggregates. The proteome is also challenged by a constant barrage of metabolic and environmental stresses (e.g., heat or heavy metals exposure, amino acid side chain oxidation, hypoxia, and toxins) that can damage them. When combined with the incidence of random errors in protein synthesis, proteotoxic stress- related protein misfolding and other types of damage are a severe threat to cell function.
Healthy young cells maintain proteostasis with a robust and highly conserved interconnected network of pathways, referred to as the proteostasis network (PN) (Figure 19.23). Using stress-responsive signaling pathways, the PN monitors proteins from their synthesis by ribosomes, through folding, refolding, transport, and degradation when their useful life is over or they are damaged. PN processes are accomplished with the aid of molecular chaperones (p. 165), stress-response transcription factors, detoxifying enzymes, and degradation processes such as the ubiquitin-proteosomal system (p. 556) and autophagy (p. 558). The resources that are devoted to proteome protection indicate the importance of the PN. For example, the human PN involves about 2000 genes. Under stressful conditions PN processes can be activated throughout the cell, that is, cytoplasm and the
FIGURE 19.23The Proteostasis Network
The proteostasis network consists of mo-lecular chaperones that assist proteins in de novo folding and in maintaining them in their native states. The network also includes enzymes and protein complexes that degrade misfolded, damaged, and obsolete proteins. As each nascent polypeptide emerges from the exit tunnel, it encounters ribosome- associated chaperones. If necessary, additional folding assistance is provided by downstream molecular chaperones such as the hsp70s and hsp90s and their associated proteins. Misfolded proteins are degraded by a combination of chaperones and E3 ubiqui-tin ligases that together recognize and target them for destruction by the UPS (ubiquitin-proteosome system). Aggregated proteins that resist digestion by proteasomes are removed by autophagy.
Autophagy
Amorphousaggregates
Chaperones
Cha
pero
nes
Chaperones
Degradation
Deg
rada
tion
Disaggregation
Aggregation
Aggregation
Oligomers
TranslationRibosome
Nascentpolypeptide
FoldingIntermediate
Misfoldedstate
Amyloidfibrils
UPS
Nativeprotein
Folding/traffic
king
Chaperones
Chaperones
Unfolding
Degradation
Unfolding
19.3 The Proteostasis Network 763
19-McKee-Chap19.indd 763 14/05/15 10:31 AM
17.2 RNA 641
Biochemistry IN PERSPECTIVE
bases. The methylation of CpG islands, which are located up-stream of most constitutively expressed (continuously produced) genes and some regulated genes, represses gene expression.
There are two classes of CpG methylating enzymes: mainte-nance methyltransferases and de novo methyltransferases. Main-tenance methyltransferases recognize methylated CpGs in the parental DNA strand and then catalyze the methylation of cyto-sines in the corresponding CpGs in the newly synthesized strand. It is this process that is responsible for the stable inheritance of DNA methylation patterns between cell generations. The addi-tion of methyl groups to previously unmodified CpGs is catalyzed by de novo methyltansferases, usually in response to various signal transduction mechanisms. The mechanism whereby CpGs are demethylated is still obscure.
Histone ModificationsHistones have a featured role in epigenetic gene expression regulation. Covalent modification of histone N-terminal tails (Figure 17B) can occur at specific amino acid residues because the unstructured tails protrude outward from the nucleosome where they are accessible to modifying enzymes. The most commonly observed modifications are methylation, acetylation, and ubiquitinylation of lysine, methylation of arginine, and phosphorylation of serine. (Histone modifications are desig-nated by histone type followed by a one-letter symbol of the modified amino acid [Table 5.1, p. 134] and an abbreviation of the modification type. For example, mono- and dimethyl modi-fications of lysine 4 on histone 3 are referred to as H3K4me and H3K4me2, respectively.) According to the histone code hypoth-esis, the pattern of histone modifications within each DNA sequence regulates gene expression by serving as a platform for the binding of specific accessory proteins. Once they are bound
Epigenetics and the Epigenome: Genetic Inheritance beyond DNA Base SequencesHow do covalent modifications of DNA and histones affect the functions of multicellular organisms? How do the more than 200 cell types in humans arise from a fertilized egg? Life scientists have known for many years that the transformation of a single cell into a multicellular organism is the result of cell specialization effected by gene expression changes that occur during the developmental process. Early signal mechanisms must “instruct” cells, each with an identical genetic blueprint, to progress down separate developmental pathways to yield termi-nally differentiated cells such as red blood cells, neurons, or skeletal muscle cells. In recent years it has become apparent that this process, the result of sequential, programmed changes in the pattern of expressed and silenced genes in each cell type, does not depend on genetic information (DNA base sequences) alone. Rather, development is the result of chromatin remodel-ing that is effected by two mechanisms: DNA methylation and histone covalent modifications. Because covalent modification–induced gene activations and repressions are heritable but do not change DNA base sequences, this phenomenon is referred to as epigenetics [epi (Gk) 5 over or above]. Epigenetic modifica-tions convert affected DNA sequences within facultative hetero-chromatin into transcriptionally active euchromatin or vice versa. DNA methylation is also a means whereby cells silence transposable elements. Each differentiated cell type has unique epigenetic modifications that are referred to as its epigenome. After a brief description of epigenetic modifications, the role of epigenetics is discussed as an interface between genomes and the environment.
DNA MethylationIn DNA methylation reactions a methyl group is donated by SAM (p. 531) to carbon-5 of cytosine residues (Figure 17A). In mammals, methylated cytosines occur predominantly in 59-CG-39 sequences, which are referred to as CpG dinucleotides or CpGs. The C-5 methyl groups of cytosine residues protrude into the major groove where they prevent binding of certain DNA-binding proteins (i.e., transcription factors). They also enable the binding of proteins with methyl-CpG binding do-mains, called methyl-CpG-binding proteins (MeCPs), that pro-mote heterochromatin formation. CpGs are relatively rare in mammalian genomes. However, there are CpG-rich regions, called CpG islands, in which CpGs are typically about 50% of
NH2
NO
O
Cytosine 5-Methyl cytosine
NH2
CH3
N
NN
O
O
FIGURE 17ACytosine Methylation
Cytosine residues in CpG dinucleotides are methylated by specific methyltransferases.
▼
17-McKee-Chap17.indd 641 14/05/15 3:31 AM
414 CHAPTER ELEVEN Lipids and Membranes
a missing or defective plasma membrane glycoprotein called cystic fibrosis transmembrane conductance regulator (CFTR). CFTR (Figure 11.33), which functions as a chloride channel in epithelial cells, is a member of a family of proteins referred to as ABC transporters. (ABC transporters are so named because each contains a polypeptide segment called an ATP-binding cassette.) The CFTR gene on chromosome 7 codes for the CFTR protein, which contains five domains. Two domains (MSD1 and MSD2), each containing six membrane-spanning helices, form the Cl– channel pore. Chloride transport through the pore is controlled by the other three domains (all of which occur on the cytoplasmic side of the plasma membrane). Two are nucleotide-binding domains (NBD1 and NBD2) that bind and hydrolyze ATP and use the released energy to drive conformational changes in the pore. The regulatory (R) domain contains several amino acid residues that must be phosphorylated by cAMP-dependent protein kinase (PKA) for chloride transport to occur.
The chloride channel is vital for proper absorption of salt (NaCl) and water across the apical (top) membrane surface of epithelial cells that line ducts and tubes in tissues such as lungs, liver, small intestine, and sweat glands. Chloride channel opening occurs in response to a signal molecule, cAMP. The cAMP-dependent kinase PKA then phosphorylates specific residues in the R domain, causing a change in its conformation that triggers the binding of ATP molecules to NBD1 and NBD2. The two nucleotide-binding domains then form a head-to-tail heterodimer-like structure with the ATP-binding sites on the inside surfaces. As a result of these intramolecular rearrangements, the chloride channel gate opens and chloride ions flow down their concentration gradient. Hydrolysis of one of the NBD-bound ATP molecules causes dimer disruption that results in channel closing. The NBD dimer acts as a timing device in that the rate of ATP hydrolysis determines the length of time that the channel is open.
KEY CONCEPTS
• Membrane transport mechanisms are classified as passive or active according to whether they require energy.
• In passive transport, solutes moving across membranes move down their concentration gradient.
• In active transport, energy derived directly or indirectly from ATP hydrolysis or another energy source is required to move an ion or molecule against its concentration gradient.
R domain
COO–
Phe508
NBD1
NBD2
Oligosaccharidechains ofglycoprotein
Inside
Outside
NH3+
FIGURE 11.33The Cystic Fibrosis Transmembrane Conductance Regulator (CFTR)
CFTR is a chloride channel composed of two domains (each with six membrane-spanning helices) that constitute the Cl2 pore, two nucleotide-binding domains (NBD), and a regula-tory (R) domain. Transport of Cl2 through the pore, driven by ATP hydrolysis, occurs when specific amino acid residues on the R domains are phosphorylated. The most commonly observed CF-causing mutation is a deletion of Phe508 in NBD1, which prevents proper target-ing of CFTR-containing vesicles to the plasma membrane. The precise structural relation-ships among the pore-forming helices remain unclear.
11-McKee-Chap11.indd 414 14/05/15 10:20 AM
MORE RELEVANT CONNECTIONS Greater emphasis on the relationship between biochemistry and human biology
74 CHAPTER TWO Living Cells
51. Techniques that the body uses to protect itself from the mi-crobe members of the human superorganism are impenetra-ble tissue barriers and __________________ system cells.
52. __________________ are phagocytic cells that engulf and digest foreign cells.
53. There are two types of living cells: __________________ and prokaryotic cells.
54. There are two types of prokaryotes: bacteria and __________________.
55. Common features of prokaryotes and eukaryotes include similar chemical composition and __________________.
56. __________________ compounds exclude water.57. The most basic and critical function of membranes is to
serve as a __________________.58. The two types of membrane proteins are peripheral and
__________________.59. Living organisms require both information and
__________________ to create order.60. In contrast to the eukaryotic cell, the prokaryotic cell is
characterized by the lack of a __________________.
Fill in the Blank
61. Why are eukaryotic cells so much larger than prokaryotic cells?
62. How does soap kill bacteria?63. What would happen if the cell membrane was covalently
linked rather than held together by relatively weak van der Waals forces?
64. Suggest a reason why phospholipids are constituents of cell membranes rather than carboxylic acids.
65. Suggest a reason why some eukaryotic cells lack cell walls.
Short Answer
66. Cyst formation causes a catastrophic loss of function in polycystic kidney disease. Genetic research has linked this disease to defects in genes that code for primary cilium proteins. Describe in general terms how malfunctioning primary cilia cause the formation of kidney cysts.
67. Primary cilia have evolved as primary sensory organelles for vertebrate cells. What structural features of these cilia make them ideal for this purpose?
68. Several pathogenic bacteria (e.g., Bacillus anthracis, the cause of anthrax) produce an outermost mucoid layer called a cap-sule. Capsules may be composed of polysaccharide or protein. What effect do you think this “coat” would have on a bacte-rium’s interactions with a host animal’s immune system?
69. In addition to providing support, the cytoskeleton immobi-lizes enzymes and organelles in the cytoplasm. What advan-tage does this immobilization have over allowing the cell contents to freely diffuse in the cytoplasm?
70. Familial hypercholesterolemia (FH) is an inherited disease characterized by high blood levels of cholesterol, xanthomas (lipid-laden nodules that develop under the skin near ten-dons), and early-onset atherosclerosis (the formation of yellowish plaques within arteries). In the milder form of this disease, patients have half the plasma membrane low-density lipoprotein (LDL) receptors needed for cells to bind to and internalize LDL (a plasma lipoprotein particle that transports cholesterol and other lipids to tissues). These patients have their first heart attacks in young adulthood. In the severe
form of FH, in which patients have no functional LDL recep-tors, heart attacks begin at about age 8, with death occurring a few years later. Based on what you have learned in this chapter, briefly describe the cellular processes that are defec-tive in FH.
71. Mycoplasmas are unusual bacteria that lack cell walls. With a diameter of 0.3 mm, they are believed to be the smallest known free-living organisms. Some species are pathogenic to humans. For example, Mycoplasma pneumoniae causes a very serious form of pneumonia. Assuming that mycoplas-mas are spherical, calculate the volume of an individual cell. Compare the volume of a mycoplasma with that of E. coli.
72. The dimensions of prokaryotic ribosomes are approximately 14 nm by 20 nm. If ribosomes occupy 20% of the volume of a bacterial cell, calculate how many ribosomes are in a typi-cal cell such as E. coli. Assume that the shape of a ribosome is approximately that of a cylinder.
73. The E. coli cell is 2 mm long and 1 mm in diameter, whereas a typical eukaryotic cell is 20 mm in diameter. Assuming that the E. coli cell is a perfect cylinder and the eukaryotic cell is a per-fect sphere, calculate the surface-to-volume ratio for each cell type (cylinder volume, V 5 pr2h; cylinder area A 5 2pr2 1 2prh; sphere volume, V 5 4/3(pr3); sphere area, A 5 4pr2). What do these numbers tell you about the evolutionary changes that would have to occur to generate an efficient eukaryotic cell, considering that most biochemical processes depend on membrane-bound transport processes?
Thought QuestionsThese questions are designed to reinforce your understanding of all of the key concepts discussed in the book so far, including this chapter and the chapter before it. They may not have one right answer! The authors have provided possible solutions to these questions in the back of the book and in the accompanying Study Guide for your reference.
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285 NEW END-OF-CHAPTER
REVIEW QUESTIONSThe most robust and
complete set of review problems of any text, with more than 1,250
end-of-chapter exercises
ATP
ADP
CREB
Nucleus
Coactivator
Ligandmolecule
Ligand-bindingsite
Receptor
Adenylatecyclase(inactive)
Outside of cell
Plasmamembrane
Inside of cellGDP
GDP
GTP
GTP
GTP αs
αs
β
γ
GDP
αsβ
γ
β
γ
αsβ
γ
Gs protein (inactive)
Gs protein (active)
2
αs
β
γ
3
4
Ligand-receptor complex
Adenylate cyclase (active)
cAMP
(+)
(+)
cAMP-dependentprotein kinase(inactive)
Phosphorylasekinase(inactive)
Phosphorylasekinase(active)
P
Cyclic AMP
AMP
Phospho-diesterase
H2O
1
cAMP-dependentprotein kinase(active)
GDP
ATP
i
ATPADP
CRE Transcription
Cytoplasm
CREB
FIGURE 16.6The Adenylate Cyclase Second Messenger System That Controls Glycogenolysis
When the receptor is unoccupied, the Gs protein as subunit has GDP bound and is complexed with the bg dimer. The binding of hormone (1) activates the receptor and leads to replacement of GDP with GTP by a GEF (not shown) (2). The activated a-subunit interacts with and activates adenylate cyclase. (3) The cAMP produced binds to and activates cAMP-dependent protein kinase. Signal transduction ends when the ligand leaves the receptor, the bound GTP is hydrolyzed to GDP by the GTPase activity within the as subunit, and the as subunit dissociates from adenylate cyclase. Cyclic AMP is deactivated by hydrolysis to AMP, a reaction catalyzed by phosphodiesterase. (4) The as subunit then reassociates with the bg dimer. Glycogen breakdown is initiated when cAMP-dependent protein kinase activates phosphorylase kinase, which in turn activates (via phosphorylation) the glycogen- degrading enzyme glycogen phosphorylase. The active subunits of cAMP-dependent protein kinase (PKA) move into the nucleus, where they activate the transcription factor CREB, allowing it to bind to CREs (cAMP-response elements) in combination with the coactivator CBP. As a result, cAMP-inducible genes are transcribed.
590
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STUNNING ART PROGRAM More than fifty new illustrations
EngAgIng pEdAgOgY
A Review of Basic PrinciplesTo ensure that all students are sufficiently prepared to acquire a meaningful understanding of biochemistry, the first four chapters—now streamlined for easier coverage and self-study assessment—review the principles of relevant topics like organic functional groups, noncovalent bonding, thermodynamics, and cell structure.
Chemical and Biological Principles in BalanceComprehensive coverage offers each instructor the flexibility to decide how much chemistry or biology should be presented. Chemical mechanisms are always presented within the physiological context of the organism.
Real-World Relevance Because students who take the survey of biochemistry course come from a range of backgrounds and have diverse career goals, the sixth edition consistently demonstrates the fascinating connections between biochemical principles and the fields of medicine, nutrition, agriculture, bioengineering, and forensics.
The Most Robust Problem-Solving Program Available• In-chapter “Worked Problems” illustrate how quantitative problems are solved and provide students with opportunities to put their knowledge into action right when new concepts are introduced
• Dozens of checkpoint questions are interspersed throughout the chapters, motivating students to think critically about high-interest topics
• Hundreds of multiple-choice and short-answer questions at the end of the chapters test students’ knowledge, develop their conceptual understanding, and encourage them to apply what they have learned
Currency With a goal of providing balanced and thorough coverage of chemistry within a biological context, the sixth edition has been thoroughly updated to present recent developments in the field. It remains focused on the “big-picture” principles that are the cornerstone of the one-term biochemistry course.
492 CHAPTER THIRTEEN Photosynthesis
PhotophosphorylationDuring photosynthesis light energy captured by an organism’s photosystems is transduced into ATP phosphate bond energy. This conversion is referred to as photophosphorylation. It is apparent from the preceding discussions that there are many similarities between mitochondrial and chloroplast ATP synthesis. For ex-ample, many of the same molecules and terms that are encountered in aerobic respiration (Chapter 10) are also relevant to discussions of photosynthesis. Al-though there are a variety of differences between aerobic respiration and photosyn-thesis, the essential difference between the two processes is the conversion of light energy into redox energy by chloroplasts. (Recall that mitochondria produce redox energy by extracting high-energy electrons from food molecules.) Another critical difference involves the permeability characteristics of mitochondrial inner mem-brane and thylakoid membrane. In contrast to the inner membrane of mitochon-dria, the thylakoid membrane is permeable to Mg21 and Cl–. Therefore, Mg21 and Cl– move across the thylakoid membrane, thereby dissipating electrical potential as protons are transported across the membrane during the light reaction. The electro-chemical gradient across the thylakoid membrane that drives ATP synthesis there-fore consists mainly of a proton gradient that may be as great as 3.5 pH units.
Experimental measurements of H1:ATP ratios indicate that the movement across the thylakoid membrane of about 12 protons in noncyclic photophosphor-ylation yields three molecules of ATP. The synthesis of these ATPs is made
The Calvin cycle (p. 493) requires an ATP:NADPH ratio of 3:2. However, ATP is also used for processes other than carbohydrate synthesis. Consequently, both noncyclic and cyclic photophosphorylation pathways are required for suffi-cient ATP synthesis during photosynthesis.
KEY CONCEPTS
• Eukaryotic photosynthesizing cells possess two photosystems, PSI and PSII, which are connected in series in a mechanism referred to as the Z scheme.
• The water-oxidizing clock component of PSII generates O2.
• The protons are used in the synthesis of ATP in a chemiosmotic mechanism.
• PSI is responsible for the synthesis of NADPH.
Calculate DG89 for the four-electron oxidation of H2O by NADP1 in the light reactions.
SOLUTIONThe overall reaction is
2 H2O 1 2 NADP1 Æ O2 1 2 NADPH 1 2 H1
The reduction potentials (DE 89) for the two half reactions are
1/2 O2 1 2 H1 1 2e2 Æ H2O (DE 89 5 1 0.82 V)
NADP1 1 H1 1 2e2 Æ NADPH 1 H1 (DE 89 5 20.32 V)
DG89 is calculated using the equation DG 5 2nFDE 89Substituting the DE 89 values for the two half reactions
DG89 5 24 (96.5 kJ/V ? mol) [20.32 V2 (0.82 V)] 5 (386 kJ/V ? mol) (21.14 V) 5 2440 kJ/mol
Describe the role of each of the following molecules in photosynthesis:
a. plastocyanin d. plastoquinone
b. b-carotene e. pheophytin a
c. ferredoxin f. lutein
QUESTION 13.5
WORKED PROBLEM 13.1
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284 CHAPTER EIGHT Carbohydrate Metabolism
In rapidly contracting muscle cells, the demand for energy is high. After the O2 supply is depleted, lactic acid fermentation provides sufficient NAD1 to allow gly-colysis (with its low level of ATP production) to continue for a short time (Figure 8.8).
In yeast and certain bacterial species, pyruvate is decarboxylated to form ac-etaldehyde, which is then reduced by NADH to form ethanol. (In a decarboxyl-ation reaction, an organic acid loses a carboxyl group as CO2.)
Pyruvate
Pyruvatedecarboxylase
CO2
Acetaldehyde
HC
CH3
O
C
CH3
O
C O−
O
Ethanol
CH3
OHCH2
Alcoholdehydrogenase
NADH NAD+
+
H+
Most molecules of ethanol are detoxified in the liver by two reactions. In the first, ethanol is oxidized to form acetaldehyde. This reaction, catalyzed by ADH, pro-duces large amounts of NADH:
H+
C H
O
+OHCH2CH3 +CH+ ADHNADHNAD
+3
Soon after its production, acetaldehyde is converted to acetate by aldehyde dehy-drogenase, which catalyzes a reaction that also produces NADH:
dehydrogenase
AldehydeC H
O
CH3 ++ NAD+ H2O
H+C O
O
+ +CH NADH3
− 2
One common effect of alcohol intoxication is the accumulation of lactate in the blood. Can you explain why this effect occurs?
QUESTION 8.1
This process, called alcoholic fermentation, is used commercially to produce wine, beer, and bread. Certain bacterial species produce organic molecules other than ethanol. For example, Clostridium acetobutylicum, an organism related to the causative agents of botulism and tetanus, produces butanol. Until recently, this organism was used commercially to synthesize butanol, an alcohol used in the production of detergents and synthetic fibers. A petroleum-based synthetic process has now replaced microbial fermentation.
The Energetics of GlycolysisDuring glycolysis, the energy released as glucose is converted to pyruvate is coupled to the phosphorylation of ADP with a net yield of 2 ATP. However, evaluation of the standard free energy changes of the individual reactions does not explain the efficiency of this pathway. A more useful method for evaluating free energy changes takes into account the conditions (e.g., pH and metabolite con-centrations) under which cells actually operate. As illustrated in Figure 8.9, free energy changes measured in red blood cells indicate that only three reactions
+ Glycerate-1,3-bisphosphate
Glyceraldehyde-3-phosphate
Pyruvate
Lactate
H+
Pi
NADH
NAD+
FIGURE 8.8Recycling of NADH during Anaerobic Glycolysis
The NADH produced during the conversion of glyceraldehyde-3-phosphate to glycerate-1, 3-bisphosphate is oxidized when pyruvate is converted to lactate. This process allows the cell to continue producing ATP under anaero-bic conditions as long as glucose is available.
Visit the companion website at www.oup.com/us/mckee to read the Biochemistry in Perspective essay on fermentation.
KEY CONCEPTS
• During glycolysis, glucose is converted to two molecules of pyruvate. A small amount of energy is captured in two molecules each of ATP and NADH.
• In anaerobic organisms, pyruvate is converted to waste products in a process called fermentation.
• In the presence of oxygen the cells of aerobic organisms convert pyruvate into CO2 and H2O.
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For InstructorsAncillary Resource Center (ARC)The McKee ARC (www.oup-arc.com/mckee) contains a wide range of lecture assessment and additional resources for instructors, including:
• A new Video and Animation Guide, with links to freely available and high-quality animated biochemical processes
• Powerpoint-based images in enhanced electronic format
• Lecture Notes Slides for each chapter of the text
• A completely revised Computerized Test Bank, with more than 700 questions
For StudentsCompanion Website (www.oup.com/us/mckee)
Student Study Guide and Solutions Manual (ISBN 9780190209919)
Written by the authors, this manual provides the solutions to all of the exercises from the text that are not included in the book itself. Each solution has been independently checked for accuracy by a panel of expert reviewers.
• Animation and Video Guide: the companion website now includes a curated guide to biochemical animations; these high-quality and free animations help students visualize complex biochemical processes
• Web Quizzes: offers more than 600 questions written by Dan Sullivan (University of Nebraska at Omaha); students receive a feedback summary with each graded quiz
• Interactive 3D Molecules: includes more than 300 interactive 3D molecules in JMOL format created by Todd Carlson (Grand Valley State University); students can manipulate and study individual molecules and their structures, take self-guided concept tutorials, and test their molecule-recognition abilities by working through the interactive self-quizzes
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