Biochem 600 ch 1-5 quizzes
The main function of the plasma membrane is to
provide a selectively permeable barrier with the aid of transport proteins
How a protein folds is determined by
the order of the amino acids found in the sequence
What gives proteins such a dominant role in biochemistry?
their ability to spontaneously fold into complex three-dimensional structures
What pairs of atoms in bases (in A, C, G, and T in DNA) are involved in hydrogen bonds?
N-H and O-H
Identify the key features that differentiate eukaryotic cells from prokaryotic cells
. The main difference between the two is the existence of membrane-enclosed compartments in eukaryotes and the absence of such compartments in prokaryotes. Prokaryotic cells, exemplified by the human gut bacterium Escherichia coli, have a relatively simple structure. They are surrounded by two membranes separated by the periplasmic space. Although human beings are composed of 100 trillion cells, we carry more than that number of bacteria in us and on us. For the most part, our attitude toward our prokaryotic colleagues is to "live and let live. —eukaryotic or prokaryotic, plant or animal—two biochemical features minimally constitute a cell: there must be (1) a barrier that separates the cell from its environment and (2) an inside that is chemically different from the environment and that accommodates the biochemistry of living.
What is the [A-]/[HA] ratio when the weak acid is in a solution one pH unit above its pKa?
10:1
Typical van der Waals energies are about:
2-4 kJ/mol
1. Know the length of a typical noncovalent bond.
4 angstroms (4 Å)
The partially positively charged hydrogen atoms of one molecule of water can interact with the partially negatively charged oxygen atoms of another molecule of water. This is called:
A hydrogen bond
Describe the basic structure of a biological membrane.
A membrane is a lipid bilayer: two layers of lipids organized with their hydrophobic chains interacting with one another and the hydrophilic head groups interacting with the environment. This membrane is impermeable to most substances, even to substances such as fuels, building blocks, and signal molecules that must enter the cell. Consequently, the barrier function of the membrane must be mitigated to permit the entry and exit of molecules and information. In other words, the membrane must be rendered semipermeable but in a very selective way. This selective permeability is the work of proteins that are embedded in the plasma membrane or associated with it
Define main chain, side chains, and disulfide bonds in polypeptides. Give the range of molecular weights of proteins
A polypeptide chain consists of a regularly repeating part, called the main chain or backbone, and a variable part, comprising the distinctive side chains (Figure 4.3). The polypeptide backbone is rich in hydrogen-bonding potential. Each residue contains a carbonyl group (C"O), which is a good hydrogen-bond acceptor, and, with the exception of proline, an amino group (NiH) group, which is a good hydrogen-bond donor. These groups interact with each other and with the functional groups of side chains to stabilize particular structures. Most natural polypeptide chains contain between 50 and 2000 amino acid residues and are commonly referred to as proteins. The largest protein known is the muscle protein titin, which serves as a scaffold for the assembly of the contractile proteins of muscle. Titin consists of almost 27,000 amino acids. Peptides made of small numbers of amino acids are called oligopeptides or simply peptides. The mean molecular weight of an amino acid residue is about 110 g mol-1 , and so the molecular weights of most proteins are between 5500 and 220,000 g mol-1 . We can also refer to the mass of a protein, which is expressed in units of daltons; a dalton is a unit of mass very nearly equal to that of a hydrogen atom. A protein with a molecular weight of 50,000 g mol-1 has a mass of 50,000 daltons, or 50 kd (kilodaltons). In some proteins, the linear polypeptide chain is covalently cross-linked. The most common cross-links are disulfide bonds, formed by the oxidation of a pair of cysteine residues (Figure 4.4). The resulting unit of two linked cysteines is called cystine. Disulfide bonds can form between cysteine residues in the same polypeptide chain or they can link two separate chains together. Rarely, nondisulfide cross-links derived from other side chains are present in proteins.
Explain what is understood about the role of protein folding in mad cow disease and Alzheimer's disease.
All of these diseases result in the deposition of protein aggregates, called amyloid fibrils or plaques (Figure 4.37). These diseases are consequently referred to as amyloidoses. A common feature of amyloidoses is that normally soluble proteins are converted into insoluble fibrils rich in b sheets. The correctly folded protein is only marginally more stable than the incorrect form. But the incorrect forms aggregates, pulling more correct forms into the incorrect form.
Understand how buffers respond to changes in [H+] or [OH−] concentration.
An acid-base conjugate pair (such as acetic acid and acetate ion) has an important property: it resists changes in the pH of a solution. In other words, it acts as a buffer. Consider the addition of OH- to a solution of acetic acid (HA): HA + OH- m A- + H2O A plot of how the pH of this solution changes with the amount of OH- added is called a titration curve (Figure 2.12). Note that there is an inflection point in the curve at pH 4.8, which is the pKa of acetic acid. In the vicinity of this pH, the addition of a relatively large amount of OH- to the buffer produces little change in the pH of the solution. In other words, the buffer maintains the value of pH near a given value, despite the addition of either protons or hydroxide ions. Figure 2.13 compares the changes in pH when a strong acid is added to pure water with the changes in pH when that same strong acid is added to a buffered solution. The pH of the buffered solution does not change nearly as rapidly as that of pure water. In general, a weak acid is most effective in buffering against pH changes in the vicinity of its pKa value. Figure 2.14 shows the buffering range of three different weak acids. Buffers Are Crucial in Biological Systems Knowledge of the workings of buffers is important for two reasons. First, much of biochemistry is experimentally investigated in vitro (in glass, or, in effect, in a test tube). Because the biomolecules that are being investigated are sensitive to pH, biochemists must use buffers to maintain the proper pH during the experiments. Choice of the proper buffer is often crucial to designing a successful experiment. Second, we need to understand buffers so as to understand how an organism controls the pH of its internal environment in vivo—that is, in the living organism. As mentioned earlier, many biochemical processes generate acids. How is the pH of the organism maintained in response to the production of acid? What are the physiologically crucial buffers? We will examine the buffering of blood pH as an example of a physiological system. In the aerobic biochemical consumption of fuels, carbon dioxide (CO2) is produced (Chapter 19). The carbon dioxide reacts with water to produce a weak acid, carbonic acid: CO2 + H2O m H2CO3 (8) The carbonic acid readily dissociates into a proton and bicarbonate ion: H2CO3 m H+ + HCO3 - (9) The conjugate acid-base pair of H2CO3/HCO3 - acts as a buffer. Protons released by an added acid will combine with bicarbonate ion, thus having little effect on the pH. The effectiveness of the H2CO3/HCO3 - buffer system is enhanced by the fact that the quantity of the buffer in the blood can be rapidly adjusted. For instance, if there is an influx of acid into the blood, reaction 9 will proceed to the left, driving reaction 8 to the left. The newly generated CO2 can then be expired from the lungs. In essence, the ratio of H2CO3/HCO3 - is maintained, which keeps the pH constant. This mechanism of blood-pH control is called compensatory respiratory alkalosis.
Which amino acid would be positively charged at physiological pH 7.40?
Arg
What do α-helices and β-sheets have in common?
Both are stabilized by hydrogen bonding involving carbonyl oxygens and amide nitrogens.
Differentiate between two major periodic structures of proteins: the α helix and the β-pleated sheet
Can a polypeptide chain fold into a regularly repeating structure? In 1951, Linus Pauling and Robert Corey proposed that certain polypeptide chains have the ability to fold into two periodic structures called the a helix (alpha helix) and the b pleated sheet (beta pleated sheet). Subsequently, other structures such as turns and loops were identified. Alpha helices, b pleated sheets, and turns are formed by a regular pattern of hydrogen bonds between the peptide NH and CO groups of amino acids that are often near one another in the linear sequence, or primary structure. Such regular folded segments are called secondary structure.
1. Describe the patterns of hydrogen bonding, the shapes, and the dimensions of these structures.
Can a polypeptide chain fold into a regularly repeating structure? In 1951, Linus Pauling and Robert Corey proposed that certain polypeptide chains have the ability to fold into two periodic structures called the a helix (alpha helix) and the b pleated sheet (beta pleated sheet). Subsequently, other structures such as turns and loops were identified. Alpha helices, b pleated sheets, and turns are formed by a regular pattern of hydrogen bonds between the peptide NH and CO groups of amino acids that are often near one another in the linear sequence, or primary structure. Such regular folded segments are called secondary structure. The a helix is stabilized by hydrogen bonds between the NH and CO groups of the main chain. The CO group of each amino acid forms a hydrogen bond with the NH group of the amino acid that is situated four residues ahead in the sequence (Figure 4.12). Thus, except for amino acids near the ends of an a helix, all the main-chain CO and NH groups are hydrogen bonded. Each residue is related to the next one by a rise, also called translation, of 1.5 Å along the helix axis and a rotation of 100 degrees, which gives 3.6 amino acid residues per turn of helix. Thus, amino acids spaced three and four apart in the sequence are spatially quite close to one another in an a helix. In contrast, amino acids spaced two apart in the sequence are situated on opposite sides of the helix and so are unlikely to make contact. The pitch of the a helix is the length of one complete turn along the helix axis and is equal to the product of the translation (1.5 Å) and the number of residues per turn (3.6), or 5.4 Å. The screw sense of a helix can be right-handed (clockwise) or lefthanded (counterclockwise). Right-handed helices are energetically more favorable because there are fewer steric clashes between the side chains and the backbone. Essentially all a helices found in proteins are right-handed. In schematic representations of proteins, a helices are depicted as twisted ribbons or rods (Figure 4.13). Not all amino acids can be readily accommodated in an a helix. Branching at the b-carbon atom, as in valine, threonine, and isoleucine, tends to destabilize a helices because of steric clashes. Serine, aspartate, and asparagine also tend to disrupt a helices because their side chains contain hydrogen-bond donors or acceptors in close proximity to the main chain, where they compete for mainchain NH and CO groups. Proline also is a helix breaker because it lacks an NH group and because its ring structure prevents it from assuming the f value to fit into an a helix. The a-helical content of proteins ranges widely, from none to almost 100%. For example, about 75% of the residues in ferritin, an iron-storage protein, are in a helices (Figure 4.14). Indeed, about 25% of all soluble proteins are composed of a helices connected by loops and turns of the polypeptide chain. Single a helices are usually less than 45 Å long. Many proteins that span biological membranes also contain a helices. Pauling and Corey named their other proposed periodic structural motif the b pleated sheet (b because it was the second structure that they elucidated). The b pleated sheet (more simply, the b sheet) differs markedly from the rodlike a helix in appearance and bond structure. Instead of a single polypeptide strand, the b sheet is composed of two or more polypeptide chains called b strands. A b strand is almost fully extended rather than being tightly coiled as in the a helix. The distance between adjacent amino acids along a b strand is approximately 3.5 Å, in contrast with a distance of 1.5 Å along an a helix. The side chains of adjacent amino acids point in opposite directions (Figure 4.15). A b sheet is formed by linking two or more b strands lying next to one another through hydrogen bonds. Adjacent chains in a b sheet can run in opposite directions (antiparallel b sheet) or in the same direction (parallel b sheet), as shown in Figure 4.16. Many strands, typically 4 or 5 but as many as 10 or more, can come together in a b sheet. Such b sheets can be purely antiparallel, purely parallel, or mixed (Figure 4.17). Unlike a helices, b sheets can consist of sections of a polypeptide that are not near one another. That is, in two b strands that lie next to each other, the last amino acid of one strand and the first amino acid of the adjacent strand are not necessarily neighbors in the amino acid sequence. In schematic representations, b strands are usually depicted by broad arrows pointing in the direction of the carboxyl-terminal end to indicate the type of b sheet formed—parallel or antiparallel. Beta sheets can be almost shown in Figure 4.16. Many strands, typically 4 or 5 but as many as 10 or more, can come together in a b sheet. Such b sheets can be purely antiparallel, purely parallel, or mixed (Figure 4.17). Unlike a helices, b sheets can consist of sections of a polypeptide that are not near one another. That is, in two b strands that lie next to each other, the last amino acid of one strand and the first amino acid of the adjacent strand are not necessarily neighbors in the amino acid sequence. In schematic representations, b strands are usually depicted by broad arrows pointing in the direction of the carboxyl-terminal end to indicate the type of b sheet formed—parallel or antiparallel. Beta sheets can be almost flat but most adopt a somewhat twisted shape (Figure 4.18). The b sheet is an important structural element in many proteins. For example, fatty acidbinding proteins, which are important for lipid metabolism, are built almost entirely from b sheets (Figure 4.19).
Distinguish between motifs and domains in protein structure.
Certain combinations of secondary structure are present in many proteins and frequently exhibit similar functions. Some polypeptide chains fold into two or more compact regions that may be connected by a flexible segment of polypeptide chain, rather like pearls on a string. These compact globular units, called domains
Explain the origin of the hydrophobic effect between nonpolar molecules and give examples of their importance in biochemical interactions
Consider the introduction of a single nonpolar molecule, such as benzene, into some water (Figure 2.9). A cavity in the water is created because the benzene has no chemical means of interacting with the water molecule. The cavity temporarily disrupts some hydrogen bonds between water molecules. The displaced water molecules then reorient themselves to form the maximum number of new hydrogen bonds. However, there are many fewer ways of forming hydrogen bonds around the benzene molecule than there are in pure water. The water molecules around the benzene molecule are much more ordered than elsewhere in the solution. The introduction of the nonpolar molecule into water has resulted in a decrease in the entropy of water. Now consider the arrangement of two benzene molecules in water. They do not reside in separate small cavities (Figure 2.9A); instead, they coalesce into a single larger one (Figure 2.9B). They become organized. The energetic basis for the formation of this order is that the association of the benzene molecules releases some of the ordered water molecules around the separated benzenes, increasing the entropy of the system. Nonpolar solute molecules are driven together in water not primarily because they have a high affinity for each other but because, when they do associate, they release water molecules. This entropy-driven association is called the hydrophobic effect, and the resulting interactions are called hydrophobic interactions. Hydrophobic interactions form spontaneously—no input of energy is required—because, when they form, the entropy of water increases. The biological significance of the hydrophobic effect is more apparent when we consider molecules more complex than benzene, such as a phospholipid (see Chapter 11). Recall that the structure of the phospholipid reveals two distinct chemical properties (see Figure 1.4). The top of the molecule, called the head group, is hydrophilic, consisting of polar and charged species. However, the remainder of the molecule, consisting of two large hydrophobic chains, cannot interact with water. Such a molecule, with two distinct chemical personalities, is called an amphipathic or amphiphilic molecule. When exposed to water, the molecules orient themselves such that the hydrophilic head groups interact with the aqueous medium, whereas the hydrophobic tails are sequestered away from the water and interact only with one another. Under the right conditions, they can form membranes. The lipids form a contiguous, closed bilayer, with two hydrophilic outsides and a hydrophobic interior, which is stabilized by van der Waals interactions between the hydrophobic tails. Membranes define the inside and outside of the cell, as well as separating the components of eukaryotic cells into distinct biochemical compartments (pp. 7 and 9). Paradoxically, order has been introduced by an increase in the randomness of water. We will return to the topic of membranes many times in this book, because membranes are vital to many aspects of energy and information transformation. Proteins play these roles because they are capable of forming complex three-dimensional structures that allow specific interactions with other biomolecules. These interactions define a protein's function. How does the hydrophobic effect favor protein folding? Consider a system consisting of identical unfolded protein molecules in aqueous solution (Figure 2.10). Each unfolded protein molecule can adopt a unique conformation—no two molecules will be in the same conformation—and so the system is quite disordered and the entropy of the collection of molecules is high. Yet, protein folding proceeds spontaneously under appropriate conditions, with all of the molecules assuming the same conformation, a clear decrease in entropy. To avoid violation of the Second Law of Thermodynamics, entropy must be increasing elsewhere in the system or in the surroundings. How can we reconcile the apparent contradiction that proteins spontaneously assume an ordered structure, and yet entropy increases? We can again call on the hydrophobic effect to introduce order. Some of the amino acids that make up proteins have nonpolar groups (p. 37). These nonpolar amino acids have a strong tendency to associate with one another in the interior of the folded protein. The increased entropy of water resulting from the interaction of these hydrophobic amino acids helps to compensate for the entropy losses inherent in the folding process. Thus, the same thermodynamic principles that permit the formation of membranes facilitate the formation of the intricate three-dimensional structures. Although the hydrophobic effect powers the folding of proteins, many weak bonds, including hydrogen bonds and van der Waals interactions, are formed in the protein-folding process to stabilize the three-dimensional structure. These interactions replace interactions with water that take place in the unfolded protein.
In higher organisms, which of the following is composed of a polymer with double-stranded phosphodiester-linked monomers?
DNA
replication-
DNA constitutes the heritable information—the genome. This information is packaged into discrete units called genes. It is this collection of genes that determines the physical nature of the organism. When a cell duplicates, DNA is copied and identical genomes are then present in the newly formed daughter cells. The process of copying the genome is called replication. A group of enzymes, collectively called DNA polymerase, catalyze the replication process.
A group of enzymes calledd________ catalyzes replication:
DNA polymerase
During transcription, ___________ is the template for a new molecule of __________.
DNA; RNA
SDS polyacrylamide electrophoresis could be used to do which of the following?
Determine the molecular weights of subunits of an oligomeric protein
1. Understand why nearly all peptide bonds are trans.
First, the peptide bond is essentially planar (Figure 4.6). Thus, for a pair of amino acids linked by a peptide bond, six atoms lie in the same plane: the a-carbon atom and CO group of the first amino acid and the NH group and a-carbon atom of the second amino acid. Second, the peptide bond has considerable double-bond character owing to resonance structures: the electrons resonate between a pure single bond and a pure double bond. This partial double-bond character prevents rotation about this bond and thus constrains the conformation of the peptide backbone. The double-bond character is also expressed in the length of the bond between the CO and the NH groups. The CiN distance in a peptide bond is typically 1.32 Å (Figure 4.7), which is between the values expected for a CiN single bond (1.45 Å) and a C"N double bond (1.27 Å). Finally, the peptide bond is uncharged, allowing polymers of amino acids linked by peptide bonds to form tightly packed globular structures that would otherwise be inhibited by charge repulsion. Two configurations are possible for a planar peptide bond. In the trans configuration, the two a-carbon atoms are on opposite sides of the peptide bond. In the cis configuration, these groups are on the same side of the peptide bond. Almost all peptide bonds in proteins are trans. This preference for trans over cis can be explained by the fact that there are steric clashes between R groups in the cis configuration but not in the trans configuration (Figure 4.8). In contrast with the peptide bond, the bonds between the amino group and the a-carbon atom and between the a-carbon atom and the carbonyl group are pure single bonds. The two adjacent rigid peptide units may rotate about these bonds, taking on various orientations. This freedom of rotation about two bonds of each amino acid allows proteins to fold in many different ways. The rotations about these bonds can be specified by torsion angles (Figure 4.9). The angle of rotation about the bond between the nitrogen atom and the a-carbon atom is called phi (f). The angle of rotation about the bond between the a-carbon atom and the carbonyl carbon atom is called psi (c). A clockwise rotation about either bond as viewed toward the a-carbon atom corresponds to a positive value. The f and c angles determine the path of the polypeptide chain. Steric exclusion, the fact that two atoms cannot be in the same place at the same time, restricts the number of possible peptide conformations and is thus a powerful organizing principle.
transcription-
Genes are useless in and of themselves. The information must be rendered accessible. This accessibility is achieved in the process of transcription through which one form of nucleic acid, DNA, is transcribed into another form, RNA. The enzyme RNA polymerase catalyzes this process (Figure 1.7). Which genes are transcribed, as well as when and where they are transcribed, is crucial to the fate of the cell. For instance, although each cell in a human body has the DNA information that encodes the instructions to make all tissues, this information is parceled out. The genes expressed in the liver are different from those expressed in the muscles and brain. Indeed, it is this selective expression that defines the function of a cell or tissue
What are the primary chemical components present in a phosphate buffer at pH 7.4?
H2PO4− and HPO4−2
Of the 20 amino acids from which proteins are made, which is most likely to be present with its R-group in a mixture of ionization states near physiological pH?
His
Which of the following is the MOST abundant element of total atoms in human beings
Hydrogen
Water-soluble proteins such as myoglobin tend to fold such that
Hydrophobic amino acid R-groups are on the interior of the protein and hydrophilic groups are on the outside.
Which of the following is a globular protein?
Myoglobin or haemoglobin
1. Explain the origin and significance of the unique amino acid sequences of proteins.
In 1953, Frederick Sanger determined the amino acid sequence of insulin, a protein hormone (Figure 4.5). This work is a landmark in biochemistry because it showed for the first time that a protein has a precisely defined amino acid sequence consisting only of l amino acids linked by peptide bonds. Sanger's accomplishment stimulated other scientists to carry out sequence studies of a wide variety of proteins. The complete amino acid sequences of millions of proteins are now known. Knowing amino acid sequences is important for several reasons. First, amino acid sequences determine the three-dimensional structures of proteins. Second, knowledge of the sequence of a protein is usually essential to elucidating its mechanism of action (e.g., the catalytic mechanism of an enzyme). Third, sequence determination is a component of molecular pathology, a rapidly growing area of medicine. Alterations in amino acid sequence can produce abnormal function and disease. Severe and sometimes fatal diseases, such as sickle-cell anemia (Chapter 9) and cystic fibrosis, can result from a change in a single amino acid within a protein. Fourth, the sequence of a protein reveals much about its evolutionary history. Proteins resemble one another in amino acid sequence only if they have a common ancestor. Consequently, molecular events in evolution can be traced from amino acid sequences; molecular paleontology is a flourishing area of research.
Two proteins are similar in the number of acidic and basic amino acids but are different significantly in size. Which of the following techniques would be best suited to separating these two proteins?
Isoelectric focusing and ion-exchange chromatography
Which of the following statements is TRUE of the proteome?
It includes the interactions of proteins that yield a functional unit.B. It varies with cell type. It varies with environmental conditions. It varies with both cell type and environmental conditions.
The three-dimensional structure of a protein is dictated by
Its amino acid sequence.
Using myoglobin and porin as examples, describe the main characteristics of native folded protein structures.
Myoglobin, a single polypeptide chain of 153 amino acids, is an oxygenbinding protein found predominantly in heart and skeletal muscle; it appears to facilitate the diffusion of oxygen from the blood to the mitochondria, the primary site of oxygen utilization in the cell. The capacity of myoglobin to bind oxygen depends on the presence of heme, a prosthetic (helper) group containing an iron atom. Myoglobin is an extremely compact molecule. the interior consists almost entirely of nonpolar residues (Figure 4.26). The only polar residues on the interior are two histidine residues, which play critical roles in binding the heme iron and oxygen. The outside of myoglobin, on the other hand, consists of both nonpolar and polar residues, which can interact with water and thus render the molecule water soluble.
1. Describe the cause and symptoms of kwashiorkor, a form of malnutrition.
Kwashiorkor means "the disease of the displaced child" in the language of Ga, a Ghanaian dialect; that is, the condition arises when a child is weaned because of the birth of a sibling. It is a form of malnutrition that results when protein intake is not sufficient. Initial symptoms of the disease are generalized lethargy, irritability, and stunted growth. If treated early enough, the effects of the disease are reversible. However, if not corrected early enough, many physiological systems fail to develop properly, including the brain. For instance, children will suffer from various infectious diseases because their immune systems, composed of many different proteins, cannot be constructed to function adequately. Likewise, the lack of protein prevents the complete development of the central nervous system, with resulting neurological problems. The most common characteristic of a child suffering from kwashiorkor is a large protruding belly (Figure 3.8). The large belly is a sign not of excess calories but of edema, another result of the lack of protein. Edema is swelling that results from too much water in tissue. Insufficient protein in a child's blood distorts the normal distribution of water between plasma and surrounding capillaries. Although the swollen belly is most obvious, the limbs of a child suffering from kwashiorkor also are often swollen. Such suffering children are a devastating display of the centrality of protein to life
Describe how the properties of water affect the interactions among biomolecules.
Many important biomolecules are neither polar nor charged. Nonetheless, such molecules can interact with each other electrostatically by a van der Waals interaction. The basis of a van der Waals interaction is that the distribution of electronic charge around an atom changes with time, and, at any instant, the charge distribution is not perfectly symmetric: there will be regions of partial positive charge and partial negative charge. This transient asymmetry in the electronic charge around an atom acts through electrostatic interactions to induce a complementary asymmetry in the electron distribution around its neighboring atoms. The resulting attraction between two atoms increases as they come closer to each other, until they are separated by the van der Waals contact distance, which corresponds to 3 to 4 Å, depending on the participating atoms (Figure 2.6). At a shorter distance, very strong repulsive forces become dominant because the outer electron clouds overlap. Energies associated with van der Waals interactions are quite small; However, when the surfaces of two large molecules with complementary shapes come together, a large number of atoms are in van der Waals contact, and the net effect, summed over many atom pairs, can be substantial.
Explain what is meant by transient chemical interactions.
Many weak bonds can result in large stable structures. This is advantageous because that weak bonds allow transient interactions. A substrate can bind to an enzyme, and the product can leave the enzyme. A hormone can bind to its receptor and then dissociate from the receptor after the signal has been received. Weak bonds allow for dynamic interactions and permit energy and information to move about the cell and organism. Transient chemical interactions form the basis of biochemistry and life itself.
Which is an appropriate statement of involvement of the hydrophobic effect in protein folding?
Nonpolar portions of the molecule associate with one another on the interior of the protein.The interior of most proteins is dominated by hydrophobic (water-fearing) groups. The protein folds in such a way as to minimize the contact of these groups with water but to facilitate their contact with each other.
Describe the nucleation-condensation model of protein folding.
Nucleation-condensation reflects the situation when secondary structure is inherently unstable in the absence of tertiary interactions whereas diffusion-collision becomes more probable with increasing stability of secondary structure
The __________ is the cellular location of _____________.
Nucleus; genetic material or Cytoplasm; protein synthesis
Essential amino acids must be:
Obtained from the diet
Relate the angstrom to other measures of length such as the meter.
One angstrom (Å) = 0.1 nanometer (nm) = 1 * 10-10 meter (m) F is the force, q1 and q2 are the charges on the two atoms (in units of the electronic charge), r is the distance between the two atoms (in angstroms), D is the dielectric constant (which accounts for the effects of the intervening medium), and k is the proportionality constant. Thus, the electrostatic interaction between two atoms bearing single opposite charges varies inversely with the square of the distance separating them as well as with the nature of the intervening medium. Electrostatic interactions are strongest in a vacuum, where D = 1. The distance for maximal bond strength is about 3 Å. Because of its polar characteristics, water (which has a dielectric constant of 80) weakens electrostatic interactions. Conversely, electrostatic interactions are maximized in an uncharged environment.
Which of the following is true regarding the chirality of amino acids found in proteins?
Only L amino acids are found in proteins
A biological molecule can serve as a hydrogen bond donor if the hydrogen is attached to
Oxygen or nitrogen
How do monoclonal antibodies differ from polyclonal antibodies?
Polyclonal antibodies are made using several different immune cells. They will have the affinity for the same antigen but different epitopes, while monoclonal antibodies are made using identical immune cells that are all clones of a specific parent cell
What is the main difference between a prokaryotic cell and a eukaryotic cell?
Prokaryotic cells do not contain membranes
proteins
Proteins are constructed from 20 building blocks, called amino acids, linked by peptide bonds to form long unbranched polymers (Figure 1.1). These polymers fold into precise three-dimensional structures that facilitate a vast array of biochemical functions. Proteins serve as signal molecules and as receptors for signal molecules. Proteins also play structural roles, allow mobility, and provide defenses against environmental dangers. Protein catalysts are called enzymes. Every process that takes place in living systems depends on enzymes.
List the key properties of proteins.
Proteins are linear polymers built of monomer units called amino acids, which are linked end to end. Remarkably, the sequence of amino acids determines the three-dimensional shape of the protein. Protein function directly depends on this three-dimensional structure. 2. Proteins contain a wide range of functional groups, which account for the broad spectrum of protein function. 3. Proteins can interact with one another and with other macromolecules to form complex assemblies. The proteins within these assemblies can act synergistically to generate capabilities that individual proteins may lack. 4. Some proteins are quite rigid, whereas others display a considerable flexibility. Rigid units can function as structural elements in cells and tissues. Proteins with some flexibility can act as hinges, springs, or levers that are crucial to protein function or to the assembly of protein complexes.
Explain how proteins relate one-dimensional gene structure to three-dimensional structure in the cell, and their complex interactions with each other and various substrates.
Proteins are the embodiment of the transition from the one-dimensional world of DNA sequences to the three-dimensional world of molecules capable of diverse activities. DNA encodes the sequence of amino acids that constitute a protein. The amino acid sequence is called the primary structure, and proteins typically consist of from 50 to 300 amino acids. Functioning proteins, however, are not simply long polymers of amino acids. These polymers fold to form discrete three-dimensional structures with specific biochemical functions. Threedimensional structure resulting from a regular pattern of hydrogen bonds between the NH and the CO components of the amino acids in the polypeptide chain is called secondary structure. The three-dimensional structure becomes more complex when the R groups of amino acids far apart in the primary structure bond with one another. This level of structure is called tertiary structure and is the highest level of structure that an individual polypeptide can attain. However, many proteins require more than one chain to function. Such proteins display quaternary structure, which can be as simple as a functional protein consisting of two identical polypeptide chains or as complex as one consisting of dozens of different polypeptide chains. Remarkably, the final three-dimensional structure of a protein is determined simply by the amino acid sequence of the protein.
Which of the following is NOT an example of a noncovalent interaction?
Salt tunnel
The transient force which, while weak, still has a large impact on how macromolecules interact is the ____________.
Van der Waals interaction
State the Second Law of Thermodynamics. Explain what is meant by entropy. pH is an Important Parameter of Biochemical Systems.
Second Law of Thermodynamics: The total entropy of a system and its surroundings always increases in a spontaneous process. The pH of a solution is a measure of the hydrogen ion concentration, with values ranging from 0 to 14. The smaller numbers denote an acidic environment, and the larger numbers denote a basic environment. Indeed, pH is an important parameter of living systems. For example, the pH of human blood is about 7.4, and a deviation of +/- 0.5 units can result in coma or death. Why is maintaining the proper pH so vital? Alterations in pH can drastically affect the internal electrostatic environment of an organism, which can alter the weak bonds that maintain the structure of biomolecules. Altered structure usually means loss of function. For instance, ionic bonds may be weakened or disappear with a change in pH, and hydrogen bonds may or may not form, depending on the pH. Given how crucial maintaining proper pH is to the correct functioning of biochemical systems, it is important to have means of describing pH.
Which amino acids contain reactive aliphatic hydroxyl groups?
Ser and Thr
1. Give the name and one-letter and three-letter symbol of each amino acid. Describe each amino acid in terms of size, charge, hydrogen-bonding capacity, chemical reactivity, and hydrophilic or hydrophobic nature.
Seven of the 20 amino acids—tyrosine, cysteine, arginine, lysine, histidine, and aspartic and glutamic acids—have readily ionizable side chains. These seven amino acids are able to form ionic bonds as well as to donate or accept protons to facilitate reactions. The ability to donate or accept protons is called acid-base catalysis and is an important chemical reaction for many enzymes. We will see the importance of histidine as an acid-base catalyst when we examine the proteindigesting enzyme chymotrypsin in Chapter 8. Table 3.1 gives equilibria and typical pKa values for the ionization of the side chains of these seven amino acids.
Solution X is at a pH of 3; solution Y is at a pH of 8. Which of the following statements is TRUE?
Solution X contains more protons than solution Y
Know and use the Henderson-Hasselbalch Equation. Given a pH value and pKa, calculate the ion concentration in a buffer system.
Very small amounts of pure water dissociate and form hydronium (H3O+) and hydroxyl (OH-) ions, with the concentration ion of each being 10-7 M. For simplicity, we refer to the hydronium ion simply as a hydrogen ion (H+) and write the equilibrium as H2O m H+ + OH. The equilibrium constant Keq of this dissociation is given by Keq = [H+][OH-]/[H2O] (1) in which the brackets denote molar concentrations (M) of the molecules. Substituting the concentration of H+ and OH- (10-7 M, each) and the concentration of water (55.5 M), we see that the equilibrium constant of water is Keq = 10-7 M * 10-7 M/55.5 M = 1.8 * 10-16 M Because the concentration of water is essentially unchanged by the small amount of ionization, we can ignore any change in the concentration of water and define a new constant: Kw = Keq * [H2O] which then simplifies to Kw = [H+][OH-] (2) Kw is the ion product of water. At 25°C, Kw is 1.0 * 10-14. The pH of any solution is quantitatively defined as pH = log10(1/[H+])= -log10[H+] (3) Consequently, the pH of pure water, which contains equal amounts of H+ and OH-, is equal to 7. Note that the concentrations of H+ and OH- are reciprocally related; thus, pH + pOH = 14, where pOH is determined by substituting the hydroxide ion concentration for the proton concentration in equation 3. If the concentration of H+ is high, then the concentration of OH- must be low, and vice versa. For example, if [H+] = 10-2 M, then [OH-] = 10-12 M. Let us consider a problem that is a bit more complex. If the [H+] equals 2.5 * 10-4 M in a solution, what would the [OH-] be? We solve this problem by first remembering the equation for the ion product of water: Kw = [H+][OH-] = 1.0 * 10-14 M2 We can determine the [OH-] by rearranging the equation to solve for [OH-] and inserting the proton concentration [OH-] = Kw [H+] = 1.0 * 10-14 M2 2.5 * 10-4 M = 4 * 10-9 M Thus, if the concentration of protons or hydroxyl ions is known, the concentration of the unknown ion can be determined. An Acid Is a Proton Donor, Whereas a Base Is a Proton Acceptor Organic acids are prominent biomolecules. These acids will ionize to produce a proton and a base. Acid m H+ + base The species formed by the ionization of an acid is its conjugate base and is distinguished from the ionized acid by having the suffix "ate." Conversely, the protonation of a base yields its conjugate acid. Let's consider acetic acid, a carboxylic acid. Carboxylic acids are key functional groups found in a host of biochemicals (see Table 2.1). Acetic acid and acetate ion are a conjugate acid-base pair. CH3COOH m H+ + CH3COOAcetic acid Acetate Acids Have Differing Tendencies to Ionize How can we measure the strength of an acid? For instance, how can we determine whether an acid will dissociate in a given biochemical environment, such as the blood? Let us examine weak acids, inasmuch as weak acids are the type found in biochemical systems. The ionization equilibrium of a weak acid (HA) is given by HA m H+ + AThe equilibrium constant Ka for this ionization is Ka = [H+][A-] [HA] (4) The larger the value of Ka is, the stronger the acid (Figure 2.11). What is the relation between pH and the ratio of acid to base? In other words, how dissociated will an acid be at a particular pH? A useful expression establishing the relation between pH and the acid/base ratio can be obtained by rearrangement of equation 4: 1 [H+] = 1 Ka [A-] [HA] (5) Taking the logarithm of both sides of equation 5 gives loga 1 [H+] b = loga 1 Ka b + loga [A-] [HA] b (6) We define log(1/Ka) as the pKa of the acid. Substituting pH for log 1/[H+] and pKa for log 1/Ka in equation 6 yields pH = pKa + loga [A-] [HA] b (7) which is commonly known as the Henderson-Hasselbalch equation. Note that, when the concentration of ionized acid molecules equals that of un-ionized acid molecules, or [A-] = [HA], the log([A-]/[HA]) = 0, and so pKa is simply the pH at which the acid is half dissociated. Above pKa, [A-] predominates; whereas, below pKa, [HA] predominates. As a reference to the strength of an acid, pKa is more useful than the ionization constant (Ka) because pKa does not require the use of the sometimes-cumbersome scientific notation. Note from Figure 2.11 that the most important biochemical acids will be predominately dissociated at physiological pH (7.4). Thus, these molecules are usually referred to as the conjugate base (e.g., pyruvate) and not as the acid (e.g., pyruvic acid).
cytoplasm/cytoskeleton-
The cytoplasm is the site of a host of biochemical processes, including the initial stage of glucose metabolism, fatty acid synthesis, and protein synthesis. Formerly, the cytoplasm was believed to be a "soup" of important biomolecules, but it is becoming increasingly clear that the biochemistry of the cytoplasm is highly organized by a network of structural filaments called the cytoskeleton. In many eukaryotes, the cytoskeleton is a network of three kinds of protein fibers— actin filaments, intermediate filaments, and microtubules—that support the structure of the cell, help to localize certain biochemical activities, and even serve as "molecular highways" by which molecules can be shuttled around the cell
The Central dogma describes
The flow of information between DNA, RNA, and protein
What is the difference between nonessential and essential amino acids?
The former are amino acids that humans can generate de novo, or from scratch. The latter cannot be made and must be ingested for the mature formation of proteins.
Describe the hydrophobic effect
The hydrophobic effect. The aggregation of nonpolar groups in water leads to an increase in entropy owing to the release of water molecules into bulk water.
translation-
The information encoded in mRNA is realized in the process of translation because information is literally translated from one chemical form (nucleic acid) into another (protein). Proteins have been described as the workhorses of the cell, and translation renders the genetic information into a functional form. Translation takes place on large macromolecular complexes called ribosomes, consisting of RNA and protein
The major conclusion of the experiment of C. Anfinsen involving ribonuclease was that
The information on how the protein should fold was contained in the amino acid sequence
organelle (nucleus)-
The largest organelle is the nucleus, which is a double-membrane-bounded organelle (Figure 1.14). The nuclear membrane is punctuated with pores that allow transport into and out of the nucleus. Such transport is crucial because the nucleus is the information center of the cell. The nucleus is the location of an organism's genome. However, the nucleus is more than a storage vault. It is where the genomic information is selectively expressed at the proper time and in the proper amount.
mitochondria-
The mitochondrion (plural, mitochondria) has two membranes—an outer mitochondrial membrane that is in touch with the cytoplasm and an inner mitochondrial membrane that defines the matrix of the mitochondrion—the mitochondrial equivalent of the cytoplasm (Figure 1.15). The space between the two membranes is the intermembrane space. In mitochondria, fuel molecules undergo combustion into carbon dioxide and water with the generation of cellular energy, adenosine triphosphate (ATP).
Define pH and pKa.
The pH is a measure of the concentration of hydrogen ions in an aqueous solution. pKa (acid dissociation constant) and pH are related, but pKa is more specific in that it helps you predict what a molecule will do at a specific pH.
List the types of interactions among amino acid side chains that stabilize the three-dimensional structures of proteins. Give examples of hydrogen bond donors and acceptors.
The polypeptide backbone is rich in hydrogen-bonding potential. Each residue contains a carbonyl group (C"O), which is a good hydrogen-bond acceptor, and, with the exception of proline, an amino group (NiH) group, which is a good hydrogen-bond donor. These groups interact with each other and with the functional groups of side chains to stabilize particular structures
Explain the conformational preferences of different amino acids in proteins and polypeptides.
The polypeptide chain therefore folds so that its hydrophobic side chains are buried and its polar, charged chains are on the surface
ELISA, enzyme-linked immunosorbent assays, are useful in biochemistry because
They involve a specific recognition between the antibody and enzyme used in the color formation.
Peptide bonds
They tend to be planar. They are generally in the trans and rarely in the cis configuration. They contain an unusually long carbon-carbon bond.
Describe the role and structure of β turns or hairpin turns and omega loops in the structure of common proteins.
Turns and loops invariably lie on the surfaces of proteins and thus often participate in interactions between other proteins and the environment. Loops exposed to an aqueous environment are usually composed of amino acids with hydrophilic R groups
Distinguish between the Fischer projection and stereochemical rendering of molecules.
a. In a Fischer projection, every atom is identified and the bonds to the central carbon atom are represented by horizontal and vertical lines. By convention, the horizontal bonds are assumed to project out of the page toward the viewer, whereas the vertical bonds are assumed to project behind the page away from the viewer. When emphasis is on a molecule's function, visualization of the shape of the molecule is more important. In such instances, stereochemical renderings are used because they convey an immediate sense of the molecule's structure and, therefore, a hint about its function. Stereochemical renderings also simplify the diagram, thereby making the function of a molecule clearer. Carbon and hydrogen atoms are not explicitly shown unless they are important to the activity of the molecule. In this way, the functional groups are easier to identify. To illustrate the correct stereochemistry of tetrahedral carbon atoms, wedges are used to depict the direction of a bond into or out of the plane of the page. A solid wedge denotes a bond coming out of the plane of the page toward the viewer. A dashed wedge represents a bond going away from the viewer and behind the plane of the page. The remaining two bonds are depicted as straight lines.
1. Classify each of the 20 amino acids according to the side chain on the α carbon as aliphatic, aromatic, sulfur-containing, aliphatic hydroxyl, basic, acidic, or amide derivative.
a. The amino acids having side chains consisting only of hydrogen and carbon are hydrophobic. The simplest amino acid is glycine, which has a single hydrogen atom as its side chain. With two hydrogen atoms bonded to the alpha carbon atom, glycine is unique in being achiral. Alanine, the next simplest amino acid, has a methyl group (iCH3) as its side chain (Figure 3.3). The three-letter abbreviations and one-letter symbols under the names of the amino acids depicted in Figure 3.3 and in subsequent illustrations are an integral part of the vocabulary of biochemists. Larger aliphatic side chains are found in the branched-chain amino acids valine, leucine, and isoleucine. Methionine contains a largely aliphatic side chain that includes a thioether (-S-) group. The different sizes and shapes of these hydrocarbon side chains enable them to pack together to form compact structures with little empty space. Proline also has an aliphatic side chain, but it differs from other members of the set of 20 in that its side chain is bonded to both the a-carbon and the nitrogen atom. Proline markedly influences protein architecture because its ring structure makes it more conformationally restricted than the other amino acids. Two amino acids with simple aromatic side chains also are classified as hydrophobic (see Figure 3.3). Phenylalanine, as its name indicates, contains a phenyl ring attached in place of one of the methyl hydrogen atoms of alanine. Tryptophan has an indole ring joined to a methylene (iCH2i)group; the indole group comprises two fused rings and an NH group. The hydrophobic amino acids, particularly the larger aliphatic and aromatic ones, tend to cluster together inside the protein away from the aqueous environment of the cell. This tendency of hydrophobic groups to come together is called the hydrophobic effect (pp. 22-23) and is the driving force for the formation of the unique three-dimensional architecture of water-soluble proteins. The different sizes and shapes of these hydrocarbon side chains enable them to pack together to form compact structures with little empty space. The next group of amino acids that we will consider are those that are neutral overall, yet they are polar because the R group contains an electronegative atom that hoards electrons. Three amino acids, serine, threonine, and tyrosine contain hydroxyl (-OH) groups (Figure 3.4). The electrons in the O-H bond are attracted to the oxygen atom, making it partly negative, which in turn makes the hydrogen partly positive. Serine can be thought of as a version of alanine with a hydroxyl group attached to the methyl group, whereas threonine resembles valine with a hydroxyl group in place of one of the valine methyl groups. Tyrosine is similar to phenylalanine but contains a hydrophilic hydroxyl group attached to the large aromatic ring. The hydroxyl groups on serine, threonine, and tyrosine make them more hydrophilic (water loving) and reactive than their respective nonpolar counterparts alanine, valine, and phenylalanine. Cysteine is structurally similar to serine but contains a sulfhydryl, or thiol (-SH), group in place of the hydroxyl group. The sulfhydryl group is much more reactive than a hydroxyl group and can completely lose a proton at slightly basic pH to form the reactive thiolate group. Pairs of sulfhydryl groups in close proximity may form disulfide bonds—covalent bonds that are particularly important in stabilizing some proteins, as will be discussed in Chapter 4. In addition, the set of polar amino acids includes asparagine and glutamine, which contain a terminal carboxamide. We now turn to amino acids having positively charged side chains that render these amino acids highly hydrophilic (Figure 3.5). Lysine and arginine have long side chains that terminate with groups that are positively charged at neutral pH. Lysine is topped by an amino group and arginine by a guanidinium group. Note that the R groups of lysine and arginine have dual properties—the carbon chains constitute a hydrocarbon backbone, similar to the amino acid leucine, but the chain is terminated with a positive charge. Such combinations of characteristics contribute to the wide array of chemical properties of amino acids. Histidine contains an imidazole group, an aromatic ring that also can be positively charged. With a pKa value near 6, the imidazole group of histidine is unique in that it can be uncharged or positively charged near neutral pH, depending on its local environment (Figure 3.6). Indeed, histidine is often found in the active sites of enzymes, where the imidazole ring can bind and release protons in the course of enzymatic reactions. The two amino acids in this group, aspartic acid and glutamic acid, have acidic side chains that are usually negatively charged under intracellular conditions (Figure 3.7). These amino acids are often called aspartate and glutamate to emphasize the presence of the negative charge on their side chains. In some proteins, these side chains accept protons, which neutralize the negative charge. This ability is often functionally important. Aspartate and glutamate are related to asparagine and glutamine in which a carboxylic acid group in the former pair replaces a carboxamide in the latter pair
Discuss how a water molecule can be considered a dipole, or polar.
a. The important properties of water are due to the fact that oxygen is an electronegative atom. That is, although the bonds joining the hydrogen atoms to the oxygen atom are covalent, the electrons of the bond spend more time near the oxygen atom. Because the charge distribution is not uniform, the water molecule is said to be polar. The oxygen atom is slightly negatively charged (designated d-), and the hydrogen atoms are correspondingly slightly positively charged (d+). This polarity has important chemical ramifications. The partially positively charged hydrogen atoms of one molecule of water can interact with the partially negatively charged oxygen atoms of another molecule of water. This interaction is called a hydrogen bond
Draw the structure of an amino acid and indicate the following features, which are common to all amino acids: functional groups, side chains, and ionic forms
a. Twenty kinds of side chains varying in size, shape, charge, hydrogen-bonding capacity, hydrophobic character, and chemical reactivity are commonly found in proteins. Many of these properties are conferred by functional groups. The amino acid functional groups include alcohols, thiols, thioethers, carboxylic acids, carboxamides, and a variety of basic groups. Most of these groups are chemically reactive. All proteins in all species—bacterial, archaeal, and eukaryotic—are constructed from the same set of 20 amino acids with only a few exceptions. This fundamental alphabet for the construction of proteins is several billion years old. The remarkable range of functions mediated by proteins results from the diversity and versatility of these 20 building blocks. Although there are many ways to classify amino acids, we will assort these molecules into four groups, on the basis of the general chemical characteristics of their R groups: 1. Hydrophobic amino acids with nonpolar R groups 2. Polar amino acids with neutral R groups but the charge is not evenly distributed 3. Positively charged amino acids with R groups that have a positive charge at physiological pH (pH 7.4) 4. Negatively charged amino acids with R groups that have a negative charge at physiological pH
Know that proteins only contain L amino acids.
a. With four different groups connected to the tetrahedral a-carbon atom, a-amino acids are chiral: they may exist in one or the other of two mirror-image forms, called the l isomer and the d isomer (Figure 3.1). Only l amino acids are constituents of proteins. What is the basis for the preference for l amino acids? The answer is not known, but evidence shows that pure l or d amino acids are slightly more soluble than a stable dl crystal. Consequently, if simply by chance, there was a small excess of the l amino acid, this small solubility difference could have been amplified over time so that the l isomer became dominant in solution. Free amino acids in solution at neutral pH exist predominantly as dipolar ions (also called zwitterions). In the dipolar form, the amino group is protonated (NH3 +) and the carboxyl group is deprotonated (COO-). The ionization state of an amino acid varies with pH (Figure 3.2). In acid solution (e.g., pH 1), the amino group is protonated (NH3 +) and the carboxyl group is not dissociated (iCOOH). As the pH is raised, the carboxylic acid is the first group to give up a proton, because its pKa is near 2. The dipolar form persists until the pH approaches 9, when the protonated amino group loses a proton. Under physiological conditions, amino acids exist in the dipolar form.
Explain the advantage of carbon over silicon as a major constituent of living cells.
a. carbon is the center of many molecules (carbon/carbon bonds stronger than silicon to silicon), used at a back bone, energy is released when these bonds go through combustion, Carbon dioxide is readily soluble in water and can exist as a gas; thus, it remains in biochemical circulation, given off by one tissue or organism to be used by another tissue or organism b.silicon is more plentiful than carbon, silicon is essentially insoluble in reactions with oxygen. After it has combined with oxygen, it is permanently out of circulation c. both can form 4 covalent bonds (crucial for large molecules)
1. Define what is meant by Brownian motion.
a. is a vital energy source for life. The movement of the particles that Brown observed is due to the random fluctuation of the energy content of the environment—thermal noise. The water and gas molecules of the environment are bouncing randomly about at a rate determined only by the temperature. When these molecules collide with pollen granules or dust motes, the particles move randomly themselves. Brownian motion is responsible for initiating many biochemical interactions. In the context of the cell, water is the most common medium for the thermal noise of Brownian motion. Water is the lubricant that facilitates the flow of energy and information transformations through Brownian motion. Enzymes find their substrates; fuels can be progressively modified to yield energy, and signal molecules can diffuse from their sites of origin to their sites of effect, all through Brownian motion. To be sure, the environment inside the cell is not as simple as just implied. Cells are not simply water-filled sacks with biomolecules bouncing about. As described in Chapter 1, a great deal of organization, such as large clusters of molecules, facilitates the Brownian-motion-driven exchange of metabolites and signal molecules. Examples of this organization will come up again many times in the course of our study of biochemistry. Water is the medium whose Brownian motion provides the motive force for biochemical interactions.
Lipids that interact with both the water and the hydrophobic region of the membrane are considered______:
amphipathic
The conversion of cysteine to cystine is what kind of reaction?
an oxidation
lipids-
are much smaller than proteins or nucleic acids. Whereas proteins and nucleic acids can have molecular weights of thousands to millions, a typical lipid has a molecular weight of 1300. Moreover, lipids are not polymers made of repeating units, as are proteins and nucleic acids. A key characteristic of many biochemically important lipids is their dual chemical nature: part of the molecule is hydrophilic, meaning that it can dissolve in water, whereas the other part, made up of one or more hydrocarbon chains, is hydrophobic and cannot dissolve in water allows lipids to form barriers that delineate the cell and the cellular compartments. Lipids allow the development of "inside" and "outside" at a biochemical level. The hydrocarbon chains cannot interact with water and, instead, interact with those of other lipids to form a barrier, or membrane, whereas the water-soluble components interact with the aqueous environment on either side of the membrane. Lipids are also an important storage form of energy. As we will see, the hydrophobic component of lipids can undergo combustion to provide large amounts of cellular energy. Lipids are crucial signal molecules as well.
Describe the composition of fuel molecules and their products after oxidation.
biological fuels react with oxygen to produce carbon dioxide and water. (combustion) provides energy for the cell
carbohydrates-
carbohydrates are an important fuel source for most living creatures. The most-common carbohydrate fuel is the simple sugar glucose. Glucose is stored in animals as glycogen, which consists of many glucose molecules linked end to end and having occasional branches (Figure 1.5). In plants, the storage form of glucose is starch, which is similar to glycogen in molecular composition. can be linked together in chains, and these chains can be highly branched, much more so than in glycogen or starch. Such chains of carbohydrates play important roles in helping cells to recognize one another. Many of the components of the cell exterior are decorated with various carbohydrates that can be recognized by other cells and serve as sites of cell-to-cell interactions.
The source of the key buffering component of plasma is ____________.
carbonic acid and bicarbonate
The rigid material which provides structural support to a plant cell is/are called the
cell wall
which amino acid is responsible for stabilizing the structure of a protein by forming pairs of sulfhydryl groups?
cysteine
Describe the process of endocytosis in eukaryotes.
endocytosis, which is the opposite of exocytosis. Endocytosis is used to bring important biochemicals such as iron ions, vitamin B12, and cholesterol into the cell. Endocytosis takes place through small regions of the membrane, such as when a protein is taken into the cell (Figure 1.19). Alternatively, large amounts of material also can be taken into the cell. When large amounts of material are taken into the cell, the process is called phagocytosis. Figure 1.20 shows an immune-system cell called a macrophage phagocytizing a bacterium. Macrophages phagocytize bacteria as a means of protecting an organism from infection.
Biomolecules can be divided into four different classes. Which of the following is NOT a major class of biomolecule?
fatty acids
The amino acid with the smallest-size side chain allowing greatest flexibility in a protein is __________.
glycine
Which amino acid has the simplest side chain?
glycine
1. List the nine essential amino acids for adult humans.
histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine
What maintains the secondary structure of a protein?
hydrogen bonds between amide hydrogens and carbonyl oxygens of the peptide backbone
The ____________ group is the functional group that makes an amino acid more reactive than nonpolar amino acids such as valine, alanine, and phenylalanine
hydroxyl
Write out Crick's original diagram for the "Central Dogma."
information flows from DNA to RNA and then to protein. Moreover, DNA can be replicated. The basic tenants of this dogma are true
Interactions between side chains of Aspartate and Arginine at neutral pH would be?
ionic
List the three kinds of noncovalent bonds that mediate interactions among biomolecules and describe their characteristics.
ionic bonds, or electrostatic interactions; Electrostatic interactions, also called ionic bonds or salt bridges, are the interactions between distinct electrical charges on atoms. They usually take place between atoms bearing a completely negative charge and a completely positive charge. Why does water weaken electrostatic interactions? Consider what happens when a grain of salt, NaCl, is added to water. Even in its crystalline form, salt is more appropriately represented in the ionic form, Na+Cl-. The salt dissolves—the ionic bond between Na+ and Cl- is destroyed—because the individual ions now bind to the water molecules rather than to each other (Figure 2.3). Water can dissolve virtually any molecule that has sufficient partial or complete charges on the molecule to interact with water. This power to dissolve is crucial. Brownian motion powers collisions among the dissolved molecules and many of these collisions result in fleeting but productive interactions. b. hydrogen bonds; Hydrogen bonds are not unique to water molecules; the unequal distribution of charges that permit hydrogen-bond formation can arise whenever hydrogen is covalently bound to an electronegative atom. In biochemistry, the two most common electronegative atoms included in hydrogen bonds are oxygen and nitrogen. Weaker than covalent bonds. , distances ranging from 2.4 to 3.5 Å separate the two nonhydrogen atoms in a hydrogen bond. Hydrogen bonds between two molecules will be disrupted by water, inasmuch as water itself forms hydrogen bonds with the molecules (Figure 2.5). Conversely, hydrogen bonding between two molecules is stronger in the absence of water. c. van der Waals interactions. d. They differ in geometry, strength, and specificity. Furthermore, these bonds are greatly affected in different ways by the presence of water.
ER
is a series of membranous sacs. Many biochemical reactions take place on the cytoplasmic surface of these sacs as well as in their interiors, or lumens. The endoplasmic reticulum comes in two types: the smooth endoplasmic reticulum (smooth ER, or SER) and the rough endoplasmic reticulum (rough ER, or RER), as illustrated in Figure 1.16 (see also Figure 1.10). The smooth endoplasmic reticulum plays a variety of roles, but an especially notable role is the processing of exogenous chemicals (chemicals originating outside the cell) such as drugs. The more drugs, including alcohol, ingested by an organism, the greater the quantity of smooth endoplasmic reticulum in the liver. The rough endoplasmic reticulum appears rough because ribosomes are attached to the cytoplasmic side. Ribosomes that are free in the cytoplasm take part in the synthesis of proteins for use inside the cell. Ribosomes attached to the rough endoplasmic reticulum synthesize proteins that will either be inserted into cellular membranes or be secreted from the cell. Proteins synthesized on the rough endoplasmic reticulum are transported into the lumen of the endoplasmic reticulum during the process of translation. Inside the lumen of the rough endoplasmic reticulum, a protein folds into its final three-dimensional structure, with the assistance of other proteins called chaperones, and is often modified, for instance, by the attachment of carbohydrates. The folded, modified protein then becomes sequestered into regions of the rough endoplasmic reticulum that lack ribosomes. These regions bud off the rough endoplasmic reticulum as transport vesicles.
Draw a peptide bond and describe its conformation and its role in polypeptide sequences. Indicate the N- and C-terminal residues in peptides.
linear polymers formed by linking the alpha carboxyl group of one amino acid to the a-amino group of another amino acid. The linkage joining amino acids in a protein is called a peptide bond (also called an amide bond). The formation of a dipeptide from two amino acids is accompanied by the loss of a water molecule (Figure 4.1). The equilibrium of this reaction lies on the side of hydrolysis rather than synthesis under most conditions. Hence, the biosynthesis of peptide bonds requires an input of free energy. Nonetheless, peptide bonds are quite stable kinetically because the rate of hydrolysis is extremely slow; the lifetime of a peptide bond in aqueous solution in the absence of a catalyst approaches 1000 years. A series of amino acids joined by peptide bonds form a polypeptide chain, and each amino acid unit in a polypeptide is called a residue. A polypeptide chain has directionality because its ends are different: an a-amino group is at one end, and an a-carboxyl group is at the other. By convention, the amino end is taken to be the beginning of a polypeptide chain, and so the sequence of amino acids in a polypeptide chain is written starting with the amino-terminal residue. Thus, in the pentapeptide Tyr-Gly-Gly-Phe-Leu (YGGFL), tyrosine is the amino-terminal (N-terminal) residue and leucine is the carboxyl-terminal (C-terminal) residue (Figure 4.2). The reverse sequence, Leu-Phe-Gly-Gly-Tyr (LFGGY), is a different pentapeptide, with different chemical properties. Note that the two peptides in question have the same amino acid composition but differ in primary structure.
Name three amino acids that are positively charged at a neutral pH
lysine and arginine
If one wanted a very precise determination of the mass of a protein, what would be the method of choice?
mass spectrometry
__________ is an amino acid with a hydrophobic side chain containing a thioether.
methionine
Understand the structures of fibrous proteins including α-keratin, made of α helical coiled coils, and collagen, which has a tight triple helix.
nd collagen. a-Keratin, which is the primary component of wool and hair, consists of two right-handed a helices intertwined to form a type of left-handed superhelix called a coiled coil. a-Keratin is a member of a superfamily of proteins referred to as coiled-coil proteins (Figure 4.21). In these proteins, two or more a helices can entwine to form a very stable structure that can have a length of 1000 Å (100 nm) or more. Collagen is the main fibrous component of skin, bone, tendon, cartilage, and teeth. It contains three helical polypeptide chains, each nearly 1000 residues long. Glycine appears at every third residue in the amino acid sequence, and the sequence glycine-proline-proline recurs frequently
Buffers are critical in maintaining proper ____________ ranges in biological systems.
pH
Two-dimensional gel electrophoresis separates proteins based on:
pI (Isoelectric point) and size
what are the three aromatic amino acids?
phenylalanine, tyrosine, tryptophan
A secreted protein would be processed through organelles in the following order
rough endoplasmic reticulum; Golgi complex; secretory vesicle; fusion of cytoplasmic membrane
which amino acids contain aliphatic hydroxyl groups?
serine and threonine
nucleic acids
store and transfer information. They contain the instructions for all cellular functions and interactions. are constructed from only four building blocks called nucleotides. A nucleotide is made up of a five-carbon sugar, either a deoxyribose or a ribose, attached to a heterocyclic ring structure called a base and at least one phosphoryl group. two types of nucleic acid: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Genetic information is stored in DNA. DNA is constructed from four deoxyribonucleotides, differing from one another only in the ring structure of the bases—adenine (A), cytosine (C), guanine (G), and thymine (T). The information content of DNA is the sequence of nucleotides linked together by phosphodiester linkages. DNA in all higher organisms exists as a double-stranded helix (Figure 1.3). In the double helix, the bases interact with one another— A with T and C with G. RNA is a single-stranded form of nucleic acid. Some regions of DNA are copied as a special class of RNA molecules called messenger RNA (mRNA). Messenger RNA is a template for the synthesis of proteins. Unlike DNA, mRNA is frequently broken down after use. RNA is similar to DNA in composition with two exceptions: the base thymine (T) is replaced by the base uracil (U), and the sugar component of the ribonucleotides contains an additional hydroxyl ( i OH) group.
The amino acid with an indol ring is __________.
tryptophan
98% of atoms are what and why?
ubiquity of water. Carbon is uniquely suited to be a key atom of biomolecules
Which of the following amino acids would most likely be soluble in a nonpolar solvent such as benzene?
valine
Which of the following is considered a noncovalent bond?
van der Waals interactions, hydrogen bonds; electrostatic interactions
