Chapter 2: The Chemical Orgin of Life

: Ribosomal RNA:

may have double stranded regions due to hairpin loop formations.

Molecular chaperones:

may prevent growing proteins from random interaction with other proteins in the cytoplasm.

Which of the following was the first protein whose tertiary structure was determined?

myoglobin

The element neon (Ne) has eight electrons in its outermost electron shell. How many covalent bonds will Ne readily form?

none

The study of proteins using siRNA's is MOST useful in determining:

the function of a protein.

The process of predicting the tertiary structure of the unknown protein by aligning the amino acids of the unknown protein onto the corresponding amino acids in the protein whose structure is known is called:

threading.

Self-assembly of complex molecular structures was first demonstrated in studies of:

tobacco mosaic virus.

: Which of the following is a pyrimidine found only in RNA?

uracil

2.12 Molecular Chaperones accelerate protein folding

"Helper proteins", or molecular chaperones, bind to short stretches of hydrophobic amino acids to help unfolded proteins achieve their proper 3D conformation. Hsp 70 family Chaperonin (triC) Figure 2.46 The role of molecular chaperones in encouraging protein folding. Not all proteins can assume their final tertiary structure by self‐assembly. Proteins undergoing folding have to be prevented from interacting non-selectively with other molecules in the crowded compartments of the cell. "Helper proteins", or molecular chaperones, bind to short stretches of hydrophobic amino acids to help unfolded proteins achieve their proper 3D conformation. Chaperones of the Hsp70 family bind to polypeptides as they emerge from the ribosome and prevent them from binding to other proteins in the cytosol. (most important) Proteins can be released by the chaperones to spontaneously fold into their native state, or repeatedly bound and released until they are fully folded. Larger polypeptides are transferred to a different type of chaperone called a chaperonin, a cylindrical protein complex that provides a folding environment. TRiC is a chaperonin thought to assist in the folding of up to 15 percent of the polypeptides synthesized in mammalian cells.

2.8 The Properties of the Side Chains: nonpolar

- alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan hydrophobic and unable to form electrostatic bonds or interact with water. Side chains of this group generally lack oxygen and nitrogen. Vary in size and shape, which allows tight packing into protein core, associating by van der Waals forces and hydrophobic interactions. Leucine and isoleucine are normally found in the hydrophobic core or the transmembrane domains of the membrane proteins Leucine, valines, isoleucine, and methionine in a peptide would be highly hydrophobic and would need detergent to be dissolved Trptophan is the bulkiest side chain of all the amino acids Hydrophobic interactions are a collective of van der waals interactions because of the dipoles in the side chains

2.4 Acids, Bases, and Buffers

-Acids release protons -bases accept protons -amphoteric molecules can act as either acids or bases. for example: water -Acidity is measure using pH scale (pH= -log [H+] -The ion product constant for water is K=[H+][OH-]=10^-14 at 25 degrees celcius -As [H+] increases, [OH-] decreases so that the product equals 10^-14 Biological processes are sensitive to pH: -changes in pH affect the ion state and function of proteins -buffers in living systems resist changes in pH -for example: bicarbonate ions and carbonic acid buffer the blood -**Strength of acids and bases chart in ppt 4 slide 21**

2.3 Noncovalent Bonds

-Electrostatic interaction -Hydrogen bonding van der Waals interaction Energy: 1-5 kcal/mol, weak interaction Collective energy of multiple noncovalent bonds drives many interactions in biology. Intra- and intermolecular interactions are governed by a variety of weak linkages (about 1 to 5 kcal/mol) called noncovalent bonds. These bonds do not depend on shared electrons but attractive forces between atoms having an opposite charge Even though individual noncovalent bonds are weak, when large numbers of them act in concert, as between the two strands of a DNA molecule or between different parts of a large protein, their attractive forces are additive. Taken as a whole, they provide the structure with considerable stability.

2.3 The Life-Supporting Properties of Water

-Polar, asymmetric, good H-bonder -High heat capacity. -Superior solvent, much better than all other solvents available. -Used in the basic processes of photosynthesis, metabolism, ATP production, etc. -Water supports the stability of proteins, DNA, and other biological molecules. Hydrogen bond formation between neighboring water molecules. Each H atom of the molecule has about four-tenths of a full positive charge, and the single O atom has about eight-tenths of a full negative charge. The structure of water is suitable for sustaining life: 1) It is asymmetric, both H atoms are on one side; 2) Both covalent O-H bonds are highly polarized; 3) All three atoms readily form H-bonds. Evaporation requires that water molecules break their hydrogen bonds, taking energy to convert water to steam. Mammals take advantage of this when they sweat because the heat required to evaporate the water is absorbed from the body, which thus becomes cooler. The cell contains a remarkably complex mixture of dissolved substances, or solutes. Water is able to dissolve more types of substances than any other solvent and helps determines the structure of molecules and their types of interactions. Water is the fluid matrix around which the insoluble fabric of the cell is constructed and the medium through which materials move between compartments. It is a reactant or product in many cellular reactions; and it protects the cell in many ways—from excessive heat, cold, or damaging radiation.

2.3 van der Waals Forces

-Transient shift of orbital electrons generates dipoles and lead to dipole-dipole interactions. -Van der Waals forces operate at optimum distances and are maximized by complementary surfaces. Van der Waals forces. (A) As two atoms approach each other, they experience a weak attractive force that increases up to a specific distance, typically about 4 Å. If the atoms approach more closely, their electron clouds repel one another, causing the atoms to be forced apart. (B) Although individual van der Waals forces are very weak, large numbers of such attractive forces can be formed if two macromolecules have a complementary surface, as is indicated schematically in this figure. Hydrophobic groups can form weak bonds based on electrostatic attractions. Covalent bonds in a nonpolar molecule can have transient asymmetric electron distributions to cause charge separation, or dipoles. Two very close molecules with transitory dipoles can have a weak attractive force, called a van der Waals force (0.1 to 0.3 kcal/ mol). Biological molecules that interact with one another often possess complementary shapes.

Which one of the following polysaccharides CANNOT be digested by humans?

cellulose

Cytoplasm has a pH of about 7. What is the concentration, in moles/liter, of the hydrogen ion?

1 x 10-7

2.0 The Chemical Origin of Life

1) The hypothesis of a pre-life RNA world is a proto-cell that has membranes and RNAs that have catalytic activity. In 1952, Urey and Miller's experiment demonstrated feasibility of producing biological molecules under pre-life conditions on earth. Many RNA enzymes have been evolved in labs. Some laboratories are attempting the formation of protocells. Researchers have hypothesized that the earliest cells (called protocells) were very simple, made up of just nucleic acids surrounded by a membrane, and that these cells may have formed in warm pools of water. In 1952, Urey and Miller simulated Earth's early atmosphere, and after two weeks, organic compounds that included a variety amino acids and sugars were formed. This supports the idea that our young planet may have been ideal for creating the organic compounds that were eventually incorporated into early cells. Some laboratories are now attempting to find conditions that would allow for the formation of protocells. -1990 diff ion enzymes found at harvrd

The human genome contains:

20,000 to 22,000 genes.

Q 1: Which of the following are needed to form a triacylglycerol molecule?

3 fatty acid molecules

How many polypeptide chains comprise a hemoglobin molecule?

4

Study of the proteome of a cell:

A Option A: requires use of a computer to compare fingerprints of extracted proteins to those of known proteins. B Option B: is furthered by mass spectrometry that provides a pattern characteristic of individual proteins. C Option C: is based on knowledge of the genome of a cell. D Option D: can reveal changes in protein composition within a cell over time. all of these

2.16 Protein Engineering Structure-based Drug Design

A library of chemicals are used to screen for hits that bind to a protein. Structure‐based drug design, relies upon knowledge of the structure of the protein target to design "virtual" drug molecules to render a protein inactive. Gleevec : an inhibitor of a tyrosine kinase (ABL) and has revolutionized the treatment of a number of relatively rare cancers, most notably that of chronic myelogenous leukemia (CML).

2.7 Lipids Fats, Steroids, phospholipids, sphingolipids

A lipid molecular may have both hydrophobic and hydrophilic parts, which is called amphipathic. Fats: a glycerol linked by ester bonds to three fatty acids, termed a triacylglycerol (TAG). Fatty acids: long, unbranched hydrocarbon chains with one terminal carboxyl group Figure 2.19, a-d Fats and fatty acids. (A) The basic structure of a triacylglycerol (also called a triglyceride or a neutral fat). The glycerol moiety, indicated in orange, is linked by three ester bonds to the carboxyl groups of three fatty acids whose tails are indicated in green. (B) Stearic acid, an 18-carbon saturated fatty acid that is common in animal fats. (C) Space-filling model of tristearate, a triacylglycerol containing three identical stearic acid chains. (D) Space-filling model of linseed oil, a triacylglycerol derived from flax seeds that contains three unsaturated fatty acids (linoleic, oleic, and linolenic acids). The sites of unsaturation, which produce kinks in the molecule, are indicated by the yellow-orange bars. Lipids dissolve in organic solvents, not water. Important cellular lipids include fats, steroids, and phospholipids. Fats have glycerol linked by ester bonds to three fatty acids, termed a triacylglycerol. Fatty acids are long, unbranched hydrocarbon chains with a single carboxyl group at one end. Fatty acids are amphipathic, with a hydrophobic hydrocarbon chain is, and hydrophilic the carboxyl group.

2.5 Functional Groups

A majority of important organic molecules in biology contain chains of carbon atoms, with certain hydrogen atoms are replaced by various functional groups. Functional groups: units that give organic molecules their physical properties and chemical reactivity. Hydrocarbons do not occur in significant amounts within most living cells. The most common linkages between functional groups are ester bonds, which form between carboxylic acids and alcohols, and amide bonds, which form between carboxylic acids and amines.

2.7 Phospholipids

A phospholipid molecule: two fatty acid chains. a phosphate group and a headgroup Figure 2.22 The phospholipid phosphatidylcholine. The molecule consists of a glycerol backbone whose hydroxyl groups are covalently bonded to two fatty acids and a phosphate group. The negatively charged phosphate is also bonded to a small, positively charged choline group. The end of the molecule that contains the phosphorylcholine is hydrophilic, whereas the opposite end, consisting of the fatty acid tail, is hydrophobic. A phospholipid molecule resembles a fat, but has only two fatty acid chains not three, so it is a diacylglycerol. The third hydroxyl of glycerol is bonded to a phosphate group, which is bonded to a small polar group like choline. Phospholipids have two ends with different properties: one end contains a phosphate group (hydrophilic); the other end has two fatty acid tails (hydrophobic). Glycerol lipids with polar head groups that are hydrophillic and fatty acid tails that are hydrophobic; amphipathic

2.13 The Human Perspective Protein Misfolding Can Have Deadly Consequences

A protein with two different structures. A contrast in structure between normal and infectious prion protein Figure 2.HP1a, b A contrast in structure. (A) Tertiary structure of the normal (PrPC) protein as determined by NMR spectroscopy. The orange portions represent alpha-helical segments, and the blue portions are short beta-strands. The yellow dotted line represents the N-terminal portion of the polypeptide, which lacks defined structure. (B) A proposed model of the abnormal, infectious (PrPSc) prion protein, which consists largely of beta-sheet. The actual tertiary structure of the prion protein has not been determined. The two molecules shown in this figure are formed by polypeptide chains that can be identical in amino acid sequence but fold very differently. As a result of the differences in folding, PrPC remains soluble, whereas PrPSc produces aggregates that kill the cell. (The two molecules shown in this figure are called conformers because they differ only in conformation.) The prion protein is encoded by a gene within the cell's own chromosomes. In normal brain tissue PrpC (prion protein cellular) is made, while in CJD patients PrpSc (prion protein scrapie) is present. PrpC is soluble and is destroyed by protein‐digesting enzymes, while PrpSc forms insoluble fibrils and is resistant to digestion. Structures are different: PrpC is mainly α‐helical and PrpSc is largely β sheet. PrpSc can bind to PrpC) and cause it to fold into the abnormal form. - Amyloid precipitate is what is thought to cause disease

2.1 Covalent Bonds Cont.

A representation of the arrangement of electrons in a number of common atoms. Electrons are present around an atom's nucleus in "clouds" or orbitals that are roughly defined by their boundaries, which may have a spherical or dumbbell shape. Each orbital contains a maximum of two electrons, which is why the electrons (dark dots in the drawing) are grouped in pairs. The innermost shell contains a single orbital (thus two electrons), the second shell contains four orbitals (thus eight electrons), the third shell also contains four orbitals, and so forth. The number of outer-shell electrons is a primary determinant of the chemical properties of an element. Atoms with a similar number of outer-shell electrons have similar properties. Lithium (Li) and sodium (Na), for example, have one outer-shell electron, and both are highly reactive metals. Carbon (C) and silicon (Si) atoms can each bond with four different atoms. Because of its size, however, a carbon atom can bond to other carbon atoms, forming long-chained organic molecules, whereas silicon is unable to form comparable molecules. Neon (Ne) and argon (Ar) have filled outer shells, making these atoms highly nonreactive; they are referred to as inert gases. The electronic structure of atoms shows the outer shell to be filled: All except hydrogen needs 8 electrons. An oxygen atom can fill its outer shell by combining with two hydrogen atoms through 2 covalent bonds, forming a molecule of water. If the bond is to be broken, the energy required is between 80 and 100 kcal per mole (kcal/mol) of molecules. -Polar: uneven distribution of electrons Nonpolar: relative even distribution H: electron donor O: electron acceptor There can be single, double and triple covalent bonds. When two atoms of the same element bond, the electron pairs of the outer shell are equally shared. When two unlike atoms bond, the positively charged nucleus of one atom (more electronegative) exerts a greater attractive force on the outer electrons than the other. Commonly present in biological molecules, nitrogen and oxygen are strongly electronegative. Electronegativity: F > O > Cl > N > S > C > P > Si 3.98 3.44 3.16 3.04 2.58 2.55 2.19 1.90

2.10 Non-covalent interactions for tertiary structures

All of the noncovalent bonds—hydrogen bonds, ionic bonds, and van der Waals forces—have been found. They may cause structural similarity between polypeptides with very low similarity in sequence. Figure 2.36 Types of noncovalent bonds maintaining the conformation of proteins. Myoglobin contains no disulfide bonds; the tertiary structure is held together by noncovalent interactions. Unlike myoglobin, most globular proteins contain both α helices and β sheets. Similarity in primary sequence is often used to decide whether two proteins may have similar structure and function. Sometimes proteins unrelated at the primary sequence level have similar tertiary structures. Interactions and enzymatic activity of a protein are deduced from the tertiary structure. Actin (eukaryotic) and MreB (prokaryotic) show no similarity at the primary level but do at the tertiary level. Individual domains coming together to form macromolecular complexes= quaternary structure You can have very different primary structure but have similar tertiary structure because it is the interactions that form the tertiary structure

2.13 Protein Misfolding Can Have Deadly Consequences

Alzheimer's disease (AD): a common disorder that strikes as many as 10 percent of individuals who are at least 65 years old. It develops with the appearance of amyloid plaques and neurofibrillary tangles. Figure 2.HP2a, b Alzheimer's disease. (A) The defining characteristics of brain tissue from a person who died of Alzheimer's disease. (B) Amyloid plaques containing aggregates of the A peptide appear extracellularly (between nerve cells), whereas neurofibrillary tangles (NFTs) appear within the cells themselves. NFTs, which are discussed at the end of the Human Perspective, are composed of misfolded tangles of a protein called tau that is involved in maintaining the microtubule organization of the nerve cell. Both the plaques and tangles have been implicated as a cause of the disease. Alzheimer's disease (AD) is a common disorder that strikes as many as 10 percent of individuals who are at least 65 years old. AD patients exhibit memory loss, confusion, and loss of reasoning ability. The brain of a person with AD contains fibrillar deposits of an insoluble material referred to as amyloid. The fibrillar deposits result from the self‐association of a polypeptide composed predominantly of β sheet.

Spongiform encephalopathy describes all of the following diseases EXCEPT:

Alzheimer's disease.

2.2 Antioxidants?

Antioxidants, which destroys free radicals in testtubes, have failed to show convincing evidence for delaying aging process or make a human live longer. A related area of research concerns the study of substances called antioxidants that are able to destroy free radicals in the test tube. Common antioxidants found in the body include glutathione, vitamins E and C, and beta‐carotene. Although these substances may prove beneficial in the diet because of their ability to destroy free radicals, studies with rats and mice have failed to provide convincing evidence that they retard the aging process or increase maximum life span.

2.8 The Properties of the Side Chains (R-groups): polar charged

At pH7.4 D, E are negatively charged K, R are positively charged. H is partially charged. Figure 2.26a The chemical structure of amino acids. These 20 amino acids represent those most commonly found in proteins and, more specifically, those encoded by DNA. Other amino acids occur as the result of a modification to one of those shown here. The amino acids are arranged into four groups based on the character of their side chains. All molecules are depicted as free amino acids in their ionized state as they would exist in solution at neutral pH. The backbone of the polypeptide is composed of that part of each amino acid that is common to all of them. The side chain or R group, bonded to the α‐carbon, is highly variable among the 20 building blocks, which gives proteins their diverse structures and activities. The side chains are important in both intramolecular interactions, which determine the structure and activity of the molecule, and intermolecular interactions, which determine the relationship of a polypeptide with other molecules, including other polypeptides. R groups usually fully charged (lysine, arginine, aspartic acid, glutamic acid) at pH 7; side chains are relatively strong organic acids & bases. Can form ionic bonds due to charges; histones with arginine bind to the negatively charged phosphate DNA backbone. Histidine is usually only partially charged at pH 7; often important in enzyme active sites due to its ability gain or lose a proton in physiologic pH ranges. Ionization reactions of glutamic acid and lysine at physiologic pH show that their side chains are almost always present in the fully charged state. Consequently, they are able to form ionic bonds with other charged species in the cell. Three types of amino acids; polar charged, polar uncharged, and nonpolar Acids give protons, bases accept protons If you change the pH you can change the protonation/deprotonation state and therefore the charge of the side chains - aspartic acid, glutamic acid, lysine, arginine, histidine

2.1 Covalent Bonds

Biological molecules are made of atoms, mainly C, H, N, O, S, and P, that are linked together. The links are covalent bonds. The covalent bonds are formed through shared electrons between atoms. The valence depends on the electron orbits of specific atoms The properties of cells and their organelles derive directly from the activities of the molecules of which they are composed. Impossible to understand cellular function without a reasonable knowledge of the structure and properties of the major types of biological molecules. The atoms that make up a molecule are joined together by covalent bonds in which pairs of electrons are shared between pairs of atoms. An atom is most stable when its outermost electron shell is filled, and the number of bonds an atom can form depends on the number of electrons needed to fill its outer shell. There can be single, double and triple covalent bonds. When two atoms of the same element bond, the electron pairs of the outer shell are equally shared. When two unlike atoms bond, the positively charged nucleus of one atom (more electronegative) exerts a greater attractive force on the outer electrons than the other. Commonly present in biological molecules, nitrogen and oxygen are strongly electronegative.

2.7 Steroids

Four hydrocarbon rings Cholesterol in animal cells, a precursor for steriod hormones; nearly absent in plants Figure 2.21 The structure of steroids. All steroids share the basic four-ring skeleton. The seemingly minor differences in chemical structure between cholesterol, testosterone, and estrogen generate profound biological differences. Steroids are built around a four‐ringed hydrocarbon skeleton. Cholesterol is found in animal cell membranes and is a precursor of the steroid hormones testosterone, progesterone, and estrogen. Cholesterol is largely absent from plant cells, which is why vegetable oils are "cholesterol‐free." - Plants have cholesterol analogs found in their body

2.5 The Nature of Biological Molecules

Biological molecules are mostly organic ones containing carbon. Carbon chemistry is extensively used because of its flexibility in forming different compounds. -Compounds produced by living organisms are called biochemicals. Most of the dry weight of an organisms consists of molecules containing atoms of carbon. The chemistry of life centers around the chemistry of the carbon atom. Having four outer‐shell electrons, a carbon atom can bond with up to four other atoms. Each carbon atom is able to bond with other carbon atoms so as to construct molecules with backbones containing long chains of carbon atoms, which may be linear, branched, or cyclic. Cholesterol: an important lipid molecule in biological membranes. It illustrates the complexity of carbon-based macromolecules. Cholesterol, whose structure illustrates how carbon atoms (represented by the black balls) are able to form covalent bonds with as many as four other carbon atoms. As a result, carbon atoms can be linked together to form the backbones of a virtually unlimited variety of organic molecules. The carbon backbone of a cholesterol molecule includes four rings, which is characteristic of steroids (e.g., estrogen, testosterone, cortisol). The cholesterol molecule shown here is drawn as a ball-and-stick model, which is another way that molecular structure is depicted. Cholesterol illustrates various arrangements of carbon atoms. The size and electronic structure of carbon make it uniquely suited for generating over several hundred thousand molecules. The simplest group of organic molecules, the hydrocarbons, contain only carbon and hydrogen atoms. As more carbons are added, the skeletons of organic molecules increase in length and their structure becomes more complex.

Section 2: The Chemical Basis of Life

Building life from scratch: computer rendering of a proto‐cell, an artificial lipid vesicle containing self‐replicating nucleic acids. The ability of such proto‐cells to self‐assemble and replicate when supplied with the right mix of chemical building blocks underscores the critical role of chemistry in the origins of life. -important for material exchange with the system

2.6 Carbohydrates

Carbohydrates (or glycans): -simple sugars (or monosaccharides) -polysaccharides: made of multiple sugar building blocks. -Carbohydrates function primarily as stores of chemical energy and as materials for biological construction. They also serve as signaling ques. Most sugars have the general formula (CH2O)n. -Metabolically important ones include n=3-7: *three carbons (trioses), *four carbons (tetroses), *five carbons (pentoses), *six carbons (hexoses), *and seven carbons (heptoses). -Carbohydrates function primarily as stores of chemical energy and as materials for biological construction.

Of the following elements, which is likely to form the least polar covalent bonds with hydrogen?

Carbon

2.13 The Human Perspective

Creutzfeld‐Jakob disease (CJD), is a rare, fatal disorder that can be inherited or acquired that attacks the brain, causing a loss of motor coordination and dementia. Eating contaminated beef from cows suffering from "mad cow disease" caused people to acquire CJD. Islanders of Papua, New Guinea contract "kuru," a spongiform encephalopathy, from eating brain tissue of a recently deceased relative. The infectious agent responsible for CJD lacked nucleic acid and instead was composed solely of protein, called a prion. - Prion disease first found in Africa from eating brain tissue of deceased

The scientist who first succeeded in reconstituting complete, fully functional 30S bacterial ribosomal subunits was:

D Option D: Masayasu Nomura.

2.9 Secondary Structure

Depending on the amino acid sequence. the backbone of the polypeptide can assume the form of a cylindrical, twisting spiral called the alpha (a) helix. Figure 2.30a,b The alpha helix. (a) The helical path around a central axis taken by the polypeptide backbone in a region of α helix. Each complete (360°) turn of the helix corresponds to 3.6 amino acid residues. The distance along the axis between adjacent residues is 15 Å. (b) The arrangement of the atoms of the backbone of the α helix and the hydrogen bonds that form between amino acids. Because of the helical rotation, the peptide bonds of every fourth amino acid come into close proximity. The approach of the carbonyl group (CO) of one peptide bond to the imine group (HN) of another peptide bond results in the formation of hydrogen bonds between them. The hydrogen bonds (orange bars) are essentially parallel to the axis of the cylinder and thus hold the turns of the chain together. SOURCE: (b): C: Illustration, irving geis. Image from the irving geis collection/ howard hughes medical institute. Rights owned by hhmi. Reproduction by permission only. Secondary structure describes the conformation of portions of the polypeptide chain. The backbone lies on the inside of the helix and side chains project outward. The helical structure is stabilized by hydrogen bonds between the atoms of one peptide bond and those situated above and below it along the spiral. The beta (b) sheet has several segments of a polypeptide lying side by side that form a folded or pleated conformation. Hydrogen bonds are perpendicular to the long axis and project across from one part of the chain to another. Sheets can be arranged either parallel or antiparallel to each other. β strands are extended and resist tensile forces. Silk has an extensive amount of β sheet, and is five times stronger than steel of comparable weight. Just need to know basic properties On beta sheets residues repeat every 2 residues, it comes to 7 A due to the partial folding Additional secondary structures include hinges, turns, loops, or finger‐like extensions. Figure 2.32 A ribbon model of ribonuclease. The regions of alpha helix are depicted as spirals and beta strands as flattened ribbons with the arrows indicating the N-terminal to C-terminal direction of the polypeptide. Those segments of the chain that do not adopt a regular secondary structure (i.e., an alpha helix or beta strand) consist largely of loops and turns and are shown in lime green. Disulfide bonds are shown in blue. Often, these are the most flexible portions of a polypeptide chain and the sites of greatest biological activity. In a ribbon model showing secondary structure, α helices are represented by helical ribbons, β strands as flattened arrows, and connecting segments as thinner strands. - Disordered parts can become folded when modified

2.11 Quaternary Structure of Proteins Protein-Protein Interactions

Different proteins can become physically associated to form a much larger multiprotein complex. Figure 2.41a, b Pyruvate dehydrogenase: a multiprotein complex. Three‐dimensional reconstruction of the bacterial pyruvate dehydrogenase E1E2 subcomplex determined by electron microscopy. Its molecular mass is 11 million daltons. (b) Molecular structure of the pyruvate dehydrogenase complex determined by fitting crystal structures of subunit proteins into the large‐scale structure seen in electron microscopy. The core of the complex consists of dihydrolipoyl acetyltransferase molecules (green). Pyruvate dehydrogenase tetramers (blue) form an outer shell around the core. The full pyruvate dehydrogenase complex contains a third protein that is not resolved here, and is even larger. SOURCE: From Jacqueline Milne et al., 2002. embo J. 21:5587-98. Different proteins can become physically associated to form a much larger multiprotein complex. Once two molecules come into close contact, their interaction is stabilized by noncovalent bonds. The pyruvate dehydrogenase complex consists of 60 polypeptide chains constituting three different enzymes. The product of one enzyme can be channeled directly to the next enzyme in the sequence without becoming diluted in the cell.

2.8 Polypeptides made of Amino Acids

During protein synthesis, an amino acid is joined to two other amino acids, forming a long polymer called a polypeptide chain. Amino acids are joined by peptide bonds from linking the carboxyl group of one amino acid to the amino group of its neighbor, with the elimination of water. Once incorporated into a polypeptide chain, amino acids are termed residues. The N‐terminus contains an amino acid with a free α‐amino group, ad the residue at the opposite end, the C‐terminus, has a free α‐carboxyl group. Usually we read the peptide from N to C terminus Periodicity is 3.6 for each amino acid

2.6 Linking Sugars Together

Figure 2.16 Disaccharides. Sucrose and lactose are two of the most common disaccharides. Sucrose is composed of glucose and fructose joined by an alpha (1 to 2) linkage, whereas lactose is composed of glucose and galactose joined by a beta (1 to 4) linkage. Sugars can be joined by covalent glycosidic bonds between the carbon atom C1 of one sugar and the hydroxyl group of another sugar, generating a C-O-C linkage. Molecules composed of only two sugar units are disaccharides and serve primarily as readily available energy stores. Sucrose is a major component of plant sap, while lactose found in milk supplies newborn mammals with fuel. Pay attention to: Fischer Projection to Haworth and Chair conformation for Glucose, and Fructose Fischer to Haworth

2.6 Structural Polysacchararides

Figure 2.17a, b Three polysaccharides with identical sugar monomers but dramatically different properties. Glycogen (A), starch (B), and cellulose (C) are each composed entirely of glucose subunits, yet their chemical and physical properties are very different due to the distinct ways that the monomers are linked together (three different types of linkages are indicated by the circled numbers). Glycogen molecules are the most highly branched, starch molecules assume a helical arrangement, and cellulose molecules are unbranched and highly extended. Whereas glycogen and starch are energy stores, cellulose molecules are bundled together into tough fibers that are suited for their structural role. Colorized electron micrographs show glycogen granules in a liver cell, starch grains (amyloplasts) in a plant seed, and cellulose fibers in a plant cell wall; each is indicated by an arrow. Figure 2.18 Chitin is the primary component of the glistening outer skeleton of this grasshopper. - Cellulose, chitin, and glycosaminoglycans (GAGs): structural polysaccharides - Cellulose: plant product made of unbranched polymers - Chitin: component of invertebrate exoskeleton made - GAGs: composed of two different sugars and found in extracellular space

2.7 Hydrophobic property of fats

Figure 2.20 Soaps consist of fatty acids. In this schematic drawing of a soap micelle, the nonpolar tails of the fatty acids are directed inward, where they interact with the greasy matter to be dissolved. The negatively charged heads are located at the surface of the micelle, where they interact with the surrounding water. Membrane proteins, which also tend to be insoluble in water, can also be solubilized in this way by extraction of membranes with detergents. Soaps owe their grease‐dissolving capability to the fact that the hydrophobic end of each fatty acid can embed itself in the grease, whereas the hydrophilic end can interact with the surrounding water. As a result, greasy materials are converted into complexes (micelles) that can be dispersed by water. Figure 2.19, a-d Fats and fatty acids. (A) The basic structure of a triacylglycerol (also called a triglyceride or a neutral fat). The glycerol moiety, indicated in orange, is linked by three ester bonds to the carboxyl groups of three fatty acids whose tails are indicated in green. (B) Stearic acid, an 18-carbon saturated fatty acid that is common in animal fats. (C) Space-filling model of tristearate, a triacylglycerol containing three identical stearic acid chains. (D) Space-filling model of linseed oil, a triacylglycerol derived from flax seeds that contains three unsaturated fatty acids (linoleic, oleic, and linolenic acids). The sites of unsaturation, which produce kinks in the molecule, are indicated by the yellow-orange bars. Fatty acids differ in their length (14-20 carbons) and presence of double bonds. Fatty acids that lack double bonds are saturated, those with double bonds are unsaturated. Naturally occurring fatty acids have double bonds in the cis configuration, which produce kinks in a fatty acid chain. The more double bonds, the less effective these long chains can be packed together. This lowers the temperature at which a fatty acid‐containing lipid melts.

2.8 Building Blocks of Proteins The Structure of Amino Acids

Figure 2.24 Amino acid structure. Ball-and-stick model (A) and chemical formula (B) of a generalized amino acid in which R can be any of a number of chemical groups. (C) The formation of a peptide bond occurs by the condensation of two amino acids, drawn here in the uncharged state. In the cell, this reaction occurs on a ribosome as an amino acid is transferred from a carrier (a tRNA molecule) onto the end of the growing polypeptide chain. Proteins are unique polymers made of amino acid monomers. Twenty different amino acids, with different chemical properties, are commonly used in the construction of proteins. All amino acids have a carboxyl and an amino group, separated by a single carbon atom, the α‐carbon. Amino acids have asymmetric carbon atoms. With the exception of glycine, the α‐carbon of amino acids bonds to four different groups so that each amino acid can exist in either a D or an L form. Amino acids used in the synthesis of a protein on a ribosome are always L‐amino acids. In a neutral solution, the α‐carboxyl group loses its proton and is negatively charged, and the α‐amino group accepts a proton and is positively charged. Alpha carbon has an amine group, carboxyl group, and proton, and a side chain; most amino acids are chiral Most AA are in the L form in the proteins Hydrolyzation of peptides breaks chains of proteins Ball stick model; ball is important atoms, stick is bonds

2.10 Tertiary Structure of Proteins

Figure 2.33 An X-ray diffraction pattern of myoglobin. The pattern of spots is produced as a beam of X-rays is diffracted by the atoms in the protein crystal, causing the X-rays to strike the film at specific sites. Information derived from the position and intensity (darkness) of the spots can be used to calculate the positions of the atoms in the protein that diffracted the beam, leading to complex structures. Secondary structure is stabilized by hydrogen bonds, while tertiary structure is stabilized by noncovalent bonds between the side chains of the protein. Secondary structure is limited to a small number of conformations, but tertiary structure is virtually unlimited. The detailed tertiary structure of a protein is usually determined using the technique of X‐ray crystallography.

2.10 Dynamic Changes Within Proteins

Figure 2.39 Dynamic movements within the enzyme acetylcholinesterase. A portion of the enzyme is depicted here in two different conformations: (1) a closed conformation (left) in which the entrance to the catalytic site is blocked by the presence of aromatic rings that are part of the side chains of tyrosine and phenylalanine residues (shown in purple) and (2) an open conformation (right) in which the aromatic rings of these side chains have swung out of the way, opening the "gate" to allow acetylcholine molecules to enter the catalytic site. These images are constructed using computer programs that take into account a host of information about the atoms that make up the molecule, including bond lengths, bond angles, electrostatic attraction and repulsion, van der Waals forces, etc. Using this information, researchers are able to simulate the movements of the various atoms over a very short time period, which provides images of the conformations that the protein can assume. Proteins are not static and inflexible, but capable of internal movements. The X‐ray crystallographic structure of a protein can be considered an average structure, or "ground state." NMR can monitor shifts in hydrogen bonds, waving movements of external side chains, and the full rotation of the aromatic rings of tyrosine and phenylalanine residues. Non-random movements within a protein triggered by binding of a specific molecule are called conformational changes. - In biology it is small changes in active sites that determine the activity of the protein called hot points or hot spots

2.11 Specific Protein-Protein Interactions

Figure 2.42a, b Protein-protein interactions. (A) A model illustrating the complementary molecular surfaces of portions of two interacting proteins. The reddish-colored molecule is an SH3 domain of the enzyme PI3K, whose function is discussed in Chapter 15. This domain binds specifically to a variety of proline-containing peptides, such as the one shown in the space-filling model at the top of the figure. The proline residues in the peptide, which fit into hydrophobic pockets on the surface of the enzyme, are indicated. The polypeptide backbone of the peptide is colored yellow, and the side chains are colored green. (B) Schematic model of the interaction between an SH3 domain and a peptide showing the manner in which certain residues of the peptide fit into hydrophobic pockets in the SH3 domain. The SH3 domain, found in more than 200 proteins, is involved in cell signaling. The surface of an SH3 domain contains shallow hydrophobic "pockets" that become filled by complementary "knobs" projecting from another protein. Structural domains act as adaptors to mediate interactions between proteins. Protein-protein interactions are regulated by modifying key amino acids with phosphate groups.

2.16 Protein Engineering

Figure 2.50a, b The computational design of a protein that is capable of binding to the surface of another protein. (A) The computationally designed protein is show in blue and its target protein (the HA protein from the H1N1 1918 influenza virus) in pink and cyan. The predicted structure of the designed protein (HB36) fits closely with that of the actual protein (shown in red) that was generated from the predicted sequence. (B) The actual interfaces of the targeted hydrophobic helix of the HA protein (gray) and the designed protein (purple). Side chains are seen to interact with sites in the HA helix. Protein biochemists know how to construct a protein that can bind the hemagglutinin (HA) protein that was present in the reconstructed 1918 influenza virus. This engineered protein is capable of binding to a hydrophobic patch on the surface of the HA protein with high affinity. The side chains from the designed protein interact in highly specific ways with sites on the α helix of HA. It is possible to design and produce artificial proteins capable of catalyzing organic reactions not catalyzed by any known natural enzyme. Choose a catalytic mechanism that might accelerate a reaction and use computer‐based calculations to construct an active site to accomplish it. Those proteins that show the greatest promise are then subjected to a process of test‐tube evolution; the proteins are mutated to create a new generation of altered proteins, which could in turn be screened for enhanced activity. Eventually, one could engineer proteins that could accelerate the rates of reaction as much as one million times that of the uncatalyzed reaction. An alternate approach is to modify those that are already produced by cells. Site‐directed mutagenesis allows a gene to be mutated in a way that substitutes an amino acid with different charge, hydrophobic character, or hydrogen‐bonding properties. Site‐directed mutagenesis is also used to modify the structure of clinically useful proteins to bring about various physiological effects. The drug Somavert, used to treat acromegaly, is a modified version of human growth hormone (GH) containing several alterations. Somavert competes with GH in binding to the GH receptor, but interaction between drug and receptor fails to trigger the cellular response.

2.16 Protein Engineering Structure-based Drug Design

Figure 2.51a-c Development of a protein-targeting drug, such as Gleevec. (A) Typical steps in drug development. In step 1, a protein (e.g., ABL) has been identified that plays a causative role in the disease. This protein is a likely target for a drug that inhibits its enzymatic activity. In step 2, the protein is incubated with thousands of compounds in a search for ones that bind with reasonable affinity and inhibit its activity. In step 3, one such compound (e.g, 2-phenylaminopyrimidine in the case of ABL) has been identified. In step 4, knowledge of the structure of the target protein is used to make derivatives of the compound (e.g., Gleevec) that have greater binding affinity and thus can be used at lower concentrations. In step 5, the compound in question is tested in preclinical experiments for toxicity and efficacy (level of effectiveness) in vivo. Preclinical experiments are typically carried out on cultured human cells (step 5a) (e.g., those from patients with CML) and laboratory animals (step 5b) (e.g., mice carrying transplants of human CML cells). If the drug appears safe and effective in animals, the drug is tested in clinical trials (step 6). (B) The structure of Gleevec. The blue portion of the molecule indicates the structure of the compound 2-phenylaminopyrimidine that was initially identified as an ABL kinase inhibitor. (C, D ) The structure of the catalytic domain of ABL in complex (C) with Gleevec (shown in yellow) and (D) with a second-generation inhibitor called Sprycel. Gleevec binds to the inactive conformation of the protein, whereas Sprycel binds to the active conformation. Both binding events block the activity that is required for the cell's cancerous phenotype. Sprycel is effective against cancer cells that have become resistant to the action of Gleevec. Researchers identified a compound called 2‐phenylaminopyrimidine that was capable of inhibiting tyrosine kinases, discovered by randomly screening a large chemical library for compounds that exhibited this particular activity. Beginning with this molecule, compounds of greater potency and specificity were synthesized using structure‐based drug design. Gleevec was found to bind tightly to the inactive form of the ABL tyrosine kinase and prevent the enzyme from becoming activated. Figure 2.51a-c Development of a protein-targeting drug, such as Gleevec. (A) Typical steps in drug development. In step 1, a protein (e.g., ABL) has been identified that plays a causative role in the disease. This protein is a likely target for a drug that inhibits its enzymatic activity. In step 2, the protein is incubated with thousands of compounds in a search for ones that bind with reasonable affinity and inhibit its activity. In step 3, one such compound (e.g, 2-phenylaminopyrimidine in the case of ABL) has been identified. In step 4, knowledge of the structure of the target protein is used to make derivatives of the compound (e.g., Gleevec) that have greater binding affinity and thus can be used at lower concentrations. In step 5, the compound in question is tested in preclinical experiments for toxicity and efficacy (level of effectiveness) in vivo. Preclinical experiments are typically carried out on cultured human cells (step 5a) (e.g., those from patients with CML) and laboratory animals (step 5b) (e.g., mice carrying transplants of human CML cells). If the drug appears safe and effective in animals, the drug is tested in clinical trials (step 6). (B) The structure of Gleevec. The blue portion of the molecule indicates the structure of the compound 2-phenylaminopyrimidine that was initially identified as an ABL kinase inhibitor. (C, D ) The structure of the catalytic domain of ABL in complex (C) with Gleevec (shown in yellow) and (D) with a second-generation inhibitor called Sprycel. Gleevec binds to the inactive conformation of the protein, whereas Sprycel binds to the active conformation. Both binding events block the activity that is required for the cell's cancerous phenotype. Sprycel is effective against cancer cells that have become resistant to the action of Gleevec.

GroEL/GroES

Figure 2.EP3a, b Conformational change in GroEL. (A) The model on the left shows a surface view of the two rings that make up the GroEL chaperonin. The drawing on the right shows the tertiary structure of one of the subunits of the top GroEL ring. The polypeptide chain can be seen to fold into three domains. (B) When a GroES ring (arrow) binds to the GroEL cylinder, the apical domain of each GroEL subunit of the adjacent ring undergoes a dramatic rotation of approximately 60 with the intermediate domain (shown in green) acting like a hinge. The effect of this shift in parts of the polypeptide is a marked elevation of the GroEL wall and enlargement of the enclosed chamber. Figure 2.EP4 A schematic illustration of the proposed steps that occur during the GroEL-GroES-assisted folding of a polypeptide. The GroEL is seen to consist of two chambers that have equivalent structures and functions and that alternate in activity. Each chamber is located within one of the two rings that make up the GroEL complex. The nonnative polypeptide enters one of the chambers (step 1) and binds to hydrophobic sites on the chamber wall. Binding of the GroES cap produces a conformational change in the wall of the top chamber, causing the enlargement of the chamber and release of the nonnative polypeptide from the wall into the encapsulated space (step 2). After about 15 seconds have elapsed, the GroES dissociates from the complex and the polypeptide is ejected from the chamber (step 3). If the polypeptide has achieved its native conformation, as has the molecule on the left, the folding process is complete. If, however, the polypeptide is only partially folded, or is misfolded, it will rebind the GroEL chamber for another round of folding. (Note: As indicated, the mechanism of GroEL action is driven by the binding and hydrolysis of ATP). Figure 2.EP1 A model of the GroEL complex built according to data from electron microscopy and molecular-weight determination. The complex is seen to consist of two disks, each composed of seven identical subunits arranged symmetrically around a central axis. Subsequent studies showed the complex contains two internal chambers. Heat shock proteins and other chaperones prevent aggregation of denatured or newly synthesized proteins. Chaperones also move newly synthesized proteins across membranes. The protein GroEL is synthesized in E. coli is essential for the proper folding of other cellular proteins. Figure 2.EP2 Reconstructions of GroEL based on high-resolution electron micrographs taken of specimens that had been frozen in liquid ethane and examined at -1700C. The image on the left shows the GroEL complex, and that on the right shows the GroEL complex with GroES, which appears as a dome on one end of the cylinder. It is evident that the binding of the GroES is accompanied by a marked change in conformation of the apical end of the proteins that make up the top GroEL ring (arrow), which results in a marked enlargement of the upper chamber. GroEL acts in conjunction with another protein, GroES. Attachment of GroES to GroEL induces a conformational change in the GroEL protein. The GroEL-GroES complex assists a protein and achieving its native state

2.13 Amyloid / beta-peptides

Figure 2.HP3 Formation of the Abeta peptide. The Abeta peptide is carved from the amyloid precursor protein (APP) as the result of cleavage by two enzymes, beta-secretase and gamma-secretase. It is interesting that APP and the two secretases are all proteins that span the membrane. Cleavage of APP occurs inside the cell (probably in the endoplasmic reticulum), and the Abeta product is ultimately secreted into the space outside of the cell. The gamma-secretase can cut at either of two sites in the APP molecule, producing either Abeta40 or Abeta42 peptides, the latter of which is primarily responsible for production of the amyloid plaques seen in Figure HP2. gamma-Secretase is a multisubunit enzyme that cleaves its substrate at a site within the membrane. The amyloid hypothesis contends that the disease is caused by the production of the amyloid /b-peptide (A/b), part of the amyloid precursor protein (APP). Aβ is released after cleavage by β‐secretase and γ‐secretase into a predominant (Aβ40) or minor (Aβ40) species. Aβ42 tends to refold into a conformation that contains considerable β sheet, and can self‐associate to form small complexes. Aβ42 overproduction can be caused by duplication of the APP gene, mutations in the APP gene, or mutations in genes (PSEN1/PSEN2) encoding for γ‐secretase. Strategies of new drugs for the prevention and/or reversal of mental decline: Prevent the initial formation of the Aβ42 peptide; Remove the Aβ42 peptide (or amyloid deposits) once it has been formed; Prevent interaction between Aβ molecules to eliminate formation of both oligomers and fibrillar aggregates.

2.13 Deposits of amyloids in brains of AD patients

Figure 2.HP4 A neuroimaging technique that reveals the presence of amyloid in the brain. These PET (positron emission tomography) scans show the brains of two individuals that have ingested a radioactive compound, called flutemetamol, that binds to amyloid deposits and appears red in the image. The left panels show a healthy brain and the right panels show a brain from a patient with AD, revealing extensive amyloid buildup. Amyloid deposits in the brain can be detected with this technique in persons who show no evidence of cognitive dysfunction. Such symptom free individuals are presumed to be at high risk of going on to develop AD. Those who lack such deposits can be considered at very low risk of the disease in the near future. Although studies with animal models for AD have shown promising results, human clinical trials have proven less successful. Aβ42 vaccination had had no effect on preventing disease progression. A "preventive trial" was begun in 2012 for early‐onset AD patients to block the future buildup of amyloid to prevent the disease. Brain‐imaging procedures reveal amyloid deposits in the brains of individuals long before any symptoms of AD have developed.

2.8 Disulfides

Formation of disulfide bonds: oxidation and reduction of bonds between two cysteine residues -S-S- bridges often form between two cysteines that are distant from one another in the polypeptide backbone or even in two separate polypeptides. Disulfide bridges help stabilize the shapes of proteins. In-text figure. Disulfide bridges often form between two cysteines that are distant from one another in the polypeptide backbone or even in two separate polypeptides. Disulfide bridges help stabilize the shapes of proteins. When someone gets a "perm" to make their hair curlier, a reducing agent breaks the disulfide bridges, letting the keratin filaments slide past each other. When the reducing agent is washed out, disulfide bridges re‐form, locking the keratin in the new positions.

2.9 Primary and Secondary Structures of Proteins Primary Structure

Four levels are described: primary, secondary, tertiary, and quaternary. Primary structure, concerns the amino acid sequence of a protein, whereas the latter three levels concern the organization of the molecule in space. Sickle cell caused by a single change in primary structure of hemoglobin Figure 2.29 Scanning electron micrograph of a red blood cell from a person with sickle cell anemia. The intimate relationship between form and function is best illustrated than with proteins. Protein structure can be described at several levels of organization, each emphasizing a different aspect and each dependent on different types of interactions. The primary structure of a polypeptide is the linear sequence of amino acids that constitute the chain. The degree to which changes in the primary sequence are tolerated depends on the degree to which the shape of the protein or the critical functional residues are disturbed. Sickle cell anemia results solely from a single change (glutamic acid to valine) in amino acid sequence within the hemoglobin molecule; significantly shortens the life span of the blood cell Secondary structure is the localized folding of the chain Tertiary structure is the secondary structure folding Quaternary structure is the folding of the tertiary structure

3: _______________ are particular groupings of atoms that often behave as a unit and give organic molecules their physical properties, chemical reactivity, and solubility in aqueous solution.

Functional groups

2.8 The Properties of the Side Chains: Side chains with unique properties

Glycine: smallest R group making backbone flexible, and allow two protein backbones to closely approach each other Proline: R group forms ring with amino group (imino acid), and is bulky so doesn't fit into orderly secondary structure Cysteine: R group has reactive -SH which forms disulfide (-S-S-) bridge with other cysteine residues often at some distance away in polypeptide backbone Glycine is only amino acid without a chiral center, it is very flexible and usually found in the flexible loop of the protein Cysteine is normally found in disulfide links Proline forms a ring within its structure and therefore can cause a kink in the structure of proteins

As a solution becomes more acidic:

H+ concentration increases and pH decreases.

2.15 Proteomics and Interactomics Interactomics

Hub proteins are more likely to be essential than non‐hub proteins. Figure 2.49 Protein-protein interactions of hub proteins. (A) The enzyme RNA polymerase II, which synthesizes messenger RNAs in the cell, binds a multitude of other proteins simultaneously using multiple interfaces. (B) The enzyme Cdc28, which phosphorylates other proteins as it regulates the cell division cycle of budding yeast. Cdc28 binds a number of different proteins (Cln1-Cln3) at the same interface, which allows only one of these partners to bind at a time. Proteins that have multiple binding partners are referred to as hubs of the protein interaction network. Hub proteins are more likely to be essential than non‐hub proteins. Some hub proteins have several different binding interfaces capable of binding a number of different binding partners at the same time. Other hubs have a single binding interface capable of binding several different partners, but one at a time

2.3 Hydrogen Bonds

Hydrogen bonds form between a bonded electronegative atom, such as nitrogen or oxygen, which bears a partial negative charge, and a bonded hydrogen atom, which bears a partial positive charge. Hydrogen bonds (about 0.18 nm) are typically about twice as long as the much stronger covalent bonds. Hydrogen bears a partial positive charge when covalently bonded to an electronegative atom. This hydrogen atom can approach a second electronegative atom to form an interaction called a hydrogen bond. Hydrogen bonds (1 kcal/mol) are easily broken and occur between most polar molecules. Since their strength is additive, the large number of hydrogen bonds between the strands makes the DNA duplex a stable structure.

2.8 Posttranslational modifications of amino acids

Important PTMs include: Phosphorylation of Ser, Thr and Tyr : reversible and regulatory. -O-PO3- Lys acetylation: -N-( CH3 )3 or -NH-CH2-CH3 PTMs can change the protein property significantly activity, life span, location, interaction with other molecules, etc PTMs can modify a protein's 3D structure, level of activity, localization within the cell, life span, and/or its interactions with other molecules. Side chains can be modified by acylation, phosphorlylation, methlyation, etc. to change the protein properties One modification can change the properties of a protein dramatically

2.3 Hydrophobic effect

In a hydrophobic interaction, the nonpolar (hydrophobic) molecules are forced into aggregates, which minimizes their exposure to the surrounding water molecules. Polar molecules associate with water and are hydrophilic. Nonpolar molecules lack the charged regions that would attract them to water molecules and are hydrophobic. They are forced into aggregates to reduce exposure to water, called a hydrophobic interaction. Not true bonds because they result from an energetic drive to exclude water away from the hydrophobic surfaces

Question NumberQ 1: Which statement(s) are FALSE regarding site-directed mutagenesis?

It does not result in a change in the structure of a protein.

2.5 Basic Biological Molecules

Macromolecules: Huge highly organized molecules that form specific structures and carry out certain activities of cells. Four major categories: -proteins -nucleic acids -polysaccharides -lipids. The first three types are polymers. Monomers and polymers; polymerization and hydrolysis. (A) Polysaccharides, proteins, and nucleic acids consist of monomers (subunits) linked together by covalent bonds. Free monomers do not simply react with each other to become macromolecules. Rather, each monomer is first activated by attachment to a carrier molecule that subsequently transfers the monomer to the end of the growing macromolecule. (B) A macromolecule is disassembled by hydrolysis of the bonds that join the monomers together. Hydrolysis is the splitting of a bond by water. All of these reactions are catalyzed by specific enzymes. Organic molecules found in cells can be divided into categories based on their role in metabolism. Macromolecules. Huge highly organized molecules that form the structure and carry out the activities of cells. Macromolecules can be divided into four major categories: proteins, nucleic acids, polysaccharides, and certain lipids. The first three types are polymers composed of a large number of low‐ molecular‐weight building blocks, or monomers.

2.10 Tertiary Structure of Proteins

Many proteins have regions that lack a defined shape like the PrP protein. These regions are flexible and can change shapes under different conditions. General Shape: fibrous proteins: elongated, globular proteins: compact. Extracellular materials are usually fibrous proteins. collagen and elastin of connective tissues, keratin of hair and skin, and silk. Most intracellular proteins are globular proteins. For many years it was presumed that all proteins had a fixed 3D structure, which gave each protein its unique properties and specific functions; however many proteins have regions that lack a defined shape like the PrP protein. Disordered segments are enriched in charged/polar residues and deficient in hydrophobic residues, and can undergo a physical transformation after binding to an appropriate partner and assume a defined, folded structure. Most proteins are categorized by shape as either fibrous proteins, which are elongated, or globular proteins, which are compact. Extracellular materials are fibrous proteins, like collagen and elastin of connective tissues, and keratin of hair and skin, and silk. In contrast, most proteins within the cell are globular proteins.

The scientist who elucidated the three-dimensional structure of hemoglobin is:

Max Perutz.

2.5 Other molecules

Metabolic intermediates (metabolites): Molecules are synthesized in a series of chemical reactions termed a metabolic pathway. The compounds formed along the pathways are called metabolic intermediates. Molecules of miscellaneous functions: -vitamins, which function primarily as adjuncts to proteins; -certain steroid or amino acid hormones; -molecules involved in energy storage, such as ATP; -regulatory molecules such as cyclic AMP; -metabolic waste products such as urea.

2.5 Locations of Biological Molecules for their function

Most macromolecules, except DNA, are short-lived. Cells provide small precursors to make them. Sugars --> polysaccharides; amino acids --> proteins; nucleotides --> nucleic acids; fatty acids --> lipids. An overview of the types of biological molecules that make up various cellular structures: The localization of these molecules can be found in a number of cell structures. The building blocks of macromolecules. Most cell macromolecules are short-lived, except DNA, and are continually broken down and replaced. Cells contain a supply of small precursors ready to be added into macromolecules. Sugars, precursors of polysaccharides; amino acids, precursors of proteins; nucleotides, precursors of nucleic acids; fatty acids, incorporated into lipids.

2.10 NMR for determining Tertiary Structure of Proteins

Nuclear magnetic resonance (NMR) spectroscopy: uses a magnetic field to probe proteins with radio waves to determine distances between atoms. It determines 3D structures without crystallization. Figure 2.34 NMR spectroscopy reveals tertiary structure without crystallization. (A) An NMR spectrum of the membrane‐spanning helix protein sensory rhodopsin II. (B) Solving the structure of sensory rhodopsin II by NMR, showing thirty compuated solutions consistent with the measured NMR spectra. The fact that all solutions agree on the overall shape indicates that we should have high confidence in the solution. SOURCE: From Antoine Guatier et al., Nature Struct. Mol. Biol., 17, 768. 2010. .34 X‐ray crystallography provides higher resolution structures for larger proteins but is limited by the ability to get any given protein to form pure crystals. NMR does not require crystallization, provides information about dynamic changes in structure, and can rapidly reveal drug binding sites, but is difficult to use on larger proteins. - Can be used to determine structure of proteins smaller than 50 kd

2.18 Nucleic Acids

Nucleic acids are polymers of nucleotides. Deoxyribonucleic acid (DNA): 2'-deoxy-ribose Ribonucleic acid (RNA) Linkage: 3'-5' phosphodiester bonds Figure 2.54 Nucleotides and nucleotide strands of RNA. (A) Nucleotides are the monomers from which strands of nucleic acid are constructed. A nucleotide consists of three parts: a sugar, a nitrogenous base, and a phosphate. The nucleotides of RNA contain the sugar ribose, which has a hydroxyl group bonded to the second carbon atom. In contrast, the nucleotides of DNA contain the sugar deoxyribose, which has a hydrogen atom rather than a hydroxyl group attached to the second carbon atom. Each nucleotide is polarized, having a 5 end (corresponding to the 5 side of the sugar) and a 3 end. (B) Nucleotides are joined together to form a strand by covalent bonds that link the 3 hydroxyl group of one sugar with the 5 phosphate group of the adjoining sugar. - Know basic structures, how 5' and 3' interact, different bases used for RNA vs DNA Each nucleotide: a five-carbon sugar, a phosphate group, and a nitrogenous base. Bases are either purines or pyrimidines. Purines: A & G Pyrimidines: T and C in DNA U and C in RNA Figure 2.55 Nitrogenous bases in nucleic acids. Of the four standard bases found in RNA, adenine and guanine are purines, and uracil and cytosine are pyrimidines. In DNA, the pyrimidines are cytosine and thymine, which differs from uracil by a methyl group attached to the ring.

A shortage of cholesterol in the body could interfere with the formation of:

Option A: progesterone. B Option B: testosterone. C Option C: cell membranes. D Option D: estrogen.

Which one of the following statements is FALSE?

Option B: Proteins with identical sequences of amino acids must also have identical folding patterns.

A sodium ion (Na+) has:

Option B: lost an electron.

The drug Gleevec is useful in the treatment of:

Option C: chronic myelogenous leukemia.

2.8 Hydrophobic core of soluble proteins

Polar residues at their surface to interact with water. Non-polar residues in the core tightly packed together, -- hydrophobic effects Figure 2.28 Disposition of hydrophilic and hydrophobic amino acid residues in the soluble protein cytochrome c. (A) The hydrophilic side chains, which are shown in green, are located primarily at the surface of the protein where they contact the surrounding aqueous medium. (B) The hydrophobic residues, which are shown in red, are located primarily within the center of the protein, particularly in the vicinity of the central heme group. The ionic, polar, or nonpolar character of side chains is very important in protein structure and function. Soluble proteins generally have polar residues at their surface to interact with water. Non-polar residues are found in the core tightly packed together, where water is excluded. Hydrophobic interactions are a driving force during protein folding and contribute substantially to the overall stability of the protein. Majority of soluble proteins have a hydrophobic core that stabilizes the protein, if it does not have a hydrophobic core then disulfide bonds are used to stabilize Polar residues surround the exterior

2.6 Nutritional Polysacchararides

Polysaccharides: polymers of sugars joined by glycosidic bonds. Glycogen: an animal product made of branched glucose polymers. Starch: a plant product made of both branched and unbranched glucose polymers. Figure 2.17a, b Three polysaccharides with identical sugar monomers but dramatically different properties. Glycogen (A), starch (B), and cellulose (C) are each composed entirely of glucose subunits, yet their chemical and physical properties are very different due to the distinct ways that the monomers are linked together (three different types of linkages are indicated by the circled numbers). Glycogen molecules are the most highly branched, starch molecules assume a helical arrangement, and cellulose molecules are unbranched and highly extended. Whereas glycogen and starch are energy stores, cellulose molecules are bundled together into tough fibers that are suited for their structural role. Colorized electron micrographs show glycogen granules in a liver cell, starch grains (amyloplasts) in a plant seed, and cellulose fibers in a plant cell wall; each is indicated by an arrow. Figure 2.17a, b Three polysaccharides with identical sugar monomers but dramatically different properties. Glycogen (A), starch (B), and cellulose (C) are each composed entirely of glucose subunits, yet their chemical and physical properties are very different due to the distinct ways that the monomers are linked together (three different types of linkages are indicated by the circled numbers). Glycogen molecules are the most highly branched, starch molecules assume a helical arrangement, and cellulose molecules are unbranched and highly extended. Whereas glycogen and starch are energy stores, cellulose molecules are bundled together into tough fibers that are suited for their structural role. Colorized electron micrographs show glycogen granules in a liver cell, starch grains (amyloplasts) in a plant seed, and cellulose fibers in a plant cell wall; each is indicated by an arrow.

2.16 Protein Engineering

Produce recombinant proteins Prediction of protein structures Prediction of functional domains. Design new proteins with novel functions. If a computer simulation program could predict the shape a protein should have to bind to the viral surface of HIV, what sequence of amino acids strung together would produce such a protein? Current technology allows the making of artificial genes that code for proteins of specific amino acids sequences. Knowledge of a protein's amino acid sequence rarely allows prediction of a protein's structure. The problem is knowing which protein might have some useful function. If a computer simulation program could predict the shape a protein should have to bind to the viral surface of HIV, what sequence of amino acids strung together would produce such a protein?

2.8 Building Blocks of Proteins

Proteins are main activity carriers. Structural protein: mechanical support Functional protein: catalysis, signaling, motion, etc. Proteins have structural shapes that determine their selectively interaction with other molecules, which defines specificity and affinity for interaction Figure 2.23a, b Four examples of the thousands of biological structures composed predominantly of protein. These include (a) feathers, which are adaptations in birds for thermal insulation, flight, and sex recognition; and (b) spider webs, made of a protein‐based silk that is among the strongest materials known. (c) human hair, composed of the protein keratin, and (d) fingernails, which are also composed of keratin. SOURCE: (a) Darrell Gulin/Getty Images, Inc. Proteins are macromolecules that carry out a cell's activities. Enzymes accelerate reactions; structural proteins provide mechanical support; hormones have a regulatory functions; receptors determine what a cell reacts to; contractile filaments and molecular motors provide biological movements. Proteins have shapes and surfaces that allow them to interact selectively with other molecules, so they exhibit a high degree of specificity. Proteins can be structural or functional; many carry out both roles Tertiary structure determines shape Proteins can recognize antibodies, sugars, DNA, etc.

2.11 Quaternary Structure of Proteins

Proteins composed of multiple subunits are said to have quaternary structure. A protein composed of two identical subunits is described as a homodimer, whereas a protein composed of two nonidentical subunits is a heterodimer. Figure 2.40a, b Proteins with quaternary structure. (a) Drawing of transforming growth factor‐β2 (TGF‐β2), a protein that is a dimer composed of two identical subunits. (b) Drawing of a hemoglobin molecule, which consists of two α‐globin chains and two β‐globin chains (a heterotetramer) joined by noncovalent bonds. When the four globin polypeptides are assembled into a complete hemoglobin molecule, the kinetics of O2 binding and release are quite different from those exhibited by isolated polypeptides. This is because the binding of O2 to one polypeptide causes a conformational change in the other polypeptides that alters their affinity for O2 molecules. SOURCE: (a) From www.rcsb.org; (b) Illustration, Irving Geis. Image From Irving Geis reproduced with permission From Aaas. Collection/ Howard Hughes Medical Institute. Rights owned by Hhmi. Reproduced by permission only.) Most proteins have more than one chain, or subunit, linked by covalent disulfide bonds or held together by noncovalent bonds. Proteins composed of subunits are said to have quaternary structure. The best‐studied multisubunit protein is hemoglobin, the O2‐carrying protein of red blood cells. Hemoglobin consists of two α‐globin and two β‐globin polypeptides, each of which binds a single molecule of oxygen. Binding of oxygen causes a bound iron atom to move closer to a heme group, which leads to increasingly larger movements within and between subunits. This revealed that the complex functions of proteins may be carried out by means of small changes in their conformation. A protein composed of two identical subunits is described as a homodimer, whereas a protein composed of two nonidentical subunits is a heterodimer. - There are often disulfide bonds that stabilize quaternary structure

2.12 Protein Folding

The linear sequence of amino acids contained all of the information required for the formation of the polypeptide's 3D conformation. Figure 2.43 Denaturation and refolding of ribonuclease. A native ribonuclease molecule (with intramolecular disulfide bonds indicated) is reduced and unfolded with beta-mercaptoethanol and 8 M urea. After removal of these reagents, the protein undergoes spontaneous refolding. The unfolding of a protein is termed denaturation, and it can be brought about by detergents, organic solvents, radiation, heat, and compounds such as urea. Ribonuclease molecules that had re‐formed from the unfolded protein were indistinguishable both structurally and functionally from the correctly folded molecules present at the beginning of the experiment. Thermodynamically the primary structure determines the tertiary structure but kinetically this happens in a long time Thermodynamics determine if a reaction will happen but not how fast Enzymes and other factors needed to drive folding process You can have the same primary sequence with different tertiary structures

2.15 Proteomics and Interactomics Proteomics

Proteome: entire inventory of proteins expressed by an organism, a particular tissue, cell or cellular organelle. Proteomics: a science of studying proteomes at different levels. Proteomics attempts to answer questions on a more comprehensive scale using large‐scale (or high‐throughput) techniques to catalog the vast array of proteins produced by a particular cell. Figure 2.47 Identifying proteins by mass spectrometry. A protein is isolated from a source (such as one of the spots on one of the gels of Figure 2.48) and subjected to digestion by the enzyme trypsin. The peptide fragments are then introduced into a mass spectrometer where they are ionized and separated according to their mass/charge (m/z) ratio. The separated peptides appear as a pattern of peaks whose precise m/z ratio is indicated. A comparison of these ratios to those obtained by a theoretical digest of virtual proteins encoded by the genome allows researchers to identify the protein being studied. In this case, the MS spectrum is that of horse myoglobin lacking its heme group. Mass spectrometry is a key technique to determine the precise mass of a molecule or fragment of a molecule, which can then be used to identify that molecule. The pattern of peaks the MS constitutes a highly characteristic peptide mass fingerprint of that protein, and the protein identity can then be elucidated from the genomic sequence of that organism. Proteomics is playing an increasingly important role in medicine. Most human diseases may leave biomarkers among the thousands of proteins present in the blood or other bodily fluids. The simplest way to find a biomarker protein is to measure the protein's interaction with a specific antibody, the basis of the PSA test for prostate cancer. Many efforts have been made to compare the proteins present in the blood of healthy individuals with those present in the blood of persons suffering from various diseases, especially cancer. The OVA1 blood test for ovarian cancer, which detects a collection of biomarkers using antibody‐based tests, was invented using data from proteomic analysis of a large number of patient samples. Figure 2.48 A network of protein-protein interactions. Each red line represents an interaction between two yeast proteins, which are indicated by the named black dots. In each case, the arrow points from an SH3 domain protein to a target protein with which it can bind. The 59 interactions depicted here were detected using two different types of techniques that measure protein-protein interactions. Global protein-protein interactions can be determined from a modified mass spectrometry to produce a map that shows all of the proteins that presumably interact inside the cell. This complete set of interactions is called the "interactome" of the cell, and the results can be presented in the form of a network.

2.17 Protein Adaptation and Evolution

Secondary and tertiary structures of proteins change much more slowly during evolution than their primary structures. Figure 2.52 Distribution of polar, charged amino acid residues in the enzyme malate dehydrogenase from a halophilic archaebacterium. Red balls represent acidic residues, and blue balls represent basic residues. The surface of the enzyme is seen to be covered with acidic residues, which gives the protein a net charge of -156, and promotes its solubility in extremely salty environments. For comparison, a homologous protein from the dogfish, an ocean-dwelling shark, has a net charge of +16. Proteins are biochemical adaptations subject to natural selection and evolutionary change, and can be compared by evolutionarily related (homologous) proteins in organisms living in very different environments. Homologous proteins can exhibit virtually identical shapes and folding patterns, but show strikingly divergent amino acid sequences. Secondary and tertiary structures of proteins change much more slowly during evolution than their primary structures. Isoforms: different versions of a proteins in individual organisms. Protein families (superfamilies) of related proteins. Figure 2.53 The dramatic effect on conformation that can result from a single amino acid substitution. In this case the substitution of a leucine for a tyrosine at a critical position within this 56-amino acid polypeptide chain results in a transformation of the entire fold of the backbone of this polypeptide. This single substitution causes 85% of the amino acid residues to change their secondary structure. The spatial distribution of the two alternate side-chains, which brings about this conformational shift, is shown in the model structures. The N-terminal amino acids are shown in orange and the C-terminal amino acids in blue.

2.19 The Formation of Complex Macromolecule Structures The Assembly of Tobacco Mosaic Virus Particles

Self‐directed assembly with constituent macromolecules. viral particles, ribosomes, nucleosomes, etc. TMV particles TMV RNA TMV proteins ( 2130 identical protein subunits) Mixing purified TMV RNA and proteins can result in infective particles after a short period of incubation.

2.8 The Properties of the Side Chains: polar charged

Side chains have a partial negative or positive charge and thus can form hydrogen bonds with other molecules including water. These amino acids are often quite reactive. Asparagine and glutamine are amides of aspartic and glutamic acid. - serine, threonine, glutamine, asparagine, tyrosine

2.14 Experimental Pathways Helping Proteins Reach Their Proper Folding State

Some proteins can self-assemble from purified subunits. Other proteins require molecular chaperones for proper folding. Molecular chaperones may protect protein structure during the heat shock response. The heat shock response involves synthesis of heat shock proteins that prevent denaturation of existing proteins.

Disulfide bridges can form between two residues of:

cysteine.

2.6 Stereoisomerism

Stereoisomerism of glyceraldehyde. (A) The four groups bonded to a carbon atom (labeled a, b, c, and d) occupy the four corners of a tetrahedron with the carbon atom at its center. (B) Glyceraldehyde is the only three-carbon aldose; its second carbon atom is bonded to four different groups (—H, —OH, —CHO, and —CH2OH). As a result, glyceraldehyde can exist in two possible configurations that are not superimposable, but instead are mirror images of each other as indicated. These two stereoisomers (or enantiomers) can be distinguished by the configuration of the four groups around the asymmetric (or chiral ) carbon atom. Solutions of these two isomers rotate plane-polarized light in opposite directions and, thus, are said to be optically active. (C) Straight chain formulas of glyceraldehyde. By convention, the D-isomer is shown with the OH group on the right. Carbon 2 as a site of stereoisomerism is referred to as an asymmetric carbon. - Glyceraldehyde, the only aldotriose, has a C atom linked to four different groups. D‐glyceraldehyde: -OH to the right, L‐glyceraldehyde: -OH to the left. -Stereoisomers or enantiomers are mirror images with the same chemical reactivity. -A multi-carbon molecules may have multiple asymmetric centers Figure 2.14 Aldotetroses. Because they have two asymmetric carbon atoms, aldotetroses can exist in four configurations. As the backbone length increases, so does the number of asymmetric carbon atoms and stereoisomers. Aldotetroses have two asymmetric carbons and four different configurations. Designation is based on the arrangement of groups attached to the asymmetric carbon atom farthest from the aldehyde. If the hydroxyl group of this carbon projects to the right, the aldose is a D‐sugar; if it projects to the left, it is an L‐sugar. - Primarily encounter the D form in biology

2.10 Protein Domains

Structural/functional domains: distinct modules, or segments, that fold independently. Protein domains are often identified with a specific function. Shuffling of domains during evolution creates proteins with unique combinations of activities. Figure 2.38 Proteins are built of structural units, or domains. The mammalian enzyme phospholipase C is constructed of four domains, indicated in different colors. The catalytic domain of the enzyme is shown in blue. Each of the domains of this enzyme can be found independently in other proteins as indicated by the matching color. Most eukaryotic proteins have two or more spatially distinct modules, or domains, that fold independently. The different domains often represent parts that function semi‐independently. Protein domains are often identified with a specific function, and the functions of a newly identified protein can usually be predicted by its domains. Shuffling of domains during evolution creates proteins with unique combinations of activities. Domain usually has specific structural or catalytic function You can form complicated tertiary structure by linking domains together which can then drive the evolution of protein structure and function This principle can be used to design proteins with novel functions/folds

2.1 Polar and Nonpolar Molecules

The O-H bonds are polarized, one atom with a partial negative charge and the other atom a partial positive charge. Polar: asymmetric distribution of charge (contain O, N, or S). Nonpolar: lack electronegative atoms and strongly polarized bonds (contain C, H). Polar molecules tend to be more reactive because reactions usually lead to electron redistribution.

2.1 Ionization

The chloride atom, has an extra electron, has a negative charge (Cl−) and is termed an anion. The sodium atom, which has lost an electron, has an extra positive charge (Na+) and is termed a cation. Hydration of ions: Na+ (H2O)4-6 Cl- (H2O)6

2.3 Ionic bonds: Attraction between charged atoms

The dissolution of a salt crystal: When placed in water, the Na+ and Cl- ions of a salt crystal become surrounded by water molecules, breaking the ionic bonds between the two ions. As the salt dissolves, the negatively charged oxygen atoms of the water molecules associate with the positively charged sodium ions, and the positively charged hydrogen atoms of the water molecules associate with the negatively charged chloride ions. A NaCl crystal is held together by an electrostatic attraction between Na+ and Cl− ions, called an ionic bond. Ionic bonds within a crystal may be quite strong, yet in water, these ions becomes surrounded by water molecules. This inhibits oppositely charged ions from approaching one another closely enough to form ionic bonds Noncovalent ionic bonds play an important role in holding the protein molecule on the right (yellow atoms) to the DNA molecule on the left. Ionic bonds form between positively charged nitrogen atoms in the protein and negatively charged oxygen atoms in the DNA. The DNA molecule itself consists of two separate strands held together by noncovalent hydrogen bonds. Although a single noncovalent bond is relatively weak and easily broken, large numbers of these bonds between two molecules, as between two strands of DNA, make the overall complex quite stable. Weak ionic bonds between oppositely charged groups of large biological molecules are of considerable importance. Negatively charged phosphate atoms in a DNA molecule are closely associated with positively charged groups on the surface of a protein through ionic bonds. Ionic bonds in a cell are weak (3 kcal/mol) due to water, but deep within the core of a protein, where water is often excluded, bonds can be much stronger.

2.6 The Structure of Simple Sugars

The structures of sugars: (A) Straight-chain formula of fructose, a ketohexose [keto, indicating the carbonyl (yellow), is located internally, and hexose because it consists of six carbons]. -(B) Straight chain formula of glucose, an aldohexose (aldo because the carbonyl is located at the end of the molecule). -(C) Self-reaction in which glucose is converted from an open chain to a closed ring (a pyranose ring). -(D) Glucose is commonly depicted in the form of a flat (planar) ring lying perpendicular to the page with the thickened line situated closest to the reader and the H and OH groups projecting either above or below the ring. The basis for the designation -D-glucose is discussed in the following section. -(E) The chair conformation of glucose, which depicts its three-dimensional structure more accurately than the flattened ring of part d. -(F) A ball-and-stick model of the chair conformation of glucose. A sugar molecule has a backbone of carbon atoms linked together in a linear array by single bonds. Each carbon atom is linked to a single hydroxyl group, except for one that bears a carbonyl (C=O) group. If the carbonyl group is located at an internal position the sugar is a ketose. If the carbonyl is located at one end, the molecule is known as an aldose. Sugars tend to be highly water soluble due to their hydroxyl groups. Sugars more than 5 carbons self‐react to produce a ring‐containing molecule. A tiny fraction of molecules in solution are linear form, but the terminal aldehyde group can react with proteins like hemoglobin. Production of a modified hemoglobin called Hemoglobin A1c is often used in blood tests to track the progress of diabetes.

Which of the following characteristics does NOT apply to water?

The water molecule readily forms hydrophobic interactions.

2.12 Protein Folding Dynamics of Protein Folding

Two different models: 2nd structure formed first Collapsed first before 2nd structure Co-translational folding: mixed process Figure 2.44 Two alternate pathways by which a newly synthesized or denatured protein could achieve its native conformation. Curled segments represent alpha-helices, and arrows represent beta-strands. Protein folding could arise by secondary structure formation followed by subsequent folding driven by hydrophobic interactions. Alternatively, initial hydrophobic collapse to form a compact structure in which the backbone adopts a native‐like shape, could be followed by secondary structure development. Most proteins probably fold by a middle‐of‐the‐road scheme in which secondary structure formation and compaction occur simultaneously. Along the folding pathway. The image on the left shows the native tertiary structure of the enzyme acyl-phosphatase. The image on the right is the transition structure which represents the state of the molecule at the top of an energy barrier that must be crossed if the protein is going to reach the native state. The transition structure consists of numerous individual lines because it is a set (ensemble) of closely related structures. The overall architecture of the transition structure is similar to that of the native protein, but many of the finer structural features of the fully folded protein have yet to emerge. Conversion of the transition state to the native protein involves completing secondary structure formation, tighter packing of the side chains, and finalizing the burial of hydrophobic side chains from the aqueous solvent. A transient structure during folding resembles the native protein but lacks many of the specific interactions between amino acid side chains. If a protein is closely related at the primary sequence level with another protein whose tertiary structure is known, then one can predict the tertiary structure of the unknown protein. Aligning the amino acids of the unknown protein onto the corresponding amino acids in the protein whose structure is known is called threading.

2.7 Fats

Unsaturated fats in liquid form at RT are oils. Solid shortenings: -CH=CH- -CH2-CH2- (reduced) cis double bonds trans fats (removal of kicked bonds). A molecule of fat can contain three identical fatty acids or it can be a mixed fat, containing more than one fatty acid. Figure 2.19, a-d Fats and fatty acids. (A) The basic structure of a triacylglycerol (also called a triglyceride or a neutral fat). The glycerol moiety, indicated in orange, is linked by three ester bonds to the carboxyl groups of three fatty acids whose tails are indicated in green. (B) Stearic acid, an 18-carbon saturated fatty acid that is common in animal fats. (C) Space-filling model of tristearate, a triacylglycerol containing three identical stearic acid chains. (D) Space-filling model of linseed oil, a triacylglycerol derived from flax seeds that contains three unsaturated fatty acids (linoleic, oleic, and linolenic acids). The sites of unsaturation, which produce kinks in the molecule, are indicated by the yellow-orange bars. Unsaturated fats in liquid form at RT are oils. Solid shortenings made from unsaturated vegetable oils have double bonds reduced with hydrogen through hydrogenation. This converts some cis double bonds into trans fats, which are straight rather than kinked. Cis bond can be converted into trans fat which is very difficult to remove and bad for your health. A molecule of fat can contain three identical fatty acids or it can be a mixed fat, containing more than one fatty acid.

In a polypeptide, when peptide bonds are formed between adjacent amino acids:

the carboxyl group of one amino acid joins with the amino group of the adjacent amino acid and water is lost.

The variability among polypeptides is primarily due to:

the diverse side chains on the different amino acids.

2.2 The Human Perspective: Do free radicals cause aging?

What is Free Radicals? Atoms or molecules that have orbitals containing a single unpaired electron tend to be highly unstable and reactive. Free radicals may be formed when a covalent bond is broken such that each portion keeps one‐half of the shared electrons, or they may be formed when an atom or molecule accepts a single electron transferred during an oxidation-reduction reaction. Free radicals are extremely reactive and capable of chemically altering many types of molecules, including proteins, nucleic acids, and lipids. In 1956, Harman: aging due to tissue damage caused by free radicals. In 1969, McCord and Fridovich: superoxide dismutase (SOD) destroys the superoxide radical (O2⋅−). Hydrogen peroxide is also a potentially reactive oxidizing agent, normally destroyed in the cell by catalase or glutathione peroxidase. Superoxide radicals are formed within cells during normal oxidative metabolism. SOD-/- : mutant bacteria or yeast does not grow with O2. Mutant mice: SOD2-/- (m.t.) die within a week Mice overexpressing SOD2, live 20% longer The importance of SOD is most clearly revealed in studies of mutant bacteria and yeast that lack the enzyme; these cells are unable to grow in the presence of oxygen. Similarly, mice that are lacking the mitochondrial version of the enzyme (SOD2) are not able to survive more than a week or so after birth. Conversely, mice that have been genetically engineered so that their mitochondria contain elevated levels of the H2O2‐destroying enzyme catalase live 20 percent longer.

2.18 Structure of Nucleic Acids

a) Ribosomal RNA b) Ribozyme (hammerhead) c) Ribosome structure. RNA may have catalytic activity; such RNA enzymes are called ribozymes. Adenosine triphosphate (ATP) : energy currency in cellular metabolism. Guanosine triphosphate (GTP) : a switch to turn on some proteins. Figure 2.56 RNAs can assume complex shapes. (A) This ribosomal RNA is an integral component of the small ribosomal subunit of a bacterium. In this two-dimensional profile, the RNA strand is seen to be folded back on itself in a highly ordered pattern so that most of the molecule is double-stranded. (B) This hammerhead ribozyme, as it is called, is a small RNA molecule from a viroid (page 24). The helical nature of the double-stranded portions of this RNA can be appreciated in this three-dimensional model of the molecule. Figure 2.57 Reconstruction of a ribosome from the cytoplasm of a wheat germ cell. This reconstruction is based on high-resolution electron micrographs and shows the two subunits of this eukaryotic ribosome, the small (40S) subunit on the left and the large (60S) subunit on the right.

Question NumberQ 2: Because they both associate with proteins that assist in the assembly of their subunits, Rubisco is MOST similar to:

antibody molecules.

Prions:

are a type of infectious agent composed only of protein.

The first protein to have its amino acid sequence determined was:

beef insulin.

Silk is composed of a protein containing a large amount of:

beta (β) sheet conformations.

Conformational changes within a protein molecule are NOT seen in the following function:

binding of calcium to myosin.

Tertiary structure of a protein is stabilized by:

bonds between side chains of amino acids.

Denaturation of a protein:

can be caused by detergents, organic solvents, or radiation.

Antioxidants are believed to:

destroy free radicals.

Hemoglobin A1c can be measured in blood tests to track the progress of which disease?

diabetes

Distinct regions of a protein that fold independently of one another are called:

domains.

3: Saturated fatty acids lack which of the following?

double bonds between carbon atoms

How many electrons are in the outer shell of a carbon atom?

four

Atoms or molecules that have an orbital with a single unpaired electron are called:

free radicals.

The liver stores energy in the form of a polysaccharide called:

glycogen.

Molecular chaperones were originally referred to as:

heat shock proteins.

An enzyme that breaks down the superoxide radical (O2-) is:

superoxide dismutase.

Weak attractions between adjacent water molecules are:

hydrogen bonds.

Polar molecules are __________; nonpolar molecules are __________.

hydrophilic; hydrophobic

Different versions of a protein, which are known as ________, are adapted to function in different tissues or at different stages of development.

isoforms

The function of a buffer is to:

maintain stable pH.

Q 1: The specific linear sequence of amino acids that form a polypeptide chain is its:

primary structure.

The major cellular macromolecules include:

proteins, nucleic acids, polysaccharides, and lipids.

Strategies to develop medications to battle Alzheimer's disease have included:

removal of the A ββ 42 peptide or the amyloid deposits that it produces.

2.6 Stereoisomerism in a ring-shaped molecule

α‐pyranose: -OH below the plane of the ring, β‐pyranose: -OH above the ring. Figure 2.15 Formation of an alpha- and beta-pyranose. When a molecule of glucose undergoes self-reaction to form a pyranose ring (i.e., a six-membered ring), two stereoisomers are generated. The two isomers are in equilibrium with each other through the open-chain form of the molecule. By convention, the molecule is an alpha-pyranose when the OH group of the first carbon projects below the plane of the ring, and a beta-pyranose when the hydroxyl group projects upward. The C1 of the pyranose ring has four different groups and becomes a new center of asymmetry within the sugar molecule. Because of this extra asymmetric carbon atom, each type of pyranose exists as α and β stereoisomers. The molecule is an α‐pyranose when the OH group of the first carbon projects below the plane of the ring, and a β‐pyranose when the hydroxyl projects upward L- vs. D-glucose