Brad Gietman's List: 2nd October 5

• he starting materials or monomers are relatively simple molecules—usually carbon  compounds derived from petroleum—which can be persuaded to link up with each other in order to form a long chain of repeating units called a polymer
• Polymers are usually classified into two types: addition polymers and condensation polymers, according to the kind of reaction by which they are made.

• Formation of a condensation polymer, on the other hand, produces H₂O, HCl, or some other simple molecule which escapes as a gas. A familiar example of a condensation polymer is nylon, which is obtained from the reaction of two monomers
• If you pull on both ends of a nylon thread, for example, it will only stretch slightly. After that it will strongly resist breaking because a large number of hydrogen bonds are holding overlapping chains together. The same is not true of a polyethylene thread in which only London forces attract overlapping chains together, and this is one reason that polyethylene is not used to make thread.

• Biochemistry is the study of chemical elements found in living systems, and how these elements combine to form molecules and collections of molecules which carry out the biological functions and behaviors that we associate with life.
• More than 99 percent of the atoms in most living organisms are H, O, N, or C.
• Many biological molecules are formed by condensation polymerization from small building-block molecules. Reversal of such condensations ( hydrolysis) breaks large molecules down into the building blocks again, allowing them to be used by another organism
• Examples of condensation reactions are the formation of lipids from fatty acids and glycerol, the formation of cellulose and starch from glucose, the formation of proteins from amino acids, and the formation of nucleic acids from ribose or deoxyribose, phosphate, and nitrogenous bases.
• Lipids may be divided into two categories: nonpolar ( hydrophobic) and polar ( hydrophilic).
• Nonpolar substances often dissolve in the hydrophobic portions of lipid tissue and may be concentrated along ecological food chains, a process referred to as bioamplification.
• Simple sugars usually contain five or six C atoms in a ring and a large number of OH groups. Disaccharides are formed from a condensation reaction between two simple sugars. Polysaccharides, such as cellulose and starch, are condensation polymers of simple sugars. Their structures and chemical reactivities are very dependent on the exact structure of the simple sugar from which they are made.
• Fibrous proteins, in which polypeptide chains are arranged parallel to one another, are fundamental components of structural tissues such as tendons, hair, etc.
• Globular proteins, on the other hand, have compact, nearly spherical structures in which the polypeptide chain folds back on itself.
• Proteins are made by polymerization of 20 different amino acids. The order of amino acid side chains along the polymer backbone constitutes primary protein structure.

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• More than 99 percent of the atoms in the human body, or any other organism for that matter, are H, O, N, and C.
• The most important of these four elements is undoubtedly carbon.
• Carbon is not the only element with unique properties in biological molecules. Hydrogen is also special and plays two important roles. You will recall that alkanes are chemically unreactive.
• It is thus quite difficult to replace a hydrogen atom attached to a carbon atom with a more stable alternative. When an organic compound reacts chemically, it is almost always a functional group which undergoes a change.
• The presence of C—H bonds renders a large proportion of the carbon chain unreactive and restricts reaction almost entirely to those sites which include an atom other than carbon or hydrogen.
• In biological molecules these other atoms are almost invariably oxygen and nitrogen, and this is no accident either
• In practice only a few of these shapes are useful, and the molecules can be "frozen" into such a useful conformation through hydrogen-bonding between various segments of the chain

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• It has been estimated that even a unicellular organism may contain as many as 5000 different substances, and the human body probably has well over 5 000 000. Only a few of these are exactly the same in both species, and so the total number of different compounds in the living portion of the earth (the biosphere) is approximately (10⁵ compounds/species) × 10⁶ species = 10¹¹ compounds.
• Fortunately nearly all the substances found in living cells are polymeric—they are built up by different combinations of a limited number of relatively small molecules.
• Water, for example, provides a solvent medium for all chemical reactions, maintains rigidity of cell walls, and serves as a thermoregulator.

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• Carbohydrates are sugars and sugar derivatives whose formulas can be written in the general form: C_x(H₂O)_y
• sucrose (ordinary cane sugar), C₁₂H₂₂O₁₁;
• glucose (dextrose), C₆H₁₂O₆
• and ribose, C₅H₁₀O₅
• fructose (fruit sugar), C₆H₁₂O₆
• Glucose is also the monomer from which the polymers cellulose and starch are built up.

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• simple sugars is shown in Fig. 1. They all contain five or six carbon  atoms, and each carbon atom, except for one, is attached to a hydroxyl group (OH).
• The remaining carbon is double-bonded to oxygen, forming a carbonyl group ). Sugars are thus all aldehydes and ketones and are usually referred to as aldoses or ketoses

• This distinguishes them from the disaccharides which are made up by condensing two sugar units.
• A familiar example of a disaccharide is ordinary cane sugar, sucrose, which may be obtained by condensing a molecule of α-glucose with one of the cyclic forms of fructose called β-fructose

• As the name suggests, polysaccharides are substances built up by the condensation of a very large number of monosaccharide units
• Cellulose, for example, is a polymer of β-glucose, containing upwards of 3000 glucose units in a chain.
• Note how the β-glucose units can condense in a straight chain because the C—O bonds on opposite sides of the ring (shown in color) are parallel to each other. Each of the chains shown in the figure is hydrogen-bonded (dashed lines) to other chains lying parallel to it and fitting snugly against it
• . Because amylose is a polymer of α-glucose, the C—O bonds at each end of the monomer are no longer parallel, and this prevents them from forming a straight chain. Instead, a spiral structure like that shown in the figure is produced. This spiral is stabilized to some extent by the occurrence of hydrogen bonding between each glucose ring and the rings immediately above it and below it in the spiral. Each spiral contains between 100 and 1000 glucose rings. The other form of starch, amylopectin, is also a polymer of α-glucose but contains many branch chains. Since these branches occur randomly in the molecule, amylopectin has no overall regular structure.
• Enzymes which are capable of hydrolyzing starch will not touch cellulose, and vice versa.

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• proteins are the most abundant organic molecules in living cells, constituting more than 50 percent of the mass once water is removed.
• The products obtained upon hydrolysis of simple proteins are all amino acids.
• In the case of conjugated proteins other organic and/or inorganic substances are obtained
• The non-amino acid portions of conjugated proteins may consist of metals, lipids, sugars, phosphate, or other types of molecules. These components are referred to as prosthetic groups.
• In the fibrous proteins long polymer chains are arranged parallel or nearly parallel to one another to give long fibers or sheets. This arrangement results in physically tough materials which do not dissolve in water.
• By contrast, polymer chains of the globular proteins fold back on themselves to produce compact, nearly spherical shapes
• . Most globular proteins are water soluble and hence are relatively mobile within a cell.
• Another class of proteins are the membrane proteins, which, as the name would suggest, reside in a cell's lipid bilayer membrane. Such proteins can act as channels for ions or other molecules unable to pass through the lipid bilayer; as signal transducers, able to respond to signal molecules on one side of a membrane to begin a molecula
• Specificity is so great in some cases that only one particular molecule can serve as the enzyme’s substrate

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• The backbone of any protein molecule is a polypeptide chain obtained by the condensation of a large number of amino acids with the elimination of water.
• If these three amino acids are now condensed, water is eliminated and a simple polypeptide contaning three amino acids is obtained:
• The two CO—NH bonds produced by this reaction are called peptide bonds. An important feature of such a peptide bond is that it is planar. This is because of the existence of two resonance structures

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• Altogether there are 20 amino acids which commonly occur in all organisms. Under most circumstances amino acids exist as zwitterions and have the general formula

  

  
  

  R represents a group called a side chain which varies from one amino acid to another.
• Notice in the above image the carbon marked with an α, has 4 different groups attached to it, and thus amino acids are chiral
• To determine if an amino acid is L or D, look at the α carbon, so that the hydrogen  atom is directly behind it. This should place the three other functional groups in a circle. Follow from COOH to R to NH₂, or CORN. If this is in a counterclockwise direction, the the amino acid is in the L-isomer. If this order is in the clockwise direction, the amino acid is a D-isomer
• On the extreme left of the figure are the six most hydrophilic side chains. All are polar, and four are actually ionic at a pH of 7. Next in the figure are the six most hydrophobic side chains. These are all large and nonpolar and contain no highly electronegative atoms like nitrogen and oxygen. The remaining eight side chains either contain small nonpolar groups or groups of fairly limited polarity, and are therefore not very strongly hydrophilic or very strongly hydrophobic.

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• This is especially true of globular proteins like enzymes. The sequence of side chains along the backbone of peptide bonds in a polypeptide is said to constitute its primary structure.
• A general formula for the number of primary structures for a polypeptide containing n amino acid units is 20ⁿ
• Determination of the primary structure of a protein is a difficult and complicated problem. It also is a rather important one—the sequence of amino acids governs the three-dimensional shape and ultimately the biological function of the protein.
• Insulin was the first protein whose amino acid sequence was determined
• In order to determine the primary structure of a protein, a known mass of pure sample is first boiled in acid or base until it is completely hydrolyzed to individual amino acids. The amino acid mixture is then separated chromatographically and the exact amount of each acid determined
• The next step is to break down the protein into smaller fragments. Disulfide bridges are broken by oxidation after which the protein is selectively hydrolyzed by enzymes, called proteases, such as trypsin or chymotrypsin.
• tandem mass spectrometry. In this method, a polypeptide is sent through an initial mass spectrometer, where only a specific species of charged peptide is allowed through.

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• . Instead the protein chain stays more or less in the same conformation all the time.
• It is held in this shape by the cooperative effect of a large number of hydrogen bond
• his is called an α helix
• A second regular arrangement of the polypeptide chain is the β sheet, the β-keratin structure found in silk and shown in Fig. 2

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• Several of the amino acid side chains are difficult to fit into either the α helix or β-sheet types of structure. An obvious example is proline, in which the R group is a ring and includes nitrogen bonded to the α carbon.
• Although myoglobins isolated from a variety of mammals differ slightly in their primary structure, they all seem to have nearly the same overall molecular shape. Apparently some of the amino acids are much more important than others in determining the bend points and other crucial features of tertiary structure.
• Finally, figure 1 shows clearly that myoglobin contains a prosthetic group. In this case it is the heme group, which contains an iron atom surrounded by four nitrogens in a flat ring structure known as a porphyrin. The porphyrin ring is not covalently bonded to the protein chain, but rather fits snugly into a “pocket” surrounded by several segments of helix. A nitrogen atom in a histidine side chain on one helix does form a coordinate covalent bond with iron in the heme group, but apart from this the prosthetic group is positioned solely by the way the protein chain is folded
• The iron in the heme group marks the active site at which the oxygen-storage function of myoglobin is accomplished.
• If an iron ion can bond to an oxygen molecule, you may wonder why the complicated porphyrin and protein structures are necessary. It is to prevent the oxidation of the iron in the heme group from the iron(II) to the iron(III) oxidation state.
• If the iron(II) atom in heme were not surrounded by the protein chain, a water molecule would be able to take part as an intermediate in the electron-transfer mechanism and reduction of the oxygen could occur.
• In some proteins there is yet a fourth level of organization, labeled quaternary structure. This may be illustrated by hemoglobin, whose function as an oxygen carrier in the bloodstream is well known. Hemoglobin consists essentially of four myoglobin molecules packed together in a single unit. Four separate polypeptide chains are each folded as in myoglobin and then nested together. The way these four subunits fit together constitutes the quaternary structure.

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• . Although more than 11400 enzymes^[1] are currently known, these constitute a very small fraction of the possible combinations of the 20 amino acids in chains of 100 or more

• Most nucleic acids are extremely long-chain polymers—some forms of DNA have molecular weights greater than 10

• Nucleic acids are made up from three distinct structural units. These are

  
  1 A five-carbon sugar. Only two sugars are involved. These are ribose (used in RNA) and deoxyribose (used in DNA). Their structures are shown in Fig. 1. Note that deoxyribose, as its name implies, has one oxygen less than ribose in the 2 position.

  

  

  Figure 1 The structure of the monosaccharides (a) ribose and (b) deoxyribose found in nucleic acids.

  2 A nitrogenous base. There are five of these bases. All are shown in Fig. 2. Three of them, adenine, guanine, and cytosine, are common to both DNA and RNA. Thymine occurs only in DNA, and uracil only in RNA.

  

  Firgure 2 Structures of the principal nitrogenous bases obtained by hydrolysis of nu-cleic acids. The hydrogen lost when the base is condensed with a sugar is shown in color. (Thymine occurs only in DNA, while the very similar uracil occurs in its place in RNA. Adenine, guanine, and cytosine occur in both DNA and RNA.)

  3 Phosphoric acid. H₃PO₄ provides the unit that holds the various segments of the nucleic acid chain to each other.
• The combination of a sugar and a nitrogenous base is called a nucleoside. A typical example of a nucleoside is adenosine, derived by the condensation of ribose and adenine:
• Nucleosides in turn can be condensed with phosphoric acid by means of the —OH group at carbon  atom 5. The result is a structure called a nucleotide.
• Finally the presence of —OH groups on both the phosphoric acid and sugar portions allows one nucleotide to link with anothe

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• They showed that each amino acid in a protein is determined by a specific codon of three nitrogenous bases in the DNA or RNA chain. The details of this genetic code are given in the table below
• Since each codon corresponds to three places in the nucleic acid chain and since there are four kinds of nitrogenous bases to fill each place, there are a total of 4³ = 64 different possible codons. Since there are only 20 amino acids, the genetic code is degenerate—several different codons correspond to the same amino acid.
• This use of multiple pairing with the third codon by tRNA is called the wobble hypothesis, and was first proposed by Francis Crick.
• There are three additional features of the genetic code. First, AUG, the codon for Methionine also serves as an initiation codon, and, with help from other signals, is where protein systhesis begins.
• A final important feature of the genetic code is the existence of three termination codons.

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• That is, DNA in the cell nucleus contains all the information necessary to control synthesis of the proteins, enzymes, and other molecules which are needed as that cell grows, carries on metabolism, and eventually reproduces.
• Thus, after DNA is replicated, each new DNA double helix will have one strand from the original DNA molecule, and one newly synthesized molecule. This is referred to as semiconservative replication.
• First, the double strand needs to be opened up to replicate each template strand. To do this, a set of proteins and enzymes bind to and open up the double helix at an origin point in the molecule. This forms replication forks, points where double stranded DNA opens up, allowing replication to occur. A helicase enzyme binds at the replication forks, with the function of further unwinding the DNA and allowing the replication fork to move along the double strand as DNA is replicated. Another enzyme, DNA gyrase, is also required to relieve stress on the duplex caused by unwinding the double strand. Further, single strand binding proteins are needed to prevent the single strands from reforming a double strand. Another essential enzyme in this initiation phase is primase, which creates an RNA primer on each single strand of DNA to begin replication from.
• All of these initial functions are necessary to prepare the DNA for the main enzyme which builds then new strands, DNA polymerase. Multiple polymerase enzymes exist, but for the moment we will DNA polymerase III, the main DNA polymerase in E. coli.
• DNA polymerase III catalyzes the reaction by which a new nucleotide is added to a growing DNA strand. That reaction is seen in figure 2. The DNA polymerase enzymes need a free 3' OH group in order to begin synthesizing a new strand, which explains the necesity of the RNA primer, which gives a 3'OH group for DNA polymerase III to start from. ^[2]
• One strand, the leading strand can be polymerized continuously since the new strand being created goes 5' to 3' from the replication fork, but since the original strands are anti-parallel, the other strand, the lagging strand is going in the wrong direction for polymerization
• This means that the lagging strand is synthesized in disconnected segments, known as Okazaki fragments, instead of continuously. Later, another DNA polymerase, in the case of E. coli, DNA polymerase I, removes RNA primers and fills in the missing discontinuities.

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• The mRNA molecules differ from DNA in three ways:

  1 RNA is generally found in a single strand form, instead of the double helix structure of DNA.

  2 RNA has a hydroxyl group () at the 2' carbon, wheras DNA simply has a hydrogen.

  3 The base uracil (U) replaces thymine (T).
• Another aspect of mRNA molecules is that they are also considerably smaller than DNA