The Structure and Function of Macromolecules

Important words and concepts from Chapter 5, Campbell & Reece, 2002 (1/14/2005):

by Stephen T. Abedon (abedon.1@osu.edu) for Biology 113 at the Ohio State University

Course-external links are in brackets

Click [index] to access site index

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(1) Chapter title: The Structure and Function of Macromolecules

(a) This chapter considers the larger biologically important organic molecules known as carbohydrates, lipids, proteins, and nucleic acids.

(b) “Understanding the architecture of a particular macromolecule helps explain how that molecule works . . . In molecular biology, as in the study of life at all levels, form and function are inseparable.”

(d) Found at this site are additional pages of possibly related interest including: [carbohydrates] [glucose model] [lipids] [proteins] [nucleic acids] [biomolecules links] [index]

BIOLOGICAL POLYMERS

(2) Polymer (monomer, subunit)

(a) Many macromolecules consist of polymers

(b) A polymer is a large molecule built up from smaller building block molecules

(d) “The inherent differences between human siblings reflect variations in polymers, particularly DNA and proteins. Molecular differences between unrelated individuals are more extensive, and between species greater still . . . The molecular logic of life is simple but elegant: Small molecules common to all organisms are ordered into unique macromolecules . . . For each class (of compound) we will see that the macromolecules have emergent properties not found in their individual monomers.”

(e) [polymer, monomer, subunit, polymer subunit (Google Search)] [index]

(3) Polymerization (condensation reaction, dehydration reaction, dehydration synthesis)

(a) Polymerization is the linking together of monomers to form polymers

(b) Polymerization in biological systems typical occurs via dehydration synthesis

(c) A condensation reaction occurs via the loss of a small molecule, usually from two different substances, resulting in the formation of a bond

(d) Dehydration reaction is synonymous with condensation reaction except that dehydration reaction is limited to those condensations in which the small molecule is water

(e) Dehydration synthesis is synonymous with dehydration reaction

(f) See Figure 5.2a, The synthesis and breakdown of polymers

(g) Energy is expended to polymerize—so all condensation/dehydration reactions require an input of energy in order to move forward!!! Energy is expended to make polymers!

(h) In biological systems, enzymes are required to polymerize—without enzymes, no polymerization; so enzymes are required to make polymers!

FAQ: What reactions or bonds take place because of dehydration synthesis? The most important thing to understand about dehydration synthesis is why it is named what it is (i.e., dehydration synthesis or condensation reaction). That is, these are reactions in which a water molecule is removed from two reactants. As a consequence of the removal of the water, what is left of the two reactants (their residues) are bonded together, hence the use of the term synthesis: Dehydration synthesis = removal of water to achieve synthesis.

Since water is removed, there have to be the ingredients of water present on the two reactants to remove. These are H-O-H. More specifically, there will exist a hydroxyl group plus a hydrogen that typically is bonded to an electronegative atom (i.e., O or N). That is, -OH and H-. Remove -OH and H- and you have all the ingredients for water. Left behind are a pair of elections which are responsible for creating the bond between what is left of the two reactants. For example:

C-OH + HO-C can react to give you C-O-C + H-O-H.

Note that only one of the carbons need be bound to an -OH (though at least one must). The other carbon could be bound to an -NH:

C-OH + HN-C can react to give you C-N-C + H-O-H.

In addition, the carbons are not limited in what else may be bonded to them nor the types of bonds (though the octet rule must always be adhered to, i.e., carbon can only have four bonds around it). Consequently, you can have dehydration synthesis between, for example, carboxyl groups and amino or hydroxyl groups:

O=C-OH + HO-C gives you O=C-O-C + H-O-H

This is how fatty acids (the carboxyl group) bind to glycerol (which supplies the hydroxyl group).

O=C-OH + HN-C gives you O=C-N-C + H-O-H

This is a peptide bond linking two amino acid residues.

In general, dehydration synthesis is how polymerization occurs in biological systems. Also, don't let the repeated use of carbon in the above examples throw you. Dehydration synthesis can occur between two non-carbon containing molecules (or ions). An example of such a reaction is the binding of two phosphates together, e.g., as in the reaction ADP + Pi --> ATP + HOH.

(i)

(j) [polymerization, condensation reaction, dehydration reaction, dehydration synthesis (Google Search)] [polymerization reactions (All About Chemistry: Polymers and Polymerization)] [index]

(4) Hydrolysis

(a) The reaction known as hydrolysis represents the opposite of condensation reaction (specifically, the opposite of dehydration reaction/synthesis)

(b) See Figure 5.2b, The synthesis and breakdown of polymers

(d) Hydrolysis liberates energy—polymers contain energy put there by dehydration synthesis; thus, some of the energy required to polymerize is returned upon hydrolysis (not all, however, due to the second law of thermodynamics)

(e) Hydrolysis plays a very important role in the liberation of usable energy within cells (see ATP hydrolysis in next chapter)

(f) Enzymes are employed in biological systems to effect most hydrolysis reactions

(g) Example: Digestion of food involves numerous hydrolysis reactions

(h) [hydrolysis (Google Search)] [dehydration reaction (nice animation of dehydration synthesis and hydrolysis) (BSC Software)] [index]

CARBOHYDRATES

(5) Carbohydrates

(a) The carbohydrates are a class of carbon-based biomolecules that include the sugars plus polymers whose monomers are sugars

(b) Carbohydrates may be classified by how many monomers are present, e.g., monosaccharide (1 subunit), disaccharide (2 subunits), and polysaccharide (>2 subunits)

(c) Carbohydrates are also classified in terms of what kind of sugars the monomers consist of as well as by how the monomers are put together (the kinds of bonds and the atoms involved in the bonds)

(d) [carbohydrates, carbohydrate chemistry (Google Search)] [carbon-based compounds, functional groups, carbohydrates (Biology at Clermont College)] [index]

(6) Monosaccharides (aldose, ketose)

(a) A monosaccharide is carbohydrate that consists of only a single monomer

(b) The molecular formula of monosaccharides is (CH₂O)_n

(d) The number of carbons (n in the formula above) varies between monosaccharide types, but for every carbon in a monosaccharide, there is also one water-molecule equivalent (count the carbon, hydrogen, and oxygen atoms in the various sugars shown in Figure 5.3)

(e) All carbons in a monosaccharide are bonded to a hydroxyl group (-OH) except for one which is bonded to a carbonyl group (=O) (note that this statement is true only for the linear form of monosaccharides) (compare Glucose, Galactose, and Fructose as shown in Figure 5.3)

(f) An aldose is a monosaccharide whose carbonyl group is found on an end carbon, i.e., aldoses are aldehyde sugars

(g) A ketose is a monosaccharide whose carbonyl group is found on a middle carbon, i.e., ketoses are ketone sugars

(h) The spatial arrangement of hydroxyl groups (-OH) around carbons varies between monosaccharides (compare Glucose and Galactose—but not Fructose, as shown in Figure 5.3)

(i) [monosaccharide, aldose, ketose (Google Search)] [monosaccharide browser (edit space-filling models of linear monosaccharides – a little clumsy, i.e., there ought to be a button that allows you to switch directly between D and L isomers, but otherwise a lot of fun) (Jon Maber)] [index]

(7) Ring form

(a) Most common monosaccharides form rings in aqueous solutions

(b) See Figure 5.4, Linear and ring forms of glucose

(c) Note how in this figure glucose is drawn without most of the carbons explicitly shown; this presentation convention allows you to see how some hydroxyl groups are found above the ring while others are found below the ring; switching –OH positions creates a different molecule (and does not occur spontaneously, except for the –OH formed upon interconversion of linear and ring forms; switching –OH positions would create a different sugar, i.e., involves a chemical reaction)

(d) (remind me to show you a model of glucose to prove to you that the above statement is indeed true)

(e) Note how the ring and linear forms of a sugar interconvert; this interconversion goes on naturally in biological systems even without the help of enzymes, but is frozen in place upon the formation of sugar polymers such as dissacharides

(f)

(8) Glucose (hexose)

(a) Glucose is the most common monosaccharide

(b) Glucose is a hexose meaning that it has six carbons (i.e., its molecular formula is C₆H₁₂O₆) (ribose, by contrast, is a pentose—it has five carbons)

(d) See Figure 5.3, The structure and classification of some monosaccharides

(e) beta-D-glucose: ; alpha-D-glucose: , with numbering:

(f) See Figure 5.4, Linear and ring forms of glucose

(g) [glucose, glucose chemistry, glucose monosaccharide, hexose, dextrose (Google Search)] [glucose, amylose, glycogen, cellulose, amylopectin (Molecules of Life)] [index]

(9) Disaccharide (glycosidic linkage, maltose, lactose, sucrose)

(a) A disaccharide is formed upon the formation of a glycosidic linkage (a type of bond) between monosaccharides

(b) This glycosidic linkage forms via a dehydration reaction:

(c)

(d) Examples of disaccharides include:

(i) Maltose = glucose + glucose (starch breakdown product)

(ii) Lactose = glucose + galactose (hydrolyzed by ß-galactocidase, an type of enzyme)

(iii) Sucrose = glucose + fructose (glucose + fruit sugar = “plant sugar”)

(e) See Figure 5.5, Examples of disaccharides

(f) [disaccharide, glycosidic linkage, maltose, lactose, lactose –tolerance –intolerance -milk, lactose chemistry, sucrose (Google Search)] [index]

(10) Sugars

(a) Sugars include both the monosaccharides and the disaccharides, i.e., these small carbohydrate molecules we call sugars

(b) [sugar, sugar chemistry (Google Search)] [sugars and sweeteners (Food Resource)] [index]

(11) Polysaccharide

(a) Polysaccharides are polymers of monosaccharides (>2)

(b) Most (all?) macromolecular carbohydrates are polysaccharides

(i) carbon and energy storage molecules (starch, glycogen) or

(ii) as structural material (e.g., in plants, insects, and fungi).

(d) [polysaccharide (Google Search)] [index]

(12) Starch (amylose, amylopectin, glycogen)

(a) Starch is a polysaccharide that consists entirely of glucose monomers

(b) Starch serves as a glucose storage molecule

(d) Starch is a low-osmolarity carbohydrate storage form (osmolarity is function of particle number, not size)

(e) In starch, the glucose monomers are linked (minimally) by 1-4 linkages (this means that the number 1 carbon of one glucose is linked by a glycosidic linkage to the number 4 carbon of a second glucose—note the labeled carbons in Figure 5.4)

(f) See Figure 5.5a, Examples of disaccharides

(g) There are a number of different kinds of starch that play similar jobs in different organisms

(i) Amylose = unbranched starch (only 1-4 linkages)

(ii) Amylopectin = branched starch (found in plants)

(iii) Glycogen = heavily branched starch (found in animals)

(h) Branches are 1-6 linkages (i.e., glycosidic linkage between a number 1 carbon and a number 6 carbon) and branched starches contain both 1-4 and 1-6 linkages, creating a very large, “fluffy” molecule

(i) See Figure 5.6, Storage polysaccharides

(j) [starch, starch chemistry, amylose, amylopectin, glycogen (Google Search)] [glucose, amylose, glycogen, cellulose, amylopectin (Molecules of Life)] [starch general information, images, and links (Food Resource)] [index]

(13) Cellulose

(a) Cellulose is a structural polysaccharide (e.g., cell walls, wood, etc.)

(b) Cellulose contrasts with amylose in that amylose contains only alpha 1-4 linkages while cellulose is a linear polymer of glucose connected only by beta 1-4 linkages

(c) Note, in Figure 5.7, the very subtle distinction between the alpha and the beta configurations of glucose; these two forms of glucose are interconvertible as the ring forms of glucose open and close (form and then convert back to the linear form), but not interconvertable once glucose has been incorporated into a polysaccharide such as starch or cellulose

(d) See Figure 5.7, Starch and cellulose structures compared

(e) See Figure 5.8, The arrangement of cellulose in plant cell walls

(f) Thus, an only subtle difference between amylose and cellulose results in one being a stiff, structural material (cellulose) and the other a flexible, energy-storage material (amylose); this idea that subtle chemical and structural differences can make a big difference in the function (or lack thereof) of biomolecules is an oft repeated theme when studying the molecules of life

(g) The following is a portion of the polymer cellulose—note the b-1,4 linkages between the glusose residues:

(h) [cellulose, cellulose structure, cellulose chemistry (Google Search)] [glucose, amylose, glycogen, cellulose, amylopectin (Molecules of Life)] [index]

(14) Digesting cellulose

(a) Most organisms cannot digest (hydrolyze) cellulose

(b) Organisms that can digest cellulose include:

(i) the microorganisms living the gastrointestinal tract of many organisms typified especially by cows and termites

(ii) many fungi (i.e., the things that “eat” the wood of fallen trees)

(15) Chitin

(a) Chitin is another example of a structural carbohydrate (cellulose is the other example that we have considered)

(b) Chitin is found in the exoskeletons of insects, spiders, and crustaceans

(c) Chitin is also found in the cell walls of fungi (though not in the cell walls of various organisms that have been incorrectly classified as fungi through the years, such as water molds)

(d) Chitin is leathery in pure form but is hardened in most uses via the deposition of calcium carbonate

(e) [a derivative of chitin called chitosan is used to sequester dietary fat to cut down on the fat calories absorbed from food, i.e., as a dieting aid (Netrition.com)]

(f) [chitin (Google Search)] [chitin (Bot 251Y: Physiology of Plants and Microorganisms)] [the chitin site (The European Chitin Society)] [index]

LIPIDS

(16) Lipids

(a) (list of phospholipids-types overhead—students need-not memorize list)

(b) Lipids are a structurally heterogeneous class of biological molecules that are, as their common characteristic, hydrophobic

(d) Examples of lipids include: Fats, phospholipids, steroids, waxes, etc.

(e) [lipids (Google Search)] [lipid links (MicroDude)] [index]

(17) Fats (triglyceride, triacylglycerol)

(a) Fats are lipids that consist of long-chain fatty acids bound by ester linkages to glycerol

(b) See Figure 5.10, The synthesis and structure of a fat, or triacylglycerol

(d) Fats function in biological systems as energy storage molecules (particular for organisms or stages of life cycles in which mobility and energy storage are simultaneously necessary, e.g., nuts, seeds, and animals)

(e) Fats possess more energy per molecule and less hydration compared with carbohydrates, resulting in fats possessing much more energy stored per unit mass or volume

(f) In animals such as ourselves, fats are stored in adipose cells

(g) Fats are also important as cushions for body organs and as an insulating layer beneath skin

(h) [fat, fats chemistry, triglycerides, triacylglycerides (Google Search)] [esters (MicroDude)] [glycerol (Molecules of Life)] [index]

(18) Fatty acid (saturated fatty acid, unsaturated fatty acid)

(a) Fatty acids are long-chain hydrocarbons with a carboxyl group (-COOH) at one end

(b) Saturated fatty acids have no C=C double bonds

(d) See Figure 5.11, Saturated and unsaturated fats and fatty acids

(e) Increasing the unsaturation of a fatty acid results in a decreasing melting point

(f) Kinks from cis-double bonds in unsaturated fatty acids inhibit close packing

(g)

(h) (I'm careful to say "cis" double bond because "trans" double bonds do not produce kinks in fatty acids—these double-bond types in fatty acids are examples of the structural isomers that are possible given double bonds—and trans-double bonds are not as readily found in naturally occurring fatty acids, though are found to some extent in animal products according to the United Soybean Board; hydrogenated vegetable oil consists of unsaturated oils made into saturated or more-saturated oils by the addition of hydrogen atoms to double bounds, and somehow in the course of hydrogenation — perhaps because the reaction is multistep and an unstable intermediate is formed that is more-free to rotate than a full double bond — trans double bonds are created; "The hydrogenation (addition of H₂) of vegetable oils eliminates carbon-to-carbon double bonds. This raises the melting point of the oils and leads to the formation of solid fats, which are commonly marketed as margarines and shortening. If the hydrogenation process is carefully controlled, hydrogenation is incomplete and the hydrogenated vegetable oils retain more carbon-to-carbon double bonds than are found in most animal fats, including butter and lard. The hydogenation process, however, does convert a portion of the nonhydrogenated cis double bonds to their trans isomers. The possible health consequences of this chemical transformation are under investigation. The results of some studies indicate that dietary trans-fats may increase heart disease risk, whereas other studies have found a correlation between the amount of trans-oleic acid stored in the body and a reduction in heart attack risk.")

(i) The amount of cis-double bonds control the melting point of the fats that unsaturated fatty acids make up

(j) Things whose body temperature is low (cold-water fish, temperate plants) tend to have unsaturated fatty acids whereas things whose body temperature is high (birds, mammals, and tropical plants) tend to have saturated fats

(k) [fatty acid, fatty acids, saturated fatty acid, unsaturated fatty acid (Google Search)] [membrane fluidity (Physiological Ecology)] [oleic acid (Molecules of Life)] [index]

(19) Oil

(a) An oil is a triacylglycerol that is liquid at room temperature

(b) [oils chemistry -essential (Google Search)] [index]

(20) Phospholipid

(a) Phospholipids are a variation on the triacylglycerol theme in which one fatty acid is replaced with a phosphate group, which in turn is bound to additional functional groups

(b) Structurally and functionally, the important thing about phospholipids is that these molecules are simultaneously hydrophobic (at one end, the fatty acid end) and hydrophilic (at the other end, the phosphate end)

(c) See Figure 5.12, The structure of a phospholipid

(d) Note clothespin symbolic representation of a phospholipid in Figure 5.12c

(e) See Figure 5.13, Two structures formed by self-assembly of phospholipids in aqueous environments

(f) Note the structures of micelles and phospholipid bilayers

(g) [phospholipids (Google Search)] [phospholipid and lipid bilayer space-filling models (many) (RasMol)] [index]

(21) Steroids

(a) All steroids possess a common ring structure

(b) These ring structures vary by attached functional groups

(c) See Figure 5.14, Cholesterol: a steroid

(d) Cholesterol is example of a steroid; cholesterol is a membrane component

(e) You should be able to recognize the structure of the steroid rings:

(f) The common steroid structure is the basis of sterol hormones including the human sex hormones (the estrogens and the androgens, including testosterone)

(g) [steroids, steroid structure (Google Search)] [cholesterol (Molecules of Life)] [cholesterol illustration (MicroDude)] [index]

PROTEINS

(22) Proteins, introduction

(a) Proteins are a major constituent of most cells (>50% dry weight)

(b) Proteins are extremely sophisticated molecules (or multi-molecular complexes)

(d) All proteins consist of polymers that are folded into specific conformations

(e) This conformation plus the chemistry of well-placed functional groups control a protein's function (another example of function follows form)

(f) Proteins are made up of 20 different types of amino-acid monomers

(g) [proteins (Google Search)] [amino acids and protein (Biology at Clermont College)] [index]

(23) Amino acids

(a) An amino acid is a short chain consisting of an amino group attached to a central carbon which is additionally attached to carboxyl group

(b) The center carbon is also bound to H plus an R group (a.k.a., a side chain)

(c)

(d) See Figure 5.15, The 20 amino acids of proteins (note that this figure is the type of thing that one memorizes in a biochemistry class, that and glycolysis, and a whole lot more)

(e) The chemistry of R groups distinguishes amino acids and their properties

(f) For example, R groups can be nonpolar (hydrophobic), polar, acidic, or basic

(g)

(h) [amino acids (Google Search)] [amino acids and protein (Biology at Clermont College)] [amino acid chemistry (Institute of Chemistry)] [index]

(24) Peptide bond (polypeptide)

(a) See Figure 5.16, Making a polypeptide chain

(b) Polypeptide = linear chain of amino acids linked by peptide bonds

(d) Backbone = -N-C-C-N-C-C-N-

(e) “’Polypeptide’ is not quite synonymous with ‘protein.’ The relationship is somewhat analogous to that between a long strand of yarn and a sweater of a particular size and shape that one can knit from the yarn. A functional protein is not just a polypeptide chain, but one or more polypeptides precisely twisted, folded, and coiled into a molecule of unique shape. It is the amino-acid sequence of a polypeptide that determines what three-dimensional conformation the protein will take.” (p. 70, Campbell et al., 1999)

(f)

(g) [“The peptide bond is named after the powerful digestive enzyme pepsin, one of the family of enzymes that cleave these bonds and so break up protein chains; ‘pepsin’ is in turn derived from the Greek root peptos, meaning cooked. Pepsin was one of the first enzymes to be prepared in pure form.” Horace Freeland Judson, 1996, The Eighth Day of Creation, Cold Spring Harbor Laboratory Press, pp. 60-61]

(h) [peptide bond, polypeptide (Google Search)] [peptide bond animated gif (John Kyrk)]

(25) Conformation = shape à function

(a) “A protein’s conformation determines how it works. In almost every case, the function of a protein depends on its ability to recognize and bind to some other molecule.”

(b) The surface chemistry of a protein is determined by the chemistry of exposed amino-acid R groups

(d) [protein conformation (Google Search)] [index]

(26) Four levels of protein structure

(a) The structure of proteins is often distinguished into four levels

(b) These are called primary, secondary, tertiary, and quaternary structure

(c) [protein structure (Google Search)] [deciphering the messages of life’s assembly (article on protein folding) (BIOL 121: Human Biology Web Site)] [index]

(27) Primary structure

(a) Primary structure is the sequence of amino acids that make up a polypeptide

(b) “Each type of protein has a unique primary structure, a precise sequence of amino acids.”

(c) See Figure 5.18, The primary structure of a protein

(d) To some extent a protein’s higher order structures are controlled by its primary structure, i.e., the order and number of amino acids

(e) Primary structure is determined and controlled by genes

(f) Genetic variations that change primary structure represent one form of mutation

(g) [primary structure (Google Search)] [index]

(28) Secondary structure

(a) Polypeptide backbones can interact in fairly predictable ways

(b) These interactions involve hydrogen bonding between carbonyl groups (=O; which possess a partial negative charge) and nitrogen-bound hydrogens (-N-H; which possess a partial positive charge)

(c) See Figure 5.20, The secondary structure of a protein

(d) Note how the bonds within the polypeptide backbone, in figure 5.20, are arranged in three dimensions

(e) (note also that the R groups and hydrogens attached to the middle carbons are not shown in this figure or in figure 5.24, yet still the secondary structure may be represented)

(f) Two most-commonly described secondary structures are the alpha helix and pleated sheet

(g) (“Four secondary structures—alpha-helices, beta-sheets, reverse turns and omega-loops—make up more than 90 percent of the conformational structure of all proteins.” George D. Rose, 1996, No assembly required, The Sciences 36(1):26-31)

(h) [secondary structure (Google Search)] [properties of protein secondary structures (table of basic structural characteristics) (Shaun D. Black)] [secondary structure animated gifs (John Kyrk)] [index]

(29) Alpha helix

(a) The alpha helix is a coiling of peptides held together every fourth peptide bond on the peptide chain/backbone

(b) See Figure 5.20

(d) [alpha helix (Google Search)] [index]

(30) Pleated sheet

(a) Portions of polypeptides that are arranged anti-parallelly can form sheets (known as pleated, or ß-pleated, or beta-pleated sheets)

(b) See Figure 5.20, The secondary structure of a protein

(c) The sheets are pleated as a consequence of the periodic bends seen in the peptide chains that result from the spatial arrangement of bonds around carbons and nitrogen found in the peptide chain

(d) Pleated sheets are often found in the hydrophobic interiors of proteins

(e) [pleated sheet (Google Search)] [index]

(31) Tertiary structure

(a) Interactions between side chains (R groups) generate additional three-dimensional structure within proteins

(b) Because of the great variety of interactions possible, the three dimensional structures generated appear as random clumps and ribbons between clumps

(i) hydrophobic interactions (hydrophobic exclusion)

(ii) hydrogen bonds

(iii) ionic bonds

(iv) disulfide bonds (bridges)

(d) See Figure 5.22, Examples of interactions contributing to the tertiary structure of a protein

(e) Tertiary structure additionally refers to the arrangement of secondary structures within the folded protein

(f) [tertiary structure (Google Search)] [interactive cytochrome oxidase (nice chime models of proteins) (Graham Palmer)] [phage 434 CRO repressor protein bound to DNA (space-filling model) (RasMol)] [index]

(32) Disulfide bridges

(a) Disulfide bonds are found between the R groups of cysteine amino acids

(b) Cysteine’s R group is a sulfhydryl group (-SH)

(d) See Figure 5.22, Examples of interactions contributing to the tertiary structure of a protein

(e) This is a covalent bond formed between different portions of a polypeptide chain

(f) Disulfide bridges serve to lock in place certain tertiary structures

(g) They can add significantly to the stability of a protein’s structure

(h) [disulfide bridge (Google Search)] [thiols (MicroDude)] [index]

(33) Quaternary structure

(a) Two or more polypeptide chains can interact together to constitute a protein’s quaternary structure

(b) See Figure 5.23, The quaternary structure of proteins

(c) Notice that when polypeptides interact they tend to retain much of their individual tertiary structures such that interactions between subunits are often superficial (i.e., occurring between surfaces of folded polypeptides, rather than involving a profound mixing together of peptides with adjacent interiors)

(d) See Figure 5.24, Review: the four levels of protein structure

(e) [quaternary structure (Google Search)] [index]

(34) Protein subunit

(a) Contrasting with the definition of subunit above, the subunit of a protein is a polypeptide chain that closely interacts with another (or more) polypeptides to form the quaternary structure of a multi-subunit protein

(b) [protein subunit (Google Search)] [index]

(35) Denaturation

(a) Given the right conditions, a protein will properly fold starting the moment it is beginning to be made

(b) Changing those conditions either during or after protein folding can correspondingly lead to an unfolding of the protein

(d) Denaturation typically results in a loss of protein function

(e) Extremes in pH, salt concentrations, temperature (especially high), and various chemicals (such as organic solvents and reducing agents) can denature proteins

(f) [denaturation (Google Search)] [index]

(36) Protein folding

(a) A few relatively simple proteins are capable of refolding properly following denaturation

(b) See Figure 5.25, Denaturation and renaturation of a protein

(c) This implies that at least in some cases all of the information necessary to specify protein conformation may be found in the protein’s primary structure

(d) This is not generally the case for more-complex (e.g., longer) proteins; as complexity increases, the temporal order of folding steps increase in importance

(e) Since denatured proteins typically do not initiate refolding in the same order as a just-synthesized (more-complex) protein, successful renaturation typically does not occur

(f) (“Biochemists now know the amino acid sequences of more than 100,000 proteins and the three-dimensional shapes of about 10,000. One would think that by correlating the primary structures of many proteins with their conformations, it would be possible to discover the rules of protein folding, especially with the help of computers. Unfortunately, the protein-folding problem is not that simple. Most proteins probably go through several intermediate states on their way to a stable conformation, and looking at the ‘mature’ conformation does not reveal the stages of folding that are required to achieve that form. However, biochemists have developed methods for tracking a protein through its intermediate stages of folding. Researchers have also discovered chaparone proteins, molecules that function as temporary braces in assisting the folding of other proteins. These breakthroughs will accelerate our understanding of protein folding.” p. 76, Campbell et al., 1999)

(g) [protein folding (Google Search)] [deciphering the messages of life’s assembly (article on protein folding) (BIOL 121: Human Biology Web Site)] [index]

(37) Chaperone proteins

(a) Organisms also possess proteins that assist the folding proteins (during and following polypeptide synthesis)

(b) Chaparone-protein-mediated assistance involves a stabilizing of unstable intermediate structures

(d) See Figure 5.26, A chaperonin in action

(e) [chaperone protein (Google Search)] [index]

NUCLEIC ACIDS

(38) Nucleic acids

(a) Nucleic acids include deoxyribonucleic acid and ribonucleic acid

(b) Nucleic acids are employed in cells as both polymers and as monomers

(d) [nucleic acid (Google Search)] [structure of DNA animated gif (John Kyrk)] [index]

(39) Nucleotides

(a) Nucleic acid monomers are called nucleotides

(b) Nucleotides consist of three parts: a sugar (deoxyribose in DNA, ribose in RNA), a phosphate group attached to the sugar, and a nitrogenous base , also attached to the sugar

(c) See Figure 5.29a, The components of nucleic acids

(d) This is the ribonucleic acid known as adenosine monophosphate (AMP)—note how the individual carbon atoms are numbered:

(e)

(f) Note the carbon that the phosphate group is attached to; this carbon is called the 5’ (five-prime) carbon

(g) Note the carbon the nitrogenous base is attached to (in this case adenine); this carbon is called the 1’ (one-prime) carbon

(h) Note that in ribose the 2’ carbon is has a hydroxyl group attached to it whereas in deoxyribose the 2’ carbon is bound instead by two hydrogens

(i) [nucleotide (Google Search)] [index]

(40) Ribonucleic acid (RNA)

(a) Two distinct types of nucleic acids are found in cells, ribonucleic acid (or RNA) and deoxyribonucleic acid (or DNA)

(b) Ribonucleic acid is distinct in that its backbone sugar is ribose rather than deoxyribose

(d) Finally, RNA is employed for different functions in the cell than DNA (though this won't make too much sense to you at this point, RNA serves roles particularly in the conversion of genotype information to phenotype information)

(e) [ribonucleic acid, RNA (Google Search)] [the RNA world (IMB Jena)] [index]

(41) Deoxyribonucleic acid (DNA)

(a) The backbone sugar of deoxyribonucleic acid, or DNA, called deoxyribose, possesses one less hydroxyl group than the backbone sugar of RNA, called ribose (this hydroxyl group is missing in deoxyribose—hence, by the way, the name—from the 2' carbon)

(b) DNA is the molecule of chromosomes and genotype in most organisms

(42) Central dogma of molecular genetics, quickie lesson

(a) See Figure 5.28, DNAàRNAàprotein: a diagrammatic overview of information flow in a cell

(b) Note how information flows from DNA to RNA to ribosomes which, in turn, synthesize polypeptides

(43) Phosphodiester linkages

(a) The nucleic acid polymer backbone consists of alternating phosphate groups and the 5’, 4’, and 3’ carbons of deoxyribose (or ribose in the case of RNA) (we will consider this latter idea more explicitly in chapter 16, e.g., Figure 16.12)

(b) That is, in the nucleic acid polymer backbone the phosphate group of an adjacent nucleotide is bound, via dehydration synthesis, to the 3’ carbon

(d) See figure 5.27b, The structure of nucleotides and polynucleotides

(e) [phosphodiester linkage (Google Search)] [index]

(44) Nitrogenous bases

(a) The backbone of DNA (or RNA) is boringly consistent

(b) The structure of DNA (or RNA) polymers varies instead in the structure of the attached nitrogenous bases

(d) See figure 5.29a, The components of nucleic acids

(e) Note that the carbons (etc.) of the nitrogenous bases are given unprimed numbers and the carbons of the sugar are given primed numbers; this serves to distinguish the numbering systems

(f) The types of nitrogenous bases are divided into two structures: purines and pyrimidines

(g) [nitrogenous base (Google Search)] [index]

(45) Purines (adenine, guanine)

(a) The purines are double-ringed structures

(b) Two types of purines are incorporated into DNA

(c) See figure 5.29a, The components of nucleic acids

(d) These differ in terms of functional groups added to the basic purine structure

(e) These types are Adenine and Guanine

(f) These are abbreviated A and G, respectively

(g) [purine, adenine, guanine (Google Search)] [index]

(46) Pyrimidines (cytosine, thymine)

(a) The pyrimidines are single-ringed structures

(b) Two types of pyrimidines are incorporated into DNA

(c) See figure 5.29a, The components of nucleic acids

(d) These differ in terms of functional groups added to the basic pyrimidine structure

(e) These types are Thymine and Cytosine

(f) These are abbreviated T and C, respectively

(g) [pyrimidine, cytosine, thymine (Google Search)] [index]

(47) Double helix

(a) Under normal physiological conditions DNA polymers are typically arranged into molecular pairs

(b) These pairs twist around each other with their sugar-phosphate backbones sticking out

(c) Together these twisted-together DNA polymers are referred to as a double helix (don’t confuse double helix with alpha helix)

(d) See Figure 5.30, The DNA double helix and its replication

(e) The DNA polymer molecules are arranged anti-parallelly when twisted together; i.e., the backbones have polarity (with 3’ and 5’ ends) and in a double helix the 3’ end of one strand is found at the same end as the 5’ end of the other strand (we will consider this latter idea more explicitly in chapter 16, e.g., Figure 16.12)

(f) [double helix (Google Search)] [index]

(48) Base pairing

(a) A double helix is held together by hydrogen bonds that form between nitrogenous bases

(b) Pair-wise hydrogen bonding typically occurs only two ways

(d) Thymine to Adenine (T-A)

(e) See Figure 5.30, The DNA double helix and its replication

(f) Note that in both cases it is a pyrimidine pairing with a purine

(g) C-A and T-G don’t hydrogen bond together well, G-A do not fit together within a double helix, and C-T together are too small to span the double helix to hydrogen bond

(h) [base pairing (Google Search)] [G-C base pairing (space-filling model) (RasMol)] [index]

(49) Strand complementarity

(a) Because of the limited base-pairing possibilities, one DNA molecule within a double helix will precisely designate what the other strand's sequence of nucleic acids must be

(b) This is not to say that the two molecules have identical sequences

(d) In other words, a sequence of ATCGCATGG will hydrogen bond to a sequence of TAGCGTACC on the complementary (other) strand within the double helix

(e) See Figure 5.30, The DNA double helix and its replication

(f) [strand complementarity (Google Search)] [index]

VOCABULARY

(50) Vocabulary [index]

(a) Adenine

(b) Aldose

(d) Amino acids

(e) Amylopectin

(f) Amylose

(g) Base pairing