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

 

 

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Vocabulary words are found below

 

 

(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."

(c)                    [structure and function of macromolecules (Google Search)] [index]

(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) (see also polymer, monomer, and subunit)

(a)                    Many macromolecules consist of polymers

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

(c)                    Monomers (a.k.a., subunits) are the 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) (see also 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, 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 (see also hydrolysis)

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

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

(c)                    Hydrolysis acts to convert polymers to monomers

(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 (see also carbohydrate)

(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) (see also monosaccharide, aldose, ketose)

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

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

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

(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)

(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)

(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)

(i)                      [monosaccharide, aldose, ketose (Google Search)] [index]

(7) Ring form (see also ring form)

(a)                    Most common monosaccharides form rings in aqueous solutions

(b)                   See Figure, 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 disaccharides

(f)                    

(8) Glucose (hexose) (see also glucose and 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)

(c)                    Glucose is an aldose

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

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

(f)                     See Figure, 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) (see also disaccharide, glycosidic linkage, maltose, lactose, and 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 beta-galactosidase, an type of enzyme)

(iii)                 Sucrose = glucose + fructose (glucose + fruit sugar = "plant sugar")

(e)                    See Figure, Examples of disaccharides

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

(10) Sugars (see also sugar)

(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 (see also polysaccharide)

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

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

(c)                    Polysaccharides typically serve as

(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) (see also starch, amylose, amylopectin, and glycogen)

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

(b)                    Starch serves as a glucose storage molecule

(c)                    Glucose can be removed from starch by hydrolysis as it is needed

(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)

(f)                     See Figure, 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, 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 (see also 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, 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 interconvertible once glucose has been incorporated into a polysaccharide such as starch or cellulose

(d)                   See Figure, Starch and cellulose structures compared

(e)                    See Figure, 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 glucose 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)

(c)                    [digesting cellulose (Google Search)] [index]

(15) Chitin (see also 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)                    [chitin (Google Search)] [index]

 

LIPIDS

 

(16) Lipids (see also lipid)

(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

(c)                    Lipids posses numerous C-H bonds (i.e., they are very hydrocarbon-like)

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

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

(17) Fats (triglyceride, triacylglycerol) (see also fat and triglyceride)

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

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

(c)                    Triacylglycerol and Triglyceride are other names for fat

(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) (see also fatty acid, saturated fatty acid, and 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

(c)                    Unsaturated fatty acid have one or more C=C double bonds

(d)                   See Figure, 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 hydrogenation 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 (see also oil)

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

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

(20) Phospholipid (see also 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, The structure of a phospholipid

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

(e)                    See Figure, 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 (see also steroid)

(a)                    All steroids possess a common ring structure

(b)                    These ring structures vary by attached functional groups

(c)                    See Figure, 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 (see also protein)

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

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

(c)                    An extremely large number of protein types exist

(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 (R group) (see also amino acid and R group)

(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, 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, polypeptide backbone) (see also peptide bond, polypeptide, polypeptide backbone)

(a)                    See Figure, Making a polypeptide chain

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

(c)                    "Attached to the repetitive backbone are different kinds of appendages, the side chains of the amino acids."

(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)]

(25) Conformation = shape --> function (see also conformation)

(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

(c)                    The interior of proteins is held together by R-group-to-R-group and backbone-to-backbone interactions

(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 (see also protein 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, 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 (see also protein 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, The secondary structure of a protein

(d)                   Note how the bonds within the polypeptide backbone, in figure, 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)] [index]

(29) Alpha helix (see also 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, The secondary structure of a protein

(c)                    Don't confuse alpha helix with double helix

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

(30) Pleated sheet (see also beta pleated sheet)

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

(b)                   See Figure, 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 (see also protein 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

(c)                    Possible interactions between R groups include:

(i)                     hydrophobic interactions (hydrophobic exclusion)

(ii)                   hydrogen bonds

(iii)                 ionic bonds (salt bridges)

(iv)                 disulfide bonds (bridges)

(d)                   See Figure, 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 (see also disulfide bridgehttp://www.biologyaspoetry.com/terms/disulfide_bridge.)

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

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

(c)                    Removing the H's the sulfurs can bond together (-SH + HS- gives -S-S-)

(d)                   See Figure, 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 (see also protein quaternary structure)

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

(b)                   See Figure, 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, 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 (see also 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

(c)                    Such unfoldings are called denaturation

(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 (see also protein folding)

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

(b)                   See Figure, 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 chaperone 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)                    Chaperone-protein-mediated assistance involves a stabilizing of unstable intermediate structures

(c)                    Chaperone proteins are especially important for successful protein folding at higher temperatures

(d)                   See Figure, A chaperonin in action

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

 

NUCLEIC ACIDS

 

(38) Nucleic acids (see also nucleic acid)

(a)                    Nucleic acids include deoxyribonucleic acid and ribonucleic acid

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

(c)                    Polymers of nucleic acids are the stuff of genes

(d)                   [nucleic acid (Google Search)] [index]

(39) Nucleotides (see also nucleotide)

(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, 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) (see also 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

(c)                    Ribonucleic acid additional employs a different nitrogenous base (uracil rather and thymine) than DNA

(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) (see also 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

(c)                    [deoxyribonucleic acid, DNA (Google Search)] [DNA (Molecules of Life)] [index]

(42) Central dogma of molecular genetics, quickie lesson (see also central dogma)

(a)                    See Figure, DNA --> RNA --> protein: 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

(c)                    [central dogma (Google Search)] [index]

(43) Phosphodiester linkages (see also phosphodiester linkage)

(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

(c)                    This bond between 3' and 5' carbons of adjacent nucleotides is called a phosphodiester linkage

(d)                   See Figure, The structure of nucleotides and polynucleotides

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

(44) Nitrogenous bases (see also nitrogenous base)

(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

(c)                    These nitrogenous bases are attached to the 1' carbon of the sugar

(d)                   See Figure, 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) (see also purine, adenine, and guanine)

(a)                    The purines are double-ringed structures

(b)                    Two types of purines are incorporated into DNA

(c)                    See Figure, 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) (see also pyrimidine, cytosine, and thymine)

(a)                    The pyrimidines are single-ringed structures

(b)                    Two types of pyrimidines are incorporated into DNA

(c)                    See Figure, 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 (see also 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, 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 (see also 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

(c)                    Cytosine to Guanine (C-G)

(d)                   Thymine to Adenine (T-A)

(e)                    See Figure, 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 (see also 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

(c)                    Instead, their sequences are complementary

(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, The DNA double helix and its replication

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

 

VOCABULARY

 

(50) Vocabulary [index]

(a)                    Adenine

(b)                    Aldose

(c)                    Alpha helix

(d)                   Amino acids

(e)                    Amylopectin

(f)                     Amylose

(g)                    Base pairing

(h)                    Carbohydrates

(i)                      Cellulose

(j)                      Central dogma of molecular genetics

(k)                    Chaperone proteins

(l)                      Chitin

(m)                  Condensation reaction

(n)                    Conformation = function

(o)                    Cytosine

(p)                    Dehydration reaction

(q)                    Dehydration synthesis

(r)                     Denaturation

(s)                     Deoxyribonucleic acid

(t)                     Digesting cellulose

(u)                    Disaccharide

(v)                    Disulfide bridges

(w)                  DNA

(x)                    Double helix

(y)                    Fats

(z)                    Fatty acid

(aa)                 Four levels of protein structure

(bb)                Glucose

(cc)                 Glycogen

(dd)               Glycosidic linkage

(ee)                 Guanine

(ff)                  Hexose

(gg)                Hydrolysis

(hh)                Ketose

(ii)                    Lactose

(jj)                    Lipids

(kk)                Maltose

(ll)                    Monomer

(mm)            Monosaccharides

(nn)                Nitrogenous bases

(oo)                Nucleic acids

(pp)                Nucleotides

(qq)                Oil

(rr)                   Peptide bond

(ss)                  Phosphodiester linkages

(tt)                   Phospholipid

(uu)                Pleated sheet

(vv)                Polymer

(ww)            Polymerization

(xx)                Polypeptide

(yy)                Polypeptide backbone

(zz)                 Polysaccharide

(aaa)             Primary structure

(bbb)            Protein folding

(ccc)             Protein subunit

(ddd)          Proteins, introduction

(eee)             Purines

(fff)               Pyrimidines

(ggg)            Quaternary structure

(hhh)            R group

(iii)                  Ribonucleic acid

(jjj)                  Ring form

(kkk)            RNA

(lll)                  Saturated fatty acid

(mmm)      Secondary structure

(nnn)            Starch

(ooo)            Steroids

(ppp)            Strand complementarity

(qqq)            Subunit

(rrr)                Sucrose

(sss)               Sugars

(ttt)                Tertiary structure

(uuu)            Thymine

(vvv)            Triacylglycerol

(www)      Triglyceride

(xxx)            Unsaturated fatty acid

(51) Practice Questions [index]

(a)                    Which is correct:

(i)                     glucose + glucose + water ---> maltose + energy

(ii)                   glucose + fructose + energy ---> maltose + water

(iii)                 glucose + maltose + water + energy ---> sucrose

(iv)                 glucose + galactose + water ---> lactose + energy

(v)                   glucose + fructose + energy ---> sucrose + water

(vi)                 fructose + glucose + energy ---> galactose + water

(b)                    Draw the linear ("two-dimensional") forms of two non-identical sugars that are both aldoses and both trioses.

(c)                    Name two carbohydrate polymers that play predominantly structural roles in various organisms.

(d)                   Name seven categories or types of lipids. Duplicate names for the same substances are acceptable. Don't differentiate categories or types in terms of lipid sources (e.g., no animal, plant, or brand names). (this was a bonus question)

(e)                    Distinguish secondary structure from tertiary structure in terms of the aspects (i.e., structure or portion) of the polypeptide which interact to hold secondary structures together or tertiary structures together. Note, I am not looking for specific kinds of bonds but instead what general parts of the polypeptide molecule are doing the bonding.

(f)                     What is the name of the amino acid that is involved in the formation of disulfide bridges?

(g)                    Draw and label the deoxyribonucleotide (i.e., DNA nucleotide) which contains the nitrogenous base, adenine. [Full credit for structures containing at least 15 correct bonds, atoms, or labels. Three incorrect bonds, atoms, or labels will be allowed. The fourth or more will serve to nullify one correct bond, atom, or label each (i.e., 20 correct entries but with eight mistakes is still worth full credit). There are a lot of possible bonds, atoms, or labels so this is not an impossible question, even if you have only a vague idea of what the correct structure might be. In fact, if you are sure of the first 15 bonds, atoms, or labels you draw, you can just stop at that point for full credit (assuming you don't inadvertently make an error, of course). One point extra credit (up to four) for each additional 10 correct bonds, atoms, or labels, with the same caveat about the cost of errors applying.]

(h)                    Other than that they probably do not correctly hydrogen bond with each other, why is it that purine to purine nitrogenous base pairing is so unlikely within a DNA double helix?

(i)                      Matching: In a deoxyribonucleotide, what is attached (e.g., functional group) to each of the below. Choose from: (a) hydrogen, (b) hydroxyl (-OH), (c) an oxygen bridge (-O-C), (d) phosphate, (e) nitrogenous base (answer hydrogen only if nothing else is attached; carbon is not an acceptable answer in any case):

(i)                     1' carbon: __________

(ii)                   2' carbon: __________

(iii)                 3' carbon: __________

(iv)                 4' carbon: __________

(v)                   5' carbon: __________

(j)                      Describe (i.e., don't just name) the chemical reaction involved in converting two typical biological monomers into a two "residues" of a polymer.

(k)                    Glyceraldehyde has the following molecular formula:

 

    H   H   H

    |   |   |

H - C - C - C = O

    |   |  

    O   O

    |   |

    H   H

 

What general class of biomolecules does this compound represent?

(l)                      What general class of biomolecules is a "residue" of the following compound a small but very important component of? (that is, what compounds are made, at least in part, from the following molecule)

 

    H   H   H

    |   |   |

H - C - C - C - H

    |   |   |

    O   O   O

    |   |   |

    H   H   H

 

(m)                  The following structure: C -- S -- S -- C is a component of proteins at what level of structure? (note that not all bonds to C are shown)

(n)                    In terms of formula weight, which is bigger, a purine or a pyrimidine or water?

(o)                    Which liberates more energy, the hydrolysis of starch or the polymerization of DNA?

(p)                    A name for a linear polymer consisting of glucose monomers (residues) connected by beta (b) 1-4 linkages.

(q)                    A name for an energy storage molecule that "hates" water, is a solid at room temperature, and consists, in part, of fatty acid residues.

(r)                     What process are chaperone proteins involved in?

(s)                     Phosphodiester linkages form between carbons number _____ and _____ of ribose in the polymerization of RNA.

(t)                     Polymers consist of __________ (a generic term) residues linked by dehydration synthesis reactions.

(u)                    Draw the two trioses labeling the aldose and the ketose appropriately.

(v)                    Name a hydrophobic molecule that is found in membranes, is not a polymer, and contains ring structures.

(w)                  Show the reaction which generates a peptide bond, showing all relevant chemical players (name the R groups R' and R'').

(x)                    What specific kind of biomolecules are genes made of?

(y)                    What macromolecule possesses a -- phosphate -- 5' -- 4' -- 3' -- phosphate -- backbone?

(z)                    Which reaction represents dehydration synthesis:

(i)                     A-OH + HO-B + H2O energy + A-O-B

(ii)                   A-O-B A-OH + HO-B + H2O + energy

(iii)                 A-OH + HO-B + energy H2O + A-O-B

(iv)                 A-O-B + H2O + energy A-OH + HO-B

(v)                   A-OH + HO-B A-O-B + H2O + energy

(aa)                 Draw the linear form of a six-carbon aldose sugar. Don't worry about making sure that the spatial arrangement around the chiral carbons is correct (i.e., I don't care if you draw glucose or galactose or whatever so long as draw a reasonable structure that is both a hexose and an aldose; hint: don't forget to check your answer using your knowledge of how many bonds you would expect to find around each carbon as well as your knowledge of the standard molecular formula of a monosaccharide)

(bb)                What type of bond connects two monosaccharides to form a disaccharide?

(i)                     Disaccharide bond

(ii)                   Ester linkage

(iii)                 Glycosidic linkage

(iv)                 Peptide bond

(v)                   Phosphodiester linkage

(cc)                 What is the difference between amylose and amylopectin?

(dd)               What is an oil?

(ee)                 How do phospholipids differ from triacylglycerols? Give two ways that/properties by which these molecules differ.

(ff)                  Pleated sheets are often found in the __________ interiors of proteins.

(gg)                What type of lipid is this molecule? (scan of cholesterol)

(hh)                Which is larger (i.e., has a greater molecular weight), cytosine, adenine, carbon dioxide, or water?

(ii)                    How many types of amino acids serve as the monomers that make up most naturally occurring proteins?

(jj)                    What is the surface chemistry of a protein determined by? (note: neither amino acids nor functional groups are sufficient answers)

(kk)                What nucleic acid makes up the chromosomes of most organisms?

(ll)                    What aspect of protein structure is controlled by genes?

(mm)            What is the functional group associated with cysteine R groups that allows these amino acids to significantly add to the stability of a protein's structure by covalently binding together different portions of the polypeptide chain?

(i)                     Amino group

(ii)                   Carbonyl group

(iii)                 Carboxyl group

(iv)                 Hydroxyl group

(v)                   Sulfhydryl group

(nn)                What is the role of chaperone proteins in macromolecular formation?

(oo)                What kind of intermolecular interactions bind a double helix together?

(pp)                The polymerization of macromolecules (e.g., proteins, DNA) occurs via __________ reactions. ("polymerization" or "-izing" is not the answer)

(qq)                Which is not a polymer in the same sense as the others?

(i)                     Carbohydrates

(ii)                   Lipids

(iii)                 Nucleic acids

(iv)                 Proteins

(rr)                   A monosaccharide with a carbonyl group found on the second carbon is called a(n) __________.

(ss)                  Carbohydrate monomers are called __________.

(tt)                   What is the most common hexose?

(uu)                Which of the following molecules does not contain any glycosidic linkages?

(i)                     Amylopectin

(ii)                   Amylose

(iii)                 Glucose

(iv)                 Maltose

(v)                   Sucrose

(vv)                Glucose may be removed from starch via a __________ reaction.

(ww)            Which two carbon atoms are involved in the bonds that form amylose, via condensation reactions, from glucose?

(i)                     1

(ii)                   2

(iii)                 3

(iv)                 4

(v)                   5

(vi)                 6

(xx)                What large organic compound do termites and cows digest (with the help of symbiotic microorganisms living within their digestive tracts), but which, for the most part, we cannot digest?

(yy)                Chitin is found in __________. [kind(s) of organism(s)]

(zz)                 In a triacylglycerol, carbon is directly bound to which other element much more often than, for example, in a carbohydrate or a nucleic acid?

(aaa)             The number of carbon-to-carbon double bonds controls the melting points of which important biological molecules?

(i)                     Deoxyribonucleic acid

(ii)                   Disaccharides

(iii)                 Fats

(iv)                 Monosaccharides

(v)                   Polypeptides

(bbb)            Conformation and specific placement of functional groups controls the chemistry and function particularly of what kind of macromolecules?

(ccc)             Ring structures, closed solely by carbon-to-carbon bonds, are most prominently present in what major type of biologically relevant organic molecule. Be precise in your answer (e.g., "protein", for example, would not be a sufficiently specific answer).

(ddd)          A long, linear (and denatured) chain consisting of many amino acids linked by peptide bonds is called a __________ ("protein" is not correct answer).

(eee)             The surface chemistry of a protein is determined by the chemistry of exposed amino-acid __________ groups. ("functional" not answer)

(fff)               Define (a) primary structure, (b) secondary structure, (c) tertiary structure, (d) quaternary structure.

(ggg)            Pleated sheets of protein are most often found where in a protein?

(hhh)            Hydrophobic interactions, hydrogen bonds, ionic bonds, and disulfide bridges are all manifestations of a protein's __________ structure.

(i)                     Primary

(ii)                   Secondary

(iii)                 Tertiary

(iv)                 Quaternary

(iii)                  Describe the covalent bonds that are capable of locking different portions, often distant in the primary structure, of a polypeptide together (i.e., within the interior of a protein).

(jjj)                  Phosphodiester linkages are found in which type of biomolecule?

(i)                     Carbohydrates

(ii)                   Lipids

(iii)                 Nucleic acids

(iv)                 Proteins

(kkk)            What is the name of the sugar that serves as part of the backbone of DNA?

(lll)                  What is the "name" of the carbon that the nitrogenous base is attached to in a nucleic acid?

(mmm)      In a double helix, where are the sugar-phosphate backbones located?

(nnn)            A more common name for the specific hydrogen bonding between nitrogenous bases that hold a double helix together is __________, which is named this because it represents an interaction between two complementary types of these nitrogen-containing structures.

(ooo)            Which has a greater molecular weight?

(i)                    A purine

(ii)                 A pyrimidine

(iii)              Three atoms of carbon

(iv)                 A base pair

(v)                   Glycine (the simplest amino acid)

(ppp)            The polymerization of macromolecules (e.g., proteins, DNA) occurs via __________ reactions. ("polymerization" or "-izing" is not the answer)

(qqq)            Which is not a polymer in the same sense as the others?

(i)                     Carbohydrates

(ii)                   Lipids

(iii)                 Nucleic acids

(iv)                 Proteins

(rrr)                A monosaccharide with a carbonyl group found on the second carbon is called a(n) __________.

(sss)               Carbohydrate monomers are called __________.

(ttt)                What is the most common hexose?

(uuu)            Which of the following molecules do not contain glycosidic linkages?

(i)                     Amylopectin

(ii)                   Amylose

(iii)                 Glucose

(iv)                 Maltose

(v)                   Sucrose

(vvv)            Glucose may be removed from starch via a __________ reaction.

(www)      In amylose, which two glucose carbon atoms are involved in the glycosidic linkage (pick 2)?

(i)                     1

(ii)                   2

(iii)                 3

(iv)                 4

(v)                   5

(vi)                 6

(xxx)            What large organic compound do termites and cows digest (with the help of symbiotic microorganisms living within their digestive tracts), but which, for the most part, we cannot digest?

(yyy)            Chitin is found in __________. [kind(s) of organism(s)]

(zzz)             In triglycerol, carbon is directly bound to which other element much more often than in, for example, carbohydrate or nucleic acids?

(aaaa)          The amount of carbon-to-carbon double bonds controls the melting point of what?

(bbbb)        Conformation and specific placement of functional groups controls the chemistry and function particularly of what kind of macromolecules?

(cccc)          Ring structures, closed solely by carbon-to-carbon bonds, are most prominently present in what major type of biologically relevant organic molecule. Be precise in your answer (e.g., "protein", for example, would not be a sufficiently specific answer).

(dddd)      A long, linear (and denatured) chain consisting of many amino acids linked by peptide bonds is called a __________ ("protein" is not correct answer).

(eeee)          The surface chemistry of a protein is determined by the chemistry of exposed __________ groups.

(ffff)            Define two of the following (be sure to indicate which two you are defining):

(i)                     Protein primary structure,

(ii)                   Protein secondary structure

(iii)                 Protein tertiary structure

(iv)                 Protein quaternary structure

(gggg)        Pleated sheets of protein are most often found where in a protein?

(hhhh)        Hydrophobic interactions, hydrogen bonds, ionic bonds, and disulfide bridges are all manifestations of a protein's __________ structure.

(i)                     Primary

(ii)                   Secondary

(iii)                 Tertiary

(iv)                 Quaternary

(iiii)                Describe the covalent bonded structure that is capable of locking different portions of a polypeptide together (i.e., within the interior of a protein).

(jjjj)                Phosphodiester linkages are found in which type of biomolecule?

(i)                     Carbohydrates

(ii)                   Lipids

(iii)                 Nucleic acids

(iv)                 Proteins

(kkkk)        What is the name of the sugar that serves as part of the backbone of DNA?

(llll)                What is the "name" of the carbon that the nitrogenous base is attached to in a nucleic acid?

(mmmm)                        In a double helix, where are the sugar-phosphate backbones located?

(nnnn)        A more common name for the specific hydrogen bonding between nitrogenous bases that holds a double helix together is called __________.

(oooo)        Which has a greater molecular weight?

(i)                    A purine

(ii)                 A pyrimidine

(iii)              Three atoms of carbon

(iv)                 A base pair

(v)                   Glycine (the simplest amino acid)

(pppp)      Bonus: Draw alpha glucose. Show all atoms in reasonably correct orientations.

(qqqq)        Before their polymerization, what is the general term for the monomers that make up polymers such as amylose? (note: "sugar" is actually not correct while "glucose" is too specific)

(rrrr)              Energy is released during hydrolysis. Consequently, the __________ reaction responsible for the synthesis of carbohydrate, protein, or nucleic acid polymers requires energy (note: looking for specific technical phrase or term that is other than "polymerization" or "endergonic")

(ssss)            Why don't disaccharides have the same general molecular formula as monosaccharides, i.e., (CH2O)n? (other than that they might differ in terms of n)

(tttt)              The position of the carbonyl group in monosaccharides divides these sugars into two general types, __________ and __________.

(uuuu)        What is the molecular formula of the pentose called ribose?

(vvvv)        Bonus: What are the substrates and products of the reactions catalyzed by beta-galactosidase? Include all relevant molecules, but note that though you should be capable of knowing which molecules must be present in this reaction, though in fact not all were presented under the heading "Examples of disaccharides" where this enzyme was briefly discussed.

(wwww)                        Which starch consists only of glucose monomers linked via alpha 1-4 linkages?

(xxxx)        Which polysaccharide consists only of glucose monomers linked via beta 1-4 linkages?

(yyyy)        Fats are lipids that consist of long-chain fatty acids bound by __________ to glycerol.

(i)                     Glycosidic linkages

(ii)                   Hydrolysis

(iii)                 Hydrophobic interactions

(iv)                 Peptide bonds

(v)                   None of the above

(zzzz)          Decreasing the __________ of/in a fatty acid results in an increasing of the melting point. (can be short answer or single-word answer)

(aaaaa)      What is an oil?

(bbbbb)    Proteins are made up of __________ different types of amino-acid monomers.

(i)                     10

(ii)                   15

(iii)                 20

(iv)                 25

(v)                   30

(ccccc)      Draw the structure of the amino acid glycine, whose R group is simply an H.

(ddddd) Hydrogen bonding between carbonyl groups and nitrogen-bound hydrogens found on a polypeptide's backbone are the interactions that give rise to a protein's __________ structure.

(i)                     primary

(ii)                   secondary

(iii)                 tertiary

(iv)                 quaternary

(v)                   none of the above

(eeeee)      Hydrophobic interactions help give rise to a protein's __________ structure.

(i)                     primary

(ii)                   secondary

(iii)                 tertiary

(iv)                 quaternary

(v)                   none of the above

(fffff)         A component of certain proteins that locks into place the protein's tertiary structure and consists of two linked sulfur atoms is called a(n) __________.

(ggggg)    Name the three components that combine to form a nucleic acid. You may use moderately general terms to describe these components if you like.

(hhhhh)    The not-base-paired backbones of nucleic acid polymers (e.g., of RNA) are held together by __________.

(i)                     Ester linkages

(ii)                   Glycosidic linkages

(iii)                 Nitrogenous interactions

(iv)                 Peptide bonds

(v)                   Phosphodiester linkages

(iiiii)              The four nitrogenous bases found in DNA are adenine, cytosine, __________, and thymine. (half credit if you can only give me the abbreviation)

(jjjjj)              Explain strand complementarity.

(kkkkk)    Describe how polymers of carbohydrates, proteins, and nucleic acids join, i.e., what is involved, chemically, that results in the binding together of carbohydrate, protein, or nucleic acid monomers into polymers. Though I'm interested specifically in what is going on at the site of bond formation (be comprehensive in your description) and much less interested in the specific chemical structures of the rest of the molecules (monomers) involved in this joining process.

(lllll)              True or False, in hydrolysis reactions, water is a product.

(mmmmm)                  Draw the structural formula of the ketose triose (a three-carbon ketone sugar).

(nnnnn)    Draw the structure of glucose in ring form. Number the carbons and indicate whether you have drawn the alpha or beta anomeric form.

(ooooo)    Of the following, circle the carbohydrates that serve more of a structural role than as sugar storage molecules:

(i)                     Amylopectin

(ii)                   Amylose

(iii)                 Cellulose

(iv)                 Chitin

(v)                   Glycogen

(ppppp)    Fats consist of glycerol bonded via ester linkages (formed upon dehydration synthesis) to three molecules of __________.

(qqqqq)    A saturated fatty acid is saturated with what?

(rrrrr)           A cis double bond found in a fatty acid results fats made up from that fatty acid remaining a liquid under what conditions as compared to fats lacking cis double bonds?

(sssss)         Common lipids possessing multiple ring structures are known as __________. (I'll accept any number of names, so long as they describe at least one example of this class of molecules.)

(ttttt)           An amino acid consists of a carbon bonded to four different (glycine is exception) groups: H, an R group, and what? (i.e., name the two additional functional groups that together make up an amino acid)

(uuuuu)    Of the four levels of protein structure, which consist mostly of well-ordered structures of folded polypeptide held together entirely by hydrogen bonding?

(i)                     Primary

(ii)                   Secondary

(iii)                 Tertiary

(iv)                 Quaternary

(v)                   None of the above

(vvvvv)    Covalent bonds that form between non-adjacent regions of polypeptide are known as __________ bridges.

(wwwww)                  What is protein denaturation?

(xxxxx)    True or False, a nucleotide consists of a phosphate group, a sugar, and a nitrogenous base.

(yyyyy)    Draw the sugar ribose and number the carbons.

(zzzzz)      Phosphodiester linkages are found in which biomolecule?

(i)                     Carbohydrates

(ii)                   Lipids

(iii)                 Nucleic acids

(iv)                 Proteins

(v)                   None of the above

(aaaaaa)   Which of the following are the purines (circle all of the purines). Hint: uracil is a pyrimidine.

(i)                     Adenine

(ii)                   Cytosine

(iii)                 Guanine

(iv)                 Thymine

(52) Practice question answers [index]

(a)                    v, glucose + fructose + energy ---> sucrose + water

(b)                    see below:

 

   HO  HO   

    |   |   

H - C - C - C = 0

    |   |

    H   H

 

   HO   H   

    |   |   

H - C - C - C = 0

    |   |

    H   OH

 

(c)                    cellulose and chitin.

(d)                   fat, fatty acid, palmitic acid, triacylglycerol, triglyceride, saturated fatty acid, unsaturated fatty acid, polyunsaturated acid, stearic acid, oleic acid, oil, hydrogenated vegetable oil, partially hydrogenated vegetable oil, phospholipid, phosphatidylcholine, steroid, cholesterol, steroid hormone, sex hormone, testosterone, estradiol, waxes, etc.

(e)                    The backbone for secondary structure and the R groups for tertiary structure.

(f)                     cysteine.

(g)                    Just drawing a phosphate group bound to the 5' carbon, then bonding the 5' carbon to the 4' and that to the 3' carbon, labeling these, and showing the various H's bound to these carbons is enough to earn full credit.

(h)                    purines are too large to base pair within the geometry of a double helix.

(i)                      (i) e, nitrogenous base, (ii) a, hydrogen, (iii) b, hydroxyl (-OH) group, (iv) c, an oxygen bridge (-O-C), (v) d, phosphate.

(j)                      A-OH + HO-B -->A-O-B + H-OH

(k)                    It is a carbohydrate

(l)                      lipids; the molecule is glycerol; the molecule it is a component (residue) of is fat (i.e., triglyceride)

(m)                  Tertiary, it is a disulfide bridge

(n)                    Purines are the larger

(o)                    hydrolysis of starch, of course, since polymerization does not yield energy

(p)                    cellulose

(q)                    fat

(r)                     protein folding

(s)                     3' and 5'

(t)                     monomer

(u)                    This is the aldose. The ketose is too difficult to draw on a computer.

 

    H   H   H

    |   |   |

H - C - C - C = O

 

    O   O

    |   |

    H   H

 

(v)                    cholesterol, steroid, etc.

(w)                  H - NH - CHR' - CO - OH + H - NH - CHR'' - CO - OH + energy --> H - NH - CHR' - CO - NH - CHR'' - CO - OH + HOH

(x)                    nucleic acids; DNA

(y)                    A nucleic-acid polymer (e.g., DNA or RNA)

(z)                    (iii) A-OH + HO-B + energy --> H2O + A-O-B

(aa)                 For example, glucose:

 

    H   OH  H   OH  OH  OH

    |   |   |   |   |   |

O = C - C - C - C C - C - H

        |   |   |   |   |

        H   OH  H   H   H

 

(bb)                (iii) Glycosidic linkage

(cc)                 Amylopectin is branched; amylose is not

(dd)               An oil is a fat that is liquid at room temperature

(ee)                 A phospholipid has one fatty acid replaced with a phosphate-containing group and consequently a phospholipid, but not a fat, possesses a hydrophilic end in addition the hydrophobic rest of the molecule

(ff)                  Hydrophobic

(gg)                A steroid, cholesterol

(hh)                Adenine (a double-ringed purine)

(ii)                    20

(jj)                    Amino acid R groups

(kk)                DNA

(ll)                    Protein primary structure (amino-acid sequence) is what is controlled by genes

(mm)            (v) sulfhydryl group

(nn)                they aid in protein folding, serving as intramolecular braces

(oo)                hydrogen bonds

(pp)                Condensation or dehydration

(qq)                (ii) Lipids

(rr)                   Ketose, ketone sugar, fructose (but not aldose or simply ketone)

(ss)                  Monosaccharides

(tt)                   Glucose

(uu)                (iii) Glucose

(vv)                Hydrolysis

(ww)            (i) 1 and (ii) 4 (not 6 because amylose contains no branches)

(xx)                Cellulose

(yy)                Fungi (cell walls), insect (and other arthropod) exoskeleton

(zz)                 Hydrogen

(aaa)             (iii) Fats (also phopholipids; "lipids" would be too general an answer)

(bbb)            Proteins

(ccc)             Steroids

(ddd)          Polypeptide

(eee)             R

(fff)               Primary structure are amino acid sequences, secondary structure are the result of interactions of the polypeptide backbone, tertiary structure are the result of interactions of R groups, and quaternary structure is the result of interactions of more than one polypeptide

(ggg)            Within the hydrophobic interior

(hhh)            (iii) Tertiary

(iii)                  -S-S-, disulfide bridge

(jjj)                  (iii) Nucleic acids

(kkk)            Deoxyribose

(lll)                  1'

(mmm)      On the outside; "sticking out"

(nnn)            base pairing

(ooo)            (iv) a base pair

(ppp)            condensation or dehydration

(qqq)            (ii) Lipids

(rrr)                ketose, ketose sugar, fructose (but not aldose or simply ketone)

(sss)               monosaccharides

(ttt)                glucose

(uuu)            (iii) glucose

(vvv)            hydrolysis

(www)      (i) 1 and (d) 4 (not 6 because amylose contains no branches)

(xxx)            cellulose

(yyy)            fungi (cell walls), insect (and other arthropod) exoskeleton

(zzz)             hydrogen

(aaaa)          fats, phospholipids; "lipids" is too general an answer

(bbbb)        proteins

(cccc)          steroids

(dddd)      polypeptide

(eeee)          R

(ffff)            A...

(gggg)        within the hydrophobic interior

(hhhh)        (iii) tertiary

(iiii)                -S-S-, disulfide bridge

(jjjj)                (iii) Nucleic acids

(kkkk)        deoxyribose

(llll)                1'

(mmmm)                        on the outside; "sticking out"

(nnnn)        base pairing

(oooo)        a base pair

(pppp)        [structure of glucose]

(qqqq)        monosaccharides

(rrrr)              dehydration or condensation synthesis or reaction

(ssss)            Because a molecule of water (but not a carbon) is removed upon dehydration synthesis to form the disaccharide from the monosaccharide

(tttt)              Aldoses and ketoses

(uuuu)        (CH2O)5

(vvvv)        Lactose + H2O --> Glucose + Galactose

(wwww)                        Amylose

(xxxx)        Cellulose

(yyyy)        (v) None of the above

(zzzz)          Saturation/number of single C-C bonds

(aaaaa)      An oil is a fat that is a liquid at room temperature

(bbbbb)    (iii) 20

(ccccc)      H2N-CH2-COOH

(ddddd) (ii) Secondary

(eeeee)      Tertiary

(fffff)         Disulfide bridge

(ggggg)    Sugar, nitrogenous base, phosphate

(hhhhh)    (v) Phosphodiester linkages

(iiiii)              Guanine (G)

(jjjjj)              Strand complementarity is the idea that the nucleotide sequence of one nucleic acid strand in a double helix can designate the nucleotide sequence of the other strand

(kkkkk)    Monomer-OH + HO-monomer + energy gives you monomer-O-monomer + H2O. Note that the second O need not be included for this to be correct.

(lllll)              False, water is a reactant

(mmmmm)                  Three carbons covalently bonded in a linear chain, the middle carbon is double-bonded to an oxygen, the two end carbons are each bonded to both a hydrogen and a hydroxyl group

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

(ooooo)    (iii) Cellulose and (iv) Chitin

(ppppp)    Fatty acids

(qqqqq)    Hydrogens

(rrrrr)           Lower temperature

(sssss)         Steroids, cholesterol, etc.

(ttttt)           An amino group and a carboxyl group

(uuuuu)    Secondary

(vvvvv)    Disulfide

(wwwww)                  The loss of a proteins conformation (shape) resulting in loss of function

(xxxxx)    True

(yyyyy)   

(zzzzz)      (iii) Nucleic acids

(aaaaaa)   (i) Adenine, (iii) Guanine

 

 

Chapter 5, Bio 113 questions:

 

(#) Draw a-D-Glucose and number all carbons.

 

A: Hexose, six-member ring with one oxygen, if beta form then starting on right of the oxygen and working around in the clockwise direction, the hydroxyl groups go up (carbon #1) then down (carbon #2) then up (carbon #3) then down (carbon #4) then no hydroxyl group (carbon #5--this hydroxyl group was lost when the ring formed) but a sixth carbon above the ring to which a hydroxyl group is attached. Remember, (CH2O)6 and that all carbon atoms must have four bonds around them (all not mentioned bonds are to hydrogen). Finally, this is not the beta form that you should be drawing so instead the hydroxyl group attached to the number 1 carbon should be pointing down.

 

(#) What general term do we use to describe the building blocks of polymers?

 

A: Monomers

 

(#) Which is the odd term out?

(i)                       Condensation reaction

(ii)                     Dehydration reaction

(iii)                    Dehydration synthesis

(iv)                   Hydrolysis

(v)                     Polymerization

 

A: (iv) Hydrolysis

 

(#) True or False, linear monosaccharides contain a carbonyl group as well as a number of hydroxyl groups.

 

A: True

 

(#) How many glycosidic linkages are found in the sugar maltose?

(i)                       zero

(ii)                     one

(iii)                    two

(iv)                   three

(v)                     four

 

A: (ii) one

 

(#) What molecule is linked together, at the very least, by 1-4 linkages?

 

A: Starch; amylose; amylopectin; glycogen; etc. even cellulose and chitin are correct answers

 

(#) What is chitin?

 

A: Chitin is a carbohydrate polymer (polysaccharide) found in the cell walls of fungi and the exoskeletons of arthropods.

 

Chapter 5b, exam questions:

 

(#) Of the four categories of organic molecules found within most bodies/cells, which typically contains the greatest proportion of C-H bonds?

(i)                       Carbohydrates

(ii)                     Lipids

(iii)                    Nucleic acids

(iv)                   Proteins

(v)                     All are similar in terms of number of C-H bonds

 

A: (ii) Lipids

 

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

 

A: False, Fats display less hydration, not more.

 

(#) Draw a 12-carbon saturated fatty acid, explicitly showing all bonds and atoms.

 

A: This should be a linear hydrocarbon chain that is 11 carbon-atoms long with a carboxylic acid group attached to one end.

 

(#) What does natural unsaturation introduce into fats?

 

A: kinks in fatty-acid chains, lower melting point, greater low-temperature fluidity, double bonds etc.

 

(#) Give an example of a substance that is simultaneously hydrophilic and hydrophobic.

 

A: fatty acids, phospholipids, cholesterol, soap, detergents, even globular proteins are a possible answer.

 

Chapter 5c, exam questions:

 

(#) Chaperone proteins are associated with __________.

(i)                       Attaching one cell to another

(ii)                     Digestion of lipids

(iii)                    Lipid metabolism

(iv)                   Membrane formation

(v)                     Protein folding

 

A: Protein folding

 

(#) What is implied by the observation that at least some proteins are capable of refolding properly following denaturation?

 

A: It means that the primary structure of these proteins supplies sufficient information to effect proper protein folding: primary structure dictates secondary, tertiary, and even quaternary structures.

 

(#) What is the technical term we use to describe what happens to a protein after exposure to excess salt, pH, or temperatures?

 

A: denaturation

 

(#) In proteins, sulfhydryl groups can bind together forming bridges that represent a portion of a protein's _________.

(i)                       Primary structure

(ii)                     Secondary structure

(iii)                    Tertiary structure

(iv)                   Quaternary structure

(v)                     Proteins don't have sulfhydryl groups

 

A: (iii) Tertiary structure, since these are interactions between R groups

 

(bonus) Draw the amino acid Alanine in fully ionized form. Alanine's R group is a methyl group: -CH3. Please be sure to indicate all atoms and charges. (Note, for whatever it is worth, "Alanine" is labeled as "Aladine" in one of the PowerPoint figures that I use.)

 

A:

    H

    |

+3HN-C-C=O

    | |

  3HC O-

 

(#) The chemistry of __________ distinguishes amino acids and their properties.

 

A: R groups.

 

Chapter 5c, exam questions:

 

(#) Number the carbons:

 


 

 

A: Starting from the below "adenine" and going clockwise they should read 1', 2', 3', 4', and 5'.

 

(#) In the above figure, what is the name of the sugar molecule?

 

A: Ribose

 

(#) A phosphodiester linkage binds together which two carbons in DNA?

 

A: the 3' and 5' carbons

 

(#) Circle the purine nitrogenous bases (and only the purine nitrogenous bases):

 

 

A: The purines are the two nitrogenous bases found on the left, above the sugars.

 

(#) In base pairing, circle all that are correct:

(i)                       Cytosine to Adenine

(ii)                     Cytosine to Cytosine

(iii)                    Cytosine to Guanine

(iv)                   Cytosine to Thymine

(v)                     Thymine to Adenine

 

A: (iii) Cytosine to Guanine, (v) Thymine to Adenine