Biochemistry Unit 2 Exam
112 flashcards · Other · by John Mark Webb
(7) Sugars (also called saccharides) are compounds containing an aldehyde or ketone group and two or more hydroxyl groups.
(7) Monosaccharides generally contain several chiral carbons and therefore exist in a variety of stereochemical forms, which may be represented on paper as Fischer projections. Epimers are sugars that differ in configuration at only one carbon atom.
(7) Monosaccharides commonly form internal hemiacetals or hemiketals, in which the aldehyde or ketone group joins with a hydroxyl group of the same molecule, creating a cyclic structure; this can be represented as a Haworth perspective formula. The carbon atom originally found in the aldehyde or ketone group (the anomeric carbon) can assume either of two configurations, α and β, which are interconvertible by mutarotation. In the linear form of the monosaccharide, which is in equilibrium with th…
(7) A hydroxyl group of one monosaccharide can add to the anomeric carbon of a second monosaccharide to form an acetal called a glycoside. In this disaccharide, the glycosidic bond protects the anomeric carbon from oxidation, making it a nonreducing sugar.
(7) Oligosaccharides are short polymers of several monosaccharides joined by glycosidic bonds. At one end of the chain, the reducing end, is a monosaccharide unit with its anomeric carbon not involved in a glycosidic bond.
(7) The common nomenclature for disaccharides or oligosaccharides specifies the order of monosaccharide units, the configuration at each anomeric carbon, and the carbon atoms involved in the glycosidic linkage(s).
(7) Polysaccharides (glycans) serve as stored fuel and as structural components of cell walls and extracellular matrix.
(7) The homopolysaccharides starch and glycogen are storage fuels in plant, animal, and bacterial cells. They consist of D-glucose units with (α1→4) linkages, and both contain some branches.
(7) The homopolysaccharides cellulose, chitin, and dextran serve structural roles. Cellulose, composed of (β1→4)-linked D-glucose residues, lends strength and rigidity to plant cell walls. Chitin, a polymer of (β1→4)-linked N-acetylglucosamine, strengthens the exoskeletons of arthropods. Dextran forms an adhesive coat around certain bacteria.
(7) Homopolysaccharides fold in three dimensions. The chair form of the pyranose ring is essentially rigid, so the conformation of the polymers is determined by rotation about the bonds from the rings to the oxygen atom of the glycosidic linkage. Starch and glycogen form helical structures with intrachain hydrogen bonding; cellulose and chitin form long, straight strands that interact with neighboring strands.
(7) Bacterial and algal cell walls are strengthened by heteropolysaccharides— peptidoglycan in bacteria, agar in red algae. The repeating disaccharide in peptidoglycan is GlcNAc(β1→4)Mur2Ac; in agar, it is D-Gal(β1→4)3,6- anhydro-L-Gal.
(7) Glycosaminoglycans are extracellular heteropolysaccharides in which one of the two monosaccharide units is a uronic acid (keratan sulfate is an exception) and the other is an N-acetylated amino sugar. Sulfate esters on some of the hydroxyl groups and on the amino group of some glucosamine residues in heparin and heparan sulfate give these polymers a high density of negative charge, forcing them to assume extended conformations. These polymers (hyaluronan, chondroitin sulfate, dermatan sulfa…
(7) Proteoglycans are glycoconjugates in which one or more large glycans, called sulfated glycosaminoglycans (heparan sulfate, chondroitin sulfate, dermatan sulfate, or keratan sulfate), are covalently attached to a core protein. Bound to the outside of the plasma membrane by a transmembrane peptide or a covalently attached lipid, proteoglycans provide points of adhesion, recognition, and information transfer between cells, or between a cell and the extracellular matrix.
(7) Glycoproteins contain oligosaccharides covalently linked to Asn or Ser/Thr residues. The glycans are typically branched and smaller than glycosaminoglycans. Many cell surface or extracellular proteins are glycoproteins, as are most secreted proteins. The covalently attached oligosaccharides influence the folding and stability of the proteins, provide critical information about the targeting of newly synthesized proteins, and allow specific recognition by other proteins.
(7) Glycomics is the determination of the full complement of sugar-containing molecules in a cell or tissue and determination of the function of each such molecule.
(7) Glycolipids and glycosphingolipids in plants and animals and lipopolysaccharides in bacteria are components of the cell envelope, with covalently attached oligosaccharide chains exposed on the cell’s outer surface.
(7) Lectins, proteins with highly specific carbohydrate-binding domains, are commonly found on the outer surface of cells, where they initiate interaction with other cells. In vertebrates, oligosaccharide tags “read” by lectins govern the rate of degradation of certain peptide hormones, circulating proteins, and blood cells.
(7) Bacterial and viral pathogens and some eukaryotic parasites adhere to their animal cell targets through binding of lectins in the pathogens to oligosaccharides on the target cell surface.
(7) X-ray crystallography of lectin-sugar complexes shows the detailed complementarity between the two molecules, which accounts for the strength and specificity of lectin interactions with carbohydrates.
(7) Establishing the complete structure of oligosaccharides and polysaccharides requires determination of the linear sequence, branching positions, the configuration of each monosaccharide unit, and the positions of the glycosidic linkages—a more complex problem than protein and nucleic acid analysis.
(7) The structures of oligosaccharides and polysaccharides are usually determined by a combination of methods: specific enzymatic hydrolysis to determine stereochemistry at the glycosidic bond and to produce smaller fragments for further analysis; methylation to locate glycosidic bonds; and stepwise degradation to determine sequence and configuration of anomeric carbons.
(7) Mass spectrometry and high-resolution NMR spectroscopy, applicable to small samples of carbohydrate, yield essential information about sequence, configuration at anomeric and other carbons, and positions of glycosidic bonds.
(7) Solid-phase synthetic methods yield defined oligosaccharides that are of great value in exploring lectin-oligosaccharide interactions and may prove clinically useful.
(7) Microarrays of pure oligosaccharides are useful in determining the specificity and affinity of lectin binding to specific oligosaccharides.
(8) A nucleotide consists of a nitrogenous base (purine or pyrimidine), a pentose sugar, and one or more phosphate groups. Nucleic acids are polymers of nucleotides, joined together by phosphodiester linkages between the 5′- hydroxyl group of one pentose and the 3′-hydroxyl group of the next.
(8) There are two types of nucleic acid: RNA and DNA. The nucleotides in RNA contain ribose, and the common pyrimidine bases are uracil and cytosine. In DNA, the nucleotides contain 2′-deoxyribose, and the common pyrimidine bases are thymine and cytosine. The primary purines are adenine and guanine in both RNA and DNA.
(8) Many lines of evidence show that DNA bears genetic information. Some of the earliest evidence came from the Avery-MacLeod-McCarty experiment, which showed that DNA isolated from one bacterial strain can enter and transform the cells of another strain, endowing it with some of the inheritable characteristics of the donor. The Hershey-Chase experiment showed that the DNA of a bacterial virus, but not its protein coat, carries the genetic message for replication of the virus in a host cell.
(8) Putting together the available data, Watson and Crick postulated that native DNA consists of two antiparallel chains in a right-handed double-helical arrangement. Complementary base pairs, A=T and G≡C, are formed by hydrogen bonding within the helix. The base pairs are stacked perpendicular to the long axis of the double helix, 3.4 Å apart, with 10.5 base pairs per turn.
(8) DNA can exist in several structural forms. Two variations of the Watson- Crick form, or B-DNA, are A- and Z-DNA. Some sequence-dependent structural variations cause bends in the DNA molecule. DNA strands with appropriate sequences can form hairpin or cruciform structures or triplex or tetraplex DNA.
(8) Messenger RNA transfers genetic information from DNA to ribosomes for protein synthesis. Transfer RNA and ribosomal RNA are also involved in protein synthesis. RNA can be structurally complex; single RNA strands can fold into hairpins, double-stranded regions, or complex loops.
(8) Native DNA undergoes reversible unwinding and separation of strands (melting) on heating or at extremes of pH. DNAs rich in G≡C pairs have higher melting points than DNAs rich in A=T pairs.
(8) DNA is a relatively stable polymer. Spontaneous reactions such as deamination of certain bases, hydrolysis of base-sugar N-glycosyl bonds, radiation-induced formation of pyrimidine dimers, and oxidative damage occur at very low rates, yet are important because of a cell’s very low tolerance for changes in its genetic material.
(8) Oligonucleotides of known sequence can be synthesized rapidly and accurately.
(8) The polymerase chain reaction (PCR) provides a convenient and rapid method for amplifying segments of DNA if the sequences of the ends of the targeted DNA segment are known.
(8) Routine DNA sequencing of genes or short DNA segments is carried out using an automated variation of Sanger dideoxy sequencing.
(8) DNA sequences, including entire genomes, can be efficiently determined in hours or days with a range of methods, including next-gen sequencing.
(8) ATP is the central carrier of chemical energy in cells. The presence of an adenosine moiety in a variety of enzyme cofactors may be related to binding- energy requirements.
(8) Cyclic AMP, formed from ATP in a reaction catalyzed by adenylyl cyclase, is a common second messenger produced in response to hormones and other chemical signals.
(8) ATP and ADP serve as neurotransmitters in a variety of signaling pathways.
(10) Lipids are water-insoluble cellular components, of diverse structure, that can be extracted from tissues by nonpolar solvents.
(10) Almost all fatty acids, the hydrocarbon components of many lipids, have an even number of carbon atoms (usually 12 to 24); they are either saturated or unsaturated, with double bonds almost always in the cis configuration.
(10) Triacylglycerols contain three fatty acid molecules esterified to the three hydroxyl groups of glycerol. Simple triacylglycerols contain only one type of fatty acid; mixed triacylglycerols, two or three types. Triacylglycerols are primarily storage fats; they are present in many foods.
(10) Because trans fatty acids in the diet are an important risk factor for coronary heart disease, their use in prepared and processed foods has become highly regulated.
(10) Waxes are esters of long-chain fatty acids and long-chain alcohols.
(10) The polar lipids, with polar heads and nonpolar tails, are major components of membranes. The most abundant are the glycerophospholipids, which contain fatty acids esterified to two of the hydroxyl groups of glycerol, and a second alcohol, the head group, esterified to the third hydroxyl of glycerol via a phosphodiester bond. Other polar lipids are the sterols.
(10) Glycerophospholipids differ in the structure of their head group; common glycerophospholipids are phosphatidylethanolamine and phosphatidylcholine. The polar heads of the glycerophospholipids are charged at pH near 7.
(10) Chloroplast membranes are rich in galactolipids, composed of a diacylglycerol with one or two linked galactose residues, and sulfolipids, diacylglycerols with a linked sulfonated sugar residue and thus a negatively charged head group.
(10) Some archaea have unique membrane lipids, with long-chain alkyl groups ether-linked to glycerol at each end and with sugar residues and/or phosphate joined to the glycerol to provide a polar or charged head group. These lipids are stable under the harsh conditions in which these archaea live.
(10) The sphingolipids contain sphingosine, a long-chain aliphatic amino alcohol, but no glycerol. Sphingomyelin has, in addition to phosphoric acid and choline, two long hydrocarbon chains, one contributed by a fatty acid and the other by sphingosine. Three other classes of sphingolipids are cerebrosides, globosides, and gangliosides, which contain sugar components.
(10) Sterols have four fused rings and a hydroxyl group. Cholesterol, the major sterol in animals, is both a structural component of membranes and precursor to a wide variety of steroids.
(10) Some types of lipids, although present in relatively small quantities, play critical roles as cofactors or signals.
(10) Phosphatidylinositol bisphosphate is hydrolyzed to yield two intracellular messengers, diacylglycerol and inositol 1,4,5-trisphosphate. Phosphatidylinositol 3,4,5-trisphosphate is a nucleation point for supramolecular protein complexes involved in biological signaling.
(10) Prostaglandins, thromboxanes, leukotrienes, and lipoxins, all of which are eicosanoids derived from arachidonate, are extremely potent hormones.
(10) Steroid hormones, such as the sex hormones, are derived from sterols. They serve as powerful biological signals, altering gene expression in target cells.
(10) Vitamins D, A, E, and K are fat-soluble compounds made up of isoprene units. All play essential roles in the metabolism or physiology of animals. Vitamin D is precursor to a hormone that regulates calcium metabolism. Vitamin A furnishes the visual pigment of the vertebrate eye and is a regulator of gene expression during epithelial cell growth. Vitamin E functions in the protection of membrane lipids from oxidative damage, and vitamin K is essential in the blood-clotting process.
(10) Ubiquinones and plastoquinones, also isoprenoid derivatives, are electron carriers in mitochondria and chloroplasts, respectively.
(10) Dolichols activate and anchor sugars to cellular membranes; the sugar groups are then used in the synthesis of complex carbohydrates, glycolipids, and glycoproteins.
(10) Lipidic conjugated dienes serve as pigments in flowers and fruits and give bird feathers their striking colors.
(10) Polyketides are natural products widely used in medicine.
(10) In the determination of lipid composition, the lipids are first extracted from tissues with organic solvents and separated by thin-layer, gas, or high- performance liquid chromatography.
(10) Phospholipases specific for one of the bonds in a phospholipid can be used to generate simpler compounds for subsequent analysis.
(10) Individual lipids are identified by their chromatographic behavior, their susceptibility to hydrolysis by specific enzymes, or mass spectrometry.
(10) High-resolution mass spectrometry allows the analysis of crude mixtures of lipids without prefractionation—the “shotgun” approach.
(10) Lipidomics combines powerful analytical techniques to determine the full complement of lipids in a cell or tissue (the lipidome) and to assemble annotated databases that allow comparisons between lipids of different cell types and under different conditions.
(11) Biological membranes define cellular boundaries, divide cells into discrete compartments, organize complex reaction sequences, and act in signal reception and energy transformations.
(11) Membranes are composed of lipids and proteins in varying combinations particular to each species, cell type, and organelle. The fluid mosaic model, with a lipid bilayer as the basic structural unit, gives a simplified and general picture of membranes.
(11) Membrane trafficking is the movement of membrane components from the endoplasmic reticulum into and through the Golgi apparatus, where they are targeted to their final destinations by covalent alterations.
(11) Integral membrane proteins are embedded within membranes, their nonpolar amino acid side chains stabilized by contact with the lipid bilayer rather than the surrounding aqueous phase. Peripheral membrane proteins associate with membranes through electrostatic interactions and hydrogen bonding with membrane phospholipids and integral proteins. Amphitropic proteins associate reversibly with membranes in response to biological signals such as phosphorylation of membrane lipids or proteins or…
(11) Many membrane proteins span the lipid bilayer several times, with hydrophobic sequences of about 20 amino acid residues forming transmembrane α helices. Multistranded β barrels are also common in integral proteins in bacterial membranes. Tyr and Trp residues of transmembrane proteins are commonly found at the lipid-water interface.
(11) Some membrane proteins have covalently attached lipids that mediate their interaction with the bilayer.
(11) Lipids in a biological membrane can exist in liquid-ordered or liquid- disordered states; in the latter state, thermal motion of acyl chains makes the interior of the bilayer fluid. Fluidity is affected by temperature, fatty acid composition, and sterol content.
(11) Flip-flop diffusion of lipids between the inner and outer leaflets of a membrane is very slow except when specifically catalyzed by flippases, floppases, or scramblases.
(11) Proteins and lipids can diffuse laterally within the plane of the membrane, but this mobility is limited by interactions of membrane proteins with internal cytoskeletal structures and interactions of lipids with lipid rafts. One class of lipid rafts is enriched for sphingolipids and cholesterol with a subset of membrane proteins that are GPI-linked or attached to several long-chain fatty acyl moieties.
(11) Caveolins are integral membrane proteins that associate with the inner leaflet of the plasma membrane, forcing it to curve inward to form caveolae, which are involved in membrane transport, signaling, and the expansion of plasma membranes.
(11) Specific proteins containing BAR domains cause local membrane curvature and mediate the fusion of two membranes, which accompanies processes such as endocytosis, exocytosis, and viral invasion. Because the inositol phospholipids PIP2 and PIP3 are specifically recognized by BAR proteins, their formation may be the signal for the intracellular processes that require membrane curvature.
(11) SNAREs are membrane proteins that act in the fusion of vesicles with the plasma membrane, in response to a signal.
(11) Integrins, cadherins, and selectins are transmembrane proteins of the plasma membrane that act both to attach cells to each other and to carry messages between the extracellular matrix and the cytoplasm.
(11) Movement of polar compounds and ions across biological membranes requires transporter proteins. Some transporters simply facilitate passive diffusion of a solute across the membrane, from a higher to a lower concentration. Others transport solutes against an electrochemical gradient; this requires a source of metabolic energy.
(11) Carriers, like enzymes, show saturation and stereospecificity for their substrates. Transport via these systems may be passive or active. Primary active transporters are driven by ATP or electron-transfer reactions; secondary active transporters are driven by coupled flow of two solutes, one of which (often H+ or Na+) flows down its electrochemical gradient as the other is pulled up its gradient.
(11) The GLUT transporters, such as GLUT1 of erythrocytes, carry glucose into cells by passive transport. These transporters are uniporters, carrying only one substrate. Symporters permit simultaneous passage of two substances in the same direction; examples are the lactose transporter of E. coli, driven by the energy of a proton gradient (lactose-H+ symport), and the glucose transporter of intestinal epithelial cells, driven by a Na+ gradient (glucose- Na+ symport). Antiporters mediate simulta…
(11) In animal cells, Na+K+ ATPase maintains the differences in cytosolic and extracellular concentrations of Na+ and K+, and the resulting Na+ gradient isused as the energy source for a variety of secondary active transport processes.
(11) The Na+K+ ATPase of the plasma membrane and the Ca2+ transporters of the sarcoplasmic/endoplasmic reticulum (the SERCA pumps) are examples of P-type ATPases; they undergo reversible phosphorylation during their catalytic cycle. F-type ATPase proton pumps (ATP synthases) are central to energy-conserving mechanisms in mitochondria and chloroplasts. V-type ATPases produce gradients of protons across some intracellular membranes, including plant vacuolar membranes.
(11) ABC transporters carry a variety of substrates (including many drugs) out of cells, using ATP as the energy source.
(11) Ionophores are lipid-soluble molecules that bind specific ions and carry them passively across membranes, dissipating the energy of electrochemical ion gradients.
(11) Water moves across membranes through aquaporins. Some aquaporins are regulated; some also transport glycerol or urea.
(11) Ion channels provide hydrophilic pores through which select ions can diffuse, moving down their electrical or chemical concentration gradients; these channels characteristically are unsaturable, have very high flux rates, and are highly specific for one ion. Most are voltage- or ligand-gated. The neuronal Na+ channel is voltage-gated, and the acetylcholine receptor ion channel is gated by acetylcholine, which triggers conformational changes that open and close the transmembrane path.
(13) Living cells constantly perform work. They require energy for maintaining their highly organized structures, synthesizing cellular components, transporting small molecules and ions across membranes, and generating electric currents.
(13) Bioenergetics is the quantitative study of energy relationships and energy conversions in biological systems. Biological energy transformations obey the laws of thermodynamics.
(13) All chemical reactions are influenced by two forces: the tendency to achieve the most stable bonding state (for which enthalpy, H, is a useful expression) and the tendency to achieve the highest degree of randomness, expressed as entropy, S. The net driving force in a reaction is ΔG, the free- energy change, which represents the net effect of these two factors: ΔG = ΔH − TΔS.
(13) The standard transformed free-energy change, ΔG′°, is a physical constant that is characteristic for a given reaction and can be calculated from the equilibrium constant for the reaction: ΔG′° = −RT ln(K'eq).
(13) The actual free-energy change, ΔG, is a variable that depends on ΔG′° and on the concentrations of reactants and products: ΔG = ΔG′° + RT ln ([products]/[reactants]).
(13) When ΔG is large and negative, the reaction tends to go in the forward direction; when ΔG is large and positive, the reaction tends to go in the reverse direction; and when ΔG = 0, the system is at equilibrium.
(13) The free-energy change for a reaction is independent of the pathway by which the reaction occurs. Free-energy changes are additive; the net chemical reaction that results from successive reactions sharing a common intermediate has an overall free-energy change that is the sum of the ΔG values for the individual reactions.
(13) Living systems make use of a large number of chemical reactions that can be classified into five general types.
(13) Carbonyl groups play a special role in reactions that form or cleave C—C bonds. Carbanion intermediates are common and are stabilized by adjacent carbonyl groups or, less often, by imines or certain cofactors.
(13) A redistribution of electrons can produce internal rearrangements, isomerizations, and eliminations. Such reactions include intramolecular oxidation-reduction, change in cis-trans arrangement at a double bond, and transposition of double bonds.
(13) Homolytic cleavage of covalent bonds to generate free radicals occurs in some pathways, such as in certain isomerization, decarboxylation, reductase, and rearrangement reactions.
(13) Phosphoryl transfer reactions are an especially important type of group transfer in cells, required for the activation of molecules for reactions that would otherwise be highly unfavorable.
(13) Oxidation-reduction reactions involve the loss or gain of electrons: one reactant gains electrons and is reduced, while the other loses electrons and is oxidized. Oxidation reactions generally release energy and are important in catabolism.
(13) ATP is the chemical link between catabolism and anabolism. It is the energy currency of the living cell. The exergonic conversion of ATP to ADP and Pi, or to AMP and PPi, is coupled to many endergonic reactions and processes.