Biochemistry Exam 2 Study Guide
Biochemistry Exam 2 Study Guide Bch4053
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This 32 page Study Guide was uploaded by Hannah Hartman on Thursday October 13, 2016. The Study Guide belongs to Bch4053 at Florida State University taught by Dr. Hong Li in Fall 2016. Since its upload, it has received 20 views. For similar materials see General Biochemistry I in Biochemistry at Florida State University.
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Biochemistry Exam 2 Protein Structures: Forces Nonbonding forces influencing protein structures Amino acids of a protein are joined by covalent bonding interactions. o This covalent bond is called a peptide bond The polypeptide is folded in three dimension by nonbonding interactions. Non binding forces are those that go "beyond the covalent bond". It goes beyond the molecule itself. T These interactions can easily be disrupted by extreme pH, temperature, denaturants, reducing reagents. We will discuss the nature of these types of forces: o Hbond interactions (1230 kJ/mol) o Hydrophobic Interactions (<40 kJ/mol) Nonpolar amino acids will help dictate the folding of the amino acid and the conjoining of various proteins. o Electrostatic Interactions (20 kJ/mol) o Van Der Waals Interactions (0.44 kJ/mol) Every pair of atoms feels these interactions! The total interatomic force acting between two atoms is the sum of all the forces they exert on each other. Hydrogen Bonds: Hydrogen bonds describe a favorable interaction between a proton bonded to an electronegative atom and an atom carrying lone pairs of electrons: DH +A = AHA Acceptors (A): carbonyl (like a peptide bond); hydroxyl groups; amine groups; Donors (D): alcohols, any atom with lone pairs of electrons This interaction is very important for maintaining protein backbone interactions. Hydrophobic interactions: Hydrophobic interactions minimizes interactions of nonpolar residues with solvent. Thus nonpolar regions of biological macromolcules are often buried in the molecules interior to exclude them from the aqueous milieu. However nonpolar residues can also be found on the surface of a protein. They may participate proteinprotein interactions. This type of interaction is entropy driven. (entropy is favorable entropy is increasing when the two nonpolar groups are coming together) o There is more entropy due to the interactions with water. The protein residue itself does not become more disordered (in fact it becomes more ordered), it is the release and interactions of water. Electrostatic Interactions: Charged side chains in protein can interact favorably with an opposing charge of another side chain according to Coulomb’s law: F = force, q = charge on the molecule, D = distance between the molecules, r = radius Examples of favorable electrostatic interaction include that between positively charged lysine and negatively charged glutamic acid. Salts have the ability to shield electrostatic interactions. o The ions will act as a competitor for the interactions Examples of electrostatic interactions: intramolecular ionic bonds between charged amino acid resides in a protein (such as glutamic acid/aspartic acid and histidine/arginine/lysine); magnesium ATP. o Note: DNA charges are always negatively charged they like to pair with positive ions such as magnesium, potassium, etc. Van der Waals Interactions van der Waals interaction between two atoms is a result of electron charge distributions of the two atoms. o These are "induceddipole" interactions. o Dipole describes the asymmetry of charge on an atom. For atoms that have permanent dipoles: o Dipoledipole interactions (potential energy ~r ) 3 5 o Dipoleinduced dipole interactions (potential energy ~r ) For atoms that have no permanent dipoles: o Transient charge distribution induces complementary charge distribution 6 (also called dispersion or London dispersion force) (potential energy ~r ) o Repulsion between two atoms when they approach each other due to 12 overlapping of electron clouds (potential energy ~r ) In general, the permanent dipole contribution are much less that the dispersi12 an6 repulsion forces. Thus the van der Waals potential can be expressed as 1/r 1/r . The characteristics of van der Waals potential is shown below: r0 is the sum of van der Waals radii for the two atoms. Van der Waals forces are attractive forces when r> r and repulsive when r< r . 0 0 The force is the derivative of the yellow curve. The force is blue curve. When they are very far apart, the force is negative. When they just past r0, they begin to repel. The distance between the two atoms is called a "van der Waals radii" Van der waals radii of common atoms (nm): o H 0.1 nm o C 0.17 nm o N 0.15 nm o O 0.14 nm o P 0.19 nm o S 0.185 nm o You don’t have to know these numbers, just recognize the trends. Note how size effects the van der waals radii. o The placement of the atoms is not only determined by van der waals reactions. It is the sum of all the interactions! Roles of Amino Acid Sequence in protein structure Weak forces operate both within the protein structure, between proteins and the water solvent; All the information necessary for folding the peptide chain into its "native" structure is contained in the amino acid sequence of the peptide; Certain loci alone the peptide chain act as nuceation points; Folded proteins avoid local energy minimum Chaperones in the cells help protein folding. Denaturation: The loss of structure order in biomolecules is called naturation; The central role of weak forces in biomolecular interactions restricts living systems to a narrow range of physical conditions. Biomolecules are folded, thus functional, only within a narrow range of environmental conditions such as temperature, ionic strength, and relative acidity; o Human proteins are stable generally around 3740 degrees, but if you raise the temperature, it will completely lose the structure. The temperature regulates the kinetic energy of the molecules. Extremes of these conditions disrupt the weak forces essential to maintaining the intricate structure and will lead to loss of their biological functions. o You can lose electrostatic interactions, hydrogen bond interactions, etc. Alzheimer Disease: Alzheimer's disease (AD) is a progressive, neurodegenerative disease characterized by memory loss, language deterioration, impaired visuospatial skills, poor judgment, indifferent attitude, but preserved motor function. AD usually begins after age 65, however, its onset may occur as early as age 40, appearing first as memory decline and, over several years, destroying cognition, personality, and ability to function. Confusion and restlessness may also occur. o The type, severity, sequence, and progression of mental changes vary widely. The early symptoms of AD, which include forgetfulness and loss of concentration, can be missed easily because they resemble natural signs of aging. . The pathogen responsible for AD is misfolded proteins, called laque . The plaque formed in patients brain binds to a receptor in the brain, thus blocking the signals, or currents, that are thought to be involved in learning and memory. o The protein is called betaamyloid peptide and is found in human and animal brain. Plaque is misfolded protein which otherwise have normal function. MORAL OF THE STORY: Alzheimer’s comes from misfolded proteins called plaques. AKA, protein folding and interactions are important! Let’s get down to Business: Protein Structures The Level of Protein Structure: Primary Structure (1º) refers to the amino acid sequences of proteins; Secondary Structure (2º) refers to segments that constitute structural conformities, or regular structures in proteins; Tertiary Structure (3º) refers to the folding of protein chains into a more compact three dimensional shape; Quaternary Structure (4º) refers to organization of subunits (one subunit is a single polypeptide chain) Restriction by Amide Plane Atoms in the peptide bond lie in a plane. Resonance stabilization energy of this planar structure is approximately 88 kJ/mol; Rotation can only occur around the two bonds connected to the Ca atom; Rotation around the Ca and carbonyl bond is called y (psi); o A psi angle is the rotation between the carbonyl carbon and alpha. o Normally phi is first and psi is second. Rotation around the Ca and nitrogen bond is called f (phi). o Phi angle is rotation between C and N Rotation of Amide Planes If (f,y) are known for all residues, the structure for the entire backbone is known. Some (f,y) are more likely than others in a folded protein Positive (f,y) values correspond to clockwise rotation around bonds when viewed from the Ca. Zero is defined when the C=O or NH bond bisects the RCaH angle. o (f,y)=(0,180), two carbonyl oxygens are too close; o (f,y)=(180,0), two amide groups are overlapping; o (f,y)=(0,0), carbonyl oxygen overlaps with amide group Ramachadran Plot: The plot uses f as horizontal Axis y as vertical axis. The , y angle for each residue can be entered on the plot. For folded proteins, their , ) angles cluster in few regions of the plot. The upper left corner arebetasheet value s and middle left are helices values. Lines signifies the number of amino acids per turn of helix (+ means righthanded, lefthanded) Normally left handed turns are in an alpha helix. Cis peptide bonds in proteins general aspects If the amino acids are on opposite side they are considered trans. Most amino acids are in a trans configuration. Occasionally you will see a cis bond. This is if the following residue is a line residue. o Due to its cyclic nature (C alpha attached to the nitrogen), this causes the protein to form a cis structure (an alpha kink) o Biologically, this cis and trans has important consequences to the protein structure. In the cell there are cis/trans flipping enzyme s (isomerases) Classes of Secondary Structure: Terms below define all classes of secondary strctures seen in proteins: o Helix Alphahelix 3(10) helix o Beta sheet Parallel Antiparallel o Betabulge o Beta turn Alpha helix: The alpha helix is a helical structure. All alpha helices in proteins are righthanded; Hbond patterns of the alpha helix: th o Alpha helix: Carbonyl oxygen of the i (I referes to any residue) residue forms Hbond with amide proton of the (i+4) residue (this is 4 amino acids away). So there are n4 Hbonds in a helix of namino acids; this is independent of side chains. o 3 10 ix: carbonyl oxygen of the i residue forms Hbond with amide proton of the (i+3) residue. 3 residues (or 10 atoms) per turn; this is very rare. Most proteins in organisms form alpha helices. o Proline is not found in ahelix except at the beginning of an ahelix; o Helix propensity of an amino acid is a measure of the likelyhood for the amino acid to be in a helix; Glu, Met, Ala, Leu have high propensities; Its not as much s the nature of the amino acid, but the pattern of the amino acid. o Examples of ahelical proteins include akeratin (structural proteins) and collagen (fibrous protein); o Linus Pauling (Nobel Prize in Chemistry, 1954) figured out the structure of keratin helix. Residues per turn: 3.6 Rise per residue: 1.5 Å; Rise per turn: 5.4 Å; (f,y)=~(60º,45º) The dipole moment of C=O increases, and the dipole moment of NH decreases. The dipole moment of the side chain decreases. We are left with a total dipole moment decrease. o Remember dipole measures the asymmetry of the molecule Helical wheel presentation of a helix can show amino acid distribution along its side. o Draw a helical wheel of the sequence “DDRILSWVAELKSE” o If you follow the pattern, the yellow position are on one side of the helical wheel and the black are on the other side. Why is this important? o IWVL are all nonpolar molecules… they form what we call a "hydrophobic strip" that can interact with another alpha helix nearby The Beta Strands: The beta strands form beta sheets in proteins Hbond patterns in beta strands: o Parallel betastrands (0.325 nm between two residues) o Antiparallel betastrands (0.347 nm between two residues) The carbonyl forms a hydrogen bond with the next strand amide group. o If you are parallel, the hydrogen bond is at an angle o If you are antiparallel beta strand, the hydrogen bond is colinear. WHERE ARE THE SIDE CHAINS? The side chains are pointing either up or down (perpendicular) of the sheet) The Beta Sheet: Formed by beta strands. Note that side chains point away from the sheet while main chains lie on the sheet. Sheets are the most extended form. Sheets consist of parallel strands are usually larger that those consist of antiparallel strands. A sheet consists of parallel strands distribute hydrophobic residues on both sides of the sheet while that consist of antiparallel strands distributes hydrophobic residues on one side Combinations of interactions will determine the overall structure and function of the protein. It is not just one or two interactions. The Beta Turn (tight turn, or betabend) Beta turns connect beta strands and reverse the direction of beta strands; Proline (due to the formation of cis bonds because of cyclic nature) and glycine (due to its small side) have high propensity for beta turns; th The carbonyl oxygen of the i residue forms Hbond with the amide proton of the (i+3) residue; beta turns are "tight" and only consist of 4 amino acids. Tight turn promotes formation of antiparallel beta sheets. The Beta Bulge: Beta bulge occurs between normal bstrands. Comprised of two residues on one strand and one on the other; Here one beta strand is curved a little because it "misses" the hydrogen bond. One amino acid is not bonded to the other strand. Bulges cause bending of otherwise straight antiparallel beta strands; Super secondary Structure: Hairpins connect two antiparallel strands; Crossovers connect two parallel beta strands, most common through an ahelix (b ab topology). All crossovers are righthanded . That is, when placing Cside strand closer and pointing right, the connecting ahelix or loop is on the top of the sheet; o Place the C strand close to you and the other strand far away fro you, the connection will be going on top of the sheet (not on the back of the sheet) for right handed crossovers. o Tertiary Structures: The classes of proteins: Based on structure and solubility, proteins can be grouped into three large classes: o Fibrous proteins these are only mentioned here; these make up the tissues, skin, bones, etc. These are structural proteins. o Globular proteins we will be focusing on globular proteins These catalyze metabolic reactions. o Membrane proteins these exist on biological membranes. We will not be talking about this now, but in second semester biochemistry we will focus on these. Fibrous Proteins Fibrous proteins contain polypeptide chains organized parallel along a single axis, producing long fibers or large sheets. They are mechanically strong , play structural roles in nature Difficult to dissolve in water o Alphakeratin and collagen are examples of fibrous proteins o These are extremely long helices that form a helical bundle. Alpha keratin: o akeratins are found in hair, fingernails, claws, horns and beaks; o Sequence consists of 311314 residue alpha helical rod segments capped with nonhelical N and Ctermini o Primary structure of helical rods consists of 7residue repeats, which promotes association of helices o bkeratins are found in silk and consist of yala repeat sequences o Alanine is small and can be packed within the sheets Collagen: a triple helix o Found in connective tissue in animals including tendons, cartilage, bones, teeth, skin and blood vessels; o 1/3 residues are lycine . Also high in roline and modified amino acids, 4 hydroxyproline (Hyp), 3hydroxyproline, and 5hydroxylysine (Hyl) Collagen is not just amino acids. It includes variable chemical groups that are modified by other enzymes, such as hydroxyl groups. o These amino acids are unsuited for either alpha helices or beta strands. Alternatively they form a tiple helix, much more extended helix than alpha helix. o Sequence determines structure: The triple helix is a structure that forms to accommodate the unique composition and sequence of collage. Every third residue faces the crowded center of the helix only glycine fits here (see next page) Proline and HyP suit the constraints of phi and psi Interchain Hbonds involving HyP stabilize helix Fibrils (formed by types I, II, and III collagen) are further strengthened by intrachain lysinelysine and interchain hydroxypyridinium crosslinks (see next page) these crosslinks are even stronger than hydrogen bonds! Collagen fibers are stabilized and strengthened by lyslys crosslinks. The gap, or hole, region seen in the electron microscope maybe the site of nucleation for the mineralization of bones. Globular Proteins Globular proteins are more numerous than fibrous proteins in cells. Globular proteins can be classified according to the type and arrangement of secondary structure Jane Richardson's classification o Antiparallel alpha helix proteins o Parallel or mixed beta sheet proteins o Antiparallel beta sheet proteins o Metal and disulfiderich proteins I will show you three dimensional structures of these types of proteins in class This classification is too simple to reflect the function and evolutionary origins of proteins Structural classification of proteins (SCOP): if you are interested in the folding of these proteins, you can go to the website and check it out! You do not need to know the exact groups or categories though. SCOP was created to to reflect both structural and evolutionary relatedness of proteins. See: http://scop.mrclmb.cam.ac.uk/scop/data/scop.b.html Family: Clear evolutionarily relationship Proteins clustered together into families are clearly evolutionarily related. Generally, this means that pairwise residue identities between the proteins are 30% and greater. Superfamily: Probable common evolutionary origin Proteins that have low sequence identities, but whose structural and functional features suggest that a common evolutionary origin is probable are placed together in superfamilies. Fold: Major structural similarity Proteins are defined as having a common fold if they have the same major secondary structures in the same arrangement and with the same topological connections. Proteins of the same fold, not necessarily of the same primary structure, generally have the same biological function o Example: The currently known allalpha protein class contain 252 superfamilies, 393 families, and 151 folds. Packing of Globular Proteins: Secondary structures pack closely to one another and also intercalate with extended polypeptide chains Most polar residues face the outside of the protein and interact with solvent Most hydrophobic residues face the interior of the protein and interact with each other van der Waals’ volume is about 7277% of the total protein volume; about 25% is not occupied by protein atoms; These cavities provide flexibility in protein conformation and dynamics; Random coil or loops maybe of importance in protein function (interacting with other molecules, enzyme reactions) Motion in Globular Proteins: Proteins are not static! Certain movements have consequences in entropy. The greater the movement, the higher the entropy (more energetically favorable). Protein structures are dynamics; o Atomic motions are random and within short distances (~0.5Å); These motions are arise from kinetic energies and are thus a function of temperature; o Collective motions refer to motions of a group of atoms as a single unit. Usually longer distance and slower; o Conformational changes involve motions of domains or segments in proteins. May occur in response to stimuli. Levinthal's Paradox: This describes how difficult it is for proteins to fold Consider a protein of 100 amino acids. Assign 2 conformations to each amino acid. 100 30 13 The total conformations of the protein is 2 =1.27x10 . Allow 10 sec for the protein to sample through one conformation in search for the overall energy minimum. The time it needs to sample through all conformations is: 13 30 17 9 o (10 )(1.27x10 )=1.27x10 sec = 4x10 years! Levinthal’s paradox illustrates that proteins must only sample through limited conformations, or fold by “specific pathways”. Much research efforts are devoted in searching for the principles of the “specific pathways”. Folding Pathways: It is hypothesized that protein folding is initiated by reversible and rapid formation of local secondary structures; Secondary structures then form domains through the cooperative aggregation of folding nuclei; Domains finally form the final protein through “Molten globule” intermediates. Molecular Chaperones: proteins that hep fold globular proteins: Molecular Chaperones are a class of proteins that assist protein folding in vivo; A well characterized chaperonin protein is hsp60 or GroEL; o Humans have many chaperones, where bacteria have few. Chaperones allow the hydrophobic part to be shielded while they are getting folded. Molecular Chaperones bind effectively to the exposed hydrophobic regions of partially folded structures. An example of Chaperonin: The bacterial chaperonin, GroEL, is composed of 14 identical subunits arranged in two rings of seven stacked backtoback with dyad symmetry. Our current understanding on how GroEL assists in protein is that an aggregationprone polypeptide binds in the open central channel of GroEL together with the co chaperonin, GroES. o Subsequent ATP hydrolysis triggers the release of both the polypeptide and GroES back into solution, when the polypeptide obtains its native conformation or rebinds to the chaperonin if it is still aggregationprone. This is a thermodynamically driven process! The middle parto fthe ring is hydrophobic. The ATP drives the protein folding. Thermodynamics of protein folding: Foldedunfolded G values will give you the delta G. If a folded protein is negative, the delta G needs to be negative. This is because the energy of the folded protein is lower DG folding foled unfolded (H foled unfolded(S foledunfolded DH foldingS folding o If we plot this on a diagram, the folded energy is negative and the unfolded energy will be higher. o Delta G is comprised of: enthalpy from the icontact of the atoms electrostatic, hydrogen, etc. favorable interactions have lower delta H values the internal energy is very low entropy These groups have higher entropy when folded This is unfavorable. A lower delta S in this term becomes a higher TS. When a protein is unfolded, it can exist in many states. o The sum of the two is a negative value. This is a battle between enthalpy and entropy. This just considers the chain itself and does not count in the water In vacuum, polypeptide chains contribute to DH foldingd DS folding The folded protein is a highly order structure, thus DS folding a negative number and thus –TDS folding a positive quantity in the equation; In vacuum, protein residues do not interact with solvent water, thus the enthalpy is favored in folded state. DH folding thus a negative quantity. Overall, the total Gibbs free energy difference is negative, thus favors the folded state. Folding in Water: Folding nonpolar residues o In aqueous solution, polypeptide chains, as well as solvent, contribute to overall DH foldingd DS foldingo o DG folding H chainDH chainDS foldingDS folding o The folded protein is a highly order structure, thus DS chains still a negative number and thus –TDS chains a positive quantity in the equation; Solvent molecules become less organized in folded state, thus DS solvent a large positive number; The driving force of the folding of the protein is water. o Protein nonpolar residues interact with one another in folded state with weak van der Waals forces, but interact more strongly with solvent through induced dipoles. Thus DH chains positive and favors unfolded state; DH solvents negative however and favors folded state. Folding nonpolar residues is driven by entropy. o In terms of enthalpy, for the chain, unfolded is a more favorable state. In the solvent, folded is the favorable state. o For the chain, it is unfavorable, entropically, to fold the protein. In a water solution, folding is entropically favored. Folding polar residues o In aqueous solution, polypeptide chains as well as solvent contribute to DH and DS , so folding folding DG folding H chainDH chainTDS foldingTDS folding o Folded protein chains are ordered. DS chains still a negative number and thus –TDS chains a positive quantity in the equation; Solvent molecules become less organized in folded state, thus DS solvents a small positive number; Here the water and the protein are the driving forces. o It is not favored to bury polar residues, but they interact favorably with solvent. Thus DH chains positive and favors unfolded state; DH solvents negative because solvent molecule interact more favorably with themselves. Quaternary Structures: Forces Driving Quaternary Association: (we skipped over this in class because it was covered in a previous lecture) Advantages of Quaternary Association: Stability: reduction of surface to volume ratio (surface area is a function of ,r2 volume is a function of )r3 Genetic economy and efficiency (less DNA is required); Bringing catalytic sites together; Cooperativity (required to regulate catalytic activity). (will be described in lecture 26) Insulin: Quaternary Structure Problem Insulin regulates glucose metabolism. Insufficient insulin lead to diabetes ; Pancreas released (active form) insulin has an quaternary structure of a monomer (two peptide chains covalently linked by disulfide bonds). In vitro produced insulin preferentially form a hexamer which prevents it from binding to insulin receptor; DNA recombinant techniques were used to convert hexamer form to monomer form that is more clinically efficient. Subunit Interactions: Many proteins exist in nature as oligomers (noncovalent assemblies of two or more monomer subunits); Interactions between subunits can be distinguished as either isologous or heterologous; Isologous interactions use the identical surface of each subunit, which results in a closed homodimer; (head to head – forms a dimer) Heterologous interactions use nonidentical surface, which results in large polymeric assemblies or cyclic structure. (head to tail – can form a polymer) Symmetry in Subunits: Cyclic symmetry: single nfold rotation axis, or Cn Dihedral symmetry: at least one 2fold axis perpendicular to an nfold axis Cubic symmetry: much less in proteins; seen in virus assembly Hemoglobin: Hemoglobin transfer oxygen from the lungs through the capillaries to the body. When hemoglobin binds to oxygen (when oxygen level is high), there is a conformational change. This motion is due to the binding of oxygen in the middle. This drags 1 particular residue, which changes the entire conformation of the residue. This is the basis for cooperativity. SWITCH! WE ARE MOVING FROM PROTEINS TO CARBOHYDRATES: Carbohydrates: Carbohydrates are the most abundant organic molecules in natures Photosynthesis energy stored in carbohydrates; Carbohydrates are the metabolic precursors of all other biomolecules; Important component of cell structures; Important function in cellcell recognition; Carbohydrate chemistry: o Contains at least one asymmetric carbon center; o Favorable cyclic structures; o Able to form polymers Carbohydrate Classes: o Monosaccharides (CH O)n:2Simple sugars, can not be broken down further; o Oligosaccharides: Few simple sugars (26). o Polysaccharides: Polymers of monosaccharides Monosaccharide (carbon numbers 37) simple sugars just 1 chain. Aldoses o Contain aldehyde o Name: aldo#oses ( e.g.,aldohexoses) o Memorize all aldoses in Figure ? (these should all be aldohexoses) o We are drawing in fischer projection, which doesn’t show literal 3 dimensional structure, but can tell you the location of the hydroxyl group. o These are asymmetical (chiral) carbons. These carbons have stereoisomers. Ketoses o Contain ketones o Name: keto#oses (ketohexoses) Stereochemistry of Monosaccharides D,L steroisomers refer to the configuration of the highest asymmetric carbon (farthest from the carbonyl carbon): in hexoses, this is normally the 5th carbon. If the hydroxyl group is on the right, it is D. If the hydroxyl group is on the left, it is an L isomer. L isomers are not common in nature. o Hydroxyl group is drawn to the right à D o Hydroxyl group is drawn to the lef à L o Note that D, L assignment does not specify the sign of rotation of plane polarized light. o D(+)glucose is dextrorotatory Dglucose; D()fructose is levorotatory D fructose o D is the preferred configuration in nature o Sugar molecules have optical activity (ability to rotate light) Each asymmetric carbon can have 2 configurations, thus for a sugar of n carbons, there are2(n possible steroisomers. o Know the following definitions: o Diastereomers Isomers that have opposite configuration at one or more carbons but are not mirror images of each other E.g. Dglucose and Dtallose are diastereomoers o Enantiomers Isomers that are mirror images E.g. LTalose and DTalose are enantiomers o Epimers Isomers that differ in only one carbon configuration E.g. DGlucose and Dmannose are epimers. Cyclic Structures of Aldohexoses Alcohols react readily with aldehydes to form hemiacetals; o Hemiacetal have an aldehyde and hydroxyl (which attacks the aldehyde) group. This takes place within the sugar itself. Linear form of aldohexoses could undergo a similar intramolecular reaction to form a cyclic hemiacetals ketones react readily with alcohols to form hemiketals; o Cyclic hemiacetals are very common and can be drawn as a Haworth Projection or a Fisher projection. Haworth Projection: (aDglucopyranose; BDglucopyranose) Fischer projection: Note that a hydroxyl group could have an up or down configuration (this determines whether it is alpha or beta). o On the same side with respect to the highest numbered carbon, the sugar is alpha. o If the hydroxyl group is on the opposite side with the fifth carbon, it will be a beta isomer. o In the example above, the sugar on top (with hydroxyl pointing down) is alpha, and the sugar on the bottom (with hydroxyl facin up) is beta. Cyclic Structures of Ketohexoses Linear form of ketohexoses could undergo a similar intramolecular reaction to form a cyclic hemiketals; Haworth Projection: o The structure with the hydroxyl group facing down is alpha. The structure with the hydroxyl group facing up is beta. Sugar Anomers: The formation of hemiketals and hemiacetals results in an asymmetric carbon atom. Isomers that differ only in their configuration about the new asymmetric carbon are called anomers, the carbonyl carbon is called anomeric carbon. o aanomer has the hydroxyl group on thesame side of o The oxygen at the highest numbered asymmetric carbon; o banomer has the hydroxyl group on theopposite side of o The oxygen at the highest numbered asymmetric carbon Monosaccharide structures: We have chair and boat conformations. Chair is the preferred (more stable) conformation. The chair conformation can flip and convert to maintain stability. Sugar Derivatives: Sugar alcohols are formed by mild reduction (with NaBH or4similar) of carbonyl groups of sugars; this just converts so you no longer have double bonded carbonyl group instead you have a straight line with all hydroxyl groups. o Add itol to the name of the parent sugar o E.g. Dglucitol (sorbitol), or DMannitol) Amino sugars contain an amino group in place of a hydroxyl group. They are found in many polysaccharides (for example, chitin). (add a NH2 group) o E.g. Dglucosamine (this is used for joint mobility), muramic acid. Acetals, Ketals, and Glycosides: Hemiacetals and hemiketals can react with alcohols in the presence of acid to form acetals and ketals. o Pyranose and furanose forms of monosaccharides react with alcohols to form glycosides. o Acetals form when the alcohol substitutes it's R group onto the hemiacetal, and recieves a hydrogen. Disaccharides: Simplest oligosaccharides; Contain two monosaccharides linked by a glycosidic bond; The free anomeric carbon is called reducing end; o The linkage carbon on the first sugar is always C1. So disaccharides can be named as sugar(a,b)1,#sugar, where a or b depends on the anomeric structure of the first sugar. For example, Maltose is glucosea1,4glucose. o The first sugar is always carbon 1. From here, look at the numbering of the second carbon to determine 1,4 or 1,6 linkage. Look at the alpha or beta configuration of the first sugar. o In the example, notice the linkage. LOOK AT THE LARGEST GROUP OFF THE 5TH CARBON. If this is going the same direction as the oxygen linkage (or hydroxyl group), it will be beta. If it is going to opposite direction, it will be alpha. Polysacchrides: Also called glycans; Starch and glycogen are storage molecules; Chitin and cellulose are tructural molecules; Cell surface polysaccharides are recognition molecules. Glucose is the monosaccharides of the following polysacchrides with different linkages and branches: Because of the differences in linkage, we need different enzymes to break these bonds! a(1,4), tarch (more branch) this molecule is used for energy storage by plants. a(1,4), lycogen (less branch) this molecules is used for energy storage by animal cells a(1,6), dextran (chromatography resins) b(1,4), cellulos (cell walls of all plants) b(1,4), Chitin similar to cellulose, but C2OH is replaced by –NHCOCH (3ound in exoskeletons of crustaceans, insects, spiders) Know these linkages!! Lipids! (AKA FATS) Lipids Lipids have low solubility in water; Lipids are amphipathic; Lipids are a principle component of biological membranes; highly reduced forms of carbon; yield large amount of energy upon oxidation in metabolism; More energy in the body come from lipids than glucose! Lipids are classified into two great classes: o Those that contain fatty acids (complex lipids); o Those that don’t (simple lipids). Fatty Acids Fatty acids = carboxyl group + a long hydrocarbon chain pKa will be very low, therefore usually deprotinated and has charge Saturated vs. Unsaturated Saturated fatty acids are single bonds in all carboncarbon bonds; Unstaurated fatty acids contain one or more double bonds in hydrocarbon chains; Fatty acids can be named in three ways. Common Fatty Acids Know these common Saturated fatty acids (Most have even number of Cs): MAKE FLASHCARDS! (#C:# Pi bonds) o Lauric acid 12:0 o Myristic acid14:0 o Palmitic acid 16:0 o Stearic acid 18:0 o Unsaturated fatty acids: o Palmitoleic acid 16:1 o Oleic acid 18:1 o Linoleic acid 18:2 o Alinoleic acid 18:3 (9,12,15) o Glinoleic acid 18:3 (6,9,12) Structural Consequences of Unsaturation Saturated chains pack tightly and form more rigid, organized aggregates (i.e., membranes); Saturated fats tend to aggregate which can lead to health issues Unsaturated chains bend and pack in a less ordered way, with greater potential for motion. Due to processing, some of the double bonds in unsaturated fats become trans, also leading to health complications. (Trans fats) Triglycerols (triglycerides) Triglycerols consist of a glycerol, esterified with three fatty acids If all fatty acid chains are the same, the molecule is called triacylglycerol (e.g., tristearin) Prochirality: (Numbering denotes the carbon # not the priority around the chiral carbon) Pretend to make C # 1 higher in priority (with D) in order to differentiate and is denoted as ProS ProR is the phosphorylated sn (stereospecific numbering) Glycerophospholipids Glycerophospholipids =1, 2diacylglycerols that has a phophate group esterified at carbon 3; (ProR position) Glycerophospholipids are a subclass of phospholipids; Glycerophospholipids are essential component of biological membranes; Phosphatidic Acid and Phosphatides Phosphatidic acid is the parent compound for the glycerolbased phospholipids; Phosphatidic acid consists of snglycerol3phosphate with fatty acids esterified at the 1 and 2positions; Phosphatides (or glycerolphospholipids) are phosphatidic acid esterified with a hydroxylcontaining organic functional group. Examples of Phosphatides: Sphingolipids Sphingosine forms the backbone of sphingolipids (rather than glycerol); Sphingosines are important components of biological membranes; Ceramide = sphingosine + fatty acid (via an amide linkage); Sphingomyelins = ceramide + phospholipids (via 1hydroxyl group) (Very important in neurological cells) Glycosphingolipids = ceramide + βlinked sugar at the 1hydroxyl moiety. Examples of Sphingolipids Waxes Waxes are esters of longchain alcohols with longchain fatty acids; Waxes are waterinsoluble due to the weakly polar nature of the ester group. Ceramide Sphingosine H O H OH H OH 2 H OH H OH C C C CH 2 C CH 2 H H NH NH 3 H H O RCOOH R fatty acid Terpenes Terpenes are a class of lipids from two or more molecules of 2methyl1,2 butadiene, or isoprene; All sterols (including cholesterol) and steroid hormones are terpenebased molecules Steroids Based on a core structure consisting of three 6membered rings and one 5 membered ring, all fused together; Cholesterol is the most common steroid in animals and precursor for all other steroids in animals; CHO alltransretinal Steroid hormones serve many functions in animals including salt balance, metabolic function and sexual function; Steroid Examples (You do not have to drawl, but be able to recognize) Function of Biological Membranes Membranes provide an enclosure to cells; Biological membranes allow exchange of materials; Biological membranes are sites of biochemical reactions that include photosynthesis, electron transfer, oxidative phosphorylation; Facilitate cell motion; Provide cell recognition and cell fusion. Spontaneously Formed Lipid Structures Hydrophobic interactions are important Micelles o Micelles are the preferred form for detergent and soaps; o Critical micelle concentration or CMC is defined as the concentration above which micelles form spontaneously; o Common detergents include triton X100 (CMC=0.24 mM), octyl glucoside (CMC=25 mM) and Dodecyl octaoxyethylene ether (CMC=0.071 mM); Lipid Bilayer Structures Hydrophobic interactions are important Phospholipids prefer to form bilayer structures in aqueous solution because their two fatty acid chains do not pack well; Phospholipids can form either unilamellar vesicles (liposomes) or multilamellar vesicles; Liposomes are highly stable and can be used as drug and enzyme delivery system; Lipid bilayers have a polar surface and a nonpolar core. The hydrophobic core provides a substantial barrier to ions and other polar entities, but a favorable environment for nonpolar molecules. Fluid Mosaic Model (S. J. Singer and G. L. Nicolson, 1972 ) The phospholipid bilayer is a fluid matrix The bilayer is a twodimensional solvent Lipids and proteins can undergo rotational and lateral movement Two classes of proteins: o peripheral proteins (extrinsic proteins) o integral proteins (intrinsic proteins) (Have large non polar portions in order to interact with the hydrophobic chain) Membrane Bilayer Mobility As an extension of fluid mosaic model, proteins and lipids on the membrane can freely move; This idea was elegantly tested by L. Frye and M. Edidin in 1970 by fusing human and mouse cells which are labeled with either red or green fluorescent antibodies; The rate of motion for integral membrane proteins can be as high as few microns per minute. Some proteins are anchored to the cytoskeleton, thus are restricted to local; Lipids can diffuse laterally as well, at a rate of few micron/sec; Transverse motion (from one layer to the other) is much slower for both proteins and lipids. Properties of the membranes allow us to withstand drastic temperature changes for limited amounts of time T mis phospholipid specific; m increases with chain length decreases with unsaturation, depends on the nature of the polar group; Phase transition are always endothermic (heatabsorbing); Transition occur over a narrow temperature range (< 1ºC); Transition temperature for biological membranes depends on lipids and proteins composition; o Cells can adjust lipid composition of their membranes to maintain proper fluidity as environmental conditions change Structure of membrane proteins Membrane proteins carry out all essential functions of membranes: Transport activity Receptor functions; o Proteins associated with membranes: Peripheral proteins (mostly globular, anchored to membrane by interacting with integral proteins); Integral proteins; Two classes: o Anchored to membrane by a single transmembrane segment (e.g., glycophorin); o Globular and largely embedded in the bilayer (e.g. bateriorhodopsin) Lipidanchored proteins o Glycophorin A Glycophorin A contains a single hydrophobic segment; Extracellular domain contains oligosaccharide units which constitute the ABO and MN blood group antigenic specificity of red cells; Extracellular domain also serves as the receptor for the influenza virus; o Other membrane proteins such as the major transplantation antigens H2 and hyman leukocyte associated (HLA) surface immunoglubulin receptors on B lymphocytes are the same class of proteins. o Bacteriorhodopsin Found in purple patches of Halobacterium halobium; Consists of 7 transmembrane helical segments with short loops that interconnect the helices; Bacteriorhodopsin clusters in hexagonal arrays resulting a C3 symmetry of packing; Bacteriorhodopsin is a lightdriven proton pump. Proton gradientgenerated potential energy is used in ATP synthesis; Lipid anchored membrane proteins New class of membrane proteins that are found to be covalently linked to lipids. The lipid moieties can insert into the bilayer, thus anchoring membrane proteins; Four types of lipid anchored proteins: o Amidelinked myristoyl anchors o Thioesterlinked fatty acyl anchors o Thioetherlinked prenyl anchors o Glycosyl phosphatidylinositol anchors Membrane and CellSurface Polysaccharides (Focus: Bacterial Cell Walls) Bacterial cell walls are composed of 1 or 2 bilayers and peptidoglycan shell; Grampositive (positive to Gram stain): One bilayer and thick peptidoglycan outer shell; Gramnegative(negative to Gram stain): Two bilayers with thin peptidoglycan shell in between; Grampositive: pentaglycine bridge connects tetrapeptides; Gramnegative: direct amide bond between tetrapeptides. Glycoproteins Glycoproteins are proteins that are covalently linked to oligo and polysaccharide groups; May be Nlinked or Olinked Nlinked saccharides are attached via the amide nitrogens of asparagine residues Olinked saccharides are attached to hydroxyl groups of serine, threonine or hydroxylysine Introduction to Membrane Transport Membrane transport studies principles of how cells exchange materials with their environment; Materials transported include inorganic electrolytes, organic metabolites, and water; The key to understand membrane transport is to understand how potential energy determines the direction of transport; The types of transport processes in biological systems include: o Passive transport o Facilitated transport o Active transport Passive Transport No special proteins needed Materials move across the membrane in the thermodynamically favored direction Facilitated Transport Passive diffusion is too slow to sustain life processes; Membrane proteins can facilitate transport; Materials moved across the membrane, still, in the thermodynamically favored direction (ΔG<0); Proteins that facilitate transport develop an affinity for the ligands transported; Facilitated transport displays saturation behavior; Saturation behavior provides a simple means for distinguishing facilitated from passive transport. Features of Transport Proteins Conformational changes in transport proteins facilitate transport; Facilitated transport does not change the difference of the total Gibbs free energy. o It reduces the energy barrier. Examples of facilitated transport systems include those for Dglucose, Chloride, cAMP, Choline, Lvaline. Active Transport Both passive and facilitated transport still can not completely satisfy the need of biological systems; Active transport moves materials across membranes AGAINST thermodynamic potential; Thus active transport mechanisms require energy. Sodium pump is inhibited by cardiac glycosides (agents that have potent effects on heart). Plant and animal steroids such as ouabain specifically inhib+t N+ , K ATPase and ion transport. It was found that people with hypertension have high blood levels of some sort of ATPase inibitor, such as ouabain. Inhibitin+ Na transport by ouabain accumulates sodium and calcium in these cells and thus narrow the blood vessels. ATPase is vital to survival. If the enzyme stops. We shut down. Ca ++ ATPase Ca has vital roles in cell signaling (muscle contract, for instance). Ca gradient is maintained by Ca ++ ATPase. Ca ++ ATPase has similar mechanism as Na, K ATPase; Gastric H +, K+ATPase The highly acidic environment (low pH) of the stomach is essential for the digestion of food for all animals; The parietal cells of the gastric muscosa is ~7.4. This proton gradient must be maintained constantly. Gastri+ H ,+K ATPase maintains pH gradient by hydrolyzing ATP. At the same time, the charge neutrality is maintained by exchanging K +for every H+ transported. Combination of active transport and counteractive diffusion allows for a balance rather than an over depolarization. This would result in a steady membrane potential with 3 Na molecules diffusion back into the cell at the same rate that 3 Na are pumped out of the cell by the Na/K pump. Nucleic Acids! Biological Function of Nucleic Acids Hereditary material (DNA); Replication (DNA); Translation (RNA); Catalysis (RNA) Gene regulation in development (RNA) Application of Nucleic Acids Recombinant DNA technology Genetically modified food; Cloning DNA vaccine DNA computing Understanding RNA viruses such as Human Immunodeficiency Virus (HIV) RNA structure and function RNA interference (RNAi) in development regulation In vitro selection Uric acid is byproduct of nucleic acid breaking down Structure and Nomenclature of Nucleotides: Start numbering with the nitrogen. We move around the first ring and then move to the next ring. The 9th hydrogen of a purine is the most important because it binds with the moeity. In a pyrmidine, all rings are numbered 16. The derivative of a purine ring gives adenine (6amino purine) and guanine (2 amino6oxy purine) Nitrogenous bases: o NH 2 O 6 7 5 N N 1N N N HN 8 2 N N N H2N N N N 4 H9 H H 3 Guanine Adenine purine (6amino purine)2amino6oxy purine) NH O 2 O 4 3 5 N NH NH N N O N O 2 N 6 H H O H 1 Cytosine Thymine Uracil pyrimidine (2oxy4oxy (2oxy4oxy (2oxy4amino pyrimidine) 5methyl pyrimidine) pyrimidine) Other Naturally Occuring Purine Derivatives: O O O H N HN N HN N HN O N N N O N N N H O H H H H
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