Biochemistry I
What do the regions of a Ramachandran represent?
(-90,-60): right-handed a helices (90,60): left-handed a helices (-90,120): B sheets
Describe competitive inhibition. What is the equation that expresses MM analysis of a competitive inhibitor? How does the inverse of this equation relate to the equation of a straight line?
-Competitive inhibition: inhibitor competes with substrate for binding to active site and does not affect catalysis (can be overcome at high substrate concentrations) -MM analysis of competitive inhibitor: v = (Vm[S])/(aKm+[S]), where a = 1+[I]/KI -Inverse of MM analysis of competitive inhibitor: 1/v = (aKm/Vm)(1/[S])+(1/Vm), where slope = aKm/Vm, x-intercept = -1/aKm, and y-intercept = 1/Vm -In competitive inhibition, the slope changes, but the y-intercept stays the same.
What expression represents an enzymatic reaction? What is the steady state approximation? What expression relates velocity to substrate concentration (MM equation)? How does the inverse of this equation relate to the equation of a straight line (LB equation)?
-E+S (k1 foward or k2 backward) ES (k3 forward) P -d[ES]/dt = 0 -V = (k3[S][Et])/([S]+((k2+k3)/k1)) or (vmax[S])/(Km+[S]), where small Km means good E and S binding and at 1/2 vmax, [S] = Km -1/V = (Km/vmax)(1/[S])+(1/vmax) relates to y = mx+b
What are carbohydrates?
-Formula Cn(H2O)n -Produced from CO2 and H2O via photosynthesis -Functions: energy source and energy storage, structural component of cell walls and exoskeletons, informational molecules in cell-cell signaling -Can be covalently linked with proteins to form glycoproteins or to lipids to form glycolipids
Describe mixed inhibition. What is the equation that expresses MM analysis of a mixed inhibitor? How does the inverse of this equation relate to the equation of a straight line?
-Mixed inhibition: inhibitor binds enzyme with or without substrate to regulatory site and inhibits both substrate binding and catalysis (can not easily be overcome at high substrate concentrations) -MM analysis of mixed inhibitor: v = (Vm[S])/(aKm+a'[S]) -Inverse of MM analysis of mixed inhibitor: 1/v = (aKm/Vm)(1/[S])+(a'/Vm), where slope = aKm/Vm, x-intercept = -a'/aKm, and y-intercept = a'/Vm -In mixed inhibition, the slope changes and the y-intercept changes.
What are monosaccharides vs an oligosaccharides vs a polysaccharides?
-Monosaccharides: a carbohydrate consisting of a single sugar unit -Oligosaccharides: short chains of monosaccharide units joined by glycosidic bonds -Polysaccharides: sugar polymers consisting of 20 or so monocaccharide units, can be branched or linear
Describe noncompetitive inhibition. What is the equation that expresses MM analysis of a noncompetitive inhibitor? How does the inverse of this equation relate to the equation of a straight line?
-Noncompetitive inhibition: inhibitor binds to ES complex (at separate site in single substrate enzyme, or to second active site in two-substrate case), does not affect substrate binding, and inhibits catalytic function (can not be overcome at high substrate concentrations) -MM analysis of uncompetitive inhibitor: v = (Vm[S])/(Km+a'[S]), where a' = 1+[I]/KI -Inverse of MM analysis of uncompetitive inhibitor: 1/v = (Km/Vm)(1/[S])+(a'/Vm), where slope = Km/Vm, x-intercept = -a'/Km, and y-intercept = a'/Vm -In noncompetitive inhibition, the y-intercept changes, but the slope stays the same.
What are some oxidation and reduction cofactors?
-Oxidized cofactors (preform oxidation reactions and are reduced): ADP+HPO2-, NAD+, NADP+, FAD -Reduced cofactors (preform reduction reactions and are oxidized): ATP, NADH, NADPH, FADH2
What kinds of biotechnology use nucleic acids?
-Polymerase chain reaction: -Sanger Sequencing: -Pyrosequencing: -Next Generation Sequencing:
What is the product of [H+] and [OH-] in a neutral pH?
10^-14 M (pH+pOH=14)
After glucose is converted into pyruvate through a sequence of 10 enzyme-catalyzed reactions (glycolysis), what are the possible metabolic fates of pyruvate?
-Under hypoxic or anaerobic conditions, it is either fermented to ethanol in yeast or fermented to lactate in vigorously contracting muscles, in erythrocytes, in some other cells, and in some microorganisms. -Under aerobic conditions, it is converted to Acetyl-CoA and sent through the citric acid cycle to yield 4 CO2 and 4 H2O molecules.
Describe the steps in gluconeogenesis.
1. 1st Bypass: Conversion of Pyruvate to Phosphoenolpyruvate Requires Two Exergonic Reactions... 2. 2 Phosphoenolpyruvate to 2 2-Phosphoglycerate 3. 2 2-Phosphoglycerate to 2 3-Phosphoglycerate 4. 2 3-Phosphoglycerate to 2 1,3-Bisphosphoglycerate
What is the flowchart for assigning the type of inhibition?
1. Does the Vmax remain the same and Km increase? (Yes = competitive, no = uncompetitive/mixed) 2. Do Vmax and Km decrease by the same factor? (Yes = uncompetitive, no = mixed)
What are distinguishing features of living organisms?
1. High degree of chemical complexity and microscopic organization 2. Extracting, transforming and using energy from the environment 3. Defined functions for organism's components and regulated interactions 4. Mechanisms to sense and respond to alterations in the surrounding 5. Self-replication and self-assembly 6. Capacity to change over time (evolve)
What are some favorable interactions in proteins?
1. Hydrophobic effect: release of water molecules from the structured solvation layer around the molecule as protein folds increases the net entropy 2. Hydrogen bonds: interaction of N−H and C=O of the peptide bond leads to local regular structures such as a helices and B sheets 3. London dispersion: medium-range weak attraction between all atoms contributes significantly to the stability in the interior of the protein 4. Electrostatic interactions: long-range strong interactions between permanently charged groups (salt bridges, especially those buried in the hydrophobic environment, strongly stabilize the protein)
How do you name a disaccharide?
1. Write the sugar with the non-reducing end on the left. 2. Give the configuration (a or b) at the anomeric carbon joining the first (on the left) and second (on the right) monosaccharide along with the identify of the sugar. 3. Indicate in parentheses the carbons being joined, with arrow connecting the two carbons. 4. Name the second residue. 5. If there are more residues, describe the second glycosidic bond by the same convention
What is a titration curve?
A plot of pH versus the equivalents of base added during titration of an acid that reveals the of the pKa of the weak acid. At the midpoint of the curve, when the concentration of acid and base are equal, pH=pKa.
What functional groups are water soluable?
Alcohols, aldehydes, ketones, and compounds containing N-H bonds all form hydrogen bonds with water and are therefore water soluble.
What is an aldose vs a ketose?
An aldose contains an aldehyde functionality. A ketose contains a ketone functionality.
What is anabolism vs. catabolism?
Anabolism converts small molecules to complex molecules (disordered to ordered, endergonic). Catabolism breaks down complex molecules to small molecules (ordered to disordered, exergonic).
What are phi and psi angles?
Angles around a-carbon (phi: amide-nitrogen bond, psi: carbonyl-carbon bond)
Phenylalanine (Phe/F)
Aromatic R groups pKa (COO-): 2 pKa (NH3+): 10
Tryptophan (Trp/W)
Aromatic R groups pKa (COO-): 2 pKa (NH3+): 10
Tyrosine (Tyr/Y)
Aromatic R groups pKa (COO-): 2 pKa (NH3+): 10 pKa (R): 10
Which amino acids absorb UV light?
Aromatic amino acids Phe, Tyr, and Trp (Tyr and Trp do until 280 nm)
What are the three forms of the double helix?
B-form/DNA (most common under biological conditions), A-form/RNA (favored in non-aqueous environments), and Z-form (left-handed DNA helix, much more compact, high salt)
Describe B-sheets.
B-sheets are assembled by H-bonding between adjacent β-strands and they can be parallel or antiparallel. Tetrahedral α-carbon in each residue causes "pleats." β turns occur frequently whenever strands in β sheets change the direction. The 180° turn is accomplished over four amino acids and stabilized by a hydrogen bond from a carbonyl oxygen to amide proton three residues down the sequence. Proline in position 2 or glycine in position 3 are common in β turns.
What are buffers?
Buffers are mixtures of weak acids and their conjugate bases. These aqueous solutions that can resist change in pH if small amounts of acid or base are added. The buffering region is where a given amount of H+ or OH added to the system has much less effect on pH than the same amount added outside the region. At the midpoint of the buffering region, where the concentration of the proton donor (acetic acid) exactly equals that of the proton acceptor (acetate), the buffering power of the system is maximal; that is, its pH changes least on addition of H+ or OH.
Describe catabolism vs. anabolism.
Catabolism includes pathways that are primarily energy-producing, while anabolism includes pathways that are primarily using energy to build complex structures. Catabolic pathways are convergent and the anabolic pathways are divergen.
What is chymotrypsin?
Chymotrypsin is a protease that increases the rate of hydrolysis of peptide bonds by 10^9. The free enzyme binds the substrate and the serine reside attacks the carbonyl carbon in the enzyme-substrate complex. The tetrahedral intermediate with the negatively charged oxygen is stabilized by the oxyanion hole. The tetrahedral intermediate then collapses and the reformation of the double bond on the carbon displaces the bond between the carbon and the amino group of the peptide linkage, breaking the peptide bond. The amino leaving group is protonated by histidine. Water attacks the new acyl enzyme intermediate and the new tetrahedral adduct is stabilized by the oxyanion hole. Collapse of this tetrahedral forms the second product, a carboxylate anion and displaces serine (release of the second product returns the active site to the initial state).
What does it mean to be amphoteric?
Compounds that have dual acid/base character. Sometimes also called ampholytes (ex: amino acids can act as weak acids or bases).
Peptide bond formation is an example of ___, while the reverse reaction is an example of ____.
Condensation (reaction type in which two compounds are joined with the elimination of water); Hydrolysis (reaction type in which a bond is broken with the addition of water)
What are conjugated proteins? What is a prosthetic group? How are conjugated proteins classified?
Conjugated proteins are proteins containing chemical components in addition to amino acids. A prosthetic group is the non-amino acid part of a conjugated protein. Conjugated proteins are classified on the basis of the chemical nature of their prosthetic groups (lipoproteins contain lipids, glycoproteins contain carbohydrates, phosphoproteins contain phosphate groups, hemoproteins contain heme groups, flavoproteins contain flavian nucleotides, and metalloproteins contain a specific metal).
Describe the structure of DNA and how it was elucidated.
DNA is a double helix (Watson and Crick modeling) and antiparallel (Franklin's X-ray crystallography). The keto tautomeric states are peredominate at neutral pH (Donahue). Bases associate together in a hydrophilic environment largely by hydrophobic interactions (entropic factor). Bases interact with each other in "stacks" (aromatic rings essentially parallel to ring systems above and below) by van der Waals interactions (enthalpic factor).
What is the equation for delta G? At equilibrium, delta G is zero, so what is delta G°?
Delta G = delta G° + RT In (Keq) Delta G° = -RT In (Keq) Where R = 0.008315 KJ/mol*K Where T = 298 K Where Keq = ((C)^c(D)^d)/((A)^a(B)^b)
What are epimers?
Epimers are two sugars that differ only in the configuration around one carbon atom
If delta G is negative, the reaction is___. If it's positive, the reaction is___.
Exergonic and thermodynamically favorable; endergonic and thermodynamically unfavorable (reverse process is favored)
Which characteristic of fatty acids will allow a researcher to separate them from amino acids? Which characteristic of nucleotides will allow a researcher to separate them from glucose?
Fatty acids are more nonpolar than amino acids. Nucleotides are physically larger molecules than glucose.
What are the roles of polysaccharides? Describe the types of polysaccharides that are involved in each role.
Fuel (glycogen, starch, dextran) -Starch, the main storage polysaccharide in plants, is a mixture of two homopolysaccharides of glucose. Amylose is a linear polymer of (α1->4) linked residues, while Amylopectin is a branched polmer of (α1->6) linkages occuring every 24-30 residues. -Glycogen is a branched polymer of (α1->6) linkages occuring every 8-12 residues. Structure (cellulose, chitin) -Cellulose is a linear homopolysaccharide of glucose. Glucose monomers form (β1->4) linked chains. Hydrogen bonds form between adjacent monomers and between chains, so structure is tough and water-insoluble. -Chitin is a linear homopolysaccharide of N-acetylglucosamine in (β1->4) linkages. Extracellular matrix (glycosaminoglycans) -Glycoseaminoglycans are heteropolysacchardies composed of repeating disaccharides and allow for diffusion of nutrients into cell.
What are globins?
Globins are oxygen-binding proteins with side chains that lack affinity for O2. The oxygen molecule is captured with heme prosthetic group that is protein bound (Myoglobin is the main oxygen storage protein and has 1 O2 binding site, while Hemoglobin is a circulating oxygen-binding protein and has 4 O2 binding sites). Free heme has two open coordination sites. In the protein, heme binds to imidazole of a His (called the proximal heme). The second coordination site is where oxygen binds.
What is the overall equation for glycoylsis?
Glucose + 2NAD+ + 2ADP + 2Pi -> 2 pyruvate + 2NADH + 2 ATP + 2H2O
What factors affect Tm?
High GC content, length, and salts/ionic strength all increase Tm.
Describe nucleophilic displacements involving ATP.
Hydrolysis relieves electrostatic repulsions from the negative charges. Phosphate is resonance stabilized.
Both DNA and RNA can undergo ___ in a test tube under ___ conditions. ___ is much more prone to this because of the ___ group
Hydrolysis, alkaline, RNA, 2'-OH
Under standard biochemical conditions, the equilibrium for the reaction above favors ___. To make ___ thermodynamically more favorable, ___.
Hydrolysis; Condensation; The carboxyl group must be chemically modified or activated so that the hydroxyl group can be more readily eliminated.
What is the relationship between K'eq, delta G'◦, and the direction of chemical reactions?
If K'eq>1, delta G'◦<1, and the reaction proceeds in the forward direction. If K'eq=1, delta G'◦=0, and the reaction is at equilibrium. If K'eq<1, delta G'◦>1, and the reaction proceeds in the reverse direction.
What is the native fold? How does it relate to stability?
Native fold is the three-dimensional confirmation of protein that makes it able to fulfill a specific biological function (has entropic cost). Stability is the tendency of a protein to maintain a native conformation.
What conformations of the ribose-base bond exist is purines and pyrimidines?
In purines, both anti (base rotated away from CH2OH moiety) and syn (base rotated toward from CH2OH moiety) conformations are possible. In pyrimidines, only the anti conformation is possible.
What is the characteristic pH at which the net electric charge is zero?
Isoelectric point (pI) = (1/2)(pKa1+pKa2), where pKa1 and pKa2 surround charge 0
What is an ionization/acid disassociation constant (Ka) and how is it related to pKa?
Ka=Keq=([H+][A-])/HA pKa = -log Ka
What is the difference between Keq and Q?
Keq is the ratio of concentrations at equilibrium, while Q is the ratio at any other time other than when the system is at equilibrium. When Keq < 1, formations of the reactants is favored. When Keq > 1, formation of the products is favored. When Q > Keq, formation of reactants is favored. When Q < Keq, formation of products is favored.
Glutamine (Gln/Q)
Polar, uncharged R groups pKa (COO-): 2 pKa (NH3+): 10
What are the categories of polysaccharides?
Linear or branched homopolysaccharides (one monomer type), linear heteropolysaccharides (two monomer types), branched heteropolysaccharides (multiple monomer types)
What is a multisubunit? What are protomers?
Multisubunit are proteins that have two or more polypeptides associated noncovalently. The individual polypeptide chains in a multisubunit protein may be identical or different. If at least two are identical the protein is said to be oligomeric, and the identical units (consisting of one or more polypeptide chains) are referred to as protomers.
Aspartate (Asp/D)
Negatively charged R groups pKa (COO-): 2 pKa (NH3+): 10 pKa (R): 3
Glutamate (Glu/E)
Negatively charged R groups pKa (COO-): 2 pKa (NH3+): 10 pKa (R): 4
When pH of solution is greater than PI, the protein will be___. When the pH of the solution is lower than PI, the protein will be ___.
Negatively charged; Positively charged
Glycine (Gly/G)
Nonpolar, aliphatic R Group pKa (COO-): 2 pKa (NH3+): 10
Alanine (Ala/A)
Nonpolar, aliphatic R Groups pKa (COO-): 2 pKa (NH3+): 10
Isoleucine (Ile/I)
Nonpolar, aliphatic R Groups pKa (COO-): 2 pKa (NH3+): 10
Leucine (Leu/L)
Nonpolar, aliphatic R Groups pKa (COO-): 2 pKa (NH3+): 10
Methionine (Met/M)
Nonpolar, aliphatic R Groups pKa (COO-): 2 pKa (NH3+): 10
Proline (Pro/P)
Nonpolar, aliphatic R Groups pKa (COO-): 2 pKa (NH3+): 10
Valine (Val/V)
Nonpolar, aliphatic R Groups pKa (COO-): 2 pKa (NH3+): 10
What is the difference between a nucleoside and a nucleotide?
Nucleoside= base+ribose Nucleotide= base+ribose+phosphate
Where are nucleotides often found?
Nucleotides are often found complexed with divalent cations. The divalent cation "neutralizes" some of the repulsions that could be present. Enzymes that utilize nucleotides also often bind divalent cation.
What are the functions of nucleotides and nucleic acids?
Nucleotides: -Energy for metabolism (ATP) -Enzyme cofactors (NAD+) -Signal transduction (cAMP) Nucleic acids: -Storage of genetic info (DNA) -Transmission of genetic info (mRNA) -Processing of genetic information (ribozymes) -Protein synthesis (tRNA and rRNA)
Serine (Ser/S)
Polar, uncharged R groups pKa (COO-): 2 pKa (NH3+): 10
Threonine (Thr/T)
Polar, uncharged R groups pKa (COO-): 2 pKa (NH3+): 10
Cysteine (Cys/C)
Polar, uncharged R groups pKa (COO-): 2 pKa (NH3+): 10 pKa (R): 8
What equation represents protein ligand interactions? What is fractional saturation? What is the relationship between association and dissociation constants? What can Kd tell us?
P+L->PL Fractional saturation (Y) is the binding sites activated divided by the total binding sites: Y = [L] / ([L]+Kd). Kd=1/Ka or Kd=k2/k1 and Ka=k1/k2 (small Kd and big Ka = higher affinity) Kd is the concentration of ligand that leads to 50% saturation (Y=0.5) of the protein.
Describe PEP.
PEP has a high energy phosphate ester bond. Hydrolysis of PEP is even more energetically favorable. Stabilization of the enol of pyruvate in the keto form contributes to the high free energy of hydrolysis.
What are some unusual DNA/RNA structures?
Palindromes occur when there are complementary regions in two strands. Mirror repeats occur where inverted repeat occurs within each individual strand of DNA.
Describe the cyclization of monosaccharides.
Pentoses and hexoses readily undergo intramolecular cyclization. The former carbonyl carbon becomes a new chiral center, called the anomeric carbon. The former carbonyl oxygen becomes a hydroxyl group; the position of this group determines if the anomer is α or β. If the hydroxyl group is on the opposite side (trans) of the ring as the CH2OH moiety the configuration is α. If the hydroxyl group is on the same side (cis) of the ring as the CH2OH moiety, the configuration is β. (Mutarotation is the interconversion of the alpha and beta configurations.)
Why are phosphorylated intermediates produced in glycolysis?
Phosphorylation traps the intermediates in the cell as negatively charged compounds do not cross the hydrophobic membrane. Energy of hydrolysis of ATP is partially conserved in formation of other phosphate esters. Binding energy of the phosphorylated compounds interacting with enzyme active sites.
What biomolecules dissolve readily in water and which do not? Why?
Polar biomolecules (glucose, glycine, aspartate, lactate, and glycerol) dissolve readily in water because they can replace water-water interactions with energetically favorable water-solute interactions. In contrast, nonpolar biomolecules (lipids and waxes) are poorly soluble in water because they interfere with water-water interactions but are unable to form water-solute interactions. In aqueous solutions, nonpolar molecules tend to cluster together. Amphipathic compounds (phenylalanine and phosphatidylcholine) contain regions that are polar (or charged) and regions that are nonpolar.
Asparagine (Asn/N)
Polar, uncharged R groups pKa (COO-): 2 pKa (NH3+): 10
Increasing pH of ___ causes the ___ group of each residue to ___. The ___ charged groups of each residue ___ each other leading to the unfolding of the a helix. Decreasing pH of ___ causes the ___ group of each residue to ___. The ___ charged groups of each residue ___ each other leading to the unfolding of the a helix.
Polyglutamates/polyaspartates, carboxyl, lose a proton Negatively, repel Polylysines/polyarginines, amino, gain a proton Positively, repel
Lysine (Lys/K)
Positively charged R groups pKa (COO-): 2 pKa (NH3+): 10 pKa (R): 10
Arginine (Arg/R)
Positively charged R groups pKa (COO-): 2 pKa (NH3+): 10 pKa (R): 12
Histidine (His/H)
Positively charged R groups pKa (COO-): 2 pKa (NH3+): 10 pKa (R): 6
What are glycoconjugates of proteins and lipids?
Proteins and lipids with small oligosaccharides attached to Asn or Ser/Thr via their anomeric carbons that play role in protein-protein recognition, folding and stability, and trafficking.
If the pH is lower than the pKa, then the compound will be ___. If the pH is higher than the pKa, then the compound will be ___. What functional group have charges?
Protonated; Deprotonated D and E have a negative charge, R and K have a positive charge, and H has a positive charge if the pH is less than or equal to 5, but is neutral is the pH is above 5.
What sugars are reducing vs. nonreducing? How do you know if a carbohydrate is reducing?
Reducing: glucose, ketose, hemiacetal, carbohydrate with free hydroxyl Nonreducing: acetal, carbohydrate without free hydroxyl Look for the carbon with the most heteroatoms attached to it (most oxidized). If it has a free hydroxyl, then it is reducing. If it is attached to another sugar through the hydroxyl, then it is not.
In coupled reactions what is the relationship between delta G° and Keq?
Standard free energies are additive and Keqs are multiplicative.
Describe the steps of glycolysis.
Step 1: Phosphorylation of glucose (phosphorylation traps glucose inside cell and lowers intracellular glucose concentration to allow further uptake, uses enzyme hexokinase and ATP as phosphate donor, irreversible) Step 2: Conversion of Glucose 6-Phosphate to Fructose 6-Phosphate (uses enzyme phosphohexose isomerase, reversible) Step 3: Phosphorylation of Fructose 6-Phosphate to Fructose 1,6-Bisphosphate (uses enzyme phosphofructokinase-1 and ATP as phosphate donor, irreversible, product used only for glycolysis) Step 4: Cleavage of Fructose 1,6-Bisphosphate to glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (uses enzyme fructose 1,6-bisphosphate aldolase, reversible) Step 5: Interconversion of the Triose Phosphates (one of the two triose phosphates formed by aldolase, glyceraldehyde 3-phosphate, can be directly degraded in the subsequent steps of glycolysis so other product, dihydroxyacetone phosphate, is immediately and reversibly converted to glyceraldehyde 3-phosphate, uses enzyme triose phosphate isomerase) Step 6: Oxidation of Glyceraldehyde 3-Phosphate to 1,3-Bisphosphoglycerate (uses enzyme glyceraldehyde 3-phosphate dehydrogenase and NAD+ as electron donor) Step 7: Phosphoryl Transfer from 1,3-Bisphosphoglycerate to ADP Step 8: Conversion of 3-Phosphoglycerate to 2-Phosphoglycerate Step 9: Dehydration of 2-Phosphoglycerate to Phosphoenolpyruvate Step 10: Transfer of the Phosphoryl Group from Phosphoenolpyruvate to ADP
What is the difference between weak vs strong acids and bases?
Strong acids and bases dissociate completely into H+ or OH- in aqueous solution (HCL or NaOH). Weak acids and bases do not completely dissociate.
Describe a phosphoryl group transfer.
Substitution from sp3 phosphorous proceeds via the nucleophilic substitution (usually associative, SN2-like) mechanism. Nucleophile forms a partial bond to the phosphorous center giving a pentacovalent intermediate or a pentacoordinated transition state.
What are the first and second laws of thermodynamics? What are enthalpy (H), entropy (S), and Gibbs free energy (G)?
The first law of thermodynamics states that energy can neither be created nor destroyed, but it can be changed from one form to another. The second law of thermodynamics states that the entropy in an isolated system always increases. Enthalpy is the heat content of the system. Entropy is the randomness or disorder of the components of a system. Gibbs free energy is the energy available in a system (delta G = delta H - T*delta S).
List and describe the processes involved in protein purification.
The first step in any protein purification procedure is to break open these cells, releasing their proteins into a solution called a crude extract, which will be subjugated to fractionation (the process of separating the proteins or other components of a complex molecular mixture into fractions based on differences in properties such as solubility, net charge, molecular weight, or function). This can be done through ion exchange chromatography (negatively charged proteins elude first when using cation-exchangers and positively charged proteins elude first when using anion-exchangers), size exclusion chromatography (large proteins emerge from the column sooner than small ones), affinity chromatography (), or SDS-gel electrophoresis (large proteins form bands on gel sooner than small ones, cannot separate sulfide bonds but DTT can).
How would an ideal oxygen carrier behave? How does this get accomplished?
The ideal oxygen carrier would bind oxygen in regions of high partial pressure (lungs), and deliver to regions of low partial pressure (tissues). Hemoglobin satisfies this by cooperative binding, which takes advantage of high and low affinity behavior. Hydrophobic interactions between alpha-beta subunits of hemoglobin change upon oxygen binding. Therefore, hemoglobin can exist in two states. The T (taut) state does not have oxygen bound (lower affinity for oxygen) and is stabilized by a number of ionic interactions at the alpha1/beta2 and alpha2/beta1 interface. The R (relaxed) state has oxygen bound (higher affinity for oxygen). The binding of oxygen to the T state triggers conformational changes to the R state.
Ionic interactions between dissolved ions are much stronger in less polar environments, because there is less screening of charges by the nonpolar solvent. Water is effective in screening the electrostatic interactions between dissolved ions because it has a high dielectric constant, a physical property that reflects the number of dipoles in a solvent. Why?
The strength, or force (F), of ionic interactions in a solution depends on the magnitude of the charges (Q), the distance between the charged groups (r), and the dielectric constant (ε, which is dimensionless) of the solvent in which the interactions occur: F = Q1Q2/εr^2
Explain the significance of non-covalent interactions.
There is far less in energy in non-covalent interactions than in covalent interactions. While they are weak, many non-covalent interactions taken together can still lead to strong interactions. Weakness allows these bonds to be made and broken, or more dynamic so the cell can respond to stimuli more rapidly and biomolecular interactions can be made and reversed.
What are the structural features shared by all amino acids?
They have a carboxyl group and an amino group bonded to the same carbon atom (the α carbon). For all the common amino acids except glycine, the α carbon is bonded to four different groups: a carboxyl group, an amino group, an R group, and a hydrogen atom; in glycine, the R group is another hydrogen atom. The α-carbon atom is thus a chiral center and amino acids have two possible stereoisomers that are enantiomers (l-Amino acids are those with the α-amino group on the left, and d-amino acids have the α-amino group on the right, and cysteine is the only amino acid that is not S-conformation besides glycine). All molecules with a chiral center are also optically active — that is, they rotate the plane of plane-polarized light.
Describe a-helices.
a helices is the protein structure in which R groups radiate outward from helical "cylinder," and it can be right- or left-handed (usually right-handed in proteins). They are stabilized by internal H-bonding between ith residue and the i+4, except those near the end of the helix (H-bonds form between the H of the amide bond and the carbonyl oxygen of the amide bonds 4 residues away). Pro (can't form hydrogen bond) and Gly (generates conformation with phi and psi angles) are destabling in helices.
What is the Henderson-Hasselbach equation?
pH = pKa + log ([A-]/[HA])
What is ph and how is it maintained?
pH=-log[H+] pH is maintained by buffers.
In D-sugars, the OH group is drawn ___ in the Fischer projection and the CH2OH moiety is drawn ____ in the Haworth projection. In L-sugars, the OH group is drawn ___ in the Fischer projection and the CH2OH moiety is drawn ____ in the Haworth projection.
right, up left, down
What is the equation for the standard free change in energy of a redox reaction? What is the equation for the free change in energy in a cell? What does this indicate?
ΔG'° = -nFΔE'°, n = #electrons and F = 96.5 kJ/mol ΔG = -nFΔE'° + RT/nFIn(acceptor/donor) (In the cell, the actual free‑energy change depends on ΔG° as well as the ratio of product concentrations to reactant concentrations.) ΔG = -RTInKeq + RTInQ (if Q<Keq, delta G will be negative and the reaction will be exergonic and go forward; if Q>Keq, delta G will be positive and the reaction will be endergonic and go backwards)