Final Exam:  December 14, 2005
[200 points total]

1.  Draw and label the complete schematic of the central dogma of biochemistry. List the individual types of RNA molecules. Indicate where each event is occurring in a eukaryotic cell.
[5 points]


2.  Identify the monomer, polymer and a higher order structure for three of the four major types of biomolecules.
[6 points]
nucleotides-->nucleic acids (oligomers) or DNA, RNA , etc.-->DNA, chromosomes
amino acids-->peptides or proteins-->proteins or any higher order protein structure
sugars/monosaccharides-->polysaccharides-->cull wall or any higher order structure
fatty acids-->lipids-->membranes


3.  Draw the condensation reaction (monomerdimer) for each of the three classes of biomolecules we discussed this semester.
[9 points]



4.  Why is the peptide bond rigid? Use resonance structures to complement your description and include the bond distances between neighboring a-carbons.
[4 points]


5.  Calculate the pH of a buffer, in which you dissolved 15.0g of Buffer X (MW=210g/mol) in 100mL of water and followed that with the addition of 56mL of 0.8 M NaOH. (Buffer X Ka ~ 4.88 x 10-7).
[3 points]
 
pH=6.31+log[0.448/(.071-.0448)]
pH=6.31+0.23=6.54

6.  What ratio of acetate ion to acetic acid exists in an acetate buffer with a pH of 5.25? (pKa = 4.74).
[3 points]
antilog(pH-pK) = antilog (0.26)=3.09

7.  Calculate the pKa of maleic acid, given that when the concentration of maleic acid is 0.022 M and the concentration of maleate is 0.041 M, the pH is 4.21.
[3 points]
pK=pH-log(.046/.019)
pK=4.21-.27=3.94

8.  Write out the multi-step reversible equilibria for the complete titration of phosphoric acid with NaOH. Draw the corresponding titration curve across the full pH range for this triprotic acid.
[5 points]


9.  Identify and describe each level of protein structure and all applicable noncovalent force(s) present in each layer.
[8 points]
primary: (linear amino acid sequence)
secondary: (hydrogen bonds involving backbone only)
tertiary: (all 4 noncovalent forces involving side chains)
quaternary: (all 4 noncovalent forces involving different polypeptide chains)


10.  Draw a reaction coordinate diagram comparing enzymes to uncatalyzed reactions. Fully label the plot and the free energy components of the reactions.
[5 points]


11. Draw each of the following curves on a single Michaelis-Menton plot (clearly labeling the axes, Km  and Vmax): [10 pts]
a.    Enzyme + substrate
b.    Enzyme + substrate + competitive inhibitor
c.    Enzyme + substrate + uncompetitive inhibitor
d.    Enzyme + substrate + positive modulator



12.  Draw a deoxynucleotide with the sequence GA hybridized with RNA, as might occur in transcription. Draw the full and complete structure.
[12 pts]

*above is shown the W/C basepairing nd the antiparallel nature of the duplex. Anti-parallel phosphosugar backbone will need to link the two residues on each side.

13.    Draw the reaction mechanism for an endonuclease (DNA). You will need to draw the side chains of thebackbone, but bases can be indicated by [Base]. [12 pts]

14.    Draw the resonance structures for keto-enol for guanine and amino-imine tautomerization for cytosine. [6 pts]


15.  Draw the following structures: [9 pts]
a.    deoxynucleoside form of 5-hydroxymethylcytidine in syn-conformation.
 

b.    oxynucleoside form of N6-methyladenine in anti-conformation.

c.    Oxynucleotide triphosphate form of 3-methylthymine in syn-conformation.


16.  If the superhelical density of a 5754 basepair plasmid is -0.08: [4 pts]
a)    What is the ideal linking number (Lko)?
548
b)    What is the actual linking number (Lk)?
504

17.   Computational approaches suggest the template strand in the middle of a gene has the following in-frame DNA sequence:
5'-CCATTTGCACTCATAAGACTGTACGTGTGA-3'
Armed with this information, answer the following questions: [10 points]

(a)  Write the coding strand of DNA (5'-->3')
5'-TCACACGTACAGTCTTATGTGCAAATGG-3'

(b)  Write the amino acid sequence (N-->C)
SER-HIS-VAL-GLN-SER-TYR-VAL-GLN-MET

18.    Experiments indicate the original coding strand has an intron with the sequence: [12 pts]
5'-TACAGTCTTAT-3'   
a.    Write the sequence of the mature mRNA (5'-->3')
5'-TCACACGGTGCAAATGG-3'
b.    Write the tRNA anticodons for each amino acid used in translation (5'-->3')
c.    Write the amino acid sequence (N-->C)
codon  UCA CAC GGU GCA AAU
anticodon UGA
 GUG
 ACC
 UGC
 AUU
amino acid SER
 HIS
 GLY
 ALA
 ASN


19.    You isolate and sequence three samples of the DNA coding strand and find three separate mutations. These are all independent mutations of the original coding strand and not cumulative effects. If we assume that base numbering begins at #1 for T, #2 for C, etc. for the original coding strand, what is the amino acid sequence for a-c below if the following mutations have occurred? [12 pts]

a.    Base #15 in the coding strand is not a T, but a C:
5'-TCACACGTACAGTCCTATGTGCAAATGG-3'
S-H-G-A-N (UNCHANGED)

b.    Between base #20 and 21 in the coding strand is an extra A:
5'-TCACACGTACAGTCTTATGTAGCAAATGG-3'
S-H-G-S-K-W
c.    Base #24 in the coding strand is missing:
5'-TCACACGTACAGTCTTATGTGCAATGG-3'
S-H-G-A-M
20.    Draw the peptide sequence you translated in question #19(b) in a solution at pH 7.0. Write the pKa for each applicable group. [15 pts]
(Draw a pentapeptide with the sequence SHGSKW). pKa values should be at the amino- and carboxy-termini, histidine, serine and lysine which should all be in the correct protonation state.
 
21.    List and describe three regulatory mechanisms that apply to enzymatic function. [3 pts]
Allosteric modulator: Reversible binding of an allosteric modulator, usually at a site remote from the active site, increases or decreases the reaction rate of an enzyme.
Feedback inhibition: When the end-product in a multi-step pathway is in high enough concentrations it acts to inhibit (usually as an allosteric effector) enzymatic function at an early step in the pathway. The effect of this is to decrease end-product formation.
Proteolytic cleavage: Inactive forms of enzymes (zymogens) exist in the cell, yet are unable to catalyze reactions until activated by proteases.

22.    Identify each stage of replication and list one enzyme that functions at each step.  
[6 points]
Initiation: Helicase, gyrase, dam methylase
Elongation: Polymerase, primase
Termination:  Ligase, topoisomerase

23.    List 4 differences between DNA and RNA (describe as needed for clarity). [4 pts]
RNA has C2’-OH, DNA does not
DNA has Thymine, RNA has Uracil
DNA is composed of 2 molecules (2 independent strands) in antiparallel orientation, whereas RNA is a single molecule.
DNA predominantly double stranded, whereas RNA has large single stranded regions
RNA is smaller
RNA has more complex structures
DNA is nuclear, RNA is made in the nucleus and functions primarily in the cytoplasm
Bases in RNA are often highly modified

24.    List 4 types of information stored in genomic DNA besides protein encoding genes. [4 pts]


25.    Matching [15 pts]: 
a.  B-form DNA __k__ the limiting rate of an enzyme catalyzed reaction at saturating [S]
b.  A-form DNA __e__ synthesized in the nucleus by RNA pol III
c.  cellulase __l__ conjugate acid/base forms of water accelerates the reaction by transferring a proton
d.  cellulose __h__ conjugate acid/base forms of an amino acid side chain from the protein or other non-water group accelerates the reaction by transferring a proton
e.  tRNA __i__ the overall rate of substrate to product conversion, also called the specificity constant
f.  mRNA __f__ synthesized by DNA-dependent RNA pol II
g.  rRNA __d__ A polysaccharide composed of linear and branched chains
h.  general acid/base catalysis __n__ successive basepairs in DNA show a rotation with respect to each other of roughly 36 deg
i.  kcat/Km __b__ rise per base 2.3 Å, 11 basepairs per turn, basepair tilt of 19deg, helix is symmetric and wider
j.  Km __m__ enzymes decrease the degrees of freedom in ternary complexes thereby enhancing the reaction rate
k. kcat __g__ synthesized in the nucleolus by RNA pol I
l.  specific acid/base catalysis __c__ an enzyme that hydrolyses the O-glycosidic linkage between sugars in a polysaccharide
m.  entropy reduction __j__ Michaelis constant, or ½(Vmax)
n.  twist __o__ two bases in a basepair exist out of plane with respect to each other
o.  propeller twist __a__ rise per base 3.4 Å, 10 to 10.5 basepairs per turn, basepair tilt of 4deg, helix is elongated and asymmetric
    
26.    True or False [15 pts]
__F___  Km occurs at lower [S] for a competitive inhibitor
__F___  A substrate binds a protein with high affinity forming a low energy and stable complex
__F___  A change in pH will have no effect on enzyme activity
__T___  A DNA duplex with a greater %GC content, will have a higher melting temperature than a duplex of the same length with higher %AT content
__T___  a-helix, g-turn and b-strand are all examples of protein secondary structure
__T___  Enzymes increase the reaction rate by increasing the lifetime of the transition state.
___F__  Mutating any amino acid in a protein will always destroy its biological function
__T___  Base-stacking is the dominant means of intra-strand stabilization
__T___  The hydrophobic effect is based on the concept that a thermodynamic driving force is associated with greasy surfaces attempting to minimize surface area that directly contacts water
___T__  Hydrogen bonding provides no net enthalpic contribution to protein folding
____F_  Prosthetic groups undergo chemical modification by enzymes
__F___  Allosteric effectors do not affect the Km, but usually change Vmax
__T___  Induced fit mechanisms are a component of the binding free energy
__F___  6M Guanidinium hydrochloride will fully oxidize cysteines
__F___  A kinase removes and a phosphorylase adds a phosphate group to a protein