BIOCHEMICAL METHODS REFERENCE EXERCISES
For each exercise below, provide:
a) the information requested.
b) the source of the information (title of source, vol., page, index number, http address, etc.).
c) the search method (e.g. "I checked the Index Volume of ...." or "I did a PubMed search that revealed ....") that you used to find the source.
Each student will be assigned a letter and will only provide the data for that letter under each exercise.
1) Give the titles and journal references of two recent papers by:
| a)Thomas Steitz | m)Robert Tjian |
| b)Joan Steitz | n)Tom Maniatis |
| c)Bernard Babior | o)David Baltimore |
| d)Sung-Hou Kim | p)Craig Venter |
| e)Paul Schimmel | q)Robert Lefkowitz |
| f)Bruce Stillman | r)John Abelson |
| g)Charles Richardson | s)Christian Raetz |
| h)Norman Pace | t)George Stark |
| i)Paul Sigler | u)Stanley Prusiner |
| j)Nadrian Seeman | v)Ralph Quatrano |
| k)Paul Modrich | w)Thomas Cech |
| l)James Darnell | x)Mary-Claire King |
2) Provide the title, authors, journal reference, and abstract of two recent
papers about the following. Give a two-sentence summary of one of the
abstracts.
a)phosphofructokinase regulation
b)tubulin structure
c)fatty acid transport
d)taurine biosynthesis
e)chloroplast DNA replication
f)cysteine proteases
g)RNA editing in mammals
h)chaperones
i)DNA methylation
j)HSP90
k)HSP70
l)TBP
m)HIV-1 protease
n)green fluorescent protein
o)ubiquitin
p)rev response element
q)sphinganine
r)sphingomyelin
s)group II introns
t)RNase P
u)STAT
v)TFIID
w)telomerase
x)GroEL
3) Give the title, authors, and journal reference of two recent papers that cite:
a)White, SA et al., Biochem. 31:1610 (1992)
b)Puglisi, JD et al., Science 257: 76 (1992)
c)Cheong C and Moore PB, Biochem. 31: 8406 (1992)
d)Liang, P and Pardee, AB, Science 257: 967 (1992)
e)Ochman, H et al., Genetics 120:621 (1992)
f)Barnes, WM, Proc. Natl. Acad. Sci. USA 91:2216 (1994)
g)Saiki, RK et al., Science 239: 487 (1988)
h)Lambowitz, AM, Cell 56: 323 (1989)
i)Cech, TR, Proc. Natl. Acad. Sci. USA 83: 4360 (1986)
j)Rani, MRS et al., J. Biol. Chem. 271: 22878 (1996)
k)Li, XX et al., J. Biol. Chem. 271: 5790 (1994)
l)Novick, D., Cell 77: 391 (1994)
m)Shuai, K. et al., Science 258: 1808 (1992)
n)Melton, DA, Nature 328: 80 (1987)
o)Zhou, QA and Sharp, PA, Science 274: 605 (1996)
p)Parada, CA and Roeder, RG, Nature 384: 375 (1996)
q)Stutz, F., Cell 82:495 (1995)
r)Moses, K. et al., Nature 340:531 (1989)
s)Stillman, B., Science 274:1659 (1996)
t)Prelich, G. and Stillman, B., Cell 53: 117 (1988)
u)Copeland, WC and Tan X., J. Biol. Chem. 270: 3905 (1995)
v)Dutta, A. and Stillman, B. EMBO J. 11: 2189 (1992)
w)Pruisner, SB, et al., Proc. Natl. Acad. Sci. USA 90:10608 (1993)
x)Harland, RM, Proc. Natl. Acad. Sci. USA 91: 10243 (1994)
4) Outline in one page a recent method to do the following:
a)detect nitric oxide induced apoptosis
b)purify lactate dehydrogenase
c)construct a phage display library
d)separate nucleic acids using HPLC
e)isolate mitochondrial tRNAs
f)purify hemocyanin
g)measure calcium transport into cells
h)purify RNase P
i)use minisatellite DNA to fingerprint wheat
j)identify RAPD markers in insects
k)use mass spectroscopy to determine protein molecular weight
l)prepare microsomes
m)assay aldolase
n)do a radioimmunoassay for progesterone
o)purify chloroplast DNA
p)quantify apolipoprotein C
q)identify a TAF
r)purify plasmid DNA using HPLC
s)identify a glucose transporter
t)measure the binding constant of insulin to its receptor
u)determine the metal content of superoxide dismutase
v)determine the titer of a herpesvirus
w)optimize a PCR reaction
x)purify carbamoyl phosphate synthetase
5) Identify three DNA sequences that show the greatest similarities to the following DNA sequence:
a)cttaacaaaatgactttaaggctttttcaagttttccatt
b)ttcttccacagggctttgtttcaaaaaataacaaaaggag
c)gtaataagttaatgtttgtccccgttataaacactgggtc
d)agtttacgatggcagcaacggaagttgtta
e)caaaaaaagggactgcgggggggttggagctcaccccccc
f)ccccattgaaaaaattcgtcgtcctgaaaagtcgcgtgct
g)ggaggtggagggtgtctaaaaccatttgcg
h)ggggacaatggaagggccggcctcgtcgtactcctgcttg
i)gtgatccacatttgctggaaggtggacagagaggccagaa
j)tggaccccccgatccacaccgagtatttgcgctccggcgg
k)ggcgatgatcttgatcttcatggggctggg
l)cgcccacgccgtgatctcttttctgatgcg
m)gccagcgatcccagggtacatggggtgccccccga
n)cactgttcaaggttttatttggcatgacacttgggt
o)ggttggttccatgatccattgcagatcttacatctcaca
p)taatattgcaatgcacactacagacacatataatatataa
q)aatatcctgtacaacatttatgcacaagatatgcatcatg
r)gacgtacacactggagccaggttatacgacttaactggga
s)actcgtcggcctaggcatgtttggtgcagggcag
t)caatgcagcaggctcacaggggtaatcgaagcctgc
u)agttggcagtgtgtctcagagacagtgggactgt
v)cacactaaccaggtcaccactacacaagtaccactt
w)ggcagcagggcagagctgtggggagtgagatgttt
x)ccccacaccatctcaacaccactgtactaaccacagctcagacga
6)Identify and provide the abstract for a grant that has been awarded to someone working on:
a)HIV-1
b)HIV-2
c)equine herpesvirus
d)ebola virus
e)mitochondrial tRNA
f)nuclear pore complexes
g)NMR of large proteins
h)protein evolution
i)protein molecular weight determination using mass spectroscopy
j)cGMP
k)p53
l)apoptosis
m)G proteins in smell
n)G proteins in vision
o)dystrophin
p)cystic fibrosis
q)transgenic rice
r)HSP70
s)cotton fiber promoters
t)telomerase and aging
u)LINE1
v)chloroplastic tRNA
w)mitochondrial DNA replication
x)transgenic fish