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Biochem 615 - Dr. Dean's Slide
Questions from Dr. Dean's Material
63
Biology
Undergraduate 3
06/02/2007

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Term
Who founded Genentech? What did he discover?
Definition
Herbert Boyer. Discovered EcoRI.
Term
Recognition sequence for EcoRI
Definition
G^AATTC
Term
What does RFLP stand for?
Definition
Restriction-Fragment Length Polymorphism
Term
HindII recognition sequence
Definition
GT Py^Pu AC
Term
EcoRV recognition sequence
Definition
GAT^ATC
Term
What are the cofactors needed for Type I, Type II, Type III?
Definition
Type I: SAM, ATP, Mg2+
Type II: Mg2+
Type III: Mg2+
Term
What people won Nobel Prizes? For what?
Definition
Werner Arber - Type I
Daniel Nathans/Hamilton Smith - Type II
Richard Roberts - split genes
Paul Berg - recombinant DNA
Michael Smith - site-directed mutagenesis
Roger Kornberg - eukaryotic transcription
Term
PvuII recognition sequence
Definition
CAG^CTG
Term
Two examples of Type I
Definition
EcoK, EcoB
Term
Two examples of Type II
Definition
EcoRI, HindII
Term
Where do the following cleave: Type I, Type II Type III?
Definition
Type I: 1000 bp away
Type II: at site
Type III: 24-26 bp away
Term
Name examples of the following cloning vectors: 1st, 2nd, 3rd, 4th generation.
Definition
1st: pSC101
2nd: pBR322
3rd: pUC8, 9, 18, 19
4th: pUC118, 119, pBluescript, pTZ18, 19
Term
What is the name of the lambda repressor?
Definition
cI
Term
Which promotes the lytic cycle, cro or cI?
Definition
Cro.
Term
Out of the promoters Pr and Prm, which promotes cro and which promotes cI?
Definition
Pr promotes cro.
Prm promotes cI.
Term
What does "YAC" stand for? Why is is important.
Definition
Yeast Artificial Chromosome. Can enable expression of larger eukaryotic genomes (better glycosylation).
Term
What did Botstein do?
Definition
Discovered cancer transcription patterns different than normal cells.
Term
What does "PD...D/ExK" mean? Which residue is most important?
Definition
Proline, Asp...Asp/Glu, anything, Lysine
Term
What did Berg get Nobel for?
Definition
Recombinant DNA.
Term
Name viruses of the following types: dsDNA, ssDNA, dsRNA, and 3 types of ssRNA
Definition
dsDNA: Herpes, Pox, Adeno, SV40
ssDNA: Roseola
dsRNA: Reo
ssRNA (acts as RNA): Polio, Rhinovirus
ssRNA (template for mRNA):Rabies, Measles, Flu
ssRNA (template for DNA): HIV
Term
What do N and Q do in lambda phage?
Definition
Produce anti-terminator proteins.
Term
What is the major repressor of the lambda lytic cycle?
Definition
cI
Term
What is the name of the repressor of the lambda repressor?
Definition
cro
Term
What are the steps of induction in lambda phage?
Definition
1. Damage to DNA (UV, etc.)
2. RecA protease attacks cI
3. Cro comes in
4. Lysing occurs.
Term
What are the two ways viruses can change their antibodies?
Definition
1. Antigenic shift: The antibody gene is replaced entirly by a new gene.
2. Antigenic drift: Point mutations occur naturally.
Term
How do you use homo-polymer tailing to join to blunt-end DNA strand?
Definition
Terminal transferase adds homo-polymer tails to both pieces of DNA. This makes sticky ends. Use ligase to stick them together.
Term
What does dpnI do in the PCR process?
Definition
Eats away methylated strands at end of rxn.
Term
Southern Blotting tests for...
Definition
DNA
Term
Northern Blotting tests for...
Definition
RNA
Term
Western Blotting tests for...
Definition
protein
Term
Draw and properly name X-Gal.
Definition
5-bromo-4-chloro-3-indoyl-B-D-galactose
Term
What are the general features of pUC18?
Definition
lac gene with MCS (multiple cloning site), amp (anti-biotic resistasnce), ori
Term
What are the general features of pUC118?
Definition
lac gene with MCS (multiple cloning site), amp (anti-biotic resistasnce), ori, M13ori
Term
What do DNA gyrase and helicase do? Which of the two needs ATP?
Definition
Helicase comes in and "jacks open" the DNA. Gyrase work on the back end, cutting the double strand DNA to relase supercoling (makes linking number -2).

Gyrase needs ATP.
Term
What is PRPP? What is it for?
Definition
5-phosphoribosylpyrophosphate (a ribose with 2 P's on one end, 1 P on the other). It transfers phosphate groups in the synthesis of AMP, GMP, IMP, OMP, UMP, etc. First committed step in PURINE biosynthesis.
Term
What is IMP? What is it for?
Definition
Inosinse monophosphate. Intermediate in PURINE biosynthesis. Converted to AMP or GMP in "branch point" of purin synthesis.
Term
What is OMP? What is it for?
Definition
Ornithine monophosphate. Intermediate in PYRIMIDINE biosynthesis.
Term
What are the purines? What are the pyrimidines? (Remember mnemonic!)
Definition
puRines: A, G (RAG)
pYrimidines: U, C (YUC)
Term
What causes Gout?
Definition
Build up of uric acid. Excess PRPP causes excess nucleotide synthesis, which causes excess uric acid.
Term
How do you treat gout?
Definition
Allopurinal. It stops hypoxanthine from being converted to uric acid (acts as analog inhibitor).
Term
How was lac discovered? By who?
Definition
Specialized transduction. Shapiro.
Term
Which mutagens cannot mutate pure DNA?
Definition
The base analogs (need replication) and nitrosoguanidine (needs cellular machinery to work).
Term
What mutagens can work on pure DNA?
Definition
EMS (Ethylmethanesulfinate), Aflatoxin, etc.
Term
How does Eckstein mutagenesis work?
Definition
You use a mutagenic primer and replicat in special "heavy" dCTPas. Then you use a "pac-man" to chew away the non-heavy strand, getting rid of non-mutated DNA. Exo3.
Term
How does Kunkel mutagenesis work?
Definition
Use M13 phage to get your start DNA. Add mutagenic primer. Grow in "-duT, -ung" E. Coli. duT represses something that would put U's everywhere. ung would normally cut out U's. But since the E. Coli is "minus" for these, the U's get put everywhere there is supposed to be a T.
Term
How does Quik-Change work?
Definition
Use double-stranded plasmid and forward and reverse mutagenic primers.
Term
What gene is put in GMO corn and cotton. Where is is form?
Definition
"Cry" gene from BT bacteria = protects from insects.
Term
Who made S&M (site-directed mutagenesis)?
Definition
M&S (Michael Smith).
Term
What is Class 1 virus?
Definition
dsDNA. Herpes, Adeno.
Term
What is Class 2 virus?
Definition
ssDNA. Roseola.
Term
What is Class 3 virus?
Definition
dsRNA. Rio virus.
Term
What is Class 4 virus?
Definition
ssRNA (acts as its own mRNA). Polio, Rhino.
Term
What is Class 5 virus?
Definition
ssRNA (is template for mRNA). Flu, Measles, Mumps.
Term
What is Class 6 virus?
Definition
ssRNA to make DNA. Hiv.
Term
What type of virus is Flu?
Definition
Orthomyxo. Class 5 (ssRNA is a template for mRNA).
Term
What on the flu virus is recognized by the human immune system (i.e. what are the antigens)?
Definition
HA and NA. These mutate frequently, which is why there are different flus every year.
Term
What are the general features of a tRNA?
Definition
Top = acceptor loop (attaches to amino acid). Left = D-loop. Bottom = anti-codon loop. Right = T-psi-C loop.
Term
What is an inactive X chromosome called?
Definition
Barr body
Term
What is "dosage compensation"?
Definition
To regulate genes on the two sets of female X chromosomes, one of the chromosomes is inactivated.
Term
How is differentiation of cells accomplished in eukaryotes?
Definition
By regulating transcription of certain genes.
Term
What is the sequence of elements in the Class II core promoter of eukaryotes?
Definition
TFIIB recognition, TATA box, Initiator, Down-stream core promoter
Term
What kind of eukaryotic genes would you expect to lack TATA boxes?
Definition
"Housekeeping genes" that are always on. I.e. they don't need to be turned on/off.
Term
What are the sequence of steps of transcription of a gene with introns?
Definition
1. Transcribe entire gene. 2. Put on Cap and Poly-A Tail. 3. Splice out introns.
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