Term
| Condensed, transcriptionally inactive chromatin |
|
Definition
|
|
Term
| Less condensed, transcriptionally active chromatin |
|
Definition
| euchromatin (Eu = true, 'truly transcribed') |
|
|
Term
| Which nucleotides have 2 rings? |
|
Definition
Purines (A, G)
PURe As Gold |
|
|
Term
| Which nucleotides have 1 ring? |
|
Definition
Pyrimidines (C, T, U)
CUT the PY |
|
|
Term
| Nucleotides are linked by: |
|
Definition
| 3' - 5' phosphodiesterase bond |
|
|
Term
| substituting a purine for a purine or a pyrimidine for a pyrimidine |
|
Definition
transition
(transItion = Identical type) |
|
|
Term
| substituting a purine for pyrimidine or vice versa |
|
Definition
transversion
(transversion = conVersion between types) |
|
|
Term
| 4 features of the genetic code: |
|
Definition
unambiguous - each codon specifies only 1 amino acid
degenerate - more than 1 codon may code for the same amino acid
commaless, nonoverlapping (except in some viruses)
universal (exceptions include mitochondria, archaeobacteria, Mycoplasma, and some yeasts) |
|
|
Term
| Rank the following mutations in severity of damage: missense, silent, nonsense |
|
Definition
| nonsense > missense > silent |
|
|
Term
Prokaryotic DNA replication and DNA polymerases:
Single origin of replication - continuous DNA synthesis on leading strand and discontinuous (______ fragments) on lagging strand.
_____ makes an RNA primer on which _____ can initiate replication. The previously mentioned enzyme elongates the chain by adding deoxynucleotides to the __ end until it reachers the primer of preceding fragment.
5'->3' exocnuclease activity of _____ degrades the RNA primer. ______ seals. |
|
Definition
Okazaki fragments
Primase
DNA polymerase III
3'
DNA polymerase I
DNA ligase |
|
|
Term
| DNA polymerase III has __ -> __ synthesis and profreads with __ -> __ exonuclease. |
|
Definition
|
|
Term
| DNA polymerase I excises RNA primer with __ -> __ exonuclease. |
|
Definition
|
|
Term
| DNA polymerase III has __ -> __ exonuclease activity to 'proofread' each added nucleotide. |
|
Definition
|
|
Term
| _________ create a nick in the helix to relieve supercoils |
|
Definition
|
|
Term
name the DNA polymerases for synthesizing:
RNA primers
leading-strand DNA
lagging-strand DNA
mitochondrial DNA
and DNA repair |
|
Definition
alpha
beta
gamma
delta
epsilon |
|
|
Term
DNA repair: single strand
Single-strand, excision repair-specific glycosylase recognizes and removes damaged base. ____ makes a break several bases to the 5' side. _____ removes short stretch of nucleotides. DNA polymerase fills the gap and DNA ligase seals. |
|
Definition
Endonuclease
Exonuclease
(EXonuclease = EXcision) |
|
|
Term
DNA repair: double strand
If both strands are damaged, repair may proceed via _____ with undamaged homologous chromosome. |
|
Definition
|
|
Term
| Name 4 diseases caused by DNA repair defects |
|
Definition
Xeroderma pigmentosum (skin sensitivity to UV light)
ataxia-telangiectasia (x-rays)
Bloom's syndrome (radiation)
Fanconi's anemia (cross-linking agents) |
|
|
Term
| DNA / RNA / protein synthesis direction |
|
Definition
DNA and RNA both 5'->3'
(Remember that the 5' of the incoming nucleotide bears the triphosphate (energy source for bond). The 3' hydroxyl of the nascent chain is the target. Imagine the incoming nucleotide bringing a gift (triphosphate to the 3' host. "BYOP (phosphate) from 5 to 3.")
Protein synthesis also proceeds in 5' to 3' direction, and amino acids are linked N to C. |
|
|
Term
| Name the three types of RNA and a quality of each |
|
Definition
mRNA is largest type of RNA
rRNA is the most abundant type of RNA
tRNA is the smallest type of RNA
(Massive, Rampant, Tiny) |
|
|
Term
In eukaryotes:
RNA polymerase I makes
RNA polymerase II makes
RNA polymerase III makes
alpha-amantin inhibits: |
|
Definition
rRNA
mRNA
tRNA
(I, II, and III are numbered as their products are used in protein synthesis)
alpha-amantin inhibits RNA polymerase II and slightly inhibits III. |
|
|
Term
Start codon is:
Stop codons are: |
|
Definition
AUG
(AUG inAUGerates protein synthesis)
UGA, UAA, UAG
(U Go Away, U Are Away, U Are Gone) |
|
|
Term
| in Eukaryotes, AUG codes for which amino acid which may be removed before translation is completed? |
|
Definition
|
|
Term
| in prokaryotes, AUG codes for what amino acid? |
|
Definition
| formyl-methionine (f-met) |
|
|
Term
| Site where RNA polymerase and multiple other transcription factors bind to DNA upstream from gene locus. |
|
Definition
promoter
(promoter mutation commonly results in dramatic decrease in amount of gene transcribed) |
|
|
Term
| Stretch of DNA that alters gene expression by binding transcription factors. May be located close to, far from, or even within (in an intron) the gene whose expression it regulates). |
|
Definition
|
|
Term
|
Definition
INtrons stay IN the nucleus (and are INtervening sequences)
EXons EXit and are EXpressed |
|
|
Term
| _____ facilitate splicing by binding to primary mRNA transcripts and forming spliceosomes |
|
Definition
| smal ribonucleoprotein particles (snRNP) |
|
|
Term
Initial RNA transcript (unprocessed) is known as _______.
The capped and tailed transcript is called _____. |
|
Definition
heterogenous nuclear RNA (hnRNA)
mRNA |
|
|
Term
RNA processing (eukaryotes only):
1)___________
2)___________
3)___________ |
|
Definition
1) capping on 5' end (7-methyl-G)
2) polyadenylation on 3' end (about 200 A's)
3) splicing out of introns
(Only processed RNA is transported out of the nucleus) |
|
|
Term
tRNA STRUCTURE:
75-90 nucleotides,
cloverleaf form
anticodon end is opposite 3' aminoacyl end. All tRNAs, both eukaryotic and prokaryotic, have ___ at 3' end along with a high percentage of chemically modified bases. The amino acid is covalently bound to the __ end of the tRNA |
|
Definition
|
|
Term
| Aminoacyl-tRNA synthetase (1 per aa, uses ATP) scrutinizes aa before and after it binds to tRNA. If incorrect, bond is hydrolyzed by synthetase. The aa-tRNA bond has energy for formation of peptide bond. A mischarged tRNA reads usual codon but inserts wrong amino acid. |
|
Definition
| Aminoacyl-tRNA synthetase and binding of charged tRNA to the codon are responsible for accuracy of aa selection. |
|
|
Term
| energy is required for what stages of protein synthesis? |
|
Definition
charging
(ATP - tRNA Activation)
translocation
(GTP - tRNA Gripping and Going places) |
|
|
Term
| Match RNA, DNA, protein to Western, Northern, Southern blot: |
|
Definition
SNoW DRoP
Southern = DNA
Northern = RNA
Western = Protein |
|
|
Term
| A rapid immunologic technique in which an antibody or an antigen is coupled to an enzyme as a means of detecting an antigenic match -- it is a test of antigen-antibody reactivity. The test challenges patients' blood samples either with an antigen to see if their immune system recognizes it or with an antibody to see whether a particular antigen is present in the sample. If the target substance is present in the sample, the test solution will have an intense color reaction indicating a positive result. |
|
Definition
Enzyme linked immunabsorbent assay (ELISA)
(ELISA is used in many laboratories to determine whether a particular antibody (e.g. anti-HIV) is present in the patient's blood sample. Both the sensitivity and specificity of ELISA approach 100%, but both false positive and false negative results do occur.) |
|
|
Term
| Small subunit of eukaryotic ribosome made of protein and RNA made by ______. |
|
Definition
|
|
Term
| Large subunit of ribosome (60S) composed of lots of _______ and _____ made from pol I, along with an oddball made by ______. |
|
Definition
| proteins, RNAs, RNA polymerase III |
|
|
Term
| Initiation of protein synthesis starts on ____ subunit. |
|
Definition
|
|
Term
| The genetic code was broken using a _________ system. |
|
Definition
| cell free protein synthesizing system |
|
|
Term
| How many nucleotides are in a tRNA? |
|
Definition
|
|
Term
| tRNAs contain many bases that are _______ |
|
Definition
|
|
Term
| A ribosome knows that a piece of mRNA is meant to be translated because it has a ____ |
|
Definition
|
|
Term
| An mRNA's 5' cap is recognized by _______. |
|
Definition
|
|
Term
| What three molecules form a complex with the 40S ribosomal subunit prior to the start of transcription? |
|
Definition
|
|
Term
| which factors must fall off in order for the 60S subunit to bind with the 40S subunit? |
|
Definition
|
|
Term
| What catalyzes GTP-dependent binding of aminoacyl-tRNA to ribosomes (docks tRNAs)? |
|
Definition
| Elongation Factor 1 (EF1) |
|
|
Term
| Which factor is required for moving mRNA through ribosome? This is GTP-dependent. |
|
Definition
| Elongation factor 2 (EF2) |
|
|
Term
| Where are uncoding regions in a eukaryotic mRNA found? |
|
Definition
| At both 3' end and 5' end (termination happens before the end of mRNA) |
|
|
Term
| How many proteins are produced per mRNA in eukaryotes? |
|
Definition
|
|
Term
| what is it called when there are multiple ribosomes translating the same mRNA at the same time? |
|
Definition
| a polyribosome (occurs in both prokaryotes and eukaryotes) |
|
|
Term
| How is a start AUG distinguished from an AUG in the middle of a gene in prokaryotes? |
|
Definition
| the shine-dalgarno sequence (a region of the 3' terminus of the 16S ribosomal RNA that is complementary to translation initiation sites). |
|
|
Term
| The first amino acids that are translated on a protein that is destined for secretion in eukaryotes are known as the _______. |
|
Definition
|
|
Term
| the signal peptide is recognized by the _____, which stops translation temporarily. |
|
Definition
| signal recognition protein (SRP) |
|
|
Term
| After being inserted through the ER membrane, the signal peptide is cleaved by _________. |
|
Definition
|
|
Term
| What sequences anchor proteins in a membrane during translation? |
|
Definition
| Stop transfer membrane anchor sequences |
|
|
Term
| Name 2 examples of proteins that are formed through alternative splicing. |
|
Definition
alpha-tropomyosin (involved in muscle contraction)
antibodies (membrane bound vs. floating around) |
|
|
Term
| A poly(A) tail, normally located at the end of an mRNA, may be found in the middle due to __________. |
|
Definition
|
|
Term
| the poly A tail on an mRNA is able to regulate protein synthesis by controlling ________. |
|
Definition
|
|
Term
| name an example of a very unstable mRNA that decays very quickly because they have short (or practically no) poly A tails. |
|
Definition
|
|
Term
| mRNA stability can be affected by _______ and _______ in addition to the length of its polyA tail. |
|
Definition
|
|
Term
| What step is most regulated in the regulation of protein synthesis? |
|
Definition
|
|
Term
| When regulating protein synthesis, the cell can phosphorylate ______ to deactivate it and thus stop overall protein synthesis. |
|
Definition
| eIF-2 (eukaryotic initiation factor 2) |
|
|
Term
| Name three things that could cause phosphorylation of eIF-2 in order to stop protein synthesis? |
|
Definition
viral infection
heme deprivation or heat shock
amino acid starvation |
|
|
Term
| What compound inhibits bacterial and eukaryotic protein synthesis by releasing the nascent polypeptide chain? It resembles the terminal portion of t-RNA, so it goes to the A site and binds to the growing polypeptide, cutting it off. |
|
Definition
puromycin
(pure and innocent looking because it resembles the tRNA, but really it is evil and can trick both prokaryotes and eukaryotes) |
|
|
Term
| What compound inhibits peptidyl transferase in prokaryotic ribosomes? |
|
Definition
Chloramphenicol
(like a doctor who is on call and has to leave his wife at night, chlorampheniCOL stops the reaction that forms a bond from happening) |
|
|
Term
| What compound inhibits binding of the formyl-methionine-tRNA to the 30S subunit in prokaryotes? |
|
Definition
Streptomycin
(Just like you wouldn't want to INITIATE making out with a girl who has STREP throat, STREPtomycin prevents INITIATION of protein synthesis) |
|
|
Term
| What compound binds to the 30S subunit and inhibits the binding of aminoacyl-tRNAs (to the A site) in prokaryotes? |
|
Definition
Tetracycline
(TetrAcycline inhibits binding of Aminoacil-tRNAs to the A site) |
|
|
Term
| What compound binds to the 50S ribosomal subunit in prokaryotes and blocks translocation? |
|
Definition
Erythromycin
(eRYTHmorycin stops the RHYTHMic movement of the mRNA through the ribosome because it blocks the translocation step) |
|
|
Term
| What compound inhibits eukaryotic peptidyl transferase? |
|
Definition
Cycloheximide
(riding on a uniCYCLE puts a HEX on your love life and any chance of forming a BOND with a woman, in the same way that chloramphenicol also prevents bond formation... the more sophisticated mnemonic points to this being a eukaryotic inhibitor) |
|
|
Term
| A toxin that inactivates EF-2 is... |
|
Definition
diptheria toxin
(rhymes with hysteria... mass hysteria stops any ordered movement from happening, the same way diptheria toxin stops ordered movement of the mRNA through the ribosome) |
|
|
Term
| A single point mutation can alter the splicing activity of an mRNA (knocking out splice sites or adding them in) by activating ________. |
|
Definition
|
|
Term
| Expression of recombinant proteins requires that their _____ be converted into _____. |
|
Definition
|
|
Term
| Name the polar and neutral amino acids (4) |
|
Definition
threonine, serine, glutamine, asparagine
THRee are SERenely GLUINg ASParagus |
|
|
Term
| Name the polar and charged amino acids (5) |
|
Definition
histidine, lysine, arginine (positive)
glutamate, aspartate
HIS LYCe ARE GLUing ASParagus |
|
|
Term
| Name the hydrophobic amino acids (9) |
|
Definition
Isoleucine, methionine, valine, alanine, leucine, tyrosine, tryptophan, phenylalanine, proline
I MET VAL and AL as LEU and TYRone took a TRYP over the PHEnway like PROs. |
|
|
Term
| When two amino acids form a peptide bond a _____ molecule is lost. |
|
Definition
|
|
Term
| An example of a medicine which is dependent on stereoisomerism is ______ |
|
Definition
| isoproterenol (a bronchodilator) |
|
|
Term
| What are the three possibilities of a mutation's effects on protein? |
|
Definition
no effect
affect function but not structure
affect structure (stability) and function |
|
|
Term
| Show how the NH3+, COOH, and COOH groups of glutamate change as the pH increases. |
|
Definition
| NH3+ and COOH and COOH <--pKa1--> NH3+ and COO- and COOH <--pKaR--> NH3+ and COO- and COO- <--pKa2--> NH2 and COO- and COO- |
|
|
Term
| What are the only ionizable groups in a peptide chain? |
|
Definition
| side chains and the ends of the chain |
|
|
Term
| What is a problem with SDS-PAGE analysis of proteins? |
|
Definition
| SDS destroys protein function and is hard to remove |
|
|
Term
| histidines, arginines, and lysines are commonly in what functional domain of a protein? |
|
Definition
|
|
Term
| ______ weakens protein interactions |
|
Definition
|
|
Term
| changing the______ will alter the net charge of a protein, allowing to elute from an ion exchange column. |
|
Definition
|
|
Term
| what is the problem with metabolic acidosis with respect to proteins? |
|
Definition
they cannot function at lower pHs!
(chloride channels shut down at higher and lower pHs than optimal) |
|
|
Term
| The combination of base and sugar is called a ________. |
|
Definition
|
|
Term
| In notation used for DNA, a p to the left of a base indicates a ________ linkage. |
|
Definition
|
|
Term
| The hydrophobic bases are pointed toward the (outside / inside) of a DNA double helix? |
|
Definition
|
|
Term
| The phosphate group in DNA are very ________ charged and point towards the outside of the helix. |
|
Definition
|
|
Term
| If twists are introduced in the same direction as the winding of DNA double helix, the DNA molecule is ________. |
|
Definition
|
|
Term
| This enzyme cleaves one strand of a DNA helix, passes DNA around the breaks, and reseals the DNA breaks. |
|
Definition
|
|
Term
| This enzyme cleaves both strands of a DNA helix, passes DNA around the breaks, and reseals the DNA breaks. |
|
Definition
|
|
Term
| This drug inactivates Topo I |
|
Definition
camptothecin
(Topo I is an unruly young child that must 'inactivated' by being sent to summer camp) |
|
|
Term
| This antitumor drug inhibits Topo II |
|
Definition
m-AMSA
(Topo II is the mom enzyme. M-AMSA makes MOM SAD) |
|
|
Term
| A left-handed DNA double helix is known as __________. |
|
Definition
|
|
Term
| __________ repeats in DNA are especially prone to bending |
|
Definition
|
|
Term
| Polypurine/polyperimidine tracts can form __________ DNA. |
|
Definition
| triple-helical DNA (H-DNA) |
|
|
Term
| How many base pairs are in the human haploid genome? |
|
Definition
|
|
Term
| How many genes are in a human? |
|
Definition
|
|
Term
| An example of a set of genes that appears to have arose from duplication and variation from an ancestral gene is the _________ located on chromosome 11. |
|
Definition
|
|
Term
| What percent of our genome encodes proteins? |
|
Definition
|
|
Term
| Sequences that are closely related to functional genes but no longer code for normal gene products are called __________. |
|
Definition
|
|
Term
| This class of pseudogenes is formed when DNA copies of RNA molecules are inserted back into an organism's genome. |
|
Definition
|
|
Term
| Sequences capable of inserting copies of themselves into new genomic locations are called: |
|
Definition
|
|
Term
| A class of transposable elements that are less than 500 nucleotides long and transpose through reinsertion of their products of reverse transcription |
|
Definition
| Short, interspersed repeat elements (SINEs) |
|
|
Term
| A class of transposable elements that are more than 500 nucleotides long and transpose through reinsertion of their products of reverse transcription |
|
Definition
| long, interspersed repetitive elements (LINEs) |
|
|
Term
| An example of a SINE family that composes about 10% of human DNA. |
|
Definition
|
|
Term
| An example of a LINE family, this one contains as many as 500,000 copies. |
|
Definition
|
|
Term
| A member of a class of transposable elements that transpose directly through DNA copies and encode their own transposase. |
|
Definition
| Simple Sequence Repeats (SSRs) |
|
|
Term
| Arrays of short (2-5 bp) nucleotide repeats. |
|
Definition
|
|
Term
| variable number of tandem repeats (VNTRs) are also known as _______. They have repeat units of 14-500 bases. |
|
Definition
|
|
Term
| A place in DNA where common variances occur is called a ___________. |
|
Definition
|
|
Term
| A member of a class of transposable elements that transpose directly through DNA copies and encode their own transposase and has repeat units varying from 5-100 bps (and are usually located on untranscribed regions of DNA like centromeres and telomeres). |
|
Definition
|
|
Term
| a core group of 8 histones with DNA wrapped around them is known is a ______ |
|
Definition
|
|
Term
| nucleosomes are ordered into _______ fibers. |
|
Definition
|
|
Term
| This protein prevents reannealing of DNA strands during DNA replication. |
|
Definition
| single strand binding protein (RPA) |
|
|
Term
| Origin recognition in humans is dependent upon a group of proteins termed ______. |
|
Definition
| the origin replication complex (ORC) |
|
|
Term
| A DNA helicase is deficient in children with __________ (significant risk of developing malignancies) |
|
Definition
|
|
Term
| A DNA helicase deficiency that causes premature aging. |
|
Definition
|
|
Term
| The leading strand is formed by |
|
Definition
|
|
Term
| pol delta and epsilon have a 3' to 5' _______ activity |
|
Definition
|
|
Term
| What enzyme cleaves individual nucleotides from the ends of polynucleotide chains? |
|
Definition
|
|
Term
| The RNA primer in lagging strands is placed by |
|
Definition
| polymerase alpha (pol-alpha primase) |
|
|
Term
| _____ is the only polymerase known to be associated with a primase |
|
Definition
|
|
Term
| After synthesis of the primer in lagging strands, the DNA nucleotides are placed by |
|
Definition
|
|
Term
| This auxiliary factor locks polymerases onto DNA |
|
Definition
| Proliferating Cell Nuclear Antigen (PCNA) |
|
|
Term
| This auxiliary factor loads pol sigma and epsilon onto DNA |
|
Definition
| Replication factor C (RFC) |
|
|
Term
| This polymerase is responsible for mitochondrial DNA synthesis |
|
Definition
|
|
Term
| This polymerase is believed to play a role in certain repair events |
|
Definition
|
|
Term
| A nucleotide analogue used to treat HIV is known as |
|
Definition
|
|
Term
| The cell cycle engine is assembled from _____ |
|
Definition
|
|
Term
| Progress through the cell cycle is regulated closely by a number of closely related molecules that are a complex of at least 2 proteins: a kinase and a cyclin. |
|
Definition
| cyclin-dependent protein kinases (Cdk) |
|
|
Term
| This protein functions as a cell cycle checkpoint at the G1/S checkpoint. When damaged DNA is detected, it arrests the cell cycle. |
|
Definition
|
|
Term
| More than half of all human malignancies diagnosed each year have a mutated or missing ______ allele |
|
Definition
|
|
Term
| In DNA mismatch repair in E.Coli, the mismatched bases are recognized by a protein termed ______ |
|
Definition
|
|
Term
| In DNA mismatch repair in E.Coli, the strand excision is catalyzed by a protein termed ______ |
|
Definition
Mut H
(Mut H Hacks and Hews DNA) |
|
|
Term
| n DNA mismatch repair in E.Coli, a protein-protein interface between Mut H and Mut S is thought to be achieved by a protein termed ______ |
|
Definition
|
|
Term
The human Mut S and Mut L homologues are called:
________
________ |
|
Definition
hMSH
hMLH
(human mut S homologue! note that hMHH has not been isolated because this just sounds weird) |
|
|
Term
| People who contain CAG repeats above the normal range in a certain gene are at risk of developing.... |
|
Definition
|
|
Term
The following are the 4 steps for _________.
1)incision
2)excision
3)resynthesis
4)ligation |
|
Definition
|
|
Term
| In E. Coli, pyrimidine dimers that are to be repaired through excision repair are recognized by a complex known as |
|
Definition
uvrABC
(ultra violet repair, a big complex) |
|
|
Term
| In E. Coli, this enzymes resynthesizes DNA that is excised by uvrABC during excision repair: |
|
Definition
|
|
Term
| When cytosine spontaneously deaminates to form uracil, ______ is the enzyme that comes to the rescue by recognizing and hydrolyzing the bonds. |
|
Definition
uracil-DNA glycosidase
(cuts the glycosidic bond) |
|
|
Term
| sites where bases are removed are called ____ |
|
Definition
AP sites
(APurinic or APyrimidic... isn't it nice that they both start with P??) |
|
|
Term
| Nitrous acid reacts with basis that contain amino groups to cause |
|
Definition
|
|
Term
| the N7 position of guanine is particularly prone to (this is bad) ______ |
|
Definition
|
|
Term
| name 2 molecules that intercalate between DNA |
|
Definition
proflavin and ethidium bromide
(proflavin means it has a delicious flavor like an unhealthy cake, which DNA is tempted too. Unfortunately, this compound fucks up DNA) |
|
|
Term
| A n-base cutter will have a cut site on average once every __ nucleotides |
|
Definition
|
|
Term
| variability of the human genome allows genetic examination of _______ |
|
Definition
| restriction fragment length polymorphisms (RFLPs) |
|
|
Term
RFLPs can be caused by two types of DNA variations:
___________
___________ |
|
Definition
single base changes and
tandem repeats of base sequences |
|
|
Term
| A strategy of detecting mutations through hybridization requires __________ |
|
Definition
| allele-specific oligonucleotide probes (ASOs) |
|
|
Term
| A modification of PCR that allows one to determine whether a specific RNA molecule is present in a sample |
|
Definition
|
|
Term
| A method that seperates DNA strands in a gel based on their conformation |
|
Definition
| Single-strand conformation polymorphism (SSCP) |
|
|
Term
| An enzymatic method for determining the sequence of a DNA molecule |
|
Definition
|
|
Term
| nucleotides that lack both the 2' and 3' hydroxyl groups on the ribose and are used in the Sanger method are known as |
|
Definition
|
|
Term
| A simple assay used to determine if a protein interacts with a particular DNA fragment |
|
Definition
|
|
Term
| Detailed information about protein-DNA interactions can be obtained by a technique known as the __________ |
|
Definition
| DNase I footprinting assay |
|
|
Term
| A DNA library constructed directly from genomic DNA and used to isolate specific fragments of genomic DNA |
|
Definition
|
|
Term
| A DNA library derived from mRNA |
|
Definition
|
|
Term
| A method that uses VNTRs to identify the source of different DNA samples is known as |
|
Definition
|
|
Term
| What is the only RNA polymerase located inside the nucleolus? |
|
Definition
|
|
Term
| What units, transcribed by RNA pol I, are arranged in multiple, tandemly arrayed copies in the genome? |
|
Definition
|
|
Term
| RNA polymerase I requires what 2 factors to bind to DNA and transcribe rRNA genes?? |
|
Definition
factor B and S factor
(does anyone else think it's BS that we have to memorize factor B and S factor??) |
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Term
| What is special about the activation region for the transcription of 5S rRNA by Pol III? |
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Definition
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Term
| What transcription factor first binds to the regulatory region of the 5S rRNA gene? |
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Definition
TFIIIC
(TFIIIC Clears the area for Binding of TFIIIB) |
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Term
| What transcription factor is recognized by pol III but can only bind DNA when TFIIIC has bound? |
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Definition
TFIIIB
(TFIIIB is the Bitch because TFIIIC always has to bind first) |
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Term
| The sole highly conserved sequence utilized during RNA pol II transcription is the |
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Definition
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Term
| What transcription factor binds to the TATA box region? |
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Definition
| TATA Binding Protein (TBP) |
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Term
| TATA binding protien is a subunit of what basal transcription factor? |
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Definition
TFIIID
(TFIII D is the only basal transcription factor that binds to DNA) |
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Term
| What is the most invariable element in a polyA site? |
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Definition
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Term
| The AAUAAA sequence is bound by the |
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Definition
| cleavage and polyadenylation specificity factor (CPSF) |
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Term
| What sort of columns can easily remove mRNA from a mixture of cell products |
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Definition
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Term
| the hairpin loop created by reverse transcriptase during production of a cDNA library can be cleaved by this enzyme ______ |
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Definition
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Term
| name 2 ways to screen colonies in a library for cDNA clones of interest: |
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Definition
nucleotide probes complementary to the cDNA
check if an expression vector was used during cloning -- in this case, antibodies can be used against the protein expressed by the desired cDNA |
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Term
| gene sites that are very accessible to enzymes such as DNAse I and are found in upstream control regions are called |
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Definition
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Term
| The expression of gene families can be regulated by an element acting over long distances known as _______________ |
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Definition
| the Locus Control Region (LCR) |
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Term
| Protein complexes such as SWI-SNF that can alter chromatin structure are said to be involved in the process of __________ |
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Definition
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Term
| Acetylation of histones leads to their activation or deactivation? |
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Definition
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Term
| Methylation of certain __ residues may be part of the process that keeps some genes in the inactive state |
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Definition
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Term
| Activators communicate to the basal factors through |
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Definition
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Term
| Activators bind to regulatory regions of DNA known as |
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Definition
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Term
| This protein is normally present in cells and is activated when temperature is increased dramatically. It then binds to DNA and is phosphorylated, causing transcription of certain genes. |
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Definition
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Term
| Current DNA microarrays contain how many genes? |
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Definition
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Term
Microarray
normal cells: green dye
transformed cell: red dye
What color will spot be if there is no difference in gene expression? |
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Definition
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Term
Microarray
normal cells: green dye
transformed cell: red dye
What color will spot be if there is more transcription of a particular gene in the transformed cell? |
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Definition
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Term
Microarray
normal cells: green dye
transformed cell: red dye
What color will spot be if there is more transcription of a particular gene in the normal cell? |
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Definition
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Term
Microarray
normal cells: green dye
transformed cell: red dye
What color will spot be if a given cDNA is not present in either cell type? |
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Definition
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Term
| One conclusion of DNA microarray studies was that the oncogene _____ is expressed at abnormally high levels in malignant breast tumor cells. |
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Definition
ErbB2
('Error in breast?') |
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Term
| Introduction of a nucleic acid complementary to an aberrantly expressed mRNA to prevent its translation is an experimental therapy known as |
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Definition
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Term
| The mechanism of sequence-specific, post-transcriptional gene silencing initiated by double-stranded RNAs homologous to the gene being suppressed is called |
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Definition
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Term
| this initiation factor interacts with the mRNA molecule before translation by associating with the m7G cap structure. |
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Definition
eIF4F
(associates with G cap. What is the letter before G? F. eIF4(Four)F)...) |
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Term
| Activation of each t-RNA requires __ high energy phosphate bonds |
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Definition
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Term
| An example of a very stable mRNA that decays very slowly is the mRNA for |
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Definition
| albumin (also hemoglobin) |
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Term
| An example of a gene that requires a complex interaction of MANY initiation factors is the _____ gene |
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Definition
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Term
Some members of this class of junk DNA encode a reverse transcriptase:
Simple sequence repeats (minisatellites)
Alu repeats
Telomeres
Processed pseudogenes
line elements |
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Definition
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Term
| mismatched bases frequently arise from replication errors: t/f? |
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Definition
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Term
| mismatched bases are removed by glycosidase that creates an AP site? t/f |
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Definition
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Term
In humans: all the of the folliwng are transcription activators of RNA pol II except:
HSF
MyoD
p53
Steroid hormone/receptor complexes
TFIIIB |
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Definition
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Term
| Erythromycin targets which subunit of prokaryotic ribosomes? |
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Definition
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Term
| The compound Gleevec is useful for treating chronic myelogenous leukemia because it: |
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Definition
| is an inhibitor of the kinase activity of the Bcr-Abl fusion protein |
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