Molecular Biology 5 Flashcards

Terms Definitions
HDAC
Histone deacetylase
pBluescript
a commercial phagemid
Transfer RNA (tRNA)
constant lengths
neurofilaments
intermediate filaments of neurons
Hydrophilic
•Polar substances that dissolve easily in water
what is HeLa?
human cell line
 
Transmission genetics
 

–Mendel’s laws of inheritance


–The chromosome theory of inheritance


–Genetic recombination and mapping


–Physical evidence for recombination
autoradiography
radioactive emissions expose film, which when developed, produces dark spots
Post-translational Modifications
i.e. phosphorylation regulates eukaryotic replication
Hershey and Chase-year?-contribution?
-1952
-used radioactively labelled bacteriophage to demonstrate that DNA is the genetic material
how many genes does A.thaliana have?
~25,000
what does a kinase do?
adds phosphate
A fragment restricted with EcoRI enzyme can be used for ligation into a plasmid that was restricted with BamHI because both the insert and the plasmid contain sticky ends. 
f
GAL4
the main transcription factor that regulates the induction of transcription of the GAL metabolic genes.
What are RFLPs used for?
DNA fingerprinting
Mention Chargaff's rules
Strands are antiparallel, complementary and the total % of purines = total % of pirimidines
Primase
Synthesizes small RNAs in opposite direction
primer
RNA chain added to begin DNA replication
Proteins
• Organic molecules that do most of the work in a cell• Assemble, disassemble, transport molecules, structure for cells and organisms• Made of amino acids and several layers of folding
what organism is ideal for studying life span, aging processes, and development?
C.elegans
at what pH does DNA completely denature
11.3
Mapping is used to establish the location of genes   relative to each other.
T
In E. coli, the antibiotic nalidixic acid, by inhibiting DNA gyrase, prevents DNA replication, which then causes positive supercoiling of the DNA. 
True
Epitope tagging.
allows addition of protein coding sequence in frame to any yeast gene. You use antibodies that are specific for the epitope you entered.
What insert size can YACs accomodate?
~1 Mb
CaCl2
- Treatment of cells with this solution makes the cell membrane leaky and permeable to plasmid DNA
cis regulators
core promoter sequence (TATA, BRE, DPE), proximal promoter region (GC box, CCAAT box), enhancers, silencers, insulators, response elements (CRE, SRE, IRE, GRE, PRE, HSRE, HMRE)
Restriction enzymes
Scan DNA for exact sequence.Highly specific. Will not cleave even if there is one change in the bases.It can slide on and off the DNA. Dimer. Structure doesn't change when bounded on DNA until it finds it exact sequence.After, DNA is cleaved on both strands and forms sticky ends and will not come back together.
codon
a triplet of adjacent nucleotides in the messenger RNA chain that codes for a specific amino acid in the synthesis of a protein molecule.
Erwin Chargaff
Chargaff's Rule: equivalences of A to T and C to G in DNA
D. RNA and protein.
"Snurps“ or snRNPs are composed of
A. epitope tagging
Which of the following would you choose to specifically collect polymerase subunits in cell extracts? 
what is the generation time of S.cerevisiae?
~90 min.
how is Z-DNA different than B-DNA?
12 bp/turn
left-handed
skinnier, longer than B
Which of the following techniques is not used to quantify the level of gene expression? 
southern blotting
The relationship between genes and enzymes was shown by 
Beadle and Tatum.
Mig1p
in the presence of glucose Mig1p binds to elements of these promoters to repress transcritipon ieven in the presence of galactose. Mig1p binds to regulatory regions of many other genes that are repressed in the presence of glucose. In the absense of glucose, Mig1p is kept in the cytoplasm as it is phosphorylated by the Snf1 kinase complex protein complex.
DNase footprinting
uses DNase to cleave DNA. Can determine where protein is bound by looking at the results of electrophoresis and finding a gap in fragments (this area is protected by the protein)
selection marker
- A bacterial gene that confers antibiotic resistance
NMDA receptor
require glutamate and glycine to allow Na and Ca influx and K efflux; irreversible antagonists: amantadine and memantine; reversible antagonists: ketamine and PCP
Frameshift Mutation
Can happen with an addition or deletion of nucleotide. With an addition and deletion it changes the entire sequence from there on.
plasmid
a segment of DNA independent of the chromosomes and capable of replication, occurring in bacteria and yeast: used in recombinant DNA procedures to transfer genetic material from one cell to another.
B. combination of histone modification on a given nucleosome near a gene's control region affects the efficiency of transcription of that gene.
 The Histone Code states that the 
what causes stationary phase?
death rate = growth rate-nutrients being depletedbacteria waste accumulating
What are the 5 attractive forces?
1. hydrophobic interactions
2. ionic
3. H-bond
4. hydrophobic cluster
5. van der waals
Phosphodiester bond in DNA
- phosphodiester bond: phosphor group is a diester linkage because there is a combination of an ester and an alcohol- the acid is phosphoric acid- two alcohol groups on either sugar ring
It is suspected that a novel histone protein only interacts with the promoter region of b-globin genes. Which of the following techniques should be used to confirm this suspicion? 
A. EMSAB. DNase footprintingC. filter bindingD. gel mobility shift assay
Roger Kornberg
Won nobel prize in 2006 for structure of yeast RNA pol II. He is the son of Arthur Kornberg.
non-template strand (sense)
The strand that looks like the mRNA.
endonuclease
- An enzyme that makes cuts WITHIN a polynucleotide strand
Function of topoisomerases in prokaryotes
Introduce negative or positive supercoiling by breaking and resealing the sugar-phosphate backbone
Missense Mutation
Change in Amino Acid from a single change in nucleotide (usually the second one)
artificial selection
a process in the breeding of animals and in the cultivation of plants by which the breeder chooses to perpetuate only those forms having certain desirable inheritable characteristics.
B. upstream element
Which of the following is not a part of the core class II promoter? 
what is the length of an average polypeptide chain unfolded? folded?
0.1-0.5 microns0.004-0.008 microns
what is a conjugated protein?
a protein with associated large biomolecule. ex. nucleoprotein (w/nuc.acid), glycoprotein (carbohydrate), lipoprotein (lipid)
Which of the following statements is true concerning DNA replication in prokaryotes? 
A. DNA replication is semiconservative.B. DNA replication is semidiscontinuous.C. DNA replication is RNA dependent.
E. There is one origin of replication.
TF II B
links TBP and polymerase, and with TF II A helps impart directionality to the PIC. Extends toward the downstream side of TBP to position polymerase toward the CAP site.
How does cloning work?
1. DNA fragms + cloning vectorResult = Chimeric plasmid w/ antibiotic resistance factor2. Put chimeric plasmid in host cells (ecoli) on media with antibiotic3. Host makes lots of copies4. Check for antibiotic resistance to make sure the plasmid is chimeric.
transcription initiation complex
formed by RNA polymerase II and TFIIs at the core promoter TATA
lac operon: glucose- lactose+
lac repressor is not bound to operator, CAP is bound due to low cAMP --> lac operon is on
genetic code is
The exact sequence of nucleotides on a DNA strand
E. They contain an inverted repeat, they contain a hairpin loop, and they contain several T's in the nontemplate strand of DNA.
Which of the following are characteristic of intrinsic terminator elements? 
what was the first eukaryotic org. to have genome completely sequenced? when?
S. cerevisiae - 1996
 
Which of the following statements is not true concerning DNA replication in prokaryotes? 
DNA replication requires only one enzyme
what 3 proteins are necessary for PolII to efficiently locate the promoter site on a gene and iniate transcription
a critical general transcription factor, the TATA binding protein, and a transcription factor protein SP1 that can bind to GC boxes
How is a genomic library constructed?
Using overlapping fragments of DNA that have been generated by mechanical shearing or partial digestion with frequently-cutting REs.Size select frags by gel purification
What are some disadvantages of Probes?
1. Expensive2. Can't detect pathogens you don't suspect. 3. May detect non-viable insignificant pathogens.4. Still have to grow for antibiotic suscept testing5. Lack of FDA approval6. Hard to choose best probe7. Lack of sensitivity
Describe the control of gluconeogenesis by response elements
1. Cortisol + zinc finger receptor bind GRE of PEPCK gene; 2. Glucagon increases cAMP --> protein kinase A --> phosphorylation of CREB --> CREB binds CRE --> upregulation of PEPCK. PEPCK converts OAA into PEP
B. CAP will assist in stimulating transcription of the lac operon if lactose is added.
Which of the following is mostly likely to occur if the level of glucose is low in a bacterial cell? 
what type of proteins are water soluble? water insoluble?
soluble - globular proteinsinsoluble - fibrous
what is the diff. between renaturation and hybridization
renaturation - same parental molecules formed
hybridization - similar but not identical strands recombine
 
During an experiment with drosophila, it was discovered that all females had red eyes. A conclusion based on this observation would be: 
A. the gene for eye color is located on the X   chromosome.B. the eye color phonotype is sex-linked.
Choosing a library: cDNA or genomic?
cDNA: if you want to clone protein-encoding genes and use them for protein expressiongenomic DNA: if you want the DNA sequence, to look at promoter regions, see introns
What is a large segment deletion? Mention two examples
Unequeal crossover in meiosis. Ex. Alpha thalasemia: deletion of alpha globin gene from chromosome 16; Cri-du-chat: 5q deletion
What are the nucleotides/bases in DNA?
There are four types of nucleotides (or 'bases') in the DNA: adenine (A), thymine (T), guanine (G) and cytosine (C).
C. reduction in the amount of rRNA made
Predict a possible effect of deleting the enhancers region of the polymerase I gene. 
Site-directed mutagenesis is used for which of the following purposes? 
to make changes to specific bases in DNA
What do you need in a good expression vector?
1. strong promoter2. inducible promoter (drug or heat inducible)3. ribosome binding site near an ATG codon
What is a triplet repeat expansion? Mention an example
Protein is longer than normal and unstable. Ex. Huntington CAG repeat codes multiple glutamines
C. binding of the activator to DNA, without activating transcription
One effect of mutation or deleting the activation domain of a transcriptional activator would be 
 
Which of the following would prevent the formation of a phosphoester bond in DNA? 
removal of an oxygen from carbon 3 of the sugar
What are 3 advantages of PCR?
1. Can detect a v. small amt of microbial cells2. Highly sensitive/specific3. Good for ID pathogens straight from the specimen.
what are the non-protein (no aa) components that may be associated with proteins?
1. Cofactors - ions, etc. that are not fixed, can move from protein to protein (Fe, Cu)
2. Prosthetic groups - fixed to a protein (heme, vitamins such as B-3)
3. Large biomolecules - nucleic acids, carbohydrates, lipids. make up conjugated proteins.
what are 3 ways proteins might be denatured?
1. heat - break covalent bonds
2. pH - neutralizes charges on side chains
3. chemical reagants - ex. SDS
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