Molecular Biology Midterm Flashcards

Terms Definitions
Carboxyl
• -COOH
F. Meicher
discovered DNA
Lipids
• Macromolecules, but not polymers• Mostly made up of hydrocarbons  mostly hydrophobic
GAL80
inhibits the transcriptional activation function of GAL4 in the absence of galactose
purines
adenine and guanine, 2 rings
Carbohydrates
• Sugars/linked chains of sugar molecules• Primary food source for cells• e.g. starch, cellulose, glucose, fructose (many are –ose)• Usually a multiple of CH2O formula
 
 
Endocytosis
materials enter the cell
membrane surface area decreases
EKLF
(erythroid Kruppel-like factor) made only in erythroid cells, where it binds to the beta globin promoter to activate transcription.
Experimental radioisotopes
32P, 35S, 14C, tritium
telomerase
enzyme that catalyzes lengthening of telomeres
Atom
•Nucleus with protons+ and neutrons, little elctrons orbit it •Number of protons in nucleus = atomic number •Atomic symbol = abbreviation, e.g. Au for gold •Mass number = sum of protons and neutrons in an atom •Ground state = electrically equal, same number of protons and electrons •Most stable with enough electrons to complete the outermost orbit level
how many genes does M.musculus have?
~25,000
SSBs
stabilize the separated strands and prevent the DNA molecule from becoming wound again
upstream element
site of transcription factor binding
concatomers
linking of genomes end-to-end in rolling circle replication. genomes are separated by cos sites.
3 Phases of Transcription
initiation, elongation, termination
Restriction
The endonuclease recognizes the GAATTC sequence and cleaves both strands of the foreign DNA to produce fragments with staggered ends. (sequence specific nucleases)
Nitrogenous bases of DNA
thymine, adenine, cytosine, guanine
Covalent bond
•Two atoms share electrons  molecule•Sometimes equal sharing (like CH4, methane)  nonpolar covalent bond•Sometimes unequal sharing (like H2O) because of deifferent electronegativity levels•Result of unequal sharing is a polar covalent bond with slightly charged parts
TFIID collaborates with TFIIA to bind to the TATA box.
TRUE
what is the Tm in humans?
>70 C
A gene can accept occasional changes, which allows organisms to evolve. 
T
In vivo, DNA polymerase III holoenzyme can synthesize DNA at a rate of 
D. 1000nt/sec
General transcription factors
(GTFs)can interact with RNA polymerases themselves and with DNA sequences near the start site of transcription to direct basal level transcription.
Western blotting (immunoblotting)
proteins are electrophoresed, blotted to a membrane, and probing with a specific antibody or antiserum to detect a particular polypeptide.
Initiation
1) Promoter binding
2) Melting of DNA strands
3) First substrate = purine ribonucleoside triphosphate
4) RNA polymerase joins second nucleotide by phosphodiester bond
alternative RNA splicing
spliceosome combines exons in different ways producinf different isoforms of the protein
RNA primer is made at the...
replication fork.
MECP2
a protein involved in silencing genes by causing chromosomes to wind into a more compact structure which is inaccessible to transcription factors.
messenger-rna
a single-stranded molecule of RNA that is synthesized in the nucleus from a DNA template and then enters the cytoplasm, where its genetic code specifies the amino acid sequence for protein synthesis.
Double Helix
• Twisted shape formed by two DNA strands• Figured out by Watson and Crick 1953• Diagram page 61
B. U2
The binding of which of the following snRNPs to spliceosome requires ATP? 
what aa often form random coils?
Gly and Pro
what is the centromere?
point of spindle fiber attachment
 
 
Hypotonic Solution
net movement of water into the cell
cell swells up and may even burst
Which of the following subunits of DNA polymerase III holoenzyme is referred to as the "sliding clamp"? 
B. b
preinitiation complex
(PIC) the complex of RNA polymerase, GTFs, and promoter DNA
RACE: method
1. hybridize incomplete cDNA to mRNA and use reverse transcriptase to extend cDNA to 5' end of mRNA.2. Use terminal transferase and dCTP to add C residues to 3' end of cDNA and use RNase H to degrade mRNA.3. Use oligo(dG) primer and DNA polymerase to synthesize a second strand of cDNA4. perform PCR with oligo(dG) as forward primer and and oligonucleotide that hybridizes to the 3' end of the cDNA as reverse primer.
recombinant
- DNA from different sources are put together

- Result of the reassortment of genes in new combinations (crossing over or in vitro)
AP1
trans factor binds PRE in response to phorbol esters
Stat-1
trans factor binds IRE in response to IFN-gamma
When a cell synthesizes a protein, amino acids become linked, one after the other, by
peptide bonds
Watson and Crick-year?-contribution?
-1953
-proposed that DNA exists as a double-helix of polynucleotide chains
what is the scientific name for zebra fish?
Daneo rerio
what is a chaperonin?
proteins that guide the folding of large proteins, reducing the risk of misfolding
 
 
Functions of Membrane Proteins:
transport materials
act as enzymes or receptors
-->cell-to-cell communication
recognize cells
-->self or non-self
structurally link cells
Which of the following is not part of the E. coli
 TerE
Which of the following is not found in RNA and DNA? 
sulfur
RNA polymerase I
Transcribes only the large rRNA genes. Enriched in the nucleolus, the site of ribosomal RNA synthesis and initiation of ribosome biogenesis
What is Microarray essentially?
Biochip technology; 1. Chip has nucleic acid array. 2. Patient sample added3. Detect hybridization
Avery, McLeod, McCarty (1944)
- isolated transforming substance
- R strain transformed from exposure even when:
o Protein was removed
o Protease added
o Ribonuclease added
- R strain did not transform when DNase added
What is genetic imprinting?
Results in mono allelic expression (Prader-Willi, Angelman)
Helicase Loader
Helps load the helicase onto the DNA strand
gene
a small portion of the genome - a sequence of nucleotides that is expressed together and codes for a single protein (polypeptide) molecule
E. snRNA and hnRNA
Which of the following are products of RNA polymerase II activity? 
how does a retrovirus work?
RNA injected, host synthesizes DNA from RNA
what is the hydrophobic effect?
folding that clusters hydrophobic aa inside protein
Erwin Chargaff’s rules
A bind with T (rougly equal percentage found in DNA)
G bins wiht C
primer extension
can map 5' end of RNA transcript to the nucleotide1. harvest cellular RNA and hybridize a labeled oligo DNA probe to transcript2. use reverse transcriptase to extend primer by synthesizing complementary DNA3. denature the hybrid and electrophorese the labeled primer.This can indicate the transcription start-site to the base.
terminal transferase (TT)
- A unique DNA polymerase that needs no template

- Used to add dCMPs to cDNA and oligo(dG) to a vector so that the cDNA can be added to a vector (fixes blunt ends)
lac operon: glucose- lactose-
lac repressor is bound to operator, CAP is bound to due to low cAMP --> lac operon is off
Double Stranded break repair
When you have a double-stranded break (ionizing radiation, free radicals)
D. Coprotease activity in RecA protein is activated and SOS response is induced.
 During an experiment to study the rate of infection of bacteria with T4, the bacterial cultures were accidentally exposed to a UV light source. Which of the following would be expected for this exposure? 
how does COOH affect pH?
COOH + H20 = COO- + H+
what does topoisomerase II do?
what is another name for it?
removes positive supercoiling, adds negative
aka - DNA gyrase
cuts both strands to do this
Put the following steps of E. coli primosome assembly in the correct order. (1) Primase binds.(2) DnaA binds to oriC at dnaA boxes.(3) DnaB binds to the open complex.(4) DnaA, RNA polymerase, and HU protein melt the DNA. 
B. 2, 4, 3, 1
considerations for choosing a plasmid (6)
1. copy number2. size of plasmid/insert3. MCS4. promoter5. selectable marker6. ability to screen/select
polylinker (Multiple Cloning Site)
- A region of DNA that contains multiple restriction sites

- Any of these sites can be used for inserting foreign DNA
Silent Mutation
No change in Amino Acid but there is a single change in nucleotide (usually the last one)
what aas are considered good alpha helix formers?
(MEAL) - methionine, glutamic acid, alanine, leucine
how do cruciform structures form?
why are they important?
when DNA unwinds, if there are palindrome sequences the single strands wind into cruciform structures
important b/c regulation and expression of genes often involve binding of proteins to cruc.structures
The notion of one-gene/one-enzyme is true or not?
False B/C

 An enzyme can be composed of more than one polypeptide.
B. Many genes contain the information for making polypeptides that are not enzymes.
C. The end products of some genes are not polypeptides.
The edges of bases
rich in information in the form of H- bonding and hydrophobic interaction potential.
What are 5 types of labels used for probes?
1. Radioactive2. Enzymatic3. Immunologic4. chemiluminescent5. Fluorescent
What are the 6 types of RNA
1. rRNA: structural component of ribosome; 2. tRNA: carries amino acids to ribosome; 3. mRNA: contain info for AA sequence; 4. hnRNA precursor of mRNA; 5. snRNA: splices mRNA; 6. Ribosymes: RNA molecules w/enzymatic activity
E. chromatography and UMP incorporation assay
You were asked to choose a method to separate a mixture of eukaryotic polymerases. Which of the following methods would you choose?
what happens to DNA when placed in pure distilled water at room temperature
will denature.  needs (+) charges stronger than those in water
Why is alpha complementation needed?
so that the entire lacZ gene does not have to be on an entire plasmid.
Type of material analyzed by Northern blot? Probe?
RNA. 32P-DNA probe. To measure sizes and amounts of mRNA
E. all of the choices are correct. OR1, OR2, OL1, & OL2
Which of the following operators is a target of cI gene production? 
what makes up the core of a nucleosome?
160 bp DNA
8 histone proteins (2 each):
H2A
H2B
H3
H4
the function of the DNA binding domain of TFs is ....
simply to tether the activation domain to the proper location.
A. The DNA is bound mainly to the sigma-subunit.
Which of the following is true about the holoenzyme of RNA pol in an open complex? 
How is the foreign (probe) dna seperated from the chimeric plasmid?
Cleave w/ RE and then seperate w/ gel electrophoresis.
Phage grown in the same strain of E. coli
will be able to infect same strain and give high yields of progeny.
/ 85
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