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Chromatin
An organized structure of DNA and protein In the Eukaryotic nucleus needs to fit up to 2m of DNA
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What are topoisomerases?
Enzymes that cut, rotate, and relegate DNA strands
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Over and underwound DNA compared to B-DNA
Overwound<10.5 bp per turn
Underwound >10.5 bp per turn
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How has molecular biology impacted energy?
(e.g., jet fuel from GMO crops)
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How has molecular biology impacted defense?
Defense (e.g., biological and chemical weapons and antidotes)
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How has molecular biology impacted Environmental sciences/toxicology?
(e.g., understanding of the mode of action of environmental pollutants)
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Which form of DNA is prevalent in vivo?
B-DNA
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Scientific name for fruit flies
Drosophila melanogaster
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Dr. Anna Stepanova's favorite plant
Arabidopsis
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How can supercoils be resolved in stranded DNA?
Matrix attachment regions- linear chromosomal DNAs anchored to a protein scaffold (helps form the superhelixes and loops to relieve strain DNA can also resolve supercoiling enzymatically with topoisomerases
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What gives an olgio a higher melting temperature?
Higher GC content than AT content
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DNA supercoils
The way that DNA relieves the torsional stress in over/underwound circular DNA molecules
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How can you monitor DNA strand separation?
Measuring UV light absorbance at 260nM- single stranded (ss) DNA absorbs more UV light than double stranded DNA
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G-quadruplex DNA
Four stranded structures forming in DNA sequences that are rich in guanines.
- The guanines are arranged in a square and held together by
- hoogsteen bonds
Form in the telomeres of chromosomes
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How are G-quadruplex DNA formations stabilized?
Monovalent cations (M+)
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What conditions are favorable for formation of triple helices?
Sequences with mirror repeat symmetries
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promoter -
a region of DNA upstream of a gene where relevant proteins (such as RNA polymerase and transcription factors) bind to initiate transcription of that gene
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codon -
A codon is a DNA or RNA sequence of three nucleotides (a trinucleotide) that forms a unit of genomic information encoding a particular amino acid or signaling the termination of protein synthesis (stop signals). There are 64 different codons: 61 specify amino acids and 3 are used as stop signals
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peptidyl transferase -
Peptidyl transferase, an integral part of the ribosome, catalyzes the formation of a peptide bond between the carboxyl group of the nascent peptide (bound as peptidyl-tRNA to the ribosomal donor site) and the amino group of the new amino acid
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snRNP -
small nuclear ribonucleoproteins, are RNA-protein complexes that combine with unmodified pre-mRNA and various other proteins to form a spliceosome, a large RNA-protein molecular complex upon which splicing of pre-mRNA occurs.
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plasmid -
A plasmid is a small circular DNA molecule found in bacteria and some other microscopic organisms. Plasmids are physically separate from chromosomal DNA and replicate independently.
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intron -
An intron is a region that resides within a gene but does not remain in the final mature mRNA molecule following transcription of that gene and does not code for amino acids that make up the protein encoded by that gene. Most protein-coding genes in the human genome consist of exons and introns.
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miRNA -
MiRNA are small, evolutionary conserved, single-stranded, non-coding RNA molecules that bind target mRNA to prevent protein production by one of two distinct mechanisms.
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The forms of DNA that are likely to exist in vivo?
A, B, and Z forms
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Minimum amount of bases that TFs can discriminate between by making just two hydrogen bonds with the bases in the DNA major groove:
4 base pairs
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How do sequence-specific transcription factors work?
They recognize certain patterns in the major groove of the DNA
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What provides chemical stability to the double helix in DNA?
Base sacking
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Distance between the 1’ carbons of the sugars on the backbone of the double helix?
(1.08nM)
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What are major and minor grooves in DNA?
Major groove: site where majority of sequence-specific DNA binding proteins go
Minor groove: (doesn’t bond?)
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The Law of Segregation:
Each inherited trait is defined by a gene pair. Parental genes are randomly separated to the sex cells so that sex cells contain only one gene of the pair. Offspring therefore inherit one genetic allele from each parent when sex cells unite in fertilization
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The Law of Independent Assortment:
Genes for different traits are sorted separately from one another so that the inheritance of one trait is not dependent on the inheritance of another.
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The Law of Dominance:
An organism with alternate forms of a gene will express the form that is dominant.
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what does each nucleotide consist of?
- Three parts:
- Five-carbon sugar (pentose)
- phosphate group (1-3 phosphates)
- base
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which type of bond attaches a base to a sugar?
glycosidic bond
=nucleoside
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nucleotide-
base+sugar+phosphate group(s)
a nucleoside + (1--3) phosphate groups= nucleotide
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How do you attach nucleotides?
They are attached via a 5' to 3' phosphodiester bond. pyrophosphate is released
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What does the 5' symbol refer to ?
the carbon in the sugar where PO4 attaches
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What does the 3' symbol refer to?
the carbon in the sugar where the hydroxyl group (OH) attaches
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The nitrogenous bases in DNA are hydro(phobic/phillic)?
hydrophobic
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Where are transcription factors likely to bind to DNA secondary structure?
Major groove
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How can a transcription factor discriminate between four possible base pairs?
by making just two hydrogen bonds with the bases in the DNA major groove
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The unusual secondary conformations of DNA:
slipped structures, cruciforms, triple helices
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How has molecular biology impacted nutrition?
(e.g., effect of food processing or molecular basis of allergenicity)
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How has molecular biology impacted forensics?
(e.g., DNA fingerprinting to incriminate a suspect or to determine paternity)
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