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100 Cards in this Set
- Front
- Back
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in (prokaryotes/eukaryotes) transcription and translation are simultaneous |
prokaryotes |
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in (prokaryotes/eukaryotes) transcription and translation are NOT simultaneous |
eukaryotes |
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what are life's primarily six elements |
CHNOPS |
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what are four kinds of strong bonds |
1. covalent 2. cis/trans isomerism 3. resonance 4. stereoisomerism |
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what are four kinds of weak bonds |
1. ionic bonds 2. hydrogen bonds 3. Van der Waals 4. hydrophobic bonds |
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what kinds of bonds are in the backbone of the protein molecule and between what atoms |
peptide bonds between carbon and nitrogen atoms |
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Draw the nucleic acids |
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more conjugated double bonds means (lower/higher) energy will be absorbed |
lower |
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what is the absorbance of DNA/RNA bases |
260mm |
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what is the absorbance of tryptophan |
280mm |
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draw the 20 amino acids |
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what does it mean to have a high energy bond and what doesn't it mean |
it doesn't mean that it is a strong bond but that is have a significant amount of energy when released |
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what kind of solvent is water |
polar and protic |
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what direct is most favorable to H bonds |
linear |
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what kind of bond do stacking interactions have |
Van der Waals |
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what help stabilize stacking interactions |
overlapping pi bonds |
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molecules (with/without) a dipole moment do not interact well with H2O |
without |
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what is the main bond type that stabilizes the folded structures of proteins |
hydrophobic interactions |
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a carboxylic acid group is a weak (acid/base) |
acid |
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an amino group is a weak (acid/base) |
base |
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what did T. H Morgan discover |
genes are located on chromosomes. |
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what did beadle and tatum discover |
genes somehow determine proteins; one gene, one enzyme |
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what did fredrick griffith discover |
he discovered that bacteria could pass on their genes by seeing if lysed cells would transfer their capsule gene onto a soft colony. |
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what did Avery discover |
proteins, RNA, or lipids were not transferred only DNA was between cells; done by purifying DNA |
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what did hershey and chase discover |
they radioactively labeled ecoli. They let it infect the cells then took off the virus coating. They found that the original host only needed the DNA and it consequently began producing viruses. |
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what does rough capsule mean |
cell without a capsule |
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what are the 3 parts of DNA |
phosphate group, deoxyribose, and nitrogenous base |
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what is the bond between the nitrogenous base and deoxyribose |
N-glycosidic |
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what is the difference between DNA and RNA |
DNA has an H on the 2nd carbon and RNA has an OH on the 2nd carbon |
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what kind of bonds connect phosphates |
phosphoanhydride bonds |
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what does adenosine nucleoside include |
base and deoxyribose |
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what kind of bond is in between phosphate and deoxyribose |
phosphomonoester bond |
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what does nucleotide include |
phosphate + sugar + base |
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what does nucleoside include |
sugar + base |
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what does 3' end with |
free hydroxyl (OH) |
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what does 5' have |
free phosphate group |
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what is chargaff's rule |
the % GC and AT varies between organisms |
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how many amps is one helical turn |
34A |
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how long is the minor groove |
6A |
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how long is the major groove |
12A |
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how thicc is that sexy helix |
20A |
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how many base pairs does one helical turn have |
10.5 base pairs |
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(right/left) handed helix |
right |
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what kind of bonds are in the DNA structure |
1. base pairing: H bonds 2. base stacking: stacking interactions 3. hydrophobic interactions of bases 4. repulsion of negatively charged phosphate groups |
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what are the abreviations for H bond acceptors, H bond donors, non polar hydrogens, and methyl groups |
A: H bond acceptors D: H bond donors H: non polar hydrogens M: methyl groups |
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what form is DNA in cells |
B form |
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what is the sequence that causes bends in DNA |
GCTCGAAAA |
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Understand beers law and how that thang works |
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what number indicates pure RNA |
2.0 |
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what number indicates pure dsDNA |
1.8 |
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contaminated DNA (can/cannot) be quantified |
cannot |
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how can you asses the purity of a DNA sample |
A/260/A280 |
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what factors can denature DNA |
1. high temp: high GC has higher melting point 2. agents like urea 3. pH > 11 4. organic solvents 5. decreased salt concentration |
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what is the hyperchromic effect |
when DNA can absorb different wavelengths based on the environment it is in |
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what factors must be considered when looking at melting point |
1. length- shorter DNA molecules have fewer H bonds and lower Tm 2. GC content- higher GC means more H bonds and higher Tm 3. chemical environment- salt concentration |
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what is heteroduplexes |
when duplex DNA has one strand that differs from the other |
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what happens when one mutant DNA strand anneals with a normal one |
the mutant sticks out and doesn't perfectly anneal with normal one |
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What are nucleases |
enzymes that cut nucleic acids by hydrolyzing backbone phosphodiester bonds
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what is the difference between exonucleases and endonucleases |
exostart at an end and endonucleases cut internally
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Does Alul endonuclease produce sticky ends |
nah |
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how can you figure out the cut frequency? |
find out how many possible bases can occur at any given position then put it to the power of how many base pairs the restriction enzyme can recognize |
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what does DNA ligase do |
religates blunt ends |
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the cathode is the (neg/pos) |
neg |
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is it anode to cathode or cathode to anode |
cathode to anode |
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what is the different between agarose and acrylamide |
agarose is looser with broad separation range and acrylamide is tighter with narrow separation range |
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how many negative charges doe DNA have |
2 negative charges per base pair |
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What is the dye that helps fluoresces and how |
ethidium bromide and absorbs UV light. When bound to DNA, the intensity increases 20x |
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how do you figure out amount of fragments that are stained by ethidium bromide |
take the size of chromosome and divide it by the cut frequency |
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what is southern blot |
there is radioactive probe and the membrane is placed on film. |
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can disulfide bonds be intra or inter molecular |
both |
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what is a salt bridge |
can form between the oppositely charged side chains |
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what structures come from the secondary structure |
alpha helix and beta sheets |
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how many amino acid residues per turn in alpha helix |
3.6 amino acid |
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what is characteristic of alpha helix that includes H bonds |
it is held together by H bonds and all H bond donors and acceptors are joined in H bond donors and acceptors are joined in H bonds except the first 4 NH and last 4 C=O |
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are beta sheets parallel or antiparallel |
both |
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what is characteristic of secondary structures |
compact and stable structures. |
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what is characteristic of tertiary structure |
proteins fold into multiple domains |
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what are the types of transmembrane proteins in tertiary structure |
alpha helical bundles and beta barrels |
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what is the best way to determine protein structure |
X ray crystallography |
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what is the rate limiting step in x ray crystallography |
getting the crystals; some proteins dont crystallize |
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what is a second option to determine protein structure |
NMR- nuclear magnetic resonance. Used for smaller proteins |
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why is leucine zipper called that |
it has a heptad repeat of leucine |
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what kind of protein interaction is tropomyosin |
coiled coil |
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what is zinc finger motif |
regulates gene expression |
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what is zip and assemble |
local structures can form quickly and then assemble into global structures |
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what are some examples of proteins that assist in folding |
GroE, disulfide bond isomerases, and peptidyl prolline isomerases |
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what is trigger factor |
interactos with proteins when they leave ribosome |
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what kinds of peptide bonds are found in turns |
cis proline bonds; formed slowly |
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what do peptidyl prolyl isomerases do |
catalyze the interconversion of cis/trans proline peptide bonds and speed up folding of proteins |
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what does protein disulfide isomerase do |
catalyze the formation and breaking of disulfide bonds as proteins fold; corrects disulfide bonds |
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what are some examples of post transnational modifications |
glycosylation, phosphorylation, acetylation, methylation |
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what does glycosylation do to a protein |
covalently attaches oligosacharides to amino acids |
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what is BME |
reduces S-S bonds to S-H and prevent them from forming |
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what is the isoelectric point |
the pH at which its net charge is zero |
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what is the concept of isoelectric focusing |
protein migrates up/down pH gradient until it comes to a location at which pH equals pI |
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what is transcriptome |
the complete set of RNA molecules transcribed from a genome. |
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what is preteome |
the compete set of proteins |
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what is metabolome |
the compete set of small molecules |
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what is cation exchange chromatography |
positively charged protein sticks to the neg charged beads while neg charged protein is does not. Positively charged protein can be eluted from the column by increasing concentration of salt in elution solution. |
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cations are (neg/positive) |
positive |
