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Flashcards in Exam 1 Deck (136)
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What is a nucleoside?

A base and a sugar -- NO phosphate


What is a nucleotide?

A base, a sugar, and a phosphate group


What is the name of the bond which attaches two nucleotides together?

Phosphodiester bond
--> Forms between the 5' end of one sugar and the 3' end of the next sugar


What is the name of the bond which holds together two phosphate groups?

Phosphoanhydride bonds


True or false: Phosphoanhydride bonds are not easily hydrolyzed

FALSE: These bonds ARE easily hydrolyzed. When the bond is hydrolyzed, energy is released


What three stabilizing forces are present in B DNA?

i) Placement on opposite sides of the double helix (on outside of helix, as opposed to inside)
ii) The negative charge on the phosphates are neutralized by positive charges of lysine and arginine residues of histone proteins
iii) The stacking of the aromatic rings of the bases that permits van der Waal interactions between the electron clouds that sandwich the rings


What is the bond between the base and the sugar in a nucleoside?

N-glycosidic bond


How does A form differ from B form? What type of DNA or RNA takes on the A form?

-Wider and more compact than B
-The structure assumed by dsRNA (double-stranded RNA)


How does the Z form differ from the B form? What type of DNA or RNA takes on the Z form?

-It is left-handed as opposed to right-handed
-Doesn't really exist in nature


Describe 3-stranded DNA

-Occurs through Hoogsteen base pairing (H-binding with N’s in 5-membered (rather than 6-membered) ring from purine)


What is 4-stranded DNA? Where does it occur?

-Called G quartets or G-quadruplexes
-Occurs in G-rich areas of DNA or RNA
-Stack on top of each other in 4G coils
-Occurs often in telomeres


What is ssDNA? Where would you find it?

-It is circular DNA (bound by a phosphodiester bond from the 3' to 5' end)-- Also called a plasmid
-Found in bacteria and archaea


Which part of a helix-turn-helix motif can fit into the major groove of DNA?

The a-helix


What part of a zinc finger motif can fit into the major groove of DNA?

The a-helix


How do DNA binding proteins work?

They recognize a specific sequence of DNA and can bind in the major groove


True or false: B-sheets can fit into the major groove of DNA

TRUE - B-sheets, along with a-helices, can both fit into the major helix of DNA in order to interact with it


How does a protein attach to DNA when interacting with it?

Through hydrogen bonds on the amino acid side chains of the protein and the phosphate backbone of the DNA (in the major groove)


Definition: Multivalency

When a lot of weak bonds all work together and the resulting bond of the two molecules is very strong (think of velcro-- only one fiber of velcro is weak, but the more you have, the better the two objects stick together)


What is the molecular basis by which proteins read DNA’s encoded information? (3 answers)

i) Hydrogen Bonding
ii) Multivalent interactions
iii) Intercalation


What does a restriction enzyme do?

Restriction enzymes chop up DNA


What does an intercalating dye do? What is an example of an intercalating dye?

-And intercalating dye stains DNA so that it can be seen under UV light (typically in a gel electrophoresis experiment)
-Ethidium bromide is an intercalating dye


What is hybridization?

When a set of bases pairs with a complementary set of bases (making hydrogen bonds)
--> When one strand of DNA binds to a new strand of DNA (not when a new strand is being formed from a template strand)


Why do higher temperatures create the more accurate hybridizations?

Only perfect matches will form at higher temps because they are the only ones strong enough to resist the heat-- weaker (imperfect) matches will be unable to stay bonded at high temps


What is a Western Blot used for?

To detect proteins


What is a Northern Blot used for?

To detect RNA


What is a Southern Blot used for?

To detect DNA


Definition: DNA sequencing

The technology to determine the order of base pairs along DNA molecules
--> Often requires cloning


When cloning via plasmids, why must you use the same restriction enzymes for both the plasmid and the DNA?

You need to use the same restriction enzymes for both so that they have matching sticky ends. The sticky ends will improve binding.


What are the two types of "Libraries"? What is the difference between them?

i) Genome Library
--Contains all genes in a genome, both coding and non-coding
ii) cDNA Library
--Contains ONLY genes that code for proteins (exons)-- no introns or non-coding areas are included


Describe blue-white colony selection using the LacZ gene

-Plasmids are made that should disrupt the LacZ gene when inserted into the bacterial genome
-After mixing plasmids and bacteria, the bacteria are grown on a plate that contains a blue galactosidase compound
-Those bacteria that grow into a blue colony can still process galactosidase (because their LacZ gene is still intact), and therefore these are UNDESIRABLE colonies (do not contain the desirable plasmid)
-Colonies that grow as a white color have a disrupted LacZ gene, therefore these colonies are selected FOR, because they have the desirable plasmid