Exam 2 Flashcards
What are the pyrimidines?
Cytosine
Uracil
Thymine
What are the purines?
Adenine
Guanine
What is the only nucleotide explicit to DNA?
thymine
What is the only nucleotide explicit to RNA?
uracil
Are purines or pyrimidines a 6 atom ring?
pyrimidines
Are purines or pyrimidines a 9 atom ring with 2 rings?
purines
Why are bases insoluble in water?
aromaticity
What are nucleosides?
nitrogen base + sugar
What bond links bases to sugars in nucleosides?
beta–glycosidic bond
What number type are sugars in DNA?
pentose
_________ makes nucleosides more water soluble than free bases
sugars
What does the hydroxyl group of at the 2-position affect?
susceptibility to hydrolysis
secondary structure
Why is DNA more stable?
it has an H and not an OH
What do syn and anti nucleosides look like?
syn: base on same side as sugar
anti: base on opposite side as sugar
What are the 4 common ribonucleosides?
- cytidine
- uridine
- adenosine
- guanosine
(–ine)
What is the two and four letter symbol for deoxyadenosine?
dA
dAMP
What is the two and four letter symbol for deoxyguanosine?
dG
dGMP
What is the two and four letter symbol for deoxythymidine?
dT
dTMP
What is the two and four letter symbol for deoxycytidine?
dC
dCMP
What is the one and three letter symbol for adenosine?
A
AMP
What is the one and three letter symbol for guanosine?
G
GMP
What is the one and three letter symbol for uridine?
U
UMP
What is the one and three letter symbol for cytidine?
C
CMP
Some minor nucleosides have “methyl” in the beginning of their name; these nucleosides are an example of a _____________ marker
epigenetic marker
N6-Methyladenosine is a minor DNA nucleoside common in _________ but not found in __________?
bacteria
eukaryotes
What 2 ways are minor DNA nucleosides helpful?
- markers own DNA to protect from degradation and degrade of bacterial DNA
- mark genes that need to be activated
The minor RNA nucleoside, ____________, is found in the wobble position
inosine
What are 2 minor RNA nucleosides?
- inosine
- pseudouridine
nucleosides are ___________ for nucleic acids
substrates
What is known as the energy carrier for nucleosides?
5’-triphosphate
Where is energy stored in nucleotides?
phosphoric bond
What does GTP drive?
protein synthesis
What does CTP drive?
lipid synthesis
What does UTP drive?
carb metabolism
What do cyclic nucleotides regulate?
regulators of cellular metabolism
(found in all cells)
What are polynucleotides?
chains of nucleic acids
What bond links nucleic acids?
3’-5’ phosphodiester bonds
What is the charge of DNA’s back bone?
negative
Is DNA or RNA more stable?
DNA
What are the 5 types of RNA?
1.ribosomal RNA
2. messenger RNA
3. transfer RNA
4. small nuclear RNA
5. small non-coding RNA
What are the 2 fundamental chemical differences between DNA and RNA?
- DNA contains 2-deoxyribose instead of ribose
- DNA contains thymine instead of uracil
How does nature solve this issue of cytosine spontaneously deaminating into uracil?
uses thymine with a 5-methyl group to replace uracil
What is Chargaff’s rule?
A=T
G=C
What did Rosalind Franklin do?
x-ray fiber diffraction to find the helix
What did Watson and Crick do?
base pairing and double helix
How many hydrogen bonds does A:T have?
two
How many hydrogen bonds does G:C have?
three
What regions of DNA are most stable?
G:C rich regions
Describe the major groove of DNA
large enough to accommodate an alpha helix from a protein
How is DNA antiparallel?
the two stands run in the opposite direction of each other
What is the consequence of DNA being antiparallel?
complementary strands
Base pairing is done by ____________ bonds
hydrogen
What is the only known left-handed DNA?
Z-DNA
What is the most common DNA?
B-DNA
What DNA is dehydrated?
A-DNA
What DNA is right handed?
A-DNA
B-DNA
What are 2 ways to sequence nucleic acids?
- Chain termination (sanger)
- base specific chemical cleavage
How are dideoxynucleotides used in chain termination sequencing?
they are randomly added to DNA being synthesized by DNA pol causing chain termination
How does base specific chemical cleavage sequencing work?
like sanger but chain is terminated by chemical agents
Can the secondary structure of DNA be denatured then renatured?
yes
what is reeannealing?
reassociation of the DNA strands into double helix
The rate of re-association is___________ proportional to genome complexity
inversely
What is the tertiary structure of DNA?
supercoils
What is the job of topoisomerase?
relaxing supercoils
o
o
What is the difference between toroidal and interwound supercoils?
toroidal: spirals out
interwound: spirals in
how do you find linking number?
L = twists + writhe
What are twists and writhes?
twists: number of helical turns
writhe: number of times helix crosses over on itself
_________ super coils makes it easier for DNA to unwind
negative
How is torsional stress on molecules resovled?
DNA is unwound
What is a type of topoisomerase?
gyrase
what does DNA gyrase do?
introduce negative supercoils
What are bacterial DNA gyrase inhibitors known for?
antibiotics
Supercoiled DNA in a torodial form wraps around ____________-
protein spools
What is an an example of a protein spool?
histones
What are the 3 parts of a chromosome?
- origin of replication
- two telomeres
- centromere
_________ is the genetic material for cellular organisms
DNA
Why is DNA replication semiconcervative?
the replication DNA is made of one new strand and one old strand
What did Meselson and Stahl’s experiment prove?
DNA replication is semiconservative
N14 and N15 created mixed strands
How is DNA replication bidirectional?
two replication forks which move in opposite directions
How id DNA replication semi-discontinous?
one strand synthesizes smoothly and one in fragments (lagging)
What does DnaA do in bacterial DNA replication?
initiator
What does DnaB do in bacterial DNA replication?
unwinds DNA