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
What does DnaG do in bacterial DNA replication?
primase
What does DnaC do in bacterial DNA replication?
helicase inhibitor
Where does DNA polymerase add nucleotides?
3’ end
What is the purpose of 3’-5’ exonuclease activity in DNA polymerase I?
proof reading
removes incorrect nucleotides
What is the purpose of 5’-3’ exonuclease activity in DNA polymerase I?
removes primer
What fixes the nick between Okazaki fragments during DNA replication?
DNA ligase
DNA polymerase III uses an _________ primer for DNA synthesis
RNA primer
What is the “real” DNA polymerase for bacteria?
DNA polymerase III
What is special about the beta subunit of bacterial DNA polymerase III?
it forms a ring around DNA
supercoiling must be compensated by ___________
DNA gyrase
why do eukaryotes have multiple origins of replication?
there are so many genes
The earlier in S phase the DNA is replicated the ________ condensed it is
less condensed
What was identified as the origin of replication identified in yeast?
ARS (autonomously replicated sequence)
What is ORC?
origin of replication
o
o
What does MCM, Cdt1 and Cdc6 do in DNA replication?
loads helicase
At ORC what is formed to start DNA replication?
Pre-RCs (prereplication complex)
______ proteins are replication licensing factors
MCM
__________ complexes control cell cycle
cyclin-Cdk
What are the 3 major cyclin types?
- G1/S-cyclin-Cdks
- S-cyclin-CDKs
- M-cyclin-CDKs
What does G1/S-cyclin-Cdks trigger?
trigger progression through the start checkpoint
What does S-cyclin-CDKs trigger?
trigger DNA replication
What does M-cyclin-CDKs trigger?
triggers mitosis
What does the inactive state of Cdk look like?
T loop
What does the partially active state of Cdk look like?
cyclin is bound
What does the active state of Cdk look like?
Cdk is phosphorylated
Checkpoints of the cell cycle depend on ________ and ________
cyclin and Cdk
DNA replication occurs _______ per cell cycle
once
What are the two steps to ensure only one DNA replication per cell cycle?
- licensing of replication (late M or early G1)
- activation of replication (S phase)
What did cell-fusion experiments give evidence of?
re-replication block
_____ phase cytoplasm contains all the factors needed to drive G1 nucleus to DNA synthesis
S phase
What are the 3 mechanisms that prevent re-replication?
- inhibition of MCM2-7 loading by geminin
- replication-dependent Cdt-1 degradation
- Cdk-dependent inhibition pf pre-RC formation
What are the two challenges of tightly packed DNA for replication?
- DNA template needs to be accessed
- nucleosomal organization has to be reproduced on daughter strands
What does PCNA do in chromatin restoration?
sliding clamp that scans for damage
directs DNA methylation
What is endoreduplication?
DNA replication without cytokinesis
___________ is replication of DNA with completion of mitosis but not cytokinesis
polyploidy
___________ is repeated replication of DNA without forming new nuclei
polyteny
What enzyme maintains telomere length?
telomerase
Telomerase uses an internal ______ template
RNA
telomerase uses _______ transcriptase activity
reverse transcriptase
What cell type lacks telomerase causing shortening telomeres?
somatic
What did Howard Temin discover?
RNA-directed DNA polymerase (reverse transcriptase)
DNA is an intermediate in RNA tumor virus replication
What is RNA-directed DNA polymerase also known as?
reverse transciptase
What are the three enzymes involved in reverse transcriptase?
- RNA-directed DNA polymerase
- RNase H
- DNA-directed DNA polymerase
What does DNA-directed DNA polymerase do in reverse transcriptase?
makes DNA duplex (seconda DNA strand) after RNase H destroys the viral genome (RNA removed)
What does RNase H do in reverse transcriptase?
degrades RNA in the DNA:RNA hybrids
All RNA tumor viruses contain ____________
reverese transcriptase
What has reverse trancriptase aided in the treatment of?
AIDs
What is the process of reverse transcriptase?
complementary DNA is synthesized using a strand of RNA
An _________ primer is required for reverse transcriptase
unusual primer
What was the first approved drug/nucleoside to treat aids?
AZT
What substrate of AZT binds to HIV reverse transcriptase?
AZTTP
___________ recombination involves similar DNA sequence
homologous
____________ recombination involves very different nucleotides sequences
non-homologous
_________________ is the enzymatic insertion of transposon
transposition
________________ and ______________ play a significant role in evolution
non-homolgous recombination
transpositions
What did Meselson and Weigle’s experiment show?
recombination of chromosomes (using heavy and light phages)
What are the 6 steps of Holliday Model Homologous Recombination?
- SYNAPSIS – two homologous DNA duplexes align
- SINGLE STRAND NICK
- STRAND INVASION – partial strand unwinding
- LIGATION – Holliday junction created
- BRANCH MIGRATION – unwinding then rewinding of two duplexes
- STRAND EXCHANGE – nick introduced to fix Holliday junction
What enzyme initiates the Holliday model and makes a nick and unwinds the DNA?
RecBDC
What enzyme is responsible for strand invasion in the Holliday model?
RecA
What enzyme is responsible for branch migration in the Holliday model?
RuvA RuvB
What enzyme is responsible for strand exchange?
RuvC
What enzyme has helicase, nuclease, and ATPase activity?
RecBCD
What is a x (chi) site?
recombinational hotspot
Why do bunny ears form when RecBCD unwinds DNA?
the rate of unwinding is faster than the rate of ssDNA release
What enzyme in the Holliday Model aids in homologous pairing?
RecA
RecA forms a __________ with a groove to accommodate the ssDNA
helical filament
Once RecA:ssDNA complex is bound what happens?
it binds to dsDNA to search for a homologous region
What is the loop called made by RecA in strand invasion of Holliday model?
D loop
What class of enzymes solve the Holliday junction?
Ruv
What Ruv cleaves the Holliday junction to fix it?
RuvC
Gene transfer techniques make it possible to introduce genes into animals by _________
transfection (transgenic animals)
What did Barbara McClintock discover?
transposons
What are class I transposons called?
retrotransposons
What is the phrase used to describe class I (retrotransposons) transposons?
copy and paste
What are class II transposons called?
DNA transposons
What is the phrase used to describe class II (DNA transposons) transposons?
cut and paste
How do class I (retrotransposons) work?
RNA is reverse transcribed into DNA and DNA is inserted back into genome in a new spot
What class of transposons require RNA intermediate?
Class I (retrotransposons)
What are transposase?
target sequence for transposons
Can RNA and DNA have mutations?
yes
Mutations are usually ________ to gene function
deleterious
Are mutations usually recessive or dominant?
recessive
Can DNA be replaced?
No, so it must be fixed
What does the Ames test indicate?
the mutagenic potential of a chemical
How does the Ames test work?
Bacteria with a mutation causing no HIS production so the bacterial will not be able to grow without HIS in environment
The bacteria is introduced to a chemical that mutates the HIS gene and now it can grow even without the presence of HIS
What are 3 major DNA repair systems?
- double stranded breaks
- direct reversal
- single-stranded damage repair
Why is double stranded breaks a dangerous DNA repair system?
the broken of strands cannot be recovered
How does the DNA repair system, direct reversal work?
chemical reactions reverse the damage of DNA
What does the DNA repair system, single-stranded damage repair, rely on to guide repair?
complementary strand
What are 3 examples of single strand damage repair?
- mismatch repair
- base excision reapir
- nucleotide excision repair
What mechanism does double stranded DNA breaks use to repair?
NHEJ
In NHEJ for double stranded breaks, what enzyme recruits the two exposed ends?
Ku70/80
double stranded break repairs cause _________ to form when its HOMOLOGOUS DNA recombination
D loops
pyrimidine dimers can be repaired by __________
photolyase
In base excision repair, __________ removes damaged bases creating _________
DNA glycosylase
AP sites
How do AP endonucleases reverse chemical damage?
cleave DNA backbone so that exonuclease can remove several residues and new ones added
What repair system repairs large regions not just bases?
nucleotide excision repair
What does photolyase break to fix chemical mutations?
rings
Base excision repair uses specific ______________
DNA glycosylases
What is an AP site?
where DNA glycosylase has removed damaged nucleotides
Why is uracil glycosylase important?
removes U from DNA because C spontaneously deaminates into U
What polymerase synthesizes new DNA at AP sites?
DNA pol I
What enzyme seals AP sites?
DNA ligase
__________ remove DNA segments for nucleotide excision repair?
excinuclease
Nucleotide excision repair in bacteria uses _________ exinucleases
ABC
Do human or bacteria have larger sections removed in nucleotide excision repair?
humans
Mismatch repair systems _______ DNA duplexes for mismatched bases
scans
How do repair enzymes know which strand is correct in bacterial methyl-directed mismatch repair?
The errors will be in unmethylated sections
What proteins are involved in bacteria methyl-directed mismatch repair?
Mut
Why is Nitrosoguanidine used in labs?
mutagen in labs
Mutations in the ____________ cause Meier-Gorlin syndrome
pre-replication complex
Do DNA polymerases require primers?
yes
What DNA polymerase lengthens Okazaki framgents?
DNA polymerase I
What DNA polymerase removes primers?
DNA polymerase I
Which DNA polymerase is very processive?
DNA polymerase III
Which DNA polymerase is specific for the lagging strand in bacteria?
DNA polymerase I
DNA polymerase III can work on _______ strands in bacteria
both
What DNA polymerase fills in Okazaki fragments in eukaryotes?
DNA polymerase I
In eukaryotes, the epsilon subunit of DNA polymerase I works of the ________ strand
leading
In eukaryotes, the delta subunit of DNA polymerase I works of the ________ strand
lagging
What DNA polymerase was the first discovered?
I
Which DNA polymerase has 5’-3’ and 3’-5’ exonuclease activity?
DNA polymerase I
Is DNA polymerase III found in eukaryotes?
No only in prokaryotes
Which DNA polymerase is enormously processive?
DNA polymerase III
Which DNA polymerase has the beta subunit ring?
DNA polymerase III
