structure of nucleic acids and synthesis of DNA Flashcards
key difference between proteins / nucleic acids
primary sequence for nucleic acids doesn’t dictate secondary/tertiary structure, like it does for proteins
N-glycosidic bond
-the bond between the sugar and the base -anti-confirmation at physiological ph (allows for H-bonding to form double stranded DNA) -bond formed at anomeric carbon, beta configuration (Be up!)
nucleoside
base + sugar
nucleotide
base + sugar + phosphate
What is the linkage/bond that holds the sugar phosphate backbone (single strand) together?
phosphodiester bond -5’ end (phosphate) to 3’ end (OH)
DNA vs. RNA
-Anti-parallel, double helix, (B-DNA form dominates in living systems), Thymine (a bit more stable than uracil) -Single stranded, helix, uracil (add destability to RNA), denatures and breaks apart in basic solution (DNA does not), *5’cap, *polyA tail, encodes proteins
mRNA
*5’cap polyA tail - for stability needs to be transported to a ribosome for protein synthesis
ribosomes
rRNA + protein **DIFFERENT subunits in Prokaryotes and Eukaryotes
tRNA
-have the anti-codon that recognizes the codon on mRNA -responsible for bringing the AA being added to the growing polypeptide
What is Tm?
temperature required for denaturation of DNA -Tm is directly proportional to the number of G-C bonds
What will a basic solution do to DNA/RNA
-it will only denature DNA (separate strands) -it will BREAK APART (its because of the OH
What happens when we cool temp back down?
hybridize = anneal = renaturation speed can tell if you have several types of DNA or just 1 type also highly repetitive sequences anneal faster
What is chromatin?
DNA is too big for free float in cell, so its supercoiled And binds to histones to form chromatin -positively charged histones attract negatively charged DNA
What about the human genome
each cell has 23 pairs of chromosomes
Zidovudine
Reverse transcriptase isn’t able to add nucleotide to 3’ end
- reverse transcriptase inhihbitor
- for treatment of HIV
5-FU
-non targeted cancer treatment (injures body cells too!) basically prevents thymine from being synthesized -without one of its precursors DNA can’t be made -this should stop cell division and slow the growth of the cancer
Azithromycin
-antibiotic -binds to prokaryotic robosomal subunit (50S) -but since mitochondrial ribosomes are similar to bacterial, the drug can affect our mitochondria
How many unique DNA molecules are possible for a 5 base pair sample
1024 = 4x4x4x4x4 (5 base pairs)
Helicase
unwinds DNA strands
topoisomerase
breaks / rejoins phosphodiester bonds to relieve supercoiling - i.e. cuts strands (single strand - type I or double - type II)
single stranded binding proteins
binds to DNA as it unwinds to prevent re-association or enzyme degradation
DNA polymerase III
adds deoxyribonucteotides in the 5’ to 3’ direction (proof reads) -can also proof read in 3’ to 5’ (exonuclease) -makes 2 new strands leading/lagging (semiconservative replication
Primase
adds RNA primers to the DNA because DNA pol needs a 3’ OH to attach its first nucleotide -eventually primers removed by DNase, DNA pol I
Leading vs. Lagging strand
continuous synthesis vs. discontinuous synthesis
DNA repair
DNA ligase DNA pol II
Cyclin dependent Kinases (CDK)
when cyclin is around it binds to a kinase this binding turns on the phosphorylating ability of the CDK -phosphorylation acts as a switch to turn on replication -cell leaves interphase and enters mitosis?
DNA replication differences: prokaryotes vs. eukaryotes
eukaryote have larger genomes Histomes / nucleosomes - unique to eukaryote Prokaryotic DNA is circular
Why is eukaryote DNA replication faster?
Multiple replication forks
DNA polymerase delta
lagging strand replication (3’ to 5’ exonuclease)
DNA polymerase epsilon
leading strand replication (3’ to 5’ exonuclease)
what is flap endonuclease
an enzyme that removes primers
Prokaryote DNA Polymerases
Eukaryote DNA Polymerases
How do we know if DNA is in the post-transciptional stage?
IF DNA is methylated then we are post-transcription
WHat is a telomere
A G rich sequence/repeats at the end of a chromosome
I guess it prevents shortening of the DNA by elongating the partent strand?
What are some example of how DNA can be damaged?
cigarettes (benzoapyrene) - binds Gaunine, stoping DNA sythesis
Sun exposure can cause thymines to start to bind together (preventing replication)
X-rays can cause the formation of free radical, which can damage cells
How can DNA be repaired?
Base Excision Repair
Nucleotide Excision Repair
Mismatched Repair
Base excision repair
- glycosylase - cleaves glycosidic bond, removing base
- AP endonuclease - chops/cleaves deoxyribose
- exonuclease removes deoxyribose and several (base) residues
- DNA pol add the propper bases back to fill gap
- DNA ligase - seals the nicks
Nucleotide Excision Repair
corrects DNA damage after sun exposure
same steps as BER, but cleaves a larger segment of DNA
Mismatched Repair
fixes errors that proof reading missed
unmatched bases produce a bulge in the DNA
must methylate the parental strand so we know to fix the incorrect base in the newly synthesized strand
Transposon
could cause or reverse a mutation
DNA jumps (copy and paste or just cut and paste) to a new locatoin in genome
Homologous recombination
genetic diversity!
exchange of nucleotide sequences between homologs (similar DNA molecules)
translocation
caused by breaks in two non-homologous chromosomes
can result in CANCER
Deamination
Thymine/cytosine can synthesized using Uracil
so thymine or cytosine (loses amino group) and forms Uracil (it’s called deamination)
C or T converted to U disrupts base pairing
But its an obvious error since U is not tipically present in DNA and our body can fix this (mismatch repair)
How to treat HIV
cocktail of reverse transcriptase inhibitors
why a cocktail?
- because reverse transcriptase can mutate
- these drugs block the 3’ OH, so reverse transcriptase cant add nucleotides
How can we fix a mutation due to smoking?
our body will probably use Nucleotide assisted repair (despite being one base guamine is large!)
What about a mutation due to sun exposure, how can our body fix that?
-2 adjacent pyrimidines mutate
again NER (because large 2 adjacent pyrimidines mutating is a large size)
Why dont you need a primase during DNA repair?
Because a 3’ OH is already present
What is special about cDNA
it contains no introns
ONLY extrons (expressed regions of DNA)
If you want to label DNA, what could you use?
Nitrogen. All bases have it
What does 5-FU do?
inhibits DNA sythesis due to Uracil
