Final: Chapter 10 - DNA and RNA Flashcards
What are nitrogenous bases?
aromatic nitrogen containing heterocycles
What is a nuceloside?
a nitrogenous base linked to a pentose sugar
What are two examples of nucelosides?
D-ribose and 2-Deoxy-D-ribose
What is a nucleotide?
A phosphate ester of a nucleoside
What is a nucleic acid?
linear polynucleotides linked by phosphodiester bridge
What are pyrimidines? Which?
smaller nitrogenous bases; cytosine, uracil, and thymine
What are purines? Which?
larger nitrogenous bases; adenine guanine
What are three properties of nitrogenous bases?
1) electron rich because aromatic with N and O
2) strong UV absorption
3) water insoluble b/c aromatic
What is the difference between uracil and thymine?
one methyl group on carbon 5
Which bases are pyrimidines? are they smaller or larger?
cytosine, uracil, and thymine; smaller
Which bases are purines? Are they smaller or larger
Adenine and Guanine; larger
What kind of bond connects nitrogenous bases and sugars?
glycosidic bond
What are the two possible confirmations of a glycosidic bond?
beta and alpha
Does a beta glycosidic bond point up or down?
up
What configuration are nucleoside glycosidic bonds typically found in?
beta
What does anti and syn rotation describe
Rotation around a glycosidic bond?
Does syn confirmation mean that nitrogenous base and sugar are stacked or staggered?
stacked
Does anti confirmation mean that nitrogenous base and sugar are stacked or staggered?
staggered
What is the function of nucleosides?
Typically no function besides adenosine
What is the function of adenosine?
Produced as a byproduct of ATP usage for energy, accumulates and promotes sleepiness
How does caffeine prevent feeling tired?
Blocks adenosine receptors because it has a similar structure
What is a nucelotides?
nucleoside with a phosphate attached at carbon 5
What is the name of a nucleoside containing cytosine?
cytidine
What is the name of nucleoside containing adenine?
adenosine
What is the name of a nucleoside containing uracil?
uridine
What is the name of a nucleoside containing guanine?
guanosine
Do nucleosides typically reside in anti or syn conformation and why?
anti because there is less steric strain
Why do nucleotides link to 5’ hydroxyl rather than 2’ or 3’ hydroxyls?
Because 5’ is a primary alcohol which is more accessible than a secondary alcohol
What are cyclic nucleotides used for?
signaling pathways
How are cyclic nucleotides formed?
Oxygen on phosphate forms ring with 3’ hydroxyl on sugar
What are three types of nucleotide reactions?
1) hydrolysis
2) functional group transfer
3) nucleic acid synthesis
What is a phosphoryl group transfer?
transfer of a phosphate group
What is a pyrophosphoryl group transfer?
transfer of two phosphate groups
What is a nucleotide group transfer?
transfer of a sugar, phosphate, and nitrogenous base
What are three characteristics of nucleic acids?
1) Always linked 3’ to 5’ by phosphodiester bonds between phosphates and sugars
2) Highly repetitive sugar phosphate backbone
3) Nitrogenous bases give unique identify to nucleic acids
What are Chargaff’s rules?
1) cytosine amount should be equal to guanine amount
2) adenine amount should be equal to thymine amount
3) purines amount should be equal to pyrimidine amount
What is the Watson and Crick model?
Describes DNA as two stranded complementary DNA helix with antiparallel strand that have H-bonding between base pairs
How many H-bonds d guanine and cytosine have between them?
3
How many H-bonds to adenine and thymine have between them?
2
Why do guanine and cytosine form more H-bonds than adenine and thymine?
guanine has a carbonyl that provides an extra H-bond acceptor; adenine does not
What is rRNA?
A complex secondary structure of RNA that is the primary component of a ribosome
How is rRNA characterized?
sedimentation coefficients; measure sedimentation velocity in response to centrifugation
What is tRNA
clover leaf shaped RNA that carries AAs to the ribosome during protein synthesis
Why is rRNA structure complex?
there is typically base pairing within the strand
What is siRNA?
short interfering RNA that is complimentary to known RNA and creates double stranded RNA to silence translation
Why doesn’t DNA contain uracil?
cytosine is likely to deaminate to uracil; if uracil was part of DNA code it would be more difficult to proofread
What is the benefit of DNA contain 2-deoxy-D-ribose instead of D-ribose?
it is more resistant to alkaline hydrolysis
Why does RNA hydrolysis occur? (3 steps)
1) in basic conditions the 3’ is deprotonated making it a good nucleophile
2) nucleophilic O attacks electrophilic phosphorus of phosphate
3) phosphate cleaved from 5’ carbon
What are two enzymes that perform enzymatic hydrolysis of nucleic acids?
1) nucleases
2) restriction endonucleases
How can nuclease cleavage vary?
Either hydrolyzes 3’ or 5’ side of phosphodiester bond
How do endonucleases cleave DNA?
identifies specific sequences of DNA and cleaves bond and specific site
