Nucleotides and Nucleic acids Flashcards by Sophie Kelly

Nucleic acids are polymers of nucleotides which are used for?

-Storage of genetic info (DNA)
-Transmission of genetic info RNA (mRNA)
-Processing of genetic info (ribozymes)
-Protein synthesis (tRNA and rRNA)

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What are nucleotides in the monomer form used for?

Cellular functions
-energy for metabolism (ATP)
-enzyme cofactors (NAD+)
-signal transduction (cAMP)

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What is a nucleotide composed of?

-nitrogenous base
-pentose
-phosphate

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What is a nucleoside composed of?

-nitrogeneous base
-pentose sugar

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How many rings do purines vs pyrimidines have?

Purines - 2
Pyrimidines - 1

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Adenine vs Guanine structure?

-Both have 2 rings
-Guanine has double bond O, adenine doesnt

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Thymine vs Cytosine vs Uracil structure

Cytosine only has 1 double bonded O whereas the others have 2
Thymine has a CH3 group amd the other 2 dont

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Charcteristics of the phosphate group?

-Neg charged at neutral pH
-Typically attached to 5’ position
- nucleic acids are built using the 5’- triphosphates version of the nucleotide (ATP,GTP,TTP,CTP)
- 2 of the 3 phosphates used for building nucleic acids form a leaving group and completed nucleic acids contain 1 phosphate moietz per nucleotide.

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What are nitrogenous bases?
What do they absorb UV light at?

-Derivatives of pyrimidine or purine
-Nitrogen containing heteroaromatic molecules
-Planar or lamost planar structures
-Absorb UV light around 250-270 nm

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Where is uracil found

RNA

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What is dAMP or dA or A abreviated for?

Deoxyadenylate - deoxyadenosine 5’-monophosphate

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What does CMP or C abbreviated for?

Cytidylate (cytidine 5’- monophosphate)

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How is the pentose ring attached to the
nitrogenous base? and what is the bond formed to?

Pentose ring is attached to the nitrogenous base via a N-glycosidic bond
The bond is formed to the anomeric carbon of the sugar in ß configuration

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Where is this bond between the pentose ring and the nitrogenous base formed?

ß-N-Glycosidic bond formed:
-to position N1 in pyrimidines
-to position N9 in purines

The bond is quite stable towards hydrolysis , especially in pyrimidines
Bond cleavage is catalyzed by acid

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Can rotation occur around the N-glycosidic bond in free nucleotides?

Yes relatively free rotation can occur

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What is the sequence chosen to defin ethis snagle of rotation in purines vs pyrimidine derivatives?

-Purines - O4’-C1’-N9-C4
-Pyrimidines - O4’-C1’-N1-C2

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What is it called if the angle corresponds to i) 0 degrees or ii) 180 degrees

0 degrees - syn conformation
180 degrees - anti conformation (found in normal B DNA)

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What limits the angle of torsion, c, possible for the N-glycosidic bond between the nitrogenous base and pentose?

Ring pucker

What are prototropic tautomers?

Structural isomers that differ in location of protons
e.g keto-enol tautomerism is common in ketones, lactam-lactim tautomerism occurs in some heterocycles (predominant at neutral pH)

What are the tautomeric forms of uracil and when do they occur?

-The lactam form predominates at pH 7.0
-Other forms (lactim, double lactim) become more prominent as pH decreases

In lactam there is a H attached to an N, this H attached to a double bonded O in lactim and the same happens with another H in double lactim

What is a common minor nucleoside found in both eukaryotic and bacterial DNA?

5-Methylcytosine

What is a common minor nucleoside only found in bacterial DNA?

N6-Methyladenosine
(small 6 meaning the methyl goup is attached to a NH group which is attached to carbon 6 instead of being directly attached to C6)

What is an epigenetic marker?

-way to mark own DNA so that cells can degrade foreign DNA (prokaryotes)
-way to mark which genes should be active (euk)

What happens to make nucleosides Inosines and where are they found?

-A H attached to a NH side group is removed and added to a doubled bonded O which becomes a single bond

-Inosine is sometimes found in the “wobble position” of the anticodon in tRNA

What is Inosine made by and what is the purpose of making it?

-Made by de-aminating adenosine -Provides richer genetic code

Minor nucleoside in RNA - Pseudouridine

-Found widely in tRNA and rRNA -More common in eukaryotes but also found in eubacteria -may stabilize the structure of tRNA -may help in folding of rRNA

What is Pseudouridine formed from, when is it formed and what is changed?

-Made from uridine by enzymatic isomerization after RNA synthesis -Distinct point of attachment to ribose -in uridine, uracil is attached through N-1, the usual point for pyrimidines, - in pseudouridine, through C5 (has 2 NHs)

What are the covalent bonds formed between the negatively charged backboness in polynucleotides?

Via phosphodiester linkages between the phosphates of each nucleotide

DNA backbone vs RNA backbone stability?

-DNA backbone is fairly stable -RNA backbone is unstable

What direction do we read the sequence?

5' to 3'

What is hydrolysis catalysed by in DNA and RNA

dna - DNASES RNA - RNASES

Examples of RNase enzymes ands what do they do?

-S-RNase - in plants prevents inbreeding -RNase P - a ribozyme (enzyme made of RNA) that processes tRNA precursors. -Dicer - an enzyme that cleaves double stranded RNA into oligonucleotides - protection from viral genomes, RNA interference technology

How many bonds is there in AT vs GC

AT - 2 GC - 3

Which kind of DNA is left handed?

Z DNA

What way do DNA strands run?

Antiparallel

What differences are there w mRNA?

-Synthesised using DNA as template and occurs as single strand -Contains ribose instead of deoxyribose -Contains uracil instead of thymine -One mRNA may code for more than one protein -Transfers genetic info from DNA to proteins w tRNA

What can form hairpin structuresß

Palindromic sequences

Temp denaturation

Two DNA strands dissociate at elevated temps and re-anneal when etmp is lowered -The reversible thermal denaturation and annealing form the basis for the polymerase chain reaction

What is DNA denaturation commonly monitored by?

UV spectrophotometry at 260nm

What is the midpoint of melting dependant on?

-Base composition - high CG increases Tm -Depends on DNA length - longer has higher Tm -Depends on pH and ionic strength - high salt increases Tm

What are 2 methods of spontaneous mutagenesis?

-Deamination -Depurination

What happens in deamination?

-very slow reactions -large number of residues -net effect is significant : 100C to U events/day in mammalian cell

What happens in Depurination?

-N-glycosidic bond is hydrolyzed -Significant for purines : 10,000 purines lost/day in a mammalian cell

Examples of radiation-induced mutagenesis

-UV light induces dimerization of pyrimidines, may be cause of skin cancer -formation of cyclobutane pyrimidine dimer introduces a bend or kink in DNA -Ionising radiation - x and gamma rays - cause ring opening and strand breaking