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Biomolecules > Nucleotides and Nucleic acids > Flashcards

Nucleotides and Nucleic acids Flashcards

1
Q

Nucleic acids are polymers of nucleotides which are used for?

A

-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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2
Q

What are nucleotides in the monomer form used for?

A

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

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3
Q

What is a nucleotide composed of?

A

-nitrogenous base
-pentose
-phosphate

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4
Q

What is a nucleoside composed of?

A

-nitrogeneous base
-pentose sugar

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5
Q

How many rings do purines vs pyrimidines have?

A

Purines - 2
Pyrimidines - 1

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6
Q

Adenine vs Guanine structure?

A

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

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7
Q

Thymine vs Cytosine vs Uracil structure

A
  • 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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8
Q

Charcteristics of the phosphate group?

A

-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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9
Q

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

A

-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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10
Q

Where is uracil found

A

RNA

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11
Q

What is dAMP or dA or A abreviated for?

A

Deoxyadenylate - deoxyadenosine 5’-monophosphate

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12
Q

What does CMP or C abbreviated for?

A

Cytidylate (cytidine 5’- monophosphate)

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13
Q

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

A

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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14
Q

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

A

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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15
Q

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

A

Yes relatively free rotation can occur

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16
Q

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

A

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

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17
Q

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

A

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

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18
Q

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

A

Ring pucker

19
Q

What are prototropic tautomers?

A

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)

20
Q

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

A

-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

21
Q

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

A

5-Methylcytosine

22
Q

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

A

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)

23
Q

What is an epigenetic marker?

A

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

24
Q

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

A

-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

25
Q

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

A

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

26
Q

Minor nucleoside in RNA - Pseudouridine

A

-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

27
Q

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

A

-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)

28
Q

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

A

Via phosphodiester linkages between the phosphates of each nucleotide

29
Q

DNA backbone vs RNA backbone stability?

A

-DNA backbone is fairly stable
-RNA backbone is unstable

30
Q

What direction do we read the sequence?

A

5’ to 3’

31
Q

What is hydrolysis catalysed by in DNA and RNA

A

dna - DNASES
RNA - RNASES

32
Q

Examples of RNase enzymes ands what do they do?

A

-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

33
Q

How many bonds is there in AT vs GC

A

AT - 2
GC - 3

34
Q

Which kind of DNA is left handed?

A

Z DNA

35
Q

What way do DNA strands run?

A

Antiparallel

36
Q

What differences are there w mRNA?

A

-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

37
Q

What can form hairpin structuresß

A

Palindromic sequences

38
Q

Temp denaturation

A

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

39
Q

What is DNA denaturation commonly monitored by?

A

UV spectrophotometry at 260nm

40
Q

What is the midpoint of melting dependant on?

A

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

41
Q

What are 2 methods of spontaneous mutagenesis?

A

-Deamination
-Depurination

42
Q

What happens in deamination?

A

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

43
Q

What happens in Depurination?

A

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

44
Q

Examples of radiation-induced mutagenesis

A

-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

Biomolecules (11 decks)

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