Nucleotides And Nucleic acids Flashcards
State the functions of nucleotides
1-coenzymes(fad,nad,nadp)
2-acts as energy storage - ATP
3-high energy intermediates in metabolic reactions UDP glycerol CHO
4-secondary messengers-cAMP, CGMP
5-precursor for RNA and DNA
Name two polymers of nucleotides
RNA
DNA
Compare and contrast between DNA and RNA
RNA
ribose sugar
Stores genetic info
DNA
Deoxyribose sugar
Carries genetic info
Catalytic function - remember we studied the catalytic function of RNA in enzymes
Describe the difference between between nucleoside and nucleotide
Nucleoside
-sugar
-base
Nucleotide
Sugar
Base
Phosphate (1,2,3)
As we know from previous knowledge that phosphate group has 4Os, 1 is bound , the other is double bounded to C , the last two are free. What is the pka value of these Os
1.0 and 6.0
That means at Ph above 1, there will be only 1negative charge, and only one o will be deprotonated
After 6.0 both, Os will be deprotonated and there will be two - signs
You know from earlier knowledge, name the purines and pyramidines
Pirines- adenosime, guanosin
Pyrimidines- thymine, cytosine
Name these 5 bases in RNA and in DNA
Guanosine
Deoxyguanosine
Guanylate
Adenosine
Deoxyadenosine
Adenylate
Thymine
Deoxythymine
Thyminylate
Cytidine
Deoxycytidine
Cytidylate
Uradine
Deoxyuradylate
Uridylate
We learned that nucleotides also act as secondary messengers. These secondary messengers are very similar to the nucleosides used in RNA. But what makes it different ?
Nucleotide in RNA have a p group at c5
However secondary messengers are cyclic nucletides
And they have p groups on C2, C3, or C2and 3
Remember when talking about nucleotides we said phospahte group (1, 2,3). Why was that so
Bcz usually in DNA or RNA m there is only one phosphate group
However, nucleosides (sugar +base) can have more then one phosphate group attached
One MAIN EXAMPLE of this is ATP- adenosine triphosphate
Ribose +adenosine+3phohate
We studied that in carbohydrates, glycosidic bonds hold sugars together, what bonds hold nucleotides together
Phosphodiester bonds sugars together
A phosphodiester bond forms between 3OH of one sugar and 5OH of another sugar
Why do we call the backbone of alternating phosphate and sugar residues
Bcz the o of phosphates attaches to3OH then 5Oh then 3OH then 5OH
Leading to a 5’end and 3’end on a same strand
State the characteristics of DNA
1-right handed double helix
2-anti parallel
3- complementary
4-de-oxy ribose sugar
5-resistant to degradation, more stable due to no Oh that can get reacted
6- G=C, A=T
7- phosphodiester bond, glucosidic bonds, h bonds, Vdw, week dipole dipole interaction
8- hydrophobic effect - by stacking of bases
9- higher freedom of configuration due to sugar phosphate backbone-it has 7 bonds that can rotate in different directions
10- has major and minor group
11-1 base = 3.4A, 1 turn has 10.6 bases, length of 1 turn = 36A
Describe how the hydrophobic effect is achieved in Nucleic Acid ?
Sugar - phosphate backbone is hydrophilic
Bases are hydrophobic
Bases stack up over each other stabilizing the strand
What is the importance of major and minor groove ?
The major and minor groove in B type DNA structure supports the gene expression control function of DNA
The proteins can attach to a nucleotide, w/o disturbing the complementary base pairing
Describe the process of denaturing of DNA
DNA standard isn’t static, it is random and has dynamic localized separation of stands and rapid reformation of strands
At high tempeand high PH, there is greater thermal motion, shifting the eq towards the separation of strand. This is called melting
What are the effects of GC on melting
Gc better stack because they are longer , allowing for greater and stronger vdq and dipole dipole forces
They also have 3 hb bonds between bases instead of 2
How can denaturation be measured
Due to the change in absorption when double stranded is converted to base
Double strand absorb ligh lower at 260nm (hypocheomacity)
When base pairing and stacking are broken, the ss absorbt light more then the ds dna (hyperchromacity)
Explain DNA replication
The double stranded the separated to single stranded and a complementary daughter strand is created out of the parent strand, using DNA polymerase.
Errors in daughter strand leads to mutations
As we know that the sugar used in rna and dna is different. What effect can this cause?
Ribse has two OH, deoxyribose has 1 OH
this makes rna less stable, as it can easily react two the two oh leadijg to the formation of 2,3 cyclic mono phosphate and shortened dna
Characteristics of rna
Antiparallel
Single stranded
Can base pair with itself
But g doesnt =c and a doesnt equal t
Weird base pairing can result
Complementary to the dna from which it was transcribed
Haipin double helix formation - base pais with itself
Bulges, interna loop
Similarities btw proteins and rnA
Rna is a tertiary structure
Very complex folds
Catalytic function
Eg - hammerhead ribosomes
Describe the process of transcription and translation
Transcription- the process in which a complementary mRNA is formed from a single dna strand using dna polymerase, rna sugar, rna bases . Mutations can occur
Translation is a process in which the mrna strand is translated/converted to a specific seq of aa using trna and genetic code
What are the modifications of mRNA
a 5’ cap- 7methyl guanosine triphosphate attach to the 5oh carbon of a 2’ methylate nucleoside through 3 phosphates
Poly A tail- addition of 20 to 250 Adenosine nucleotides at the end
Function of cap and tail
Prevents degradation- stabilize
Recognition by rib
Assist in translation
Trna characteristics
73 to 93 nucleotide long
Carries aa
Clover leaf shape
ACC at3’ end
Has an anticodon region st bottom that recognizes the codon of mRNA
At least 20 trna ,1 or more for each aa
Draw the trna
Rrna
Ribosome is a large cytoplasmic structure that translates the mrna into a specific seq of amino acids
Made of 4 Rrna and 80 proteins
2 main nucleoproteins are
60S
28s 5.85s, 5s,
50 polypeptide
40S
18s
30 polypeptide
Eukaryotic ribosomes vs prok rib
60s and 40s
28s 5.85 s 5s , 18s
50s and 30s
23s, 5s, 16s
Mirna
Snall -22 nucleotides
Precursor was 100 nuc transcribed but then cut into smaller pieces by nucleases
Complementary to particular mrna seq
Bonds and formes a complex
Preventing certain genes to be translated
The complex is destroyed by enzymes sometimes
Sometimes it isn’t destroyed by enzymes- so mrna bcms silent
Mirna prevents overproduction of particular proteins in imp biological process eg embryonic dev
Mutations
1- deamination 1/10^-7
2- depurination 1/10^-5
Deamination
T- base pair to U instead of C
One imp why dna doesnt use U
Depurination
Removal of purine base from phosphodiester backbone
Drawings end
Uv light
Causes photoproducts in areas of consecutive T
Forms
Cyclobutane thymine dimer
6-4 photoproduct
Oxidative damage
H2o2 forms free radicals
Chemicals
Alkylating agenets
Base analoggs
Nitrous acid
Mutages cause
Aging , cancer
Uncontrolled growth
Modify / change growth patterns
Cancer have 2 to 3 mutations in growth regulations
When you plota graph , tm vs percentage degradeation .
You will see that 1/2 deg is tm
Tm is the melting point when 1/2 of the dna is double and half is single stranded
When more G and Cs are present ,
The graph will be longer, higher so the tm inc
