Biochem 2- Week 1 Flashcards
what is the pyrimidine numbering system
1- priority goes to nitrogen adjacent to C double bonded to C
2- look for second nitrogen in ring and that is the direction that numbering will take
what is the numbering system in purine
1- assign priority to nitrogen in larger ring and one that is furthest from ring junction
2- look for the second nitrogen in larger ring
3- number rest of larger ring
4- move to smaller ring and number double bonded nitrogen as 7
5- number rest of atoms in smaller ring using clockwise direction
what are the seven naturally occuring nucleotide derivatives
1- hypoxanthine which come from deamination of adenine
2- xanthine which comes from deamination of guanine
3- 4 thiouridine which come from replacing carbonyl group of uracil with thiol
4- inosine which is a hypothanine attachedc to ribose sugar
5- ribothymidine which is thymine with ribose sugar
6- psrudiouridine which is identical to uracil but links to ribose sugar at c-5 instead of
c-1
7- dihydrouridine which is made from hydrogenation of double bonds in uracil
Why do we have thymine in DNA instead of uracil like in RNA
the difference between uracil and thymine is that thymine has a methyl group amd that is important for maintaining the correct sequence of DNA because cytosine in the correct DNA sequence can be converted to uracil due to hydrolytic deamination caused by oxidative stress and this is a mutation that DNA enzymes will fix by removing these deaminated cytosine and put new cytosine
if DNA was to have uracil in teh sequence, then the enzymes will just see them as mutation even if they are part of correct sequence and replace them with cytosine, which will make sequence incorrect, so there will be misunderstanding between teh correct and mutated cytosine so the uracil was methylated ( got additional methyl group) and became thymine
what is teh linkage between nuecleotide bases
are known as 3’-5’ phosphodiester bridges
what is difference between sugar of DNA and that of RNA
in RNA, the sugar is a ribose sugar with a hydroxyl group at C-2’ but in DNA that carbon loses its hydroxyl group and there is only hydrogen at C-2’ to increase stability of DNA
what is the linkage between sugar and base called
a B or N glycosidic linkage and this molecule is also known as adenosine=nucleoside
between what carbon adn nitrogen do the B glycosidic linkages occue in purine and pyrimidine
in purine: between 1’C of sugar and N9 of nase
in pyrimidine: between 2’C and N1 base
what is the linkage between phosphate groups called
phosphoanhydride bonds
what was teh start to helping find structure of our DNA
all the way back to 1868 where Miescher was able to discover a phosphate containing substance which he called nuclein
how did Leven and Jacobs further the findings from nuclein
they found 4 distinct species which has pentose and nitogenous base in 1909 and then proposed a model om 1912 which was a carbohydrate polymer and close to that time, Steudal also proposed his model which was a phosphate polymer and more correct than carbohydrate one
what was another discovery made in 1930 that helped with finding DNA structure
they were able to define the sugar-base connectivity
what were some proposed models in 1935 due to a discovery made then
discovery of 1:1;:1;:1 ratio was reported for A,C,G, and T
so Levene and Tipson proposed tetrameric structure while Takahashi proposed a cyclic structure
what helped scientists gets back on track after the whole tetrameric model
in 1938, Hammerson was able to find molecular weight of DNA and was around 1 milion which disproved the tetrameric structure
Astbury also used X ray fibre diffraction to find extended structure and the 3.4A spacing
what was discovered in 1940 by Gullard
he discovered teh H-bonding by using enolic tautomers in structural models but it was teh wrong H-bonding
What was an improtant discovery taht helped Watson and Crick, and Franklin and Wilkins come with correct DNA model
in early 1950s, Chargaff reported the correct ratio of nucleotide of G:C and A:T which helped those scientists come with strcuture but at same time, another scientist called Pauling also came up with the 3-stranded structure which is as we know incorrect
what was wrong with phosphate based polymer proposed by Steudel
the model has bases naging off phosphate backbone
what was incorrect with carbohydrate based polymer porposed by Levene and JAcobds
the bases and phospjates are hanging off the carbohydrate backbone
what was incorrect about the tetranucleotide hypothesis by Takahashi
he correctly depicted the base sugar connectivity but incorrectly syggested DNA to be comprimised of independent tetranucleotide units
What was incorrect about the secodn proposed structure of tetranucleotide hypothesis by levene and tipson
the correctly had teh sugar0base-phosphate link but incoreectly suggested DNA to be comprimised of independent tetranucleotide units
how did Astbury/Bell model of single stranded DNA help but was also incorrect about
also known as penny staking model and the same scientist also measured distance between nucleotide
the model showed DNA to be single stranded with planar sugar and bases stacked on top of another so was incorrect as DNA is double stranded as we knwo now and that sugar and bases aren;t planar
what are teh forms of base tautomers and how are they significant
keto and enol are the two types of base tautomers and each form differ as keto is a hydrogen bond acceptor while enol is hydorgen bond donator, carboxyl into hydroxyl, which will affect the hydrogen bonding in DNA
so only keto forms can be found to allow for A/T bonding and C/G bonding
What made Pauling’s inside out structure incorrect
it correctly identified the linear connectivity of DNA and its extended structure and that it is multiple strands but he proposed DNA to be triple interwind strands that formed a triple helix connected with phosphates in teh middle which was physically impossibe due to repulsive forces between phosphate groups
What is Chargaff’s rule and how did that contribute to finding teh double helix of DNA
using molar ratios by conducting pairwise comparison between the bases and was able to seee ratio of 1:1 between A/T and 1:1 btw G/C while other pairing ratios wheren’t close to 1 so proved the hydrogen bonding to be between A/T and G/C
what are the forces that stablizie DNA structure
H-bonding, dipole interactions, and hydrophobic effect
what are the three major types of H-bonding between nitrogenous bases and how do they differ
1- Canonical Waston-Crick base pairs where teh correct configuration of rpurine is that it uses larger ring and atoms at position 1+6+(2 for G) while pyrimidine use the opposite face of its N-Glycosidic vond and unsed position 4+3+(2 for C) for hydrogen bonding and this is the most stable form of the three and one seen in DNA as the C-G pair has stability becaise of extra H-bond
2- Hoogsten base pair is also known as any variation as any H-bond pattern that is different from Waston-Crick one will apply here and these are mostly in RNA as there is possibility of distorations due to sugar molecules being close
3- wobble base pair is a speciifc type of Hoogston and mostly in RNA and tRNA as it allow for more flexibility in possible H-bond
what does hoogsten hydrogen bonding found in DNA belong to
such bonding will only be at end of DNA if found there and it will be known as telomers as it form G-quadruplexes between the guanine rich strands to prevent degradation of telomers
so telomers are guanine rich strands
how does melting temperature reflect DNA stability
it was shown that DNA has unique ability to absorb light due to teh ring nitrogenous bases
can observe change from DS to SS DNA to know melting temp using denaturing experiment which involve increasing temp little by little and the created sigmodial curve will idnicate the DNA denaturing and show it to be cooperative process
why can SS DNA absorb more light than DS DNA
that is because the rings in single stranded are more exposed to the light
what are the three effects that will influence melting temperature
1- more C/G rich DNA as there will be more H-bond so higher melting temp
2- replacing electronegative atom with elctropositive one will increase staking effect which increase melting temp
3- if nitogenous bases were able to be repalced by more hydrophobic bases, that will increase hydrophobic effect which will increase melting point
what is the dipole effect an dhow does it effect DNA stability
also know as base styacking where adjacent bases are stacked on top of each other and experience weak dipole dipole with each other amd having many dipole dipole will make that bonding stronger and have effect on stability of DNA by also increasing its melting temp
changing electronegative atom to electropositive one will decraese the dipole dipole effect
why does DNA still get distabilized by nonpolar solvent
in nonpolar solvents, there is no hydrophobic effect so hydrophobic bases are exposed and duplex get destabilized rsulting in single stranded DNA
hydrophobic effect increase stability of DNA by increasing entropy of water so mising that will allow for hydrophobic bases to act freely and lose those hydrogen bonds
how does hydrophobic effect in polar solvents increase stability of DNA
base stacking occur in hydrophobic effect which means forming double helix DNA releases water molecules and this increases entropy of water which increases stability of DNA
