Chapter 3 and 24: Nucleotide Structure and Function Flashcards
what is cAMP?
a secondary messenger
Draw and label the two purines
adenine and guanine
Draw and label the three pyrimidines
thiamine, cytosine and uracil
What’re the three main functions that the structure of DNA must permit?
1) must allow for the duplication of information
2) must allow for the expression of information- easy conversion of information into protein product
3) must allow for the stable storage: Structure must be manageable in size and stable over long periods of time.
A purine has ___ ring(s) and a pyrimadine has ___ ring(s)
purine has 2 rings and a pyrimadine has 1 ring
What is the sugar differences in a deoxyrobonucleotide and a ribonucleotide?
deoxyribonucleotide has 2’ deoxy sugar with NO 2’OH group, ribonucleotide uses ribose.
Differences between nucleotide and nucleoside
nucleosidedoes not have a phosphate group PO3- on the 5’ Carbon
Draw deoxyribonucleotie and deoxyribonucleotide with a thiamine base attached to proper carbon.
Base should attach to 1’ carbon, phosphate group should attach to 5’ carbon. deoxy should not have an OH at the 2’ position
What’re the three main components of ATP
adenine, phosphate groups, and RIBOSE sugar.
From what group of the ATP molecule is used for chemical energy?
hydrolysis of the phosphate groups
What is a phosphodiester linkage?
linkage between a nucleotide residue in RNA and RNA
What is a phosphoester/phosphoanhydride linkage?
linkages between ATP’s phosphate groups.
Why is ATP metastable?
Metastability is a term referring to molecules in which the thermodynamic breakdown is energetically favored, ATP can readily undergo hydrolysis because the reaction is spontaneous
When connecting two nucleotides to form nucleis acid structure, the phosphate bridge bond connecting the 3’ and 5’ positions is called _____
a phosphodiester linkage
Phosphates of polynucleotides are in _____ in physiological pH
deprotonated
Is the phosphate sugar backbone of a nucleid acid hydrophillic or phobic?
hydrophillic
Explain chargaffs rules
concentration of A equals the concentration of T, and concentration of G equals the concentration of C
Explain the Watson and Crick double stranded helix structure
2 helical chains of DNA wound around the same axis to form a right handed double helix.
Base pairs are complementary and the two strands run antiparallel to each other.
Each DNA strand can act as a template for the synthesis of its complimentary strand.
Each nitrogenous base is ____bonded to a base in the opposite strant to form a base pair (covalently, ionically, or hydrogen)
Hbonded
C-G pairs have ___ Hbonds between them and A-T pairs have ____Hbonds between them
CG have 3 Hbonds, AT have 2 Hbonds
The hydrophillic backbone of DNA are on the ____ of the double helix to allow for favorable interactions with H2o, while the aromatic base pairs are stacked ____ the double helix to allow ___________interactions
outside of the helix, aromatic base pairs are stacked inside the double helix to allow favorable base stacking interactions/
Transcription vs Translation
Transcription: process by which DNA nucleotides are copied into RNA molecules
Translation: RNA to protein
T/F Hydrogen bonding between nitrogenous bases is a large factor that allows DNA to have a high stability.
False. Hbonding is only required for specificity of base pairing more than anything. If you were to denature the DNA, the bases would just Hbond with water because they are energetically similar.
Base stacking is _____driven, whereas Protein stacking is____ driven
base stacking in enthalpically driven, and proteins are entropically driven.
Two main reasons as to why base stacking interactions are favorable
1) London dispersion forces are larger than expected, delocalized pi electron cloud allows them to be more responsive to spontaneous dipoles
2) Favorable electrostatic interactions occur between stacked bases. Many polar bonds in bases due to O and N atoms, and the staggering allows atoms with opposite partial charges to be stacked and interact with each other.
The higher the proportion of GC base pairs, the _____stable Dna is is due to _______
more stable DNA is due to stronger stacking interactions.
How do cations aid in increasing thermal stability?
Cations shield the negative chargs in the phosphate sugar backbone to allow more favorable interactions with water. With cations shielding the negative portions, there are less repulsive interactions between water and the backbone and less repulsive interactions between the phosphate groups themselves
When a DNA duplec is heated above a characteristic temperature, its native structure collapses and its two complementary strands separate and assume random conformations, this process is called
denaturation.
what is the hyperchromic effect?
absorbance levels increase by 40% upon denaturation because of the electronic interactions amond neighboring bases.
What is Tm?
melting temperature. temp at which half of the maximum absorbance increase is attained.
TM ___ as [GC pairs] increase because of their _____
Tm increases because of their greater stacking energies that make the DNA strand more stable
To denature a strand of DNA, a _____ solvent should be used
non polar solvent. less solvent-DNA interactions would be taking place.
What’re annealing conditions
condition where DNA completely renatures.
What is it called when RNA pairs with DNA to form a “combination” double helices?
hybridization
How does the structure of DNA allow itself to duplicate?
it has strand complimentarity, one strand acts as a template as the other gets duplicated
DNA of a gene is ___ to produce an RNA molecule that is complimentary to the DNA
transcribed
RNA sequence is then ____ into corresponding sequence of amino acids to form a protein
translated
What is the central dogma of molecular biology?
DNA of a gene is transcribed to produce an RNA molecule that is complimentary to the DNA, and then the mRNA is then translated into corresponding squence of amino acids to form a protein
RNA strands are synthesized from free _____
ribonucleotideTRIPHOSPHATES
DNA and mRNA is read in a x’ to y’ direction
5’ to 3’ direction
What part of the structure allows DNA to be found efficiently?
the outer surface of the double helix contains major and minor grooves, and sequence specific DNA binding proteins can discriminate among the four base pairs according to the functional groups that the base pairs project into the grooves.
What makes the major groove wider than the minor groove?
The fact that the base pairs are slightly asymmetrically attached to the backbone.
What kind of interactions allow sequence specific proteins to recognize specific grooves?
edges and functional groups contain different hydrogen donors and acceptors for potential specific interactions with protein. most of the interactions are vanderwaal and Hbond forces. Some ionic interactions with phosphate backbone groups.
What is a repressor
a protein that binds on or near a gene to prevent transcription.
What type of cells contain repressors?
prokaryotic cells.
What does a repressor recognize?
a recognition site on the DNA fragment called an operator
what is indirect readout
phenomenon where protein senses the base sequence of DNA through the DNA’s backbone conformation and flexibility.
What is a leucine zipper transcription factor?
a eukaryotic transcription factor that contains leaucine at every 7th position and are shaped as alpha helices.
Recall that in every 7th position of an alpha helices contains a hydrophobic side chain AA, allowing them to form coiled coils. in a leucine zipper, the non polar leu side chains lock together like fingers or a zipper.
More often than not, binding proteins tend to form hydrogen bonds and vanderwaal interactions with the ____ groove of the DNA
major groove, not minor
WHat’re the three main factors that allow DNA to be stored over a long period of time?
1) no uracil
2) no 2’ hydroxyl group
3) they’re wrapped around histones.
Why is no uracil a factor having DNA high stability?
1) dna recognizes uracil as foreign. If it didn’t, large amounts of mutations would occur
Why is not having a 2’hydroxyl important for having high DNA stability?
allows DNA to be more resistant to hydrolysis. There is less chance of bond breaking because there is no OH to act as a nucleophile.
Name the 5 major classes of histones
H2a H2b H3 H4 H5
How do histones contribute to DNA stability?
the histones are positively charged amino acids that can interact with the negative charges on DNA’s sugar phosphate backbone to reduce the overall polarizing effects.
T/F the interactions between DNA and histones are sequence specific
False, the histones interact with the DNA backbone and not the bases, thus, it does not matter where the histone binds, unlike other binding proteins like leucine zippers in eukaryotic cells or repressors in prokaryotic cells.
Define a nucleosome
a DNA segment wrapped around 8 histones
When the histone tail is _____, the DNA is inaccessbile and the genes are inactive
when the histone tail is methylated, the dna is inaccessible
When the histone tail is____, the DNA is accessible and the genes are active
The DNA is accessible, the gene is active.
Define polysome
single strand of mRNA that can be simultaneously translated by large clusters of 10-100 ribosomes
Why is RNA more susceptible to hydrolysis?
because RNA has a hydroxyl group at the 2’ location. During base catalysis, the OH2’ group can get deprotonated and act as a nucleophile, attacking adjacent phosphorus in the backbone of RNA, cleaving the backbone.
