Chapter 4 - DNA, RNA Flashcards
The central dogma
DNA -> RNA -> Protein
Nucleotide
Sugar, a phosphate, and one of four bases
DNA
Has a deoxyribose sugar and lacks an OH at carbon 2
Phosphodiester bridges
The 3’hydroxyl group of the sugar moeity of one nucleotide is joined the the 5’ group of the adjacent sugar
RNA
Is a long unbranched polymer with phosphodiester linkages. Ribose contains a 2’-hydroxyl group. RNA is uracil instead of thymine
Phosphodiester bridges
Have a negative charge. This negative charge repels nucleophilic species such as hydroxide ions, which are capable of hydrologic attack on the phosphate backbone
Nucleoside
Base and sugar joined by a glycosidic linkage
Nucleotide
Sugar, base and phosphate. Joined by ester linkages
Nucleotide triphosphates
The monomer that are linked to form RNA and DNA. The energy, ATP, released from it is used to power many cellular processes
Nucleotide functions
Energy for metabolism
Enzyme cofactors
Signal transduction
Nucleic acid function
Storage of genetic information
Transmission of genetic info (mRNA)
Processing of genetic info
Protein synthesis tRNA, rRNA
Double helix structure
Double helical structure facilitates the replication of genetic information
Watson Crick model of DNA
Right handed screw
Anti parallel strands, opposite directionality
Sugar phosphates on the outside, and purine and pyrimidines on the inside
Length of DNA
Bases are separated 3.4A
10.4 bases per turn of helix
20A diameter
Intermediate shape
The base pairs are held by
Hydrogen bonds which contribute stability in the helix due to their large numbers in a DNA molecule
Stacking of base pairs
Millions of bases together become very strong
Rings are planar.
Held by van der Waals
For,action of the double helix
Is facilitated by the hydrophobic effect
Base stacking is favored by the confirmations of the somewhat rigid five ,embedded rings of th backbone sugars
Supercooling is important because
Is more compact and less reactive
May hinder the capacity of the double helix to unwind
DNA denaturing
Can happen by heating DNA or changing the ph.
Melting temperature
When half of the DNA molecule helical structure is lost
Helicases
Use chemical energy from ATP to disrupt the helix
Denaturing
Covalent bonds stay intact
Hydrogen bonds are broken
Base stacking is lost
Hydro chronic effect
Increase in absorption upon denaturing due to release of base pairing
DNA is replicated by polymerase
Promote the formation of the bonds joining unite of the DNA backbone
DNA synthesis needs
Deoxynucleoside triphosphates
-dATP, dGTP, dCTP, dTTP and Mg ion
Preexisting DNA template
Primer having a free 3’ hydroxyl
Nucleases
Enable DNA fidelity because it enables mismatched nucleotides
Polymerization is driven forward by
The hydrolysis if pyrophosphate to yield PPi
Where do you want to radiolabel?
In the alpha carbon
Reverse transcriptase
Makes viral DNA
Possess several activities and catalyze the synthesis of a complementary DNA strand, the digestion of the RNA and the subsequent synthesis of the DNA strand
RMA polymerase
The synthesis of RNA from DNA is called Transcription and is catalyzed by the RNA polymerase enzyme
RNA synthesis
Does not require a primer of nuclear activity
Fidelity by base sequence studies
If RNA polymerase doesn’t have a promoter, how does it bind?
Bonds to promoter site
Cap structure
Guanosine nucleotide with a 5’-5’ triphosphates linkage
PolyA tail
Important to have because the cell can tell whether the mRNA was made correctly
Genetic code is degenerate
Amino acids are encoded by more than one codon
Important of degenerate code
The probability of mutation to chain termination would be much higher
What physical property is going to change between the prokaryotic start signal and eukaryotes?
There’s going to be a charge difference.
The N terminator, for euk, must be able to interact with glutamate so its needs that positive charge.
Splicing is carried out by
Spliceosomes
Introns
Start with GU and end with AU that precedes by a pyrimidine rich tract
