Module 4 - Nucleic Acids and Information Flow

who determine genetic material and how

Griffith studied virulent and mutant, non virulent strep on mice and determined DNA from the dead virulent cells were transferred to the nonvirulent

who identified DNA as the genetic materail

Avery, macleod and mccarty. tested if deal virulent protein dna or rna caused transformation of nonvirulent

deoxyribose vs ribose structure

deoxyribose missing O on 2’ C

what happens to phosphate at physiological pH

ionization, hydroxyl groups lose H giving it 2 negative charges

what does DNA having polarity refer to

directionality, has different ends

what end does a DNA code read when it is not specified (eg AGCT)

5’ to 3’

who built the 3D model of DNA and whos research was it based on

watson and crick. based on x ray crystallography by franklin and wilkins and chargaffs rule

which way does DNA coil, what is the directions of the 2 strands described as

right, antiparallel 

what causes major and minor groves in DNA

the tight coiling

what are the 2 main factors affecting stability of DNA

hydrogen bonds (weak individually but strong together) and base stacking (interactions between bases on the same strand)

genome and some examples

genetic material of an organism eg bacterial genome, nuclear genome, mitochondrial genome

gene

unit of heredity, affects one or more traits

gene expression

functional gene product, example is protein

where does transcription occur in eukaryotes

nucleus

where does transcription occur in prokaryotes

cytoplasm

why is RNA less stable than DNA

the OH group on the 2’ C

what is the difference in the 5’ ends of DNA vs RNA

typically DNA has a monophosphate and RNA has a triphosphate

what is needed for transcription to occur

DNA template, RNA polymerase, ribonucleotide triphosphates (ATP CTP GTP UTP)

template strand, direction of reading

strand used to synthesize mRNA, read 3’ to 5’

which direction does RNA grow during transcription

5’ to 3’

what are the 3 steps of of transcription

initiation, elongation, termination

initiation of transcription in prokaryotes

RNA polymerase recognizes promoter with the help of a sigma factor, sigma factor associates with RNA Pol

initiation in eukaryotes

activator proteins bind to the enhancer region, general transcription factor bind to promoter region and RNA pol 2 is recruited

what does the mediator complex do in initiation of transcription

associates with transcription factors and RNA Pol 2

what is the significance of the DNA looping in initiation of transcription

bring activator proteins in contact with transcription factors, THIS initiates transcription

what is the RNA-DNA duplex

8 pairs in length of RNA bound to DNA, found within the bubble of 14 base pairs unwound 

transcription elongation; how do the nucleotide triphosphates enter polymerase, and how does DNA enter and exit, and how is the complete transcript released

channels!

steps of polymerization (elongation) in transcription

RNA pol detects ribonucleotide triphosphates and joins them to the transcript by orienting the oxygen on the 3’ end of the strand to break off a pyrophosphate group

why is it important that a P-p (pyrophosphate) group is removed from the ribonucleotide triphosphates during transcription

provides the energy for the phosphodiester bond

primary transcript

RNA straight from the template strand

why is the mRNA different in eukaryotes and prokaryotes

in prokaryotes the mRNA is the primary transcript but in eukaryotes the primary transcript is processed first to become mRNA

polycistronic mRNA

in prokaryotes, primary transcript containing code for more than 1 gene

why isn’t eukaryotic mRNA considered polycistronic

each mRNA only codes for 1 gene

RNA processing modifications

5’ cap, 3’ poly-A tail, removal of introns

why is it important for a 5’ cap to be added post transcription in eukaryotes, what kind of bond is it 

5’-5’ bond, protects mRNA from exonucleases and provides stability

why is it important for a polyA tail to be added post transcription in eukaryotes, how long is it

250 adenines, important for transcription termination, mRNA export, protection from exonucleases

why is intron removal post transcription important

they don’t contribute to protein function

what is alternative splicing

1 gene can produce diverse mRNA due to unique exon combinations

what is polyadenylation

addition of poly-A tail in RNA processing

typical sequence for promoter region

TATA box, 5’ TATAAA 3’ and 25 bases away from the first transcribed base