Module #4 - Nucleic Acids and Information Flow
Intro
DNA (deoxyribonucleic acid) has a common structure across all organisms
Structure of DNA is linked to its function
Storing genetic info
Copy itself to transmit the genetic information from one generation to the next
How do we now DNA is the genetic material?
Experiiments conducted by F. Griffith in 1928
Results:
When the debris of dead virulent cells was mixed with the nonvirulent cells became virulent →
How Do We KNow?
Research conducted by Avery, MacLeod & McCarty in 1944 identified the molecule that transformed the nonvirulent bacteria
Key evidence that DNA is the genetic material
What is DNA Made Of?
Recall that DNA is a linear polymer of four different subunits → nucleotides
A nucleotide consist of three parts:
A five-carbon sugar
a nitrogenous base
A phosphate group
Bases can only be added to the 5’ to the 3’ direction
3D Structure of DNA
Watso and Crick build a 3D model of DNA based on results from other researchers:
X-ray crystalllography by Rosalind Franklin and Maurice Wilkins
Resuls from biochemistry expirements from Erwin Chargaff.
%C = %G and %T = %A
The two strands run in opposite directions → antiparrallel
Recall that bases pair with specificity
A pairs only with T
C pairs with G
Q: Why is there specificity of base pairing?
A: Specificty arises due to hydrogen bonds that form between A and T and between C and G
Genome
Q: What is a genome?
A: The genetic material of an organism
Some examples:
In bacteria -
Gene Expression
Q: What is a gene?
A: “The unit of heredity
The Central Dogma
DNA is transcribed into RNA, which is then translated into protein
This is the central dogma
The term transcription is used for the generation of RNA from DNA → DNA is the template
Emphasizes that DNA and RNA use the same “language” of nucleic acids
Protein synthesis is dependent on the “code” carried
Transcription
The process of transicription is to create a complementary copy a DNA sequence into an RNA sequence
The DNA serves as a template for RNA production in the cell
Despite the differences in transcriptional location the processes are similar in both prokaryotes (cytoplasm) and eukarytotes (nucleus)
What is needed for transcription to occur?
Answer: Need the following:
A DNA template
RNA Polymerase → this is the enzyme needed for transcription
Polymerase moves in 3’ to 5’ direction along template DNA strand → RNA grows in 5’ to 3’ direction
Ribonucleotide triphosphates
ATP, GTP, CTP. UTP
Provides energy to drive the anablic/synthetic reaction
RNA - Differences
Nitrogenous base → uracil
Replaces thymine found in DNA
How does it take place?
A region of DNA unwinds, and one strand will be used as a template for the RNA transcript
The key is the new RNA strand grows in the 5’ → 3’ diresction
This means the template DNA strand is read in the 3’ - > 5’ direction by RNA polymerase
Transcription takes place in 3 stages → initiaion, elongation & termination
always places nucleotides on 3’ end
Initiation of Transcription
Transcription is initiated at a specific region of DNA → promoter
This is a double-stranded DNA sequence that proteins knows as transcription factors and RNA polymerase bind
Promoter sequences are conserved DNA sequences
One very common base pair sequence in eukaryotes is 5’ - TATAAA - 3’ called the TATA box
The first nucleotide to be transcribed is usally found ~25 base pairs away from the TATA box
Transcription proceeds until RNA gets to a terminator
In bacteria, promoter recognition is mediated by a protein → sigma factor
This protein associates with RNA polymerase (RNA Pol) and RNA Pol’s binding to specific promotes
In prokaryotes - all transcription is performed b a single type of RNA polymerase
In Eukaryotes…
at least six proteins must work together to initiate transcription → general transcription factors
They bind to the promoter region
Transcriptional activator proteins will bind to enhances sequences on the DNA
This recruits RNA polymerase complex II (RNA Pol II)
In eukaryotes there are 3 distinct RNA polymerases
RNA Pol II to make mRNA
Initiation
The mediator complex associates with the genral transcription factors and RNA Pol II
The looping of the DNA brings activator proteins into contact with the proteins bound at the promoter region -
a “bubble” that is about 14 base pairs in length
The RNA-DNA duplex in the bubble is about 8 base pairs in length
It is very, very small
Elongation
RNA Pol (prokaryotes) and RNA Pol II (eukaryotes) allows for unwinding of the DNA → this allows complementary nucleotides to be added to the growing messenger RNA (mRNA) transcript
RNA nucleotide trisphosphates can enter via channels
There are also channels for:
The DNA double elix to enter/exit
An exit of the growing mRNA
The release of the mRNA when transcription is terminated
Prokaryotic Transcription (missing parts)
The RNA tr
For genes that code for a protein → the primary transcript (mRNA) has the information to direct the ribosome to translate
Both transcription & translation occur in the cytoplasm
Recall that there is no nuclear envelope
In prokaryotes, the pri
If this is the case, then the mRNA is called polycistronic mRNA
Eukaryotic Primary Transcript
There is an added layer of complexity between transcription and tranlation in eukaryotes → due presence of the nuclear membrane
The primary transcript needs to be modified so the message can move from the nucleus to the cytoplasm
RNA Processing of Eukaryotic mRNA
First → addition of a 5’ cap of 7-methylguanosine to the 5’ end of the primary trancscript
The
The addition of the 5’ cap is neede since the ribosome would not recognize the mRNA → this translation could not occur
The second major modification is the addition of about 250 consecutive adenines to the 3’ end of the mRNA → call the poly(A) tail
THis process is knows as polyadenylation
Serves an important role in:
Transcription termination
Export of the mRNA to the cytoplasm
Protection from degradation by exonucelases
The transcript also undergoes the excision of certain squences → introns
This leaves intact exons
This process is knows as RNA splicing
Some genes can produce primary transcripts that are spliced in different ways → alternative splicing
This means that asingle gene may produce different, but related, protein products in different cells → splicing results in different mRNAs