Central Dogma and Genetic Transfer

Molecular Transfer of Genetic Information and Central Dogma

• DNA is transcribed into RNA which then translates into proteins, describing the flow of genetic information in a biological system.
• RNA polymerase synthesizes RNA from DNA in the 5' to 3' direction during transcription, resulting in an RNA transcript
• Ribosomes, transfer RNA (tRNA), and amino acids synthesize proteins from mRNA in the 5' to 3' direction in translation, resulting in a functional protein.
• Genetic information is expressed and regulated by the central dogma of molecular biology.

Exceptions to Linear Genetic Transfer

• Retroviruses such as HIV use RNA as genetic material and reverse transcriptase to convert their RNA genome to DNA.
• The synthesized DNA from retroviruses integrates into the host cell's genome, is transcribed into mRNA, and subsequently translated into viral proteins.
• Retroviruses follow this process: RNA -> DNA -> RNA -> Protein
• RNA viruses like influenza, polio, and coronaviruses directly use RNA for translation without converting it to DNA.
• The translation follows: RNA -> Protein
• Viruses can hijack host ribosomes immediately after infection to translate their RNA into proteins.
• Prions are misfolded proteins that induce other proteins to misfold without nucleic acids (DNA or RNA)
• Protein aggregation for prions: Protein -> Protein
• Transposable elements that change their position within a genome and some transcribe into RNA, then reverse back into DNA, integrating into different genomic locations
• DNA for transposons uses: DNA -> RNA -> DNA

Bacteria and Eukaryote Gene Expression Similarities

• Both bacteria and eukaryotes: employ transcription and translation to express genes, both follow the central dogma (DNA -> RNA -> Protein).
• Regulatory proteins with transcription factors bind to specific DNA sequences to enhance or inhibit transcription.
• Both have promoter regions where RNA polymerase binds to initiate transcription.
• Have clusters of genes that are functionally related called operons.

Bacteria and Eukaryote Gene Expression Differences

• Bacteria lack a nucleus, transcription and translation occur simultaneously in the cytoplasm.
• Eukaryotes have a nucleus, which separates transcription (in the nucleus) and translation (in the cytoplasm).
• Bacteria gene expression uses repressors or activators at the transcriptional level.
• Eukaryotes gene expression involves multiple transcription factors, enhancers, silencers, and chromatin remodeling at multiple levels.
• Bacterial mRNA is translated immediately after transcription with very little processing.
• Eukaryotic pre-mRNA undergoes splicing to remove introns, and also has a 5' cap and polyadenylation at its 3' end before translation.
• Bacteria use sigma factors that are part of the RNA polymerase holoenzyme to begin transcription.
• Eukaryotes use a set of transcription factors to form the pre-initiation complex at the promoter.
• Bacteria respond rapidly to changes using mechanisms like the lac operon to regulate lactose metabolism based on its availability.
• Eukaryotes have more signaling pathways to regulate gene expression and integrate multiple signals.

Eukaryotic Gene Expression Regulation Levels

• Transcription Regulation controls DNA to RNA transcription with promoter and enhancer elements that regulate RNA polymerase activity.
• Transcription factors are proteins that act as activators or repressors to influence transcription initiation.
• Chromatin structure affects DNA accessibility for transcription machinery.
• Post-Transcriptional Regulation controls RNA processing and stability after transcription
• RNA splicing removes introns and joins exons to create different mRNA isoforms.
• 5' capping and 3' polyadenylation enhance mRNA stability and aid translation.
• RNA interference (RNAi) uses small RNA molecules (siRNA and miRNA) that bind to mRNA that leads to degradation or inhibiting translation. Translational Regulation controls mRNA translation into protein.
• Initiation factors help assemble the ribosome on the mRNA, and availability influences translation efficiency.
• The secondary structure of mRNA can affect ribosome binding and translation initiation.
• Regulatory proteins can bind to mRNA to promote or inhibit translation.
• Post-Translational Regulation controls protein function and stability after translation.
• Chemical modifications like phosphorylation can alter protein function, activity, and stability.
• Proteolytic cleavage activates/inactivates proteins by cleaving into smaller peptides.
• Protein degradation via the ubiquitin-proteasome pathway regulates protein levels in the cell.
• Epigenetic Regulation involves heritable changes in gene expression without changes to the DNA sequence.
• DNA methylation (addition of methyl groups to DNA) can silence gene expression.
• Histone modification changes to histones that can influence chromatin structure and gene accessibility.

Functions of Different RNA Types

• Messenger RNA (mRNA) carries genetic information from DNA to the ribosome
• mRNA contains codons, which are three-nucleotide sequences that specify amino acids.
• Before translation, mRNA undergoes 5' capping, polyadenylation, and splicing.
• Transfer RNA (tRNA) translates mRNA codons into amino acids during protein synthesis
• tRNA has an anticodon complementary to a codon, carries a corresponding amino acid and a 3' end, and ensures the correct amino acid sequence.
• Ribosomal RNA (rRNA) is structural/functional components of ribosomes, the locations for protein synthesis.
• rRNA combines with proteins to form ribosomal subunits, catalyzes peptide bond formation during translation, and is involved in the alignments of mRNA and tRNA during translation.
• Small Nuclear RNA (snRNA) is involved in splicing pre-mRNA in the nucleus.
• snRNA forms complexes with proteins to create small nuclear ribonuclear proteins while recognizing and removing introns from pre-mRNA, to facilitate exon joining.
• Small Nucleolar RNA (snoRNA) modifies/processes rRNA.
• snoRNA guides chemical modifications of rRNA like methylation and pseudouridylation; and assembly of rRNA into ribosomal subunits.
• Micro RNA (miRNA) regulates gene expression by targeting mRNA for degradation/translational repression.
• miRNAs are short, non-coding RNA molecules in mRNA.
• miRNAs influence various biological processes through post-transcriptional regulation.
• Small Interfering RNA (siRNA) regulates gene expression and defends against viral RNA using short, double-stranded RNA molecules to silence specific genes by promoting mRNA degradation.
• siRNAs play a role in the cellular response to foreign RNA like viruses.
• Long Non-Coding RNA (lncRNA) regulates gene expression and chromatin remodeling.
• lncRNA molecules do not code for proteins, but interact with DNA, RNA, and proteins to influence transcription and chromatin structure.

mRNA Structure

• The 5' cap being a modified guanine nucleotide that protects mRNA from degradation and it assists ribosome binding during translation.
• 5' Untranslated Region (5' UTR) regulates translation between the 5' cap and the start codon (AUG).
• Coding Sequence portion contains codons that specify amino acids.
• 3' Untranslated Region (3' UTR) is the region that follows the stop codon- mRNA stability and translation efficiency are controlled.
• Poly(A) Tail is a stretch of adenine nucleotides that enhances its stability and facilitates export from the nucleus towards the 3' end.

mRNA Synthesis

• RNA polymerase II binds to the promoter region of the gene, is aided by transcription factors during initiation.
• RNA polymerase II synthesizes directionally 5' to 3' of the complementary RNA strand along the DNA template strand during elongation
• The release of the synthesized pre-mRNA new happens since RNA polymerase II has come across a termination signal for its termination

mRNA Maturation

• Capping occurs shortly after transcribing.
• Functions to protect mRNA from damage and assists ribosome binding.
• The spliceosome a complex of snRNA and proteins, performs splicing for exons and introns.
• Polyadenylation enhances stability and export from the nucleus after 3' end poly(A) tail additions that come following termination.

mRNA Lifecycle

• Mature mRNA goes through nuclear pores and then get exported nucleus to cytoplasm.
• Protein recognizes 5' end cap and poly(A) tail aids the process.
• Protein binds and initiations translation where codons assembles for every amino acid in polypeptide chain inside cytoplasm.
• mRNA molecules has a finite lifespan and is eventually degraded by exonucleases and endonucleases to remove the 5' cap and poly(A) tail after translation.

Transcription Initiation in Prokaryotes

• RNA polymerase binds to the promoter, which contains -10 and -35 regions on the DNA.
• RNA polymerase unwinds the DNA double helix when bound, creating a transcription bubble to show the template strand.
• RNA polymerase starts synthesizing RNA through the incorporation of ribonucleotides following the DNA template strand.

Transcription Elongation in Prokaryotes

• RNA polymerase elongates along the DNA template strand.
• RNA will be synthesized in the 5' to 3' direction.
• Transcription continuously unwinds and re-anneals the DNA.

Transcription Termination in Prokaryotes

• Intrinsic termination occurs when the RNA forms a GC-rich-stem-loop structure followed by a poly-U sequence and then RNA polymerase encounters a specific sequence on the RNA.
• Rho-dependent termination occurs when Rho protein binds to the RNA transcript and causes RNA polymerase causes the polymerase to fall off because they were moving toward it

Transcription Initiation in Eukaryotes

• Transcription factors (TFs) bind to the promoter region and include the TATA box, to allow form the pre-initiation complex (PIC).
• After the pre-initiation complex assembles then RNA polymerase II is recruited to the promoter.
• RNA polymerase II unwinds the DNA and forms a bubble on the transcription to allow entry for template strand

Transcription Elongation in Eukaryotes

• RNA polymerase II still synthesizes directionally 5' to 3' while using the DNA template.
• C-terminal domain of RNA polymerase II becomes phosphorylated, and allows RNA processing factors and transition from initiation to elongation.
• RNA forms co-transcriptional processing that undergoes splicing and capping.

Transcription Termination in Eukaryotes

• RNA is cleaved and has a poly-A tail to aid export from the nucleus and stabilize mRNA.
• Termination is impacted through effects from CTD and presence of factors.

Transcription Direction and Template

• RNA will be directionally formed 5' to 3' in eukaryotes and prokaryotes.
• Template Strand is used directionally 3' to 5' for RNA usage during transcription.
• Non-Template contains a same sequence but replacement for thymine then replaced into uracil.
• RNA polymerase is bonded towards the DNA with template strand using prokaryotes.
• Any strand of DNA is transcribed through varied gene expression.
• RNA polymerase II then non-template stays untranscribed. Capping and splicing undergoes processes to turn pre-mRNA eukaryotes.

RNA Polymerase and Promoter Elements

• Typically has one RNA for core enzyme made of sigma factor and subunit enzyme towards prokaryotes.
• Includes recognizing from its sequence (TATAAT) at start and crucial binding of RNA to bind and -10 Region (Pribnow Box) start region.
• The site of region for also RNA by 35 Region downstream.
• RNA Polymerase has III levels for RNA and Eukaryotes. TATAAA sequence conserved around for the complex TATA box for region

5' and 3' UTR usage

• prokaryotes - short and contains Shine-Dalgarno essential sequence to allow initiation translation.
• a upstream site ribosome and Shine-Dalgarno aligns RNA to allow for initiation.
• 3'UTR includes a termination signal.
• 5'UTR has 7mG cap with ribosome in Eukaryotes
• Contains elements that may alter function.
• Various regulations inside of the roles in 3'URT.
• It has a polyadenylation signial, that signals to allow initation to occur and the contain protein binding sits.

Splicing

• Catalyzed to form mature RNA from small proteins and RNA for introns and exons that can be joined by spliceosome.
• Involves transesterification reactions using hydroxyl group .
• Constitutive splicing joins both introns and exons to allow the most joining of it.
• Alternative splicing increases by genes containing exons to remove them by gene that has been produced inside gene.

Evidence and Polydenylation

• R-loop structures form displacing RNA for introns on non template creating displaced non template form DNA.
• it indicates rna forms the transcript does not directly match.
• Polydenylation has no process inside prokaryotes
• Adds eukaryotes that have poly a tails after end
• It signals the Poly A tail. Poly A facilitates with promoting.

Translation

• binding of it to mRNA beings at subunit Shine-Dalgarno sequence.
• Ribosome contains tRNA initiator and its binds.
• After this the ribosome complex completes and is complex is initiated.
• RNA enters and helps assist.
• Amino bond formation requires ribosome.
• elongation factors are involved for rna to be delivered.
• The encounter results for termination to encounter UAG for termination.
• release factors bind, and hydrolysis occurs.
• RNA goes from its subunits and will encounter as ribosome.

Structure

• Prokaryotic are 70s subunits and has subunits.
• Has sites known as amino or A site that have rna attached. PepSite holds growing side for formation of it and P site. Exit for donation from site.

Structure and Function

• Ribsomes are Eukaryotic and subunits for site
• A Site similar to rna in Prokaroutes.

Functions

• Catalyzes for binding of it.
• Ensures its accurate for the formation.
• Trna will move, ribosome after is formed. This action will allows site for mRNA

tRNA Structure

• tRNA in Molecules and has cloverleaf characteristics.
• 3 dimensional shapes can be found. Has site attached to acids.

Function and Genetic Code

• Accuracy by codon.
• Pairing with each that have rule bases to follow.
• UAC will bond to ensure.
• tRNA
• Specifics follow rna that attaches and determine to add which rna.

Genetic Organisation

• Codons have triplet, every one has specific acids.
• They are a signa.
• AUG that comes then all follow end.
• ORF has frame begins for it.

Chracteristics

• That share for beings for genetic.
• Degeneracy with multiple codes for codes.
• Non over lapping That come up and are part Starts and stops with code being signalled. Shifts then that and alteration in 3ds.

Effects

• Adding causes a shift, resulting into amino for the mutations.
• causes of proteins.

Somatic

• Mutation from non cells.
• Are not passed to offspring.
• That all can functions effects
• Mutatins that cause smoking. GermLine Definition: sperm and eggs. Phenotype : These are inheritable to the gene. Associated mutations comes.

Effect

• affect an individual.

DNALesion

• Loss can be detected
• Damage that is fixed to take damaged site Insertion
• Is there can replication done. Bases has modification
• repair helps address code
• Unrepaired can lead. Pyrimidine
• Covalent Linkages with pyrimidine.
• Excision has a repair damage DsB has effects Hormon.

Lesions

• Alkylating groups by DNA
• Source due to chemotherapy
• Damages is cause.
• Byproducts with aerobic metabolism.
• Removed by amine that base.
• Has a altered pair.

Depiction

• high can effect to cause. UV light. Causes a pyrimidine base.
• Heat causing can. It has structure alteration.

Point

• Can be caused by acids having some mutations. Effects Can take place on amino acid by some.
• That happens and has a phenotype issue

coding

• Location from regions helps it in its function that important that a essential Mutations: factors and changes affects is a change. They disrupt or the ability to act.
• That increase can take in a diseases.
• Affect the changes signals as it may happen.

Polymerase

• Dna polymerase temporarly dissociates at the enzyme or template.
• It follows a repeatition with place. Type of slilpage
• The polyemrase re associate helps replication leading to strand If the associate repeats with 1s and skips resulting to new strains.

Consequences

• Results from alteration if they come during genes
• non functional with alter .
• That happens all may take function

DNA and Siippage

• Regions with long stretches
• increased the likeliness of mis alignment fidelity Accuracy of the rate increasing liklines of it
• cellular Increase with occur.
• Tauermation comes. Process converts new phases. Forms an altering

Mispairing

• occurs when wrong code is replicated. Mechanism by errors as well Transition It helps with properties. Changes with correct functions of acids

Modification

• With radiation affecting high level The result for it to code wrong

Depurination

• That can occur during 100s a day A incorrect will come out as this.

Deamination and repair

• It helps during and will affect it.

Oxidative

• React to make variations
• That is a repair of it.

Test

• used to find components by looking at salmonella It cannot increase but need it to surivive has steps.

BER

• damage by it comes glysoylases are the recognitions. creating the AP site endinuclease creates break.
• and add template strand