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Biology, Regulation of Gene expression 2, Regulation of Gene Expression 1,…
Biology
Regulation of Gene expression 2
lvls of regulation of gene expression in euks.
transcriptional
post-transcriptional
translational
post-translational
Signature Motifs of transcription factors
Zinc finger
helix-turn-helix
Leucine zipper
Promoter-proximal elements & enhancers
Promote-proximal elements
Enhancers
properties
Insulators
DNA sequences that control transcription bind to:
General (basal) transcription factors
Special (specific) transcription factors
Gal pathway
Gal4 functionally independent domains
DNA binding
Activation
Gal80 & galactose regulates Gal4
transcriptional activator proteins recruit transcriptional machinery:
co-activation via the mediator complex
Cytoplasmic control of mRNA stability
Gene silencing by RNA interference (RNAi)
RNA interference (RNAi)
Triggered by formation of double-stranded RNA in cells
in research
phenocopy
Chromatin structure (histone/nucleosome)
regulation
influence
macrolevel
Gene level
heterochromatin
spreading
position-effect variegation
histone modifications
histone code
open vs close chromatin states
euchromatin
heterochromatin
Regulation of Gene Expression 1
Constitutive, iducible & repressible gene expression
Constitutive
Inducible
Repressible
Operon system in bacteria
Inducible operon
repressible operon
The Lactose (Lac) Operon
Induction & (-) feedback
regulatory role of LacO (I, O, P)
Inhibitor (repressor) (trans regulator)
Operator (cis regulator)
repression
cis / trans effects of LacO mutations
diploid cell for LacO genes can contribute twice the enzyme activity than a haploid cell can
IPTG and X-Gal use to decouple induction & (-) feedback
IPTG
X-Gal
Complexities of LacO
operator only acts in cis (Oc mutations)
represser acts in cis & trans
repressors are trans-acting (I- mutations)
I^s (super repressor) mutation reveal allosteric interaction pocket in repressor
activation/repression by Lactose/Glucose
The Ara Operon
Regulation of repressible/Inducible systems
repressible
(-) control
(+) control
Inducible
(-) control
(+) control
Regulating gene expression in bacteria
regulatory proteins control transcription
(+) regulation
(-) regulation
Induction of enzyme synthesis
repression of enzyme synthesis
cis and trans regulation
cis acting factor
trans acting factors
Role of allosteric interactors
(+) & (-) control of gene expression
(+) control
(-) control
DNA Dmg, Repair & Mutation
types of mutations
Somatic
Germinal
Mutation create phenotypic variability but also threatens cells
DNA instability as source of mutations
Point mutations
Base substitutes:
(4) transition (purine replaced by purine) [A=G];[G=A] or (pyrimidine replaced by pyrimidine) [C=T];[T=C]
(8) transversion (purine replaced by pyrimidine) [A=C]; [A=T]; [G=C]; [G=T]. (pyrimidine replaced by purine) [C=A]; [C=G]; [T=A]; [T=G]
functional consequence in coding region (ORF)
Silent mutations
Missense mutations
Nonsense mutations
Indels
frameshift mutation
functional consequence in non-coding regions
point mutations in regulatory regions needed for gene expression or mRNA processing & stability may affect how much protein made
Indels
Base insertion
Base deletion
Origin of mutations- spontaneous & random
Errors in replication
1) DNA pol slippage (indels)
2) mispairing
Tautomerization of nucleotides lead to purine-pyrimidine mismatches & transition mutations
DNA dmg
Ionization
Depurination
Deamination
Oxidative dmg
mutations
Spontaneous
Induced
mutagen
Types:
Chemical
ROS
Intercalating agents
DNA adducts
Base analogs
Alkylating agents
Physical
UV/Ionizing radiation
determining mutagenicity
Screening for revertants (organism)
bacterial based reversion approach (cell)
The Ames test
DNA Repair Systems
Base excision repair (BER)
Nucleotide excision repair (NER)
Mismatch repair (MMR)
Translation synthesis (TLS)
Homologous recombination repair (HR)
Non-homologous end-joining (NHEJ)
Direct repair
modus operandi
Surveillance
excision (resection)
polymerization
strand ligation
Population genetics
Violations of HWP
Non-random mating bias
(+) mating
disassortative mating
geographic isolation bias
inbreeding bias
Inbreeding & pop size
mutation
natural selection
changes in allele freq in pops
neutral mutation
deleterious mutation
adaptive mutation
Genes are multi-allelic units
theory of allele freqs
Gene pool concept
allele freqs & genotype freqs
HW equilibrium (HWE)
The Genetic Code
hachimoji DNA
Wobble rules
x^n = y
Amber suppressors
Stop codons
Molecular Genetics
Molecular transfer of genetic info
DNA(genotype) --> RNA --> Protein(phenotype)
Biochemistry of DNA
Replication
Transcription
Where?: RNA synthesized in nucleus, transported to cytoplasm
Phages
in Prokaryotes
Stage (1)
Stage (2)
Stage (3)
Termination signals in bacteria
Rho (p)-dependent termination
Intrinsic (p)-independent termination
in Eukaryotes
RNA polymerase 2 (Pol2)
Initiation
Co-transcriptional processing of RNA during elongation
Capping
7-methyl guanosine (7-MG) cap
Splicing
Exons
Introns
2 main mechanisms of splicing
self splicing
RNA/Protein complex-mediated splicing
Poly A polymerization
3' poly(A) tail
Translation
RNA molecules
Coding
Non-coding
Central Dogma
DNA 🔄(DNA pol) --RNA polymerase--><--Retrotranscription-- RNA 🔄(RdRP) --Amonioacyltransferase--> Protein 🔄(prions)
Flow of info between Biological polymers
RNA
Can replicate itself
Can be retrotranscribed to DNA
Characteristics
General features of synthesis
RNA polymerases
Prion
PrP^c --> PrP^sc
Self-replicable
Prokaryotes
Eukaryotes
Sequencing
Recombinant DNA & Genomic Analysis
Gene isolation & manipulation
Recombinant DNA techniques
PCR (vitro)
Gene cloning (vivo)
DNA amplification
recombinant protein synthesis
Vector & insert
Plasmids
Phages
life cycle
components
Strategies
Digestion strategy
selection systems in plasmids
selection for plasmid background
selection for an insert
Gel electrophoresis
DNA sequencing
Systems biology (omics)
Bioinformatics
Comparative genomics
Functional genomics
Sanger sequencing
new generation sequencing
Blast & DNA sequence database
Genome structure
Coding
Non-coding
Exome sequencing
Proteins & their Synthesis
Prok. & Euk. transcription & translation compared
Translation
mechanics
Stages
polypeptide chain initiation
chain elongation (peptide bonds)
chain termination
Ribosomes: decoding hubs
tRNA
unmatched residue & anticodon info
possibility 1
possibility 2