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Basic Principles of Molecular Biology - Coggle Diagram
Basic Principles of Molecular Biology
Central Dogma
DNA = code
RNA = Decoder
DNA
Transcription
mRNA
Transcription
Protein
Nucleic Acids
Biopolymers composed of nucelotides
Nucleotides
Monomeric units
Joined by phosphodiester bonds
Sugar-phosphate backbone
Constant
Variable bases
Guanine
Cytosine
Adenine
Thymine
DNA
Uracil
RNA
Guanine - cytosine
3 H bonds
Adenine - thymine
2 H bonds
Sugar
DNA - deoxyribose
RNA - ribose
Nucleoside
Nucleotide without phosphate i.e. sugar + base
Oligonucleotide
Short RNA/DNA molecules
Replication primer
5' phosphate binds 3' hydroxyl
Synthesis in 5'-3' direction
Positive supercoil
Major and minor grooves
Glycosidic bond position
DNA replication
5'-3' direction only
DNA polymerase + accessory proteins
dNTP's
A, C, G, T
Unwound duplex (-ve coil)
Right solutes
Semi-conservative
DNA organisation
Prokaryotes
Single chromosome
Circular
Can be linear e.g. Agrobacterium
Plasmid
Bacteria
Active chromatin
Always unwound (-ve supercoil)
Allows protein access
Inactive chromatin
Typically condensed
Unless transitioning
Eukaryotes
Multiple chromosome
Linear
Viral episomes
Supercoiling
Unwinding of DNA
Active chromatin
Always unwound (-ve supercoil)
Allows protein access
Inactive chromatin
Not always condensed
Gene organisation
Prokaryotes
Minimal features
Single promoter
RNApol binding site
RNApol recognition site
5' - 3' UTR (leader/trailer)
Function coding region
cDNA
1-3 open reading frames
No gaps
Terminator
Promoters
\(\sigma\) subunit binds - initiation of RNApol, left when RNApol activates
RNApol binds at TATA box
Transcription
Antileader is G/C rich
Between promotor and coding regions
Antitrailer + termination regions are G/C rich
Terminators
Blocks RNApol
2 ways
\(\rho\) protein-independent
G/C rich hairpin
Stalls RNApol
A/T rich gene, 6U after hairpin
RNApol falls off
No accessory proteins
\(\rho\) dependent
No U after hairpin
G rich RNApol stall
\(\rho\) displaces RNApol
Operons
Lac operon
2 promoters
1 has an inhibitor
Lactose binds preventing inhibitor binding promoter
Allowing transcription
Proteins for lactose breakdown translated
Multiple proteins from one mRNA
E.coli ribosomal operon
Extremely long compared to cell dimensions
Positive or negative supercoiling by topoisomerase
Induce additional turns in DNA helix
Break DNA polynucleotide
Rotate 2 ends relative to each other
Enzyme rejoins ends
Polynucleotide winds up on itself
Databases record genes in mRNA 5'-3' direction
Eukaryotes
Gene
Single promoter
5' and 3' UTR
Function coding region
Exons >1
Introns >0
Terminator
Primary transcript
pre-mRNA
Contains introns and exons
Capping, polyadenylation + splicing
mRNA
RNA processing
5'-capping
7'-methyl cap added
Linked via 5'-5' triphosphate bridge to first base on 5' UTR
Polyadenylation at 3' UTR
Polyadenylation signal (PAS) at AAUAA
CA cleavage
GU rich region follows downstream
Polyadenylation at 3' end
3' UTRs key to mRNA stability + regulation
Splicing
Introns removed
Introns
Splice donor site (5'end) GU
Splice acceptor site (3' end) AG
Function possibility?
Cryptic exons
Non-coding RNA (ncRNA)
Structural/regulatory
Ribosomal RNA (rRNA)
Introns + exons
Very highly conserved
18S in all eukaryotes
Small nucleolar RNA (snoRNA)
Ribosome formation
Transfer RNA (tRNA)
pre-tRNA
Large part of 5' end cleaved off
3 RNA polymerases
Pol I
rRNA only - 98% cell RNA
Pol II
mRNA + ncRNA TU's
Pol III
tRNA, rRNA, snoRNA + some ncRNA - in all cells
Pol I + III stopped at specific termination sequences
Pol I
On DNA - transcription termination factor (TTF-1)
Polymerase falls off
Pol III
4-7 U on 3' end
Mechanism unknown
Pol II random termination
Cleavage at AAUAA
Pre-initiation complexes
Transcription factors
TBP - TATA binding protein
Activators + repressors
On promoter
Upstream of coding region
Operators
Repressors
Activated by signalling molecules
Bind to operator when activated
Clusters + arrays
Clusters
product of duplication and divergence
Hox, globin genes
cis or trans
Expanded protein family functionality
Co-expressed
Few kb distance
Arrays
Consecutively repeated genes
No intergenic space
Prokaryotic-like
Function almost identical
rRNA genes
Viruses
DNA or RNA
Very economical
Piece of DNA can be part of 2 different ORFs
Short genome ~ 10 proteins
Polycistronic
mRNA encoding several viral proteins
Single or double stranded
1 or more gene segments
Minimal non-function sequences
1-2 promoters
Episomal
Unless fully integrated into host DNA
Plasmid DNA (pDNA)
Circular dsDNA
1-many copies per cell
Prokaryotes/yeasts
1 kbp -100,000s kbp
Independently replicating
Additional functional genes
Antibiotic resistance
Can integrate to genome
Usually don't have own polymerase gene
Proteins
Protein Structure
Primary
Amino acid sequence
Secondary
Folding into \(\alpha\)-helices and \(\beta\)-pleated sheets
H-bonds
Tertiary
3D
H-bonds
Disulphide bridges (covalent)
Ionic bonds/salt bridges
VdW's/hydrophobic interactions
Quarternary
Complexes of multiple subunits
Post-translational modifications
Organisation
Domains
Exons can represent single functional units within a protein
Exon 1 = domain 1 etc.
Translation
mRNA threaded through ribosome
tRNA bound to amino acid
Ribosome catalyses formation of peptide bond
Multiple ribosomes on one mRNA
64 possible codons
20 amino acids
Stop codon
Redundancy
Robust
Mutation may not lead to change in amino acid
Speed of translation affected by codon mutations
Amino acid biochemistry
Back bone
Carboxylic acid group
H
Amino group
Charged (NH3+, COO-)
Side chain differs
Charge
Acidic/basic
Hydrophilic/hydrophobic
Planar/linear
Polar/non-polar
N terminus to C terminus
Macromolecule functions
DNA
RNA
ncRNA
RNA interference (RNAi)
miRNAs
DNA
Primary miRNA
Processing
pre-miRNA
Processing
miRNA
1 more item...
Translational repression
Evolutionarily conserved
Expression
Intergenic
5'-UTR
Exonic
Intronic
3'-UTR
Protein
Transcriptional units vs. genes
TU's
Anything made into RNA molecule
Gene
Anything made into a protein
Both have
Introns + exons
5' + 3'-UTRs
Engineering gene expression
Simplicity is important
Requirements
Promoter
Pro/eurkaryotic
Expresses in right conditions
5' + 3' UTRs
Function coding region
cDNA
Terminator