Flow of information Flashcards
Central dogma of molecular biology
The central dogma of molecular biology – a fundamental framework that describes the flow of genetic information within a biological system
Central dogma outlines the process by which genetic information is transferred from DNA to RNA then to protein
Begins with transcription, where a segment of DNA is used as a template to synthesise mRNA. During translation, ribosomes read the mRNA sequence and synthesise a corresponding protein by linking together specific amino acids in the order dictated by the mRNA. Process is crucial because proteins are essential for virtually all cellular functions, from structural roles to catalysing biochemical reactions
Central dogma emphasises the directional flow of information (DNA – RNA – protein) underscoring the pivotal roles of genetic information in the functioning and regulation of living organisms
DNA, RNA and flow of genetic info
Functional unit of genetic information is the gene
Genes are a part of genetic elements – large molecules and/or chromosomes
Genome – all genetic elements
DNA (genetic blueprint) RNA (transcription product), mRNA translated into protein
Informational macromolecules = nucleic acids and proteins
DNA and RNA
- Nucleotides = nucleic acid monomers
- DNA and RNA = polynucleotides
- Three components = pentose sugar, nitrogenous base, phosphate
- DNA = deoxyribose, RNA = ribose
- DNA is double stranded, RNA is single stranded
The genetic code
The genetic code – a set of rules by which the information encoded within DNA or RNA sequences is translated into proteins by living cells. The code is universal to almost all organisms, highlighting the shared evolutionary origins of life. It consists of sequences of three nucleotides (codons) each of which corresponds to a specific animo acid or a stop signal during protein synthesis.
64 possible codons, but only 20 amino acids, so the genetic code is redundant – meaning several codons can code for the same amino acid. Redundancy serves as a protective mechanism against mutations, as it chances in the DNA sequence might not necessarily alter the protein produced
Genetic exchange
Genetic exchange – the process by which genetic material is transferred between organisms or exchanged between different parts of the genome within the organism.
Genetic exchange of genetic information introduces genetic diversity, which is essential for evolution adaptation and survival
There are several mechanisms where genetic exchange can occur – both in sexually reproducing organisms (vertical gene transfer) and in asexual organisms such as bacteria (horizontal gene transfer)
8% of human genomes consists of viral DNA sequences, mainly from retroviruses that have migrated into our DNA over revolutionary time
Vertical and horizontal gene transfer
Vertical gene transfer – transmission of genetic material from parent to offspring during sexual or asexual reproduction
Genetic exchange between eukaryotes occurs when two gametes fuse together and homologous chromosomes exchange genetic information
Horizontal gene transfer – process by which organism transfers genetic material to another organism that is not its offspring
Allows for the direct exchange of genes between organisms, often across different species
Common in bacteria and plays a significant role in evolution, especially in microorganisms
1. Transformation – prokaryote uptakes DNA from the environment and recombines it into its genome
Cells that could take up DNA from the environment = competent cells
Genetic competence is transient state that depends on the cells physiological state
Some species are naturally competent
Cells can be artificially made competent in the lab
2. Conjugation – genetic exchange among microbes based on the ability of certain plasmids to transfer from cell to cell
Can be responsible for rapid spread of antibiotic resistance (many plasmids carry gene encoding antibiotic resistance)
3. Transduction – transfer of genetic material by a virus (bacteriophage or phage)
When phages pack their DNA during assembly, they also take DNA from one host to another
Two different kinds of mistakes
i. Phages randomly pack and exchange any of the hosts genes (generalised transduction
ii. Phages only pack and exchange specific genes from the host (Specialised transduction)
How natural transformation was discovered - Griffiths experiment
1928, Frederick Griffith
Noticed Streptococcus pneumoniae capsule-bearing strains (S) killed mice, but capsule-free strains (R) did not
Capsule – made of polysaccharides/amino acids, helps microbes to adhere and form biofilms, prevents microbes from being eaten up by white blood cells, protects against phagocytosis
On agar plate, S colonies are smooth in appearance, R colonies are rough in appearance
Conclusions – heat-killed virulent bacteria could transform non-virulent bacteria into a virulent form, genetic information can be transferred between organisms, Streptococcus pneumonia is one of the few bacteria that can become naturally competent
Molecular mechanism behind natural transformation
- Exogenous double stranded DNA (dsDNA) binds to proteins of the competent system in the cell membrane
- dsDNA is fragmented into smaller pieces
- One strand of the dsDNA is degraded by a nuclease, while the other strand enters the cells
- The strand in the cytoplasm is coated by transformation-specific DNA-binding protein (RecA proteins) protecting inserted DNA from degradation by nucleases in the cytoplasm
- If the strand is homologous to and existing DNA region of the cell, the strand gets integrated in the chromosome = single-strand assimilation
- RecA (protein essential for the repair and maintenance of DNA) invades the homologous region in the cell chromosome, displacing one of the existing strands and replacing it with the new DNA (forming a stretch of hybrid DNA or heteroduplex)
Homologous = similar in position, structure, and evolutionary origin by not necessarily in function
Artificial transformation: implications in gene cloning
Gene cloning – recombinant DNA is introduced in cells artificially
DNA is introduced into bacteria in two ways – chemically competent cells and the heat shock method, electrocompetent cells and an electroporator
Chemically competent cells and the heat shock method
- Cells treated with chemicals (CaCl2) that alter the cell membrane permeability, facilitating DNA uptake
Ca2+ ions attracted to negatively charged DNA and negatively charged cell membrane
Electrocompetent cells and electroporation
Conjugation in gram negative bacteria
- Sex pilus of the donor bacterium (F+) attaches to the recipient bacterium (F-) where F=fertility
- Sex pilus retracts, dragging the cells together
- A single strand of the plasmid is cut and unwound, and the DNA is transferred to the recipient cells while the donor plasmid creates a new second strand
- Once in the recipient cell a second strand is replicated in the recipient cell where it becomes the new donor (F+) cell
Recombination events
Very rarely the conjugative plasmid (F factor) can get integrated into the chromosome of the donor bacteria by site specific recombination
Regions within the plasmid sequence and the chromosome where the plasmid will integrate must be similar
These cells are called Hfr (high frequency recombination cells)
Site specific recombination
Requires – specific DNA sequences, occurs between the circular and linear DNAs at specific sequences (IS = insertion sequence), two DNA partners, a specialised recombinase protein that is responsible for recognising the sites and breaking and rejoining the DNA
Once integrated the Hfr cells now contains the F factor and can produce sex pili
Hfr cell connects with the donor cell and genes in the chromosomes of the donor cell are transmitted to the recipient
Length of time of attachment defines how much DNA is transferred
Once in the donor cell the DNA fragment integrates by homologous recombination in the chromosome of the recipient cell
Homologous recombination
Donor DNA recombines within the recipient’s chromosome via at areas of similar or identical sequence (homologous = same)
Double crossover inserts the donor DNA into the recipient’s chromosome (does not necessarily contain the F factor)
Conjugation among gram-positive bacteria
Conjugation similar to that in gram-negative bacteria. Major differences between conjugation in gram-negative and gram-positive bacteria is the mechanisms that establish cell-cell contact in order to initiate conjugal transfer
Gram-positive bacteria clump together to bring the donor and recipient close
Gram-positive bacteria do not form sex pilli
1. Bacteria clump together
2. & 3. Conjugative plasmid replicates in the donor and the recipient cell
Quorum sensing (QS) in conjugation
Some gram-positive bacteria (recipient) produce pheromones to attract the plasmid of the donor cell
1. Recipient cell produces a pheromone (cA) that interacts with a plasmid (pA) in the donor cell
2. Plasmid in the donor cell encodes for genes producing aggregation substances (AS)
3. AS migrate to the cell surface of the donor cell
4. AS bind binding substances (BS) on the surface of the recipient cell
5. Cells clump together, and genetic exchange occurs
The plasmid in the donor cell usually carries a gene encoding for cA too, but its expression is repressed by a regulatory gene in the plasmid (pA), so aggregation occurs only among donor and recipient cells
Specialised transduction
- Phage DNA in integrated into the bacterial chromosome as a prophage
- Normal phage excision produces a circular phage again
- Abnormal excision results in some of the neighbouring bacterial DNA being carried over in the circular phage while some DNA phage is left behind in the bacterial chromosome
Can result in bacteria being more virulent as it acquires new genes, less virulent as random integration can damage normal gene function
Transduction in practical application
What happens to bacterial after infection with a lytic phage – bacterial chromosomes are being degraded
Cells are being lysed and bacteria killed
