Chapter 8-Microbial Genetics
I. Evolution (not in the book, but you should know)
A. Biology, and in particular microbiology, only makes sense through the lens of evolution. Without evolution, all of biology is a set of unrelated facts. (slightly modified from a famous quote by E.O. Wilson)
B. Evolution
1. Simple: Change over time, resulting in new species
2. Advanced: The change of population gene frequencies with resultant speciation through selection of naturally occurring genetic variants that are adequately adapted to their contemporary environment.
3. Important points
a. Genetic variation is inherent to biological systems and essentially random
b. Selection is not directional or with purpose, it simple selects for those organisms adequately adapted to their present environment to reproduce
4. What is a species?
a. Even microbiologists do not have a firm grasp on how to define species.
b. The hallmark of macrobiotic species, sexual isolation, is not applicable to bacteria.
c. A general definition for a bacterial species is a group of bacteria that have a consistent group of measurable phenotypes, a shared environmental niche and limited diversity in their genetic sequence.
i. Phenotype: measurable exhibited traits
ii. Genotype: genetic sequence traits (may or may not be expressed).
5. Controversies
a. Contrary to how the popular media portrays the events, there is no serious debate in the scientific community as to the current validity of Evolutionary Theory.
b. Evolutionary Theory is the most parsimonious solution to all the evidence available about the progressive development of life on Earth.
c. The nature of Science-
i. Science is testable by experimentation
ii. Science relies on natural processes to explain observation
iii. Science is falsifiable
iv. Science relies on uniformity of observation
v. This does not invalidate the realms of Religion and Philosophy, but they do not have a place in Scientific Theory.
d. Intelligent Design
i. The current rival to Evolution is the so called theory (notice small ‘t’) of Intelligent Design
ii. Intelligent design states that life exhibits too much complexity and interconnection to be random and as such must be the work of a designer.
iii. Though this debate is fueled more by political motivation than science (see 5.a.) I will approach the topic on the level of science, as this is a science class.
iv. Intelligent design suffers from four logical flaws that preclude it from being a Scientific Theory.
a. ID is not testable, it is impossible to construct an experiment to judge whether a “designer” is responsible for the formation of a complex system.
b. ID is not falsifiable
c. ID does not make predictions
d. ID does not take into account the advantage of precursor structures, in ID an eye is of no use if it is not a complete eye, while in reality it can be of great selective advantage.
e. ID relies on supernatural explanation, this is a true ‘nail in the coffin,’ science must rely on natural processes to explain how things work, not a dues ex machina. This leads to the “god unemployment line” phenomenon.
v. Contrary to popular depictions, ID is not a new idea, just a fresh veneer on an old idea (you can look back to the philosopher John Ray in the 1600s for the same basic idea).
II. Structure and Function of the Genetic Material
A. Genetics – the science of heredity
1. The totality of genetic information in a cell is referred to as the genome, contained in both the chromosome and any ancillary genetic material.
a. Chromosome – The physical construct of DNA that carries the majority of an organism’s genetic information, bacteria typically have a single chromosome.
b. ancillary genetic material – genetic material outside the chromosome that can be used by an organism, i.e. plasmids, typically these are not needed for survival, but confer an advantage to the organism.
2. Gene – a segment of DNA (RNA in some viruses) that codes for a functional product.
B. The Flow of Genetic Information
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C. DNA Replication
1. DNA is composed of four nuclear bases, with a sugar-phosphate backbone (coded 5’-3’)
a. Adenine (A)
b. Cytosine (C)
c. Guanine (G)
d. Thymine (T), replaced by Uracil (U) in RNA
2. The nuclear bases pair in a specific way:
a. A:T (or A:U in RNA)
b. C:G
3. This specific base pairing means that even if you only have one strand of the DNA double helix, you have a template for the second strand.
4. DNA replication is termed semiconservative which means that each new double helix has one new strand and one old strand.
5. DNA Replication is accomplished through an enzyme called DNA Polymerase.
6. The Basic Process of DNA Replication
a. The parental DNA is unwound and stabilized, with a separation of strands (termed the Replication Fork) being formed at a fixed site (the origin of replication, ori)
b. One strand is formed continuously by DNA Polymerase in a 5’-3’ direction, this is the leading strand
c. Since DNA Polymerase can only produce DNA strands in a 5’-3’ direction the other stand (with is unzipped in a 3’-5’ direction) has to be produced in staggered small pieces (the lagging strand) and connected together by a separate enzyme.
7. In most bacteria replication occurs bidirectionally around the circular chromosome from the ori.
8. In bacteria the error rate is very low, on the order of 1 mistake for every 1010 nucleotides added.
C. RNA and Protein Synthesis
1. Transcription – the synthesis of a complementary strand of RNA from the DNA template.
a. RNA Polymerase binds to the DNA (unwound and separated) called a promoter, again RNA is synthesized 5’à3’
b. RNA forms the new chain, using base pairing as the guide
c. RNA synthesis continues down the DNA chain, until a terminator sequence is reached
d. At the terminator the RNA polymerase and newly formed RNA strand are released.
2. Translation – The conversion of the RNA nuclear code into protein amino acid sequences.
a. Ribosomes translate the nuclear code into proteins.
b. The nuclear code is read in frames of three bases, ie. ATG
c. The groups of three bases are called codons
d. The ribosome uses the codons to determine the next amino acid in a sequence
e. The genetic code (figure 8.8) is the translation matrix for this conversion.
AUG à Methionine (start)
CUU à Leucine
f. The mechanism of translation is based on recognition of the codons by anticodons on special RNA molecules called tRNA (transfer RNA) that have a anticodon on one end and a specific amino acid linked to that anticodon on the other.
III. The Regulation of Bacterial Gene Expression
A. We will be covering only some of this material, and not to the level of detail in the text, be aware of the contents for these notes.
B. Genes are regulated by a variety of mechanisms, typically at the level of transcription.
1. Constitutive – genes that are constantly produced at a fixed rate
2. Repression – regulation that inhibits the production of specific gene products, the gene’s default state in on.
3. Induction – regulation that turns transcription on, the gene’s default state is off.
C. Operon Model – Genes in prokaryotes tend to be clustered into functional groups, which share a common regulation system.
IV. Mutation: Change in the Genetic Material
A. Mutation – a change in the base sequence of DNA.
B. Types of Mutations
1. Base Substitution – a single base change in the sequence
a. Missense Substitution – a mutation that results in an amino acid change.
b. Nonsense Substitution – a mutation that results in a stop codon.
2. Frame-Shift Mutations – one or a few bases are inserted into or deleted from a sequence, throwing off the codon sequence.
C. Mutations can occur in the absence of any apparent reason (spontaneous mutation) or can be the result of exposure to some substance that causes a mutation (mutagen).
D. Mutagens can be chemical in nature, or can be caused by radiation (remember the use of radiation in microbial control).
E. Mutations are constantly being repaired by the cell, though some do persist over time.
V. Genetic Transfer and Recombination
A. Genetic Recombination refers to the exchange of genes between two DNA molecules that allow for novel new arrangements.
B. Recombination happens between areas of DNA that have high homology (similar sequence).
C. Like mutation, recombination is a driving force in evolution in that whole genetic segments can be rearranged in novel ways.
D. Gene Transfer can happen in two ways.
1. Vertical Gene Transfer – passing genes from parent to offspring.
2. Horizontal Gene Transfer – passing genes between microbes in the same generation (bacterial sex).
E. There are a variety of specific mechanisms for horizontal gene transfer
1. Transformation – the uptake and incorporation of naked DNA
a. Griffith’s (with follow-up and expansion by Avery) Experiment dealing with Rough/Smooth Streptococcus pneumonia.
b. Transformation in nature occurs due to a natural state called competence, occurring during starvation.
2. Conjugation – the direct transfer of DNA between bacteria through a physical connection.
a. DNA is passed through a pilus.
b. Typically controlled by a sex plasmid, though this can become integrated into the chromosome (resulting in a high frequency recombination bug)
3. Transduction – the movement of DNA through the use of a virus
a. Mediated by viruses of bacteria, called bacteriophage
b. Results from a failed virus particle.
F. Plasmids – Small, self-replicating circular pieces of DNA that comprise 1-5% of some bacterial genomes.
1. Plasmids can be gained and lost and are not necessary for the basic survival of a bacteria.
2. Plasmids typically confer some selective advantage to the host, such as antibiotic resistance or toxin production.
G. Transposon – small pieces of DNA that can move themselves around the genome.