Introduction: Bacteria & Phage Flashcards
DNA is complexed with other molecules such as ____
protein
Information in the genome (not just the “gene”) is present in the form of a ______ and not in the accessory proteins
linear sequence of bases
Central Dogma: Bacteria genome are made of deoxyribonucleic acid (DNA) (_______ bases) and transcribed into ribonucleic acid (RNA) (______ bases) which is translated into protein (______ code)
- ATCG bases
- AUCG bases
- one letter amino acid
Nomenclature: Genes are identified by _________ letters which indicated the _____ the gene product is involved in. Then followed by ____ letter signifying the individual gene. (ex. ______)
-three lowercase italicized
-pathway
-capital
-lacZ (lac-pathway Z- gene encoding B-galactosidase) -lac is italicized
In bacteria, transcription & translation occur in _____
the same cell compartment
Plus (+) superscript on a gene indicates _____
wild-type (no mutations)
Minus (-) superscript on a gene indicates _____
a mutant allele (likely non-functional)
Delta (Δ) before a gene name indicates that ______
-the gene has been deleted.
Proteins/gene products are not _____, and the first letter of the protein name is _____ (ex. ____ = β-galactosidase enzyme)
-italicized
-capitalized
- LacZ
6 reasons to study Bacterial Genetics
- Model system for higher organisms
- Bacteria are more complex than once thought
- Bacteria are interesting
- Essential to ecology of Earth
- Symbiosis
- Role in Disease
Many scientific principles are discovered using _____. _______ and ________ make good genetic models
-“simple” cells
-Bacteria
-Bacteriophages
Crisper/Cas is the bacteria’s _____
ancient immune system that cleaves virus DNA
Three Domains of Life
- Archaea
- Bacteria
- Eukaryotes
Domains of Life are distinguished through ______
sequences of ribosomal RNAs (rRNAs)
Bacterial lineages diverged ______ years ago but mammals diverged _______ years ago
-billions
-millions
Bacterial lineages look the same morphologically but ________
highly divergent genetically (has high sequence diversity)
Bacteria can be ___-celled or ______ and shape?
-single
-multicellular
-rod-shaped/spherical
1 colony = ____
1 cell reproduced to form 10^10 cells
Streptomyces coelicolor (descr.)
- Form stalks of spores –> hyphae (multiple cells in a row)
- Produce antibiotics
-gram +
Escherichia coli (descr.)
- Single-celled rods
- Model organism & pathogen (after acquiring specific genes)
5 properties that make bacteria good genetic models
-bacteria are PROKARYOTES
-no nuclear membrane
-transcription & translation occur simultaneously
-single chromosome
-bacteria are HAPLOID facilitates genetic analysis
Transcription & Translation happening at the same time means that _____
transcription of DNA is immediately reflected in translation of mRNA
eukaryotes general descriptions.
-More complex cell structure -> organelles
eg. mitochondria, choloroplasts, endoplasmic reticulum
-Diverse -> plants, animals, fungi, protists
-Very similar at biochemical level (macromolecular synthesis)
Mitochondria derived from early symbiosis with ______
alphaproteobacterium (uses proton capture to generate energy)- (gram -)
Chloroplasts derived from early symbiosis with ______
cyanobacterium (photosynthesis) - gram -
In bacteria, transcription and translation are tightly coupled. Ribosome translates mRNA as it is being synthesized by ______ which produces _____
-RNA polymerase
-polyribosome (many ribosomes on mRNA)
5’ end of polyribosome has the _____
most recently attached ribosome attached
Bacterial chromosome (def.) & condensed in a structure called ____. DNA is arranged in _____
-single, supercoiled, double-stranded circular DNA molecule
-nucleoid
-supercoiled loops
DNA of bacterial chr is highly compacted around _____
histone-like (not histone) proteins
Adding nick to chr removes ___
supercoils
Gram +/ Gram - colours
-retain more dye (purple/crystal violet)
-retain little dye (counterstain pink/ safranin)
Gram positive membrane
cytoplasmic membrane
cell wall (peptidoglycan- polymer of sugars and peptides- thick)
Gram negative membrane
cytoplasmic membrane
cell wall (peptidoglycan - thin)
periplasmic space - soluble space dense with proteins
outer membrane - very impermeable due to LPS
differences in ____ determine bacterial cell shape
peptidoglycan
types of media for bacterial growth
-complex (broth, complex extract from biological material, rich in organic molecules)
-minimal (no organic compounds other than carbon, ions, basic nutrients to keep cell alive)
prototrophs grow on ____
minimal media (WT), supports their own growth
auxotrophs require ____ & grow on _____
- other organic substance than carbon source, mutants of prototroph
- complex media
agar is from ____
seaweed
solid media is made by____
adding agar to media and pouring in plate
plating def.
the act of depositing bacteria on the agar surface
bacterial genomes are haploid meaning that? effect?
-one copy(allele) of each gene
-easy to identify mutations as most mutations have immediate effect but can’t maintain lethal mutations (gene is essential)
Bacteria have short generation times (def.)
time the organism takes to reach maturity and give rise to offspring
ASEXUAL REPRODUCTION (def.)
bacteria multiply asexually by cell division
-produces CLONES - all progeny are genetically identical to parent and to each other
colony (def.)
visible cluster of bacteria originating from a single bacterium (number of colonies represents initial number bacteria)
how to find # bacteria from colony
colonies formed/ml plated x dilution before plating = # viable cells/ml undiluted
How to isolate strains from mixed culture
-identify and pick colony & streak on new plate (x2) =pure culture
How to screen strains from mixed culture
Identify mutants by screening for a differential phenotype, so both WT and mutants can grow but they will look different
How to select strains from mixed culture
Isolate (select for) desired strain/mutant under selective conditions where only the desired bacteria can grow (Eg. nutrient agar, antibiotics, or selective
temperatures)
Bacteria make good genetic models (7 reasons)
-simple growth requirements
-haploid
-short generation times
-asexual reproduction
bacteria counted easily
-easy to screen and isolate
-easy to select
archaea (descr.) -mix of euk & prok elements
- Single celled organisms (like bacteria)
¤ Lack a nucleus (like bacteria)
¤ Basic cellular processes more similar to that of eukaryotes (e.g. transcription, translation, DNA replication)
Many archaea are ______ + examples
-extremophiles/Extreme condition loving
- High temperature sulfur springs
- Ocean floor
- High osmolarity : Dead Sea
bacteriophages (descr.)
-bacteria eaters
-viruses that grow in bacterial cells/foundation of genetic principles
_____ are the most numerous “organisms” on Earth; 10^31particles; 10-fold more than bacteria (10^30); major life form on earth
-Phages
phages turn over ____ of bacteria everyday; mahor players in carbon cycling and nutrient turnover in biosphere
40%
Only ______ of phage genes are of known function
-30-50%
They can carry foreign DNA to new hosts, and therefore are responsible for some _______
-bacterial evolution
Phages are ____ bacterial parasite
obligate (can only multiply in actively metabolizing bacterium)
Minimal functions of phages for survival
1)-protection of nucleic acid
2)-delivery of nucleic acid to inside of a bacterium
3)-conversion of bacterium into a phage “factory” to produce more phages
4)-release of progeny phage
structure of phages
-DNA, RNA, single or double stranded, linear, or circular
-nucleic acid surrounded by a protein COAT or CAPSID
- helical (rod or thread-like), isometric (spherical, many icosahedral)
two types of phage lifecycle
1) Lytic / Virulent
- infecting phage converts bacterium into a phage factory to produce many more phages
2) Lysogenic / Temperate
- phage DNA becomes integrated into the bacterial
chromosome and is silent; phage genome in this state is called a PROPHAGE
phage that undergo only lytic growth are called ____
-VIRULENT
the bacterium harbouring the prophage is referred to as a _____
- process of integration termed ______
-LYSOGEN
-LYSOGENY
bacteriophage capable of lysogeny = ______ bacteriophage
-TEMPERATE (or lysogenic)
The Lytic Lifecycle Steps
1) Adsorption of phage to specific receptors on the bacterial surface
2) Passage of DNA from phage through bacterial cell wall
3) The bacterium is turned into a phage factory
- EARLY GENE products allow phage DNA to begin to replicate
- LATE GENES encode structural proteins for the phage head and tail
4) Phage particles are assembled- This is also called MORPHOGENESIS
5) Release of newly synthesized phage
the release of the phage require which two proteins?
holin - protein that disrupts cytoplasmic membrane
lysozyme - protein that degrades cell wall
LYSATE (def.) & the number of phage released per bacterium is called the _____
-the collection of lysed cells and new phages
-BURST SIZE
The Lysogenic Lifecycle steps
1) phage adsorption and injection of phage DNA into host cell
2) brief period of transcription -a REPRESSOR PROTEIN and SITE-SPECIFIC RECOMBINATION enzyme synthesized
3) the phage DNA molecule recombines into the bacterial chromosome -occurs by recombination between attachment mediated by INTEGRASE
4) phage DNA is now replicated with the bacterial chromosome as the bacterium grows
5) lytic growth may be triggered again after many cell generations by a process known as INDUCTION
Lysogeny may provide a _____ advantage
-selective growth
- pure phage stocks purified from _____
-PLAQUES
PLAQUES (def.)
regions of clearing that develop in a lawn of bacteria due to the lytic growth cycle
one plaque originates from _____
-one phage
number of plaques = _______
original number of phage
Efficiency of Plating (EOP) (def.)
- the fraction of phage particles that can form a plaque
- usually 1 or very close to 1 for most phages
Multiplicity of Infection (MOI) (def.)
- refers to the number of adsorbed phage per bacterium
- determines how many bacteria will be infected by phage
Isolation of Phage Stocks (def.)
- phage produce more rapidly than bacteria (100 phage vs. 2 bacteria per generation time),
- if mixed 1:1, all the bacteria will be lysed (PHAGE LYSATE)
5 reasons phage make good genetic models
-Bacteriophage are Haploid (mutations manifest immediately)
-Short Generation Times
-Multiply Clonally (pure stocks for further manipulation)
-Easy to Cross Phage Strains (infect same bacteria with different mutant phage stocks at high MOI, some bacteria infected by both phage, can examine plaques to study interaction of genes (RECOMBINATION) (COMPLEMENTATION))
- Easy to Select Mutants (millions of phage can be mixed with bacteria and grown under SELECTIVE
CONDITIONS that allow growth of only specific mutant phage)
