Microbiology 3 Flashcards
(191 cards)
1
Q
Genetics
A
the science of heredity
2
Q
Chromosomes
A
structures containing DNA that carry genes, microbes only have a single chromosome, we have a set of 2
3
Q
Prokaryote chromosome
A
have a circular chromosome, genes are much more simple than eukaryotes
4
Q
Eukaryote chromosome
A
have a linear chromosome (us), can preform gene splicing, genetics are very complex
5
Q
Genes
A
the molecular unit of heredity
6
Q
Alleles
A
different versions of genes, seen in eukaryotes only
7
Q
Mutations
A
a source for different types of genes
8
Q
DNA structure
A
double stranded helix, nucleic acid composed of nitrogenous bases
9
Q
Nitrogenous bases
A
the base components of DNA and RNA, made of 5 carbon sugar and a phosphate group, they form the rungs of the structure
10
Q
Nitrogenous base pairings DNA
A
C makes 3 hydrogen bonds with G, T makes 2 hydrogen bonds with A
11
Q
Nitrogenous base pairings RNA
A
C makes 3 hydrogen bonds with G, U makes 2 hydrogen bonds with A
12
Q
Genetic information transfer
A
DNA replication
Transcription
Translation
entire process takes place in the cytoplasm, all steps can occur at the same time, this can’t happen in eukaryotes
13
Q
DNA replication
A
occurs before binary fission, must move from 5’ to 3’, is a semi-conservative process because each new DNA molecule contains one original strand and one new strand of DNA
14
Q
DNA is anti-parallel
A
top strand is synthesized from 5’ to 3’, bottom strand synthesizes from 3’ to 5’ because it synthesizes in the opposite direction
15
Q
Leading strand
A
DNA strand that continuously synthesizes
16
Q
Lagging strand
A
DNA strand that synthesizes discontinuously
17
Q
Origin
A
where DNA synthesis begins
18
Q
Replication bubble
A
where the DNA strand opens up to be synthesized
19
Q
Enzymes/molecules involved in DNA replication
A
DNA polymerase DNA ligase Helicase Single strand DNA binding proteins RNA primase Ribozyme
20
Q
DNA polymerase
A
synthesizes DNA, can add nucleotides to the 3’ end only (OH), has a proof reading function to correct mutations
21
Q
DNA ligase
A
covalently links the Okazaki fragments in lagging strand synthesis
22
Q
Helicase
A
seperates the 2 strands of DNA and unwinds them
23
Q
Single stranded DNA binding proteins
A
stabilize the strand of DNA, keeps the 2 strands separate by not allowing them to connect their hydrogen bonds
24
Q
RNA primase
A
puts down RNA primer that is later removed and replaced with nucleotides, this allows us to have a 3’ hydroxyl for DNA polymerase
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Ribozyme
RNA enzyme that removes introns and splices exons together, capable of acting as an enzyme
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RNA synthesis
only one strand is copied
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RNA polymerase
begins transcription when it binds to the DNA at the promoter site, synthesis continues until it reaches the terminator site on the DNA
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Promoter sequence
indicate the start of a gene
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RNA types (3)
rRNA
mRNA
tRNA
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rRNA
forms integral part of ribosomes
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Ribosomes
a minute particle consisting of RNA and associated proteins, cellular machinery for protein synthesis, bind mRNA and tRNA to build polypeptides and proteins, found in large numbers in cell ctoplasm
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mRNA
carries coded information that must betranslated, ultimately results in a protein
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tRNA
structural RNA, involved in protein synthesis
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Important tRNA sites
amino acid binding site, anticodon
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mRNA codons
there are 64 codons and only 20 amino acids, the code will be redundant
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Genetic code
is redundant, universal or nearly universal, 64 codons, 61 are sense codons, 3 are non-sense codons
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Sense codons
code for an amino acid
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Non-sense codons
aka stop codons, you hit one about 5% of the time
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AUG
is the start codon
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Regulation of metabolism
80% of bacteria are not regulated
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Constitutive
bacteria that are not regulated and are being produces all the time
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Feedback inhibition
enzymatic, end product is threonine which goes back to enzyme 1 and shuts down the pathway through non-competitive inhibition
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Genetic regulation of metabolism
uses operons, I gene is upstream from the operon and is always on
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Mutation types
point mutation
| frame shift
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Point mutations
silent
missense
nonsense
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Silent mutations
base substitution, has no effect on the organism
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Missense mutations
coding for the wrong amino acid
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Nonsense mutations
base substitution mutation, codes for a stop codon then the sequence is not completely done
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Causes of mutations
spontaneous
induced
chemical mutations
radiation
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Spontaneous mutations
arise during replication
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Induced mutations
chemical mutagens
| ex: acridine: frame shift, wedges into double helix causing a frame shift
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Chemical mutations
Base analog
| 5-bromouracid is inserted into DNA instead of thymine, base pairs with Guanine
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Radiation
causes adjacent pyrimidines to bond, transcription of mRNA stops at the gap
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DNA repair
Light repair
Dark repair
uses DNA polymerase, ligase, endonucleases, and exonuclease
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Light repair
light activates photolyases that break dimers
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Dark repair
can occur with or without light, uses nucleotide excision repair
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Ways to acquire mutation
Induced
| spontaneous
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Induced mutations
exposure to an antibiotic induced a change in an organism, mutations occur only in the presence of antibiotics
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Spontaneous mutations
allows the organism to grow in an antibiotic, this selects for the resistant mutant, there will be large fluctuations in the number of resistant organisms per culture, a mutation can occur early or late in the incubation period
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Fluctuation test
used to determine whether mutations were spontaneous or induced
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Replica plating method
used to study mutations, sterile velveteen pad is imprinted on master plate, in the same orientation, the pad is used to inoculate an agar plate with the antibiotic
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Conclusor
used to study mutations, bacteria on the antibiotic plate had resistance without exposure, this demonstrates the spontaneous nature of mutations
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Ames test
used to screen chemicals for their mutagenic properties, uses histidine autotrophes of salmonella, upon exposure to mutadine, they have the ability to revert back to histidine synthesizing capability
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Carcinogens
tend to be mutagens
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Auxotroph
nutritionally deficient mutant
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Resistance plasmids
aka R plasmids, resistance is not induced by antibiotics, resistant strains are selected for by antibiotic use
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Genetic engineering
the direct manipulation of genes for practical purposes
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Genetic engineering techniques
protoplast fusion, recombinant DNA cloning
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Protoplast fusion
protoplasts of 2 strains can be mixed to allow for genetic recombination of desired characteristics
EX: slow growing, good producer of substance fuse when there is polyethylene glycol with a fast growing poor producer to get a fast growing good producer
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Protoplast
organism with its cell wall enzymatically removed
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Recombinant DNA
DNA from 2 different sources covalently linked to create a single DNA
If a plasmid is cut with the same restriction enzyme, the 2 DNAs will have compatible "sticky ends", can covalently link the 2 DNA with DNA ligase, this makes recombinant DNA
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Gene cloning
the production of multiple copies of a gene carrying pieces of DNA, recombinant plasmid is used to transform bacteria, recombinant bacteria are selected for using media with an antibiotic, clonal population of cells create multiple copies of the gene
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Viruses
obligate intracellular parasites, can only replicate inside a host cell
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Virus nucleoproteins
nucleic acid covered by a protein coat, viral genome may be either DNA or RNA
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Viral components
nucleic acid core
capsid
envelope
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Viral nucleocapsid
naked (no envelope)
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Viral nucleic acid core
genome may be DNA or RNA, ss- or ds-, linear, circular or segmented
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Viral capsid
protein coat that surrounds the genome, composed of capsomeres
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Viral envelope
bilayer membrane spikes, glycoproteins attach to host receptor
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Viral size
must be viewed with an EM, ribosome = 25-30nm
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Viral shapes
Heilcal
Polyhedral
Complex capsid
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Helical shape
capsid forms helix around genome
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Polyhedral shape
capsid is many sided, most common
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Icosahedron
20 triangular faces
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Complex capsid shape
combination of helical and icosahedral shapes
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Viral host range
the spectrum of hosts that a virus can infect
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West Nile virus
a good example of a broad host range
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Viral specificity
Virus is selective in the organisms it infects, the type of cells and disease it produces
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What is used to classify viruses
based on type and structure of nucleic acid genome
DNA or RNA genome
Double or single stranded
linear, circular or segmented
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Virus families
-viridae
| are distinguished on the basis of nucleic acid type, capsid shape, presence of envelope and size
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RNA virus chromosomal arrangements
is a single strand, viruses do not have both + and –
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+ sense RNA viruses
during infection, RNA acts like mRNA and is translated
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- sense RNA viruses
RNA acts as a template for the production of + sense RNA, must carry RNA polymerase with the virion
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Rhabdoviridae
sense RNA virus, enveloped, helical, 70-180nm in size, virion contains an RNA dependent RNA polymerase
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Rhabdoviridae Ex
Rabies virus
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Double stranded RNA viruses
one family with the virion, has segmented dsRNA
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RNA virus families
picornaviridae
retroviridae
rhabdoviridae
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Picornaviridae
+ sense RNA virus, naked, polyhedral shape, 18-30nm in size, translated to produce an RNA , dependent RNA polymerase
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Picornaviridae Ex
polio virus
100
Retroviridae
+ sense virus, retro transcription, enveloped, spherical, nm in size, virion contains 2 copies of the genome and the enzyme reverse transcriptase (makes DNA from RNA template)
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Retroviridae Ex
provirus: before transcription, new DNA is incorporated into the host genome
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DNA virus families
grouped on basis of DNA structure, only one family has ssDNA
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Herpesviridae
linear dsDNA virus, enveloped, polyhedral, 120-200nm in size, viral dsDNA can exist as a provirus, causes latent infections
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Latent infections
virus remains in the host for a long time, can still replicate
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Viral, Bacteriophage and anvimal DNA virus replication steps
```
Adsorption
Penetration
Synthesis
Maturation
Release
```
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Viral Adsorption
the attachment of viruses to host cells
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Viral Penetration
entry into host cells
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Viral synthesis
creation of new nucleic acid molecules, capsid proteins using the host’s metabolic matching
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Viral maturation
assembly of these components into infectious virions
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Viral release
departure of new virions, generally killing the cell
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T-even bacteriophage
dsDNA, complex, naked, capsid head collar
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T-even bacteriophage host Ex
E. Coli
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Bacteriophage adsorption
specific proteins on the tail fibers bind to specific receptors on host cells
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Bacteriophage penetration
Lysozyme weakens the cell wall, the tail sheath contracts, viral genome is “injected” from head into bacterial cell
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Bacteriophage synthesis
phage directs host cell to make phage products, bacterial DNA is disrupted
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Bacteriophage maturation
viral components are assembled into infectious virions
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Bacteriophage release
lytic phage lyse the host cell and inject neighboring cells
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Bacteriophage growth curve stages
Eclipse period
Latent period
Viral yield
119
Bacteriophage growth curve eclipse period
spans from penetration through synthesis
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Bacteriophage growth curve latent period
spans from penetration to phage release
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Bacteriophage growth curve viral yield
number of viruses per injected cell
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Plaque assay
used to determine phage number
| reported in pfu (plaque forming units)
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Plaques
clear areas where phage has infected host and surrounding cells
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Temperate bacteriophage
Lysogeny
| Bacteriophage doesn’t kill host
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Lysogenic conversion
prevents adsorption of similar phage and biosynthesis of prophage
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Lysogenic prophage
produces proteins that repress viral replication
127
Lysogenic induction
spontaneous or induced excision of prophage resulting in lytic cycle
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Animal DNA virus adsorption
enveloped viruses have spikes that bind receptors
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Animal DNA virus penetration
Nucleic acid and capsid enter cell
| uses uncoating
130
Animal DNA virus synthesis
Viral DNA genome is replicated and viral proteins are synthesized, viral proteins move to the nucleus where they combine with new viral DNA
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Animal DNA virus maturation
the complete virion is assembled; enveloped viruses bud through a host membrane where viral lipids and glycoproteins are present
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Animal DNA virus release
Budding of new virions does not necessarily kill the host cell
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Transcription
occurs before we express a protein, is the synthesis of a complimentary strand of RNA from a DNA template
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Translation
decodes the "language of nuclaic acids to proteins, occurs on the ribosome
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Translation steps
Initiation
Elongation
Termination
136
Translation elongation steps
codon recognition
peptide bond formation
translation
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Polyribosome
transcription and translation occurring at the same time
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Genetic regulation of metabolism steps
enzyme induction
| enzyme repression
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Enzyme reperssion
uses lac operons and trpoperons
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Operon consists of
Promoter sequence
operator
structural genes
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Enzyme repression: Operator
binds to repressor
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Enzyme repression: Structural genes
make a protein code for enzymes
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Lac operon without lactose
repressor bound to operator
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Lac operon with lactose
lactose is converted to allolactose
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allolactose
the inducer, binds to repressor and inactivates it so it no longer binds to the operator
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Trp operon
I gene makes an inactive repressor, default position is on
147
Trp operon Tryptophan
acts as a co-repressor, tyrp binds to the repressor and activates it
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Trp + repressor
would bind to the operator and shut down transcription
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Bacteriophage
a virus that infects bacteria, nucleic acid core is covered by a protein coat
150
Bacteriophage life cycle
2 possible outcomes:
lytic cycle
lysogenic cycle
151
Bacteriophage lytic cycle
characteristics of virulent phages, the cell is lysed releasing hundreds of bacteriophages
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Bacteriophage lysogenic cycle
initiated by a temperate phage, phage is incorporated into bacterial chromosome and replicated with it
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Emerging viruses
increase in viral disease
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Emerging virus causes
previously endemic viruses can spread due to global warming
ex: delongue fever
tropical islands are farmed and contact viral vectors
ex: yellow fever
viral host range spread to other species, becomes a mutant virus not recognized by the immune system
ex: swine flu pandemic of 1918
155
Bacteriophage structural components
Genome
tail sheath
plate and tail fibers
156
Bacteriophage genome function
carries the genetic information necessary for replication of new phage particles
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Bacteriophage tail sheath function
retracts so that the genome can move from the head into the host cell's cytoplasm
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Bacteriophage plate and tail fibers function
attach phage to specific receptor sites on the cell wall of a susceptible host bacterium
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Prophage
Phage genome is incorporated into host nucleic acid
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Lysogen
Bacterium and temperate phage
161
Uncoating
enzymes digest the protein coat releasing the DNA
162
RNA viruses examples
polio
HIV
both are + sense ssRNA
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Polio adsorption
naked viruses have proteins that bind to complementary proteins on the host
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Polio penetration/uncoating
most naked viruses enter the cell by endocytosis
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Polio synthesis
mRNA and viral proteins are produced, + sense RNA acts as template to make - sense RNA, -sense RNA is the template for making many copies of the + sense RNA viral genome
166
Polio maturation
new virions are assembled in the cytoplasm
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Polio release
kills the host cell
168
HIV adsorption
glycoprotein spikes in the envelope recognize protein receptors on the host cell surface
169
HIV penetration/uncoating
fusion with the host
170
HIV synthesis
2 copies of + sense RNA copied into ssDNA by reverse transcriptase, second strand of DNA is synthesized, dsDNA inserts into host cell genome as a provirus, provirus genes are transcribed and translated
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HIV maturation
2 copies of + sense RNA are packed into each capsid
172
HIV release
mature HIV nucleocapsids bud from the plasma membrane
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Culturing animal viruses
```
eggs
cell culture
primary cell culture
diploid fibroblast strains
continuous cell line
cytopathic effects
```
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Culturing-eggs
fertilized, intact eggs used to grow animal viruses, difficult to study cellular effects caused by viruses
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Cell culture
animal cells are grown in monolayers, animal cells are treated with proteolytic enzymes, cells can be subcultured after growth
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Primary cell culture
comes directly from the animal, cells usually divide a few times
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Diploid fibroblast strains
immature cells that produce collagen, derived from fetal tissue, retain capacity for repeated cell division
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Continuous cell line
will reproduce for extended number of cell divisions
| ex: HeLa line = cervical cancer
179
Cytopathic effects
CPE
visable effect viral infection has on cells
ex: cells change shape, detatch from culture container
180
Virus effects
transformation
| teratogenesis
181
Viral transformation
another CPE caused by viruses, the conversion of normal cells to malignant ones
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Viral teratogenesis
induction of defects during embryonic development
183
Teratogen
drug or agent that causes defects, viruses can act as teratogens
ex: CMV, HSV and rubella
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Virus like agents
viroids
| prions
185
Viroids
infectious RNA particles smaller than a virus, no protein products are produced, disrupt host cell metabolism, cause lethal plant diseases
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Prions
proteinaceous particles, proteins exist in normal form and prions proteins stick together and eventually kill cells
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Tumor or neoplasm
localized accumulation of cells
188
HPV
human papillomavirus, causes cancer, dsDNA, exists as a provirus, production of excess viral replication protein causes uncontrolled cell growth
189
Cancer from a virus
15% of cancer comes from a virus, discovered in 1911
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Oncogenes
a gene that causes uncontrolled cell growth
191
Proto-oncogenes
a normal gene that when under the control of a virus can act as an oncogene
