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165 Cards in this Set
- Front
- Back
- 3rd side (hint)
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Structure of DNA
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Structure of DNA
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Structure of DNA
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Archaea DNA structure is similar to that of
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eucaryotic cells
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DNA replication in most prokaryotes
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bidirectional from a single origin of replication
Some Archaea have more than one origin |
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DNA polymerase rxn
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DNA polymerases
DNA synthesis is in 5’ to 3’ direction These enzymes require? |
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Eukaryotes use chromatin to...
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wrap DNA around histones which we call nucleosome
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What polymerase enzymes require?
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-Helicase (unwinds DNA)
-Single stranded binding proteins keep in DNA in open form -DNA primase II adds nucleotides -DNA tropiomerase II relieves tension on end of strand -DNA polymerase replaces the primers left over in the lagging strand |
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Helicase
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unwinds DNA
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What causes the lagging and leading strands of DNA
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antiparrellel
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Okazaki fragments
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The fragments that formed in the lagging strands
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Transcription in Bacteria
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-Polygenic mRNA often found in bacteri and Archea
-contains directions for >polypeptide -Knows where to start because why? |
the sigma factor on DNA polymerase recognizes it
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Transcription in the Archaea
-similarities with eucaryotes? |
introns present in some archaeal genes
-Similarites with similarities with other procaryotes |
mRNA is polygenic |
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Genes that Code for Proteins – The Coding Region
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Begins with the mRNA sequence 5’-AUG-3’
codes for N-formylmethionine coding region ends with a stop codon |
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Organization of the Code
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code degeneracy
stop (nonsense) codons UGA, UAG, UAA do not encode amino acids |
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name three stop codons
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UGA, UAG, UAA
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Translation
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Ribosome in procaryotes
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70S ribosomes = 30S + 50S subunits
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Ribosomal in eucaryotes
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80S ribosomes = 40S + 60S subunits
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the goal of Initiation
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the goal –
position ribosome properly at 5' end of mRNA |
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tRNA binding sites of ribosome
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peptidyl (P) site
aminoacyl (A) site exit (E) site |
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Elongation
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Termination of Protein Synthesis
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takes place at any one of three codons
nonsense (stop) codons – UAA, UAG, and UGA |
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Termination
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takes place at any one of three codons
nonsense (stop) codons – UAA, UAG, and UGA |
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Regulation of Transcription Initiation
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Negative control
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Operons
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The lac Operon
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Operons
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Operons
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The lac Operon
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Regulation of lac operon
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The Tryptophan (trp) Operon
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Regulation of the trp Operon
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Positive Control
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Catabolite Activator Protein (CAP)
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exists two forms
-active form when 3’,5’-cyclic adenosine monophosphate (cAMP) is bound -inactive form when it is free of cAMP |
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cAMP
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cAMP structure
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Regulation of the lac Operon by the lac Repressor and CAP
*4 Scenarios know these |
1. lactose present but no glucose
2. lactose and glucose 3. neither lactose or glucose 4. glucose but no lactose |
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Regulation of Gene Expression in Archaea
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Mutations
-define -Why detectable in prokaryotes? |
-"a change"
-Prokaryotes are haploid so no dom/recessive alleles |
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chemical that causes a mutation
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mutagens
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Initiation codon
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AUG
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Translation
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direction of synthesis is N terminal -> c-terminal
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ribosome
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-site of translation
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tRNA
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single stranded fold back on themselves
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Induced Mutations
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caused by agents that directly damage DNA
-base analogs -DNA modifying agents -Intercalating agents |
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Bromauracil
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Ultraviolet (UV) damage of DNA
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-results in formation of thymine dimers
-the resulting DNA can no longer serve as a template -Thymine bonds with itself -dimer means two -there are repair mechanism to fix this |
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Thymine dimers pic
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Mutations (types)
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Point mutations
-silent mutation -missense mutation -nonsense mutation Frameshift mutation |
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Point mutation
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one nucleotide
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Point: Silent mutation
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no consequence for protein
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Point: missense mutation
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code for different amino acid
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point: nonsense mutation
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you want a protein but can't get it (stop)
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Frameshift
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-caused by insertion of 1 or 2 or several insertions or deletions
-in general worse than point shift -uv light will cause frameshift |
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Base analogs
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cause point mutations
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two causes of fram shift mutations
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UV light
Acridine dyes |
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More Types of Mutations
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-mutations in regulatory sequences
-Mutations in tRNA and rRNA genes |
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Detection and Isolation of Mutants
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-mutations are generally rare
one per 10e7 to 10e11 cells -finding mutants requires sensitive detection methods and/or methods to increase frequency of mutations |
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Carcinogenicity Testing
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-based on observation that most carcinogens are also mutagens
-tests for mutagenicity are used as screen for carcinogenic potential -e.g., Ames test |
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Ames test
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DNA Repair
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proofreading
-correction of errors in base pairing made during replication -errors corrected by DNA polymerase other DNA repair mechanisms also exist |
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Direct Repair
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Direct repair of a methylated base
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Creating Genetic Variability
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mutations are subject to selective pressure
Recombination process in which one or more nucleic acids are rearranged or combined to produce a new nucleotide sequence |
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Bacterial Plasmids
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conjugative plasmids such as the F plasmid can transfer copies of themselves to other bacteria during conjugation
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Bacterial Conjugation
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F+ x F- Mating
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-a copy of the F factor is transferred to the recipient and does not integrate into the host chromosome
-donor genes usually not transferred |
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F+ conjugation
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HFr Conjugation
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-donor HFr cell has F factor integrated into its chromosome
-donor genes are transferred to recipient cell -a complete copy of the F factor is usually not transferred |
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F plasmid integration
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Hfr conjugation
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F’ Conjugation
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F’ x F- Mating
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Bacterial Transformation
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uptake of naked DNA by a competent cell followed by incorporation of the DNA into the recipient cell’s genome
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Bacterial transformation pic
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Transduction
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Transduction
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Lytic and Lysogenic Cycles of Temperate Phages
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Generalized transduction
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generalized transduction (diagram)
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Genomics
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The study of the whole DNA of an organism
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Insights from Microbial Genomes
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identification of genes for which no function has been found
-example= Neisseria meningitidis ~50% of genes have known function 16% of ORFs match genes of unknown function in other organisms ~25% have no database match at all |
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Interesting findings in genomics
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Haemophilus influenzae
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> 33% of genes have unknown function
-lacks complete set of Krebs cycle genes |
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minimal genome size needed for free-living existence
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minimal genome size needed for free-living existence
based on analysis of Mycoplasma genitalium genome one of smallest procaryotic genomes sequenced ~108-121 genes not required for growth in laboratory ~300 genes required for growth in laboratory |
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comparison of S. aureus and S. epidermidis genomes
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used to track evolution of antibiotic resistance and virulence
both strains thought to have acquired ability to synthesize a capsule from Bacillus anthracis |
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Bacillus anthracis (cause of anthrax)
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genomic analysis suggests it was derived from an insect-infecting ancestor
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Genomes of Extremophiles
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-studied to help understand mechanisms used by microbes to survive in harsh environments
-Deinococcus radiodurans can survive drying, oxidizing agents and g radiation |
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Environmental Genomics
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-also called metagenomics
-finding rhodopsin-like genes in marine procaryotes is an example of an exciting discovery that requires a reassessment of oceanic carbon cycles |
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Construction and Screening of Genomic Libraries Directly from the Environment
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Principles of Virus Taxonomy
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Major phage families and genera
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Characteristics used for virus classification by the ICTV
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Genome structure
Replication strategy Morphology Genetic relatedness |
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Taxonomy of Eucaryotic Viruses
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most of the ~5,000 known viruses infect eucaryotic organisms
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Taxonomy of Eucaryotic Viruses
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viruses that infect vertabrates
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Ds DNA viruses: Adenoviridae
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Adenoviridae
“gland” Naked, with linear DNA Stable in acid and heat Cause of respiratory infections One of the most common vectors tried in gene therapy |
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Ds DNA viruses:Herpesviridae
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Herpesviridae
“creeping” Enveloped, with linear DNA DNA can be a provirus Latency Wide range of diseases |
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Cold sores vs. genital herpes
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caused by herpes simplex type 1 vs. 2, respectively
transmitted sexually and to infant during vaginal delivery (congenital or neonatal herpes) |
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Chickenpox/shingles?
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-caused by varicella-zoster virus
-humans serve as reservoir and source -acquired by droplet inhalation into respiratory system |
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Mononucleosis (Infectious)
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caused by Epstein-Barr virus (EBV)
-infects B cells -also associated with Burkitt’s lymphoma spread by mouth-to-mouth contact clinical manifestations -enlarged lymph nodes and spleen, sore throat, headache, nausea, general weakness and tiredness, and mild fever -self-limited disease, lasting 1 to 6 weeks |
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Cytomegalovirus
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Cytomegalovirusvirus shed in semen and cervical solutions
>can also be transmitted by blood transfusions and organ transplants teratogen |
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Ds DNA viruses:Poxiridae
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Poxviridae
Enveloped with linear DNA Largest and most complex group We are familiar with the orthopoxviruses -Have some host cytoplasm within them -Smallpox (Variola) infects humans, cowpox (Vaccinia) infects cows, etc. |
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Poxviridae: small pox
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Eradication of Smallpox
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Protection from Smallpox
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Ds DNA viruses
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Papovaviridae
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“Pa”: papilloma, “po”: polyoma, “va”: vacuolating
Papilloma group causes warts and is strongly associated with cervical cancer |
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Venereal Warts (anogenital condylomata)
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Hepatitis B
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Hepatitis B: prevention
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Ss DNA viruses: Parvoviridae
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Ds RNA virus: Reoviridae
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“respiratory, enteric, orphan” viruses
Naked, polyhedral Rotavirus Most common cause of severe diarrhea in children |
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Ss (+) RNA viruses: Picornaviridae
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Poliomyelitis
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Polio vaccines
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Coronaviridae
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Coronavirus got its name from the Latin for “crown” (corona)
SARS |
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Ss (+) RNA viruses: Noroviridae
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gastroenteritis
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Ss (+) RNA viruses: Togaviridae
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-Small, enveloped, polyhedral
-Mammalian and arthropod vectors -Transmitted by mosquitoes -Encephalitis in humans and horses -Rubella (human to human transmission) |
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Rubella (German Measles)
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Congenital rubella syndrome results from infection of pregnant women in frist trimester
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Ss (+) RNA viruses:Flaviviridae
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-Enveloped, polyhedral
-Transmitted by mice and ticks -Encephalitis -Yellow fever -Hepatitis C |
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Ss (+) RNA viruses: Retroviriade
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Acquired Immune Deficiency Syndrome (AIDS)
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caused by human immunodeficiency virus (HIV)
occurs world wide, causing the great pandemic of the second half of the twentieth century |
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Transmission of HIV
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acquired and can be passed from person to person
-when infected blood, semen or vaginal secretions come in contact with uninfected person’s broken skin or mucous membranes |
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HIV attaching to host cell
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CDC Classification System for Stages of HIV-Related Conditions
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Diagnosis of HIV
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Antivirals used against HIv
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RNA gene changes extremely quickly
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Ss (-) RNA viruses:Paramyxoviridae
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Causes measles, mumps, viral pneumonia
-some bronchitus |
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Measles (Rubeola)
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enters body through respiratory tract
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Koplik's spots
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characteristic lesions of
oral cavity Indicative of measles |
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subacute sclerosing panencephalitis
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rare progressive degeneration of central nervous system caused by measles virus
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symptomatic/supportive therapy
attenuated measles vaccine -MMR vaccine (measles, mumps, rubella) |
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Mumps
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Ss (-) RNA virus: Rhabdoviridae
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Rhabdoviridae
-“rod” -Enveloped, helical capsid- -Bullet-shaped -Rabies virus |
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Rabies
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Ss (-) RNA viruses: Orthomyoxviriade
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-“straight”
-Enveloped -Genome segmented into 8 pieces -Influenza A (birds, other animals) -Influenza B (humans) |
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Influenza (Flu)
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classified into subtypes based on hemagglutinin (HA) and neuraminidase (NA), membrane surface glycoproteins
H5N1 subtype (known as bird flu) vs. H1N1 Antigenic drift vs. antigenic shift |
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Influenza (Flu)
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Flu…
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Flu clinical manifestations
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H5S1
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bird flu
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Antigenic drift vs. antigenic shift
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How these flu viruses are changing
Proteins change a little bit but body still recognizes antigen (antigenic drift) Antigenic shift->big change |
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Defining procaryotic species
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Strains
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Biovars
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differ biochemically and physiologically
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morphovars
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differ morphologically
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serovars
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differ in antigenic properties
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Type strain
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-usually one of first strains of a species studied
-often most fully characterized -not necessarily most representative member of species |
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genus –
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well defined group of one or
more species that is clearly separate from other genera |
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Binomial System of Nomenclature
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devised by Carl von Linné (Carolus Linnaeus)
each organism has two names -genus name – italicized and capitalized (e.g., Escherichia) -species epithet – italicized but not capitalized (e.g., coli) can be abbreviated after first use (e.g., E. coli) |
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Techniques for Determining Microbial Taxonomy and Phylogeny
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Classical Characteristics
-morphological -physiological -biochemical -ecological -Genetic: comparing DNA sequence of rRNA genes |
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The Second Edition of Bergey’s Manual of Systematic Bacteriology
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largely phylogenetic rather than phenetic
procaryotes are divided between two domains and 25 phyla |
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E. coli replication machinery: DNA gyrase
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Relieves supercoiling of DNA produced as DNA strands are separated by helicase; separates daughter molecules in final stages of replication
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E. coli replication machinery: Helicase loader
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helps direct DNAB protein (helicase) to DNA template
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E. coli replication machinery: DNA primase
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synthesis of RNA primer, component of primosome
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DNA polymerase III holoenzyme
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Complex of about 20 polypeptides catalyzes most of the DNA synthesis that occurs during DNA replication; has 3'->5' exonuclease (proofreading activity)
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DNA polymerase I
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Removes RNA primer; component of primosome
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Phylum Spirochaetes
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Treponema pallidum:
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Borrelia burgdorferi:
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Spirochete Motility
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current thought:
axial fibrils rotate, causing corkscrew-shaped outer sheath to rotate and move cell through surrounding liquid |
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Phylum Bacteroidetes
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