Mesnage (Autumn) Flashcards
What are the 3 domains?
- bacteria
- archaea
- eukarya
Who defined the 3 domains system?
- Carl Woese
What are the characteristics of bacteria?
- haploid genome
- rapid multiplication
- horizontal gene transfer
- conjugation
What is the purpose of conjugation?
- injection of genetic info
- used for passing on antibiotic resistance
What is phylogeny?
- study of evolutionary history of organisms
How are evolutionary relationships measured?
- by comparing genetic info
What is the role of molecular clock DNA seqs?
- encoding conserved proteins w/ similar function
- undergoing random and neutral mutations
How are DNA seqs compared?
- find % divergence
- find gene present in all organisms, but has diff seq
What do phylogenetic trees show, and what are they based on?
- show genetic distance between organisms
- based on comparative analysis of rRNA gene seq
Who defined binomial nomenclature?
- Carl Linnaeus
What is taxonomy?
- discipline that deals w/ classification of organisms
What are the taxonomic subdivisions?
- domain
- kingdom
- phylum
- class
- order
- family
- genus
- species
What is the only method of phenotypic analysis where pure isolates are not required?
- morphology/differential staining
What are the diff methods of phenotypic analysis?
- morphology/differential staining –> also give info about cell wall composition
- metabolic properties –> compared w/ known standards
- phage typing
- FA profiles –> extract FA, derivatise to form methyl esters, gas chromatography, compare patterns of peaks from various FA methyl esters to patterns in database
- mass spec
Why are genotypic analyses more reliable?
- shape can vary w/ conditions
What are the diff methods of genotypic analysis?
- DNA/DNA hybridisation
- FISH
- rDNA (16S) sequencing –> doesn’d distinguish between dead and alive MOS
- MLST (multi locus seq typing)
- whole genome seq
How is diversity gen in bacteria?
- binary fission
- haploidy
- genetic plasticity
What is the nucleus the site of? (euks)
- mRNA, tRNA and rRNA synthesis
What is the ER important in? (euks)
- protein trafficking
What is the structure and role of the RER? (euks)
- membrane protein covered w/ ribosomes
- outer face site of protein synthesis
- specific sorting signals allow import into RER
What is the role of the SER? (euks)
- no protein synthesis
- contributes to lipid synthesis and of steroids
- toxin breakdown
What is the role of the golgi? (euks)
- carb synthesis
- mod of proteins for specific targeting
Where do lysosomes originate from and what is their role? (euks)
- originate from golgi
- can fuse w/ other vesicles
- contain digestive enzymes to hydrolyse macromolecules
Where do peroxisomes originate from and what is their role? (euks)
- originate from ER
- incorp lipids and proteins from cyto
- oxidise alcohols and FAs (role in lipid metabolism)
Which organelles have their own DNA/translation machinery and multiply by division? (euks)
- mito
- chloroplasts
What is the structure and role of chloroplasts? (euks)
- made of thylakoids (forming grana)
- in stroma
- convert light to organic compounds via Calvin cycle
What is the structure of flagella/cilia and how do they work? (euks)
- bundle of 9 pairs of MTs connected to adjacent ones via nexin molecules and surrounding central pair (axoneme)
- ATP hydrolysis drives motion, carried out by dynein molecules
- MTs slide against each other, giving whip like movement
What is the structure of a nucleoid? (proks)
- usually singular, circular chromosome
- DNA complexed w/ histone like proteins
- genetic material also inc plasmids
What is the structure of the cyto and what does it contain? (proks)
- compartment enclosed by membrane w/ dedicated psychological function
- usually no organelles, some proks do
- contains proteins, tRNAs, mRNAs and ribosomes
- can contain several inclusion bodies (protein bounded) –> carboxysomes, storage granules and gas vesicles
What is the structure of the envelope, from inner to outer? (proks)
- cyto membrane
- peptidoglycan
- polymers covalently to peptidoglycan
- outer membrane
What is the structure and role of appendages? (proks)
- projecting parts w/ distinct appearance and function
- pilus –> dedicated to conjugation
- fimbriae –> adherence to host cells/surfaces, antigenic structures made o f 1 major protein
- flagella –> supramolecular assembly involved in bacterial motility
What did stable incorporation of endosymbiotic bacteria result in?
- formation of mito and chloro
What are the 2 theories of endosymbiotic origin of euks, and the assoc problems?
- nucleus appears before acquisition of mito and chloro, but doesn’t account for fact that proks have similar lipid composition
- mito originated from engulfment of hydrogen prod bacterium by hydrogen consuming archaea, genes for lipid synthesis transferred to host, giving rise to nucleus, chloro acquired later by endosymbiosis leading to 1st phototrophic euks
What are the general properties of viruses?
- obligatory parasites (need hosts metabolic machinery to rep)
- small
- made of NA genome surrounded by protein coat (capsid) and facultative lipid membrane (envelope)
- can infect all living organisms
What is the genome composition of virus nucleic acid?
- DNA: ss or ds
- RNA: ss (+/-) or ds
How does genome composition effect size of virus?
- ds larger than ss
- DNA larger than RNA
How many molecules make up virus nucleic acid?
- usually 1
- can be fragmented
What is the composition of virus capsid?
- made of protein (1 or more), called capsomeres
What is the structure of the virus capsid?
- self assembly products
- highly ordered
What is the composition of virus envelope?
- lipid bilayer w/ (glyco)proteins from host or virus encoded
What is the role of virus envelope?
- allows entry into host cell by fusion or endocytosis
What are some examples of complex viruses?
- bacteriophages –> contain mixture of icosahedral/ filamentous structure
- non-symmetrical viruses, eg. smallpox
What can viruses be named after?
- disease caused
- place 1st reported
- host and signs of disease
- shape
- discoverer
- supposed transmission mechanism
- combo
What is the Baltimore classification of viruses?
- DNA viruses = Group I, II, VII
- RNA viruses = Group III, IV, V, VI
How do the diff Baltimore groups of viruses replicate?
- I = semi conservative
- II = semi conservative, discard (-) strand
- VII = transcrip, then reverse transcrip
- III = transcribe ssRNA (+) to give ssRNA (-)
- IV = transcribe ssRNA (-) to give ssRNA (+)
- V = transcribe ssRNA (+) to give ssRNA (-)
- VI = transcribe (-) strand of dsDNA to make ssRNA genome
What is the life cycle of a virus?
- attachment
- genome injection
- prod of NAs and proteins
- maturation (assembly of viral particles)
- release
What are the different morphologies of bacteria?
- cocci
- rods
- curved
- spiral (helical)
- exotic
Why can bacteria be coloured?
- prod pigments
Why can bacteria smell?
- odors result from bacterial metabolism
What is the method for carrying out a Gram stain?
- stain w/ crystal violet
- fix w/ idoine
- wash w/ alcohol
- counterstain w/ safarin
What do the results of a Gram stain mean?
- +ve = no outer membrane and thick cell wall
- -ve = outer membrane and thin cell wall
What are bacterial capsules made of?
- most of polysaccharides
- some of AAs
How are capsules attached to bacteria?
- covalently bonded to cell wall or outer membrane
What is the role of bacterial capsules?
- confer resistance to host phagocytes/bacteriophages
- keep env hydrated
What are the characteristics of exopolysaccharides in bacteria?
- homo/heteropolysaccharides
- non covalently attached to cell surface
- important for biofilm formation
- some economically important
What are the characteristics of S layers in bacteria?
- facultative structures
- non covalently bound to cell surface
- proteinaceous crystalline arrays, self assembly products
What is the structure of the outer membrane in bacteria? (gram -ve)
- phospholipids
- proteins inc porins (trimeric assembly for solute transport)
- lipoproteins covalently linked to peptidoglycan
- LPS (endotoxin), potent activator of IS
What is the structure and role of peptidoglycan in bacteria?
- complex polymer
- elastic 3D network
- subcellular compartment
- dynamic reg of exchanges w/ env
What is present in the cyto membrane of bacteria?
- phospholipids (unsat FAs cause kink, modulate fluidity and permeability)
- hopanoids (equivalent to steroids in euks)
- proteins
What is the structure of chromosomes in bacteria?
- ds DNA
- usually single circular
- variable size (0.5Mbp - 9.5Mbp)
- organised as nucleoid (histone like proteins)
What is the structure of bacterial plasmids?
- ds DNA
- usually circular
- variable copy no. (1-100s)
- size 2kbp to 600kbp
- can be self transferable
- carry resistance gene
What is the structure of bacterial genome?
- no introns (cont coding seq)
- operons, w/ 1 promoter and several ORFs
- relatively small genes
How is transcrip initiated in bacteria?
- RNA pol scans DNA, forming loose complex
- σ factor binds to 2 specific seqs upstream of start codon (“close complex”)
- DNA unwound allowing formation of “open complex”, transcrip starts and σ released
How is transcrip terminated in bacteria? (2 possibilities)
- req palindromic GC rich region, upstream of AT rich seq
- forms hairpin structure when GC rich region transcribed, which makes RNA pol fall apart, helped by AT rich seq
- ——-OR———
- Rho proteins recognise and bind 72 GC rich residues
- due to RNA dependent ATPase activity, wraps downstream RNA around itself
- when reaches pol, Rho unwinds RNA-DNA duplex and releases RNA pol
How does RNA differ in bacteria from euks?
- transcrip in cyto in bacteria (nucleus in euks)
- 1 RNA pol in bacteria, 3 in euks
- in euks termination involves AAUAAA seq
- mRNA mod in euks
What are the differences in gene expression between bacteria and euks?
- ribosomes different
- 80S bind mRNA in tRNA absence
- 40S subunit guided by 5’ cap on mRNA
- 30S subunit recognises SD seq
- translation coupled w/ transcrip in proks
- euk translation spec inhibited by acycloheximide
How can bacteria be classified by their metabolism?
- sunlight = photo
- preformed molecules = chemo
- organic = organo
- inorganic = litho
- organic compounds = heterotroph
- inorganic compounds = autotroph
