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45 Cards in this Set

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genetic material
both prok and euk CELLULAR organisms are ds-DNA
virus:ds or ss, DNA or RNA
genes assembled on chrom's
(all genetic material of a cell or virus is the genome)
genetic information
sequence order of the purine and pyrimidine in the polynucleotide chains of DNA and/or RNA provides the info for assembly of all prot and functional RNA's.
what is a gene
stretch of DNA(RNA)the specifies the aa sequence
unit of complementation(cistron)
unit of mutation(outdated)
unit of expression(outdated)
unit of inheritance(outdated)
alleles
(diff forms of same gene and located at the exact same psotion in genome)
>400 of e.coli trpA gene
dominant,recessive,co-dominant
cells can be homo,heteo,hemi
duplicate genes located at diff positions on genome arent alleles of each other
steps in genetic info flow
1.DNA poly(rep):start at origin of rep,primer,make lead/lag strands
DNA
2.RNA pol(transcr):one strand template,start at promotors,no primer
RNA
3.ribo&tRNA (transl):codons read,begin at start/end at stop
PROTEIN
genetics of prok and euk
(rep,trancrip/lation, occur in ALL organisms)
1.prok have 1 circular chrom in the cyto
2.euk have lots linear chrom in the nucleus
3.euk genes have coding/non (in/extrons)
size, numbers, shapes of chromosomes in domain of life
bacteria:mycoplasma .58
streptomyces 8.66
archaea:nanoarchaeum .49
sufolobus 2.99
eukarya:giardia 12
tetrahymena 210
gene expression in prokaryotes
chrom & rib in the cyto allow for coupling of translation to transcription
several genes are transcribed from a common promotor to a single long mRNA
gene expression in eukaryotes
1.separation of scrip/lation: chrom in nucl,ribo in cyto
2.genes split into ex/introns
3.1mary script must be extensively processed before exported to ctyo for translocation(mRNA)
DNA double helix: major and minor grooves and protein contact points
proteins interact with DNA mainly by binding to atoms of bases exposed in the major groove.
(minor:small at top
major:deep, next one down)
inverted repeats
form stem-loop in dsDNA
binding sites for proteins,including transcriptional regulators
provide info for the formation of stem-loop structures in RNA
effect of heat on DNA
ds from .8-1 relative abs
Tm=85degC
melting=1-1.2
ss levels at ~1.2
supercoiled DNA
relaxed covalently closed
(break one strand)
relaxed nicked circular
(rotate one end of broken strand around helix and seal)
supercoiled circular DNA
[inside cells DNA is highly supercoiled and associated with proteins]
enzymes are necessary to increase or decrease DNA supercoiling:gyrase and topoisomerases
number of strands passed thru and resealed=less supercoiled
topoI:figure 8
topoII and gyrase:egg shaped
(such enzymes are essential for replication transcription and DNA repair)
organization of prokaryotic chromosomes
DNA is tightly compressed into nucleoids and spreads when cells are gently lysed.
in eukaryotes DNA is packaged with histones into nucleosomes
chromatin fiber
euchro/htereochromatin
highly condensed,duplicated chromosomes of dividing nucleus
non-chromosomal genetic elements
(types of extrachromosomal elements)
1.virus:UQ in pro and euk
2.plasmid:UQ in prok, in mito of fungi/plant, sometimes in yeast and protezo
3.mito and chlor DNA:remmants of bacterial chroms only in euk
viruses
DNA or RNA
some are integrated into host chrom's for replication
often are responsible for diseased state of host
plasmids
small(circular,linear) of DNA, replicate independently of cellular chrom's
carry info for own replication
not essential for normal cell metab,growth,reproduction
survival advantages
types of plasmids
fertility(transfer of DNA)
resistance(Abiotic)
bacteriocin(pduce toxins)
virulence(disease-causing)
cryptic(unknown)
mito and chloro DNA's
1-5
both contain mtDNA and cpDNA
circular, similar to prok
code for small # of indispensable proteins
contain genes for proteins involved in oxidative phosphorylation and photosynthesis and 2 RNA's
mito and chloro DNA's
6-8
chrom's are episomes and dont follow mendelian inheritance
circular,linear DNA plasmids can be present in mito of fungi and plants
chlor of some algae are non-pathogenic small circular ds-plamidlike RNA
transposable elements
(semiautonomous genetic elements)
(segments of DNA that can move from on eplace on a chrom or genome to another)
replicate of a chrom(plasmid or virus)
transposable elements
in prokaryotes(have at least 4 transposons)
1.insertion sequences(IS):carry genes required for movement to new locations
2.transposons:carry other genes in addition to ones for movement
3.genetic elements that proliferate by hopping around in the genomes of their hosts and are transmitted to other cells like viruses
4.conjugative transposons(cells produce sex pili)
transposable elements in eukaryotes(have at least 2 transposons)
1.DNA resembling prok transposons
2.retrotransposons:elements that exist as DNA in the genomes but are transcribed into an RNA copy which is used for template for RT into a DNA copy inserted at a new location in the genome.
DNA replication
1953 Watson&Crick:predicted is semiconservative
1958 Messelson&Stahl:confirmed its conservative.
properties of DNA polymerases
synthesize DNA 5'-3'
require template and primer(can be DNA or RNA)
exonuclease 3'-5'
I&II have a 5'-3'exonuclease for the degradation of primers during rep
III w/ DNA repair prot 5'-3'
DNA strand elongation
1.DNA pol use deoxyribonucleoside tri-P as substrates and addthem to 3'
2.DNA pol are processive and add one nucleotide to infor by complementary bases in the template strand
functions of primers and templates in DNA synthesis
1.RNA pol dont need primer
2.primases are RNA pol
3.primers are ~30 nucleotides
4.DNA pol start synthesis at 3'-OH of RNA primers
DNA replication:initiation
begins at origin of rep
prok,have 1 origin on chrom
euk,each chrom has many origins
DNA rep is bidirectional
only some plasmid or viral DNA are unidirectional mode
(best origin of replication is ori-C of the e.coli chrom)
DNA replication starts at...
origins of replication
The ori-C site of e.coli is 245bp long with 11 GATC/CTAG Dam methylation sites and 4DnaA boxes
Dam:deoxyadenosine methyl transferase
DNA replication:the process
1.rep bubble made by binding DnaA protein to ori-DNA
2.DNA helicase (DnaB) unwinds
3.ss are kept separate by ss binding protein (SSB)
4.primase (DnaG) makes RNA primers
DNA replication:elongation
lead/lag strand replication
elongation continued...
GTC:sites for the intiation of RNA primer synthesis
gyrase,helicase,okazaki fragments, primase
completion of lagging strand synthesis
1.pol III starts at primer and replicates until it reaches primer of prior okazaki fragment
2.III released from lagging, and snaps back to start new fragment
3.I degrades primer bw fragment in 5'-3', fills gap
4.ligase seals last gap
bidirectional replication
rep starts at origins of rep and goes in both directions until one rep complex collides with another going in the opposite direction
termination of replication
most bacterial chrom have rep termination sites
euk and viruses termination appears to occur when rep complexes collide.
proofreading and editing
mismatch in pairing at the terminal base pair causes the DNA pol to pause:the last base in the new strand is removed by 3'-5' exonuclease of the pol before rep continues.
replication of linear chromosomes: the end problem
no primer synthesize DNA at the ends of chromosomes bc theres no template for primase to make primer
DNA pol cant replace RNA primer bc it cant synthesize 3'-5' and cant initiate 5'-3' unless it is primed
replication of linear chromosomes (some solutions to the end problem)
linear chrom of some bacteriophages have ss cohesive ends and are circularized after entry into the host cell
replication of linear chromosomes(soln #2 to the end problem)
ends of some linear chromosomes and plasmids are covalently closed hairpin structures.
replication of linear chromosomes (soln#3 to the end problem)
some linear chromosomes replicate by initiation from a nucleotide linked to a protein
replication of linear chrom (soln#4)
euk solve by extending their 3' by means of a RT that has its own RNA template:telomerase
(some telomeres are 100-200Kb)
antibiotics that block DNA replication
ciprofloxacin GyrA of gyrase
trimethoprim reductase
inhibitors of DNA synthesis
4-quinolone:2hex
nalidixix acid:2hex,N,OH
ciprofloxacin:3hex,N,NH,F,OH
mitomycin C:hex,2pent,NH2
novobiocin:6hex