Exam 2 - Part 2 Flashcards
RNA synthesis is under the direction of DNA
- RNA produced has complementary sequence to the template DNA
three types of RNA are produced - mRNA carries the message for protein synthesis
- tRNA carries amino acids during protein synthesis
- rRNA molecules are components of ribosomes
- a single RNA polymerase catalyzes
components of bacteria RNA polymerases
- core enzyme = catalyzes RNA synthesis
- sigma factor = no catalytic activity, helps the core enzyme recognize the start of genes
- holoenzyme = 1 + 2
transcription
- initiation, elongation, and termination
- only a short segment of DNA is transcribed
promoter
site where RNA polymerase binds to initiate transcription (is not transcribed)
transcription termination
occurs when core RNA polymerase dissociates from template DNA
- two types: intrinsic and rho-dependent
transcription in bacteria
- Polycistronic mRNA often found in bacteria and archaea
- Contains directions for >1 polypeptide catalyzed by a single RNA polymerase–reaction similar to that catalyzed by DNA polymerase
transcription eukaryotes
- differs from bacterial transcription in a few ways
eukaryotes have 3 major RNA polymerases - promoters differ from those in bacteria by having combinations of many elements
- RNA polymerase II is a large aggregate, containing 10 or more subunits
- catalyzes production of heterogeneous nuclear RNA (hnRNA) which undergoes posttranscriptional modification to generate mRNA
eukaryotic genes
initially made up of exons (expressed sequence) and introns (intervening sequence)
- spliceosome splits out introns
- alternative splicing gives variety
what is considered genes?
- DNA sequences that code for tRNA and rRNA are considered genes
- genes coding for tRNA may code for more than a single tRNA molecule or type of tRNA
ribozymes
spacers between the coding regions are removed after transcription, some by the use of special ribonucleases
the genetic code
Universal Remained unchanged First two letters of each codon Initiation codon Termination codons (non-sense) Code degeneracy Wobble hypothesis
prokaryotic ribosome
70S ribosome, split into 30S and 50S subunits
eukaryotic ribsosome
80S ribosome, split into 40S and 60S
- in mitochondria or chloroplasts
translation
- synthesis of polypeptide directed by sequence of nucleotides in mRNA
- It is coupled with transcription
- Ribosome: site of translation–polyribosome (polysome)
polyribosome
complex of mRNA with several ribosomes
amino acid activation
-tRNA has to be charged with an amino acid before it goes to the ribosome
aminoacyl-tRNA synthetase proofreads and adds on the correct amino acid
elongation
- sequential addition of amino acids to a growing polypeptide
peptidyl (donor-P) site
binds initiator tRNA or tRNA attached to growing polypeptide (peptidyl-tRNA)
aminoacyl (acceptor-A) site
binds incoming aminoacyl-tRNA
exit (E) site
briefly binds empty tRNA before it leaves ribosome
what are the three stop codons?
UAA, UAG, UGA
what are the purposes of release factors?
- aid in recognition of stop codons
- 3 RFs function in prokaryotes
- only 1 RF active in eukaryotes
molecular chaperones
- proteins that aid the folding of nascent polypeptides
- protect cells from thermal damage - e.g., heat-shock proteins
- aid in transport of proteins across membranes
- examples: DNAj and DNA k
overview of gram positive and gram negative protein secretion
- gram-positive and gram-negative bacteria have different problems secreting proteins based on the differences between the structure of their walls
- Both G+ and G- use the Sec-dependent pathway for transporting proteins across the membrane
- Other secretion pathways also exist, but all systems require energy
SEC dependent pathway
- general pathway
- translocate proteins from cytoplasm across or into plasma membrane
- Attached to pre-protein is signal peptide which: delays the folding, chaperone proteins keep preproteins unfolded, and removed once pre-protein emerges from plasma membrane
protein secretion in gram negative
- Type I, II, II, IV, and V–- Transport across the OM
–Transport across Periplasmic space
Type 1 (ABC) protein secretion pathway
- ubiquitous in prokaryotes
- transports proteins from cytoplasm across both plasma membrane and outer membrane
Type 3 protein secretion pathway
secretes virulence factors of Gram-negative bacteria from cytoplasm, across both plasma membrane and outer membrane, and into host cell
Type 4 protein secretion pathway
are unique because they secrete proteins and transfer DNA during conjugation
where does the regulation of gene expression occur?
- transcription initiation
–transcription elongation
–translation
–posttranslation
operons
the sequence of bases coding for one or more polypeptides along with the promoter and operator or activator binding sites
- unique to bacteria
- normally controls sugar metabolism
lac operon is an example of what type of control and types of genes?
negative transcriptional control of inducible genes
the lac operon
contains genes needed to catabolize lactose
- negative control with the lac repressor to the operator
- positive control with the CAP
global regulatory systems
- regulatory systems that affect many genes and pathways simultaneously
- important for bacteria since they must respond rapidly to a wide variety of changing environmental conditions
- controls multiple operons that can be related or unrelated
regulon
genes or operons controlled by a common regulatory protein
modulon
operon network under control of a common global regulatory protein but individual operons are controlled separately by their own regulators
what are some examples of global regulatory systems?
- regulatory proteins
–alternate sigma factors
–two component signal transduction (regulatory) systems
–phosphorelay systems
diauxic growth
biphasic growth pattern in which there is preferential use of one carbon source over another when both are available in environment
–lag occurs after preferred substrate is exhausted followed by the resumption of growth using the second source
- catabolite repression plays a role in this pattern of growth
mutations
stable, heritable changes in sequence of bases in DNA
- in prokaryotes usually produce phenotypic changes
- can occur spontaneously or be induced by chemical mutagens or radiation
- mistakes are usually made and fixed before it moves onto the next generation
- is only considered a mutation when it is passed on from a parent cell to a daughter cell
point mutation
silent mutation – change nucleoside sequence of codon – but not the encoded amino acid
missense mutation
a single base substitution that changes codon for one amino acid into codon for another amino acid
nonsense mutation
converts a sense codon to a stop codon
frameshift mutation
results from insertion or deletion of one or two bases pairs in the coding region of the gene
induced mutations
caused by agents that directly damage DNA
base analogs
- structurally similar to normal bases
- mistakes occur when they are incorporated into growing polynucleotide chain
DNA modifying agents
alter a base causing it to mispair
intercalating agents
distort DNA to induce single nucleotide insertions and deletions
Ames test
- based on observation that most carcinogens are also mutagens
- tests for mutagenicity are used as screen for carcinogenic potential
- Reversion rate in presence of suspected carcinogen reversion rate in absence of suspected carcinogen
proofreading
- correction of errors in base pairing made during replication
–errors corrected by DNA polymerases
direct repair
- used to directly repair thymine dimers
–thymines separated by photochemical reaction using visible light catalyzed by photolyase - called photoreactivation
- can break the bond with a photo reaction from light, can be repaired with enzymes
mismatch repair
-type of excision repair
–mismatch correction enzyme scans newly synthesized DNA for mismatched pairs
–mismatched pairs removed and replaced by DNA polymerase and DNA ligase
DNA methylation
- to distinguish old DNA strands from new DNA strands
–old DNA (template strand) methylated; new DNA not methylated
–the repair system cuts out the mismatch from the unmethylated strand - catalyzed by DNA methyltransferases
SOS response
- inducible repair system
- a global control network
- used to repair excessive damage that halts replication, leaving many gaps
–RecA protein initiates recombination repair
–RecA protein also acts as protease, destroying a repressor protein and thereby increasing production of excision repair enzymes - a highly error-prone repair used in a life-or-death situation
- used a response to the environment
Horizontal gene transfer
- occurs via three mechanisms (conjugation, transformation, and transduction) evolved by bacteria to create recombinants
- all three mechanisms depend on some type of recombination
- genes can be transferred to the same or different species
bacterial conjugation
- the transfer of genes between bacteria that depends on: direct cell to cell contact mediated by the F pilus, a type IV secretion system, and rolling circle replication of plasmid
- direct contact of 2 bacteria via a pili
vertical gene transfer
transfer of genes from a parent cell to a daughter cell
mutations can be induced by physical mediums
- x-ray and gamma = penetrating, very harmful, will break up DNA into pieces
UV = not penetrating, effects the surface, can cause a thymine dimer
DNA binding domain: helix turn helix
- alpha helix with a turn and another alpha helix
- can hold the DNA
- structure dictates function
- CAP is a type of helix turn helix
what is the role of CAP proteins in catabolic repression?
- used in dioxic growth
- CAP is activated by cAMP, which acts as a hunger signal
- when there is low glucose, there is more cAMP
- cAMP is used to activate CAP, and to make it bind to the CAP binding site
sigma 24
make more flagella for movement away from chemotaxis
sigma 60
metabolize nitrogen
sigma 70
exponential growth
sigma 32
heat shock proteins
what are some DNA binding domains?
- leucine zipper
- zinc finger
CAP binding
- effect RNA polymerase binding
what is the purpose of sigma factors?
- prelude the RNA polymerase complex to find the promoter region
- each sigma factor controls a group of genes
small RNA
- 50-100 base pairs
- regulatory mechanisms
- makes RNA from the complementary strand
antisense RNA
- if a copy of DNA is made from the coding strand instead of the complementary strand
- opposite of the complementary strand, and it can find to mRNA
- can prevent ribosomes and complexes from binding and synthesizing the mRNA
attenuation of trp operon
- slows down from a stem-loop formation
- if a loop forms in the 1:2 region it pauses or if it forms in the 3:4 region it stops
- the 2:3 region loop allows it to continue
allolactose
- binds to the lac repressor and inhibits it, prevents lac operon from binding
- acts as a corepressor
negative transcription control
proteins bind to DNA and inhibit expression
regulatory proteins
- regulate transcription
- inducers and repressors
- compete in the promoter region and can determine if RNA pol will bind
inducible genes
- genes that are normally off but will get turned on when needed
- lac operon
- catabolic
repressible genes
- genes that are normally on unless turned off deliberately
- synthetic
- trp operon
