Lecture 11 Flashcards
23S rRNA
- catalytic RNA
- caalyzes peptide bond formation between amino acid on tRNA at A site and growing peptide chain bond to rRNA in P site
peptidyl transferase
cataltic activity of 23S rRNA
structure domains of ribosomal RNA
-50S (23S and 5S) of 70S prokaryotes
functional domains of proteins
- sequences with 50-300 amino acids
- fold into stable, unique conformation
- LDL receptor protein domains
- exon shuffling
chromosome mutations
- change in total number of chromosomes
- depletion or duplication of genes/segments of chromosomes
- rearrangements of genetic material within or among chromosomes
deletions and duplications in the alterations of chromosomes
-total amount of genetic info in chromosome changes
inversions and translocations in alternations of chromosomes
-genetic material remains the same but rearranged
what is a mutation?
- an alteration in DNA sequence in DNA sequence
- any base-pair change in sequence
- singe base-pair substitution
- deletion or insertion of base pairs
- major alteration in chromosomal structure
where may chromosomal mutations occur?
- somatic or germ cells
- coding or noncoding regions
point mutation (base substitution)
-change from one base pair to another
missense mutation
results in new triplet code for different amino acid
nonsense mutation
results in triplet code for for stop codon (translation terminated prematurely)
silent mutation
A mutation that changes a single nucleotide, but does not change the amino acid created.
frameshift mutation
- results from insertations or deletions of base pair
- loss or addition of nucleotide causes shift in reading frame
- frame of triplet reading during translation is altered
loss of function mutation
reduces/eliminates function of gene product
null mutation
results in complete loss of function
dominant mutation
results in mutant phenotype in diploid organism
dominant gain of function mutation
results in gene with enhanced, negative or new function
lethal mutations
interrupt essential process and result in death (highly conserved genes; natural selection does not tolerate alterations)
lethal conditional mutations
dependent on organism’s enviroment
neutral mutation
majority of mutations occur in a noncoding region, effect on genetic fitness of organism is neither beneficial nor detrimental
spontaneous mutation
- changes in nucleotide sequence that occur naturally
- arise from normal biological or chemical processes that alter nitrogen bases
induced mutation
result from influence of extraneous factors, either natural or artificial
what do mutations arise from?
- replication
- replication is imperfect
- DNA polymerase occasionally persists after proofreading
- errors due to mispairing predominantly lead to point mutations
replication slippage
- if loop occurs in template strand during replication, DNA polymerase musses lopped out nucleotides, and small insertion and deletion occur
- more common in repeat sequences
- hot spots for DNA mutations
- contribute to hereditary diseases
DNA repair system
maintains the integrity of genetic material; repairs systems, counteracts genetic damage that can result in genetic disease and cancer
DNA polymerase
proofreads, removes, and replaces incorrectly inserted nucleotides
mismatch repair
- activated when proofreading fails
- mismatches are detected, cut, and removed (by endonuclease and exonuclease) and the correct nucleotide is inserted by DNA polymerase
strand discrimination
- adenine methylase recognizes DNA sequences and adds methyl group to adenine residues on old strand
- newly synthesized strand of replication remians unmethylated
- mismatch repair recognizes unmethylated strand and repair
postreplication repair
- responds after damaged DNA has escaped repair and has failed complete replication
- RecA protein directs recombination exchange with corresponding region on undamaged parental strand
excision repair
- light independent DNA repair
- exonuclease recognizes and cuts distortion/error
- DNA polymerase inserts complementary nucleotides in missing gap
- DNA ligase seals final nick
inducible enzymes
bacteria adapt to environment by producing inducible enzymes only when specific substrates are present
constitutive enzymes
enzymes are continuously produced regardless of chemical makeup of environment
repressible system
- presence of specific molecule inhibit gene expression
- abundance of end product in environment represses gene expression
negative control
genetic expression occurs unless shut off by regulator molecule
positive control
transcription occurs only when regulator molecules directly stimulates RNA production
lactose
galactose and glucose containing disaccharide; lactose is an inducer
-gene activity is repressed when lactose is absent and induced when available
where are gene responsible for coding for enzymes located?
- organized into clusters
- regulatory regions are located upstream of gene cluster they control
- on the same strand; cis-acting
cis and trans acting sites
- regulatory site events determine if genes are transcribed into mRNA
- binding of trans-acting element at cis-acting site regulates gene cluster negatively or positively
lac Z
encodes beta-galaosidase, an enzyme that converts disaccharide lactose to monosaccharides glucose and galactose; conversion is necessary for lactose to serve as primary energy source in glycolysis
Lac Y
specifies primary structure of permease, an enzyme that facilitates entry of lactose into bacterial cell
Lac A
encodes enzyme transacetylase, which may be involved in removal of toxic by products of lactose digestion from the cell
Lac I
located close to but not part of lac operon structural genes. produces repressor molecule, which regulates transcription of structural genes
lac operon structural genes
- lacZ, lacY, and lacA
- all three are transcribed as a single unit
- results in polycistronic mRNA
constitutive mutations
genes with these mutations produce enzymes regardless of lactose presence/absense
operon
group of genes is regulated and expressed together as a unit
lac operon: negative control
-operon subject to negative control
-transcription occurs only when repressor fails to bind operator region
-repressor normally binds DNA sequence in operator region
-inhibits RNA polymerase
-represses transcription of
structural genes
summary of the operon
- invoked series of molecular interactions between proteins and DNA
- no lactose, enzyme are not needed and expression of genes encoding enzymes are repressed
- lactose present, indirectly induces activation of genes by binding repressor
I- mutation
the repressor protein is altered or absent and cannot bind to the operator region
-structural genes are always turned on
Oc mutant
the nucleotide sequence of the operator DNA is altered and will not bind with a normal repressor molecule
-the structural genes are always turned on
how is gene regulation more complex in eukaryotes?
- Greater amount of D N A that is associated with histones and other proteins
- mRNA s must be spliced, capped, and polyadenylated prior to transport from nucleus
- Genes on numerous chromosomes are enclosed in a double membrane nucleus
- mRNAs have a wide half life range
cis-acting DNA sequences
- located on same chromosomes as gene that it regulates; required for accurate regulated transcription of genes
- promoters, enhancers, and silencers
promoters (core and proximal)
nucleotide sequences that serve as recognition sites for transcription machinery
- located immediately adjacent to regulatory genes
- critical for transcription initiation
core promoter
-determines accurate initiation of transcription
proximal-promoter elements
modulate efficiency of basal levels of transcription
focused promoters
specific transcription initiation at start sire; major type of initiation for lower eukaryotes
dispersed promoters
direct initiation from several weak transcriptional start sites
promoter structure DNA sequence is made up of?
- initiator
- TATA box
- TFIIB recognition element
- downstream promoter element
- motif ten element - loss of transcriptional activity upon mutation of a TATA-box or DPE can be compensated by the addition of an MTE
enhancers
- regulate transcription of eukaryotic genes, cis-acting transcription of regulatory elements
- located on either side of gene, some distance from gene, or even within gene, important in reaching maximum level of transcription
insulators
found between an enhancer and a promoter for a nontarget gene; allow some enhancer-promoter interactions and block others
silencers
- regulate transcription
- repress the level of transcription initiation
transcription factors
- transcription regulatory proteins
- target cis-acting sites of genes regulating expression
- multiple transcription factors bind to several different enhancers and promoter elements and fine-tune the level of transcription initiation
activators
-increase transcription initiation
repressors
-decrease transcription initiation
DNA-binding domain
- transcription factor functional domain
- binds to specific DNA sequences in the cis-acting regulatory site
trans-activating domain
- transcription factor functional domain
- activates or represses transcription by binding to other transcription factors or RNA polymerase
helix-turn-helix (HTH)
- characteristic domains of DNA binding proteins
- present in both eukaryotic and prokaryotic transcription factors
zinc-finger
- found in wide range of transcription factors that regulate gene expression
- DNA binding proteins
basic leucine zipper
- allows for protein-protein dimerization
- DNA binding proteins
general transcription factors (GTF)
- required at promoter to initiate basal or enhanced levels of transcription
- assembly of proteins in specific order forms pre-initiation complex
- PIC provides platform for RNAP2 to recognize transcription start sites
coactivators
- interact with proteins and enable activators to make contact with promoter-bound factors
- coactivators form complex enhanceosome
enhanceosome
- interacts with transcription complex
- repressors proteins at silencer elements decrease rate of PIC assembly and RNAP2 release
