Overall Themes - 2nd half
February 12, 2013
9:42 PM
Prokaryoticenvironmentvs Eukaryotic environment
What's the information in DNA?
• Protein-coding information
• RNA-coding information
• Codons - specify amino acids
○ Start codon - AUG
○ Stop codons - UAA, UAG, UGA
○ Trp codon - UGG
• Promoter- attracts the attention of RNA polymeraise
• UTR (untranslated region) - stretch of DNA between Promotersegment and start codon.
○ Transcribed into RNA, but NOT translated because it's 'upstream' of the start codon'
• SD Box (located in the UTR) - helps the initiation of translation (in bacteria) by complementary
base pairing before the start codon
• Operator - regulatory DNA sequence in the operon; binding sequence for a regulatory protein.
• Enhansers - proteins bind to enhanse transcription levels of genes in a gene cluster,
eukaryotesonly?
• TATA box - region where TATA binding protein is bound to the promoterattracts RNA
polymeraiseand other transcription factors
• Peptide tag - aminoacid sequence that tells the cell where the RNA should go from the
chloroplast (i.e. to the; ER, nucleus, chloroplast)
○ This sequence appers in the coding region of the DNA
How to get information out of DNA
• RNA polymerase - itentifies and transcribes genes
• Ribosomes - assemblesproteins from
• Operons
○ Repressor (regulatory protein); when bound to DNA, reduces the likelyhoodthat genes
will be transcribed
○ Activator ( regulatory protein); when bound to DNA, increases the likelyhood that genes
will be transcribed
• Promoters -
• Enhansers -
• Regulating enhansers/promoters= different expression of genes (by binding proteins onto
them)
• Eukaryotes - 5' phosphate cap - recognized by the small ribosomalsubunit and begins the
ribosomescanning along the mRNA
Examples of the importance of complementary basepairing:
• mRNA pairs with itself
• tRNA pairs with itself
• In DNA structure
• In Transcription
• SD box
• snRNApairs with itself
• ALL RNAs PAIR WITH THEMSELVES
• - & snRNPs
Stop Codon vs Termination Sequence
• Stop codon signals the end of translation by the ribosome • Stop codon signals the end of translation by the ribosome
• Terminatorsequence base pairs with itself into a hairpin structure to stop RNA polymeraiseby
dissassociating the mRNA sequence, causing it to 'fall off'
○ Terminatorsequenc is located after the stop codon
How to Study
• Make pictures of genes showing the relative location of signals
• Make a chart of signals and how they are understood
○ Release factor in the ribosome - is always competetingto ge into the ribosome,but
while translation is happening, it's out competedby tRNA (which binds more readily)
Is a PROTEIN, does not base pair.
• Make a list of RNA functions
○ Xist-Tsix regulation (non-coding RNAs regulating gene expression)
• Make a diagram of gene expression that highlights complementarybase pairing
• Make a chart comparing proks to euks
This picture is important
Transcriptional regulation
Determines
Chromatin •Regulation of transcription initiation which genes
•Chromatin remodeling to make genes are transcribed
accessible for transcription
pre-mRNA
Posttranscriptional regulation Determines
•Variations in pre-mRNA processing types and
•Removal of masking proteins availability of
•Variations in rate of mRNA breakdown mRNAs to
ribosomes
•RNA interference
• Mature
RNAs Ribosome
Translational regulation Determines rate
•Variations in rate of initiation of proteat which proteins
synthesis are made
New polypeptide chains
Posttranslational regulation Determines
Finished proteins •Variations in rate of protein processing availability
•Removal of masking segments of finished
•Variations in rate of protein breakdown proteins
Protein
breakdown
Fig. 14.6, p. 316
In general,
the location of different types of information coded in DNA and how is each one “understood” by
the cell
how prokaryoticgene structure/expressionis different than eukaryotic
role of various types of RNA in gene expression
role of complementarybase pairing in gene expression
likely effect of mutations in various DNA signals Lec 11 - Intro to prokaryotic Gene Structure
February 12, 2013
9:43 PM
Lecture Outcomes
• relative sizes of typical mitochondrial, chloroplast and nuclear genomes
Nucleus - 120 00 kilobases
Mitochondrial - 16 kilobases
Chloroplast - 200 kilobases
• rubisco structure and assembly from componentscoded by different genomes
• possible reasons why modern organelle genomeshave become dramatically smaller over
evolutionarytime
○ Evolvedto be very specific - only carry out specific processes
○ Some redundant genes have been deleted
Mutation/deletion
Lateral gene transfer - transfer to the nucleus
□ Redundant genes:
Flagella, movementgenes
Hexokinease,glycolysis genes not needed in organelles
○ Mitochondria with smaller genomes may have had selective advantage because they'd
be easier to replicate.
• possible reasons why genes have movedto the nucleus from organelles over evolutionary
time
So the nucleus can have more control - coordinated control
So that the cell won't reject the cell
So that oxygen ( produced in this cell) doesn’t react with important genes - causes
mutations and damage.
Nuclear DNA can undergo sexual reproduction, which generates genetic diversity
(positive)
• possible reasons why certain genes have not movedto the nucleus from organelles
○ Genes in the organell need local control - need to be inside in order to sense problems
○ Too hard to transport proteins and products from those genes from the cytosolinto the
organelle
○ Too big to move - structure just doesn't work in the nucleus.
○ Environmentin organelles in prokaryotic [vs eukaryoticenvironmentin the cell]
Difference in these environments - something has to change
○ Just Chance - genetic drift; hasn't been enough time for them to move over
• basic mechanism of transcription and translation in prokaryoticorganelles vs. eukaryotic
nuclear environments
• basic structure and function of RNA polymeraseand ribosome
○ RNA polymeraseitentifies and transcribes genes - including it's own
Basic protein structure (amino acid chains etc.)
○ Ribosomes are primarily made up of RNA ( the catilytic part) and then protein (the
structiral part)
Are responsible for assembling the proteins of the cell
• examples of complementarybase pairing in gene expression
○ RNA pairs with itself ( complementarybase pairing)
tRNA pairs withself inorder to obtain proper strcture
RibosomalRNA basepairs with itself to achieve 3D structure inorder to be
catalytic. Lec 12 - Prokaryotic Gene Function Reviewing Chapter 13, Gene structureand expression. Focus on prokaryoticgenes
February 13, 2013
3:22 AM
Independent Study Outcomes
1. identify the sequence of standard "start" and "stop" codons
a. Start: AUG
b. Stop: UAA, UAG, UGA
2. identify the function of "start" and "stop" codons
a. Start: The first codon read in an mRNA in translation
b. Stop: A codon that does not specify amino acids - AKA nonsense codons.
3. compare the overall gene expression of prokaryotic vs. eukaryotic cells.
a. The same codons specify for the same amino acids in all living organisms and even viruses (with some
exceptions)
Lecture Outcomes
• relative location of such DNA sequence “signals” as promoter, 5’ and 3’ UTR, “SD box”, start codon, stop codon,
transcription terminator etc.
○ 5' to 3', the order of things in the DNA:
Promoter
UTR (untranslated region) - AKA, the SD box
Start Codon
Gene(s)
Stop Codon
Transcription terminator
• mechanism by which each signal is interpreted, or understood, by the cell
○ Promoter - attracts the attention of RNA polymerase
○ UTR (Untranslated Region) - Transcribed into RNA, but NOT translated because it's 'upstream' of the start
codon'
Is the first region transcribed
tRNA doesn't pair with UTR
□ SD Box (part of the UTR)- In bacteria, rRNA (ribosomal RNA) pairs with it to help the initiation
of translation
○ Startcodon - starts translation by the ribosome
Not the first 3 bases transcribed (that's the UTR)
○ Genes - transcribed by DNA polymeraise, translated by ribosomes into proteins.
Three major stages of translation:
□ Initiation: translation components assemble on the start codon of the mRNA
□ Elongation: the assembled complex reads the string of codons in the mRNA one at a time,
while joining the specified amino acids into the polypeptide
□ Termination: completes the translation process when the complex disassembles after the last
amino acid of the polypeptide (specified by the mRNA) has been added
○ Stop Codon - stops translation by the ribosome
○ Transcription terminator - is transcribed by the RNA polymerase, base pairs with itself and creates a
'hairpin loop' this tells the RNA polymerase to stop.
Destabilises mRNA still bound to the DNA (by base pairing) such that mRNA falls off
Only understood as RNA
• relationship between DNA sequence of signals and their function (ie. how would low efficiency promoters be
different than high efficiency promoters?
• characteristics of promoters that require a particular position and direction
○ When polymeraise binds onto a promoter they have to go 3' to 5'
i.e Where ever the start codon is, is the way it must travel.
• change in amino acid coded, given a change in the DNA sequence (and Genetic Code table)
○ WTF DOES THAT EVEN MEAN. DO YOU EVEN GRAMMAR, HAFFIE?
○ A change in the DNA sequence would cause another amino acid to be coded, or the same one to be coded
or a sequence for Start or Stop?
• base sequence of start and stop codons as mRNA and DNA
○ Start:
mRNA: AUG
DNA: TAC
○ Stop:
mRNA: UAA, UAG, UGA
DNA: ATT, ATC, ACT
• the location of various signals given a diagram of gene expression
promoter startcodon Stop codon
Outcomes Midterm 2 Page 4 Transcription
SDbox terminator
Outcomes Midterm 2 Page 5 Lec 13 - Prokaryotic Gene Regulation Reviewing Chapter 14, Control of gene expression;
especially the Sections 14.1a and 14.1b.
February 25, 2013
2:14 AM
Independent Study Outcomes
1. identify the main features of bacterial operons
○ Operon - a cluster of prokaryotic genes & DNA sequences involved in their regulation
○ Operator - regulatory DNA sequence in the operon; binding sequence for a regulatory protein.
Repressor (regulatory protein); when bound to DNA, reduces the likelyhood that genes will be
transcribed
Activator ( regulatory protein); when bound to DNA, increases the likelyhood that genes will
be transcribed
○ Transcription unit - cluster of genes transcribed into a single mRNA (operon transcribed as a unit
from the promoter)
2. identify the function of repressor proteins
○ Repressor (regulatory protein); when bound to DNA, reduces the likelyhood that genes will be
transcribed
This is because it blocks RNA polyerase from binding to the promoter
Sometimes it slips off
3. identify location of various components of the lac operon
(In order:)
○ Regulatory gene - encodes lac repressor
○ Promoter - binds RNA polymerase
○ Operator - binds Lac Repressor
○ lacZ - gene; encodes for the enzyme B-Glactosidase
○ lacY- encodes a permease enzyme that transports lactose actively into the cell
○ LacA - encodes a transacetylase enzyme (relevant to metabolism of compounds other than lactose)
Lecture Outcomes
• DNA signals in RNA-coding genes
(see first part of lec 12 outcomes)
• DNA sequence of anticodon in tRNA gene, given the codon
○ UGG on the mRNA,ACC on the tRNA
• likely effect of base sequence substitutions in various DNA signals
○ Promoter:
Can't recognise the gene
Might inhibit polymeraise binding
Could increase it's effeciency
(can have bothe positive and negative effects)
○ SD Box:
Effect on the effecency of translation (more or less)
○ Start Codon:
You can break it. - destroys it and kills the gene
○ Stop Codon:
If you destroy the stop codon; the ribosome won't stop translation
□ It will continue to read through, and won’t stop until it reaches another stop codom
□ Often we find redundant stop codons
○ Transcription Terminator:
Changes its effeciency (works better or worse)
• change in amino acid coded, given a change in the DNA sequence (and Genetic Code table)
○ Silent mutations
Codon changed for another of the same amino acid
○ Missense mutations - mutated basepair from a normal
Changes the gene into a different codon
○ Nosense muatations
Changes the gene
○ Indel mutations - fairly severe; insertion of a base pair
Disrupts reading frame downstream - new set of amino acids
• base sequence of start and stop codons as mRNA and DNA • base sequence of start and stop codons as mRNA and DNA
• the location of various signals given a diagram of gene expression
• basic structure of lac operon
Regulatory gene Transcription unit of three structural genes
lacI lacZ lacY lacA
Promoter Operator
DNA
○ Transcription termination site
initiation
site
Lac repressor β-Galactosidase Permease Transacetylase
RNA polymerase
• mechanism of action of lac repressor
○ Functions as a dimer (binds as a dimer) - loops out the promoter so the RNA polymeraise can't get
past the loop.
• function of lac operon in the presence, and absence, of lactose
In the absence of lactose, lac repressor binds to operator and prevents transcription
In the presence of lactose - allolactose (an inducer and isomer of lactose) changes the repressor's
shape so that it can no longer bind to the operator and prevent ranscription
• possible location of mutations in lac operon that give rise to a given phenotype
• phenotype that would arise from a given mutation in lac operon under given conditions Reviewing sections relating to eukaryotic gene structure and
Lec 14 - Eukaryotic Genes function: 13.4 and 14.2, 14.3. In particular, see Fig. 13.19 and
February 27, 2013 14.15. As usual, watch the "Concept Fixes".
1:40 AM
Lecture Outcomes
• basic structure of eukaryotic vs prokaryotic cell with respect to gene expression
Eukaryotes Prokaryotes
Ribosomes initially away from mRNA (because of the nuclear membrane, allows for more Ribosomes attach to mRNA even as mRNA is still being
oppurtunity for gene regulation transcribed from the nucleus
•Transcription Control
•Post-Transcriptional Control
•Translational Control
•Post-Tranlational Control
Nuclear gene structure is more complicated Promoter only
•Promoter proximal region + p
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