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UMD / OTHER / BSCI 222 / What is the purpose of topoisomerases?

What is the purpose of topoisomerases?

What is the purpose of topoisomerases?

Description

School: University of Maryland - College Park
Department: OTHER
Course: Intro to Genetics
Professor: Kimberly paczolt
Term: Spring 2017
Tags:
Cost: 50
Name: Exam 2 Study Guide: Bsci222, StLeger
Description: This study guide covers material that will be on the 2nd midterm for Dr. StLeger, Spring2018. Good luck!
Uploaded: 03/26/2018
14 Pages 12 Views 4 Unlocks
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Genetics Exam 2 Study Guide Saturday, March 24, 2018 12:57 PM


What is the purpose of topoisomerases?



8/

Packaging of DNA affects the expression of genes.

Bacteria--- operons are the length of a cell,  so 1000x compaction is needed ○ chromosomes are supercoiled by topoisomerases

Eukaryotes---- chromatin= 1/3 DNA, 1/3 Histones, 1/3 non-histone proteins

Dispersed euchromatin easier to transcribe than condensed  

heterochromatin

DNA wrapped around histones, not supercoiled

▪ Histones bond ionically w/ DNA and form nucleosome beads

Extra folding with condensinand chromosomal scaffolding  


What is the purpose of euchromatin?



proteins

How is DNA accessed?  

Diverse specificity proteinsthat unwind small regions to activate  

genes

Types of DNA sequences vary.

Unique- mostly genes

○ ENCODE searches for functionality of entire genome

Moderately repetitive--- duplicated genes (tandem repeats) & transposons  (interspersed repeats)

Highly repetitive -------telomeres, centromeres, microsatellites ○ Usually not transcribed because of structural or no function

Microsatellites(short tandem repeats) can impact gene regulation  


What is the purpose of heterochromatin?



We also discuss several other topics like esm 2104 vt

when inserted into promoters… used in DNA fingerprinting

STRs found in any bodily excretion except vomit- Innocence  

Project

▪ mtDNA fingerprinting used in identification too (more copies)

Transposable elements---sequence rearrangements (e.g. Horizontal gene transfer) ○ Provide a mechanism for macroevolutionary change

Transposons = cut/paste… DNA jumps

○ Contain gene for Transposase… Know the jumping process ○ 1/3 of our genes are mix/matched via transposition… new genes or  functions

Retrotransposons = copy/paste… reverse transcriptase used

Transposons = cut/paste… DNA jumps

○ Contain gene for Transposase… Know the jumping process ○ 1/3 of our genes are mix/matched via transposition… new genes or  functions We also discuss several other topics like kathleen moore jmu

Retrotransposons = copy/paste… reverse transcriptase used

Always replicative: 42% of human genome, 30% of variation among  

humans

▪ Selfish (junk) DNA is parasitic

LINEs… 17% human genome

□ long and contain their own RNA polymerase gene SINEs… 11% human genome

Short, may have promoter or response element, but  parasitize LINEs

○ 1/3 of our genes are mix/matched via retrotransposition… new genes or  functions

Human endogenous retroviruses(Hervs) make up 1-8% of the human genome • Example: Placental development

Transposable elementsprovide a mechanism for macroevolutionary change

Diversity can be produced very rapidly thanks to jumping genes

Ex. Gc salic acid gene is turned off in all mammal brains

▪ Larger brains & better synapses

○ Ex. Neuronal plasticity variation & personality diversity 9/

DNA replication has evolved so that problems are solved  efficiently.

Issues with Replication

○ Double helix must be uncoiled so genes can be accessed ○ DNA strands have to be separated

○ Complementary base-pairing must be maintained and established ○ Covalent bonds must form within new strands If you want to learn more check out bio 196

○ Termini of linear chromosomes  We also discuss several other topics like angle θ is in standard position. if sin(θ) = − 1 3 , and π < θ < 3π 2 , find cos(θ).

Theta replication in E. coli

• Initiator proteins (DnaA) bind to origin of replication & separate strands

DNA Polymerase 3 is the builder in bacteria.

• Nucleotides are added to 3' OH at the end of an existing strand (reads 5' to 3')

Differential addition due to antiparallel  strands If you want to learn more check out extently

Leading Strand produced 5' to 3'… chasing replication  fork ○ If you want to learn more check out humanistic psychologists maintain each of the following about self disclosure except one. which one?

• Initiator proteins (DnaA) bind to origin of replication & separate strands

DNA Polymerase 3 is the builder in bacteria.

• Nucleotides are added to 3' OH at the end of an existing strand (reads 5' to 3')

Differential addition due to antiparallel  strands

Leading Strand produced 5' to 3'… chasing replication  fork

▪ Template has its 3' end away from fork

○ Lagging Strand produced in short backwards pieces… Okazaki fragments •

RNA primer precedes each new nucleotide segment

DNA Polymerase 1 replaces these rna primers

▪ bidirectional exonuclease activity & 5' to 3' polymerase activity

○ DNA ligase "stitches" DNA fragments together

Linear replication in eukaryotes is much more complicated. • Origin Recognition Complexesbind in many spots & recruit helicases

Replisome complex forms at the replication fork

○ Helicases…" unzipper"… plow through H-bonds, breaking double strand ○ DNA gyrase… "relaxer"…  unwinds "knotted" DNA ahead of fork ○ Single-stranded DNA binding proteins… "Straighteners"… •

DNA replication machinery work together to form a complex that replicates  both the leading and lagging strands concurrently

• Histones synthesizedduring G2 so that nucleosome formation occurs

Telomeres are at the termini of linear  chromosomes.

• The end of the lagging strand cannot be fully replicated

Non-coding DNA at the end of chromosomes are sacrificed to keep coding  genes safe

Telomerase can add to the length of telomeres

▪ Longer telomeres associated with increased lifespan (e.g. narwhal)

Germ cells & cancer cells have telomerase activity; somatic cells  

don't.

▪ Telomere shortening due to stress… causes premature aging 10/

The Central Dogma: DNA---> mRNA ---> protein

• Usually changes in gene expression underlie evolution more than changes in  the gene

DNA is transcribed into an mRNA strand that codes for proteins. • Problems with Transcription are essentially the same as in DNA replication • DNA binding proteinsturn gene transcription on/off at promoter sequences  on DNA

○ These proteins have motifs that fit into major groove, form H-bonds w/  DNA

• Problems with Transcription are essentially the same as in DNA replication • DNA binding proteinsturn gene transcription on/off at promoter sequences  on DNA

○ These proteins have motifs that fit into major groove, form H-bonds w/  DNA

Transcription in Bacteria

• Initiation

• RNA Polymerase binds at two consensus sequences on promoter of gene ○ Bacterial  polymerase requires a sigma factor to bind to the promoter ○ Promoter indicates specificity (on/off), along with:

▪ Which strand will be copied: 3' to 5'; the sense strand

▪ Beginning of the transcription unit (+1)

• Elongation: mRNA synthesized in 5' to 3' direction from sense strand template ○ Energy from ribonucleotide triphosphate monomers

• Terminationsignal triggers end of transcription and release of mRNA ○ Rho independent termination

▪ Inverted repeats enable hairpin secondary structure, and weak AU  bonds trigger release of mRNA transcript

○ Termination factor rho unwinds RNA from DNA ("helicase binds at rut")

Transcription in Eukaryotes

• RNA polymerase 2 (for mRNA) must be induced…  

○ RNA polymerase 1 (rRNA) and 3 (tRNA) are constitutive

• Eukaryotic Promoters are more complex and variable.

○ Transcription factors must bind to promoters to turn transcription  on/off

○ Promoters exposed when topoisomerases, chromatin remodeling  complexes, and acetylating enzymesloosen the chromatin DNA  structure

• Core promoter =  conserved consensus sequences include TATA box ○ Basal transcription factors (TF) help RNA polymerase bind to the  promoter

▪ Example: positioning preassembled holoenzyme

• Regulatory promoter = multiple consensus sequences that provide binding  sites for different regulatory transcriptional factors (transcriptional activators) ○ Mixed and matched so unique combo of TA's regulate each gene ○ Response elements = consensus sequences shared by many genes so  that they respond to the same signal mediated by TA

▪ Example: glucocorticoid response element for cells that care  about stress

○ Enhancer, insulator, and silencer  sequences away from promoter loop  around to brin activators or reressors onto reulator romoter

○ Response elements = consensus sequences shared by many genes so  that they respond to the same signal mediated by TA

▪ Example: glucocorticoid response element for cells that care  about stress

○ Enhancer, insulator, and silencer  sequences away from promoter loop  around to bring activators or repressors onto regulatory promoter

mRNA is long-lived in eukaryotes thanks to processing. • Primary mRNA transcripts are processed in nucleus:

○ 5' cap - modified guanine nucleotide structure recognized by ribozyme ○ 3' RNA cleavage by ribonuclease

▪ Poly-A tail… 6-200 Adenine added to the new 3' end by poly-A polymerase

□ Determines how many times mRNA will be translated

○ Introns are unintelligible, so removed (stretches of non-coding  transcript)

○ Keep exons& nested genes(exons within introns of other genes; 25% of  our genes)

• Specific proteins transport mRNA through nuclear pore complexes out to  cytosol

Alternative RNA splicing for one gene to produce many proteins • RNA splicingproduces a primary transcript by cutting introns and rearranging  exons

○ snRNPs (small nuclear ribonucleoproteins) form spliceosome and fuse  exon mRNAs

▪ Introns cut out by ribozyme

○ *Bacteria lack introns… # of genes reflect fitness

• Alternative Splicing-single gene can encode multiple proteins via mix/match  of exons

○ Different domains have different functions, so mix/match effects  function

▪ Multiple 3' cleavage sites can lead to different proteins too

• Fruitless Gene encodes behavior

○ Behavioral switch gene via nervous system development… "gay  drosophila"

• DrosophilaDescam (Down Syndrome cell-adhesion molecule) • Neurodevelopment implications for mammalian proto-cadherins in synapses ○ Alternative promoter selection

○ Trans-splicing: combine exons from several mRNA transcripts ▪ Nerve cells cadherins' expressed in billions of combinations for  synaptic formation

      • Neurodevelopment implications for mammalian proto-cadherins in synapses ○ Alternative promoter selection

○ Trans-splicing: combine exons from several mRNA transcripts ▪ Nerve cells cadherins' expressed in billions of combinations for  synaptic formation

Translation of mRNA codons into a polypeptide sequence • mRNA transcript's nucleotides grouped into 3nucleotide frames ○ 61 codons code for 20 amino acids, and 3 are stop codons

Each amino acid's aminoacyl tRNA synthetase binds it to appropriate tRNA  (charging) 

• Ribosomesself-assemble and produce polypeptide chains

▪ Most of our metabolism dedicated to ribosome production &  functioning

○ 2 subunits in eukaryotes

▪ Small = 1 rRNA (18S) + 33 proteins…. Attaches to mRNA

▪ Large =  2 rRNA (28S & 5S) + 49 proteins … contains 3 binding sites  for tRNA

□ A, P, E sites

• Initiation

○ Small ribosomal subunit recognizes 5' cap (eukaryotes) or Shine Delgarno sequence (bacteria)

○ Eukaryotes, ribosomal subunits bind to mRNA at Kozak Consensus  Sequence 

• Elongation

○ A ribozyme creates peptide bond between amino acids in A & P sites… ○ Then ribosome moves down mRNA in 5' to 3' direction… translocation ▪ Next tRNA binds… wrong one will wobble, so it is corrected

• Termination

○ Protein release factors bind to terminator codon in A-site, causing  ribosomal subunits to dissociate… mRNA & polypeptide sequence are  released

• Message amplificationenables protein production to sustain the cell ○ 1 gene transcribed 1000s of times, each mRNA translated 1000s of times ○ Polyribosometranslation speeds the process up

○ Bacteria simultaneously transcribe and translate the same gene (no  nucleus)

Gene Regulation in Prokaryotes

The operon includes promoter, operator, and genes

• Transcription unit - multiple functionally related genes transcribed into one  mRNA

• Operator- on/off switch for transcription of transcription unit

Gene Regulation in Prokaryotes

The operon includes promoter, operator, and genes

• Transcription unit - multiple functionally related genes transcribed into one  mRNA

• Operator- on/off switch for transcription of transcription unit • Promoter - binding site for RNA polymerase

• Regulator gene- produces repressor protein that binds to operator, blocking  transcription

Lac operon- negative inducible… (catabolic pathways)

• Empty repressor binds DNA, but lactose = inducer binds repressor so DNA  transcribed

• Transcription unit contains 3 genes

Tryptophan operon- negative repressible… (anabolic pathways) • "empty" repressor needs corepressor = Trp to bind so that it can bind DNA@  operator, inhibit transcription

Global regulators  coordinate control of many genes, usually using positive  transcriptional control 

• Ex. cAMP pathways coordinate breakdown of glucose/lactose

Genetics Exam 2 Study Guide Saturday, March 24, 2018 12:57 PM

8/

Packaging of DNA affects the expression of genes.

Bacteria--- operons are the length of a cell,  so 1000x compaction is needed ○ chromosomes are supercoiled by topoisomerases

Eukaryotes---- chromatin= 1/3 DNA, 1/3 Histones, 1/3 non-histone proteins

Dispersed euchromatin easier to transcribe than condensed  

heterochromatin

DNA wrapped around histones, not supercoiled

▪ Histones bond ionically w/ DNA and form nucleosome beads

Extra folding with condensinand chromosomal scaffolding  

proteins

How is DNA accessed?  

Diverse specificity proteinsthat unwind small regions to activate  

genes

Types of DNA sequences vary.

Unique- mostly genes

○ ENCODE searches for functionality of entire genome

Moderately repetitive--- duplicated genes (tandem repeats) & transposons  (interspersed repeats)

Highly repetitive -------telomeres, centromeres, microsatellites ○ Usually not transcribed because of structural or no function

Microsatellites(short tandem repeats) can impact gene regulation  

when inserted into promoters… used in DNA fingerprinting

STRs found in any bodily excretion except vomit- Innocence  

Project

▪ mtDNA fingerprinting used in identification too (more copies)

Transposable elements---sequence rearrangements (e.g. Horizontal gene transfer) ○ Provide a mechanism for macroevolutionary change

Transposons = cut/paste… DNA jumps

○ Contain gene for Transposase… Know the jumping process ○ 1/3 of our genes are mix/matched via transposition… new genes or  functions

Retrotransposons = copy/paste… reverse transcriptase used

Transposons = cut/paste… DNA jumps

○ Contain gene for Transposase… Know the jumping process ○ 1/3 of our genes are mix/matched via transposition… new genes or  functions

Retrotransposons = copy/paste… reverse transcriptase used

Always replicative: 42% of human genome, 30% of variation among  

humans

▪ Selfish (junk) DNA is parasitic

LINEs… 17% human genome

□ long and contain their own RNA polymerase gene SINEs… 11% human genome

Short, may have promoter or response element, but  parasitize LINEs

○ 1/3 of our genes are mix/matched via retrotransposition… new genes or  functions

Human endogenous retroviruses(Hervs) make up 1-8% of the human genome • Example: Placental development

Transposable elementsprovide a mechanism for macroevolutionary change

Diversity can be produced very rapidly thanks to jumping genes

Ex. Gc salic acid gene is turned off in all mammal brains

▪ Larger brains & better synapses

○ Ex. Neuronal plasticity variation & personality diversity 9/

DNA replication has evolved so that problems are solved  efficiently.

Issues with Replication

○ Double helix must be uncoiled so genes can be accessed ○ DNA strands have to be separated

○ Complementary base-pairing must be maintained and established ○ Covalent bonds must form within new strands

○ Termini of linear chromosomes  

Theta replication in E. coli

• Initiator proteins (DnaA) bind to origin of replication & separate strands

DNA Polymerase 3 is the builder in bacteria.

• Nucleotides are added to 3' OH at the end of an existing strand (reads 5' to 3')

Differential addition due to antiparallel  strands

Leading Strand produced 5' to 3'… chasing replication  fork ○

• Initiator proteins (DnaA) bind to origin of replication & separate strands

DNA Polymerase 3 is the builder in bacteria.

• Nucleotides are added to 3' OH at the end of an existing strand (reads 5' to 3')

Differential addition due to antiparallel  strands

Leading Strand produced 5' to 3'… chasing replication  fork

▪ Template has its 3' end away from fork

○ Lagging Strand produced in short backwards pieces… Okazaki fragments •

RNA primer precedes each new nucleotide segment

DNA Polymerase 1 replaces these rna primers

▪ bidirectional exonuclease activity & 5' to 3' polymerase activity

○ DNA ligase "stitches" DNA fragments together

Linear replication in eukaryotes is much more complicated. • Origin Recognition Complexesbind in many spots & recruit helicases

Replisome complex forms at the replication fork

○ Helicases…" unzipper"… plow through H-bonds, breaking double strand ○ DNA gyrase… "relaxer"…  unwinds "knotted" DNA ahead of fork ○ Single-stranded DNA binding proteins… "Straighteners"… •

DNA replication machinery work together to form a complex that replicates  both the leading and lagging strands concurrently

• Histones synthesizedduring G2 so that nucleosome formation occurs

Telomeres are at the termini of linear  chromosomes.

• The end of the lagging strand cannot be fully replicated

Non-coding DNA at the end of chromosomes are sacrificed to keep coding  genes safe

Telomerase can add to the length of telomeres

▪ Longer telomeres associated with increased lifespan (e.g. narwhal)

Germ cells & cancer cells have telomerase activity; somatic cells  

don't.

▪ Telomere shortening due to stress… causes premature aging 10/

The Central Dogma: DNA---> mRNA ---> protein

• Usually changes in gene expression underlie evolution more than changes in  the gene

DNA is transcribed into an mRNA strand that codes for proteins. • Problems with Transcription are essentially the same as in DNA replication • DNA binding proteinsturn gene transcription on/off at promoter sequences  on DNA

○ These proteins have motifs that fit into major groove, form H-bonds w/  DNA

• Problems with Transcription are essentially the same as in DNA replication • DNA binding proteinsturn gene transcription on/off at promoter sequences  on DNA

○ These proteins have motifs that fit into major groove, form H-bonds w/  DNA

Transcription in Bacteria

• Initiation

• RNA Polymerase binds at two consensus sequences on promoter of gene ○ Bacterial  polymerase requires a sigma factor to bind to the promoter ○ Promoter indicates specificity (on/off), along with:

▪ Which strand will be copied: 3' to 5'; the sense strand

▪ Beginning of the transcription unit (+1)

• Elongation: mRNA synthesized in 5' to 3' direction from sense strand template ○ Energy from ribonucleotide triphosphate monomers

• Terminationsignal triggers end of transcription and release of mRNA ○ Rho independent termination

▪ Inverted repeats enable hairpin secondary structure, and weak AU  bonds trigger release of mRNA transcript

○ Termination factor rho unwinds RNA from DNA ("helicase binds at rut")

Transcription in Eukaryotes

• RNA polymerase 2 (for mRNA) must be induced…  

○ RNA polymerase 1 (rRNA) and 3 (tRNA) are constitutive

• Eukaryotic Promoters are more complex and variable.

○ Transcription factors must bind to promoters to turn transcription  on/off

○ Promoters exposed when topoisomerases, chromatin remodeling  complexes, and acetylating enzymesloosen the chromatin DNA  structure

• Core promoter =  conserved consensus sequences include TATA box ○ Basal transcription factors (TF) help RNA polymerase bind to the  promoter

▪ Example: positioning preassembled holoenzyme

• Regulatory promoter = multiple consensus sequences that provide binding  sites for different regulatory transcriptional factors (transcriptional activators) ○ Mixed and matched so unique combo of TA's regulate each gene ○ Response elements = consensus sequences shared by many genes so  that they respond to the same signal mediated by TA

▪ Example: glucocorticoid response element for cells that care  about stress

○ Enhancer, insulator, and silencer  sequences away from promoter loop  around to brin activators or reressors onto reulator romoter

○ Response elements = consensus sequences shared by many genes so  that they respond to the same signal mediated by TA

▪ Example: glucocorticoid response element for cells that care  about stress

○ Enhancer, insulator, and silencer  sequences away from promoter loop  around to bring activators or repressors onto regulatory promoter

mRNA is long-lived in eukaryotes thanks to processing. • Primary mRNA transcripts are processed in nucleus:

○ 5' cap - modified guanine nucleotide structure recognized by ribozyme ○ 3' RNA cleavage by ribonuclease

▪ Poly-A tail… 6-200 Adenine added to the new 3' end by poly-A polymerase

□ Determines how many times mRNA will be translated

○ Introns are unintelligible, so removed (stretches of non-coding  transcript)

○ Keep exons& nested genes(exons within introns of other genes; 25% of  our genes)

• Specific proteins transport mRNA through nuclear pore complexes out to  cytosol

Alternative RNA splicing for one gene to produce many proteins • RNA splicingproduces a primary transcript by cutting introns and rearranging  exons

○ snRNPs (small nuclear ribonucleoproteins) form spliceosome and fuse  exon mRNAs

▪ Introns cut out by ribozyme

○ *Bacteria lack introns… # of genes reflect fitness

• Alternative Splicing-single gene can encode multiple proteins via mix/match  of exons

○ Different domains have different functions, so mix/match effects  function

▪ Multiple 3' cleavage sites can lead to different proteins too

• Fruitless Gene encodes behavior

○ Behavioral switch gene via nervous system development… "gay  drosophila"

• DrosophilaDescam (Down Syndrome cell-adhesion molecule) • Neurodevelopment implications for mammalian proto-cadherins in synapses ○ Alternative promoter selection

○ Trans-splicing: combine exons from several mRNA transcripts ▪ Nerve cells cadherins' expressed in billions of combinations for  synaptic formation

      • Neurodevelopment implications for mammalian proto-cadherins in synapses ○ Alternative promoter selection

○ Trans-splicing: combine exons from several mRNA transcripts ▪ Nerve cells cadherins' expressed in billions of combinations for  synaptic formation

Translation of mRNA codons into a polypeptide sequence • mRNA transcript's nucleotides grouped into 3nucleotide frames ○ 61 codons code for 20 amino acids, and 3 are stop codons

Each amino acid's aminoacyl tRNA synthetase binds it to appropriate tRNA  (charging) 

• Ribosomesself-assemble and produce polypeptide chains

▪ Most of our metabolism dedicated to ribosome production &  functioning

○ 2 subunits in eukaryotes

▪ Small = 1 rRNA (18S) + 33 proteins…. Attaches to mRNA

▪ Large =  2 rRNA (28S & 5S) + 49 proteins … contains 3 binding sites  for tRNA

□ A, P, E sites

• Initiation

○ Small ribosomal subunit recognizes 5' cap (eukaryotes) or Shine Delgarno sequence (bacteria)

○ Eukaryotes, ribosomal subunits bind to mRNA at Kozak Consensus  Sequence 

• Elongation

○ A ribozyme creates peptide bond between amino acids in A & P sites… ○ Then ribosome moves down mRNA in 5' to 3' direction… translocation ▪ Next tRNA binds… wrong one will wobble, so it is corrected

• Termination

○ Protein release factors bind to terminator codon in A-site, causing  ribosomal subunits to dissociate… mRNA & polypeptide sequence are  released

• Message amplificationenables protein production to sustain the cell ○ 1 gene transcribed 1000s of times, each mRNA translated 1000s of times ○ Polyribosometranslation speeds the process up

○ Bacteria simultaneously transcribe and translate the same gene (no  nucleus)

Gene Regulation in Prokaryotes

The operon includes promoter, operator, and genes

• Transcription unit - multiple functionally related genes transcribed into one  mRNA

• Operator- on/off switch for transcription of transcription unit

Gene Regulation in Prokaryotes

The operon includes promoter, operator, and genes

• Transcription unit - multiple functionally related genes transcribed into one  mRNA

• Operator- on/off switch for transcription of transcription unit • Promoter - binding site for RNA polymerase

• Regulator gene- produces repressor protein that binds to operator, blocking  transcription

Lac operon- negative inducible… (catabolic pathways)

• Empty repressor binds DNA, but lactose = inducer binds repressor so DNA  transcribed

• Transcription unit contains 3 genes

Tryptophan operon- negative repressible… (anabolic pathways) • "empty" repressor needs corepressor = Trp to bind so that it can bind DNA@  operator, inhibit transcription

Global regulators  coordinate control of many genes, usually using positive  transcriptional control 

• Ex. cAMP pathways coordinate breakdown of glucose/lactose

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