Unit 6: DNA Synthesis

• Linking Number
◦ = base pairs/10.5
◦ Number of times one closed circular DNA is wound about another
• What kind of bond joins the sugar to the base? N-glycosyl
• Which bases have higher melting points? Why?
◦ Anything with Guanine b/c Guanine makes 3-H bonds with Cytosine
• Satellite DNA: Highly repetitive sequences of DNA
• Telomeres:
◦ Repeated sequences at the ends of eukaryotic DNA to help stabilize it
• Telomerase:
◦ Adds telomeric ends,
◦ a reverse transcriptase enzyme
◦ Template is RNA segment in telomerase
◦ Primer: 3' end of chromosome
◦ Germ cells have this
• Why is it advantageous for cells to maintain their DNA in the underwound state?
◦ Easier to package DNA
◦ Easier to separate DNA
• Topoisomerase
◦ An enzyme that increases or decreases the extent of DNA underfunding
◦ Type 1: Acts transiently breaking one of the two DNA strands, passing the unbroken strand through
the break and rejoining broken ends, changes LK in increments of 1
◦ Type 2: Breaks both DNA strands and change LK in increments of 2
• How does E.Coli topoisomerase I remove negative supercoils?
◦ 1. Active site Tyr attacks phosphodiester bond in one DNA strand, cleaving it and creating a
covalent 5' phosphotyrosol protein DNA linkage
◦ 2. Enzyme changes to open conformation
◦ 3. The unbroken DNA strand passes through break in 1st strand
◦ 4. Enzyme in closed conformation, the liberated 3'OH attacks 5' phosphotyrosyl DNA line
• Histones
◦ Proteins that package and order dan, rich in Arg/Lys residues
◦ Basic and positive so DNA backbone is attracted
◦ DNA wraps around histone like beads
◦ DNA wraps around 8 histones
• Base Stacking Interactions
◦ Stabilizes double helix
◦ Hydrophobic interactions
• Semi-conservative Replication:
◦ Each DNA strand serves as template for the synthesis of a new strand, produces two new DNA
molecules each w/ 1 new strand, 1 old strand
• DNA synthesis
◦ occurs in what direction?
‣ 5' -> 3'
◦ Template strand is read in what direction?
‣ 3'-> 5'
◦ Leading Strand
‣ Replicated continuously in 5'-> 3' direction,
‣ same direction as replication fork
◦ Lagging strand
‣ Discontinuously replicated
 ‣ Opposite direction as replication fork
‣ Composed of ozaki fragments in 5'-> 3' direction
◦ Equation:
‣ dNTP + dMTP (n) -> dMTP (n+1) + PPi
◦ Exonuclease:
‣ Degrade nucleic acids from one end of the molecule
‣ Removes primers
‣ Can either go 5'-> 3' or 3'-> 5'
◦ Endonuclease:
‣ Degrade nucleic acids at specific internal sites,
‣ Performs proof reading
◦ Processivity:
‣ The average # of nucleotides added before a polymerase dissociates from substrate
• How does proofreading work?
◦ 1. Polymerase makes mistake
◦ 2. Polymerase repositions mispaired 3' terminus into exonuclease site
◦ 3. Exonuclease hydrolyzes it
◦ 4. 3' terminus repositions back into polymerase
◦ 5. Polymerase incorporates correct nucleotide
• Enzymes involved in DNA Synthesis
◦ Types of DNA polymerase:
‣ DNA Polymerase 1
• 3' -> 5' proof reading (exonuclease activity)
• 5' -> 3' exonuclease activity: replaces RNA primers w/ DNA,
• slow rate of polymerization, low processivity
‣ DNA Polymerase III
• 3' -> 5' proof reading
• no 5'-> 3' exonuclease activity (can't remove primers)
• High rate of polymerization
• High processivity
‣ Has 2 B subunits that form a clamp and surround DNA so it can't dissociate
◦ Helicase:
‣ Enzyme that moves along DNA and separate strands using ATP
‣ Unwinds in 5'-> 3' direction
◦ Topoisomerase:
‣ Relieves topological stress in helical DNA from helicase by introducing positive or negative
supercoils
◦ DNA-binding proteins:
‣ Stabilizes separate DNA strands so the strands don't reanneal
◦ Primase
‣ Synthesizes RNA primers
◦ DNA Ligase
‣ Repairs nick that remains when a primer is replaced by DNA via DNA Pol I
• DNA Initiation of Replication Steps
◦ 1. DnaA binds in its ATP-bound state to R and I sites in OriC
◦ 2. It polymerizes and forms a complex that denatures DUE b/c it induces positive supercoiling
◦ 3. DnaC loads DnaB helices onto both strands which then unwinds DNA in 5'-> 3' direction
◦ 4. Helices creates two replication forks moving in opposite directions
◦ 5. Initiation ends once DNA pol III is loaded onto strand
• DUE:
◦ DNA Unwinding Element
◦ Rich in A=T base pairs, makes it easier to denature cause weaker bond then G=C
• I site
◦ Binds DnaA only when its active
◦ R Site: binds DnaA regardless of if its active
• What contributes to the high accuracy of DNA replication?
◦ 1. Base excision repair
◦ 2. Proof reading
◦ 3. Substrate specificity
• Spontaneous cytosine deamination reaction:
◦ NH2 on C turns to O on U
◦ Uracil is produced as a result
• Base Excision Repair Process
◦ 1. DNA glycolyase recognizes a damaged incorrect base and cleaves between its backbone
◦ 2. AP endonuclease cleaves phosphodiester bond near AP site
◦ 3. DNA polymerase 1 initiates repair synthesis from the 3'OH removing and replacing portion of
damaged strand
◦ 4. Nick sealed by DNA ligase

Unit 7: Transcription
• Monocistronic mRNA:
◦ Carries the code for one polypeptide
◦ Eukaryotes
• Polycistronic mRNA
◦ Carries the code for multiple polypeptides
◦ Prokaryotes
• RNA Polymerase:
◦ Substrate: NTP
◦ Doesn't require a primer: binds promoters instead
◦ Synthesis direction: 5' -> 3'
◦ Reading direction: 3'-> 5'
◦ Claw Shaped
‣ 6 subunits
‣ Sigma subunit
• Directs core to promoter, dissociates during elongation
• Only in prokaryotes
◦ No exonuclease proofreading activity
‣ B/c many copies of RNA are produced by a single gene and they can be degraded and replaced
• Consensus Sequence:
◦ A DNA or AA sequence consisting of residues that most commonly occur at each position in a set of
similar sequences
◦ Stronger promoter: if it matches consensus sequence
‣ Results in better binding w/ RNA polymerase
‣ Results in faster rate of transcription
• Significance of -35 -> -10 region
◦ Where promoter sequence is in prokaryotes
• RNA initiation of Transcription Steps:
 ◦ 1. RNA pol core and sigma subunit bind DNA promoter
◦ 2. Transcription bubble forms
◦ 3. Transcription initiated, conformational changes convert complex to elongation form
◦ 4. Transcription complex moves away from promoter: promoter clearance
◦ 5. Sigma subunit dissociates, NUSA binds
◦ 6. When transcription is complete, both NUSA and RNA pol dissociate
• What are two distinguishing features of the termination signal in rho independent termination of
transcription in prokaryotes?
◦ Has a region that is self complementary: Hairpin loop forms
◦ Conserved string of A=U bonds at 3' end
‣ Becomes unstable from hairpin nearby
‣ so RNA dissociates because of the stress of the hairpin
• Transcription Factors:
◦ An array of proteins required by RNA pol II,
◦ Affect regulation and initiation by binding regulatory site and interacting w/ RNA pol II and other
transcription factors
• Primary transcript
◦ Newly synthesized RNA molecule
◦ Formed into mRNA by:
‣ RNA splicing
‣ Addition of 5' cap
• protects mRNA from degradation
• assists in ribosome binding
‣ Addition of 3' poly A tail
• Types of Gene Expression
◦ Constitutive:
‣ Unvarying expression of gene
◦ Regulated
‣ Controlled expression of gene in response to signals

• RNA splicing
◦ Signals:
‣ At the 5' end, the intron has the sequence GU
‣ At the 3' end, the intron has sequence AG
‣ snRNPS complementary bind these sites via snRNAs
◦ Splicesosome:
‣ Large protein complex involved in splicing mRNAS
‣ Composed of snRNPs
• Specialized RNA protein complex containing snRNAs involved in splicing
◦ How do snRNAs locate consensus sequences to cut out introns?
‣ U1 snRNA has a sequence complementary to splice site at 5' end of intron
‣ U2 is paired to the intron at a position w/ A residue
• Lariat
 ◦ Lasso-like structure caused by bulge-pairing of U2 snRNA
◦ Splicing Mechanism
‣ 1. Inactive spliceosome loops intron and brings active A close to 5' end of intron
‣ 2. 2'OH of adenosine in intron acts as nucleophile and attacks phosphate at 5' splice site
forming lariat structure
‣ 3. 5' exons 3'OH is free
‣ 4. 5' exons 3'OH acts as nucleophile and cuts off intron
‣ 4. Intron floats until degraded
• Poly A tail
◦ Binding site for one or more specific proteins
◦ Protects mRNA from enzymatic destruction
◦ Not encoded in gene
◦ Made by polyadenylate polymerase
‣ Does not require template
‣ Needs cleaved mRNA (primary transcript as primer)
◦ Poly A addition mechanism:
‣ 1. RNA polymerase II synthesizes RNA beyond transcript segment w/ cleavage signal
‣ 2. Cleavage signal gets bond by enzyme complex composed of endonuclease and
polyadenylate polymerase
‣ 3. Endonuclease cleaves at cleavage signal
‣ 4. Polyadenlyate synthesizes large poly A tail
• RNA World Hypothesis:
◦ 1. Prebiotic formation of simple compounds from atmosphere
◦ 2. Synthesis of short RNA or RNA like molecules
◦ 3. Selective replication of these short RNA molecules
◦ 4. Polypeptide synthesis catalyzed by RNA
◦ 5. Peptide use in RNA replication
◦ 6. RNA gets copied into DNA
◦ 7. DNA genome is translated on RNA protein complex w/ RNA and protein catalysts
• Evidence for RNA world
◦ Prebiotic Chemistry Experiments:
‣ Shows that it was possible for nucleotides to emerge in prebiotic conditions
◦ Catalytic RNAs
‣ RNAs discovered to be catalysts
◦ Expanding catalytic repertoire of ribozymes
‣ Ribozymes could synthesis precursors
◦ Ribosome structure
‣ RNA can synthesize proteins
◦ Vestiges of RNA world
‣ Parasitic RNAs can passively self replicate
◦ Progress in Search for RNA replicator
‣ Progress in research in finding a ribozyme that can self replicate

• Lac Operon
 ◦ Equation
‣ Lactose + H2O-> Galactose + Glucose
• Performed by B-Galactosidase
◦ Diagram (in order)
‣ PI:
• Promoter for lac repressor gene
‣ Lac1:
• codes for lac repressor gene
‣ O3:
• Secondary operator for lac repressor
‣ P:
• Promoter for Lac Genes
‣ O1:
• Operator
‣ LacZ:
• Codes for B-galactosidase
◦ Hydrolyzes Lactose
‣ O2:
• Secondary operator for lac repressor
‣ LacY
• Codes for Galactoside Permease
◦ Allows lactose to enter cell
‣ LacA
• Codes for Thiogalactosidase transacetylase
◦ Rids toxic byproducts of the reaction
◦ Regulation:
‣ Negative Regulation
• When Lactose is present:
◦ Allolactose
‣ Inducer
‣ Binds lac repressor
‣ Prevents lac repressor from binding operator and blocking RNA pol from
binding
‣ Allows for transcription to occur
‣ Positive Regulation
• Catabolite Repression
• When Glucose is not present
◦ CRP-cAMP receptor protein binds to site near promoter and stimulates transcription
◦ Summary:
‣ Need lactose and no glucose
‣ Transcription can weakly occur with no glucose

• 5 Features that Distinguish regulation of gene expression in eukaryotes from prokaryotes:

◦ 1. The activation of transcription is associated w/ changes in chromatin structure
◦ 2. Positive regulation is more prominent
◦ 3. Regulator mechanisms involving lncRNAs are common
◦ 4. Eukaryotic cells have larger multimeric regulatory proteins
◦ 5. Transcription in nucleus is separate from translation in cytoplasm
• Heterochromatin:
◦ More condensed form of chromatin
◦ Transcriptionally inactive
◦ Most of Y chromosomes
• Euchromatin
◦ Less condensed chromatin
◦ Mostly what DNA is
◦ Some active, some not

• Riboswitches:
◦ Segment of mRNA that binds to specific ligand and affects translation or processing of mRNA
◦ Cis-regulation
‣ b/c self-regulates
◦ Mechanism:
‣ Terminate transcription, block translation w/ slicing
‣ Regulate their own translation through folding -> induces conformational change
‣ Binding of mRNAs to appropriate ligand causes conformation change in mRNA
‣ Negative feedback loop
‣ Transcription inhibited by hairpin or loop
‣ Translation inhibited by blocking of ribosome binding site
• miRNA
◦ Noncoding genes that silence genes
◦ Has internally complementary sequences -> forms hairpins
◦ Mechanism
‣ Endonuclease cut hair pin, another cuts loop
• Results in two DNA strands
• One is degraded
• The other binds to mRNA and silences it by degrading it
• RNAi
◦ Process where small interfering RNAs (siRNA) bind mRNA and silence it
◦ Can tell you protein function

Unit 8: Translation

• During Translation, mRNA is read in 5'-> 3' direction

• Activation: Uses aminoacyl-tRNA synthetases

◦ 2 bonds (n) from breaking of AA-AMP and PPi hydrolysis
‣ C terminus of AA attacks the ATP-> AMP + PPi
‣ tRNA attacks the AA-AMP intermediate causing AMP to break off
◦ Activates AA for peptide bond formation
◦ Ensures appropriate placement of AA in growing polypeptide

• Initiation in prokaryotes:
◦ 1 bond: If-2-GTP -> If2-GDP + Pi
‣ 1) Small subunit binds IF-1 at the A site and binds IF-3 at the E-site
‣ 2) mRNA binds, AUG is now at the P site. mRNA is by Shine Dalgarno Sequence interaction
with 16s ribosome
‣ 3) IF-2 bound to GTP binds to subunit, along with initiating fMet-tRNA
‣ 4) The large subunit binds, IF2-GTP -> IF-2 GDP + Pi, IF's dissociate

• Elongation:
◦ 2 bonds total (n-1): Ef-Tu-GTP hydrolysis, Ef-G-GTP hydrolysis
‣ 1) the Next tRNA comes into A site bound to EF-Tu-GTP. Ef-Tu-GTP will hydrolyze the GTP.
• Creates lag and allows for incorrectly base paired tRNAs to dissociates "proofreading" .
 Ef-Tu-GDP dissociates and will be recycled to Ef-Tu-GTP with the help of Ef-Ts
‣ 2) Accommodation: rRNA in the large subunit catalyzes peptide bond formation by moving AA
close together. NH2 of Amino acid on A site binds AA on P site, bond between AA on P site
and P site breaks
‣ 3) Translocation: want growing peptide in P-site. Ef-G-GTP translocate binds to the A site,
hydrolyzes GTP, moves tRNA with nothing on it in E site and moves growing polypeptide
from A site to P site

• Termination: 1 high energy bond Ef-G-GTP hydrolysis

◦ 1) Signaled by a stop codon in the A site, termination factor will bind at the A site
◦ 2) Termination factor binds and hydrolyzes the bond between the polypeptide and the tRNA in the P
site
◦ 3) EF-G-GTP (translocate) translocate the ribosome, ribosome dissociates

• What are the two filters in place to ensure tRNA binds the correct AA?
◦ First filter:
‣ initial binding of AA to enzyme
◦ Second filter:
‣ separate active site on enzyme that only wrong substrate fits, hydrolyzes intermediate from
AA-AMP to AA + AMP

Unit 9:

• DNA Cloning Procedure:

◦ 1. Obtaining DNA sequence to be cloned
‣ Using restriction endonuclease as molecular scissors to cut out the DNA sequence
◦ 2. Selecting a cloning vector
‣ A small molecule that can carry DNA and is capable of self-replication
◦ 3. Joining gene of interest to carrier molecule
‣ DNA ligase pastes them together so they are no longer held by H-bonds
‣ Now bound by covalent bonds
◦ 4. Move DNA into host cell w/ machinery to replicate cloning vector
‣ Plasmids: transformation
• Put cell under environmental stress, cell picks up DNA from environment
‣ Viral DNA
• Can infect the cell
◦ 5. Selecting/identifying host cells with recombined DNA
‣ Use selectable marker
• Antibiotic resistance
• GFP
• Metabolic activity
• Sticky Ends: EcoRI generates
• Blunt ends: HaeIII generates
• What do plasmid contains before cDNA is inserted?
◦ Ori
◦ Promoter
◦ Gene for operator
 ◦ Operator
◦ Ribosome Binding Site
◦ Transcription termination sequence
• Site Directed Mutagenesis: Method to replace individual amino acids
◦ Oligonucleotide directed mutagenesis
‣ 1) Denature double stranded plasmid into 2-circular single stranded pieces of DNA
‣ 2) Anneal oligonucleotide primers w/specific mutation
‣ 3) Use DNA polymerase to extend and incorporate primers w/mutation
‣ 4) Digest non-mutated parental DNA w/ methylation nuclease
‣ 5) Anneal newly synthesize strands
‣ 6) Transform new DNA into cells and end up with mutated plasmids
◦ Synthetic Insert Method
‣ 1) Cut out area of interest
‣ 2) Replaced w/ synthetic insert w/ desired mutation
• PCR
◦ Heating
◦ Cooling
◦ Replication
◦ 2^x copies (x is # of cycles)
• RT-PCR
◦ Reverse transcriptase PCR
◦ Reverse transcriptase converts RNA -> cDNA
◦ then PCR occurs like normal
• Q-PCR
◦ Quantitive PCR
◦ Can be used to estimate the relative copy #s of a particular sequence
◦ Fluorescent probe w/ quenching molecule complementary binds
◦ Binding of target DNA sequence separates quencher and allows for it to be fluorescent
• How are epitope tags used to identify interacting proteins?
◦ 1) Gene of interest is cloned next to a gene w/ epitope tag
◦ 2) The resulting fusion is precipitated by antibodies to the epitope in a column
◦ 3) Any other proteins that interact precipitate, allows us to understand protein functions
• Epitopes: part of protein that binds with antibodies

• Pyrosequencing
◦ Individual dNTPs are added to a mix of lucerifase one at a time
◦ when individual dNTPS are added, PPi is released when correct binding occurs
◦ PPi forms ATP
◦ ATP reacts w/ lucerifase to emit light
◦ When it emits light, the computer tracks which dNTP is added
• Next generation reversible terminator sequence:
◦ 1. dNTPS with blocked 3'OH groups are added by DNA polymerase and each are flourescently
labeled w/different colors
◦ 2. The block allows only one dNTP to be added at a time, fluorescent color is added
◦ 3) the block and fluorescent is removed and process is repeated
◦ 4) Eventually transformed into contains by computer aligning overlapping sequences
• Ion semiconductor sequencing
◦ DNA sequencing technology in which nucleotide additions are detected by measuring electrons
released
◦ The four dNTPS are introduced one by one in a repeating cycle, each being removed before the next
 is added
• Single-molecule real-time (SMRT) sequencing:
◦ DNA sequencing technology in which nucleotide additions are detected as flashed of fluorescent
colored light w/sensitivity enhanced
‣ A single molecule of DNA polymerase immobilized in pores on flow cell
‣ Polymerase captures fragmented genomic sequences as they diffuse into pore
‣ The labelled dNTPs diffuse in each newly added nucleotide releasing its colored group as it
adds each nucleotide
‣ A light detection system records color of light flash
• Human Genome:
◦ How many protein coding genes are there?
‣ 20,000
‣ makes up 1.5%
◦ What fraction of human genome consists of genes?
‣ 27.4%
◦ Transposons:
‣ Segments of DNA that can move from one location to another
‣ 2.9%
‣ Some active, but most inactive
◦ SNP
‣ Single nucleotide polymorphisms
• Changing in one base that cause for genetic variation with alleles

Practice Prelim Items:

• Name a specific example of RNA editing:
◦ Cytosine deamination reaction
• Protein that delivers fmet-tRNA to ribosome in initiation
◦ IF-2
• Site on ribosome where fmet-tRNA is delivered
◦ P-site
• Name protein that delivers aminoacyl-tRNAS to the ribosome during elongation
◦ Ef-tu
• Complete enzyme activity that is part of large subunit ribosomal RNA that forms peptide bond
◦ Peptidyl transferase
• RNA enzyme name:
◦ ribozyme
• Name enzyme that shifts ribosome position on mRNA during translation
◦ EF-G
• Name two cellular processes benefit by maintenance of DNA in this state
◦ DNA replication
◦ DNA transcription
• What is the name used by molecular biologists describe the interaction between Aminoacyl tRNA
synthetaste and tRNAs that contributes to fidelity of translation?
◦ Second genetic code

• Crazy weird DNA graph:

◦ A= enhancer
◦ B= transcription factors
◦ C= co-activator
‣ Co-activator interacts w/ transcription activators and sends activating signals to prininitation
complex
• When would you choose a to use an expression vector to clone a gene?
◦ When you want to express the cloned gene
• Name the cutting edge technology to create a targeted modification in any gene?
◦ CRISPR
• Name the procedure used in the lab to exploit biology of microRNAS?
◦ RNAi
◦ Tells us about gene function
• How many genes are there in the human genome?
◦ 23,000-25,000
• Two enzymes required to add Poly A tail
◦ Endonuclease and polyadenylate polymerase
• What is chromatin remodeling?
◦ Changing position of nucleosomes
◦ using variant histones
◦ covalent modification of nucleosomes
• Pyrosequencing:
◦ Add nucleotides one at a time
• What is the general purpose of RNAi?
◦ It is used to degrade a specific mRNA in a cell (or block translation of that specific RNA) in order to
see how the phenotype of a cell or organism is affected in the absence of that specific protein.
• Describe the RNAi method
◦ A plasmid is created that, when transcribed, will create an mRNA with a hairpin structure. That
mRNA will then be processed as if it were a microRNA. After processing, the short single-stranded
RNA that results will cause mRNA degradation or block translation.
• On a DNA microarray, what is implied if a sector does not fluoresce?
◦ The gene represented by that sector is not expressed in either sample.
• On a DNA microarray where one cDNA preparation has been labeled red and the other labeled green,
what does it mean if the sector fluoresces yellow?
◦ The gene represented by that sector is expressed similarly in
both samples.
• Correct order of events in initiation of transcription by E.coli RNA polymerase?
◦ Protein binding, closed complex formation, open complex formation, RNa synthesis, promoter
clearance
• (2 points) Translation in eukaryotes differs from that in prokaryotes (bacteria) in that (circle all that are
true
◦ in prokaryotes it is initiated with fMet whereas in eukaryotes it is initiated with Met.
◦ in prokaryotes it is initiated at an AUG near a Shine-Dalgarno sequence in the mRNA.
◦ in eukaryotes the 3' end of the mRNA is associated with the 5' end during initiation whereas in
prokaryotes it is not.
◦ i n prokaryotes translation and transcription are coupled whereas in
eukaryotes they are not
• List three key processes that contribute to this high fidelity of DNA replication
◦ 1) base selection by the polymerase
◦ 2) 3' to 5' exonuclease (proofreading)
◦ 3) DNA repair
• Basic explanation of RNA world
◦ parent of all life was a self-replications RNA
• Procedure used to tag proteins thereby facilitating their purification using affinity chromatography
techniques
1. Ligate the gene for GST to the gene that encodes your protein of interest and
2. introduce into an expression vector.
3. Transform the recombinant vector and over-express in E. coli.

• ^^ Allows identification of interacting partners – when the affinity column binds the fusion protein,
 interacting partners will also be retained on the column
• Why don't you need telomeres in prokaryotes?
◦ B/c DNA is circular, so replication forks eventually meet
• If stop codon: it will not be attached to tRNA
• Which would make it go from a closed to an open complex?
◦ Supercoiling
• Translation: amino acid + ATP → aminoacyl-AMP + PPi

• The Nobel Prize in Chemistry was recently awarded for work that revealed the 3-
D structure of the ribosome at highresolution. Discuss the key aspect of this high
resolution structure that supports the RNA World Hypothesis.
◦The rRNAs form the structural core of the ribosome with the proteins being
located more superficially. In fact, there is no protein within 18Å of the active
site for peptide bond formation.

• Two popular techniques for protein interaction

◦Co-immunoprecipitation

◦Yeast 2-hybrid analysis

• Gyrase: introduces negative supercoils using ATP, type 2 topoisomerase

• What feature is critical for telomere formation?

◦Repeating sequences allow it to bind to a few nucleotides at a time on the chromosome

and slide down to keep elongating the 3' end of the chromosome

• Chromatin:

◦Tightly packed DNA + protein

• miRNA: trans regulation

• Why do scientists use RNAi

◦To determine a proteins function by seeing how cells/organisms change when it isn't
present

• After a replication bubble is formed:

◦the linking # becomes 0

◦Outside the bubble is greater than 384

• True or false:

◦After DNA strand is lengthened, telomerase serves as template F

◦Telomerase tends a DNA strand by adding to 5' end F

◦Telomerase is active in somatic cells F

◦Teloermase protects ends of linear chromosomes by preventing shortening in DNA

replication F

• mRNA editing

◦Cytosine deamination of the mRNA encoding apolipoprotein B

• Specific name of enzyme that forms peptide bond

◦Peptide transferase