Genetics Unit 2

A form of DNA

Right handed helix, compact, has a smaller major groove

B form DNA

Right handed with major and minor groove

C:G bonds are blank than A:T bonds

stronger/more stable

What does topoisomerase do?

Enzymes that manage DNA supercoiling and topology by creating transient cuts in the DNA strands.

Is ligase + or - charged

Positive

what is a direct repeat?

Arrows (direction of transcription) are facing the same way. Creates a deletion and a piece of circular DNA.

What is an Indirect repeat?

Direction of transcription is going opposite ways. Contort the arrows so they’re facing the same way then cross over. Creates an inversion.

Acetylation

Binds to the histones tails. Opens DNA for replication or transcription.

Methylation

Turns off genes by adding a methyl group to the 5th carbon of the sugar in DNA’s backbone

Euchromatin

Open DNA active in gene expression

heterochromatin

closed DNA, inactive in gene expression

Will blood cells produce enzymes needed in the brain?

No, that part of the genome will be turned off since the cell isnt speciallized for that

Highly repetitive DNA

heterochromatin (aka satellite DNA)

Tandem repeats

short repeats (not long)

Interspaced repeats

Long sequences scattered throughout the genome, most of them non-coding regions

semi-conservative replication

How human DNA replicates. One parent strand and one new strand in each replication.

Conservative DNA replication

Parent DNA is kept whole while a double stranded daughter replicate is made out of two new strands.

Dispersive DNA replication

Double stranded DNA is a mix of new and old in no particular order having new and old in both the 3’-5’ and 5’-3’ strands.

rolling circle

how prokaryotes replicate

What does DNA polymerase need before it starts replicating the DNA?

A primer with a 3’ OH group

What direction is DNA synthesized?

5’ to 3’

How does prokaryote initiation occur?

Proteins must accumulate in a high enough concentration that they bind to the DNA and trigger the formation of a replication bubble

what does DNA pol 1 do?

in prokaryotes it removes the primers once replication is complete and replaces the RNA primers with DNA nucleotides

what is Gyrase?

Cuts the DNA to release supercoiling tension

what does DNA pol III do?

Starts replicating DNA at the primers and has proofreading capabilities where it can identify the mistake and fix it.

What does ARS stand for?

Autonomous replication sequence (the origin of replication in eukaryotes)

what is OrC and what does it do?

Origin recognition complex is a protein bound to an ARS which signals the formation of a replication fork.

What is a transposon?

A sequence that can jump from one location of the genome to another

What is a cut and paste DNA transposon?

The physical material is cut out and put into another part of the genome

What is copy and paste DNA transposition?

The sequence is replicated and then inserted elsewhere in the genome.

What is an Ac transposon in the context of maize?

The activator insertional sequence (IS) with the functional Trn gene that codes for transposase

What is “Ds” in the context of maize transposons?

Dissociator = crippled version of Ac, causes unstable mutation of maize

When is maize purple?

Purple is dominant to yellow. If there is at least one C+ gene the corn will be purple

When is maize yellow?

Since purple is dominant there needs to be a Ds strand and a C- for it to be negative.

What is hybrid dysgenesis? (in fruit flies)

When a “P” (parental) element is present in one parent but not the other. This can impact the sterility of the offspring.

What happens when you cross a “P” female fly with a “M” male fly?

Since the gene is present in the egg the P gene will be able to express itsself and produce repressor proteins that will then inhibit its transposition and the offspring will be viable

What happens when a “M” female fly mates with a “P” male fly?

Since the P factor is in the sperm cell the repressor protein isn’t made and transposition occurs making all offspring sterile

In order, what are the components of prokaryotic transcription?

-35 and -10 promoters, +1 start site, uses hairpin to terminate

Christmas tree (rna branching off a strand of DNA) what way is it replicating if the longer rna strands are on the left?

to the left. idk why

How does Rho independent termination work? (prok)

transcribed RNA sequence forms a hairpin. The hairpin is followed by 6-U’s (6-A’s in the DNA but its U in the RNA) The A:U pairing causes the RNA to fall off since its a weak bond

What does poly-astronic mean?

Multiple reading frames where theres multiple start and stops

Explain Rho Dependent termination

The RNA will have a RUT sequence that the Rho protein can bind to. Rho functions as a helicase for DNA and assists in termination of the RNA strand from the DNA.

In order, what are the components of eukaryotic transcription?

regulatory sequences (promoters of silencers), -25 (TATA box), +1 start sequence, ORF (open reading frame)

How does the TATA box work?

TFIID binds to TATA, TFIIB brings RNA pol with it and binds to TFIID, TFIIH binds to the whole complex and helps unwild DNA template and dissociate RNA pol at the terminator.

What processing happens to euk mRNA?

1. Addition of 7-methyl Guanine cap @ 5’end

2. Poly-a tail added @ 3’ end

3. Splicing (remove introns + alternative splicing)

Grace meets an alien. what is the aliens name.

Rocky

How does the removal of introns work?

The OH group is attacked nuclearphillically to break the phosphodiester bond and the reaction continues down the mRNA until all of the intron bonds are broken

WTF is an autocatalytic intron

intron splicing that doesnt require a splicosome because a guanosine provides a free OH to breal the phosphodiester bosd

Group 3 splicing in mRNA using a spliceosome

blah blah blah 5’ to 2’ Ilariate linkage forms an Ilariate look at the branch point between intron and exon that a spliceosome then cuts.

Are all of the exons transcribed and used for coding proteins?

Nope. that would be too easy. mRNA will have an open reading frame. The untranslating parts are called untranslated regions isnt that neat.

Whats the Shine-Dalgano sequence?

tells ibs where to bind so the small ribisomal subunit can find it and bind to prepare for translation. only need one per mRNA sequnece in euk but you need one for each cistron in prok.

what does “constitutive” mean?

A gene that is always on or constantly being expressed

What is an inducible gene? (example: Lac operon)

Only on when a certain something (lactose) is present

What is a repressible gene? (example: Trp operon)

is on until a certain something (glucose) is present then it stops transcription

What is a positive control?

the molecule activates the system

what us a negative control?

the molecule is a repressor

What is the order of Lac genes?

lac i (codes for repressor), promoter, operator, +1, Lac Z (beta-galactose), Lac y (permiase for getting lactose into the cell), Lac A (transacytlase)

What is polycistronic mRNA? (example: the lac gene)

One gene that codes for multiple proteins or products

How does glucose work as a corepressor for the lac gene?

When glucose levels are high there will be low levels for cAMP which leads to a weak expression of lacz. When there are low levels of glucose (and therefor high cAMP) it will bind to a region of the DNA upstream on the promoter and help RNA pol to bind, increasing the levels of lac expression. Important thing to remember is that the lac gene is always off unless lactose is present.

what is the Trp operon?

Thee Trp repressor cannot bind to the Trp operator unless tryptophan is present. Without it the repressor is produced and gene expression is halted.

How is transcription of the Trp operon terminated? *prok

When tryptophan levels are high the tRNA is highly charged and theres no transcription of Trp because the 3 to 4 Rho independent termination occurs. But if there are low levels of tryptophan the ribosome stalls at the Trp codon which causes a 2 to 3 anti-terminator sequence which breaks up the terminator sequence and leads to transcription of Trp E gene.

What happens to gene expression of the shine-dalgano sequence is deleted?

For the Trp gene since it’s off unless levels of trp are low and you get ribosomal stalling it remains off even when levels are low because the sine-dalgano sequence is responsible for assembling the robosome and without it no transcription can take place.

What happens if the 6 A sequence for the Trp E gene were deleted?

Transcription would take place reguardless of the amount of tryptophan present because the 3 to 4 stop sequence would be ineffective.

Give an example of a negativly inducable system and explain.

Lac because it’ll shut itself off when lactose is no longer present or when a better food source is avaliable. In other words it is inducible because adding something causes a reaction by binding to the repressor and its negative because it has a repressor thats always expressed.

Example of a negative repressible system

Trp because when tryptophan is present it will bind to the repressor and halt gene expression but otherwise it wouldn’t be able to bind and RNA pol could transcribe the sequence.

what does Omp stand for?

Outer membrane protein (used in the lac operon to let lactose through the membrane and into the cell, another example is an aquaporin)

what does micF do?

micF is antisence RNA that binds to Omp F and inhibits its translation (Post transcriptional control)

What happens in the lytic cycle

cell go pop, lysis, Cro gene is produced and CII is degraded

Lysogenic cycle

longer word = longer cycle. When cell is sad it will incorperate the bacteriophage genes into its genome.

What happens to a bacteria if lambda is repressed by CI?

The cell enters lysogenic cycle

Explain operator affinity and why its important for lytic and lysogenic cycles?

There are three operators and the lambda repressor has the highest affinity for (OR1 >OR2 >OR3). However the Cro dimer has the highest affinity for (OR1<OR2<OR3) they work together as an on off switch for lytic and lysogenic cycles.

What happens when Rec A is produced in a cell

Happens when the cell is under UV stress, the Rec A will stop dimerization of lambda repressor and trigger the lytic cycle as Cro binds to the operators instead.

Basic eukaryotic gene regulation. Explain.

UAS (upstream activation sequence), promoter, +1 start sequence, GAL 1 gene.

What is needed for a eukaryotic UAS to trigger gene expression of GAL1

When galactose is present it keeps the activation domain of GAL4 open so when GAL 80 binds its not restricting the binding of RNA pol. If the domain is active than transcription is active. GAL 80 still binds just not in that spot.

what are the three transcription factors we talked about in class?

Helix-turn-helix (lambda repressor), helix-loop-helix, and zinc finger

how is transcription effected when wrapped around a histone

Can still happen but at much lower levels because enhancing factors that assist with RNA pol binding aren’t able to bind since they’re too big to fit with the histone in the way.

what is lucine zipper?

Lucines are interspaced evenly every 3-4 amino acids and it forms a zipper that can help when connecting dimers together.

what is HAT?

histone acetyl transferase. it removes the negative charge on lysine (neutralized the DNA) to increase gene expression and allow TFIID to bind and trigger RNA pol binding.

What is HDAC

Histone De-Acetylation Complex. keeps DNA in a closed confirmation