Module B Flashcards

Question

B2- numbering convention (upstream vs downstream)

Answer 1

The first nucleotide transcribed is the +1 nucleotide Upstream: the untranscribed stuff and is expressed as a negative number. The greater the number, the farther away it is from the +1 nucleotide Downstream: opposite of upstream

Answer 2

polycistronic-many genes on a single transcript eg. lac operon promoter causes all three genes to be transcribed on to Cistron- a unit of DNA/RNA that corresponds to a single gene

Answer 3

unit of genetic expression that consists of 1 or more regulated genes, its operator, and promoter sequences.

Answer 4

5 Core subunits for RNAP in E.coli 1 sigma factor- number denotes the size(molecular weight) the sigma factor binds to the core and directs it to the binding site **RNAP II in eukaryotes contains 12 subunits

Answer 5

6 subunits of RNAP make up the holoenzyme | Holoenzyme: catalytically enzyme, an enzyme with all subunits, phosphate groups, and cofactors

Answer 6

In normal conditions, the use of this subunit is predominant. However, if the cell receives an insult (eg. heat) then it may use other subunits like sigma 32 to change cell physiology to adapt to the enviroment.

Answer 7

In eukaryotes, sometimes activator and promoter sites are far apart. Proteins called architectural regulators help loop the DNA to bring the two sites closer.

Answer 8

The amount of expression determined solely by the promoter | no repressor and no promoter

Answer 9

Open complex: During initiation of transcription, the bound DNA in the -10 region is partually unwound but still intact. Closed: the bound DNA is intact. once transcription is initiated, the complex will convert to the elongation form

Answer 10

The unwinding of DNA is considered helicase activity since helicase is the enzyme that unwinds DNA in replication. In transcription, the unwinding is done by THIIF at the inr sequence to form an open complex.

Answer 11

The DNA in opened and the CTD has been phosphorylated by the CK9 (though kinase activity).

Answer 12

The step before elongation, it is the process of the complex moving away from the promoter

Answer 13

proteins required for the elongation step of translation are called elongation factors. In bacteria this consists of: EF-Tu, EF-Ts, and EF-G. NusA replaces the sigma factor subunit once the subunit leaves. NusA prevents premature termination and also speeds up transcription of some (BOXA)

Answer 14

It only makes one type of RNA -pre-ribosomal RNA and differ greatly from one species to another

Answer 15

pre-rRNA cannot be used until it has been spliced, and after splicing it becomes an rRNA (ribosome)

Answer 16

Blocks RNAP II and in high conc. it will also block RNAP III. However, this will affect only eukaryotes since bacteria use bacterial RNAP. Also the mushroom's own RNAP II is not blocked.

Answer 17

It makes the most of the mRNA in eukaryotes. It creates the mRNA templates for proteins

Answer 18

Factors with the label TFII are highly conserved across eukaryotes (similar) These are very important to forming the initiation complex

Answer 19

around -30 of the inr sequence, composed of a bunch of TATA

Answer 20

TBP binds to the TATA box, if the promoter has no TATA box then it will arrive as a complex called TFIID

Answer 21

repeats of an amino acid code of YSPTSPS It is separate from the main body of the enzyme by a linker sequence. Also the CTD helps to up the methylated cap at the 5' end of the mRNA and it coordinates interactions between complexes in post-transcription (splicing)

Answer 22

Phosphorylation of the CTD is required for elongation complex to form since it coordinates interactions between complexes in post-transcription (splicing)

Answer 23

produces tRNA and some special RNA's | and has a highly specific promoter sequence

Answer 24

Addition of a transcription factor into the complex.

Answer 25

Once the all the parts (THIIF and THIIE are the last ones) attach you form a closed complex. Then the THIIF will promote unwinding of the DNA at the start site.

Answer 26

Elongation complex: the complex after promoter clearance | Termination: after CTD dephosphorylate, and elongation factors dissociate as well as termination factors

Answer 27

transcription of a gene. If the gene is being transcribed than it is being expressed.

Answer 28

Genes that are generally expressed constantly. | eg. genes that produce tRNA or other central metabolic pathway

Answer 29

constitutive: unvarying expression regulated: expression responds to molecular signals

Answer 30

This is the rate of transcription determined SOLEY by the promoter sequence. The promoter will determine the affinity for RNAP and its transcription factors

Answer 31

Inducible/induction: able to be induced/ being induced | repressible: can be repressed

Answer 32

negative: regulated by a repressor positive: regulated by an activator positive and negative regulation does not mean increasing and decreasing transcription, however repressor always represses and activator always promotes eg. CRP+cAMP

Answer 33

Activator: bind to DNA and enhance RNAP activity at the promoter Repressor: bind to DNA to inhibit RNAP binding to the DNA. regulated by effector eg. allolactose is the effector for the lac repressor protein

Answer 34

makes the RNAP bind to a specific promoter sequence eg. TBP makes RNAP bind to promoters with a TATA box sigma 70 makes it bind to promoters with -35/-10

Answer 35

Operator is where repressor binds | promoter is where RNAP binds.

Answer 36

regulates the binding of the repressor/activator to DNA eg. cAMP->CRP allolactose->lac repressor

Answer 37

The binding of the effector to the repressor's allosteric site changes the conformation of the repressor, releasing it from the DNA

Answer 38

diffusible factor: things like repressors or activators that will act on all strands. (trans: other) Operator: changes to the operator will only affect the gene that the operator is on. (cis=same) it acts on the same strand

Answer 39

Sugar linked to a functional group via anomeric bond at the 1-carbon replacing the H of the OH. If it the orientation is above the plane, then it is an alpha-glycoside and if it is below the plane then it is a beta-glycoside.

Answer 40

Galactose vs Glc: Galactose has a different orientation of the hydroxyl group at the 4-carbon Arabinose: the isomer of glucose. Straight chain, and an aldehyde

Answer 41

glycoside with a glucose and a galactose respectively

Answer 42

INTRA molecular rearrangement of electrons that result in an isomer of the original and the overall oxidation states remain the same

Answer 43

the mechanism used to form glycoside bonds and is how beta-galactosidase creates allolactose

Answer 44

lactose is a sugar created by the dehydration of glucose and galactose.

Answer 45

thiogalactoside transacetylase detoxifies the cell by acetylating non-metabolic pyranosides to remove them from the cell.

Answer 46

substitute for allolactose in lab setting, it is made of galactose and substituting the OH on the 1-carbon with a sulfur-methyl.

Answer 47

Gene is the DNA the codes for the mRNA equivalent of the product gene product: is either the fRNA or the protein that the DNA codes for

Answer 48

combination of three genes that are required to use lactose as a carbon source, its promoter and operator. The Lac I gene is not part of the lac operon because it has its own promoter.

Answer 49

Lac Z is the first gene in the sequence, and codes for beta-galactosidase which hydrolyzes lactose to form glucose and galactose. Allolactose is also a minor side product.

Answer 50

Lac Y codes for beta-galactoside permease which faciliates intake of lactose

Answer 51

Lac A, the last gene in the operon. Processes toxic galactose, to remove from the cell.

Answer 52

O1: between the promoter and the lac z gene and is the tightest bond. O2: is inside the lac Z gene O3: inside the lac I gene

Answer 53

Lac I repressor: a tetramer made of 4 identical monomers, the gene product of Lac I binds to the operator to inhibit transcription of the lac operon. Conformation changes if allolactose binds to the allosteric site.

Answer 54

activator for secondary sugar operons. | homodimer with binding sites for DNA and cAMP

Answer 55

molecules that bind to repressors/activators to regulate gene expression eg. allolactose is the inducer for the lac operon

Answer 56

co-activator for CRP. binds to CRP to create a complex which can bind to DNA to induce transcription

Answer 57

regulatory mechanism to choose a more favourable source of over other alternative sources.

Answer 58

network that share a common regulator | eg. cAMP/CRP are common to the secondary sugars- lactose and arabinose.

Answer 59

Helical turn: 1 complete physical turn in the DNA. | positive coil will be tighter, thus less nucleotides per turn.

Answer 60

Form A and B are right handed (counterclockwise going up) in regards to helical sense.

Answer 61

The center which the DNA rotates/spiral around. The B-form (watson-crick) lines up with the axis perfectly. The A-form is tilted around the helical axis.

Answer 62

base stacking interaction help stablize the DNA and mantain its double helix structure.

Answer 63

aromatic ring= benzene ring

Answer 64

Major: 4 functional groups on one side- allows for more specificity minor: 3 functional groups on one side

Answer 65

hydrophilic: water loving (polar) hydrophobic: water-hating (non polar)

Answer 66

small recognizable structural characteristic of folding patterns in amino acids. made of small beta sheets and alpha sheets and is between a tertiary and secondary structure.

Answer 67

Stable configuration with a specific function. may consist of multiple motifs. Part of a protein with its own specific function.

Answer 68

motif on the outside of a protein that serves to carry out a function

Answer 69

Domain with motifs such as helix turn helix or zinc fingers that can recognize specific DNA patterns and bind to those regions

Answer 70

hydrogen bonds can form between the major(or minor) groove of the DNA bases with parts of the R group of amino acids which allows proteins to recognize specific parts of the DNA. However, A=T (or C=G) does not only bind to only one amino acid.

Answer 71

called the alpha helix, is a part of the helix turn helix that recognizes sequences in the DNA

Answer 72

Major: Methyl, H donor, H acceptor and other H (stray hydrogen)

Answer 73

hydrogen-bond acceptor will be an atom with strong electro-negativity. This is how most nucleotide pairs are recognized.

Answer 74

This non-polar group at 5-carbon allows thymine to be easily distinguished from cytosine.

Answer 75

most common are helix turn helix and zinc finger. And they interact with the DNA via hydrogen bonding.

Answer 76

helix turn helix: used to recognize specific DNA, it is about 20 nucleotides long. There are two alpha-helices about 7-9 nucleotides long and a beta sheet to connect them. looks like a trapezoid shape. Zinc finger: a zinc ion stabilizes to 4 amino acids which link to approximately 30 nucleotides which form a loop which interacts with DNA

Answer 77

Proteins often require binding to another protein eg. RNAP to regulatory proteins/subunits Thus, there are domains for dimer formation which contains motifs that facilitate such binding.

Answer 78

leucine zipper: is a amphipathic (hydrophobic and hydrophilic) alpha helix with one side hydrophobic. This allows for the dimer to form. zipper can side. Helix loop helix: Helix loop helix can bind to another HLH to form a dimer.

Answer 79

Homo dimer: identical proteins that make up a dimer | Hetero dimer: two different proteins make a dimer.

Answer 80

Genes, especially in eukaryotes, are controlled by more than 1 factor. There are activators and repressors, enhancers and silencers that control the expression of a gene.

Answer 81

UAS: Region farther away from the promoter, is another regulatory region

Answer 82

Basal (general) transcription factors:

Answer 83

Large protein with 20-30 polypeptides that binds tightly to CTD of RNAP initiation complex and activator.

Answer 84

sometimes the activator and the inr sequence are far apart. The architectural regulator will bind to the DNA and fold it to bring the inr closer to the activator which allows the mediator to connect the transcription activators on the UAS with the RNAP on the inr.