Exam 2, Neilson :)

Front 1

Anabolic vs. catabolic reactions

Back 1

Catabolic reactions release energy that is used to drive chemical reactions--like breaking down sugars. Anabolic reactions require energy and build new molecules--like amino acids.

Front 2

Constitutive expression

Back 2

a gene that is transcribed continually, rather than only transcribed when needed

Front 3

Most bacterial gene promoters have

Back 3

an activator, a repressor, or both

Front 4

cistron

Back 4

part of the operon that encode for different proteins

Front 5

Operons

Back 5

common in bacteria. Contain two+ genes that are often involved in the same pathway

Front 6

Lac Operon: LacY

Back 6

galactoside permease--membrane protein that that transports lactose into the cell. (It is found when there is no lactose in the cell because of basal level transcription)

Front 7

Lac operon: lacZ

Back 7

encodes forβ-galacosidase--converts lactose to galactose and glucose. It coverts small amounts of lactose into allolactose (still two rings, connected at a different spot)

Front 8

What is responsible for negative regulation of the lac operon?

Back 8

the Lac repressor. When an inducer is not present, the Lac repressor is bound to the operator to prevent RNA polymerase from leaving the promotor site. Allolactase is the inducer/effector--with it, the Lac operon changes conformation and can no longer bind to the operator

Front 9

How many binding domains does the Lac repressor have?

Back 9

It has 3--two that will bind to different operator sequences (of 3) that makes the DNA loop

Front 10

IPTG

Back 10

An effector of the lac operon. It is a gratuitous inducer, which means it will not be metabolized. This is helpful for scientific studies because it will not disappear.

Front 11

Positive regulation of the Lac operon is done by what? how?

Back 11

CRP, which is activated by cAMP when glucose levels are low (cAMP levels rise). CRP--cAMP binds to the operon, and if lactose is present, high levels of transcription occur.

Front 12

what is the name of the enzyme that catalyzes the formation of cAMP?

Back 12

Adenylate cyclase

Front 13

What does DNA footprinting show us? What are the basics?

Back 13

Where sigma factors are bound to the DNA. Sigma factors bind to the promoters because of osmotic shock.

Front 14

The Lac I gene, according to Jacob and Monod..

Back 14

Is the repressor. It acts in trans, and is diffuseble

Front 15

The Lac O gene, according to Jacob and Monod..

Back 15

Acts in cis and is not produce a product. It's the operator

Front 16

In the Lac operon, X-gal functions as.... and produces what?

Back 16

a substrate but not inducer of the operon; when cleaved, it produces a blue color.

Front 17

How does the AraC regulator work?

Back 17

If arabinose is present, then it forms a dimer on two segments of the gene that are close together and acts as an inducer. If arabinose is not present, then it forms a dimer, connecting to segments of the gene that are pretty far apart and they form a loop, making it hard for RNA polymerase to bind.

Front 18

Trp repressor naturally is...

Back 18

not on the trp gene until tryptophan is present, tryptophan acts as an effector, which allows the pressor to bind to the gene, stopping translation.

Front 19

Attenuation

Back 19

mRNA has four segments of genes. Segment 3 can stably bond to either segment 4 or 2. Segment 1 of the gene encodes for a protein that has tryptophan residue in it, so when tryptophan (trp+tRNAtrp) is readily available, the ribosome moves quickly (covering up 2 quickly) and segments 3 and 4 bind. This creates a termination sequence, because of the UUUU sequences it finds. When tryptophan is not super high, the ribosome moves slowly because it is searching for the correct amino acids, this allows segments 2 and 3 to bind. The binding of these two segments does not terminate translation.

Front 20

What does the TPP riboswitch do?

Back 20

When TPP is present, the thiamine pyrophosphate(TPP)riboswitch, THI box sequesters the shine-delgarno sequence, which prevents translation. When TPP is not present, the shine-delgarno sequence is free. mRNA is involved in making vitamin B

Front 21

Studies of the glmS gene showed us that

Back 21

When the metabolite binds it cleaves thegene– different matabolites=don’t always work.

Front 22

What were the three propsed models for DNA replication?

Back 22

Conservative: parent strands end up together at the end

Semiconservative: each new strand is 1/2 parent strand and 1/2 new strand

Dispersive: the strands do not stay together completely 1/4 old and 3/4 new in the second generation

Front 23

which was the light DNA and which was the heavy DNA? Why?

Back 23

The heavy DNA was the normal parent strand DNA, the light DNA was made out N14 instead of the normal N15

Front 24

SSB proteins

Back 24

keep DNA strand apart during DNA replciation

Front 25

Template strand

Back 25

What the DNA polymerase reads so that it can make the complementary new DNA match the coding strand

Front 26

Coding strand

Back 26

WHat we want the new strand of DNA to look like

Front 27

•DNAa

Back 27

Recognize Origin of Replication and recruit

Front 28

Helicase

Back 28

unzips the two strands of DNA

Front 29

DNA primase

Back 29

Adds RNA primers as a place for Pol to start

Front 30

Clamp Loader

Back 30

holds everything together

Front 31

B-Clamp

Back 31

place for DNA pol. to sit, it increases the processivity of polymerase

Front 32

DNA Pol. III

Back 32

main guy, synthesizes DNA in the 5'-->3' direction

Front 33

•DNAPol. I

Back 33

Remove RNA primer and fill in with DNA

Front 34

Topoisomerase I

Back 34

– Adjust linking number by 1, relieve strain

Front 35

•Topoisomerase II –

Back 35

Adjust linking number by 2, untangle--negative super coils

Front 36

•Dam Methylase –

Back 36

Adds methyl groups to newly synthesized strand (GATC sequence), takes a little while for it to go to work after replication.

Front 37

HU

Back 37

stimulates open complex at oriC

Front 38

DnaC

Back 38

helicase loader

Front 39

DnaB

Back 39

helicase

Front 40

Gyrase

Back 40

type II topoisomerase

Front 41

Pol II holoenzyme

Back 41

chromosomal replicase, consists of Pol III core, B clamp, and y complex clamp loader

Front 42

RNaseH

Back 42

removes RNA primers before processing

Front 43

hda

Back 43

induces DnaA to hydolyze ATP

Front 44

tus

Back 44

participates in replication termination

Front 45

topoisomerase IV

Back 45

helps detangle completed chromosomes

Front 46

What proofreading tool for DNA polymerases have?

Back 46

3'-->5' exonuclease that can remove an incorrectly inserted base pairs before continuing

Front 47

DNA polymerase I has a nick translation activity...what does that mean?

Back 47

It has a 5'-->3' exonuclease which remoces RNA primers from Okazaki fragments

Front 48

What cofactor is required for both DNA sythesis and proofreading activities? Why?

Back 48

Mg++, It counters the negative charge of the DNA

Front 49

WHat helps DNA polymerase be processive?

Back 49

the B clamp

Front 50

Back 50

Fast stop

Front 51

Back 51

Slow stop

Front 52

Examples of fast stop proteins

Back 52

helicase, DNA polymerase II

Front 53

Examples of slow stop proteins

Back 53

DNAa, topoisomerase,DNA polymerase I

Front 54

How many origins of replication are there in bacteria?

Back 54

ONLY ONE

Front 55

What is the ter site?

Back 55

THe termination site of replication in E. COli

Front 56

cis elements

Back 56

part of the DNA so they cannot move. Examples--tata box, sequences

Front 57

trans element

Back 57

CRP activator, anything that is not actually part of the DNA. Examples: repressor

Front 58

define merodiploid

Back 58

a new copy of the gene, inserted plasma to make the bacteria diploid for the lac operon to be able to test different things

Front 59

Super repressors

Back 59

binds to sequence continually except when the operon is constituive

Front 60

Tata binding proteins

Back 60

Tbp, tf2b, tf2d, tf2d recruits RNA polymerase

Front 61

EMSA shows...

Back 61

when DNA is bound to a protein

Front 62

How do cells regulate the r protein?

Back 62

They do so by a translational feedback loop, one of the proteins that is encoded for the the operon is a repressor

Front 63

nonsense mutations

Back 63

point mutation that makes an early stop codon

Front 64

Missense

Back 64

point mutation that changes the protein

Front 65

Transition mutations/what are they caused by?

Back 65

changes a purine to a different purine or a pyrimidine to a different pyrimidine. They can be caused by a replication error or a mutagen

Front 66

Tranversion mutations, cause of

Back 66

purine to pyrimidine or pyrimidine to purine.They can be caused by a replication error or a mutagen--reactive oxygen species

Front 67

Deletion mutations

Back 67

possibly causes frameshifts, not reversible

Front 68

What type of mutagen causes transversion mutations, and how do you fix them?

Back 68

Oxygen radicals. Repaired by base excision repair.

Front 69

How does base excision work? know the names of all proteins

Back 69

Glycoslyase flips out the base that is wrong. AP endonuclease cuts the strand and removes the wrong part. Pol I comes and replaces the sequences, then ligase seals it in

Front 70

What type of mutagen causes pyrimidine dimers or 6-4 photoproducts? How do you repair it?

Back 70

UV light. Nucleotide excision repair, or photorepair for organisms without placentas

Front 71

draw out nucleotide excision repair, make sure you know the proteins

Back 71

UvrA and UvrB move along the DNA scanning for damage, when it encounters damage UvrA leaves and UvrC then comes and cuts the DNA around where the damage was located. Then UvrD(helicase) comes and separates the two strands. Then Pol. I and ligase do their work to fix the strand.

Front 72

What type of mutation causes bulky adducts? What are bulky adducts? How are they repaired?

Back 72

Alknation (mustard gas). Bulky adducts are covalent links between bases.They are repaired either through nucleotide excision repair (usually) or base excision repair (maybe). Can lead to cancer.

Front 73

What causes deamination? what is deamination? how do you fix it?

Back 73

Deanimation is when an aminio group is removed from a C or A base. Nitrous acid causes it. It is repaired by base excision repair

Front 74

What mutagen causes double stranded breaks? How are they fixed.

Back 74

Caused by X-rays. Fixed by homologous recombination

Front 75

Describe homologous recombination and the proteins that play a role in it

Back 75

RecB/C/D come and bind at the break, they eatthe DNA until it reaches the chi site, then it leaves a 3’ end and codes itwith RecA. RecA finds a homologous strand and makes a D loop with a holidayjunction. Make sure that you can draw this. RuvA/B bindat the holiday junction, RuvC cuts it. Can allow for branch migration.

Front 76

what causes mismatches? How are they fixed?

Back 76

Replication errors cause mismatches. The mismatch repair system fixes them.

Front 77

Describe the mismatched repair

Back 77

MutS looks for mismatches, MutL binds to MutS when it finds a mismatch. Then MutH is called over and binds to the nearest methylated strandand MutS/L fold over to make a loop as they bind to MutH. MutH nicks the strand that is not methylated, and then exonuclease comes and removes the stand that has the mismatch, and the DNA polymerase III comes and replaces the bases.

Front 78

What is the purpose of SPO11?

Back 78

It initiates meiotic recombination, by purposely creating double-strand breaks on

Front 79

3-base insertion mutations are probably due to

Back 79

template slippage during DNA replication

Front 80

What is Xeroderman pigmentosum

Back 80

A disease in which a person is extremely sensitive to UV light and susceptible to cancer. It happens when there is a defect in NER

Front 81

Two examples of direct repair

Back 81

photolyase, and direct repair of methylated nucleotide bases by methyltransferase (when there is a methyl group on a G). Methyltransferase is the suicide enzyme

Front 82

lysine, arginine, and histadine are... positive ones are

Back 82

basic

Front 83

What is the role of the mediator?

Back 83

activators bind to the enhance region of the DNA and the mediator bring the enhancer sequences closer to the promoter region, so that they can attract RNA polymerase better

Front 84

SWI/SNF

Back 84

Are chromatin remodeling complexes

Front 85

Reporter genes

Back 85

reports if something is expressed or not. LacZ is an example of a reporter gene.

Front 86

what makes tRNA?

Back 86

Pol III

Front 87

Gal4p

Back 87

For the Gal(galactose operon in eukaryotes) increases transcription, it has a DNA binding domain and an activation domain. It has to be on the UAS sequences to be active. Both ends of the sequence of the Gal4p are essential, the C and N terminus. We know this cause we can measure the activity of the gene based on production of beta galactasidase

Front 88

UAS

Back 88

is the upstream activator for the GAL1 promoter in yeast

Front 89

Gal80p

Back 89

binds to Gal4 and prevents activation

Front 90

Gal3p

Back 90

binds to Gal80p making it have a conformational change and so Gal80p leaves and Gal4p can work

Front 91

Gal4p is dependant on the present of... what are the two repressors? When are they present?

Back 91

galactose, unless glucose is present. Tup1 and Mig1 are present unless there is no glucose.

Front 92

Nucleosomes in heterochromatin have ... are are transcriptionally...

Back 92

histone H1 bound, are tightly packed together, and the DNA is transcriptionally silent.

Front 93

Nucleosomes in euchromatin are... and are transcriptionally...

Back 93

spaced farther apart, and the DNA can be decondensed so that it becomes accessible for binding by transcription factors and other proteins.

Front 94

What is a global means of gene inactivation?

Back 94

histone deacetylation, which leads to tighter association of the DNA in chromatin

Front 95

If an organism is more complex, why are its promoter sequences more complex?

Back 95

Because many genes need to be expressed at a intermediate level, not just turned on and off

Front 96

HAT

Back 96

acetylates histones, making the gene more easily expressed

Front 97

RecA

What does it need?

Back 97

bacterial recombinase, needs ATP. Cannot use ATPyS because it doesn't actually release energy.

Front 98

RecB and RecD

Back 98

3'-->5' helicase, forms 3' strand extensions

Front 99

RecC

Back 99

Binds to chi, forms 3' strand extensions

Front 100

RuvA

Back 100

binds to DNA and promotes branch migration

Front 101

RuvB

Back 101

DNA translocase, promotes branch migration

Front 102

Ruv C

Back 102

resolvase, resolves hilliday intermediate

Front 103

nonhomologous end joining in eukaryotes

enzymes involved in the process

Back 103

does not conserve the original DNA sequence, some of the ends are removed so some information is lost. It is important in somatic cells but is mutagenic in germ cells

Ku70&80, artemis, pol, XRCC4, XLF, Ligase

Front 104

Nonhomologous end-joining that results in the loss of genes encoding what can lead to a predisposition to cancer?

Back 104

NHEJ

Front 105

The Ames test

Back 105

Is uused to screen for carcinogens. A bacteria needs histadine to grow, but is plated on a bunch of medias that do not contain histadine, a mutagen is then used to see if it can make the cell grow without the histidine

Front 106

What is the order of DNA packaging?

Back 106

Histone(+DNA)-->nucleosome-->chromatin(DNA and RNA)-->chromosome

Front 107

Nucleosomes are inactive when

Back 107

H1 levels are high, NUcleosomes are tightly packed (because of deactylation) and chromodomain**

Front 108

Nucleosomes are active when

Back 108

H1 is low, nucleosomes are acetylated, bromodomain

Front 109

Nucleosomes are made out of

Back 109

An octomer mostly composed of arginine and lysine. Remember they have N-terminal tails!

Front 110

Why are different sigma factors important for bacterial promoters?

Back 110

DIfferent sigma factors allow RNA polymerase to recognize different promoters with other consensus sequences.

Front 111

The closer a sequence is to the consensus sequences (-10 and -35)... and how did they find this out?

Back 111

The stronger the binding of the sigma factor is. Mutational analysis--mutated to be more like the TATAAT and TTGACA sequence=greater binding

Front 112

RNA polymerase can proofread in two different ways, what are they?

Back 112

Removing the misincorporated base before proceeding or removing a short stretch of bases (like it went a little too far without catching the error)

Front 113

rho-independent termination

Back 113

requires a hairpin to form/stemp-loop structure to form which causes the RNA polymerase to fall off. In Prokaryotes!

Front 114

rho-dependent termination

Back 114

requires the rho-protein to move along the DNA strand until it runs into RNA polymerase, when it reaches it then RNA polymerase falls off

Front 115

What are the RNA products and the promoter elements for RNA Pol I? EUKARYOTIC

Back 115

RNA products: rRNAs

Promoter elements: UCE, core sequence

Front 116

What are the RNA products and the promoter elements for RNA Pol II? EUKARYOTIC

Back 116

RNA products: mRNA, microRNAs, some noncoding RNAs

Promoter elements: Inr, DPE, tata box, bre

Front 117

What are the RNA products and the promoter elements for RNA Pol III? EUKARYOTIC

Back 117

RNA products: tRNA, rRNA

Promoter elements: Box A, Box B, Box C, and the TATA box

Front 118

Bacterial RNA polymerase is very similar to what what Eukaryotic RNA polymerase? Are the the same?

Back 118

Eukaryotic RNA polymerase II, no, the eukaryotic one is more complex with more subunits

Front 119

What makes up the core promoter that RNA polymerase II binds to?

Back 119

BRE, TATA, INR, DPE. The promoter should have at least one of these

Front 120

What is the biggest different in the transition betweentranscription and translation in bacteria and eukaryotes?

Back 120

They are coupled in bacteria, but transcription happens inside of the nucleus and translation happens outside of the nucleus in eukaryotes

Front 121

Basal level transcription always

Back 121

happens! So there is always some level of the gene

Front 122

What is the function of Pol II, IV, and V.

Do they have exonuclease 3'-->5'?

Do they have exonuclease 5'-->3'?

Back 122

translesion synthesis.

exonuclease 3'-->5'--only Pol II (Pol III does too)

exonuclease 5'-->3' --No (only Pol I has this)

Front 123

telomerase

Back 123

synthesizes more TTGGGG repeats (uses an internal RNA molecule as a template) at the end of chromosomes. It should be absent in normal somatic cells, if it is activated it will form tumors

Front 124

When a replication fork is damaged, how can it be repaired?

Back 124

With double-strand break repair

Front 125

Bromodomains

Back 125

Acetylated nucleosomes are recognized by bromodomain proteins to help stabilize an open chromatin state

Front 126

Chromodomains

Back 126

Methylated histones are recognized bychromodomain proteins to help promote theclosed state.

Front 127

What sequence is methylated by the Dam methylase?

Back 127

GATC

Front 128

In bacteria, the sigma factor associates wit the core enzyme to

Back 128

provide promoter specificity