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Flashcards in ch 7.1 Deck (60):
1

What are some different techniques used to determine DNA and proteins?

Gel mobility shift
size exclusion chromatography
affinity chromatography
DNA foot printing

2

What is gel mobility shift used for?

To find the sequence of the protein binding DNA preference

3

What is size exclusion chromatography used for?

To find the DNA binding preference of regulatory protein

4

what is affinity chromatography used for?

protein binding to a specific DNA sequence

5

How do you find a specific DNA sequence from a binding protein?

DNA footprinting

6

What is DNA foot printing?

1) label one strand with p53
2) mix one strand with protein that binds to that site and one with out
3) add nucleases to the mixture of both strands
4) run on a gel
5) the protein protects the posphodiester bonds so if compare strands DNA sequence is determined

7

how is tryptophan synthesized?

tryptophan prescence shuts off promoter
trytophan absence shuts on promoter

8

How many enzymes synthesize tryptophan?

five enzymes all transcribed from a single promoter

9

What is the tryptophan operator?

regulatory element that lies in the promoter region
it recognizes the the repressor protein

10

What is the repressor protein for tryptophan?

TRP repressor
a helix turn helix protein

11

What does the repressor blocks?

access to the promoter by RNA poly

12

When is the promoter in tryptophan active?

When there is tryptophan present, the tryptophan binds to repressor and activates the repressor. the repressor then binds to the promoter and prevents trancription of enzymes

13

how does tryptophan bind to the repressor?

it binds to two of the helices in the repressor and increases the distance

14

What is negative control?

when a DNA binding protein turns off transcription

15

What is positive control?

when regulatory protein binds to promoter for transcription

16

What is the repressor for the LAC operon?

LAC repressor

17

What is the activator for the LAC operon?

CAP (catabolite activator protein)

18

What are the three genes of the LAC operon?

lacZ
lacY
lacA

19

What does lacZ for?

it makes the beta -galactosidase for converting glucose into galactose

20

What is lacY for?

lactose permease

21

What is lac A for?

transacetylase

22

What does CAP allow for?

use alternative carbon in the absence of glucose

23

What happens in a no lactose condition?

lac repressor is bound
gene is off

24

what happens in a lactose presence condition?

lac repressor is removed

25

What happens when glucose is present?

cAMP is not bound to CAP
LAC operon is off

26

How operators does the LAC operon have?

several operators

27

How many operators can a repressor bind?

two simultaneously
simultaneous binding strengthens overall repression

28

How does one repressor binds to a major and auxiliary operator?

DNA looping

29

What is the gene control region?

regulatory protein binding sequences spread over a large stretch of DNA in eukaryotes

30

How many regulatory proteins does the human genome encode for?

~2000

31

What does eukaryotic cells need to begin trancription?

activator
regulator
gene regulatory proteins

32

What do activators promote?

The assembly of RNA poly and general transcription factors at transcription start point
Activators bind to DNA enhancer sequences

33

What do activators attract to the promoter?

attract and position transcription factors, mediators and RNA poly

34

What do activators also help modify?

chromatin structures (histone modifications, nucleosome remodeling:remova; and replacement)

35

Eukaryotes does repressors compete for binding to DNA binding sites with polymerase?

no

36

What are ways that repressor will block activator?

overlap in binding site
masking activator surface
blocking assembly of transcription factors
recruit remodeling complex (turn chromatin into transcription silence)
recruit deacetylase
recruits methyl transferase

37

What are ways to regulate gene regulator proteins?

protein synthesis
ligand binding
covalent modification
addition of second subunit
unmasking
stimulation of nuclear entry
release from membrane

38

Where is the beta globin gene exclusively expressed at?

red blood cell
on the chromosome as a cluster.

39

What does cluster of globin contain?

embryonic
fetal
adult globin genes
each has its on set of regulatory gens

40

What is a locus controlled region?

long stretch of DNA that controls every gene of the globin gene
located far upstream from gene cluster it controls

41

How do locus controlled regions bring regulatory proteins in proximity of genes it controls?

looping DNA occurs for transcription

42

What does LCR have to prevent the spread of heterochromatin?

barrier sequences

43

What is the difference in gene control in eukaryotes and prokaryotes?

bacteria has one operon that controls many genes
eukaryote genes has their own operator

44

What can turn a switch on and off in eukaryotes?

despite being controlled by a combination of regulatory genes, a single regulatory gene can turn a switch off and on

45

What is methylated in mammal DNA?

Cytosine at CG in DNA
CG in promoters in actively transcribed genes remains unmethylated

46

What methylates the cytosine?

CPG methylase (methyl transferase)

47

When are CG in promoters methylated?

when the promoter is off
turns to nonmethylated when the promoter is on

48

How is cytosine methylated?

into 5-methylcytosine

49

after replication what recognizes the unmethylated C strand?

methylase

50

What recruits the DNA methylase?

histone modyfying reader writer complex

51

What is genomic imprinting?

expression of a gene is depended on if it is inherited from mother or father

52

What is prader-willis syndrome?

maternal imprint

53

What is angelmann syndrome?

paternal imprint

54

What is RNA editing?

changes in RNA after transcription

55

in what was RNA editing first discovered?

trypanosoms -large number of Uracils were incorporated into the gene

56

What inserts Uracils into the RNA in trypanosoms?

guide RNAs
40-80nts long
5` end complementary to region of transcript to be edited

57

What is ADAR?

Adenisine deaminase acting on RNA
they deaminates Adenine to inosine

58

What is the structure for ADAR binding?

as secondary hairpin

59

What edit deaminates C to U apolioprotein B?

intestine cells
liver does not express editing enzyme

60

Why will the deamination of C to U give a truncated apoliproprotein B?

because its last AAs cod e is CAA when C is deaminated to U it gives a premature stop codon UAA

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