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Flashcards in finals - DNA binding proteins Deck (82):
1

_____ Gene regulatory proteins that recognize and bind to specific DNA sequences and either promote or inhibit gene transcription by RNA pol

DNA-Binding Proteins

2

____ the two domains of DNA binding proteins

DNA binding domain and Transcription activation (inhibition) domains

3

(T/F) Surface of proteins are exactly complementary to surface topography of recognized DNA sequence

true

4

which of the ff is not an interaction made between DNA binding proteins and DNA?
a. ionic bonds
b. covalent bonds
c. hydrogen bonds
d. hydrophobic interactions

B

5

(T/F) each of the protein- DNA binding is strong

false

Each protein-DNA interaction is weak but typical DNA-binding protein subunit forms about 20 contacts with DNA to generate tight interaction

6

___ The protein motifs that mediate DNA-binding on the major groove

αhelices or βpleated sheets

7

which of the ff is not a major DNA-binding motif?
a. Helix-turn-helix (HTH)
b. Carboxy-terminal portion
c. Zinc fingers
d. Leucine zipper

B

this is part of HTH

8

which of the ff does not apply to helix-turn-helix?
a. 2 αhelices is connected by lysine in its β turn region
b. Each α helical region spans about 8 amino acids separated by 3.4 amino acid β turn
c. The amino acids of HTH motifs tend to be highly conserved among different HTH proteins
d. Found in hundreds of DNA-binding proteins in prokaryotes and eukaryotes

A

glycine is in the turn coz its small

9

_____ the HTH recognition helix that regulates
sequence-specific binding of protein to DNA and fits into the major groove

Carboxy-terminal portion

10

______ helps align or position recognition HTH along DNA

N-terminal helix

11

*(T/F) HTH proteins are typically polymers

false

are dimers

12

(T/F) regions of proteins outside HTH motif can vary considerably in structure (sequence) among different proteins and each may also contact the DNA to modulate the interaction

true

13

(T/F) binding region on DNA for each recognition helix of each member of the dimer is separated by exactly two turn of DNA helix

false

by one turn only! one turn = 3.4nm

14

which of the ff does not apply to the DNA binding by dimeric proteins?
a. recognition helices of the dimer bind symmetrically to symmetrical DNA sequences
b. each monomer forms nearly identical contacts with the DNA region
c. symmetrical interactions significantly increases the binding affinity of the proteins for the DNA
d. none of the above

D. all applies :)

15

(T/F) zinc finger motifs and HTHs contain amino acids plus zinc ions

false

this only applies to Zn finger motifs

16

which of the ff does not apply to Zn finger motifs?
a. exists as a monomer
b. can exist in clusters of direct repeats
c. Zinc ions coordinate two cysteine and two histidine residues at base of a 12 amino acid loop
d. zinc holds together an α helix and a β sheet (secondary structure)

A

either in clusters (multiple fingers) or dimeric

17

_____ example of molecules that have multiple Zn finger repeats

Transcription factor for RNA pol lll, TFlllA,

18

which of the ff does not apply to multiple zinc finger proteins?
a. Zinc fingers follow one another along the major groove
b. Multiple repeats mediates strong and specific binding to DNA
c. Number of zinc finger repeats are similar among different proteins
d. Provides a mechanism for cells to regulate the strength of DNA binding
among different transcription factors

C

it VARIES among diff proteins

19

*(T/F) Arginine and histidine residues in multiple Zince fingers form hydrogen bonds with guanine bases

true

20

(T/F) β-pleated sheet regions of zinc fingers mediate binding to major groove of the DNA

false

this is done by alpha helices

21

(T/F) zinc finger repeats varies among different proteins but zinc fingers have similar amino acid sequences and contact DNA bases in similar ways

true

22

*_____ the aa that is commonly iinvolved in the DNA-multiple zinc protein binding Interactions

arginine

23

*(T/F) DNA-protein interaction occurs between arginine of a DNA-binding protein and guanine in DNA which has a specific arrangement of hydrogen-bond acceptors that is
unambiguously recognized by the side chain of arginine in the major groove

true

24

(T/F) Dimeric zinc finger proteins are mostly of extracellular receptors

false

intracellular

25

(T/F) Each monomer forms a structure similar to that of HTH motif except it has two α helices that are held together by a zinc ion

true

26

which of the ff is not true about dimeric zinc proteins?
a. both α helices interacts with major groove
b. structure is similar to HTH proteins
c. are intracellular receptors
d. its helices are held together by zinc ions

A

only ONE of the two helices interact w/ major groove

27

____ is the third major type of DNA binding motif

Basic Region-Leucine Zipper Motif

(BRLZM)

28

which of the ff is not true about BRLZ motif?
a. has arginine
b. leucine residues every 6th position
c. has histidine
d. has lysine

B

leucine residues every seventh position

29

______ the basic aa that BRZL motif contains

Lys, arg, his

30

___ # of aa every one turn of α helix

3.6 aa

31

(T/F) all lysine residues in BRLZ motif line up on one side of α helix

false

all LEUCINE

32

which of the ff is not true about BRLZ motif?
a. can be homo or heterodimeric
b. leucine residues mediate hydrophobic interactions between monomers
c. leucines hold monomers together at one end
d. one side interacts with phosphate groups in the major groove

all is true

33

(T/F) Basic residues at other end form electrostatic interactions with the
phosphate groups of the DNA backbone and permit interactions between the side chains of amino acids with the major groove

true

34

(T/F) Some transcription factors also use β sheet structure to recognize information on the surface of the major groove

true

35

_____ Regulates genes encoding enzymes involved in methionine synthesis in bacteria by binding to dimeric repressor and alters its conformation so that it can associate with DNA and shut off genes involved in met synthesis

met repressor

36

which of the ff is not true about mRNA processing in eukaryotes vs prokaryotes?
a. both mRNA are spliced to remove introns from exons
b. only euk mRNA have 5’ cap and 3’ polyadenylation
c. prok mRNA is polycistronic
d. euk have the ability to synthesize several proteins from same gene

A

splicing is only in eukaryotes

no introns in prokaryotes

37

(T/F) both eukaryotes and prokaryotes have mRNA transcripts that are covalently modified at both ends that allows cell to determine whether both ends of mRNA are intact for export out of nucleus and into cytoplasm

false

this only applies to eukaryotes.

mRNA end in prokaryotes not modified

38

(T/F) in eukaryotic mRNA, 5’ end modified by addition of a 7'-methylguanosine cap while the 3’ end is modified by addition of a poly A tail

true

39

____ the process where eukaryotes can produce multiple proteins from same gene

alternative splicing

40

(T/F) the C- terminal
domain of RNA pol ll must be first phosphorylated before it can shed most of the general transcription factors and begin transcription of mRNA

true

41

which of the ff is not true about the mRNA pol II in humans?
a. has aa repeats that contain two serine residues that can be phosphorylated
b. a total of 104 negatively charged phosphate
groups can be produced
c. phosphorylation both dissociates proteins of the initiation complex and allows a new set of proteins to bind
d. Enzymes jump from nascent RNA transcript to tail of enzyme

D

from enzyme tail to RNA = transcribes and processes the new RNA transcript at same time

42

(T/F) 5’ end of RNA transcript is modified by addition of a modified guanine nucleotide after about 25 ribonucleotides have been added

true

43

(T/F) the final mature cap consists of a guanylate (GMP) residue that is methylated at the N7
position and bound to the adjacent residue by a reverse 5’-5’ triphosphate linkage

true

not the regular 5’ to 3’ phosphodiester linkage

44

____ the methylated regions in eukaryotic mRNA

the 2’-hydroxyl group of first 2 ribonucleotides

45

_____ the term for the methylated ribonucleotides and presence of the
7-methylguanosine cap in eukaryotic mRNA

2’-O-methylribosyl groups

46

which of the ff is not a function of 7-Methylguanosine mRNA cap?
a. marks 3’ end of mRNA
b. helps to distinguish mRNA’s from other types of
RNA’s in the cell
c. protects the mRNA from degradation by exonucleases
d. functions in the processing, exporting, and translation of the mRNA in
the cytosol

A

marks 5' end

47

______ a group of proteins that bind the 7-Methylguanosine mRNA cap in the nucleus

cap-binding complex (CBC)

48

____ are eukaryotic genes that contain both introns and exons

split genes

49

(T/F) both introns and exons are present in initial mRNA transcript but only exons occur in final mRNA products

true

50

_____ process by which introns are removed from the mRNA product

mRNA splicing

51

(T/F) RNA splicing applies to all types of RNA

false

primarily restricted to production of mRNA

52

____mRNA which has not been spliced

precursor-mRNA or pre-mRNA

53

(T/F) only after 5’ and 3’ processing and splicing has occurred is RNA product
referred to as mRNA

true

54

(T/F) both initial pre-mRNA and mature mRNA transcript contains introns and 5’ and 3’ untranslated regions

false

mature mRNA = exons only & 5’ and 3’ ends modified with a 7-methylguanosine and poly-A tail

55

which of the ff is not an advantage of RNA splicing?
a. facilitate the evolution of new proteins by recombination with new set of exons
b. permits a single gene to encode multiple proteins by alternative splicing of different exons
c. produce protein isoforms with varying regulatory and specialized functions
d. yield different protein encoding mRNAs (60% of genes)

C

isoforms of related but specialized functions

56

_____ the molecular machinery about a size of a ribosome that splices out introns, consists of complex of 5 other RNAs and over 50 proteins

spliceosome

57

which of the ff does not apply to mRNA spliceosome?
a. hydrolyzed ATP per splicing event
b. can recognize and manipulate only one type of intron at a time
c. ensure accuracy of splicing
d. prevent defective splicing

B

on all types of introns!

58

(T/F) in RNA splicing, the 2’ OH of a specific adenine in intron sequence attacks and cuts phosophodiester bond at the 5’ splice site

true

59

(T/F) in RNA splicing, the cut 5’ end of the intron becomes linked to the adenine to form loop structure at the “branch site”

true

60

(T/F) in RNA splicing, the released 5 ‘OH end of exon sequence reacts with 3’ end of adjacent exon to join the two exons and release lariat-shaped intron

true

61

(T/F) spliced introns are recycled

false

are degraded

62

(T/F) the mRNA splice sites are marked by poly-A sequences the the 3' end of introns

false

introns have GU at 5’end and AG at 3’ end

63

____ the conserved sequence at the branch site at base of intron loop

PyNPyPuAPy

64

(T/F) Branch site typically occurs 18 to 40 bases upstream from 3’ splice site

true

65

(T/F) RNA splicing is performed primarily by proteins

false

by short RNA molecules (snRNAs)

66

which of the ff is false about the snRNAs of the spliceosome?
a. 100 to 200 nucleotides long
b. Recognize intron-exon
borders and intron branch sites through complementary base pairing
c. has high content of uridine residues
d. snRNA is complexed with at least 7 different proteins to form BBPs

D

forms snRNPS

67

which of the ff is not a component of the spliceosome?
a. U7 snRNA
b. snRNPS forms the core
c. U2AF protein
d. branch-point binding protein (BBP)

A

there's no such thing :)

68

which of the ff does not apply to the spliceosome?
a. recognize splicing consensus sequences on premRNA
b. bring the two ends of intron together
c. catalyze splicing reactions
d. none of the above

D

all applies :)

69

____ a fatal autoimmune disease frequently caused by generation of
autoantibodies against proteins associated with U1 snRNP. Onset is often in late adolescence/early adulthood and causes rash on cheeks and forehead

Systemic Lupus Erythematosus

70

___ & ___ recognize the branch-point site of introns during the splicing reaction

BBP and U2AF protein

71

(T/F) during the splicing reaction, U2 snRNP displaces BBP and U2AF and the U1 snRNP binds to the 5’ splice site through complementary base pairing

true

72

(T/F) the splicing mechanisms and arrangements of snRNPs are independent of ATP

false

73

(T/F) introns and exons both tend to be uniform in size

false

introns vary, exons are uniform in size

74

(T/F) Binding of serine and arginine rich proteins to exons of the nascent RNA molecules regulate selection of splice sites by
spliceosomes

true

75

(T/F) association of spliceosome components with the RNA as it is synthesized regulate selection of splice sites by
spliceosomes

true

76

which of the ff does not apply to splice-site selection of spliceosome?
a. Assembly of spliceosome begins as soon as 5’ end of premRNA emerges from Pol ll
b. Spliceosome components are bound to phosphorylated N- terminal
tail of Pol ll
c. By binding 5’ splice site as it is synthesized splicing apparatus may be able to
keep track of the very next splice site (3' end of same intron)
d. spliceosome assembly may occur during transcription but splicing occurs post transcription

B

bound to C-terminal

77

_____ are components of spliceosomes that assemble on exon sequences and mark off 5’ and 3’ splice sites of each intron/exon border which enhances fidelity of splicing mechanism

SR proteins (serine and arginine rich)

78

which of the ff is not true?
a. SR proteins mark exons
b. hnRNP proteins preferentially bind introns
c. U1 snRNP at 5’ splice site
d. U3 snRNP at 3’ splice site

D

U2 snRNP at 3' site

79

____ is the complex where long introns are packaged. This facilitate the ability of splicesomes to differentiate
introns from exons and are larger than nucleosomes

heterogeneneous nuclear
ribonucleoprotein (hnRNP) complexes

80

___ introns that catalyze removal of their own introns without help of proteins or any other RNAs

Self- Splicing Introns

81

_____ RNA molecules that are capable of catalyzing their own chemical reactions

ribozymes

82

____ discovered the first ribozyme - The self-splicing pre-rRNA of the ciliate Tetrahymena

Thomas Cech