BCH 453 Exam 2 Practice
0.0(0)
Studied by 0 people
Call Kai
Learn
Practice Test
Spaced Repetition
Match
Flashcards
Knowt PlayCard Sorting
1/143
Earn XP
Description and Tags
Last updated 1:23 PM on 3/7/23
Name | Mastery | Learn | Test | Matching | Spaced | Call with Kai |
|---|
No analytics yet
Send a link to your students to track their progress
144 Terms
1
New cards
What does non-specific mean?
Protein recognizing any piece of DNA
2
New cards
What does specific mean?
Protein recognizing only a specific piece of DNA
3
New cards
What do you want the polymerase to be?
Non-specific
4
New cards
What is an example of non-specific DNA binding?
When DNA needs to be in a denatured state
5
New cards
What contains OB fold?
Non-specific binding
6
New cards
What type of binding is a gradient?
Specific
7
New cards
How many binding proteins are site specific?
2400
8
New cards
Which groove are most site specific proteins inserted in?
Major
9
New cards
What is an example of cis?
Sequence on DNA
10
New cards
What is an example of trans?
Amino acids
11
New cards
Palindromic
Binding of dimers
12
New cards
Repetitive
Binding of higher order multimers
13
New cards
Bridging
Chromatin compaction and transcriptional regulation
14
New cards
DNA Looping
interactions between recognition sites
15
New cards
What are the two domains of trans factors?
DNA binding and trans activation
16
New cards
\
Which groove is larger?
Which groove is larger?
Major
17
New cards
What groove can fit alpha helix and beta sheets?
Major
18
New cards
What has a function of bending the DNA?
Minor groove
19
New cards
Where do proteins have less space for binding?
Minor groove
20
New cards
What is biochemical definition of a gene?
Region of DNA that is transcribed into RNA
21
New cards
When a gene is encoded, it is highly _____
Regulated
22
New cards
RNA Polymerase
Makes RNA copy
23
New cards
Template DNA
DNA that gets copied and serves as an outline
24
New cards
Nucleotides
Put the DNA together
25
New cards
Regulatory Factors
To make sure the gene and location are correct
26
New cards
What is the transcription start site?
\+1 site
27
New cards
Nontemplate Strand
Sense strand coding strand
28
New cards
Which direction does DNA get copied?
Left to right
29
New cards
Where is the -10/-35 region located from the start site?
Upstream
30
New cards
Where is the +5 region located from the start site?
Downstream
31
New cards
How are nucleic acids synthesized?
5’ to 3’
32
New cards
What is needed as the point of attachment in transcription?
Hydroxyl group
33
New cards
What direction is the template strand read in?
3’ to 5’
34
New cards
Pyrophosphate
Provides energy to fuel a reaction
35
New cards
Pyrophosphatase
Assures stability of all DNA generated
36
New cards
What results in a positive delta G?
Hydrolysis of one phosphoric anhydride
37
New cards
What results in a negative delta G?
Hydrolysis of pyrophosphate
38
New cards
What is the purpose of EMSA?
To tell us whether a DNA binds or not
39
New cards
What does EMSA look for?
Mobility shift
40
New cards
What must be done to DNA before using in EMSA?
To be radio labeled
41
New cards
What happens in 5’-end-labeling?
Phosphate group is removed and replaced with a radioactive version
42
New cards
What is used to remove gamma phosphate group?
Alkaline Phosphatase
43
New cards
What transfers the gamma 32P?
Polynucleotide Kinase
44
New cards
How does Ethidium Bromide make DNA visible?
By intercalating with the double strand
45
New cards
What is the first step of EMSA?
Label target DNA
46
New cards
What is the second step of EMSA?
Incubate hot probe with protein of interest
47
New cards
What is the third step of EMSA?
Run samples on gel with control samples
48
New cards
What kind of gel is used in EMSA?
Native
49
New cards
What is the fourth step of EMSA?
Dry gel and expose to film
50
New cards
What does EMSA Analysis conclude?
If an interaction exists
51
New cards
Protein can bind to either cold or hot #1 probes means there is?
Competition
52
New cards
Protein cannot bind to unrelated cold #2 probe means there is?
No competition
53
New cards
What does competition EMSA conclude?
There is a specific interaction
54
New cards
What is super shifting EMSA used for?
To identity the exact protein
55
New cards
Does DNA migrate slower or faster if interacting with a protein?
Slower
56
New cards
What is footprinting used for?
To identify where the protein reacts in the DNA
57
New cards
What type of footprinting uses DNase I?
Enzymatic W
58
New cards
What type of footprinting uses DMS?
Chemical
59
New cards
What is the first step of footprinting?
Label DNA
60
New cards
What is the second step of footprinting?
Incubate DNA with protein
61
New cards
What is the third step of footprinting?
Incubate DNA with something that will chop it
62
New cards
What is the fourth step of footprinting?
Look at regions of footprint
63
New cards
What does enzymatic footprinting do?
Gives a large gross picture of protein/DNA interaction region
64
New cards
What does chemical footprinting do?
Gives a very fine resolution of protein/DNA interaction region
65
New cards
DNase I
Cleaves DNA at phosphodiester bonds or near a pyrimidine
66
New cards
Which is a larger protein, DNase I or DMS?
DNase I
67
New cards
What type of gel is used to see footprinting results?
Denaturing polyacrylamide gel
68
New cards
What are the two primary types of gel?
Native and denaturing
69
New cards
What are the secondary types of gel?
Agarose and polyacrylamide
70
New cards
Why might DNase I footprinting have negative numbers?
It is after the +1 site and downstream
71
New cards
What is the first step of DMS footprinting?
Expose DNA to methylation by DMS to modify the G residues (with/without protein)
72
New cards
What is the second step of DMS footprinting?
Purify DNA away from protein
73
New cards
What is the third step of DMS footprinting?
Cleave DNA backbone with hot alkali and run on sequencing gel
74
New cards
What is the fourth step of DMS footprinting?
Compare G band intensity in samples with/without the protein
75
New cards
Where do decreased DMS cleavages happen?
\-6, -14, -32
76
New cards
Where do enhanced DMS cleavages happen?
\-2, -34, -37
77
New cards
What is Modification Interference Method (MIM) used for?
To identify which nucleotide residues are required for contact with the protein
78
New cards
What question does MIM ask?
If I mess with the DNA, can I prevent the protein from binding?
79
New cards
Where will modified residues show up?
In unbound fractions
80
New cards
What is the first step of MIM?
Label DNA
81
New cards
What is the second step of MIM?
Modify 32P DNA with DMS on N7 of guanine
82
New cards
What is the third step of MIM?
Incubate DNA with protein
83
New cards
What is the fourth step of MIM?
Run on native gel and isolate bound and unbound complexes
84
New cards
What is the fifth step of MIM?
Purify DNA and cleave with hot alkali
85
New cards
What is the sixth step of MIM?
Run cleavage products on denaturing polyacrylamide gel
86
New cards
What is the seventh step of MIM?
Compare G residues in minus and plus protein lanes
87
New cards
When to use polyacrylamide gel?
When looking at nucleotides (DNA)
88
New cards
When to use agarose gel?
When looking at proteinsW
89
New cards
What is denaturing polyacrylamide gel based on?
Size
90
New cards
What does Alanine Screening Substitution answer?
Which region of the protein is binding to the DNA or RNA?
91
New cards
What does NMR DNA Analysis answer?
What is the detailed structure of the complex?
92
New cards
Function of small nuclear RNAs
RNA processing
93
New cards
Function of small nucleolar RNAs
Methylate rRNA
94
New cards
Trans Acting Factors
Anything not in the same molecule
95
New cards
Cis Acting Factors
Like nucleic acids
96
New cards
What does DNA dependent RNA polymerase (DdRp) do?
Initiates making nucleic acids W
97
New cards
Which is an example of Trans acting factors?
DNA binding proteins
98
New cards
Which is an example of Cis acting factors?
Promoter
99
New cards
How many polymerases do prokaryotes have?
1
100
New cards
How many polymerases do eukaryotes have?
3
Note 
Flashcards (34)