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BIO 1A03 > T3- M3&4 > Flashcards

T3- M3&4 Flashcards

1
Q

What did all cells derive from

A

Fertilized eggs

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2
Q

What determines a cell’s fate

A

Which genes are turned on/off

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3
Q

Why are signals important

A

To control gene expression

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4
Q

Define proteome

A

The complete set of proteins made by an organism

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5
Q

What are transcription factors

A

Proteins which bind to specific DNA sequences

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6
Q

Why are transcription factors essential

A
  • Determine pathway for cell type
  • Work with other proteins that result in gene expression changes
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7
Q

How are transcriptional regulation in prokaryotes and eukaryotes similar

A
  • Both activate and repress transcription
  • both use RNA polymerase to bind to promotors
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8
Q

How are the DNA in eukaryotes and why

A

Highly compact chromatin- easy way to fit DNA in nucleus

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9
Q

What do chromatin do

A

Allow DNA to move around in cell divison

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10
Q

Are genes in tight chromatin expressed?

A

No, need to unwind

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11
Q

What is DNA wrapped around

A

Histone proteins

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12
Q

How many histone proteins does each nucleosome have

A

8 with 150 base pairs

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13
Q

What is chromatin remodelling

A

The rearrangement of chromatin from a condensed state to a transcriptionally accessible state

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14
Q

What is needed for chromatin remodelling

A

Activator protein or transcription factor

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15
Q

How is DNA tightly bound

A

Due to positive tails of histones and negatively charged phosphate in DNA

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16
Q

What is the activator protein recruited for histone modifications

A

Coactivator enzyme histone acetyltransferase

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17
Q

What does coactivator enzyme histone acetyltransferase do

A

Attaches acetyl groups to lysine amino acids along positive tails of nucleosome histone proteins

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18
Q

What happens once positive tails are acetylated

A

Positive charge is reduced and interactions between histones and DNA reduced

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19
Q

What other modifications assist in transcription initiation

A

Methylation of lysine and arginine
Phosphorylaton of serine and theanine

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20
Q

4 types of transcription factor proteins

A
  • include basic helix loop helix
  • helix turn helix
  • zinc finger
  • leucine zipper
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21
Q

What bonds are between alpha helical domains

A

Hydrogen bonds

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22
Q

What is the promotor sequence in eukaryotes

A

TATA box

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23
Q

What is a core promotor

A

A binding site for RNA polymerase and other transcription factors

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24
Q

What is recognized by TATA box

A

TATA binding protein or TBP subunit of transcription factor TF2D

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25
What is the BRE region
Promoter for eukaryotes
26
What is BRE region bound by
TF2B factor
27
What are enhancer regions
Bind cell or region specific transcription factors - facilitates formation of transcriptional complex
28
Where are enhancer sequences in eukaryotes
Distant from promotor
29
What happens once transcriptional components bound
Flexible DNA allows factors and RNA poly to loop
30
What do adaptor or mediator proteins do
Connect enhancer proteins to promotor proteins
31
What are silencer proteins
Bind transcriptional repressors to halt transcription - positioned upstream of target gene
32
What does silencer region activation cause
Interference of general transcription factor assembly and mediator activity
33
What type of cells specialize to hemoglobin
Blood cell progenitors/ stem cells
34
What must happen before progenitor cells differentiate into red blood cells
Transcription of globin proteins
35
What hemoglobin proteins are in both fetus and adults
2 alpha globin proteins
36
What hemoglobin protein is unique to fetus
2 gamma globin proteins
37
What hemoglobin proteins are unique to adults
2 beta globin proteins
38
Why do fetuses need gamma globin proteins
Gamma globin proteins bind more oxygen, allowing the fetus to use it for development in womb
39
What does chromatin of beta globin gene do in fetus
It is tightly wrapped to prevent transcription
40
What does chromatin of beta globin gene do in adult
It is loose to allow transcription
41
What does methylation of nucleotide bases do
Inhibit transcription
42
What is the most common nucleotide modification in DNA
Addition of methyl group to cytosine base
43
What are CpG islands
A string of cytosine and guanine bases where methyl group is added
44
What does p represent in CpG islands
Phosphate group
45
Where are CpG islands located
Near promotors
46
What happens when CpG islands not methylated?
DNA binding proteins recognize promotor and transcription occurs
47
What happens when CpG islands methylated?
Shape of DNA binding site is changed and protein cannot bind- no transcription
48
Define HDAC
Histone Deacetylases - Bind to DNA and promote removal of acetyl group from neighboring proteins
49
What is the purpose of HDAC proteins
Allow nucleosomes to reassemble and mask enhancer and promotor sequences * repress transcription
50
What is the default nature of chromatin in prokaryotes
Default "off"
51
What is the default nature of chromatin in eukaryotes
Default chromatin "on"
52
What does amount of gene product vary upon
- changing conditions - different signals
53
Where can gene expression be regulated
- transcription/ initiation - RNA processing - stability of RNA - Protein synthesis - Protein modification/ transport - Protein degregation
54
Describe In Situ Hybridization
Lab technique used to identify which cells and tissues express gene by undertaking analysis of finding mRNA in organism development
55
How was mRNA detected
Complimentary probe with tag
56
What does complimentary probe have
Fluorescently labelled short, single stranded segment of DNA/RNA which binds complimentary to mRNA
57
Describe DNA microarray
Lab technique where glass slides with known DNA act as probes to detect gene expression in a pattern
58
What can microarrays show
Thousands of genes at once and help visualize variation in gene expression in different cell types
59
What must happen to mRNA to be labelled
Isolated from cell
60
What needs to be made as a template for mRNA
Complementary cDNA molecules using *reverse transcriptase enzyme* - florescent nucleotides used and become part of new cDNA molecule
61
Describe how mRNA from normal and epithelial cells were combined in hybridization
Equal amounts were placed with normal being green and cancer being red
62
How to know if gene is active
Produces a lot of mRNA and lots of cDNA- BRIGHT SPOT
63
What did it mean if the spot was green?
Specific gene is expressed more in normal cells
64
What did yellow spots mean
Gene equally expressed in both
65
What does no brightness mean?
Gene not expressed
66
What must happen to mRNA to stop gene expression
Must be degraded
67
How was poly a tail affect mRNA
Needed for stability
68
Describe miRNA
short, non coding regulatory double stranded molecules which to become part of the silencing complex
69
What does miRNA form
Hairpin loops due to complimentary base pairing
70
What do the miRNA hairpin loops do
Process into single stranded mRNA fragments which activate RNA interference machinery
71
What do miRNA and RISC complex do
Bind to target mRNA sequence for translation miRNA
72
What is siRNA
Small interfering RNA which is associated with RISC complex - exact compliments of mRNA target
73
Purpose of proteasomes
Degrade unneeded or damaged proteins by marking them

BIO 1A03 (10 decks)

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