Lecture 3 Flashcards
1
Q
Principles of Gene and Devlopement (Mechanisms of Cell differentiation)
A
- Genomic equivalence
- Selective gene expression
2
Q
All cells contain an identical set of genes
A
Genomic equivalence
3
Q
Different cells activate different genes at different time.
A
Selective gene expression
4
Q
The project that aims to physically map the human genom
A
The Human Genome Project
5
Q
How long and who completes HGP
A
10 year (1998-2003)
Completed by International Human Genome Sequencing Consortium
6
Q
Who led HGP
A
NHGRI (National Human Genome Research Insititute)
Department of Energy
7
Q
First leader of HGP
Nobel Laureate
A
Dr. James Watson
8
Q
Led the HGP since 1993
NHDRI director
A
Dr. Franis S. Collins
9
Q
Total no. of genes in HGP
A
30K
10
Q
The shortest gene (Based on HGP)
A
Histone (500 NT)
11
Q
Large genes (based on HGP)
A
DMD (dystrophin) 2,200 Kb)
12
Q
How many genes does Chromosome 1 have
A
2968 genes
13
Q
How many genes does Chromosome 2 have?
A
231 genes
14
Q
The chromosome associated with Diseases
A
Chromosome 17
15
Q
Structures of Eukaryotic Gene
A
- Promoter
- Cap Sequence
- ATG codon
- Exons
- Introns
- Translation Terminal Codon
- 3’ Untranslated region
16
Q
binding site of RNA polymerase and subsequent initiation of transcription.
A
Promoter Region
17
Q
- Transcription initiation site
- Represents the 5’ end of RNA “cap” sequence vary among genes; necessary for the
binding of mRNA to
ribosomes and its translation
A
Cap Sequence
18
Q
Structure for initiation of translation
A
ATG codon
19
Q
o Intervening sequence between initiation points of transcription & translation
o Determines the rate of translation initation
A
Leader sequence
20
Q
Base pairs coding for a protein
A
Exons
21
Q
- Non-coding sequences interspersed among the exons
- Maybe longer and more numerous than exons
A
Introns
22
Q
- Transcribe but not translated into protein
AATA sequence where a “tail” of adenylate residues (200
300) are added
A
3’ untranslated region
23
Q
Confers stability and
translatability on the
mRNA
A
Poly (A) tail
24
Q
Requirements for RNA to be active protein
A
- Processed into mRNA
- Translocated (from nucleous to cytoplasm)
- Translated
- Post-transtionally modified
25
Two types of regulatory elements
- Cis-regulators
- Trans-regulators
26
Represents specific DNA sequences on a given chromosomes which act only on adjacent genes.
Cis-regulators
27
Where can cis-regulators be found
5',3' ends and introns
28
Types of Cis-regulators
- Promoters
- Enhancers
29
-Required for binding of RNA polymerase and accurate initiation transcription
- Specific the times and places of transcription
Promoters
30
- Activate the utilization of the promoter
- Control the efficiency and rate of transcript
Enhancers
31
Structure of promoter
- TATA sequence
- 30 base pairs
32
Functions of promoter
- Bind RNA polymerase
- Specify places and time the transcription can occur
33
Euk. RNA poly. cannot bind to naked DNA sequence, it needs ____
Additional protein factors
34
Protein encoding genes are transcribe by____ ____ ___
RNA polymerase II
35
- recognized the TATA box through one of its subunits.
- Serves as foundation of the transcription initiation complex, serves to keep nucleosomes from forming in this region.
TFIID
36
TFII binds once stabilized by
TFIID → once stabilized by ___
TFIIA
37
Once TFIIB is in place___ can bind to complex
RNA
38
Once TFIIB allows rna to bind in place =
Other transcription factors are used to release rna polymerase, the transcription start
39
Requirement for Enhancer to function
- DNA sequence
- Primary elements
- Transcription factors
40
Can activate utilization of a promoter in enhancer
DNA sequence
41
responsible for tissue-specific transcription in enhancer
Primary elements
42
Function by binding specific regulatory proteins in ehancer
transcription factors
43
Functions of enhancer
Regulate the temporal and tissue-specific expression
44
- An enzyme that is not found in mammalian
cells
- Can be used as reporter gene
CAT (Chloramphenicol acetyltransferase)
45
Importantance of CAT
- required by genes for transcription
- major determinant of differential transcription
46
the combination of transcription factors that causes particular genes to be transcribed
Modular
47
negative enhancers, can be used to repress the
transcription of other genes.
Silencers
48
- Soluble molecules from one gene and interact with genes on the same
or diff. chromosomes
- W/ sequence specific DNA binding domain
Trans-regulators
49
enables that transcription factor to interact with proteins
trans-activating domain
50
Three major domains of Transcription factor
1. DNA-binding domain
2. Trans-activating domain
3. Protein-protein interaction domain
51
– recognizes a particular DNA sequence
DNA-binding domain
52
53
activate or suppress the transcription of the gene. Enables the transcription factor to interact with proteins involved in binding RNA polymerase
Trans-activating domain
54
allows the transcription factor’s activity to be modulated by TAFs or other transcription factors.
Protein-protein interaction domain
55
Produces serum albumin and liver in fetal mouse
Endodermal cell
56
fetal mouse liver makes serum albumin, but only after ______
certain stage of gut development
57
When is endodermal tube instructed to begin forming liver and specific genes
after contact with cardiac mesoderm in the heart precursors
58
Examples of trans-regulatory factors
1. Homeodomain proteins
2. Zinc finger standard
3. Basic helix-loop helix TF (bHLH)
4. Basic Leucine Zipper (bZip)
5. Nuclear Hormone Receptors
6. Sox-2 TF
59
critical for specifying the anterior-posterior body axes
Homeodomain proteins
60
Example of homeodomain proteins
Hox TF and POU transcription factor
61
region that comprises the homeodomain and the 2nd DNA-binding region
POU domain
62
Pituitary-specific factor that activates the genes encoding GH, prolactin and other pituitary proteins
Pit-1 (GHF1)
63
ubiquitous protein that recognizes a certain eight-basepair sequence (octabox)
oct1
64
B-cell specific factor recognizes a certain 8-base pair sequence called Octa box & activates Ig genes.
Oct2
65
a nematode gene product involved in determining the fates of neurons.
UNC-86
66
has two or more “DNA binding Fingers” helical domains . Zn ions link and stabilize the fingers, coordinated by 2 cysteines and 2 histidines.
Zinc finger standard
67
Example of Zinc Finger standard
WT and Krox 20
68
critical for kidney & gonads development.
WT
69
for hindbrain development
Krox 20
70
binds to DNA via a region of basic AA (10-13 res.). May form a dimer with positive or negative regulators.
Basic Helix-Loop Helix TF (bHLH)
71
Example of Basic Helix-Loop Helix TF (bHLH)
E12 and E 47
72
complexed with Myo D or Id (inhibitor of different) proteins for muscle specificatio
E12 and E47
73
α- helix with several leucine residue that bind with other bZip proteins -> “Leucine
Zipper” dimer.
Basic Leucine Zipper (bZip)
74
Liver differentiation and
adipogenesis
CCAAT
75
mediate the effect of hormones on genes
Nuclear hormone receptors
76
Types of RNA polymerase
RNA Polymerase: I, II and III
77
RNA polymerase transcribes
Large ribosomal RNAs
78
RNA polymerase II transcribes ____
mRNA precursors
79
RNA polymerase III transcribes
5S ribosomal DNA
80
addition of 7-methyl guanylate to the 5‘ end of pre-mRNA.
CAPPING
81
a chain of 150-200 adenylate nucleotide is attached to the 3’ end of the pre-mRNA after transcription.
Polyadenylation
82
removal of non-coding
sequences (introns) from pre-mRNA to produce the mature mRNA.
Splicing
83
Chemical modifications in a gene
DNA Methylation
84
Three areas that DNA methy. can contribute to diff gene activity
a. methylation of promter
b. responsible for distinguishing between egg and sperm derived genes in mammals
c. Continues repression of the gene of one or two X chromosome
85
Where does methylation occurs?
Lysine 9 of histone 3 (H3-K9)
86
How does methylation lowers gene accessability
by closing chromatin structure
87
- chromatin of the inactive X chromosome
- condensed and replicates after most of the chromatin
heterochromatin
88
Condensed, inactive member pair of X chromosome in the cell
The barr body
89
What does mutant X chromos. do to nice embryo?
Ectodermal cell death
Absence of mesoderm formation
Embryonic death
90
removal of acetyl group (H4 of lysine 16)
Deactylation
91
removes the positive charge from histone reducing the force of attraction w/ DNA leading to wider opening of the chromatin
Acetylation of lysine
92
restores the positive charges and promotes close attraction between histone & DNA -> Condensed chromosome
Deactylation
93
200/so adenyl is added to the 3' end
Polyadenylation
94
initiates transcription producing 20-25 NT -5 triphosphorylated transcript.
CTD (carboxyl terminal domain)
95
DNA bending protein that wraps a 60- bp coil of DNA around the transcriptional activators
HMG-1
96
Control of Gene Expression Before Transcription
1. Seletive gene amplification
2. gene arrangement
97
Control of Gene Expression After Transcription
3. Chemical modification
98
affect nucleosome
stability
Chemical modification
99
Selective RNA processing
Posttranscriptional
100
which nuclear transcripts are processed into cytoplasmic messages “Chosen few”
Censorship
101
the same nuclear RNA is spliced into different mRNAs.
hnRNA splicing
102
Also called as RNA interference or RNAi
- process results in down regulation of a gene at the RNA level
Post-transcriptional Gene Silencing
103
Alternative RNA splicing
- Alternative 5' splicing
- Alternative 3' splicing
- intron retention
- mutually exclusive exons
- exon skipping
104
a part of an exon may be included in the splicing at 5’ end.
Alternative 5' splicing
105
part of an exon may be included in the splicing at the 3’ end
Alternative 3' splicing
106
an intron is included in the final mRNA. 2-5% human genes
Intron retention
107
different exons found in 2 different mRNAs.
Mutually exclusive exons
108
Translation control
1. Differential mRNA longevity
2. Selective inhibition of mRNA translation
109
- the longer an mRNA persists, the more protein can be translated from it.
- messenger RNAs can be selectively stabilized
at specific times in specific cells
Differential mRNA longevity
110
length of its poly(A) tail depends upon sequences in the 3´ untranslated qregion
Stability of message
111
Post transcriptional control
- Phosphrylation
- Lipidation
- Glycosylation
- Ubiquitination
- Disulfied bonds
- acetylation
112
adds phosphate to seriene, threonin or tyrosine
Phosphorylation
113
attaches a lipid, such as fatty acid to a protein chain
lipidation
114
adds ubiquitinatin to a lysine residue of a target protein marketing it for destruction
Ubuquitination
115
covalently links the "S" atoms of two different cysteine residues
Disulfied bond
116
Adds acetyle group to the N-terminus of a protein to a increase stability
Acetylation
117
Attaches a sugar, usually to an "N" or "O" atom in an amino acid side chain
Glycosylation
118
genes are active only if derived from paternal
Gene imprinting
