Regulation Of Gene Expression- Exam III Flashcards
All letters in a gene name are:
Italicized
In human genes _____ letters are capitalized and in rodents and other species:
Human genes: all letters capitalized
Other species genes: first letter capitalized
What are the general requirements for gene expression control?
Transcriptional machinery
What are the gene specific requirements for gene expression control? (4)
- Intracellular hormone-receptor complexes
- Intracellular 2nd messengers
- Gene specific (class specific) transcription factors
- Gene regulatory sequences
Activates or increases gene expression
Activator
Activates increases gene expression but requires a buddy system
Coactivators
Transcription factors that decreases gene expression
Repressors
Transcription factor that decreases gene expression but requires buddy system
Corepressors
Islands of CpG dinucleotide sequences to produce 5-meC
DNA methylation
DNA methylation adds a 5 methyl group on the cytosine which causes:
Compaction of DNA into heterochromatin
DNA exists in a highly condensed _____ form.
Nucleosome
Dependent upon if you are looking at the major or minor groove:
Different molecules will be available interact with
A DNA binding protein motif: common in transcription factors and consists of alpha helices bound by a looping stretch of amino acids
Helix-loop helix
A DNA binding protein motif: that has multiple types, but all have a bound zinc metal ion associated with the protein. Some have an alpha helix plus a beta sheet structure, while others have a more helix turn helix structural motif.
Zinc finger motifs
Zinc finger motifs can be ____ or ______.
Monomer or dimers
A DNA binding protein motif: consisting of two alpha helices joined by a short stretch of amino acids.
Helix-turn-helix
A DNA binding protein motif: two proteins each with an alpha helix (formed largely by consecutive leucine residues) form a Y-shaped and coil-coiled structure. It results in both protein and DNA binding.
Leucine Zipper
The majority of DNA binding proteins function as (2)
- Dimers
- Tandem clusters
A particular sequence of amino acids or nucleic acids that has associated with it some type of function- shared sequences
Motif
A motif that is capable of promoting both DNA binding and dimerization of itself.
Leucine zipper
_____ have a specific nucleotide sequences so they can position certain critical nucleotides in the correct groove.
Consensus nuclear response element
In prokaryotes, the repressors and activator binding sites are generally closely juxtaposed to the:
RNA polymerase binding site
In eukaryotes, it’s believed that the DNA regulator sequences can be located at greats distances relative to the _________ of transcription.
Start site
Contains the start site of transcription for many RNA polymerase II genes and binds TFIID
INR
Site located at +30 BP 3’ to the start site and binds TFIID
DPE
Sequence located at -35 5’ of the start site that binds TFIIB
BRE
What does BRE bind?
TFIIB
What does DPE bind?
TFIID
What does INR bind?
TFIID
What does the TATA box bind?
TBP subunit of TFIID
Many DNA proteins have DNA binding activity but may not have:
Transactivating activity
Transactivating activity:
Turns on the expression of a gene
If a DNA protein does not have transactivating activity, they must have:
Another protein paired with them to turn on the gene
When you have a gene activator that binds to chromatin, what occurs next?
Chromatin remodling- to open up
The chromatin remodeling process often involves:
Histone modification enzymes - associated with the nucleosomes
Histone modifications will:
Methylate or demethylate or acetylate or deacetylate to relax the nucleosome structure
Mediators, general transcription factors, and RNA polymerase assemble ______ at the Promotor.
Pre-initiation complex
The autosomes and X-chromosomes are amenable to linkage mapping studies because:
They undergo recombination
The Y-chromosome with the exception of the pseudoautosomal region does:
Not undergo recombination
The most commonly used technology for identifying mutations in genes is:
DNA/RNA sequencing coupled with databases
What allows us to identify causal mutations in those cases where a large family suitable for linkage analysis is not available?
Exome sequencing
Sequencing the entire genome:
Genome sequencing
Only sequencing the bits of information that code for proteins
Exomic sequencing
A means to look at what genes are being expressed inside a cell:
Transcriptomic sequencing or RNA-seq
What allows us to look at DNA methylation, ChIP sequencing, and ribosome profiling?
Epigenomics
OPPG individuals bone density is:
Extremely low
What gene is mutated in the HBM individual?
LRP5
Loss of function mutations give rise to _______, while gain of function mutations give rise to_____
OPPG, and HBM
HBM mutation in LRP5 is due to
A single amino acid change
LRP5 and LRP6 had a role in the ______ pathways
WNT/Beta-catenin signaling pathway
Beta catenin is known to be a ____ so it needs to be tightly regulated
Oncogenic gene
Sclerostin binds LRP5/6 and inhibits:
Wnt/Beta-catenin signaling
Protein that forms a complex with DNA and may or may not have transactivating ability:
DNA binding protein
DNA sequence that modulates transcription in and orientation and location independent fashion
Enhancer
DNA sequence or Promotor that serves to bind transcriptional regulatory proteins
Nuclear response element
Transcription factors that bind DNA, “read” the DNA sequence based upon interaction between specific ____ in their DNA binding motif, and ______ that are present in the major and minor grooves of the DNA.
Amino acids; proton donors/acceptors
Different types of DNA binding proteins use different types of _______ structure motifs to interact with the major and minor grooves of DNA
Secondary/tertiary
