Topic 2, Lecture 1 Flashcards
sWhat accounted for the different between a neuron and liver cell?
the function of the cells come from the structure of the protein. later we learned that TF’s can alter the liver to a neuron by just 3 MASTOR REGULATORS ( transcription factors)
What were the differences in the protein expression of two tissues?
each tissue has its own genome
and all tissues have the same genome but different mechanism (time- specific regulation)
Where does regulation happen?
at the transcription level
Remember the examples of the dolly and bonnie
due to genomic equivalence this proves that all cells have the same genome needed to control proteins (transcribed and then made)
What are the important specific protein structure regulation thingys?
tissue-specific
gene-specific
Time-specific
BUT MOST IMPORTANTLY
right protein
right time
right amount
be able to draw out drawing of the gene and +1 site with appropriate labels to help with concepts
DRAW THAT DUDE
Central Dogma
flow of genetic information from DNA to RNA to protein
Regulation at transcription or at translation level?
it is more efficient to regulate at transcription because it is easier and it saves energy
what makes DNA an acid?
phosphodiester bonds (how we regulate gene transcription)
backbone is a (-) charge
how many genes encode, how many proteins?
30,000 genes, 24,000 proteins
what is the complete nucleotide of human genome
3.2x10^9 billion
how many nucleotide pairs are in chromosome 22
48 million
DNA laid end to end is what?
2 meters
Nucleus is what diameter
6um
A protein encoding gene is every
130 meters
an average gene would extend
30 meters
Chromatin is what?
fibrous, nucleoproteins (DNA/Proteins) complexed within the nucleus
what does chromatin consists of?
DNA, histones, Nucleosomes, and non-histone proteins.
It is about 1/3 DNA and 2/3 proteins
Chromosomes are
linear, double-stranded DNA molecule and associated proteins it is highly condensed DNA
DNA double helix is decondensed proteins that form a what? but it is also only transcribed at what length? (beads on a string)
chromosome scaffold
11mm
Chromosomes are formed from? but the way they look is determined by what?
formed from chromatin
look is determined by stage of cell cycle
What is the typical structure of the histone fold?
H2A and H2B form dimer through an intersection called a handshake
How many turns does the DNA helix make around the histone octomer?
1.7 tight turns
Histone tails are
tails that stick out (8) on n- terminus
11-37 AA on n-terminus that extend from nucleosome
Tails can under go what?
MODIFICATIONS
Linker Histone is
the linker that keeps the tails close to the histone core
what are the tails doing?
help like one nucleosome to next nucleosome
beings everything together (paper clip holding paper)
heterochromatin
highly condensed regions of chromosome that stain darkly
transcriptionally inactive
heterochromatin undergoes two stages
facultative
constitutive
facultative
decondensed and go back and forth from hetero to euchromatin
constitutive
stays condensed as hetero and rarely if ever transcribed
euchromatin
light regions
less condensed regions of chromatin
site of gene transcription
If modifying histones to induce heterochromatin what formation must be tightly packed?
histone tails - hetero
specific proteins lock heterochromatin in place, not just a matter of DNA being tightly packed but keeping it condensed to bind to proteins.
What percent open-active chromatin in the cell (housekeeping gene encodes)?
20%
what falls under constitutive heterochromatin?
centromere and telomere
What do the modifications of the tails do to histones?
how tails pack
hetero- tightly condensed
euchromatin- spread out (transcribed)
But what’s the story behind modifications?
histone modification, morphology of nucleus, and degree of transcription
are all apart of the story
Lampbrush
the dark area is the scaffolding, fuzzy loops
Lambrush loops contain how many nucleotide pairs?
50,000 to 200,000 nucleotide pairs
the extended loops are
the active sites of transcription at 11nm
the tight loops are
30nm
nuclear neighborhoods
subcompartments that can accelerate complete sets of chemical reactions
locked on the loop of the 30nm fiber
MOLECULAR GLUE THAT KEEPS WHAT NEEDS TO BE HERE IN PLACE
Why have a gene that would not be transcribed in a nuclear neighborhood? (active or passive approach)
active or passive approach to regulating gene transcription
passive would NOT DO IT
some want ACTIVE
cannot transcribe a gene, so lock it in NUCLEAR NEIGHBORHOODS with heterochromatin
REMEMBER MOLECULAR GLUE
histones include how many nucleosome pairs of DNA
200
50 in between and 150 wrapped
typical diploid human cell contains how many nucleosomes
30 million
small basic portions of histones
H1 H2A H2B H3 H4
how many bonds are btw dna and histone core? and how many of these form between the AA and phosphodiester backbone
142 and 1/2 of these form btw AA and phosphodiester backbone
how many copies of each histone per cell in humans
60 million
