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all the coding and noncoding regions of DNA that is hetitable
Characteristics of a good genome
- adaptability over evolutionary time, yet stable
What is the relationship between genes and proteins?
25000 genes don't make 25000 proteins.
Due to alternative splicing, we make more due to the ability to splice out different regions.
What was the experiment done to determine that DNA was the genetic material?
Frederick Griffith used smooth and rough strains and injected them nto mice.
Smooth strain produces glycoprotein that it coats self with--> mice die
Rough strain lacks glycoprotein--> mouse lives
Heat-killed S strand and living rough strain--> transformation of R strain--> mice die
groove in the helix that is more spacious, allowing proteins invovled in fixing/ replicating DNA to approach; canning sequences
smaller regions that contains certain dinucleotides that are easy to compress
Why is the base pairing important?
G-C and A-T content are important because there should be more G-C bonds to ensure that there are enough hydrogen bonds to hold the helix together
tells us what the protein sequence will be
Difference between DNA and RNA
T versus U
deoxyribose versus ribose
ds versus ss
forever versus temporary
nucleotide sequence of DNA closely resembling that of a functional gene, but containing numerous mutations that prevent its proper expression; most arise from duplication of a functional gene followed by accumulation of damaging mutations in one copy
what does a gene contain?
coding and uncoding regions (exons and introns, respectively)
regulatory DNA sequences where most proteins land in transcription
What are the three characteristics all chromosomes must have?
telomere: during rep, on one strand of DNA, the machine has difficulty at the end and can't copy to the end of the strand; telomeres cap the strand to maintain the sequence; carried out by telomerase to make sure the telomere is the right length
centromere: place where growing MT can attach to pull the chromosomes apart
origin of replicaiotn: during synthesis, machines need a starting point because its hard to separate DNA due to numerous H bonds; a sequence that tells proteins where to start
What makes up a gene?
- 1) long interspersed nuclear elements
2) short interspersed nuclear elements
3) retroviral like elements
4) DNA only transposon fossils
5) segmental duplications
6) simple sequence repeats
1) introns and protein-coding regions= gene
Not sequenced yet:
What is special about introns?
they have some functionality and contain regulatory sequences or have no assigned function yet
Is it beneficial to have junk?
yes because they have a potential that a new gene can occur
mutations can hit everything, making the probability that important regions would get mutated small
Why are mitotic chromosomes so condensed?
to separate into daughter strands
core particle and one linker DNA
Why is DNA shrunken down?
DNA is too big to fit into nucleus. We increase its mass by adding proteins, which can allow DNA to wrap around them
What experiment determined nucleosomes?
unfolded chromatin was exposed to nucleases, which degraded the linker NA, but not the core histones.
This left the nucleosome, which was placed in a buffer of high salt concentration, causing dissociation of the histone and DNA due to the ionic bonds
Four pairs of histones were found, which made eight subunits
Amino acids in histones are __, which bind to the __.
- positively chared
- negative backbones of DNA
What is similar about the histone structre?
Each of the core histones contains an N-terminal tail, which is subject to several forms of covalent modificaiton, and a histone fold region
subunits interact with each other in a handshake way
fold into a histone fold; shorter alpha helices loop around the center one
about 100 amino acids long
Explain the bending around the histones.
minor groove outside prefers GC because it holds together better
AA, TT, and AT dinucleotides preferred inside because they can be easily compressed
helps regulate angle of DNA to allow control
binds to DNA outside and then binds DNA and puts them together, shrinking them down
What do tails on the histones do?
they stick out and come in contact with adjacent nucleosome
What is a way of control with the nucleosomes?
for efficiency, take cells you don't need and pack them away. The regions that we need will be structured out and more accessible.
A nucleosome can expose the DNA, allowing access by transcription factors
IF there is a transcription factor, it can bind to that piece of DNA and transcribe
Explain the chromatin remodeling complex.
we want to alter the DNA in some way
Using ATP hydrolysis (by subunits), nucleosome sliding occurs
It binds both to the protein core of the nucleosome and to the double-stranded DNA that winds around it. The subnit changes the structure of the nucleosome temporarily, making the DNA less tightly bound to the histone core. By pulling the nucleosome core along the DNA double helix, they make the nucleosomal DNA available to other proteins in the cell. They can remove all or part of the nucleosome core from a nucleosome
Explain the code reader complex.
it will bind tightly only to a region of chromatin that contains several of the different histone marks that it recognizes. Thereofre, only a specific combination of marks will cause the complex to bind to chromatin and attract additional protein that catalyze a biological function
Essentially, it takes a code that has been printed; reads it; and attracts other proteins and commences to write or carry out function
Which protein has the best indication of mutation?