Chapter 4 Ppt

all the coding and noncoding regions of DNA that is hetitable

• fixing 
• regulation
• adaptability over evolutionary time, yet stable 
• reproductivity

25000 genes don't make 25000 proteins. 

Due to alternative splicing, we make more due to the ability to splice out different regions.

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

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

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

coding and uncoding regions (exons and introns, respectively) 

UTRs

regulatory DNA sequences where most proteins land in transcription

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

• Repeats:
• 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

Unique:

1) introns and protein-coding regions= gene

Not sequenced yet: 

1) heterochromatin

they have some functionality and contain regulatory sequences or have no assigned function yet

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

to separate into daughter strands

core particle and one linker DNA

DNA is too big to fit into nucleus. We increase its mass by adding proteins, which can allow DNA to wrap around them

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

• positively chared
• negative backbones of DNA

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

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

they stick out and come in contact with adjacent nucleosome

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

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

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

fibrinopeptides