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DNA makes a template for...
chromosomes replicated into a pair of sister chromatids
when is DNA distinguishable/condensed?
G1, S, G2
What phases are in interphase?
What phase are cells in most of the time?
What is S phase
chromosome easily visualized because it is in most condensed state
region on chromosome that allows for separation of sister chromatids (usually in the middle)
complex of proteins that form at the centromere that attach the chromosome to the mitotic spindle, allowing them to be pulled apart
location on DNA where replication begins
How many replication origins do prokaryotes have
more than 1
how many replication origins do eukaryotes have?
ends of a chromosome where it contains repeated nucleotide sequences.
they get shorter
What happens to the telomeres as cells keep dividing over time?
histones and non-histone proteins
two classes of proteins that bind DNA to form the chromosome
made up of histones, non-histone chromosomal proteins, and nuclear DNA
what is responsible for the nucleosome
histones are wrapped in what usually?
2 of H2A, H2B, H3, H4
What are histones made up of
When do histones assemble into nucleosomes?
2 proteins come together
lysine or arginine
more than 1/5 of amino acids on core histones are...
The positive charge of the histone does what to the negative charge of the backbone?
dependent on presence of tightly bound proteins to DNA
Dependent on ATP-dependent chromatin remodeling complexes
linker histone that allows for compacting nucleosomal DNA
N terminal histone tails
acetylation of lysines.
mono, di, trimethylation of lysines
exposed with amino acid and can be modifies with acetylation and methylation
histone acetyl transferase (HATs) add acetyl groups to lysines
trimethylation of Histone H3 attracts heterochromatin protein HP 1 and contributes to the spread of heterochromatin
covalent modifications that can determine multiple outcomes
recognizes particular of markings on chromatin which attracts additional proteins (what needs to be added)
variety of proteins that bind histones
cooperate with chromatin remodeling complexes
remove certain dimers from nucleosome
the N terminal tails can be...
Acetylation (Histone acetyl transferase)
what is looser association and removes the positive charge on the lysine.
methylation (Histone methyl transferase
what condenses the chromatin structure where the DNA cannot be replicated
what has more methylation: parent or new strand?
looser so that it can be used for DNA replication
tightly condensed chromatin that cannot be used for DNA replication
what does cancer turn off with methylation?
each daughter strand inherits original and one new strand
What is used to add a nucleotide because it can also give energy off?
what is the primase made up of to add to the primer strand?
5' to 3' (the leading strand has to be 3' to 5')
what way does DNA polymerase synthesize?
synthesis in the 5 to 3 direction and then joined together after synthesis
1 mistake is every how many nucleotides?
what enzyme proofreads before the new nucleotide is added? (correct nucleotides are energetically favorable)
What occurs when incorrect nucleotide is added that has difficulty extending off improperly based paired 3 OH end?
opens the replication fork hydrolyze ATP when bound to single strands of DNA
single stranded binding proteins (SSBs)
binds tightly and expose single strand DN without covering the bases; aid helicases by stabilizing the unwound single strand conformation; mainly used in the lagging strand
DNA polymerase I
what takes off RNA primer?
what is synthesized by DNA primase?
joins the DNA fragment ends in the lagging strand
PCNA sliding clamp
keeps DNA polymerase firmly on DNA when moving but releases as soon as the polymerase runs into double stranded DNA; a ring around DNA polymerase
protein complex responsible for assembly of the clamp, requires ATP hydrolysis
primer is essential for what?
okazaki fragments are made up of what?
origin recognition complex (ORC)
multisubunit initiator of protein that binds to a minimal DNA sequence required for directing DNA replication initiation
phosphorylate helicases that activates replication but when phoshphorylates ORC it is not able to accept new helicase
replicates the ends of chromosomes; stabilizes the end of the chromosome
contain tandem repeats of short sequences (GGGTTA) and at the end of the chromosome
put nicks to release tension in the DNA and then puts them back together; prevents tangling during replication
produces transient single strand breaks; break allows two sections of DNA helix on either side of the nick to rotate freely
associates with both strands at the same time; forms covalent linkage to both strands of the DNA HELIX AT THE SAME TIME
strand directed mismatch repair
detects the potential for distortion in the DNA helix from the misfit between non-complementary base pairs
create permanent mutation
what would happen if there was a change in a nucleotide in the template strand?
nicks/ single strand breaks
newly synthesized lagging strand DNA contains....
after DNA replication
when does the repair of DNA occur?
MutS and MutL
what two proteins scan DNA to detect nicks in the new strand?
recognizes a specific type of altered base DNA and catalyze its hydrolytic removal
AP endonuclease and phosphodiesterase
enzymes tat recognize the blank space in a DNA strand
nucleotide excision repair
can repair damage cause by large change in the structure of DNA double helix
ionizing radiation, replication errors, oxidizing agents, radicals
how can double strand breaks occur on DNA?
nonhomologous end joining (NHEJ)
-broken ends are rejoined by DNA ligation (lose portions of chromosome)
loss of nucleotides -quick and dirty solution
exchange of DNA strands between a pair of homologous duplex DNA sequences
can repair double stranded breaks accurately without loss or alternation of nucleotides at site of repair
looks at other chromosome, scan to recognize what portion is missing or similar
does homologous recombination lose diversity?
ATM/ATR kinase protein
transducing DNA damage signals to checkpoint control proteins
kinase and phosphatase
what two enzymes help regulate the cell cycle
what is between M and S?
what is between S and M?
gap phases (G1 and G2)
allows time for growth of the cell
resting state of no replication
can use DNA binding fluorescent dyes: reveals condensation of chromosomes in mitosis
antibodies against microtubules
artificial thymidine analog
can incorporate into DNA during DNA replication