chromosomes replicated into a pair of sister chromatids
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M phase
when is DNA distinguishable/condensed?
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G1, S, G2
What phases are in interphase?
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interphase
What phase are cells in most of the time?
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DNA synthesis
What is S phase
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miotic chromosome
chromosome easily visualized because it is in most condensed state
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centromere
region on chromosome that allows for separation of sister chromatids (usually in the middle)
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kinetochore
complex of proteins that form at the centromere that attach the chromosome to the mitotic spindle, allowing them to be pulled apart
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replication origin
location on DNA where replication begins
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1
How many replication origins do prokaryotes have
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more than 1
how many replication origins do eukaryotes have?
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telomere
ends of a chromosome where it contains repeated nucleotide sequences.
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they get shorter
What happens to the telomeres as cells keep dividing over time?
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histones and non-histone proteins
two classes of proteins that bind DNA to form the chromosome
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chromatin
made up of histones, non-histone chromosomal proteins, and nuclear DNA
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histones
what is responsible for the nucleosome
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DNA
histones are wrapped in what usually?
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2 of H2A, H2B, H3, H4
What are histones made up of
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S phase
When do histones assemble into nucleosomes?
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dimer
2 proteins come together
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lysine or arginine
more than 1/5 of amino acids on core histones are...
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neutralize
The positive charge of the histone does what to the negative charge of the backbone?
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nucelosome positioning
1. dependent on presence of tightly bound proteins to DNA 2. Dependent on ATP-dependent chromatin remodeling complexes
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H1
linker histone that allows for compacting nucleosomal DNA
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N terminal histone tails
1. acetylation of lysines. 2. mono, di, trimethylation of lysines 3. phoshphorylation serines 4. exposed with amino acid and can be modifies with acetylation and methylation
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acetylation
histone acetyl transferase (HATs) add acetyl groups to lysines
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methylation
trimethylation of Histone H3 attracts heterochromatin protein HP 1 and contributes to the spread of heterochromatin
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histone code
covalent modifications that can determine multiple outcomes
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reader complex
recognizes particular of markings on chromatin which attracts additional proteins (what needs to be added)
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histone chaperones
variety of proteins that bind histones - cooperate with chromatin remodeling complexes - remove certain dimers from nucleosome
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covalently modified
the N terminal tails can be...
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Acetylation (Histone acetyl transferase)
what is looser association and removes the positive charge on the lysine.
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methylation (Histone methyl transferase
what condenses the chromatin structure where the DNA cannot be replicated
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parent
what has more methylation: parent or new strand?
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euchromatin
looser so that it can be used for DNA replication
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heterochromatin
tightly condensed chromatin that cannot be used for DNA replication
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tumor-suppressing gene
what does cancer turn off with methylation?
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semiconservative
each daughter strand inherits original and one new strand
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deoxyribonucleoside triphosphate
What is used to add a nucleotide because it can also give energy off?
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RNA
what is the primase made up of to add to the primer strand?
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5' to 3' (the leading strand has to be 3' to 5')
what way does DNA polymerase synthesize?
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okazaki fragments
synthesis in the 5 to 3 direction and then joined together after synthesis
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10^7
1 mistake is every how many nucleotides?
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DNA polymerase
what enzyme proofreads before the new nucleotide is added? (correct nucleotides are energetically favorable)
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exonucleolytic proofreading
What occurs when incorrect nucleotide is added that has difficulty extending off improperly based paired 3 OH end?
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DNA helicase
opens the replication fork hydrolyze ATP when bound to single strands of DNA
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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
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DNA polymerase I
what takes off RNA primer?
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RNA primer
what is synthesized by DNA primase?
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DNA ligase
joins the DNA fragment ends in the lagging strand
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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
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clamp loader
protein complex responsible for assembly of the clamp, requires ATP hydrolysis
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DNA polymerase
primer is essential for what?
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DNA
okazaki fragments are made up of what?
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origin recognition complex (ORC)
multisubunit initiator of protein that binds to a minimal DNA sequence required for directing DNA replication initiation
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protein kinase
phosphorylate helicases that activates replication but when phoshphorylates ORC it is not able to accept new helicase
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telomerase
replicates the ends of chromosomes; stabilizes the end of the chromosome
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telomeres
contain tandem repeats of short sequences (GGGTTA) and at the end of the chromosome
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DNA topoisomerases
put nicks to release tension in the DNA and then puts them back together; prevents tangling during replication
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topoisomerase I
produces transient single strand breaks; break allows two sections of DNA helix on either side of the nick to rotate freely
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topoisomerase II
associates with both strands at the same time; forms covalent linkage to both strands of the DNA HELIX AT THE SAME TIME
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strand directed mismatch repair
detects the potential for distortion in the DNA helix from the misfit between non-complementary base pairs
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create permanent mutation
what would happen if there was a change in a nucleotide in the template strand?
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nicks/ single strand breaks
newly synthesized lagging strand DNA contains....
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after DNA replication
when does the repair of DNA occur?
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MutS and MutL
what two proteins scan DNA to detect nicks in the new strand?
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DNA glycosylase
recognizes a specific type of altered base DNA and catalyze its hydrolytic removal
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AP endonuclease and phosphodiesterase
enzymes tat recognize the blank space in a DNA strand
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nucleotide excision repair
can repair damage cause by large change in the structure of DNA double helix
-broken ends are rejoined by DNA ligation (lose portions of chromosome) - loss of nucleotides -quick and dirty solution
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homologous recombination
- 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
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yes
does homologous recombination lose diversity?
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ATM/ATR kinase protein
transducing DNA damage signals to checkpoint control proteins
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kinase
phosphorylates
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phosphatase
de-phosphorylates
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kinase and phosphatase
what two enzymes help regulate the cell cycle
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G1
what is between M and S?
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G2
what is between S and M?
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gap phases (G1 and G2)
allows time for growth of the cell
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G0
resting state of no replication
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microscopy
- can use DNA binding fluorescent dyes: reveals condensation of chromosomes in mitosis - antibodies against microtubules
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artificial thymidine analog
- can incorporate into DNA during DNA replication
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flow cytometer
- rapid analysis of a alrge number of cells - measures DNA content in a cell population and sorts the data
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late in G1
start/restriction point - is environmental favorable?
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G2/M transition
- controls system triggers early mitotic events that lead to chromosome alignment on the mitotic spindle in metaphase. - is all DNA replicated? - is environment favorable?
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metaphase/anaphase transition
- control system stimulates sister-chromatid separation leading to completion of mitosis and cytokinesis - are all chromosomes attached to the spindle?
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cyclin dependent kinase (CDK)
-members of a family of kinases - rise and fall throughout the progression of the cell cycle - cyclical changes in phosphorylation of intracellular proteins
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cyclin protein
CDK regulator - CDK is dependent on this - made and destroyed though the cell cycle
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G1-S cyclins
activates CDKs late in G1 - levels fall in S phase
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S cyclin
- binds CDKS after progression through start - stimulate chromosome duplication - remain elevated until mitosis
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M cyclin
- activates CDKS that stimulate into mitosis at G2/M transition - fall in mid-mitosis usually around metaphase/anaphase