Cell and Molec Exam 2

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DNA makes a template for...
chromosomes replicated into a pair of sister chromatids
M phase
when is DNA distinguishable/condensed?
G1, S, G2
What phases are in interphase?
What phase are cells in most of the time?
DNA synthesis
What is S phase
miotic chromosome
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
replication origin
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
S phase
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?
nucelosome positioning
1. dependent on presence of tightly bound proteins to DNA 2. Dependent on ATP-dependent chromatin remodeling complexes
linker histone that allows for compacting nucleosomal DNA
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
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
histone code
covalent modifications that can determine multiple outcomes
reader complex
recognizes particular of markings on chromatin which attracts additional proteins (what needs to be added)
histone chaperones
variety of proteins that bind histones - cooperate with chromatin remodeling complexes - remove certain dimers from nucleosome
covalently modified
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
tumor-suppressing gene
what does cancer turn off with methylation?
each daughter strand inherits original and one new strand
deoxyribonucleoside triphosphate
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?
okazaki fragments
synthesis in the 5 to 3 direction and then joined together after synthesis
1 mistake is every how many nucleotides?
DNA polymerase
what enzyme proofreads before the new nucleotide is added? (correct nucleotides are energetically favorable)
exonucleolytic proofreading
What occurs when incorrect nucleotide is added that has difficulty extending off improperly based paired 3 OH end?
DNA helicase
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?
RNA primer
what is synthesized by DNA primase?
DNA ligase
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
clamp loader
protein complex responsible for assembly of the clamp, requires ATP hydrolysis
DNA polymerase
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
protein kinase
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
DNA topoisomerases
put nicks to release tension in the DNA and then puts them back together; prevents tangling during replication
topoisomerase I
produces transient single strand breaks; break allows two sections of DNA helix on either side of the nick to rotate freely
topoisomerase II
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?
DNA glycosylase
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
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
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
flow cytometer
- rapid analysis of a alrge number of cells - measures DNA content in a cell population and sorts the data
late in G1
start/restriction point - is environmental favorable?
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?
metaphase/anaphase transition
- control system stimulates sister-chromatid separation leading to completion of mitosis and cytokinesis - are all chromosomes attached to the spindle?
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
cyclin protein
CDK regulator - CDK is dependent on this - made and destroyed though the cell cycle
G1-S cyclins
activates CDKs late in G1 - levels fall in S phase
S cyclin
- binds CDKS after progression through start - stimulate chromosome duplication - remain elevated until mitosis
M cyclin
- activates CDKS that stimulate into mitosis at G2/M transition - fall in mid-mitosis usually around metaphase/anaphase