exam 4: lecture 11 dna structure and function Flashcards
What are the levels of chromatin packing?
a) nucleosomes (“beads on a string)
-dna double helix (default, naked state, no proteins)
=> 1st level packing: the DNA wrap around 8 histones twice (9th histone: lock+hold the protein from falling apart)
b) 30nm chromatin fiber-> solenoid (a bunch of solenoid)
c) looped domains (300 nm)
-attached to scaffold proteins
d) heterochromatin (700nm)
-coiled coil (loop around themselves)
e)highly condensed, duplicated chromosome ( 1400nm)
-compact the coil down
-chromatin: decondensed state
-chromosome: condensed state (easy to move around)
What is the order of the cell cycle?
Interphase:
*Gap 1: preparation for S (getting the cells ready for S: nucleotides,dNTP, enzymes, ribosomes)
-G1 checkpoint: ensure the cells have everything it needs to replicate DNA
*Synthesis (S): chromosomes are being duplicated (4x the point of DNA)
*Gap 2: preparation for division (enzymes, aa, size)
-G2 checkpoint: ensure the DNA is copied correctly, all needed components to divide
Mitosis
*Mitosis: PMAT
-M checkpoint: ensure every chromosome is attached w the correct #
factors for speed (length of cell cycle)
- Age: newborn’s new cycles are shorter
- Species: bamboo can grow an 1.5 inch/ day=rapid cell cycle
- Tissue: gut cell(digestive) & blood cells have shorter cell cycles compared to nerve cells
- Temp (vitro): only in culture (lab) will fo thru cycle if temp is raised until plateau
Animal Cells: Mitosis-interphase
interphase (G1, S, G2)
-2 centrosomes w/ centriole pairs
-chromatin
-nucleolus
-nucleus envelope
Animal Cells: Mitosis-prophase + prometaphase
Prophase:
-MTs (spindle fibers) being synthesized w centrioles at the ends
-nucleolus (nuclear lamin) starts to degrade/ break down
-sister chromatids (2 long chromatins) on the way to being condensed
-centromere ( hold the sister chromatids tgt)
Prometaphase:
-fragments of nuclear envelope
-centrioles (+) at the end of poles
-chromosomes wandering around
-centromere -> kinetochore
Animal Cells: Mitosis-Metaphase
-Astray MT
-Polar MT
-Kinetochore MT
-mitotic spindle connecting to centrioles
-metaphase plate with chromosomes line up at the center
Animal Cells: Mitosis- Anaphase
-daughter chromosomes are pulled apart to go to opposite poles
Animal Cells: Mitosis-Telophase & Cytokinesis
-nuclear envelope forming
-chromosomes decondensing
-cleavage furrow (cytokinesis)
The purpose of mitosis (the number of diploid)
G1: diploid (2n-46)
S: tetraploid (4n-92)
G2: 4n
P: 4n
M: 4n
A: 4n
T+C: split into 2n & 2n
purpose: to get 2 new identical daughter cells
The human life cycle
genetic diversity:; variations w/in offsprings
-haploid gametes (n-23)—> fertilization: diploid zygote (2n-46)/ multicellular diploid adults (2n-46)—–> meiosis
haploid (n/23)+ haploid (n/23)= diploid (2n/46)
Meiosis
-cell division of gametes
-a single germ cell divides into 4 unique daughter cells (to create haploid cells)
-daughter cells have half the # of chromosomes as the parent cell, so they are considered haploid
1 pair of blue & 1 pair of red (2n)—–INTERPHASE——> homologous chromosomes: blue & red shuffled tgt (4n)—–MEIOSIS I—–> daughter cells (2n) & (2n)—-MEIOSIS II—–> daughter cells II: 4 pairs (n)(n)(n)(n)
Genetic Shuffling of Meiosis I
- crossing over in prophase I: swap DNA-rearrangement of chromosomes
synapsis in prophase I: lining of homologous chromosomes - independent assortment in metaphase I (sister chromatid stays a pair: di. not ger pulled apart)
The duplicated homologous chromosomes pair and CROSSING OVER
2 pairs: 1 pair of red & 1 pair of blue
-> small sections of red and blue gets exchanged: chiasma
=recombinant chromatids
Independent Assortment
possibility 1: possibility 2:
blue-red blue-red
blue-red red-blue
——————————– metaphase II ———————————
blue. red blue red
blue red red blue
———————————— ————————–
(4blue)(4blue)(4red)(4red) (2blue/2red)X2 (2red/2blue)X2
Meiosis vs Mitosis
mitosis:
-high fidelity (ability to accurate duplicate)
-results in 2 daughter cells
-results in diploid somatic cells
-rarely synapsis
-rarely cross-over
-chromatids separate in anaphase
-one division
meiosis:
-variable
-results in 4 gametes
-results in haploid cells
-synapsis common
cross-over common
-chromatids separate in anaphase ii
-two divisions
what are nucleotides made up
-nitrogen bases
-5 carbon sugar (ribose)
-phosphate groups
pyrimidines vs purines
pyrimidines (1 ring)
-thymine
-cytosine
-uracil
purines (2 rings)
-adenine
-guanine
phosphates are attached at 5’ carbon
bases are attache at 3’ carbon
A-T tastes less energy to break
DNA @ 95
denatures into separate strands
when cool, the bases come back tgt correctly (hydrogen bonds come back)
The purpose of major and minor grooves?
in order enzymes to access the DNA
groove allows to access enzymes that have the ability to cut, paste, copy DNA
what holds the bases tgt?
diester bonds
Semi-conservative replication
a hybrid of old and new
curly & straight
conservative replication
two DNA copies are produced from one original DNA
every time a cell divide, the cell keeps 1 original strand another one new
II ~~
I~. ~~
how does replication begin
bacteria only has 1 orgin w 2 replication forts; only 1 direction
eukaryotes has an origin every 50000 bp
replication starts @ the orgin (replication forks)
replication bundles: merging forks tgt until the whole comes apart to have 2 whole strands
occurs in S phase (when DNA replicates)
What are the limitations of DNA polymerase?
1) can onky travel 5’>3’ to synthesize DNA (unidirectional synthesis)
2)can not synthesize DNA de novo (“from newness”)
(DNA polymerase need someplace to start from; need a short piece to start from)
3) must have “primer” to start synthesis, but it can not make its own
4)can not unwind the DNA by itself and hold it open for replication
(need help to keep the fork open
*5’ phosphate attached to 3’ hydroxyl
The process of unwinding in DNA at the Origin
Origin: where dna polymerase binds and begins to replicate the DNA
unidirection
the function of topoisomerases
cut the strand
twist
attach it
a mechanism by which a single strand break (a nick) ahead of a replication fork to allows rotation
the function of ligases
attach DNA strand
if 2 dna pieces have matching ends
what is the leading strand?
nucleotides are being added at the 3’ end (same direction as direction fork)
synthesized continuously
what is the lagging strand?
synthesized discontinuously, resulting in Okazaki fragments and later connected by DNA ligase
function of helicase
unwinds dna at the replication fork
SSB proteins
single-strand proteins binds and stabilize single-stranded DNA at the replication fork (keep them from binding tgt, holding the strands apart)
How does DNA begin replication, if DNA polymerase cannot start on its own?
RNA polymerase (primase)
what is the Trombono model?
the leading and lagging strand replication proteins approach each other and the lagging strand creates a loop
-describe the idea how replication takes place in bacteria (feeding thru the 2nd ring)
function of DNA polymerase I
remove RNA + replace w/ DNA
