exam 4: lecture 11 dna structure and function

Question 1

What are the levels of chromatin packing?

Answer 1

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)

Question 2

What is the order of the cell cycle?

Answer 2

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 #

Question 3

factors for speed (length of cell cycle)

Answer 3

1. Age: newborn’s new cycles are shorter
2. Species: bamboo can grow an 1.5 inch/ day=rapid cell cycle
3. Tissue: gut cell(digestive) & blood cells have shorter cell cycles compared to nerve cells
4. Temp (vitro): only in culture (lab) will fo thru cycle if temp is raised until plateau

Question 4

Animal Cells: Mitosis-interphase

Answer 4

interphase (G1, S, G2)
-2 centrosomes w/ centriole pairs
-chromatin
-nucleolus
-nucleus envelope

Question 5

Animal Cells: Mitosis-prophase + prometaphase

Answer 5

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

Question 6

Animal Cells: Mitosis-Metaphase

Answer 6

-Astray MT
-Polar MT
-Kinetochore MT
-mitotic spindle connecting to centrioles
-metaphase plate with chromosomes line up at the center

Question 7

Animal Cells: Mitosis- Anaphase

Answer 7

-daughter chromosomes are pulled apart to go to opposite poles

Question 8

Animal Cells: Mitosis-Telophase & Cytokinesis

Answer 8

-nuclear envelope forming
-chromosomes decondensing
-cleavage furrow (cytokinesis)

Question 9

The purpose of mitosis (the number of diploid)

Answer 9

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

Question 10

The human life cycle

Answer 10

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)

Question 11

Meiosis

Answer 11

-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)

Question 12

Genetic Shuffling of Meiosis I

Answer 12

1. crossing over in prophase I: swap DNA-rearrangement of chromosomes
   synapsis in prophase I: lining of homologous chromosomes
2. independent assortment in metaphase I (sister chromatid stays a pair: di. not ger pulled apart)

Question 13

The duplicated homologous chromosomes pair and CROSSING OVER

Answer 13

2 pairs: 1 pair of red & 1 pair of blue
-> small sections of red and blue gets exchanged: chiasma
=recombinant chromatids

Question 14

Independent Assortment

Answer 14

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

Question 15

Meiosis vs Mitosis

Answer 15

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

Question 16

what are nucleotides made up

Answer 16

-nitrogen bases
-5 carbon sugar (ribose)
-phosphate groups

Question 17

pyrimidines vs purines

Answer 17

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)

Question 18

The purpose of major and minor grooves?

Answer 18

in order enzymes to access the DNA
groove allows to access enzymes that have the ability to cut, paste, copy DNA

Question 19

what holds the bases tgt?

Answer 19

diester bonds

Question 20

Semi-conservative replication

Answer 20

a hybrid of old and new
curly & straight

Question 21

conservative replication

Answer 21

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~. ~~

Question 22

how does replication begin

Answer 22

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)

Question 23

What are the limitations of DNA polymerase?

Answer 23

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

Question 24

The process of unwinding in DNA at the Origin

Answer 24

Origin: where dna polymerase binds and begins to replicate the DNA
unidirection

Question 25

the function of topoisomerases

Answer 25

cut the strand
twist
attach it

a mechanism by which a single strand break (a nick) ahead of a replication fork to allows rotation

Question 26

the function of ligases

Answer 26

attach DNA strand
if 2 dna pieces have matching ends

Question 27

what is the leading strand?

Answer 27

nucleotides are being added at the 3’ end (same direction as direction fork)
synthesized continuously

Question 28

what is the lagging strand?

Answer 28

synthesized discontinuously, resulting in Okazaki fragments and later connected by DNA ligase

Question 29

function of helicase

Answer 29

unwinds dna at the replication fork

Question 30

SSB proteins

Answer 30

single-strand proteins binds and stabilize single-stranded DNA at the replication fork (keep them from binding tgt, holding the strands apart)

Question 31

How does DNA begin replication, if DNA polymerase cannot start on its own?

Answer 31

RNA polymerase (primase)

Question 32

what is the Trombono model?

Answer 32

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)

Question 33

function of DNA polymerase I

Answer 33

remove RNA + replace w/ DNA