BIOL 3000 Exam 3

cell division

process by which a parental cell divides into two daughter cells

why is cell size limited?

the ability to transport food and oxygen into the interior becomes harder, as well as the outside cannot keep up with the quick growth of the inside

cell cycle

G0, G1, S, G2, M

G0 phase

resting phase, cell senescence

cell senescence

the period in a cell's lifespan when it loses the ability to divide and grow; cell aging

G1 phase

growth phase, cell increases in size and prepares for DNA synthesis

S phase

DNA is replicated

G2 phase

second growth phase, cell gets larger and prepares for mitosis and cell division

M phase

cell growth stops and cell divides into two daughter cells

why was frederick griffith's transforming principle important?

it was the first suggestion of DNA as a heritable material

why was the avery-macleod & mccarty experiment important?

it confirmed griffith's work and isolated DNA as the heritable material

why was the hershey-chase experiment important?

it confirmed that DNA was the genetic material

image B51

x-ray diffraction image of DNA, used later to determine its double helical structure

semi-conservative model

double stranded DNA contains one parental and one daughter strand following replication

DNA replication is a ____ process

semi-conservative

conservative model

both parental strands stay together after DNA replication and the daughter molecules contain all new nucleotides

dispersive model

parental and daughter DNA are interspersed in both strands; consists of old and new strands

meselson-stahl experiment

used isotope of nitrogen to change the weight of DNA N15 and N14, demonstrated that the semi-conservative model is the best description of replication

DNA replication

use of an existing strand of DNA as a template for the synthesis of new, identical strand

how common are errors in DNA replication?

one error occurring every 1 billion nucleotides

origin of replication

a particular sequence in a genome at which replication is initiated

origin of replication in bacteria

OriC

what is responsible for the timing of DNA replication?

GATC methylation sites

DnaA boxes

AT rich region that is the site for the binding of DnaA protein

initiator proteins

proteins that bind to DNA and mark the point where strand separation will occur

DnaA is an ____

initiator protein

replication bubbles

sections of DNA that look like a bubble where the two strands separate in order to enable replication to occur rapidly

replication occurs.....

bidirectionally

replication fork

a y-shaped region on a replicating DNA molecule where new strands are growing

DNA replicates from ____ to ____

5' to 3'

topoisomerase (gyrase)

reduce torsional strain causing unwinding of double helix

helicase

breaks hydrogen bonds between complementary nucleotides

unwinds DNA to form transcription bubble

single-strand binding proteins

stabilize ssDNA until elongation begins

primase

RNA polymerase that adds a ribonucleotide primer to ssDNA

how long are primers?

typically 10-12 bases in length

when are DNA primers removed?

following elongation. they are replaced with DNA nucleotides in this step

DNA polymerase (prokaryotic)

enzyme that catalyzes attachment of nucleotides to make new DNA during replication

DNA polymerase I

removes RNA primer and starts synthesis

DNA polymerase III

responsible for most of replication process

DNA polymerase II, IV, V

repairs DNA

T/F: prokaryotes contain the enzymes DNA polymerase alpha, sigma, beta

false, prokaryotes have DNA polymerase I, II, III, IV, V

polymerase alpha

synthesizes primer

polymerase sigma

synthesizes leading strands

polymerase epsilon

synthesizes lagging strand

T/F: DNA polymerase can initiate DNA by itself given the right conditions

false, DNA polymerase requires primers in order to initiate synthesis

DNA polymerase can only synthesize in the _ to _ direction

5' to 3'

are the sugars on the outside of the double helix hydrophilic or hydrophobic?

hydrophilic

1st step of elongation

new DNA is synthesized from deoxyribonucleic triphosphates (dNTPs)

2nd step of elongation

in replication, the 3' OH group on last nucleotide "attacks" the 5' phosphate group of incoming dNTP

3rd step of elongation

two phosphates are cleaved off of incoming dNTP

4th step of elongation

a phosphodiester bond form between the two nucleotides

5th step of elongation

phosphate ions are released

t/f: in DNA replication, both parental strands are replicated at the same time

true

DNA ligase

joins together newly synthesized DNA strands by creating a covalent phosphodiester bond

what does high fidelity mean in terms of DNA replication?

mistakes are very rare

exonuclease activity

located in DNA pol III, backs up in 3' to 5' direction to fix mistakes

what is unique about prokaryotic DNA replication?

- single circular plasmid DNA

- one origin (oriC)

- DNA is free floating in cytoplasm

what is unique about eukaryotic DNA replication?

- multiple large linear chromosomes

- multiple origin sites

- DNA tightly packed around histone proteins

- telomeres

telomerase

an enzyme that catalyzes the lengthening of telomeres in eukaryotic cells

how does telomerase work?

1. binds to overhand using complementary RNA primer

2. synthesizes DNA to make it double stranded

3. DNA pol binds to double stranded DNA and fills in the gap

4. ligase joins strands together

cancer

uncontrolled cell division or replication

aging

cell senescence or lack of cell division (werner syndrome)

disease

especially related to DNA repair defects (bloom syndrome)

site of replication

replicon

t/f: replication only occurs on ssDNA

true

chromatin

DNA and protein complex that compacts DNA

t/f: chromatin is only found in eukaryotes

true

histones

proteins found in chromatin, provides structure, shape and gene regulation of chromosomes

euchromatin

lightly packed chromatin rich in gene concentration. is most often under active transcription

heterochromatin

tightly packed chromatin consisting mainly of genetically inactive sequences

in chromosomes, when gene transcription occurs, what is likely the chromatin formation?

euchromatin

facultative heterochromatin

gene silencing; barr bodies

the condensed, inactive X chromosomes found in females is an example of.....

barr bodies

constitutive heterochromatin

VERY gene poor; centromeres and telomeres

folded-fiber model

DNA and protein model that proposed a single, long chromatin fiber makes up each chromosome

folded fiber model: type A fiber

chromatin fiber 1-10 nm. DNA packing ratio is 6:1

folded fiber model: type B fiber

chromatin fiber 20-25 nm. DNA packing ratio 10:1

according to the folded fiber model, what type of fiber is folded more tightly?

type B

according to the folded fiber model, extensive folding of type ____ forms a chromatid

B

nucleosome model

most accepted DNA packing model. proposes nucleosomes to be the packing unit of eukaryotic chromatin, made up of a double DNA strand wrapped core histones

which DNA packing model is better fit for protein biosynthesis?

nucleosome model

which of the following statements is true regarding core histones?

I. H2A, H2B, H3, and H4 are core histones

II. they were highly conserved during evolution

III. have a very basic charge due to being made of cystine and arginine

IV. consist of approximately 120 amino acids each

I, II, and IV

which of the following statements is true regarding linker histones?

I. consists of 200 amino acids

II. they were highly conserved during evolution

III. tissue specific expression

IV. closely associated with core particle

H1 is in what histone class?

linker histones

how many core histones are in a nucleosome?

8, two of each type

how many linker histones are in a nucleosome?

1

what is the importance of 10 nm fiber in nucleosome formation?

they are the primary packing of chromatin

solenoid formation

helical coiling of 10 nm

fibers consisting of 6 nucleosomes

what histone is found in the center of a solenoid, and what is it used for?

H1, used for packing

how does H1 histone work?

binds linker DNA and 146 bp portion of central core DNA, compacts up to 40x!

zig zag model formation

due to the limited flexibility of DNA, straight linker DNA connects opposite nucleosomes

t/f: both solenoid and zig zag typologies may both simultaneously be present in chromatin fiber

true

chromatin loops

higher order of coiling with 300 nm chromatin fiber built around scaffold of topoisomerase II

chromatin loops share the same level of compaction as....

euchromatin

metaphase chromosome

condensed chromatin loops looped around spiral scaffold composed of topoisomerase II and about 15 non-histone proteins

metaphase chromosomes have the same level of compaction as...

heterochromatin

2 nm - 10 nm fibers are known as _____ and are found in the _____ phase

DNA and nucleosomes; G1

30 nm fibers are known as _____ and are found in the _____ phase

chromatin; early G2

300 nm fibers are known as ____ and are found in the _____ phase

chromatin loops; late G2

700 nm fibers are known as _____ and are found in the _____ phase

condensed chromatin loops; beginning prophase