Exam 4 Eukaryotes

semiconservative replication

each daughter duplex contains one strand from the parent structure

temperature sensitive (ts) mutants

unable to replicate their chromosomes at elevated temperatures

• have been important in the study of DNA synthesis for replication, DNA repair, and genetic recombination

origin

specific site on the bacterial chromosome where replication begins

replication forks are sites where:

1. parent double helix is undergoing strand separation

2. nucleotides are being incorporated into the newly synthesized complementary strands

DNA polymerases

the enzymes that synthesize new DNA strands from a template

3’ → 5’ direction

DNA polymerase molecules move along a template in a:

primase

an RNA polymerase that assembles short RNA primers

helicase

unwind a DNA duplex in a reaction that uses energy released by ATP hydrolysis

DnaB

major helicase during replication in E. coli

single-stranded DNA-binding proteins (SSB)

stabilize single stranded DNA

DNA polymerase III holoenzyme

contains various subunits having different functions in the replication process

beta clamp

holds the polymerase to the DNA as it moves along the template strand and synthesizes the complementary strand in bacteria

DNA polymerase I

involved in DNA repair

• has 5’→3’ exonuclease function and 3’→5’ exonuclease function

5’→3’ exonuclease function

removes nucleotides from the 5’ end of a single-strand nick

• involved in RNA primer removal

3’→5’ exonuclease function

removes mispaired nucleotides from the 3’ end of the growing DNA strand

• DNA repair

replicon

a DNA segment that replicates from a single origin of replication, acting as a unit of replication

autonomous replicating sequences (ARSs)

contains the origin of replication in eukaryotic cells

origin recognition complex (ORC)

multisubunit protein complex that binds the ARS

eukaryotic DNA polymerases:

1. alpha

2. beta

3. gamma

4. delta

5. epsilon

DNA polymerase alpha

eukaryotic polymerase that initiates Okazaki fragment synthesis

DNA polymerase gamma

eukaryotic polymerase that replicated mDNA

DNA polymerase beta

eukaryotic polymerase that is involved in DNA repair

DNA polymerase delta

eukaryotic polymerase involved in lagging strand synthesis

DNA polymerase epsilon

eukaryotic polymerase involved in leading strand synthesis

nucleotide excision repair (NER)

operates by a cut-and-patch mechanism that removes a variety of bulky lesions

• 2 NER pathways: transcription-coupled and global genomic pathway

base excision repair (BER)

operates to remove altered nucleotides generated by reactive chemicals present in the diet or produced by metabolism

• initiated by a DNA glycosylase that recognizes the alteration and removes the altered base by cleavage of the glycosidic bond holding the base to the deoxyribose sugar

mismatch repair (MMR)

correction of mistakes that escape the DNA polymerase proofreading activity

• recognizes distortions caused by mismatched bases

double strand break (DSB) repair

can be separated into 2 pathways:

1. nonhomologous end joining

2. homologous recombination

nonhomologous end joining (NHEJ)

a complex of proteins binds to the broken ends of the DNA duplex and catalyzes a series of reactions that rejoin the broken strands

homologous recombination

requires a homologous chromosomes to serve as a template for repair of the broken strand

continuously, leading strand

the DNA strand growing toward the replication fork grows _______ in a 5’→3’ direction as the replication fork advances and is called the _________

cell division

the process by which new cells arise from other living cells

mitosis

leads to the production of cells that are genetically identical to their parent

• basis for producing new cells

meiosis

leads to the production of cells with half the genetic content of the parent

• basis for producing new sexually reproducing organisms

2 major phases of the cell cycle:

M phase and interphase

M phase

includes the process of mitosis and cytokinesis

interphase

the period between cell divisions, is a time when the cell grows and engages in diverse metabolic activities

• lasts longer than M phase

G1

takes place after the end of mitosis

• cell grows and carries out normal metabolism and organelles duplication

S phase

DNA replication and chromosome duplication

G2 phase

occurs between the end of S phase and the beginning of mitosis

• cell grows and prepares for mitosis

3 categories of cells based on their capacity to grow and divide:

1. cells that are highly specialized and lack the ability to divide

2. cells that normally do not divide but can be induced to begin DNA synthesis and divide when given an appropriate stimulus

3. cells that normally possess a relatively high level of mitotic activity

maturation-promoting factor (MPF)

initiates entry of a cell into M phase

• contains a kinase subunit and a regulatory subunit called cyclin

START

the first transition point that occurs in late G1

• once a cell has passed START it is committed to replicating its DNA and completing the cell cycle

• requires the activation of cdc2 by one or more G1/S cyclins

G2/M transition

passage from G2 to mitosis

• requires activation of cdc2 by mitotic cyclins

progress through the cell cycle can be arrested at a checkpoint by:

1. sensors that detect chromosomal abnormalities

2. transmitters that signal the information

3. effectors that inhibit cell cycle machinery

mitotic stages:

1. prophase

2. prometaphase

3. metaphase

4. anaphase

5. telophase

prophase

formation of the mitotic chromosome

• chromosome compaction/condensation occurs in early prophase

• cohesin and condensin are responsible for compaction

cohesin

holds the two sister chromatids together continuously through G2 and into mitosis, when they are ultimately separated

primary constriction

an indentation on a mitotic chromosome that marks the position of the centromere

kinetochore

found on the outer surface of centromeres and are the sites where the chromosomes attach to the microtubules of the mitotic spindle

organelles during prophase:

• nuclear pore complexes are disassembled

• nuclear lamina is disassembled

• nuclear membranes are disrupted mechanically

• membranous organelles remain relatively intact

• Golgi complex may become incorporated into the ER or become fragmented to form small vesicles

prometaphase

mitotic spindle assembly is completed

• chromosomes are moved by microtubules into the center of the cell

metaphase

chromosomes are aligned at the spindle equator

• microtubules of the metaphase spindle can be divided into 3 groups

3 groups of microtubules of the metaphase spindle:

1. astral microtubules

2. chromosomal (or kinetochore) microtubules

3. polar (or interpolar) microtubules

astral microtubules

radiate outward from the centrosome into the region outside the body of the spindle

• help position the spindle apparatus in the cell and may help determine the plane of cytokinesis

chromosomal (or kinetochore) microtubules

extend between the centrosome and the kinetochores of the chromosomes, exert a pulling force on the kinetochores, maintaining the chromosome in the equatorial plane

polar microtubules

extend from the centrosome past the chromosomes

• form a structural basket that maintains the integrity of the spindle

anaphase

begins when the sister chromatids of each chromosome split apart and start their movement towards opposite poles

anaphase A

movement of chromosomes toward the poles

• tubulin subunits are lost from both ends of the chromosomal microtubules, resulting in shortening and movement of chromosomal fibers

anaphase B

two spindle poles move further apart due to the elongation of microtubules

• tubulin subunits are added to the plus ends of polar microtubules

telophase

mitotic spindle disassembles

• nuclear envelopes of the two nuclei are reassembled

• chromosomes become dispersed

cytokinesis

process where one cell is divided into 2 daughter cells

contractile ring theory

suggests that a thin band of actin and myosin filaments generates the force to cleave the cell

motor protein roles:

• keep the poles apart

• bring chromosomes to the metaphase plate and keep them there

• elongate the spindle during anaphase B

cohesin

what is responsible for holding sister chromatids together after replication? it holds the two chromatids together through G2 and into mitosis.

preprophase band

a dense ring of cytoskeleton filaments and proteins, including microtubules, actin, organelles, and accessory proteins

• band disappears by prometaphase but the cell “remembers” its original location

• formed during interphase (G2)

cell plate

simple precursor of new cell wall

phragmoplast

assembly of cytoskeletal proteins, membranes, and other components needed for the formation of the cell plate

meiosis

ensures the production of a haploid phase in the life cycle

meiosis I

homologous chromosomes pair and then segregate, ensuring that daughter cells receive a full haploid set of chromosomes

• genetic recombination takes place

• starts with diploid parent cells and ends with 2 haploid daughter cells

meiosis II

separates sister chromatids

sister chromatids

identical copies of a single chromosome, formed after DNA replication

homologous chromosomes

pairs of chromosomes, one from each parent

gametic (terminal) meiosis

includes all multicellular animals and many protists

• meiosis occurs during gamete formation

• in males spermatogonia become spermatocytes

• in females oocytes enter extended meiotic prophase and meiosis completes after fertilization

zygotic or initial meiosis

found in protists and fungi

• meiotic divisions occur just after fertilization, forming haploid spores

• spores divide by mitosis to produce a haploid adult generation

• diploid phase is brief

sporic (intermediate) meiosis

includes plants and some algae

• diploid zygote undergoes mitosis and develops into a diploid sporophyte

• sporogenesis occurs, producing spores that germinate directly into a haploid gametophyte

• gametophyte produces gametes by mitosis

spermatid

an immature male sex cell formed from a spermatocyte that then undergoes differentiation to become a highly specialized sperm cell

oogonium

an immature female reproductive cell that gives rise to primary oocytes by mitosis

prophase I of meiosis:

1. leptotene

2. zygotene

3. pachytene

4. diplotene

5. diakinesis

leptotene

first stage of prophase I during which the chromosomes become compacted

zygotene

2nd stage of prophase I, when homologous chromosomes pair in process called synapsis

pachytene

3rd stage of prophase I where synapsed chromosomes form tetramers

diplotene

stage of prophase I when crossing over occurs

diakinesis

final stage of prophase I when the chromosomes are prepared for attachment to the spindle fibers

chiasmata

covalent junctions between the homologous chromosomes

anaphase I

homologous chromosomes separate

anaphase II

sister chromatids separate

interkinesis

stage between the 2 divisions of meiosis

extracellular messenger molecules

what cells usually communicate with one another through

autocrine signaling

the cell that is producing the messenger expresses receptors on its surface that can respond to that messenger

paracrine signaling

messenger molecules travel short distances through extracellular space

• usually limited in their ability to travel around the body because they are inherently unstable, or are degraded by enzyme, or they bind to the extracellular matrix

endocrine signaling

messenger molecules reach their target cells through the bloodstream

first messenger/ligand

a molecule that binds to the receptor

receptors

specifically recognize and bind to messenger molecules

2 different types of signal transduction:

1. activated by a diffusible second messenger

2. activated by the recruitment of cytoplasmic proteins to the plasma membrane

effector

enzyme that is gets signal from receptor and generates the second messenger in response

second messenger

small molecules that act as activators or inhibitors of specific proteins

kinases

add phosphate groups

phosphatases

remove phosphate groups

signal transduction

the overall process in which information carried by extracellular messenger molecules is translated into changes that occur inside a cell