Bio 303 Final

• G0, G1, S, G2 phases are called interphase
• G0, G1, G2 are gap phases
• cells in G0 are neither dividing or preparing to divide
• S phase is synthesis phase and is when DNA replication
• M phase stands for mitotic phase and is when cell divides

• prophase - each replicated chromosome consisting of two sister chromatids condense; two centrosomes move apart and assemble the mitotic spindle
• prometaphase - breakdown of the nuclear envelope; beginning of attachment of microtubules to kinetochores on the chromosomes
• metaphase - chromosomes align at equator of the spindle; paired kinetochore microtubules on each chromosome attach to opposite poles of the spindle
• anaphase - sister chromatids are separated to opposite poles; kinetochore microtubules are shortened while non-kinetochore microtubules grow longer and slide past each other
• telophase - the two sets of chromosomes arrive at the poles of the spindle; a new nuclear envelope reassembles around each set to form two nuclei

• considered the sixth stage of M phase
• process in which cytoplasm from a mitotic cell is divided to the two daughter cells
• starts at anaphase and ends at the end of telophase
• contractile ring made of actin and myosin is attached to membrane-associated proteins in the cytoplasmic face of the plasma membrane
• sliding motion decreases diameter of ring until the plasma membrane is cleaved in two
• unlike in muscle contraction, contractile ring gradually becomes smaller and completely disassembles after the cell is cleaved

• cyclin concentration increases during interphase and peak at M phase
• Cdk concentration remains constant but its activity increases in M phase
• activity of Cdk is dependent on cyclin

• cyclin-Cdk complex remains inactive after binding
• kinases add the inhibitory phosphate and the activating phosphate to the complex but remains inactive
• an activating protein phosphatase removes the inhibitory phosphate, and cyclin-Cdk is now active

can trigger condensation of chromosomes, phosphorylation of nuclear lamins, rearranging microtubule cytoskeleton to form mitotic spindle

• the active cyclin-Cdk complex regulates its own activity
• the complex activates the enzyme (ubiquitin ligase) that ubiquitylates (process of adding ubiquitin) cyclin protein
• ubiquitin targets cyclin for degradation in proteosome, thus inactivating Cdk

• levels of Cdc6 increase during G1 phase
• Cdc6 binds to DNA at origin of replication to form, along with other proteins, the origin recognition complex (ORC)
• ORC facilitates DNA replication
• S phase cyclin binds with Cdk to form S-Cdk
• S-Cdk triggers cell to undergo S phase by acting as a transcription factor for the synthesis of other proteins that assemble into a replication fork, where DNA replication begins
• another S-Cdk substrate also phosphorylates Cdc6 which tags it for degradation, making sure replication happens once

• checkpoints are key places that ensure quality control for the cell
• G1 - damaged DNA, unfavorable extracellular environement
• S - damaged or incompletely replicated DNA
• G2 - damaged or incompletely replicated DNA
• M - chromosome improperly attached to mitotic spindle

• p53 is a protein that is phosphorylated by kinases when DNA damage is detected by the cell
• activated p53 is a transcription factor that leads to synthesis of p21 protein
• p21 acts as a Cdk inhibitor protein that inactivates S-Cdk complex, preventing cell from going into S phase
• system acts as a G1 checkpoint before a cell can move into S phase

• two combine to form inactive M-Cdk complex
• M-Cdk complex is activated by two kinases, Wee 1 phosphorylates the inhibitory site and Cak the activating site on the M-Cdk complex
• a phosphatase called Cdc 25 removes the inhibitory phosphates, thus activating the M-Cdk complex
• M-Cdk promotes mitosis in cell
• M-Cdk also activates Cdc 25, resulting in positive feedback
• M cyclin is targeted for destruction by APC

• happens in prometaphase
• nuclear lamins, made of intermediate filaments, and nuclear pores are phosphorylated leading to their breakdown
• microtubules of the mitotic spindle can now attach to chromosomes
• nuclear envelope reforms when lamins and pores are dephosphorylated

• centrioles are microtubule organizing centers and are located inside of centrosomes 
• centrioles are replicated in S phase and create two centrosomes
• centrosomes migrate to opposite sides of nucleus
• connections form between microtubules and chromosomes following nuclear membrane breakdown
• when centrosomes form spindles they are called spindle poles

• kinetochore microtubule attaches to a chromosome at centromere
• non-kinetochore microtubule functions to separate chromosomes in anaphase

• cohesion rings hold replicated DNA (sister chromatids) together
• cohesion rings form the centromere
• point where microtubules connect to centromere is called the kinetochore

• the metaphase checkpoint exists to make sure all chromosomes are attached to kinetochore microtubules from separate centrosomes
• attachment of microtubules to the centromeres deactivates inhibitors (Mad2, BubR1) of anaphase-promoting complex (APC), thus making APC active
• APC tags securin for degradation via ubiquitylation, which separates from the now active protein called separase
• separase breaks the cohesion linkages holding the sister chromatids together, allowing anaphase to occur

• in anaphase a, sister chromatids are pulled to opposite spindle poles and at the same time the kinetochore microtubules are depolymerized
• in anaphase b, non-kinetochore microtubules push against each other and elongate mitotic spindle pushing two ends apart
• dynein is motor protein used in anaphase a, kinesin used in anaphase b

• a structure that forms in plant cells during late cytokinesis
• phragmoplast forms from remains of non-kinetochore microtubules at equator of old mitotic spindle
• vesicles from the Golgi carry polysaccarides and glycoproteins needed for the cell wall to the phragmoplast
• vesicles fuse to form a membrane structure until they reach the plasma membrane, dividing the original cell into two
• later, cellulose microfibrils are laid down to complete construction of the new cell wall

germ cells become haploid after meiosis I

• in order for homologous chromosomes to remain at the equator of spindle (by maintaining tension of microtubules) at prophase of meiosis 1, homologs interact in a process called crossing over
• synapsis is alignment of homologs, and the points of attachment are called chiasmata
• matching regions on homologous chromosomes can break and reconnect to the other chromosome
• cohesin rings at chiasmata, but not at centromere, are then degraded by separase

the principle stating that the laws of chance govern which particular characteristics of the parental pairs will occur in each individual offspring

• rosettes are cellulose synthesizing complexes that help synthesize the cellulose microfibrils that make up the cell wall
• glucose from G3P synthesized in chloroplasts act as the enzyme substrate (along with ATP since this is an anabolic reaction) to create cellulose
• force of polymerization moves rosette assembly along plasma membrane (fluid mosaic)
• a pair of microtubule fibers keep assembly  of cellulose in a straight line; fibers are tethered to the plasma membrane by a MAP

openings in plant cell walls that allow them to communicate with each other

• collagen is a connective tissue made up of complex collagen proteins that act as ECM that cells can attach to
• actin inside cell can bind to extracellular fibronectin via integrin proteins, fibronectin can then attach to collagen
• collagen is made up of smaller collagen fibrils and smaller triple-stranded collagen molecules, called pro-collagen
• assembly of collagen fiber from triple-stranded pro-collagen is regulated by presence and absence of amino and carboxyl domains (by proteases) of the pro-collagen
• regulation by enzymes is also influenced by availability of vitamins C and D in diet

• proteins with cores composed of sugar groups that can form a hydrated gel
• they absorb water

ECM produced by connective tissue and used as a substrate for epithelial cells to attach to

• caspases are killer proteins that destroy:
• protein kinases, focal adhesion proteins, nuclear lamins, cytoskeletal proteins, DNA

• shrinkage of cell body
• condensation of the nucleus
• fragmentation of the DNA
• loss of attachment to other cells
• membrane blebbing
• formation of apoptopic bodies

• triggered by internal signals like DNA damage, oxidative stress (reactive oxygen species/H2O2), ER stress, excessive levels of Ca+2, and viral or bacterial infection
• proteins Bak and Bax are activated, and form channels in the outer mitochondrial membrane
• cytochrome c exits the mitochondria and leads to formation of capsase complexs called apoptotsomes
• apoptotsomes then activate caspase 3 as well as other caspases

• triggered by external signals (ligands) like exposure to toxin, high temperature, or TNF-alpha (tumor necrosis factor or "death factor")
• TNF-alpha can bind to TNFR1 and initiate a signal pathway that activates caspase 8 via post-translational cleavage
• caspase 8 activates caspase 3 which degrades various proteins in the cell

• a way for a cell to stay alive during times of stress or low resources
• autophagy does not usually lead to cell death
• allows the cell to recycle old or damaged organelles, or to metabolize proteins when ATP levels are low

• during autophagy, a double-membraned phagophore forms; membrane comes from ER and outer mitochondria membrane
• the phagophore encloses cytoplasmic components forming an autophagosome
• the autophagosome can fuse with a lysosome to form an autolysosome, then digestion of contents occur
• beclin 1 and ATGs help form the autophagosome