CellBiology

Question 1

Nucleus

Answer 1

Consists of the Nuclear Envelope, Outer nuclear membrane,perinuclear space inner nuclear membrane, ER membrane, ER lumen, ER lumen, , nuclear pores

contains the DNA
where transcription occurs

Question 2

Endosome

Answer 2

important for the uptake of nutrients, inactivation of signaling receptors after receiving a growth or differentiation signal, and fine regulation of cell physiology such as the potentiation response in neuronal cells.
Has different subcompartments for different fates; cargo can be sorted by its coat, by lipid dependent partitioning, and/or by geometric sorting methods

Question 3

Lysosome

Answer 3

involved in protein degradation, cricitical for cell homeostasis which monitors improper protein folding, turnover damaged/denatured proteins, removes signaling proteins etc
part of the endocytic/late secretory pathway (autophagy)
phagocytosis is an important for large protein degradation
contain lots of hydolytic enzymes ( > 40) including proteases, glycodiases, reductases, and esterase’s. dey digest errything.

Question 4

Golgi appartus

Answer 4

The Golgi is composed of cisternae, which are cis (facing the ER), medial, and trans. It is important for modifying, sorting, and packaging macromolecules for secretion or integration into the cell membrane or for use in non-secretory vesicles like lysosomes.

all secretory/cell surface/vacuolar pathway glycoproteins need to pass through it
and it’s ribbon is dependent on microtubules

Question 5

mitochondrion

Answer 5

powerhouse of the cell

Question 6

vesicles

Answer 6

mediators of transport between components of the secretory system , they bud from one compartment with a specific type of cargo that is meant to be transported to another compartment. then fuse to target compartment and deliver their cargo. SNARE proteins are important for this process (docking and fusion)

synaptic or large desnse core granules which differ in fxn

Question 7

COPI and COPII systems

Answer 7

are important for budding and fusion in vesicular transport, specifically in the coating step that takes place after the budding.

Question 8

endoplasmic reticulum

Answer 8

contiguous with the nuclear membrane, and composed of smooth and rough ER. Smooth synthesizes lipids and steroids and rough is the site of transcription for secreted proteins and cell surface proteins and studded with ribosomes, and where all integral proteins are translated, protein folding compartment
role in metabolism of carbohydrates, regulation of calcium concentration, detoxification of drugs
ready proteins are exported from ER to golgi and beyond but needs protein folding QC

Question 9

nuclear lamina

Answer 9

repressed gene environment

Question 10

nuclear pores

Answer 10

unlike lamina/envelope, it is an active gene environment. Along w/ nuclear envelope, you see nuclear pores with decondensed, active chromatin. These pores are used for transport between the nucleus and cytoplasm.

Question 11

Nuclear pore complex(NPC)

Answer 11

made up of NUP, nuclear pre proteins, which can be split into different categories. They affect transfer rate, etc. The nuclear pre has stable scaffold proteins, but dynamic peripheral proteins.

Question 12

Synaptotagmin

Answer 12

Ca2+-binding protein that mediates calcium sensing by secretory cells.

Question 13

integral membrane proteins

Answer 13

integral membrane proteins are defined as those where the membrane must be disrupted in order to release them; span the lipid bilayer. Transmembrane proteins encounter at least three very different environments: cytosolic, lipid bilayer, and the lumen.

Question 14

nuclear transportation

Answer 14

very important, NPCs are essential, as they are stationary vessels for transportation of ‘cargo’. Signals are important in transportation, including the nuclear localization signal(NLS) and nuclear export signal(NES), RAN-GTPase cycle

Question 15

Ran-GTPase cycle

Answer 15

the small GTPase RAN is essential for nuclear transport. RanGTP concentrations are high in the nucleus and low in the cytoplasm. In the nucleus, RCC1 converts RanGDP to RanGTP. in the cytoplasm, RanGAP1 converts RanGTP to RanGDP. RanGTP promotes export cargo/receptor interaction as well as import. cargo/receptor dissociation.

Question 16

importin

Answer 16

importin receptor that is important for stimulating nuclear import. They bind to NLS or NES of their cargo, the FG domains in Nups, allowing docking at the NPCs, and also bind directly to the GTP bound form of the small GTPase Ran which regulates nuclear transport receptor-cargo binding.

Question 17

exportin

Answer 17

mediate nuclear export, i.e. Crm1

Question 18

cytoplasm

Answer 18

makes up most of the volume of the cell (50%) contains ribosomes, proteosomes, chaperone complexes, and ribonucleoprotein complexed

Question 19

ribosomes

Answer 19

are protein synthesis machines, which are large multi-subunit RNA enzymes that catalyze peptide bond formation and “decode” the triplet code of nucleotides –> AA. May catalyze protein synthesis/translation in the cytoplasm or on the surface of the ER membrane
large ribosomal subunit + small ribosomal subunit
mRNA binds between the subunits of the ribosome, with 3 functionally defined tRNA binding sites , A P E(acceptor, peptidyl-tRNA,
Folding begins at the exit tunnel
SRP(signal recognition particle) directs the ribosomes to a specific receptor in the rough ER membrane.

Question 20

chaperone complexes

Answer 20

important for protein folding, many are HS proteins, which are unregulated during cell stress. They cover up hydrophobic regions, disrupt hydrophobic interactions to give proteins another chance to fold correctly, and or isolate proteins so all other chaperones to work. present at high levels, interact with substrate proteins

Question 21

ribonucleoprotein complexes

Answer 21

RNPs are typically important for mRNA processing and transport

Question 22

Vacuolar system and Vacuoles

Answer 22

secretory and endocytic pathways, used for communication with the extracellular milieu

Vacuoles: A membrane-bound organelle which is present in all plant and fungal cells and some protist, animal, and bacterial cells. Essentially enclosed compartments filled with water containing both inorganic and organic molecules including enzymes.

Question 23

Misfolded proteins

Answer 23

not all can be degraded so they become aggregates which leads to many neurodegenerative diseases

unfolded protein responses
important for detecting when midsfolding events occur ( 3 pathways: translation control, protein refolding, and protein degradation)

Question 24

Mechanisms for endocytosis

Answer 24

clathrin-mediated, non-specific, cholesterol mediated, clathrin/cholesterol-independent, caveolae-mediated, and receptor-mediated.

Question 25

3 types of autophagy

Answer 25

macroautophagy = encircling intracellular material with a membrane then fusing it lysosomes(cytoplasmic only)

microphagy = where material is isolated directly at the lysosomal membrane by invagination of the limiting membrane

chaperone-mediate autophagy = where substrates are directly delivered to the lysosome by a chaperone protein

Autophagy is an essential process for both cell survival (generation of ATP, degrading misfolded proteins, etc) as well as in apoptosis.

Question 26

Proteosomes

Answer 26

degrade proteins that are defective or no longer needed (in addition to lysosomes), and are the catalytic machine that degrades ubiquitinated substrates

does the actual degradation. It is a huge protein complex, with a core 20S protease complex that associates with 19S to form 26S proteasomes. 20S proteasome has an unusual catalytic process, which is mediated by an N-terminal threonine that is exposed upon autocatalytic cleavage.

Question 27

Ubiquitin

Answer 27

76 amino acid heat stable polypeptide, when it is covalently attached to a substrate protein, that protein is targeted for degradation.

conjugated to substrate proteins through the ATP-dependent activity of ubiquitin conjugating enzymes, and those complexes are degraded by ATP- depdendent activity of the proteasome.

removed by de-ubiquitinating enzymes (DUBs), so the entire process is highly regulated.


Question 28

ubiquitin conjugating enzymes

Answer 28

subclassified into E1, which activates ubiquitin for transfer to E2, which is the ubiquitin conjugating enzyme (Ubc) that forms a bond with Ub and often transfers Ub to the substrate or to E3, which facilitates the transfer of Ub from E2 to the substrate.

E3 ubiquitin ligases confer specificity of degradation.

Question 29

SUMO-1/Smt3p

Answer 29

cytosolic degradation system with homology to ubiquitin and therefore competes with ubiquitination.

Question 30

Glycolysis

Answer 30

the process of metabolizing glucose into pyruvate and other molecules
glucose –> fructose 6-phospate –> fructose 1,6-biphosphate –>phosphenolypyruvate –> pyruvate

Question 31

gluconeogenesis

Answer 31

reciprocal of glycolysis

Question 32

tricarboxylic acid cycle (TCA cycle)

Answer 32

aerobic respiration: starts w/ pyruvate –> ATP energy to the coenzyme NADH–> electron transport process in the mitochondrial membrane –>energy used by protein complexes => proton gradient t–> ATP synthase

Question 33

Apoptosis

Answer 33

regulated cell death: removes unwanted or damaged cells. occurs during normal cell turnover, tissue homeostasis, embryogenesis, induction and maintenance of immune tolerance, and development of the nervous system.

Question 34

Apoptotic cells exhibit

Answer 34

• cell body shrinkage and formation of membrane-bound apoptotic bodies, which are engulfed by healthy cells
• cleavage between nucleosomes.

Question 35

necrosis

Answer 35

accidental or pathological cell death results in rupture of the plasma membrane and the release of cellular contents

Question 36

caspases

Answer 36

kill cells by cleaving a discrete set of proteins, which inactivates apoptosis inhibitors, destroys cell structures, and separates regulatory and catalytic domains. Caspase activation often occurs in a cascade due to autoregulatory function. Caspase activation is also regulated by at least four groups of proteins.

Question 37

inhibitors of apoptosis protein (IAP)

Answer 37

inhibit caspase activation by binding to mature caspases and inhibiting their protease activity.

Question 38

mitochondria/cytochrome c pathway

Answer 38

Apaf-1 activates caspase-9 through oligomerization. Apaf-1 is activated by the binding of cytochrome c to dATP, and cytochrome c must be released from the mitochondria in order for this to happen

Question 39

tumor necrosis factor receptor (TNFR) superfamily

Answer 39

death receptors leads to caspase activation via auto-proteolytic processing as well as the release of cytochrome c.

Question 40

wnt signaling pathway

Answer 40

activated by binding a Wnt-protein ligand to a Frizzled family receptor, which passes the biological signal to the protein dishevelled inside the cell. Results in gene expression, cell shape, calcium regulation.