bio 221 final

What are the parts of mitochondria and chloroplasts?

Inner + outer membrane, matrix, intracellular space, thylakoids (chloroplasts only)

How is ATP produced?

In mitochondria: oxidative phosphorylation + membrane based mechanism called chemiosmotic coupling

What are the 3 major enzyme complexes in mitochondria that electrons pass through?

NADH dehydrogense complex. cytochrome C reductase complex, cytochrome C oxidase complex

Where do electrons go in mitochondria?

2 electrons pass through each complex; 1 hydrogen is pumped into the inner membrane space for each complex, and oxygen is the final electron acceptor

How many electrons are needed to form 1 water in mitochondria?

4

What does ATP synthase use for energy?

Stored energy from the proton gradient (it can be reversible)

What do chloroplasts do?

Capture light energy to make ATP + NADPH

Which photosystem comes first?

PSII comes before PSI

What is the final electron acceptor in chloroplasts?

NADP+ (turns into NADPH)

What increases along the electron transport chain?

Redox potential

What is the structure of microtubules?

13 parallel protofilaments arranged in a cylinder; have alpha (+) and beta (-) ends

What do microtubules display?

Dynamic instability

Where does GTP bind on microtubules?

Beta subunit

When does the microtubule grow?

When GTP-bound tubulin dimers are added faster than GTP is being hydrolyzed by the dimers (shrinks when vice versa)

Where do GTP-bound tubulin dimers do? (where do they add?)

create a GTP cap (which is then lost during tGTP hydrolysis of beta-tubulin dimers)

What direction are microtubules arranged?

Depends on the cell (+end towards the outside of cell = anterograde, +end towards nucleus = retrograde)

What drives intracellular transport?

Kinesin + dynein “walking” on microtubulesWh

What are the steps for kinesin/dynein movement?

What is the structure of actin filaments?

Twisted chain of globulin actin monomers; monomers have distinct ends that point in one direction; filaments have didstinct +/- ends; thinner and more flexible than microtubules

What are actin filaments important for?

Muscle contraction

What happens during muscle contraction?

During a simultaneous shortening of all sarcomeres; when myosin heads walk along actin filaments by cycling through attaching/detaching; myosin heads are propelled along actin filaments through ATP hydrolysis; actin filaments slide past myosin filaments (attach and release of myosin heads)

What triggers muscle contraction?

Sudden rise in cytosolic Ca²⁺; action potential is triggered by neurotransmitter open Ca²⁺ in T-tubule which opens Ca²⁺ release channel on sarcoplasmic reticulum which triggers myofibril contraction

How is muscle contraction usually prevented?

Myosin binding sites on actin monomers are blocked by tropomyosin; but the troponin protein present in the troponin complex triggers the shift of tropomyosin in the presence of Ca²⁺ , myosin binding sites are not blocked after the shift of tropomyosin which allows for contraction

How are genes activated?

through the cyclic AMP pathway; signal molecule binds to GPCR, then adenyl cyclase is activated which cleaves ATP to form cyclic AMP, cAMP activates protein kinase A which phosphorylates other kinase which activates glycogen phosphorylase to break down glycogen, then PKA inactivates glycogen synthase (prevents glycogen from being made)

How does the inositol pathway trigger a rise in intracellular Ca²⁺?

signal molecule binds to GPCR which activates G-protein subunits; G-protein a;pha beta and gamma activate phospholipase C; phospholipase C cleaves inositol phospholipid to diaglycerol and inositol 1,4,5-triphosphate (IP₃) which diffues through cytosol and binds to Ca²⁺ channels on ER surface; Ca²⁺ ions flood into the cytosol; diacylglycerol recruits protein kinase C (PKC) to membrane and activates kinase; PKC phosphorylates downstream intracellular proteins

What do activated receptor tyrosine kinases (RTKs) do?

They recruit a complex of intracellular proteins; enzyme coupled receptors contain protein binding domains exposed to the extracellular space and enzyme domains in the intracellular space; enzyme domains in the intracellular space serve to cross-phosphorylate the other domain; activated receptors recruit and activate other signaling/scaffolding proteins to its cytoplasmic tails and trigger signal cascade

What do most RTKs activate?

Monomeric GTPase Ras (a small monomeric GTP binding protein that is downstream from RTKs

What does activated Ras trigger?

Kinase cascade → activates MAP (mitogen activate protein kinase which is important for division) kinase kinase kinse; MAPKKK activates MAPKK; MAPKK activates MAPK which changes gene expression and protein activity of other downstream proteins

What happens when RTKs activate phosphoinositide 3-kinase?

Lipid docking sites are formed in the PM → inositol phospholipids in the PM are phosphorylated, phosphorylated inositol proteins serve as docking sites for intracellular signaling proteins (relocate to PM); survival signal IGF (intracellular growth factor) activates RTK which recruits PI 3-kinase; recruitment of protein kinase I and Akt to membrane allows Akt to propagate signal; activated Akt phoshporylates Bad, inactivting it, releasing it from Bcl2, Actovated Bcl2 promotes cell surviva;’ when Bad is active, cell suicide apoptosis happens

How do you study cell signaling pathways?

Mutation of specific amino acids from Tyr to other amino acids changes ability of downstream signaling proteins to bind; by mutating individual amino acids to a non-phosphorable amino acid (no OH group) allows researchers to study the identity of downstream proteins and their relationship with RTKs; to study order of proteins in a signaling pathway, you need to mutate an individual protein to render it non-functional OR overactivate a protein to make it extra functional;

How can you tell the order of proteins after affecting one of the proteins?

if the protein is downstream from the mutated protein, there will be no effect as a result of the changes; if the protein is upstream of the mutated protein, then a defect in the signaling protein abolishes signaling; proteins can be placed in order based on the order of signaling deduced experiments

How are different steps in the cell cycle triggered?

Different cyclin-Cdk complexes because levels of cyclin proteins are specific to each phase which drives assembly and activation of cyclin-Cdk complexes (cyclinCdk complexes cannot be assembled without the respective cyclin; transcription and translation of cyclins will only be triggered during a specific point in the cell cycle phase and continue to accumulate)

How are cyclin concentrations regulated?

By transcription and proteolysis (cyclin protein levels must be rapidly reduced going into the next phase; cyclin proteins are rapidly degraded by slatinf cyclins for destruction through tagging with ubiquitin; anaphase promoting complex or cyclosome (APC/C) tags cyclin-Cdks with ubiquitin; tagging with ubiquitin slates proteins for destruction in the proteasome; once cyclin is destroyed, Cdk returns to inactive state

How is the activit5y of Cyclin-Cdk complexes controlled?

By phosphorylation, dephosphorylation and Cdk inhibitor proteins (inhibiting kinase adds inhibitory phosphates to M-cdk leaving it inactive; phosphates must be removed by Cdc25 for Cdk complex to become active; binding of Cdk inhibitory proteins prevents Cdk from phosphorylating target proteins; P27 maintains Cdk in inactive state during G1 phase; pausing can give G1 more time to grow)

What can reverse the effects of Cdks?

Phosphatases downstream of active Cdks

What do mitogens do?

Promote production of cyclins that stimulate cell division (mammalian cells will only multiply if they are stimulated by extracellular signals; mitogens are produced by other cells; if there are no mitogens the cell will enter G0; to escape cell cycle arrest there must be an accumulation of cyclins; mitogens switch on cell signaling pathways that stimulate synthesis of G1-cyclins, G1-S-cyclins and other proteins for DNA synthesis and chromosome duplication)

What does S-Cdk do?

Initiates DNA replication and blocks re-replication (DNA prepares to replicate by recruiting proteins to sites where replication will begin (origins of replication); an origin replication complex is a complex of proteins that sits on the origin of replication and it recruits Cdc6 (which rises in G1); ORC + Cdc6 positions helicase to open up the replication bubble; S-Cdk activates helicase and recruits rest of replication machinery; S-Cdk also prevents re-replication by phosphorylating Cdc6 and ORC (cannot reinitiate replication again in the same cycle))

How can the cell cycle be arrested in G2?

Incomplete replication of DNA (when DNA replication stalls, single stranded DNA at the replication fork triggers a DNA damage response; DNA damage response inhibits Cdc25 phosphatase which prevents M-Cdk from triggering M-phase

What does M-Cdk do?

Drives into mitosis; helps prepapre duclipactec chromosomes for segregation and induces assembly of the mitotic spindle; accumulation happens throughout G2 but M-Cdk is only active at the end of G2; active M-Cdk activates more Cdc25 in a positive feedback loop; once activated, M-cdk drives cell into mitosis irreversibly, M-Cdk is also responsible for reducing levels of itself at the end of mitosis (activated M-Cdk turns on APC/C which marks M-cyclins for destruction))

what does proteolysis do?

Triggers sister-chromatid separation at anaphase (anaphase begins with breakage of linkages that hold sister chromatids together in duplicated chromosome; active AOC/C ubiquilates securin (inhibitory protein for separase); during metaphase the spindles are attaches to the kinetochore complex; in anaphase separase cleaves cohesion allowing mitotic spindles to pull apart sister chromatids