Cell Bio Final

Difference between Prokaryote and Eukaryote organelles

Prokaryotes lack membrane bound organelles and only contain:

• Ribosomes

• nucleoid

• cell membrane

• cytoplasm

Organelle functions to know

• Mitochondria

• Chloroplast

• Nuclear envelope

• Golgi apparatus

• Peroxisome

• Lysosome

• ER

• Ribosome

How do cilia and flagella move

Have a structure rich in double microtubules and dynein arms that move towards minus end closer to cell body causing the power stroke to occur which fully extends cilia. Movement of dynein allows for cilia to move and therefore the entire cell.

Three major filaments of cytoskeleton

• Microtubules

• Intermediate filaments

• Actin filaments

How does cytoskeleton move cargo around cell

Through motor proteins bound to microtubules by globular heads

Two motor proteins that move on cytoskeleton

• dynein (moves toward minus end)

• Kinesin (moves toward plus end)

motor proteins walking steps

• Initial position has leading head bound to ADP and lagging head bound to ATP

• ATP gets hydrolyzed which leads to weak association and release from microtubule

• leading head binds to ATP causing a conformational change that throws lagging head ahead

• original position is restored

Dynamic instability

Rapid switch from growth and shrinkage between microtubules on a centrosome due to GTPase activity of B-subunit. Important for Anaphase A to work.

Sarcomere

Highly organized actin and myosin filaments that make up contractile component of myofibril

Muscle contraction process

• Acetylcholine binds to cell surface receptor causing a signaling sequence within cell

• Sarcoplasmic reticulum is signaled to release Ca2+ into cytoplasm

• Ca2+ binds to troponin complex causing a conformational change

• This change also moves bound tropomyosin that blocked myosin II from binding to actin

• Myosin II binds to actin and walks toward plus end, bringing Z-disks closer together

• Muscle contracts

Myosin II walking on actin process

• Attached: Myosin II is bound to Actin in a rigor conformation

• Released: ATP binds to cleft on myosin II head, changing its conformation and causing it to release from actin

• Cocked: Myosin II cleft closes and moves it closer to actin plus end. head also has ATPase activity that hydrolyzes it to ADP and Pi

• Force generating: Myosin II bound to ADP and Pi has weak affinity to actin so Pi is released. The change in shape due to release generates force that allows head to regain original shape and release ADP

• Attached: Myosin II head is bound to no active carriers and binds to actin

Cohesin and Condensin

• Cohesin: ring shaped protein complex that joins sister chromatids together after replication in S-phase

• Condensin: Ring shaped protein complex that condenses chromosomes at prophase to prepare for proper separation

Cohesin cleavage process

APC indirectly cleaves cohesin through activating another enzyme that cleaves at metaphase, allowing mitosis to proceed into anaphase

CDK function

Enzyme that triggers events in cell cycle through a series of phosphorylation’s. Cell cycle control system depends of CDK activity. Must bind to cyclin to be activated

M-CDK

Responsible for initiation of mitosis.

Must be dephosphorylated to be active. Is inhibited by inhibitory kinase Wee1 and activated by activating phosphatase Cdc25.

G1-CDK and G1/S-CDK

Responsible for initiation of S-phase

They phosphorylate and inactivate Rb protein therefore allowing transcription factors to be released and bind to genes responsible for DNA replication

S-CDK

responsible for chromosome duplication

activates helicase during S-phase to begin DNA replication

How are CDKs regulated

regulatory proteins that bind to CDK to block binding or activity of cyclin-CDK complexes.

ex.

• p27

• p21

Atomic number and atomic mass

• Atomic number: number of protons in an atom

• Atomic mass: number of protons and neutrons in atom nucleus

Covalent bonds vs Noncovalent bonds

• Covalent Bond: sharing of electrons (strong bonds)

• Noncovalent Bond: transfer of electrons (weak bonds)

Reduction and oxidation

• Reduction: Addition of an electron, loss of an oxygen, or gain of hydrogen. Charge decreases

• Oxidation: Loss of electron, gain of oxygen, or loss of hydrogen. Charge increases

These occur together

Electron carriers function

NADH and NADPH are activated carriers of electrons. They abstract energy by oxidizing organic molecules, becoming reduced, and then donating them elsewhere.

favorable rxns vs unfavorable rxns

• favorable reaction: spontaneously occur and release free energy (-G)

• unfavorable reaction: require an input of energy therefore product has more free energy than reactant (+G)

General relationship between oxidation and reduction with favorability

oxidation is favorable and associated with breakdown of complex molecules

reduction is unfavorable and associated with building of complex molecules

G as reaction proceeds

As reactants are used up and more product forms G moves closer to equilibrium or 0

How are unfavorable reactions able to proceed

Coupling with a favorable reaction such as ATP hydrolysis. If overall free energy change is negative than reactions can proceed.

Enzymes help with favorable reactions

They lower activation energy required to initiate a spontaneous reaction. This speeds up reactions.

Condensation reaction

Energetically unfavorable reaction that uses energy stored in ATP to join molecules together with the release of water

Fibrous proteins

• coiled coils

• keratin

• intermediate filaments

• microtubules

Have the ability to form into filaments, sheets, or spheres

Protein folding

Proteins fold into most energetically favorable (lowest energy) structure. This occurs naturally and sometimes with the help of chaperone proteins.

What ultimately determines protein shape

amino acid sequence (primary structure)

2 Chaperone protein actions

• Physically assist polypeptide into forming most energetically favorable structure

• Encapsule protein and allow it to refold

Enzymes to know

• hydrolase

• Nuclease

• Protease

• Ligase

• Isomerase

• Polymerase

• Kinase

• Phosphatase

• oxido-reductase

• ATPase

Cell membrane structure

Amphipathic (hydrophobic and hydrophilic)

• Polar hydrophilic head: at exterior of membrane made of choline, phosphate, and glycerol

• Nonpolar hydrophobic tails: make up inside of membrane made of C-H interactions

Cell membrane formation in ER process

• phospholipid synthesis adds to cytosolic side of ER membrane

• Scramblase will then randomly flip-flop phospholipids from one monolayer to the other

• ER membrane will have symmetric growth on both lumen and cytosolic sides

Cell membrane formation in Golgi process

• New membrane is delivered from ER to Golgi

• Flippase transfers specific phospholipids to cytosolic side

• Golgi will have asymmetric growth

Brca 1 gene

Tumor suppressor gene that when mutated causes breast and ovarian cancer

How do drugs treat mutations to Brca1 gene

Inactivate mutated tyrosine kinases to block activation and proliferation

ex. Gleevec

Cell cortex

Mesh of peripheral proteins rich in actin, underlying the cell membrane for support.

Spectrin

cytoskeleton protein that is found in red blood cells cell cortex to give bi-concave appearance.

Mutation will lead to anemia

Transporter vs channel

• Transporter: allows solute to enter opening and then release on the other side

• Channel: allows ions to passively pass into membrane through opening

Transporter is have specificity and go through conformational changes. Channels are openings that rely on passive transport

Valium

Tranquilizer that binds to GABA gated Cl- channels to facilitate their opening. High amounts of Cl- flow into cell and polarize it making it harder for an action potential to occur.

Gated ion channels

Control flow of ions

• Voltage gated channel: dependent on membrane potential

• Ligand gated channel: dependent on binding of small molecule

• Mechanical gated channel: opens due to physical force

aerobic respiration

sugar + O2 → CO2 + H2O (ATP)

break down of sugar to generate energy in the presence of oxygen

Anaerobic respiration

Break down of sugar into lactic acid or ethanol, yielding much less energy

Protein entering nucleus process

• Protein with nuclear localization signal (lots of Lys) is recognized by a nuclear import receptor

• Nuclear import receptor guides protein to nuclear pore by interacting with cytosolic fibrils

• guidance into pore passes through protein meshwork that allows for specification of entry into nucleus

• The protein is released when inside nucleus

Does protein structure change when entering nucleus

No it remains unchanged

nuclear import receptor energy process

• When in nucleus with protein, Ran-GTP binds and protein dissociates from receptor

• receptor bound to Ran-GTP passively diffuses through nuclear pore back into cytoplasm

• Ran hydrolyzes GTP to power nuclear import receptors binding and guidance of other nuclear bound proteins

protein translocator

transports unfolded (naked) proteins across mitochondrial and chloroplast membranes through a narrow opening. Proteins are unfolded when going through and refolded when inside organelle.

Wnt signal

Binds to G-coupled receptor activating a signaling pathway that deactivates APC. molecules that are usually degraded are able to bind to transcription factors and uncontrollably stimulate gene expression and cell proliferation in gut stem cells

G-protein-coupled receptor

Largest family of cell surface receptors that spans membrane 7 times

G protein parts

alpha, Beta, Gamma subunits

G protein activation process

• all parts are bound together with a-subunit holding a GDP

• when a signaling molecule binds to receptor, a conformational change occurs that releases GDP

• B,Y-subunits dissociate from a, and GTP binds to a-subunit

• the two complexes are activated and trigger a signaling pathway

G protein inactivation process

• a-subunits GTPase activity hydrolyzes GTP to GDP and releases Pi

• inactive a-subunit reassembles with B,Y complex to reform inactive G protein

Cell cycle phases

• G1: Cell growth and monitoring of internal and external environment to ensure DNA replication is ready

• S: chromosome duplication occurs

• G2: Cell growth and monitoring of internal and external environment to prepare for mitosis. Organelles duplicate

• M: Mitosis and cytokinesis

Cell cycle checkpoints

• G1 checkpoint: is cell environment favorable for DNA dup.

• G2 checkpoint: is DNA replicated or is DNA damage repaired

• M checkpoint: are chromosomes properly attached at spindles

Cdc25 controlling cell activity

is an activating phosphatase that takes away phosphates in M-CDK to activate it and start mitosis. Positive feedback loop is created between Cdc25 and M-CDK.

centrosome structure

• two central centrioles at right angle

• Protein matrix creating sphere

• Y-tubulin rings where microtubules grow out of

centrosome function

microtubule organizing center and important for mitosis and anaphase