Cell Bio Final Exam

Review, Cell Signaling, Cell Cycle, and Apoptosis

How is genetic material stored in cells?

In DNA

What happens to the parent strands during DNA replication?

They are used as a template for the new strands

Endosymbiotic theory

Mitochondria and chloroplasts evolved from symbiotic bacteria captured by an ancient archaea. Both have their own circular DNA and replicate independently of the cell.

What makes up proteins? What links them together?

amino acids, peptide bonds

Protein families

proteins with similar sequences and conformations. Evolutionarily related. May have distinct functions. Ex: serine proteases break down amino acids by targeting different peptide bonds

Lysozymes

cut the polysaccharides in bacterial cell walls. Amino acids in the active site interact with glycosidic bonds.

Motor proteins

proteins capable of movement. Ex: actin and myosin

Enzymes

proteins that catalyze reactions by lowering the activation energy

3 domains of living organisms

Bacteria, archaea, eukaryotes

Prokaryote characteristics

No membrane-bound organelles, no nucleus, single circular chromosome, divide via binary fission, smaller, peptidoglycan cell walls, simultaneous transcription and translation

Eukaryote characteristics

membrane-bound organelles, have a nucleus, paired linear chromosomes, divide via mitosis, larger, polysaccharide cell walls (if present), separate transcription and translation

Condensation vs hydrolysis

Condensation - joining 2 subunits with the elimination of water, frees electrons for covalent bonding, anabolic

Hydrolysis - breaking bonds between 2 molecules by adding water, releases energy, catabolic

How are cell respiration and photosynthesis connected?

The products of photosynthesis (glucose, O2) are used for cellular respiration, and the products of cellular respiration (CO2, H2O) are used for photosynthesis

Catabolism vs anabolism

Catabolism - breakdown of larger molecules into subunits, releases energy

Anabolic - joins smaller molecules together, requires energy

How do organisms obtain energy from food? What carrier molecules are reduced? What is the main product?

Cell respiration, FAD and NAD (to FADH2 and NADH), ATP

What component determines the physical properties of an amino acid?

the side chain (R group)

Ligand

a substance that is reversibly bound to a protein. Ex: hemoglobin and oxygen, antibodies and antigens

SRC protein kinase activation steps

1. A phosphate is released from the SH2 domain (regulatory) to loosen the structure of the protein

2. The SH3 domain (also regulatory) moves and binds to an activating ligand

3. Tyrosine is phosphorylated and the active site opens

Characteristics of life (8)

1. Response to stimuli

2. Metabolism

3. Growth and development

4. Cellular organization

5. Homeostasis

6. Reproduction

7. Heredity

8. Evolution

What forces stabilize a proteins 3D structure?

Weak (non-covalent) forces - Van der Waals interactions, hydrophobic interactions, H-bonding, ionic bonds

DNA vs RNA

DNA: double stranded, A-T, deoxyribose, forms helix

RNA: single stranded, A-U, ribose, forms hairpins

Chromosomes

paired, linear, segmented packages of DNA

Transcription vs translation

Transcription: making an RNA copy of DNA

Translation: using RNA to make proteins

What enzyme is involved in transcription?

RNA polymerase

When does translation end?

When the ribosome encounters the stop codon in the A site

Chaperones

proteins that help guide the folding of other proteins

Polyribosome

a single RNA being translated by multiple ribosomes at once, forms a spiral

Why are phospholipids good membrane components?

They are amphipathic - hydrophilic head and hydrophobic tails

Components of cell membranes

phospholipids, cholesterol, and proteins

Phospholipid movement in membranes

Can move laterally within the membrane very quickly, but require flippase proteins to flip between inner and outer leaflets

What secondary structure do membrane proteins usually have?

alpha-helices

What are detergents used for?

Extracting membrane proteins. They are hydrophobic and hydrophilic, so they can surround the protein and take it out of the membrane.

How does the cytoskeleton affect protein diffusion?

it restricts proteins into certain domains, but proteins can occasionally cross over into other domains

What molecules can pass through the membrane easily? What molecules cannot?

Small hydrophobic molecules and gases pass through the easiest, followed by small polar molecules (water), large molecules (glucose), and ions (need transporter).

Aquaporins

protein channels that transport water through passive diffusion

What molecules is required for the uptake of glucose into enterocytes?

Na+

P-type ATP pump

transporter phosphorylates itself during pumping, maintains ion gradients through active transport, relies on hydrolysis of ATP, has conformational change. Ex: Ca2+ transport into sarcoplasmic reticulum of muscle cells

Voltage-gated channel

change in voltage across the membrane opens the gate. Ex: depolarization in Na channels

Why is it beneficial to be able to stop translation of broken mRNAs?

Broken mRNAs could code for incorrect proteins, inhibiting the cell’s function

Components required for translation

ribosomes, mRNA, tRNA, and amino acids

If the distance between the A site and P site was increased by 2 bases, how would it affect translation?

The protein would be coded incorrectly because the incoming codon would not sit correctly in the A site. Peptide bond synthesis would also be inhibited because the amino acid chain in the P site would be too far from the new amino acid in the A site.

Lipid raft

a concentration of lipid and protein components that perform a specialized function and move as a unit. They are often used for signaling, endocytosis, and vesicle transport.

Why do enterocytes have tight junctions?

The tight junctions keep proteins bound in specific domains and keep them from dispersing throughout the cell. Enterocytes need SGLT1 (brings in glucose) to stay on the lumen side of the cell, while GLUT2 (moves glucose into the blood) needs to stay on the capillary side.

Cholesterol

Membrane component found in many cells. Made of four fused hydrocarbon rings with a polar charged head group and a hydrophobic tail. Embedded within the lipid bilayer. Helps maintain fluidity at extreme temperatures and aids in signaling.

Channel vs transporter

Channel: protein that forms a pore across the membrane. Both sides are open at the same time, but it can be closed or blocked. Used for ion transport. Ex: aquaporins

Transporters: alternate between 2 conformations and have a binding site for the molecule being transported. Trigger induces a conformational change. Ex: SGLT1

Why do gram negative bacteria have an auxiliary transport mechanism? How does it work?

They have an extra outer membrane so molecules have to be transported twice. The outer membrane has channels/pores, while the inner membrane has transporters. Proteins in the periplasmic space bring molecules to the transporters.

Signal sequence

sequence of amino acids that tags a protein for transport to a specific location in the cell

Endoplasmic reticulum

Structurally and functionally diverse. One continuous structure that becomes more enclosed and tube-like as you get further from the nucleus. Spread throughout the cell and is in close contact with mitochondria and the plasma membrane. Proteins (unfolded) are translocated into the rough ER through ribosomes embedded in the membrane.

What happens when a protein cannot be folded correctly in the ER?

First, glucosyl transferase glycosylates the protein again and calnexin retains it. If it continues to be folded incorrectly, the unfolded protein response is triggered. The protein leaves the ER and ubiquitin binds to it to mark it for degradation by a proteasome.

Peroxisomes

Bud from the ER and acquire proteins from the ER membrane and cytosol. Contain oxidative enzymes. Functions: phospholipid synthesis, synthesis of myelin sheath on neurons, breakdown of alcohol, produce H2O2.

Protein transport into the chloroplast

Requires 2 signal sequences. One directs proteins into the stroma (through binding with TOC and TIC), the other directs it to the thylakoid membrane.

Transport into the nucleus

Occurs through nuclear pores. Ran-GTPase imposes directionality. Cargo proteins bind receptor and enter the nuclear pore. Then Ran-GTPase binds the receptor, causing the release of the cargo, and the Ran-GTPase-receptor complex exits through the pore.

How are organelle comportments recognized by vesicles?

Based on their phosphoinositides (PIPs)

SNARE proteins

Mediate membrane diffusion. Found in pairs. T snares (on target) and V snares (on vesicle) coil around each other after Rab binding and push water out of the way. The outer cytosolic leaflets fuse and separate, then the inner leaflets do the same.

Two types of transport through the golgi

1. Vesicle transport - movement of cargo from one cisterna to the next via vessicles

2. Cisternal maturation - new cisterna continually form from the ER. Each layer successively moves down as a new one is added. Trans golgi network gets smaller and buds off to form vesicles. Proteins move with cisterna.

Synaptic vesicles

Vesicle components are trafficked to membrane and prepped before signaling to allow for rapid response. The components move from golgi → membrane → endosome → vesicle. They are filled with neurotransmitters, which are released in response to an action potential.

Lysosomes

membrane-bound compartment filled with acid hydrolases (enzymes active in acidic environment) that break down macromolecules. Maintain internal acidity via H+ transport through ATPase. Generated from endosomes.

Steps of Cellular Respiration

1. Glycolysis - sugar splitting. In the preparatory phase, PO4 from ATP is added to glucose. In the payoff phase, the sugar molecules are rearranged. Produces net 2 ATP, 2 NADH, and 2 pyruvate.

2. Conversion of pyruvate - coenzyme-A is added to pyruvate. Produces 2 Acetyl-CoA, 2 CO2, and 2 NADH

3. Citric Acid Cycle - acetyl-CoA binds to oxaloacetate to form citrate, which is rearranged and oxidized. Completes the breakdown of glucose. Produces 6 NADH, 2 FADH2, 4 CO2, and 2 ATP

4. Oxidative phosphorylation - high-energy electrons from NADH and FADH2 are used to create a H+ gradient, which powers ATP synthesis. Produces ~32 ATP

Steps of Photosynthesis

1. Light reactions - harvest energy from the sun and store it in ATP and NADPH. Driven by a H+ gradient and excitation of electrons in chlorophyll. Split water to replace electrons. Occurs in the thylakoids.

2. Calvin Cycle - energy from ATP and NADH is used to fix carbon and make sugar. Occurs in the stroma.

How could you test if a series of amino acids is a signal sequence?

Fluorescently tag the protein and remove the signal sequence. If the protein ends up dispersed through the cell (in cytosol) instead of localized in one place (target), it is likely a signal sequence.

Golgi

Made of ordered, stacked membrane compartments called cisterna. Has 2 faces: cis face is near the nucleus and trans face is near the plasma membrane. The compartments each have different functions, and proteins move through each compartment for modifications (such as glycosylation), sorting, and packaging into vesicles.

Why are the components of the ETC and ATP synthesis localized in the cristae?

They make compartments that allow H+ ions to build up and increase surface area for ATP synthesis.

What do the mitochondria and chloroplasts have in common? (6 things)

1. Energy conversion

2. Compartmentalization - cristae and thylakoids

3. Ion gradients (via electron carriers) and ATP synthesis

4. Oxidation/reduction reactions

5. CO2 ←→ O2

6. Semiautonomous

How are mitochondria and chloroplasts different?

1. The inner membrane of the chloroplast is not folded, but the inner membrane of the mitochondria is

2. Chloroplasts have extra compartments (thylakoids)

3. Mitochondria break down glucose for energy, chloroplasts store energy in glucose

Signaling

How cells communicate. Response to the environment. Can be within an organism or between two organisms. Important for growth, division, and differentiation. Occurs in the multiple steps and often involves gene expression. Can affect metabolism, cell shape, and movement. Many pathways occur simultaneously

Quorum sensing

group of bacteria in a liquid together signal to each other

Insulin signaling

Insulin is a hormone released from the pancreas that controls cellular uptake of glucose. Insulin binds to insulin receptors, which triggers a series of reactions and phosphorylation of membrane phospholipids. GTP is hydrolyzed and binds to Rab10, which activates GLUT4 to go to cell surface and bring in glucose.

Extracellular signals can act over _______ distances

short and long

4 Pathways of extracellular signaling

1. Contact-dependent - direct membrane to membrane contact (ex: cardiomyocytes)

2. Paracrine - one cell releases several signaling mediators to act on neighboring cells

3. Synaptic - neurons secrete neurotransmitters to nearby target cells

4. Endocrine - hormones are secreted into the bloodstream and act over a longer distance

Extracellular signaling molecules

Receptor-specific. Hydrophilic molecules bind to cell-surface receptors. Hydrophobic molecules bind to intracellular receptors after being brought into cell by carrier proteins.

Cells response to extracellular signals

Cells are programmed to respond to specific combos of signals. Different cells can respond differently to the same signal. Receptors can be similar or different. Ex: Acetylcholine can trigger decreased firing in the heart, secretion in the salivary gland, and contraction of skeletal muscles (different receptor).

3 Major classes of cell-surface receptor proteins

1. Ion-channel coupled - binding of a signal molecule opens/closes the ion channel and facilitates transport of the ion. Short and rapid pathway, usually has 2 components, cell to cell signaling.

2. G-Protein Coupled (GPCR) - involves a trimeric GTP-binding protein that is anchored to the cytosolic side of the membrane. Signal molecule binds receptor, which interacts with G protein, which then activates target protein. Often activates enzymes.

3. Enzyme-coupled - function as a receptor and an enzyme. 2 subunits are separated and inactive until a dimer molecule brings them together and activates them. Usually involves phosphorylation. Ex: insulin

Mediators

AKA secondary messengers. Small molecules that transfer messages from one component/cell to another.

2 methods of mediator activation

1. Phosphorylation - molecule binds to receptor and protein kinase phosphorylates mediator using ATP hydrolysis. Mediator-PO4 is activated and transmits a signal to the next mediator. Protein phosphatase removes PO4, deactivating the original mediator.

2. GTP binding - signal is off and mediator is bound to GDP. Signal molecule binds receptor, causing mediator to release GDP and bind GTP. GTP-bound mediator is activated and transmits signal to the next mediator. GTP is hydrolyzed and mediator is deactivated.

3 ways that intracellular signaling complexes form

1. Preformed signaling complex - receptor is bound to a scaffold and all intermediates are constantly present, even when off

2. Assembly on activated receptor - intermediates bind after signal molecule binsd

3. Assembly on phosphoinositide docking site - signal molecule leads to phosphorylation and intermediate activation

Cyclic AMP and gene expression

1. Signal molecule binds to a GPCR

2. Activated G protein activates adenylyl cyclase, which converts ATP to cAMP

3. cAMP binds to and activates PKA (kinase)

4. PKA enters the nucleus and phosphorylates CREB (protein)

5. CREB-PO4 bind CRE

6. CREB-binding protein binds and activates gene transcription

Cytokines

chemical mediators associated with inflammation. Induce conversion of monocytes to macrophages.

JAK-STAT pathway

JAK - janus kinase

STAT - signal transducer and activators of transcription

1. Cytokine binds to 2 JAK receptors and brings them together

2. JAKs phosphorylate each other

3. Each JAK phosphorylates its own receptor at the cytoplasmic end, creating a docking site for STAT

4. SH2 on STAT binds the docking site

5. JAK phosphorylates STAT

6. STAT-PO4 is released and forms a dimer

7. STAT dimer enters the nucleus and binds the cytokine-responsive element, which activates transcription of the target gene

Many signaling pathways involve what?

Dimers

What is cell division needed for?

Growth, reproduction, and cell replacement

Phases of eukaryotic cell cycle

Interphase and Mitotic phase (mitosis and cytokinesis)

Stages of interphase

1. Gap 1 (G1) - cell grows and does normal function

2. Synthesis (S) - DNA is replicated, cell is committed to division at this point

3. Gap 2 (G2) - preparation for cell division

What is G0?

A resting phase. Cells may enter this during unfavorable conditions, such as a lack of resources and space. Some cells, such as neurons, do not divide at all and stay in this phase.

Cancer

unregulated cell division

The cell cycle is a ______ process

tightly controlled

3 checkpoints in the cell cycle

1. End of G1 - cell determines if it has enough space and resources to divide, commits to cell division

2. End of G2 - cell determines if DNA was replicated correctly and if there are enough proteins/resources, commits to mitosis

3. Between metaphase and anaphase - cell determines if the spindle is bound to the sister chromatids and if they are lined up correctly

Cell cycle control

Dependent on cyclin dependent protein kinases (Cdk). Cyclin is a mediator that is specific to each stage. Cdk is expressed constantly but only active in the presence of cyclin, so cyclin expression controls phase changes. Cdks are activated sequentially and the steps regulate each other. Protein phosphatase removes PO4 to deactivate Cdk.

Kinetochores

proteins on the centromere of chromatids

What is the mitotic spindle made of?

actin and myosin

Phases of mitosis

1. Prophase - DNA is duplicated before entry. Sister chromatids condense and spindle starts to form

2. Prometaphase - fragmentation of nuclear envelope, spindle binds to kinetochores, movement of chromosomes (via motor proteins: kinesin and dynein)

3. Metaphase - sister chromatids line up in the center of the cell and the spindle is attached to kinetochore on both sides

4. Anaphase - sister chromatids split, outer spindle retracts and middle spindle fibers push chromatids apart, individual chromosomes go to opposite poles

5. Telophase - 2 sets of daughter chromosomes arrive at the poles, nuclear envelope reforms around each new nuclei, division of cytoplasm begins

Cytokinesis

Animal cells - contractile ring of actin and myosin causes the membrane to pinch inwards (outside in)

Plant cells - golgi derived vesicle accumulate between the 2 nuclei and fuse to form the cell plate, which later becomes the cell wall (inside out)

Cells divide into _____ cells

smaller

Meiosis

DNA is duplicated once. 2 rounds of cell division. Homologous chromosomes are pulled to separate sides, then sister chromatids are split. Produces 4 cells with ½ of the chromosomes. Crossing over allows daughter cells to be nonidentical.

Apoptosis

programmed cell death. Cell collapse, apoptotic bodies degrade cell components. Fragmentation of the nucleus. Cell is engulfed by phagocytes.

Necrosis

death in response to an acute event. Cell bursts. Inflammatory response to surrounding tissues.

What is apoptosis critical for?

Development. Ex: webbing between fetal mouse paws must die

What controls apoptosis?

An intracellular cascade mediated by caspases. Caspases are proteases that cleave each other to activate after signal binding.

Caspase-activated DNAase

Caspase cleaves iCAD from CAD, then active CAD cleaves DNA.