Lecture Notes Flashcards – Cell Biology, Macromolecules, RNA & Protein Regulation, Endomembrane System, Translation & Targeting

What is the nucleus, and where is it located?

The nucleus is the cell’s command center, enclosed by the nuclear envelope in the center of eukaryotic cells. It stores DNA and is the site of transcription (DNA → RNA).

What is the nucleolus, and what is its function?

The nucleolus is a dense region inside the nucleus where rRNA is synthesized and ribosomal subunits are assembled.

What are nuclear pores, and what do they do?

Nuclear pores are protein complexes in the nuclear envelope that regulate transport of RNA and proteins between the nucleus and cytoplasm.

What is the nuclear envelope, and what is its structure?

A double membrane surrounding the nucleus with pores that control entry/exit of molecules; it is continuous with the endoplasmic reticulum.

What are ribosomes, and where are they found?

Ribosomes are molecular machines made of rRNA and proteins that carry out protein synthesis; they can be free-floating in the cytosol or bound to the rough ER.

What is the rough endoplasmic reticulum (rough ER), and what is its function?

A network of flattened sacs studded with ribosomes that synthesizes, folds, and modifies proteins.

What is the smooth endoplasmic reticulum (smooth ER), and what does it do?

A network of tubules without ribosomes that synthesizes lipids, detoxifies drugs, and stores calcium.

What is the Golgi apparatus, and what is its role?

A stack of membrane sacs that modifies, sorts, and packages proteins and lipids for secretion or delivery to organelles.

What are transport vesicles, and what is their function?

Small membrane-bound sacs that move proteins and lipids between organelles or to the plasma membrane.

What are lysosomes, and what do they do?

Acidic vesicles containing digestive enzymes that break down macromolecules, old organelles, and pathogens.

What are mitochondria, and what are their functions?

Double-membrane organelles that produce ATP via cellular respiration; contain circular DNA and replicate independently.

What are chloroplasts, and where are they found?

Double-membrane organelles found in plant cells that carry out photosynthesis; contain circular DNA and replicate independently.

What is the plasma membrane, and what is its role?

A phospholipid bilayer surrounding the cell that controls entry/exit of molecules and maintains homeostasis.

What is the cytosol vs cytoplasm?

Cytosol is the fluid portion of the cell where many reactions occur; cytoplasm includes cytosol plus organelles (excluding the nucleus).

What are microtubules, and what do they do?

Hollow tubes of tubulin that provide structure, act as tracks for motor proteins, and form spindle fibers during mitosis.

What are microfilaments, and what is their function?

Thin filaments of actin that control cell shape, support movement (crawling), and assist in cytokinesis and muscle contraction.

What are intermediate filaments, and what do they provide?

Rope-like fibers that provide tensile strength, resist stretching, and form the nuclear lamina under the nuclear envelope.

What are centrioles, and where are they located?

Cylindrical microtubule structures located near the nucleus in animal cells that organize spindle fibers during mitosis.

What can light (brightfield) microscopy show?

Live or dead cells up to ~1000x magnification; can view nucleus, chloroplasts, and cell boundaries; detailed view often requires staining.

What can fluorescence microscopy show?

Visualizes specific proteins or organelles using fluorescent tags; higher detail than light microscopy; usually dead cells unless GFP used.

What can TEM (transmission electron microscopy) show?

Internal ultrastructure of cells down to DNA strands with high resolution (~1 nm); images are grayscale (often false-colored).

What can SEM (scanning electron microscopy) show?

3D surface detail of cells and specimens with resolution ~3–20 nm; images grayscale (often false-colored).

What evidence supports endosymbiosis for mitochondria and chloroplasts?

Double membranes, circular DNA, own ribosomes, independent replication, and size similar to prokaryotes.

Which organelles are made of a phospholipid bilayer?

All membrane-bound organelles: nucleus, ER, Golgi, lysosome, plasma membrane, vesicles, mitochondria, chloroplasts.

Which organelles have a double membrane?

Nucleus (nuclear envelope), mitochondria, chloroplasts.

Where does transcription and RNA processing occur?

Inside the nucleus.

Where does translation occur?

In the cytosol, on ribosomes (free or ER-bound).

Where are ribosomal subunits made?

In the nucleolus.

Which organelle is the site of lipid synthesis?

Smooth ER.

Which organelles are involved in protein modification and sorting?

Rough ER and Golgi apparatus.

Which organelle produces ATP?

Mitochondria.

Which organelle breaks down macromolecules in an acidic lumen?

Lysosome.

What structures are continuous with each other?

Nuclear envelope and rough/smooth ER.

What structures are involved in mitosis?

Centrioles and spindle fibers (microtubules).

What are the four classes of biological macromolecules?

Carbohydrates, lipids, proteins, and nucleic acids.

What are the monomers of each macromolecule?

Carbohydrates: monosaccharides; Lipids: glycerol + fatty acids; Proteins: amino acids; Nucleic acids: nucleotides.

What types of bonds link the monomers?

Carbohydrates: glycosidic bonds; Lipids: ester bonds; Proteins: peptide bonds; Nucleic acids: phosphodiester bonds.

What are the main functions of carbohydrates?

Short-term energy, structural support (cell walls), and cell recognition/signaling.

What are the main functions of lipids?

Long-term energy storage, membrane structure, signaling molecules (steroids, hormones).

What are the main functions of proteins?

Enzymes, structural support, transport, defense (antibodies), and cell signaling.

What are the main functions of nucleic acids?

Store and transmit genetic information, direct protein synthesis.

What is the central dogma of biology?

DNA → RNA → Protein.

Where does transcription occur, and what is produced?

In the nucleus; produces RNA from DNA.

Where does translation occur, and what is produced?

In the cytoplasm on ribosomes; produces proteins from RNA.

What is the difference between genome and proteome?

Genome = entire DNA of a cell; Proteome = all proteins expressed in a cell (varies with conditions).

What sugar does DNA contain, and how does it differ from RNA sugar?

DNA contains deoxyribose (no 2’ OH); RNA contains ribose (2’ and 3’ OH).

What bases are found in DNA vs RNA?

DNA: A, T, C, G. RNA: A, U, C, G (U replaces T).

Which is more stable, DNA or RNA, and why?

DNA is more stable because it lacks the 2’ OH group, reducing reactivity.

What is dehydration synthesis, and what does it do?

A reaction that removes water to form covalent bonds between monomers, building polymers.

What is hydrolysis?

A reaction that uses water to break covalent bonds, splitting polymers into monomers.

Which process builds macromolecules, and which breaks them?

Dehydration synthesis builds; hydrolysis breaks.

What is ATP, and what is its role?

Adenosine triphosphate; the main energy currency of the cell.

What is GTP, and what is its role?

Guanosine triphosphate; used in protein signaling and microtubule function.

What are cyclic nucleotides (cAMP and cGMP)?

Modified nucleotides that act as second messengers in cell signaling pathways.

How are cyclic nucleotides made and broken down?

Cyclase enzymes convert ATP/GTP → cAMP/cGMP; phosphodiesterase enzymes degrade them.

What are GTPase, GAP, and GEF proteins?

GTPases switch between active (GTP-bound) and inactive (GDP-bound); GAP accelerates GTP hydrolysis to GDP; GEF swaps GDP for GTP, activating the protein.

DNA is converted to RNA through what process?

Transcription.

RNA codes for protein through what process?

Translation.

Where does DNA replication occur?

In the nucleus.

What molecule has only a 3’ OH on ribose?

DNA nucleotide.

What molecule has a 2’ and 3’ OH on ribose?

RNA nucleotide.

Which molecule uses peptide bonds?

Proteins.

Which molecule has CH2O as a general formula?

Carbohydrates.

Which molecule has cholesterol as a component?

Lipids.

Which molecule must fold properly to function?

Proteins.

What are the monomers of proteins, nucleic acids, carbohydrates, and lipids?

Proteins: amino acids; Nucleic acids: nucleotides; Carbohydrates: monosaccharides; Lipids: fatty acids/glycerol.

What are phosphorylation reactions carried out by?

ATP or GTP (nucleotides).

What is the primary structure of a protein?

The linear sequence of amino acids connected by peptide bonds.

What stabilizes primary protein structure?

Covalent peptide bonds between amino acids.

What is secondary structure in proteins?

Regular folding patterns such as α-helices and β-sheets.

What stabilizes secondary structure?

Hydrogen bonds between backbone atoms.

What is tertiary protein structure?

The overall 3D folding of a single polypeptide chain.

What stabilizes tertiary structure?

Weak forces (hydrogen bonds, hydrophobic interactions, ionic bonds, van der Waals) and strong disulfide bridges.

What is quaternary protein structure?

Association of two or more polypeptide subunits into one functional protein.

What forces stabilize quaternary structure?

Similar to tertiary: weak interactions and disulfide bridges.

What is denaturation of a protein?

Loss of structure (secondary, tertiary, quaternary) without breaking the primary sequence.

How does urea cause denaturation?

Disrupts hydrogen bonds and weak interactions, breaking secondary and tertiary structure.

Why is β-mercaptoethanol used in denaturation?

It breaks disulfide bridges (covalent), which urea cannot disrupt.

What are chaperones?

Helper proteins that prevent misfolding and aggregation, assisting in folding/refolding.

What happens when proteins misfold?

They can form aggregates that clog the cytoplasm and may cause cell death (linked to neurodegenerative diseases).

Where do hydrophobic amino acids tend to be located in globular proteins?

In the protein’s interior, away from water.

Where do hydrophilic amino acids tend to be located?

On the protein’s surface, exposed to water.

What is a biomolecular condensate?

A membraneless compartment that organizes proteins/RNA for activity (e.g., stress granules).

How is a biomolecular condensate different from a lysosome?

Condensates have no membrane and don’t degrade; lysosomes are membrane-bound and degrade contents.

What is the role of enzymes?

Lower activation energy, speeding up chemical reactions without being consumed.

What is feedback inhibition?

End product of a pathway binds allosterically to an enzyme at the start, stopping the pathway.

What is competitive inhibition?

A molecule resembling the substrate binds the active site, blocking substrate binding.

What is allosteric regulation?

Binding of a molecule at a regulatory site changes enzyme shape and activity.

How does phosphorylation regulate enzymes?

Kinases add a phosphate group (activates/inactivates); phosphatases remove it (reverses regulation).

What are GTP-binding proteins?

Proteins that act as molecular switches: active when bound to GTP, inactive when bound to GDP.

What is the difference between GEF and GAP?

GEF swaps GDP for GTP (activates); GAP hydrolyzes GTP to GDP (inactivates).

In the reaction E + S ↔ ES → EP ↔ E + P, what does ES represent?

The enzyme–substrate complex.

What does EP represent in the enzyme reaction?

The enzyme–product complex (transition state).

Why is the first step reversible, but the second step not?

Binding is weak and reversible; once bonds are broken/made in the transition state, the reaction goes forward.

Why does the enzyme (E) appear on both sides of the equation?

Because the enzyme is not consumed in the reaction and is regenerated.

What does chromatography do, and what can it tell you?

Separates molecules by size, charge, or affinity; can purify proteins but does not identify them unless affinity-based.

What is immunoprecipitation, and what does it reveal?

Uses antibodies to pull down a specific protein and its interacting partners, revealing complexes.

What is SDS-PAGE, and what does it measure?

Separates denatured proteins by size using an electric field; indicates protein size and abundance.

What does Western blotting do?

Uses antibodies to detect specific proteins after SDS-PAGE, showing presence and quantity.

What is immunofluorescence used for?

Uses fluorescent-tagged antibodies to locate proteins inside cells under a microscope.