Biology Flashcard Hell

What is an organic compound?

A compound containing carbon covalently bonded to hydrogen (C-H bonds); the basis of biological molecules (proteins; lipids; carbohydrates; nucleic acids).

What is an inorganic compound?

A compound that does NOT contain C-H bonds.

Why is CO2 classified as inorganic even though it contains carbon?

Because it has no C-H bonds and behaves chemically like simple inorganic gases rather than undergoing typical organic reactions.

What are saturated fats - solid or liquid at room temperature?

Fatty acids with no C=C double bonds; straight chains pack tightly giving a higher melting point; so they are typically SOLID at room temperature (e.g. animal fats).

What are unsaturated fats - solid or liquid at room temperature?

Fatty acids with one or more C=C double bonds (usually cis) which create kinks that prevent tight packing giving a lower melting point; so they are typically LIQUID at room temperature (e.g. plant oils).

How does saturation affect a fat's melting point?

More saturation = tighter packing = higher melting point (solid); more unsaturation = looser packing = lower melting point (liquid).

What monomers build carbohydrates?

Sugars (monosaccharides) linked by glycosidic bonds.

What monomers build proteins?

Amino acids linked by peptide bonds.

What monomers build nucleic acids (DNA/RNA)?

Nucleotides linked by phosphodiester bonds.

What monomers build lipids?

Fatty acids esterified to glycerol.

What is a hydrogen bond?

A weak attraction between a hydrogen bonded to an electronegative atom (O or N) and another electronegative atom; important in water; DNA base pairing; and protein structure.

What is an ionic bond?

An electrostatic attraction between oppositely charged groups or ions.

What are van der Waals forces?

Very weak short-range attractions arising from transient fluctuations in electron distribution; important when molecular surfaces fit closely together.

What are hydrophobic interactions?

The clustering of nonpolar molecules away from water; driven by the entropy gain of surrounding water molecules; important in protein folding and membrane formation.

What did Griffith's transformation experiment (1928) show?

That a 'transforming principle' could pass from heat-killed virulent bacteria to live non-virulent bacteria; making them virulent (and lethal to mice).

What did the Avery-MacLeod-McCarty experiment (1944) prove?

That DNA specifically is the 'transforming principle' identified in Griffith's experiment - i.e. DNA is the genetic material.

What did the Hershey-Chase experiment (1952) prove and how?

That DNA (not protein) is the genetic material. They used bacteriophages labeled with 35S (protein coat) and 32P (DNA) and showed only the DNA entered bacteria to direct infection.

What is a karyotype?

The complete chromosome complement of a cell/organism; characterized by chromosome number; size; and shape.

What is a karyogram?

A visual/photographic display of a karyotype with chromosomes arranged into matched homologous pairs; used to detect chromosomal abnormalities.

What is a nucleosome?

The basic repeating unit of chromatin: ~147 bp of DNA wrapped around a histone octamer (2 copies each of H2A; H2B; H3; H4).

What are histones and what is their function?

Small positively charged proteins that neutralize and organize the negatively charged DNA backbone by forming the core around which DNA wraps (nucleosomes).

What is euchromatin?

Loosely packed chromatin that is accessible to transcription machinery - transcriptionally active.

What is heterochromatin?

Densely packed chromatin that is inaccessible to transcription machinery - transcriptionally silent.

What is depurination?

Spontaneous hydrolysis of the N-glycosidic bond that releases a purine base (A or G); leaving an abasic (AP) site in DNA.

What is deamination and what is the classic example?

Loss of an amino group from a base; classic example is cytosine to uracil; which causes a C to T mutation if unrepaired before replication.

What is mutagenesis?

The overall process by which mutations arise - from replication errors; spontaneous chemical damage; radiation; or chemical mutagens.

What causes Xeroderma Pigmentosum and what is the consequence?

Defective nucleotide excision repair (NER) genes; causing extreme UV sensitivity and a very high risk of skin cancer.

What does nucleotide excision repair (NER) do?

Removes bulky helix-distorting lesions (e.g. UV-induced pyrimidine/thymine dimers) by excising a short damaged segment and resynthesizing it using the intact strand as a template.

What is homologous recombination and when does it occur?

A DNA double-strand break repair mechanism that uses the sister chromatid as a template; occurs in S/G2 phase; high fidelity/accurate.

What is non-homologous end joining (NHEJ)?

A DNA double-strand break repair mechanism that directly ligates broken ends without a template; can occur in any cell cycle phase; fast but error-prone.

What causes sickle cell anemia and what is the mechanism?

A point mutation in the beta-globin gene (Glu6->Val) producing hemoglobin S; which polymerizes under low oxygen; distorting red blood cells into a sickle shape and causing vessel blockage and hemolysis.

What causes Progeria and what is the effect?

A mutation in the LMNA gene (encoding lamin A); producing an abnormal protein ('progerin') that disrupts the nuclear lamina; leading to nuclear instability and a premature-aging phenotype.

What is collagen and what is its function?

The most abundant structural protein in the extracellular matrix; forms a triple-helix fibril that provides tensile strength to skin; tendons; bone; and cartilage.

What roles do actin and myosin play in muscle contraction?

Myosin (thick filament) heads use ATP hydrolysis to cyclically bind and pull actin (thin filament); producing the sliding-filament mechanism of contraction.

What are microtubules made of?

Alpha/beta-tubulin dimers polymerized into hollow polar cylindrical filaments.

What is the GTP cap on a microtubule?

GTP-bound tubulin subunits at the growing plus end that stabilize the microtubule and promote continued growth.

What is dynamic instability?

The stochastic switching of microtubules between growth and rapid shrinkage phases; triggered by loss of the GTP cap (causing 'catastrophe').

What is the central dogma of molecular biology?

DNA -> RNA (via transcription) -> Protein (via translation); DNA replication (DNA->DNA) is also part of the information flow.

How does DNA polymerase differ from RNA polymerase in primer requirement?

DNA polymerase requires a primer to begin synthesis; RNA polymerase does not.

How does DNA polymerase differ from RNA polymerase in proofreading/fidelity?

DNA polymerase has 3'->5' exonuclease proofreading activity (high fidelity); RNA polymerase generally lacks proofreading (lower fidelity).

What is the function of mRNA?

Carries the genetic code copied from DNA to the ribosome for translation.

What is the function of tRNA and what is an anticodon?

tRNA is an adaptor molecule that carries a specific amino acid; its anticodon (a 3-nucleotide sequence) base-pairs with the mRNA codon.

What is the function of rRNA?

Structural and catalytic component of the ribosome; catalyzes peptide bond formation.

What is a codon?

A 3-nucleotide sequence on mRNA that specifies one amino acid (or a stop signal).

What is an anticodon?

The complementary 3-nucleotide sequence on tRNA that base-pairs with an mRNA codon.

What is the function of the mRNA 5' cap?

A 7-methylguanosine cap added co-transcriptionally that protects the 5' end from degradation and is required for efficient translation initiation.

What is the function of the mRNA poly-A tail?

Added post-transcriptionally at the 3' end; protects against degradation and assists in nuclear export and translation efficiency.

What is the EJC (exon junction complex)?

A protein complex deposited at exon-exon junctions during splicing that marks the mRNA's processing history and influences export; translation efficiency; and nonsense-mediated decay.

What is an mRNP?

A messenger ribonucleoprotein particle - the mRNA packaged with associated proteins (cap-binding complex; EJCs; poly-A binding proteins) during export/processing.

What is the spliceosome?

A large ribonucleoprotein complex (snRNPs U1; U2; U4; U5; U6) that recognizes splice sites and catalyzes intron removal/exon joining in the nucleus.

What is the difference between introns and exons?

Introns are non-coding intervening sequences that are removed during splicing; exons are coding sequences that are retained and joined together.

What is endocrine signaling?

A hormone is released into the bloodstream and acts on distant target cells.

What is paracrine signaling?

A signal diffuses locally to affect nearby cells.

What is autocrine signaling?

A cell signals to itself or to identical neighboring cells of the same type.

What is synaptic signaling?

A neurotransmitter is released across a synapse to a closely apposed target cell.

What is contact-dependent signaling?

Signaling that requires direct membrane-to-membrane contact between cells (e.g. Notch-Delta signaling).

What is the difference between fast and slow signaling responses?

Fast responses modify pre-existing proteins (e.g. phosphorylation; channel opening) within seconds-minutes; slow responses require new gene transcription/protein synthesis and take minutes-hours.

What does a kinase do in signaling?

Transfers a phosphate group from ATP onto a Ser/Thr/Tyr residue of a target protein; altering its activity/conformation.

What does a phosphatase do in signaling?

Removes a phosphate group from a protein; reversing phosphorylation.

How do ion-channel-linked receptors work?

Ligand binding directly opens or closes an ion channel - the fastest receptor response type.

How do GPCRs (G-protein coupled receptors) work?

Seven-transmembrane receptors that; upon ligand binding; activate an associated heterotrimeric G protein.

How do RTKs (receptor tyrosine kinases) work?

Ligand binding causes receptor dimerization and trans-autophosphorylation of tyrosine residues; creating docking sites for downstream signaling proteins.

How does cholera toxin cause disease?

It ADP-ribosylates Gs-alpha; locking it in its active GTP-bound state; causing continuous adenylyl cyclase activity; excess cAMP; and CFTR hyperactivation - leading to massive water/electrolyte loss (watery diarrhea).

How does pertussis toxin work?

It ADP-ribosylates Gi-alpha; locking it in its inactive state so it cannot inhibit adenylyl cyclase; resulting in abnormally elevated cAMP.

What are the steps of the adenylyl cyclase (Gs) signaling pathway?

Ligand (e.g. adrenaline) binds GPCR -> activates Gs -> activates adenylyl cyclase -> produces cAMP -> activates PKA -> downstream effects.

What are the steps of the phospholipase C (Gq) signaling pathway?

Ligand binds GPCR (Gq) -> activates phospholipase C -> cleaves PIP2 into IP3 and DAG; IP3 triggers Ca2+ release from ER; DAG activates PKC.

What is Ras and how does it function as a molecular switch?

A small GTPase that is active when bound to GTP and inactive when bound to GDP.

What does a GEF (guanine nucleotide exchange factor) do?

Promotes release of GDP so GTP can bind; activating Ras (or other small GTPases).

What does a GAP (GTPase-activating protein) do?

Stimulates the intrinsic GTP hydrolysis of Ras; inactivating it (GTP -> GDP).

What is the order of the Ras-Raf-MEK-ERK pathway?

RTK activation -> GEF (e.g. Sos) -> Ras-GTP -> Raf -> MEK -> ERK -> altered gene expression and cell proliferation.

How do Ras mutations contribute to cancer?

Mutations (e.g. G12V) lock Ras in its active GTP-bound state or impair GAP-stimulated hydrolysis; causing constitutive proliferative signaling - among the most common oncogenic mutations in human cancers.

What are the three tiers of the MAP-kinase cascade?

MAP3K -> MAP2K (e.g. MEK) -> MAPK (e.g. ERK); each phosphorylating and activating the next to amplify the signal.

What does the TOR (Target Of Rapamycin) pathway regulate?

Integrates nutrient and growth-factor signals to regulate cell growth; protein synthesis; and autophagy.

What is the nuclear lamina?

A meshwork of lamin intermediate filament proteins lining the inner nuclear membrane; providing mechanical support and helping organize chromatin.

How does colchicine affect microtubules and why is this useful in cancer treatment?

It binds free tubulin dimers and prevents polymerization; causing microtubule depolymerization; this arrests rapidly dividing cells (like cancer cells) in mitosis since they rely on microtubule-based spindles.

How does taxol affect microtubules (in contrast to colchicine)?

Taxol over-stabilizes microtubules and prevents depolymerization; also arresting cells in mitosis - the opposite mechanism from colchicine; but the same end result of blocking spindle function.

What is the diameter/subunit/function of microtubules?

~25 nm (thickest); subunit is tubulin (alpha/beta dimers); functions: mitotic spindle; intracellular transport tracks; cilia/flagella.

What is the diameter/subunit/function of actin filaments?

~7 nm (thinnest); subunit is G-actin (forms F-actin); functions: cell shape; motility; muscle contraction; cytokinesis.

What is the diameter/subunit/function of intermediate filaments?

~10 nm; subunits vary (keratins; vimentin; lamins); function: mechanical strength/structural support (not used for motor-based movement).

Which direction does kinesin generally move cargo?

Toward the microtubule plus end (usually outward from the cell center).

Which direction does dynein generally move cargo?

Toward the microtubule minus end (usually inward toward the cell center).

How does myosin function in intracellular transport?

Moves cargo (e.g. vesicles) along actin filaments; powered by ATP hydrolysis (e.g. myosin V).

How do troponin and tropomyosin regulate muscle contraction?

Tropomyosin blocks myosin-binding sites on actin at rest; when Ca2+ rises; troponin (bound to tropomyosin) shifts tropomyosin to expose the binding sites; allowing contraction.

What is the sliding filament model of muscle contraction?

Myosin heads bind exposed actin sites and undergo a Ca2+/ATP-driven power stroke that pulls actin filaments toward the sarcomere center; then release (requires ATP) to reset for another cycle - shortening the sarcomere.