BMSC 3404 — Exam 2 Review

• Informational macromolecules = nucleic acids (DNA + RNA) and proteins.
• Anchor vocab: gene = functional unit · genome = all genetic elements in a cell · DNA = blueprint · RNA = transcription product; proteins = translation products (from RNA).

• DNA is a double helix (double-stranded), runs antiparallel, with complementary base pairing (A–T, C–G).
• Built from nucleotides, each = nitrogenous base + deoxyribose (5-C sugar) + phosphate.
  • A nucleoside is just base + sugar (no phosphate) — distractor, not a property.

• Within a strand: phosphodiester bonds (covalent) link nucleotides along the sugar–phosphate backbone.
• Between strands: hydrogen bonds link the two nucleic-acid chains (A–T, C–G).
  • A–T = 2 H-bonds, G–C = 3 → GC-rich DNA is more stable (foundation, not the direct answer).

• The central dogma is the one-directional flow DNA → RNA → protein.
• Transcription makes RNA from a DNA template; translation makes protein from mRNA (read by the ribosome).
  • Replication (DNA → DNA) copies the genome — related machinery, but not part of the central dogma's flow.

• Bacteria and Archaea: a single, circular, double-stranded DNA chromosome.
• Eukaryotes: 2 or more linear chromosomes.
  • Eukaryotic DNA is housed in a membrane-bound nucleus; prokaryotic genomes are generally smaller (E. coli = 4.64 Mbp).

• Supercoiling = DNA twisting and coiling on itself to compact the chromosome so it fits inside the cell.
  • Unwound, the chromosome is several hundred times longer than the cell.

• Negative supercoiling = clockwise → DNA gyrase and topoisomerase II.
• Positive supercoiling = counterclockwise → DNA topoisomerase I.

• Positive supercoiling helps prevent melting (denaturing) of DNA at high temperatures.

• An operon = a cluster of genes (often for one biochemical pathway) transcribed and regulated as a single unit.
  • They share one regulatory region and produce a single polycistronic mRNA; operons are the exception, not the rule.

• Through the operon's regulatory region:
  • Promoter → RNA polymerase binds.
  • Operator → binds regulatory proteins.
• A repressor (from a separate repressor gene) blocks the promoter until an activating molecule binds it.
  • lac operon: the repressor binds lactose, releases from the operator, and frees the promoter so transcription proceeds.

• A plasmid = a small, circular, double-stranded DNA molecule separate from the chromosome that replicates independently and is nonessential.
  • May influence host cell physiology.

• Plasmids carry nonessential but advantageous genes — useful traits, not survival basics.
  • Common categories: virulence factors, bacteriocins, nitrogen fixation, hydrocarbon degradation and other metabolic functions.
• The key one: antibiotic resistance, carried on R plasmids and spread cell-to-cell by horizontal gene transfer.

• Nonessential (cell survives without it) vs the chromosome's essential core genes.
• Much smaller than the chromosome.
• Replicates independently of the chromosome.
• Transferable between cells via horizontal gene transfer; the chromosome generally isn't.
  • Similarities: both plasmids and chromosomes are circular, double-stranded DNA, so shape isn't a distinguishing feature.

1. Starts at the origin of replication (oriC).
2. dnaA binds the origin and opens (melts) the double helix.
3. dnaC loads the helicase (dnaB) onto the open complex.
4. Helicase unwinds and separates the two strands.
5. Single-stranded binding proteins (SSBs) stabilize the open strands.
6. Gyrase / topoisomerase relieves supercoiling ahead of the fork.
7. Primase (dnaG) lays an RNA primer to start synthesis.

• DNA polymerase III adds nucleotides to the 3′ end of the growing strand; synthesis runs only 5′ → 3′.
• Because of that directionality (and antiparallel templates):
  • Leading strand — built continuously toward the fork (one primer).
  • Lagging strand — built discontinuously, away from the fork, in short pieces called Okazaki fragments, each with its own RNA primer.

• General process: the RNA primers are removed and replaced with DNA, then the fragments are sealed into one continuous strand.

• Originates at the origin of replication; terminates at the terminus of replication (~opposite the origin).
• Replication is bidirectional — two forks leave the origin in opposite directions around the circular chromosome.
• FtsZ partitions the DNA — it forms the division ring (Z-ring) at midcell that drives cell division, separating the two chromosome copies into the daughter cells.

• RNA polymerase recognizes and binds the promoter region of the DNA template strand to start transcription.
• The sigma (σ) factor is the part that recognizes the promoter. With σ attached, RNA pol is the holoenzyme; once transcription begins, σ dissociates, leaving the core enzyme to elongate.

• What binds & where: the sigma (σ) factor binds the promoter (at the initiation site).
• Specific sequences recognized: the −10 region (TATAAT, the Pribnow box) and the −35 region (TTGACG).
• If mutated (the −10/−35 promoter or σ): RNA pol can't recognize/bind → transcription doesn't initiate for that gene.

• The template strand is the complement of both the coding strand and the mRNA (it's the strand RNA pol reads).
• The coding strand is identical to the mRNA, except RNA carries uracil (U) where DNA has thymine (T).

• RNA polymerase adds nucleotides to the 3′ end of the growing RNA, moving down the DNA template as it goes (same 3′-end, 5′→3′ logic as replication).
• This produces a transcriptional unit — a DNA segment transcribed into one RNA molecule, with one initiation and one termination site.

• A single mRNA that carries multiple open reading frames (ORFs) — i.e., multiple genes transcribed together.
• These are co-transcribed genes organized as operons, regulated as a unit.

• General process: RNA pol reaches a termination sequence, the RNA folds into a hairpin loop (stem-loop), and the entire complex dissociates — releasing the RNA.
• What initiates it — two modes:
  • Intrinsic (rho-independent): a GC-rich inverted repeat folds into the hairpin, immediately upstream of a run of uracils (poly-U) → the complex destabilizes and releases.
  • Rho-dependent: termination at a rho-dependent termination site.

• Rifampin and actinomycin.
• They prevent RNA synthesis by blocking the RNA polymerase active site (rifampin) or RNA elongation (actinomycin).
• Why effective: no RNA gets built → no mRNA → no proteins → growth and division stall.

• A codon is a triplet (3 ribonucleotides) on the mRNA that codes for one amino acid.
• Each amino acid is carried by a tRNA whose anticodon is complementary to and base-pairs with the codon — that's how the correct amino acid gets matched to each codon.
• There is one start codon (AUG) and three stop codons.

• General process: the small (30S) subunit + initiation factors bind the mRNA → at the start codon (AUG) → the first tRNA (fMet) joins, forming the initiation complex → the large (50S) subunit binds.
• What the ribosome binds: the mRNA at the start codon (AUG) — that's the recognition point that gets initiation started.
  • (The specific ribosome-binding site — the Shine-Dalgarno sequence in bacteria — comes up in the bacteria-vs-eukarya comparison.)
• If the AUG region is mutated: the ribosome can't recognize the correct start codon, so translation can't initiate properly → no functional protein.
  • How you know it's ribosome binding, not something earlier: the mRNA is still present and normal — transcription worked. A transcription problem would leave you with no/abnormal mRNA. So normal mRNA + no protein = a binding/initiation problem.

• General process: the mRNA threads through the ribosome and tRNAs add amino acids to the growing polypeptide chain one at a time; the ribosome advances 3 nucleotides at a time.
• Order a tRNA moves: A → P → E
  • A site — incoming charged tRNA is loaded (via elongation factor EF-Tu).
  • P site — the growing polypeptide chain attaches to the prior tRNA.
  • E site — the now-empty tRNA exits.

• Termination: the stop codon is recognized → release factors cleave (release) the polypeptide → the complex dissociates.
• Ribosome recycling: once released, the ribosome can be reused — it's freed to start translating again.
• The process can also repeat on one mRNA to form polysomes (many ribosomes on a single transcript).

• Puromycin — binds the A site of the 70S ribosome, inducing chain termination (premature release of the polypeptide).
• Aminoglycosides (e.g., streptomycin) — target the 16S rRNA of the 30S subunit, causing error-filled proteins that inhibit growth.

• Point mutation = a change in only one base pair (a base-pair substitution). The phenotypic effect depends on the exact location.

• Frameshift mutation = insert or delete a base pair.
• End result: it scrambles the entire downstream polypeptide (the reading frame shifts). Can cause gain/loss of hundreds to thousands of base pairs — often due to transposable elements.
• More detrimental than a point mutation: a point mutation changes at most one codon, while a frameshift misreads every codon downstream.

• Induced mutations are caused environmentally or deliberately by mutagens — chemical, physical, or biological agents that increase mutation rates.

• Benefit of mutations: they generate genetic variation — the raw material for adaptation. Mutation fuels evolution; some are beneficial.
• Reversion = returning a mutation to its original form / restoring the wild-type phenotype (possible because point mutations are typically reversible). A revertant = a strain in which the original phenotype is restored.
  • Same-site revertant — the mutated base is restored to the original sequence (the original mutation is undone).
  • Second-site revertant — a mutation at a different site restores the wild-type phenotype without fixing the original = a suppressor mutation. It can be in the same gene, another gene, or another gene that makes a compensating enzyme.
  • Suppressor tRNA (nonsense case) — a tRNA's anticodon mutates to read the STOP as an amino acid → full-length protein restored, preventing a lethal mutation.

• Transformation = free DNA is incorporated into a recipient cell (only a small portion of a gene at a time).
• Host requirement: a competent host — a cell able to take up DNA and be transformed.
• What integrates it: RecA integrates the DNA if it is homologous with the chromosome.
• Process: homologous recombination — DNA binds → taken up as single-stranded DNA (a nuclease degrades the other strand) → RecA recombines it into the genome.

• Transduction = transfer of DNA from one cell to another by a bacteriophage (the phage is the vehicle; the DNA moved is the donor bacterium's genes).
• Generalized: DNA from any portion of the host genome is packaged inside the virion. Donor genes can't replicate independently → lost without recombination.
• Specialized: DNA from a specific region of the host chromosome is integrated directly into the virus genome (typically replacing some viral genes); integrated during lysogeny / via homologous recombination.
• Benefit of specialized: lysogenic conversion — altering the host phenotype by lysogenization, and the lysogen becomes immune to further infection by the same phage.

• Conjugation = mating; genetic exchange requiring cell-to-cell contact (plasmid-encoded DNA exchange).
• Process: donor has a conjugative (F) plasmid; sex pilus pairs the cells; TraI nicks the plasmid; transfer by rolling-circle replication → replicated in both cells so each ends with a complete plasmid.
• F+ = has a non-integrated F plasmid (donor); F− = lacks the plasmid (recipient).
• End result: two F+ cells (the recipient becomes F+). Once F+, surface receptors are altered, so the cell can no longer be a conjugate recipient or take up a second plasmid.
• Hfr = F plasmid integrated into the chromosome → can mobilize chromosomal/genomic DNA; F transfers last, so the recipient stays F− (and, being F−, can still take up another plasmid).
• More efficient (at transferring chromosomal genes): Hfr.

• Immunization (acquisition) — Cas recognizes the PAM in viral DNA → captures the adjacent protospacer → inserts it as a new spacer in the CRISPR array (repeats + spacers = memory bank).
• Interference — the array is transcribed/processed into crRNA → crRNA:Cas recognizes the matching foreign DNA → Cas cleaves/destroys it. Requires the spacer to already be present.

• All characterized archaeal viruses have DNA genomes (no RNA archaeal virus isolated to date).
• Most are double-stranded and circular (only two known are single-stranded).

• Genome: single-stranded DNA virus; small genome with overlapping genes; icosahedral virion. (Baltimore Class II.)
• How it replicates: rolling circle replication — but first it makes a double-stranded replicative form (RF) from the ssDNA, and rolls off that.
• Basic steps:
  1. Nick — gene A protein nicks the + strand of the RF at the origin → free 3′ end.
  2. Roll & copy — DNA pol extends from the 3′ end, copying around the circular − strand template (new + strand).
  3. Displace — the original + strand is peeled off (displaced) as the polymerase rolls.
  4. One revolution = one genome's worth of displaced + strand.
  5. Cleave & circularize — gene A protein cleaves/ligates the displaced strand into a circle → one new plus-strand ssDNA genome; RF rolls again.

• Terminal repeats = the same sequence repeated at both ends of the linear genome (terminal redundancy).
• Concatemer = a long DNA molecule of several genome copies linked end-to-end.
• Virus: bacteriophage T7 — double-stranded DNA, Baltimore Class I (transcribes the − strand).
• General process (concatemer formation):
  1. T7 replicates its linear DNA bidirectionally from an internal origin, leaving unreplicated terminal repeats at the ends.
  2. The terminal repeat of one molecule pairs with the matching repeat of another; DNA pol + ligase join them end-to-end → a concatemer (several genome units).
  3. A cutting enzyme makes single-stranded cuts and DNA pol fills in → individual mature T7 genomes, each with terminal repeats restored, ready to package.

• Genome: linear double-stranded DNA virus; Baltimore Class I (transcribes the − strand).
• How it replicates — cyclic DNA formation: on entering the host, lambda's cohesive "cos" ends (complementary single-stranded overhangs) base-pair, so the linear DNA cyclizes into a circle (sealed at the cos site). The circle then replicates by rolling circle replication.
• Difference from bacterial replication: the bacterial chromosome is already circular and replicates bidirectionally (theta replication) from its origin. Lambda starts linear, so it must cyclize first, then uses rolling circle — not bidirectional theta.

• Special: double-stranded RNA virus; Baltimore Class III (makes ssRNA / + strand).
• Replication type: conservative replication — the only known genome to do this. Genomic dsRNA is synthesized only off the + strand: the replicase makes the − strand, which is used to form the dsRNA genome (parental duplex stays conserved).
• Where: in the cytoplasm, inside the viral core / nucleocapsid (the genome never leaves the core).
• Animal virus that replicates there (cytoplasm): Pox virus (replicates in the cytoplasm, not the nucleus).

Unique animal viruses (where): Pox replicates in the cytoplasm (not the nucleus) — same location as reovirus. Adenovirus uses leading-strand replication on both strands.

• Cause: tumors in small mammals (e.g., SV40, a circular dsDNA polyomavirus).
• How: the viral DNA integrates into the host DNA → tumor-inducing genes are transcribed → tumor-induction proteins are made → these transform the cell to a tumor state.

• Must do first: its RNA genome must be transcribed by its replicase into + RNA, in two classes — (1) mRNAs encoding viral proteins, and (2) full-length + RNA as a template for new genomic − RNA.
• Why: the genome is negative-sense (−) RNA (Rabies; Baltimore Class V), which ribosomes can't read — only + sense is mRNA — so it must make + RNA first.

• Expect: a gene encoding RNA replicase (an RNA-dependent RNA polymerase).
• Why: to replicate the viral RNA — the host has no enzyme to copy RNA from RNA, so the virus must encode its own (it makes − RNA off a + template, then + RNA off the − template).

• RNA viruses came first.
• Why — the RNA-world idea: RNA can do both jobs at once — store genetic information (like DNA) and catalyze reactions (ribozymes, like protein enzymes) — so RNA could self-replicate before the DNA-and-protein system existed. DNA (more stable) and protein enzymes evolved later.

• Polyprotein = a single giant protein translated from one long ORF, then cleaved post-translationally into smaller functional proteins.
• How to tell: the genome is translated as one continuous product, yet the virus needs many proteins — i.e., more proteins than genes/start codons (one big protein being cut up). Classic case: + ssRNA viruses like poliovirus.
• What cleaves it: a protease.

• Reverse transcriptase — it synthesizes DNA from an RNA template (RNA → DNA), the reverse of normal transcription. (Baltimore Class VI.)

• What's unique: a filamentous phage with helical symmetry (circular ssDNA, Class II) that is released without lysing the host.
• How it attaches: to the host pilus.
• How it releases: extruded through the membrane without lysis — coat protein covers the DNA as it exits. Because the cell isn't killed, there is no intracellular accumulation and the cells grow without forming plaques.
• Infection type: a chronic (persistent) infection — the host keeps growing and producing virus.

• Genome: linear dsDNA, with a head-and-tail morphology.
• Lifestyle: a temperate phage — it can run either cycle:

Whichever repressor accumulates first controls the outcome. Loop: cI ⊣ Cro, Cro ⊣ CII, CII → cI.

• Most infect hyperthermophilic Crenarchaeota (think acidic hot springs).
• All archaeal viruses have DNA genomes — almost all dsDNA and circular.
• They show unusual, diverse morphologies — the hallmark being spindle-shaped (lemon-like) virions, plus rods and filaments.

RNA replicase — an RNA-dependent RNA polymerase (RdRp).

• Both are + ssRNA viruses — Class IV, so the genome acts directly as mRNA.

• Influenza has a segmented genome (it's −ssRNA, enveloped, pleiomorphic).
• That segmentation enables antigenic shift: when two strains infect the same cell simultaneously, their segments reassort → a hybrid / unique strain.

Released by budding.

• They carry reverse transcriptase and convert their RNA genome into DNA — every other RNA virus stays RNA (uses RNA replicase, never makes DNA).
• That dsDNA has long terminal repeats (LTRs) used to integrate into the host genome.
• Also distinctive: enveloped and carry two copies of the genome; thought to be of ancient origin (RNA-to-DNA transition).

An infectious agent simpler than a virus — it's missing a core component. A viroid is nucleic acid only (no protein); a prion is protein only (no nucleic acid).

MAVS aggregation in humans is a beneficial prion-like behavior: it triggers interferon production in response to viruses — part of the antiviral immune response.

• What it's for: the most widespread CO₂-fixation pathway — it fixes CO₂ into organic carbon for biosynthesis.
• Who uses it: oxygenic phototrophs (cyanobacteria, algae, plants), purple bacteria, and most aerobic chemolithotrophs.
• How to recognize it: the cell contains carboxysomes — proteinaceous microcompartments holding Rubisco that protect it from oxygen.

Because different pigments absorb different wavelengths of light. Carrying both bacteriochlorophylls and chlorophylls lets the organism capture a broader range of the light spectrum — harvesting more light energy than a single pigment could.

Chlorosomes — their large, highly efficient light-harvesting antenna structures.

Phycobiliproteins (phycobilins).

Check whether it produces oxygen. Oxygenic splits water as its electron donor, releasing O₂ as waste; anoxygenic uses another donor (e.g., H₂S) and makes no oxygen.

Anoxygenic photosynthesis was first.

How we know: oxygenic phototrophs (cyanobacteria) run two photosystems, and they acquired both via horizontal gene transfer. Since anoxygenic phototrophs each carry only one photosystem, the single-photosystem (anoxygenic) form is the ancestor; the two-photosystem (oxygenic) form was assembled later by combining two pre-existing systems.

• If PSII is blocked, some oxygenic organisms can run on PSI alone — meaning they switch to anoxygenic photosynthesis.
• Since PSII is what splits water, they can no longer use water as the donor (no O₂), so the reducing power for CO₂ must come from another donor — e.g., H₂S in cyanobacteria.

It oxidizes reduced sulfur compounds (H₂S, S⁰, thiosulfate, sulfite) all the way to sulfate (SO₄²⁻), funneling electrons to the ETC for energy (these colorless sulfur bacteria also release H⁺, so they're acidophilic).

The pathway breaks at that step — sulfur can't be fully oxidized to sulfate, so electrons never reach the ETC and the cell can't conserve energy from sulfur oxidation. Each protein is a required link in the chain.

• Acidithiobacillus ferrooxidans, Leptospirillum ferrooxidans, and Ferroplasma.
• They oxidize Fe²⁺ → Fe³⁺ as chemolithotrophs (fixing CO₂ via the Calvin cycle), and are acidophilic — some grow at pH < 0.

Extensive ferric iron (Fe³⁺) precipitates — the rust-colored deposits — together with acidic (low-pH) water. Because Fe²⁺ → Fe³⁺ precipitates and lowers pH, both signs appear together.

The rule: "Nitroso-" = ammonia oxidizer; "Nitro-" (no -so) = nitrite oxidizer.

Nitrate reducers (denitrifiers like Pseudomonas and Paracoccus) run dissimilative anaerobic respiration on nitrate. The benefit: they remove fixed nitrogen — stripping nitrate from fertilizer runoff — which makes them useful for bioremediation and water treatment.

Bonus pollutant-clearers from the same lecture: Dehalobacter / Dehalococcoides dechlorinate pollutants, and Desulfotomaculum detoxifies arsenic.

The nitrogen oxide products of denitrification cause three problems:

• Acid rain
• Ozone consumption (depletion)
• Greenhouse gas — N₂O (nitrous oxide)

A single compound is simultaneously oxidized AND reduced, splitting into two separate products — one more oxidized, one more reduced.

Both are carried out by Gram-positive, non-sporulating bacteria.

Pyrococcus furiosus is a hyperthermophilic archaeon that obtains 4 ATP from a modified glycolysis — double the usual 2 ATP of standard glycolysis.

Two microbes cooperate to carry out a reaction neither can do alone, linked by interspecies electron transfer. Most syntrophic reactions are secondary fermentations.

• Gene loss — the trait was lost during divergence over time (both descended from an ancestor that had it).
• Convergent evolution — the trait evolved independently in two or more lineages via nonhomologous genes.
• Horizontal gene transfer — the genes encoding the trait were exchanged between distantly related lineages.

• Cell walls contain peptidoglycan (Gram-negative-type envelope).
• Akinetes = resting structures with a thickened cell wall (survive stress/dormancy).
• Hormogonia = short motile filaments that facilitate dispersal during stress.
• Gas vesicles = buoyancy control for light-intensity positioning.

No flagella, but motility still varies: gliding motility, phototaxis and chemotaxis, and Synechococcus has non-flagellated swimming motility.

• Most abundant ocean phototrophs = Synechococcus and Prochlorococcus.
• They drive ~80% of marine photosynthesis (≈35% of total global photosynthesis).
• Nitrogen fixation is the dominant input of new nitrogen in the oceans.
• Widely distributed; more tolerant of extremes than eukaryotic algae.

They form freshwater blooms that release potent neurotoxins, toxic blooms, and geosmins (taste/odor compounds) into water.

• Looks like: small, highly motile, curved cells; obligate aerobes (oxidize amino acids and acetate).
• Targets: Gram-negative bacteria, using host cytoplasmic contents as nutrients.
• Mechanism: attaches → penetrates → replicates in the periplasm, forming a spherical bdelloplast.
• Found in: aquatic habitats, soils, and sewage.

• Looks like: vegetative cells are simple Gram-negative rods, but the life cycle builds strikingly colored, elaborate multicellular fruiting bodies.
• Unique: the most complex behavior known in bacteria — they swarm as a self-organizing unit, excrete a slime trail, lyse other bacteria for nutrients, then aggregate into mounds and differentiate into fruiting bodies.

• Gram-negative, tightly coiled, slender and flexuous.
• Endoflagella sit in the periplasm, surrounded by an outer sheath → corkscrew-like motion → lets them burrow through viscous material or tissue.
• Found in: aquatic sediments and within animals.

• Syphilis = Treponema pallidum.
• Lyme disease = Borrelia burgdorferi.
• Leptospira interrogans = leptospirosis (localizes in the kidney → renal failure); it's the "L" in the canine distemper–leptospira–hepatitis vaccine for dogs.

• Prosthecae = cytoplasmic extrusions — hyphae, stalks, and appendages.
• They allow attachment to particulate matter, plant material, and other microbes in aquatic environments.
• Examples: Hyphomicrobium (budding replication) and Caulobacter (stalk extension + replication).

It reproduces by budding via unequal cell growth: the mother cell forms a hypha, a bud forms at the hypha's end, enlarges, grows a flagellum, breaks loose, and swims away (then loses the flagellum). The daughter is entirely new while the mother retains its original identity.