Microbiology Photosynthesis, DNA, Gene Transfer, and Protein Synthesis

What is phototrophy?

Using light-excited electrons to obtain energy for cell growth; light energy becomes chemical energy.

How does the electron transport system produce ATP?

Electron transfer builds a proton motive force (PMF); H+ flowing through ATP synthase drives ATP production.

What is photoexcitation?

Absorption of light by a pigment raises an electron to a higher-energy state.

What is photolysis?

Light-driven removal of electrons from an electron donor such as H2O or H2S.

What three components are common to photolytic systems?

A light-harvesting complex, an electron transport system, and energy carriers.

What is bacteriorhodopsin?

A single-protein light-driven proton pump; it builds PMF without a chlorophyll-based photosystem.

Where is bacteriorhodopsin found?

In halophilic archaea; related proteorhodopsin occurs in marine proteobacteria.

How do folded photosynthetic membranes help purple bacteria?

They increase membrane surface area for capturing photons and carrying out energy conversion.

What are the three photosynthetic systems in these slides?

Anaerobic photosystem I, anaerobic cyclic photosystem II, and oxygenic Z pathway.

Which organisms use anaerobic photosystem I in the lecture?

Green sulfur bacteria (Chlorobia).

What can donate electrons to anaerobic photosystem I?

H2S, organic molecules such as succinate, or Fe2+.

Where do electrons end up in anaerobic photosystem I?

In reduced electron carriers such as NADH or NADPH, supporting CO2 fixation and biosynthesis.

What is the key benefit of NADPH in photosynthesis?

It provides reducing power (high-energy electrons) for biosynthesis and CO2 fixation.

Which bacteria use cyclic photosystem II in these slides?

Purple sulfur and purple nonsulfur bacteria (alphaproteobacteria in the lecture).

Why is anaerobic photosystem II called cyclic?

Excited electrons travel through an ETS and return to bacteriochlorophyll.

What is the main product of cyclic photophosphorylation?

ATP from PMF; the returning electrons do not yield net NADPH in the cycle.

What donates and ultimately receives electrons in cyclic photosystem II?

Bacteriochlorophyll donates excited electrons and receives them back after ETS cycling.

Why does cyclic electron flow generate ATP without net electron consumption?

Electron cycling pumps protons, but the electrons return to their original pigment.

Which organisms use oxygenic Z-pathway photosynthesis?

Cyanobacteria and plant chloroplasts.

What is the electron donor in oxygenic photosynthesis?

Water (H2O); splitting water releases O2.

Where do electrons ultimately end up in oxygenic photosynthesis?

NADP+ is reduced to NADPH.

Why are both photosystem II and photosystem I needed in the Z pathway?

PSII extracts electrons from water; PSI re-excites them so NADP+ can be reduced.

What are the main products of the oxygenic Z pathway?

O2, ATP, and NADPH; ATP and NADPH help fix CO2.

What distinguishes oxygenic from anoxygenic photosynthesis?

Oxygenic uses water and releases O2; anoxygenic uses other electron donors and does not release O2.

If a phototroph releases oxygen, what was the electron source?

Water, because oxygen is released when H2O is split.

What does the Winogradsky column illustrate?

Different phototrophic and sulfur-cycling microbes occupy layers with different light, oxygen, and sulfur conditions.

Why are cyanobacteria often near the top of a Winogradsky column?

They require light and use water as electron donor, releasing oxygen near the illuminated surface.

What is a genome?

The complete genetic information of a cell.

How do gene and chromosome differ?

A gene is a functional DNA segment; a chromosome is a larger DNA structure containing many genes.

What is the central dogma?

DNA is transcribed into RNA, and RNA is translated into protein.

How are replication, transcription, and translation different?

Replication: DNA→DNA; transcription: DNA→RNA; translation: RNA→protein.

What exception to the central dogma is mentioned?

Retroviruses can reverse-transcribe RNA into DNA before producing RNA and protein.

What did Griffith's experiment demonstrate?

Bacteria can acquire a heritable trait from material released by other bacteria: transformation.

What did Avery and colleagues establish?

DNA is the transforming substance in Griffith-style bacterial transformation.

What are the three components of a DNA nucleotide?

A nitrogenous base, deoxyribose sugar, and phosphate.

Which DNA bases are purines and pyrimidines?

Purines: A and G; pyrimidines: C and T.

What bonds connect nucleotides within a DNA strand?

Covalent 5′-3′ phosphodiester bonds in the sugar-phosphate backbone.

What holds complementary DNA strands together?

Hydrogen bonds between A-T and G-C base pairs.

What does antiparallel mean in DNA?

One strand runs 5′→3′ while the complementary strand runs 3′→5′.

Why is GC-rich DNA harder to denature?

G-C pairs have three hydrogen bonds versus two for A-T; GC-rich duplexes are generally more stable.

What is DNA denaturation?

Separation of double-stranded DNA into single strands, often by heating.

How does a bacterial nucleoid differ from a nucleus?

The nucleoid is a DNA-rich region without a nuclear membrane.

How is bacterial DNA compacted?

It forms protein-anchored loops and supercoils in the nucleoid.

What is a plasmid?

Usually a small, autonomously replicating extrachromosomal DNA molecule.

Why do plasmids matter clinically?

They can carry transferable antibiotic-resistance genes.

How do bacterial and eukaryotic chromosomes typically differ?

Bacteria usually have one circular chromosome; eukaryotes have multiple linear chromosomes packaged with histones.

How are archaeal chromosomes and information processing unusual?

Archaea share bacterial-like cell organization but replication, transcription, and translation often resemble eukaryotes.

What is positive supercoiling?

DNA is overwound relative to its relaxed state.

What is negative supercoiling?

DNA is underwound relative to its relaxed state.

What do topoisomerases do?

Cut and reseal DNA to change supercoiling and relieve torsional stress.

How do type I and type II topoisomerases differ?

Type I cuts one strand; type II cuts both strands.

What is DNA gyrase?

A bacterial type II topoisomerase that uses ATP to introduce negative supercoils.

Which antibiotic class targets bacterial DNA gyrase?

Quinolones.

What is vertical gene transfer?

Transmission of genetic information from parent to offspring.

What is horizontal gene transfer?

Transfer of genetic material between cells rather than directly from parent to offspring.

What are the three main mechanisms of horizontal gene transfer?

Transformation (free DNA), conjugation (cell contact), and transduction (phage-mediated).

What is transformation?

Uptake of naked extracellular DNA by a competent bacterial cell.

What does competence mean?

The ability of a cell to take up extracellular DNA.

What is the uptake of naked extracellular DNA by a competent bacterial cell?

Transformation

Why can transformation change a recipient's traits?

Incoming DNA may recombine with the chromosome or otherwise persist and be expressed.

What is conjugation?

Direct transfer of DNA from donor to recipient through a cell-contact transfer system.

What is an F+ cell?

A donor carrying the F-factor plasmid needed for conjugative transfer.

What is an F− cell?

A recipient that lacks the F-factor plasmid.

What does an F plasmid encode?

Machinery for pilus formation and DNA transfer between cells.

What is an Hfr cell?

A bacterium with F factor integrated into its chromosome; it can transfer chromosomal genes efficiently.

Why is Hfr conjugation useful for chromosomal gene transfer?

Transfer starts from integrated F DNA and can carry adjacent bacterial chromosome sequences.

What is homologous recombination?

Exchange or incorporation of DNA between matching or closely related sequences.

What is transduction?

Transfer of bacterial DNA from one cell to another by a bacteriophage.

How do generalized and specialized transduction differ?

Generalized can transfer various host DNA segments; specialized transfers genes near a prophage integration site.

What mechanism allows a bacterium to gain resistance after taking up DNA from dead cells?

Transformation: the donor DNA was free in the environment.

What mechanism allows two bacteria to exchange a resistance plasmid through contact?

Conjugation: DNA moves through a contact-dependent transfer system.

What mechanism involves a phage accidentally carrying a bacterial gene to another cell?

Transduction: a virus serves as the DNA carrier.

What does semiconservative replication mean?

Each daughter DNA duplex contains one original strand and one newly synthesized strand.

What does bidirectional replication mean?

Two replication forks move away from an origin in opposite directions.

Where does bacterial chromosome replication begin?

At the origin of replication, oriC.

In what direction does DNA polymerase synthesize DNA?

5′→3′, by adding nucleotides to a preexisting 3′-OH.

Why is a primer needed for DNA replication?

DNA polymerase cannot start a strand from nothing; it extends an existing 3′-OH.

What does DnaA do?

Initiates replication by binding oriC and promoting origin opening.

What does DnaB helicase do?

Unwinds the DNA double helix at the replication fork.

What does DNA primase do?

Synthesizes short RNA primers for DNA polymerase to extend.

What is the main job of bacterial DNA polymerase III?

Synthesizes most of the new DNA on both strands.

What does DNA gyrase do during replication?

Relieves positive supercoiling that builds ahead of the fork.

What does bacterial DNA polymerase I do?

Removes RNA primers and replaces them with DNA.

What does DNA ligase do?

Seals nicks in the DNA backbone, joining adjacent fragments.

What does topoisomerase IV do at replication termination?

Separates interlinked daughter circular chromosomes (decatenation).

Why is the leading strand synthesized continuously?

Its template orientation permits 5′→3′ synthesis in the same direction the fork advances.

Why is the lagging strand synthesized in fragments?

Polymerase works only 5′→3′, opposite the fork's movement on that template.

What are Okazaki fragments?

Short DNA pieces synthesized discontinuously on the lagging strand and later joined.

Why does the lagging strand need multiple primers?

Each Okazaki fragment needs a new starting 3′-OH.

What is the correct order for completing an Okazaki fragment?

Primase makes RNA primer → Pol III extends → Pol I replaces primer → ligase seals nick.

What provides energy for DNA chain extension?

Incoming nucleotide triphosphates; their high-energy phosphate bonds drive addition.

How can E. coli divide every 20 minutes if copying DNA takes 40 minutes?

It starts new rounds of chromosome replication before earlier rounds finish.

What do Tus and ter do?

Tus binds ter sites and helps stop replication forks in the termination region.

What does SeqA do in replication control?

Binds hemimethylated oriC DNA and helps prevent immediate reinitiation.

How is eukaryotic replication initiation different from bacterial replication?

Linear eukaryotic chromosomes typically use multiple replication origins.

Which eukaryotic polymerases synthesize leading and lagging strands?

Pol ε mainly synthesizes leading; Pol δ mainly synthesizes lagging.

What is the end-replication problem?

Conventional DNA polymerases cannot fully copy the ends of linear chromosomes after primer removal.

What does telomerase do?

Extends telomere repeats using its internal RNA template.

What is PCR?

Polymerase chain reaction: in vitro amplification of a chosen DNA region.

What are the three repeated PCR steps?

Denaturation → primer annealing → extension.