exam 2 flashcards~Microbiology lecture

What is metabolism?

The buildup and breakdown of nutrients within a cell to provide energy and sustain life.

What are the two main types of metabolic reactions?

• Catabolism: Breaks down complex molecules -> releases energy.

• Anabolism: Builds complex molecules -> requires energy.

How are catabolism and anabolism connected?

They are linked by ATP, which stores and transfers energy between them.

What is the role of enzymes in chemical reactions?

Enzymes are biological catalysts that speed up chemical reactions by lowering the activation energy without being consumed.

What are the components of a holoenzyme?

• Apoenzyme: Protein part

• Cofactor: Non-protein part (e.g., metal ions)

• Coenzyme: Organic cofactor (e.g., NAD+, FAD, CoA)

• Holoenzyme = Apoenzyme + Cofactor/Coenzyme

What factors influence enzyme activity?

Temperature, pH, substrate concentration, inhibitors.

What is the difference between competitive and noncompetitive enzyme inhibition?

• Competitive inhibitor: Competes with substrate for active site.

• Noncompetitive inhibitor: Binds to a different site (allosteric site) and changes enzyme shape.

What are the three types of phosphorylation that generate ATP?

1. Substrate-level phosphorylation – Direct transfer of phosphate to ADP (glycolysis, Krebs).

2. Oxidative phosphorylation – Uses the ETC to generate ATP.

3. Photophosphorylation – Light energy used to produce ATP (photosynthesis).

How does oxidative phosphorylation work?

Electrons pass through the ETC, releasing energy to pump protons. Protons flow through ATP synthase -> ATP is produced.

Where does glycolysis occur and what are its products?

Cytoplasm; produces 2 pyruvate, 2 ATP, and 2 NADH.

What is the purpose of the pentose phosphate pathway?

Produces NADPH and pentoses for DNA/RNA and amino acids. Operates alongside glycolysis.

What is the Entner-Doudoroff pathway and where is it found?

• Produces 1 NADH, 1 NADPH, and 1 ATP.

• Found in Pseudomonas, Rhizobium, Agrobacterium.

Where does the Krebs cycle occur?

• Prokaryotes: Cytoplasm

• Eukaryotes: Mitochondrial matrix

What are the main products of the Krebs cycle?

NADH, FADH2, ATP, and CO2.

Why is it important to oxidize NADH and FADH2 back to NAD+ and FAD?

To keep glycolysis and the Krebs cycle running; without recycling, energy production stops.

What is chemiosmosis?

The movement of protons across a membrane down their gradient to drive ATP synthesis.

What is the final electron acceptor in the ETC?

Molecular oxygen (O2), which combines with electrons and protons to form water.

How much ATP is produced from NADH and FADH2 in the ETC?

• Each NADH -> 3 ATP

• Each FADH2 -> 2 ATP

Total ATP yield per glucose molecule in prokaryotes?

38 ATP

Does fermentation require oxygen?

No, it is an anaerobic process.

What is the final electron acceptor in fermentation?

An organic molecule like pyruvate.

What are the two main types of fermentation and their products?

• Lactic Acid Fermentation: Lactic acid only (homolactic) or lactic acid + other compounds (heterolactic).

• Alcohol Fermentation: Ethanol + CO2.

How does fermentation differ from aerobic respiration?

• No Krebs cycle or ETC used.

• Produces small amounts of ATP.

How are lipids broken down for energy?

• Lipids -> Glycerol + Fatty acids.

• Glycerol -> Glycolysis.

• Fatty acids -> Beta-oxidation -> Acetyl-CoA -> Krebs cycle.

How are proteins catabolized for energy?

• Proteins -> Amino acids.

• Amino acids are deaminated -> organic acids -> Krebs cycle.

How are organisms classified based on energy and carbon sources?

• Photoautotrophs: Light energy, CO2.

• Chemoautotrophs: Chemical energy, CO2.

• Photoheterotrophs: Light energy, organic molecules.

• Chemoheterotrophs: Chemical energy, organic molecules.

Compare aerobic respiration, anaerobic respiration, and fermentation.

• Aerobic Respiration: O2 final electron acceptor, produces most ATP.

• Anaerobic Respiration: Inorganic molecule (not O2) is final electron acceptor, moderate ATP.

• Fermentation: Organic molecule is final electron acceptor, very little ATP.

What is genetics?

The study of what genes are, how they carry information, how information is expressed, and how genes are replicated and passed between organisms.

Define genome.

All the genetic material in a cell, including chromosomes and plasmids.

Define chromosome.

Structures containing DNA that carry hereditary information.

Define gene.

A segment of DNA that codes for a functional product like a protein or RNA.

Define genotype vs phenotype.

• Genotype: The organism’s genetic makeup.

• Phenotype: The physical expression of those genes.

Define genomics.

The study of an organism’s complete genetic information (genome).

What enzymes unwind and relax DNA strands during replication?

• Helicase: Unwinds the DNA double helix.

• Topoisomerase & DNA gyrase: Relieve supercoiling.

What does DNA polymerase do?

Adds nucleotides to the growing DNA strand in the 5’ → 3’ direction and proofreads the new strand.

What are Okazaki fragments?

Short fragments made on the lagging strand, later joined by DNA ligase.

What is semi-conservative replication?

Each new DNA molecule consists of one original strand and one new strand.

List the three main types of RNA and their functions.

• mRNA (messenger RNA): Carries genetic code from DNA to ribosome.

• tRNA (transfer RNA): Brings amino acids during protein synthesis.

• rRNA (ribosomal RNA): Structural and catalytic component of ribosomes.

What is transcription?

The process of making mRNA from a DNA template.

Where does transcription occur in prokaryotes vs. eukaryotes?

• Prokaryotes: Cytoplasm

• Eukaryotes: Nucleus

What enzyme synthesizes RNA?

RNA polymerase.

What are the steps of transcription?

1. RNA polymerase binds to the promoter.

2. DNA unwinds and complementary base pairing occurs.

3. RNA synthesis proceeds in the 5’ → 3’ direction.

4. Process stops at a terminator sequence.

What is translation?

The process where mRNA is decoded to build a protein.

What are codons and how many sense codons are there?

Codons are groups of 3 nucleotides on mRNA that specify amino acids. There are 61 sense codons.

What is the start codon and what are the stop codons?

• Start codon: AUG

• Stop codons: UAA, UAG, UGA

What is degeneracy of the genetic code?

Multiple codons can code for the same amino acid.

What is the role of tRNA in translation?

tRNA brings the correct amino acid and has an anticodon that pairs with the mRNA codon.

What are exons and introns?

• Exons: DNA regions that code for proteins.

• Introns: Noncoding regions that are removed before translation.

What is the role of snRNPs?

Remove introns and splice exons together.

What is an operon?

A group of genes controlled by a promoter and an operator.

What are constitutive genes?

Genes that are always expressed at a fixed rate.

What are inducible vs. repressible genes?

• Inducible genes: Default OFF, turned ON by inducer.

• Repressible genes: Default ON, turned OFF by repressor.

How does the lac operon work?

• No lactose: Repressor binds to operator → transcription blocked.

• Lactose present: Lactose binds to repressor → transcription occurs.

How does the tryptophan operon work?

• Low tryptophan: Genes are expressed.

• High tryptophan: Tryptophan acts as corepressor → stops transcription.

What is catabolite repression?

Inhibits cells from using other carbon sources when glucose is available.

Define mutation.

A permanent change in the DNA sequence.

List types of point mutations.

• Silent mutation: No change in protein.

• Missense mutation: Changes one amino acid.

• Nonsense mutation: Creates a stop codon.

• Frameshift mutation: Insertion/deletion shifts reading frame.

What are mutagens?

Agents that cause mutations.

Give examples of chemical mutagens.

• Nitrous acid

• Nucleoside analogs

What damage does UV radiation cause to DNA?

Forms thymine dimers.

How does the cell repair UV damage?

• Photolyase repair: Separates thymine dimers.

• Nucleotide excision repair: Cuts out damaged bases and replaces them.

Define vertical vs. horizontal gene transfer.

• Vertical: Parent to offspring.

• Horizontal: Between cells of the same generation.

List the mechanisms of horizontal gene transfer.

• Transformation

• Conjugation

• Transduction (generalized and specialized)

• Transposons

What is genetic recombination?

Exchange of genes between two DNA molecules, increasing genetic diversity.

What is transformation in bacteria?

Genes transferred as naked DNA from one bacterium to another.

What is conjugation in bacteria?

Transfer of plasmids via sex pili requiring direct cell-to-cell contact.

What is transduction in bacteria?

Transfer of DNA from one cell to another by a bacteriophage (virus).

What are transposons?

Segments of DNA that move to different locations (“jumping genes”).

• May carry antibiotic resistance genes.

Why is regulation of gene expression important?

It allows the cell to conserve resources and respond to environmental changes.

Compare the three main methods of horizontal gene transfer.

• Transformation: Naked DNA uptake.

• Conjugation: Plasmid transfer via direct contact.

• Transduction: Virus-mediated DNA transfer.

What is the difference between generalized and specialized transduction?

• Generalized: Any bacterial gene may be transferred.

• Specialized: Only specific bacterial genes are transferred.

Who is considered the founder of virology and when?

In 1892, viruses where discovered to be filterable; this marked the founding of virology.

What is variolation?

An early method in China and Japan to protect against smallpox.

Example of a disease caused by coxsackie virus strain A?

Hand, foot, and mouth disease.

Example of a disease caused by coxsackie virus strain B?

Dilated cardiomyopathy, pleurodynia (chest pain).

List general characteristics of viruses.

Obligatory intracellular parasites

• contains DNA or RNA (not both)

• Protein coat (capsid)

• May have envelope with spikes

• No ribosomes

• No ATP-generating mechanisms

Differentiate a virus from a bacterium.

Viruses lack plasma membrane, binary fission, both DNA and RNA, ribosomes, and ATP metabolism; sensitive to interferon not antibiotics.

What is difference between enveloped and unenveloped viruses?

Enveloped: sensitive to pH, heat, dryness, disinfectants; exit via budding; harder immune target.

Unenveloped: Resistant, exits through lysis, easier immune target.

What determines a virus’s host range?

Specific host attachment sites and host cellular factors.

How are viruses classified?

• Order: ends in -virales (ex. Articulavirales)

• Family: ends in -viridae (ex. Orthomyxoviridae)

• Genus/Species: ends is -virus (ex. Influenza A virus)

• Viral species: group sharing genetic info and ecological niche.

How are bacteriophages cultured?

Grown in bacteria, form plaques on agar (measured as PFUs).

How are animal viruses cultured?

In cell cultures, embryonated eggs, or live animals.

Methods to identify viruses?

Serological tests (ELISA), nucleic acids (PCR).

What are the steps of the lytic cycle (T-even phages)?

Attachment → Penetration → Biosynthesis → Maturation → Release.

What is lysogeny?

Phage DNA integrates into host genome as a prophage, replicated with host; can later enter lytic cycle.

How do animal viruses multiply?

Attachment → Entry (endocytosis/fusion) → Uncoating → Biosynthesis → Maturation → Release (budding/lysis).

Where do DNA viruses replicate?

DNA in nucleus; capsid proteins in cytoplasm; slower, stable, vaccines available.

Where do RNA viruses replicate?

In cytoplasm, using RNA-dependent RNA polymerase; rapid replication, high mutation rate.

What are retroviruses?

RNA viruses that use reverse transcriptase to make DNA, integrate into host as provirus (ex. HIV).

What is an oncogene?

A gene that can transform normal cells into cancerous cells when turned “on”.

Examples of DNA oncogenic viruses?

EBV(Burkitt’s lymphoma), HPV(cervical cancer), HBV(liver cancer).

Examples of RNA oncogenic viruses?

HTLV-1 and HTLV-2 (adult T cell leukemia/lymphoma).

What is a latent viral infection?

Virus remains inactive in host cell, can reactivate (ex. Herpes, shingles).

What is a persistent viral infection?

Virus is continuously released over time, often fatal (ex. HIV,HBV,SSPE).

How do plant viruses enter cells?

Through wounds or insect vectors.

What are viroids?

Short, naked RNA molecules causing plant diseases (ex. Potato spindle tuber disease).

What type of virus is hepatitis A?

+ssRNA, naked, picornaviridae; transmitted fecal oral (ex. Shellfish), prevented with inactivated vaccine.