Midterm 2 microbio

What is genetics?

The study of heredity and expression — transmission of traits, gene expression into proteins, variation via mutation, and the structure/function of genetic material.

What is a genome?

The total genetic material of an organism. Bacteria have DNA genomes; viruses can have DNA or RNA.

Why do RNA viruses generally mutate faster?

Because RNA genomes have higher mutation rates.

How is bacterial DNA organized?

As a single circular chromosome; no specific organelle stores it — all genetic processes occur in the cytoplasm.

Where do eukaryotes store DNA?

In multiple linear chromosomes; DNA also appears in mitochondria and chloroplasts.

What are plasmids?

Circular double-stranded DNA that replicates independently, carries non-essential genes (like antibiotic resistance and virulence factors), and is used in biotech.

What is the difference between genotype and phenotype?

Genotype is the genetic makeup; phenotype is the observable traits produced when genes are expressed as proteins.

What makes up a nucleotide?

A sugar, phosphate group, and nitrogenous base.

What forms the backbone of DNA?

Phosphodiester bonds between nucleotides.

What are the complementary base pairs in DNA?

A–T (double bond) and G–C (triple bond).

Why are G–C pairs harder to separate than A–T pairs?

G–C has triple bonds vs. the double bonds of A–T.

Why do origins of replication have more A–T bases?

A–T pairs are easier to open (double bonds), requiring less energy to initiate replication.

What does "antiparallel strands" mean in DNA?

The two strands run in opposite directions (5'→3' and 3'→5'), which is key for enzyme directionality and is targeted by antibiotics.

Why do cells replicate DNA?

Each daughter cell needs a complete copy of the genome before cell division.

What is the origin of replication?

The site where DNA replication is initiated; has a high concentration of A–T base pairs.

What does "semiconservative replication" mean?

Each daughter molecule retains one original strand from the parent molecule.

What does Topoisomerase II (gyrase) do?

Relaxes supercoiled DNA to make it accessible for replication initiation; targeted by fluoroquinolone antibiotics.

What does helicase do?

Opens the DNA helix by breaking hydrogen bonds between nitrogenous bases.

What does primase do?

Synthesizes RNA primers needed to start replication.

What does DNA polymerase III do?

Adds nucleotides in the 5'→3' direction; the main replication enzyme.

What does DNA polymerase I do?

Removes RNA primers and replaces them with newly synthesized DNA.

What does ligase do?

Seals gaps between Okazaki fragments on the lagging strand to create one continuous DNA strand.

What is the leading strand?

Made continuously in the 5'→3' direction toward the replication fork; only one RNA primer needed.

What is the lagging strand?

Made discontinuously in Okazaki fragments, each requiring its own RNA primer; replicates away from the fork.

What is the Central Dogma of biology?

DNA → RNA → Protein (transcription then translation).

What are the three types of RNA?

mRNA (carries code to ribosomes), tRNA (carries amino acids to ribosomes), rRNA (forms ribosomes and participates in protein synthesis).

Which RNA types are translated?

mRNA and tRNA are involved in translation; rRNA is not translated.

What happens during transcription initiation?

RNA polymerase binds to the promoter region upstream of the gene; the sigma factor helps RNA polymerase recognize the promoter.

Does RNA polymerase need a primer?

No — unlike DNA polymerase, RNA polymerase does not require a primer.

What strand does RNA polymerase read, and in what direction is RNA synthesized?

Reads the DNA template 3'→5'; synthesizes RNA 5'→3'.

What replaces thymine in RNA?

Uracil.

What happens during transcription termination?

RNA polymerase reaches a termination sequence and releases the mRNA transcript.

Why can bacteria begin translation before transcription finishes?

Because transcription and translation both occur in the cytoplasm and can overlap.

What is a codon?

A 3-base sequence on mRNA that specifies one amino acid.

What is the start codon and what does it code for?

AUG; codes for methionine.

What are the three stop codons?

UAA, UAG, and UGA.

Is the genetic code universal?

Yes — it applies to all organisms.

What is the anticodon?

A 3-base sequence on tRNA that pairs with the complementary mRNA codon.

Where is the amino acid attached on tRNA?

At the 3' end.

What are the A, P, and E sites of the ribosome?

A = incoming tRNA site; P = growing polypeptide chain site; E = exit site.

What do polyribosomes (polysomes) do?

Multiple ribosomes translate one mRNA simultaneously, increasing protein production speed.

What does the small ribosomal subunit do?

Binds mRNA.

What does the large ribosomal subunit do?

Forms peptide bonds between amino acids.

What is a mutation?

A heritable change in DNA sequence that may alter protein structure and function, resulting in a changed phenotype.

What is a point mutation?

A single nucleotide substitution that alters one DNA base pair.

What is a silent mutation?

A base substitution where the amino acid remains unchanged due to genetic code redundancy; minimal phenotypic effect though may cause loss of stability or efficiency.

What is a missense mutation?

A base substitution that changes one amino acid, altering the protein's primary structure; effects vary by location.

What is a nonsense mutation?

A mutation that creates a premature stop codon, producing a truncated and usually nonfunctional protein; often severe effect.

What is a frameshift mutation?

An insertion or deletion of nucleotides that shifts the mRNA reading frame, altering all downstream codons; usually produces nonfunctional proteins and is often severe.

How does rifampin resistance arise?

A mutation alters RNA polymerase so the antibiotic can no longer bind effectively.

What antibiotic class targets DNA gyrase/topoisomerase?

Fluoroquinolones.

Why do bacteria adapt so quickly?

Rapid reproduction, large population sizes, frequent mutations, gene sharing (HGT), and strong selective pressures.

What are the two sources of genetic variation in bacteria?

Mutation (changes in DNA sequence) and recombination (acquisition of new DNA via HGT).

What are the three mechanisms of horizontal gene transfer (HGT)?

Conjugation (direct cell contact via pilus), transformation (uptake of free DNA via pore), and transduction (bacteriophage-mediated via phage).

How does HGT differ from normal inheritance?

HGT transfers DNA between unrelated cells, not parent to offspring.

What is conjugation?

Direct transfer of DNA between bacteria requiring physical cell contact, mediated by a conjugative pilus; commonly involves plasmid transfer.

What is the F plasmid?

The fertility plasmid; F+ cells carry it and act as donors, F− cells lack it and act as recipients.

What does the F plasmid encode?

Conjugation machinery including pilus formation and DNA transfer proteins; it can spread itself.

What are Hfr cells?

Cells where the F plasmid has integrated into the chromosome; during conjugation they transfer chromosomal DNA, but the entire F factor is rarely transferred and the recipient usually remains F−.

What clinically important traits does conjugation spread?

Antibiotic resistance, virulence factors, toxin genes, biofilm-associated traits (e.g., CRE, MRSA, ESBL-producing bacteria).

What is transformation?

Uptake of free DNA from the environment by a competent bacterium, which incorporates foreign DNA into its chromosome.

What are competent cells?

Cells capable of taking up environmental DNA; some bacteria are naturally competent, others become competent under stress (starvation, DNA damage, temperature/salt changes).

What are biotechnology applications of transformation?

Recombinant DNA technology, vaccine production, and therapeutic production (e.g., insulin).

What is transduction?

DNA transfer mediated by bacteriophages; a phage accidentally packages bacterial DNA and transfers it to a new host.

What virulence factors are spread by phages?

Cholera toxin (Vibrio cholerae), Shiga toxin (E. coli/Dysentariae), Botulinum toxin (C. botulinum), diphtheria toxin (C. diphtheriae), erythrogenic toxin causing scarlet fever (S. pyogenes).

Why are bacteria used in biotechnology?

They grow rapidly, are cheap, easily accept plasmids/free genes, and are easy to genetically modify for efficient protein production.

What is recombinant human insulin?

Human insulin gene inserted into a plasmid → plasmid transformed into bacteria → bacteria produce human insulin → purified for patient use; the first major recombinant therapeutic.

What is Corynebacterium glutamicum used for industrially?

Production of L-glutamic acid → MSG.

What is D-ribose used for?

As a sweetener, nutritional supplement, and starting compound for synthesizing riboflavin and antiviral drugs.

Are viruses alive?

Debated — they contain genetic material, can evolve, and can reproduce (inside hosts), but lack metabolism outside the host and cannot reproduce independently.

What does "acellular" mean for viruses?

Not made of cells; they are obligate intracellular parasites.

What do all viruses contain at minimum?

A genome (DNA or RNA) and a capsid (protein coat).

What do viruses lack that cells have?

Ribosomes, ATP generation, and independent metabolism.

Can a virus have both DNA and RNA?

No — viruses contain DNA or RNA, never both.

What is a virion?

A complete, infectious virus particle.

What are the general steps of the viral replication cycle?

Attachment → Penetration → Uncoating → Synthesis → Assembly → Release.

What is host range?

The spectrum of cells a virus can infect.

How do enveloped viruses enter cells?

By fusion with the host membrane.

How do naked viruses enter cells?

By endocytosis.

What is the eclipse period?

The stage between uncoating and assembly where no complete virions exist inside the host cell.

Where do DNA viruses assemble?

In the nucleus.

Where do RNA viruses assemble?

In the cytoplasm.

What type of virus is HIV?

An enveloped retrovirus; positive-sense ssRNA virus.

What cells does HIV primarily target?

CD4 T cells.

What enzyme does HIV use and why is it important?

Reverse transcriptase converts RNA → DNA, and then integrase (a separate enzyme) integrates it.

What are the stages of HIV disease?

Early infection (flu-like symptoms) → Chronic stage (may be asymptomatic, slow immune decline) → AIDS (severe immune suppression, opportunistic infections, very low CD4 count).

How is HIV transmitted?

Blood, sexual contact, needle sharing, mother-to-child. NOT through hugging, saliva, casual contact, food sharing, or mosquitoes.

What does U=U mean?

Undetectable = Untransmittable; people on consistent ART with fully suppressed viral load cannot sexually transmit HIV.

What are the major drug targets for HIV?

Entry/fusion inhibitors, reverse transcriptase inhibitors, integrase inhibitors, protease inhibitors; combination therapy (cocktails) is used because HIV rapidly mutates.

What is PrEP and PEP?

PrEP = pre-exposure prophylaxis; PEP = post-exposure prophylaxis.

What is a capsid made of?

Capsomeres (protein subunits) that protect the genome, aid host cell attachment, and help deliver the genome into the host.

What are the two major capsid shapes?

Helical (cylindrical) and icosahedral (polyhedral — symmetrical, highly stable).

What is a viral envelope?

A lipid membrane acquired from the host cell membrane that surrounds the capsid; contains viral spikes.

What do viral spikes do?

Bind host cell receptors to determine host specificity and enable viral entry (e.g., SARS-CoV-2 spike, influenza hemagglutinin, HIV gp120).

How do naked viruses differ from enveloped viruses in survival?

Naked viruses are more resistant and survive longer on surfaces; enveloped viruses are fragile and sensitive to detergents and soaps.

How are naked viruses released?

By lysis (cell explosion).

How are enveloped viruses released?

By budding.

What are bacteriophages?

Viruses that infect bacteria; extremely abundant, usually contain dsDNA, and often have complex structures (head, tail sheath, base plate, tail fibers).

What is the function of bacteriophage tail fibers?

They recognize and attach to bacterial cells.

What is the lytic cycle?

Attachment → genome injection → viral synthesis → assembly → host cell lysis → release of new phages; host bacterium is destroyed.