MICRO EXAM 2

What is genetics?

The study of inheritance (heredity) of living things.

What is a genome?

The sum total of genetic material of an organism.

What forms can a genome take?

Mostly chromosomes, but also plasmids or organelle DNA (mitochondria/chloroplasts) in eukaryotes.

What nucleic acid makes up the genome of all cells?

DNA exclusively; virus genomes can be DNA or RNA.

What is a chromosome?

A distinct cellular structure composed of a neatly packaged DNA molecule.

How do eukaryotic and bacterial chromosomes differ?

Eukaryotic: DNA wound around histones, in the nucleus, diploid/haploid, linear. Bacterial: DNA condensed by histone-like proteins, usually one circular chromosome.

What are the three categories of genes?

Structural genes (code for proteins), genes coding for RNA machinery, and regulatory genes (control gene expression).

What is genotype?

An organism's distinctive genetic makeup (sum of all gene types).

What is phenotype?

The expression of the genotype as observable traits (structures/functions).

What three parts make up a DNA nucleotide?

Phosphate, deoxyribose sugar, and a nitrogenous base.

What holds nucleotides together in a DNA strand?

Covalent sugar-phosphate bonds forming the backbone (5′ to 3′ linkages).

What bonds hold the two DNA strands together?

Weak hydrogen bonds between complementary bases.

What are the base-pairing rules of DNA?

Adenine (A) pairs with thymine (T); guanine (G) pairs with cytosine (C).

What are the two purine bases and two pyrimidine bases in DNA?

Purines: adenine, guanine. Pyrimidines: cytosine, thymine.

What does 'antiparallel' mean for the DNA double helix?

The two strands run in opposite directions — one 5′ to 3′, the other 3′ to 5′.

What does 'semiconservative replication' mean?

Each new DNA molecule contains one original (parental) strand and one newly synthesized strand.

What enzyme unwinds the DNA helix at the origin?

Topoisomerase.

What enzyme breaks hydrogen bonds to separate the two DNA strands?

Helicase.

What do single-strand binding proteins do?

Keep the separated DNA strands apart during replication.

What enzyme adds new nucleotides to the growing DNA strand?

DNA polymerase III.

What enzyme lays down a short RNA primer before DNA synthesis begins?

RNA primase.

What is the leading strand?

The strand synthesized continuously in the 5′ to 3′ direction toward the replication fork.

What is the lagging strand?

The strand synthesized discontinuously, in short fragments, away from the replication fork.

What are Okazaki fragments?

Short DNA fragments (100–1,000 bases) making up the lagging strand.

What enzyme joins Okazaki fragments together?

DNA ligase.

How fast can bacteria replicate DNA?

Up to 750 bases per second at each replication fork.

How often do replication errors occur?

Roughly every 10^9 to 10^10 bases.

What is transcription?

Using DNA as a template to synthesize an RNA molecule.

What is translation?

Using RNA to produce a protein.

How do retroviruses break the normal DNA→RNA→protein flow?

They use RNA as a template to make DNA (reverse transcription).

What are the three steps of transcription?

Initiation, elongation, termination.

What enzyme carries out transcription?

RNA polymerase.

What DNA sequence does RNA polymerase bind to start transcription?

The promoter.

How does RNA differ structurally from DNA?

RNA is single-stranded, contains uracil instead of thymine, and contains ribose instead of deoxyribose.

What is a codon?

A three-nucleotide sequence on mRNA that specifies one amino acid.

What is an anticodon?

The three-nucleotide sequence on tRNA that pairs with an mRNA codon.

What is the function of tRNA?

Carries a specific amino acid to the ribosome and pairs its anticodon with the mRNA codon.

What is the function of mRNA?

Carries the genetic code (codons) from DNA to the ribosome.

What is the function of rRNA?

Forms the structure of the ribosome (with proteins) and catalyzes peptide bond formation.

What size are bacterial ribosomes, and what subunits make them up?

70S, composed of 50S and 30S subunits.

What size are eukaryotic ribosomes, and what subunits make them up?

80S, composed of 60S and 40S subunits.

How many possible codons are there, and how many amino acids do they specify?

64 codons specify 20 amino acids.

What is 'wobble' in the genetic code?

Only the first two nucleotides of a codon are usually needed to specify the amino acid, so the third can vary without changing the amino acid.

What is the start codon, and what amino acid does it specify in bacteria?

AUG; it specifies formyl methionine (f-Met) in bacteria.

What are the three stop (termination) codons?

UAA, UAG, and UGA.

Why do stop codons terminate translation?

No tRNA anticodon corresponds to them.

What is a polyribosome (polysome)?

Multiple ribosomes translating the same mRNA strand simultaneously.

How do bacteria and eukaryotes differ in mRNA coding capacity?

Bacterial mRNA can code for several genes in series; eukaryotic mRNA codes for only one protein.

Where do transcription and translation occur in bacteria vs. eukaryotes?

Bacteria: both occur simultaneously in the cytoplasm. Eukaryotes: transcription in the nucleus, translation in the cytoplasm.

What are introns and exons?

Introns are non-coding sequences that must be edited out; exons are the protein-coding sequences that remain in eukaryotic genes.

What is an operon?

A coordinated set of genes regulated as a single unit, found only in bacteria and archaea.

What is the difference between an inducible and a repressible operon?

Inducible (catabolic) operons are turned on by their substrate; repressible (anabolic) operons are turned off by their product.

What are the three parts of the lac operon?

The regulator (codes for the repressor), the control locus (promoter + operator), and the structural locus (three enzyme-coding genes).

What happens to the lac operon when lactose is absent?

The repressor protein binds the operator, blocking transcription (operon is off).

What happens to the lac operon when lactose is present?

Lactose binds the repressor, causing it to release from the operator, allowing RNA polymerase to transcribe the structural genes (operon is on).

What is phase variation?

A heritable, reversible switching of genes on/off that produces phenotypic changes, often affecting bacterial surface traits.

What is horizontal gene transfer (HGT)?

Transfer of DNA that gives an organism new genes not inherited from a parent.

What is a plasmid?

A small, circular, independently replicating piece of DNA that is not essential for survival but can carry useful traits.

What are the three modes of horizontal gene transfer in bacteria?

Conjugation, transformation, and transduction.

What is conjugation?

Direct transfer of DNA (often a plasmid) from a donor to a recipient cell via a pilus.

What is the F factor?

A fertility plasmid that allows a donor (F+) cell to form a conjugative pilus and transfer DNA to a recipient (F-) cell.

What is an Hfr donor?

A cell in which the F factor has integrated into the chromosome, allowing high-frequency transfer of chromosomal genes during conjugation.

What are R (resistance) plasmids?

Plasmids carrying genes for antibiotic resistance, commonly shared via conjugation.

What is transformation?

Uptake of free DNA fragments from the environment by a competent recipient cell.

What is transduction?

Transfer of bacterial DNA between cells via a bacteriophage.

What is generalized transduction?

A lytic phage mistakenly packages random fragments of host DNA and transfers them to a new host.

What is specialized transduction?

A temperate prophage excises imprecisely, carrying adjacent host genes into new phage particles.

Which HGT mechanism is direct (cell-to-cell contact), and which are indirect?

Conjugation is direct; transformation and transduction are indirect.

What are transposons?

Mobile 'jumping genes' that can shift position within or between the chromosome and plasmids, or between cells.

What roles can transposons play?

Changing surface traits, replacing damaged DNA, and spreading drug resistance between bacteria.

What is a mutation?

Any change to the nucleotide sequence in the genome.

What is the difference between a spontaneous and an induced mutation?

Spontaneous mutations arise from random replication errors; induced mutations result from exposure to mutagens (e.g., UV light, X rays, nitrous acid).

What is a wild type organism?

One with the natural, nonmutated characteristic, as opposed to a mutant strain.

What is a missense mutation?

A base substitution causing an amino acid change (may or may not affect function).

What is a silent mutation?

A base substitution that does not change the amino acid produced, due to code redundancy.

What is a frameshift mutation?

An insertion or deletion of bases that shifts the reading frame, altering all downstream codons.

What is a single nucleotide polymorphism (SNP)?

A heritable mutation altering just one nucleotide; important in personalized medicine.

What is excision repair?

A repair process where enzymes remove defective bases and DNA polymerase I and ligase fill the gap.

How does UV damage repair work?

The enzyme DNA photolyase uses visible light to repair a limited number of UV-induced mutations.

Are most spontaneous mutations beneficial?

No, but a small number create variants that adapt better, especially when the environment changes (e.g., drug resistance).

What happens to DNA when heated and then cooled?

It denatures into single strands when heated, then reanneals with complementary strands when cooled.

What is a restriction endonuclease?

An enzyme that recognizes and cuts DNA at a specific sequence, often producing 'sticky ends.'

Why are 'sticky ends' useful?

They let DNA from different sources be joined together if cut with the same restriction enzyme.

What is PCR?

Polymerase chain reaction — a method to rapidly amplify DNA from a few copies to billions in hours.

What are primers in PCR?

Short DNA strands (15–30 bases) that mark where DNA amplification should begin.

Why is Taq polymerase used in PCR?

It's a heat-stable DNA polymerase from Thermus aquaticus that survives the high temperatures PCR requires.

What are the three steps of a PCR cycle?

Denaturation (~94°C), priming/annealing (50–65°C), and extension (~72°C).

How does DNA quantity change with each PCR cycle?

It doubles exponentially each cycle.

What is gel electrophoresis used for?

Separating DNA fragments by size using an electrical current, since DNA migrates toward the positive pole.

Why do smaller DNA fragments move faster in electrophoresis?

They pass through the gel matrix more easily than larger fragments.

What is shotgun sequencing?

A method that breaks the genome into fragments, clones and sequences them, then uses computer overlap analysis (contigs) to reconstruct the full sequence.

What are the '-omics' fields?

Genomics (genes), proteomics (proteins), metagenomics (genomes in an ecological niche), and metabolomics (small metabolic chemicals in a cell).

What is the goal of recombinant DNA technology?

To combine genetic material from different organisms, often so bacteria can mass-produce hormones, enzymes, or vaccines.

What are the basic steps of gene cloning?

Excise the gene with restriction enzymes, insert it into a vector (plasmid/virus), and let a host (bacteria/yeast) replicate and express it.

What is synthetic biology?

Creating new biological molecules and organisms from scratch (e.g., the 2010 self-replicating synthetic cell).

What is gene therapy?

Replacing a faulty disease-causing gene with a normal gene from a healthy organism.

What is CRISPR used for?

Cutting an organism's DNA at a precise chosen location to fix a genetic defect.

What is CAR T-cell therapy?

Engineering T cell receptors to recognize cancer cell antigens for targeted cancer treatment.

What are the four aspects genetics explores?

Transmission of traits, how traits are expressed, structure/function of genetic material, and how that material changes.

Where in a eukaryotic cell can genetic material be found besides the nucleus?

Mitochondria and chloroplasts.