Genetic Emergency

What are the three parts of a nucleotide?

Nitrogenous base, pentose sugar, and phosphate group(s).

How are DNA nucleotides linked into a chain?

A phosphodiester bond connects the 3′ position of one sugar to the 5′ phosphate of the next nucleotide.

In what direction do DNA and RNA chains grow?

5′→3′; new nucleotides are added to the free 3′-OH end.

How do complementary bases pair?

DNA: A–T (2 hydrogen bonds), G–C (3); RNA: A–U and G–C. Strands pair antiparallel.

What is the complement of DNA 5′-ATGC-3′, written antiparallel?

3′-TACG-5′.

What does semiconservative DNA replication produce?

Two DNA molecules, each with one parental strand and one newly synthesized strand.

What are the steps of cellular DNA replication in order?

Start at origin → unwind DNA → synthesize RNA primers → extend new DNA 5′→3′ → remove/replace primers → ligate fragments and proofread.

What is an origin of replication?

A DNA location at which replication begins, usually generating two replication forks.

What does helicase do during replication?

Unwinds/separates the two DNA strands at the replication fork.

What does primase do?

Makes short RNA primers that provide the 3′-OH needed by DNA polymerase.

Why does DNA polymerase need a primer?

It can extend an existing free 3′-OH, but cannot begin a DNA strand from scratch.

What are dNTPs used for?

Incoming deoxyribonucleotide triphosphates are substrates for building new DNA; cleavage of their triphosphates drives addition.

What does DNA polymerase do, and in which direction?

Reads a template 3′→5′ and synthesizes complementary DNA 5′→3′.

What is the difference between leading and lagging strand synthesis?

Leading strand: continuous toward fork. Lagging strand: discontinuous Okazaki fragments that are later joined.

Why are Okazaki fragments made?

Because DNA polymerase only synthesizes 5′→3′ while the templates are antiparallel.

What happens to the RNA primers on the lagging strand?

Primers are removed and replaced with DNA; DNA ligase seals remaining nicks.

What does DNA ligase do?

Forms phosphodiester bonds that seal nicks between adjacent DNA fragments.

What does DNA polymerase proofreading do?

Removes an incorrectly incorporated nucleotide and allows correct DNA synthesis to continue.

Name the three PCR steps in order.

Denaturation (heat separates strands) → annealing (DNA primers bind) → extension (thermostable DNA polymerase synthesizes DNA). Repeat cycles.

What ingredients are required for PCR?

Template DNA, forward/reverse DNA primers, dNTPs, thermostable DNA polymerase, appropriate salts/buffer (including Mg²⁺).

How does PCR differ from replication in cells?

PCR uses heat to unwind DNA and DNA primers; cells use helicase and RNA primers. PCR lacks cellular replication forks/Okazaki-fragment machinery.

How does Sanger sequencing work?

Extend primer with DNA polymerase in presence of normal dNTPs and labeled ddNTPs → random termination → separate products by length → read 5′→3′ sequence.

Why do ddNTPs stop DNA synthesis?

They lack a 3′-OH, so DNA polymerase cannot add another nucleotide.

What are the three stages of transcription?

Initiation: polymerase binds/promoter region → elongation: RNA made 5′→3′ from DNA template → termination: transcript released.

What is the coding strand compared with the template strand?

mRNA matches coding DNA except U replaces T; it is complementary and antiparallel to template DNA.

DNA template 3′-TAC CGA ATT-5′: what RNA is made?

5′-AUG GCU UAA-3′.

What is a promoter?

DNA regulatory region where transcription machinery assembles to begin transcription.

How do enhancers, silencers, and transcription factors affect gene expression?

Transcription factors bind regulatory DNA; enhancers increase transcription, silencers decrease it.

What are the major steps in eukaryotic mRNA maturation?

Add 5′ cap → remove introns and join exons by splicing → cleave/process 3′ end and add poly-A tail → mature mRNA can be exported.

What happens during RNA splicing?

Introns are removed from pre-mRNA and exons joined together.

How can alternative splicing increase protein diversity?

Different combinations of exons from one gene produce different mature mRNAs and potentially different proteins.

What does aminoacyl-tRNA synthetase do?

Uses ATP to attach the appropriate amino acid to its matching tRNA (charges the tRNA).

What happens during eukaryotic translation initiation?

Small ribosomal initiation complex associates with 5′ mRNA end, scans for AUG, initiator Met-tRNA occupies P site, then large subunit joins.

What happens during translation elongation?

Charged tRNA enters A site → peptide bond transfers chain to A-site amino acid → ribosome translocates → empty tRNA exits E site; repeat.

What do ribosomal A, P, and E sites do?

A: incoming aminoacyl-tRNA; P: tRNA with growing peptide; E: empty tRNA exits.

What happens during translation termination?

A stop codon (UAA, UAG, UGA) enters A site; release factor binds, polypeptide is released, ribosome dissociates.

How do you translate an mRNA sequence into amino acids?

Read mRNA 5′→3′ in triplet codons from start codon AUG; use genetic code; stop at UAA/UAG/UGA (no amino acid for stop).

What is Mendel’s law of segregation, physically?

Homologous chromosomes separate in meiosis I, so each gamete receives only one allele of each autosomal gene.

What is independent assortment, physically?

Different homologous chromosome pairs orient independently at metaphase I, generating different allele combinations for unlinked genes.

What happens at fertilization genetically?

Two haploid gametes unite, restoring a diploid genotype with one homolog from each parent.

How do you solve a monohybrid Punnett square?

Identify parental genotypes → determine gametes → combine in grid → count offspring genotypes and phenotypes.

What ratio comes from Aa × Aa with complete dominance?

Genotypes 1 AA:2 Aa:1 aa; phenotypes 3 dominant:1 recessive.

How do you solve a dihybrid cross?

List gametes for each parent (AaBb → AB, Ab, aB, ab) → combine in 4×4 grid or multiply independent single-gene probabilities.

What is the phenotype ratio for AaBb × AaBb (unlinked, complete dominance)?

9 A_B_ : 3 A_bb : 3 aaB_ : 1 aabb.

How does a testcross reveal an unknown dominant-phenotype genotype?

Cross with homozygous recessive. Recessive offspring reveal the unknown parent carries a recessive allele.

How is a chi-square genetics test performed?

Choose predicted ratio → compute expected counts → χ²=Σ(O−E)²/E → df=categories−1 → find p → p<0.05 rejects the model.

What does a large chi-square value mean?

Observed counts deviate substantially from expected counts relative to expected frequencies; at fixed df, larger χ² means smaller p.

What happens in mitosis in order?

Chromosomes condense → nuclear envelope breaks down and spindle attaches → chromosomes align → sister chromatids separate → nuclei reform → cytokinesis.

What happens in meiosis I?

Homologs pair and may cross over in prophase I → pairs align in metaphase I → homologs separate in anaphase I → two haploid cells form.

What happens in meiosis II?

Without another S phase, individual chromosomes align; sister chromatids separate, producing typically four haploid cells.

How does crossing over create genetic variation?

Nonsister chromatids of homologous chromosomes exchange DNA during prophase I, producing recombinant chromatids.

How is sex-chromosome inheritance determined in typical human XX/XY crosses?

Egg contributes X; sperm contributes X or Y. Father passes X to daughters and Y to sons.

How do you solve an X-linked recessive Punnett square?

Write alleles on X chromosomes; include Y for XY parent; combine gametes and calculate son and daughter outcomes separately.

How is DNA packaged into chromatin?

DNA wraps around histone octamers to form nucleosomes; higher-order folding compacts chromatin.

What is chromosome condensation?

Additional compaction of chromatin, especially during prophase of mitosis/meiosis, creating visible condensed chromosomes.

What is the centromere–kinetochore–spindle sequence?

Centromeric chromatin assembles kinetochore → spindle microtubules attach → forces segregate chromosomes/chromatids.

What does telomerase do?

Helps maintain repetitive DNA at the ends of linear chromosomes, counteracting end-replication shortening.

What is meiosis I nondisjunction and its gamete outcomes?

Homologous chromosomes fail to separate in meiosis I; if meiosis II is normal, gametes: n+1, n+1, n−1, n−1.

What is meiosis II nondisjunction and its gamete outcomes?

Sister chromatids fail to separate in one meiosis II cell; gametes: n, n, n+1, n−1.

How can nondisjunction cause trisomy or monosomy?

An n+1 or n−1 gamete fuses with a normal n gamete, yielding a 2n+1 trisomic or 2n−1 monosomic zygote.

What is a reciprocal translocation?

Exchange of chromosome segments between nonhomologous chromosomes, often a balanced rearrangement.

What is a chromosome inversion?

Chromosome segment breaks and reinserts in reverse orientation; usually balanced.

What is a chromosome deletion?

A chromosome segment is missing; unbalanced loss of DNA.

What is a chromosome duplication?

A chromosome segment occurs in extra copy/copies; unbalanced gain of DNA.

How can recombination errors cause chromosome rearrangements?

Incorrect exchange between nonhomologous or repeated DNA sequences can produce translocations, inversions, deletions, or duplications.

What is mitochondrial inheritance?

Mitochondrial DNA is transmitted mainly through the egg/maternal line; an affected father does not typically transmit mtDNA.

What is Y-linked inheritance?

Y-linked alleles pass from father to son and not to daughters.

How do you determine inheritance mode from a pedigree?

Assume complete penetrance/no new mutations unless stated → test AD, AR, XD, XR → rule out inconsistent models using parent-child trios → consider rarity and probabilities.

What is Bardwell Rule 1?

Unaffected parents have affected child → rule out autosomal dominant and X-linked dominant (under class assumptions).

What is Bardwell Rule 2?

Two affected parents have unaffected child → rule out autosomal recessive and X-linked recessive (under class assumptions).

What is Bardwell Rule 3?

Unaffected mother has affected son OR affected father has unaffected daughter → rule out X-linked dominant.

What is Bardwell Rule 4?

Affected mother has unaffected son OR unaffected father has affected daughter → rule out X-linked recessive.

How do you use the rare disease clue?

For a rare trait, multiple unrelated carriers marrying into a family are unlikely under recessive inheritance; affected founders are often taken as heterozygotes under dominant inheritance. It is probabilistic, not absolute.

How do you calculate pedigree disease risk?

Assign possible genotypes → update using known unaffected/affected status → multiply conditional transmission probabilities across generations.

Why is an unaffected sibling of an AR-affected child 2/3 likely to be a carrier (Aa×Aa)?

Remove aa (affected) from 1 AA:2 Aa:1 aa; among the three unaffected outcomes, two are Aa.

How do you recognize balanced versus unbalanced rearrangements?

Balanced: no net substantial loss/gain (often reciprocal translocation/inversion). Unbalanced: loss/gain of DNA (deletion/duplication).