BSC2010 Exam 2

Cell division—four core events

Division signals, DNA replication, DNA segregation, cytokinesis; together yield two daughter cells.

Asexual vs sexual reproduction

Asexual: genetically identical clones (variation via mutations). Sexual: meiosis → haploid gametes → fertilization → genetic diversity.

Diploid (2n)

Having two sets of chromosomes in homologous pairs.

Haploid (n)

Having one set of chromosomes (one homolog from each pair).

Homologous chromosomes

Chromosome pair (one maternal, one paternal) carrying corresponding genes.

Gamete

Haploid reproductive cell produced by meiosis.

Zygote

Diploid cell formed by fusion of two haploid gametes.

Eukaryotic cell cycle phases

G1 (normal function), S (DNA replication), G2 (prep for mitosis), M (mitosis + cytokinesis); G0 = arrested non-dividing state.

Mitosis—prophase

Chromosomes condense; kinetochores form; centrosomes orient.

Mitosis—prometaphase

Nuclear envelope breaks; chromatids attach to kinetochore microtubules; spindle fully formed.

Mitosis—metaphase

Chromosomes align at the metaphase plate.

Mitosis—anaphase

Centromeres divide; sister chromatids separate and move to poles.

Mitosis—telophase

Nuclear envelopes reform; spindle breaks down; chromosomes decondense.

Cytokinesis (animals vs plants)

Animals: actin–myosin contractile ring pinches membrane. Plants: Golgi vesicles form cell plate and new wall.

Chromosome movement in mitosis

Kinetochore motor proteins and microtubule shortening draw chromosomes to poles.

Binary fission (prokaryotes)

Replication starts at ori, proceeds toward ter; segregates as replication proceeds; cell constricts, new wall deposited.

Meiosis—overview

Two divisions after one replication produce four genetically distinct haploid cells.

Meiosis I vs Meiosis II

Meiosis I separates homologs (sister chromatids stay together); Meiosis II separates sister chromatids (like mitosis).

Crossing over

Exchange between nonsister chromatids at chiasmata during prophase I; yields recombinant chromatids.

Independent assortment

Independent alignment and segregation of homolog pairs create gamete variety; underlies Mendelian ratios.

Nondisjunction

Failure of homologs/sister chromatids to separate; leads to aneuploidy (abnormal chromosome number).

Aneuploidy example

Trisomy 21 (Down syndrome) is a survivable human aneuploidy.

Polyploidy

Triploid (3n), tetraploid (4n), etc.; common in plants/fungi; usually deleterious in animals.

DNA is genetic material—evidence

DNA is nuclear/chromosomal, doubles in S-phase, diploid > haploid amounts; bacterial transformation and phage injection experiments implicate DNA.

DNA structure

Antiparallel double helix with specific base pairing (A–T, G–C), major/minor grooves for protein binding.

Semiconservative replication

Each daughter DNA has one old and one new strand.

DNA synthesis direction

Polymerases add nucleotides to 3′ end; synthesize 5′→3′ while reading template 3′→5′.

Leading vs lagging strands

Leading strand synthesized continuously; lagging strand in Okazaki fragments with repeated priming and ligation.

Initiation of replication

Origin (ori) unwinds; helicase separates strands; primase makes RNA primers; forks move away from ori.

Lagging-strand processing

Primer removal, DNA fill-in by another polymerase, final nick sealed by DNA ligase.

End-replication problem

Lagging-strand ends not fully replicated; telomeres buffer ends and telomerase extends them in certain cells.

Telomerase—note

Telomerase extends telomeres in some cell types; telomeres shorten with repeated divisions.

Mutation—definition

Heritable, permanent DNA sequence change from replication errors or damage; raw material for evolution.

Spontaneous vs induced mutations

Spontaneous: polymerase errors, tautomeric shifts, deamination. Induced: chemicals and radiation (e.g., UV).

Proofreading

DNA polymerase excises mispaired bases during synthesis; fixes most mismatches.

Mismatch repair

Post-replication protein complex removes and replaces mismatched bases.

Excision repair

Damaged nucleotides removed and replaced with normal ones.

Photoreactivation

Photolyase uses light energy to repair UV-induced thymine dimers.

Point mutations—protein effects

Silent (no change), missense (amino acid substitution), nonsense (premature stop), frameshift (indel not multiple of 3; broad disruption).

Loss-of-function vs gain-of-function

Loss: reduced/absent normal activity (often recessive). Gain: novel/overactive function (often dominant).

Conditional mutations

Phenotype expressed only under certain environments (e.g., temperature-sensitive pigment enzymes).

Chromosomal rearrangements

Deletions, duplications, inversions, translocations; often from double-strand break misrepair or aberrant crossover.

Central Dogma

Information flows DNA → RNA → protein; transcription followed by translation.

Coding vs template DNA strands

Template is read 3′→5′ to synthesize RNA; coding strand matches mRNA (U replaces T).

Promoter

Sequence specifying where RNA polymerase initiates transcription; helps choose which strand to transcribe.

Transcription—steps

Initiation at promoter, elongation 5′→3′ adding ribonucleotides, termination releases RNA.

RNA splicing

Introns removed and exons joined by spliceosome (snRNPs).

5′ cap and poly(A) tail

Cap aids ribosome binding and protects from decay; poly(A) tail assists nuclear export and stabilizes mRNA.

Codon, degeneracy, start/stop

Codon = 3 nt word; multiple codons per amino acid (degenerate) but unambiguous; AUG = start (Met), UAA/UAG/UGA = stops.

tRNA anticodon

Triplet complementary to an mRNA codon; guides correct amino acid incorporation.

Anticodon orientation

Anticodon pairs antiparallel to the codon (5′↔3′ orientation matters).

Wobble

Flexibility at codon 3rd base allows one tRNA to recognize multiple synonymous codons.

Ribosome sites

A site (tRNA entry), P site (peptide bond formation), E site (tRNA exit); large subunit has peptidyl transferase activity.

Translation initiation

Small subunit binds mRNA, Met-tRNA binds AUG, large subunit joins; initiation factors assemble complex.

Translation elongation

Cycle of tRNA entry, peptide bond formation, translocation; ribosome moves 3′ along mRNA.

Translation termination

Stop codon recruits release factor; polypeptide is hydrolyzed from P-site tRNA and released.

Polysome

Multiple ribosomes translating one mRNA simultaneously.

ER targeting (signal sequence)

N-terminal signal pauses translation, ribosome docks at ER, co-translational translocation; signal often cleaved.

Proteolysis

Protease-mediated cleavage of signal peptides or polyproteins to activate/mature proteins.

Glycosylation

Addition of carbohydrate chains forming glycoproteins (ER/Golgi); affects folding, stability, targeting.

Phosphorylation

Addition of phosphate groups by kinases; changes protein conformation/activity.

Gene expression—levels

Regulated at transcription, RNA processing, translation, and after translation; networks of regulators control outputs.

Inducers, repressors, constitutive genes

Inducers turn on inducible genes; repressors shut down repressible genes; constitutive genes are expressed continuously.

Positive vs negative regulation

Positive: activators increase transcription; negative: repressors block transcription.

lac operon (inducible)

Allolactose binds repressor, detaching it from operator; RNA polymerase transcribes lactose-utilization genes.

trp operon (repressible)

Tryptophan (corepressor) enables repressor to bind operator, shutting off transcription when product is abundant.

Eukaryotic core promoter/TATA

General transcription factors assemble at core promoter (often TATA box) with RNA Pol II to start basal transcription.

Enhancers/silencers & mediator

Distant DNA elements bound by specific factors; mediator bridges to basal apparatus to modulate transcription rate.

Basal transcription apparatus

RNA Pol II + general transcription factors at the core promoter.

Combinatorial control

Different transcription factor combinations specify cell phenotypes and coordinate multi-gene programs.

Chromatin & nucleosomes

DNA wrapped around histones forms nucleosomes; packing controls accessibility for transcription.

Histone acetylation/deacetylation

Acetylation loosens chromatin (activates); deacetylation compacts chromatin (represses).

Histone methylation/phosphorylation

Additional reversible histone modifications that modulate transcriptional activity.

DNA methylation & CpG islands

5-methylcytosine at CpGs recruits repressors and silences genes; promoter CpG islands typically unmethylated in active genes; heritable yet reversible.

Euchromatin vs heterochromatin

Euchromatin: diffuse, unmethylated, transcriptionally active; heterochromatin: condensed, methylated, silenced.

Genomic imprinting

Parent-specific methylation marks cause monoallelic expression; often crucial in embryonic development.

Alternative splicing

Generates multiple mature mRNAs/proteins from one gene; major source of proteome diversity.

mRNA stability

Regulated by nucleases and RNA-binding proteins that expose or protect recognition sites.

miRNAs

Regulatory RNAs that pair with mRNAs to inhibit translation or induce degradation.

Translational regulation—three modes

miRNA binding, 5′ cap modification (uncapped mRNAs not translated), translational repressors blocking ribosome binding/movement.

Ubiquitin–proteasome degradation

Polyubiquitin tags target proteins to proteasomes for proteolysis; ubiquitin is recycled.

Virus—basic structure

Genome (DNA or RNA) within a protein capsid; sometimes envelope; dependent on living cells to replicate.

Lytic vs lysogenic cycles

Lytic: rapid virion production and host lysis; lysogenic: genome integrates, replicates with host, can later induce lytic.

Phage gene timing (lytic)

Early genes shut off host, replicate viral genome; late genes encode coat and lysis enzymes.

HIV lifecycle highlights

Infects CD4+ immune cells; reverse transcriptase makes DNA that integrates and can remain latent for years.

Gene structure (eukaryote)

Enhancers/silencers, core promoter (± TATA), 5′ UTR, exons/introns, 3′ UTR, termination sequences; integrates multi-level regulation.

Where processes occur

Transcription/RNA processing in nucleus; translation in cytosol or on ER; post-translational mods in ER/Golgi/cytosol.

Sequence conversion—mRNA → coding DNA

Coding DNA sequence is the same as mRNA but T instead of U (mind 5′/3′ orientation).

Sequence conversion—mRNA → template DNA

Template DNA is the reverse complement of mRNA (keep antiparallel orientation).

Sequence conversion—coding DNA → mRNA

Replace T with U and maintain 5′→3′ orientation (mRNA matches coding strand).

Sequence conversion—template DNA → mRNA

Read template 3′→5′ and write complementary mRNA 5′→3′ with U for T.

Roles of RNA in translation

mRNA (message), tRNA (anticodon + amino acid), rRNA (ribosomal catalysis/structure).

Protein modifications—where occur

Proteolysis, glycosylation, phosphorylation; ER/Golgi/cytosol depending on modification.

Mendel—character vs trait

Character = general feature (e.g., seed shape); trait = specific form (e.g., round).

Allele, genotype, phenotype, locus

Allele = variant; genotype = allelic makeup; phenotype = observable expression; locus = gene’s chromosomal location.

Homozygous vs heterozygous

Homozygous: two identical alleles; heterozygous: two different alleles at a locus.

Dominant vs recessive

Dominant trait appears in heterozygote; recessive trait masked in heterozygote.

Parental (P), F1, F2 generations

P: original cross; F1: first filial generation; F2: offspring of selfed F1.

Monohybrid cross ratios

F2 phenotypes ~3:1; genotypes ~1:2:1; supports equal allele segregation.

Law of segregation

Alleles separate equally into gametes; gametes combine at random in fertilization.