Exam III

Biology

Reproductive cycle vs. Cell cycle

The reproductive cycle is the process by which whole organisms produce offspring to continue the species, whereas the cell cycle is the sequence of events by which individual cells divide within an organism for growth, maintenance, and repair.

Somatic cells vs. Gametes

Somatic cells are diploid body cells ($2n$), whereas gametes are haploid sex cells ($n$), such as sperm and eggs, specialized for sexual reproduction.

Parthenogenesis

A form of asexual reproduction where offspring develop directly from an unfertilized egg without the fusion of gametes.

Binary fission sequence in prokaryotes

1. DNA replication begins at the origin of replication; 2. The single circular chromosome is copied; 3. The cell elongates and copies separate; 4. FtsZ proteins organize division; 5. A septum forms; 6. The cell splits into two daughter cells.

$G_0$ phase

A quiescent, non-dividing state outside the active cell cycle where cells perform their normal physiological functions.

Interphase phases and activity

Composed of the $G_1$, $S$, and $G_2$ phases; it is an active growth and preparation period rather than an inactive resting stage.

Effect of $S$ phase on chromosome number

A typical human cell goes from $46$ unreplicated chromosomes to $46$ replicated chromosomes containing $92$ chromatids. DNA amount doubles; ploidy remains $2n$.

Semiconservative replication

The mechanism of DNA replication in which each newly synthesized double helix consists of one conserved parental strand and one newly formed strand.

Homologous chromosomes vs. Sister chromatids

Homologues are maternal and paternal chromosomes carrying the same genes at identical loci, often with different alleles; sister chromatids are initially genetically identical copies of a single chromosome joined at the centromere (crossing over during meiosis can make sister chromatids differ).

Centromere and kinetochore

The ______ is the constricted region holding sister chromatids together, where protein complexes called ______ assemble to attach spindle microtubules.

Karyotype

An organized visual display of an individual's complete set of chromosomes, evaluated by size, banding pattern, and centromere position.

Stages of mitosis in order

Prophase (chromatin condenses, spindle forms), Metaphase (chromosomes align at the equator), Anaphase (sister chromatids separate to opposite poles), and Telophase (nuclear envelopes reform, chromosomes decondense).

Animal vs. plant cell cytokinesis

______divide via a contracting cleavage furrow of microfilaments; ________ construct a rigid cell plate that develops into a new cell wall.

Cell cycle checkpoints ($G_1$, $G_2$, M)

$G_1$ checkpoint assesses cell size, nutrients, DNA integrity, growth factors, and whether division is needed; $G_2$ checkpoint verifies complete and accurate DNA replication; M (spindle) checkpoint checks that all chromosomes are properly attached to spindle fibers.

Proto-oncogenes vs. Tumor-suppressor genes

Proto-oncogenes encode proteins that stimulate normal cell division (overactivation creates oncogenes); tumor-suppressor genes (e.g., p53, BRCA1) produce proteins that halt the cell cycle, repair DNA, or trigger apoptosis.

Multiple-hit model of cancer

The principle that cancer progression requires an accumulation of multiple successive mutations in growth-promoting and tumor-suppressing genes over time.

Key difference between Meiosis I and Meiosis II

Meiosis I separates homologous chromosome pairs, reducing ploidy from diploid ($2n$) to haploid ($n$); Meiosis II separates sister chromatids without changing ploidy.

Sources of genetic diversity in sexual reproduction

Crossing over (nonsister chromatids exchange DNA segments during prophase I), independent assortment (random alignment of homologous pairs during metaphase I), and random fertilization (which occurs after meiosis when distinct gametes unite).

Nondisjunction and aneuploidy

________is the failure of homologous chromosomes or sister chromatids to separate properly, resulting in _____cells with monosomy (one missing chromosome) or trisomy (one extra chromosome).

Central dogma of molecular biology

The directional flow of genetic information: $\text{DNA} \rightarrow \text{RNA} \rightarrow \text{protein}$ (via transcription and translation).

DNA nucleotide structure and antiparallel strands

A DNA nucleotide consists of a deoxyribose sugar, a phosphate group, and a nitrogenous base (RNA nucleotides contain ribose instead of deoxyribose); DNA strands run in opposite directions ($5' \rightarrow 3'$ antiparallel to $3' \rightarrow 5'$) joined by complementary base pairs ($A=T$ with 2 hydrogen bonds, $G \equiv C$ with 3).

Degenerate and unambiguous genetic code

_______ means multiple distinct triplets/codons can specify the same amino acid; ________ means each specific codon designates only one unique amino acid or termination signal.

Usual start codon and stop codons

The ________ is AUG (encoding methionine); ______ are UAA, UAG, and UGA, which terminate polypeptide elongation.

Template strand vs. Coding strand

The template strand ($3' \rightarrow 5'$) is read by RNA polymerase to synthesize complementary RNA; the coding strand ($5' \rightarrow 3'$) shares the identical sequence with the resulting RNA, substituting T for U.

Eukaryotic mRNA processing

Post-transcriptional modifications including the addition of a $5'$ methylated cap, addition of a $3'$ poly-A tail, and removal of noncoding introns with splicing together of exons by the spliceosome.

Alternative splicing

A process where different exon combinations from a single pre-mRNA transcript are spliced together, enabling one gene to produce multiple distinct protein isoforms.

tRNA and aminoacyl-tRNA synthetase

tRNA delivers specific amino acids using its anticodon loop to base-pair with mRNA codons; aminoacyl-tRNA synthetase is the enzyme that attaches the correct amino acid to its corresponding tRNA.

Frameshift mutation

An insertion or deletion of nucleotides within a coding sequence not divisible by three, which changes the downstream reading frame, usually altering the amino acid sequence and often producing an early stop codon.

Epigenetic modification

Heritable or lasting alterations in gene expression (such as DNA methylation or histone acetylation) that modify chromatin accessibility without altering the underlying DNA nucleotide sequence.

Genotype vs. Phenotype

Genotype is the specific allelic combination of an organism (e.g., $GG$, $Gg$, $gg$); phenotype is the observable physical or biochemical trait resulting from genotype-environment interaction.

Sexual vs. asexual reproduction

Sexual reproduction combines genetic information through gametes. Asexual reproduction occurs without gamete fusion and usually produces genetically similar offspring.

Budding vs. regeneration

Budding: a new organism develops as an outgrowth of a parent. Regeneration: regrowing lost parts; in some organisms, a separated piece can develop into a new individual.

Functions of mitosis

Growth, maintenance, repair, and asexual reproduction in many eukaryotes.

$G_1$, $S$, and $G_2$ phases

$G_1$: growth and normal functions. $S$: DNA replication. $G_2$: further growth and preparation for division.

DNA polymerase

Enzyme that builds new DNA strands by adding complementary nucleotides and forming covalent bonds in the sugar-phosphate backbone.

Histones, chromatin, and locus

_______ are proteins DNA wraps around. _____ DNA plus associated proteins. ______a gene's location on a chromosome.

Human autosomes and sex chromosomes

Typical human somatic cells contain $44$ autosomes, or $22$ pairs, and two sex chromosomes, or one pair.

Amniocentesis

Sampling amniotic fluid, which can provide fetal cells for chromosome testing.

Apoptosis

Programmed cell death used in development, maintenance, and removal of damaged or unnecessary cells. Proteases break down proteins; nucleases break down nucleic acids.

Ras, Cdk, p53, and BRCA

Ras participates in growth signaling. Cdks regulate cell-cycle progression. p53 can stop the cycle or trigger apoptosis. BRCA1 and BRCA2 help repair DNA.

Benign, malignant, and metastatic tumors

Benign: does not invade or spread. Malignant: invades nearby tissue. Metastatic: has spread to another body location.

Immortalized cells

Cells that escape the usual limits on repeated cell division.

Carcinogen and course-listed cancer risk factors

Carcinogen: an agent that can cause cancer. Course-listed risk factors include tobacco, alcohol, dietary patterns, inactivity, increasing age, and frequent cell division.

Overall results of mitosis vs. meiosis

Mitosis: one division, usually two genetically similar cells with chromosome sets maintained. Meiosis: two divisions after one DNA replication, usually four genetically varied haploid products.

Fertilization and zygote

Fertilization combines haploid gametes: $n + n \rightarrow 2n$. The resulting cell is a zygote.

Germ-line cells

The cell lineage that gives rise to gametes; mutations transmitted through gametes can be inherited.

Euploidy vs. aneuploidy

Euploidy: complete chromosome sets. Aneuploidy: extra or missing individual chromosomes.

Chromosome-condition examples

Down syndrome: usually trisomy $21$. Klinefelter: usually XXY. Triple-X: XXX. Turner: usually $45\text{, }X$.

Maternal age and Down syndrome

The probability of having a child with Down syndrome increases with maternal age.

Red Queen hypothesis and coevolution

Coevolution: interacting species evolve in response to one another. The Red Queen hypothesis proposes that continued evolutionary change may be needed to keep up with other evolving organisms.

Bacterial DNA exchange

Bacteria can exchange genetic information without producing gametes; their reproduction occurs through cell division.

Gene, genome, and allele

Gene: DNA sequence used to produce a functional RNA or protein product. Genome: complete set of DNA. Allele: an alternative version of a gene.

How DNA influences traits

DNA sequence affects amino acid sequence, which affects protein shape and function, which can affect phenotype.

Four levels of protein structure

Primary: amino acid sequence. Secondary: local folds, including alpha helices and beta sheets. Tertiary: overall shape of one polypeptide. Quaternary: multiple polypeptide subunits together.

Enzyme and active site

An ____speeds a chemical reaction. Its ________is the region where substrate binding and catalysis occur.

Chargaff's rule

In double-stranded DNA, $A = T$ and $G = C$. All four percentages total $100\%$.

Codon totals

$64$ possible codons: $61$ specify amino acids and three are stop codons. The standard code specifies $20$ amino acids.

Stages of transcription

Initiation: machinery assembles at the promoter. Elongation: RNA is synthesized. Termination: transcription ends.

RNA polymerase

Enzyme that uses a DNA template to build RNA in the $5' \rightarrow 3'$ direction.

Promoter, transcription factors, and TATA box

Promoter: DNA region where transcription machinery assembles. Transcription factors help regulate and initiate transcription. A TATA box is a sequence found in some promoters.

mRNA, tRNA, and rRNA

mRNA carries the message; tRNA delivers amino acids; rRNA forms part of ribosomes and helps catalyze peptide-bond formation.

Translation

Ribosomes read mRNA codons and join amino acids into a polypeptide. Stages: initiation, elongation, termination.

Locations of transcription and translation

For nuclear genes in eukaryotes, transcription occurs in the nucleus; translation occurs on ribosomes in the cytoplasm, including those attached to rough ER.

Spliceosome and snRNA

The __________ removes introns and joins exons. ____________, together with proteins, are components of the splicing machinery.

Post-translational changes

Proteins may fold, be cleaved, assemble with other subunits, or receive chemical modifications after translation.

Selective gene expression

Different cell types express different subsets of genes, allowing cells with largely the same DNA to have different functions.

Activators and repressors

Regulatory proteins that increase or decrease gene expression.

Noncoding DNA

DNA that does not encode proteins. Some produces functional RNAs, regulates genes, or serves structural roles; not all noncoding DNA has an established regulatory function.

miRNA, siRNA, and RNA interference

Small RNAs can reduce gene expression, commonly by promoting mRNA destruction or blocking translation.

Substitution, insertion, and deletion

a base is replaced. bases are added. bases are removed.

Mutagens and mutation effects

Mutagens increase mutation frequency. Mutations can have harmful, neutral, or beneficial effects.

Sickle-cell disease and progeria

_____________ involves a substitution affecting beta-globin. Hutchinson–Gilford ______ typically involves a new mutation affecting lamin A processing.

Mutation and natural selection

Mutation generates new genetic variants; natural selection changes the frequency of variants through differences in reproductive success.

Epigenome, methylation, and histone modification

Epigenome: chemical marks on DNA and associated proteins. DNA methylation and histone changes can affect gene activity without changing the DNA sequence.

Dutch Hunger Winter example

Prenatal nutritional conditions were associated with later health outcomes in offspring.

Agouti mouse example

Maternal diet and epigenetic marks can influence gene expression and offspring traits, including coat color and tendency toward obesity.

Maternal care in rats

Early maternal care can influence epigenetic regulation of genes involved in stress responses.

Homozygous vs. heterozygous

________ two matching alleles, $GG$ or $gg$. ________ two different alleles, $Gg$.

Dominant vs. recessive

Under complete dominance, the dominant allele's effect appears in a heterozygote; the recessive allele's effect is masked. Dominant does not mean more common or better.

OCA2 and melanin

____ helps support pigmentation through melanosome function. ____ contributes to skin, hair, and eye color and helps protect against UV damage.