V. Genetics

Key focus of this chapter: DNA and chromosomes

This chapter reviews DNA and chromosomes, cell division, Mendelian genetics, protein synthesis, and mutations.

A. Cell Division

1. Cell cycle

a. Controlling cell cycle

G1 checkpoint

– checks cell size, nutrients, growth signals, and DNA integrity before entry into S phase; cells may enter the nondividing G₀ state.

– cell growth checkpoint

G2 checkpoint

– checkpoint before M phase.

– verifies that DNA replication is complete and checks for DNA damage before mitosis.

– mitosis-promoting factor (MPF), a cyclin–Cdk complex, promotes entry into mitosis when activated.

M checkpoint

– prevents anaphase until chromosomes are properly attached to the spindle through their kinetochores.

b. Mitosis

Normally produces genetically identical daughter nuclei while maintaining ploidy (e.g., 2n → 2n in diploid somatic cells).
Occurs during tissue repair and organismal growth.

Cell phases		Classification	Descriptions
Interphase		G1 phase	• Cell growth • First gap phase • Duration varies by cell type and conditions
		S phase	• DNA synthesized • Duplicated chromatin
		G2 phase	• Cell growth and preparing for mitosis • Second gap
M phase	Mitosis	Prophase	• Chromosomes condense • Spindle microtubules begin to form • Centrosomes move toward opposite poles in animal cells • The nuclear envelope breaks down in late prophase/prometaphase
		Metaphase	• Chromosomes align at the metaphase plate • Sister kinetochores are attached to spindle microtubules from opposite poles
		Anaphase	• Sister chromatids separate and move toward opposite poles
		Telophase	• Nuclear envelopes re-form • Chromosomes begin to decondense
	Cytokinesis	Cytokinesis	• Two daughter cells form • Plant cell: forms cell plate • Animal cell: forms cleavage furrow

c. Meiosis

A cell division process required for sexual reproduction; produces haploid spores or gametes, depending on the life cycle.
Reduces chromosome sets from diploid to haploid (2n → n).
Genetic diversity increases through crossing over and independent assortment.

** DNA replication occurs during S phase before mitosis and before meiosis I; no DNA replication occurs between meiosis I and meiosis II.

Meiosis I	Prophase I	• Chromosomes condense; homologs pair by synapsis to form tetrads • Crossing over occurs between nonsister chromatids of homologous chromosomes • Spindle microtubules form, and the nuclear envelope breaks down • Centrosomes move toward opposite poles in animal cells
	Metaphase I	• Homologous chromosome pairs align at the metaphase plate • Homologs attach to spindle microtubules from opposite poles; sister chromatids remain together
	Anaphase I	• Homologous chromosomes separate and move toward opposite poles; sister chromatids remain joined
	Telophase I & Cytokinesis	• Two haploid cells form; each chromosome still has two sister chromatids • Plant cells form a cell plate; animal cells form a cleavage furrow • No DNA replication occurs before meiosis II
Meiosis II	Prophase II	• Spindle microtubules re-form • Centrosomes move toward opposite poles in animal cells
	Metaphase II	• Chromosomes align along the metaphase plate • Spindle fibers attach to the kinetochores
	Anaphase II	• Sister chromatids separate and move toward opposite poles
	Telophase II & Cytokinesis	• Nuclear envelopes re-form • Chromosomes decondense • Haploid daughter cells form • Plant cells form a cell plate; animal cells form a cleavage furrow

2. Sexual life cycle

Gametes

– reproductive cells that fuse during fertilization

– haploid cells (n)

– e.g., sperm and eggs

Zygote

– fertilized egg

– diploid cell (2n)

Somatic cells

– body cells outside the reproductive germ line

B. Population genetics

1. Hardy-Weinberg equilibrium

a. Equation

b. Conditions

Large population
Isolation (no gene flow)
No mutation
Random mating
No natural selection

2. Genetic Drift

: random changes in allele frequencies due to chance, especially in small populations; genetic variation may be lost.

a. Bottleneck effect

A sharp reduction in population size leaves a chance sample of the original alleles.

b. Founder effect

A small group establishes a new population whose allele frequencies may differ by chance from those of the source population.

3. Genotype Frequency

a. Inbreeding

Mating between relatives increases homozygosity and reduces heterozygosity in offspring; by itself, it does not change allele frequencies.

b. Hybridization

Crossing genetically different populations or species can produce new combinations of alleles. Hybrids between species may have reduced fertility.

C. Mendelian genetics

1. Terminology

Allele

– alternative form of a gene.

– e.g., P: dominant allele, p: recessive allele

Phenotype: observable trait
Genotype: genetic constitution
Dominant allele

– under complete dominance, determines the heterozygote’s phenotype for the trait.

– the dominant phenotype appears in both dominant homozygotes and heterozygotes.

Recessive allele

– its phenotypic effect is masked by the dominant allele in a heterozygote under complete dominance.

– the recessive phenotype appears in recessive homozygotes and can also appear in hemizygotes.

Hemizygous – having only one copy of a gene or locus, as for most X-linked genes in XY males.
Pair of homologous chromosomes.

– carry the same genes at corresponding loci, but may carry different alleles; generally similar in length, centromere position, and staining pattern.

Homozygous: two identical alleles at a given locus.
Heterozygous: two different alleles at a given locus.

Pair of homologous chromosomes	Homozygous	Heterozygous
	AA, aa	Aa

Law of segregation

– The two alleles of a gene separate during gamete formation, so each gamete receives one allele.

Law of independent assortment

– Alleles of unlinked genes assort independently during gamete formation. Genes on different chromosomes follow this rule; linked genes may not.

Testcross

– cross an individual with a dominant phenotype but unknown genotype with a homozygous recessive individual.

– a homozygous dominant parent is expected to produce only dominant-phenotype offspring. In a finite sample, all dominant offspring support but do not prove homozygosity.

– a heterozygous parent is expected to produce a 1:1 dominant-to-recessive phenotypic ratio under complete dominance.

2. Mendelian experiments

Classification	Figures	Features
P generation
F1 generation
F2 generation

Monohybrids

– A monohybrid cross follows inheritance of one characteristic.

– e.g., Bb × Bb → expected 3:1 phenotypic ratio with complete dominance.

Dihybrids

– A dihybrid cross follows inheritance of two characteristics.

– e.g., BbDd × BbDd → expected 9:3:3:1 phenotypic ratio with independent assortment, complete dominance at each locus, and no epistasis, assuming equal gamete and offspring viability.

3. Laws of probability

For independent events, multiply their probabilities to find the probability that both occur.
For mutually exclusive outcomes, add their probabilities to find the probability that either occurs.

Traits	Figures	Features and diseases
Sex-linked traits		• X-linked recessive alleles are carried on the X chromosome • An unaffected XY father × heterozygous carrier mother: each son has a 50% chance of being affected; each daughter has a 50% chance of being a carrier • Under the standard recessive model, an affected XX daughter inherits an affected allele from each parent • Examples: hemophilia A or B and common red-green color vision deficiencies
Autosomal traits		• Autosomal dominant: one disease-associated allele can produce the phenotype; heterozygotes are affected under complete penetrance • Homozygous dominant genotypes may be affected or more severe; in some disorders they are lethal • Examples: achondroplasia, Huntington disease, and Hutchinson–Gilford progeria syndrome
Autosomal traits		• Autosomal recessive: two disease-associated alleles are generally required; affected individuals may be homozygous or compound heterozygous • Examples: sickle cell anemia, phenylketonuria (PKU), oculocutaneous albinism, galactosemia, and Tay–Sachs disease

4. Pedigrees

Autosomal traits

– autosomal genes are on nonsex chromosomes, and traits can affect either sex. An affected daughter with an unaffected father is inconsistent with typical X-linked recessive inheritance under standard assumptions, but does not by itself establish autosomal inheritance.

Dominant traits

– usually appear in successive generations when penetrance is complete; incomplete penetrance can cause apparent generation skips.

Recessive traits

– for an autosomal recessive trait, two unaffected heterozygous parents can have an affected child; recessive traits may skip generations.

5. Inheritance

a. Complete dominance

The heterozygote has the same phenotype as the dominant homozygote.
Example: true-breeding purple-flowered × white-flowered pea plants → purple-flowered F1 offspring.

b. Incomplete dominance

The heterozygote has a phenotype intermediate between those of the two homozygotes.
Example: true-breeding white-flowered × red-flowered snapdragons → pink-flowered F1 offspring.

c. Codominance

Both alleles are expressed in the heterozygote.
Example: people with the MN blood group express both M and N antigens.
Example: ABO blood groups have three main alleles (I^A, I^B, and i). I^A and I^B are codominant; both are dominant to i.

Phenotype	Genotype	Antibodies
A		Anti-B
B		Anti-A
AB		None
O		Anti-A, Anti-B

d. Pleiotropy

A single gene affects multiple phenotypic traits.
e.g., Sickle cell disease

e. Epistasis

A gene at one locus masks or modifies the phenotypic effect of a gene at another locus.
e.g., Color of mice

f. Polygenic inheritance

Multiple genes contribute to one trait, often producing continuous variation.
e.g., Skin color

g. Penetrance

Percentage of individuals with a particular genotype who express its associated phenotype.

h. Multifactorial disorder

A disorder influenced by both genetic and environmental factors.

i. Maternal inheritance

In humans, mitochondrial DNA is typically inherited from the mother.

D. Experiments identifying genetic material

1. Griffith’s transformation experiment

a. Experiment

– 1) Inject living S cells (encapsulated bacteria) into a mouse → mouse dies

– 2) Inject living R cells (nonencapsulated bacteria) into a mouse → mouse lives

– 3) Inject heat-killed S cells into a mouse → mouse lives

– 4) Inject a mixture of heat-killed S cells and living R cells into a mouse → mouse dies

b. Conclusion

The living R bacteria were converted into the pathogenic S bacteria by an unidentified transforming factor from the heat-killed S bacteria.

2. Avery–MacLeod–McCarty experiment

a. Experiment

– 1) Protease-treated extract from heat-killed S cells + living R cells → transformation produces living S cells.

– 2) Ribonuclease-treated extract from heat-killed S cells + living R cells → transformation produces living S cells.

– 3) Deoxyribonuclease-treated extract from heat-killed S cells + living R cells → no transformation into S cells.

b. Conclusion

DNA is the transforming factor.

E. Chromosome basics

1. Chromosomes in humans

46 chromosomes in diploid cells (2n).
23 chromosomes in haploid gametes (n).
Typically 44 autosomes and two sex chromosomes (usually XX or XY).

2. Chromosome appearances

Classification	Features
Metacentric	Centromere near the middle of the chromosome
Acrocentric	Centromere near one end of the chromosome
Telocentric	Centromere at the end of the chromosome

3. Level of chromosomal organization

Histones: proteins around which eukaryotic DNA wraps to form nucleosomes, helping package DNA.

4. Linked genes

: genes on the same chromosome tend to be inherited together; crossing over can separate them.

Recombination frequency estimates genetic distance between nearby linked genes: 1% recombination corresponds to about 1 map unit (centimorgan).
Recombination frequency generally increases with distance but cannot exceed 50%; multiple crossovers can cause it to underestimate long distances.
Linkage map

5. Sex-linked genes

: genes on X or Y chromosomes.

Examples of X-linked recessive traits

– hemophilia A and B

– common red-green color vision deficiencies

Barr body: a largely inactive X chromosome; some genes escape X inactivation

6. Chromosomal alteration

a. Changing chromosome number

Nondisjunction

– failure of homologous chromosomes to separate in meiosis I, or of sister chromatids to separate in meiosis II or mitosis.

Aneuploidy

: gain or loss of individual chromosomes, often caused by meiotic or mitotic nondisjunction.

– monosomic (2n –1): one copy of a particular chromosome instead of the usual pair

– trisomic (2n+1): three copies of a particular chromosome instead of the usual pair

Polyploid

: more than two sets of chromosomes.

– triploidy (3n)

– tetraploid (4n)

b. Changing chromosomal structures

Translocation

– transfer of a chromosome segment to a nonhomologous chromosome; reciprocal translocations exchange segments.

Deletion

– loss of a chromosomal segment.

Duplication

– an additional copy of a chromosomal segment.

Inversion

– reversal of a segment’s orientation within the same chromosome.

7. Human disorders

a. Down syndrome

Usually caused by nondisjunction producing trisomy 21; translocation and mosaic forms also occur.
Typically 47 chromosomes in full trisomy 21.

b. Klinefelter syndrome

An extra X chromosome, usually resulting from meiotic nondisjunction.
Typically 47,XXY; small testes and reduced testosterone are common.
Infertility is common, but features and fertility vary.
Mosaic forms may contain both 46,XY and 47,XXY cells.

c. Turner syndrome

Complete or partial absence of one X chromosome.
Short stature and ovarian insufficiency are common; fertility varies.
Monosomy X is a common form; mosaic and structural X-chromosome variants also occur.
45,X in monosomy X.

F. DNA replication

1. DNA structure

Rosalind Franklin and Raymond Gosling produced X-ray diffraction images that helped reveal DNA structure.
James Watson and Francis Crick proposed the double-helix model of DNA.
DNA backbone: alternating deoxyribose sugars and phosphate groups.
Purine: A (adenine), G (guanine).
Pyrimidine: C (cytosine), T (thymine).
Two hydrogen bonds between A and T, three hydrogen bonds between G and C.
For comparable DNA molecules under similar conditions, higher GC content generally increases melting temperature.

2. Chargaff’s rules

In double-stranded DNA, A = T and G = C; therefore A + G = C + T.
e.g., A = 30%, G = 20%, C = 20%, T = 30%

3. Semiconservative model

The two parental DNA strands separate, and each serves as a template for a new strand.
Each daughter DNA duplex contains one parental strand and one newly synthesized strand.
If parental strands are labeled and replication uses unlabeled nucleotides, each daughter duplex contains one labeled and one unlabeled strand after one round.

4. DNA replication

DNA replication	RNA replication
A ⇔ T G ⇔ C	A ⇔U G ⇔ C

a. Origins of replication
– Sites where DNA replication begins.

Replication fork

– A Y-shaped region where helicase unwinds the parental DNA.

– New DNA strands are synthesized at each replication fork.

b. Elongation (bacterial replication: E. coli model)

Leading strand

– DNA polymerase III synthesizes the leading strand continuously in the 5′ → 3′ direction.

– Synthesis proceeds in the same direction as replication-fork movement.

Lagging strand (Okazaki fragments)

– DNA polymerase III synthesizes each Okazaki fragment in the 5′ → 3′ direction.

– Each fragment elongates away from the replication fork.

– Lagging-strand synthesis is discontinuous; all new DNA is synthesized 5′ → 3′.

c. Enzymes for DNA synthesis

Topoisomerase

– Relieves torsional strain ahead of the replication fork by transiently breaking and rejoining DNA.

Helicase: Separating the parental double strands of DNA
Single-strand binding protein

– Stabilizes unwound single-stranded DNA and prevents reannealing.

Primase

– Synthesizes short RNA primers on the DNA template, providing a free 3′-OH for DNA polymerase.

DNA polymerase

– DNA Pol III (E. coli): adds deoxyribonucleotides to the 3′ end of growing DNA.

– DNA Pol I (E. coli): removes RNA primers and replaces them with DNA.

– Many DNA polymerases proofread using 3′ → 5′ exonuclease activity.

DNA ligase

– Seals nicks in the sugar-phosphate backbone, joining adjacent DNA fragments.

Telomerase

– Uses its RNA template to extend the 3′ ends of eukaryotic chromosomes, helping maintain telomeres. In humans, it adds TTAGGG repeats; activity is low or absent in most somatic cells.

d. Repairing DNA

G. Protein synthesis

1. Central dogma

2. Transcription

a. Initiation (eukaryotic RNA polymerase II)

① General transcription factors assemble at the promoter. At TATA-containing promoters, TATA-binding protein recognizes the TATA box; not all promoters contain one.

② RNA polymerase II and transcription factors form an initiation complex at the promoter.

③ RNA polymerase II begins synthesizing pre-mRNA at the transcription start site, using the DNA template strand.

b. Elongation

RNA polymerase II elongates pre-mRNA in the 5′ → 3′ direction.

c. Termination

RNA polymerase II continues beyond the RNA cleavage site and eventually dissociates from DNA, ending transcription. The cleaved pre-mRNA undergoes 3′-end processing.

3. RNA processing

a. Modification of pre-mRNA ends

A cap is added to the 5′ end, and most eukaryotic pre-mRNAs receive a poly(A) tail at the 3′ end.

b. RNA splicing

: spliceosome removes introns from pre-mRNA and splices exons together to make mRNA.

Introns: intervening sequences removed from a pre-mRNA during splicing
Exons: sequences retained in mature RNA; they may include protein-coding regions and untranslated regions (UTRs)
Spliceosome: snRNPs + other proteins

4. Translation

a. Codons and anticodons

Codons: three-nucleotide sequences in mRNA that specify an amino acid or a stop signal

– start codon: AUG (methionine)

– stop codons: UAA, UAG, UGA; recognized by release factors rather than tRNAs

Anticodons: three-nucleotide sequences in tRNA that pair antiparallel to complementary mRNA codons
Wobble: flexible base pairing between the third nucleotide of an mRNA codon and the first nucleotide of the tRNA anticodon; some tRNAs recognize more than one synonymous codon (degeneracy of the genetic code)

b. tRNA

Features

– a single RNA strand folds through intramolecular hydrogen bonding to form base-paired stems and unpaired loops.

– may contain modified nucleosides, such as inosine, pseudouridine, and 4-thiouridine.

Aminoacyl-tRNA synthetase uses ATP to attach the correct amino acid to the 3′ end of a tRNA

c. Ribosomes

: read mRNA from 5′ to 3′ and synthesize a polypeptide from its N-terminus to its C-terminus; initiation and elongation factors use GTP.

A site

– binds incoming aminoacyl-tRNA during elongation; the initiator tRNA starts in the P site.

P site

– holds the tRNA carrying the growing polypeptide chain.

– peptide-bond formation transfers the growing chain from the P-site tRNA to the A-site amino acid; translocation then moves the peptidyl-tRNA from A to P.

E site

– exit site for deacylated (uncharged) tRNA.

H. Mutation

1. Point mutation: base substitution

: a base substitution replaces one nucleotide (one base pair in double-stranded DNA) with another.

Missense: a coding-sequence change alters a codon so that it specifies a different amino acid.
Nonsense: a change converts an amino acid codon into a premature stop codon.
Silent (synonymous): a codon changes but still specifies the same amino acid.

2. Frameshift

: an insertion or deletion of a number of nucleotides not divisible by three within a coding sequence, shifting the downstream reading frame.

Can alter downstream amino acids and introduce a premature stop codon; effects depend on the mutation’s location
Insertions or deletions in multiples of three are in-frame and do not shift the reading frame.

3. Cancer

Oncogenes: activated or overexpressed forms of proto-oncogenes that promote excessive cell growth or survival.
Cancer usually develops through an accumulation of genetic changes, including activation of oncogenes or loss of tumor-suppressor function; a single mutation in an arbitrary somatic gene does not necessarily cause a tumor.

I. Gene technology

1. Polymerase chain reaction (PCR)

Rapidly amplifies a specific DNA region defined by primers through repeated cycles of DNA synthesis.
Useful for critical forensic analysis.

2. X-ray diffraction

Uses X-ray diffraction patterns to determine three-dimensional molecular structure.
X-ray crystallography.

3. DNA fingerprinting

Compares variable DNA regions to help distinguish individuals or assess biological relationships.

4. Transgenic organism

An organism engineered to contain introduced DNA, often a gene from another species.