V. Genetics

Key focus of this chapter: DNA and Chromosome

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

A. Cell Division

1. Cell cycle

a. Controlling cell cycle

G1 checkpoint

– determines whether cell cycle goes to S phase or the nondividing G₀ state.

– cell growth checkpoint

G2 checkpoint

– checkpoint before M phase.

– Checks completion of DNA replication and DNA damage.

– MPF is a cyclin–CDK complex that promotes entry into mitosis.

M checkpoint

– Checks that all kinetochores are properly attached to spindle microtubules before anaphase.

Scientific schematic — Checkpoint-position correction: the G₂ checkpoint precedes entry into mitosis; the spindle checkpoint acts at the metaphase-to-anaphase transition, not cytokinesis. G₀ is a nondividing state entered from G₁.

b. Mitosis

Typically produces genetically identical daughter cells while preserving ploidy (e.g., 2n → 2n in diploid somatic cells).
Occurs for repairing tissues and growing organisms.

Cell phases		Classification	Descriptions
Interphase		G1 phase	• Cell growth • First gap • Duration varies by cell type
		S phase	• DNA synthesized • Duplicated chromatin
		G2 phase	• Cell growth and preparing for mitosis • Second gap
M phase	Mitosis	Prophase	• Nuclear envelope disappears • DNA condenses into chromosomes • Spindle microtubule begins to form • Centrosomes move into opposite ends of the cell
		Metaphase	• Chromosomes align along the metaphase plate • Spindle fibers attach to the kinetochores
		Anaphase	• Separating and moving sister chromatids to opposite poles by spindle fibers
		Telophase	• Nuclear envelopes reappear • Chromosomes begin to be less condensed
	Cytokinesis	Cytokinesis	• Two daughter cells form • Plant cell: forms cell plate • Animal cell: forms cleavage furrow

c. Meiosis

Sexual reproduction resulting in spores or gametes.
Reducing chromosome sets from diploid to haploid (2n → n) in germ line cells.
Independent assortment and crossing over increase genetic diversity.

** DNA replication occurs during interphase before mitosis or meiosis I; it does not occur between meiosis I and II.

Meiosis I	Prophase I	• Nuclear envelope disappears • DNA condenses into chromosomes and then forms homologous chromosome pairs (tetrad) • Synapsis and crossing over of homologous chromosomes at chiasma • Spindle microtubule begins to form • Centrosomes move into opposite ends of the cell
	Metaphase I	• Pairs of homologous chromosomes line up along the metaphase plate • Spindle fibers attach to the kinetochores
	Anaphase I	• Pairs of chromosomes separate and move to opposite poles by spindle fibers.
	Telophase I & Cytokinesis	• Forming two haploid daughter cells • Plant cell: forming cell plate • Animal cell: forming cleavage furrow
Meiosis II	Prophase II	• Spindle microtubule begins to reform • Centrosomes move into opposite ends of the cell
	Metaphase II	• Chromosomes align along the metaphase plate • Spindle fibers attach to the kinetochores
	Anaphase II	• Chromosome separate and sister chromatids move to opposite poles by spindle fibers
	Telophase II & Cytokinesis	• Nuclear envelopes reappear • Chromosomes begin to be less condensed • Haploid daughter cells form • Cell plate of plant cell and cleavage furrow of animal cell

2. Cycle of sexual life

Gametes

– reproductive germ-line cells

– haploid cells (n)

– eg/ Sperm and eggs

Zygote

– fertilized egg

– diploid cell (2n)

Somatic cells

– forming body of eukaryotic species except reproductive germ-line cell

B. Population genetics

1. Hardy-Weinberg equilibrium

a. Equation

b. Condition

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

2. Genetic Drift

: random changes in allele frequencies, especially in small populations.

a. Bottleneck effect

A sharp reduction in population size can change allele frequencies by chance.

b. Founder effect

A small founding group may have allele frequencies unlike the source population and reduced diversity.

3. Genotype Frequency

a. Inbreeding

Mating between relatives increases offspring homozygosity; it does not by itself change allele frequencies.

b. Hybridization

Crossing genetically distinct individuals or varieties can combine parental alleles; outcomes vary.

C. Mendelian genetics

1. Terminology

Allele

– alternative form of a gene.

– eg/ P: dominant allele, p: recessive allele

Phenotype: observable trait
Genotype: genetic constitution
Dominant allele

– expressed in a heterozygote under complete dominance.

– the dominant phenotype appears in dominant homozygotes and heterozygotes.

Recessive allele

– masked by the dominant allele in a heterozygote under complete dominance.

-only appearance of the traits from recessive homozygotes.

Hemizygous – having one copy of a locus, such as most X-linked loci in an XY male.
Pair of homologous chromosomes.

– homologs carry the same gene loci, typically have similar size and centromere position, and may carry different alleles. One homologous pair contains two chromosomes; the image’s “1” means one pair, not one chromosome.

Homozygous: A pair of identical alleles.
Heterozygous: A pair of different alleles.

Pair of homologous chromosomes	Homozygous	Heterozygous
	AA, aa	Aa

Law of segregation

– the two alleles at a locus segregate so each gamete receives one.

Law of independent assortment

– alleles at unlinked loci assort independently during gamete formation; closely linked loci may not.

Testcross

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

– all dominant offspring are expected if the unknown parent is homozygous dominant; a small sample cannot prove this genotype.

– a heterozygous parent gives an expected 1:1 dominant-to-recessive phenotype ratio.

2. Mendelian experiments

Classification	Figures	Features
P generation
F1 generation
F2 generation

Monohybrids

– crossing between two heterozygotes of F1 generation having a single characteristic.

– eg/ Bb × Bb → Phenotypic ratio with 3:1

Dihybrids

– crossing between two heterozygotes of F1 generation having two characteristics.

– eg/ BbDd × BbDd → An expected F2 phenotype ratio of 9:3:3:1 with independent assortment and complete dominance at both loci

3. Law of probability

Traits	Figures	Features and diseases
Sex-linked traits		• Passing the traits on X chromosome to offspring • For an X-linked recessive trait, sons are affected if they inherit the recessive allele from their mother • Daughters usually need a recessive allele from each parent; a carrier mother alone is insufficient. • Eg/ Hemophilia, color blindness
Autosomal traits		• Dominant traits are expressed in heterozygotes and, when viable, dominant homozygotes • Eg/ Achondroplasia dwarfism, Huntington’s disease, progeria (premature aging)
Autosomal traits		• Diseased offspring with homozygous recessive • Eg/ Sickle cell anemia, PKU disease, albinism, Galactosemia, Tay-Sachs disease

4. Pedigrees

Autosomal traits

– with full penetrance, an affected daughter and unaffected father exclude the usual X-linked recessive pattern; this observation alone does not prove autosomal inheritance.

Dominant traits

– often appear in successive generations; reduced penetrance or a new mutation can alter this pattern.

Recessive traits

– unaffected carrier parents can have an affected offspring; recessive traits may skip generations.

5. Inheritance

a. Complete dominance

The heterozygote has the same phenotype as the dominant homozygote.
Purple flower × white flower → purple flower

b. Incomplete dominance

The heterozygote has a phenotype intermediate between the two homozygotes.
Eg/ White flower × red flower → pink flower

c. Codominance

Both alleles are expressed in the heterozygote.
Eg/ roan cattle: intermingled red and white hairs illustrate codominance
Eg/ blood group (I^A, I^B, i), (multiple alleles or polymorphism)

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

d. Pleiotropy

One gene influences multiple phenotypic traits.
Eg/ Sickle-cell disease

e. Epistasis

One gene modifies or masks the phenotypic expression of another gene.
Eg/ Color of mice

f. Polygenic inheritance

Multiple genes contribute to a trait, often producing continuous variation.
Eg/ Skin color

g. Penetrance

The percentage of individuals with a given genotype who express its associated phenotype.

h. Multifactorial disorder

A disorder influenced by both genetic and environmental factors.

i. Maternal effect

The mother’s genotype determines offspring phenotype through products deposited in the egg. This differs from maternal mitochondrial inheritance.

D. Gene experiment

1. Griffith transforming experiment

a. Experiment

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

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

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

– 4) injection 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.

2. Avery, MacLeod, and McCarty experiment

a. Experiment

– 1) mixture heat-killed S cells, living R cells, and protease → living S cells

– 2) mixture heat-killed S cells, living R cells, and ribonuclease → living S cells

– 3) mixture heat-killed S cells, living R cells, and deoxyribonuclease → no living 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	Location of centromere at middle of chromosome
Acrocentric	Location of centromere at close to end of chromosome
Telocentric	Location of centromere at end of chromosome

3. Level of chromosomal organization

Histone: DNA packing molecules composed of protein.

4. Linked genes

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

Recombination frequency estimates genetic distance: 1% recombination ≈ 1 centimorgan for short intervals.
Increased probability of crossing over with greater the gap between two linked genes.
Linkage map

5. Sex-linked genes

: genes on X or Y chromosomes.

Sex-linked recessive traits

– hemophilia

– color blindness

Barr body: an inactivated x-chromosome

6. Chromosomal alteration

a. Changing chromosome number

Nondisjunction

– separation failure of pairs of homologous chromosomes in meiosis I or sister chromatids in meiosis II.

Aneuploidy

: abnormal number of chromosomes from the nondisjunction of meiosis I or II.

– monosomy (2n − 1): one chromosome of a homologous pair is missing

– trisomy (2n + 1): three copies of one chromosome

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.

Deletion

– lost chromosomal segment.

Duplication

– repeating chromosomal segment.

Inversion

– reverse attachment of chromosomal segment.

7. Human disorders

a. Down syndrome

Usually trisomy 21 from nondisjunction; translocation and mosaic forms also occur
47 chromosomes

b. Klinefelter syndrome

Nondisjunction of X chromosome
Usually an XXY male with impaired fertility
May include gynecomastia and reduced testicular function
47 chromosomes

c. Turner syndrome

Nondisjunction of X chromosome
Usually a female with a 45,X karyotype and ovarian insufficiency; mosaic forms occur
Monosomy of sex chromosome
45 chromosomes

F. DNA replication

1. DNA structure

Rosalind Franklin made X-ray diffraction photograph.
James Watson and Francis Crick proposed the DNA model of double helix structure.
DNA backbone: deoxyribose sugars bound to 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.
With comparable length and conditions, higher GC content generally increases DNA melting temperature.

2. Chargaff’s rules

A+G = C +T
Eg/ A = 30%, G = 20%, C = 20%, T = 30%

3. Semiconservative model

The parental strands separate and each serves as a template for a new complementary strand.
Each daughter DNA molecule contains one parental strand and one newly synthesized strand.
After one replication in unlabeled medium, parental label constitutes half the total DNA if only parental DNA was labeled.

4. DNA replication

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

a. Origins of replication

Replication fork

– Y shaped site by helicases.

– places of elongation of new strand DNA.

b. Elongation

Leading strand

– DNA Pol III elongates continuously new strand of DNA from 5´ to 3´.

– same direction with movement of replication fork.

Lagging strand (Okazaki fragments)

– DNA Pol III creates short segments of new DNA from 5´ to 3´.

– opposite direction against movement of replication fork.

– each Okazaki fragment is synthesized 5′ → 3′; fragment formation proceeds away from the moving fork.

c. Enzymes for DNA synthesis

Topoisomerase

– relieving the strain of tighter twisting from untwisting of parental DNA.

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

– stabilizing single-stranded DNA and preventing reannealing.

Primase

– synthesizing short segments of RNA primer which is nucleotide chain for starting point of DNA synthesis and putting down the RNA primer on new strands of DNA.

DNA polymerase

– In bacteria, DNA Pol III adds nucleotides to extend DNA; eukaryotes use different replicative polymerases.

– In bacteria, DNA Pol I removes RNA primers and replaces them with DNA.

– proof reading (DNA error correction).

DNA ligase

– joining the ends of new strand of DNA.

Telomerase

– uses an RNA template to extend telomeres (TTAGGG repeats in humans), helping offset replication-associated shortening.

d. Repairing DNA

G. Making protein

1. Central dogma

2. Transcription

a. Initiation

① In eukaryotic RNA polymerase II transcription, general transcription factors assemble at the promoter; some promoters contain a TATA box.

② RNA polymerase binds to promoter along with the transcription factors.

③ RNA polymerase binding on DNA begins to synthesize pre-mRNA.

b. Elongation

RNA Polymerase elongates pre-mRNA from 5´ to 3´

c. Termination

Finishing pre-mRNA transcript

3. RNA processing

a. Modifying of pre-mRNA ends

Adding 5´cap and poly-A tail to pre-mRNA ends

b. RNA splicing

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

Introns: noncoding segments of nucleic acid
Exons: sequences retained in mature RNA; they can include coding regions and untranslated regions
Spliceosome: snRNPs + other proteins

4. Translation

a. Codons and anticodons

Codons: triplet nucleotides at mRNA and translated into amino acids

– start codon: AUG (met)

– stop codon: UAA, UAG, UGA

Anticodons: triplet nucleotides at the end of tRNA and complementary on codon
Wobble: flexible pairing at the third base of a codon lets some tRNAs recognize multiple codons; this contributes to genetic-code degeneracy

b. tRNA

Features

– hydrogen bonds with short double stranded RNA.

– presence of unusual bases: methylated bases, pseudouridine, 4-thiouridine.

Aminoacyl-tRNA synthetase binds an amino acid to 3´ end of tRNA

c. Ribosomes

: synthesizes a polypeptide while reading mRNA 5′ → 3′; initiation, elongation, and termination use GTP.

A site

– aminoacyl-tRNA binding site.

P site

– holds the tRNA carrying the growing peptide. Peptidyl transferase transfers the peptide to the amino acid on the A-site tRNA; translocation then moves tRNAs through the sites.

E site

– exit of tRNA site.

H. Mutation

1. Point mutation

: substitution of one nucleotide molecule.

Missense: result of a different amino acid by altering codon
Nonsense: result of stop codon
Silent: result of same amino acid although altering codon

2. Frame shift

: insertion or deletion of a number of nucleotides not divisible by three within a coding sequence.

Can disrupt downstream codons and protein function
Missing or insertion

3. Cancer

Oncogenes: genes leading to cancer.
Cancer usually develops through accumulated changes in growth-control genes, including oncogenes and tumor-suppressor genes.

I. Gene technology

1. Polymerase chain reaction (PCR)

Quickly copy and amplify an original double strand of DNA.
Useful for critical forensic analysis.

2. X-ray diffraction

Method to know the three-dimensional molecular structure.
X-ray crystallography.

3. DNA fingerprint

Identification of an individual’s DNA by their DNA profiles.

4. Transgenic organism

An organism containing introduced genetic material from another source.