Genetics Notes

Genetics

Basic Genetic Terminology

  • Gene: The smallest unit of inheritance that codes for specific protein chains, each with a specific function in cell physiology.
  • Codon: Three base sequences grouped together that code either for a specific amino acid or serve a regulation function, such as starting or stopping protein chain synthesis.
  • Nucleoside: A nitrogenous base attached to a carbohydrate without a phosphate group.
  • Nucleotide: A nucleoside with one or more phosphates.

Nitrogenous Bases of DNA

  • Nitrogenous bases are nitrogen-containing molecules that are weakly basic.
  • Two families of nitrogen bases in DNA:
    • Pyrimidines: Heterocyclic aromatic organic compounds containing two nitrogen atoms.
      • Cytosine
      • Thymine
    • Purines: Heterocyclic aromatic organic compounds consisting of a pyrimidine ring fused to an imidazole ring.
      • Adenine
      • Guanine

Nucleosides: Ribose vs. Deoxyribose

  • The carbohydrate in nucleosides comes in two forms:
    1. Ribose: Found in RNA (ribonucleic acid).
    2. Deoxyribose: Found in DNA (deoxyribonucleic acid).

Nucleosides vs. Nucleotides

  • The most basic component of DNA is the base itself.
  • A nucleoside is a nitrogenous base attached to a carbohydrate with no phosphate.
  • A nucleotide is a nucleoside with one or more phosphates.

DNA Nucleotide Chain

  • DNA is formed by nucleotides joined together by 3’ -5’ phosphodiester linkages.
  • One end is called the 5’ end, whereas the other is the 3’ end.
  • DNA is always read in the 5’ to 3’ direction.
  • Replication (duplication of DNA) and transcription (copying DNA into RNA) also take place in the 5’ to 3’ direction.

Nucleotide Base Pairing

  • Nucleotides on opposite strands of DNA pair with one another in a specific manner.
    • Thymine pairs with adenine, connected with two hydrogen bonds.
    • Cytosine pairs with guanine, connected with three hydrogen bonds.

Double Helix

  • DNA forms a double helix, stacked like a spiral staircase along the central axis.
  • Stabilized by van der Waals interactions, the hydrophobic properties of the nitrogen bases, and the hydrogen bonds between the nitrogen bases.
  • The double helix can be wound in either a left-handed or right-handed direction.
  • Major and minor grooves are sections of double helix DNA that are exposed and can interact with proteins and other molecules.

Histones

  • Histones are proteins that function in the packaging of DNA.
  • Nucleosome: Organizing unit of chromatin, a complex of eight histone molecules (2 copies each): H2A, H2B, H3, H4.
  • DNA is wrapped around the nucleosome.

Chromatin

  • Chromatin is a form of DNA packaging, a complex of DNA and proteins.
  • Nucleosome: Basic unit of DNA packaging, consists of a segment of DNA wound in sequence around eight histone protein cores.
  • Solenoid structures: Strings of nucleosomes wound into helical, tubular coils.

Ribonucleic Acid (RNA)

  • Present in the majority of living organisms.
  • Exists mostly in the single-stranded form with a variety of lengths and structures.
  • Contains the following nitrogenous bases: Adenine, Guanine, Uracil, and Cytosine.
  • Three Major Types of RNA:
    • Messenger RNA (mRNA)
    • Transfer RNA (tRNA)
    • Ribosomal RNA (rRNA)

Nitrogenous Bases of RNA

  • Same nitrogenous bases as DNA except RNA uses uracil in place of thymine.
  • One other key difference between RNA and DNA: the sugar molecule in the nucleotides.
    • RNA has ribose.
    • DNA has deoxyribose.
  • RNA can hybridize with DNA.
    • Guanine pairs with Cytosine.
    • Adenine pairs with Uracil.

Central Dogma

  • All the activities of the cell are coordinated by information encoded by DNA.
  • The DNA is copied into another type of nucleic acid (RNA) through a process called “transcription.”
  • The transcribed RNA is then decoded into proteins by a process termed “translation.”
  • The proteins then function in the cell to relay information.

Transcription

  • Transcription is the process by which a single-stranded RNA molecule is made that is complementary to the DNA strand used as a template.
  • Genes must be transcribed before their information can be used by the cell.

RNA Synthesis

  • During transcription, RNA is synthesized using DNA as a template.
  • Synthesis of the new RNA molecule occurs in the 5’-to-3’ direction.

RNA Polymerase

  • RNA polymerase is an enzyme that uses DNA as a template to synthesize an RNA molecule.
  • Four functional regions:
    1. Jaws: Clamp around DNA template and holds it in place.
    2. Ribonucleoside triphosphate tunnel: Allows entry of free ribonucleoside triphosphates into the active site.
    3. Active site: Site of ribonucleoside triphosphate addition to the growing RNA molecule.
    4. RNA exit channel: Point of exit for newly formed RNA molecule.

Translation

  • Translation is the conversion of the information in RNA into protein.
  • Because there are only 4 different nucleotides in mRNA but 20 different amino acids in a protein, the translation cannot be accounted for by a direct one-to-one correspondence between a nucleotide in RNA and an amino acid in protein.
  • Codons: Three-letter (nucleotide) sequence of RNA that represents a specific amino acid; most amino acids are associated with multiple codons.

Reading Frames

  • An RNA sequence can be translated in three different reading frames, depending on where the coding process begins.
  • Only one of the three possible reading frames of an mRNA specifies the correct protein.

Genotype vs. Phenotype

  • Genotype: The genetic information for an organism.
  • Phenotype: The physical manifestation of the genetic information.
  • Allele: A form of a gene that occurs at the same locus on homologous chromosomes; different alleles of ABO blood groups are an example.
  • Locus: The locations of allelic genes on a chromosome.
  • Polymorphism: The existence of ≥ 2 different phenotypes resulting from ≥ 2 alleles.

Causes of DNA Mutations

  • Spontaneous mutations:
    • Depurination
    • Deamination
  • Induced mutations:
    • Chemicals
    • Radiation

Depurination

  • Depurination results in the loss of a purine nitrogen base (adenine or guanine) without breaking the phosphodiester DNA “backbone.”
  • When the replication machinery encounters a missing purine on the template strand, it can skip to the next complete nucleotide, producing a nucleotide deletion in the newly synthesized strand.

Deamination

  • Deamination is the conversion of a cytosine to uracil.
  • The DNA replication machinery inserts an adenine when it encounters a uracil on the template strand.

Induced Mutations

  • X-rays:
    • Excites water in the cell, leading to the generation of hydroxyl radicals.
    • Hydroxyl radicals react with DNA, altering the structure of the bases or cleaving the DNA strands (double-strand breaks).
  • Ultraviolet light:
    • Causes formation of pyrimidine dimers.
    • Mutations that result in the formation of covalent bonds between carbons in adjacent thymines (thymine dimers).
  • Chemicals:
    • Benzo[a]pyrene: Aromatic polycyclic hydrocarbon, highly mutagenic.
    • When oxidized by cytochrome P450, forms bulky adducts with guanine residues in DNA.

Types of DNA Mutations

  • Point mutations
  • Insertion/deletion
  • Trinucleotide Expansions
  • Chromosomal mutations

DNA Point Mutations

  • Point mutations: A mutation that causes a change in a single nucleotide in the DNA sequence.
    • Missense: Results in a codon that codes for a different amino acid.
    • Nonsense: Results in a premature stop codon.
    • Insertion: Extra nucleotide is added, can change the reading frame and result in a frameshift mutation.
    • Deletion: Loss of a nucleotide, can change the reading frame and result in a frameshift mutation.

Trinucleotide Expansion

  • Results from slippage during DNA replication.
  • The newly synthesized strand dissociates from the template strand, a kink is formed, and repeat sequences allow the new strand to re-anneal in the wrong location, creating a duplication of that region.
  • The greater the number of repeats, the more likely that a disease will occur or the severity of a disease will increase.
  • Clinical Correlation: Huntington's disease is caused by a trinucleotide expansion mutation.

Chromosomal Mutations

  • Mutations can occur at the level of a chromosome, through chromosomal breakage:
    • Deletion: Loss of a piece of DNA from a chromosome. Deletion of a gene or part of a gene can lead to a disease or abnormality.
    • Duplication: Production of one or more copies of any piece of DNA, including a gene or even an entire chromosome.
    • Inversion: Reversal of a piece of DNA.
    • Insertion: A type of chromosomal abnormality in which a DNA sequence is inserted into a gene, disrupting the normal structure and function of that gene.
    • Translocation: Breakage and removal of a large segment of DNA from one chromosome, followed by the segment's attachment to a different chromosome.
    • Recombination: Unequal crossing over during meiosis.

Translocations

  • Gross chromosomal rearrangements resulting from breaks in chromosomes.
  • The free ends of the DNA at the breakpoint re-seal with the free ends of a different broken chromosome.
  • Frequently observed in cancer cells.
  • Some hereditary diseases are associated with chromosomal translocations.

DNA Repair Process

  • Two major types of DNA damage that need repair:
    • Single nucleotide defects
      • Excision repair
        • Nucleotide excision repair
        • Base excision repair
      • Mismatch repair
    • Double-stranded breaks in DNA
      • Non-homologous end joining
      • Homologous recombination

Types of Excision DNA Repairs

  • Nucleotide Excision Repair:
    • Specific repair endonucleases cleave the abnormal chain and remove the damaged region.
    • The gap is then filled by a DNA polymerase that adds deoxyribonucleotides, one at a time, to the 3’-end of the cleaved DNA, using the intact complementary DNA strand as a template.
    • The newly synthesized segment is joined to the 5’- end of the remainder of the original DNA strand by a DNA ligase.
  • Base Excision Repair:
    • DNA glycosylase cleaves the N-glycosidic bond that joins the damaged base to deoxyribose.
    • The sugar-phosphate backbone of the DNA now lacks a base at this site.
    • An endonuclease cleaves the sugar-phosphate strand at this site.
    • DNA polymerase fills in the gap.
    • DNA ligase joins the newly synthesized segment to the original DNA strand.

Mismatch Repair

  • Active during DNA replication when an incorrect but normal base is incorporated into the growing chain.
  • Mismatched bases do not form normal base pairs.
  • The mismatch is recognized by the mismatch repair enzyme complex.
  • The mismatch repair enzyme complex removes a segment of the newly synthesized DNA that includes the mismatched bases.
  • DNA polymerase and ligase repair the gap.
  • DNA mismatches are due to replication error.

Non-Homologous End Joining

  • Non-homologous end joining (NHEJ) is the most common mechanism for repairing double-strand breaks in somatic cells.
  • Does not require a homologous chromosome as a template.
  • Following a double-strand break, nucleases process the broken ends to form blunt ends; during this process, some nucleotides are lost, and mutations may be introduced.
  • The ends are then brought together by a specialized group of enzymes and rejoined by DNA ligase (works like a glue).
  • A “quick and dirty” DNA repair mechanism.
  • Double-strand breaks in DNA are most often caused by exposure to ionizing radiation (X-rays, radioactive material).

Homologous Recombination

  • Error-free method for repairing double-strand breaks.
  • Requires the presence of a homologous chromosome to be used as a template.
  • Commonly used for repair of newly replicated DNA.
    1. Two homologous chromosomes become aligned.
    2. A nuclease generates single-stranded ends at the break by chewing back one of the complementary strands.
    3. One of the single strands then invades the homologous DNA duplex by forming base pairs with its complementary strand. A significant number of bases must pair to produce a branch point where one strand from each duplex crosses.
    4. The invading strand is elongated by DNA polymerase, using the complementary strand as a template.
    5. The branch point migrates as the base pairs holding together the duplexes break, and new ones form.
    6. Additional DNA synthesis and ligation complete the repair.

Chromosomal Inheritance

  • Humans have 23 pairs of chromosomes:
    • 22 pairs of autosomal chromosomes
    • 1 pair of sex chromosomes (XX or XY)
  • Autosomal inheritance refers to the alleles located on autosomal chromosomes.
  • One autosomal allele for each gene is passed down from each parent.
  • Autosomal alleles are passed equally to both genders.

Dominant and Recessive

  • Dominant: Only one allele of a pair is required to manifest a phenotype.
  • Recessive: Both alleles must be the same for a particular phenotypic expression.
  • Homozygous: Both alleles are the same.
  • Heterozygous: Each allele is different.

Mendelian Inheritance

  • Four classifications of Mendelian inheritance:
    • Autosomal Dominant
    • Autosomal Recessive
    • X-Linked Recessive
    • X-Linked Dominant

Autosomal Dominant Inheritance

  • Characteristics of autosomal dominant inheritance:
    • The affected offspring has one affected parent unless the gene for the abnormal effect was the result of a new mutation.
    • Unaffected persons do not transmit the trait to their children.
    • Males and females are equally likely to transmit the trait to males and females.
    • The trait is expected in every generation.
    • The presence of two mutant alleles generally presents with a more severe phenotype.

Autosomal Recessive Inheritance

  • Characteristics of autosomal recessive inheritance:
    • Most affected individuals are children of phenotypically normal parents (both are heterozygous carriers).
    • Often, more than one child in a large siblingship is affected.
    • On average, one-fourth of siblings are affected.
    • Males and females are equally likely to be affected.
    • Affected persons who marry normal persons tend to have phenotypically normal children.
    • When a trait is exceedingly rare, the responsible allele is most likely recessive if there is an undue proportion of marriages of close relatives among the parents of the affected offspring.

X-Linked Dominant Inheritance

  • Distinguishing feature between an X-linked dominant and an X-linked recessive disorder:
    • There are no carriers; expression of disease occurs in both males and females.
    • Like X-linked recessive disorders, females transmit the mutant allele to both male and female offspring, but males can only transmit to females.
    • All of an affected male’s daughters will have the disorder.

X-Linked Recessive Inheritance

  • Characteristics of X-linked recessive inheritance:
    • Unaffected males do not transmit the disorder.
    • Affected males cannot transmit the disorder to male offspring.
    • All the daughters of an affected male are heterozygous carriers.
    • Heterozygous women transmit the mutant allele to 50% of the sons and to 50% of the daughters.
    • Affected males will transmit the mutant allele to all of his daughters.