Chapter 02 Basic Genetics

• Genetics is an important area of modern biology and blood banking.
• A solid understanding of classic genetics: Mendel's laws of inheritance, the Hardy-Weinberg formulas, cellular concepts that control chromosomes, mitosis and meiosis, and the biochemistry of molecular structures is required to understand modern genetics.

Introduction

• Genetics is a dynamic science with direct applications especially relating to blood group genetics and pathogen testing for blood supply safety.
• The antigens follow straightforward codominant inheritance patterns in blood group systems (ABO, Rh, Kell, Kidd, etc.).
• Cellular and molecular genetics are becoming as important as population genetics and inheritance patterns.
• Modern genetic techniques analyze blood donors and recipients, previously relying only on serologic testing.
• Molecular methods require training and skill in restriction mapping, sequencing, polymerase chain reaction (PCR), and gene array technology.
• Genetics is overviewed at population, cellular, and molecular levels.
• Chapter 4 explains modern testing methods of molecular biology, including recombinant DNA technology, Southern and Northern blotting, restriction fragment length polymorphism analysis, PCR techniques, cloning, and sequencing.

Classic Genetics

• Genetics is vital for understanding blood group antigens and disease marker testing in transfusion medicine.
• Modern genetics relies on biochemistry and biophysics of nucleic acids like DNA, RNA, and chromosomal proteins, and population studies and epidemiology.
• Inheritance patterns and biochemical reactions causing gene mutations are important, as new alleles can lead to new blood groups and diseases affecting donors and recipients.
• Genetics influences all areas of transfusion medicine, including HLA typing, cell processing, parentage studies, viral testing, and blood services.
• Genotyping donor or recipient DNA using leukocytes determines which antigens may be present and which antibodies can be made against them.

Population Genetics

• Mendel's laws of inheritance, the Hardy-Weinberg principle, and inheritance patterns are major concerns.

Early Genetics and Mendel's Laws of Inheritance

• Carolus Linnaeus started classifying living things in the 17th century based on physical traits and observations
• No attempts were made to understand why specific traits occur
• In 1859, Charles Darwin sought to understand life diversity and how organisms gain an advantage referred to as natural selection
• Gregor Mendel studied physical traits inheritance in sweet pea plants.
• He determined physical traits are due to elementen, modernly known as genes.
• Mendel studied flower color, seed color, and seed shape.
• Mendel's first law of inheritance, the law of independent or random segregation, is based on these results.
• The first generation, the parental/pure/P1, bred true for generations.
• The plants were homozygous for either red flowers (RR, dominant trait) or white flowers (rr, recessive trait).
• The second generation, the F1 filial, resulting from crossbreeding, had all red flowers.
• The trait that was observed was dominant.
• F2 generation plants crossbred to a 3:1 ratio of red to white flowers.
• F1 generation plants are heterozygous (hybrid) for flower color, i.e. Rr.
• F2 generation has a 3:1 ratio, where the R gene results in red flowers, either RR homozygous or Rr heterozygous.
• Mendel's first law illustrates each gene passes to the next generation independently.
• Alleles of genes have no permanent effect on one another when present in the same plant, but segregate unchanged by passing into different gametes.
• Partial dominance occurs when alleles exhibit it.
• The phenotype of a heterozygous organism is a mixture of homozygous phenotypes seen in the P1 generation.
• Plants with red and white flowers having offspring with pink flowers or flowers that have red and white sections gives an example.
• F1 generation has the heterozygous Rr genotype, even if the phenotype doesn't show dominance.
• Blood group genes are inherited in a codominant manner.
• Both alleles are expressed, and their gene products express at the phenotypic level.
• An example is the MNSs blood group system; a heterozygous MN individual would type as both M and N antigen positive.
• Mendel's second law is the law of independent assortment that states genes for different traits are inherited separately from each other.
• If a homozygote dominant for two traits is crossed with a homozygote recessive for both, the F1 generation exhibits the phenotype of the dominant parent.
• The F2 generation yields parental and a new phenotype, a reciprocal type with dominant feature of one plant and recessive feature of another.
• Recombinant types occur in both combinations using different types of seeds produced by peas.
• Mendel studied that they can be colored and textured in any combination.
• Mendel's laws apply to sexually reproducing diploid organisms, microorganisms, insects, plants, animals, and people. but there are exceptions.
• Genes closely linked on a chromosome may be inherited as a single unit.

Hardy-Weinberg Principle

• G. H. Hardy and W. Weinberg developed the mathematical formula p + q = 1 that allows the study of Mendelian inheritance, addressing recessive persistent traits.
• Criteria in Box 2-1 must be met for proper equations use.
  • The population studied must be large.
  • Mating among all individuals must be random.
  • Mutations must not occur in parents or offspring.
  • There must be no migration, fertility, or mortality of genotypes studied.
• It is almost impossible to use this formula in humans, as mating is not random.
• There is population mixing and gene mutations commonly occur.
• Hardy-Weinberg is used to study the frequencies of the Rh antigen, D, in a population.
• In a simple example, there are two alleles D/d.
• To determine the frequency of each allele, the corresponding phenotype number is counted (remembering both Dd and DD will appear as Rh-positive) and divide by the total number of alleles. This is value p in the Hardy-Weinberg equation.
• Counting the alleles lets us determine value q.
• When p and q are added, it must equal 1.
• The ratio of homozygotes and heterozygotes is determined using the other form of the Hardy-Weinberg equation, p² + 2pq + q2 = 1.
• An example tests 1,000 blood donors for the D antigen and find that DD and Dd (Rh-positive) occurred in 84% of population and dd (Rh-negative) occurred in 16%.
• Gene frequency calculations:
  • p = gene frequency of D
  • q = gene frequency of d
  • p2 = DD, 2pq = Dd, which combined are 0.84
  • q2 = dd, which is 0.16
  • q = square root of 0.16, which is 0.4
  • p + q = 1
  • p=1-q
  • p = 1 - 0.4
  • p = 0.6
• A three-allele system would require p + q + r = 1 or p² + 2pq + 2pr + q2 + 2qr + r2 = 1.
• Using this formula is complex, but it can be found in advanced genetics textbooks.

Inheritance Patterns

• Pedigree analysis needs data figures representation understanding.

• Males are represented as squares and females as circles.

• A line indicates a mating, a double line between male and female indicates consanguineous mating.

• A stillbirth or abortion is a small black circle.

• Deceased family members have a line crossed through them.

• The propositus has an arrow indicating it and indicating something unusual of that member.

• Pedigree analysis follows common inheritance patterns.

• Autosomal-recessive inheritance where autosomal refers to traits not carried on sex chromosomes.

• A recessive trait is carried by either or both parents but isn't seen unless both parents carry the trait

• A recessive trait can be genetically expressed in a heterozygous individual but may not be seen in the phenotype level

• Dominant X-linked: the father carries the trait, he has no sons with it, but all his daughters will.

• Women can be either homozygous or heterozygous for an X-linked trait.

• Sons have a 50% chance of inheriting trait, so they'll express it because the trait is dominant (i.e. Xga system)

• X-linked recessive: the father always expresses the trait but never passes it on to his sons but instead his daughters, who are carriers.

• Each individual has the allele due ot one of the parents carrying the trait (gene is expressed if only one copy is present), doesn't differ between sexes, unlike X-linked traits

• If an individual doesn't have the autosomal or X-linked trait, they can be a carrier that passes it, as recessive seem to skip generations

• Autosomal dominant traits, like blood group genes, are encountered in blood banking often.

• Traits are passed on from generation to generation.

• Unusually rare traits in every generation and/or general population, is the result of related individuals mating

Cellular Genetics

• Organisms are divided into:

  • Prokaryotic - no nuclei
  • Eukaryotic - nucleus

• Humans and mammals are eukaryotic.

• The nucleus contains genetic material required for replication

• Nuclear material is chromatin of nucleic acid of structural protein, defined by staining patterns

• Heterochromatin - dark bands, usually not active

• Euchromatin - swollen, active in RNA synthesis

• Most nuclei contain chromatin, made of DNA polymers and histones, and compressed to form chromosomes.

• Each organism has as specific number of chromosomes.

• Humans have 46 arranged in pairs with one each from parents.

• Humans contain 22 autosomes and 1 set of sex chromosome.

• 2N is normal for all human cells

• The gametes are an exception.

• N refers to pairs of chromosomes in a cell.

Terminology

• Two gametes make a fertilized egg (2N) which combines genetic information

• Each parent contains 1N

• 2N maintains genes for health

• The genetic material has a complex pattern of organization evolving for millions of years

• Genes = DNA arranged linearally with structural proteins for wound bundles

• DNA are organized at chromosomes (incredibly long duplex DNA strands)

• Genes' nucleotide sequence and location determine a gene

• Various gene functions occur upstream (start site) and downstream

• Locus is a gene location (loci for plural) which contains many forms for genes (allele)

• A genotype makes DNA sequence, where as the phenotype describes results/functions in the body such as controlling an enzyme via controlling a blood group antigen; as well as influencing physical characteristics such as muscle fibre ratio, skin/eye, hair colour

• A trait/phenotype may result from multiple genes

• Homozygous vs Heterozygous

• "Silent" Gene: Hemizygous -Silent" is amorph which does not produce detectable traits

• Hemizygous refers to when one chromosome has the gene copy while the other is deleted

Mitosis

• A cell divides, chromosomes reproduce identical daughter cells for viability

• Quantitative and qualitative identical DNA is delivered

• Mitosis is broken into stages, characterized by chromosome movement.

• Interphase

• Prophase

• Metaphase

• Anaphase

• Telophase

• Interphase - DNA dispersed throughout the nucleus via in chromatin form

• Prophase - DNA condenses to chromosomes/nuclear envelope breaks

• Metaphase - Chromosomes line to nucleus and pair with corresponding chromosome where cytogenetics preparations occur

• Anaphase - Cellular spindle apparatus forms and chromosomes pull to opposite ends

• Cell get pinched in middle

• Telophase - Cell pulls apart with division ending as chromosomes & cytoplasm separates into 2 daughter cells

Meiosis

• Meiosis is a process for creating unique daughter cells when creating gametes or germ or sex cells

• Allows for genetic diversity/controls chromosome's # within dividing cells

• Contains 1N if 2N chromosomes paired resulting in non viable 4N daughter cells

• Meiosis only happens at germinal tissues and is critical for reproduction -Without meiosis, there is no differentiation, thus evolution doesn't occur from generation

• Meiosis stages are identical to Mitosis, where there's condensation, homologous chromosome pairing at prophase/aligning chromosome at cell center

• Anaphase & Telophase: cell then enters interphase

• Prophase II - Chromosome condensation + Metaphase II

• Centromeres divide

• Anaphase & Telophase II - Cell divides resulting in 1N cells

• Crossing over + Recombination w/ maternal/paternal- chromosomes occurs during meiosis allowing for new DNA sequences.

• Due to random segregation, creating DNA is possible + In humans with 23 pairs of chromosomes makes over millions

• Cell division is a critical process that occurs constantly, described in stages

• Cells exist in Four stages

• G0 - Resting

• G1 - pre Replicating

• S - DNA synthesized

• G2

• M - Mitosis and division

• Chromosomes are between G0 and G2 during interphase:

• Nerves are G0

• Cancer cells undergo cell divisions + consume nutrients + overcrowd nearby cells, the same can be said with leukemia and tumor

Molecular Genetics

• Molecular genetics is the study of biochemistry of molecules and their structure+ their biochemical nature with nuclear/protein polymers

• DNA (Deoxyribonucleic acid) is a heredity backbone with chromatin chromosomes built by basic proteins

• Nucleic is aided with the DNA in the pH, allowing it to stabilized complex structure.

• DNAs protein are found at nucleosome tightly packaged within nucleus within inches in cell

• Hela Conformation protein protects when not transferred or replicated

• DNAs consists of 2 strand duplexes that is directional, also anitparallel composed of a:

• 4 Nitrogenous bases

• Deoxyribose + P group

• Backbone consist of phosphodiester linkages by hydrogen/Van Der Waals bonding

• Little force between same strands allows DNA to be strong by flexible

• 4 Different kinds of bases consist of Adenine (A), Cytosine (C), Guanine (G), Thymine (T).

• Adenine + Guanine --> Purines, a double ring

• Cytosine + Thymine --> Pyrimidines, single ring structure

• Bonding within DNA is specific to A-T (with 2 hydrogen bonds) and C-G (stronger with 3 bonds)

• Classic Watson-Crick base is shown with B-Form

• In 1950s Watson and crick discovered that DNA exists as Z-DNA (helix with 3 dimension) , using different carbon attachments at 1st carbon

• Phosphates @ DNA backbone attaches to the sugar at the 3rd to 5th carbons

• Linkage of purine bases to the sugar is @ carbon one therefore the 2 DNA strains are antiparallel

• the 5' to 3' end

• Complementary strand contains sequence

• RNA's (messenger/m) correspondence is template/coding

• with only 4 different kinds of construction, nucleotides cant code on unique amino acids (20 different AA)

• Triplets or Codon codes one specific amino acid

• AA w/ multiple traplets has redundant genetic code. The more common these are, the higher Codon they have

• Four special codons are used only in initiation of transcriptions/translations in every process, called start codon

• 3 for stop Codons that doesn't charge AA to result in terminating peptide through mRNA translation

Replication

• Replication is copying DNA through enzymes, small nucleic molecules, and the helix within DNA that serve as template

• Must be perfect for mitosis for duplication of DNA at daughter cell w/ similar sequencing and quantity.

• Nearly bidirectional DNA replica is semiconservative that splits a strand of DNA in half to have 1 to 3 pairing while the other section opens

• New synthesis adds w/ parent strands is show w/ figure 2-12

• Enzymes and proteins enables for DNA with correct replica along parent sequences

• DNA relication happens at:

• Sections are uncoiled

• Strands kept apart, usually done with DNS Gyrase(open supercoils) + DNA Helicase using energy/ATPhydro

• DNA polymerase III allows at 3-5 direction at the lead strands

• Single strand binding proteins prevents H bonding when not needed during replication

• The Polymerase checks for additions to new strands + can eliminate incorrect bases

• oligonucleotide helps replications though connecting at the beginning @ region in replicating

  • "Primes" + RNA Primer allows replication through primase enzymes, then annealing at parent strands

• The newly replicated zones of parental strands are the Okazaki fragments joining to make continue strand via DNA Polymerase I + Ligases -- Isomerase, the enzyme allows recoiling DNS + edits the strand and proceeds with process and editing

Errors

• DNS errors, which affects life is fixed by editing on the complex replications
• Mechanisms detects, changes + edits + corrects
• DNA polmerases edits both 5' and 3' allowing backtracking and removal of nucleotide and is inserted
• A second form of is mismatching repair - correct nucleotide is removed and replace for another -Chemical + Enviromental factors alters (ie. alkylating/reac with guanine which results in depurination)
  • Radiation + strong oxydizing agents damage strands
• Some treats creates cancer by cell replicating greater damages and risk for cell death
• Mutations are defects via errors
• This includes photomismatch reair, recombinational, eecisions, SOS repair, (missing bases with alterations)
• Thymine dimers or lights active photomatch or enzymatic clears of thymine damages+ DNA cut+ removed

Mutations:

• Proofreading+ repairing doesn't prevent systems nor mutation from being fool proof

• When entered to strands, it may/may to be altered ( protein wise) depending on if change affect AA

• Mutation - any changes within structures + sequence or in biochemical settings via external factors also causing mutant that differs or original wild type.

• point mutation happens w/in single nucleotide w/ substitutes, deletions and insertations

  • The changed or altered tripet/Codon wouldn't change AA sequence, which affects protein

• Silent Mutations - where there isn't much effects with cells (enzyme functions)

• Transition vs Transversion - The type of mutation can have major effects on AA leading to effects on protein

  • Mistake mutations - results in changes + can be acomodated w/ peptide

• Nonense is bad since, causes one 3 possible STOP codon

• Inserts + deletions (not multiples of 3) causes bigger problems

• Unusual genetique changes can be happen with replication and lower frequency of replication, duplicates due to pseudogenes/ Junk DNA.

• A large part of DNA includes junk/necessary effects with Alus Duplication of DNA contains short tandem

• Glycoporin and rhCD4 occurs with duplication within C4

• Mutations involve recombination/crossing over happens the sex cells.

  • The recombination breaks 2 DNS for a exchange across DNA, then resolves strands Crossover - single, double triple that can happens and result Hybrid.

• Genes w/ the (MNSs) blood + (Dantu/Mix) Group and the recombination within systems (D, V, J genes help the immune globes).

• Deletion of DNA occurs 100s of or 1000s of nucleotides that aren't editable, resulting in less functionality with cell, thus leading 30kD deletations of (Rogers +21 )

Isolation

• Successfully separating DNS enables optimal performance to procedures like the 4th chapter
• Alkinie denaturation that leads to precipations enables purification to un-cellular components Bead Technology helps isolates DNA for charge interactions as the process becomes automated Traditional Methods
• Mechanical damage + chemicals and sonications helps breaks cell walls , and disrupting other things + centrifugation allow isolated nucleic acids
• Greater care allows in obtaining a read, sequence intact but not readily degrading
• Synthesizing helps the body that is converted allow synthesis and allows various modifications for complex analysis

Techniques

• Knowledge through biochemical factors allows it to study with detailed definitions through interaction in order to cells/cells grouped, humans and organisms 1 the isolation/intact and structed damage uses chemicals that interacts the cell (uses salt gradients, detergents, enzyme activaiton 2 locates and visualisation, DNA by connecting through molecules (like H)

• Separation is requires through many sub species like sequencing and nucleic gel binding, through colums or membranes 4 - A method + changes with radiations+ emissions, detects the data