Introduction to DNA

• Each person's DNA quantity is enough to stretch to the Sun and back 300 times.
• A human genome (a haploid set of chromosomes in a gamete) contains nearly 3 billion DNA base pairs.
• The human genome is packaged into 23 chromosomes.
• Most cells are somatic cells (body cells), which are diploid with 23 pairs of chromosomes, containing approximately 6 billion DNA base pairs per cell.
• Each base pair (Thymine-Adenine; Cytosine-Guanine) is 0.34 nanometers long.
• Each haploid cell contains 2 meters of DNA.
• A human body has approximately 50 trillion cells, which is about 100 trillion meters of DNA per human.
• DNA is packed together to create chromatin, then a chromatid, which join together to form a chromosome.
• DNA stands for deoxyribonucleic acid, and carries genetic information.
• DNA is a double helix with two strands known as polynucleotides.
• Polynucleotides are composed of simpler units called nucleotides.
• Each nucleotide has three components:
  • A nitrogen-containing nucleobase (Thymine-Adenine; Cytosine-Guanine)
  • A monosaccharide sugar called deoxyribose
  • A phosphate group
• Nucleotides are joined by a covalent bond (hydrogen bond) between the sugar of one nucleotide and the phosphate of the next.
• This results in an alternating sugar-phosphate backbone.
• T-A base pairs are joined by 2 hydrogen bonds, while C-G base pairs are joined by 3 hydrogen bonds.
• Purines and pyrimidines are nitrogenous bases in DNA and RNA.
• Two-carbon nitrogen ring bases (adenine and guanine) are purines.
• One-carbon nitrogen ring bases (thymine and cytosine) are pyrimidines.
• Purines contain two carbon-nitrogen rings and four nitrogen atoms.
• Pyrimidines contain one carbon-nitrogen ring and two nitrogen atoms.
• Negatively charged DNA wraps around 8 positively charged histone proteins and forms a nucleosome (bead on a string).
• A bunch of nucleosomes together is called chromatin.
• Certain proteins, called histones, compact chromosomal DNA into the microscopic space of the eukaryotic nucleus.
• Histones are proteins that provide the energy required to fold DNA.
• Histones allow chromatins to be packaged into a smaller volume than DNA alone.
• DNA is negatively charged due to the phosphate groups in its phosphate sugar backbone, thus histones bind very tightly.
• Chromatin is a complex of DNA-proteins that forms chromosomes within the nucleus of a eukaryotic cell.
• Chromatin has 2 forms:
  • Euchromatin is less condensed and can be transcribed. Transcription allows for proteins to be built.
  • Heterochromatin is highly condensed and typically cannot be transcribed.
• Chromatins look like beads on a string, which are called nucleosomes.
• Each nucleosome is DNA wrapped around 8 histones (proteins).
• Each chromosome is one continuous thread-like DNA molecule coiled tightly around proteins.
• Each chromosome contains a portion of the 6.4 x 10^9 base pairs.

Cell Division and Genetic Material

• Genetics is the biology field that studies how genetic information is passed from one generation to the next.
• The Cell Theory states that
  • All living things consist of one or more cells
  • Cells are the smallest units of living organisms
  • New cells come only from pre-existing cells by cell division
• Traits must be passed from one cell (parent) to new cells (daughter).
• Genetic information is passed through DNA (deoxyribonucleic acid).
• When a cell divides, each new cell receives genetic information from the parent cell.

The Cell Cycle

• Cells reproduce through controlled growth and division in the cell cycle.
• Somatic cells, the body cells of plants and animals, go through the cell cycle, but exclude reproductive cells.
• Each cell cycle results in two cells.
• Functions of cell division in multicellular organisms:
  • Growth of the organism
  • Repair of damaged tissues and organs
  • Maintenance to replace dying or dead cells
• Actively dividing animal cells take around 12-24 hours to complete the cycle.
• The cell cycle has 3 main stages: interphase, mitosis, and cytokinesis.

Interphase

• Interphase is the stage where the cell carries out normal functions, grows, and makes copies of genetic material before the next stage.
• As the cell copies its DNA, it prepares for division. Interphase is divided into 3 phases:
  • G1 (Growth 1) is the major growth period. The cell synthesizes new molecules to prepare for the next phase
  • S (Synthesis) stage is when cellular DNA is copied or replicated. DNA exists as uncondensed fibers, called chromatin
  • G2 (Growth 2) stage synthesizes new molecules prior to mitosis and cell division

Mitosis

• Mitosis divides the cell’s nucleus and genetic material. The copied genetic material is separated and prepares to split into two cells.
• The key actions during mitosis:
  • Prophase: The cell’s chromatin condenses into chromosomes, the DNA gets copied. The chromosome exists as two copies
  • Sister chromatids are the two chromosome arms, which are genetically identical (held together at the centromere)
  • The nuclear membrane breaks down and the nucleolus disappears.
  • Spindle fibres (microtubule structures that facilitates the movement of chromosomes within a cell) are formed from the centrosomes
  • Centrosomes move apart to opposite poles of the cell.
  • Metaphase: Spindle fibres guide the chromosomes to the equator (center line) of the cell.
  • Spindle fibres from opposite poles attach to the centromere of each chromosome
  • Biologists consider each pair of sister chromatids to be a single chromosome as long as the chromatids remain joined at the centromere
  • Anaphase: Each centromere splits apart, and the sister chromatids (now chromosomes) separate from each other.
  • Spindle fibres shorten, pulling the chromosomes to opposite poles of the cell.
  • At the end of anaphase, one complete chromosome set has been gathered at each pole of the cell.
  • Telophase: Chromosomes have reached opposite poles of the cell
  • Chromosomes unwind into less-visible chromatin stands
  • Spindle fibres break down and a nuclear membrane forms around the new chromosome set
  • A nucleolus forms within each new nucleus

Cytokinesis

• Mitosis is the process of nuclear division, which is followed by cytokinesis (division of the cytoplasm), completing two new daughter cells.
• During cytokinesis in animal cells, an indentation forms in the cell membrane along the cell’s equator.
• The indentation continues to deepen until the cell is pinched into two.
• Animal cell cytokinesis is accomplished by microfilaments that constrict to pinch the cytoplasm, ending with two genetically identical daughter cells, now in G1 of interphase.
• Plant cells create a cell plate structure between two daughter nuclei and cell walls form on either side.
• The cell plate results in two genetically identical plant cells.
• Prokaryotic cells do not have a nucleus, completing division through binary fission.
• The DNA is duplicated, copies attach to the cell membrane, and DNA molecules are pulled apart.

The Structure of Genetic Material

• DNA has 2 long strands that form a double helix.
• DNA exists as chromatin fibre strands during most of the cell cycle
• The chromatin condenses into distinct chromosomes once mitosis begins.
• Nucleotides are the individual units of each of the DNA strands, consisting of a phosphate group, a sugar group, and a base.
• Sugar and phosphate groups form the backbones of the two nucleotide strands.
• Bases protrude inward at regular intervals.
• The 4 DNA bases are adenine (A), guanine (G), thymine (T), and cytosine (C).
• Nucleotides are identified by their bases, each paired in a particular manner.
• Adenine is paired with thymine and guanine is paired with cytosine, called complimentary base pairs.
• A DNA or genetic mutation is a nucleotide sequence change of DNA.
• The complete DNA sequence in every cell of an organism is the organism’s genome.
• During interphase, when DNA is replicated, the double helix unwinds and each strand of DNA serves as a template for a new strand.
• Copied DNA results in the new double-stranded DNA molecules containing one original and one new DNA strand.
• Each new DNA molecule conserves half of the original DNA, called semi-conservative.

Chromosome Organisation

• Human somatic cells have 46 chromosomes in 23 pairs.
• For each pair, one chromosome is from the father, and the other chromosome is from the mother.
• Sex chromosomes (X or Y) determines the genetic sex of an organism.
  • A human female has two X chromosomes
  • A human male has one Y chromosome and one X chromosome
• The sex chromosomes are always counted as a pair.
• Autosomes are the remaining 22 pairs of chromosomes are not involved in determining sex.
• Autosomes are chromosomes not involved in determining the sex of the organism.
• Chromosomes are paired based on similar characteristics.
• Homologous chromosomes are pairs of chromosomes that appear similar in length, centromere location, and banding pattern under dyes, but are not identical.
• Genes are DNA sections containing genetic information for specific trait inheritance.
• Homologous chromosomes carry genes for the same traits, but different forms of the same gene are called alleles.
• A karyotype is an individual’s particular set of chromosomes.
• Cell samples collected and stained creates a banding pattern on chromosomes for organizing into a karyotype.
• Autosomes are numbered from 1-22, sex chromosomes are labelled X or Y, the Y chromosome is much smaller than the X chromosome
• Chromosome pairs are put in order according to size.
• The tallest pair of homologous chromosomes goes to pair #1, the second tallest is pair #2, etc. until the shortest homologous chromosomes ends at pair #22
• Homologous chromosomes are matched based on lengths, banding patterns (where genes are located), and centromere location.
• SS chromosomes collected in mitosis.

Reproduction

• Asexual reproduction reproduces one parent for genetically identical offspring.
• Mitosis results in clones.
• Sexual reproduction uses 2 parents for genetically distinct offspring.
• Sexual reproduction involves male reproductive cell (sperm) fusion with a female reproductive cell (egg).
• These are called gametes, and the fusion cell is a zygote, called fertilization.
• Fused gamete cells result in the same number of chromosomes as the somatic cells.
• Gametes contain half the number of chromosomes as the parent cells.
• Gametes are called a haploid for having single unpaired chromosomes.
• A haploid has half the number of chromosomes as the parent cell, designated as n.
• Each human gamete is haploid, designated as n = 23.
• Cells with pairs of chromosomes (all somatic cells) are called diploid
• Diploids contain pairs of homologous chromosomes.
• After fertilization, the zygote cell is diploid (2n chromosomes)
• N chromosomes comes from the female parent, and n chromosomes comes from the male parent, bringing the diploid in humans to 46.
• Remember, n represents the number of chromosome pairs in an organism.
• 2 human gametes combine for 23 pairs of homologous chromosomes.
• The number of genetically distinct gametes is calculated as 2^n (n = # of pairs).
• For humans, there are 23 pairs of chromosomes resulting in 2^23, therefore 8.4 million options.
• Meiosis is the cellular process that produces cells containing half the number of chromosomes as the parent cell, producing gametes with a haploid number of chromosomes.
• Meiosis has 2 key outcomes:
  • Genetic Reduction: meiosis is a cell division form producing daughter cells with half the number of chromosomes as the parent cell;
  • Genetic Recombination: meiosis products having different allele combinations, giving rise to offspring that are genetically different and increasing the genetic variation in a population.
• Cells divided by meiosis proceed with interphase growth and the synthesis phase before dividing
• Chromosome replication is included.
• At the start of meiosis, a cell contains duplicated chromosomes, each with a pair of identical sister chromatids held together at the centromere.
• Each pair of homologous chromosomes lines up side by side (1 chromosome from each parent).
• Lining up homologous chromosomes is called synapsis.
• Synapsis causes the segments of chromosomes to attach along their lengths to form a tetrad (made of up the 4 chromatids).
• Genetic information is then exchanged with one another (crossing over), which is a part of genetic recombination.
• Crossing over occurs at a site on the chromosomes called the chiastmata.
• The centrosomes move to the poles of the cell and the spindle apparatus forms.
• Pairs of homologous chromosomes line up along the equator of the cell.
• The spindle fibres attach to the kinetochore (protein complex assembled on the centromere) of each homologous chromosome.
• The homologous chromosome pairs line up at the cell equator in determined via independent assortment, an element of genetic recombination.
• Independent assortment formula = 2^n (n = the number of pairs of chromosomes that are within the cell), which gives the number of distinct gametes produced with this cell.
• Homologous chromosomes separate and move to opposite poles of the cell.
• The centromeres do no split. .
• One chromosome (2 chromatids) moves from each homologous pair to each pole.
• Chromosome numbers are reduced from diploid, 2n -> haploid, n
• The homologous chromosomes uncoil and the spindle fibres disappear.
• Cytokinesis occurs via a nuclear membrane around each group of homologous chromosomes to form two cells.
• Each new cell is now haploid.
• Phases of meiosis II are similar to those of mitosis.
• The cell undergoing division during meiosis II is haploid instead of diploid.
• Haploid chromosome numbers line up at the equator during metaphase II.
• During anaphase II, the spindle fibres pull the sister chromatids apart at the centromere.
• Chromosomes move toward opposite poles of the cell.
• Chromosomes reach the poles during telophase II, and the nuclear membrane and nuclei reform.
• During meiosis II, cytokinesis results in 4 haploid cells (each with "n" number of chromosomes)
• Meiosis I: genetic recombination, separation of homologous pairs, diploid -> haploid.
• Meiosis II: DS -> SS (the number of chromosomes stays the same) for all 4 daughter cells.
• In genetics, a trait is a specific characteristic or feature of an organism
• An Austrian monk, Gregor Mendel, answered, "How are traits inherited?”
• Pea plants reproduce through sexual reproduction and self-fertilize.
• The same pea plant offers both male and the female gametes.
• Plants that self-fertilize to produce offspring with consistently the same traits generation after generation are called true breeding.
• Selectively fertilizing a female gamete with a male leads to predictable traits via a process called cross-pollination.
• Mendel began each experiment with true-breeding plants, or a parental/P generation.
• Organisms initially are crossed and are typically true breeding.
• True breeding plants with one trait variety were crossed with true-breeding plants with other trait forms
• Plants were crossed green-colored seeds with yellow-colored seeds.
• P generation crosses result in the first filial or F1 generation.
• One trait is monitored in the cross and hybrid plants (those made from parents of differing forms of traits), called a monohybrid cross.
• Monohybrid cross = crossing two individuals that differ by one trait.
• Yellow-seed and green-seed plants are crossed, for example. Offspring/F1 generation resulted in only yellow seeds.
• The green form of seed color “disappeared”
• Contrasting forms of traits resulted in a single trait expression amongst offspring.
• The second filial or F2 generation is a cross of F1 generation plants.
• The green form of seed color shows again in F2 generation
• The ratio of plants with yellow seeds to plants with green seeds in the F2 generation was 6022:2001, or 3.01:1 (3:1).
• The Mendelian ratio of 3:1 is for the phenotype after crossing 2 heterozygotes.
• Hereditary’ factors/alleles result in every trait studied.
• Alleles are gene differences with two alleles for each gene in diploid organisms.
• Mendel’s pea plants have two alleles for seed colour.
• Although all the F1 generation seeds were yellow, they all had a copy of each seed color gene form.
• Therefore, they each had an allele for yellow and one for green seeds, from both parents.
• Yellow is the form of a trait that always appears when an allele for it is present or the dominant form, while green required two alleles for expression or the recessive form.
• Mendel’s law of segregation=traits are determined by pairs of alleles that separate during meiosis yielding one allele per gamete
• Each offspring upon fertilization, contains one allele from each parent.
• The trait that is expressed depends on whether the individual inherits dominant or recessive alleles for the trait.
• A dominant allele means the dominant trait will be expressed.
• Expression of the recessive form requires that an individual has two recessive alleles for the trait.
• Alleles are expressed using upper- and lower-case letters.
• A dominant allele results in the upper-case first letter and the recessive utilizes the same letter in lower case.
• Y=allele for yellow represents yellow seeds in Mendel's pea plants
• y = allele for green seeds
• Every diploid organism for each contains two alleles for each gene which results in three possible allele combinations:
  • Two copies of the dominant form (YY) or homozygous dominant
  • Two copies of the recessive form (yy) or homozygous recessive
  • One copy of each form (Yy) or heterozygous
• An organisms combination of alleles is the genotype.
• The genotype is an organism’s entire genetic build.
• A phenotype is an expression of a genotype that represents the physical and physiological traits of an organism.
• For example: each pea and seed of a color YY or genotype Yy yields a phenotype of yellow.
• The yellow seed color is the dominant phenotype.
• Green color is yields the recessive phenotype.
• Only the pea plants with yy yield seeds of green.
• An individual has two identical alleles, are homologous for that, for example YY or yy.
• An individual yielding two alleles results in the trait to be heterozygous for that e.g. Yy.
• Every cell contains two alleles per gene and results in two possible outcomes of meiosis.
• The probability of a specific sorting of is ½ or 50, while probability will allele showing at twice (since every geno also has two 25 phenotype.

Punnett Squares

• Punnett Square analysis is a gene expression and grid combination of results from genetic crosses.
• A monohybrid cross has the Punnett squares, the grid to be designed as: Draw the line dividing the sides which result in small squares. Result on the genotype over the gametes on parent top while the alleles also must be done. Genotype has alleles. that alleles. A a gene for gene as is dominant from an genetic