DNA Nucleotide Structure

• DNA contains the instructions for an organism's development, survival, and reproduction.
• A nucleotide is the basic building block of nucleic acids like DNA and RNA.
• The three parts of a nucleotide includes a phosphate group, a sugar (deoxyribose in DNA, ribose in RNA), and a nitrogenous base (A, T, C, G in DNA; A, U, C, G in RNA).
• DNA nucleotides have deoxyribose sugar and thymine (T), while RNA nucleotides have ribose sugar and uracil (U) instead of thymine.
• The four nitrogenous bases that make up DNA include adenine (A), thymine (T), guanine (G), and cytosine (C).
• Phosphate groups and deoxyribose sugars make up the backbone of a DNA double helix.
• Nitrogenous base pairs (A-T and C-G) make up the "rungs" of a DNA double helix.
• Nitrogen bases connect to the backbone through covalent bonds between the sugar and the base.
• Hydrogen bonds hold the two DNA strands together between complementary base pairs.
• Nitrogen bases connect to each other within the DNA double helix by hydrogen bonds.
• Adenine (A) pairs with thymine (T) via two hydrogen bonds, and cytosine (C) pairs with guanine (G) via three hydrogen bonds.

DNA and RNA Base Pairing

• Adenine (A) pairs with Thymine (T) in DNA.
• Cytosine (C) pairs with Guanine (G) in DNA.
• Adenine (A) pairs with Uracil (U) in RNA.
• Cytosine (C) pairs with Guanine (G) in RNA.

DNA Replication

• An organism replicates its DNA to ensure each new cell receives an identical copy of genetic information, crucial for growth, repair, and reproduction.
• DNA replicates during the S phase (Synthesis phase) of the cell cycle.
• The process of replication involves:
  • Unwinding: Helicase unwinds the DNA.
  • Priming: Primase adds RNA primers.
  • Elongation: DNA polymerase builds new strands.
  • Joining: DNA ligase connects fragments.
• DNA replication is called "semiconservative" as each new DNA molecule has one original and one newly synthesized strand.
• Helicase unwinds the DNA double helix, separating the two strands.
• DNA polymerase adds complementary nucleotides to the growing strand and proofreads to correct errors.
• DNA ligase joins Okazaki fragments on the lagging strand and seals breaks in the DNA backbone.
• The structure of DNA facilitates replication as the double helix allows the two complementary strands to separate easily, providing templates for new strands.
• Accurate copying of genetic information is ensured by base pairing, where A pairs with T and C pairs with G.
• Enzymes work efficiently in opposite directions due to antiparallel orientation on each strand during replication.

Protein Synthesis

• A gene is a segment of DNA containing instructions for making a specific protein or RNA molecule, which determines traits or functions in an organism.
• DNA is the molecule that carries genetic information.
• A gene is a segment of DNA that codes for a specific protein or RNA.
• A protein is a molecule made by ribosomes from instructions in the gene, carrying out various functions in the cell.
• A chromosome is a structure made of DNA and proteins that contains many genes. Humans have 46 chromosomes.
• Homologous pairs of chromosomes are pairs of chromosomes (one from each parent) that have the same structure and carry genes for the same traits.
• Transcription produces messenger RNA (mRNA), a copy of the gene's DNA sequence.
• mRNA carries genetic information from the DNA in the nucleus to the ribosome for protein synthesis.
• Translation produces a protein and mRNA is decoded by ribosomes to assemble amino acids into a specific polypeptide chain, which then folds into a functional protein.

Types of RNA

• mRNA (messenger RNA) carries the genetic code from DNA to the ribosome for protein synthesis.
• tRNA (transfer RNA) brings amino acids to the ribosome during translation, matching them with the mRNA codons.
• rRNA (ribosomal RNA) combines with proteins to form the ribosome, the site of protein synthesis.
• During translation, amino acids are brought to the ribosome by tRNA.
• The ribosome reads the mRNA codons, and each codon specifies an amino acid.
• Amino acids are linked together in a specific sequence by peptide bonds to form a polypeptide chain, which then folds into a functional protein.
• A codon is a sequence of three nucleotides in mRNA that codes for a specific amino acid, found on the mRNA molecule.
• During protein synthesis (translation), the ribosome reads the mRNA codons and each codon specifies an amino acid, and tRNA brings the corresponding amino acid to the ribosome.
• Amino acids are then linked together to form a protein.
• An anticodon is a sequence of three nucleotides on tRNA that is complementary to a codon on mRNA.
• During protein synthesis, the anticodon on the tRNA matches with the codon on the mRNA in the ribosome, ensuring the correct amino acid is added to the growing protein chain.
• Multiple codons will code for some of the same amnio acids as there are 64 codons and only 20 amino acids.
• This phenomenon of multiple codons coding for the same amnio acid is known as the redundancy or degeneracy of the genetic code.
• AUG is generally the start codon and codes for methionine (amino acid).

Mutations

• Point mutation/Substitution:
  • One nucleotide is replaced by another.
  • May change one amino acid, potentially altering protein function and can cause silent, missense, or nonsense mutations.
• Addition/Deletion (Frameshift mutation):
  • Nucleotides are added or deleted, shifting the reading frame.
  • Changes the entire amino acid sequence, often making the protein nonfunctional.
• A protein's shape is determined by its amino acid sequence. The sequence influences how the protein folds into its functional 3D structure through various interactions like hydrogen bonds and ionic bonds.

Mitosis

• Mitosis is the process of cell division that results in two identical daughter cells, each with the same number of chromosomes as the original cell.
• Stages of mitosis includes prophase, metaphase, anaphase, and telophase.
• Single-celled organisms go through cell division for reproduction, resulting in the formation of two genetically identical daughter cells. This is known as asexual reproduction.
• The phases of the cell cycle include interphase and M phase.
• Interphase prepares the cell for division and grows, consisting of:
  • G1 phase: Cell growth.
  • S phase: DNA replication.
  • G2 phase: Final preparation for mitosis.
• M phase: Cell division occurs, consisting of:
  • Mitosis: Division of the nucleus (prophase, metaphase, anaphase, telophase).
  • Cytokinesis: Division of the cytoplasm, resulting in two daughter cells.
• The phases of mitosis include:
  • Prophase: Chromosomes condense, nuclear membrane breaks down, spindle forms.
  • Metaphase: Chromosomes line up at the cell center.
  • Anaphase: Sister chromatids are pulled apart.
  • Telophase: Chromatids reach poles, nuclear membrane reforms.
  • Cytokinesis: Cytoplasm divides, creating two daughter cells.
• Chromosomes are long, thread-like structures made of DNA and proteins, carry genetic information, and are found in the nucleus of cells. Humans have 46 chromosomes (23 pairs).
• Chromosomes are visible during mitosis, specifically in the prophase stage, when they condense and become distinct structures.
• Cancer is a disease where cells grow uncontrollably and spread to other parts of the body.
• Cancer begins when mutations occur in the DNA of a cell, causing it to bypass normal regulatory mechanisms of the cell cycle, leading to uncontrolled division.

Genes Involved in Cancer

• Oncogenes are mutated or overactive versions of normal genes (proto-oncogenes) that promote cell growth and division, thus they can drive uncontrolled cell proliferation when mutated.
• Tumor suppressor genes normally prevent uncontrolled cell division and promote cell repair, but cells can divide uncontrollably when these genes are mutated or inactivated.
• DNA repair genes fix errors in DNA, and mutations in these genes can lead to the accumulation of additional mutations, contributing to cancer development. An example is the p53 gene.
• Somatic cells are diploid (2n), containing two sets of chromosomes, one from each parent and make up the body of an organism, performing regular functions like growth, repair, and maintenance.
• Sex cells (gametes) are haploid (n), containing one set of chromosomes, half the number of somatic cells and are responsible for reproduction in humans, sperm (male) and eggs (female) combine during fertilization to form a diploid zygote.
• Autosomes are non-sex chromosomes that determine most traits and humans have 22 pairs of autosomes (44 total).
• Allosomes are sex chromosomes that determine an organism's sex and humans have 1 pair of allosomes: XX (female) or XY (male).
• Gametes are reproductive cells (sperm in males and eggs in females) that carry half the genetic information of an organism (haploid, n).
• Gametes combine during fertilization to form a zygote, which is diploid (2n).
• There are 46 chromosomes in human somatic cells and 23 pairs.
• There are 23 chromosomes in human gametes and 0 pairs.
• Human gametes have 22 autosomes (non-sex chromosomes) and 1 sex chromosome (either X or Y).
• The two sex chromosomes in humans are X and Y.
• A double division is necessary in meiosis to reduce the chromosome number by half, so gametes are haploid. This ensures the zygote will have the correct diploid number after fertilization.
• Crossing over is the exchange of genetic material between homologous chromosomes during meiosis.
• Crossing over creates new combinations of genes, increasing genetic variation in offspring and is important for evolution and diversity in a population.
• A locus is the specific location or position of a gene on a chromosome.
• Mendel's Law of Independent Assortment states that genes for different traits are inherited independently of each other, however it is only true if the traits are located on different chromosomes or far apart on the same chromosome.
• Genes that are close together on the same chromosome tend to be inherited together because they are physically linked, which is related to their locus—the position of the genes on the chromosome. The closer the two loci are, the less likely they are to assort independently.

Mitosis vs. Meiosis

• Mitosis: Produces 2 identical diploid cells and is for growth, repair, and asexual reproduction.
• Meiosis: Produces 4 non-identical haploid cells (gametes) and is for sexual reproduction, with genetic variation due to crossing over and independent assortment.
• Gregor Mendel was an Austrian monk and scientist known as the father of modern genetics.
• Mendel's major contribution was discovering the basic principles of heredity through experiments with pea plants; he established the Law of Segregation and the Law of Independent Assortment, laying the foundation for understanding how traits are inherited.
• Advantages to using peas to study inheritance:
  • Distinct traits: Peas have easily recognizable traits (e.g., seed color, plant height).
  • Self-pollination and cross-pollination: Peas can reproduce both ways, making controlled breeding easy.
  • Short generation time: They grow quickly, allowing for rapid observation of multiple generations.
  • Large number of offspring: Produces many seeds per plant, increasing the reliability of results.
• A Punnett Square is used to predict the genotypes and phenotypes of offspring based on the genotypes of their parents.
• Genotype is the genetic makeup of an organism, referring to the specific alleles it has for a given trait (e.g., AA, Aa, aa).
• Phenotype: The physical expression or appearance of a trait in an organism, determined by its genotype (e.g., tall or short plants).
• A flower heterozygous for two traits can create 4 unique combinations of gametes.
• Blood type follows codominant inheritance and multiple alleles, following the ABO blood group system that has three alleles: A, B, and O.
• A and B are codominant, meaning both can be expressed when present (e.g., AB blood type).
• O is recessive to both A and B.
• Possible blood types are A, B, AB, and O.
• Antibodies can be used to test for blood type by mixing blood with anti-A and anti-B antibodies.
• Clumping with anti-A means blood type A.
• Clumping with anti-B means blood type B.
• Clumping with both means blood type АВ.
• No clumping means blood type O.
• Traits are influenced by both genetics (nature) and environmental factors (nurture).
• Gene expression is the process by which information from a gene synthesizes a functional product, usually a protein involving two main steps: transcription and translation.
• Transcription includes the gene's DNA being copied into mRNA.
• Translation includes the mRNA being used to build a protein at the ribosome.
• This process determines the traits of an organism.
• Epigenetics refers to changes in gene expression or activity that do not involve changes to the DNA sequence itself.
• These changes can be influenced by environmental factors and can affect how genes are turned on or off.
• Epigenetic modifications can be passed down influencing future generations without altering the underlying genetic code.

Effects of Methylation or Acetylation on Genes

• Methylation: Adding a methyl group (-CH3) to DNA, typically at cytosine bases silences genes by preventing transcription, so genes cannot be expressed.
• Acetylation Adding an acetyl group (-COCH3) to proteins activates genes by loosening the DNA structure, allowing easier transcription machinery access, therefore leading to gene expression.
• An example of epigenetic inheritance is DNA methylation when a parent's DNA is heavily methylated at certain genes (silencing them), this methylation pattern can be passed down to offspring, potentially affecting the expression of those genes without changing the DNA sequence, influencing various traits or susceptibility to diseases across generations.