DNA and RNA structure

• These are highly detailed study notes on the provided text
• They contain comprehensive information that you can use to prepare for tests

Structure of DNA

• Rosalind Franklin used X-ray crystallography to study DNA structure.
• Watson & Crick pieced together the DNA molecule puzzle, using Franklin's data in 1953.

Structural Components of DNA

• The building blocks of DNA are nucleotides.
• Nucleotides comprise deoxyribose (5-carbon sugar), a phosphate group, and a nitrogenous base.
• The four types of nitrogenous bases in DNA are adenine (A), guanine (G), cytosine (C), and thymine (T).
• Adenine (A) and guanine (G) are double-ringed purines.
• Cytosine (C) and thymine (T) are smaller, single-ringed pyrimidines.
• Base-pairing takes place between a purine and pyrimidine.
• Adenine (A) pairs with thymine (T).
• Guanine (G) pairs with cytosine (C).

RNA Composition

• RNA consists of a nitrogenous base, a five-carbon sugar, and a phosphate group.
• The five-carbon sugar in RNA is ribose, not deoxyribose.
• Ribose has a hydroxyl group at the 2' carbon, unlike deoxyribose.
• RNA contains the nitrogenous bases adenine, cytosine, and guanine.
• RNA contains uracil (U) instead of thymine.

Organization of Genetic Material

• Eukaryotes contain a well-defined nucleus.
• Prokaryotes contain a chromosome that lies in the cytoplasm in an area called the nucleoid.
• Eukaryotic chromosomes compact through several levels of organization: DNA double helix, DNA wrapped around histones, nucleosomes coiled into a chromatin fiber, further condensation of chromatin, and the duplicated chromosome.

Information Storage on a Double Helix

• DNA is a double helix made of two strands twisted around each other and DNA is composed of nucleotides.
• Nucleotides consist of a phosphate group, a deoxyribose sugar, and a nitrogenous base, such as Adenine (A), Thymine (T), Cytosine (C), Guanine (G).
• The two strands of DNA are held together by hydrogen bonds between specific base pairs.
• Adenine (A) pairs with Thymine (T).
• Cytosine (C) pairs with Guanine (G).
• The two strands of DNA are complementary, meaning the sequence of bases in one strand determines the sequence of bases in the other strand.

Chromosomes and Karyotype/Organization of Genomes

• Prokaryotic genomes are a single, circular DNA molecule in the nucleoid.
• Some prokaryotes have plasmids, which are small, extra loops of DNA.
• Eukaryotic genomes consist of multiple, linear DNA molecules bound with proteins to form chromosomes inside the nucleus.
• Somatic cells (body cells) contain a diploid (2n) set of chromosomes, with humans having 46 total.
• Gametes (sex cells: sperm and egg) contain a haploid (n) set of chromosomes, with humans having 23.
• Homologous chromosomes are pairs of chromosomes (one from each parent) with the same genes but different versions (alleles).
• Genes are functional units of chromosomes that code for specific proteins.
• Traits are the different variations of a characteristic (e.g., blood type can be A, B, or O).
• Genetic variation comes from the combination of genes inherited from both parents.
• Sex chromosomes (X and Y) have different genes, unlike homologous chromosomes.
• A small homologous region is needed for reproduction.

Cell Cycle Overview

• The cell cycle includes interphase (growth and DNA replication) and the mitotic phase (nuclear and cytoplasmic division).
• The cell cycle ensures the formation of two genetically identical daughter cells.

Interphase: Preparation for Division

• G1 Phase (First Gap): The cell grows, synthesizes proteins, and accumulates energy for DNA replication.
• S Phase (Synthesis Phase): DNA replication occurs, forming sister chromatids, and the centrosome is duplicated.
• G2 Phase (Second Gap): The cell continues to grow, synthesizes proteins for mitosis, and prepares for division.

Mitosis: Nuclear Division

• Mitosis occurs in five stages: prophase, prometaphase, metaphase, anaphase, and telophase.
• Prophase: Chromosomes condense, spindle fibers emerge, and the nuclear envelope breaks down.
• Prometaphase: Spindle fibers attach to chromosomes at their kinetochores.
• Metaphase: Chromosomes align at the metaphase plate.
• Anaphase: Sister chromatids separate and move toward opposite poles.
• Telophase: Chromosomes decondense, and the nuclear envelope reforms.

Cytokinesis: Cytoplasmic Division

• Cytokinesis is the second part of the mitotic phase, where cell division is completed by physical separation into two daughter cells.
• In animal cells, a cleavage furrow forms, splitting the cell.
• In plant cells, a cell plate forms, creating a new cell wall between daughter cells.

Sexual Reproduction and Life Cycles

• Meiosis is a specialized cell division process that reduces chromosome number by half, producing haploid gametes from diploid cells.
• Meiosis includes one round of DNA replication and two rounds of nuclear division (Meiosis I and Meiosis II).

Stages of Meiosis

• Interphase: DNA replication occurs, forming sister chromatids.
• Meiosis I (Reduction Division): Prophase I involves homologous chromosomes pairing up and exchanging genetic material via crossing over.
• Metaphase I involves homologous chromosomes aligning randomly (independent assortment).
• Anaphase I involves homologous chromosomes separating to opposite poles.
• Telophase I & Cytokinesis involves the formation of two haploid cells, but chromosomes still have sister chromatids.
• Meiosis II (Similar to Mitosis): Prophase II involves chromosomes condensing again.
• Metaphase II involves chromosomes aligning at the center.
• Anaphase II involves sister chromatids separating.
• Telophase II & Cytokinesis result in four genetically unique haploid cells.

Key Differences Between Meiosis and Mitosis

• Mitosis produces two genetically identical diploid cells for growth and repair.
• Meiosis produces four genetically unique haploid cells for sexual reproduction.
• Crossing over and independent assortment in meiosis generate genetic diversity.
• Meiosis I reduces chromosome number, while mitosis maintains it.

Inheritance - Gregor Mendel

• He studied inheritance using pea plants to study inheritance, which were ideal given they had clear, distinct traits, could self-fertilize and be cross-pollinated manually, had short generation times, allowing multiple generations to be studied quickly, and produced large sample sizes, making results statistically reliable.
• Mendel's work challenged the blending inheritance theory, instead, finding traits were inherited as dominant or recessive factors.
• A monohybrid cross is a cross between two true-breeding parents differing in one trait.
• P Generation (true-breeding) → F1 Generation (all showed dominant trait) → F2 Generation (3:1 ratio of dominant to recessive traits).
• Traits do not blend; dominant traits mask recessive ones but do not eliminate them.
• Dominant traits are expressed in hybrids (e.g., violet flowers).
• Recessive traits are hidden in F1 but reappear in F2.
• Genes exist in pairs, with each parent passing one allele to offspring.
• Mendel's work laid the foundation for modern genetics but was not widely recognized until 1900.

Laws of Inheritance

• Genotype is the genetic makeup of an organism (e.g., YY, Yy, or yy for seed color).
• Phenotype is the physical appearance based on the genotype (e.g., yellow or green seeds).
• Dominant alleles (capital letter, e.g., Y) show up in the phenotype even if there is only one copy.
• Recessive alleles (lowercase letter, e.g., y) only appear if two copies are present.
• A monohybrid cross studies one trait at a time.
• P Generation (Parents) are true-breeding plants (YY x yy).
• F1 Generation (First Offspring) are all Yy (yellow).
• F2 Generation (Second Offspring) has a 3:1 ratio of yellow to green.
• A Punnett square predicts possible offspring by combining alleles from each parent.
• Law of Dominance: a dominant allele masks a recessive one in hybrids (Yy looks yellow, not mixed).
• Law of Segregation: each parent passes only one allele per gene to offspring.
• Law of Independent Assortment: traits are inherited separately unless genes are linked.
• Test Cross: used to determine if an organism with a dominant trait is homozygous (YY) or heterozygous (Yy).
• Cross the unknown dominant plant with a homozygous recessive (yy) plant.
• If all offspring are yellow, the unknown plant is YY.
• If offspring are 50% yellow, 50% green, the unknown plant is Yy.

Non-Mendelian Inheritance

• Incomplete Dominance: neither allele is completely dominant, and heterozygous offspring shows a blended trait between both parents.
• Example: Snapdragon flowers exhibit incomplete dominance, with Red (RR) x White (WW) = Pink (RW).
• The pink flower is an intermediate of red and white.
• Codominance: both alleles are fully expressed at the same time in a heterozygote.
• Example: Human Blood Types (ABO system): Blood type A (IAIA) and blood type B (IBIB) are dominant.
• A person with IAIB has both A and B proteins on red blood cells (AB blood type).
• Neither allele is hidden; both appear together.
• Multiple Alleles: some genes have more than two alleles in a population.
• Blood type has three alleles: IA (A type), IB (B type), and i (O type).
• A person can inherit any two of these alleles from their parents.
• Six possible genotypes exist (IAIA, IAIB, IBIB, IAi, IBi, ii).
• Sex-Linked Traits: some genes are located on the X chromosome and do not appear on the Y chromosome.
• Males (XY) have only one X chromosome, so they express any gene on it.
• Females (XX) can have a dominant and a recessive allele, making them possible carriers.
• Males inherit X-linked traits from their mother and color blindness and hemophilia are human examples of X-linked traits.

Epistasis (Gene Interaction)

• One gene can "turn off" or block another gene, for example, coat Color in Mice.
• Gene A controls black or brown fur and Gene C determines if any color is produced at all.
• If a mouse inherits cc (homozygous recessive), no pigment is produced, and the mouse is albino, regardless of the A gene.
• A 9:3:4 ratio appears instead of Mendel's 3:1.

Two Functions of DNA

• DNA replication involves DNA unwinding at the origin of replication.
• New bases are added to the complementary parental strands, one new strand is made continuously, while the other strand is made in pieces.
• Primers are removed, new DNA nucleotides are put in place of the primers and the backbone is sealed by DNA ligase.
• Transcription: DNA encodes RNA, which then encodes proteins and genetic information flows from DNA → mRNA → Protein.
• Transcription occurs in three steps: initiation, elongation, and termination.

Transcription Steps

• Initiation: RNA polymerase binds to a promoter (a specific DNA sequence).
• The DNA unwinds, creating a transcription bubble where RNA synthesis starts.
• Elongation: RNA polymerase reads the template strand of DNA.
• It builds a complementary mRNA strand, replacing thymine (T) with uracil (U).
• The new RNA strand grows in the 5' to 3' direction.
• Termination: a stop signal in the DNA causes RNA polymerase to detach and the completed mRNA strand is released.

Genetic Processes

• In prokaryotes (bacteria), transcription happens in the cytoplasm and can occur at the same time as translation.
• In eukaryotes, transcription occurs in the nucleus, and the mRNA must be processed before it leaves for translation.
• Proteins are essential for cell function where the process of translation builds proteins by decoding an mRNA sequence into a chain of amino acids.
• Translation requires mRNA to carry genetic instructions from DNA, ribosome (the site where proteins are made, of a large and small subunit), tRNA to transfer specific amino acids to the ribosome and amino acids to act as the building blocks of proteins.
• Ribosomes in prokaryotes are found in the cytoplasm, while in eukaryotes, they are in the cytoplasm and rough ER.
• The genetic code uses groups of three nucleotides (codons) to specify one amino acid.
• There are 64 codons, but only 20 amino acids, meaning some codons code for the same amino acid.
• AUG (start codon) signals the beginning of translation.
• Stop codons (UAA, UAG, UGA) signal the end of translation.
• The genetic code is universal, meaning nearly all living organisms use it.

Stages of Protein Synthesis

• Initiation: the small ribosomal subunit binds to mRNA, a tRNA carrying the amino acid methionine (AUG) binds to the start codon and the large ribosomal subunit attaches, forming the initiation complex.
• Elongation: new tRNA molecules bring amino acids to the ribosome, the ribosome moves one codon at a time, adding amino acids to the growing polypeptide chain and the process continues, powered by GTP (energy source similar to ATP).
• Termination: a stop codon is reached (UAA, UAG, UGA), a release factor causes the polypeptide to detach, and the ribosome breaks apart, and the protein is complete.

DNA Technology

• Blood-Typing: blood-typing is used to identify a person's blood group based on the presence of specific antigens on red blood cells.
• This is determined by the presence of A and B antigens.
• Type A blood has A antigen, anti-B antibodies.
• Type B blood has B antigen, anti-A antibodies.
• Type AB blood has A and B antigens, no antibodies (universal recipient).
• Type O blood has no antigens, anti-A and anti-B antibodies (universal donor).
• Testing uses anti-A and anti-B antibodies to check for agglutination (clumping), which indicates the presence of antigens.
• Applications for blood-typing include forensics (Murder Lab), paternity tests, and medical transfusions.
• DNA Fingerprinting is identifying individuals by analyzing unique patterns in their DNA.

Key Steps in DNA Fingerprinting

• DNA Extraction – Cells are lysed to release DNA.
• Restriction Enzyme Digestion – Enzymes cut DNA at specific sequences.
• Polymerase Chain Reaction (PCR) – Amplifies DNA segments.
• Gel Electrophoresis – Separates DNA fragments based on size.
• Analysis of Banding Patterns – DNA fragments create unique banding patterns.
• Applications: crime scene investigations (Murder Lab) and paternity tests.
• DNA is useful for identifying genetic mutations in research.

Consumer Genotyping

• Defined as identifying genetic variations using single nucleotide polymorphisms (SNPs) to determine ancestry, health risks, and traits.
• SNPs (Single Nucleotide Polymorphisms) are small variations in the genome that may be associated with specific traits or diseases.
• Genome-Wide Association Studies (GWAS) identify SNPs linked to diseases through case-control studies.
• Companies offering consumer genotyping: 23andMe, AncestryDNA, MyHeritage DNA.
• Applications: ancestry tracking, predicting disease risks (e.g., APOE SNPs for Alzheimer's), and personalized medicine (Pharmacogenomics).

CRISPR (Gene Editing)

• This is useful as a powerful tool that allows scientists to edit DNA precisely.
• Guide RNA (gRNA) directs the Cas9 enzyme to a specific DNA sequence.
• Cas9 Enzyme cuts the DNA at the target site.

DNA Repair Mechanisms

• Non-Homologous End Joining (NHEJ): Introduces small mutations.
• Homology-Directed Repair (HDR): Uses a DNA template to introduce specific changes.
• Applications include gene therapy, agriculture and forensics & research.
• Gene therapy is defined as correcting genetic mutations (e.g., sickle cell anemia).
• Ethical considerations include potential unintended mutations, designer babies and genetic enhancement and regulation and ethical use in humans.

CURE Labs 1&2

• Mockingbird Songs: Clear, repeated phrases, distinct pitch changes.
• Background Noise: Irregular, non-repetitive (e.g., wind, car sounds, rustling leaves).