RNA and Protein Synthesis, Cell Division, Genetics and other patterns of inheritance

RNA and Protein Synthesis

RNA: The Role of RNA

• RNA (ribonucleic acid) is a nucleic acid similar to DNA.
• It's a long chain of nucleotides.
• The base sequence of RNA guides protein production.
• Cell proteins determine phenotypic traits.

Ribonucleic Acid (RNA) Components

• RNA contains four nitrogenous bases:
  • Guanine (G)
  • Uracil (U)
  • Adenine (A)
  • Cytosine (C)
• The chemical structures of each base are depicted with their respective atoms and bonds.
• Each nucleotide includes a ribose sugar and a phosphate group.

Differences between RNA and DNA

• Sugar: RNA contains ribose, while DNA contains deoxyribose.
• Strands: RNA is generally single-stranded, whereas DNA is double-stranded.
• Bases: RNA has uracil (U) instead of thymine (T) found in DNA.

RNA as a Disposable Copy of DNA

• RNA serves as a temporary copy of specific DNA segments.
• Most RNA molecules participate in protein synthesis.

Types of RNA

• Messenger RNA (mRNA): Carries instructions for polypeptide synthesis from the nucleus to ribosomes.
• Ribosomal RNA (rRNA): Forms a crucial part of ribosomes where proteins are assembled.
• Transfer RNA (tRNA): Transports amino acids to the ribosome, matching them to the mRNA code.

Functions of RNA Types

• mRNA encodes proteins.
• tRNA carries amino acids.
• rRNA forms the ribosome.

Transcription

• RNA synthesis primarily occurs during transcription.
• DNA segments act as templates for producing complementary RNA molecules.
• Prokaryotes: RNA and protein synthesis occur in the cytoplasm.
• Eukaryotes: RNA is produced in the nucleus and moves to the cytoplasm for protein production.

Transcription in Eukaryotic Cells

• RNA polymerase binds to DNA, separating the strands.
• One DNA strand acts as a template for assembling RNA nucleotides.

Role of Promoters

• RNA polymerase binds to promoters, which are specific DNA base sequences.
• Promoters signal RNA polymerase where to start making RNA.
• Similar signals indicate when to stop transcription.

RNA Editing

• RNA is edited before use.
• Introns, portions that are cut out and discarded.
• Exons, the remaining pieces, are spliced together to form the final mRNA.

Ribosomes and the Genetic Code

• A specific DNA base sequence provides directions for forming a polypeptide (amino acid chain).
• The sequence and types of amino acids determine the protein's properties.
• The mRNA base sequence constitutes the genetic code.
• The four bases (A, C, G, U) act as letters.
• Each three-letter "word" (codon) corresponds to a single amino acid.
• Some codons signal the start or stop of protein synthesis.

Amino Acid Codon Wheel

• The codon wheel illustrates how each three-letter codon corresponds to a specific amino acid.
• It also indicates start and stop codons.

Translation

• Ribosomes use mRNA codons to assemble amino acids into polypeptide chains.
• Translation is the process of decoding an mRNA message into a protein.
• mRNA is transcribed in the nucleus and then enters the cytoplasm.
• Translation starts at the start codon on the ribosome.
• Each codon attracts a complementary anticodon on tRNA.

Role of tRNA in Translation

• Each tRNA carries a specific amino acid.
• Codon-anticodon matching ensures the correct amino acid is added.
• Amino acids bind together as the ribosome moves along the mRNA.
• The process ends when a stop codon is reached, releasing the polypeptide and mRNA.

Molecular Basis of Heredity

• Molecular biology explains living organisms at the molecular level (DNA, RNA).
• The central dogma: Information flows from DNA to RNA to protein.
• Gene expression is how DNA, RNA, and proteins put genetic information into action.
• The genetic code is generally universal across organisms.

The Central Dogma

• DNA is transcribed into mRNA, which is then translated into a polypeptide.

Mutations

• Mutations are heritable changes in genetic information.
• Germline mutations are heritable.
• Somatic mutations occur after conception and aren't heritable.

Types of Mutations

• Gene mutations affect a single gene.
  • Point mutations involve one or a few nucleotides.
    • Substitutions: One base is changed to another.
    • Insertions: A base is added to the DNA sequence.
    • Deletions: A base is removed from the DNA sequence.
• Insertions and deletions cause frameshift mutations, altering the reading frame.
• Frameshift mutations can drastically change the amino acid sequence.

Chromosomal Mutations

• Changes in chromosome number or structure.
  • Deletion: Loss of part or all of a chromosome.
  • Duplication: Extra copy of part or all of a chromosome.
  • Inversion: Reversal of a chromosome's direction.
  • Translocation: Part of one chromosome breaks off and attaches to another.

Effects of Mutations

• Mutations can be caused by natural events or artificial means.
• Errors during replication.
• Environmental conditions can increase mutation rates.

Mutagens

• Mutagens are chemical or physical agents that cause mutations.
  • Radiation (UV, X-rays).
  • Chemicals (carcinogens, preservatives, cosmetics).
  • Infectious agents (viruses, bacteria).

Mutation Effects on Genes

• Some mutations have little to no effect.
• Some produce beneficial variations (e.g., polyploidy in plants).
• Some disrupt gene function or change protein structure, causing genetic disorders (e.g., sickle cell disease).

Gene Regulation and Expression

• Prokaryotes regulate genes to conserve energy, producing only necessary genes.
• DNA-binding proteins control transcription in prokaryotes.
• An operon is a group of regulated genes.

Lactose Operon Example

• The lac operon in E. coli is a group of three genes that must be activated together to use lactose as food.
• When lactose is absent, the lac repressor binds to the operator, switching the operon off.
• When lactose is present, it binds to the repressor, causing it to detach from the operator and turning the operon on.

Eukaryotic Gene Regulation

• Transcription factors are DNA-binding proteins controlling gene expression in eukaryotes.
• Gene promoters have multiple binding sites for transcription factors.
• RNA interference (RNAi) occurs when microRNA (miRNA) molecules prevent mRNA molecules from passing on protein-making instructions.
• RNAi technology holds potential for treating diseases by turning off specific genes.

Genetic Control of Development

• Regulating gene expression is crucial for multicellular organism development.
• Gene regulation leads to cell differentiation.
• Master control genes trigger specific development and differentiation patterns.

Homeotic and Hox Genes

• Homeotic genes are master control genes regulating organ development in specific body parts.
• Homeobox genes share a 130-base DNA sequence and code for transcription factors involved in cell development.
• Hox genes are homeobox genes that control cell differentiation as the body grows.

Homeobox vs Homeotic vs Hox Genes

• Homeobox
  • A conserved DNA sequence regulating gene expression.
  • Occurs in all eukaryotes.
  • Encodes homeodomain, which binds to DNA.
• Homeotic
  • Genes regulating the development of anatomical structures.
  • Occur in all eukaryotes.
  • Serve as transcription factors, which regulate the development of body parts.
• Hox
  • A subset of homeobox genes specifying body plan regions.
  • Occur only in bilateral animals.
  • Serve as transcription factors, which regulate the development of body parts.

Environmental Factors and Gene Expression

• Environmental factors can affect gene expression (e.g., Himalayan rabbits and temperature).

Habitats, Niches, and Species Interactions

• A habitat refers to the physical and biological environmental factors that affect the organisms living there.
• Every species has a range of tolerance for environmental conditions.
• Within a habitat, a species occupies a niche, including the range of conditions it can survive and reproduce in.

Competition and Species Interactions

• Competition within and among species determines the numbers and types of species in a community and their niches.
• Predator-prey and herbivore-plant populations influence each other and often cycle.
• The competitive exclusion principle states that no two species can occupy the same niche in the same habitat at the same time.

Symbiosis

• Symbiosis is the interdependent relationship between two species.
  • Commensalism: One organism benefits, and the other is unaffected (e.g., sharks and remora fish).
  • Mutualism: Both species benefit (e.g., bees and flowers).
  • Parasitism: One organism benefits, and the other is harmed (e.g., fleas on dogs).

Keystone Species

• A keystone species has a significant impact on community structure.
• Changes in its population size can dramatically alter an ecosystem.

Succession

• Ecological succession is a series of predictable changes in a community over time.
• Primary succession occurs on bare rock with no remnants of an older community (e.g., after volcanic eruptions).
• Pioneer species are the first species to colonize a barren area.

Primary Succession Stages

• Bare rock → Lichens → Small annual plants → Perennial herbs, grasses → Grasses, shrubs, shade-intolerant trees → Shade-tolerant trees (Climax community).

Secondary Succession

• Secondary succession occurs when some members of an older community remain (e.g., after wildfires or human activities).
• New communities replace older ones.

Secondary Succession Stages

• Fire → Annual plants (1-2 years) → Grasses and perennials (3-4 years) → Grasses, shrubs, pines, young oak, and hickory (5-150 years) → Mature oak and hickory forest (150+ years).

Climax Community

• Secondary succession can reproduce the original climax community or take different paths.
• A climax community is the final, relatively stable stage of succession until a disturbance occurs.

Examples of Climax Communities

• Forest
• Desert
• Grassland
• Coral reef

Biodiversity, Ecosystems, and Resilience

• Biodiversity is the total genetically-based variation in all organisms in the biosphere.
• Biodiversity includes ecosystem, species, and genetic diversity.

Types of Biodiversity

• Ecosystem diversity: Variety of habitats, communities, and ecological processes.
• Species diversity: The number and relative abundance of species.
• Genetic diversity: Sum of genetic information in individual organisms.

Importance of Biodiversity

• Biodiversity contributes to medicine, agriculture, and adaptation to change.
• Ecosystems with higher biodiversity are more resilient to disturbances.

Ecosystem Services

• Ecosystem services are benefits provided to humans by ecosystems.
• Examples:
  • Food production
  • Nutrient cycling
  • Water purification
  • Carbon storage
  • Pest regulation
  • Crop pollination
  • Buffering effects of extreme weather events.

Purifying Water

• Wetlands and forests filter and clean groundwater.

Buffering Effects of Weather

• Mangrove forests protect shorelines.
• Dune and salt marsh grasses do the same in temperate regions.

Pollinating

• Bees, flies, and butterflies pollinate crop plants.

Regulating Pests

• Birds and bats eat insects that spread diseases and damage crops.

Food Production

• Oceans provide large fishes.
• Wild plants produce food for humans.

Nutrient Cycling

• Forests remove carbon dioxide.
• Bacteria and fungi fix nitrogen.

Maintaining Soil Structure

• Detritivores and soil organisms aerate soil.
• Bacteria and fungi produce humus.

Other Patterns of Inheritance

• Non-Mendelian inheritance patterns.

Incomplete Dominance

• A dominant allele does not completely mask the recessive allele, resulting in a blending of traits.

Codominance

• Two different alleles of the same gene are expressed separately in different parts of an organism.
• Both traits appear instead of one being dominant.

Multiple Alleles

• Multiple alleles exist when there are many variations of a gene in a population.

Polygenic Traits

• Polygenic traits are controlled by multiple genes.
• Genes may be located near each other or on separate chromosomes.
• They do not follow Mendel’s inheritance patterns and are often represented as a range of continuous variation.
• Examples include height, skin color, eye color, and hair color.

Sex-Linked Traits

• Sex-linked traits are associated with genes found on sex chromosomes (X and Y in humans).
• Examples include hemophilia and color blindness.

The Process of Cell Division

• Genetic information is passed on via chromosomes.
• Cells copy their DNA before division.
• Each daughter cell receives its own copy.
• Cells have a specific number of chromosomes.

Prokaryotic Chromosomes

• Prokaryotic cells lack nuclei.
• DNA is found in the cytoplasm.
• Most prokaryotes have a single, circular DNA molecule.

Eukaryotic Chromosomes

• Located in the nucleus and made of chromatin.
• Chromatin consists of DNA and histone proteins.
• DNA coils around histone proteins to form nucleosomes.
• Nucleosomes interact to form coils and supercoils, which make up chromosomes.

The Prokaryotic Cell Cycle

• Regular cycle of growth, DNA replication, and cell division.
• DNA replication begins when cells reach a certain size.
• Binary fission is a form of asexual reproduction producing two genetically identical cells.

The Eukaryotic Cell Cycle

• Four phases: G1, S, G2, and M.
• Interphase: G1, S, and G2 phases (growth period).
• M phase: Cell division period.

Phases of the Eukaryotic Cell Cycle

• G1 Phase: Cell growth; synthesis of new proteins and organelles.
• S Phase: DNA replication.
• G2 Phase: Production of molecules required for cell division.
• M Phase: Cell division, including mitosis and cytokinesis.

Important Cell Structures in Mitosis

• Chromatid: Strand of a duplicated chromosome.
• Centromere: Area where chromatids are joined.
• Centrioles: Structures that organize the spindle.
• Spindle: Microtubule structure that separates chromatids.

Stages of Mitosis

• Prophase: Chromosomes condense and become visible; centrioles move to opposite sides of the nucleus; the spindle forms; the nuclear envelope dissolves.
• Metaphase: Chromosomes line up across the center of the cell; spindle fibers connect to centromeres.
• Anaphase: Centromeres are pulled apart; chromatids separate and move to opposite poles.
• Telophase: Chromosomes spread out into chromatin; nuclear envelopes re-form; spindle breaks apart; nucleolus becomes visible.

Cytokinesis

• Division of the cytoplasm.
• Animal Cells: The cell membrane is drawn inward, pinching the cytoplasm into two equal parts.
• Plant Cells: A cell plate forms between divided nuclei and develops into cell membranes; a cell wall then forms.

Cellular Respiration: An Overview

Chemical Energy and Food

• Food provides the chemical building blocks needed for growth and reproduction.
• Food molecules contain chemical energy released when bonds are broken.
• Energy is stored in units of calories.
  • 1 \text{ Calorie} = 1 \text{kilocalorie} = 1000 \text{calories}
• Cells use fats, proteins, and carbohydrates for food.

Overview of Cellular Respiration

• If oxygen is available, organisms can obtain energy from food through cellular respiration.
  • 6O2 + C6H{12}O6 \rightarrow 6CO2 + 6H2O + \text{Energy}
  • Oxygen + Glucose → Carbon dioxide + Water + Energy

Stages of Cellular Respiration

• Three main stages: glycolysis, Krebs cycle, and electron transport chain.

Glycolysis

• Glucose is broken down into two molecules of pyruvic acid.
• ATP and NADH are produced.
• Glycolysis produces a small amount of energy, with most remaining locked in pyruvic acid.

Krebs Cycle (Citric Acid Cycle)

• Pyruvic acid is used to make carbon dioxide, NADH, ATP, and FADH2.
• The cycle “turns” twice for each glucose molecule.

Electron Transport Chain

• Most energy is produced using oxygen.
• High-energy electrons from NADH and FADH2 are passed down the chain.
• Water is formed when oxygen accepts electrons and H+ ions.
• Energy is used to move H+ ions across the mitochondrial membrane.

ATP Synthase

• H+ ions pass back through ATP synthase, causing it to rotate and produce ATP.

Oxygen and Energy Pathways

• Aerobic processes require oxygen (Krebs cycle, electron transport chain).
• Anaerobic processes do not require oxygen (glycolysis).
• Glycolysis occurs in the cytoplasm.

Comparing Photosynthesis and Cellular Respiration

• Opposite processes; energy flows in opposite directions.
• Photosynthesis “deposits” energy, and cellular respiration “withdraws” energy.
• The reactants of cellular respiration are products of photosynthesis, and vice versa.
• Cellular respiration occurs in plants, animals, fungi, protists, and bacteria.
• Photosynthesis occurs only in plants, algae, and some bacteria.

Homeostasis and Cells

The Cell as an Organism

• Unicellular organisms perform all life functions.
• Homeostasis: Relatively constant internal physical and chemical conditions.
• Unicellular organisms grow, respond to the environment, transform energy, and reproduce to maintain homeostasis.
• Unicellular organisms include prokaryotes and eukaryotes.
• Prokaryotes (especially bacteria) are adaptable and live almost everywhere.
• Eukaryotes also spend their lives as single cells (e.g., algae, yeast).
• Homeostasis is an issue for every unicellular organism; they need to find energy, maintain mineral levels, and respond to the environment.

Multicellular Life

• Cells of multicellular organisms are interdependent and work together.
• Cells are specialized for particular tasks and communicate to maintain homeostasis.

Cell Specialization

• Cells have different roles (movement, reaction, production).
• Each specialized cell contributes to the overall homeostasis.

Specialized Animal Cells

• Example: Lung cells are full of mitochondria to keep particles out of the lungs.

Specialized Plant Cells

• Pollen grains are light and small with thick cell walls and tiny wings for breeze.

Levels of Organization

• Cells → Tissues → Organs → Organ Systems.
• Tissue: A group of similar cells performing a particular function.
• Organ: Many tissues working together to perform complicated tasks.
• Organ System: A group of organs working together to perform a specific function.
• The organization creates a division of labor and allows for homeostasis.

Cellular Communication

• Cells communicate via chemical signals.
• Signals speed up or slow down cell activities.
• Cells form connections (cellular junctions).
  • Some junctions hold cells firmly together.
  • Others allow small molecules to pass from cell to cell.
• To respond to signals, cells must have receptors.

Cell Growth, Division, and Reproduction

Information "Overload"

• Living cells store critical information in DNA.
• As cells grow, demands on information increase.
• Unlimited growth would cause an “information crisis”.

Exchanging Materials

• Food, oxygen, and water enter, and waste exits through the cell membrane.
• The rate of exchange depends on surface area.
• The rate of usage and production depends on volume.
• The ratio of surface area to volume is key.

Ratio of Surface Area to Volume

• As the cell grows, volume increases faster than surface area, decreasing the ratio.
• Too large, the cell is not efficient in exchange.

Division of the Cell

• Cells divide into two “daughter” cells before growing too large.
• DNA is copied, and each daughter cell receives a complete set.
• Cell division reduces cell volume and increases the surface area to volume ratio.

Asexual Reproduction

• A single parent produces an offspring.
• Offspring are usually genetically identical.
• Simple, efficient, and effective for producing large numbers of offspring.
• Both prokaryotic and eukaryotic single-celled organisms, and some multicellular organisms can reproduce asexually.

Examples of Asexual Reproduction

• Bacteria reproduce using binary fission.
• Kalanchoe plants form plantlets.
• Hydras reproduce via budding.

Sexual Reproduction

• Offspring are the fusion of two sex cells from two parents.
• Offspring inherit genetic information from both parents.
• Most animals and plants and many single-celled organisms reproduce sexually.

Comparing Sexual and Asexual Reproduction

• Asexual:
  • Produces genetically identical offspring.
  • Quick and produces large numbers of offspring.
• Sexual:
  • Produces genetically diverse offspring.
  • Genetic diversity aids species survival during environmental changes.