Alessandro Buccini Grade 11 Bio Notes PDF

Sept 9 2024 Intro to Bio Cells and Cell Theory What Exactly is Life? For something to have life it must have all 3 of these properties To be considered alive, something must have these three properties: 1. CELLULAR: All living things are made up of cells. They can be: ○ Unicellular: Single-celled organisms like bacteria, yeast, or amoebas. ○ Multicellular: Organisms made of many cells, like toadstools, frogs, plants, and humans. 2. PROPAGATE: Living things reproduce. They can: ○ Asexually: Reproduce on their own. ○ Sexually: Combine genetic material with others. 3. METABOLIZE: Living things use chemical reactions to get energy and build the molecules they need to stay alive. What is a cell? At its simplest, a cell consists of: A plasma membrane (outer boundary) Cytoplasm (internal fluid) Hereditary material (DNA) What are life functions? Life functions are the processes that keep an organism alive, like metabolism, growth, and reproduction. Organisms Single-celled organisms: Perform all life functions with just one cell. Multicellular organisms: Have many cells that work together to perform life functions. Cell Theory Robert Hooke stated the cell theory is… 1. All living things are made up of 1 or more cells 2. Cells are the basic structural and functional units of life 3. All cells come from another division of cells Prokaryotes Prokaryotic cells are small, single, simple cells that don't have a nucleus Structures include DNA, cell membrane, cell wall, and ribosomes. Some have extra features like pili or flagella for movement. Eukaryotes Eukaryotic Cells: Larger and more complex cells with a nucleus. Found in plants, animals, fungi, and protists (like algae). The nucleus contains DNA and controls cell activities. Cell Structure All cells have DNA cytoplasm ribosomes and a cell membrane Eukaryotic cells have membrane bound organelles and specialized structure within the cell that performs certain tasks These organelles float around in the cytoplasm which is mostly made up of water This combination is called Cytosol Organelles and Their Functions Unit 1 Chapter 1.1 Classifying life's diversity Organization Organisms are grouped into: 3 Domains: Bacteria, Archaea, Eukarya. 6 Kingdoms: Bacteria, Archaea, Protista, Plantae, Fungi, Animalia. Organisms are grouped according to shared characteristics. In the past the groupings were determined by shared physical characteristics. The advances in biochemistry this century has added to the sophistication of these groupings. The Three Domains Eukarya contains the greatest biological diversity in the Kingdom Protista Protists have lived on earth for a longer time than plants and animals Which means that it has had a longer time to diversify and change! What is our grouping? THE GROUPS, IN ORDER OF SIZE: with the group names for humans A. KINGDOM - Animalia (The LARGEST grouping) B. PHYLUM - Chordata C. CLASS - Mammalia D. ORDER - Primata E. FAMILY - Hominidae F. GENUS - Homo G. SPECIES - sapiens (The smallest grouping) ANIMALIA: motile, multicellular, eukaryotic consumers. PLANTAE: sessile, multicellular, eukaryotic producers. FUNGI: sessile, multicellular, eukaryotic decomposers. PROTISTA: Mostly unicellular eukaryotes, can be producers or consumers. Eubacteria: Unicellular prokaryotes, can be producers, consumers, or decomposers. Most bacteria are usually classified under this Kingdom. Archaebacteria: Unicellular prokaryotes living in extreme conditions (deep sea thermal vents, hot springs, etc.) different from other bacteria. Virus: A fourth group of biological entities, the viruses, are not organisms in the same sense that eukaryotes, archaeans, and bacteria are. However, they are of considerable biological importance. Cladograms A cladogram is a stylized diagram that looks like a series of Y's or forks in a road. At each branch, or "Y" junction, novel characters of evolutionary origin are used to separate off one group from the rest. Cladograms are a useful way of organizing, in a visual way, the relationships between creatures that share and do not share derived characters. Cladograms can be constructed for any group of organisms. For example, the following organisms are a set from which a cladogram can be made; kangaroo, earthworm, amoeba, lizard, cat, sponge, and salmon. Each of these creatures has an evolutionary relationship to one another. They all share a common origin, and their current forms are all derived from branching events somewhere in the phylogenetic past. Jaws Lungs Claws/nails Feathers Mammary Fur Glands Hagfish Perch yes Salamander yes yes Lizard yes yes yes Pigeon yes yes yes yes Mouse yes yes yes yes yes Chimp yes yes yes yes yes Sept 10 2024 Phylogenetic Trees A diagram that shows the evolutionary relationships between species based on their similarities and differences. Sept 11 2024 Chapter 1.2: Determining how Species are related What is Evolution? Evolution: The gradual change in species over time. Species: A group of organisms that can mate and produce fertile offspring. Determining how species are related Modern classification uses morphological similarities and evolutionary history to assign a species to taxa. Hypotheses about the evolutionary history and relationships among different species are made based on three types of evidence: Modern classification uses: 1. Anatomy: Study of the structure of organisms. 2. Physiology: Study of the functions and processes within organisms. 3. DNA: Genetic material used to compare species. Homologous vs Analogous Homologous: Similar traits from a common ancestor. Analogous: Similar traits that evolved independently. Homology can be distinguished from analogy by comparing fossil evidence and the degree of complexity. The more complex two similar structures are, the more likely it is that they are homologous. Homologous Analogous Similar anatomy Not similar anatomy Not similar functions Similar functions Genes come from common Genes not inherited from ancestors ancestors Chapter 1.3 The Three Domains and Their Kingdom The Three Domains of Life Organisms are categorized by: Cell Type: Prokaryotic (simpler) vs. Eukaryotic (complex). Ability to Make Food: Autotrophs (make their own food) vs. Heterotrophs (consume other organisms). Number of Cells: Unicellular (one cell) vs. Multicellular (many cells). All cells can be broken into 2 basic categories: PROKARYOTIC (simplest) EUKARYOTIC (most complex) Aerobic: needs oxygen Anaerobic: does not need oxygen Point of comparison Eukaryotic Prokaryotic Size (Micrometers) 100-1000 1-10 Internal Structure - Membrane - No organelles bound organelles - Most anaerobic - Most aerobic Nucleus - DNA in nucleus - DNA in loop as chromosomes - No membrane - Bound by membrane Kingdom Protista, plants, fungi, Bacteria, Archaea animals Which type of cell originated first (Prokaryotic or Eukaryotic) Prokaryotic Cells: Believed to have originated first, around 3.5 billion years ago. Eukaryotic Cells: Evolved from prokaryotic cells about 1.5 billion years ago, likely through endosymbiosis. Endosymbiosis Endosymbiosis: Theory that mitochondria and plastids originated from prokaryotes living inside other cells. Key evidence supporting an endosymbiotic origin of mitochondria and plastids: Similarities in inner membrane structures and functions. These organelles transcribe and translate their own DNA. Their ribosomes are more similar to prokaryotic than eukaryotic ribosomes. Sept 12 2024 The First Single Celled Organism Stromatolites: Oldest known fossils (3.5 billion years ago), showing layered bacteria. The First Multi Celled Organism Eukaryotic Cells: Oldest fossils date back 2.1 billion years. Multicellularity led to the evolution of algae, plants, fungi, and animals. The common ancestor of multicellular eukaryotes lived about 1.5 billion years ago. The oldest multicellular eukaryotic fossils are of small algae (1.2 billion years ago). Advances in Classification More kingdoms were identified from two in the 1800s to six in 2010, based on cell types and similarities. The 3 Domains The 3 Domains Eukarya: Includes all eukaryotic cells (four kingdoms). Bacteria and Archaea: Prokaryotic domains with significant genetic and cellular differences. The second most general rank, kingdom, includes six different taxa. There is incredible structural diversity (internal and external forms) within the kingdoms even though species are grouped. Masters of Adaptation Prokaryotes: Thrive in extreme environments and have high genetic diversity. Two Domains of Prokaryotes: Bacteria: Found in various environments. Archaea: Live in extreme environments (e.g., salty or hot). Nutritional and Metabolic Adaptations Phototrophs: Get energy from light. Chemotrophs: Get energy from chemicals. Autotrophs: Use CO2 as a carbon source. Heterotrophs: Require organic nutrients. Domain: Archaea Archaea are prokaryotes and share certain traits with bacteria and other traits with eukaryotes. Some archaea live in extreme environments and are called extremophiles. Extreme halophiles live in highly saline, salty environments. Extreme thermophiles thrive in very hot environments. Main Characteristics of Kingdoms When classifying only to the kingdom rank, the following characteristics can be used: number of cells (unicellular or multicellular) cell wall material (if present) nutrition (autotroph or heterotroph) primary means of reproduction (asexual or sexual) Sept 13 2024 Chapter 2.1 Viruses and Prions What is a Virus? A virus is a tiny infectious particle that: Exists almost everywhere and can infect all types of life. Can only reproduce by entering a living cell and using that cell's machinery. Is made up of genetic material (either DNA or RNA, but never both) inside a protective protein shell called a capsid, and sometimes a layer from the host's cell membrane. Are Viruses Alive? (NO) All living organisms are made of cells (eukaryotic or prokaryotic). Viruses are not cellular and thus lack cytoplasm, organelles, and cell membranes. Viruses are dependent on the internal physiology of cells to reproduce. How Big Are Viruses? They vary in size from 20-40 nm (nanometers). 1 nm = one billionth of a meter (1/1,000,000,000). Structure of a Virus All viruses contain: - A protein sheath (Capsid) - DNA and/or RNA How Are Viruses Classified? Size and shape of the capsid Shape and structure of the virus Type(s) of diseases the virus causes What the virus infects (animal, plant, fungi) Genome (set of genes) and type of genetic material (RNA or DNA) Method of reproduction How Does a Virus Reproduce? Viruses replicate inside a host cell. Many more viruses are constructed by the host cell, not the virus itself. Viruses have two possible cycles of reproduction: - Lytic Cycle - Lysogenic Cycle Lytic vs Lysogenic Cycle What is the Lysogenic Cycle? What is a Retrovirus? A retrovirus is a type of virus with single-stranded RNA. It uses an enzyme called reverse transcriptase to turn its RNA into DNA, which is the opposite of the usual process. This is why it's called "retro," meaning "backwards." How Does a Retrovirus Work? Retroviruses carry RNA and reverse transcriptase that converts the viral RNA into DNA in the host cell. The DNA then integrates into the host’s chromosomes, becoming a provirus. Every descendant cell has this viral DNA copied within its genome. What is a Vaccine? Vaccines help your body be ready to fight off viral infections. They mimic an infection to activate the body’s natural defenses. They contain an antigen, a substance that triggers the immune system to make antibodies. The antigen could be: - Weakened or killed bacteria or viruses - Bits of their exterior surface or genetic material - Bacterial toxin treated to make it non-toxic Viruses and Biotechnology Biotechnology involves technology used to manipulate DNA, also known as genetic engineering. DNA is the genetic material of all living organisms, and genes from one organism can be put into another. A virus’s DNA can be altered by removing its original DNA, splicing in new DNA, and putting the modified DNA back into the virus. This virus can then be used to deliver new genetic material into a host cell. What is a Prion? A prion is not a virus but a type of infectious agent discovered in the 1980s. Prions are made of protein and are the only known non-genetic disease-causing agents. They become harmful when they change molecular shape and remain infectious even after exposure to radiation. Examples of Prions: Creutzfeldt-Jakob disease (CJD) and its variant, Creutzfeldt-Jakob disease (vCJD) Bovine spongiform encephalopathy (BSE or Mad Cow Disease) Sept 18 2024 Chapter 2.2 Bacteria Heterotrophs: Bacteria classified as heterotrophs get energy from breaking down complex organic compounds in the environment. ○ Includes saprobes, bacteria that feed on decaying material and organic wastes. ○ Also includes parasites, which absorb nutrients from living organisms. Aerobic vs. Anaerobic Bacteria: Aerobic: Bacteria that require oxygen to live. Anaerobic: Bacteria for which oxygen is deadly. Examples: - Green patches: Green sulfur bacteria. - Rust patches: Purple non-sulfur bacteria. - Red patches: Purple sulfur bacteria. Archaebacteria Methanogens: Anaerobic archaebacteria that produce methane (natural gas) as a waste product. ○ Found in swamps, sewage, and buried landfills. ○ Could be used to produce methane in sewage treatment or landfill operations. Halophiles: Salt-loving archaebacteria that grow in salty environments like the Great Salt Lake (Utah) or salt ponds in San Francisco Bay. ○ Large populations can turn these waters dark pink due to pigments similar to rhodopsin (found in the human retina). ○ Perform a type of photosynthesis that does not produce oxygen. ○ Aerobic organisms, meaning they require oxygen and perform aerobic respiration. Extreme Halophiles: Live in extremely salty environments and are mostly photosynthetic autotrophs. ○ They use a pigment called bacteriorhodopsin instead of chlorophyll, making them appear purple. Thermophiles: Archaebacteria that live in hot environments like hot springs, with some growing at temperatures above boiling. ○ Anaerobic, performing anaerobic respiration. ○ Notable for their heat-stable enzymes, such as Taq polymerase, used in DNA replication for medical and research purposes. - Taq polymerase, first isolated from Thermus aquaticus in Yellowstone hot springs, has an annual market value of roughly half a billion dollars. Eubacteria Cyanobacteria Definition: A group of bacteria that includes both single cells and chains of cells. Appearance: Often seen as "green slime" in aquariums or ponds. Photosynthesis: ○ Capable of modern photosynthesis, producing oxygen from water. ○ This ability is inherited by all plants from cyanobacteria. Historical Significance: ○ First organisms on Earth to perform modern photosynthesis. ○ Responsible for creating the first oxygen in the Earth's atmosphere. Bacteria Overview Common Misconceptions: Often viewed negatively due to association with diseases. Beneficial Types: ○ Actinomycetes: Produce antibiotics like streptomycin and nocardicin. ○ Gut Bacteria: Live symbiotically in animal guts. Produce vitamin K, essential for blood clotting. ○ Nitrogen-Fixing Bacteria: Reside on plant roots. Convert nitrogen into a usable form. ○ Fermentation: Contribute to the tang in yogurt and the sour flavor in sourdough bread. ○ Saprobes: Help break down dead organic matter. Ecological Role: Serve as the base of the food web in many environments. Bacteria Characteristics Cell Structure: ○ Prokaryotic and unicellular. ○ Possess cell walls. ○ Contain circular DNA called plasmids. Metabolism: ○ Can be anaerobes (do not need oxygen) or aerobes (require oxygen). ○ Can be heterotrophs (consume organic material) or autotrophs (produce their own food). Reproduction: ○ Asexual: Primarily through binary fission. ○ Sexual: Occurs through conjugation. Endospores: ○ Some bacteria can produce endospores to survive unfavorable conditions. Bacteria Shapes and Gram Staining Shapes: Various shapes (circles, ovals, squiggly lines) Gram Staining: ○ First step in bacterial identification. Classification: ○ Gram-Positive: Stained purple due to thick peptidoglycan and teichoic acid in cell walls. ○ Gram-Negative: Stained pink due to thin peptidoglycan and lipopolysaccharides, lacking teichoic acid. Staining Process: ○ Gram-Positive: Purple crystal violet stain is trapped by the thick peptidoglycan layer. ○ Gram-Negative: Outer membrane prevents initial staining; after acetone treatment, pink safranin counterstain is trapped by the peptidoglycan layer. Sept 26 2024 Unit 2 Chapter 4.1: The Nature of Hereditary Genetics is the study of heredity (how traits are passed from parents to offspring) and variation (differences in traits). DNA (Deoxyribonucleic Acid) is a molecule containing genetic instructions for the development and functioning of all living organisms. Genes are sections of DNA with specific nucleotide sequences, located on chromosomes, that code for proteins. The Structure of Genetic Material DNA is made up of 4 nucleotide bases: ○ Adenine (A) ○ Guanine (G) ○ Thymine (T) ○ Cytosine (C) Base Pairing: ○ Adenine pairs with Thymine (A-T) ○ Guanine pairs with Cytosine (G-C) DNA structure consists of: ○ Phosphate group ○ Deoxyribose sugar ○ Nitrogenous base Purines: Double-ringed bases (Adenine and Guanine). Pyrimidines: Single-ringed bases (Thymine and Cytosine). DNA bases are held together by hydrogen bonds. The Cell Cycle Mitosis: The process of cell division that results in two identical daughter cells with the same genetic material as the parent cell. It occurs in somatic cells. A cell’s total inherited DNA is called its genome. Phases of the Cell Cycle 1. Interphase (growth phase) → Mitosis (division of the nucleus) → Cytokinesis (division of the cell). 2. Interphase is subdivided into: ○ G1 Phase (Gap 1): Rapid growth and metabolic activity. ○ S Phase (Synthesis): DNA synthesis and replication. ○ G2 Phase (Gap 2): Centrioles replicate, preparing the cell for division. Mitosis Mitosis is the division of the cell’s nucleus, ensuring the daughter cells receive the same number of chromosomes and genetic makeup as the parent cell. Mitosis consists of five stages: Stages of Mitosis 1. Interphase: ○ The cell is growing and preparing for division. ○ Chromosomes are dispersed in the form of chromatin. ○ DNA replication occurs. 2. Prophase: ○ Centrioles move to opposite sides of the cell. ○ Chromosomes condense and become visible. ○ The nuclear membrane breaks down. ○ Spindle fibers form, which will help separate the chromatids. 3. Metaphase: ○ Chromosomes line up at the cell’s equator. ○ Spindle fibers attach to the centromeres of the chromosomes. 4. Anaphase: ○ Chromatids (the two halves of each chromosome) are pulled apart and move toward opposite poles of the cell. 5. Telophase: ○ Early Telophase: The nuclear membrane reappears around each set of chromosomes. Chromosomes begin to decondense back into chromatin. Spindle fibers disappear as nuclear division completes. ○ Late Telophase: Cytokinesis occurs, dividing the cytoplasm into two separate daughter cells. The cell membrane pinches in the middle to separate the cells. Cytokinesis The final step of cell division, where the cytoplasm separates, forming two new daughter cells. Occurs after mitosis. Homologous Chromosomes Homologous chromosomes are pairs of chromosomes that are similar in length, centromere position, and banding patterns. Genes A gene is the basic unit of heredity and contains DNA instructions to make proteins. Human genes can vary in size from hundreds to millions of DNA bases. The process of protein synthesis: DNA → RNA → Protein. Alleles An allele is a variant form of a gene. Different alleles are found at the same location (genetic locus) on a chromosome. Humans are diploid organisms, meaning they have two alleles for each gene, one from each parent. Human Karyotype A karyotype displays chromosomes as pairs, arranged by size. The first 22 pairs are autosomes, coding for all characteristics except sexual traits. The 23rd pair determines sexual characteristics. Errors in Mitosis 1. Mutations: ○ Permanent changes in DNA, caused by mutagens like toxic chemicals, radiation, or viruses. ○ These errors can be passed on during anaphase, affecting a group of cells. 2. FHIT Gene: ○ Located on chromosome 3. ○ A mutation in the FHIT gene can lead to rapid cell division, resulting in tumor formation. 3. Oncogenes: ○ Genes that, when mutated, can trigger uncontrolled cell division, leading to cancer. ○ Examples include mutations causing retinoblastoma, Wilms' tumor, and breast cancer. Oct 7 2024 Chapter 4.2 - 4.3: Sexual Reproduction Sexual Reproduction Sexual reproduction requires two parents and produces genetically distinct offspring. It involves the fusion of male (sperm) and female (egg) reproductive cells called gametes. The resulting fertilized cell is called a zygote, which has the same number of chromosomes as a somatic cell. Each gamete carries one set of homologous chromosomes. The human diploid number is 2n = 46. Haploid vs. Diploid Cells Haploid (n): Cells with one set of chromosomes (one gene per trait). All gametes are haploid and result from meiosis. Diploid (2n): Cells with homologous chromosomes (two genes per trait). All somatic cells are diploid and created through mitosis. Chromosome Types: Autosome: Any chromosome that is not a sex chromosome (X or Y). Sex Chromosome: X or Y, responsible for biological gender. Meiosis Meiosis is the process that produces gametes with a haploid number of chromosomes. It involves two complete cycles: Meiosis I and Meiosis II. Phases of Meiosis: 1. Prophase I: Homologous chromosomes align (synapsis) and exchange segments. 2. Metaphase I: Homologous chromosomes line up at the equator. 3. Anaphase I: Homologous chromosomes are separated. 4. Telophase I: Chromosomes uncoil and spindle fibers disappear. Cytokinesis: Results in two haploid cells. Meiosis II: 1. Prophase II and Metaphase II: Similar to mitosis. 2. Anaphase II: Sister chromatids are separated. 3. Telophase II and Cytokinesis: Results in four haploid cells. Gamete Formation in Animals Spermatogenesis: The process that produces sperm in males, starting at puberty. Oogenesis: The process that produces eggs in females; it begins before birth and completes monthly after puberty, with only one egg maturing from meiosis. Multiple Births Genetic Variation Genetic variation refers to differences in DNA sequences that lead to unique traits (e.g., hair color, skin color). This variation results from subtle differences in DNA that create different alleles (gene forms). Independent Assortment Gametes are created that carry different combinations of maternal and paternal chromosomes. Occurs during metaphase I when each homologous chromosome is randomly oriented towards one of the poles. This process can produce over 8 million different chromosome combinations. Crossing Over Genetic material between maternal and paternal chromosomes is exchanged. Occurs during prophase I. Involves non-sister chromatids exchanging genetic material in multiple sections. Errors in Chromosome Number Non-Disjunction: The failure of chromosomes to separate during meiosis, resulting in gametes with abnormal chromosome numbers. Trisomy: The presence of three copies of a chromosome. Key types include: Trisomy 21: Down Syndrome. Trisomy 13: Patau Syndrome – severe defects; short lifespan. Trisomy 18: Edward's Syndrome – severe organ system effects; short lifespan. Sex Chromosome Trisomies: XXY: Klinefelter Syndrome – male, sterile, some female characteristics. XYY: Male, often taller, below average intelligence. XXX: Female, generally normal. Monosomy: A single chromosome copy error. The only survivable type is Monosomy X (XO), also known as Turner Syndrome – female, short stature, sterile, normal intelligence. Prenatal Genetic Testing Prenatal genetic testing is available to pregnant women and is covered by the Ontario Health Insurance Plan. The decision to undergo testing can be complex and may involve considerations about potential pregnancy termination. Oct 18 2024 Chapter 4.3: Reproductive Technologies Reproductive Technologies in Agriculture Selective Breeding: Breeding plants and animals to enhance specific, desirable traits. Example 1: Breeding cows for increased muscle mass. Example 2: Creating various dog breeds. Artificial Insemination: The artificial transfer of semen into a female’s reproductive tract. Semen is processed and stored before use. Increases access to high-quality males with desirable traits (healthy, strong). Farmers can purchase semen online and have it shipped instead of acquiring the entire animal. Embryo Transfer: Involves fertilizing an egg artificially, allowing it to develop into an embryo, and then transferring it into a female. Facilitates easy shipping of embryos, allowing animals to be born and raised in one location. The fused cell formed when a sperm fertilizes an egg is called a zygote. Reproductive Technologies for Humans Artificial Insemination: Similar to the process in animals, sperm is collected from a male and introduced into a woman’s reproductive system. In Vitro Fertilization (IVF): Designed for women with blocked fallopian tubes. Immature eggs are retrieved from the woman and combined with sperm in a lab. After fertilization, the embryo is placed in the uterus to develop into a fetus. Cloning: The process of producing genetically identical organisms. Achieved by removing the haploid nucleus of an egg cell and replacing it with the diploid nucleus from a donor's somatic cell. The egg becomes diploid and develops into an embryo with identical DNA to the donor. Oct 23 2024 Chapter 5.1: Understanding Inheritance Traits Characteristics that can be passed on - Examples: hair color, eye color, height Early Ideas about Heredity Breeding of animals and plants without understanding inheritance First widely accepted theory: pangenesis proposed by Aristotle - Suggested sperm and egg contained tiny particles from all body parts - Males and females formed genes in every organ - Genes moved through blood to genitals and into children Some believed only sperm contained this essence, with homunculus theory - By the 1800s, the idea emerged that traits from parents were blended in offspring - Example: red flower plus white flower equals pink flower None of these theories had scientific evidence The Science Genetics is the branch of biology dealing with the principles of variation Mendels laws form the theoretical basis for understanding genetics and inheritance Key innovations by Mendel - Developed pure lines - Counted results and kept statistical notes Why Peas Mendel worked with garden peas, which had clear characteristics for easy tracking Selected seven traits, each with only two variations Round versus wrinkled seeds - Yellow versus green color - Tall versus short plants Mendel's Research on Particulate Inheritance Created pure breeding lines for different traits in pea plants Traits studied included - Plant height tall versus short - Pea color green versus yellow - Pea texture round versus wrinkled Mendels Discoveries Parents came from pure bred lines known as the P generation Offspring were the F1 generation Expected blended offspring for traits like pea color and texture F1 generation results: all individuals looked the same Crossed F1 lines to produce F2 generation Three fourths of the F2 individuals resembled one parental line One fourth resembled the other parental line New Terms Mendel introduced two new terms - Dominant: the allele that expresses itself at the expense of an alternate allele; phenotype seen in the F1 generation from the cross of two pure lines - Recessive: an allele whose expression is suppressed in the presence of a dominant allele; phenotype that disappears in the F1 generation and reappears in the F2 generation Allelic Expression When two alleles are present, if one is dominant and the other is recessive, the dominant allele may prevent the expression of the recessive allele in the phenotype; masks it from being seen Writing Alleles Alleles are written as upper and lower case letters A dominant allele is represented by an upper case letter; usually the first letter of the allele’s description The recessive allele is the lower case of the same letter Example - Yellow pea allele: Y - Green pea allele: y Possible combinations in each plant: YY, Yy, or yy; this is the plant’s genotype The actual color of the peas is the plant’s phenotype Traits Mendel Tested Mendels experiments were called monohybrid crosses because only one trait was monitored at a time He studied seven different traits For all traits, the F1 generation showed one of the two characteristics The F2 generation showed both characteristics in a 3 to 1 ratio Law of Segregation Mendel's First Law states that traits are determined by pairs of alleles that segregate during meiosis Each gamete receives one allele Inherited traits are determined by pairs of genes; allelic pairs like DD, Dd, or dd These genes segregate in the gametes in the sex cells, either sperm or egg Each parent can only give one allele - If you possess DD, you can only give D or D - If you have Dd, you can give either D or d to your children What is an Allele An allele is one of several alternative forms of a specific gene, each with a unique nucleotide sequence - Examples: tall and dwarf are the alleles for pea plant height - Other examples: the gene for human eye color may be expressed in several forms such as blue, brown, green If a person has one gene for blue eyes and one for brown, they have two alleles for that particular gene Evolution proceeds by changes in the frequency of alleles in a population over time What You See and What It Is Phenotype: the visible appearance of a trait in an organism Genotype: the specific allelic combination for a certain gene or set of genes, representing the genetic makeup of an organism Oct 28 2024 Chapter 5.2: Modeling Punnett Squares Recall Any pair of genes on homologous chromosomes may have different alleles Different Alleles Different alleles may result in different versions of a trait Homozygous Alleles - If the alleles for a characteristic in a homologous pair are the same, the organism is said to be homozygous for that characteristic Heterozygous Alleles - If the alleles for a characteristic in a homologous pair are different, the organism is said to be heterozygous for that characteristic Dominant or Recessive The phenotype for a particular characteristic depends on which allele is dominant and which allele is recessive Dominant alleles are always expressed in a cell’s phenotype Only one copy of the dominant allele needs to be inherited for it to be expressed Dominant alleles are represented by an uppercase letter (e.g., ‘B’ for brown eyes) Recessive alleles are only expressed if two copies are present If only one copy is present, its effect is masked by the dominant allele Recessive alleles are represented by a lowercase letter (e.g., ‘b’ for blue eyes) Fertilization Two haploid cells combine to make one diploid cell Monohybrid Crosses Monohybrid Crosses In a monohybrid cross, organisms differing in only one trait are crossed Reading Punnett Squares A Punnett square shows the probability that parents will have certain offspring Results can be written as percentages, fractions, or ratios The only 100% certainty occurs after the baby is born Finding the Genotype For some characteristics, the genotype of a homozygous recessive individual can be determined from their phenotype - Example: The allele for brown fur (B) in mice is dominant over the allele for white fur (w) - All white mice must have the genotype 'ww' What is a Test Cross? During a test cross, an individual with an unknown genotype is crossed with a homozygous recessive individual The phenotype of the offspring will reveal the unknown genotype If all the offspring display the dominant phenotype, then the parent of unknown genotype must be homozygous for the characteristic If half the offspring show the dominant phenotype and half show the recessive phenotype, then the parent must be heterozygous for the characteristic Dihybrid Crosses Mendel also designed experiments to follow the inheritance pattern of two traits Determined if the inheritance of one trait affected another The Law of Independent Assortment Mendel’s second law Found a 9:3:3:1 ratio for every dihybrid cross performed This ratio is expected only if the inheritance of one trait has no influence on the inheritance of another trait Alleles for one trait segregate independently from alleles of another trait during gamete formation Each allele combination is equally likely to occur Mendel's Experiment Crossed true-breeding plants that produced yellow, round seeds (YYRR) with true-breeding plants that produced green, wrinkled seeds (yyrr) F1 generation all displayed the dominant trait for both traits (yellow and round) F1 generation self-fertilized to create the F2 generation F2 generation had a mix of four phenotypes close to the ratio 9:3:3:1 (yellow, round: yellow, wrinkled: green, round: green, wrinkled) Nov 1 2024 Chapter 5.3: Human Pedigrees, Autosomal Inheritance and Sex Linked Inheritance Human Pedigrees Pedigrees are a convention for keeping track of human genetic traits used to infer genotype. They are the human equivalent of test crosses. Visualization of a Pedigree Males are designated with square symbols. Females are designated with round symbols. Lines indicate matings, parent-offspring relationships, and sibling relationships. Generations Generations are numbered from the top of the pedigree using uppercase Roman numerals (I, II, III, etc.). Individuals in each generation are numbered from the left with Arabic numerals as subscripts (III1, III2, III3, etc.). Example of Autosomal Dominant Pedigree Autosomal means not on the sex chromosomes. It refers to situations where a single copy of an allele is sufficient to cause expression of a trait. Autosomal Dominant Inheritance 1. Every affected person should have at least one affected parent. 2. Males and females should be equally often affected. 3. An affected person has at least a 50% chance of transmitting the dominant allele to each offspring. Examples of Autosomal Dominant Disorders Progeria: A mutation causing rapid aging; individuals typically die before reproducing. Huntington’s Disease: Affects the central nervous system, typically breaking down around age 30. Autosomal Recessive Inheritance This refers to situations where two recessive alleles must be present for a trait to be expressed. Characteristics of Autosomal Recessive Inheritance 1. An affected person may not have affected parents; parents would be carriers. 2. It affects both sexes equally and can appear to skip generations. 3. Two affected parents will have affected children 100% of the time. Examples of Autosomal Recessive Disorders Albinism: A genetic condition resulting in a loss of pigment in hair, skin, and eyes. Tay-Sachs Disease: A genetic disorder causing a buildup of fatty deposits in the brain, leading to fatal outcomes. Difference Between Autosomes and Sex Chromosomes Autosomes: The first 22 pairs of human chromosomes that do not influence the sex of an individual. Sex Chromosomes: The 23rd pair of chromosomes that determine the sex of an individual. Patterns of Inheritance Crossing a white-eyed male with a red-eyed female results in roughly ¼ of the population being white-eyed females. Crossing a white-eyed female with a white-eyed male gives 100% white-eyed offspring. Crossing a white-eyed female with a red-eyed male results in all white-eyed males and all red-eyed females. Sex Determination The sex of an individual is determined by the sex chromosomes contributed by the sperm and the egg. In humans (and fruit flies): ○ An egg can donate an X chromosome. ○ A sperm can donate either an X or Y chromosome. Therefore, the sperm determines the sex of the child. Sex-Linked Inheritance Mothers always give an X chromosome to their offspring (it's all they have). Fathers can give either an X or a Y chromosome. Girls receive one X from their mother and one X from their father, while boys receive one X from their mother and one Y from their father. Inheritance of Sex-Linked Traits Traits located on sex chromosomes depend on the sex of the parent carrying the trait. The gene must be located on the X chromosome. For sex-linked traits, symbols for the genes are not used in the Punnett Square. Instead, sex chromosomes are used, with symbols for the dominant and recessive alleles written as superscripts. Examples of Sex-Linked Disorders Most known sex-linked traits are X-linked (carried on the X chromosome) because the X chromosome is much larger than the Y chromosome. Risk and Inheritance of Sex-Linked Disorders Males are at a greater risk for inheriting sex-linked disorders because they only inherit one X chromosome. If that X carries the allele for a disorder, they will be affected. Females can be carriers of the trait (having the recessive allele masked by a dominant allele on the other X chromosome). There are no male carriers. Recessive lethal X-linked traits result in death. Examples of Sex-Linked Traits and Disorders Male pattern baldness Red-green color blindness Myopia Night blindness Hemophilia Sex-Linked Inheritance in Practice Punnett squares are used to predict the outcome of sex-linked inheritance. Assume the trait is X-linked unless stated otherwise. Most disorders are recessive, but some are dominant; the question will specify. Definition of a Carrier A "carrier" is a female who is heterozygous for the trait. X-Linked Recessive Inheritance This refers to situations where a recessive allele on the X chromosome can lead to a trait, condition, or disorder. Males are affected more often than females, with a ratio of about 8:1. Affected males will transmit the allele to all daughters but not to sons. Homozygous recessive females can arise only from matings where the father is affected and the mother is affected or a carrier. Examples of X-Linked Recessive Disorders Hemophilia: The inability of the blood to clot properly. Duchenne Muscular Dystrophy: Causes progressive and degenerative muscle weakness. X-Linked Dominant Inheritance Refers to situations where a single dominant allele on the X chromosome can lead to a trait or condition. This is very uncommon. Characteristics of X-Linked Dominant Inheritance 1. Twice as many females are affected as males. 2. Usually, half the children of an affected female will be affected, regardless of sex. 3. All daughters of an affected male will be affected, but none of the sons. Example of X-Linked Dominant Disorder Vitamin D resistant rickets: Can lead to bone deformities, particularly in the lower limbs (bowed legs) Nov 4 2024 Chapter 6.1: Beyond Mendels Laws Incomplete Dominance Definition: Incomplete dominance occurs when neither of the two alleles for the same gene is completely dominant. The heterozygote's phenotype is a mixture of both alleles. Example: Flowers - P Generation: True breeding red and white flowers - F1 Generation: 100% pink flowers - F2 Generation: 25% red, 50% pink, 25% white (1:2:1 ratio) Notation: Superscripts are used for alleles in incomplete dominance. Human Example: Familial hypercholesterolemia is a disorder that exhibits incomplete dominance. Animal Example: Andalusian Chickens Codominance Definition: Codominance occurs when both alleles are fully expressed. The heterozygote shows both phenotypes simultaneously. Example: Roan animals (e.g., red and white roan bovine). Human Example: Sickle Cell Anemia Misshapen red blood cells can't transport oxygen efficiently. Heterozygotes have both normal and sickled red blood cells. Advantage: Heterozygotes are resistant to malaria. Multiple Alleles Definition: Some traits result from the interaction of more than two alleles for one gene. - Example: Human Blood Types Alleles: IA (A antigen, codominant), IB (B antigen, codominant), i (no antigen, recessive). - Example: Rabbit Coat Colour Four alleles with an order of dominance: - Agouti (C) > Chinchilla (Cch) > Himalayan (Ch) > Albino (c). - Example: Clover Leaf Pattern - Seven different alleles for leaf pattern. Environmental Effects on Inheritance Definition: Environmental factors can influence whether a gene is active. - Example: Himalayan rabbits exhibit dark coloration due to a gene active only at lower temperatures. Polygenic Inheritance Definition: Traits that show continuous variation and vary gradually from one extreme to another, controlled by multiple genes. - Examples: Height and skin color in humans, kernel color in wheat, ear length in corn. Note: Dominant alleles contribute to the phenotype, while recessive alleles do not. Chapter 6.2: Inheritance of Linked Genes Linked Genes Definition: Alleles on the same chromosome do not assort independently and do not follow Mendel’s laws. Genes located on the same chromosome are inherited together, known as linked genes. Linkage Group: All genes on one chromosome form a linkage group, tending to be inherited together. Crossing Over: During meiosis I, crossing over can unlink genes on the same chromosome. hromosome Mapping: Scientists have found that linked genes separate with predictable frequency based on their proximity on the chromosome. This understanding of inheritance is known as chromosome mapping and is useful in rapidly reproducing plants and animals. Sex-linked Inheritance Thomas Hunt Morgan: A geneticist who studied fruit flies (Drosophila melanogaster). He discovered that eye color is sex-linked. Eye Color Experiment: - Crossed a male white-eyed fly with a red-eyed female. - F1 Generation: All offspring had red eyes. - F2 Generation: Observed all females with red eyes, half of males with red eyes, and half with white eyes. - Conclusion: The gene for eye color is on the X chromosome. Definition: Traits controlled by genes on the X or Y chromosome are called sex-linked traits. X and Y Chromosomes: - The X chromosome has about 2,000 genes; the Y chromosome has fewer than 100. X-linked Dominant Disorders: - Affected males pass the allele to their daughters (100% chance). - Affected females can pass the dominant allele to both sons and daughters (all would have the disorder). X-linked Recessive Disorders: - A son needs one recessive allele to be affected; a daughter needs two. - Example: Red-green color vision deficiency (CVD) can be tracked using a pedigree. Notation: A superscript is used on the X or Y chromosome for sex-linked traits. CVD is an X-linked recessive disorder. Punnett Squares: Used to predict the outcome of crosses involving sex-linked traits. Barr Bodies X Chromosome Inactivation: Females have two X chromosomes, but only one is active in each cell, while the other becomes inactive and forms a Barr body. Timing: This deactivation occurs early in embryonic development, and which X chromosome is inactive varies among cells. Calico Cats Example: In heterozygous female cats, 50% of cells express the orange allele and 50% express the black allele, depending on which X chromosome is active. Nov 14 2024 Chapter 7.1: Introduction to Evolution What is Evolution? In biology, evolution is the change in the inherited traits (genes/alleles) of species or populations over time. Three main processes that influence the rate of evolution: 1. Variation within a species – Each individual is unique, meaning there are differences in their traits. 2. Reproduction – How and how often a species reproduces affects its rate of evolution. 3. Selection – Traits that are beneficial in an environment are more likely to be passed on (through natural selection or sexual selection). Evolution by Natural Selection Charles Darwin's theory of evolution by natural selection states that organisms best suited to their environment are more successful at passing on their traits to the next generation. Darwin’s Key Idea: Species change over time because individuals with advantageous traits survive longer and reproduce more. Darwin’s Influences Darwin originally wanted to be a doctor but abandoned the idea due to his aversion to blood. He later considered becoming a minister but was more interested in animals than studying. Darwin became fascinated with taxonomy (classification of organisms) and biology. John Stevens Henslow, a botany professor, mentored Darwin and recommended him for a position as a naturalist on the HMS Beagle, a voyage around the world led by Captain Robert Fitzroy. Voyage of the HMS Beagle: The voyage lasted 5 years, and Darwin studied plants, animals, and fossils. He noticed similarities between extinct animal fossils and modern species, especially on the Galapagos Islands. Darwin observed finches on the Galapagos that looked similar to birds in South America but not to those in Africa, despite similar environments. Two Types of Evolution 1. Convergent Evolution: Unrelated species become more similar as they adapt to similar environments. 2. Divergent Evolution: New species form from an existing species adapting to new environments. Phylogenetic Tree A phylogenetic tree shows the evolutionary relationships among species, illustrating divergent evolution over time. All Species Have Genetic Variation Every species has variation within itself. No two individuals are identical. Variation can be passed down to future generations. Adaptation and Variation Organisms face environmental challenges such as weather, famine, and competition (for food, space, and mates). Species produce more offspring than can survive, leading to competition. Individuals with traits better suited to the environment will survive and reproduce more successfully, passing on favorable traits. Over time, genes for less favorable traits are eliminated from the gene pool. For example, giraffes with longer necks can reach higher branches, so they are more likely to survive and pass on their long-neck trait. Adaptation and Survival Adaptation refers to any structure, behavior, or physiological process that helps an organism survive and reproduce in its environment. Examples of adaptations: ○ Camouflage: Hiding from predators. ○ Hibernation: Sleeping through harsh seasons. ○ Mimicry: Harmless species resemble harmful ones (e.g., Viceroy butterfly mimics Monarch butterfly to avoid being eaten). Development of Adaptations Adaptations are the result of gradual, cumulative changes that help organisms survive and reproduce. Adaptations arise from random mutations in the DNA of organisms. Not all variations are adaptations—only those that improve survival or reproduction. Variation Within Species Genetic variation within a species comes from mutations, which create new genetic information. Mutations are permanent changes in the DNA of an organism and can occur spontaneously or due to external factors (e.g., UV rays, cigarettes). ○ Mutations in somatic cells (body cells) do not affect future generations. ○ Mutations in gametes (reproductive cells) can be passed on to offspring. Beneficial mutations can provide a selective advantage, improving an organism’s survival. Rapid Reproduction and Selective Advantage Some species, like bacteria, reproduce rapidly (e.g., doubling in under 10 minutes). Rapid reproduction means that new beneficial alleles can spread quickly through a population when the environment changes, giving the organisms with these traits a selective advantage. Example: People with the sickle cell trait have a selective advantage in areas with malaria because the mutated gene helps protect against the disease. Nov 18 2024 Chapter 7.2: Natural vs Artificial Selection Old Theories of Evolution Jean Baptiste Lamarck (early 1800s) - Theory: "The Inheritance of Acquired Characteristics" - Lamarck suggested that traits an organism acquires during its lifetime can be passed on to its offspring. - Example: Giraffes' long necks evolved because their ancestors stretched their necks to reach higher leaves. This acquired trait was passed down to future generations. Charles Darwin (1859) - Influenced by Charles Lyell: Lyell’s book, (Principles of Geology), - helped Darwin realize that natural forces gradually change Earth's surface. These same forces are still at work today. - Main Work: *On the Origin of Species by Means of Natural Selection* (1859) Key Points: - Species did not exist in their current form but evolved from ancestral species. - Natural Selection is the mechanism driving evolution. Variation Within Species Variation is the difference in traits among individuals in a species. It’s caused by different combinations of genetic information (alleles) inherited from parents. Mutation is the primary source of genetic variation. A mutation is a permanent change in DNA, and only mutations in the DNA of gametes (sperm or egg cells) can be passed to offspring. Selective Advantages Selective Advantage refers to a genetic trait that improves an organism’s chances of survival and reproduction. A mutation may initially be a disadvantage but could later provide a survival benefit in a changing environment. Phenotype: The trait must show up in the organism’s appearance or behavior for natural selection to act on it. Organisms that reproduce quickly, like bacteria, adapt quickly to new conditions. - Example: Staphylococcus aureus (S. aureus) bacteria mutate rapidly and can become resistant to antibiotics. These beneficial mutations help the bacteria survive and spread to future generations. Natural Selection Natural Selection (also called "Differential Reproduction") means individuals with favorable traits are more likely to survive and reproduce, passing those traits on to their offspring. - Example: The English peppered moth (Biston betularia) has both light and dark forms. Dark moths are more likely to survive in polluted environments, while light moths are more visible to predators. Artificial Selection Artificial Selection is the process where humans selectively breed plants or animals for specific traits. Examples: - Cats bred for specific appearances. - Cows are bred to increase muscle mass for meat. - Chickens are bred to lay more eggs. Wild Mustard Plant: Through artificial selection, this one plant species has been bred into many different crops (e.g., cabbage, broccoli, cauliflower). Corn Selection Experiment (1896): Corn was selectively bred for high or low oil content, showing how human intervention can drastically change plant traits over time. Consequences of Artificial Selection Negative Effects: Selecting for one trait can unintentionally harm other traits. - Example: English bulldogs bred for flat faces often suffer from respiratory problems. Reduced Genetic Diversity: Artificial selection often leads to lower genetic diversity in a population, making them less adaptable to environmental changes. Monoculture Farming: In agriculture, monocultures (growing large fields of one type of crop) are more vulnerable to diseases or environmental changes because they lack genetic diversity. Gene Banks: To preserve genetic diversity, gene banks store seeds from wild plants and early cultivars that have traits modern crops may have lost. Nov 21 2024 Chapter 8.2: Sources of Evidence of Evolution Evidence of Evolution Biogeography Study of species distribution across the world (past and present). Helps understand how species are spread and evolved geographically. Fossil Record Fossils found in sedimentary rock layers. Order of fossils in layers shows how life has changed over time. Considered strong evidence of evolution. Taxonomy System of classifying organisms from broad categories (kingdom) to specific ones (species). Shows relationships between different organisms. Homologous Structures Similar body parts in different species due to a common ancestor. Structures may have different functions (studied in comparative anatomy). Comparative Embryology Study of embryo development in different species. Early embryos look alike but develop into different organisms. Suggests common evolutionary origin. Molecular Biology Study of DNA, RNA, and proteins (amino acids). All organisms share similar nucleotide bases in DNA and RNA. Shows common genetic foundation among all life forms. Nov 26 2024 Chapter 9.1: Evolution and Speciation Evolution The processes that have transformed life on Earth from its earliest forms to the vast diversity we see today. A change in the genes!!! Charles Darwin Wrote "On the Origin of Species by Means of Natural Selection" in 1859. Two main points in his theory: 1. Species were not created in their present form, but evolved from ancestral species. 2. Darwin proposed Natural Selection as the mechanism of evolution. Key Terms Population: A localized group of individuals of the same species. Species: A group of populations whose members can interbreed and produce viable (fertile) offspring. Gene Pool: The total collection of genes in a population at any given time. Hardy-Weinberg Principle The Hardy-Weinberg Principle states that the shuffling of genes during sexual reproduction alone cannot change the overall genetic makeup of a population. For this principle to apply, five conditions must be met: 1. Very large population. 2. Isolation from other populations (no gene flow). 3. No net mutations (no changes in genes). 4. Random mating (no preference in mate selection). 5. No natural selection (everyone survives equally). If all conditions are met, the population is in equilibrium—this means no evolution is occurring (no genetic changes). Microevolution Refers to evolutionary changes in a species over relatively short periods of geological time. It involves changes in a population's gene pool over generations. Five Mechanisms of Microevolution 1. Genetic Drift Changes in the gene pool of a small population due to chance events. Two key examples: Bottleneck Effect: Occurs when a population is drastically reduced in size, often due to a disaster. The small surviving group has reduced genetic variation, and any recovery may be limited to the genes of this small group. Founder Effect: Happens when a new colony is established by a small number of individuals from the original population. This small group may have: Less genetic variation than the original population. A non-random sample of the genes from the original population. Unit 4 Dec 3 2024 Chapter 10.1a: Nutrition and Digestion Nutrition – Diet: Humans are Heterotrophic, meaning they need to consume other organisms for food. Functions of Nutrients: Energy Growth & Repair Insulation Health Types of Nutrients: 1. Carbohydrates – provide energy. 2. Fats – provide energy and help with insulation. 3. Proteins – are needed for growth and repair. 4. Water – needed for cellular activity. 5. Vitamins – support various body functions. 6. Minerals – help with body functions. 7. Fibre (Roughage) – helps maintain a healthy colon. Energy: Energy from food is measured in Joules (J) (SI units). ○ 1 Calorie = 4.2 Joules ○ 1 gram of Carbohydrate or Protein = 16.8 Joules ○ 1 gram of Fat = 37.8 Joules Energy Requirements: The amount of energy a person needs depends on several factors: Age – Children require more energy than older adults. Gender – Men typically need more energy than women, except for pregnant or lactating women. Occupation – Physically demanding jobs need more energy than sedentary ones. Climate – Cold climates need more energy for warmth compared to hot climates. Basal Metabolic Rate (BMR): BMR is the minimum energy needed for your body to function at rest. Energy Expenditure Breakdown: Liver: 27% Brain: 19% Other Organs: 19% Skeletal Muscles: 18% Kidneys: 10% Heart: 7% Dec 9 2024 Chapter 10.1b: Macromolecules Hydrolysis Reaction A hydrolysis reaction involves the breaking apart of two subunits through the addition of a water molecule. Hydration Synthesis Hydration synthesis is a catabolic reaction that releases energy. Carbohydrates Carbohydrates are produced by plants and algae through photosynthesis. Carbohydrates are used for: 1. Energy 2. Building materials 3. Cell identification and communication. Carbohydrates contain carbon (C), hydrogen (H), and oxygen (O) in a 1:2:1 ratio. General formula: (CH₂O) , where n represents the number of carbon atoms. Carbohydrates are classified into three groups: 1. Monosaccharides 2. Disaccharides (Oligosaccharides) 3. Polysaccharides Monosaccharides Monosaccharides are simple sugars, like glucose, galactose, and fructose. They have 5 or more carbon atoms. ○ In their dry state, they are linear, but they form a ring structure when dissolved in water. Types of glucose: ○ α-glucose: 50% chance the OH group on C1 will be below the plane of the ring. ○ β-glucose: 50% chance the OH group on C1 will be above the plane of the ring. Disaccharides Disaccharides (or oligosaccharides) are formed by joining 2 or 3 monosaccharides through glycosidic linkages, which are created by condensation (dehydration synthesis) reactions. Examples: ○ Maltose ○ Sucrose Polysaccharides Polysaccharides consist of hundreds to thousands of monosaccharides connected by glycosidic linkages. They are used for energy storage and structural support. ○ Starch and Glycogen are used for storage. ○ Cellulose and Chitin are used for structure. Lipids Lipids are hydrophobic molecules that are generally nonpolar. They are made of carbon (C), hydrogen (H), and oxygen (O). Lipids are used for: ○ Energy storage ○ Building membranes ○ Chemical signals. Types of lipids: ○ Fats ○ Phospholipids ○ Steroids (e.g., cholesterol and sex hormones) ○ Waxes (e.g., waterproof coating on plants and animals) Fats Triglycerides are made of glycerol and 3 fatty acids formed by ester linkage (esterification). Saturated fats: ○ Typically from animals. ○ Solid at room temperature due to increased van der Waals forces. ○ Used for long-term energy storage, insulation, protection, and to help dissolve fat-soluble vitamins. ○ No double bonds between carbon atoms. Unsaturated fats: ○ Typically from plant oils. ○ Liquid at room temperature. ○ Contain one or more double bonds between carbon atoms. ○ The rigid kinks from the double bonds reduce the number of van der Waals attractions. Esterification of a Triglyceride The hydroxyl group of glycerol reacts with the carboxyl group of three fatty acids. This reaction forms an ester linkage. Phospholipids Phospholipids are made of 1 glycerol, 2 fatty acids, and a highly polar phosphate group. They form cellular membranes (the phospholipid bilayer). ○ The phospholipid bilayer is: Virtually impermeable to macromolecules. Relatively impermeable to charged ions. Quite permeable to small, lipid-soluble molecules (e.g., O₂ and CO₂, which diffuse through easily). ○ Larger molecules pass through the membrane via carrier proteins (facilitated diffusion). Steroids (Sterols) Steroids are made of 4 fused hydrocarbon rings and functional groups. Examples: ○ Cholesterol ○ Testosterone ○ Estrogen ○ Progesterone Waxes Waxes consist of long-chain fatty acids linked to alcohols or carbon rings. They have a firm, pliable consistency and are used as a waterproof coating on plants and animals. Proteins Proteins are made of one or more amino acid polymers that have been coiled together. Of the 20 amino acids that make up proteins, we must consume 8 essential amino acids (because we cannot produce them on our own): ○ Tryptophan (Trp) ○ Methionine (Met) ○ Valine (Val) ○ Threonine (Thre) ○ Phenylalanine (Phe) ○ Leucine (Leu) ○ Isoleucine (Ile) ○ Lysine (Lys) The bonds holding amino acids together are called peptide bonds. Amino Acids Each amino acid has 3 components: 1. Amino group (NH₂) 2. Central (α) hydrogen atom 3. Carboxyl group (COOH) The Four Levels of Protein Folding 1. Primary structure: The sequence of amino acids in a polypeptide chain, determined by the nucleotide sequence of a gene. 2. Secondary structure: The folding and coiling of the polypeptide chain into shapes like pleated sheets or alpha helices. 3. Tertiary structure: The polypeptide chain undergoes further folding due to interactions between side chains (R-groups). 4. Quaternary structure: Two or more polypeptide chains come together to form a functional protein, such as in collagen and hemoglobin. Denaturation Changes in temperature or pH can cause a protein to unravel (denature). A denatured protein is unable to perform its biological function. Dec 11 2024 Chapter 10.2: Digestive System Obtaining Food Different animals use various methods to capture food for energy. Filter Feeders Filter feeders collect small food particles using sieve-like organs in their mouths. Examples include: ○ Whales ○ Oysters ○ Mussels ○ Many aquatic organisms. Fluid Feeders Fluid feeders ingest their nutrients in the form of liquids. Examples include: ○ Tapeworms ○ Leeches ○ Mosquitoes ○ Hookworms Spiders Spiders are also fluid feeders. After prey is captured and killed, digestive enzymes are pumped into the prey to break it down. Hairy Little Legs Many animals use appendages with rows of hairs to capture food or molecules from the surrounding fluid, to enable movement, or to move fluids past themselves. Open Tube Arrangement Grasshoppers have an open tube arrangement with separate entrances and exits for food and waste. Other organisms, like hydra and sea anemones, have only one opening for both food intake and waste expulsion. This is called closed tube digestion. Amoeba Amoeba refers to members of the genus Amoeba and other protozoa with pseudopodia (false feet). They are uninucleate (lack a true nucleus) and have no fixed shape. They reproduce by binary fission. Amoebas move by extending their pseudopods, which also help them take in food. Food particles are digested in vacuoles through intracellular digestion. Intracellular Digestion Amoeba and Paramecium use intracellular digestion. ○ They form vacuoles around food by phagocytosis (engulfing food). ○ Digestion occurs inside the cell. ○ Waste residue is expelled from the cell after digestion. The Mammalian Digestive System Upper Digestive Tract Mechanical Digestion: The large food particles that are ingested are broken into smaller pieces, which can then be acted upon by enzymes. This process begins with chewing (mastication) in the mouth. Movements: After ingestion and mastication, food moves from the mouth to the pharynx, then down the esophagus. This movement is called deglutition or swallowing. Digestive System Mammals have specialized external organs made up of cells designed specifically for digestion. Peristalsis Peristalsis is the wave-like movement that pushes food through the digestive tract. The muscles in the organ contract and narrow, then propel the food and fluids forward in a coordinated wave, much like ocean waves. Digestion in the Stomach Mechanical Digestion Mixing movements in the stomach occur due to smooth muscle contraction. These repetitive contractions mix food particles with digestive enzymes and fluids. Peristalsis continues in the stomach to move food through the digestive system. Chemical Digestion Chemical digestion breaks down complex molecules of carbohydrates, proteins, and fats into smaller molecules that can be absorbed and used by the cells. This is done through hydrolysis, which uses water and digestive enzymes to break down the molecules. Enzymes speed up this slow process. Small & Large Intestines Absorption The simple molecules resulting from chemical digestion pass through the cell membranes of the small intestine lining and enter the blood or lymph capillaries. This process is called absorption. Elimination Indigestible food molecules are eliminated from the body. These are removed through the anus in the form of feces during defecation. Jan 6 2024 Chapter 11.1 Function of Respiratory System The Respiratory System The respiratory system is a group of organs that help bring oxygen into the body and remove carbon dioxide from each cell. Stages of Respiration There are four stages of respiration: 1. Breathing (Inhalation and Exhalation) – the process of air moving in and out of the lungs. 2. External Respiration – the exchange of gases (oxygen and carbon dioxide) between the lungs and the blood. 3. Internal Respiration – the exchange of gases between the blood and the body’s cells. 4. Cellular Respiration – the process where cells release energy by using oxygen and producing carbon dioxide. Breathing Breathing is the movement of air into and out of the lungs. Inspiration (Inhalation): Air is drawn into the lungs when the diaphragm and rib muscles contract, expanding the chest cavity and lowering air pressure inside the lungs. Expiration (Exhalation): Air is pushed out of the lungs when the diaphragm and rib muscles relax, reducing lung volume and increasing air pressure. External Respiration This is the exchange of gases (oxygen and carbon dioxide) between the lungs and the blood. Oxygen moves from the lungs into the blood, while carbon dioxide moves from the blood into the lungs to be exhaled. Internal Respiration Internal respiration happens in the tissues. Oxygen moves from the blood into the cells, and carbon dioxide moves from the cells into the blood. Respiratory Surfaces For gas exchange to happen efficiently, respiratory surfaces need to meet two key requirements: 1. Large Surface Area – to allow enough gas exchange to meet the body’s needs. 2. Moist – gases need to dissolve in water to diffuse properly. This is why some animals live in moist or aquatic environments. Types of Respiratory Surfaces Different animals have developed different types of respiratory surfaces for gas exchange: 1. Outer Surface (Skin) ○ Some animals use their entire outer surface for respiration, where gases diffuse directly through the skin. ○ These animals must live in moist environments to facilitate gas exchange. 2. Gills ○ Gills are extensions of the body surface that increase surface area for gas exchange. ○ Gills are used by animals living in water (like fish), where oxygen in water diffuses into the blood and carbon dioxide diffuses out. 3. Tracheal System ○ Insects use a system of tubes called tracheae to exchange gases directly between their cells and the environment, without involving blood. 4. Lungs ○ Larger animals use lungs, which are internal sacs lined with moist tissue. Lungs increase surface area for more efficient gas exchange. ○ Blood carries oxygen from the lungs to cells and removes carbon dioxide. Aquatic Gas Exchange In aquatic animals, gas exchange happens as water enters the mouth and flows over the gills. Oxygen in the water diffuses into the blood, while carbon dioxide in the blood diffuses out through the gills into the water. Terrestrial Gas Exchange On land, air must be moved into and out of the lungs for gas exchange to occur. The brain controls the breathing rate and monitors lung air volume. The diaphragm (a muscle beneath the lungs) and intercostal muscles (between the ribs) control lung pressure, allowing air to flow in (inhalation) and out (exhalation). Air Pressure in the Lungs Inhalation (Inspiration): The diaphragm and intercostal muscles contract, expanding the chest cavity. As the volume increases, the pressure inside the lungs decreases, causing air to flow in. Exhalation (Expiration): The diaphragm and intercostal muscles relax, reducing lung volume. This increases pressure inside the lungs, forcing air out. Breathing During inhalation, the rib cage moves upward and outward, and the diaphragm contracts downward, expanding the lungs and drawing air in. During exhalation, the rib cage relaxes back to its normal position, and the diaphragm moves upward, causing the lungs to contract and air to be pushed out. Spirographs A spirometer is used to measure the amount of air moving in and out of the lungs. The results are shown on a spirograph, which helps measure lung function. Measuring Respiratory Volume The following terms describe lung volumes: 1. Tidal Volume (TV) – the amount of air inhaled or exhaled in a normal breath when the body is at rest. 2. Inspiratory Reserve Volume (IRV) – the extra air you can inhale after a normal breath with maximum effort. 3. Expiratory Reserve Volume (ERV) – the extra air you can exhale after a normal breath with maximum effort. Chapter 11.2-11.3 Human Respiratory System Chapter 11.2 Human Respiratory System Humans are land animals, so we use lungs to breathe. The respiratory tract is the pathway that air takes to reach the lungs, where gas exchange happens. It begins at the nose and continues through various structures to the lungs. The respiratory system's main job is to exchange oxygen (O₂) from the air with carbon dioxide (CO₂) in the blood. Components of the Respiratory System The respiratory system includes the following parts: Nasal Cavity (nose) Pharynx (throat) Larynx (voice box) Trachea (windpipe) Bronchi (tubes that lead into the lungs) Lungs (where gas exchange occurs) Physical Properties of Lung Tissue Lung tissue has three key properties that help it expand and contract during breathing: 1. Extensibility – Lung tissue can stretch easily without being damaged, allowing the lungs to expand and bring in air. 2. Elasticity – When stretched, lung tissue recoils back to its normal size. 3. Compliance – This refers to how easily the lung volume can expand. Lungs with good compliance stretch easily when a small vacuum (negative pressure) is created. Upper Respiratory Tract Air enters through the nose or mouth. Inside the nasal passages, small bones called turbinate bones increase the surface area. These bones help warm the air with a network of blood vessels and clean the air using mucus from ciliated membranes. Air then moves into the pharynx (throat), passes the glottis (opening to the larynx), and enters the larynx (voice box). The epiglottis covers the glottis during swallowing to prevent food from entering the windpipe (trachea). The larynx is made of cartilage and is important for sound production (voice). After passing through the larynx, air enters the trachea, which is about 10–12 cm long and kept open by semicircular cartilage rings. Lower Respiratory Tract The trachea branches into two bronchi (one for each lung). Each lung is surrounded by a protective pleural membrane. The left lung has two lobes, and the right lung has three lobes. The bronchi divide many times into smaller tubes called bronchioles, which end in tiny, grape-like clusters of sacs called alveoli (singular: alveolus). There are around 500 million alveoli in each lung. Alveoli and Gas Exchange Each alveolus is surrounded by a network of capillaries (tiny blood vessels). The walls of both the alveoli and capillaries are very thin (only one cell thick), which allows for quick gas exchange through diffusion. Oxygen (O₂) moves from the air in the alveoli into the blood, because the O₂ concentration is higher in the alveoli than in the blood. Carbon dioxide (CO₂) moves from the blood into the alveoli, where it is then exhaled. Transporting Gases About 99% of oxygen (O₂) in the blood is carried by hemoglobin, a protein found in red blood cells. When carbon dioxide (CO₂) leaves the body’s cells, about 23% of it is carried by hemoglobin. The rest is carried in the blood plasma (fluid). Bronchi and Bronchioles The bronchi branch repeatedly into smaller tubes called bronchioles. These end in clusters of alveoli, where gas exchange takes place. Chapter 11.3 Respiratory System Disorders Tonsillitis Cause: A bacterial or viral infection of the tonsils (located in the pharynx at the back of the throat). Function of Tonsils: They help keep harmful substances, like bacteria, out of the respiratory system. Symptoms: Red, swollen tonsils, sore throat, fever, and swollen glands. Treatment: Tonsils can be surgically removed if necessary. Laryngitis Cause: Inflammation of the larynx (voice box) due to infection or overstraining the voice. Symptoms: Hoarseness or loss of voice. Treatment: Typically clears up on its own in a few days. Pneumonia Cause: Inflammation and fluid buildup in the alveoli (air sacs in the lungs), caused by bacteria or viruses. Types: Lobular and bronchial pneumonia. Treatment: Antibiotics (for bacterial pneumonia), antiviral medications, and vaccines. Bronchitis Cause: Inflammation of the bronchi (airways), leading to redness and excess mucus production. Symptoms: Coughing up mucus. Types: ○ Short-term (acute): Caused by bacteria. ○ Long-term (chronic): Caused by repeated exposure to irritants (dust, chemicals, or cigarette smoke), which damage the cilia in the lungs. Chronic Bronchitis (COPD): Leads to infections, persistent cough, and mucus buildup. Treatment: While it can’t be cured, chronic bronchitis can be managed with medications, quitting smoking, and special exercise programs. Asthma Cause: Inflammation of the bronchi and bronchioles, often triggered by pollen, dust, or smoke. Symptoms: Wheezing, coughing, chest tightness, and shortness of breath. Treatment: Cannot be cured but can be managed with inhalers and muscle-relaxing medications. Emphysema Cause: Damage to the walls of the alveoli, which lose their elasticity and reduce the respiratory surface area for gas exchange. Symptoms: Labored breathing due to collapsed bronchioles. Type of COPD: Incurable, but symptoms can be treated with inhalers or low-flow oxygen tanks. Main Causes: Smoking and airborne irritants. Cystic Fibrosis Cause: A genetic condition that causes the cells lining the airways to release thick, sticky mucus that clogs the lungs. Symptoms: Difficulty breathing and increased bacterial infections due to mucus buildup. Treatment: No cure, but mucus-thinning medications and antibiotics help. Gene therapy has been used since 1993 to attempt to correct the genetic defect. Lung Cancer Cause: Uncontrolled cell division forms a mass (carcinoma or tumor), which can reduce the respiratory surface area. Symptoms: Persistent cough, difficulty breathing, chest pain, and loss of appetite. Metastasis: The tumor can spread to other areas of the body. Main Cause: Smoking is the leading cause, though there are other risk factors. Prognosis: Lung cancer is the leading cause of cancer deaths in Canada, and over 80% of people diagnosed die within five years. Diagnostic Tools CT Scanning (Computed Tomography) Purpose: A major diagnostic tool for respiratory disorders. How it Works: A rotating X-ray machine takes detailed images (or "slices") of the body’s interior. Spiral CT Scanning: A more advanced CT scan that creates clearer, more detailed images of internal tissues and blood vessels. Use: It’s especially useful for detecting early lung cancer and identifying internal injuries. Bronchoscopy Purpose: A procedure that allows doctors to examine the trachea and lungs using an endoscope (a flexible tube with a camera). How it Works: The endoscope is inserted through the mouth or nose under general anesthesia. It can also be used to collect tissue or mucus samples for diagnosis, remove tumors, and repair damaged tissues. Uses: It helps diagnose conditions like asthma, lung infections, and tumors. Jan 7 2024 Chapter 12 The Circulatory System An imaging technology called Magnetic Resonance Angiography (MRA) enables doctors and scientists to examine the circulatory system in great detail. The heart, which is the pump for the entire system, beats 100 000 times a day, delivering oxygen and nutrients via blood to every organ, tissue, and cell. Chapter 12.1 The Function of Circulation 12.1 The Function of Circulation Multicellular organisms need nutrients, oxygen, and waste removal to function properly. The circulatory system performs the following essential tasks: Transports gases, nutrients, and waste products Regulates internal body temperature and transports chemical substances Protects against blood loss and diseases/toxins Major Components of the Circulatory System 1. Heart: A muscular organ that pumps blood through the body. 2. Blood Vessels: Hollow tubes that carry blood. 3. Blood: Fluid that transports nutrients, oxygen, carbon dioxide, and other substances. Two Types of Circulatory Systems Open Circulatory System: Blood flows freely in the body cavity and directly contacts organs/tissues. Examples: Insects, crustaceans. Example: A grasshopper's blood (hemolymph) is pumped through a vessel and re-enters via small pores called ostia. Closed Circulatory System: Blood is contained within vessels, circulating in a continuous path. Examples: Earthworms, birds, humans. Example: An earthworm has five aortic arches near its head that pump blood. The Mammalian Circulatory System Double Circulation: Blood passes through two circuits: 1. Pulmonary Circulation: Heart to lungs and back. 2. Systemic Circulation: Heart to the rest of the body and back. The heart is responsible for cardiac circulation, pumping blood through these systems. The Human Heart Located slightly left of the chest, made of cardiac muscle. Oxygen-rich blood is separated from oxygen-poor blood. Has 4 chambers: two atria (top) and two ventricles (bottom), separated by a septum. The Structure of the Human Heart Blood Flow: Right side: Receives deoxygenated blood from the body (via the vena cavae), pumps it to the lungs (via pulmonary arteries). Left side: Receives oxygenated blood from the lungs (via pulmonary veins), pumps it to the body (via the aorta). Valves: Atrioventricular valves: Tricuspid (right) and bicuspid (left) valves allow blood from the atria to ventricles. Semilunar valves: Pulmonary (right) and aortic (left) valves allow blood to flow from ventricles into arteries. Blood Vessels Arteries (and arterioles): ○ Carry blood away from the heart. ○ Have thick, elastic walls. ○ Carry oxygenated blood (except pulmonary artery). ○ No valves, high-pressure blood flow. Veins (and venules): ○ Carry blood to the heart. ○ Carry deoxygenated blood (except pulmonary veins). ○ Have one-way valves to ensure blood flows forward. ○ Thin, non-elastic walls. Capillaries: ○ Site of material exchange between blood and body cells. ○ Have a single layer of cells for easy exchange. Blood and Its Components 1. Plasma (fluid portion): ○ Contains water, dissolved gases, proteins, sugars, vitamins, minerals, and waste products. 2. Formed Elements (solid portion): ○ Red Blood Cells (RBCs): Transport oxygen and some carbon dioxide. ○ White Blood Cells (WBCs): Defend the body against infections. ○ Platelets: Help with blood clotting. Blood Plasma and its Functions 92% Water. 7% proteins (albumin, globulins, fibrinogen). 1% other substances (glucose, fatty acids, vitamins, salts, gases). Red Blood Cells and Their Functions 44% of blood volume. Specialized for oxygen transport via hemoglobin. Lack a nucleus and can carry a small amount of carbon dioxide. 500-1000 RBCs for every WBC. White Blood Cells and Their Functions 1% of blood volume. Five types: ○ Neutrophils (most common) – fight infections. ○ Eosinophils – in mucus, combat parasites. ○ Basophils – attract phagocytes to infection sites. ○ Lymphocytes – produce antibodies. ○ Monocytes – destroy bacteria. Platelets and Their Function Small, membrane-bound cell fragments involved in blood clotting. When injury occurs, they release chemicals to form a clot (fibrin). The Functions of Blood 1. Transport: Carries nutrients, gases, and waste products to/from cells. Transports glucose, amino acids, and other substances. 2. Temperature Regulation: Blood flow near the skin can change to either release (vasodilation) or conserve (vasoconstriction) heat. 3. Countercurrent Heat Exchange: Deep arteries and veins in extremities lie close to each other, allowing heat transfer from warm blood flowing out to cooler blood returning, helping maintain core body temperature.

Alessandro Buccini Grade 11 Bio Notes PDF

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