Biology Primer CEER 2024 PDF

CEER 2024 BIOLOGY PRIMER Cell - The basic structural and functional unit of all living organisms. Cell —> Tissue—> Organ—> System—>Organism PROKARYOTES EUKARYOTES Revised Cell Theory...

CEER 2024 BIOLOGY PRIMER Cell - The basic structural and functional unit of all living organisms. Cell —> Tissue—> Organ—> System—>Organism PROKARYOTES EUKARYOTES Revised Cell Theory No membrane bound Membrane bound nucleus nucleus 1. All organisms are composed Cell walls made of Cell walls, if present, is of cells. peptidoglycan made of cellulose (chitin in 2. The cell is the basic unit of fungi) life. 3. All cells come from No membrane bound Membrane bound organelles organelles pre-existing cells. (compartmentalization) Prokaryotic vs. Eukaryotic Cells Have pili & fimbriae (for Have cilia or flagella (for adhesion) and flagella movement) Prokaryotic cell - a single celled organism (for propulsion) that does not contain a nucleus. single -celled Single-celled or multicellular Eukaryotic cell - a more complex cell (e.g., plant and animal cells) that Single circular Multiple linear chromosome chromosome contains nucleus and many other organelles. Cell Organelles Cell wall – rigid layer that protects and encloses the cell (plant cells and some Cell (plasma) membrane –phospholipid bacteria) bilayer that protects and encloses the cell; controls transport; maintains homeostasis Chloroplast– captures solar energy for photosynthesis (plant cells, some algae) Cytoplasm – fluid-like substance that contains various membrane-bound Vacuole – stores substances structures (organelles) that perform various functions **Nitroplast (new discovery, this 2024)- for nitrogen-fixation, formed via primary Cytoskeleton –provides internal structure endosymbiosis Ribosome – produces proteins Building Blocks of Life Nucleus – contains DNA which controls 1. Carbohydrates - organic compounds cellular activities made up of carbon, hydrogen, and oxygen. Endoplasmic Reticulum– site of chemical reactions (production of proteins, - Monosaccharides, metabolism and transportation of lipids, and disaccharides, detoxification of poisons) polysaccharides - ROUGH: contains ribosomes 2. Lipids - class of large biomolecules that are not formed through - SMOOTH: lipid production polymerization. Golgi Body – packages, distribute products - They have diverse structures but are all Lysosomes– digest excess products and non-polar --- hydrophobic food particles behavior Mitochondria – transform energy through Functions: respiration Energy storage  Cushioning of vital organs Types: and for insulations Diffusion - movement of Important role in plasma substances across the plasma membrane structure membrane from an area of high concentration to an area of low 3. Proteins - account for more than concentration 50% of the dry mass of most cells, and they are instrumental in almost Facilitated transport - a carrier everything organisms do. molecule embedded in the plasma membrane transports a Functions: substance across the plasma speed up chemical reactions membrane following the Defense high-to-low concentration Storage gradient Transport cellular communication Osmosis - diffusion of water Movement across the plasma membrane structural support from areas of high concentration to areas of lower concentration 4. Nucleic acids - polymers made of monomers called nucleotides. 2. Active transport - movement of substances across the plasma - store, transmit, and help membrane that requires the use of the express hereditary cell’s energy and carrier molecules; information substances are moving from an area of low concentration to an area of higher - DNA, RNA, Proteins concentration (against the concentration gradient) Transport Mechanisms in Cells Types: 1. Passive transport - movement of Endocytosis - large particles substances across the plasma are brought into the cell membrane without the use of the cell’s Phagocytosis - "cellular energy (with the concentration gradient) eating"  Pinocytosis - "cellular ribose sugar, and drinking" three phosphate groups. Exocytosis - large particles leave the cell Cellular Respiration Equation: Homeostasis - internal equilibrium; the C6H12O6 + 6O2 --> 6CO2 + 6H2O + plasma membrane regulates what enters Chemical Energy (in ATP) and leaves the cell; a selectively permeable membrane only allows certain substances or to pass through C6H12O6 (glucose) + 6O2 (oxygen) → Effect of Concentration on a cell 6CO2 (carbon dioxide) + 6H2O (water) + Chemical Energy (in ATP) Hypotonic – water moves in; cell bursts Stages: Hypertonic – water moves out; cell shrivels 1. Glycolysis (anaerobic) Isotonic – no net movement a. Location: cytoplasm/cytosol b. What happens: glucose is broken down into pyruvate Cellular Respiration c. Function: plays a key role in the way organisms extract - series of chemical reactions that energy from nutrients convert glucose into energy (ATP) d. Net yield per glucose necessary to power various molecule: 2 ATP, 2 Pyruvate, reactions inside the body 2 NADH - Adenosine triphosphate 2. Citric Acid Cycle/Krebs Cycle (ATP) is a molecule that acts (aerobic) as the primary energy carrier a. Location: mitochondrial in cells during cellular matrix respiration. b. What happens: pyruvate is - ATP is made up of further broken down, CO2 is three parts: a nitrogenous base,  released, NADH & FADH2 c. Function: produces the are produced largest amount of ATP, c. Function: produces ensures efficient energy high-energy electron carriers extraction from nutrients (NADH and FADH2) that are d. Net yield per glucose used in the next step molecule: 26-28 ATP, water d. Net Yield per glucose molecule: 6 NADH, 2 Photosynthesis FADH2, 2 ATP, 4 CO2 3. Oxidative Phosphorylation, Electron - the process by which plants use Transport Chain and Chemiosmosis sunlight, water, and carbon dioxide (aerobic) to create oxygen and energy in the a. Location: inner mitochondrial form of sugar. membrane - CO2 enters and O2 leaves b. What happens: the leaf (organ) through i. Electron Transport microscopic pores called Chain- NADH and stomata. FADH2 donate - Chloroplast: The site of electrons to the ETC, photosynthesis in plants. This cell which are passed organelle is found in plant cells and through a series of contains chlorophyll, a protein complexes. green-coloured pigment. Proton gradient is - In plants, chloroplasts are created found particularly in the ii. Chemiosmosis- parenchyma cells of the leaf Protons flow back into mesophyll (the internal cell the mitochondrial layers of a leaf). matrix through ATP synthase, driving the synthesis of ATP from Stages: ADP and inorganic phosphate 1. Light dependent reactions  a. Location: Thylakoid through an electron membrane transport chain (ETC) b. What happens: Solar energy that includes is converted into chemical cytochrome b6f and energy in the form of ATP plastocyanin. and NADPH which fuels the b. This movement of Calvin cycle for the synthesis electrons releases of glucose and other energy that pumps carbohydrates. H2O is protons (H+) from the splitted, releasing O2. stroma into the c. The light-dependent thylakoid lumen. reactions, through linear c. The proton gradient electron flow, convert light created is used by energy into chemical energy ATP synthase to in the form of ATP and generate ATP through NADPH. a process called photophosphorylation The Stages of linear electron flow in. the light-dependent reactions of 3. Reduction of NADP+ photosynthesis: a. Electrons from PSI are further excited 1. Photosystems Absorb Light and passed to Energy ferredoxin, then to a. Photosystems, like ferredoxin-NADP+ Photosystem II (PSII) reductase, which and Photosystem I reduces NADP+ to (PSI), capture light NADPH. energy using b. This process pigments in the produces NADPH, thylakoid membrane. which carries 2. Electrons Move Down the high-energy electrons Electron Transport Chain for use in the Calvin a. In PSII, high-energy cycle. electrons are passed  Cell Division 2. Calvin Cycle (also known as the Comparison between Mitosis & Meiosis Light-independent reactions) a. Location: Stroma MITOSIS MEIOSIS b. What happens: Plants use carbon dioxide, along with Chromosom 2n n the energy from ATP and es NADPH produced in the light-dependent reactions, to Synapsis None Prophase I produce glucose and other (Zygotene) carbohydrates. Crossing-ov Rare Prophase I The light-independent reactions of er (Pachytene) the Calvin cycle can be organized Metaphase Chromosom Tetrads into three basic stages: es align align 1. Fixation - Carbon dioxide (metaphase from the air combines with a I); sister 5-carbon molecule (RuBP) to chromatids form a 6-carbon compound, now which quickly splits into two considered 3-carbon molecules. as 2. Reduction - The 3-carbon chromosom molecules (3-PGA) receive es align energy from ATP and (metaphase electrons from NADPH, II) turning into a sugar called DNA 1 During G3P. Replication interphase I 3. Regeneration - Some of the only G3P molecules are used to remake the original 5-carbon # of division 1 2 molecule (RuBP) with the (reductional help of ATP.  & nuclear envelope fragments equational) Metaphas Spindle fibers from centriole # of 2 (each 4 (each e attach to the centromere daughter diploid is haploid (n)); Chromosomes gradually cells 2n); genetically migrate to the midline of the genetically non-identica cell (equatorial plate) oriented identical to l to mother between the two centrioles mother cell cell and to each other Anaphas Begins with the separation of e the centromere Cell type Somatic Gametes Spindle fibers will pull cells centromeres toward centrioles Mitosis Homologous chromosomes move to opposite poles Poles of cells move apart Stage Main Events Telophas The two sets of Interphas G1: growth, metabolic e chromosomes reach the e activity, organelles begin to opposite poles where they double begin to uncoil S: DNA replication, Telophase ends with chromosome duplication cytokinesis (cellular division) G2: growth and formation of two Prophase Chromosomes coil and daughter cells condense Nucleus contain diploid Centrioles divide and spindle number of cells apparatus appears Chromosomes have no apparent orientation in the cell Nucleolus disappears and Meiosis Telophase The spindle apparatus I continues to separate the Stage Main Events homologous chromosomes until they reach the Interphase Same in mitosis poles. Each pole now has a Prophase I Synapsis: homologous haploid chromosome chromosomes come side set. by side to form a tetrad. Prophase Spindle apparatus forms Crossing-over: homologous II and the chromosomes chromosomes progress toward the exchange segments at metaphase II plate intersections called Chiasmata. Metaphase Chromosomes align at the II center Anaphase The centromeres of sister II chromatids separate. Each sister chromatid now becomes individual chromosomes. Telophase Nuclei begin to form at II opposite poles. Metaphase Chromosomes are now There are now four daughter I arranged in metaphase cells. Each with a haploid plates, still in homologous number of chromosomes. pairs. Anaphase Homologous chromosomes I migrate to opposite poles. Sister chromatids still intact. DNA RNA - Deoxyribonucleic acid- carries the - Ribonucleic acid genetic instructions for the - Function: gene expression, development, functioning, growth, regulation, protein synthesis and reproduction - Function: for storage and Structure (single helix) transmission of genetic information, replication, and protein synthesis 1. Nitrogenous bases a. Pyrimidines: Uracil (U), Structure (double helix): Each nucleotide Cytosine (C) unit is composed of: b. Purines: adenine (A),guanine (G) 1. Nitrogenous bases c. Base-pairing rule: A-U, C-G a. Pyrimidines: thymine (T), 2. Phosphate- Links the ribose sugars cytosine (C) together b. Purines: adenine (A),guanine 3. Ribose sugar- has an extra hydroxyl (G) group compared to deoxyribose in c. Base-pairing rule: A-T, C-G DNA 2. Phosphate- Links the sugars together 3. Deoxyribose sugar Types of RNA 1. Messenger RNA (mRNA)  a. Function: Carries genetic Central Dogma of Molecular Biology information from DNA to the ribosomes for protein synthesis. b. Role: Involved in transcription and translation processes. 2. Transfer RNA (tRNA) a. Function: Brings amino acids to ribosomes during protein synthesis. b. Structure: Cloverleaf shape 1. DNA Replication with an anticodon region that a. DNA → DNA pairs with the corresponding b. Process: codon on mRNA. i. Initiation: Helicase 3. Ribosomal RNA (rRNA) unwinds the DNA a. Function: Forms the core of double helix, creating the ribosome’s structure and a replication fork. catalyzes protein synthesis. ii. Elongation: DNA b. Role: Together with proteins, polymerase adds rRNA forms the ribosomes. complementary nucleotides to each original strand, forming two new strands. iii. Termination: The replication process completes, resulting in two identical DNA molecules. 2. Transcription a. DNA → RNA b. Process:  i. Initiation: RNA the ribosome polymerase binds to according to the the promoter region mRNA codon of DNA and starts sequence. Peptide unwinding the DNA bonds form between strands. amino acids, creating ii. Elongation: RNA a growing polypeptide polymerase chain. synthesizes the RNA iii. Termination: The strand by adding RNA ribosome reaches a nucleotides stop codon, which complementary to the does not code for an DNA template strand. amino acid. The iii. Termination: RNA completed polymerase reaches polypeptide chain is a terminator released, and the sequence, and the ribosome newly formed RNA disassembles. molecule is released. 3. Translation Patterns of Inheritance a. RNA → Protein b. Process: Gene: A segment of DNA that encodes a i. Initiation: The specific protein or function. ribosome assembles Allele: Different versions of a gene. around the mRNA and the first tRNA, Genotype: The genetic makeup of an which carries the start individual (combination of alleles). amino acid (methionine) and Phenotype: The physical expression of the recognizes the start genotype (observable traits). codon (AUG). ii. Elongation: tRNAs bring amino acids to Dominant Allele: An allele that expresses its trait even in the presence of a different 4. Polygenic Inheritance allele. Pattern: Traits are controlled by multiple genes. Recessive Allele: An allele that expresses Characteristics: Results in a continuous its trait only when two copies are present. range of phenotypes. Examples: Height, skin color. 1. Codominance Pattern: Both alleles in a heterozygous 5. Multifactorial Inheritance individual are fully expressed. Pattern: Traits are influenced by multiple Characteristics: Results in a phenotype that genes and environmental factors. shows both traits equally. Characteristics: Complex traits that do not Examples: ABO blood group system (AB follow simple Mendelian inheritance. blood type). Examples: Heart disease, diabetes, obesity. 2. Incomplete Dominance Mendel’s Law of Heredity Pattern: The heterozygous phenotype is intermediate between the two homozygous 1. Law of Segregation phenotypes. Definition: Each individual has two alleles Characteristics: Results in a blending of for each gene, which segregate during traits. gamete formation so each gamete receives Examples: Snapdragon flower color (red, only one allele. white, pink). Key Points: 3. Mitochondrial Inheritance (Maternal Alleles separate during meiosis. Inheritance) Gametes carry only one allele for each Pattern: Genes are passed from mother to gene. offspring through the mitochondria in the Offspring inherit one allele from each egg. parent. Characteristics: Affects both males and females, but only females pass the trait to Example: Crossing heterozygous pea plants their children. (Pp) results in a 3:1 ratio of purple Examples: Leber’s hereditary optic (dominant) to white (recessive) flowers in neuropathy (LHON). the offspring. 2. Law of Independent Assortment markers, and gene editing to Definition: Genes for different traits assort develop new products. independently during gamete formation. Key Points: Genetic Engineering - sometimes Inheritance of one trait does not affect called biotechnology inheritance of another. Applies to genes on different chromosomes - process of transferring a or far apart on the same chromosome. gene (DNA) from one Results in genetic variation. organism to another Example: Crossing pea plants with different - Organisms with transferred traits (seed shape and color) results in a gene now produce 9:3:3:1 phenotypic ratio in the F2 “recombined” genetic code ( generation. called “recombinant DNA”) - Ex: insulin produced Biotechnology through bacteria - Ex: oil-eating bacteria - Has - A technology that uses biological application in medicine, systems, living organisms, or environment, industry, derivatives thereof, to develop or agriculture, selective modify a product or process for breeding specific purpose (UN Convention on Biological Diversity, Art.2) Gene Editing - precise method used - Traditional biotechnology - to alter the DNA sequence of an methods are primarily organism. Targeted cuts in the DNA focused on plant and animal are made, allowing for the addition breeding, and fermentation or deletion of bases that code for that uses microbes to specific genetic functions. produce wine, beer, yoghurt, Examples of Techniques: etc. 1. CRISPR-Cas 9 - utilizes - Modern biotechnology - guide RNA to direct the Cas9 involves the application of enzyme to a specific DNA molecular techniques, such sequence for cutting as recombinant DNA 2. TALENS - uses technology, molecular custom-designed proteins to  bind specific DNA sequence and create double-strand Developed by: Carl Linnaeus breaks Format: Two-part scientific name (Genus 3. Zinc Finger Nucleases species), e.g., Homo sapiens (ZFNs) - employs engineered Importance: Provides a standardized zinc finger proteins to naming system, reducing confusion. recognize and bind specific DNA sequences, paired with 3. Domains of Life nucleases to cut the DNA. Bacteria: Unicellular prokaryotes with Taxonomy and Classification peptidoglycan cell walls. Archaea: Unicellular prokaryotes without Taxonomy is the science of classifying peptidoglycan, often in extreme organisms based on shared characteristics. environments. Eukarya: Unicellular and multicellular 1. Taxonomic Hierarchy eukaryotes (includes Protista, Fungi, Plantae, Animalia). Levels: Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species 4. Kingdoms Mnemonic: "Dear King Phillip Came Over For Good Soup" Bacteria: Corresponds to the domain Species: The most specific level, Bacteria. representing a group of individuals that can Archaea: Corresponds to the domain interbreed and produce fertile offspring. Archaea. Protista: Mostly unicellular eukaryotes, Example: Taxonomic hierarchy of humans diverse group. Fungi: Unicellular or multicellular Kingdom – Animalia, Phylum- Chordata, eukaryotes, heterotrophic, with chitin cell Class- Mammalia, Order – Primates, walls. Suborder – Haplorhini, Family – Hominidae, Plantae: Multicellular eukaryotes, Subfamily – Homininae, Genus – Homo, autotrophic, with cellulose cell walls. Species – Homo sapiens Animalia: Multicellular eukaryotes, heterotrophic, without cell walls. 2. Binomial Nomenclature 5. Modern Classification Systems Phylogenetics: Classification based on evolutionary relationships and genetic information. Cladistics: Method of classification based on common ancestry, using cladograms to show relationships.