Biology of the Cell - BIO 14 LEC - A.Y. 2024-2025 PDF

BIO 14 LEC Biology of the Cell A.Y. 2024-2025 | 1st Semester Cell Cycle and Cell Division Cell Division Process where parent cell divides to form two daughter cells Prokaryotic cell division is simpler then eukaryotic cell division ○ Prokaryote → singular circular chromosome,...

BIO 14 LEC Biology of the Cell A.Y. 2024-2025 | 1st Semester Cell Cycle and Cell Division Cell Division Process where parent cell divides to form two daughter cells Prokaryotic cell division is simpler then eukaryotic cell division ○ Prokaryote → singular circular chromosome, no nucleus, and few organelles ○ Eukaryote → multiple chromosomes, nucleus, organelles All parts are duplicated then separated as cell divides Cell Cycle Repeating series of events including growth, DNA synthesis, and cell division Asexual Reproduction ○ In prokaryotes → cell grows, DNA replicates, cell divides Eukaryotic Cell Cycle 1. Mitotic Phase (M) → mitosis and cytokinesis ○ When nucleus and cytoplasm divide 2. Interphase (G1, S, and G2) ○ Cell grows, performs life processes, prepares to divide Interphase Growth Phase 1 (G1) Cell spends most of time here Rapid growth and performs routine functions Biosynthetic and metabolic activities occur at a high rate Synthesis of amino acids and proteins ○ Including those needed for DNA replication If cell is not dividing, the cell enters the G0 phase G0 Phase Resting phase; cell has left the cycle and stopped dividing Cells may remain here for a long time → such as neurons ○ Also cells that are completely differentiated Cellular senescence ○ Cell stops dividing due to issues of sustainability or viability of daughter cells ○ Such as DNA damage or degredation ○ Occurs when normal diploid cells lose ability to divide → after 50 cell divisions Cells are in quiescent stage → inactive Synthesis Phase (S) DNA replication BIO 14 LEC Biology of the Cell A.Y. 2024-2025 | 1st Semester ○ Both strands of double helix is used as templates for two new complementary strands ○ Strands hydrogen bond to template strands and two double helices form Amount of DNA has doubled, but the cell remains a diplod Sister chromatids are produced → attached at the centromere Centrosomes are duplicated during S phase ○ Consists of a pair of rod-like centrioles composed of tubulin and other proteins ○ Sit at right angles to one another Mitotic spindle → two resulting centrosomes ○ Orchestrates movement of chromosomes during mitosis Growth Phase 2 (G2) Shortened growth period where organelles are reproduced or manufactured Parts necessary for mitosis and cell division Cell replenishes energy stores Cytoskeleton is dismantled to give resources for mitotic spindle Mitotic Phase Cell division occurs through mitosis and cytokinesis Mitosis Multi-phase process where nucleus divides Nuclear envelope/membrane breaks down and then reforms Chromosomes are sorted and separated to ensure complete set BIO 14 LEC Biology of the Cell A.Y. 2024-2025 | 1st Semester Prophase Chromatin condenses into chromosome, becoming visible with its identical partner → sister chromatid X-shape is formed Nucleolus disappears, as well as nuclear envelope Centrioles → origin point for microtubules, pair of centrioles: centrosome Centrosomes move apart as microtubules extent Thus, Mitotic spindle is formed from the centrosomes and microtubules Kinetochore → protein structure on centromere that attaches mitotic spindle and sister chromatids → prometaphase Metaphase Sister chromatids and microtubules line up in the middle of cell Metaphase plate → plane through the center of spindle, where sister chromatids are positioned Microtubules are ready to pull apart chromatids and bring one to opposite side of cell Anaphase Sister chromatids are separated, forming individual chromosomes again Pulled to opposite ends as the microtubules shorten Two new daughter cells contain identical genetic material Telophase Formation of two new daughter nuclcei Surround genetic material as it uncoils to chromatin Nucleoli reappears with new nuclei Mitotic spindle breaks apart Cell is beginning to split in half Cytokinesis Also occurs in prokaryotes Cytoplasm divides and two daughter cells form In Animal Cells ○ Contractile ring forms inside plasma membrane at the metaphase plate → composed of actin filaments ○ Cleavage furrow is formed In Plant Cells ○ New cell wall must form because cleavage furrow is not possible → due to rigid cell walls ○ During interphase, Golgi apparatus accumulates enzymes, structural proteins, and glucose molecules before being divided BIO 14 LEC Biology of the Cell A.Y. 2024-2025 | 1st Semester ○ During telophase, golgi vesicles move on microtubules and collect on metaphase plate ○ Cell plate is formed → fused vesicles ○ Cell plate enlarges until it merges with cell well ○ Enzymes use accumulated glucose to build new cell wall with cellulose ○ Golgi membranes become plasma membrane on the sides of the cell wall Control of the Cell Cycle Controlled by regulatory proteins ○ Signals cell to start or delay the next phase of the cycle ○ Ensure that previous phase is completed Key checkpoints ○ G1 checkpoint → before S phase, decides if cell is big enough to divide Aka restriction point If not, the cell goes to G0 ○ DNA synthesis checkpoint → S checkpoint determines if DNA was replicated properly ○ Mitosis Checkpoint → ensures chromosomes are aligned before cell division Aka spindle checkpoint Will not proceed until kinetochores are firmly anchored to spindle fibers of opposite sides Cancer and the Cell Cycle Occurs when cell cycle is not regulated; due to damaged DNA ○ Resulting in mutations in the genes regulating cell cycle Can occur due to exposure to radiation or toxic chemicals Cancer cells divide faster ○ May form a mass of abnormal cells → tumor ○ Take up nutrients and space ○ Can damage tissues and organs, leading to death When in bone marrow, abnormal blood cells are produced HeLa Cells From Henrietta Lacks, a cancer patient Taken without her knowledge to a researcher Her cells continued to divide, copies are still used worldwide BIO 14 LEC Biology of the Cell A.Y. 2024-2025 | 1st Semester Meiosis Process producing haploid genes Cell division in which chromosome number is halved Only occurs in special cells Homologous chromosomes separate and haploid cells are formed Composed of Meiosis I and Meiosis II Meiosis I Prophase I homologous chromosomes pair up ○ In mitosis and meiosis II, they do not form pairs Crossing-over of chromosomes occurs Metaphase I Spindle fibers attach to chromosome pairs and line up on the equator ○ In mitosis and meiosis, sister chromatids line up Anaphase I Spindle fibers shorten and pairs separate to opposite poles Telophase I and Cytokinesis Spindle breaks down and new nuclear membranes form Cytoplasm divides and two haploid daughter cells are created Go on to meiosis II ○ DNA does not replicate between meiosis I and meiosis II BIO 14 LEC Biology of the Cell A.Y. 2024-2025 | 1st Semester Meiosis II Prophase II Nuclear envelope breaks dorn and spindle forms in each haploid daughter cell Centrioles begin to separate Metaphase II Spindle fibers line up the sister chromatids of each chromosome along the center Anaphase II sister chromatids separate to opposite poles Telephose II and Cytokinesis Spindle breaks down and new nuclear membrane forms Cytoplasm divide and four haploid cells are formed Cellular Differentiation Development Zygote → product of sperm meeting egg, single cell Axes → head vs tail During development, zygote grows into body with axes and organs ○ Different cell types are also produced Basic Processes of Development Number of cells increase through division Body axes must form Tissues, organs, and structures must form Individual cells acquire cell type identities → differentiation Sources of Information in Development 1. Intrinsic information (lineage) ○ Inhereted from mother cell via cell division ○ Cell inherits molecules telling it that it belongs to the nerve cell-producing lineage of the body 2. Extrinsic information (positional) ○ Information received from cell’s surroundings ○ Chemical signals from a neighbor, instructing it to become a photoreceptor Differentiation, Determination, and Stem Cells Cells become more restricted in development potential ○ Type of cells made through cell division becomes fewer Totipotent → gives rise to wide range of cells (ex. zygote) BIO 14 LEC Biology of the Cell A.Y. 2024-2025 | 1st Semester Pluripotent → restricted in development potential Germ Layers a. Mesoderm Lungs, skeletal muscle, endothelial cell, cardiac muscle, red blood cell b. Endoderm Lining of digestive tract, columnar epithelial cell, liver cell c. Ectoderm Skin, central nervous system, hair, epithelial cells, neuron Process of Cell Status a. Specified → has certain fate but able to switch given the right cues b. Determined → irreversibly committed to a certain fate c. Differentiate → stable, final identity Adult Stem Cells Some cells retain the ability to produce multiple cell types Multipotent → adult stem cells Undergo asymmetric cell division ○ Two daughter cells that are different from one another ○ One daughter remains a stem cell through self-renewal ○ The other takes on a different identity Meristems Centers of cell division and growth ○ In animals, totipotent stem cells differentiate into any tissue type in the early stages of development ○ In plants, these are present their whole lives Apical Meristems ○ Located at the ends of shoots → shoot apical meristem ○ Located at the roots → root apical meristem ○ Produces three types of primary meristems Protoderm → makes epidermis, surrounding the plant Ground meristem → ground tissue with functions in photosynthesis, storage and support Procambium → vascular tissue, functions in transport Lateral Meristems or Secondary Meristems ○ Result in secondary growth, a woody increase in girth ○ Vascular cambium Arises from procambium and pericycle in roots In stems, arises from procambium cells of vascular bundles → fascicular cambium BIO 14 LEC Biology of the Cell A.Y. 2024-2025 | 1st Semester And parenchyma cells between vascular bundles → interfascicular cambium Gives rise to secondary phloem (part of the bark) and secondary xylem (wood) ○ Cork Cambium Arises form pericycle in roots and parenchyma cells of the cortex in stems Produces periderm, secondary dermal tissue (part of bark) Intercalary Meristems → elongate stem from the middle, in between nodes Marginal Meristems → located along leaf edges for leaf development Central Dogma of Molecular Biology DNA AND RNA: NUCLEIC ACIDS DNA and RNA Nucleic acids that carry out cellular processes, especially the regulation and expression of genes Key Terms ○ Nucleotide → monomer comprising DNA or RNA molecules; consists of nitrogenous heterocyclic base of purine or pyrimidine, a five-carbon pentose sugar, and a phosphate group ○ Genome → cell’s complete genetic information packaged as a double-stranded DNA molecule ○ Monomer → relatively small molecule which can be covalently bonded to form a polymer Types of Nucleic Acids DNA ○ Genetic material in living organisms ○ Found in nucleus, chloroplast, and mitochondria of eukaryotes ○ In prokaryotes, DNA is free-floating within cytoplasm ○ In eukaryotes, combines with histone proteins to form chromatin Substance of chromosomes RNA ○ Involved in protein synthesis ○ In eukaryotes, DNA uses messenger RNA to communicate with rest of cells ○ Other RNA: rRNA, tRNA, microRNA Nucleotides Monomers of DNA and RNA Made up of the following a. Nitrogenous base b. Pentose or five-carbon sugar BIO 14 LEC Biology of the Cell A.Y. 2024-2025 | 1st Semester c. Phosphate group Carbon numbering in pentose sugar ○ Numbered 1′ to 5′ ○ Base attached to 1′ carbon ○ Phosphate attached to 5′ carbon Polynucleotide Formation ○ 5′ phosphate of incoming nucleotide attaches to 3′ hydroxyl group of growing chain Types of Pentose Sugars 1. Deoxyribose (in DNA) → has an H at the 2′ position 2. Ribose (in RNA) → Has an OH at the 2′ position Nitrogenous Base Contain carbon and nitrogen Contain amino group that binds extra hydrogen ○ Decreases hydrogen ion concentration ○ Makes the environment more basic Adenine, Guanine, Cytosine, Thymine ○ Adenine, guanine → purines; two carbon-nitrogen rings ○ Cytosine, thymine, uracil → pyrimidine; single carbon-nitrogen ring Phosphate Group Attached to hydroxyl group of the 5’ carbon of one sugar and hydroxyl group of 3’ carbon → 5’3’ phosphodiester linkage ○ Formation involves removal of two phosphate groups DNA Double Helix Twisted staircase with sugar and phosphate backbone surrounding complementary nitrogen bases Key Terms ○ Mutation → error in base pairing during DNA replication ○ Sugar-phosphate backbone → outer support of ladder; strong covalent bonds between monomers of DNA ○ Base pairing → AT and GC Double Helix Structure Sugar and phosphate backbone Nitrogenous bases bound by hydrogen bonds Antiparallel orientation → strands of helix run in opposite directions BIO 14 LEC Biology of the Cell A.Y. 2024-2025 | 1st Semester DNA Replication Each strand is copied Forms a daughter DNA double helix with one parental DNA strand and one new strand DNA Packaging Key terms ○ Nucleosomes → subunit of chromatin; composed of two turns of DNA wrapped around eight histones ○ Histones → chief protein component of chromatin; spool where DNA winds Eukaryotic and Prokaryotic Cells Eukaryotic → Well-defined nucleus ○ DNA wrapped around histones to form nucleosomes ○ Nucleosome links to each other using Linker DNA ○ Heterochromatin → tightly packed region ○ Euchromatin → less dense region Prokaryotic → Chromosome lies in cytoplasm in the nucleoid ○ DNA is twisted by supercoiling → either under-wound or over-wound ○ Proteins involved in supercoiling ○ Proteins and enzymes maintain supercoiled structure: DNA gyrase Types of RNA Key Terms ○ Codon → sequence of three adjacent nucleotides; encodes for a specific amino acid during protein synthesis or translation ○ Transcription → synthesis of RNA under direction of DNA RNA Structure and Function Nitrogenous base pairings are different: AU and GC Types of RNA 1. Messenger RNA ○ Carries code out of nucleus to ribosomes for assembly of proteins 2. Transfer RNA (tRNA) ○ Translates information from mRNA ○ Reads codon sequences and form amino acids 3. Ribosomal RNA ○ Ribosome → holds all players in position and facilitates base pairings ○ Ribosomal RNA function inside ribosome BIO 14 LEC Biology of the Cell A.Y. 2024-2025 | 1st Semester CENTRAL DOGMA: GENES TO TRAITS DNA Encodes mRNA and mRNA Encodes Protein Transcription → DNA to mRNA Translation → mRNA to amino acid Genetic Code is Universal and Redundant Codons → three nucleotide segments 64 possible combination ○ 61 codons code for one of the 20 common amino acids ○ 3 codons are stop codons or nonsense codons ○ AUG is also a start codon → initiates translation Genetic code is universal → proof that life shares a common origin Genetic code is redundant → more nucleotide triplets than amino acids ○ Reduces negative impact of mutations MUTATIONS Point Mutation Single base changed in DNA sequence 1. Missense Mutation ○ Causes different amino acid to be inserted in the protein ○ Sickle-cell disease 2. Nonsense Mutation ○ Changes a codon into a stop codon 3. Silent Mutation ○ Changing a codon to another codon, but same amino acid is produced Frameshift Mutation Insertion or deletion of extra base pairs from a gene Very big consequences BIO 14 LEC Biology of the Cell A.Y. 2024-2025 | 1st Semester Chromosome Mutations Large-scale mutation at chromosome level Deletion, duplication, inversion, translocation ○ Deletion and duplication cause serious problems ○ Inversions and translocation are often not problematic → but may cause problems during reproduction Results of Mutations 1. Beneficial 2. Neutral 3. Deleterious TRANSCRIPTION Process of making an RNA copy of a gene Mediated by RNA polymerases ○ Synthesized in a 5’ → 3’ direction Template strand → template to create complementary copy of DNA Coding strand → nearly identical to RNA copy Initiation site → first nucleotide pair in DNA; where first RNA nucleotide is transcribed ○ Also known as the +1 site ○ Nucleotides before initiation site are given negative numbers and designated upstream ○ Nucleotides after are given positive numbers and designated downstream Three stages: initiation, elongation, termination Initiation of Transcription Promoters ○ Specifies where to begin transcription and which DNA strand to copy ○ Exist upstream of the genes they regulate ○ Sequence determines if gene is transcribed all the time, sometimes, or infrequently ○ TATA box → in prokaryotes, -10 region where promoter binds ○ Sigma → subunit of RNA polymerase, binds to -35 sequence Initiation Complex Transcription factors → in eukaryotes, regulates frequency of transcription Initiation complex → transcription factors and RNA polymerase bound to promoter Transcription bubble → region of unwinding of DNA for RNA synthesis Transcription Elongation RNA polymerase synthesizes mRNA in 5’ to 3’ direction; 40 nucleotides per second BIO 14 LEC Biology of the Cell A.Y. 2024-2025 | 1st Semester Transcription Termination Polymerase dissocate from DNA template and new mRNA In prokaryotes, two kinds of termination signals a. Rho-dependent termination Controlled by rho protein Tracks behind polymerase on growing mRNA chain Near end of gene, polymerase encounters run of G nucleotides and stalls Rho protein collides with polymerase and releases mRNA from transcription bubble b. Rho-independent termination Controlled by sequences on DNA template strand Polymerase encounters region rich in C-G nucleotides mRNA folds back on itself and the C-G nucleotides bind together Hairpin is produced and causes polymerase to break away