BIO01 PDF - Cell Biology Overview

CO1 Overview of the cell Information - the traits onto offspring Membrane - are built of structures called cell Metabolism - Digestion , break down of particles to tiny particles Growth - Development Reproduce - Multiply “cloning” asexual reproduction Homeostasis - Maintains balance Are viruses c...

CO1 Overview of the cell Information - the traits onto offspring Membrane - are built of structures called cell Metabolism - Digestion , break down of particles to tiny particles Growth - Development Reproduce - Multiply “cloning” asexual reproduction Homeostasis - Maintains balance Are viruses considered living or nonliving - They are in a gray line - Neither living or non living ( requires a host to live ) - Are proteins with a genetic material The levels of organization ( simplified ) ( abiotic - environment , biotic - living things ) - Cellular level - Organism level - Population level - Population - Community - Ecosystem WHAT ARE CELLS Cells - smallest unit of life (exhibits the the characteristics of life ) THE DISCOVERY OF CELLS Robert Hook - invented the microscope , coined the name cell form cellula - Discovered dead cells from observing the cork board Antonie Van Leeuwenhoek - increase the magnification of the cell - Saw alive cells The Cell Theory (Subcellular Structures and Organelles) - Cell is basic unit of life - All life forms are made of one or more cells - Cells come from preexisting cells GENETIC MATERIAL  - Every Cell contains DNA as genetic material - DNA contains genes PROKARYOTES Contain single circular molecule of DNA found near the center of the cell called the nucleoid ( Bacteria) - Small simple cells - Lack a nucleus - Lack a membrane-bound organelles Parts: Cell wall - provide support and protection Capsule - outer gelatinous covering Pili - cell attachment to surfaces and other cell Flagellum - mobility EUKARYOTES Contain DNA organized into linear chromosomes segregated into nucleus that is surrounded by a nuclear envelope ( Plant Cell and Animal Cell ) Cytoplasm - (cytosol (fluid part) found only in EUKARYOTES) semifluid that fills the inside of the cell contains sugars , amino acids and proteins Membrane bound organelles - compartmentalization in eukaryotes Ribosomes - composed of RNA and proteins that synthesize all cellular proteins - The protein synthesis machinery - Made of two subunits (large and small) made of RNA and proteins Free Ribosomes - floating in the cytoplasm , synthesizes proteins found in the cytoplasm Membrane associated ribosomes - synthesize proteins in the endomembrane systems Organelles - is the structure inside a cell surrounded by a plasma membrane Plasma Membrane - encloses a cell and separates its contents from it surroundings ( defines cell boundaries and retains contents ) - Regulate transports of materials into and out of the cell - Cell recognition , connection and adhesion , cell communication Nucleus - (roughly spherical) Information center of the eukaryotic cell (has the genetic material/contains genetic information ) largest organelle within eukaryotic cell (located in the central region of the cell) - Site of DNA replication and transcription in eukaryotes Parts: Nucleolus - where ribosomes are made , site of ribosomal RNA synthesis Nuclear Envelope - two phospholipid bilayer membranes Nuclear pores - holes where nutrients pass through , regulate the passage of molecules between nucleus and cytoplasm Chromatin - loose Chromosome - compact Endomembrane System - Series of membrane throughout the cytoplasm - Divides the eukaryotic cell into the compartments - Different functions (connected to each other) - Channels the passage of molecules through the cell interior - Synthesizes Lipids and proteins Endoplasmic Reticulum - Largest internal membrane - Composed of phospholipid bilayer - Characterized by cisternae( flattened) Types: Rough endoplasmic reticulum (blue structure) (produces protein) - Ribosomes attached to its surface ( protein synthesis) - Site of synthesizing proteins meant for export - After protein is receive RER performs initial glycosylation (glycosylations - adds short chain carbohydrates) -connected RER sa Nuclear Envelope (they receive…. ) Functions of RER - Protein synthesis in the attached ribosome - Initial glycosylation of proteins - Proper folding of proteins Smooth Endoplasmic Reticulum (green structure) - Lack bound ribosomes - Synthesis of lipids (steroid,hormones,membrane fluid) - Stores calcium ions - Detoxification of organic molecules Golgi Apparatus ( cisternae) - Composed of two phase (cis phase and trans phase) - Collects the products of (RER and SER) and distributes - Modifies proteins and lipid (performing glycosylation final - Synthesis of cell wall components Vesicles - packaging of the products of golgi apparatus The Functions of Golgi Complex - Glycosylation of glycoproteins and glycolipids - Synthesis of most of the cells complex polysaccharide - Modification of proteins in the RER Protein Transport through Endomembrane System (located in the RER but pinched off and delivers to the golgi apparatus ) - Proteins and Lipids manufactured on the SER and RER are transported into the golgi apparatus and modified as they pass through it Cis phase - receives the transport vesicles Trans phase - packages the product (secretory vesicles delivers to the outside of the cell ) Lysosome - digestive vesicles (contains acid hydrolases - can degrade macromolecules (organelles) when contact is made ) ( repair (breakdown) by degrading damage old organelles and recycle their component molecules ) Peroxisome - performs oxidation for fatty acids ( secretes hydrogen peroxide “toxic”) cointains catalyst(catalase) that decomposes hydrogen peroxide Central vacuole (plant cell) - helps maintain osmotic balance and tonicity - Specialized membrane-bound structure found in plant cells - Breakdowns macromolecules - Detoxifies foreign substances Cellular Generators Similarities (Mitochondria and Chloroplast ) - Double membrane (walls) - Contains their own DNA(circular) and protein synthesis machinery (they make their own )(ribosomes) - Energy metabolism (generate energy) Mitochondria (folded inner) (all cells) Two membranes - Outer (smooth ) - Inner (folded) ( cristae - numerous contiguous layers ) - intermembrane space (between outer and inner(folded) membrane - Matrix (located DNA and Ribosomes) - Synthesize ATP(adenosine triphosphate) energy that cells use to process,converts chemical energy stored in chemicals bonds of macromolecules into a form that is more useful and readily used by cells ( electricity to power a house) - ATP from macromolecules  - Outer membrane many holes so food molecules can enter so mito can process to produce atp Chloroplast smooth - Found in plant cell only - Difference between chloroplast ( organelles) and chlorophyll (pigment of the plant) - Thylakoid disc shaped light capturing photosynthesis (location chlorophyll nakasiksik) - Stacks of thylakoid (grana) (granum-singular) - Stroma fluid matrix (part) (where DNA, Enzymes and Ribosomes are located) - Chloroplast- collect solar energy to produce food= glucose/carbohydrates - Proceed to mitochondria to be process into atp Endosymbiont theory - believed some of the organelles in eukaryotic cells were once prokaryotic microbes Cytoskeleton - a network of protein fibers that support the shape of the cell(made of protein fibers) , anchor organelles to fixed location Types of fiber composing the cytoskeleton - Actin Filaments (Microfilaments) - responsible for cell movement - Microtubules - moving materials within the cell (organize the cytoplasm) - Intermediate Filaments - provide structural stability Centriole ( found in animal cells but not in plants cells) - Centrosome region surrounding the pair - made of microtubules in pairs ( each centriole composed of 9 (triplets of microtubules)) - Help organize microtubules Flagella and Cilia - (extension like hair) aid of the movement of certain particles Plant cell wall - provides protection and support , made of carbohydrate polymers Parts: Primary Cell wall -is thin provides flexibility and allow cell to increase in size ( made of cellulose , hemicellulose , glycans and pectin ) Secondary Cell Wall - formed between the primary cell wall and the plasma membrane ( made from successive layers of strong cellulose ) EXTRACELLULAR STRUCTURES Extracellular matrix - collagen fibers and elastin fibers embedded within the complex web of glycoproteins that form a protective layer over the cell surface - Provide animal cells strength to present tearing - Structural support in cells that move - Scaffold where cells can organize - Cell signaling CO2 Cell cycles - a series of events involving growth synthesis , and regulations in a cell that results in cell division Cell Divisions - Reproduction - A parent cell produces daughter cells PROKARYOTIC CELL DIVISION Binary Fission - process in which bacteria reproduce themselves Clonal - each cell produced by cell division is an identical copy of the original cell Steps EUKARYOTIC CELL DIVISION DNA strand collects histones and produce nucleosomes which then coils then supercoils then chromosome Chromosomes - Humans 46 chromosomes in 23 nearly identical pairs - Each 46 contains hundreds to thousands genes - Genes (traits) play an important role in determining growth , development and functions Autosomes - numbered chromosomes , numbered roughly in relation to their size Sex Chromosomes - determine the biological sex and sex linked traits Haploid - one set of chromosomes Diploid - twice the haploid , tidal number of chromosomes in a cell Homologous Chromosomes - are maternal and paternal copies of the same chromosomes Sister Chromatids - are replicas of single chromosomes held together at their centromeres by cohesion proteins(cohesin) KInetochore protein ( gilid ng sister chromatids) Karyotyping - test to examine chromosomes in a sample of cells. Karyotype - array of chromosomes an organism possess Cell Cycle G1 and G2 - interphase G1 - cell grows and carries out normal metabolism organelles duplicate ( cell size , nutrients , growth factor and DNA damage) G2 - cell grows and prepares for mitosis ( cell size and DNA damage ) S phase - DNA replication and chromosome duplication M phase - division phase ( mitosis , miosis and cytokinesis ) ( chromosomes attachment to spindle ) Eukaryotic Cell Cycle - five phases Interphase ( preparatory ) G1 ( GAP 1 Phase) - Primary growth phase of the cell - Cell performs normal functions - Cell organelles are duplicated - Cell grow - Longest phase S ( synthesis phase) - DNA replication G2 ( GAP 2 Phase ) - Second growth phase - Double checks replicated chromosomes for possible errors - Cell continues to prepare for mitosis - Cell produces proteins that help in sorting chromosomes M phase Mitosis - Nuclear division - Occurs in somatic cells - Parent cell produced two new daughter cells ( genetically identical) - Distribute duped chromosomes - Five stages Cytokinesis - Division of the cytoplasm - Result of two daughter cells from one parent cell STAGES OF MITOSIS Prophase - Chromosomes condense ( visible ) - Appear as two sister chromatids held together at the centromere - Cytoskeleton disassembles - Spindle fibers form - Golgi apparatus and ER disperse - Nuclear envelope breaks down Prometaphase - Chromosomes attach to microtubules at the kinetochore - Chromosomes move to the equator of the cell - Centrosomes move toward opposite poles Metaphase - All chromosomes are aligned at the equator (metaphase plate ) of the cell Anaphase - Proteins holding the centromeres of sister chromatids are degraded , freeing , individual chromosomes - Chromosomes are pulled to opposite poles  - Spindle poles move apart Telophase - Chromosomes are clustered at the opposite poles and decondense - Nuclear envelopes reform around chromosomes - Golgi apparatus and ER reforms - Spindle is disassembles Cytokinesis - Animal cell , cleavage furrow forms to divide cell - Plant cell , cell plates forms to divide cell Importance of mitosis - Necessary for growth and development of an organism - Needed to form more complex structure in an organism such as tissues and organs - Necessary when an organism needs new and genetically identical cells to replace those that are already old , lost and or damage MEIOSIS - type of cell division that occurs in gametes - a parent cell produces 4 daughter cells that are genetically unique from each other - occurs after a cell finishes the stages of the interphase - has two divisions: Meiosis I Meiosis II MEIOSIS I Prophase I - Chromosomes begin to condense. - Spindle fibers begin to form. - Each chromosome consists of two sister chromatids attached at the centromere. - Homologous chromosomes form a bivalent through a process called synapsis - Crossing over occurs in the chiasmata. SYNAPTONEMAL COMPLEX - joins homologous chromosomes (paired homologues, each composed of two sister chromatids) - forms bivalent or tetrad - ( It's like a zipper that holds the chromosomes together so they can exchange genetic material (crossing over)) GENETIC RECOMBINATION - crossing over - allows homologues to Exchange chromosomal material - occurs in the chiasmata Metaphase I - Pairs of homologous chromosomes randomly align at the equator of the cell. - Chiasmata keep homologous pairs together.  - A kinetochore microtubule from one pole of the cell attaches to one homologue of a chromosome, while a kinetochore from the other pole attaches to the other homologue of a pair. Anaphase I - Kinetochore microtubules shorten. - Homologous pairs are pulled apart. - Sister chromatids do not separate. Telophase I - The separated homologues form a cluster at each pole of the cell. - Nuclear envelope re-forms around each daughter cell. - Cytokinesis may occur. - Resulting cells have half the number of chromosomes of the original cell. MEIOSIS II Prophase II - New spindle fibers form in each cell. - Nuclear envelope breaks down. Metaphase II - Chromosomes consisting of sister chromatids joined at the centromere align along the equator (metaphase plate) of each cell. - Kinetochore microtubules from opposite poles attach to kinetochores of sister chromatids. Anaphase II - Kinetochore microtubules shorten. - Sister chromatids are pulled to opposite poles of the cells. Telophase II - Nuclear membranes reform. - Cytokinesis occurs and four haploid cells are formed. - No two cells are alike due to the random alignment of homologous pairs at metaphase I and crossing over during prophase I. CANCER - Anything that damages DNA, such as environmental factors or UV radiation in sunlight, can lead to mutations. - Random mutations arise with each round of DNA replication. If a gene is mutated that encodes one of the proteins involved in cell division, this can lead to uncontrolled growth. - acquired condition - characterized by uncontrolled cell division - may arise from exposure to carcinogens - initially diagnosed via the presence of a tumor BENIGN TUMOR - excessive proliferation - does not spread to other parts of the body MALIGNANT TUMOR - can metastasize PROTO-ONCOGENES - normal cellular genes that become oncogenic when mutated - only one allele needs to be mutated TUMOR-SUPPRESSOR GENES - normal cellular genes that when mutated can lead to cancer - both alleles lose function p53 GENE - tumor-suppressor gene which encodes the p53 protein - “guardian of the genome” ✓ involved in the G1/S checkpoint ✓ promote DNA repair ✓ promote programmed cell death (apoptosis) - When a mutation removes p53 gene function, the cell can proceed through the cell cycle with damaged DNA, leading to further mutations that lead to cancer CO3 UNCOMPLETE Diffusion: The movement of molecules from an area of higher concentration to an area of lower concentration. Simple Diffusion: The movement of molecules across a selectively permeable membrane from an area of higher concentration to an area of lower concentration. It does not require energy input. Facilitated Diffusion: The movement of molecules across a selectively permeable membrane from an area of higher concentration to an area of lower concentration with the help of a transport protein. It does not require energy input. Osmosis: The movement of water across a selectively permeable membrane from an area of higher water concentration to an area of lower water concentration, or from an area of lower solute concentration to an area of higher solute concentration. Osmolarity: The relative total solute concentration inside or outside the cell. Kinetic Energy: The energy of motion. Equilibrium: A state where there is no net movement of molecules across a membrane because the concentration of the molecules is the same on both sides. Action Potential Propagation: The transmission of an action potential down the axon of a neuron. Trigger Zone: The area of a neuron where action potentials are initiated. Axon Terminal: The end of an axon where neurotransmitters are released to communicate with other neurons. Erythrocyte Plasma Membrane: The cell membrane of a red blood cell. Capillaries: Tiny blood vessels that connect arteries and veins.  Carbonic Acid (H2CO3): A weak acid formed by the reaction of carbon dioxide and water. Chloride-Bicarbonate Anion Exchange Protein (Antiporter Carrier Protein): A membrane protein that transports chloride ions into the red blood cell and bicarbonate ions out of the cell. Transport Proteins: Membrane proteins that facilitate the movement of molecules across the membrane. Conformational Change: A change in the shape of a protein. Hydrophilic Channel: A channel in a membrane protein that allows water-soluble molecules to pass through. Carrier (Transporters or Permeases) Proteins: Proteins that bind to specific molecules and transport them across the membrane. Channel (Pores) Proteins: Proteins that form channels through the membrane, allowing specific molecules to pass through. Bulk Transport: Requires energy! The movement of large quantities of molecules across the membrane in vesicles. Exocytosis: The process by which a vesicle fuses with the plasma membrane and releases its contents outside the cell. Endocytosis: The process by which the plasma membrane folds inward to form a vesicle that brings molecules inside the cell. Permeability: The ease with which a substance can cross the membrane. Electrochemical Gradient: The combination of the electrical gradient and the concentration gradient that drives the movement of ions across the membrane. Electrical Gradient: The difference in electrical potential across the membrane. Concentration Gradient: The difference in concentration of a molecule across the membrane. Resting Membrane Potential: The electrical potential difference across the plasma membrane of a cell when it is not actively signaling. Passive Transport: The movement of molecules across the membrane without the input of energy. Examples include simple diffusion and facilitated diffusion. Active Transport: The movement of molecules across the membrane from an area of lower concentration to an area of higher concentration, against the concentration gradient. It requires energy input from ATP. Unassisted Movement Down the Gradient: The movement of molecules across the plasma membrane without the assistance of proteins. Fluid Mosaic Model: A model of the cell membrane that describes it as a fluid bilayer of phospholipids with embedded proteins. Membrane Lipids: Lipids that make up the cell membrane. Glycerophospholipids (Phospholipids): The most abundant type of lipid in the cell membrane, consisting of glycerol, a phosphate group, and two fatty acid chains. Glycerol: A three-carbon alcohol. Phosphate Group: A negatively charged group. Fatty Acid Chains: Long chains of hydrocarbons.  Amphipathic/Amphiphilic Molecule: A molecule with both hydrophilic and hydrophobic regions. Polar Head: The hydrophilic region of a phospholipid molecule. Non-polar Tail: The hydrophobic region of a phospholipid molecule. Diacylglycerol Kinase: An enzyme that catalyzes the phosphorylation of diacylglycerol to phosphatidic acid. Diacylglycerol: A glycerol molecule with two fatty acid chains attached. Phosphoric Acid: A strong acid and a phosphate group. Phosphatidic Acid: A key intermediate in the synthesis of phospholipids and triacylglycerols. Membrane Proteins: Proteins that are embedded in the cell membrane. Proteins: Polymers of amino acids. Polymers of Amino Acids (Polypeptide): A chain of amino acids linked together by peptide bonds. Alpha Carbon: The central carbon atom in an amino acid. Amino Group: A nitrogen-containing group (-NH2). Carboxylic Acid Group: A carbon atom double-bonded to an oxygen atom and single-bonded to a hydroxyl group (-COOH). Residue (Side Chain): The portion of an amino acid that determines its properties. Peptide Bond: The covalent bond that links amino acids together in a polypeptide chain. Transport: The movement of molecules across the membrane. Transmembrane Protein Channels: Channels formed by proteins that span the membrane. Ion Channels: Channels that allow the passage of ions across the membrane. Porins: Channel proteins that allow the passage of small molecules. Aquaporins: Channel proteins that allow the passage of water. K+ Channel: A type of ion channel that allows the passage of potassium ions. Active Transport: The movement of molecules across the membrane from an area of lower concentration to an area of higher concentration, against the concentration gradient. It requires energy input from ATP. Protein-Mediated Movement Up the Gradient: The movement of molecules across the membrane against the concentration gradient with the assistance of transport proteins. Acid Anhydride Bond: A bond that forms between two carboxylic acid groups. High Energy Bond: A bond that releases a significant amount of energy when it is broken. Phosphorylated Forms of Adenosine: Forms of adenosine that have been modified by the addition of phosphate groups. Hydrolysis: The breakdown of a molecule by the addition of water. Synthesis of ATP: The process of generating ATP from ADP and inorganic phosphate. Proton Ion Gradient: A difference in the concentration of protons across the membrane. ATPase: An enzyme that catalyzes the hydrolysis of ATP. Na+/K+ ATPase Pump (Antiporter): A membrane protein that transports sodium ions out of the cell and potassium ions into the cell. It requires ATP to function.