Bio Sci 93 Notes PDF

Bio Sci 93 Lec 1 Structural organization of cells 1. Atoms (O, H, C) a. Foundation 2. Molecules (lipids, proteins, etc) a. Formed by combinations of atoms 3. Cells a. Formed by combinations of molecules Cell compositions 1. Water (70-95%) 2. carbon-based...

Bio Sci 93 Lec 1 Structural organization of cells 1. Atoms (O, H, C) a. Foundation 2. Molecules (lipids, proteins, etc) a. Formed by combinations of atoms 3. Cells a. Formed by combinations of molecules Cell compositions 1. Water (70-95%) 2. carbon-based molecules (the rest)\ 3. Elements a. Can’t be broken down into other substance (they are composed by only one type of atom) b. 92 elements, 25 essential for life i. 96% of living matter is made from 4 elements: 1. C, O, N, H (S, Ca, K, P ~ 4%) ii. Trace elements (Fe, I, Zn, Cu) 4. Atoms: smallest unit of chemical elements a. Use chemical bonds to combine and form molecules and compounds i. Strong bonds (intramolecular) 1. Covalent: sharing of electrons by two atoms a. non polar: equal sharing of electrons b. Polar: unequal sharing of electrons 2. Ionic: transfer of electrons between two atoms ii. Weak bonds (intermolecular) 1. Hydrogen bond: the H atom forms a covalent bond with another atom in the same molecule where it is present, and a second weaker bond (the hydrogen bond) with an atom in another molecule a. 5. Molecules: two or more atoms combined 6. Compounds: molecules made up of two or more elements combined in a fixed ratio a. Sodium, chlorine, sodium chloride (table salt) NaCl Cohesion Molecular structure and chemical properties of water 1. Composed of H and O 2. Two H atoms covalently bonded to one O atom 3. Polar covalent bonds: electrons are not shared equally a. O attracts electrons, it has a partial negative charge b. H has a partial positive charge (H+) 4. The structure of water provides special function properties  a. Cohesion: interactions between water molecules i. Formation of hydrogen bonds between water molecules 1. H and O of adjacent water molecules ii. Maximum of 4 partners b. Solvent: interactions between water and other molecules i. Formation of hydrogen bonds between water and other charged molecules ii. NaCl iii. Na+: bonds with water O iv. Cl-: bonds with water H 1. Solvent: A substance in which another substance dissolves 2. Solute: a dissolved substance 3. Solution: mixture of solute and solvent 5. Solid and liquid water a. Solid water (ice): hydrogen bonds are stable b. Liquid water: hydrogen bonds break and reform 6. Hydrophilic and hydrophobic substances a. Hydrophilic substances: i. Affinity for water - substances with polar covalent or ionic bonds that can form hydrogen bonds with water ii. Ex: NH3, NaCl, proteins with ionic or polar regions b. Hydrophobic substances i. Repel water: non polar covalent bonds ii. Lipids: dominant bonds C-C and C-H with equal sharing of electrons Dissociation of water molecules and pH 1. Water can dissociate into a hydrogen ion and hydroxide ion: a. Pure water: b. Biological solutions: 2. Acids increase the proton [H+] concentration of a solution a. (CIH ←→ Cl-) hydrochloric acid dissociation in water 3. Bases decrease the proton [H+] concentration of a solution a. (NH3 + H+ ←→ NH4+ + OH-, then OH- + H- ←→ H2O) Buffers 1. Chemical processes taking place in cells are sensitive to pH changes a. Buffers: resist change in pH solution i. Donate H+ when the solution is depleted of H+ (acids) ii. Donate OH- or accept H+ when there is an excess of H in the solution (bases) b. Human blood: pH 7.4 i. Buffered by carbonic acid and bicarbonate ii. Maintaining blood pH between 7.37 and 7.43 creates an optimal environment for cellular enzyme activity and membrane integrity Lec 2 Cell composition 1. Water (70-90%) a. Carbon based compounds (rest) i. Carbon-carbon bond ii. Carbon bonded to other elements 1. H, O, N, S, P 2. Carbohydrates, lipids, proteins, and DNA Carbon atoms 1. Building blocks of biological molecules 2. Carbon atom has 4 valence electrons 3. Can form 4 covalent bonds Molecular Diversity of Carbon compounds 1. Carbon chains form the skeleton of most organic compounds 2. Large variation in the arrangement of the carbon skeleton a. Diversity in length, # branches, double bonds, ring structure Chemical Groups 3. Properties of an organic molecule also depend on the chemical groups attached to the carbon skeleton a. Various chemical groups can replace one or more hydrogens of a hydrocarbon b. They help give each molecule its unique properties and are directly involved in chemical reactions i. thus also known as functional groups 4. Hydroxyl group a. Compound name: alcohol i. Polar due to electronegative oxygen ii. Forms hydrogen bonds with water 5. Carbonyl group a. Compound name: ketone or aldehyde i. Sugars with ketone groups are called ketosis; those with aldehydes are called aldoses 6. Carboxyl group a. Compound name: carboxylic acid or organic acid i. Acts as an acid 7. Amino group a. Compound name: amine i. Acts as a base  8. Sulfhydryl group a. Compound name thiol i. two–SH groups can react, forming a “cross-link” that helps stabilize protein structure 9. Methyl group a. Compound name: methylated compound i. Affects the expression of genes ii. Affects the shape and function of sex hormones 10. Phosphate group a. Compound name: organic phosphate i. Contributes negative charge ii. When attached, confers on a molecule the ability to react with water, releasing energy Chapter 5: Carbon based molecules 1. Polymer: long molecule built from similar subunits (monomers) linked by covalent bonds a. Carbohydrates, proteins. Nucleic acids 2. Lipids a. Diverse group of hydrophobic molecules b. Built from two or more different types of smaller subunits 1. Carbohydrates: central to the chemistry of life a. Simplest carbohydrates are monosaccharides: i. Vary in location of carbonyl group (e.g. aldose vs. ketose) ii. Vary in length of carbon skeleton (e.g. 3, 5, 6 are common) b. Glucose is the main fuel of cellular respiration c. Carbon skeletons serve as raw material for synthesis of other molecules including amino acids and fatty acids 2. Lactose a. Present in milk and products made from milk (cheese and ice cream) b. Lactose intolerance:  i. Without the enzyme, lactose passes into the colon where it feeds bacteria that generate gas and fluid resulting in bloating, cramps, and diarrhea 3. Polysaccharides a. Polymers of 100s-1000s of monosaccharides i. Structure: 1. Cellulose (cell in plants) b. Energy storage i. Starch (in plants) ii. Glycogen (animals) 1. Starch and glycogen are polymers of glucose 4. Lipids a. Diverse group of hydrophobic molecules i. Built from two or more different types of smaller subunits b. Hydrophobic i. Nonpolar C-H covalent bonds c. Three forms i. Fats ii. Phospholipids iii. Steroids d. Fats: glycerol combines with 3 fatty acid chains i. Saturated fats (lard, butter) 1. No C=C double bounds ii. Unsaturated fats ( oils, margarine) 1. C=C double bonds 5. Hydrogenated fats and trans fats a. Hydrogenated fats i. Synthetically converted to saturated fat by adding hydrogen], allowing them to solidify (peanut butter) ii. Process of hydrogenating oils can produce trans fat 6. Phospholipids a. Glycerol + two fatty acids + phosphate group + choline 7. Steroids a. Carbon skeleton with 4 rings and varying functional groups b. Cholesterol  i. Component of membrane ii. Precursor of all other steroids including testosterone and estrogen Hydroxyl groups are characteristics of alcohol The electronegativity of nitrogen means that amino groups tend to pick up hydrogen ions Thiols are characterized by the presence of a sulfhydryl group Phosphate groups are a component of ATP Play a major role in energy transfer By donating hydrogen ions, carboxyl groups act as an acid Lec 3 : Macromolecules 2: Proteins and Nucleic Acids Proteins 1. Function a. Support, storage, transport, signaling, receptors, movement, catalysis, defense i. Enzymatic proteins: 1. Function: selective acceleration of chemical reactions 2. Ex: digestive enzymes catalyze the hydrolysis of bonds in food molecules ii. Defensive proteins 1. Function: protection against disease 2. Ex: antibodies inactivate and help destroy viruses and bacteria iii. Storage proteins 1. Function: storage of amino acids 2. Ex: casein- the protein of milk, is the major source of amino acids for baby mammals iv. Transport proteins 1. Function: transport of substances 2. Ex: hemoglobin-the iron containing protein of vertebrate blood-transport oxygen from lungs to other parts of body v. Hormonal proteins 1. Function: coordination of an organism’s activities 2. Ex: insulin, a hormone secreted by the pancreas, causes other tissues to take up glucose, thus regulation blood sugar concentration vi. Receptor proteins 1. Function: response of cell to chemical stimuli 2. Ex: receptors build into the membrane of a nerve cell direct signaling molecules released by other nerve cells 2. Structure a. Amino acids: monomers, combine to form polymers b. Polypeptide: polymer of AAs in specific sequence c. Protein: one or more polypeptides with specific #-D conformation i. Amino acids → polypeptides → proteins Structure of amino acid 1. Amino group 2. Hydrogen 3. Carboxyl group 4. R group: variable side chain a. Nonpolar; hydrophobic (9/20) b. polar ; hydrophilic (6/20) c. ionized (charged at cellular pH)  i. Acids and bases ii. Hydrophilic (5/20) 5. Formation of polypeptides a. AA are joined by dehydration reactions i. Peptide bond (covalent) b. Polypeptide i. Amino end 1. N terminus ii. Carboxy end 1. C terminus iii. Few to thousands of monomers(aa) Conformation of proteins Structures 1. Primary structure a. Determined by AA sequence b. Effect of single change in primary structure can have pleiotropic consequences 2. Secondary structure a. Hydrogen bonding by atoms in the polypeptide backbone (N-H- - - -O=C) i. Alpha helix (coils) ii. Beta pleated sheets (folds) 3. Tertiary structure (overall shape of polypeptide) a. R group interactions i. Weak: 1. Hydrogen bonds 2. Ionic bonds 3. Hydrophobic 4. Van der waals interactions ii. Strong 1. Disulfide bridges (covalent) 4. Quaternary structure a. Overall protein structure resulting from combined polypeptides: i. 2 or more ii. Stabilized by R group interactions Conformation is influenced by environment 1. Influenced by: a. pH b. High salt conc. c. Temperature Proteasome degradation 1. Damaged or misfolded proteins are actively degraded a. Tagged with ubiquitin (kiss of death) b. Delivered to proteasomes c. Proteases chop proteins into short peptides for recycling  i. Abnormal proteasomal degradation is associated with serious clinical conditions such as cancer, cystic fibrosis and neurodegenerative diseases Sickle cell anemia 1. Caused by a. Single based change in DNA b. Single base change in mRNA c. Single AA change in protein Nucleic Acids 1. Function a. Store and transmit hereditary information 2. Structure a. Polymers of nucleotide monomers b. Nucleotide monomers i. Pentose sugar ii. Nitrogen base iii. Phosphate group 3. Two types of nucleic acids a. Deoxyribonucleic acid (DNA) i. Double stranded ii. Nitrogen bases: C, G, A, T iii. Deoxyribose sugar iv. Phosphate group b. Ribonucleic acid (RNA) i. Single stranded ii. Nitrogen bases: C, G, A, U iii. Ribose sugar iv. Phosphate group Sugar-phosphate backbone of polynucleotides 1. Polynucleotides (nucleic acid polymer) a. Sugar connected to phosphate group of adjacent nucleotide i. Phosphodiester linkage (dehydration reaction) b. Backbone: sugar-phosphate units c. Side chains: nitrogen bases i. Purines: two rings ii. Pyrimidines: one ring Macromolecules, polymers, and monomers 1. Macromolecules consist of carbohydrates, proteins, and nucleic acids a. Polymer: long molecule made up of many similar or identical building blocks(monomers) linked by covalent bonds  i. ii. Enzymes: specialized macromolecules (usually proteins) that speed up chemical reactions 1. Condensation reaction: reaction that connects a monomer to another monomer or a polymer a. Two molecules are covalently bonded to each other with the loss of a small molecules Lec 4: Single Cell Dynamics Plasma membrane components 1. Thin barrier: 8nm thick 2. Composition a. Lipids i. Phospholipids are amphiphile or amphipathic molecules; They form the membrane bilayers ii. Cholesterol regulates membrane fluidity b. Proteins i. Embedded in bilayer ii. Regulate traffic across the membrane c. Carbohydrates i. On extracellular surface of the membrane ii. Important in cell-cell recognition iii. Also glycoproteins and glycolipids 3. Membrane proteins can diffuse laterally The cellular membrane is fluid 1. Evolutionary adaptations provide adequate fluidity in extreme environments 2. Some organisms change the lipid composition of the cell membrane “on demand” a. Phospholipids drift laterally in the plane of the membrane b. Held together by weak hydrophobic interactions 3. Cholesterol stabilizes the fluidity of the membrane a. Reduces membrane fluidity at moderate temps but at low temps Lec 6: Membrane function, active transport Crossing 1. Traffic across the plasma membrane is selectively permeable a. Osmosis: diffusion of water across a permeable membrane i. Direct passage through lipid bilayer ii. Passage mediated by transport proteins 1. Passive transport 2. Active transport iii. Vesicular transport or bulk transport 2. Direct passage through lipid bilayer a. Hydrophobic molecules like steroids b. Small hydrocarbons, nonpolar molecules (gasses like CO2, O2) c. Diffuse down the concentration gradient (no energy) 3. Passage mediated by transport proteins a. Hydrophilic, charged ions, larger molecules b. Specific transport protein for each substance c. Passive (no energy) or active (require energy) i. Passive: facilitated diffusion ii. Active: electrogenic pump (generates a voltage across the membrane, maintains high intracellular K+ and low Na+) 4. Two forms of glucose transport in animal cells a. Facilitated diffusion i. [glucose] inside cell < [glucose] outside cell ii. Transport protein (specific for glucose) iii. No energy used b. Co transported with Na+ i. No transported into cell ii. Glucose co-transported 5. Passage mediated by vesicular transport (large molecules like proteins and carbohydrates) a. Endocytosis i. Vesicle formed from the plasma membrane ii. Bringing external molecules inside cell b. Exocytosis i. Internal membrane vesicle fuses with plasma membrane ii. Releases molecules to outside iii. Types: 1. Phagocytosis 2. Pinocytosis 3. Receptor-mediated endocytosis c. Receptor mediated endocytosis i. Ex: uptake of cholesterol 1. Human cells need cholesterol 2. Cholesterol travels in blood (LDL: low density lipoproteins ) 3. Stimulates endocytosis Lec 7 Cytoskeleton in eukaryotic cells 1. A network of fibers, extending throughout cytoplasm a. Structural support i. Mechanical support ii. Anchors internal cellular components b. Motility (interaction w/ motor proteins) i. Movement of cell from place to place ii. Movement within the cell c. Structural elements of cytoskeleton i. Microfilaments (MF) ii. Microtubules (MT) iii. intermediate filaments (IF) 2. Cytoskeleton elements a. Composed of subunits (polymers composed by monomers) b. Polarized (MT and MF) i. They display + and a - end c. Dynamic structures i. Rapid assembly and disassembly (MF and MT) ii. IF are more stable MF function 1. Cell shape a. Structure: ex: microvilli increase the absorbing area of intestinal cells; shape maintained by MF b. Intracellular transport of cellular components over short distances (with myosin motor proteins) c. Cell motility (crawling) d. Contraction of muscle: actin and myosin (motor proteins) i. Crawling movement: mediated by the interaction of myosin motors and microfilaments and the alternate polymerization and depolymerization of MF in different regions of the cytoplasm Intermediate filaments 1. Supercoiled into thick cables 2. Different types of IF with different subunits depending on cell type (e.g. keratins, neurofilaments, etc) a. Function: i. Cell shape, resist tension ii. Cell and nuclear anchorage iii. Formation of nuclear lamina  1. Lamin is the IF that forms the nuclear lamina 2. Lamin mutations cause accelerated aging in humans (progeria) Microtubules 1. Structure a. Hollow cylindrical rods b. Made of tubulin dimers c. Cytoplasmic tubules grow out from centrosome i. + end, growing tip ii. - end, near the centrosome or MTOC 2. Function a. Cell shape and organization of cytoplasmic components b. Track for movement of cellular components i. Vesicle and organelle movement (long distances) ii. Chromosome movement during cell division iii. Requires interaction with motor proteins c. Kinesins (move towards the + end of the MT) d. Dyeins (move toward the - end of MT) Motor proteins move cargoes along MT tracks 1. Bind to the cargo and the cytoskeletal polymer 2. Adapter region that is specific for each cargo (mitochondria, lysosomes, vesicles, etc) 3. Changes in protein shape result in movement a. Dyneins move toward minus(-) end microtubules b. Kinesins move toward plus(+) end microtubules Requires energy for movement (ATP): Motor proteins are ATPases Microtubules in cilia and flagella 1. Function in movement of appendages a. In unattached cells, they move cells from one place to another b. In attached cells they move fluid over tissue i. Ex: the ciliated lining of the digestive tract helps move substances from one location to another Extracellular matrix 1. Animal tissues have a complex extracellular matrix mainly composed of glycoproteins (secreted by the cells) a. Most abundant: collagen fibers 2. Integrins in the plasma membrane link ECM proteins such as fibronectin with the cellular cytoskeleton a. Facilitating the crosstalk between the cell and its environment Mitochondria and chloroplasts 1. Energy transformers of cell 2. Enclosed in membranes but not part of the rest of the cell’s endomembrane system 3. Semi Autonomous  a. grow and reproduce within the cell 4. Location in cell is not fixed a. move around the cytoplasm using cytoskeletal tracks Peroxisomes 1. Membrane bound organelle formed by proteins and lipids in the cytosol (not part of the endomembrane system) a. Breaks down fatty acids b. Detoxify alcohol and other poisons 2. Compartmentalization a. Byproduct is H2O2 (hydrogen peroxide)-toxic b. Produces enzyme to convert H2O2 to H2O Lec 8: Nucleus, Ribosomes, Endomembrane system Nucleus 1. Contains the genetic library of eukaryotic cells a. Chromatin: DNA and associated proteins (histones) i. Synthesis of messenger RNA (mRNA) ii. Nucleus: synthesis of ribosomal RNA (rRNA) - formation of ribosomal subunits 2. Enclosed by a double membrane a. Nuclear pores composed of nucleoporins b. Mediate transport in and out of the nucleus i. Substances that travel through the pores have tags called nuclear localization signals that allow them to pass through the pore complexes Ribosomes: synthesize proteins 1. Composed of rRNA combined with cytosolic proteins a. 2 subunits, large and small 2. Free ribosomes a. Synthesize cytosolic proteins 3. Bound ribosomes (to the rER) a. Synthesize integral membrane proteins and secreted proteins Endoplasmic reticulum 1. Continuous with nuclear envelope a. Membrane tubules b. Cisternae: internal membrane stracks 2. Smooth ER: rich in metabolic enzymes a. Ribosome free b. Large portion of sER in specialized cells i. Synthesis of lipids (eg. phospholipids) - gonads (ovary and testis) synthesis of steroid hormones ii. Metabolism of carbohydrates - liver: breakdown of glycogen iii. Detoxification of drugs and poisons - liver: metabolization of toxic substances iv. Calcium sequestration: 1. In muscle cells: regulation of calcium stores that mediate muscle contraction 2. In secretory cells: calcium regulates vesicle secretion a. Gonad (sex gland or reproductive gland): is a mixed gland that produces the gametes (sex cells) and sex hormones of an organism, in the female of the species the reproductive cells are the egg cells and in the male the reproductive cells are the sperm 3. Rough ER a. Ribosomes attached to outer membrane  b. Processing proteins synthesized by Er-bound ribosomes i. Secreted proteins 1. Enter cisternal space (through special pores) 2. Protein folding, processing 3. Transported in lumen of vesicles ii. Membrane proteins 1. Synthesized and inserted into membrane, folding and processing 2. Transported in membrane of vesicles c. Membrane factory i. Synthesize phospholipids from precursors in the cytosol ii. Membrane transferred in vesicles to other organelles or cell membrane Golgi Apparatus: finishes, sorts, and ships 1. Flattened membranous sacs a. Cisternae: internal space b. Cis face: receiving side c. Trans face: shipping side Lec 9: cell communication Cell communication 1. Essential for multicellular organisms a. Cells must communicate to coordinate their activities. b. Communication between cells is also important for many unicellular organisms. c. Cell signaling mechanisms have been highly conserved Cell signaling 4 types of signaling 1. Secreted signals that act lonely a. Paracrine signaling i. Growth factors b. Synaptic signaling i. Neurotransmitters 2. Secreted signals that act at distant sites: Hormones a. Travel to target cells at distant sites b. Animal cells: travel in circulatory system c. Plant cells: travel in vessels, cell to cell, or diffusion in air 3. Intracellular signals a. Important in adjacent tissue cells 4. Cell surface signals a. Important during development and for immune response Signal reception 1. Signal (ligand) binds to receptor a. Includes change in location/shape of the receptor 2. Receptors a. Plasma membrane proteins i. Ligands: secreted, hydrophilic, water soluble, or membrane bound b. Cytoplasmic or nuclear proteins i. Ligands: hydrophobic, lipid soluble Plasma membrane (or cell surface) receptors 1. G-protein-coupled receptor (GPCR)  a. Ligands include hormones, neurotransmitters b. Important in sensory reception i. Ex: vision, smell, taste 2. Tyrosine kinase receptors (TKR) a. Ligands are generally growth factors b. Can activate multiple cellular responses (different than G proteins) c. Abnormal TKR activation (even without ligands) are involved in different types of cancer 3. Ligand-gated ion channels a. Ligands: neurotransmitters b. Ions such as Na+ or Ca+ (depending on the receptor) flow in or out of the cell c. Important for communication between nerve cells d. Some are present in the membrane of organelles (ex: sER) 4. Intracellular receptors a. Ligands can directly cross the membrane bilayer b. Receptor in cytosol or nucleus Transduction 1. Two common mechanisms are a. Protein phosphorylation cascades b. Second messengers (ex: calcium, IP3, or cAMP)