All Lectures of Biology 190
All Lectures of Biology 190 BIOL 190
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BIOL190: Biology for Health Professions Dr. Shah (Fall 2015) Lecture Notes (Lectures 1-24) DNA and Gene Expression (Lecture 1-4) Deoxyribonucleic Acid (DNA) 2 nucleotide strands twisted into a double helix o Each strand is made up of repeating nucleotide subunits o Each nucleotide contains a phosphate group (PO ),4glucose, nitrogen base o Strands oriented in opposite directions (anti-parallel) Base-Pairs link strands to each other: big base + small base o Hydrogen Bond o A--T (2 bonds) and G---C (3 bonds) Bases in DNA o Adenine (A) , Guanine (G) Purines (Big, Double-Ring) o Thymine (T) , Cytosine (C) Pyrimidines (Small, Single-Ring) o Sugar Phosphate backbone: directly held together with strong covalent bonds o Neighboring Bases are NOT directly linked by the sugar phosphate backbone o DNA is a double-stranded molecule where each strand is a chain of nucleotides Hershey and Chase Experiment Definitive demonstration that DNA is the genetic material Used a bacterial virus called T2 Phage (bacteriophage) that reproduces by infecting bacterial cells (E.coli) and the infection proceeded even if virus particles shaken off (blender) after brief attachment period How the experiment was carried out? o Prepared 2 separate batches of virus radioactively label DNA (CHONP) or Protein (CHONS) Method 32 35 o Virus: radioactive DNA : p/ Protein: S o 1. Infected bacterial cells o 2. Blender (shake off parts of virus that didn’t enter cells: “virus leftovers” o 3. Centrifuge cells = pellet, virus leftovers = liquid o Centrifugation: extended forces will be drawn down (example: sand and water) Results: The pellet after centrifugation (contains heavier bacterial cells) showed radioactive phosphorous labeled DNA ( p)2 Conclusion: since radioactive phosphorous was detected in bacterial cells pellet. It suggests that DNA was internalized in bacterial cells and hence- DNA is the genetic material o DNA must have entered into heavier bacterial cells o 3S was found in the liquid- so T2 Phage proteins must have stayed outside cells Watson and Crick Made a 3D model of DNA Strand Polarity: 5’ P4 end, 3’ sugar end Rosalind Franklin and Maurice Wilkens X-Ray Diffraction of DNA: From measurement Purines and Pyrimidines must be paired together to keep constant 2 nm helix width Erwin Chargaff: chemical analysis of DNA o Amounts of A=T, G=C in any as DNA sample o Order of A-T, G-C differed across samples o Proportions (%) of A-T, G-C differed in samples DNA Replication 2 ways cells use the genetic info stored in DNA: 1. Control: DNA controls cell structure/ function (Transcription and Translation) o Codes directly for all proteins in cells o Proteome: specific array of proteins in a given cell, determines cell make-up and what jobs it can do, ex. Carry O (red blood cells), fight disease ( white cells), contrast (muscle cells) 2 2. Heredity: complete copy of genetic info physically passed from generation (Replication) o DNA must be copied (replicated) replication of DNA o DNA copies passed on to offspring from 2 parents in sexual reproduction o Inherited through generations DNA replication: part of HEREDITY function of DNA o Cell division: 1 parent cell 2 daughter cells o Daughter cells are genetically identical to parent cell o Must copy cell’s DNA 2 copies (copying occurs in S-Phase of cell cycle) o DNA Replication is Semi-Conservative: Parental molecule in split in half with daughter o DNA Replication: the parental strands separate and serve as templates and 2 identical daughter molecules of DNA are formed DNA replication is semi-conservative o Covalently linked by DNA Polymerase (enzyme) o At origins DNA Strands begin to unwind and separate with the help from Helicase (enzyme) o DNA Polymerase can ONLY add new nucleotides at 3’ end, direction is always 5’ to 3’ o Separate fragments need to be linked (ligated) together covalently by DNA Ligase (enzyme) o Lagging Strand: new strand is made 5’3’ o Leading Strand: leading the synthesis o First thing in DNA replication is to unwind the strand with the enzyme, Helicase. DNA Polymerase which helps join the nucleotides during complementary pairing (links them covalently): synthesis in the 5’ 3’ and Ligase joins molecule Proofreading : DNA Polymerase o Removes any incorrect base pairing o Errors that remain – Gene mutations o Mutation: Permanent change in the DNA Base sequence Gene Expression: control role of DNA Influence of genetic info (in DNA) on cell structure and function o Through production of PROTEINS that make up the structure and carry out the function of the cell o Proteins are coded for by genes: segment of DNA in chromosomes Control role of DNA is NOT related to the heredity role of DNA Genes: segments of the DNA in each chromosome o Each chromosome has a different set of genes, often separated by non-coding regions of DNA o Each gene codes for a specific gene product in the cell: mostly protein; some RNA o Which part of the DNA structure carries the code? Sequence of Bases Requires 2 Processes: o DNA Transcription: copying of DNA info into RNA copies; Used to make mRNA, tRNA, rRNA; takes place in the nucleus where DNA is; Final RNA products then go to the cytoplasm o mRNA Translation: interpretation of mRNA code, synthesis of protein, take place in the cytoplasm, involves mRNA message, tRNA interpretation, and ribosomes (rRNA and ribosomal proteins) RNA Sugar: ribose , Bases: A , U , G , C (no T) , Single stranded DNA Replication DNA Transcription Occurs in synthesis (S) phase of cell cycle Occurs in preparation phase of cell cycle (G1 and G2) Enzyme- DNA Polymerase Enzyme- RNA Polymerase Both strands of DNA are template One strand of DNA is template Utilizes nucleotides – ATGC Utilizes nucleotides – AUGC Entire genome copied Only individual genes transcribed Product formed remains bound to parent DNA Products formed detach from DNA and goes to molecule cytoplasm Steps of DNA Transcription RNA Polymerase binds at ‘promoter’ region of TEMPLATE strand of gene RNA polymerase unwinds DNA locally as it moves along template; no helicase needed Free RNA- type nucleotide covalently to 3’ end of growing RNA molecule; RNA made in 5’3’ direction Process stops at terminator region, RNA comes off (many more copies made), DNA comes back together and rewinds into helix, RNA goes to the cytoplasm through nuclear pore ONLY a GIVEN GENE TRANSCIRBED, NOT WHOLE GENOME DNA Coding Each gene codes for a specific product molecule o A few genes code ribosomal RNA (rRNA) o Several genes code for transfer RNA (tRNA) o All other genes code for messenger RNA (mRNA) and each mRNA codes for a specific protein o mRNA, tRNA, rRNA all made by DNA transcription o mRNA, tRNA , rRNA all needed for protein synthesis (mRNA Translation) mRNA: messenger RNA Each mRNA molecule- made by DNA transcription of a particular protein- coding gene (in nucleus) Processed in nucleus o 5’ cap (modified G) and 3’ tail sequence (poly-A tail) added for mRNA o Introns (spacer regions) cut out o Exons (expressed regions) spliced together Goes out to the cytoplasm Brings the genetic info from one protein-coding gene to the cytoplasm o Coding units = ‘codon’ tRNA: transfer RNA tRNA molecule- made by DNA transcription of tRNA- coding genes (in nucleus) Go out to the cytoplasm Appropriate amino acid then attached to each tRNA at its amino acid binding site Requires a specific loading enzyme and ATP (energy) Anticodon of each tRNA complementary to specific codon in mRNA Base-Pairing of anticodon and codon allow tRNA to deliver amino acid to correct place during translation rRNA: ribosomal RNA rRNA molecule- made by DNA transcription from particular rRNA-coding genes (in nucleus) specific rRNA molecules then assembles with specific ribosomal proteins (brought in from cytoplasm) to form 2 subunits of ribosomes: Large and small ribosomal subunits Codon-Sequence of 3 Adjacent Nucleotides on a Strand Constitutes genetic code for specific amino acid that is to be added to polypeptide chain Codon Chart: mRNA o Specific, but o Redundant-same amino acid that is to be added to polypeptide chain o AUG= start (amino acid met = methionine) o UAA, UAG,UGA = STOP Codon to terminate protein synthesis Given an mRNA sequence, how do you translate it? Use the genetic code Record abbreviation of amino acid Find the start codon STOP when you reach a stop codon Mark off the triplet code DO NOT do anything with anticodons Look up each codon (in mRNA) in the “dictionary” Example: CGUCUAUG/UAU/GGC/CAU/GCC/CCA/UGA/UAC/G met tyr gly his ala pro STOP Translation (Protein Synthesis) Nucleic acid language to protein language Initiation Elongation Termination Translation- Initiation Formation of functioning complex o 1 (initiator) met- loaded tRNA binds to small ribosomal subunit o Small ribosomal subunit and tRNA met binds to beginning of mRNA o Small ribosomal subunit moves along mRNA until start codon (AUG) o Stops there b/c UAC anticodon on tRNA met base pairs with AUG in mRNA o Large ribosomal subunit then joins complex o A site is open ready for tRNA called for by codon in the A site Translation- Elongation (codon-anticodon interaction) Next tRNA amino acid diffuses in with its amino acid to dock at the next codon (A site) Correct tRNA amino acid comes in b/c its anticodon is complementary to codon in A site Previously added amino acid breaks off of the tRNA that brought it in and links covalently to the next amino acid o This is the actual synthesis step, catalyzed by peptidyl transfer enzyme in large ribosomal subunit The now empty tRNA in the P site diffuses away; will be reloaded for next job Ribosome moves along mRNA to the next codon (translocation) Process repeats itself Translation- Termination At stop codon o Release factor binds to stop codon, signaling end of translation o Complex disassembles: finished protein released into cell, empty tRNA falls out of the complex-will be reloaded for the next job, ribosomal subunits come apart- will be reused for further protein synthesis, Further ribosomes have come behind the first, make more copies of the same protein Protein Enzyme Function One of major function of protein: serves as enzymes o Enzymes speed up chemical reactions o Required for chemical reactions to run at body tempt./ in the cell Ex: chemical reaction to make RNA during DNA transcription If RNA polymerase gene is mutated, it may not be expressed properly or at all so no functional enzyme made! DNA codes for protein enzymes presence/absence of lipids/carbs (indirectly control over these molecules) How can gene expression change in cells? Level of Name Reversibility Description change Using vs. not Regulation of gene Reversible Cell can turn using the info expression: normal expression of process in cells genes on/off depending on need, conditions Changing the Mutation: result of Not reversible Mutation is a info errors/damage (once permanent proofreading change in the step is finished) base sequence Francis Jacob and Jacques Monod Observed bacteria, E.coli, and noticed that o If the nutrient sugar, lactose, was added to cells’ nutrient medium, all 3 enzymes needed for it use appeared in the cells o If lactose was absent, all 3 enzymes were absent o Lactose seemed to be “turning on” o Control of the 3 genes seemed to be coordinated Proposed the idea of an operon: o Segment of DNA in bacteria that includes promoter sequence ( where RNA polymerase binds), operator sequence (where a repressor protein binds), a group of structural (protein- coding) genes Gene Mutation Permanent change in the base sequence of DNA in one gene region Leads to mistakes in RNA, protein encoding What are the 2 ways gene mutation can arise? o DNA replication error not corrected by proofreading o Environmental mutagens; radiation, chemicals, viruses When in the cell cycle would each of these be most likely to occur o Proofreading error: “S” (during DNA Replication) o Environment damage: throughout the cycle Biomolecules (Lecture 5-8) Proteins: functional categories Transport: movement of materials around body or into/out of cells o Potassium channel [facilitates movement of (charged) K ions across membrane] o Hemoglobin (in red blood cells-carries oxygen from lungs to body cells) Hormones: chemical signaling in the body o Insulin, glucagon (regulate blood sugar levels) Contractile: contraction o Actin, myosin (muscle contraction) Structural: structural support, toughness o Collagen ( in extracellular matrix, around the cell) o Keratin (epidermal layer) Protection o Antibodies (immunity in white blood cells) Enzyme: needed to facilitate every reaction in the body o Trypsin (digests proteins in the small intestines) o Amylase (digests starch in the saliva) Storage: nutrient storage for growing embryo o Endosperm proteins (in seeds) Protein monomers = amino acids Amino group, central carbon, hydrogen atom, carboxyl group Mass of 1 amino acid measured in Dalton R-group: also called side chains, variable groups How do the R groups vary? o Size (a single hydrogen to a long chain/ bulky ring structure) o Charge (+ or – or neutral) o Polarity (partial charge on an atom resulting of unequal sharing of electrons) Water Solubility o Charges and polar R groups = hydrophilic (water soluble) o Uncharged and non-polar R group = hydrophobic (not water soluble) Formation of a covalent (peptide) bond between 2 amino acids to form a chain (polypeptide) This chemical reaction is called Dehydration Synthesis o Removal of –OH from one amino acid and –H from other amino acid, releasing a H2O molecule o Allows direct covalent linkage between 2 amino acids o So water is taken out (dehydration) as a larger molecule is made The covalent bond between two amino acids (monomers) in a polypeptide ( polymer) = PEPTIDE BOND Dehydration synthesis to make a polypeptide chain is translation Polypeptide: a chain of amino acids produced by dehydration synthesis/translation Primary (1°) Structure Linear chain of amino acids held together in a sequence by covalent bonds from dehydration synthesis What determines the specific order of amino acids in the chain? o mRNA translation Secondary (2°) Structure Distribution of alpha helices and beta pleated sheets along a protein chain Spatial arrangement of amino acids residues that are nearby in sequence/local regions of the polypeptide chain Regular coils (helices) and folds (pleated sheets) with connected segments Hydrogen bonds between part of backbone; R group NOT involved Tertiary (3°) Structure Overall 3D shape where 2° structure folded into a 3D shape Refers to the spatial arrangement of amino acid residues that are far apart in the sequence and to the pattern of disulfide bonds (covalent) protein Hydrophobic interactions: always on the inside of the protein with no interact H2O Quaternary (4°) Structure Refers to the spatial arrangement of subunits and the nature of their interactions Functional proteins consisting of more than 1 individual polypeptide chain Polypeptide Protein Linear chain of amino acid chain with 1 ore more polypeptides with appropriate coiling/folding which has NOT acquired levels of structure to make it able to normal 3D shape required for its function function Polypeptide chain can NOT perform Gives native conformation of proteins functional in the cells Normal, form, structure Can perform function in the cells Non- polar R groups internalize to minimize interaction with water Polar and charged R groups position themselves o On the exterior where they will interact with water be in positions to interact with each other What stabilizes 3° structure? o Hydrophobic interaction, Hydrogen Bond, Disulfide Bond, Ionic Bond Proteins Glucagon: functional at 2° structure ; pancreatic hormone ; raises blood sugar if the level gets too low Amylase: functional at 3 ° structure ; enzyme that hydrolyzes starch in the mouth (saliva) Hexokinase: functional at 3° structure ; enzyme that catalyzes the first reaction in glycolysis Hemoglobin: functional at 4° structure ; contained in red blood cells, which efficiently carries oxygen from the lings to the tissues of the body, also helps transport CO2 and H ions back to the lungs + K (Potassium ion) channel: functional at 4° structure ; membrane transport protein Collagen: functional at 4 ° structure ; holds ligaments, tissue, muscle, etc. together Proteases: enzymes which hydrolyzes the protein Trypsin: hydrolyzes proteins at lysine and arginine Gene Mutation: Permanent changes in the base sequence of DNA What are 2 ways gene mutations can arise? o DNA replication errors not corrected by proofreading o Environmental Mutagens: radiation, chemicals , virus What are the 2 main classes of gene mutation? Base Substitution and Base insertion/deletion Base Substitution o Silent Mutation: no change in the protein because the amino acid did not change o Nonsense Mutation: premature stop because the amino acid changed to a STOP amino acid o Missense Mutation: amino acid substitution Base Insertion/Deletion o Frameshift Mutation: the reading frame of codons is shifted by one or two nucleotides o Amino Acid insertion: an extra codon inserted, but the same reading frame Sickle Cell Anemia Missense mutation (TA to AT) Change in amino acid: Glu (a negatively charged R group) to Val (a hydrophobic R group) so sickle hemoglobin (has a changed 3D shape, less efficient binding of O2, stacks in RBSs and distorts their shape) Sickled RBCs get stuck in capillaries, block blood flow, cause pain cries, destroyed by spleen anemia Protein Structure/Function Relationship Protein function depends on the pockets and grooves of the molecule’s normal 3D structure Anything that alters the normal 3D structure will alter the function o Anywhere from slight change to total loss of function o Depends on extent of change What can alter the 3D shape of a protein? o Denaturation of the protein molecule o Mutation in the DNA coding for the protein o Hydrolysis of Protein Different interactions/ bonding help stabilize structure Backbone of proteins are covalent, which is a peptide backbone Several kinds of non-covalent, interactions/bonding are very important in protein structure (MAJOR ROLE) o These forces are H bonding, hydrophobic interactions, ionic/electrostatic bonds o These non-covalent interactions help to maintain overall 3D structure Covalent like Disulfide bonds (S-S) bonds (MINOR ROLE) Non-Covalent interactions help in forming/stabilize structure Hydrogen Bonding: can be made whenever possible within a given protein structure Hydrophobic interactions: form due to non-polar R groups of amino acid and other non-polar regions which try to go away from water minimizing interactions with water Ionic/Electrostatic Bonds: interactions which arise between opposite charges 4 Main Type of Biomolecules Nucleic Acids o Polymers: DNA and RNA (mRNA, tRNA, rRNA) o Monomer: nucleotides Carbohydrates o Polymers: Polysaccride and Disaccharides o Monomers: Monosaccride Lipids o Polymers: Triglycerides o Monomers: Fatty Acids and Glycerol o Fats and Oils, Phospholipids, Steroids, Waxes Proteins o Monomers: amino acids o Support (Collagen) , hormone (insulin) , contractile (myosin) , enzyme (hexokinase) Carbohydrates Monosaccride (simple/single sugar) Polysaccride (complex carbs.) o Different Monosaccride contain different numbers and/or arrangements of the C, H, O atoms Dehydration Synthesis of Disaccharides o Maltose = Glucose + Glucose o Sucrose = Glucose + Fructose o Lactose = Glucose + Galactose Polysaccharide (aka complex CHO) o Starch, glycogen, cellulose o Humans cannot digest cellulose: lack enzyme to hydrolyze o Another name of cellulose (main component of plants cell walls) = “dietary fiber” o Glycogen = animals = stores energy o Potato = starch = chain of glucose o Cellulose = structure for plants (We cannot digest) ; hydrogen bonds Carbohydrate: function Mono- , Disaccharides o Glucose, fructose (mono) ; sucrose, lactose, maltose (di) o Short term energy storage Macromolecules- all glucose polymers o Starch: long term energy storage in plants o Glycogen: long term energy storage in animals o Cellulose: structural in plant cell walls and is indigestible fiber (roughage) for humans Lipids What atoms are present? Mostly C + H (very little O) Lack of chare and polarity making the molecule hydrophobic ( NOT water soluble) Fatty Acids o Monomer of triglycerides/ phospholipid molecules o With C/C single bonds called saturated H are on the same side BAD o With C/C double bonds called unsaturated b/c it contains fewer hydrogens Cis or trans hydrogen are in the opposite side Saturated (or trans) fat o Straight, close-packed fatty acids; solid at room tempt. ; vascular damage, stroke, heart attack ; all hydrogen Unsaturated (oil) fat o Kinks at double bonds of fatty acids that doesn’t lead to clogging= healthier o Loosely packed; liquid at room tempt. Lipids: structural categories o 2 major categories of lipids: Triglycerides-Fats and Oils (3 Fatty Acids and 1 Glycerol) and Phospholipids-amphipathic[hydrophilic head, hydrophobic tail] (2 Fatty Acids, PO4group, 1 glycerol) Steroid: 4 basic fused ring structure ; example: cholesterol Lipid Function o Fats and Oils- long term energy storage, insulation and cushioning o Phospholipids- membrane structure, separate H2O filled cells from H2O environment o Steroids- hormones, membrane structure and fluidity in the membrane o Waxes- protection, prevent dehydration Nucleic Acids ATP Adenosine Triphosphate o Adenine base and ribose sugar and 3 phosphate groups o Immediate energy molecule in all cells o Used as a monomer for making RNA (end phosphate group comes off) Two Kinds of Covalent Bonds Nonpolar: partner atoms share electron pairs equally; hydrophobic Polar: partner atoms share electron pairs unequally; hydrophilic Water is Polar Glucose is also Polar Charged particles are also water soluble so they are polar Methane is nonpolar What do all 4 classes have in common? Organics, contain 1 or more chemical groups, dehydration synthesis (making), hydrolysis (breaking) Chemical Groups Hydroxyl: -OH , polar Carboxyl: -COOH , acid , negatively charged Amino: -NH ,2base , positively charged Phosphate: -OPO 23, buffer , negatively charged Methyl: -CH ,3nonpolar , reduces polarity Where are chemical groups found? Hydroxyl: sugars, CHOS, glycerol, Estradiol Carboxyl: amino acids, protein, fatty acids Amino: amino acids, proteins, phospholipids head Phosphate: nucleic acids, ATP, phospholipid head Methyl: fatty acids, lipids, Testosterones Differences Chemical Composition o Proteins: CHON (S) , -COOH charged, NH (charg2d) , variety of R groups , hydrophilic o Carbohydrates: 1C:2H:1O , lots of OH (polar) , hydrophilic o Lipids: CHO, Phospholipid N and P , mostly hydrocarbon and CH (non-pol3r) hydrophilic o Nucleic Acids: CHONP, PO (cha4ged) , OH (polar) on backbone, various (polar) on bases, hydrophilic What makes them this way? Their chemical groups Cells (Lecture 9-12) What is a cell? A basic unit of life (cell theoryall life consists of one or more cells) All Properties of Life: o Presence of DNA, ordered structure, reproduction, growth and development, energy processing, response to the environment, regulation (homeostasis) What are the 4 basic structural features common in ALL cells? Plasma Membrane o Outer boundary: separates cell from surroundings o Encloses the cell o Controls what leaves or enters the cells Cytoplasm o Fills space within the boundary o Suspends or supports internal structure and inclusions Genetic center: DNA o Controls cell structure and function o Governs heredity Ribosomes o Serves as site of protein synthesis o Expression of genetic info to develop structure/ function Prokaryotes Eukaryotes Size 1-10 µm 10-100+ µm DNA DNA circular, no limiting DNA linear and paired, within membrane, nucleoid membrane, true nucleus Inclusions Few; none membrane- enclosed Many; most enclosed in 1-2 (organelles membrane ) Ribosomes Smaller Larger Cellular Differentiation Normal process by which immature undifferentiated cell develops distinct structures and functions of specialized cells Underlying mechanism: differential expression of genes in DNA o Genes turned on = expressed genes turned off = silenced Results: change in proteome of the cell o Defines morphology and specialized function Begins with an undifferentiated cell (stem cell) Undifferentiated Cells Differentiated Cells Immature cells Specialized, mature cells Non-descript morphology Small nucleus, large cytoplasm Large nucleus, small cytoplasm Specific protein and internal structures to Absence of specialized protein and internal perform function structures associated with specialized o Contract (muscles) o Transport oxygen (Red Blood cells) function Examples: most cells in very early embryo, o Produce insulin (pancreas) very small number in each organ o Transmit electric signals (neurons) 2 Main Categories of Stem Cells: Embryonic and Somatic Stem cells are the undifferentiated cells that can differentiated into specialized cells Embryonic Stem Cells o Source: surplus embryos from in vitro fertilization (IVF) clinics o From inner cell mass (KM) of blastocyst stage embryo (~5 days after fertilization, before implantation) o Pluripotent o Not from absorbed fetuses Somatic Stem Cells o From fetus- adult tissue, e.g. umbilical cord, bone marrow o Multipotent to unipotent o Unipotent= a cell between myeloid stem cell and erythrocyte (RBC) o Mature RBC has no nucleus Cell Type Potency Specialize to Examples Zygote (fertilized Totipotent All type of cells, egg) including placenta Inner Cell Mass Pluripotent Nearly all cell types, no placenta Hematopoietic Multipotent Many cell types Bone, Cartilage, SC Fat Mesenchymal SC Proerythroblast Unipotent One cell type RBC/Erythrocytes What three features define Stem Cells? Unspecialized/ Undifferentiated Able to specialize/ differentiate into different levels of potency (plasticity) Able to self-renew: produces 1 replacement SC and 1 daughter cell ready to differentiate Induced Pluripotent Stem Cells (iPSC) Adult differentiated cell ( e.g. skin keratinocyte) Treated with 4 genes to genetically reprogram the cells Results: cell revert to earlier less differentiated state and act like pluripotent SC Research and medical treatment of patient without rejection Extracellular Matrix (ECM) ECM: mostly protein material at outer surface of cells (plasma membrane) and between cells ECM molecules on outer surface o Allows cells to attach to other cells and to ECM o Includes receptors for hormones, growth factors o Provide cell recognition/ identity to self o Are entry points for viral infections ECM materials between cells provide o Scaffolding for tissue architecture (collagen and other fibers) o Anchoring for cells ECM act as a signal for stem cells to differentiate Phospholipid (P-L) Main component: phosphate group and glycerol (Hydrophilic head and Hydrophobic fatty acid tail) Bilayer Barrier between watery cytoplasm and cell’s watery environment o Prevents: loss of material from cell and entry of material from outside the cell o Hydrophobic tails won’t let dissolved hydrophilic material through Plasma Membrane Structure o Proteins: intracellular junctions, transport, signal transduction, attachment to the cytoskeleton and ECM, Enzymatic activity, cell to cell recognition, receptors (for hormones) o Cholesterol: no cholesterol in membrane = cell is rigid, membrane flexibility, lateral movement within the cell o Carbohydrate= Glycoprotein: short chain of sugars attached to a protein Glycocalyx: identity tag Plasma Membrane Function o Limiting boundary: separate cell from its environment o Transport: material in and out of the cell o Identification and Recognition: of many different molecules (ex. ABO blood type) o Communication: cells able to communicate with each other o Attachment Membrane Function #2: Transport Diffusion: movement of atoms/ions/molecules down their concentration gradient from high to low concentration until equilibrium is reached, no external energy input needed Osmosis: the movement of water molecules from high to low concentration through a membrane Concentration Gradient: a difference in concentration across space Equilibrium: particles are equally distributed in space Types of barriers o Fully Permeable: everyone can go through o Semi/Selectively Permeable: allows certain molecules to go through o Impermeable: doesn’t allow anything to pass Solution = Solute + Solvent (e.g. salt water = salt + water) Solution: solute (starts as a solid) dissolved in a solvent (liquid) Tonicity: the amount of solute in a solution Isotonic: one solution = solute = another solution Hypertonic: more solute, the cell shrives because too much water is leaving the cell Hypotonic: less solute than another solution, the cell burst because too much water is coming into the cell Size + Polarity/ Charge Can it cross the phospholipid bilayer? Very small particles, no charge Yes, it can go through the P-L tails Very small particles, charged NO, it cannot go through the P-L tails Small particles, no charge Yes, it can go through the P-L tails Large structure, no charge Yes, it can go through the P-L tails Larger structure, charged NO, it cannot get through the P-L tails Polymer, charged or uncharged NO, much too large to pass though What limits ability to cross the P-L Bilayer? Size and Polarity/Charge Simple Diffusion Facilitated Active Transport Diffusion Concentration DOWN DOWN UP (AGAINST) Gradient Cellular energy NO NO YES required Transport Protein NO YES YES required Examples O2 CO2 ethanol Ions amino acids steroid H2O nucleotides Endocytosis: plasma membrane indents; forms pocket around material; vesicle sides fuse; closed vesicle drops into cytoplasm o Example: amoeba engulfing a food particle ; white blood cells engulfing a disease agent o INTO the cell and YES cellular energy is needed Exocytosis: cellular material to be transported packaged in a vesicle; vesicle fuses with plasma membrane; vesicles opens up; releases cell product o Example: pancreatic cell releasing digestive enzyme ; fibroblast releasing collagen fibers into extracellular space o OUT of the cell and YES cellular energy is needed Membrane Function #3: Identification and Recognition ID tags on cells: CHO chains on the outside of the plasma membrane are responsible for cell recognition Example: ABO blood groups o All humans have either A, B, AB, O blood type o Immune system recognizes foreign blood types because different short CHO chains o A blood specific sugar chains o B blood specific sugar chains o O lacks sugar chains Membrane Function #4: Communication General schemes of intracellular signaling in animals o Endocrine Signaling: hormones in the blood stream o Paracrine Signaling o Autocrine Signaling: cancer cells have this o Signaling by plasma membrane- attached proteins Signal transduction: series of molecular changes that converts (amplifying) a signal received on outside of cell’s membrane o Across the membrane, through the cytoplasm, to the target molecule/structure in cell to elicit a response o One molecule alters another molecule, which then alters a third molecule, etc. (called a domino effect process cannot stop, the end product of signal transduction is a new protein) o Transmit the message to the appropriate parts of the cell o A signal molecule is released by a cell in one part of the body, received by a target cell elsewhere, the receipt of the signal is via binding of signal molecule to a specific receptor proteins on outside of the target cell membrane Membrane Function #5: Attachment (cell can attach to the ECM and other cells) Cell attachment via “Junction” junctions has no physical connection with cells except gap junctions Tight junction Anchoring junction Gap junction Tight Junction o Looks like the adjacent membranes are sewn together o Forms a water tight seal between the two membrane o Prevents passage of material between the cells Anchoring Junction o Cytoskeleton element connect to assist with structure o Connect the intermediate filaments of the cytoskeletons of adjacent cells (desmosomes) o May also anchor to a cell’s intermediate filaments to ECM o Provide mechanical strength to the tissue by connecting many cells together Gap Junction o Forms pores that provide direct connection between the cytoplasm of adjacent cells o Allow flow of molecules and ions from one cell to the next o Permit communication between adjacent cells that coordinate the tissue’s reaction Internal membranes have the same structure as plasma EXCEPT: no glycocalyx Eukaryotic Organelles What are organelles? Structures within a cell which with characteristic morphology and specialized function What separates one organelle (compartment) form another and from the surrounding (cytoplasm)? Membrane What are examples of organelles surrounding by o One membrane: ER(SER + RER) , Golgi , lysosome o Two membranes (2 adjacent phospholipid bilayers): nucleus and mitochondria o No membrane: ribosomes, fibers of cytoskeleton What are the specific advantages of compartmentalization? Increased surface area: e.g. inner mitochondrial membrane Increased concentration of reactants used in chemical reactions: reactant concentrations control rate of reaction Separation of incompatible reactions/reaction environment o Synthesis vs. degradation: e.g. RER vs. lysosome o Reactions that need different environment: pH 7 (cytoplasm), pH 5 (lysosome) Separation of products based on whether they are for internal use ( inside a membrane-enclosed organelle or free-floating in cytoplasm) and export (collagen of ECM, insulin, digestive enzyme) Organelles 1) Nucleus: double membrane (nuclear envelope) continuous w/ ER; stores DNA: to control cell’s structure/function an heredity 2) Nucleolus: site of rRNA-coding genes; ribosomal subunit assembly of rRNA and ribosomal proteins 3) Chromatin: stretched out form of chromosomes/DNA; active gene expression 4) Nuclear Pores: protein and RNA traffic 5) Ribosome: contains Large and small subunits, empty tRNA leaving the ribosome, tRNA in the P site, tRNA in the A site 6) Free Ribosome: floating ribosomes in the cytoplasm making proteins in the cytoplasm a. Translation of proteins used in cytoplasm e.g. hexokinase and hemoglobin 7) Bound Ribosome: ribosomes attached to RER, involved with translation of membrane proteins a. Proteins to be inserted into the P-L bilayers of the membrane b. Proteins for export from cell by exocytosis c. Proteins for membrane-enclosed cellular organelles 8) Smooth endoplasmic reticulum (SER): single membrane, lipid synthesis, synthesis of new membrane, synthesis of testosterone and estrogen, detoxification (liver cells) , calcium ion storage (esp. muscle cells) 9) Rough endoplasmic reticulum (RER): single membrane, ribosomes that attach to ER membrane, membrane associated proteins, proteins for delivery, proteins for release our of cells 10)Golgi apparatus: single membrane, finishes, sorts, packages, ships cell production 11)Lysosomes: single membrane, contain mixture of hydrolytic enzymes- ACID HYDROLASES, works in acidic conditions (have optimum pH in acidic range), intracellular digestion, cell recycling center (unneeded molecules and damaged organelles) 12)Mitochondria: double membrane, cellular respiration: ATP Synthesis, huge surface area, thrown into long folds (cristae) in order to fit inside of the smaller outer membrane, site of mitochondrial electron transport chain (ETC) 13)Cytoskeleton: 3D network of protein fibers in the cytoplasm for structural support (scaffolding) and cell movement a. Microfilaments: thinnest fibers, can be assembled and reassembled, protein = actin (globular protein), function = cell shape and whole cell movement b. Intermediate Filament: intermediate fibers; generally not disassembled and reassembled, various fibrous proteins, function = cell shape, reinforcement of cell junction, organelle placement c. Microtubules: thickest fibers, hollow tubes, can be disassembled and reassembled, protein = tubulin (globular protein), function = arrangement of organelles, intracellular transport, cell motility, the separation of chromosomes during mitosis Properties Plasma/ Cell Membrane Cell Wall Chemical Mostly lipid (+proteins+ some Mostly cellulose Composition carbohydrates) Thickness Thin Thick Flexibility Flexible, laterally fluid Stiff ,rigid Permeability Selectively permeable Porous v. permeable Location Outer layer of cell External to P.M. Function Gatekeeper Structural support Cell type w/ ALL! Plant cells, some fungi this structure Metabolism (Lecture 13-16) Matter and Energy Matter: anything that takes up space and has mass Energy: ability to do work Kinetic Energy: energy of motion; example: heat, light, anything moving Potential Energy: stored energy, energy of position/ arrangement; example: chemical arrangement, physical placement Kinetic Energy Potential Energy Skier going downhill: mechanical Skier poised at top of hill: position H2O flowing down slope from dam Battery: arrangement Electrons moving in a wire: electrical Chemical bond energy: arrangement Random thermal motion of atoms and Concentration gradient: arrangement molecules: heat Photon moving: light H2O above a dam Molecule/ion flowing down concentration Molecule-energy in bonds holding atom gradient: mechanical together: arrangement What rules govern energy use? The Law of Thermodynamics 1 law: the quantity of energy in the universe is constant: energy cannot be created or destroyed, only converted from one form to another but the total amount of energy in the universe doesn’t change 2ndlaw: the quality of energy in the universe is NOT constant: the amount of useful energy declines spontaneously meaning that energy transformations occur but are NOT 100% efficient because some useful energy is lost as heat energy Metabolism Sum total of all the chemical reactions that occur in a cell o How cells function and dictate o How cells manage matter and energy o Consists of many interconnected metabolic pathways Metabolic Pathways st A series of chemical reactions in which product of the 1 reaction is substrate (starting material) of the 2nd reaction, product of the 2 ndreaction is the substrate of the 3 reaction, etc. Linear Pathway example: glycolysis Cyclical Pathway example: Krebs cycle Two Parts of Metabolism Anabolism (making/synthesis reactions) o Synthesis, production, manufacture o Requires energy consumption o E.g. dehydration synthesis (monomerpolymer) of all biomolecules; production of monomers form inorganic molecules (photosynthesis) Catabolism (breaking down reactions) o Breakdown, degradation o Releases energy: making energy available for the cell o E.g. hydrolysis (polymermonomer) of all biomolecules; non-water mediated breakdown of an organic monomerinorganic parts ( C H O 6 12 a6d H O2glucose2catabolism) Chemical Reaction Chemical reaction: change in bonding relationship between/among atoms without any loss of starting atoms (conservation of mass) It’s the rearrangement of atoms (basic unit of matter) Most chemical reactions go in either direction. The direction is usually determined by relative concentration of reactant vs. product. Heating can provide needed kinetic energy to get reactants moving and colliding In cells, ENZYMES are used to avoid damaging high temperature Exergonic Reactions: Catabolic Endergonic Reactions: Anabolic Releases energy: makes energy available to Consumes energy: requires energy input by cells cell Energy in reaction is higher than energy in Requires/ needs energy for reaction to take products which is lower so energy is place released out of the system Starting reactant is low Energy of reactants is greater than the Energy of reactants is less than the energy energy of the products of the product Energy released/out Energy required/in Order to random Random to order Degradation or breaking down of complex Synthesis/ building a more complex structure to smaller structure structure from less complex material Energy Hull Diagram (EHD) Endergonic Reactions: MES (Max, End, Start) [think you enter the room as a mess] Exergonic Reactions: MSE (Max, Start, End) [think you exit the room messy] ΔG: difference in potential energy levels of reactants and products EA: energy of activation: kinetic energy input needed for reactants to reach transition state [start to max] o Enzymes reduces the energy of activation (E ) A Transition State: the max energy level in the chemical reaction; reactant bonds are breaking, product bonds are forming; when reached, the chemical reaction finishes and products are release [start to end] Coupled Reactions (or processes) Two reactions are coupled if something from the 1 reaction is essential/ needed from the 2 nd reaction The ‘something’ can be a molecule: in 2 sequential reactions, the product of the 1 reaction is the reactant for the next reaction The ‘something’ can be energy: the energy needed to run an endergonic reaction. These 2 reactions are said to be energetically coupled Exergonic and endergonic reactions are connected “coupled” in cells o Energy released from exergonic reactions is used to drive endergonic reactions So cell uses two sets of coupled reactions: o One set uses energy from food to make (to restore) supplies of ATP o Another set uses ATP breakdown to fuel cellular work ATP is coupling molecule in the middle: appears in both sets of coupled reaction o First being made o Then being consumed Enzyme Biological Catalysts- Help the reaction to take place, but are not used up in the chemical reaction Substrate (Reactants) + Enzyme Products + Enzyme Speed up the rate of chemical reactions- speeds up reaction ~ 10 fold by lowering the E (no A change in ΔG) Makes the reaction easier because the transition state is easier to reach But does NOT provide energy Why are enzymes essential to living systems? o Cells utilize many kinds of BIOCHEMICAL reactions like o Anabolic reactions- endergonic or Catabolic reactions- exergonic At body temperature of 98.4°F/37°C, chemical reactions wouldn’t be able to take place at a sufficient rate w/o an enzyme APOENZYME (protein part of enzyme) + COENZYME (organic)/COFACTOR (inorganic) = whole/ complete ENZYME Enzyme, 3D conformation: enables enzyme to have many small pockets and grooves (active site and allosteric site) Active Sites of Enzymes Is a 3D region formed by groups that come from different parts of amino acids sequence Is a relatively small part of the total volume of an enzyme Directly participate in the making or breaking of bonds Is structurally complementary to the substrate o Shape-lock and key concept of enzyme substrate binding o Chemical composition (charge, polarity) o Substrates bind by a multiple weak attraction with R groups of enzymes Anything/ any agent which causes the change in shape of active site will affect the enzyme activity or function o Inhibition of enzyme o Denaturation of enzyme o Permanent alteration in gene level Is the site where a competitive inhibitor binds if present The Catalytic cycle of an enzyme 1. Enzyme available with empty active site 2. Substrate binds to enzyme with induced fit a. Keeps substrate from diffusing away b. Holds substrate in close proximity and current orientation to help bond formation and breaking c. Strains/ stresses the substrate bond, making them easier to break 3. Substrate is converted to product a. Water is added 4. Products are released a. Chemical reaction occurs b. Induced fit is released c. Products are released How does the catalytic cycle accelerate the rate of a chemical reaction? Reduces the E Af reaction through induced fit: o Keeps substrates from diffusing away o Holds substrate close to each other, and o Incorrect orientation in active site o Strains reactant bonds makes reaction easier NO effect on ΔG (free energy difference between energy of reactants and products) Control of enzyme activity Enzymes are proteins-if disrupt 3D shape, change/lose enzyme activity How can that happen? o Heat over 45°C, Extremes of pH, Extremes of salt, Foaming, Mutation Would these conditions ever be used by cells to control enzyme activity? o Cells maintain constant internal conditions: homeostasis o High fever from illness: would cause mild (reversible) denaturation, but not used as a wat to control enzymes o Mutations: may occur through error, but again, not a control mechanism Control of enzyme activity by cells Rate of synthesis and its rate of degradation controlled Start or stop making the enzyme: certain genes can be “turned on” or “turned off”, e.g. lac operon in E.coli, the presence of lactose Accessibility of substrate: the transfer of substrates from one compartment of a cell to another can serve as a control point (controlling the entry of substrates can regulate enzyme activity) Isolate active enzyme in a separate compartment: enzymes are often confined to specific locations in the cell and work only there Activation: some enzymes are made in an immature, inactive form, and get activated where/when appropriate Enzyme Inhibitors Competitive inhibitor: inhibitor can bind on the active site of enzyme complex as it resembles substrate o Irreversible: inhibitor covalently bound to the active site o Reversible: inhibitor loosely bound can diffuse off Non-competitive/ Allosteric inhibitors: inhibitor and substrate can bind simultaneously to an enzyme molecule at different binding sites other than the active site Competitive Inhibitor: blocks active site Non-competitive or Allosteric inhibitor: changes shape of active site o Binding is reversible- activity is restored if inhibitor comes off o Binds and changes 3D shape of enzyme, indirectly closing off active site Feedback inhibition = example of non-competitive inhibitor (NOT a type) o Pathway on: enzyme present and active; all substrate present o Pathway off: enzyme “a” present but inactive; thus no substrate B,C,D,E present o Specific example of feedback inhibition: pathway that converts threonineisoleucine o Isoleucine is a different amino acid Two types of carrier molecules involved in glucose catabolism - + e /H carrying coenzyme o NAD /NADH and FAD/FADH 2 o Hold energy temporarily; later ‘cashed in’ for ATP Energy carrier molecule o ADP/ATP o ATP = immediate energy molecule used in all cells - + + e /H carrying coenzymes: NAD and FAD Picks up HIGH ENERGY electrons and accompany hydrogen ions, H (aka protons), from the substrate in the active site of the enzyme Carrying them to another location in the cell where they can be used Empty out their ‘cargo’ in that location Come back in empty states to assist the same reaction again What do NADH and FADH do2with their e /H ? + - + Hold the e /H for only a short time Shuttle e /H from one place to another WITHIN the cell o From where they are picked up: glucose o To where they can be used: mitochondria (ETC) Once cargo is delivered, empty (oxidized) carriers go back for more (shuttle service) What can delivered e /H be used for? Produce ATP Reduction and Oxidation Type of chemical reaction that transfers electrons from 1 structure to another The 2 reactions occur together o When one structure gives up electrons o Another structure receives it/them o So electrons is/are transferred Together called Redox reaction o Oxidation: is the loss of electron the structure that loses electrons becomes oxidized o Reduction: is the gaining of electrons the structure that gains electrons is reduced o This is counter-intuitive (i.e. a reduction is gain) o When the (CH O)2 is oxidized (loses hydrogens), NAD and FAD pick them up (reduced) Limited ATP/ADP supplies in the cell Can’t be passed from cell to cell Very hard for cell to make from scratch ATP/ ADP+P neei to be cycled constantly within cell If a cell can’t cycle ADP back to ATP it will die Reactions of Glucose Catabolism 1 C 6 12+ 6 O 6 2O + 6 H 2 + 36-32 ATP (40% ATP + 60% heat) C 6 12+ 6NAD+ + 2ADP + 2P 2 Pyruvaie + 2 NADH + 2 ATP - Oxygen absent = Fermentation - Oxygen Present = Cellular Respiration ATP Synthesis ATP synthesis is an endergonic process Energy transformations are 40% efficient, 60% energy is lost as heat What is the main source of energy to produce ATP? o KE of electrons removed from organic molecules during catabolism o Flowing down mitochondrial ETC + o Producing protons/H gradient across inner mitochondrial membrane o Potential energy in this gradient is used to synthesize ATP by chemiosmosis How does a cell make ATP from ADP+P? i Direct Phosphorylation/ aka Substrate Level Phosphorylation o Requires an enzyme o Requires a phosphate group donor which has high energy phosphate group transfer potential compared to ATP o Energetically coupled w/ exergonic reactions in the glucose catabolism pathway: Glycolysis (cytoplasm) and Krebs cycle (Mitochondria) o Source of ~10% of a cell’s ATP Chemiosmosis o Source of ~90% of a +ell’s ATP o Energy source- H / proton gradient from ETC drives ATP synthesis by chemiosmosis o Occurs in mitochondria in eukaryotes o Occurs in cytoplasm in prokaryotes Three categories of cellular work CHEMICAL Category MECHANICAL Category TRANSPORT Category Endergonic Rxns, e.g. - Muscle contraction - Active transport across - DNA synthesis - Motor proteins inside of membranes cells - RNA synthesis - Protein synthesis - Lipid synthesis What is an e transport chain (ETC)? - A series of e transport protein inserted in the P-L bilayer of the inner mitochondrial membrane Each protein can accept 2e - Each protein then passes these e to the next protein in the series - The flow of e down the chain provides kinetic energy There must be an e donor at the start and a final e acceptor at the end of the chain - + + ETC: energy from e flow along ETC used to pump (actively transport) H across membrane H gradient across membrane + Chemiosmosis: ATP Synthesis (from ADP+P) using enirgy from flow of H ions back down gradient (facilitated diffusion) through channel protein/ ATP Synthesase complex Glucose Catabolism: Glycolysis, Prep Stage, Krebs cycle, ETC, Chemiosmosis Glycolysis o 1 Glucose 2 Pyruvates 2 ADP 2ATP 2 NAD+ 2 NADH + H + o ATP is made by substrate level phosphorylation o Glucose is broken down by enzymes st o 1 enzyme used in glycolysis to breakdown glucose is Hexokinase o Occurs in the cytoplasm o Breaks down glucose into 2 3-C molecules, Pyruvates o 9 step metabolic pathway o Anaerobic: doesn’t consume O2 or indirectly dependent on O2 Transition Stage/ Prep Stage o Pyruvate is converted to Acetyl CoA which enters the Mitochondrial Matrix o CO2 molecule is released o End Products of Prep Stage: 2 Acetyl CoA and 2 NADH+H + o Enzyme Responsible: pyruvate Dehydrogenase o Aerobic Krebs Cycle o 6 NAD+ 6 NADH+ 6 H + 2 ADP 2 ATP 2 FAD+ 2 FADH 2 o ATP made by substrate level phosphorylation; occurs in mitochondrial matrix o End Product of Krebs Cycle: 2 FADH2 , 2 ATP , 6 NADH2 , 4 CO2 o 1 FADH2 = 2 ATP o 1 NADH = 3 ATP o Aerobic o 4 remaining carbons from pyruvates as CO2 o A cyclical metabolic pathway ETC o NADH and FADH2 shuttles through until it reaches O2 which is the final electron acceptor. H+ actively transport outer mitochondrial membrane o ETC embedded in inner mitochondria membrane Series of electron acceptors e source (NADH and FADH2) and a final e acceptor (Oxygen) Chemiosmosis o H+ has stored potential energy which drives H+ through channel in ATP Synthase (facilitated d
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