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Midterm notes on lecture material and textbook from Introduction to Molecular and Cellular Biology course...

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BIO 1090 Midterm Notes: LECTURES #1 & #2:

1.1-1.4 PG 1-13 KARP

What does it take to make life? 1. INFORMATION (biological) tells us/our cells to do things 2. CHEMISTRY When did life start? Miller-Urey Experiment (1952): Earth’s Atmosphere:  

N, Ammonia, Methane, CO2, H2O, H+ ↓ Urea, Cyanide, Formaldehyde, AMINO ACIDS

The Cell Theory:   

Cells are the structural unit of life All organisms are composed of 1 or more cells Cells are made from pre-existing cells through division

Basic Properties of the Cell:          

Highly complex & organized Cellular activity controlled by genetic program Can reproduce Assimilate & utilize energy (from the sun) Carry out chemical reactions (enzymes) Engage in mechanical activities Respond to stimuli Capable of self-regulation They evolve Cytoskeletal Elements: (actin filaments, microtubules ect) contribute to cell shape & movement, provide structural support and support transport of material

Two Classes of Cells on Earth: 1. Prokaryotic: Structurally simpler (NO nucleus) ex. Bacteria 2. Eukaryotic: Structurally more complex (Nucleus) ex. Plants, Fungi, Protists, Animals

Viruses and Virons: Viruses(V): non-cellular macromolecular packages that threat function & reproduce only WITHIN living cells -

-

Bind to cell surface and use proteins to enter cell o Once inside V hijacks cellular machinery to synthesize nucleic acids and proteins o Assembles new virus particles Wide Host-Range: Rabies infect cells in dogs, bats and humans Narrow Host-Range: Cold & Flu in humans First viruses were the TMV’s (Tobacco Mosaic Virus)

Two Main Types of Viral Infection: 1. LYTIC: Production of virus particles ruptures & kills cells (ex. Influenza) 2. NON-LYTIC or INTEGRATIVE: viral DNA is inserted in host genome (making a PROVIRUS), cell can survive but is usually impaired (ex. HIV) Virons: Virus outside of living cells (inanimate particle), composed of DNA & RNA ex. Protein capsule

LECTURE #3: BIOLOGICAL MEMBRANES

Function of Biological Membranes:      

Cell boundary (PM only) Define/enclose compartments Control mvmts of material into/out of cell Allow response to external stimuli (PM only) Enable interactions b/t cells (PM only) Provide scaffold for biochemical activities (including energy transduction) o Allows reactions to occur in membrane

Fluid Mosaic Model: By Singer & Nicolson (1972)   

 

-4.1 (review) -4.3 (to end of section “The Asymmetry of Membrane Lipids”) -4.4 (pg. 130-132, through to end of 2nd paragraph after heading -“Integral Membrane Proteins”; pg. 137 “Peripheral Membrane -Proteins”; “Lipid-Anchored Membrane Proteins”) -4.5 -4.6 (1st 2 paragraphs) -4.7 (pg. 147, 1st 2 paragraphs; pg. 149 “Diffusion of Substances -Through Membranes”, 1st 3 paragraphs; pg. 151 “The Diffusion of Ions -Through Membranes” to end of list of 3 types of channels on pg. 152.)

Individual lipid molecules can move Different particles penetrate the lipid layer Bilayer of amphipathic (molecule having both hydrophobic: non-polar and hydrophilic: polar parts) lipids Components are mobile Components can interact

3 Classes of Membrane Proteins:

Structure of Biological Membranes:  

All mems share common properties o 6nm thick (with associated water), stable, flexible, capable of self-assembly Different mems contain different types of lipids and proteins o Mems have different functions, in different cells and within an individual cell

EX. The inner mem of the mitochondria contains a very high concentration of protein 

WHY? Myelin sheath of a neuron contains a very low amounts of protein. Myelin sheath consists of layers of plasma mem, forming insulation around the nerve axon Biological Mems are Asymmetrical o Two leaflets have distinct lipid composition o In many plasma mems the outer leaflet contains GLYCOLIPIDS & GLYCOPROTIENS (lipids and proteins with carbohydrate attached)

Fluidity: an Important Function of Biological Mems: Mem fluidity is determined by: 



Nature of lipids in mem o UNSATURATED lipids INCREASE fluidity o SATURATED lipids REDUCE fluidity Temperature o WARMING INCREASES fluidity = liquid crystal o COOLING DECREASES fluidity = crystalline gel

Mem Fluidity is Crucial to Cell Function: 

 

Balance b/t ordered structure and disordered structures allows: o Mechanical support and flexibility, dynamic interactions b/t mem components (proteins can come together reversibly) & mem assembly and modification Mem fluidity must be maintained In response to changes in temp, lipid composition of mem can be changed by 1. Desaturation of lipids 2. Exchange of lipid chains

Biological Membranes are Dynamic:   

Lipids move easily, laterally, within leaflet Lipid mvmt to other leaflets is slow Mem proteins can diffuse within bilayer o Mvmt of proteins is restricted, some proteins do not move, rapid mvmt is spatially limited, long range diffusion is slow, biochemical modification can dramatically alter protein mobility in the mem (part of signal transduction) o

CHAPTER 4, 4-4 TO 4-7 LECTURE #4: TRANSMEMBRANE SUBSTANCE MOVEMENT

Lipid Rafts: Membrane Microdomains: Small areas of plasma mem enriched in certain types of lipids (cholesterol)   

Rafts are rigid Some mem proteins contain rafts My form ‘functional compartment’

Movement of Substances Across Cell Membranes    

Lipid bilayers do not allow many compounds to pass through them freely SMALL, UNCHARGED molecules cross mems relatively easily LARGE, POLAR, CHARGED compounds cannot easily cross lipid bilayers Mechanisms exist for controlled transport of many substances across mems

4 Ways to Move Molecules 1. Simple Diffusion: very small molecules, uncharged, down a concentration gradient EX. O2, CO2, H2O OSMOSIS

2. Diffusion Through a Channel: small, charged molecules, down a conc gradient EX Na+, K+, CA2+ Cl- (flow is ‘downhill’) ION CHANNEL: selective channels allowing only one type of ion to pass, own a conc gradient, often channels are gated A) Voltage-gated channels : respond to changes in charge within mem EX. K+ Channel B) Ligand-gated channels: Channel responds to binding to specific molecule EX. Acetylcholine C) Mechano-gated channels: Channels respond to physical force on mem EX. Cation channel in ear 3. Facilitated Diffusion: Compound binds specifically to integral mem protein called ‘FACILITATIVE TRANSPORTER’, change in transporter conformation allows compound to be released on other side of mem, compound moves down a conc gradient 4. Active Transport: Compound binds specifically to integral mem protein called ‘ACTIVE TRANSPORT’, change in transport conformation allows compound to be realeased on the other side of mem, compound moves AGAINST conc gradient, requires input of energy

LECTURE #5: THE EXTRACELLULAR MATRIX, CELLULAR COMPARTMENTS, MITOCHONDRIA & OXIDATIVE PHOSPHORYLATION Readings for ch 5 & 6 Extracellular Matrix: Glyocalyx: (found in most cells) the assembly of carbohydrate groups attached to proteins & lipids on the outside of plasma mem    

Mediates cell-cell and cell-ECM interactions Provides mechanical protection Serves as a barrier to some particles Binds regulatory factors

Proteogylcans: Proteins with chains of polysaccharides ECM serves important functions like:     

Sites for cell attachment Physical support for cells Separate/defines tissues Substrate through which cells can move Contains regulatory factors (signals)

-Chapter 7 - Introduction; section 7.1 pg. 236 – 238 up to (not including) section on ‘Collagen’; section 7.6 (Cell Walls) -Chapter 5 - Introduction; section 5.1; section 5.3 - 1st 2 paragraphs (mitochondria and ATP) -Chapter 15 - section 15.8 pg. 656-657 (apoptosis) (Fig. 15.37) -Chapter 8 - Introduction; section 8.1 (endomembrane system); -8.2 pg. 273 “Insights Gained From the Use of the Green -Fluorescent Protein” -1st paragraph; section 8.5 “Types of -Vesicle Transport and Their Functions”-1st 2 paragraphs

Plant Cell Walls: composed of cellulose microfibrils embedded in a polysaccharide matrix

   

Composed of cellulose, hemicellulose, pectin and proteins Provide structural support to cell and organism as a whole Protect cell from mechanical damage and pathogen attack Contain biochemical signals for cell

Origin of Eukaryotic Cells: THE ENDOSYMBIONT THEORY:

Mitochondria has 2 membranes: 1. Outer Mitochondrial Membrane (OMM)  Contains enzymes with diverse metabolic functions  Porins: large channels, when open mem is freely permeable 2. Inner Mitochondrial Membrane (IMM)  High protein:lipid ratio (3:1)  Double-layered folds = cristae  Cristae: increase mem surface area, conatin machinery for aerobis respiration and ATP formation  Rich in phopholipid called cardiolipin

Oxidative Phosphorylation: ATP synthesis in the mitochondria Step 1: Electron transport and proton pumping: generates an electrochemical gradient     

High energy elecrons pass from coenzymes in the matrix to electron carriers inIMM Series of ekectron carriers Energy transfer at each comples uased to pump protons (H+) from matrix into intermembrane space Ultimately low energy electrons are transferred to terminal accepter H2O produced

Step 1: Controlled movement of protons back across IMM  

Via ATP synthase Potential energy in electrochemical gradeitn across IMM converted to ATP in the matrix

LECTURE #6: APOPTOSIS, CTYOPLASMIC MEM SYSTEMS & VESICULAR TRANSPORT Mitochondria Play an Important Role in Programmed Cell Death (APOPTOSIS): Apoptosis: A normal occurrence in which a coordinated sequence of events leads to the death of a cell Characterized by:     

Shrinkage of cell Blebbing of the plasma mem Fragmentation of dna and nucleus Loss of attachment to other cells Engulfment by phagocytosis

Intrinsic Pathway: Initiated by intracellular stimuli (genetic damage, hypoxia, virus), proapoptic proteins stimulate mitochondria to leak protiens (cutochrome C), release of apoptotic mitochondrial proteins commits the cell to apoptosis

Cytoplasmic Endomembrane System: 

Early EM work revealed (within cytoplasm): mem bound organelles and vesivles, extensive network membranous canalds and stacks of sacs (= cisternae) o Endoplasmic reticulum (ER), Golgi complex, Lysosomes, Vacuoles, Endosomal Transport Vesicles

Polarized Structure of a Secretory Cell: Secreted Protein EX. Mucin, glycoprotein of mucus 

Synthesized in the rough ER, processed in ER, further processed in Golgi, concentrated in vesicles, delivered to PM

Using GFP to Track Cell Components:    

The Green Fluorescent Protein from jellyfish can be genetically fused with a cellular protein The fusion protein can be expressed in cells The cellular:GFP fusion protein fluoresces and can be visualized under a microscope Observation of the fusion protein provides information about the endogenous protein

Vesicular Transport (Trafficking) 



1. 2. 3. 4.

Transport of material between compartments o Organelle-PM (& vice versus) o Organelle-organelle o Utilizes transport vesicles: small, spherical membrane-enclosed organelles that bud off donor compartment and fuse with acceptor compartment targeted movement (directed) o uses cytoskeleton and motor proteins o sorting signals recognized by receptors movement of vesicle – uses ctyoskeleton and motor proteins Tethering vesicle to target compartment – via protiens calls Rabs Docking of vesicle to target compartment – uses proeins called SNAREs Fusion of vesicle and target mem  Orientation of a protein with respect to the cytoplasm and interior of mem-bound compartments is maintained during its travel through the endomembrane system

Examples of Vesicular Transport: ER  Golgi, Organelle  PM = exocytosis (eg secretion og neurotransmitter), PM  organelle, Organelle  organelle =endocytosis

LECTURE #7:ENDOPLASMIC RETICULUM & GOLGI TO ER VESICULAR TRANSPORT Readings for 7 & 8

Endoplasmic Reticulum (ER): is an interconnected network of mem enclosed tubules and flattened sacs  

Interior (=lumen) is separate from the sytosol ER mem is continuous with the outer mem of the nucleus

Smooth ER:   

Production of steroid hormones EX endocrin cells Detoxification EX liver cells Sequestration EX in muscle cells

Rough ER:    

Protein synthesis, modification & transport – for proteins targeted to ER Synthesis of mem phospholipids Glycosylation of proteins – addition of carbohydrate chains Protein folding (quaity control)

-Chapter 8- 8.3 pg. 279 – to end of 3rd paragraph on pg. 283 -“The Endoplasmic Reticulum”; pg. 289 “From the ER to the Golgi Complex: The First Step in Vesicular Transport” - 8.4 pg 290-292 to end of section “Glycosylation in the Golgi Complex” - 8.5 “Types of Vesicle Transport and Their Functions”- 1st 3 paragraphs (pg. 295)

Protein Synthesis: (PS) In the cytoplasm ribosomes synthesize polypeptides from mRNA (=translation) 1) Translation completed on free ribosomes: cytosolic proteins, peripheral mem proteins , these proteins will be targeted to nucleus, mitochondria, peroxisomes, chloroplasts 2) Translation completed by ribsomes attached to ER mem (rough ER) PS in the Rough ER: Secreted proteins, integral mem proteins, soluble proteins associated with the inside (lumen) of endomem system Ribosomes are targeted to the ER mem by a ‘signal sequence’ Cotranslational Protein Imports: After translation of Signal Sequence 1) 2) 3) 4)

Signal Recognition Particle (SRP) binds to signal sequence- translatin STOPS Targeting of translation complex to ER – SRP beinds to SRP receptor Srp is released and ribosome binds TRANSLOCON – protein synthesis resumes Polypeptide enters the ER (through translocon) as it is translated

Once a protein is fully synthesized and properly folded it has 1 of 2 options: 1) It is retained in the ER if that is where the protein functions 2) It is transported from the ER to the golgi complex for further modification and delivery to distal parts of the the biosynthetic/secretory pathway Exit sites: mem and ER lumen bud off to form TRANSPORT VESICLES  

ER-Golgi Intermediate Compartment (ERGIC) Transport vesicles fuse to form larger vesicles & interconnected tubules

Golgi Complex:    

Structure: smooth, flattened, disk-like, cisternae, curved like shallow bowl, show polority CGN acts as a sorting station TGN sorts proein into different types of vesicles Functions: processing plant of the cell, modification of proteins and lipids, transports and sorts proteins= Chapter 8 - Cytoplasmic Membrane

COPI & COPII: Proteins assemble on the cytosolic surface of donor mems at sites where budding takes place  

COPI – coated vesicles move in retrograde direction COPII – coated vesicles move in entorograde direction

LECTURE #9: LYSOSOMES, PLANT CELL VACUOLES, CYTOSKELETON

Systems - 8.6: “Lysosomes” - 8.7: “Plant Cell Vacuoles” Readings for Lectures 9 and 10 Chapter 9 - The Cytoskeleton and Cell Motility - Introduction - 9.1: “Overview” - 9.3: “Microtubules” pg. 330 - 335 (including section “Kinesins”, 1st 3 paragraphs); pg. 337 - 339 (“Cytoplasmic Dynein”); pg 339 (“Microtubule-Organizing Centers” 1stparagraph). - 9.4: “Intermediate Filaments” (1st 3 paragraphs, pg. 354)

Clathrin: coated vesicles move from TGN to other vesicles (lyso, endo, vac) Lysosomes: digestive Organelles    

25nm-1000nm, ph of 4.6 Hydrolytic enzymes – acid hydrolases Lysosomal mem – glycosylated proteins – protective lining next to lumen Function: 1. Autophagy = organelle turnover (destruction of organelles and their replacement), lysosome fuses with ER-derived autophagic vacuole (forms autolysosome), contents enzymatically digested (forms residual body: released = exocytosis, retained = lipofuscin granules) 2. Degradation of internalized material EX PM components, Bacteria

Plant Vacuoles: fluid-filled, mem bound, takes up ~90% of cell Tonoplast: vacuolar mem, contains active transport systems that generate high interior (ion) 

Function: 1. Intracellular digestion- low ph 2. Storage – solutes & and macromolecules, chemical storage 3. Mechanical support; turgor pressure, gives rigidity to plant, stretches cell wall during growth

Cytoskeleton:  

Dynamic network of interconnected filaments and tubules that extends throughout the cytosol of eukaryotes Function: 1. Structural support 2. Spatial organization within cell 3. Intracellular transport 4. Contractility and motility

Microtubules:   

 



largest cytoskeletal element (25nm diameter) polymer of a-tubulin B-tubulin 2 major types: o Axonemal MT: highly organized, stable, part of structuresninvloved in cell mvmt o Cytoplasmic MT: loosely organized, very dynamic, located in cytosol Fast-growing plus end, slow-going minus end Micro-associated proteins (MAPs) o Motor MAPs: 2 main types: kinesin and dynein, use ATP to generate force, can move along MT track, can generate sliding force b/t MT’s o Non-Motor Maps: Control MT organization in cytosol Dynein: minus end-directed, Kinesin: plus end-directed o Both are motor proteins that use ATP as power, transport vesicle ect along MT tracks, direction of mvmt is polarized D(- to +), K(+to-), composed of heavy & light protein chains

LECTURE #10: CYTOSKELETON, MT IF MF, MAPS AND MOTOR PROTEINS Intermediate Filaments: non-polar and provide structural and mechanical support  



Intermediate size (10-12nm), exclusize to multicellular animals, provie structural support, mechanical strength, stable (relative to MT), fibrous proteins, contain central a-helical domain 5 class (I-V); examples o Keratins: epithelial cells o Neurofilaments: neurons o Lamins: nucleus of all cells Structure: o A-helical domains wrap around each other forming rope-like dimer o Monomers are aligned in parallel; if dimers are polar molecules o 2 dimers associate anti-parallel to make tetramer therefore assembled filaments are not polar

Microfilaments (MF): polymers made up of G-actin monomers- important for cell shape   





Smallest cytoskeletal element (~8nm) Polymer of protein actin Polypeptide o Individual molecules o Polymerized microfilament Several well-characterized functions o Maintenance of cell shape o Vell mvmt o Cytokinesis o Muscle contraction F-actin MF o G-actin monomers have polar structure o Monomers are incorporated into the filament in the same orientation o F-actin filament is polar: plus & minus ends

LECTURE #11: MAPS AND MOTOR PROTEINS, MYOSIN AND ACTIN-BINDING PROTEINS, THE NUCLEUS Actin-binding proteins: 

EX



o Nucleating proteins, monomer-polymerizing proteins filament-depolymerizing Directed Cell Motility: coordinated activity of actin-binding proteins controls microfilament formation in a lamellipodium to allow directed cell movement

Myosin: actin associated motor protein



Large family of proteins, most move toward plus end of microfilament, divided into 2 broad groups 1. Conventional mysosins: type II, primary motors for cmuscle contraction 2. Unconventional myosins: type I and III-XVIII

Nucleus: 



Function: o Storage, replication and repair of genetic material, exression of genetic material (transcription: mRNA, tRNA, rRNA & splicing) ribosome bios...