Biol 1090 Flashcards
Enucleation
The process where cells (red blood cells) eject their nucleus.
Differentiation
Cells specialize
Miller Urey Experiment and key takeaways
Simulated conditions on early earth and found that that simple inorganic compounds in the presence of energy can form simple then later more complex organic compounds. Some of which are amino acids.
Primordial Hypothesis
(Oparin’s and Haldane’s)
Commonly accepted conditions on primative earth favored chem rxns that synthesis more complex organic compounds from simpler inorganic precursors.
Cell Theory
- All living organisms are composed of 1 or more cells
- Cell is the most basic unit of life (first 2 by Schleidon and Shwann)
- All cells come from cells (Virchow)
Basic Properties of Cells
- Highly complex and organized
- Activity controlled by genetic programing
- Can reproduce
- Assimilate and Use energy
- Carry out chem rxns (enzymes)
- Engage in mechanical activities (engulf)
- Respond to Stimuli
- Capable of self regulation
- Evolve
Prokaryotes
Bacteria and Archaea
- no defines nucleus or organelles
- single celled orgs
- 1-10 nanometers
- small ribosomes
- reproduce asexually
- genetic material in nucleoid
- DNA is circular fashion (plasmid)
Eukaryotes
Fungi, plants, animals, protozoa
- multicellular organisms
- 10-100 nanometers
- nucleus and organelles
- ribosomes are large
- genetic material in nuclear compartment (chsomes)
Eukaryotes - Animals
- lysosomes
- microvilli
Eukaryotes - Plants
- cell walls
- vacuoles (turgor pressure)
- chloroplasts
- plasmodesmata (connect neighboring plant cells)
Virus Genome
DNA or RNA
Virus
macromolecular packages that can function and reproduce only with living cells.
Virion
Inanimate particle outside cells
Virus Baltimore Classification
Retrovirus - RNA type, can insert a copy of its genome into a DNA host cell
Hepadnavirus - DNA type
Filovirus - single stranded negative sense DNA
Adenovirus - resperatory illness
Bacteriophage - Infects and replicates within bacteria and archaea
Negative Sense RNA
must be transcribed to mRNA
Positive Sense RNA
can be directly translated into proteins
Host Range
Narrow - infect cells in just a specific part of humans
Wide - (rabies) can infect humans, bats, foxes, racoons
Non-lytic
Viral DNA or RNA inserts into host genome (provirus). Infected cell can survive often with impaired function
Lytic
Production of virus particles ruptures and kills the cell
Monopartite
Entire genome occupies one nucleic acid molecule
Multipartite
Genome occupies several nucleic acid segments
RNA Vaccines
Tricking body cells into producing fragments of a virus (antigens).
Can be made more effective by incorporating instructions for a replicase (to make more antigens)
HIV
Retrovirus - inserts copy of genome into DNA host cell (stays in DNA forever_
Hepadnavirus
Hepatitis B
Filovirus
Ebola
Adenovirus
Cold and Flu
Bacteriophage
Attack bacteria and archaea
Slime molds
- eukaryotic single celled organisms
- reproduce with spores
- many nuclei
- can move around and respond to environment
Virus (Yes) can/are
- complex and organized
- controlled by genetic programing
- reproduce (yes and no)
- evolve
Only in plant cells
- chloroplasts
- cell wall
- vacuoles
- plasmodesmata
Only in animal cells
- lysosomes
- microvilli
Phospholipid bilayer properties
- trilaminar (lipid bilayer)
- made of lipids (phospholipids)
- hydrophobic and hydrophilic parts (phospholipids are amphipathic)
Phospholipids Structures/patterns
Micelle - circular no lumen
Liposome - circular two layers lumen
Bilayer sheet - (trilaminar)
Phospholipids (structure)
- 2 fatty acyl molecules (esterified 1,2)
- glycerol
- phosphate (3 by phosphate residue)
- variable portion of head group (choline, serine, inositol)
Sphingolipid
- glycerol replaced with sphingosine
- amide linked to fatty acid and phosphate group
enriched in nervous system (signal transduction + cell recognition)
Fluid mosaic includes
- phospholipids
- peripheral, transmembrane proteins
- ## cholesterol
Lipid Rafts
Portions of the bilayer that include a higher concentration of specific proteins like sphingolipids or cholesterol
Types of membrane proteins
- integral
- peripheral
- lipid anchored
Integral proteins and functions
- transport of nutrients and ions
- cell-cell communication
- attachment
How can temperature affect lipid structure
- denaturation of lipids
- exchange of lipid chains
Transmembrane protein structure
- ## hydrophobic portion within bilayer (alpha helices) (transmembrane protein domain)
TM4SFs Tetraspanins
- 4 alpha helices
- 2 extracellular domains
cell, adhesion, motility, proliferation
Simple Diffusion
- passive
- non-mediated
- will concentration gradient (down)
- small uncharged particles (CO2, O2)
Diffusion through Channel
- passive
- non-mediated
- through channels
- small charged particles
Na+, K+, Ca2+, Cl- - down concentration gradient
- channels are selective
Facilitated Diffusion
- passive
- mediated
- substrate binds directly to facilitative transporter
- change in conformation allows compound to be released on other side
- down concentration gradient
Active Transport
- active
- mediated
- substrate binds to active transporter
- hydrolysis of an ATP molecule allows molecules to be released on other side
- against gradient
Na+/K+ transporter (maintains action potential) - 3Na+ out, 2K+ in for each ATP
- against gradient
Ion Channels
Allows channels to respond to stimuli
1) voltage-gated (Na+, K+)
- respond to changes in charge (action potential)
2) Ligand-gated (acetylcholine)
- responds to binding of a specific molecule on surface of ligand
- causes a conformational change to channel
Ways of targeting ion channels
TTX - Na+ channel blocker
- binds to voltage-gated Na+ channels and blocks passage of Na+ (inhibits firing of action potentials)
Curare - competitive antagonist
- occupies same position on receptor and causes no response
Symporter
- rely on chem gradient of another molecule to push a compound up its concentration gradient
- Na+ glucose symporter (2Na+ 1 glucose) (Na+ is with gradient into cell)
Antiporter
- concentration gradient of one molecule is used to transfer a second molecule in opposite direction
- Na+/H+ exchanger
- Na+ into cell, H+ out of cell
Cell Structure (hypertonic, hypotonic, isotonic)
Hypertonic - more solute out of cell, shrink
Isotonic - normal
Hypotonic - more solute in cell, burst/lysed
Signal Transduction
- binding of ligand to a receptor
- signal transduction via second messenger (cAMP, calcium, G-protein)
- cellular response
Glycogenolysis
epinephrin converting glycogen in liver to glucose
- glycogenin(acts as a primer to polymerize first glucose molecule) surrounded by glucose units
Anchor Proteins
- interact with components of the ECM
ECM (extracellular matrix) roles
Abundant in connective tissues
- cell adherence
- communication between cells - - cell shape, mechanical support, structural integrity
- serves as barrier, filters out some particles
ECM components
- proteins (collagen)
- glycoproteins (laminin, fibronectin)
- proteoglycans (proteins with chains of polysaccharides)
Plant Cell Walls (ECM)
- cellulose, hemicellulose, pectin, proteins
- structural support
- protection
Theory of Endosymbiosis and Evidence
- organelles from euk cells with two membranes (mit, chlo) are formerly free living prokaryotes taken inside one another in endosymbiosis
Evidence:
1) binary fission of mitochondria and plastids
2) circular DNA in organelles like bacteria
Aerobic cellular respiration
Converting glucose to energy (stored in ATP) in the presence of oxygen
Outer Mitochondrial Membrane
- contains many enzymes (monoamine oxidases)
- has porins (for ATP, sucrose)
Inner Mitochondrial Membrane
- high protein to lipid ratio (3:1)
- double layers fold called cristae
- rich in cardiolipin - phospholipid (optimal membrane function)
Mitochondrial Matrix Makeup
Matrix - high protein content, gel like consistency, contains mitochondrial ribosomes and DNA
Substrate level phosphorylation
*specific to glycolysis
- hydrolysis rxns release enough energy to phosphorylate ADP to ATP
12% or ATP
Oxidative phosphorylation
- chemical energy of organic molecules is transferred first to electron carriers to create an electrochemical gradient to power ATP synthesis
88% of ATP
Electron Carriers
Oxidized - accepts e
Reduced - donates e
NAD+, NADH
FAD, FADH2
Photosynthesis
building carbs using energy from sunlight and CO2
Light-Dependent Reactions
- occurs in thylakoid membranes
- chlorophyll is light harvesting complex
-e enters ETC
H+ pumped into thylakoid lumen
Light-Independent Reactions
Calvin Cycle
- occurs in stroma
- ATP and NADPH made in light reaction used to make CH2O
Apoptosis
Death of a cell in a coordinated sequence of events
Roles of Apoptosis
bmp - expression of non-active MnpReceptors in duck embryonic limbs results in webbed feet (reduces apoptosis)
Plants - uses apoptosis to cause fenestrated leaves
Apoptotic Cells (characteristics)
- shrinkage
- blebbing (bulging of plasma membrane)
- fragmentation of DNA or nucleus
- engulfment by phagocytosis
Cytochrome C
causes production of caspases
- disrupts cell adhesion
- destroy lamins
- breaks down cytoskeleton
- activates DNase
Apoptosis and Diseases
too little - cancer
too much - alzheimers, parkinsons
Cytoplasmic Endomembrane system
- ER
- endosomal transport vesicles
- golgi complex
- lysosomes
- vacuoles
Secreted Proteins (mucin)
- synthesized in rough ER
- processed in the ER
- processed in golgi
- concentrated in vesicles
- delivered to plasma membrane for secretion
GFP Tracking
Green Fluorescent Protein from Jellyfish
- can be fused with other cellular proteins
- can be expressed in cells when fused
Vesicular Transport
uses transport vesicles
- movement - uses cytoskeleton and motor proteins (anterograde or retrograde)
- tethering - via RAB proteins
- docking - uses SNARE proteins (provides energy for fusion)
- fusion - fuses vesicle and target membrane
Exocytosis + Endocytosis
Exocytosis - e.g organelle to plasma membrane
e.g secretion of neurotransmitters
Endocytosis - e.g PM to organelle
e.g Activity-dependent internalization pf AMPA receptors
Rough ER
- have ribosomes
- protein processing
- synthesis of membrane phospholipids
- glycosylation of proteins
- protein folding and quality control (chaperone)
- Protein synthesis, modification, and transport
Smooth ER
-no ribosomes
- lipid synthesis
- production of steroid hormones
- detoxification
- sequestration (storage of Ca2+)
Ca2+ in cytosol is:
- bound by Ca2+ binding proteins
- forced through pumps and transporters
- or sequestered (in sinks)
Where are proteins translated (free vs. bound)
- free - cytosolic prots, peripheral membrane prots, prots to nucleus, mitochondria, peroxisomes, or chloroplasts
- bound - secreted prots, integral membrane prots, soluble prots associated with lumen of endomembrane system
- all protein translation begins on free ribosomes not associated with the ER
Signal Sequence
to target ribosomes to ER membrane
- amino terminus
- contains consecutive hydrophobic amino acids
- directs synthesis to ER compartment
Endocytic Pathways of Protein Sorting
1) protein retained in ER
2) transported to golgi (futher modifications), and delivered to distal parts of secretory pathway (maybe outside the cell)
Zellweger Syndrome
- no peroxisomes made (mutation)
- autosomal recessive
- brain development defects
- hypomyelination
- apnea
- abnormal renal function
- does not survive a year
Cystic Fibrosis
- mutation in CFTR
- deletion of 3 nucleotides
- loss in phenylalanine (508)
- proteins degraded in ER fail to reach surface
OR - CFTR transporter affected
- cannot produce proper lubricating fluid in lungs
- sticky lung
ER to Golgi pathway
Proximal to distal
Cis to Medial to Trans
Golgi Complex Structure
- smoot flattened cisternae
- about 8 cisternae per stack
- few to thousand of stacks per cell
- curved
- polarity
- cisternae biochemically unique (different enzymes to modify)
- membrane supported by protein skeleton (actin, spectrin)
- scaffold linked to motor proteins that direct movement of vesicles into and out of golgi
CGN and TGN
CGN - sorting station (should proteins continue on to next golgi or back to ER)
TGN - sorts proteins into different types of vesicles (diff destinations)
Golgi Function
Processing plant
- sorts
- modifies
- ships (vesicles)
- synthesis of polysaccharides and modification of proteins and lipids
(glycosylation and proteolytic modification)
Coat Proteins
COPI (retrograde/reverse), COPII (anterograde/forward)
- helps form vesicles
- helps select “cargo”
Regulated and constitutive secretory pathways
Constitutive (continual) - mucin secretion
Regulated - insulin and neurotransmitter release
Lysosomes
- digestive organelles
- 25 nm to 1 (weird u)m
- internal pH or 4.6 (proton pump or H+-ATPase regulated)
- contains hydrolytic enzymes (acid hydrolases)
- membrane has glycosylated proteins that act as a protective lining against acidic lumen
Coatomers
Clathrin and AP complex - AP/clathrin coated vesicles move from TGN to other vesicles and help form endocytic vesicles to move from PM to endo/lysosomes
Autophagy
normal dissembly of unecessary or disfunctional cell components (organelle turnover) by lysosomes
Degredation (lysosomes)
recycling of PM components and destroying pathogens (only in phagocytic cells)
Lysosome Functions
Autophagy and degredation of internalized material
Plant Vacuoles
Intracellular digestion - regulate cytoplasmic pH (pH about 5) acid hydrolases
- sequestration of toxic ions
Mechanical support - regulate turgor
Storage - store amino acids, sugar, CO2 in form of malate, and chemical storage (anthocyanin)
Cytoskeleton Function
1) structural support
2) spatial organization within cells
3) intracellular transport
4) contractility and motility
Components of the Cytoskeleton
- Microfilaments (MF)
- Microtubules (MT)
- Intermediate filaments (I)
Microtubules (MT)
Polymer of alpha-tubulin and beta-tubulin
Types of Microtubules
Axonemal MT:
- highly organized and stable
- part of structures involves in cell movement
Cytoplasmic MT:
- loosely organized and unstable
- located in cytosol
MT assembly/disassembly
- rapid turnover of MTs in vivo
- shrinking occurs rapidly at plus end (catastrophe)
- formation if MT is regulated
- MTOC is central site of MT assembly
MT Proteins (MAPs)
- modulate assembly (MAP2 or Tau)
- mediate interaction with other cells (vesicles/organelles)
Classes of MAPs
1) Non Motor MAPs - control MT organization in cytosol (Tau)
2) Motor MAPs - kinesin and dynein
- use ATP to generate force
- can move material along MT tract
- can generate slide force between MTs
Non motor MAPs
Control MT organization in cytosol
- stabilize MTs
- stimulate assembly
Defects in Tau
- cause neurofibrillary tangles
- cause alzheimer’s disease
Motor MAPs
- power intracellular transport
- kinesin (+end directed)
- dynein (- end directed)
They move along MT - can generate a sliding force btw MTs
Kinesin and i Dynein in Zebrafish
- survival mechanism
- in dark melanin granules are dispersed outward by kinesin (appears darker)
- in light melanin granules are aggregated forward by dynein (lightly coloured)
MTOC
Central site of MT assembly
- only in euk cells
2 types:
1) basal bodies (cilia, flagella)
2) centrosomes (spindle formation)
Actin Molecules
- central component of MFs
- monomer: G-actin or globular
- polymer: F-actin or fibrous
Actin binds and slowly hydrolyzes ATP
Intermediate Filaments
- arrangement of non fibrous alpha helical proteins
- non polar
provides structural support and mechanical strength - stable compared to MTs and MFs
- not used in transport
Microfilaments
- double helix of actin monomers
- maintains cell shape
- cell movement
- vesicle transport
- muscle contraction
- cytokinesis
Actin Associated Motor Proteins
Myosins (motor proteins):
- primarily move towards the + end of MF
1) conventional myosins: type 1, for muscle contraction
2) unconventional myosins: type 1 and type III-XVIII
- generate force
- contribute to motility in non muscle cells (lamellipodium/push)
(pull)
Functions of the Nucleus
- storage repair and replication of genetic material
- expression if genetic material (transcription, RNA splicing)
- ribosome biosynthesis
Nuclear Lamina
- made of lamins (intermediate filaments) only found in animals cells (the lamin)
- bound to inner membrane
- provide structural support for nuclear envelope
- attachment sites for chromatin
Nuclear Pore complex
- composed of NUPs (nucleoporins)
- octagonal symmetry/basket like
- projects into cytoplasm and nucleoplasm
Transport: - passive: under 40 kDA, rapid, 100 molecules/minute/pore
- regulated: larger molecules, slow, 6 molecules/minute/pore
