bio exam

• 1. information
• 2. chem
• 3. compartments

• -cell = structural unit of life
• -all organisms are composed of one or more cell types
• -cells can arise only by the division of a preexisting cell

• -highly complex and organized
• -activity is controlled by a genetic program
• -can reproduce and make copies of themselves
• -assimilate and utilize energy
• -carry out many chemical reactions
• -engage in mechanical activities
• -respond to stimuli
• -capable of self regulation
• -they evolve

• prokaryotic
• eukaryotic

• bacteria 
• structurally simpler

• protists, fungi, plants, animals
• structurally more complex
• large number of parts
• compartments- membrane bound structures dedicated to a particular function and components

• highly complex and organized
• large number of parts
• organized with respect to time and space
• parts interact with little tolerance of error
• fidelity of interactions is mantained through control of regulation of parts 
• cellular organization is very consistent
• conserved throughout evolution

enables movement of molecules into and out of the nucleus

• actin filaments
• microtubules
• intermediate filaments

• contribute to cell shape and movement
• provide structural support
• support transport of materials

• non cellular macromolecular packages that can function and reproduce only within living cells
• outside of cells a virus exists as an inanimate object called viron

• dna 
• rna
• protein capule (capsid)

a cell surface via proteins

rabies can infect cells in dogs bats humans

human cold infects epithelial cells of human resp system

• hijacks cellular machinery to synthesize nucleic acids/proteins
• assembles new virus particles

• lytic
• nonlytic/ integrative

production of viral particles ruptures/kills cell ex influenza

• viral dna is inserted in host genome=provirus
• viral progeny bud at cell surface
• cell can survive but impared function

• cell boundary
• enclose compartments
• control movement in and out of cell
• allow response to external stimuli 
• enables interactions between cells
• provides scaffold/ support for biochemical activities

individual lipid molecules can move

different particles penetrate the lipid layer

• bilayer of amphipathic lipids
• amphipathic= both hydrophobic and hydrophilic regions

non polar

polar

• integral 
• peripheral 
• lipid anchored

span lipid bilayer

associate with surfaces of lipid bilayer

attach to a lipid in the bilayer

• interact and are mobile 
• contain hydrated lipid bilayer

• 6 nm thick
• stable
• flexible
• capable of self assembly

• lipids and proteins
• have different function in different cells and within the same cell

• ex inner membrane of mitochondria contains high conc of protein
• myelin sheath of a neuron contains low protein

asymmetrical

• 2 leaflets have distinct lipid composition 
• outer leaflet has glycolipids and glyco proteins

glyco means they have carbohydrates

• nature of lipids in membrane 
• unsaturated lipids increase fluidity 
• saturated lipids decrease fluidity
• temperature 
• warming =inc fluidity = liquid crystal
• cooling = dec fluidity = crystalline gel

• mechanical support and flexibility 
• dynamic interactions between membrane components
• membrane assembly and modification

crucial to cell function

• temp
• desaturation of lipids
• exchange of lipid chains

regulates membrane fluidity

laterally within leaflet

slow

• proteins movement is restricted
• some dont move
• rapid movement is spatially limited
• long range diffusion is slow
• biochemical modification can dramatically alter protein mobility in the membrane (signal transduction)

• small area of plasma membrane that are enriched in certain types of lipids eg cholesterol
• relatively rigid
• membrane proteins accumulate in rafts
• may form functional compartment

• lipid bilayers do not allow many compounds to pass through them freely 
• small uncharged molecules cross membranes relatively easily (02 c02 no h20)
• large polar charged compounds cannot easily cross lipid bilayers
• specific mechanisms exist for the controlled transport of many substances across membranes

• simple diffusion
• diffusion through channel 
• facilitated diffusion 
• active transport

• passive, nonmediated
• small molecules uncharged move down concentration gradient

• passive non mediated 
• small charged molecules 
• move down concentration gradient

• integral membrane proteins that are aqueus 
• selective allow one kind to pass
• move down 
• channels gated can open and close

• channels are selective, allowing
• only one type of ion to pass
• • ions move down concentration
• gradient
• • often channels are ‘gated’ (can be
• open or closed)

• Voltage-gated channels (e.g. K+ channel)
• Ligand-gated channels (e.g. acetylcholine)
• Mechano-gated channels

• ➡ Channel responds to changes in charge across
• membrane

• Channel responds to binding of specific molecule
• (a ‘ligand’)

• Channel responds to physical force on
• membrane (e.g. stretch)

• • Compound binds specifically to
• integral membrane protein called a
• ‘FACILITATIVE TRANSPORTER’
• • Change in transporter conformation
• allows compound to be released on
• other side of membrane
• • Compound moves down a
• concentration gradient

• • Compound binds specifically to
• integral membrane protein called
• an ‘ACTIVE TRANSPORTER’
• • Change in transporter
• conformation allows compound
• to be released on other side of
• membrane
• • Compound moves against a
• concentration gradient
• • Requires input of ENERGY

The Na+/K+ ATPase maintains cellular [Na+] and [K+] using ATP

• Glycocalyx = assembly of carbohydrate groups attached to
• proteins and lipids on the outside of the plasma membrane
• - mediates cell-cell and cell-ECM interactions
• - provides mechanical protection
• - serves as a barrier to some particles
• - binds regulatory factors

• organized network of material
• produced and secreted by cells

• sites for cell attachment
• - physical support for cells
• - substrate through which cells can move
• - contains regulatory factors (signals)
• - separate/define tissues

proteins with chains of polysaccharides

• • composed of cellulose, hemicellulose, pectin and
• proteins
• • provide structural support to cell and to organism
• as a whole (~ ‘skeleton’)
• • protect cell from mechanical damage and pathogen
• attack
• • contain biochemical signals for cell

• cellulose microfibrils
• embedded in a polysaccharide matrix

• protein synthesis, many metabolic
• pathways

• contains genome, DNA, RNA synthesis,
• ribosome assembly

synthesis of lipids, synthesis of proteins

• protein modification, packaging of
• proteins and lipids

degradation of cellular material

sorting and recyclingq

• atp synthesis 
• apoptosis

• photosynthesis
• atp synthesis

oxidation of toxic molecules

• ancestral prokaryote
• infolding of plasma membrane 
• endosymbiosis 
• ancestral eukaryote

fusion and fission

• outer mitochondrial membrane
• inner mitochondrial membrane

• contains many enzymes with diverse metabolic functions 
• porins 
• - large channels 
• -when open membrane is feely permeable

• high protein lipid ratio 3:1
• double layered folds = cristae
• rich in phopholipid called cardio lipin

• increase membrane surface area 
• contain machenery for aerobic respiration and atp formation

• intermembrane space 
• matrix

• high protein - gel like 
• mitochondrial ribosomes
• mitochondrial dna

• electron transport and proton pumping 
• generates and electrochemical gradient 
• hihg energy electrons pass from coenzymes (NADH an FADH2 ) in the matrix to electron carriers in IMM
• series of e carriers = electron transport chain 
• energy transfer at each complex used to pump protons from matric into intermembrane space 
• low energy e is transferred to terminal e acceptro O2
• water is produced

controlled movement of protons back across IMM

via atp synthase 

potential energy in electrochemical gradient across inner mitochondrial membrane converteed to atp in the matrix

normal occurrence in which a coordinated sequence of events leads to death of a cell

• shrinkage of cell 
• blebbing of the plasma membrane
• framentation of DNA and nucleus
• loss of attachment to other cells
• engulfment by phagocytosis

• initiated by intracellular stimuli
• proapoptotic proteins stimulate mictochondria to leak proteins
• release of apoptotic mitochondrial proteins commits the cell to apoptosis

• disrupts cell adhesion
• destroys lamins
• breaks down cytoskeleton 
• activates DNase

• within the cytoplasm contains membrane boudn organelles and vesivles 
• extensive network of membranous canals and stack of sacs = cisternae

stacks of sacs

• endoplasmic reticulum 
• golgi complex
• lysosomes
• vacuoles
• endosomal transport vesicles

• synthesized in the rough er
• processed in the er
• further processed in golgi 
• concentrated in vesicles
• delivered to plasma membrane

use green fluorescent protein t

• transport of material between ompartments 
• uses transport vesicles
• targeted movement --directed and uses cyto seleton and motor proteins and sorting signals are recognized by receptors

small spherical membrane enclosed organelles that bud off donor compartment and fuse with acceptor compartment

via Rabs

proteins called snares

maintained

organelle to plasma membrane

plasma membrane to organelle

• inter connected network of membrane encoled tubules and flattened sacs
• inerior = lumen and separate from cytosol
• er membrane is continuous with the outher membrane of the nucleus

• production of steroid hormones
• detoxification -- contains enzymes that modify foreign compounds 
• sequestration/ storage of Ca 2+

• protein synthesis modification and transport 
• synthesis of membrane phospholipids
• gycosylation of proteins -- add carbohydrate
• protein folding - quality control

• In the cytoplasm,
• ribosomes synthesize
• polypeptides from mRNA
• (= translation)

• All protein translation begins on free ribosomes
• 1) Translation completed on free ribosomes
• - cytosolic proteins
• - peripheral membrane proteins
• - these proteins will be targeted to nucleus,
• mitochondria, peroxisomes, chloroplasts
• 2) Translation completed by ribosomes attached to ER
• membrane (rough ER)

• secreted proteins
• ✤ integral membrane proteins
• ✤ soluble proteins associated with inside
• (lumen) of endomembrane system
• ‣ e.g. proteins that function within the
• ER, Golgi, lysosomes

• protein contains ‘signal sequence’
• - located at its amino-terminus (N-terminus)
• - contains several consecutive hydrophobic
• amino acids
• •
• ‘signal sequence’ directs synthesis to ER
• • protein moves through channel into ER
• = COTRANSLATIONAL IMPORT

• 1) Signal Recognition Particle (SRP) binds
• to signal sequence – translation STOPS

• 2) Targeting of translation complex to ER
• [SRP/ribosome/new polypeptide]
• - SRP binds to SRP receptor
• 3) SRP is released and ribosome binds
• TRANSLOCON
• - protein synthesis resumes
• 4) Polypeptide enters the ER (through the
• translocon) as it is translated

• 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 biosynthetic/secretory
• pathway.

exocytosis

endocytosis

• membrane and ER
• lumen bud off to form
• TRANSPORT VESICLES

• - region between ER & Golgi complex
• - transport vesicles fuse to form larger vesicles &
• interconnected tubules
• = Vesicular-Tubular Clusters (VTCs)
• - these then form the ‘cis-Golgi network’

ER to GOLGI

cis medial trans

• -smooth, flattened, disk-like cisternae
• (~ 0.5 - 1 micron in diameter)
• ~ 8 (or fewer) cisternae/stack
• (range from a few to several 1000 stacks per cell)
• - curved like a shallow bowl
• - shows polarity:
• ‣ cis - medial - trans cisternae
• ‣ cisternae are biochemically unique
• - membrane supported by protein “skeleton” (actin, spectrin)
• - scaffold linked to motor proteins that direct movement of
• vesicles into and out of the Golgi

• acts as a “sorting station”
• i.e., sorts whether proteins
• should continue on to the next
• Golgi station or be shipped back
• to the ER

• sorts protein into different types
• of vesicles
• - Vesicles go to Plasma membrane
• or other intracellular destinations
• (e.g. lysosomes)

step wise

• ‘
• • synthesis of complex polysaccharides
• • modification of proteins and lipids
• - glycosylation (glycoproteins & glycolipids)
• - proteolytic modification
• • TRANSPORT and sorting of proteinsprocessing plant’ of the cell

• trans
• cisterna, enter the trans-Golgi
• network (TGN) and are then
• sorted and delivered to their
• final destinations
• ➡ endosomes
• ➡ secretory granules
• ➡ lysosomes
• ➡ plasma membrane

• coat has 2 functions
• (i) helps form the vesicle
• (ii) helps select ‘cargo’

• COPI and COPII proteins assemble on the cytosolic surface
• of donor membranes at sites where budding takes place.

• coated vesicles move
• from TGN to other vesicles
• (e.g. lysosomes, endosomes,
• plant vacuoles)

retrograde direction

• COPII-coated vesicles move
• in anterograde direction

• constitutive 
• regulated

digestive organelles

• AUTOPHAGY = organelle turnover
• - lysosome fuse with autophagic vacuole forms autolysosome 
• - contents enzymatically digested
• ➡ forms residual body
• 2. Degradation of internalized material
• e.g. - plasma membrane components
• - bacteria (in phagocytic cells)
• released (exocytosis)

• tonoplast
• = vacuolar membrane
• - contains active transport
• systems that generate
• high interior [ion]

• ✤ intracellular digestion
• - low pH, acid hydrolases
• ✤ mechanical support; turgor pressure
• - gives rigidity to plant - supports soft tissues
• - stretches cell wall during growth
• ✤ storage
• - solutes and macromolecules
• - chemical storage (no excretory system)
• ‣ isolate toxic compounds
• ‣ sequesters pigments (e.g. anthocyanin)

• Dynamic network of interconnected filaments
• and tubules that extends throughout the cytosol
• (and some organelles) of eukaryotes

• 1) structural support
• 2) spatial organization within cell
• 3) intracellular transport
• 4) contractility and motility

• ‣ largest cytoskeletal element (25 nm diameter)
• ‣ polymer of proteins α-tubulin and β-tubulin
• ‣ 2 major types:
• (i) axonemal MT
• - highly organized, stable
• - part of structures (axoneme) involved in cell
• movement (e.g cilia, flagella)
• (ii) cytoplasmic MT
• - loosely organized, very dynamic
• - located in cytosol

• - α/β heterodimers form long protofilaments
• - 13 protofilaments form longitudinal array
• ‣ hollow cylinder
• - heterodimers aligned in same direction (head to tail)
• ‣ STRUCTURAL polarity
• - MTs have fast-growing ‘plus’ end
• and slow-growing ‘minus’ end

• Dynamic
• Assembly and Disassembly

• - in vivo, this leads to rapid turnover of most MTs
• within cell (half-life is minutes)
• ‣ ‘dynamic instability’
• - shrinkage can occur very rapidly at the ‘plus’ end
• (termed ‘catastrophe’)
• - formation of MTs is regulated/controlled
• - Microtubule-Organizing Center (MTOC)
• = central site of MT assembly

• - several different proteins that bind MTs
• ‣ modulate assembly, function
• ‣ mediate interactions with other cellular
• structures (e.g vesicles/organelles)
• 21
• Microtubule-associated Proteins (MAPs)
• - often stabilize MTs or stimulate assembly

• 1. Motor MAPs:
• - 2 main types: kinesin and dynein
• - use ATP to generate force
• - can move material along MT ‘track’
• - can generate sliding force between MTs
• 2. Non-Motor MAPs:
• - control MT organization in cytosol
• (e.g. Tau in neurons)

minus end directed

plus end

• • intermediate size (10-12 nm diameter)
• • exclusive to multicellular animals
• • provide structural support, mechanical strength
• • stable (relative to MTs or microfilaments)
• • fibrous proteins, contain central α-helical domain

• - keratins: epithelial cells
• - neurofilaments: neurons
• - lamins: nucleus of all cells

• • α-helical domains wrap
• around each other
• forming rope-like dimer
• (coiled-coil = )
• Structure of Intermediate Filaments
• Fig. 9.42 22
• 2
• • 2 dimers associate antiparallel
• to make tetramer
• Therefore assembled
• filaments are NOT polar
• 3
• • monomers are aligned in
• parallel; IF dimers are polar
• molecules

• • smallest cytoskeletal element (~ 8 nm)
• • polymer of protein actin
• • polypeptide = 42 kDa, binds ATP
• - individual molecules = G-actin (globular)
• - polymerized microfilament = F-actin

polymerized microfilament

individual molecules

• - maintenance of cell shape
• - cell movement
• - cytokinesis
• - muscle contraction

• nucleation (slow)

• elongation (fast)

• Polymerization/Depolymerization
• and
• Structure/Organization
• - are regulated by actin-binding proteins
• Fig. 9.70 Fig. 9.75
• - filaments can be loose arrays/networks or
• tight bundles/cables

• Examples of actin-binding proteins
• • nucleating proteins; e.g. Arp2/3
• • monomer-polymerizing proteins; e.g. profilin
• • filament-depolymerizing proteins; e.g. cofilin

• Arp2/3 nucleates
• polymerization at
• branch points

• Coordinated activity of actin-binding proteins
• controls microfilament formation in a lamellipodium to
• allow directed cell movement

• an Actin-associated Motor Protein
• - large family of proteins
• - most move toward plus end of microfilament
• - divided into 2 broad groups
• 1) conventional myosins
• - type II
• - primary motors for muscle contraction
• 2) unconventional myosins
• - type I and types III-XVIII

• generate force and
• contribute to motility in non-muscle cells

• based and microfilament-based motors
• can cooperate in intracellular transport
• Movement of
• pigment granules
• via the cytoskeleton

• ๏ storage, replication, and repair of genetic material
• ๏ expression of genetic material
• - transcription
• mRNA, tRNA, rRNA
• - splicing
• ๏ ribosome biosynthesis

• ๏ Nuclear envelope
• - nuclear membrane
• - nuclear pores
• - nuclear lamina
• • Nuclear contents
• - chromatin
• - nucleoplasm
• - nucleolus

• 2 parallel phospholipid bilayers
• • separated by 10-50 nm
• • Outer membrane (ONM) binds ribosomes and is
• continuous with rough endoplasmic reticulum
• • Inner membrane (INM)
• - bears integral proteins
• - connects to nuclear lamina

lumen

• • separates nuclear content from cytoplasm
• - separates transcription & translation
• • selective barrier
• - allows limited movement of molecules
• between nucleus and cytoplasm
• • supported by nuclear lamina

• • thin meshwork of filamentous proteins
• - lamins (class V intermediate filaments)
• • bound to inner membrane of NE by integral
• membrane proteins
• • provides structural support for NE
• • attachment sites for chromatin

• • gateways between cytoplasm & nucleoplasm
• • 3,000 to 4,000 pores/nucleus
• • pores occur where inner and outer membranes fuse
• • pores have a complex protein structure
• ‣ Nuclear Pore Complex (NPC)

• - composed of nucleoporins (NUPs)
• - octagonal symmetry
• - projects into cytoplasm and
• nucleoplasm

• • passive diffusion of molecules smaller than 50 kDa
• ‣ rapid (100/min./pore)
• • regulated movement of larger molecules
• ‣ slow (6/min./pore)
• 24
• Regulated movement of proteins into the nucleus
• requires a Nuclear Localization Signal (NLS)
• NLS = a short stretch of positively charged
• amino acids within the protein sequence

• Ribosome Biogenesis
• • synthesis of rRNA
• • rRNA processing
• • assembly of subunits
• (rRNA + proteins)
• • 40S and 60S subunits are
• exported to cytoplasm