Quiz 2

How do cells solve the problem of protecting and compartmentalizing cellular components?

Lipid bilayers

Fluid-Mosaic Model

* Within the “sea” of membrane lipids, integral membrane proteins are floating around
* All cellular membranes have lots of proteins embedded in them

What does it mean that lipid bilayers are selectively permeable?

Certain substances can readily diffuse across the membrane, certain substances can cross the membrane (but not easily), and certain substances cannot pass the membrane at all

What factors affect the rate of diffusion across a membrane?

1. Size
2. Charge

Structure of a phospholipid

Hydrophilic head


1. Polar group
2. Phosphate group
3. Glycerol

Hydrophobic tails


1. 2 fatty acid chains

Amphipathic

Having a hydrophilic part and hydrophobic part (ex. phospholipid)

What is the most chemically variable portion of a lipid?

* The polar group/head group
* Can confer unique functions to the lipid

How can fatty acid tails in a lipid vary?

* Length
* # of kinks (C=C bonds)

Micelles

* Spherical structure spontaneously formed by single layer of lipids
* Formed by cone-shaped phospholipids (1 fatty tail)

Liposome

* Spherical structure spontaneously formed by double layer of lipids
* Formed by cylinder-shaped phospholipids (2 fatty tails)

Cone-shaped phospholipid

* 1 fatty tail
* Forms micelles

Cylinder-shaped phospholipid

* 2 fatty tails
* Form liposomes/bilayers

Saturated hydrocarbon chains

Hydrocarbons have maximum hydrogen bonding and no C=C double bonds

Unsaturated hydrocarbon chains

* Missing some hydrogens, so have C=C bonds
* Causes a bend or __**kink**__ in the chain
* Prevents close packing of hydrocarbon tails and reduces hydrophobic interactions

Why are hydrocarbon chains called (fatty) acids?

Because they have a hydroxyl group that can act as an acid and give up H+

Cis-double bonds in fatty acid tails

* Occur naturally
* Two H on the same side
* Two non-H on the same side
* Cis = same

How do saturated vs. unsaturated fatty acids affect membrane permeability?

* No unsaturated fatty acids = low permeability
* Many unsaturated fatty acids = high permeability
* More porous

Cholesterol

* Makes membranes more rigid, less permeable, a stabilized to fluidity changes
* Steroid molecule


* Present in most eukaryotic membranes


* Amphipathic structure

How does temperature affect membrane fluidity and permeability?

* ==Higher temperature== = higher fluidity = higher permeability
* ^^Lower temperature^^ = lower fluidity = less permeability

How does the length of fatty acid tails affect membrane permeability?

* Longer tails = less permeable
* Shorter tails = more permeable

Diffusion

* Ions and molecules diffuse spontaneously from regions of higher concentration to regions of lower concentration
* Driven by entropy (tendency of the universe to become more disordered)

What types of molecules can diffuse through a membrane?

* Small mostly non-polar molecules
* Very small polar molecules (ex. water)

Osmosis

* The movement of water across a semipermeable membrane
* Water is drawn toward higher *solute* concentration

What happens to a cell in a hypertonic solution?

Cell shrinks

* Water moves out of the cell to area of higher solute concentration

What happens to a cell in a hypotonic solution?

Cell swells/lyses

* Water moves into the cell to an area of higher solute concentration

Hypertonic solution

Compared to cell, solution has higher solute concentration

Hypotonic solution

Compared to cell, solution has lower solute concentration

Transmembrane/integral membrane proteins (def’n, characteristic, shape)

* Transverse the entire membrane
* Tend to contain hydrophobic amino acid residues (that interact with the hydrophobic core of the membrane)
* Usually form alpha helix

Peripheral membrane proteins

* Reversibly associated with either the internal or external side of the membrane
* Could be bound to a lipid or another protein embedded in the membrane

How do ion channels and transporters influence membrane permeability?

By allowing specific polar solutes to pass that are normally impermeable

Ion channels

* Open to allow a specific solute to pass (usually ions)
* Either open or closed
* Open/closed status is regulated: “gated”

Transporters/carrier proteins

* Undergo conformational (shape) change
* Bind solutes on one side of the membrane and release them on the other

Passive transport

* Occurs when a solute moves down its concentration gradient (high to low concentration)
* Occurs spontaneously (no energy input needed) due to diffusion
* Can occur through the membrane directly or through a channel/transporter protein

Active transport/pumping

* Occurs when a cell expends energy (usually ATP) to move a solute against its concentration gradient (low to high concentration)
* Requires a protein pump

Simple diffusion

Solute passes through the membrane along its concentration gradient by itself (no channel/transporter protein or energy required)

* Passive transport

Facilitated diffusion

Solute passes through membrane via a transporter or channel protein along its concentration gradient

* Passive transport

Sodium-potassium pump (+ where does it get energy)

* Uses energy of ATP hydrolysis to create electrochemical gradient
* Animal cells
* Pumps Na+ ions out of the cell
* As a result, Na+ higher outside the cell
* Pumps K+ ions into the cell
* As a result, K+ is higher inside the cell

Gradients are a form of ________ energy

Stored (potential)

Coupled transport

* One molecules moves down its concentration gradient, releasing energy
* Potential energy of electrochemical gradient (generated by active transport)


* Another molecule is driven with this energy to move against its concentration gradient

What types of things can pass through cell surface transporters? Why?

* Amino acids and nucleotides can pass
* Small monomers
* Nucleic acids and proteins cannot pass
* Larger
* Reason: there is a size limit to what can enter cells through transporters/channels; transporters/channels are selective

Selective

Binds/recognizes or allows passage of some things but not others

What do all cells have?

1. __Plasma membrane__ (separates cell from its environment)
2. __DNA__ (genome = entire chromosomal DNA seq. of cell)
3. __Cytosol__ (aqueous interior of cell)
4. __Ribosomes__ (‘machines’ for protein synthesis)
5. __Cytoskeleton__ (structural support)

What are things that only some cells have?

1. Nucleus (encloses genome)
2. Organelles (membrane-enclosed sub compartments)
3. Cell wall (protective outer layer)
4. Flagellum/cilium (projection for movement)

Plasma membrane

Acts as a selective barrier against the extracellular environment

What is characteristic of eukaryotic cells?

* Nucleus
* Bigger
* Organelles (many intracellular membranes)

Motile

Many __bacteria__ are motile (can move) due to the presence of __flagella__

Plasmid

Prokaryotes may contain a small, __circular piece of extra-chromosomal DNA__ called a plasmid

* Easily shared
* Often where bacteria have genes conferring antibacterial resistance

Nucleoid

Circular chromosome is supercoiled into nucleoid (one big packaged chromosome)

Cell wall (bacteria)

Almost all bacteria have a __semi-rigid__ but __permeable__ cell wall composed of __peptidoglycan__ that __prevents osmotic lysis__

Mitochondria

* Harness energy from chemical compounds (e.g. glucose, fats)
* Convert energy into ATP
* Present in virtually all eukaryotes (including plant cells)
* Double membrane with aqueous compartment in between

Chloroplasts

* Capture the sun’s energy
* Synthesize simple sugars via photosynthesis
* Double membrane with additional third interior membrane (thylakoid membrane)

Life originated as _____________

Prokaryotic (no nucleus nor intracellular membranes)

Endomembrane system

* Evolved from inner folds of the plasma membrane
* Pinched off and enclosed DNA (nucleus)
* Created eukaryotes
* Refers to the set of intracellular organelles that are interconnected via vesicular traffic

Membranes of which organelles are __*not*__ part of the endomembrane system?

* **Mitochondria**
* **Chloroplast**
* These were engulfed: endosymbiotic theory
* They grow and multiply independently of other membrane compartments

Endosymbiotic theory

Mitochondria and chloroplasts evolved from __engulfed prokaryotes__ that gave an advantage to the host eukaryotic cell

Zip code hypothesis

Proteins are directed to the correct cellular location by signals within their amino acid sequence

* Usually encoded by primary amino acid sequence


* Zip codes are most prevalent in eukaryotes

What is the default location for a protein in the absence of a specific signal/zip code?

Cytoplasm/cytosol

Nuclear envelope

* Double-membrane structure that contains nucleus
* Continuous with __ER__
* Supported by __nuclear lamina__ (cytoskeletal structure)
* Perforated by __nuclear pore complexes__ that act as gates

Nuclear pore complexes (NPCs)

Allow selective passage of molecules between nucleus and cytoplasm

Vesicular traffic

Refers to when membrane bound structures are budding off and/or fusing with another membrane bound structure

Members of endomembrane system

1. ER
2. Golgi
3. Lysosome
4. Endosomes
5. Plasma membrane

Exocytosis

A vesicle that has budded off from the endomembrane system can fuse with the plasma membrane and deliver its contents into the extracellular space

* Things are sent out of the cell

Endocytosis

Material from outside the cell is brought into a vesicle that can then fuse with other organelles

* Bringing things into the cell

Vesicular transport

A vesicle can pinch off of one membrane and fuse with another

What characteristic of cells allows vesicular transport to occur?

Lipid bilayers are fluid and can fuse and intermix with each other

Rough ER vs. smooth ER

* Rough ER: integral membrane and lumenal protein synthesis
* Has ribosomes bound to it (in the process of translating something)
* Smooth ER: primary site of lipid synthesis
* No ribosomes

Where are integral membrane proteins and proteins inside the endomembrane system synthesized?

ER

Secretion/exocytosis

Vesicular transport out of the cell

What is the secretary pathway through the cell?

1. ER
2. Golgi
3. Plasma membrane

Note: some proteins that are needed to function in the ER or Golgi can be retained there by mechanisms similar to the zip code concept

Glycosylation

* Proteins that go through the ER and Golgi are __glycosylated = covalently attached to carbohydrate chains__ (modified by carbohydrates)
* Occurs in the lumen of the Golgi
* This is why cell-surface and extracellular proteins are glycoproteins
* For integral plasma membrane proteins, the lumenal, glycosylated portions end up in the extracellular space

Endoplasmic reticulum structure

Forms a continuous network of __interconnected membrane tubules__ (some rough, some smooth)

Cisternae

The Golgi apparatus consists of a series of __flattened membrane sacs__ called cisternae

Endocytic pathway

Stuff outside the cell or in the plasma membrane can be brought __into the cell__ by endocytosis

* Endocytic cargo can be recycled (sent back to the plasma membrane) or directed to a lysosome
* This is *not* done because the cell wants the protein it is bringing in (if that were the case, the cell would just make the protein itself); it is usually about bringing something in to be degraded

Lysosomes

* Acidic and degradative organelles
* They break down any biological molecule brought to them into building blocks for reuse
* Cellular compost bin

How do lysosomes maintain an acidic pH?

Proton pumps

Lysosomal/acidic hydrolases

Degrading enzymes that only work at low pH

Signal/signal sequence

* Signal within protein that is currently being translated directed a ribosome to the surface of the ER
* At the ER, the ribosome associates with a translocation channel through which the protein’s synthesis is completed, resulting in a lumenal protein or integral membrane protein

Series of events leading to synthesis of lumenal/membrane protein

1. Signal recognition particle __(SRP)__ binds to a signal sequence in the amino end of the growing polypeptide, __halting translation__
2. SRP binds to SRP receptor on ER membrane
3. SRP receptor brings ribosome to transmembrane channel (SRP dissociates)
4. Protein synthesis resumes; growing polypeptide chain is threaded through the channel
5. Protein ends up in the lumen of the ER where it will remain, be transported to the lumen of another organelle, or be secreted out of the cell

Signal anchor sequences

* Signal anchor sequences become transmembrane domains in transmembrane proteins
* Hydrophobic portion
* They are released from the translocation channel into the ER membrane and diffuse laterally into its lipid bilayer

General cytoskeletal functions

1. Structure and support


1. Shape, strength
2. Shape could include controlling membrane projections
2. Intracellular transport
3. Contractility and motility
4. Spatial organization

What types of subunits does the cytoskeleton consist of?

Noncovalent polymers of protein

* Microtubules (smallest)
* Microfilaments (biggest)
* Intermediate filaments (middle)

Microtubule

* Smallest
* Hollow tube formed from tubulin dimers
* More rigid than actin or intermediate filaments and rupture when stretched
* Globular shaped
* Consists of alpha and beta tubulin

Microfilaments

* Largest
* Double helix of actin monomers
* Actin = 3º protein structure that binds to itself
* Flexible
* Most concentrated just beneath the plasma membrane

Intermediate filaments

* Strong fiber composed of intermediate filament proteins
* Fibrous (stringy) subunits; rope-like
* Doesn’t fold into globular shape
* Provide cell mechanical strength
* Very flexible