BIO130 Final Exam

A detailed set of flashcards on information tested on in the final exam (second half of the course + labs)

What are the two things animal cells have but plant cells don’t?

Lysosomes → degradation

Extracellular matrix

What are the three things plant cells have but animal cells don’t? And what are their purposes?

Cell wall → cell shape, protection against mechanical stress

Vacuoles (2 types) → degradation (like animal lysosome), storage

Chloroplast → photosynthesis

Cytoplasm vs Cytosol vs Lumen

Cytoplasm: everything but nucleus (includes organelles)

Cytosol: everything but membrane bound organelles (aqueous part of cytoplasm)

Lumen: inside of organelles

3 types of lipids that compose membranes

phospholipids, sterols, glycolipids

phosphoglyceride and structure

type of phospholipid with glycerol group

• glycerol group: 3 C with O connected. 2 Os connects to the hydrocarbon tails, the other connects to the phosphate group.

liposome

artificial lipid bilayer in sphere (because that’s energetically favorable)

Uses:

• drug delivery into cells

• study lipid and membrane protein properties

Describe the ways phospholipids can move (fluid)

Phospholipids rapidly move within each leaflet

• lateral diffusion (side to side, deeper into plane)

• rotate

• flex

• and rarely “flip flop” - move from one leaflet to another on their own

effect of temperature on membrane fluidity

lower temperature → more viscous, less fluid

factors affecting membrane fluidity (membrane composition)

1. phospholipid saturation

   1. cis-double bonds increase fluidity (reduce tight packing)

   2. phospholipid tail length (shorter tails increase fluidity because lipid tails interact less)

   3. lipid composition (addition of cholesterol stiffens membrane)

cholesterol

most common sterol in animal membranes.

Decreases mobility of phospholipid tails, makes plasma membrane less permeable to polar molecules.

scramblase

aka “Phospholipid translocator”

Enzyme in the ER that catalyzes the flip-flopping of random phospholipids from one leaflet to the other.

Why is scramblase needed?

Phospholipids are synthesized in cytosolic leaflet of ER which means the membrane needs to be evened out.

Flippase

The two faces of the plasma membrane have different lipids. This asymmetry is maintain by the enzyme Flippase in the Golgi membrane.

• flip flops specific phospholipids to the cytosolic leaflet

4 steps to new phospholipids being made and added to the cell membrane

1. in ER membrane you make a ton of lipids

2. there’s some scramblases that flip them to other side to even things out

3. transport vesicles takes it to Golgi

4. Flippases sorts things out to get specificity —which from then on stays consistent

note: from then on, “stays consistent”

glycolipids/glycoproteins

Formed when sugar groups are added to lipids/proteins on luminal face. Protects the membrane from harsh environments.

integral membrane proteins

membrane proteins that insert in some way into the lipid bilayer

• transmembrane - pass through entire membrane

• monolayer associated

• lipid-linked

peripheral membrane proteins

no not insert into the lipid bilayer. They are associated with the membrane noncovalently, bound to either lipids or other proteins.

properties of transmembrane proteins

amphipathic - AA side chains are either polar or not polar

• the nonpolar region is typically 20-30 hydrophobic amino acids.

Have specific orientations important to function

X-ray crystallography

technique used to determine the 3D structure of proteins

Turns proteins into crystals, light is shown through them, and the diffraction pattern is measured

Hydrophobicity plots

x-axis: AA number. Starts on N-terminus, goes to C-terminus.

high y value = very hydrophobic, low y value = very hydrophillic

• each stretch of 20-30 hydrophobic AAs is a transmembrane domain

Monolayer Associated Membrane Proteins

A type of integral membrane protein

• protein is anchored on cytosolic face by amphipathic alpha helix.

Ex. Sar1 - involved in membrane bending, vesicle formation

lipid-linked membrane proteins

type of integral membrane protein

2 types:

• Protein with GPI anchor on noncytosolic face

• Protein with lipid anchor on cytosolic face

Use of detergent

extraction of membrane proteins

FRAP (Fluorescence Recovery After Photobleaching

Experiment to observe lateral diffusion of membrane proteins.

• you can measure the speed of lateral diffusion by looking at the slope of recovery

membrane transport proteins

2 classes: channel proteins, transporter proteins

Transport polar and charged molecules (small, nonpolar molecules can just simply diffuse on their own)

• selective

channel proteins

Type of membrane transport protein for passive transport

Binds weakly to transported molecule; does not change conformation a lot

Selective for size and charge

Transporter proteins

type of membrane transport protein - can do passive and active transport

Solute binds strongly; conformation changes a lot during transport

membrane potential

the difference in charge across the membrane

electrochemical gradient

concentration gradient + membrane potential (but we take concentration gradient to be more significant)

describe channel proteins in more detail

passive transport

Hydrophilic pore across membrane

Selective for size and charge

Example = ion channel

ion channels and their 2 kinds

passive transport of ions - selective for ion size and charge.

2 kinds:

1. Non-gated Ion Channels - always open

   1. ex. K+ leak channel

2. Gated Ion Channels - signal required to open channel

4 types of gated ion channels

comparison of transporter-mediated diffusion and simple diffusion/channel-mediated transport (rates of transport)

Uniport

Passive transport transporter protein (down electrochemical gradient)

Uni → “one” solute

ex. glucose transporter (GLUT Uniporter)

Gradient driven pump

Type of active transport transporter protein

1 solute down its gradient, 2nd solute against its gradient

ATP-driven pumps (ATPases)

type of active transport transporter protein

Requires ATP hydrolysis to move solute against its gradient

light driven pump

type of active transport transporter protein in bacteria

Describe the 2 types of gradient driven pumps

1. symport

   1. 2 solutes moved in same direction

2. antiport

   1. 2 solutes moved in opposite direction

For both, free energy from 1st solute moving down its electrochemical gradient is used to transport the 2nd solute against its electrochemical gradient.

How is the Na+ electrochemical gradient maintained?

Symports and Antiports are present

Na+ - K+ pump (plasma membrane ATP-driven pump) in animal cells.

How is cytosolic pH regulated?

Antiport: Na+ - H+ exchanger on plasma membrane

What are the three kinds of ATP-driven pumps"?

1. P-type pumps

2. ABC transporter

1. V-type pump

P-type pumps (ATP driven pump)

Generates and maintains electrochemical gradients

• ex. Sodium Potassium pump (3 Na+ out, 2 K+ in)

• ex. H+ pump in plant cell plasma membranes

* “pees itself” → phosphorylated during pumping cycle

(note: another example is Flippase)

why is the Na+ gradient important?

Transport nutrients into cells (e.g. glucose)

maintain pH

How does the Na+ - K+ pump work?

1. 3 sodiums bind

2. the pump phosphorylyzes itself triggering conformational change

3. 3 sodiums ions ejected, 2 potassium ions bind

4. pump dephosphorylates itself, returns to original conformation and the potassium is ejected.

ABC Transporter

type of ATP-driven pump

Uses 2 ATP to pump small molecules across cell membrane

V-type pump

Type of ATP-driven pump

Uses ATP to pump H+ into organelles to acidify the lumen

Found in lysosomes and plant vacuoles

V-type proton pump vs F-type ATP Synthase

They are structurally related but opposite modes of action.

V-type proton pump uses ATP to pump H+ against the electrochemical gradient.

but F-type ATP Synthase uses the H+ electrochemical gradient to produce ATP.

How is glucose transferred from the intestine to the bloodstream?

Lining the gut lumen are epithelial cells, each separated by tight junctions (so glucose can’t go between them).

Na+ driven glucose symporter on the apical domain brings Na+ and glucose into the cell, then Na+ - K+ pump and passive glucose uniport (GLUT Uniporter) on the basal domain remove Na+ and glucose from the cell.

Which transporter proteins are involved with the generation and maintanence of membrane potentials?

K+ leak channel (passive transport)

• outward flow of K+

Na+ - K+ pump (P-type pump)

• Net 1 (+) ion pumped out

^ net result = outside is more + than outside

for plants: H+ pump (P-type pump)

K+ leak channel

Important channel for maintaining membrane potential

Na+ - K+ pump

~10% of membrane potential

• maintains Na+ gradient w low cytosolic [Na+] and K+ gradient with high cytosolic [K+]

Electrogenic:

• 3 Na+ ions pumped out

• 2 K+ ions pumped in

• Net 1 (+) ion pumped out

H+ pump and generation of membrane potential in plant cells

Generates H+ electrochemical gradient, which is used by gradient-driven pumps like H+ Driven Symporter.

• good for electrical signaling and pH regulation

resting membrane potential

When membrane potential is as equilibrium - Voltage difference is steady

• for animals, is from -20 mV to -200 mV

• for plants, is from -120 mV to -160 mV

note: is from perspective of the inside of the membrane

What molecules diffuse rapidly?

small, nonpolar, and sometimes if small enough uncharged polar

ex. O2, CO2

briefly what are the functions of the organelles?

What is cytosol?

50% of the cell volume

Protein synthesis and degradation

many metabolic pathways

contains cytoskeleton

pancreatic exocrine cell

secretes digestive enzymes

rough ER and smooth ER

rough

• has membrane-bound ribosomes

• involved in synthesis of soluble proteins and transmembrane proteins for the endomembrane

smooth

• phospholipid synthesis

• detoxification

Which organelles are not membrane bound?

Nucleolus and Centrosome

Simply, how are proteins sorted?

If they have a sorting signal called a signal sequence they are directed to the right place.

Signal sequence

AA sequence in a protein that directs protein to the correct compartment

• recognized by sorting receptors

encoded in the genome

sorting receptors

recognize signal sequences and take proteins to their destination

2 ways protein sorting is done:

1. post translational sorting

   1. proteins are already fully synthesized in the cytosol before sorting

2. co-translational sorting - for proteins going to ER

   1. have an ER Signal Sequence

   2. proteins complete synthesis on the ER membrane

Post-Translational Protein Sorting

Depending on destination, proteins are either folded or unfolded

• folded: nucleus, peroxisomes

• unfolded: mitochondria, plastids

How does protein sorting into nucleus work?

Post-translational. Protein already folded.

Travel through nuclear pores.

Protein has nuclear localization signal

how are proteins sorted into peroxisomes?

Post translational. Folded.

Proteins imported through transmembrane protein complex.

How are proteins sorted into mitochondrion and chloroplasts

Post translational. Unfolded.

Proteins are unfolded for import by hsp70 chaperone proteins

Co-Translational Protein Sorting

For proteins that enter the ER - the entry point to the Endomembrane system

ER Signal sequence is hydrophobic

Endomembrane system

ER, Golgi apparatus, endosomes, lysosomes

In general what are the steps of co-translational sorting?

Translation starts on ribosomes in the cytosol per usual, but then once ER Signal Sequence is translated the protein is inserted into the ER (“co-translational translocation)

The process looks different depending on if the protein is:

1. soluble

2. or transmembrane

Describe the process of co-translational sorting of a soluble protein

SRP recognizes and binds to ER signal sequence once translated, translation stops.

Connects to SRP-ribosome complex (SRP receptor + translocon)