Unit 2

Question 1

4 features of biological membranes

Answer 1

1. ) the membrane is a bilayer, made up of both lipids and proteins
2. ) the membrane is selectively permeable (aka permeability is different for different molecules)
3. ) the membrane is organized but fluid
4. ) the membrane is asymmetric

Question 2

Ectotherms

Answer 2

“Cold-blooded” animals manipulate their membrane compositions (the nature of major structural proteins) to control fluidity as T or P changes

Question 3

Endotherms

Answer 3

Animals like us. Membranes are maintained in a strictly controlled environment (T and P). They have limited capacity to changes in T and P

Question 4

3 features that affect fluidity

Answer 4

1) degree of saturation - the more double bonds, the more fluid the bilayer
2) the number of carbon atoms in the fatty acid chains - the shorter the fatty acid tails, the more fluid the membrane
3) the sterol control of the membrane. Cholesterol is a type of sterol. At high T, it decreases the fluidity of the membrane. At low T, it increases the fluidity of the membrane by preventing tight packing of phospholipid hydrocarbon tails

Question 5

Difference between lipid bilayer and biological membrane

Answer 5

Lipid bilayers are made exclusively of lipids while biological membranes include proteins of various sizes, shapes, and functions. An example of a biological membrane is a plasma membrane

Question 6

Why can lipids form membranes and why are they special?

Answer 6

They can form membranes because they are amphipathic, where the head forms H-bonds and the tails are nonpolar and cannot form H-bonds. Their spontaneous assembly allows the membrane to be self-healing, self-healing, and can self-assemble

Question 7

Is lipid bilayer and phospholipid bilayer interchangeable?

Answer 7

I dont know ask someone lol

Question 8

Why do lipid bilayers form spontaneously?

Answer 8

It is because it’s energetically favourable. It’s stable because association of hydrophobic groups results in less disruption of the hydrogen bonded structure of the surrounding water molecules. Overall free energy is reduced because of the entropy of the system, which is negative. Entropy increases

Question 9

How do the levels of protein structures form? STRUCTURE DICTATES FUNCTION

Answer 9

Primary structure: the long chains of amino acids that are covalently bonded together based on the sequence read from the mRNA. Determines the proteins 3D structure

Secondary structure: the backbone interacts non-covalently with itself. Ex. alpha helices and beta-sheets

Tertiary structure: R-groups interact with other R-groups or backbone atoms. Makes covalent disulphide bonds. Overall 3D structure of entire polypeptide

Quaternary structure: different polypeptide chains come together to form a protein. Multiple subunits

Question 10

What can cross the membrane?

Answer 10

Small, nonpolar molecules (O2, CO2, NO) can cross easily

Large molecules cannot because of their size (AA, nucleotides, glucose)

H20 can cross, but rate varies with different proteins

Question 11

Describe the asymmetry of the membrane. What contributes to the asymmetry?

Answer 11

Each side of the bilayer have different functions and membrane proteins need to be inserted specifically or the bilayer function will be compromised, therefore, membrane sides are not interchangeable. Carbohydrates (only found on the non-cytosolic side) contribute to membrane asymmetry

Question 12

Lipid rafts

Answer 12

Membranes have regions with varying fluidity. Rafts are regions with reduced fluidity (more ordered), having a higher concentration of sphingolipids and cholesterol. Thicker region

Question 13

Why is fluidity important?

Answer 13

It must be in certain limits for the membrane to function properly. If it is not fluid enough, proteins and other components may freeze. If it’s too fluid, it will be difficult to keep organized and unwanted ions/molecules may cross

Question 14

Fluorescence Recovery After Photobleaching (FRAP)

Answer 14

Used to examine how mobile various membrane components are within the cell. It couples a fluorescent dye to a specific component of the membrane (lipid or protein). If the dye exposed to a very bright light, it’s destroyed, or “bleached”. Recovery depends on how fluid the membrane is (the more fluid, the faster it will recover)

Question 15

Why is membrane asymmetry important?

Answer 15

It ensures specific lipids are on the correct side of the membrane so they can do their job. For example, the cell identification molecules are on the extracellular side of the cell membrane and the lipids for organelle identification are on the cytoplasmic side

Question 16

What do flippases, floppases, and scramblases do?

Answer 16

They move lipids from one side of the membrane to the other. They’re important for the growth of membranes

Question 17

Integral proteins

Answer 17

Embedded within the phospholipid bilayer or covalently bound to lipid molecules. Extractable with strong detergents. Cannot be removed without destroying the membrane

Question 18

Peripheral proteins

Answer 18

Attached to the outer/inner surface of the membrane. Extractable with milder salt solutions. Attached to the membrane with non-covalent interaction and is easily disrupted

Question 19

What are transmembrane proteins? How are they held in place? Which level of structure do they use to pass through the membrane?

Answer 19

Extended throughout the membrane and has stuff sticking out either membrane side. Held in place via interactions of hydrophobic AA side chains of the protein with hydrophobic core of the membrane

They pass through the membrane using secondary structures. It is because the backbone of the polypeptide chain is always polar and can form H-bonds, making it hard to cross the hydrophobic core

Question 20

What are secondary structures and what is their 2-fold effect?

Answer 20

They are local, repeating structure that’re formed via H-bonding of backbone atoms to other backbone atoms

2-fold effect:

1) satisfy H-bonding requirements of the protein backbone, making them thermodynamically favourable structures
2) Push R-groups towards the outside of the structure where they interact with the environment

Question 21

Alpha-helix

Answer 21

AA side chains extend outwards from the core of the helix, and the backbone is in the center. Usually made up of 20+ AAs with hydrophobic side chains.

They are amphipathic because they have to exist in the hydrophobic center and aqueous parts. Core surface is hydrophobic and other regions are hydrophilic

Nothing can pass through it, but multiple ones can form a pore/channel that allow things to pass through it

Question 22

Beta-sheet

Answer 22

The edges of the sheets (or strand) will have exposed backbone that don’t easily interact with the hydrophobic core of the bilayer.

They can turn into beta-barrels, which satisfies thermodynamic requirements. The outside of the barrel interacts with the environment and helps hold the protein in the environment and the inside creates space that allows H2O and other small molecules to pass through the membrane

Question 23

4 functions of membrane proteins

Answer 23

1) Structural - anchors help attach the membrane to organelles, the extracellular matric, or other cells. Linkers help connect several proteins in the membrane and provides shape
2) Transport - transports different molecules across the membrane (ex. helices and sheets)
3) Enzymes - membrane proteins have enzymatic activity for cellular functions, like synthesizing, modifying enzymes, flippases, scramblases, or kinases
4) Receptors - span across membrane and binds to small molecules. other proteins outside the cell. The interaction causes a chain of events that transmits a signal in the cell. Many receptors are also enzymes

Question 24

Bioinformatics approach: Hydropathy plots

Answer 24

Can only do predictions. Analyzes the sequence of AAs in a protein and looks for alpha-helical transmembrane domains. Looks for linear stretch of AAs that’re “hydrophobic enough” to allow them to exist stably within the confines of the hydrophobic core of the lipid bilayer

Question 25

Sodium-Dodecyl-Sulphate PolyAcrylamide Gel Electrophoresis (SDS-PAGE)

Answer 25

Tests predictions experimentally. Used for protein separation. Molecules of all sizes migrate the same rate if other factors are equal. However, larger molecules travel more slowly because they spend more time impeded in the strands of the gel than the small molecules We want to know if proteins are integral or peripheral. Or if proteins have portions exposed on either side of the membrane, or both

Question 26

2 ways to study the mobility of a membrane component (liquid or protein) within a membrane

Answer 26

1) Fluorescence Recovery After Photo-bleaching (FRAP) - protein/lipid of interest is labelled with fluorescent tag and followed by confocal fluorescence microscopy. Laser points to the area of fluorescent tags, which emits photons and are extinguished (called bleaching). If it is fluid, the bleached are will recover some of its fluorescence as fluorescent tags flow back into the are and bleach tags move out 2) Hybrid cell experiments - two surface proteins are labelled with antibodies that are attached to a fluorophore and each have different colours (ex. red and green). They are then fused to become a single "cell" and the colours are initially distinct. If they're mobile, the fluorescent markers will intermingle because of the membrane fluidity

Question 27

Why is a plasma membrane a biological membrane?

Answer 27

It has a network of proteins that can be on the inside and outside Has integral and peripheral proteins, which allow them to be thicker than just lipid bilayers Cells use networks made up of proteins and polysaccharides to shape/support the plasma membrane

Question 28

Glycocalyx

Answer 28

a coating of carbohydrates that covers the exteriors of the plasma membrane in animal cells. Provides protection and unique identifiers. In plant cells, this coating joins together with secreted carbohydrates to form the cell wall

Question 29

Component of glycocalyx: glycolipids

Answer 29

An integral protein that fatty acid tails hold firmly in place in the membrane. The polysaccharide potion interacts with polar aqueous phase and other polar groups They are synthesized on the cytosolic side of the ER and flipped to the interior side for addition/modification of carbohydrates

Question 30

Component of glycocalyx: glycoproteins

Answer 30

Integral protein. Proteins that carry attached polysaccharides. Has hydrophobic domains embedded in the central hydrophobic region of the bilayer. The carbohydrates are attached to exterior part of the protein Process begins in the ER, but modification finalization is in the Golgi

Question 31

Protein domain

Answer 31

A subsection of a protein that has a very specific structure/function Ex. transmembrane domain, catalytic domain, and DNA-binding domain

Question 32

Which two components of the glycocalyx are important for cell identity markers?

Answer 32

Both glycolipids and glycoproteins are important for cells having an identity because of their configuration on the surface of the membrane. An example of this are blood types

Question 33

Types of non-covalent interactions

Answer 33

Electrostatic attractions (ionic bonds) Hydrogen bonds Van der Waal attractions - their electrons are distributed asymmetrically Hydrophobic forces - caused by a pushing of nonpolar molecules out of the hydrogen-bonded water network

Question 34

Membrane proteins

Answer 34

Protein hydrophobic domains are embedded in the hydrophobic core of membranes. They are free to move in the bilayer unless they're restrained, like being bound or being confined by the cytoskeleton

Question 35

LIPID BILAYERS ARE NOT IDENTICAL TO BIOLOGICAL MEMBRANES

Answer 35

Bilayers refer to lipid components and biological membranes refer to the lipids + proteins and everything else. They are NOT SYNONYMOUS

Question 36

Properties of lipids that allows it to form bilayers

Answer 36

It must be the correct shape and be amphipathic. 2 tails and a kink

Question 37

Why do bilayers spontaneously form?

Answer 37

The free energy of the system is minimized if the hydrophobic regions cluster together to limit contact with H2O. It increases the motional freedom of H2O. It is thermodynamically favourable H2O minimizes interactions with nonpolar molecules by reorganizing into a "cage" around the hydrophobic molecule

Question 38

Composition of membrane lipids

Answer 38

Mostly phospholipids, but also glycolipids and sterols

Question 39

Lateral diffusion vs. transverse diffusion

Answer 39

Lateral diffusion is when a molecule can traverse across the same leaflet. it is energetically favourable for it to move around Transverse diffusion is when a molecule flips to the other leaflet. Not favourable since the hydrophilic head would have to travel through the hydrophobic area. Very slow and rare. Enzymes can help

Question 40

Factors that affect membrane fluidity

Answer 40

1) Temperature (higher T generally makes a membrane more fluid) 2) Unsaturation (fast response) - increases double bonds and introduces kinks and that decreases how tightly packed they are 3) Shorter fatty acid tails (slow response) - less interactions 4) Cholesterol (slow response) - when cholesterol is present, high T decreases fluidity. At low T, it increases fluidity as it interferes with Van der Waal interactions between fatty acid tails

Question 41

Where is carbohydrate asymmetry generated?

Answer 41

It is generated in the Golgi. Its lumen is the site of glycosylation. The orientation of the membrane is preserved when being transported via vesicles.

Question 42

Where are lipids synthesized?

Answer 42

All new membranes come from the ER. New lipids are made in the SER, which are made by proteins attached to the membrane

Question 43

Transmembrane domain

Answer 43

Part of a membrane protein that passes through the lipid bilayer. They are amphipathic. Most transmembrane domains are alpha helices, but some can be beta-barrels

Question 44

Biochemical approach

Answer 44

Protein purification and experiments to determine membrane protein type, components, and orientation. Salts are usually used to isolate membrane proteins Once they are separated, gel electrophoresis or SDS-PAGE can be used

Question 45

Factors that affect membrane protein mobility

Answer 45

1) Linked to the cell cortex (cytoskeleton) - anchored to the cytoskeleton 2) Linked to proteins outside the cell (extracellular matrix) 3) Linked to proteins in neighbouring cells - cell to cell adhesion proteins link plasma membranes 4) Cells can have diffusion barriers - tight junctions are adhesions between neighboring epithelial cells that prevent leaks between the cells. It's a large protein complex that blocks areas