BIO 200 MIDTERM 1 > UNIT 2 > Flashcards

UNIT 2 Flashcards

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1
Q

Macromolecules

A
  • composed of monomers joined by covalent bonds
  • assemble into functional structures
  • fundamental to biological structure and function
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2
Q

Denaturation of Macromolecules

A

Macromolecules can be denatured (lose their structure) due to increased energy (e.g., heat) or chemical agents. (can sometimes refold if conditions are normalized)

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3
Q

Types of macromolecules

A

proteins, lipids, carbohydrates and nucleic acids

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4
Q

Features of biological membranes

A

the membrane is:
- bilayer (favorable conformation)
- organized and fluid ( related to un sat fatty acids, fatty acid tail length, cholesterol concentration)
- permeable
- asymmetric and has different permeability

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5
Q

Lipids

A
  • have high hydrophobic content
  • phospholipids, sterols, fatty acids and triacylglycerols
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6
Q

phospholipids

A
  • in aqueous env form bilayers
  • they have the right shape to form bilayers (they have a hydrophilic head and two hydrophobic fatty acid tails)
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7
Q

sterols

A
  • in aqueous env form monolayers
  • influence fluidity and keep membrane stable by injecting themselves into phospholipids
  • most common is cholesterol
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8
Q

fatty acids

A
  • in aqueous env form micelles
  • not bilayers (cannot form h bonds)
  • can be sat or unsat
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9
Q

triacylglycerols

A
  • don’t form anything
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10
Q

What is necessary for bilayer formation?

A
  • amphipathicity
  • they have to be the right shape
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11
Q

thermodynamics of the hydrophobic effect

A

forming the most stable conformation (bilayer assembly) achieved by minimizing the exposure of hydrophobic groups to water

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12
Q

Why is there no water within the hydrophobic core of bilayer?

A

water cannot h-bond with fatty acid tails

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13
Q

when we talk about membrane fluidity, what kind of movement do we mean?

A

lateral diffusion

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14
Q

What is the fluid mosaic model?

A

describes the structural features of biological membranes

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15
Q

FRAP

A

A specific area of the membrane labeled with a fluorescent marker (such as GFP) is photobleached using a laser. After bleaching, the movement of unbleached fluorescent molecules into the bleached area is monitored over time.
- to study protein mobility

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16
Q

How to interpret FRAP results

A

The rate at which fluorescence returns to the bleached area indicates the fluidity of the membrane

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17
Q

What does rapid recovery mean?

A

high fluidity, indicating that molecules can move freely within the membrane.

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18
Q

What does slow or no recovery mean?

A

Indicates low fluidity, meaning that the movement of membrane components is restricted.

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19
Q

effect of temp on lipids

A
  • cold temp: membrane bilayers freeze - more ordered, less fluidity and fragile
  • warm temp/normal: less order, more fluidity
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20
Q

why is there less fluidity in membrane bilayers at cold temp?

A

as temp decreases, molecular motion slows down and molecules are trapped in van der waals interactions

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21
Q

How could a cell change its lipids to maintain appropriate fluidity?

A

adjusting:
- fatty acid saturation
- fatty acid tail length
- sterol content

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22
Q

Higher number of saturated lipids lead to..

A

-more tightly packed phospholipids (more van der waals interactions)
- less fluidity

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23
Q

Higher number of unsaturated lipids

A
  • more kinks in the fatty acid tails due to double bonded structures
  • less van der waals interactions
  • more fluidity
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24
Q

Phospholipids with shorter/longer fatty acid tails are more fluid

A

shorter because less surface area, therefore fewer van der waals interactions

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25
cholesterol at high temp
increases fluidity by preventing tight packing of fatty acids which reduces van der waals interactions
26
cholesterol at low temp
stabilize the membrane by filling spaces between phospholipids, making the membrane less permeable and more rigid - less fluid since there are more van der waal interactions
27
High Saturation & Long Fatty Acids
-less fluidity due to tight packing of saturated fatty acids
28
High unsaturation and short fatty acids
- more fluidity as the kinks from unsat fatty acids and their shorter length reduce packing (van der waal interactions)
29
Factors that affect membrane fluidity
1. Temperature 2. Lipid composition (sat of lipid tails, length of fatty acid tails, sterols in the membrane) 3. Membrane organization ( lipid rafts, attachment to structures inside/ outside the cell and barriers to diffusion)
30
Lipid rafts
- are microdomains in the plasma membrane rich in specific types of lipids (sphingomyelin & cholesterol) - thicker and less fluid - more ordered than surrounding membrane
31
Membrane protein adhesion to other molecules
connected to internal structures like the cytoskeleton (e.g., the cell cortex) and external structures like the extracellular matrix (ECM). This anchoring stabilizes the membrane and helps maintain its shape and organization.
32
Cell to cell adhesion
cadherins link the plasma membrane of neuronal cells
33
Diffusion barriers
Tight junctions: create barriers between neighboring cells and regulate what substances can pass between cells and help maintain the directional flow of molecules
34
How is permeability in the cell?
proteins allow the cell membrane to be selectively permeable
35
permeability depends on...
the properties of the molecules
36
diffusion of gases and hydrophobic molecules
diffuse freely across lipid bilayers
37
diffusion of small uncharged polar molecules
diffuse fairly well across lipid bilayers
38
Diffusion of large uncharged polar molecules
negligible
39
charged substances (ions)
cannot diffuse across lipid bilayer
40
Protein primary structure
linear amino acid sequence of peptide-bonded amino acids; this sequence determines the protein’s 3D structure
41
Protein secondary structure
Localized folding of the polypeptide chain into structures such as α-helices and β-pleated sheets, stabilized by hydrogen bonds between backbone amide groups.
42
Protein tertiary structure
overall 3-D structure (‘fold’) of entire polypeptide; stabilized by side-chain interactions (non-covalent and disulfide bonds) as well as interactions between side chains and backbone atoms.
43
Protein Quaternary structure
3-D arrangement of polypeptides in a protein composed of multiple subunits; similar stabilization as tertiary.
44
How are bilayer assembly and protein structure formation similar?
- both driven by thermodynamics - non covalent and covalent interactions ensure the most stable conformational state - increase stability of the system - allows for molecular self-assembly
45
Types of membrane proteins
integral proteins and peripheral proteins
46
integral proteins
directly attached to the membrane and are amphipathic
47
peripheral proteins
bound to membrane surfaces through non covalent association with other membrane proteins
48
Transmembrane proteins
allow certain substances to cross the lipid bilayer by acting as gateways
49
Transmembrane domain
- part of a membrane protein that passes through the lipid bilayer - some are alpha helices and some are beta barrerls
50
How do we study membrane proteins (and their asymmetry)?
A. Bioinformatics approach: hydropathy plots B. Protein purification & biochemical experiments
51
Bioinformatics approach: hydropathy plots
-To predict alpha helical transmembrane domains - Based on properties of the aa in peptide sequence - Peaks above threshold indicates potential transmembrane alpha-helices - No beta sheets - Reads entire sequence of protein
52
Why are hydropathy plots only for alpha helical domains?
because beta sheets alternate hydrophobic and hydrophilic residues, unlike alpha-helices that have continuous hydrophobic segments.
53
In transmembrane beta sheets (like beta-barrels), the hydrophobic residues face... while the hydrophilic ones face...
the lipid bilayer, aqueous env (inward)
54
Protein purification & biochemical experiments
- to determine membrane protein type, components & orientation
55
Steps of protein purification & biochemical experiments
1. break open the cells to release all the proteins, including both peripheral and integral proteins. Once the cells are lysed, the two types of proteins are separated differently 2. Unfold proteins by adding SDS and break disulfide bonds 3. Separate proteins by size with SDS-PAGE
56
Isolation of peripheral proteins
are isolated by using high-salt solution
57
Why do we use high salt solution to disrupt peripheral proteins?
high salt tends to weaken their non covalent interactions with the membrane
58
Isolation of integral proteins
isolated by using detergents like SDS
59
Why do we use detergents to isolate integral proteins
because these proteins are embedded in the membrane, therefore we need detergents disrupt the membrane to solubilize the integral proteins by surrounding their hydrophobic regions
60
What are detergents
have both hydrophilic (water-attracting) and hydrophobic parts, similar to lipids. When added to the solution, detergents disrupt the membrane by breaking up the lipid bilayer.
61
Step 2. Unfold/linearize proteins by adding SDS & break disulfide bonds
Add SDS to denature the protein and add mercaptoethanol to break disulfide bonds.
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SDS' role
SDS is a detergent that disrupts the natural 3D structure of proteins and coats proteins with a negative charge
63
Step 3. Separate proteins by molecular weight (size) with SDS-PAGE
proteins will move toward the positive side at the bottom of the gel - smaller proteins move faster and travel farther - larger proteins move slower and don't travel as far - we can visualize the proteins with dyes and fluorescent markers
64
Other method to size proteins and DNA and RNA
gel electrophoresis
65
Nucleic acids separation (DNA, RNA) using gel electrophoresis
Uses a gel called agarose. DNA and RNA already have a consistent charge because of their structure, so they separate based on their size as they move through the gel.
66
Questions we can answer using SDS-PAGE
1. Which side of the membrane is the protein facing? 2. Is the protein integral or peripheral?
67
Why do we use protease digestion?
to tell which part of the integral protein is facing the inside or outside of the membrane.
68
what is a protease
protease is an enzyme that breaks down proteins. If the protease is added to intact cells, it will only digest the part of the protein that is exposed on the outside of the membrane
69
Why do we say the membrane is asymmetric?
the two leaflets of the membrane are different. - lipid composition of outer and inner leaflet of bilayer are different - proteins have specific orientation within the membrane - carbohydrates are only found on the non-cytosolic side
70
what are flippases
enzymes that move phospholipids from one leaflet to the other
71
role of flippases
they help generate or maintain lipid asymmetry
BIO 200 MIDTERM 1
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