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Biochemistry 2 > Chapter 12- Lipids and cell membranes > Flashcards

Chapter 12- Lipids and cell membranes Flashcards

1
Q

Biological membranes

A

Dynamic structures in which proteins float in a sea of lipids. The lipid component prevents molecules generated inside the cell from leaking out and unwanted molecules from diffusing in. The protein components act as transport systems that allow the cell to take up specific molecules and remove unwanted ones. Membranes also define the boundaries of the cell

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2
Q

Internal membranes of the cell

A

Eukaryotic cells contain internal membranes that form the boundaries of organelles like the mitochondria, chloroplasts, peroxisomes, and lysosomes. Evolution has allowed for functional specialization and the development of these components

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3
Q

Common features of biological membranes (8)

A
  1. Membranes are sheetlike structures, only 2 molecules thick, that form closed boundaries between different compartments
  2. Consist mainly of lipids and proteins
  3. Membrane lipids form lipid bilayers
  4. Specific proteins mediate distinctive functions of membranes
  5. The proteins and lipid molecules of the membrane are held together by noncovalent cooperative interactions
  6. Membranes are asymmetric- the 2 faces of the membrane are different
  7. Membranes are fluid structures- lipids and proteins move around inside the membrane
  8. Most cell membranes are electrically polarized
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4
Q

Lipid bilayers

A

Membrane lipids have hydrophilic and hydrophobic components and spontaneously form closed bimolecular sheets in aqueous media. They are barriers to the flow of polar molecules

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5
Q

Functions of membrane proteins

A

Proteins act as pumps, channels, receptors, energy transducers, and enzymes. Membrane proteins are embedded in lipid bilayers, which create appropriate environments for their functions

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6
Q

Electrical polarization of the membrane

A

The inside of the cell is negative, typically -60 mV. Membrane potential plays a role in transport, energy conversion, and excitability

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7
Q

Fatty acids

A

Long hydrocarbon chains of various lengths and degrees of unsaturation that terminate with carboxylic acid groups

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8
Q

3 major kinds of membrane lipids

A
  1. Phospholipids
  2. Glycolipids
  3. Cholesterol
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9
Q

Functions of lipids

A

Water insoluble biomolecules that are highly soluble in organic solvents (like chloroform). They act as fuel molecules, highly concentrated energy stores, signal molecules and messengers in signal transduction pathways, and components of membranes

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10
Q

4 components of a phospholipid molecule

A
  1. One or more fatty acids- provide a hydrophobic barrier. The rest of the molecule has hydrophilic properties, which enables interaction with an aqueous environment
  2. A platform to which the fatty acids are attached
  3. A phosphate
  4. An alcohol attached to the phosphate
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11
Q

Phospholipid platform

A

Could be made of glycerol (3 carbon alcohol) or sphingosine (a complex alcohol)

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12
Q

Phosphoglycerides

A

Phospholipids derived from glycerol. They consist of a glycerol backbone to which 2 fatty acids and a phosphorylated alcohol are attached.

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13
Q

Phosphoglyceride structure

A

The hydroxyl groups at C-1 and C-2 of glycerol are esterified to the carboxyl groups of the 2 fatty acid chains. The C-3 hydroxyl group of the glycerol backbone is esterified to phosphoric acid. The resulting compound is phosphatide, the smallest phosphoglyceride- used to synthesize other phosphoglycerides

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14
Q

How are major phosphoglycerides derived from phosphatidate?

A

By the formation of an ester bond between the phosphate group of phosphatidate and the hydroxyl group of one of several alcohols

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15
Q

Common alcohol components of phosphoglycerides (5)

A
  1. Serine
  2. Ethanolamine
  3. Choline
  4. Glycerol
  5. Inositol
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16
Q

Common phosphoglycerides found in membranes (5)

A
  1. Phosphatidylserine
  2. Phosphatidylcholine
  3. Phosphatidylethanolamine
  4. Phosphatidylinositol
  5. Diphosphatidylglycerol (cardiolipin)
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17
Q

Sphingomyelin

A

A phospholipid found in membranes that is not derived from glycerol. It has an amino acid called sphingosine as a backbone, which contains a long, unsaturated hydrocarbon chain. The amino group of the sphingosine backbone is linked to a fatty acid by an amide bond. The primary hydroxyl group of sphingosine is esterified to phosphorylcholine

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18
Q

Glycolipids

A

Sugar containing lipids that are derived from sphingosine. The amino group of the sphingosine backbone is acylated by a fatty acids. In glycolipids, one or more sugars are attached to the primary hydroxyl group of the sphingosine backbone.

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19
Q

Cerebroside

A

The simplest glycolipid, which contains a single sugar residue (glucose or galactose)

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20
Q

Gangliosides

A

Complex glycolipids that contain a branched chain of as many as 7 sugar residues. Glycolipids are oriented in an asymmetric fashion- the sugar residues are always on the extracellular side of the membrane

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21
Q

Where are the carbohydrate components of glycolipids located?

A

The carbohydrate components of glycolipids are on the extracellular surface of the cell membrane, where they
play a role in cell–cell recognition.

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22
Q

Cholesterol structure

A

The third type of membrane lipid. It is a steroid that is built from 4 linked hydrocarbon rings. A hydrocarbon tail is linked to the steroid at one end, and a hydroxyl group is attached to the other end. In membranes, the molecule is parallel to the fatty acid chains of the phospholipids, and the hydroxyl group interacts with the nearby phospholipid head groups

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23
Q

Where is cholesterol found?

A

It is not found in prokaryotes, but is found in different amounts in almost all animal membranes. It makes up almost 25% of the membrane lipids in certain nerve cells, but is basically absent from some intracellular membranes

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24
Q

Amphipathic characteristics of membrane lipids

A

Membrane lipids are considered amphipathic because they contain hydrophilic and hydrophobic components. The fatty acid tail components provide the hydrophobic properties, whereas the alcohol and phosphate components, called the polar head group, provide the hydrophilic properties. The fatty acid chains are mostly parallel to each other, while the polar component points in the opposite direction

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25
Q

Relationship between membrane lipids and membrane proteins

A

Membrane lipids form a permeability barrier and establish compartments, while specific proteins mediate nearly all other membrane functions. They transport chemicals and information across a membrane. Membrane lipids create the appropriate environment for the action of such proteins

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26
Q

How does protein content vary between membranes?

A

Myelin has a low content of protein (18%), since relatively pure lipids are better suited for insulation. The plasma membranes of most other cells are more metabolically active. They contain many pumps, channels, receptors, and enzymes. The protein content of these plasma membranes is typically 50%. Energy transduction membranes, like the internal membranes of mitochondria and chloroplasts, have the highest content of protein, around 75%

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27
Q

Myelin

A

A membrane that serves as an electrical insulator around certain nerve fibers. It plays a critical role in enabling the rapid transmission of action potentials. Oligodendrocytes/Schwann cells wrap their plasma membranes multiple times around the axon.

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28
Q

How does myelination of the brain change over time?

A

Significant myelination of neurons in the brain occurs during infancy but persists throughout adolescence. The brain actively develops throughout childhood.

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29
Q

How are the protein components of a membrane visualized?

A

By SDS-polyacrylamide gel electrophoresis. The electrophoretic mobility of many proteins in SDS-containing gels depends on the mass rather than the net charge of the protein. Each membrane contains many proteins, but has a distinct protein composition. This is because membranes performing different functions contain different repertoires of proteins

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30
Q

Myelination

A

The process of a Schwann cell/oligodendrocyte wrapping its membrane around an axon

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31
Q

Multiple sclerosis

A

An example of a demyelination disease, impairing myelin
assembly or damaging existing myelin

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32
Q

Integral membrane proteins

A

Interact extensively with the hydrocarbon chains of membrane lipids, and can be released only by agents that compete for these nonpolar interactions. Most of these proteins span the lipid bilayer

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33
Q

Peripheral membrane proteins

A

Bound to membranes by electrostatic and hydrogen-bond interactions with the polar head group of lipids. These polar interactions can be disrupted by adding salts or by changing the pH.

34
Q

How are peripheral membrane proteins anchored to the lipid bilayer?

A

Some are bound to the surfaces of integral proteins on the intracellular or extracellular side of the membrane. Others are anchored to the lipid bilayer by a covalently attached hydrophobic chain (like a fatty acid)

35
Q

Bacteriorhodopsin

A

An archaeal protein that uses light energy to transport protons from inside to outside the cell. It generates a proton gradient used to form ATP. Bacteriorhodopsin is built almost entirely of 7 alpha helices. Most of the amino acids in these membrane spanning alpha helices are nonpolar and only a few are charged.

36
Q

How are membrane proteins distributed?

A

In bacteriorhodopsin, most of the amino acids in the membrane spanning alpha helices are nonpolar and only a few are charged. This distribution of nonpolar amino acids makes sense, because these residues are either in contact with the hydrocarbon core of the membrane or with one another. Membrane spanning alpha helices are the most common structural motif in membrane proteins

37
Q

Motifs (supersecondary structures)

A

Combinations of secondary structure that are present in many proteins and frequently exhibit similar functions. A helix-turn-helix is an example

38
Q

Alpha helix

A

A rod-like secondary structure. A tightly coiled backbone forms the inner part of the rod and the side chains extend outward in a helical array. It is stabilized because the CO group of each amino acid forms a hydrogen bond with the NH group of the amino acid that is situated 4 residues ahead in the sequence. All main chain CO and NH groups are hydrogen bonded except for the terminal amino acids

39
Q

Porin structure

A

A protein found in the outer membranes of bacteria, like E. coli. The protein is built entirely of beta strands (does not have alpha helices).

40
Q

Arrangement of beta strands in porin membrane proteins

A

Each strand is hydrogen bonded to its neighbor in an antiparallel arrangement, which forms a single beta sheet. The beta sheet curls up to form a hollow cylinder that forms a pore (channel) in the membrane. The outside surface of the porin is nonpolar because it interacts with the hydrocarbon core of the membrane. The inside of the channel is hydrophilic and is filled with water. The alternation of hydrophobic and hydrophilic amino acids along each beta strand allows for the hydrophobic and hydrophilic surfaces of the protein

41
Q

Beta sheets

A

Composed of two or more polypeptide chains (beta strands). The beta strands are almost fully extended, instead of being tightly coiled like an alpha helix. The sheet is formed by linking two or more strands lying next to one another hydrogen bonds. The strands can be parallel, antiparallel, or mixed, and the sheets can include 10 or more strands, but typically has 4 or 5. The sheets can be flat or somewhat twisted. Fatty acid binding proteins are built mostly from beta sheets

42
Q

Antiparallel beta sheets

A

Adjacent strands in a beta sheet that run in opposite directions. The NH group and the CO group of each amino acid are hydrogen bonded to the CO group and NH group of another amino acid on the adjacent chain

43
Q

Parallel beta sheets

A

Adjacent strands in a beta sheet that run in the same direction. For each amino acid, the NH group is hydrogen bonded to the CO group of one amino acid on the adjacent strand. The CO group is hydrogen bonded to the NH group on the amino acid two residues further along the chain

44
Q

Prostaglandin H2 synthase-1

A

Catalyzes the conversion of arachidonic acid into prostaglandin H2. It is a homodimer with a complicated structure that consists mainly of alpha helices. It lies along the outer surface of the membrane and is firmly bound by a set of alpha helices with hydrophobic surfaces that extent from the bottom of the protein into the membrane. This is a strong linkage that can only be disrupted by detergents- detergents can release the protein from the membrane. It is classified as an integral membrane protein even though it doesn’t span the membrane

45
Q

Conversion of arachidonic acid into prostaglandin H2 (2 steps)

A
  1. A cyclooxygenase reaction
  2. A peroxide reaction
46
Q

Prostaglandin H2

A

Promotes inflammation and modulates gastric acid secretion. In response to an injury or infection, prostaglandins promote the inflammatory response and cause swelling, pain, and fever.

47
Q

How does localization of prostaglandin H2 synthase impact its function?

A

Arachidonic acid is a substrate for this enzyme. Arachidonic acid is hydrophobic and reaches the active site of the enzyme from the membrane without entering an aqueous environment by traveling through a hydrophobic channel in the protein. Drugs like aspirin and ibuprofen block this channel and prevent prostaglandin synthesis by inhibiting the cyclooxygenase activity of the synthase

48
Q

Aspirin mechanism

A

Acts through the transfer of its acetyl group to a serine residue that lies along the path to the active site. It blocks the channel in the prostaglandin synthase that its substrate travels through to reach the active site.

49
Q

Cyclooxygenase inhibitors

A

Blunt the inflammatory response, provide pain relief and fever reduction. Aspirin inhibits cyclooxygenase activity by obstructing the channel.

50
Q

The cyclooxygenase (COX) activity of prostaglandin H2 synthase-1 is dependent on

A

a channel connecting the
active site to the membrane interior

51
Q

Membrane anchors

A

Hydrophobic groups that are covalently attached to proteins and tether the proteins to the membrane. They allow soluble (hydrophilic) proteins to associate with the hydrophobic membranes. Examples- palmitoyl groups, farnesyl groups, and GPI anchors

52
Q

Using amino acid sequence to predict transmembrane helices

A

One approach is to ask whether a postulated helical segment is likely to be more stable in a hydrocarbon environment or in water. What is the free energy change when a helical segment is is transferred from the interior of a membrane to water? We can use the amino acid sequence and estimate free energy changes of a hypothetical alpha helix when transferred from the membrane to water

53
Q

Hydropathy plot

A

Plots the free energy change when the protein is transferred from the membrane to water, against the first amino acid at the window. Empirically, a peak of +84 mol or more in a hydropathy plot based on a window of 20 residues indicates that a polypeptide segment could be a membrane spanning alpha helix. Hydropathy plots can identify potential membrane-spanning helices when sequence but little additional information is known for a protein. However, a peak in a hydropathy plot does not prove that a segment is a transmembrane helix. Even soluble proteins can have nonpolar regions

54
Q

Window

A

A stretch of 20 amino acids

55
Q

How many residues would be able to traverse a lipid bilayer?

A

An α helix consisting of 20 residues can traverse a lipid bilayer.

56
Q

Hydrophobicity of each amino acid can be quantified by

A

Hydrophobicity of each amino acid can be quantified by determining the free energy required to transfer the amino acid from a hydrophobic to a hydrophilic environment.

57
Q

Polarity Scale for Identifying
Transmembrane Helices

A

Shows the free energy for the transfer of an amino acid residue in an alpha helix from the membrane interior to water

58
Q

Glycophorin

A

A protein found in the membranes of red blood cells- it is predicted to have one membrane-spanning helix based on free energy findings. The hydropathy plot has a peak of +168 (greater than +84). The hydrophobic residues buried in the bilayer form a transmembrane alpha helix. The carboxyl terminal part of the molecule is located on the cytoplasmic side of the membrane. It is rich in negatively and positively charged residues

59
Q

Purpose of having 2 membranes

A

Bacteria like E. coli have 2 membranes separated by a cell wall. The inner membrane acts as the permeability barrier, and the outer membrane and the cell wall provide additional protection. The outer membrane contains porins and is therefore very permeable to small molecules

60
Q

Periplasm

A

The region between the two membranes in bacteria, which contains the cell wall

61
Q

Gram staining

A

A technique used to distinguish between 2 types of bacterial membranes. Crystal violet dye is added to a sample of bacteria. Then, iodine is added to trap the dye in the cell. Alcohol is used to wash out the dye. Bacteria can be Gram negative or Gram positive. In Gram positive bacteria, the trapped dye binds tightly and does not wash out

62
Q

Gram positive bacteria

A

Bacterial cells that have a thick cell wall- the trapped dye binds tightly and does not wash out. These bacteria stain dark purple

63
Q

Gram negative bacteria

A

Bacterial cells that have a thin cell wall- the dye washes out quickly and the bacteria stain pink, due to the addition of a second stain at the conclusion of the experiment

64
Q

Why are Gram staining results important?

A

It is an important method for the initial classification of a bacterial sample, especially in fluid samples from an infected patient. Rapid identification of bacterial type is critical for the selection of antibiotic treatment

65
Q

Cell walls

A

Cell walls are made from proteins, peptides, and carbohydrates. Bacteria contain cell walls, as do plants. In plant cells, the cell wall is on the outside of the plasma membrane. Animal cells do not have cell walls

66
Q

Eukaryotic cells

A

Eukaryotic cells, with the exception of plants, do not have cell walls. They are surrounded by a single membrane, known as the plasma membrane (or cell membrane). Eukaryotic cells have membranes inside the cell that allow compartmentalization of function, unlike prokaryotic cells. Example- the nuclear envelope is a double
membrane connected to another membrane system of
eukaryotes, the endoplasmic reticulum.

67
Q

Nuclear envelope

A

The double membrane that surrounds the nucleus. It consists of a set of closed membranes that come together at structures called nuclear pores. The pores regulate transport into and out of the nucleus. The nuclear envelope is linked to the endoplasmic reticulum

68
Q

Endoplasmic reticulum

A

Another membrane defined structure that is attached to the nuclear envelope. It plays a role in drug detoxification and the modification of proteins for secretion.

69
Q

Receptor mediated endocytosis

A

The process by which cells take up molecules. A protein or larger complex binds to a receptor on the cell surface. Once the molecule binds, specialized proteins act to cause the membrane in this region to invaginate. The invaginated membrane eventually breaks off and fuses to form a vesicle

70
Q

Clathrin

A

A specialized protein that causes the membrane to invaginate for receptor mediated endocytosis. It polymerizes into a lattice network around the growing membrane bud (also called a clathrin-coated pit). This helps to internalize receptors bound to their cargo.

71
Q

Which molecules utilize receptor mediated endocytosis to get into the cell?

A

Various hormones, transport proteins, and antibodies. This process occurs in reverse (a vesicle fusing with the membrane) to release neurotransmitters into the synaptic cleft

72
Q

Disadvantage of receptor mediated endocytosis

A

This pathway is available to viruses and toxins as a means of invading cells

73
Q

Transferrin

A

The protein that binds iron in the bloodstream. Iron is crucial for the functions of many proteins, like hemoglobin and myoglobin. However, free iron ions are highly toxic to cells because they can form free radicals. The transport of iron atoms from the digestive tract to the cells where it’s needed has to be tightly controlled

74
Q

Transferrin receptor

A

The receptor for transferrin that is expressed in the plasma membranes of cells that require iron. Formation of a complex between the transferrin receptor and iron-bound transferrin initiates receptor mediated endocytosis

75
Q

Endosomes

A

Vesicles that internalize protein complexes formed during receptor mediated endocytosis. Transferrin receptor and iron bound transferrin complexes are internalized in endosomes.

76
Q

Use of endosomes in transporting iron into the cell

A

As the endosomes mature, proton pumps in the vesicle membrane lower the pH of the lumen to 5.5. Under these conditions, the affinity of iron ions for transferrin is reduced. The ions are released and are free to pass through channels in the endosomal membranes into the cytoplasm. The iron-free transferrin complex is recycled to the plasma membrane. Transferrin is released back into the bloodstream.

77
Q

SNARE proteins

A

Membrane fusion needs to be specific. Proteins from both membranes that help draw appropriate lipid bilayers together by forming tightly coiled 4-helical bundles. Once these membranes are close to each other, the fusion process can proceed

78
Q

Structure of cardiolipin

A

Diphosphatidylglycerol (cardiolipin) has an unusual structure compared with the other
phosphoglycerides shown earlier. It has a net charge of −2 and an inverted cone shape, unlike most phosphoglycerides.

79
Q

Cardiolipin

A

Most often found in the membranes of bacteria,
archaea, and the inner membranes of mitochondria. In
mitochondria, the cardiolipin is involved in the structure and function of the respirasome, which is essential in ATP synthesis.

80
Q

Tafazzin

A

Proper synthesis and maintenance of cardiolipin levels requires the enzyme tafazzin, which catalyzes the transfer of linoleate chains from phosphatidylcholine to immature cardiolipin

81
Q

Barth syndrome

A

Results from mutations that reduce the catalytic
activity of tafazzin. Symptoms include dilation of the heart chambers, exercise intolerance, and impaired growth. These
individuals have malformed mitochondria with distorted inner
membranes and poorly functioning respirasomes due to improper assembly of the protein complexes.

Biochemistry 2 (12 decks)

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