BIOL 3362 BIOCHEMISTRY II Exam 3 (MOVED TO TUESDAY APRIL 14TH!

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STUDY GUIDE
Chapter 8 Lipids
How the fatty acids are denoted according to IUPAC nomenclature rules?
The longest carbon chain in the molecule determines the prefix. Since the highest priority
functional group of fatty acids is the carboxyl group, the suffix is oic acid. Example: A 12carbon, fully saturated fatty acid is called dodecanoic acid.
In the case of unsaturated fatty acids, an cen- is added. Example: A 16-carbon, unsaturated
fatty acid with a double bond at the 9th carbon is called 9-hexadecenoic acid.
^^^ a -cen is not added, rather an -en is added as it contains an alkene. HEXADECen-oic acid
12:0 - lauric acid
14:0 - myristic acid
16:0 - palmitic acid
18:0 - stearic acid
18:1(9) - oleic acid
18:2 (9,12) - linoleic acid

What are the unique structural features of fatty acids?

- They are hydrophobic (little/no affinity for water.)
- insoluble in water, soluble in non-polar compounds (like dissolves like)
- amphipathic: have a polar and non-polar end.
- long hydrocarbon hydrophobic tail + carboxyl hydrophillic head
- carbanion-based condensations of thioesters and/or by carbocation based
condensation of isoprene units and ketoacyl units

6-7

How does lipid unsaturation affect the material properties of fats and oils?
Each cis double bond causes a kink in the chain. Fatty acid double bonds are usually cis.
Takes less thermal energy to further disorder poorly ordered arrays of FA. Therefore,
unsaturated FAs have a lower Tm (i.e., olive oil is more liquid at room temperature than is butter
or beef fat). Presence of cis double bonds reduce the compaction/stacking of the fatty acids.

What is lipid chirality? Why it is important in biological molecules?

-Chirality in glycerolipids is due to the fact that the central carbon in glycerol has four different
substitutions, thus it is a stereogenic center/chiral center.
--Chirality determines the stereochemistry of biological molecules - many biochemical
pathways are stereoselective.
--Recent studies show that the chirality of phospholipids makes fluid lipid bilayers piezoelectric
-Piezoelectric properties brought by chiral lipids is believed to play a central role in the
functioning of cell membranes as active couplers such as mechanoreception,
magnetosensitivity, as well as in-plane proton membrane transport and related phenomena
such as adenosine triphosphate (ATP) synthesis.
-Piezoelectricity is the charge that accumulates in certain solid materials in response to applied
mechanical stress (electricity resulting from pressure)

--Lipid chirality in cell membrane has been proposed to be the determining mechanistic factors
in a hypothesis for the origin of the three domains of life.

What is saponification?
Process that produces soap by alkali hydrolysis of triacylglycerols with lye which yields
glycerol and salt of free fatty acids (soap) strong bases
What are waxes?
Esters of long chain alcohols with long chain fatty acids. Usually insoluble due to mostly
hydrocarbon composition. Have high melting point, are solid at room temperature. Function as
energy stores and act as water impermeable coatings. Biological roles: preventing water loss,
abrasion, and infection.
What is an essential fatty acid?
Essential fatty acids, or EFAs, are fatty acids that humans and other animals must ingest because the
body requires them for good health but cannot synthesize them.
-linoleic acid
-precursor for the synthesis of eicosanoids, such as prostaglandins.
-Omega-6 fatty acid:
--pro-inflammation
--Linoleic
--2 double bonds
--found mostly in fresh fruits, vegetable, olive oil, corn oil
-Omega 3 fatty acid:
--anti-inflammation
--Alpha-linolenic acids
--3 double bonds
--found mostly in fish and flaxseed; consist of DHA and EPA

What is a trans-fatty acid?

-Can occur due to fat hydrogenation

-Partial hydrogenation of polyunsaturated oils contain substantial levels of various trans fat, and clinical
research has shown that chronic consumption of processed foods containing partially hydrogenated
vegetable oils can contribute to cardiovascular disease

-As a byproduct of hydrogenation or when heated to high temperatures or repeatedly re-used, oils with
high content of unsaturated fatty acids can form unhealthy trans-fatty acids

-A trans-fatty acid is an unsaturated fatty acid that contains at least one double bond in the trans
conformation, rather than the usual cis conformation.
What is the effect of heat on lipids? (in terms of chain length, saturation)
At low temperatures: bilayer lipids are highly ordered
Tm increases with:
increase in chain length
decrease in unsaturation
depends on the polar head group
please give more information (saturation, chain length)
What are the properties of triacylglycerols? Where are they found in the cell?
-Composed of glycerol which is esterified with three fatty acids (esterification- bond between a hydroxyl
group and a carboxyl group)
-Fats and oils - triglycerides, found in adipocytes
-Are chiral even though glycerol is not; attachment of fatty acids is what makes them chiral

What are the molecular movements available to lipids in a membrane structure? (Ch. 9 slide
42)
-Lateral (in the plane of the membrane)
-Rotational
-Segmental (tails waving)
-Bobbing (up and down in the bilayer)
-Flip flop (slow process, does not occur to any significant rate in artificial membranes, only living cells)
Due to flippases (phospholipid translocases) which also control lipid asymmetry
catalytic alpha subunit of P4 ATPase and regulatory beta subunit of Cdc50 protein family

Why lipids are the biomolecules of choice for storage of metabolic energy?
-Contain highly reduced carbons, large amounts of energy released in the oxidative reactions of
metabolism
-Ex: 1 g of triglyceride 38 kJ of energy
They are not hydrated like mono and disaccharides so can be compacted.
the energy available in fats (lipids) in the average person far exceeds the energy available from protein,
glycogen and glucose

 Why diets high in trans-fatty acids and saturated fatty acids are not good for health?
Diets high in trans-fatty acids raise plasma LDL (bad) cholesterol levels and triglyceride levels while
lowering HDL (good) cholesterol levels.
-The effects of trans-fatty acids on LDL, HDL, and cholesterol levels are similar to those of saturated fatty
acids.
-Diets aimed at reducing the risk of coronary heart disease should be low in both trans and saturated fatty
acids.
-Trans-fatty acids along with saturated fatty acids form a very compact structure in triglyceride form. Since
there is no kink in the hydrocarbon tail, their structure is very stable and hard to break. This
compactness causes them to have very high melting point and require high temperature to break down.
This will cause accumulation of fat residues in the body and eventually cause diseases such as blood
vessel coagulation leading to heart problems, stroke, and many other heart-related complications

How do unsaturated fatty acids provide fluidity to membranes?

- The double bonds found in fatty acids are nearly always in the cis configuration. This causes a bend or
kink in the fatty acid chain. This bend has very important consequences for the structure of biological
membranes.
- Unsaturated fatty acids prevent such close packing and produce flexible, fluid aggregates. Increased
fluidity means that it will have a lower melting point and this will make the fatty acid stay in liquid phase in
lower temperatures (37C)

What are the properties of glycerophospholipids?

- Similar to fats but have only two fatty acids esterified to the carbons 1 and 2 position of the
glycerol backbone. The carbon 3 position is esterified to a phosphate group that is linked to a
polar head group alcohol.
Glycerophospholipids are:
-amphipathic (hydrophobic tail consisting of hydrocarbons, hydrophilic head consisting of the
phosphate group and its attachment)
-essential components of cell membrane
-(USUALLY) contain one fatty acid that is unsaturated, typically on the carbon 2 position of the
glycerol backbone
-the phosphate group is negative in electrical charge (its possible that the head group contains
either ethanolamine or choline, which would make it (NET) neutral though)
What are the common head groups in glycerophospholipid?
Hydrogen
Serine
Inositol
Glycerol.
Ethanolamine (+) @ pH 7
Choline (+) @ pH 7
Ethanolamine and choline are positively charged at neutral pH, balancing out the negative
charge from the phosphate to give a net charge on the polar head region of zero. When the
head group has no net charge, the glycerophospholipid is negatively charged due to the
negatively-charged phosphate.

 How do phospholipases cleave glycerophospholipids?

Enzymes that convert phospholipids into fatty acids by hydrolyzing ester bonds in phosphoglycerides

There are 4 phospholipases: A1, A2, C, and D. Phospholipases A1 and A2 cleave the fatty
acids of glycerophospholipids from the 1, and 2 glycerol carbon positions, respectively.
This produces lysophospholipids. Phospholipases C and D hydrolyze on either side of
the phosphate in the polar head group.
What is a sphingolipid? What are the derivatives and their functions?
A class of lipids with sphingosine as the backbone instead of glycerol. (Sphingosine is an 18-C
amino alcohol). A fatty acid is joined to the sphingosine via an amide linkage to form a ceramide.
Derivatives:
phosphosphingolipids, also called sphingomyelins, represent a phosphorus
containing subclass of sphingolipids that are especially important in the nervous tissue of
higher animals
glycosphingolipids: consist of a ceramide with one or more sugar residues in a
beta-glycosidic linkage at the 1-hydroxyl moiety; glycosphingolipids with one sugar are
cerebrosides, ceramides with 3 or more sugars, one of which is a sialic acid, are
gangliosides
What do phospholipids participate in cellular signaling events?
Phospholipids participate in transmission of ligand receptor induced signal from the plasma
membrane to intracellular proteins, primarily PKC, which is maximally active in the presence of
calcium ion and diacylglycerol. PKC activity is mediated by receptor that are coupled to
activation of phospholipase C.

What is a ceramide?
A fatty acid joined to a sphingosine via an amide linkage

What are plasmalogens?

A variant of an ether glycerophospholipid in which the fatty alcohol has a double bond between
carbons 1 and 2. (Remember an ether phospholipid is a variant on the phospholipid in which
one of the fatty acids has been replaced by a fatty alcohol thereby making the connection to the
glycerol an ether linkage rather than an ester linkage. See slide 75 for structure).
Plasmalogens easily react with a variety of free radicals in and around the lipid membrane
preventing the oxidation of highly polyunsaturated fatty acids, therefore can be classified as
antioxidants.
What is the difference between omega-3 and omega-6 fatty acids? How are they processed in
the cells?
Omega-3 (Found in fish biggest deficiency):
made from alpha-linolenic acid,
long chain polyunsaturated fats ranging from 18-20 Cs long.(ALA, EPA, DHA),
site of unsaturation between 3 and 4 C from omega side.
highly curved structure,

 ALA EPA (3 reactions)--> DHA (4 reactions),

anti-inflammatory mediators
Omega-6 (hard to have deficiency found in vegetable oils)
made from linoleic acid
Linoleic GLA DGLA arachidonic acid (precursor to eiconasoids-prostaglandins)
site of unsaturation between 6 and 7 C from omega side
pro-inflammatory mediators
What are terpenes/terpenoids/isoprene/isoprenoids compounds? How are they formed?
-roles include modulation of membrane fluidity, chemical defense and communication, energy
transfer and growth regulation
-Give plants their fragrance
-Small plant-made molecules that turn into vapor at relatively low temperatures and waft easily
through the air
-Building block is the hydrocarbon isoprene
-Larger structures of terpenes are assembled from several isoprene units, usually by head-totail linked isoprene units
What are some of the common terpenes?
-Vitamin A

-Menthol
-Cholesterol
-Steroids
What is caldarchaeol?
a membrane-spanning lipid in thermoacidophilic archaea. the hydrophobic core consists
of C40C40 caldarchaeol
A membrane-spanning lipid found in hyperthermophilic archaea. Membranes made up of
caldarchaeol are more stable since the hydrophobic chains are linked together, allowing the
microorganisms to withstand high temperatures.
ether linked glycerol to isoprene chains
Which steroid hormones do participate in the control of carbohydrate, protein and lipid
metabolism? cortisol
Glucocorticoids (Ex: cortisol)
What are sterols? List some of the common steroids. cortisol, testosterone, estradiol,
progesterone
A steroid (the cholesterol-looking molecules) that contains an oxygen bonded to the carbon at
the 3 position. The oxygen can be double bonded, as a ketone; or single bonded, as an alcohol.
What is the backbone of steroid hormones?
gonane is this correct? yes

 What are the plant stenols?

fully reduced sterols, they mimic cholesterol and bind to cholesterol receptors on intestinal cells
and block the absorption of cholesterol. Stenols arent absorbed.

Chapter 9 - Membranes and Membrane Transport

Why do lipids spontaneously form ordered structures in water? What types of arrangements do
they undergo?
-Waters tendency to form hydrogen bonds and share in polar interaction, and the hydrophobic effect,
which promotes self-association of lipids in water to maximize entropy, are the basis for the interactions of
lipids and proteins to form membranes
-Lipids are amphiphiles. Amphiphiles have both water soluble and insoluble parts. When an amphiphile is
put in water, the water-INsoluble or apolar portion wants to avoid contact with water
- form monolayer, bilayer, micelle, or liposomes
What is critical micelle concentration?

CMC= concentration of surfactants above which micelles form and all additional surfactants added
to the system go to micelles. Once surface tension reaches a certain point, all additional molecules will go
to micelles since the tension is at its limit.

Micelles only form above CMC temperature. Below this monomers/lipids are present.

Molecules -> spherical micelles -> cylindrical micelles -> middle phase -> viscous isotropic phase->
neat phase

Ex: washing clothes- starts off w/ greater concentrations than CMC in water, waits for equilibrium,
the surfactant concentration goes below CMC & no micelles form.
The lipid concentration at which micelle formation will occur. If the lipid concentration is below the CMC,
then micelles will not form; instead, individual lipid molecules will predominate in solution. If the lipid
concentration is above the CMC, then micelles will form. CMC values vary from lipid to lipid.
What are liposomes? What are the uses of liposomes?
-Also known as unilamellar vesicle (single lipid bilayer)
-Artificially prepared (bilayers) lipid vesicles, which are highly stable and can be subjected manipulation
such as gel filtration and dialysis
-Liposomes can be prepared to mimic/resemble cell membrane structure and function. Hence, they are
very useful to deliver drug or diagnostic reagents into the body
Liposomes are vesicles that have a membrane composed of phospholipids with a single lipid bilayer
structure (unilamellar vesicles).

What are the properties and characteristics of biological membranes that account for their
broad influence on cellular processes?
-What makes the cell membrane special is the presence of different proteins on the surface that are used
for various functions such as cell surface receptors, enzymes, surface antigens, and transporters
-Proteins carry out most of the cell membranes functions
1.Membrane transport proteins (integral membrane proteins)
2.Membrane receptor proteins (integral membrane proteins)
3.Cell adhesion proteins (integral membrane proteins)
4.Cell-recognition proteins (integral membrane proteins)

5.Virus, toxin and drug-fixing proteins

6.Shape and cell migration-related proteins

How do sugars occur on the cell membrane?

Branched oligosaccharides covalently bonded to lipids or proteins used for recognition of cells and
separation of the cell from local environments

How are the peripheral proteins attached to membrane?

-Peripheral (extrinsic) proteins are associated with the surface of the bilayer surface via ionic interactions
(electrostatic) and H-bonds.
-Some proteins bind to extracellular side via covalent bond to GPI
-Can also be bonded via myristoylation, palmitoylation, and isoprenylation
-These proteins can be removed from the membrane by agents that disrupt ionic interactions and
hydrogen bonds (high salt concentrations, urea or extremes of pH)
-In most cases, peripheral proteins are found on the intracellular side of the membrane
-2 major groups of peripheral membrane proteins
-Most peripheral proteins are linked to the intracellular side of the membrane through an
enzymatically-mediated covalent bond to a lipid chain, enabling anchorage of a protein to the cell
membrane or to other membranes
-Other proteins are linked to a transmembrane (integral) protein through a non-covalent bond.
This protein will be located on predominantly on the intracellular side of the membrane

How do proteins associate with cell membrane?

They associate as either peripheral or integral proteins. Associating as peripheral or integral
depends on whether they are hydrophobic and can attach into the bilayer or hydrophilic and must stay on
the outside of the bilayer via ionic interactions or H bonds. Integral proteins usually must be removed with
detergents.
peripheral - surface of bilayer via ionic interaction/ h bond- do not extend into hydrophobic interier
integral- associated with bilayer- some portion inserted into hydrophobic interior of bilayer

How does the presence of cholesterol affect lipid membrane?

-Helps stabilize the membrane
-At body temp, cholesterol makes the membrane less fluid by restraining the movement of phospholipids.
-But because cholesterol hinders the close packing of phospholipids, it also lowers the temperature
required for the membrane to solidify

How does temperature affect lipid membrane?

1. At low temperatures, bilayer lipids are highly ordered, forming a gel phase with the acyl
chains nearly perpendicular to the plane of the membrane plane. This state is called the solidordered state, and the lipid chains are tightly packed and undergo relatively little motion. The
lipid chains are in their fully extended conformation, the surface area per lipid is minimal, and
the bilayer thickness is maximal.
2. At higher temperatures, the acyl chains undergo much more motion. The membrane is then
said to be in a liquid crystalline phase or liquid-disordered state. In this less ordered state,
the surface area per lipid increases and the bilayer thickness decreases.
Also: The transition from the gel phase to the liquid crystalline phase is a true phase transition,
and the temperature at which it occurs is referred to as a melting temperature (Tm).

 How are the proteins attached to cell membrane via lipids?

-myristoylation: add myristic acid on N-terminal Gly through amide bond= cotranslational
-palmitoylation: add palmitic acid on C-terminal Cys by thioester bond = posttranslational
-isoprenylation: add fanesol and geranylgeraniol to C-terminal Cys = posttranslational
What are the lipid rafts? How do they form and what is their function?
Regions of the lipid membrane that are unable to be structurally characterized in the solid
ordered state or the liquid disordered state. This unique state that is only found in certain
regions of the membrane (rather than the whole of the membrane) is called the liquid-ordered
state. It is characterized by a high degree of acyl chain ordering (like in the solid ordered state)
but has the translational disorder characteristic of the liquid disordered state. The regions that
exhibit these characteristics are called lipid rafts (or membrane rafts) and are postulated to be
aggregates of specific proteins, cholesterol, and glycosphingolipids with long, saturated fatty
acyl chains. They are transient, with lifetimes from a tenth of a millisecond or less to a few
seconds or more. They function in a complementary role to proteins involved in signaling
processes.
What is meant by asymmetric structure of biological membranes?
The two monolayers of the lipid bilayer have different lipid compositions and different
complements of proteins. The membrane composition is also different from place to place
across the plane of the membrane. It is said that both the lipids and the proteins of membranes
exhibit lateral heterogeneity and transverse asymmetry.
Which organelle in the eukaryotic cell synthesizes phospholipids, glycolipids and cholesterol?
smooth endoplasmic reticulum and golgi by lipid transfer proteins
How does transport occur across biological membranes?
Through one of these three types of membrane transport processes: passive diffusion,
facilitated diffusion, or active transport. (Or secondary active transport)
What is antiport, uniport, and symport?
Symport, in which the solutes are sent in the same direction
Uniports simply move solutes from one side to another.
Antiport, in which they are sent in opposite directions
What is the effect of temperature on transport across lipid membrane?
Low temperatures should inhibit transport across the lipid membrane, as lipids become
more rigid and less fluid. Higher temperatures should increase transport (up to certain point).

What is active transport and secondary active transport?

Active transport is the movement of molecules against their natural direction with the
assistance of ATP hydrolysis, light, or a concentration gradient.

Ex: sodium-potassium Atpase pump: pumps sodium out, potassium in.

(High concentration of potassium inside, and low outside. Negative charge on inside.)

Secondary active transport: transport driven by ion gradients. (concentration gradients)

How does Na+,K+-ATPase function?

it uses the energy derived from hydrolysis of ATP to drive the active transport of
potassium ions inside and sodium outside cells in 2:3 stoichiometry.
Main role: establishment & maintenance of an electrochemical gradient across plasma
membrane, critical for processes such as neuronal communication, osmotic regulation
of cell volume, ion homeostasis.
ATP hydrolysis occurs via an E-P intermediate.
Cardiac glycosides inhibit by binding to outside.
3 Na+ bind intracellularly, the ATPase is phosphorylated favoring P-enz II, Na+ is moved
to the outside the cell
2 K+ bind extracellularly, ATPase is dephosphorylated favoring P-enz I, K+ is moved to
inside the cell
Why water transport across lipid membrane requires a protein?
Because water only moves by osmosis, in order to direct the movement of water,
cells in the kidney set up strong osmotic gradients using Na+. By regulating these
gradients and specific channel proteins, kidney cells exert precise control over loss or
retention of water and electrolytes.
Lipid bilayers of plasma membrane have limited water permeability, thus
AQUAPORINS are necessary, which forms channels through which water can diffuse.

What are the common head groups in glycerophospholipids?

H, serine, inositol, glycerol, choline, ethanolamine

Ethanolamine and choline are positively charged at neutral pH, which balances the
negative charge of the phosphate, so that the net charge on the polar head region of the
lipid is zero.
What is passive diffusion?
When the transported species moves across the membrane in the thermodynamically favored
direction without the help of any specific transport system/molecule.
How does facilitated diffusion occur?
The transported species moves across the membrane in the thermodynamically favored
direction with the help of integral membrane proteins that show specificity for the transported
solute. This diffusion type can exhibit saturation behavior when the solute concentration is high
enough; this is similar to saturation kinetics with enzymatic reactions.
How does energy input drive active transport processes?
-Some transport must occur such that solutes flow against their thermodynamic potential

-Energy input drives such transport

-Energy source and transport machinery are coupled

-Energy source may be ATP, light or a concentration gradient

How are certain transport processes driven by light energy?
There are two well-characterized proteins that use light energy for transporting substances:
bacteriorhodopsin, the light-driven H+ pump, and halorhodopsin, the light driven Cl- pump.
These transmembrane proteins use light energy to set up electrochemical gradients across
membranes. The energy from this electrochemical gradient is then used for secondary active
transport (using symports and antiports) of various substances, such as amino acids and
sugars.
How are amino acid and sugar transport driven by ion gradients?
Amino acids & sugars are accumulated by cells in transport processes driven by Na+ and H+
gradients. Many are symports. Secondary active transport

What type of molecular movements can we observe in the membrane?

What are the flippases?
Enzymes that can transport phosphatidylserine (PS), a phospholipid found in membranes, and
to a lesser extent phosphatidylethanolamine (PE), another phospholipid found in membranes,
from the outer leaflet to the inner leaflet of the plasma membrane. These enzymes are ATPdependent. They are essential for the creation and maintenance of transverse lipid
asymmetries.
-ATP-dependent flippases that transport PS, and to a lesser extent PE, from the outer leaflet to the inner
leaflet of the plasma membrane

-ATP-dependent flippases that transport a variety of amphiphilic lipids, especially

cholesterol,Phosphatidylcholine PC, and sphingomyelin from the inner leaflet to the outer leaflet

What is lipid phase transition?

It is when the membrane undergoes a transition from the gel phase (lower temp phase, bilayers
are more ordered) to the liquid crystalline phase (higher temp phase, bilayers are less ordered),
and vice versa. This transition occurs at a specific temperature referred to as the melting
temperature (Tm). Particular phospholipids display characteristic melting temperatures. The
melting temperature increases with chain length, decreases with unsaturation, and depends on
the nature of the polar head group.
Give an example for transmembrane protein?
glycophorin (single pass transmembrane protein)
bacteriorhodopsin (multiple pass transmembrane protein)
-Na+, K+ ATPase (sodium pump)
What is the characteristic structural motif in the porin proteins?
Beta-barrels (pg 271)
What are the lipid-anchoring motifs?

myristoylation, palmitoylation, isoprenylation

Amide-linked myristoyl anchors, thioester-linked fatty acyl anchors, thioether-linked prenyl
anchors, and amide-linked glycosyl phosphatidylinositol anchors.
Passive diffusion versus facilitated diffusion: how do the transported molecules move across
the membrane?
In passive diffusion, the molecules enter into the lipid of the membrane and travel across with
no aid by proteins. In facilitated diffusion, the molecules diffuse through integral membrane
proteins. Neither process requires the input of energy; they both occur spontaneously.
What is the most noticeable characteristic of hydropathy plots for transport proteins?

-Hydrophobicity (or hydrophilicity) plots are designed to display the distribution of polar and apolar
residues along a protein sequence

-The analysis is commonly used to predict membrane-spanning segments (highly hydrophobic) of

proteins. It is also applied to understand and predict regions that are likely exposed on the surface of
proteins (hydrophilic domains) and therefore potentially antigenic.

-The most noticeable characteristic will be that the hydropathy index is positive if there are hydrophobic
proteins

Which transport mechanism is used by the anion transporter of erythrocytes?

The antiport transportation mechanism.
What is secondary active transport?
The original ion gradient is said to arise from a primary active transport process, and the transport that
depends on the ion gradient for its energy input is referred to as a secondary active transport process.
The gradients of H+, Na+, and other cations and anions established by ATPases and other energy
sources can be used for secondary active transport of various substrates.

What is the most unique characteristic of active transport?

The use of energy to drive solutes across a membrane in the thermodynamically unfavorable
direction.
Give two examples for H+ , Na+ ATPases and their biological function.
-Gastric Mucosal cell: uses the energy of hydrolysis of ATP to pump H+ out of the mucosal cells and into
the stomach interior in exchange for K+ ions. This transport is electrically neutral, and the K+ that
transported into the mucosal cell is subsequently pumped back out of the cell together with Cl- in a
second electroneutral process. Thus, the net transport affected by these two systems is the movement of
HCl into the interior of the stomach.

-Vacuolar ATPases: various H+-transporting ATPase found in osteoclasts provide a source of circulating
calcium for soft tissues such as nerves and muscles. Once growth is complete, the body balances
formation of new bone tissue by cells called osteoblasts with resorption of existing bone matrix by
osteoclast

Where is the majority of calcium ions sequestered inside the cell?

In muscle fibers (or muscle cells), nearly all of the calcium ions are sequestered inside the
sarcoplasmic reticulum.
Explain H+, K+-ATPase activity in the context of high blood pressure.
People with hypertension have high blood levels of ouabain, an endogenous Na+, K+-ATPase
inhibitor (it's a cardiac glycoside), which causes inhibition of the sodium pump in the cells lining
the blood vessel wall that results in accumulation of sodium and calcium in these cells and the
narrowing of the vessels to create hypertension.
Explain H+, K+-ATPase activity in the context of cardiac glycosides.
In the presence of cardiac glycosides, which are certain plant and animal steroids, the Na+,K+ATPase is inhibited. These inhibitory molecules bind exclusively to the extracellular surface of
Na+,K+-ATPase when it is in the E2-P state (the enzyme's conformation with a relatively low
affinity for Na+ but a high affinity for K+), forming a very stable E2-P (cardiotonic steroid)
complex, rendering the enzyme inactive. This is talked about on p.296
What is the function of bacteriorhodopsin?
-The structure has been verified for bacterial photosynthetic reaction center

-Driven by light energy rather than by ATP. 2 well-characterized system: bacteriorhodopsin, the lightdriven H+-pump, and halorhodopsin, the light-driven Cl- pump.

-Light energy drives transport of proton through bacteriorrhodopsin, providing energy for the bacterium in
the form of a transmembrane proton gradient. Proton hop from site to site across bacteriorhodopsin. Light
absorption converts retinal from all-trans to the 13-cis configuration, triggering conformation changes that
induce pKa changes and thus facilitate H+ transfer and net H+ transport across the membrane
It's function is to capture light energy and use it to move protons across the membrane out of the cell. The
resulting proton gradient is subsequently converted into chemical energy.

How do gap junctions mediate cell-to-cell communication?

-A gap junction between cells is formed when 2 hexameric arrays of subunits in separate cells contact
each other and form a pore through which cellular contents may pass

-Gap junctions close by means of a twisting, sliding motion in which the subunits decrease their tilt with
respect to the central axis. Closure of the gap junction is Ca2+-dependent

Considering the effect of temperature on membrane, how can you distinguish the activities of
mobile carriers and pores/channels?
-Channels are comparatively insensitive to membrane phase transitions and show only a slight
dependence of transport rate on temperature.
-Mobile carriers, on the other hand, function efficiently above a membrane phase transition, but
only poorly below it. Consequently, mobile carrier systems often show dramatic increases in
transport rate as the system is heated through its phase transition.

Chapter 23 - Fatty Acid Catabolism

What is the form of lipid storage in our body?
In animals, fat is stored mainly in the form of triglycerides in specialized cells, adipocytes or
adipose cells

 What is the difference between brown fat and white fat?

White fat stores energy as triglycerides while brown fat burns lipids for thermogenesis. Brown
fat has mitochondria that can uncouple to produce heat rather than ATP which helps control
body weight. White fat contains a single large lipid droplet while brown fat has cytoplasmic
space and contains multiple lipid droplets
What is the importance of brown fat?
Brown fat cells have an extraordinary number of mitochondria, which are involved in heat
generation. Brown fat thermogenesis also seems to be of considerable importance to animals
coming out of hibernation, allowing them to rewarm.
What is the sequence for activation of the release of fatty acids from cells?
One of the hormone messengers bind to receptors on the plasma membrane of adipose cells
and lead to the activation of adenylyl cyclase, which forms cyclic AMP from ATP. Then, cAMP
activates protein kinase A, which phosphorylates and activates a triacylglycerol lipase that
hydrolyzes a fatty acid from C-1 or C-3 of triacylglycerols. Subsequent actions of diacylglycerol
lipase and monoacylglycerol lipase yields fatty acids and glycerol. The adipose cell then
releases the fatty acids into the blood, where they are bound to serum albumin, which transports
free fatty acids to sites of utilization.
Which hormone induces the mobilization of fatty acids from adipose cells?
Adrenaline(epinephrine), glucagon, and adrenocorticotropic hormone (ACTH)
What is the function of fatty acid binding proteins?`
Fatty-acid (FA) trafficking accompanied by the fatty acid-binding proteins (FABPs) in the
cell. As lipid chaperones, FABPs have been proposed to play a role in the transport of lipids to
specific compartments in the cell: to lipid droplets for storage; to the endoplasmic reticulum for
signalling, trafficking and membrane synthesis; to the mitochondria or peroxisome for oxidation;
to cytosolic or other enzymes to regulate their activity; to the nucleus for the control of lipidmediated transcriptional programs via nuclear hormone receptors (NHRs) or other transcription
factors that respond to lipids; or even outside the cell to signal in an autocrine or paracrine
manner.
Why bile salts are important in the digestion of triacylglycerols?
They act as detergents to emulsify the triacylglycerols and facilitate the hydrolytic acitivity of the
lipases and esterases.
What is the function of pancreatic lipase?
Large micelles can not be absorbed through the intestinal mucosa. Digestion via pancreatic
lipase yields a smaller micelle that can be absorbed by the intestinal mucosa
Which enzyme digests the majority of lipids after a meal?
Lipase
How are the lipids transported in the blood stream?
Serum albumin, which is the most abundant protein in blood serum.
What is a chylomicron?

Lipoprotein aggregates assembled with fatty acids and monoacylglyerols that are absorbed
through the intestinal wall
Where in the cell are fatty acids condensed with coenzyme A to form acyl-CoA?
fatty acids must be activated in the CYTOPLASM before being oxidized in the mitochondria.
Activation is catalyzed by fatty acyl-CoA synthetase, which condenses fatty acids with CoA.
^^^Only long chain FA must be activated in the cytoplasm. Short chain FA can diffuse into the
mitochondrial matrix and there be activated with acetyl CoA.
How is the long-chain fatty acyl groups carried across the membrane?
Unlike the short- and medium- length fatty acids, long-chain fatty acids cannot enter into the
mitochondrial matrix directly. They must first be converted to O-acylcarnitine by the enzyme
carnitine acyltransferase I, which is associated with the outer mitochondrial matrix. The Oacylcarnitine is then transported across the inner membrane of the mitochondria by a
translocase. Once inside the matrix, the O-acylcarnitine is passed to carnitine acyltransferase II,
which is on the matrix side of the inner membrane, and which transfers the fatty acyl group back
to CoA to reform the fatty acyl-CoA, leaving free carnitine, which can return across the
membrane via the translocase.

What is the function of carnitine in fatty acid metabolism?

Combines with the long chain FA to enter the intermembrane mitochondrial space via Carnitine
acyltransferase I
What is the sequence for transport of fatty acyl groups across the inner mitochondrial
membrane?
- fatty acids become fatty acyl coA via acyl coA synthetase
- this marks them for transport into mitochondria
- short and medium FA-CoA can diffuse into mitochondria as free FAs
Which enzyme performs the first oxidation in the -oxidation of saturated fatty acids?
Acyl-CoA dehydrogenases. There are 4 different kinds: (1) very long-chain acyl-CoA
dehydrogenase (VLCAD); (2) long-chain (LCAD); medium-chain (MCAD); and short-chain
(SCAD).
Which enzyme performs the oxidation of the C-C bonds?
Acyl-CoA Dehydrogenase performs the oxidation of the alpha-beta bond. The second oxidation
(carried out by hydroxyacyl-CoA dehydrogenase) only oxidizes the beta hydroxyl group on the
beta carbon.
What happens to acetyl-CoA produced during -oxidation?
It is further metabolized in the TCA cycle. It can also be used as a substrate in amino acid
biosynthesis.

 How many times must the -oxidation cycle be repeated for the complete oxidation of a 16carbon saturated fatty acid ?
[palmitic acid, in lecture slides]
Seven,,,, how did we obtain this number??
16 /2 -2 ATP.. split into couplets 7 FADH/7NADH .. couplets are acetyl Coa (10
ATP each acetyl CoA)
2-/-2-/-2-/-2-/-2-/-2-/-2-/-2
You need seven rounds of oxidation (/)
How many NAD+ are reduced in the -oxidation of stearoyl-CoA to form nine molecules of
acetylCoA?
Eight, I think.
How many NADH are generated from the complete oxidation of palmitoyl-CoA to CO2?
7 NADH are generated from beta-oxidation. 8 Acetyl-CoA, created from beta-oxidation, enter
the TCA cycle and used to create 24 more NADH. So there are a total of 31 NADH molecules
generated. (24+7=31 ) 8(3 NADH per CoA)=24 in TCA cycle
When is propionyl-CoA produced during lipid breakdown?
When the fatty acid has an odd number of carbons
What is omega oxidation? Where does it occur?
Alternative pathway to beta oxidation that involves oxidation of the Omega carbon as opposed
to the beta carbon. Used when B oxidation is defective (Ex: lack of carnitine). Enzymes for this
reaction are located in the ER of liver and kidney cells. Also used to increase speed of oxidation
process since both ends may be oxidized at the same time.
What are the three most common ketone bodies?
Acetone, acetoacetate and beta-hydroxybutyrate
Where are the ketone bodies synthesized?
Occurs only in the mitochondrial matrix.
mitochondria of liver.
How do the ketone bodies transported in the body?
Acetoacetate and beta-hydroxybutyrate are transported through the blood from liver to target organs and
tissues, where they are converted to acetyl-CoA. Ketone bodies are easily transportable forms of fatty
acids that move through the circulatory system without the need for complexation with serum albumin and
other fatty acid binding proteins.-++

What is the difference between thiolase activity in -oxidation and thiolase activity in ketone
body formation?
Ketone body formation uses reverse thiolase to produce Acetoacetyl-CoA
The thiolase enzyme is the same enzyme that carries out the thiolase reaction in beta-oxidation
and ketone body formation. The difference between the two pathways is the direction of the
reaction: In beta-oxidation, thiolase produces acetyl-CoA; In ketone body formation, thiolase
consumes acetyl-CoA to form acetoacetyl-CoA

 What is the major source of energy for the brain during starvation?
Ketone Bodies
How do the ketone bodies enter the major metabolic pathways of the cells?
The ketone bodies are converted back to acetyl-CoA in the mitochondria
What is non-shivering thermogenesis? How is it mediated and how is it regulated?
Fatty acids are oxidized in the mitochondria and produce heat due to the uncoupling protein in
brown fat. Exposure to cold activates sympathetic nervous system which releases
norepinephrine to activate SERCA mediated heat production which activates brown tissue

How is brown fat involved in thermogenesis? burns lipids

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