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Lipids and Amino Acids: Structures, Functions, and Metabolism, Summaries of Biochemistry

University of Saint La Salle (USLS)Biochemistry

A comprehensive overview of the different classes of lipids, including simple lipids (triglycerides), complex lipids (phospholipids and sphingolipids), and steroids. It delves into the structure, properties, and metabolism of fatty acids, as well as the degradation and synthesis processes. Additionally, the document covers the classification, structure, and properties of amino acids, highlighting their amphoteric nature and their role in the formation of peptides and proteins. The information presented in this document would be highly relevant for students studying biochemistry, molecular biology, or related fields, as it lays the foundation for understanding the fundamental building blocks of living organisms and their metabolic pathways.

Typology: Summaries

2022/2023

Uploaded on 12/19/2023

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LIPIDS .
CLASSIFICATION OF LIPIDS BY
FUNCTION
●Lipids serve as a storage for
energy. While plants store energy in
the form of starch, animals (including
humans) prefer fats as an economical
source of energy. It is said that the
burning of fats has twice higher
production of energy (9kcal/g)
compared to the burning of
carbohydrates in the form of
glycogen.
●Lipids function as a membrane
component of the cell. Unlike
carbohydrates and proteins which are
mostly soluble in water, our body’s
cell needs constituents that are
insoluble in water for protection.
Lipids serve this function as a barrier
between inside and outside of the cell.
● Lipids also serve as chemical
messengers. Some lipids deliver
signal from one part of the body to
another (steroid hormone) while
others function as mediator of the
hormone response (prostaglandins
and thromboxanes).
Triglyceride = glycerol + 3 Fatty
Acids → SIMPLE LIPIDS
aka - triglycerols
WAXES FOUND IN NATURE
● Bee wax - weax “substance
made by bees”
● Birds Feather
● Carnauba Palm
● Spermaceti Wax - sperm
whale
● Plant leaf surface
CLASSIFICATION BY STRUCTURE
● Simple Lipids
● Complex Lipids
● Steroids
● Prostaglandins, thromboxanes and
leukotrienes
1. Simple Lipids
- Animal fats and plant oils are
regarded as triglycerides
(triglycerol), which are simple
lipids. Triglycerides are
triesters of glycerol and fatty
acids. Structurally, glycerol is
an organic compound
(alcohol) that contains three
carbons, five hydrogens, and
three hydroxyl (OH) groups.
Fatty acid, on the other hand,
is a long chain of hydrocarbon
containing a carboxyl group
(-COOH). All fatty acids have
common characteristics.
These are the following:
● All are unbranched carboxylic
acids
● Hydrocarbon chain ranges
from 4 to 36; the most
common are 12-20 carbons
● Contain even number of
carbons
● Only -COOH as a functional
group except for some do
have double bonds
Glycerol + Fatty Acids = Triacylglycerol
2. Complex Lipids
- Phospholipids contain an
alcohol, two fatty acids, and a
phosphate group. These are
major components of the
plasma membrane. A
phospholipid is considered an
amphipathic molecule, which
means that it contains the
hydrophilic head and a
hydrophobic tail.
Phosphatidylcholine and
phosphatidylserine are two
important phospholipids that
are found in plasma
membranes. Choline and
serine are attached to the
phosphate group labeled as
the R via the hydroxyl group.
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LIPIDS.

CLASSIFICATION OF LIPIDS BY

FUNCTION

● Lipids serve as a storage for energy. While plants store energy in the form of starch, animals (including humans) prefer fats as an economical source of energy. It is said that the burning of fats has twice higher production of energy (9kcal/g) compared to the burning of carbohydrates in the form of glycogen. ● Lipids function as a membrane component of the cell. Unlike carbohydrates and proteins which are mostly soluble in water, our body’s cell needs constituents that are insoluble in water for protection. Lipids serve this function as a barrier between inside and outside of the cell. ● Lipids also serve as chemical messengers. Some lipids deliver signal from one part of the body to another (steroid hormone) while others function as mediator of the hormone response (prostaglandins and thromboxanes). Triglyceride = glycerol + 3 Fatty Acids → SIMPLE LIPIDS aka - triglycerols WAXES FOUND IN NATURE ● Bee wax - weax “substance made by bees” ● Birds Feather ● Carnauba Palm ● Spermaceti Wax - sperm whale ● Plant leaf surface CLASSIFICATION BY STRUCTURE ● Simple Lipids ● Complex Lipids ● Steroids ● Prostaglandins, thromboxanes and leukotrienes

1. Simple Lipids

  • Animal fats and plant oils are regarded as triglycerides (triglycerol), which are simple lipids. Triglycerides are triesters of glycerol and fatty acids. Structurally, glycerol is an organic compound (alcohol) that contains three carbons, five hydrogens, and three hydroxyl (OH) groups. Fatty acid, on the other hand, is a long chain of hydrocarbon containing a carboxyl group (-COOH). All fatty acids have common characteristics. These are the following: ● All are unbranched carboxylic acids ● Hydrocarbon chain ranges from 4 to 36; the most common are 12-20 carbons ● Contain even number of carbons ● Only -COOH as a functional group except for some do have double bonds **Glycerol + Fatty Acids = Triacylglycerol
  1. Complex Lipids**
  • Phospholipids contain an alcohol, two fatty acids, and a phosphate group. These are major components of the plasma membrane. A phospholipid is considered an amphipathic molecule, which means that it contains the hydrophilic head and a hydrophobic tail. Phosphatidylcholine and phosphatidylserine are two important phospholipids that are found in plasma membranes. Choline and serine are attached to the phosphate group labeled as the R via the hydroxyl group.

There are two types of phospholipids: a. Glycerophospholipids – also called phosphoglycerides are cell membrane components throughout the body. It is structurally composed of glycerol esterified by two fatty acids and and a phosphate group, which is esterified to another alcohol.

  • Examples of phosphoglycerides are lecithins, cephalins and phosphatidylinositols. The second carbon on these phospholipids is always esterified to unsaturated fatty acid. Lecithin molecule (figure below), which is a major component of egg yolk, is composed of a stearic acid (saturated) on one end and linoleic acid (unsaturated) in the middle. Phosphatidylinositols do not only serve as important constituent of the plasma membrane but also function as signaling molecules in chemical communication. b. Sphingolipids – are components of the myelin, the coating of the nerve axon. Sphingomyelin is a phospholipid that is derived from sphingosine instead of glycerol in glycerophospholipids. Sphingosine is an amino alcohol that contains a long chain and unsaturated hydrocarbons. The amino group in sphingosine backbone is linked to a fatty acid by an amide bond, which forms into sphingomyelin. Additionally, the primary hydroxyl group of sphingosine is esterified to phosphorylcholine. Glycolipids are sugar-containing complex lipids with ceramide. Like sphingolipids, ceramide molecule is a combination of fatty acids and sphingosine (Figure). Cerebrosides are glycolipids which occur in the brains and nerve synapses. In this complex lipid, the fatty acid of the ceramide part may contain either 18-carbon or 24-carbon chains. Other glycolipids are the gangliosides which contain a more complex carbohydrate structure. In a ganglioside, an oligosaccharide chain is linked to the terminal hydroxyl group of ceramide by a glucose residue. This oligosaccharide chain contains at least one acidic sugar, either N-acetylneuraminate or N-glycolylneuraminate. These acidic sugars are called sialic acids.
  1. Steroids are another major class of lipids which contain ring structures composed of three cyclohexane rings and a fused cyclopentane ring. Cholesterol - is the most common and abundant steroid in the human body. It is mainly synthesized in the liver. Also, it is the precursor to many steroid hormones such as testosterone and estradiol, which are secreted by the gonads and endocrine glands. It is also the precursor to Vitamin D and essential component of the plasma membrane, which is found within the phospholipid bilayer, for example, in red blood cells. Lipoproteins : Carriers of Cholesterol ● High-density lipoprotein (HDL) (“good cholesterol”), which consists of about 33% protein and about 30% cholesterol ● Low-density lipoprotein (LDL) (“bad cholesterol”), which contains only 25% protein but 50% cholesterol ● Very-low-density lipoprotein (VLDL), which mostly carries triglycerides (fats) synthesized by the liver
  • The properties of fatty acids and lipids derived from them are markedly dependent on chain length and degree of saturation.
  • Unsaturated fatty acids have lower melting points than saturated fatty acids of the same length. Fatty Acid Degradation and Synthesis
  • Four processes involved in the degradation of fatty acids to convert them to activated acetyl units (acetyl CoA) that can be processed through the citric acid cycle. If the fatty acid is an even number, the process is just repeated until the fatty acid is completely converted to acetyl-coA units. The reverse processes are referred to as the synthesis of fatty acid. Degradation: ● Oxidation of activated fatty acid (attachment of CoA) to form a double bond fatty acid ● Hydration of the double bond to form alcohol (with hydroxyl group) ● Oxidation of alcohol to a ketone ● Cleavage of fatty acid by coA to yield acetyl CoA and fatty acid chain two carbon shorter Synthesis: ● Condensation of acetyl unit and a malonyl unit to form a four-carbon unit Carbonyl to a methylene group: ● Reduction ● Dehydration ● Reduction Beta- Oxidation of Fatty Acids
  • Beta-oxidation (ß-oxidation) is the catabolic process by which fatty acid molecules are broken down in the cytosol in prokaryotes and in the mitochondria in eukaryotes to generate acetyl-CoA.
  • Acetyl-CoA enters the citric acid cycle while NADH and FADH2, which are coenzymes, are used in the electron transport chain.
  • It is referred to as “ß-oxidation” because the ß-carbon of the fatty acid undergoes oxidation to a carbonyl group. ß-oxidation takes place in the mitochondria of eukaryotes while in the cytosol of prokaryotes. Substrates: Free fatty acids; H2O. Products: One acetyl CoA, one NADH, and one FADH2 for every removal of a two-carbon group from the fatty acid chain. The pathway of ß-oxidation:
  1. Dehydrogenation catalyzed by acyl-CoA dehydrogenase, which removes two hydrogens between carbons 2 and 3.
  2. Hydration catalyzed by enoyl-CoA hydratase, which adds water across the double bond.
  3. Dehydrogenation catalyzed by 3-hydroxy acyl-CoA dehydrogenase, which generates NADH.
  4. Thiolytic cleavage catalyzed beta-ketothiolase, which cleaves the terminal acetyl-CoA group and forms a new acyl-CoA, which is two carbons shorter than the previous one. The shortened acyl-CoA then reenters the beta-oxidation pathway. Enzymes of ß -Oxidation Metabolism of Dietary Lipids
  • Most lipids are ingested in the form of triacylglycerols and must be degraded to fatty acids for absorption across the intestinal epithelium.
  • Intestinal enzymes called lipases , secreted by the pancreas, degrade triacylglycerols to free fatty acids and monoacylglycerol.
  • Lipids present a particular problem because these molecules are not soluble in water.
  • Triacylglycerols in the intestinal lumen are incorporated into micelles composed of bile salts, amphipathic molecules synthesized from cholesterol in the liver and secreted from the gall bladder.
  • The ester bond of each lipid is oriented toward the surface of the micelle, rendering the bond more susceptible to digestion by lipases in aqueous solution.
  • The final digestion products are carried in micelles to the intestinal epithelium, where they are transported across the plasma membrane. Dietary Lipids Are Transported in Chylomicrons
  • In the intestinal mucosal cells, the triacylglycerols are resynthesized from fatty acids and monoacylglycerols and then packaged into lipoprotein transport particles called chylomicrons, stable particles approximately 2000 Å ( nm) in diameter.
  • These particles are composed mainly of triacylglycerols, with apolipoprotein B-48 (apo B-48) as the primary protein component. Protein constituents of lipoprotein particles are called apolipoproteins. Chylomicrons also transport fat-soluble vitamins and cholesterol. - The chylomicrons are released into the lymph system and then into the blood. These particles bind to membrane-bound lipases, primarily at adipose tissue and muscle, where the triacylglycerols are once again degraded into free fatty acids and monoacylglycerol for transport into the tissue. The triacylglycerols are then resynthesized inside the cell and stored. In the muscle, they can be oxidized to provide energy. METABOLISM OF CHOLESTEROL

AMPHOTERIC PROPERTIES OF

AMINO ACIDS

  • In solutions, amino acids are amphoteric means that they can act either as an acid or a base due to the presence of an acidic group (carboxyl group) and a basic group (amino group), depending on the pH of the media.
  • While amino acids are commonly written in their unionized forms, each one is more properly written as a zwitterions. A zwitterion results when both carboxyl and amino groups undergo ionization in water. And at physiological pH (7.4) , a zwitterion will form. PEPTIDES
  • polymers of amino acids joined together by peptide or amide bonds NAMING PEPTIDES
  • In naming of peptides, we start at the N-terminus (left side) and ends with the C-terminus (right side).
  • By convention, on the left side is the amino or N- terminal end and on the right side is the carboxyl or C-terminal end.
  • So, the beginning of the peptide is the N-terminal end and the end of the peptide is the C-terminal end.
  • In reading an amino acid sequence, it is read from left-to-right, starting with the N-terminal end and ending with the C terminal end. Full amino acid names can be used, three-letter code abbreviation, and one-letter code for especially long peptides. For full amino acid names, we change the amino acid suffixes like –ine, -ate, -an to –yl, except for the C-terminal amino acid. ● Glutamine will become Glutaminyl. Glutamate (Glutamic Acid) will become Glutamyl. ● Aspartate (Aspartic Acid) will become Aspartyl. Proteins - Levels of Structure ● Primary structure – one-dimensional first step in specifying the three-dimensional structure of a protein; the order in which the amino acids are covalently linked together ● Secondary structure – a three-dimensional structure of a single polypeptide chain; the arrangement in space of the atoms in the peptide backbone (the conformations of the side chains are not included in the structure) ● Tertiary structure – the three-dimensional arrangement of all the atoms in the protein, including those in the side chains and in any prosthetic groups (groups of atoms other than amino acids) ● Quaternary structure – the arrangement of subunits with respect to one another .
  • Subunits are multiple polypeptide chains.
  • Not all proteins have all four levels. For example, only proteins with multiple polypeptide chains have primary structure.
  • The function of a protein depends on its tertiary structure. If this is disrupted, it loses its activity.

Protein Conformation and Functions Protein Denaturation

  • In denaturation, the secondary, tertiary and quaternary structures are disrupted. The primary structure is not affected. If a protein is denatured, it therefore becomes biologically inactive. Factors which can bring about denaturation include the following physical and chemical agents: ● Heat ● UV radiation ● Organic compounds ● Acids and bases ● Heavy metal ions/salts ● Detergent ● Altered pH ● Agitation / Violent shaking
  • Denaturation may be permanent or temporary.
  • Permanent denaturation is irreversible as the inactive protein cannot revert back to its active state.
  • Temporary denaturation is reversible as the inactive protein can revert back to its active state. The protein, in this case, regains its biological activity. Protein Metabolism The Urea Cycle The specific steps of the Urea Cycle are listed below.
  1. Synthesis of carbamoyl phosphate by Carbamoyl Phosphate Synthetase I (occurs in the mitochondria of the liver)
  2. Synthesis of citrulline from carbamoyl phosphate and ornithine by Ornithine Transcarbamoylase (in mitochondria)
  3. Synthesis of argininosuccinate by condensation of citrulline and aspartate by Argininosuccinate Synthetase
  4. Argininosuccinate cleaved by Argininosuccinase to produce fumarate and arginine
  5. Urea production and the regeneration of ornithine from arginine by Arginase After the formation of urea, urea will diffuse out of the liver cells into the blood, with the kidneys filtering it out, and excreted in the urine. A normal adult can excrete 25 to 30 g of urea daily but this will vary with the protein content of the diet.

Enzyme Classification

  • Enzymes are commonly given names derived from the reaction that they catalyze and /or the compound or type of compound on which they at. For example, lactate dehydrogenase speeds up the removal of hydrogen form lactate (an oxidation reaction).
  • the name of the enzyme
  • end in –ase. Some enzymes , however, have older names, which were assigned before their actions were clearly understood.
  • Among these are pepsin, trypsin, and chymotrypsin—all enzymes of the digestive tract. Enzymes can be classified into six (6) major groups according to the type of reaction they catalyze. Factors that Influence Enzyme Activity Enzyme activity is a measure of how much reaction rates are increased. 1. Temperature and pH
  • Temp. Changes conformation of the enzyme. In uncatalyzed reactions, rate usually increases with temperature. When starting at low temperature, an increase in temperature first causes an increase in rate. However, protein conformations are very sensitive to temperature changes. Once the optimal temperature is reached, any further increase in temperature alters the enzyme conformation. 2. Enzyme and Substrate Concentration
  • Enzymes have a saturation point.
  • once all the enzymes added are occupied by the substrate molecules, its activity will be ceased.
  • When the reaction begins, the velocity of enzyme action keeps on increasing on further addition of substrate.
  • However, at a saturation point where substrate molecules are more in number than the free enzyme, the velocity remains the same. The type of substrate is another factor that affects the enzyme action. ● The chemicals that bind to the active site of the enzyme can inhibit the activity of the enzyme and such substrate is called an inhibitor. ● Competitive inhibitors are chemicals that compete with the specific substrate of the enzyme for the active site. They structurally resemble the specific substrate of the enzyme and bind to the enzyme and inhibit the enzymatic activity. This concept is used for treating bacterial infectious diseases. Each enzyme operates best at a certain pH. However extreme pH values denatures enzymes irreversibly.

Mechanisms of Enzyme Action

1. Lock -and- Key Model - This model assumes that the enzyme is a rigid, 3D-body. The surface that contains the active site has a restricted opening into which only one kind of substrate can fit. - According to the lock-and-key model, an enzyme molecule has its particular shape because that shape is necessary to maintain the active site in exactly the conformation required for that particular reaction. An enzyme molecule is very large (typically consisting of 100 to 200 amino acid residues), but the active site is usually composed of only two or a few amino acid residues, which may be well located at different places in the chain. This arrangement emphasizes that the shape and the functional groups on the surface of the active site are of utmost importance in recognizing a substrate. 2. Induced-Fit Model

  • From x-ray diffraction, we know that the size and shape of the active site cavity change when the substrate enters.
  • Daniel Koshland introduced this model to explain this phenomenon. He compared the changes occuring in the shape of the cavity upon substrate binding to the changes in the shape of a glove when a hand is inserted.
  • The enzyme modifies the shape of the active site to accommodate the substrate. Both lock-and-key and the induced-fit model explain the phenomenon of competitive inhibition. The inhibitor molecule fits into the active site cavity in the same way the substrate does, thereby preventing the substrate from entering. The result: whatever reaction is supposed to take place on the substrate does not occur.