Biochemistry Notes 2

Fatty Acid Structures and Properties

Straight-chain fatty acid
Branched-chain fatty acid
- iso-methyl: e.g., iso-17:0 (15-Methylhexadecanoic acid)
- anteiso-methyl: e.g., anteiso-17:0 (14-Methylhexadecanoic acid)
- poly-methyl: e.g., Phytanic acid (3,7,11,15-Tetramethylhexadecanoic acid)
Structures of Palmitate & Palmitic Acid
- Fatty acids are ionized at physiological pH, existing as carboxylate forms.
- Palmitate: ionized form
- Palmitic acid: unionized form

Variations in Fatty Acids

Fatty acids in biological systems typically contain an even number of carbon atoms.
- The 16- and 18-carbon atom chains are most common.
- Examples:
  - Palmitate (ionized form of palmitic acid)
  - Oleate (ionized form of oleic acid)

Cis and Trans Configurations

Double bonds, when present, are commonly in the cis configuration.
- Examples:
  - Stearate
  - trans-Oleate

General Nomenclature

In polyunsaturated fatty acids, double bonds are separated by at least one methylene group.
- Example: 18:1 (Δ9) Cis-9-Octadecenoic acid (oleic acid)
- n-Octadecanoic acid (stearic acid)
- octadec: 18 carbons
- ane: single bonds
- en: double bonds
- oic: acid
- dien: 2 double bonds
- Methylene group: $CH_2$

Carbon Atom Numbering

Fatty acid carbon atoms are numbered starting with the carboxyl terminal carbon atom.
- Carbon atoms 2 & 3 are also referred to as α & β, respectively.
- Double bond positions are indicated with the symbol Δ, with the first atom of the double bond indicated by a superscript #.
- Example:
  - 18:4 cis-Δ6,9,12,15

Omega (ω) Carbon Numbering

Fatty acids can also be numbered from the methyl carbon atom (omega carbon).
- Example:
  - 18:4 cis-ω3,6,9,12

Naturally Occurring Fatty Acids in Animals

Table of Common Fatty Acids:
- Includes Number of carbon atoms, Number of double bonds, Common name, Systematic name, Formula.
 - Laurate: 12:0, n-Dodecanoate, $CH3(CH2)_{10}COO^-$
 - Myristate: 14:0, n-Tetradecanoate, $CH3(CH2)_{12}COO^-$
 - Palmitate: 16:0, n-Hexadecanoate, $CH3(CH2)_{14}COO^-$
 - Stearate: 18:0, n-Octadecanoate, $CH3(CH2)_{16}COO^-$
 - Arachidate: 20:0, n-Eicosanoate, $CH3(CH2)_{18}COO^-$
 - Behenate: 22:0, n-Docosanoate, $CH3(CH2)_{20}COO^-$
 - Lignocerate: 24:0, n-Tetracosanoate, $CH3(CH2)_{22}COO^-$
 - Palmitoleate: 16:1, cis-Δ9-Hexadecenoate, $CH3(CH2)5CH=CH(CH2)_7COO^-$
 - Oleate: 18:1, cis-Δ9-Octadecenoate, $CH3(CH2)7CH=CH(CH2)_7COO^-$
 - Linoleate: 18:2, cis, cis-Δ9,12-Octadecadienoate, $CH3(CH2)4(CH=CHCH2)2(CH2)_6COO^-$
 - Linolenate: 18:3, all-cis-Δ9,12,15-Octadecatrienoate, $CH3CH2(CH=CHCH2)3(CH2)6COO^-$
 - Arachidonate: 20:4, all-cis-Δ5,8,11,14-Eicosatetraenoate, $CH3(CH2)4(CH=CHCH2)4(CH2)_2COO^-$

Chain Length and Unsaturation on Fatty Acid Properties

Properties are dependent on chain length & degree of unsaturation.
- Short chain length & cis double bonds enhance fluidity.
- Lack of tight packing limits van der Waals interactions.
Melting Point Example
- Stearate (saturated): 69.6 °C
- trans-Oleate: 13.4 °C

Most Important Fatty Acids in Triglycerides

Includes Carbon Atoms, Double Bonds, Structure, Common Name, Melting Point (°C)
- Lauric acid: 12:0, $CH3(CH2)_{10}COOH$ , 44
- Myristic acid: 14:0, $CH3(CH2)_{12}COOH$ , 58
- Palmitic acid: 16:0, $CH3(CH2)_{14}COOH$ , 63
- Stearic acid: 18:0, $CH3(CH2)_{16}COOH$ , 70
- Arachidic acid: 20:0, $CH3(CH2)_{18}COOH$ , 77
- Palmitoleic acid: 16:1, $CH3(CH2)5CH=CH(CH2)_7COOH$ , 1
- Oleic acid: 18:1, $CH3(CH2)7CH=CH(CH2)_7COOH$ , 16
- Linoleic acid: 18:2, $CH3(CH2)4(CH=CHCH2)2(CH2)_6COOH$ , -5
- Linolenic acid: 18:3, $CH3CH2(CH=CHCH2)3(CH2)6COOH$ , -11
- Arachidonic acid: 20:4, $CH3(CH2)4(CH=CHCH2)4(CH2)_2COOH$ , -49

Melting Point Differences in C18 Length

As the # of cis double bonds inc., the MP dec.
Longer fatty acid chains allow for more van der Waals interactions resulting in an increased melting point.

C18 Fatty Acids

Stearate: n-Octadecanoate, $CH3(CH2)_{16}COO^-$ , 69.6 °C
Oleate: cis-Δ9-Octadecenoate, $CH3(CH2)7CH=CH(CH2)_7COO^-$ , 13.4 °C
Linoleate: cis, cis-Δ9,12-Octadecadienoate, $CH3(CH2)4(CH=CHCH2)2(CH)6COO^-$ , -5 °C
Linolenate: all-cis-Δ9,12,15-Octadecatrienoate, $CH3CH2(CH=CHCH2)3(CH2)6COO^-$ , -11 °C

Major Categories Based on Structure & Function

Lipids that contain fatty acids (complex lipids):
- Storage lipids: Triacylglycerols
- Membrane lipids: Phospholipids, Glycolipids
  - Glycerophospholipids
  - Sphingolipids
  - Galactolipids (sulfolipids)
Lipids that do not contain fatty acids: cholesterol, vitamins, pigments, etc.

Storage and Membrane Lipids

Storage Lipids: Triacylglycerols
- Glycerol + 3 fatty acids
Membrane Lipids:
- Phospholipids
  - Glycerophospholipids: Glycerol + 2 fatty acids + Phosphate + Alcohol
  - Sphingolipids: Sphingosine + Fatty acid + Phosphate + Choline
- Glycolipids: Sphingolipids: Sphingosine + Fatty acid + Mono- or oligosaccharide Galactolipids (sulfolipids): Glycerol + 2 fatty acids + Mono- or disaccharide

Triacylglycerols

Fatty acids are stored as triacylglycerols in which 3 fatty acids are esterified to one molecule of glycerol.
In mammals, the major site for triacylglycerol storage is adipose tissue.
- Each adipocyte (adipose/fat cell) contains a large lipid droplet in which the triacylglycerols are housed.
Formation of Triacylglycerols:
- Three fatty acid chains are bound to glycerol by dehydration synthesis, forming a triglyceride or neutral fat and 3 water molecules.

Energy Storage

Triacylglycerols are energy-rich, storing energy compactly (9 cal/g) compared to carbohydrates & proteins (4 cal/g).
They are hydrophobic & reduced.
Anhydrous fat stores >6 times the energy of hydrated glycogen.
Fats Provide Efficient Fuel Storage
- Fatty acids carry more energy per carbon because they are more reduced
- Fatty acids carry less water per gram because they are nonpolar
Glucose & glycogen are for short-term energy needs & quick delivery
Fats are for long-term (months) energy needs, good storage, & slow delivery
- Solid: longer chains saturated (only C-C); ex: animal fat, butter
- Liquid: unsaturated (C=C); ex: vegetable oils.

Common Types of Membrane Lipids

Phospholipids
Glycolipids
Cholesterol

Phospholipids

Major class of membrane lipids, made of ≥2 fatty acids, a platform, a phosphate, & alcohol.
Two common platforms: glycerol & sphingosine.
Phospholipids with glycerol platform are phosphoglycerides or phosphoglycerols.

Structure of Phosphatidate

Major phospholipids are derived from phosphatidate.

Common Phosphoglycerides Found in Membranes

Includes Fatty acid, Phosphate, Alcohol.
- Phosphatidylserine
- Phosphatidylethanolamine
- Phosphatidylcholine
- Phosphatidylinositol
- Diphosphatidylglycerol (cardiolipin)

Sphingolipids

Phospholipids built on a sphingosine platform.
Sphingomyelin is common in the myelin sheath of nerve cells.

Glycolipids

Carbohydrate-containing lipids located on the extracellular surface of the cell membrane.
- Plays a role in cell-cell interactions.

Steroids

Lipids built on a tetracyclic platform of 3 cyclohexane rings & a cyclopentane ring fused together.
Cholesterol is a key example.

Membrane Lipids

Amphipathic molecules with hydrophobic & hydrophilic properties.
- Fatty acid components provide hydrophobic properties.
- Alcohol & phosphate components (polar head group) provide hydrophilic properties.

Lipids Summary

Structurally & functionally diverse, poorly soluble in H2O.
Triacylglycerols are main storage lipids.
Phospholipids are main constituents of membranes.
Sphingolipids play roles in cell recognition.
Cholesterol is both a membrane lipid and precursor for steroid hormones.
Some lipids carry signals from cell to cell & tissue to tissue.

Digestion Overview

Digestion prepares large biomolecules for metabolism.
Proteases digest proteins into amino acids & peptides.
Dietary carbohydrates are digested by α-amylase.
Lipid digestion is complicated by hydrophobicity.

Purpose of Digestion

Degrade components of a meal (proteins, lipids, & carbohydrates) into small molecules for absorption & transport.
Accomplished by diverse hydrolytic enzymes.

Mechanical vs. Chemical Digestion

Mechanical digestion: physical process of breaking food into smaller pieces without chemical change.
Chemical digestion: biochemical process of changing macromolecules into smaller molecules for absorption & transport.

Digestive Enzymes

Most digestive enzymes are secreted as inactive precursors (zymogens or proenzymes).
- Trypsinogen from the pancreas is activated by enteropeptidase in the small intestine.
- Trypsin, in turn, activates other pancreatic proenzymes.

Gastric & Pancreatic Zymogens

Pepsinogen -> Pepsin (Stomach)
Chymotrypsinogen -> Chymotrypsin (Pancreas)
Trypsinogen -> Trypsin (Pancreas)
Procarboxypeptidase -> Carboxypeptidase (Pancreas)
Proelastase -> Elastase (Pancreas)

Digestion Process

Digestion is a form of catabolism.
It occurs when food moves through the digestive system.
Digestion begins in the mouth w/ mechanical degradation.
- Chewing converts food into a slurry for hydrolytic enzymes.
Mechanical digestion includes chewing and swallowing.
Chemical digestion of carbohydrates, fats.
Mechanical digestion includes peristaltic mixing and propulsion.
Chemical digestion of proteins, fats.
Absorption of lipid-soluble substances such as alcohol and aspirin.
Mechanical digestion includes mixing and propulsion, primarily by segmentation.
Chemical digestion of carbohydrates, fats, polypeptides, nucleic acids.
Absorption of peptides, amino acids, glucose, fructose, fats, water, minerals, and vitamins.
Mechanical digestion includes segmental mixing and propulsion.
No chemical digestion (except by bacteria).
Absorption of ions, water, minerals, vitamins, and organic molecules.

Protein Digestion in the Intestine

Food movement from the stomach to the intestine stimulates secretion of key hormones by cells of the small intestine:
- Secretin: causes release of sodium bicarbonate, which neutralizes stomach acid.
- Cholecystokinin (CCK): stimulates release of digestive enzymes from the pancreas & secretion of bile salts from the gallbladder.
Proteins are digested into small fragments called oligopeptides.
Peptidases on the surface of intestinal cells cleave the oligopeptides into amino acids & di- & tripeptides, which are conveyed into the intestinal cell by transporters.
The amino acids are subsequently released into the blood by antiporters.

Carbohydrate Digestion

Primary source of carbohydrates is starch.
Several enzymes participate in carbohydrate digestion.
- α-Amylase: initiates digestion by cleaving α-1,4 bonds but not α-1,6 bonds.
- Other enzymes (α-glucosidase & α-dextrinase): complete digestion.
Sucrose & lactose are digested by sucrase & lactase, respectively.
Glucose & galactose are transported into the intestine by the sodium-glucose linked transporter, & the transporter GLUT5 allows entry of fructose.

Digestion Enzymes

α-Amylase: cleaves α-1,4 bonds but not α-1,6 bonds
α-glucosidase & α-dextrinase: complete the digestion

Monosaccharide Uptake

Glucose & galactose are transported into the intestine by the sodium-glucose linked transporter (SGLT).
The transporter GLUT5 allows entry of fructose.

Emulsification

Grinding & mixing in the stomach converts lipids into an emulsion.
Process of dispersion of lipids into small droplets by reducing surface tension.
Bile salts, secreted by the gallbladder, insert into lipid droplets, rendering them more accessible to digestion by lipases.

Lipase

Pancreatic lipases convert triacylglycerols into 2 fatty acids & monoacylglycerol.

Micelle Formation

Digestion products are carried as micelles to the intestinal epithelial cells for absorption.

Chylomicron

Triacylglycerols are re-formed from fatty acids & monoacylglycerol and packaged into lipoprotein transport particles called chylomicrons in the intestine.
The chylomicrons eventually enter the blood so that the triacylglycerols can be absorbed by tissues.

Energy Needs

Energy is required to meet 3 fundamental needs: performance of mechanical work in muscle contraction & cellular movement, active transport of molecules & ions, synthesis of macromolecules & other biomolecules from simple precursors.

Metabolism

Metabolism consists of many interconnecting rxns. ATP is the universal currency of free energy.
Oxidation of carbon fuels is an important source of cellular energy.
Metabolic pathways contain many recurring motifs.
Metabolic processes are regulated in 3 principle ways.

Energy Generation

Stages of the Generation of Energy from Food
- Large molecules in food are broken down into smaller molecules in the process of digestion.
- Small molecules are processed into key molecules of metabolism, mainly acetyl CoA.
- ATP is produced from the complete oxidation of acetyl CoA.
  - Lipids -> Fatty acids and glycerol
  - Polysaccharides -> Glucose and other sugars
  - Proteins -> Amino acids
Molecules are degraded/synthesized stepwise in metabolic pathways.
ATP is the energy currency of life.
ATP can be formed by the oxidation of carbon fuels.
A limited # of rxn types that involve particular intermediates are common to all metabolic pathways.
Metabolic pathways are highly regulated.

Metabolic Reactions

Metabolism: entire network of chemical rxns carried out by living cells.
Metabolites: small molecule intermediates in degradation or end product of metabolism.
Catabolic reactions: degrade molecules to create smaller molecules (produces energy).
Anabolic reactions: synthesize molecules for cell maintenance, growth, & reproduction (required energy).
Glucose Metabolism: The eventual fate of glucose is to convert it to CO2 & H2O w/ generation of ATP. The aerobic fate of pyruvate is to produce 3 CO2 molecules.

Metabolic Pathways

Many metabolic pathways are linked together, including the Metabolism of Complex Carbohydrates, Complex Lipids, Cofactors and Vitamins, and Other Amino Acids..

Energy Reactions

Metabolic pathways are divided into 2 types: Catabolic pathways: combust carbon fuels to synthesize ATP or ion gradients Anabolic pathways: use ATP & reducing power to synthesize large biomolecules Some pathways, called amphibolic pathways function anabolically or catabolically

Metabolic Reactios

The Individual rxns must be specific. The pathway in total must be thermodynamically favorable.
A thermodynamically unfavorable rxn in a pathway can be made to occur by coupling it to a more favorable rxn.

ATP

Energy derived from fuels or light is converted into adenosine triphosphate (ATP), the cellular energy currency. Consists of three phosphate groups, ribose, and adenine.

Phosphorylation

The hydrolysis of ATP is exergonic because the triphosphate unit contains 2 phosphoanhydride bonds that are unstable. The energy released on ATP hydrolysis is used to power a host of cellular functions.

Energy

ATP has a high phosphoryl - transfer potential b/c electrostatic Repulsion Resonance stabilization Increase in entropy Stabilization by hydrolysis
• ATP has a phosphoryl-transfer potential that is intermediate among the biologically important phosphorylated molecules

Biochemical Processes With Phosphate

Phosphate & its esters are prominent in biology for several reasons: Phosphate esters are thermodynamically unstable, yet they are kinetically stable Phosphate esters are stable b/c the inherent negative charges resist hydrolysis Because phosphate esters are kinetically stable, they are ideal regulatory molecules
Cells maintain a very high concentration of ATP Recent research suggests that ATP may function as a biological hydrotrope ATP prevents the formation of protein aggregates & dissolves those that form so another role of ATP is maintaining protein solubility

Cellular Energy

ATP is the immediate donor of free energy for biological activities
The amount of ATP is Hence ATP must be constantly recycled to provide energy to power:
Motion* Active transport* Biosynthesis* Signal amplification

Oxidation

Amino acids, monosaccharides & lipids are oxidized in the catabolic pathways Oxidizing agents: accept è & is reduced Reducing agents: lose e & is oxidized Oxidation of one molecule must be coupled w/ the reduction of another molecule
Oxidation rxns involve loss of e-. That must be coupled to reactions that gain e: oxidation-reduction (redox) rxns C atoms in fuels are oxidized to yield CO2, & the è are accepted by oxygen to form H2O The more reduced a C atom is, the more free energy is released upon oxidation. Fats are a more efficient food source. Fats than glucose btc fats are more reduced
Compounds w/High Phosphoryl - Transfer Potential Can Couple Carbon Oxidation to ATP Synthesis, The essence of catabolism is capturing the energy of carbon oxidation as ATP Oxidation of the C atom form ATP a compound w/ high phosphoryl - transfer potential that can then be used to synthesize Oxidation of glyceraldehyde 3-phosphate to 3-phosphoglyceric acid Ran does not occur to one step

Metabolic Pathways

Activated carrier: small molecule carrying a chemical group in a high-energy linkage, serving as a donor of energy or of the chemical group in many different chemical rxns (ex: ATP, NADH, acetyl CoA) 2 characteristics: carriers are kinetically stable in the absence of specific catalysts and the metabolism of activated groups is accomplished w/ a small # of carriers.
Activated ATP is an activated carrier of phosphoryl groups. Other activated carriers are the same in biochemistry, often they are derived from vitamins Nicotinamide adenine dinucleotide (NAD+) & flavin adenine dinucleotide (FAD) carry e- derived from the oxidation of fuels Activated Carriers Nicotinamide adenine dinucleotide phosphate (NADP+) is to reductive biosynthesis carriers of electrons for fuel Oxidation
A redox dehydrogenation RXN
Activation Carriers of Electrons for the Synthesis of Biomolecules Nicotinamide adenine dinucleotide phosphate (NADP+) is an activated carrier of e- for reductive biosyntheses NADPH is exclusive used for reductive biosynthesis & NADH is primarily for ATP generation Reactive site Keto Group of a Two-Carbon Unit Being Reduced to a Methylene Group NADPH/mediated reduction Activated Carrier of Two-Carbon Fragments Coenzyme (ACCoA or group CoA-SH) is an activated carrier of acyl groups including the acetylacyl The transfer of the acyl group is exergonic b/c the thioester is unstable Reactive group

Metabolic Processes

Homeostasis, a stable biochemical environment, is maintained by careful regulation of biochemical processes. 3 regulatory controls are especially prominent The amount of enzymes present The catalytic activity of enzymes The accessibility of substrates The Amounts of Enzymes Are Controlled The quantity of enzyme present can be controlled @ the level of gene transcription Catalytic Activity Is Regulated Catalytic activity is regulated allosterically or by reversible covalent modification
Hormones coordinate metabolic activity, often by instigating the covalent modification of allosteric enzymes Energy charge regulates metabolism Product of a pathway controls the rate of synthesis by inhibiting an early step The Accessibility of Substrates Is Requested Compartments Opposing rxns such as fatty acid synthesis & degradation may occur in different cellular the flux of substrates b/w compartments is used to regulate metabolism

Glycolysis

Oxidative phosphorylation: oxidative energy (e movement) used in mitochondria to generate Phosphorylation: light energy captured in chloroplasts of plants to make ATP Characteristics of Metabolism Metabolic pathways are most inreversible Every metabolic pathway has a committed 1st step All metabolic pathways are regulated Metabolic pathways in eukaryotic cells occur in specific cellular locations.
Glycolysis: Energy Conversion Pathway, Glycosis comes from a combination of 2 Greek words Glykys = sweet Lysis = breakdown Central pathway for glucose catabolism. Glycolysis is the sequence of 10 enzyme catalyzed rxns to pyruvate converts I mol of I this oxidative of I mol of produce of major cell process of cell The enzymes of glycolysis are another glycolytic increases enzyme * ATP

Glycolysis Parts

Glycolysis occurs in 2 stages: Stage I traps glucose in the cell & modifies it to for to of phosphorylated Stage 2 to *ATP is accumulating the increases enzyme 2 ATP I is glucose to

Glycolysis Phases

Phase 1: Preparatory Phase of glycolysis in which the phosphate by glucose biphosphate biphosphate * ATP
Phase 2: Payoff Phase rxns ADP * ATP ATP' 2 molecules are oxidized phosphate dehydrogenase of rate

The Process

Step 1: Phosphorylation Glucose is phosphorylated by ATP to form sugar phosphate Transfer Reactions that catalyze Transfer of phosphoryl group from phosphoryl to ADP from ATP to 2: chemical of oxygen aldose fructose phosphate is B Transfer of and the as a carrier phosphoryl molecules

Glycolysis, Cont

Hexokinase Glucose in the Cell Begins Glycolysis, Specific transported Protein kinase removes phosphonates from ATP to an acceptor
Step 2: Isomerization oxygen from * phosphate Conversion 6phosphate phosphate
Step 3: Phosphorylation to * ATP the * is enzyme Step to produce Two molecule glyceraldehyde DHAP Glyceraldehyde the enzyme Glyceraldehyde -OH is the rate Step catalyzed carbon is an and the enzyme in rate
Energy Profiles for Glyceraldehyde Oxidation Acyl -Formation Transfer important levels reactions glyceraldehyde glyceraldehyde phosphate synthesis in muscle is all

Last Steps

*Step 8: phosphate with by to level enzyme the reactions ADP the net reactions involved ADP the steps

Carbohydrates

Several in to into to and the

Reactions of Glycolysis

Each molecule of glucose gives 2 molecules of glyceraldehyde-3-phosphate Therefore, the net equation of glycolysis can be summarized as Glucose +2 P+2 ADP + 2 NAD+ > 2 pyruvate+2 ATP+ 2 NADH+ 2H+ + 2 H2O The simultaneous rxns involved are Glucose is oxidized to pyruvate NAD+ is reduced to NADH ADP is phosphorylated to ATP ATP GenerationConsumption in Glycolysis
Reaction ATP ATP 1 glucose glucose-6-phosphate glucose-6-phosphate 3 fructose-6-phosphate fructose-6-phosphate fructose-1,6-biphosphate fructose-1,6-biphosphate 7 1,3,-diphosphoglycerate 1,3,-diphosphoglycerate diphosphoglycerate 3-phosphoglycerate3-phosphoglycerate 10 10
phosphoenolpyruvatphosphoenolpyruvate pyruvate pyruvate Net Gain of = BBYJU' A 4-2=2

Glycolysis Pathways

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Anaplerotic reactions

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