metabolism a collective name for the many reactions that go on in the cells of living organisms...

Metabolism • A collective name for the many reactions that go on in the

cells of living organisms• Catabolism

• The group of metabolic pathways that break down larger molecules into smaller ones

• Pathways are often exergonic and release energy• Anabolism

• The group of metabolic pathways that build up larger molecules from smaller ones

• Pathways are often endergonic and absorb energy

An Overview of Metabolism

Catabolic pathways for the degradation of food and the production of biochemical energy


Catabolic stages:Stage 1 • Food is digested by hydrolysis of ester, glycoside (acetal),

and peptide (amide) bonds to yield primarily fatty acids plus glycerol, simple sugars, and amino acids

Stage 2 • Molecules are further degraded in the cytoplasm of the cells

to yield acetyl groups attached by a thioester bond to the large carrier molecule coenzyme A• The resultant compound, acetyl coenzyme A (acetyl

CoA), is a key substance in the metabolism of food molecules and in numerous other biological pathways


• The acetyl group in acetyl CoA is linked to the sulfur atom of phosphopantetheine, which is itself linked to adenosine 3’,5’-bisphosphate


Stage 3 Citric acid cycle• Acetyl groups are oxidized inside cellular mitochondria to

yield CO2

• This stage releases a large amount of energy

Stage 4 The electron transport chain• Energy made in the last stage used during the fourth stage

to accomplish the endergonic phosphorylation of ADP with hydrogen phosphate ion (HOPO3

2-, abbreviated Pi) to give ATP


Gibbs Stuff

• Reactions that are not favored.• What can we do?

ATP, the final result of food catabolism, has been called the “energy currency” of the cell• Energy production and use in living organisms revolve around

the ATP⇆ADP interconversion• Catabolic reactions “pay off” in ATP by synthesizing it from

ADP plus phosphate ion• Anabolic reactions “spend” ATP by transferring a phosphate

group to another molecule, thereby regenerating ADP


ADP and ATP are phosphoric acid anhydrides

• Contain linkages analogous to the linkage in carboxylic acid anhydrides

• React with alcohols by breaking a P-O bond and forming a phosphate ester, ROPO3

2-. The reaction is a nucleophilic acyl substitution at phosphorus

• Phosphorylation

reactions with ATP require the presence of divalent metal cation in the enzyme, usually Mg2+,to form a Lewis acid-base complex with the phosphate oxygen atoms and neutralize some negative charge


An energetically unfavorable reaction “couples” with an energetically favorable reaction so that the overall free-energy change for the two reactions together is favorable

Coupled reactions• Imagine that reaction 1 does not occur to any reasonable

extent because it has a small equilibrium constant and is energetically unfavorable, the reaction has ∆G > 0

(1) A + m B + n ∆G > 0

where A and B are the biochemically “interesting” substances undergoing transformation, while m and n are enzyme cofactors, H2O, or other substances


Imagine that the product n can react with substance o to yield p and q in a second, strongly favorable reaction that has a large equilibrium constant and ∆G << 0:

(2) n + o p + q ∆G << 0

Because the two reactions are coupled through n, the transformation of A to B becomes possible

• When an amount of n is formed in reaction 1, it undergoes a complete conversion in reaction 2, thereby removing it from the first equilibrium and forcing reaction 1 to continually replenish n until the reactant A is gone

• The two reactions added together have a favorable ∆G < 0• The favorable reaction 2 “drives” the unfavorable reaction 1


Coupled Reactions• Phosphorylation reaction of glucose to yield glucose 6-phosphate plus

water• The reaction of glucose with HOPO3

2- does not occur to any degree because it is energetically unfavorable, with ∆Gº′ = +13.8 kJ/mol


Coupled ReactionsWith ATP, glucose undergoes an energetically favorable reaction to

yield glucose 6-phosphate plus ADP• ATP drives the phosphorylation reaction of glucose:


ATP• Able to drive unfavorable phosphorylation reactions

• The resultant phosphates are more reactive as leaving groups in nucleophilic substitutions or eliminations.


Reactions that make water

• A series of reactions that produce water follow.

Peptides and proteins are amino acid polymersResidues • An amino acid in a protein chain• Joined together by amide bonds, or peptide bonds

An amino group from one residue forms an amide bond with the carboxyl group of a second residue

• Alanylserine is the dipeptide that results when an amide bond is formed between the alanine carboxyl and the serine amino group

19.4 Peptides and Proteins

Two dipeptides can result from reaction between alanine and serine, depending on which carboxyl group reacts with which amino group

• If the alanine amino group reacts with the serine carboxyl, serylalanine results

Peptides and Proteins

Proteins• The protein’s backbone is continuous chain of atoms

running the length• The repetitive sequence of –N–CH–CO–atoms

Polypeptides• Convention for writing peptides:

• N-terminal amino acid on the left • Peptides with the free –NH2 group

• C-terminal amino acid on the right• Peptides with the free –CO2H group

• The name of the peptide is indicated using abbreviations• Alanylserine is abbreviated Ala-Ser or A-S • Serylalanine is abbreviated Ser-Ala or S-A


Amide Bonds• Amide nitrogens are nonbasic because their unshared electron

pair is delocalized by interaction with the carbonyl group• The overlap of the nitrogen p orbital with the p orbital of the carbonyl

group imparts a certain amount of double-bond character to the C-N bond and restricts rotation around it

• The amide bond is planar • The N-H is oriented 180º to the C=O


Aldehydes and ketones undergo a rapid and reversible nucleophilic addition reaction with alcohols to form hemiacetals

Monosaccharides undergo intramolecular nucleophilic additions• The carbonyl and hydroxyl groups of the same molecule react to form

cyclic hemiacetals

21.5 Cyclic Structures of Monosaccharides: Anomers

Two anomers formed by cyclization of glucose

Cyclic Structures of Monosaccharides: Anomers

Some monosaccharides also exist in a five-membered cyclic hemiacetal form called a furanose

• D-Fructose exists in both the pyranose and the furanose forms • The two pyranose anomers result from addition of C6 –OH group to

the C2 carbonyl• The two furanose anomers result from addition of C5 –OH group to

the C2 carbonyl


• When a sample of either pure anomer of D-glucopyranose is dissolved in water its optical rotation slowly changes and reaches a constant value of +52.6• The specific rotation of -D-glucopyranose decreases

from +112.2 to +52.6 when dissolved in aqueous solution

• The specific rotation of -D-glucopyranose increases from +18.7 to +52.6 when dissolved in aqueous solution

• This change in optical rotation is due to the slow conversion of the pure anomers into a 37 : 63 equilibrium mixture and is known as mutarotation


Ester and Ether Formation• Monosaccharides exhibit chemistry similar to

simple alcohols• Usually soluble in water but insoluble in organic

solvents• Do not easily form crystals upon removal of water• Can be converted into esters and ethers

• Ester and ether derivatives are soluble in organic solvents and are easily purified and crystallized

21.6 Reactions of Monosaccharides

• Esterification is normally carried out by treating the carbohydrate with an acid chloride or acid anhydride in presence of base• All –OH groups react including the anomeric –OH group

Reactions of Monosaccharides

Glycoside Formation• Hemiacetals yield acetals upon treatment with an alcohol and an

acid catalyst

• Treatment of monosaccharide hemiacetals with an alcohol and acid catalyst yields an acetal, called a glycoside


Biological Ester Formation: Phosphorylation

Glycoconjugates• Carbohydrates linked through their anomeric center

to other biological molecules such as lipids (glycolipids) or proteins (glycoproteins)

• Constitute components of cell walls and participate in cell-type recognition and identification


Palmitic acid (C16) and stearic acid (C18) are the most abundant saturated fatty acids

Oleic and linoleic acids (both C18) are the most abundant unsaturated fatty acids

Waxes, Fats, and Oils

• Fats and oils are triglycerides, or triacylglycerols• Triesters of glycerol with three long-chain carboxylic acids

called fatty acids• Fats are used by animals for long-term energy storage

• Less highly oxidized than carbohydrates• Provide about six times as much energy as an equal weight of

glycogen

Waxes, Fats, and Oils

Phospholipids are diesters of phosphoric acid, H3PO4

23.3 Phospholipids

Two general kinds of phospholipids• Glycerophospholipids

• Based on phosphatidic acid• Acyl group at C1 is usually saturated and

the one at C2 is usually

unsaturated• The phosphate group

at C3 is also bonded

to an amino alcohol

such as choline,

ethanolamine,

or serine• Compounds are

chiral at C2 with an

L or R configuration

Phospholipids

• Sphingomyelins• Have sphingosine or a related dihydroxyamine as their

backbone• Abundant in brain and nerve tissue• Major constituent of the coating around nerve fibers

Phospholipids

Nucleic acids are biopolymers• Composed of nucleotides which are joined together to form a long chain• Nucleotide

• Composed of nucleosides bound to a phosphate group• Nucleoside

• Composed of an aldopentose sugar linked through its anomeric carbon to the nitrogen atom of a heterocyclic purine or pyrimidine base

24.1 Nucleotides and Nucleic Acids

metabolism a collective name for the many reactions that go on in the cells of living organisms...

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