Molecules

topics

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Section ~ Nucleobases, nucleosides, nucleotides : molecules • bases nucleosides nucleotides • adenine • AMP • ATP • cAMP • cytosine • C to T • C to U • guanine • purine pyrimidine • thymine • T U mismatch • uracil

Section ~ Amino Acids : molecules : amino acids • amino acid chart • alanine • arginine • asparagine • aspartic acid • cysteine • glutamic acid • glutamine • glycine • histidine • isoleucine • leucine • lysine • N-formylmethionine • methionine • phenylalanine • proline • serine • threonine • tryptophan • tyrosine • valine

Section ~ DNA, RNA : molecules : • DNA, RNA and nucleotides • adenosine • CDP • DNA RNA • GDP • GMP • GTP • UDP • UMP

Section ~ Lipids, Fatty Acids : molecules : φ Lipids fatty acids φ eicosanoids φ prostaglandins φ sphingolipids φ triacylglycerols

Section ~ Cholesterol, Steroids : molecules : • steroids

Section ~ Neurotransmitters : molecules : • neurotransmitters • acetylcholine • dopamine • epinephrine • GABA • glycine • norepinephrine • serotonin

Section ~ Hormones : molecules : • hormones

Section ~ Sugars : molecules : • sugars • glucose • ribose deoxyribose

Section ~ Energy : molecules : • energy • ATP • NADPH : : energy organelles • chloroplast •

Section ~ Cofactors, Coenzymes, Intermediates : molecules • Acetyl Co-Enzyme A • NADH : NAD⁺ : NADPH : NADP⁺ : Nicotinamide adenine dinucleotide : • pyruvate

bases nucleosides nucleotides

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Bases (nucleobases) are heterocyclic purine and pyrimidine analogues found in DNA and RNA.

Nucleosides comprise the RNA bases bound to a ribose sugar molecule -- examples are cytidine, uridine, adenosine, guanosine, thymidine and inosine. Deoxyribonucleosides comprise bases bound to a molecule of the sugar deoxyribose.

Nucleotides are nucleosides attached to a phosphate (phosphorylated by specific kinases), and deoxynucleotides are phosphorylated deoxyribonucleosides.

• adenine • AMP • ATP • cAMP • cytosine • C to T • C to U • guanine • thymidine • T U mismatch • uracil

adenine

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AMP

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ATP

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Adenosine triphosphate is produced by the enzyme ATP synthase, which possesses highly conserved structure and genetic coding – that is, the structure and genetic code for ATP synthase is remarkably similar in all known forms of life.

ATP synthase is powered by a transmembrane electrochemical potential gradient, usually in the form of a proton gradient, which is generated by an electron transport chain. In all living organisms, a series of redox reactions are employed to produce the transmembrane electrochemical potential gradient required for phosphorylation reactions:
AMP + Pi → ADP + Pi → ATP. (Pi is inorganic phosphorus)

Redox reactions are chemical reactions in which electrons are transferred from a donor molecule to an acceptor molecule. The Gibbs free energy of the reactants compared to the products provides the chemical potential enegy for redox reactions.

The Gibbs free energy is the energy available (“free”) to do work. Any reaction that decreases the overall Gibbs free energy of a system (reactants → products) will proceed spontaneously with release of that energy. The transfer of electrons from a high-energy donor molecule to a lower-energy acceptor molecule can be spatially separated into a series of intermediate redox reactions within an electron transport chain. The spatial separation permits biological control of the reactions.

Harvard University provides a wonderful video explaining operation of the F1-F0 ATPase.

cAMP

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cytosine

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C to T

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cytosine (C) conversion to thymine (T) by alkylation followed by deamination.

C to U

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cytosine (C) conversion to uracil (U) by deamination.

guanine

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purine pyrimidine

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Adenine and guanine are purines and cytosine, uracil, and thymine are pyrimidines.

Left - purine (smaller molecule with bigger name) and (right) pyrimidine (larger molecule with smaller name)

grey - carbon / white - hydrogen / blue - nitrogen

thymine

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T U mismatch

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thymine (T) and uracil (U) differ only in the CH3 group on T, and may be mismatched.

uracil

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Molecules in Motion

2007-12-19T16:24:00.000-05:00

Atheistic molecules, that is.
A-Deistic
Adeistic
Black Out
cosmos
Eine Kleine Nattermusing
eMusings
eVolition
Galaria
Godborygmi
Godspell Follies
Gray Matters
MetaThoughts
Mimble Wimble
Naturalism
bLogodaedaly
palimpsest
Salient
Science of Evolution
Sechuam
Sintheist
Tabula Flexuosa
The Scarlet A
Weltschauung

amino acids

2006-11-30T23:59:00.000-05:00

Essential amino acids in adult humans: lysine, leucine, isoleucine, methionine, phenylalanine, threonine, tryptophan, and valine.
Additional amino acids essential to children: histidine and arginine.

• amino acid chart • alanine • arginine • asparagine • aspartic acid • cysteine • glutamic acid • glutamine • glycine • histidine • isoleucine • leucine • lysine • N-formylmethionine • methionine • phenylalanine • proline • serine • threonine • tryptophan • tyrosine • valine

External links: Alanine Arginine Asparagine Aspartic acid Cysteine Glutamic acid Glutamine Glycine Histidine Isoleucine Leucine Lysine Methionine Phenylalanine Proline Serine Threonine Tryptophan Tyrosine Valine Essential amino acid Protein Peptide Genetic code Isoleucine and valine biosynthesis Leucine biosynthesis

amino acid chart

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alanine

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Non-polar amino acid Ala A RNA code: GCU, GCC, GCA, GCG

arginine

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Basic amino acid Arg R RNA code: CGU, CGC, CGA, CGG, AGA, AGG

asparagine

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Polar amino acid Asn N RNA code: AAU, AAC

aspartic acid

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Acidic amino acid Asp D RNA code: GAU, GAC

cysteine

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Polar amino acid Cys C RNA code: UGU, UGC

glutamic acid

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Acidic amino acid Glu E RNA code: GAA, GAG

glycine

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Non-polar amino acid Gly G RNA code: GGU, GGC, GGA, GGG

glutamine

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Polar amino acid Gln Q RNA code: CAA, CAG

histidine

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Basic amino acid His H RNA code: CAU, CAC

Histidine's imidazole side chain has a hydrogen-bound nitrogen atom that is slighty acidic and another nitrogen that is slightly basic. The almost neutral pKa of histidine ensures that its charge will change in response to relatively small shifts in cellular pH.

Histidine functions as a co-ordinating ligand in metalloproteins, and at the catalytic site of some enzymes. In catalytic triads, the basic nitrogen of histidine extracts a proton from serine, threonine or cysteine, activating the nitrogen as a nucleophile. In a histidine proton shuttle, histidine rapidly shuttles protons by abstracting a proton onto the basic nitrogen to generate a positively-charged intermediate before passing a proton from the acidic nitrogen. Carbonic anhydrases employ the histidine proton shuttle to rapidly shuttle protons away from a zinc-bound water molecule to quickly regenerate the active form of the enzyme.

isoleucine

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Non-polar amino acid Ile I RNA code: AUU, AUC, AUA

leucine

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Non-polar amino acid Leu L RNA code: UUA, UUG, CUU, CUC, CUA, CUG

lysine

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Basic amino acid Lys K RNA code: AAA, AAG

N-formylmethionine

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N-Formylmethionine (fMet) is an amino acid that is found in all living cells. It is a derivative of the amino acid methionine, in which a formyl group has been added to methionine's amino group (catalyzed by the enzyme transformylase when Met is attached to tRNA.fMet, but not to tRNA.Met).

N-Formylmethionine plays a crucial role in the protein biosynthesis of bacteria, archaea, mitochondria and chloroplasts. Bacteria utilize N-formylmethionine (f-Met) rather than methionine at the N-terminal of the elongating polypeptide chain.

Compare to methionine.

f-Met amino acid RNA code: AUG tRNA.fMet & tRNA.Met

methionine

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Non-polar amino acid Met M amino acid RNA code: AUG (also stop codon)

phenylalanine

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Aromatic Non-polar amino acid Phe F RNA code: UUU, UUC

proline

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Non-polar amino acid Pro P RNA code: CCU, CCC, CCA, CCG

serine

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Polar amino acid Ser S RNA code: UCU, UCC, UCA, UCG, AGU, AGC

Serine is a biosynthetic derivative of glycine, and a biosynthetic precursor of purines and pyrimidines, cysteine, tryptophan, and other metabolites.

Serine is found in the active sites of many enzymes including the serine proteases chymotrypsin and trypsin.

Serine is important in signal transduction because it is phosphorylated by serine/threonine kinases.

threonine

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Polar amino acid Thr T RNA code: ACU, ACC, ACA, ACG

Threonine is an essential amino acid in humans.

Threonine is important in signal transduction because it is phosphorylated by serine/threonine kinases.

tryptophan

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Aromatic Non-polar amino acid Trp W RNA code: UGG

tyrosine

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Aromatic Polar amino acid Tyr Y RNA code: UAU, UAC

Tyrosine plays an important role in signal transduction because protein tyrosine kinases and receptor tyrosine kinases can phosphorylate the amino acid within proteins.

Tyrosine is a biosynthetic precursor of the thyroid hormone thyroxine (T4) and triiodothyronine (T3), the pigment melanin, the catecholamine neurotransmitter dopamine and norepinephrine, the neurotransmitter/hormone epinephrine, and in the opium poppy, morphine.

valine

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Non-polar amino acid Val V RNA code: GUU, GUC, GUA, GUG

DNA, RNA and nucleotides

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• adenosine • CDP • DNA RNA • GDP • GMP • GTP • UDP • UMP

adenosine

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CDP

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DNA RNA

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GDP

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GMP

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GTP

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Above – phosphorylation of GDP (left) yields GTP (right), which is hydrolysed back to GDP by GTPases.

GTP is generated in the citric acid cycle, and is an important energy molecule. GTP is most important in its role as a molecular switch in signal transduction.

GTPases hydrolyze GTP to GDP + Pi in the highly conserved domains of G-proteins, which are associated with GPCRs (guanine nucleotide-binding protein-coupled receptors, G-protein coupled receptors, serpentine receptors, 7TM receptors, or heptahelical receptors).

Above GTP

UDP

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UMP

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Lipids fatty acids

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Phospholipids are formed from four components: fatty acids, a negatively charged phosphate group, an alcohol and a backbone. Phospholipids with a glycerol backbone are known as glycerophospholipids or phosphoglycerides. (left - click to enlarge image)

Essential fatty acids are required in the diet because, lacking the necessary desaturase enzymes, humans are unable to biosynthesize omega fatty acids, though we do possess the bio-machinery for their interconversion. The two closely related families of EFAs are : omega-3 (ω-3, or n-3) α-linolenic acid (18:3), and omega-6 (ω-6, n-6) linoleic acid (18:2). The EFAs serve as substrates for the biosynthesis of longer, more desaturated fatty acids (long-chain polyunsaturates).

Only sphingomyelin has a sphingosine backbone. Sphingomyelin is present in all eukaryotic cell membranes, but is mainly present in cells of the nervous system. Phospholipids, along with glycolipids and cholesterol, are a major component of all biological membranes.

tags [Biochemistry] [Molecular Biology] [eicosanoid] [phospholipid]

eicosanoids

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Eicosanoids, or Icosanoids function as autocrine and paracrine mediators, and are oxygenated hydrophobic derivatives of 20-carbon polyunsaturated essential fatty acids, predominantly arachidonic acid (AA) in humans. Dihomo-gamma-linolenic acid (DGLA) and eicosapentaenoic acid (EPA, icosapentaenoic acid, timnodonic acid) also serve as eicosanoid precursors. Eicosanoids include leukotrienes with four double bonds and prostanoids with two double bonds (prostaglandins and prostacyclins with five-membered rings, and thromboxanes with heterocyclic oxane structures).

Eicosanoid biosynthesis begins with phospholipase catalyzed release from phospholipids (A2) or diacylglycerol (C) of a 20-carbon essential fatty acid (EFA) containing three, four, or five double bonds (ω-6 DGLA, ω-6 AA or ω-3 EPA, respectively).

Physiological activity of the short-lived eicosanoids is mediated by specific receptors:
Leukotrienes:
● CysLT1 (Cysteinyl leukotriene receptor type 1)
● CysLT2 (Cysteinyl leukotriene receptor type 2)
● BLT1 (Leukotriene B4 receptor)
Prostanoids:
● PGD2: DP-(PGD2)
● PGE2:
– ● EP1-(PGE2)
– ● EP2-(PGE2)
– ● EP3-(PGE2)
– ● EP4-(PGE2)
● PGF2α: FP-(PGF2α)
● PGI2 (prostacyclin): IP-(PGI2)
● TXA2 (thromboxane): TP-(TXA2)

Eicosanoid Actions

tags [Molecules] [biochemistry] [eicosanoid]

phospholipids

2006-08-09T16:09:00.000-04:00

Phospholipids are formed from four components: fatty acids, a negatively charged phosphate group, an alcohol and a backbone. Phospholipids with a glycerol backbone are known as glycerophospholipids or phosphoglycerides.

Only one type of phospholipid possesses a sphingosine backbone – sphingomyelin. Sphingomyelin is present in all eukaryotic cell membranes, but is mainly present in cells of the nervous system. Phospholipids, along with glycolipids and cholesterol, are a major component of all biological membranes. (click to enlarge image)

Phospholipases are enzymes that hydrolyze specific ester bonds in phosphoglycerides or glycerophosphatidates, converting the phospholipids into fatty acids and other lipophilic substances. Phospholipases are involved in signaling cascades. Phospholipase A1 hydrolyzes the acyl group attached to the 1-position, while phospholipase A2 hydrolyzes the acyl group attached to the 2-position to form fatty acid and lysophospholipid products. Phospholipase A2 is responsible for the release of arachidonic acid from membranes (flow diagram PLA2 pathway). Arachidonic acid is a signalling molecule and is the precursor for eicosanoid signaling molecules, which include leukotrienes and prostaglandins. Some eicosanoids are synthesized from diacylglycerol, and are released from the lipid bilayer by phospholipase C.

tags [Biochemistry] [Molecular Biology] [eicosanoid] [phospholipid]

prostaglandins

2006-08-09T06:10:00.000-04:00

Prostaglandins (PG) are diffusible, physiologically active C20 signaling molecules with a 5-carbon ring, which belong to the prostanoid subclass of eicosanoid fatty acid derivatives (left - PGE1)

▼ actions : autocrine : biosynthesis : classification : diversity : immune system (insect) : mediators : paracrine : PG-receptors (GPCRs) : prostacyclin : secretion : side-chain substitutions : structural differences : thromboxane : transporters ▼

Prostaglandins occur in almost all tissues and act as lipid mediators affecting platelets, endothelial cells, mast cells, etc. Prostaglandins are potent but have a short half-life before being inactivated and excreted, so their effects are confined to paracrine (local) or autocrine (same cell) functions. Prostaglandins exhibit subtle differences in their chemical structures on the basis of different side-chain substitutions. Classification is based on these structural differences. PGA to PGE and PGJ rings have a keto group and are some have double bonds or hydroxyl groups in various positions. The PGF ring has two hydroxyl groups while PGK has two keto substituents on the ring. PGG and PGH are bicyclic endoperoxides. (diagram)

These small structural variations are considered responsible for the immense diversity of physiological effects characteristic of prostaglandins. Adding to their physiological diversity, the same prostaglandins can elicit different responses in different tissues. [] basic PG structure (Jmol) []

Prostaglandins, with their fellow eicosanoids, are synthesized from C20 fatty acids in response to hormonal signals. (diagram, diagram 2) Approximately a dozen different prostaglandins have been identified, each associated with different activities plus different effects on various tissues. Prostaglandin secretion is mediated by the multidrug resistance protein 4 (MRP4, ABCC4) transporter, which is a member of the ATP-binding cassette transporter superfamily. Various prostaglandins ligate members of the G-protein-coupled receptors (DP1-2, EP1-4, FP, IP, and TP) that can have opposing effects on cAMP, IP turnover, and Ca2+ levels. (diagram PGE2→EP)

Prostaglandins have a wide variety of actions:
● muscular contraction
● relaxation of vascular smooth muscle (vasodilation)
● mediation of inflammation (diagram PGE2)
● calcium movement
● ion transport
● lipolysis
● hormone regulation
● cell growth control
● temperature regulation

Table Eicosanoid Actions

Thromboxane is released by platelets and causes platelet aggregation and vascular constriction. Prostacyclin is secreted by vascular endothelial cells and is antagonistic to thromboxane.

Eicosanoid Actions

Prostaglandins and other eicosanoids mediate cellular immune responses to bacterial infections in insects – eicosanoids mediate insect microaggregation and nodulation responses to bacterial infections.[s]

[] prostaglandin gallery []

▲ Top ▲

tags [Biochemistry] [Molecular Biology] [eicosanoid] [prostaglandins]

sphingolipids

2006-08-08T16:16:00.000-04:00

Ceramide is a well-characterized sphingolipid metabolite and second messenger that participates in numerous biological processes. In addition to serving as a precursor to complex sphingolipids, ceramide is a potent signaling molecule capable of regulating vital cellular functions. Perhaps its major role in signal transduction is to induce cell cycle arrest, and promote apoptosis. In contrast, little is known about the metabolic or signaling pathways that are regulated by the phosphorylated form of ceramide. It was first demonstrated that ceramide-1-phosphate (C1P) had mitogenic properties, and more recently it has been described as potent inhibitor of apoptosis and inducer of cell survival. C1P and ceramide are antagonistic molecules that can be interconverted in cells by kinase and phosphatase activities. An appropriate balance between the levels of these two metabolites seems to be crucial for cell and tissue homeostasis. Switching this balance towards accumulation of one or the other may result in metabolic dysfunction, or disease. Therefore, the activity of the enzymes that are involved in C1P and ceramide metabolism must be efficiently coordinated to ensure normal cell functioning. Gomez-Munoz A. Ceramide 1-phosphate/ceramide, a switch between life and death. Biochim Biophys Acta. 2006 May 19; [Epub ahead of print]

triacylglycerols

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Triacylglycerols are the molecules employed for fat storage in adipose tissue.

steroids

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neurotransmitters

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acetylcholine • dopamine • epinephrine • GABA • glycine • norepinephrine • serotonin

acetylcholine

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dopamine

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epinephrine

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GABA

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glycine

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norepinephrine

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serotonin

2006-06-12T23:46:00.000-04:00

hormones

2006-05-31T23:59:00.000-04:00

sugars

2006-04-30T23:59:00.000-04:00

glucose

2006-04-18T00:03:00.000-04:00

Glucose is an aldohexose - the natural form, D-glucose is also called dextrose. Glucose is biologically important, and is one of the products of photosynthesis by plants and some prokaryotes. Glucose is an important precursor in the synthesis of glycogen (animals), polysaccharides, lactose, cellulose and starch (plants), proteins and lipids, and vitamin C (plants, most animals).

Glucose is an important fuel in energy yielding catabolic pathways such as glycolysis, the pentose phosphate pathway, and the citric acid cycle. In the catabolic pathway gluconeogenesis, animals convert non-carbohydrate intermediates such as pyruvate and glycerol into glucose. Animals and fungi convert glycogen to glucose (glycogenolysis), while plants hydrolyse the storage form starch into glucose.

Glycosylation involves the addition of saccharides to proteins and lipids, and is one of four principal co-translational and post-translational modification steps in the synthesis of membranous and secretory proteins. Most proteins synthesized in the rough ER undergo glycosylation, which is an enzyme-directed site-specific process, as opposed to the non-enzymatic chemical reaction of glycation (below). There are two types of glycosylation: N-linked glycosylation to the amide nitrogen of asparagine side chains and O-linked glycosylation to the hydroxy oxygen of serine and threonine side chains.

Glucose can form formaldehyde under abiotic conditions, a propery that probably was utilized by primitive biochemical systems. A more important property of glucose to advanced metabolic forms is the low tendency of glucose, in comparison to other hexose sugars, to react non-specifically with the amino groups of proteins. This glycation reaction reduces or destroys the function of many enzymes. Glucose's low rate of glycation is due to the tendency of glucose to adopt the less reactive cyclic isomeric form (below). Nevertheless, many of the long-term complications of diabetes, such as blindness, kidney failure, and peripheral neuropathy probably result from the glycation of proteins or lipids.

Glucose can take up a linear or a cyclic form. The ring form results from bonding between the aldehyde C atom and the C-5 hydroxyl group, creating an intramolecular hemiacetal. By virtue of the ring form's resemblance to pyran, glucose is also termed glucopyranose.

Glucose has 4 optic centers, so glucose has (4²-1) = 15 possible optical stereoisomers, of which only 7 occur biologically. Of these galactose (Gal) and mannose (Man) are the most important. The eight isomers (including glucose) are all diastereoisomers in relation to each other and all belong to the D-series.

An additional asymmetric center at C-1 (called the anomeric carbon atom) is created when glucose cyclizes, so two ring structures, called anomers, α-glucose and β-glucose. The α-and β- forms differ structurally in the orientation of the hydroxyl group linked to C-1 in the ring. The designation α means that the C-1 hydroxyl group is below the plane of the ring in the Haworth projuection, while the β means it is above the ring. The α and β forms slowly interconvert in aqueous solution in a process called mutarotation solution to a final stable ratio of α:β = 36:64.

Image of glucose representations from Fisher to Haworth.
Animated image of D-Glucose shifting into β-D-glucose.

polysaccharides

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Polysaccharides are sugar macromolecules.

ribose deoxyribose

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The molecules differ in the presence of an -OH group on carbon 2 of the pentose ring. Ribose is found only in RNA, as is uracil, and deoxyribose is found only in DNA, as is thymine.

energy

2006-03-31T23:59:00.000-05:00

• ATP • GTP • Pathways •

chloroplast

2006-03-28T16:12:00.000-05:00

The chloroplast is the site of photosynthesis in eukaryotic cells, and is the site of the Calvin cycle just as the mitochondrion is the site of oxidative phosphorylation.

The thylakoid membrane, with its embedded photosystems, is the structural unit of photosynthesis. Both photosynthetic prokaryotes and eukaryotes possess membranes with embedded photosynthetic pigments. Only eukaryotes, which have a nuclear membrane and membrane-bound organelles, possess chloroplasts with an encapsulating membrane. The chloroplast has three compartments, while the mitochondrion has only two. Compartments within a chloroplast are the intermembranous space [3], the stroma [6], and the thylakoid lumen (8) within stromal and granal thylokoids [4,5].

1. outer membrane
2. inner membrane
3. intermembranous space
4. stromal thylakoid
5. granal thylakoid
6. stroma (cytosol)
7. granum (a stack of thylakoids)
8. internal lumen of granal and stromal thylakoids
(click to enlarge image)

The typical higher plant chloroplast is lenticular and approximately 5 microns at its largest dimension. Plant cells contain from 1 to 100 chloroplasts, depending on the type of cell. The mature chloroplast is typically bounded by outer (1) and inner (2) membranes that possess significantly different chemical constituents. In addition to enzymes that function in photosynthesis, chloroplasts also contain a circular DNA molecule and the protein-synthetic machinery characteristic of prokaryotes (below).

The smooth outer membrane (1) is freely permeable to molecules, and resembles the chemical constitution of the eukaryotic plasma membrane. The smooth inner membrane (2) contains many integral transporter proteins that regulate the passage of small molecules like sugars, and proteins (synthesized in the cytoplasm of the cell, but utilized within the chloroplast). The inner membrane chemically resembles prokaryotic cell membranes.

The folded thylakoid membranes perform the light reactions of photosynthesis utilizing Photosystems I and II, both of which include chlorophyll and carotenoid molecules. Thylakoid membranes also contain Cytochromes b and f and ATP synthase. The fluid stroma surrounding the thylakoid membranes includes the RUBISCO enzymes that perform the light-independent reactions of conversion of CO₂ into organic molecules such as glucose. The stroma also includes the chloroplast genome (cpDNA genes) comprising many identical, circular molecules of DNA.

Each chloroplast contains about 40 to 80 grana (7), and each grana comprises about 5 to 30 thylakoids. The thylakoids are membranous disks about .25 to .8 microns in diameter, which contain protein complexes, pigments, and other accessory components. The phospholipid bilayer of the thylakoid is folded repeatedly into stacks of grana. (details) These stacks are connect by channels to form a single functional compartment – the internal lumen.

The thylakoid is the site of oxygenic photosynthesis in eukaryotic plants and algae, and in prokaryotic Cyanobacteria. Cyanobacteria possess thylakoid membranes, but as prokaryotes they do not contain chloroplasts. Chlorophyll, accessory pigments, and other integral membrane proteins transduce light energy to provide excited electrons (excitons) to electron transport chains, powering the formation of NADPH and ATP during photophosphorylation.

The current consensus is that chloroplasts originated from Cyanobacteria that have become endosymbionts. This is an origin analogous to the endosymbiotic origin of mitochondria, which are believed derived from "purple bacteria", alpha-proteobacteria most closely related to Rickettsiales.

The cpDNA genes encode some of the molecules needed for chloroplast function. Hundreds of others are transcribed from genes in cellular nucleus, translated into proteins in the cytoplasm, and transported into the chloroplast. It has been experimentally demonstrated that endosymbiotic engulfment of prokaryotes is followed by Endosymbiotic Gene Transfer.

Chloroplast RNA-binding and pentatricopeptide repeat proteins
Chloroplast gene expression is mainly regulated at the post-transcriptional level by numerous nuclear-encoded RNA-binding protein factors. In the present study, we focus on two RNA-binding proteins: cpRNP (chloroplast ribonucleoprotein) and PPR (pentatricopeptide repeat) protein. These are suggested to be major contributors to chloroplast RNA metabolism. Tobacco cpRNPs are composed of five different proteins containing two RNA-recognition motifs and an acidic N-terminal domain. The cpRNPs are abundant proteins and form heterogeneous complexes with most ribosome-free mRNAs and the precursors of tRNAs in the stroma. The complexes could function as platforms for various RNA-processing events in chloroplasts. It has been demonstrated that cpRNPs contribute to RNA stabilization, 3´-end formation and editing. The PPR proteins occur as a superfamily only in the higher plant species. They are predicted to be involved in RNA/DNA metabolism in chloroplasts or mitochondria. Nuclear-encoded HCF152 is a chloroplast-localized protein that usually has 12 PPR motifs. The null mutant of Arabidopsis, hcf152, is impaired in the 5´-end processing and splicing of petB transcripts. HCF152 binds the petB exon–intron junctions with high affinity. The number of PPR motifs controls its affinity and specificity for RNA. It has been suggested that each of the highly variable PPR proteins is a gene-specific regulator of plant organellar RNA metabolism.

T. Nakamura, G. Schuster, M. Sugiura and M. Sugita Chloroplast RNA-binding and pentatricopeptide repeat proteins Biochem. Soc. Trans.. (2004) 32, (571–574)

mitochondria

2006-03-12T15:04:00.000-05:00

The mitochondrion (pl. mitochondria) is the 'power house of the eukaryotic cell, performing oxidative phosporylation. Mitochondria have two internal, membrane-bound spaces, unlike chloroplasts, which have three internal spaces.

The outer mitochodrial membrane is similar in constitution to the eukaryotic cell’s plasma membrane, while the inner membrane is similar in chemical composition to bacterial membranes. This difference is one of several lines of evidence for the serial endosymbiotic origin of mitochondria as phagocytozed purple bacteria.

Above left – click to enlarge : simplified diagram of a mitochondrion showing:
1. space between inner and outer membranes
2. matrix
3. christae
4. junction between membranes
5. inner membrane
6. outer membrane

The image at right (click to enlarge) is based on reconstruction of serial tem slices through a mitochondrion. The outer membrane (violet) surrounds the organelle. The inner membrane (pale blue) is contiguous, at membrane junctions (pale blue connecting to green at lower center), with the inner membrane that forms the walls of cristae (green).

The matrix – a soup factory – lies between the cristae, and contains mitochondrial DNA and the components of intermediary metabolism. image - mitochondrion cut : tour mitochondrion :

The outer and inner membranes are composed of phospolipid bilayers studded with proteins, much like the cell membrane. However, the composition of the inner and outer membranes is very different.

The inner mitochondrial membrane contains more than 100 different polypeptides. The protein to phospholipid ratio is very high – more than 3:1 by weight, having about 1 protein for 15 phospholipids. The inner membrane is also rich in an unusual phospholipid, cardiolipin, which is usually characteristic of bacterial plasma membranes. This composition, along with other evidence, has led to the assumption that the inner membrane is derived from endosymbiotic prokaryotes. The endosymbiotic theory of eukaryotic evolution is now widely accepted.

In contrast, the outer membrane, which encloses the entire mitochondrion, is similar in composition to the cell membrane and comprises about 50% phospolipids by weight and contains a variety of enzymes. The enzymes carry out activities such as the oxidation of epinephrine (adrenaline), the degradation of tryptophan, and the elongation of fatty acids.

The plant chloroplast is the site of photosynthesis : animation - chloroplast : tour the chloroplast : Virtual Cell Textbook - Cell Biology

Cofactors, Coenzymes, biosynthetic intermediates

2006-02-28T23:59:00.000-05:00

In general, a cofactor is any substance required to cooperate with an enzyme that catalyzes a specific reaction. Cofactors are non-proteinaceous substances that assist enzymes in performing catalytic actions. Cofactors may be cations (metal ions) or organic molecules known as coenzymes (vitamins).

Cofactors may be altered temporarily during the reaction which they assist, but they return to their original state after participating in catalysis, so they are not ultimately changed by the reaction.

Cofactors may be loosely or tightly bound to the enzyme. Organic, loosely bound cofactors are called coenzymes, and play an accessory role in enzyme-catalyzed processes, often by acting as a donor or acceptor of a substance involved in the reaction. When combined with an inactive apoenzyme, coenzymes form a complete, active enzyme called the holoenzyme. ATP and NAD⁺ are common coenzymes, and are loosely bound to the enzyme. Many coenzymes are phosphorylated water-soluble vitamins. Heme is tightly, covalently bound, and as such is a prosthetic group.

Prosthetic groups differ from cofactors in being tightly (often covalently) bound to a particular enzyme molecule. Haem is an example of a prosthetic group found in cytochromes and haemoglobin, which carries electrons and/or oxygen.

In molecular genetics, cofactors are proteins that interact with transcription machinery, transducing regulatory information between core RNA polymerase machinery and gene-specific transcription factors. 'Mediator' is the most universal cofactor known today – it is a modular complex serving as the interface between gene-specific RNA pol II machinery. Mediator is also needed for response to other regulatory proteins such as activators and repressors of transcription.

Many molecules are important intermediates in biochemical pathways.

• acetyl-CoA • NADH : NAD+ : NADPH : NADP+ : Nicotinamide adenine dinucleotide : • pyruvate • • •

Acetyl Co-Enzyme A

2006-02-24T21:36:00.000-05:00

The main function of coenzyme A is transfer of acyl groups, such as the acetyl group, or of thioesters. A molecule of coenzyme A carrying an acetyl group is also referred to as acetyl-CoA.

Coenzyme A is sometimes referred to as 'CoASH' or 'HSCoA' because when it is not attached to an acetyl group, it is attached to a thiol group, -SH. CoA is adapted from β-mercaptoethylamine, panthothenate and adenosine triphosphate.

The coenzyme is a very important biological intermeditate in the synthesis and β-oxidation of fatty acids and in generation of pyruvate for the citric acid cycle.

Acetyl Co-A is chiefly employed to convey the carbon atoms of the acetyl group to the citric acid cycle to be oxidized for energy production. Acetyl-CoA is the precursor to HMG CoA, which is a vital component in cholesterol and ketone synthesis. Acetyl C0-A contributes an acetyl group to choline in the synthesis of acetylcholine, in a reaction catalysed by choline acetyltransferase.

NADH

2006-02-11T11:42:00.000-05:00

Nicotinamide adenine dinucleotide
is an important cofactor. NADH is the reduced form, while NAD⁺ is the oxidized form. Phosphorylation through an ester linkage at the 2' position of the adenosyl nucleotide yields NADP.

Phototrophs obtain NADPH (along with ATP) through the noncyclic fom of photophosphorylation during the light-reactions of photosynthesis (image Z-scheme). A photon is absorbed by Photosystem II and the two resultant excited electrons are passed to Photosystem I, which employs a second photon to further boost their energy for the overall reaction: NADP⁺ + H⁺ + 2e^- → NADPH. Non-phototrophic organisms manufacture NADH during oxidative phosphorylation, where NADH & FADH2, the energy carrier molecules generated by the citric acid cycle enter an electron transfer chain that generates a proton gradient by pumping protons (H⁺) across the membrane. Glycolysis generates the energy carrier molecules ATP and NADH in addition to intermediates (3-C or 6-C) for biosynthetic pathways.

Nicotinamide adenine dinucleotide phosphate (NADP) is employed in anabolic reactions, such as fatty acid biosynthesis and nucleic acid synthesis, which require NADPH as a reducing agent.

In chloroplasts, the light-reactions of noncyclic photophosphorylation produce both ATP and NADPH, which act as energy-transfer, reducing agents in the light-independent (“dark”) reactions of the Calvin cycle.

MH2 + NAD⁺ → NADH + H⁺ + M: + energy, where M is a metabolite.

Two hydrogen ions (a hydride ion and an H⁺ ion) are transferred from the metabolite. One electron is transferred to the positively-charged nitrogen, and one hydrogen attaches to the carbon atom opposite to the nitrogen.

NAD is synthesized from the vitamin niacin in the form of nicotinic acid or nicotinamide. At right is adenine.

Left: space fill molecule of NADH

C black : H white : O red : P orange : N blue

oxaloacetate

2006-02-10T01:57:00.000-05:00

oxaloacetate

pyruvate

2006-02-09T01:06:00.000-05:00

Left: pyruvic acid -click to enlarge image.

Pyruvate is the carboxylate anion of the alpha-keto acid. As the output compound of glycolysis, where one molecule of glucose yields 2 pyruvate, pyruvate is an important intermediate in metabolism. Pyruvic acid unites several key metabolic reactions because it can be converted to carbohydrates via gluconeogenesis, to fatty acids, to energy through acetyl-CoA, to the amino acid alanine, and to ethanol.

Provided that sufficient O2 is available, pyruvic acid is converted to acetyl-CoA, which enters the Krebs cycle. Pyruvate is also converted to oxaloacetate in an anaplerotic reaction, and ultimately yields 4 molecules of CO2.

In anaerobic conditions, pyruvic acid is converted to lactic acid and ethanol by plants. Pyruvate generated by glycolysis is converted by anaerobic respiration (lactate fermentation) to lactate using the enzyme lactate dehydrogenase and the coenzyme NADH. Pyruvate is converted, in alcoholic fermentation, to acetaldehyde and then to ethanol.

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