Agriculture
Water, ions, salts, and gases all are types of inorganic molecules that are essential to cellular function. The chemical properties of water make it an ideal solvent and buffer for the chemistry that occurs inside cells.
The capillary action that helps water travel up plant tissues from the roots is a direct consequence of the polarity of the water molecule.
The chemistry of life on earth is carbon and water chemistry. Water is the most abundant compound in living cells and makes up as much as 90 percent of the weight of most plant tissues. Many of the molecules that are part of larger macro molecules in cells are linked together chemically by dehydration synthesis, or the loss of water.
These macromolecules are broken up into their component units by the addition of a water molecule between the units, a process known as hydrolysis. The chemical properties of water make it an ideal solvent and buffer for the chemistry that occurs inside cells.
Because the electrons of the covalent bonds within the water molecule are more often orbiting the oxygen atom, the oxygen atom gains a slightly negative charge.
The hydrogen atoms are slightly positive. This separation of charge across the water molecule is said to make it polar. Because of its polar nature,water is able to dissolve, or ionize, a variety of molecules. This gives water its buffering capacity.
Water molecules are attracted to one another because of this polarity. This weak attraction, which occurs in the form of hydrogen bonds, has great chemical consequences when many molecules of water are involved.
Hydrogen bonding allows water to have surface tension. The capillary action that helps water travel up plant tissues from the roots is a direct consequence of the polarity of the water molecule.
Water is also able to absorb heat without vaporizing (changing from a liquid to a gas state) quickly. Therefore, physiological temperatures can be maintained as water molecules absorb the heat from metabolic reactions.
Water, ions, salts, and gases all are types of inorganic molecules that are essential to cellular function. Inorganic molecules are chemical molecules that do not contain carbon. The remainder of the molecules within cells are built around the unique properties of the carbon atom and are called organic molecules.
Organic Macromolecules
There are four major classes of organic molecules in cells: carbohydrates, lipids, nucleic acids, and proteins. All of these molecules contain carbon backbones, and almost all of them contain oxygen and hydrogen as well as other elements.
Some or all of the members of each class of organic molecules occur as very large molecules, called macromolecules, that are polymers of smaller molecules joined together by covalent bonds.
For example, starch and cellulose are carbohydrate polymers of simpler carbohydrates called sugars. Likewise, fats and oils are lipid polymers composed of smaller lipids called fatty acids and the sugar alcohol called glycerol.
Carbohydrates
Carbohydrates are molecules that consist of primarily carbon, hydrogen, and oxygen atoms. Carbohydrates are the primary source of stored energy in most living organisms. They can also serve as structural molecules in cell walls and as markers on some cell membranes, identifying different types of cells.
Simple sugars, or monosaccharides, are sugars that are small molecules composed of a chain of covalently bonded carbon atoms with associated hydrogen and oxygen atoms.
These molecules always have a ratio of one carbon atomto two hydrogen atoms to one oxygen atom(CH2O). The monosaccharide glucose is the primary sugar produced from simpler sugars made in photosynthesis.
When two simple sugars are covalently linked together, they form a disaccharide. In plants, the disaccharide sucrose, which is composed of one fructose molecule and one glucose molecule, is the most common sugar. Sucrose is the same thing as so-called table sugar, which is harvested from sugar cane or sugar beets.
Many sugars can be linked together to form a carbohydrate polymer, or polysaccharide. Starch is composed of many glucose molecules linked together and is the major form of carbohydrate storage in plants.
When energy is required, the individual sugars of the polysaccharides are hydrolyzed (broken down to simpler molecules), and the glucose that is released is used by the mitochondria to generate energy.
Polysaccharides are also important structural molecules in plants. Themost abundant polysaccharide in nature is cellulose, another polymer of glucose and a major component of plant cell walls.
Lipids
Lipids are diverse group of unrelated molecules which includes fats, oils, steroids and sterols, waxes, and other water-insoluble molecules.
Lipids are characterized by their hydrophobic, or ?water-fearing,? chemical behavior, which is what makes them insoluble in water. Unlike other molecules that ionize and are dissolved by water, lipid molecules are nonpolar.
They are repelled by the polar nature of water and tend to aggregate in aqueous solutions. Lipids also are used to store energy and are especially abundant in seeds because lipids contain more energy by weight than carbohydrates.
Examples of lipids commonly found in biological systems include fats and oils that are storage molecules known as triglycerides. A triglyceride consists of glycerol (a three-carbon molecule) and three fatty acid molecules, long-chain hydrocarbon molecules that are attached to each of the three glycerol-carbon atoms by ester linkages.
The long chain of carbon atoms of the fatty acid can be saturated or unsaturated with respect to hydrogen content. Saturated fatty acids contain as many hydrogen atoms as allowed bonded to each carbon atom. Saturated fats tend to be solid at room temperature and include substances such as butter and lard.
Unsaturated fatty acids do not have the maximum number of hydrogen atoms because some of the carbon atoms form double bondswith adjacent carbon atoms in the chain. Unsaturated fats tend to be liquid at room temperature and include substances such as corn oil and olive oil.
Plants have many lipids that are unique to them. For instance, cutin and suberin are two lipid polymers that form structural components of many plant cell walls.
These two molecules form a mesh work that secures another type of lipid polymer found in plants, wax. Waxes are long-chain lipid compounds that are integrated into the cutin and suber in mesh work and are important in preventing water loss for plants. Waxes give apple peels their characteristic shiny appearance.
Phospholipids are a type of lipid molecule that is found in all living organisms. They are structurally similar to triglycerides, except instead of having three fatty acids attached to glycerol, they have only two.
Replacing the third fatty acid is a charged phosphate group. This unique structure results in one end of the molecule being hydrophilic (the phosphate end, often called the head) and the other being hydrophobic (the end with the two fatty acids, often called the tail).
Consequently, phospholipids will spontaneously form an oily layer at the water surface, orienting their charged phosphate heads toward the water and their fatty acid tails away fromthewater and toward the air. This is the basis for the phospholipid bilayer structure that underlies the formation of all cellular membranes.
In the case of a lipid bilayer, because there is water on both sides, the two layers are tail to tail, with their heads oriented to the inside and outside of the membrane, where they come into contact with water.
Nucleic Acids
The information that directs all cellular activity is containedwithin the chemical structure of the nucleic acids. Nucleic acids are polymers of smaller molecules called nucleotides.
Nucleotides, in turn, are composed of three types of covalently linked molecules: a ribose sugar, a phosphate group, and a nitrogen-containing base. The two major nucleotides that are found in cells are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).
DNA contains the genetic information that directs the development and activity of the organism. In eukaryotic cells DNA resides in the nucleus in linear molecules of repeating nucleotide units, although there are circular molecules of DNA found in the mitochondria and chloroplasts of eukaryotic cells.
DNA nucleotides are composed of a fivecarbon deoxyribose sugar, a phosphate group, and one of four possible bases: adenine (A), thymine (T), cytosine (C), and guanine (G). The information of the DNA molecule is found in the sequence of the nitrogenous bases along its length.
Any region of DNA that directs a cellular function or encodes another molecule is called a gene. Not all DNA regions encode proteins. Some regions encode the instructions for RNA molecules that are used as catalysts and for protein synthesis reactions.
Some genes are regulatory, controlling the time and place where certain genes are expressed. In many eukaryotes, genes only account for 10 percent of the DNA. Although some of the remaining 90 percent carries various structural functions, most of it is of uncertain function.
In 1953 Francis Crick and James Watson constructed a molecular structure for the DNA molecule, relying heavily on the experimental data generated by Rosalind Franklin. The structure they proposed,which has since been supported by additional experimental data, was that of a double helix.
The DNA molecule can be envisioned as a ladder. The sugars and phosphates of the nucleotides alternate with each other to formthe backbone, the outside vertical support, and the bases form the individual rungs of the ladder.
The ladder is twisted to create a helical structure. DNA can exist as single strands and in other confirmations in the cell, but the ?B-form? of the DNA double helix is the most common form in the cell.
RNA molecules are also polymers of nucleotides, but the nucleotides of the RNAmolecule differ slightly from those of the DNAmolecule. RNA nucleotides contain a five-carbon ribose sugar, a phosphate group, and one of four bases. Three of the four bases are the same as found in DNA: adenine, guanine, and cytosine. Instead of thymine, RNA uses the base uracil.
RNA bases can pair in essentially the same way as DNA bases, but most often RNA exists as single-stranded molecules in cells. These long strands of RNA can often pair with other bases in short regions, causing the RNA to fold up into highly complex, three-dimensional structures important for RNA function.
RNAis found throughout cells. Messenger RNA (mRNA) is made by the cell using the DNA sequence in genes as a template for making a complementary strand of RNA in a process called transcription.
In After being transcribed and modified in certain complex ways, most mRNA is transported to the cytoplasm where it is used to direct the synthesis of proteins.
Ribosomal RNA (rRNA) is a major component of ribosomes, which are responsible for coordinating protein synthesis, along with transfer RNA (tRNA). Some RNA molecules, like protein molecules, can also catalyze chemical reactions. Catalytic RNA molecules are called ribozymes, and they play roles in gene expression and protein synthesis.
Single nucleotides and compounds that are made fromthemare involved inmany cellular processes. The universal unit of ?energy currency? in the cell is adenosine triphosphate (ATP).
Guanosine triphosphate (GTP) is amolecule that is involved in relaying signals received at the cell membrane to the nucleus of the cell. Compounds, such as NADH and NADPH, that are involved in metabolic reactions in themitochondria and in energy capture reactions in the chloroplasts also contain nucleotides.
Proteins
Protein molecules are large, complex molecules with a huge variety of structures and functions within cells. Most chemical reactions in cells are catalyzed by proteins called enzymes.
Proteins form the basis of the cytoskeleton of cells, providing structure andmotility. Proteins are also essential for the communication between cells and within cells. In plants, the largest concentration of proteins can be found in some seeds.
Proteins are polymers of nitrogen-containing molecules called amino acids. The amino acids are much simpler molecules than the nitrogenous bases found in nucleic acids. The same twenty amino acids is are used in the manufacture of proteins in the cells of all living organisms.
An amino acid is built around a single carbon atomcalled the alpha carbon. Bonded to the alpha carbon are a hydrogen atom(H), a carboxyl group (COOH), and an amino group that contains nitrogen (NH2).
A specialized ?R? group is attached at the last site. The R-groups are different for each of the twenty amino acids, and their chemical properties, such as charge, hydrophilic or hydrophobic nature, and size, dictate protein function and shape.
The order and number of amino acids that are linked together to form a protein are determined by the order of the codons in the DNA that encode that protein.
The order and number of the amino acids in a protein is called the primary structure, and it ultimately determines the shape of the protein. Proteins can have secondary structures formed by hydrogen bonding between the peptide bonds that link the amino acids together.
The two common secondary structures in proteins are the alpha helix and the beta pleated sheet. The amino acid chain (also called a peptide chain) can fold up on itself to form globular structures. This is known as tertiary structure.
Tertiary structure is determined by the number and order of amino acids in the protein and is formed when molecules in the R-groups of the amino acids interact with one another. When two or more peptide chains interact to form a single functional molecule, the protein is said to have quaternary structure.
- Carbohydrates
Common organic chemicals found in all living organisms, important in energy metabolism and structural polymers, carbohydrate molecules are made up of carbon, hydrogen, and oxygen. Carbohydrates are made of carbon, hydrogen, and oxygen molecules in a...
- Genetic Code
Genetic Code The genetic code defines each amino acid in a protein, or polypeptide, in terms of a specific sequence of three nucleotide called codons, in the DNA. The genetic code is therefore the key to converting the information contained in genes int...
- Lipids
LipidsLipids are a diverse group of compounds sharing the common property of being hydrophobic (insoluble in water). Lipids include fatty acids, fats, oils, steroids (sterols), waxes, cutin, suberin, glycerophospholipids (phospholipids), glyceroglycolipids...
- Nucleic Acids
Nucleic acids are the genetic material of cells, including DNA and the various types of RNA. Nucleic acids were discovered in the mid-nineteenth century, but their role as genetic material was not substantiated until the mid twentieth century. When chromosomes...
- Proteins And Amino Acids
Proteins and Amino AcidsProteins are found in all cells and carry out a variety of important cellular functions. Within any one cell there may be thousands of different proteins having a variety of sizes, structures, and functions. Proteins are also important...
Agriculture
Plant Cells, Molecular Level
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| Plant Cells, Molecular Level |
The capillary action that helps water travel up plant tissues from the roots is a direct consequence of the polarity of the water molecule.
The chemistry of life on earth is carbon and water chemistry. Water is the most abundant compound in living cells and makes up as much as 90 percent of the weight of most plant tissues. Many of the molecules that are part of larger macro molecules in cells are linked together chemically by dehydration synthesis, or the loss of water.
These macromolecules are broken up into their component units by the addition of a water molecule between the units, a process known as hydrolysis. The chemical properties of water make it an ideal solvent and buffer for the chemistry that occurs inside cells.
Because the electrons of the covalent bonds within the water molecule are more often orbiting the oxygen atom, the oxygen atom gains a slightly negative charge.
The hydrogen atoms are slightly positive. This separation of charge across the water molecule is said to make it polar. Because of its polar nature,water is able to dissolve, or ionize, a variety of molecules. This gives water its buffering capacity.
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Water molecules are attracted to one another because of this polarity. This weak attraction, which occurs in the form of hydrogen bonds, has great chemical consequences when many molecules of water are involved.
Hydrogen bonding allows water to have surface tension. The capillary action that helps water travel up plant tissues from the roots is a direct consequence of the polarity of the water molecule.
Water is also able to absorb heat without vaporizing (changing from a liquid to a gas state) quickly. Therefore, physiological temperatures can be maintained as water molecules absorb the heat from metabolic reactions.
Water, ions, salts, and gases all are types of inorganic molecules that are essential to cellular function. Inorganic molecules are chemical molecules that do not contain carbon. The remainder of the molecules within cells are built around the unique properties of the carbon atom and are called organic molecules.
Organic Macromolecules
There are four major classes of organic molecules in cells: carbohydrates, lipids, nucleic acids, and proteins. All of these molecules contain carbon backbones, and almost all of them contain oxygen and hydrogen as well as other elements.
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| Organic Macromolecules |
Some or all of the members of each class of organic molecules occur as very large molecules, called macromolecules, that are polymers of smaller molecules joined together by covalent bonds.
For example, starch and cellulose are carbohydrate polymers of simpler carbohydrates called sugars. Likewise, fats and oils are lipid polymers composed of smaller lipids called fatty acids and the sugar alcohol called glycerol.
Carbohydrates
Carbohydrates are molecules that consist of primarily carbon, hydrogen, and oxygen atoms. Carbohydrates are the primary source of stored energy in most living organisms. They can also serve as structural molecules in cell walls and as markers on some cell membranes, identifying different types of cells.
Simple sugars, or monosaccharides, are sugars that are small molecules composed of a chain of covalently bonded carbon atoms with associated hydrogen and oxygen atoms.
These molecules always have a ratio of one carbon atomto two hydrogen atoms to one oxygen atom(CH2O). The monosaccharide glucose is the primary sugar produced from simpler sugars made in photosynthesis.
When two simple sugars are covalently linked together, they form a disaccharide. In plants, the disaccharide sucrose, which is composed of one fructose molecule and one glucose molecule, is the most common sugar. Sucrose is the same thing as so-called table sugar, which is harvested from sugar cane or sugar beets.
Many sugars can be linked together to form a carbohydrate polymer, or polysaccharide. Starch is composed of many glucose molecules linked together and is the major form of carbohydrate storage in plants.
When energy is required, the individual sugars of the polysaccharides are hydrolyzed (broken down to simpler molecules), and the glucose that is released is used by the mitochondria to generate energy.
Polysaccharides are also important structural molecules in plants. Themost abundant polysaccharide in nature is cellulose, another polymer of glucose and a major component of plant cell walls.
Lipids
Lipids are diverse group of unrelated molecules which includes fats, oils, steroids and sterols, waxes, and other water-insoluble molecules.
Lipids are characterized by their hydrophobic, or ?water-fearing,? chemical behavior, which is what makes them insoluble in water. Unlike other molecules that ionize and are dissolved by water, lipid molecules are nonpolar.
They are repelled by the polar nature of water and tend to aggregate in aqueous solutions. Lipids also are used to store energy and are especially abundant in seeds because lipids contain more energy by weight than carbohydrates.
Examples of lipids commonly found in biological systems include fats and oils that are storage molecules known as triglycerides. A triglyceride consists of glycerol (a three-carbon molecule) and three fatty acid molecules, long-chain hydrocarbon molecules that are attached to each of the three glycerol-carbon atoms by ester linkages.
The long chain of carbon atoms of the fatty acid can be saturated or unsaturated with respect to hydrogen content. Saturated fatty acids contain as many hydrogen atoms as allowed bonded to each carbon atom. Saturated fats tend to be solid at room temperature and include substances such as butter and lard.
Unsaturated fatty acids do not have the maximum number of hydrogen atoms because some of the carbon atoms form double bondswith adjacent carbon atoms in the chain. Unsaturated fats tend to be liquid at room temperature and include substances such as corn oil and olive oil.
Plants have many lipids that are unique to them. For instance, cutin and suberin are two lipid polymers that form structural components of many plant cell walls.
These two molecules form a mesh work that secures another type of lipid polymer found in plants, wax. Waxes are long-chain lipid compounds that are integrated into the cutin and suber in mesh work and are important in preventing water loss for plants. Waxes give apple peels their characteristic shiny appearance.
Phospholipids are a type of lipid molecule that is found in all living organisms. They are structurally similar to triglycerides, except instead of having three fatty acids attached to glycerol, they have only two.
Replacing the third fatty acid is a charged phosphate group. This unique structure results in one end of the molecule being hydrophilic (the phosphate end, often called the head) and the other being hydrophobic (the end with the two fatty acids, often called the tail).
Consequently, phospholipids will spontaneously form an oily layer at the water surface, orienting their charged phosphate heads toward the water and their fatty acid tails away fromthewater and toward the air. This is the basis for the phospholipid bilayer structure that underlies the formation of all cellular membranes.
In the case of a lipid bilayer, because there is water on both sides, the two layers are tail to tail, with their heads oriented to the inside and outside of the membrane, where they come into contact with water.
Nucleic Acids
The information that directs all cellular activity is containedwithin the chemical structure of the nucleic acids. Nucleic acids are polymers of smaller molecules called nucleotides.
Nucleotides, in turn, are composed of three types of covalently linked molecules: a ribose sugar, a phosphate group, and a nitrogen-containing base. The two major nucleotides that are found in cells are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).
DNA contains the genetic information that directs the development and activity of the organism. In eukaryotic cells DNA resides in the nucleus in linear molecules of repeating nucleotide units, although there are circular molecules of DNA found in the mitochondria and chloroplasts of eukaryotic cells.
DNA nucleotides are composed of a fivecarbon deoxyribose sugar, a phosphate group, and one of four possible bases: adenine (A), thymine (T), cytosine (C), and guanine (G). The information of the DNA molecule is found in the sequence of the nitrogenous bases along its length.
Any region of DNA that directs a cellular function or encodes another molecule is called a gene. Not all DNA regions encode proteins. Some regions encode the instructions for RNA molecules that are used as catalysts and for protein synthesis reactions.
Some genes are regulatory, controlling the time and place where certain genes are expressed. In many eukaryotes, genes only account for 10 percent of the DNA. Although some of the remaining 90 percent carries various structural functions, most of it is of uncertain function.
In 1953 Francis Crick and James Watson constructed a molecular structure for the DNA molecule, relying heavily on the experimental data generated by Rosalind Franklin. The structure they proposed,which has since been supported by additional experimental data, was that of a double helix.
The DNA molecule can be envisioned as a ladder. The sugars and phosphates of the nucleotides alternate with each other to formthe backbone, the outside vertical support, and the bases form the individual rungs of the ladder.
The ladder is twisted to create a helical structure. DNA can exist as single strands and in other confirmations in the cell, but the ?B-form? of the DNA double helix is the most common form in the cell.
RNA molecules are also polymers of nucleotides, but the nucleotides of the RNAmolecule differ slightly from those of the DNAmolecule. RNA nucleotides contain a five-carbon ribose sugar, a phosphate group, and one of four bases. Three of the four bases are the same as found in DNA: adenine, guanine, and cytosine. Instead of thymine, RNA uses the base uracil.
RNA bases can pair in essentially the same way as DNA bases, but most often RNA exists as single-stranded molecules in cells. These long strands of RNA can often pair with other bases in short regions, causing the RNA to fold up into highly complex, three-dimensional structures important for RNA function.
RNAis found throughout cells. Messenger RNA (mRNA) is made by the cell using the DNA sequence in genes as a template for making a complementary strand of RNA in a process called transcription.
In After being transcribed and modified in certain complex ways, most mRNA is transported to the cytoplasm where it is used to direct the synthesis of proteins.
Ribosomal RNA (rRNA) is a major component of ribosomes, which are responsible for coordinating protein synthesis, along with transfer RNA (tRNA). Some RNA molecules, like protein molecules, can also catalyze chemical reactions. Catalytic RNA molecules are called ribozymes, and they play roles in gene expression and protein synthesis.
Single nucleotides and compounds that are made fromthemare involved inmany cellular processes. The universal unit of ?energy currency? in the cell is adenosine triphosphate (ATP).
Guanosine triphosphate (GTP) is amolecule that is involved in relaying signals received at the cell membrane to the nucleus of the cell. Compounds, such as NADH and NADPH, that are involved in metabolic reactions in themitochondria and in energy capture reactions in the chloroplasts also contain nucleotides.
Proteins
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| running your car on water |
Proteins form the basis of the cytoskeleton of cells, providing structure andmotility. Proteins are also essential for the communication between cells and within cells. In plants, the largest concentration of proteins can be found in some seeds.
Proteins are polymers of nitrogen-containing molecules called amino acids. The amino acids are much simpler molecules than the nitrogenous bases found in nucleic acids. The same twenty amino acids is are used in the manufacture of proteins in the cells of all living organisms.
An amino acid is built around a single carbon atomcalled the alpha carbon. Bonded to the alpha carbon are a hydrogen atom(H), a carboxyl group (COOH), and an amino group that contains nitrogen (NH2).
A specialized ?R? group is attached at the last site. The R-groups are different for each of the twenty amino acids, and their chemical properties, such as charge, hydrophilic or hydrophobic nature, and size, dictate protein function and shape.
The order and number of amino acids that are linked together to form a protein are determined by the order of the codons in the DNA that encode that protein.
The order and number of the amino acids in a protein is called the primary structure, and it ultimately determines the shape of the protein. Proteins can have secondary structures formed by hydrogen bonding between the peptide bonds that link the amino acids together.
The two common secondary structures in proteins are the alpha helix and the beta pleated sheet. The amino acid chain (also called a peptide chain) can fold up on itself to form globular structures. This is known as tertiary structure.
Tertiary structure is determined by the number and order of amino acids in the protein and is formed when molecules in the R-groups of the amino acids interact with one another. When two or more peptide chains interact to form a single functional molecule, the protein is said to have quaternary structure.
- Carbohydrates
Common organic chemicals found in all living organisms, important in energy metabolism and structural polymers, carbohydrate molecules are made up of carbon, hydrogen, and oxygen. Carbohydrates are made of carbon, hydrogen, and oxygen molecules in a...
- Genetic Code
Genetic Code The genetic code defines each amino acid in a protein, or polypeptide, in terms of a specific sequence of three nucleotide called codons, in the DNA. The genetic code is therefore the key to converting the information contained in genes int...
- Lipids
LipidsLipids are a diverse group of compounds sharing the common property of being hydrophobic (insoluble in water). Lipids include fatty acids, fats, oils, steroids (sterols), waxes, cutin, suberin, glycerophospholipids (phospholipids), glyceroglycolipids...
- Nucleic Acids
Nucleic acids are the genetic material of cells, including DNA and the various types of RNA. Nucleic acids were discovered in the mid-nineteenth century, but their role as genetic material was not substantiated until the mid twentieth century. When chromosomes...
- Proteins And Amino Acids
Proteins and Amino AcidsProteins are found in all cells and carry out a variety of important cellular functions. Within any one cell there may be thousands of different proteins having a variety of sizes, structures, and functions. Proteins are also important...