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    Biology Molecule Essay (2035 words)

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    Unit 1 – Man is approximately 50-60% water. The distribution of water in the body is divided into three compartments: 1) intracellular – 28 liters, 2) intercellular/interstitial fluid – 11 liters (80%), and 3) blood plasma – 3 liters (20%). Women generally contain less water than men. Organisms can contain anywhere from 60-80% water, while bacteria have a lot of water and fat cells have very little. Water’s properties result from its structure and molecular interactions. Water is polar due to its polar covalent bonds and asymmetrical shape, which give it opposite charges on opposite sides. Electrons spend more time around oxygen, giving hydrogen a slight positive charge. Hydrogen bonds form between the oxygen of one molecule and the hydrogen of another. Cohesion is the substance being held together by hydrogen bonds. Hydrogen bonds are transient, but enough is always held together to give water more structure than almost any other liquid. Beads and meniscus are formed by cohesion and also help upward transport of water in plants. Adhesion counteracts the downward pull of gravity. Water has greater surface tension than most liquids because surface molecules are hydrogen bonded to molecules below and around them. Surface tension can hinder life, such as beading in the alveoli of lungs, but surfactants can be used to counteract this. Water has a high specific heat, which allows it to resist extreme temperature changes. It also has a high heat of vaporization, which causes it to require a lot of energy to change states. When sweating, heat energy is utilized to change states from liquid to gas, causing a drop in temperature. As a solid, water is less dense than as a liquid and will float. Charged regions of molecules have an electrical attraction to charged ions. Water surrounds ions, separating and shielding them from one another. Polar compounds are generally soluble, and charged regions of water are attracted to oppositely charged regions of other polar molecules. Polar molecules are miscible in other polar liquids. Most water molecules don’t dissociate (~1/554 million do). The hydrogen atom in the hydrogen bond between the two water molecules may shift from the oxygen atom it is covalently bonded to the unshared orbitals of the oxygen that it is hydrogen bonded to. The hydrogen ion is transferred, creating a hydronium ion and leaving a hydroxide ion. The solvent is water itself, and at equilibrium, water is not dissociated. At equilibrium in pure water at 25°C, [H+] = [OH-], and the pH of this solution is 7 (neutral). A high pH means low acidity. Acids are substances that increase the relative [H+] and remove OH-, because it tends to combine with H+ to form water. If [H+] * [OH-], it is acidic and has a pH between 0 and 7. Bases are substances that reduce the relative [H+] in a solution and may increase the [OH]. If [H+] * [OH-], it is basic and has a pH greater than 7. Buffers are important in the body to keep the pH range between 6 and 8, and the pH of blood is between 7.34 and 7.

    44 – Mustn’t shift below 7.2 or acidosis will occur. Some body zones may have a pH as low as 0.5 or as high as 10. Buffers minimize sudden changes and are a combination of hydrogen donors and hydrogen acceptors. Ions are accepted when in excess and donated when in short supply. In biological systems, an example is the bicarbonate buffer. In response to a rise in pH, the carbonic acid dissociates to form a carbonate ion and a hydrogen proton. If there is a drop, it is reversed (pH up = to the right, pH down = to the left). Equilibrium is established, but it is always moving to the left or the right. A balance is the optimum pH. Other body buffers include protein molecules which donate and accept amino acids to stabilize pH. Most of the rest of organisms is made up of carbon-based compounds like carbs, lipids, proteins, nucleic acids. Carbon compounds are known as organic. Vitalism is the belief in a life force outside the control of chemical laws. This has been disproved as water, ammonia, hydrogen, and methane have been combined in a lab to form organic substances. C+O+H = carbohydrates. C+H+N = amino acids, urea, proteins, lipids. Carbon atoms are the most versatile building blocks. Each has 4 valences where bonds can form. Carbon chains form the skeleton of most organic molecules. They may be straight or branched, long or short, or in closed rings. Hydrocarbons contain only hydrogen and carbon. They form when organic matter decomposes and functional groups break off, leaving a skeleton. Hydrocarbon chains, branches, and rings can be modified by other elements which are joined on in a particular matter. These are components of organic molecules that are often involved in chemical reactions. They replace 1 or more hydrogens in a hydrocarbon.

    Carbohydrates: sugars and starches. Nonsugars include plant starch, animal starch, cellulose, and chitin. They come from pasta, rice, flour, fruit, and syrups. They are an important source of energy, can be oxidized to release energy, and improve your mood. They contain C, H, and O, with generally 2 times as much H as O. Sugar names usually end with -ose and are named depending on the number of carbons in them (e.g. triose, pentose). 6 carbon sugars, hexoses, are most important. The general formula is C6H12O6, and in living systems, the state is aqueous. Solids exist in chains, and liquids as rings. The molecular formula is the same for different hexoses, but the structural formula differs. Other isomers of glucose can be reorganized by cells into alpha glucose, and then oxidized. Glucose is the major nutrient for cells, and its carbon skeleton is raw material for the synthesis of other organics.

    Disaccharides: 2 hexose sugars. The most common are sucrose, lactose, and maltose. Glucose + glucose = maltose + water. Glucose + fructose = sucrose + water. Glucose + galactose = lactose + water. This process is known as condensation or dehydration synthesis. Synthesis of disaccharides doesn’t happen in the human body, but usually, they are eaten and digested, through a process known as hydrolysis or disaccharidases.

    Polysaccharides: These are macromolecules that are made by condensation when monosaccharides are joined. The general molecular formula is C6H12O5. Common polysaccharides are amylose, amylopectin (plant starch), glycogen (animal starch), cellulose (cell wall material), and chitin (leathery covering of invertebrates). Plants use glucose to grow, and extra is stored in the roots in a soluble form which is then reactivated in the spring. This reactivates the growing process year after year. Animal starch is stored in special cells (the average person has a 24-hour supply) and can readily be converted into glucose for use. Cellulose and chitin are structural carbohydrates. Amylose is formed when glucose molecules join in a 1-4 linkage pattern. The first carbon of one glucose links to the fourth carbon of another. This is a covalent bond or a glycosidic link. The bond is angular and forms a spiral called an alpha helix. If it branches, amylopectin is formed. Cellulose is a 1-4 linkage of beta glucose. This creates a straight strand and not a helix. These bonds are rigid and require special enzymes (cellulase) to break them. The position of the beta glucose molecules alternates.

    Lipids: Humans rarely eat pure lipids. Cell membranes are primarily lipid, and lipids can easily enter cells, carrying a food’s flavor with them. A diet should have less than 30% fat, 55-65% carbs, and 10-15% protein. Lipids are important as a source of energy, insulation (adipose tissue), cushions for the internal organs, as a lubricant, as an emulsifying agent (cholesterol in bile), as a structural component of cells (1/6 of the brain is fat), cholesterol as a precursor molecule for vitamin D, cortisone, testosterone, progesterone, and estrogen. Lipids are the simplest biological molecules and are composed mostly of C, H, and a few Os. They are energy-rich because of the high C to H ratio. Fat consists of a glycerol molecule connected by ester bonds to a 3 fatty acid molecule (this is a triglyceride). If the bonds between the carbons are single bonds, the fatty acid is saturated (fat formed is a saturate). If they have multiple bonds, it is an unsaturated fat. A polysaturate is more than one fatty acid held together by single bonds. Multiple bonds can be broken, and extra hydrogens added through hydrogenation. Short-chained fats of unsaturated fatty acids are soft with a low boiling point.

    Long-chained fats of saturated fatty acids are harder with a high boiling point. The length of chains affects boiling point the most. To make an oil from a solid, you must hydrogenate it. Saturated fatty acids can be converted to the steroid cholesterol. Triglycerides are monitored more closely in the blood than cholesterol. The amount of saturates converted to cholesterol is genetic. Abnormal genes can cause excessive production (1 gene = severe heart disease, 2 = shortened life span). The liver produces cholesterol. Steroids have a 5-ring shape. Examples are androgens, estrogens, and cortisone. There are 20 amino acids, 8 of which are essential and can be converted into any of the other 12. Protein-rich foods are digested into amino acids, and the body absorbs them to make their own proteins. Liver cells convert them into absent aminos = transamination. Proteins are synthesized on ribosomes in the cytoplasm of cells or on polysomes (ribosome chains). DNA codes proteins by copying its info onto a shorter strand known as mRNA (m = a message to synthesize a protein). The message is received, and a protein is synthesized. For synthesis, all 20 are required. The number, sequence, and type of amino acids making up the protein are the primary structure. This is determined by DNA. Secondary structure is the coiling or pleating of amino acid chains, caused by rigid peptide bonds that are bent by strong intermolecular attraction between hydrogens and oxygens of every fourth amino. This results in a regular, repeating twist or an alpha helix. Chains lie parallel to one another and form hydrogen bonds between themselves. This is a beta sheet but is not very common. Secondary structure is determined by intermolecular bonds. Tertiary structure refers to the folds in the coiled chain. This is called by a thiol called cysteine. This can form a bridge when it meets another cysteine. When 2 cysteines meet, a disulfide link is formed. Insulin has 6 cysteine amino acids and forms 3 bridges and a slightly globular protein. The more cysteine amino acids there are, the more folds or joints that result, and the more globular the protein is. Globular proteins are the doers” that function because they have a particular shape due to the cysteine-cysteine sulfur bridges. Some proteins may be a bunch of polypeptide chains close together. This is quaternary structure, which very few proteins have. All proteins have a primary and secondary structure, but few have a tertiary structure, and even fewer a quaternary. Proteins can be 50-50,000 amino acids long. Amino acids are joined by peptide bonds, a covalent bond between the C of one amino acid and the N of a neighbor. A polypeptide chain is a string of aminos not long enough to be a protein. Amino acids are so named because of their two functional groups, the amine group and the carboxylic acid group. All living cells contain DNA and RNA. These carry instructions for making proteins and specify the sequence in which amino acids should be linked together. DNA and RNA are polynucleotides, polymers of nucleotides. Nucleotides consist of a phosphate group + a pentose + a nitrogenous base. They can be linked together by condensation to form a polynucleotide. If a nucleotide contains ribose, it becomes Ribo Nucleic Acid. These are always just a single strand but may be looped into 3-dimensional shapes. If the nucleotide contains deoxyribose, Deoxyribo Nucleic Acid results. DNA molecules are far longer than RNA molecules and can never contain Uracil. 4 possible bases are adenine, guanine, cytosine, and thymine. DNA molecules contain two polynucleotide strands, held together by hydrogen bonds between the bases. Hydrogen bonds can only be formed between specific base pairs: Adenine – Thymine, Cytosine – Guanine. A sense strand is a sequence of bases that tells the order in which to string together the amino acids. A length of DNA coding the sequence for a polypeptide is called a gene. Three bases, a codon, specify an amino acid. There are 64 possible arrangements of bases in a codon. Polypeptides are made when 2 strands of DNA split up, and an RNA molecule builds up against the sense strand. The base sequence of RNA must match that of the DNA molecule. A complete RNA molecule then peels off and travels to the location where polypeptides are made. The sequence of bases on a DNA molecule is the same for a human or a bacterium. A slightly different version of one of the nucleotides that forms RNA is ATP. ATP contains ribose, adenine, and 3 phosphate groups instead of 1. Phosphate groups may be lost one at a time to make ADP (di) or AMP (mono). All living cells make ATP as an energy currency; it is produced constantly. ATP molecules usually last less than a minute before being broken down. 40 kg is produced in a day. If a cell needs energy, it hydrolyzes ATP and releases energy in small packets. NAD contains ribose sugar, adenine, and 2 nucleotides. One nucleotide does not contain any of the 5 bases but instead a nicotinamide ring. They can accept hydrogens and become NADH. Hydrogens are accepted or passed on during respiration or photosynthesis.

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