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Chapter 5 The structure and function of large biological molecules…

- - - - Ex 1.- A protein may consist of thousands of atoms that form a molecular colossus with a mass well over 100,000 Daltons.
      - Considering the size and complexity of macromolecules, it is noteworthy that biochemist have determined the detailed structure of so many of them.
        
        The architecture of a large biological molecule plays an essential role in its function.
        
        Ex 1.- Water and other simple organic molecules, large biological molecules exhibit unique emergent properties arising from the orderly arrangement of their atoms.
- - - - In the cells, these process are facilitated by Enzymes, specialized macromolecules that speed up chemical reactions .
        
        Monomers are connected by a reaction in which two molecules are covalently bonded to each other, with the loss of a water molecule, which is called Dehydration reactions.
        
        When a bond forms between two monomers, each monomer contributes part if the water molecule that is released during the reaction.
        
        Ex . 1- One monomer provides a hydroxyl group (-OH), while the other provides a hydrogen (-H).
        This reaction is repeated as monomers are added to the chain one by one, making a polymer
        
        Polymers are disassembled to monomer by Hydrolysis, which is the process that is essentially the reverse of the dehydration reaction. ( Hydrolysis means water breakage (from the Greek word hydro, water, and lysis, to break.
        
        The bond between monomers is broken down by the addition of a water molecule, with a hydrogen from water attaching to one monomer and the hydroxyl group attaching to the other.
        
        Ex 1. A good example of hydrolysis within our bodies is the process of digestion.
        1st - The bulk of the organic material in our food is in the form of polymers that are much to large to enter our cells.
        2nd - Within the digestive tract, various enzymes attack the polymers, speeding up hydrolysis.
        3rd - It then releases monomers that then absorbed into the bloodstream for the distribution to all body cells.
        4th - Lastly, Those cells can then be use dehydration reactions to assemble the monomers into new, different polymers that can preform specific functions required by the cell.
  - - - Ex 1.- The inherited differences between close relatives such as human siblings reflect small variations in polymers, particularly DNA and proteins.
      - Molecular differences between unrelated individuals are more extensive, and those between species greater still.(The diversity of macromolecules in the living world is vast, and the possible variety is effectively limitless).
        
        These molecules are constructed from only 40 to 50 common monomers and some others that occur rarely. (Building a huge variety of polymers from such a limited number of monomers is analogous to constructing hundreds of thousands of words from only 26 letters of the alphabet).
        
        The key is arrangement - the particular linear sequence that the units follow. But, this analogy falls short of describing the great diversity of macromolecules. Because most biological polymers have more monomers than the number of letters in a word.
        
        Ex 1.- Proteins, are built from 20 kinds of amino acids arranged in chains that are typically hundreds of amino acids long.
        Ex 2.- The molecular logic of life is simple but elegant: Small molecules that are common to all organisms are ordered into unique macromolecules.
        
        Despite this immense diversity, molecules structure and function can still be grouped roughly by class. ( For each class, the large molecules have emergent properties not found in their individual building blocks).
  - - - The repeating units that serve as the building blocks of a polymer are small molecules called *Monomers ( from the Greek monos, single).*
        (Some monomers also have other function of their own.
- - - - Glucose (C6H12O) the most common monosaccharide, is the central importance in the chemistry of life.
        In the structure of glucose, we can see the trademark of sugar: The molecule has a carboxyl group (CO) and multiple hydroxyl groups (-OH).
        
        Depending on the location of the carboxyl group, as sugar is either an Aldose (Aldehyde), or Ketose (Ketone sugar).Another criterion for classifying sugars is the size of the carbon skeleton, which ranges from 3 to 7 carbons long.
        
        Ex 1.- Glucose; for example is an aldose.
        Fructose; is an isomer of glucose, and its ketose.
        (Most names for sugar end in -ose).
        
        Another source of diversity for simple sugars is in the spatial arrangement of their parts around asymmetric carbon.
        Ex 1.- Glucose and galactose, for example differ only in the placement of parts around one asymmetric carbon.
        (May not seem like much, but just a significant to give them two distinct shapes and binding activities).
        
        Monosaccharides, mostly glucose are major nutrients for cells.
        The process known as cellular respiration, cells extract energy from glucose molecules by breaking them down in a series of reactions.
        
        Simple sugars area major fuel for cellular work, their skeletons also serve as raw material for the synthesis of other types of small organic molecules, such as amino acids and fatty acids.
        (Sugar molecules that are not immediently used in these ways are generally incorporated as monomers into disaccharides or polysaccharides.
        
        A Disaccharide consists of two monosaccharides joined by a Glycosidic linkage. Which is a covalent bond formed between two monosaccharides by dehydration reaction.
        
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  - - - Some serve as a storage material, hydrolyzed as needed to provide sugars for cells. Others serve as building material for structures that protect the cell or the whole organisms.
        (the architecture and function are determined by its sugar monomers and the position of its glycosidic linkage.
      - Storage Polysaccharides
        
        Both plants and animals store sugars for later use in the form of storage polysaccharides.
        (Plants store Strach, a polymer of glucose monomers, as granules with cellular structures known as plastids. Which include chloroplast).
        
        Synthesizing starch enables the plants to stockpile surplus glucose. Because, glucose is a major cellular fuel, starch represents stored energy.
        ( The sugar can later be withdrawn from this carbohydrate "blank" by hydrolysis, which can break the bond between the glucose monomers).
        
        Most of the glucose monomers in starch are joined by 1-4 linkages ( #1 Carbon to # 4 Carbon), like glucose units in maltose.
        Ex 1.- The simplest form of starch, Amylose is unbranched. Amylopectin, a more complex starch is branched with 1-6 linkage at the branch points.
        Ex 2.- Animal store polysaccharides called Glycogen, a polymer or glucose that is like amylopectin but more extensively branched.
        
        Vetabrates store glycogen mainly in the liver and muscles cells. Hydrolysis of glycogen in these cells releases glucose when they demand for sugar increases.(The stored fuel cannot sustain in an animal for long).
        Ex 1.- In humans, glycogen stores are depleted in a about a day unless they are replenished by consumption of food.
      - Structural Polysaccharides
        
        Organisms are built of strong materials from structural polysaccharides.
        The polysaccharides called Cellulose is a major component of the tough walls that enclose plant cells.
        Ex 1. - On a global scale, plants produce almost 10^14 kg ( 10 billion tons)of cellulose per year.
        
        Like starch, cellulose is a polymer of glycose, but the glycosidic linkage in these two polymers are different.
        The difference is based on the fact that there are actually two slightly different rings structures for glucose .
        
        When glucose forms a ring, the hydroxyl group attached to the number 1 Carbon is positioned either below or above the plane of the ring. The two rings forms for glucose are called Alpha, and Beta.
        (In starch, all glucose monomers are in a Alpha configuration).
        
        The differing glycosidic linkage in starch and cellulose gives the two molecules distinct 3-D shapes.
        Cellulose is never branched, and some hydroxyl groups on its glucose monomers are free to hydrogen-bond with the hydroxyl ofnotehr cellulose molecules lying parallel to it.
        
        Enzymes that digest starch by hydrolyzing its Alpha linkages, are unable to hydrolyze the Beta linkage of cellulose due to the different shape these two molecules.
        Although clellulose is not a nutrient for humans, it is an important part of a healthy diet.
        
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- - - - They may have some polar bonds associated with oxygen, lipids consist mostly of hydrocarbon regions. Lipids are varied in form and function. They also include waxes and certain pigments.
  - - - Glyceral is an alcohol; and each of its 3 carbons bears a hydroxyl group. A Fatty acid has a long carbon skeleton, usually 16 or 18 carbons in length.
        The carbon at one end of the skeleton is part of the carboxyl group, the functional group that gives these molecules the name fatty acid.The rest consists of a hydrocarbon chain.
        
        Fats separate from water because the water molecules hydrogen-bond to one another and exclude the fats. In making a fat, three fatty acid molecules are joined to glycerol by an ester linkage. A bond formed by a dehydration reaction between a hydroxyl group and a carboxyl group
        
        The resulting fat, is called Triacylglycerol. Tri meaning 3. The fatty acids in a fat can all be the same, or they can be of two or three different kind.
        The terms saturated fats and unsaturated fats are commonly used in the context of nutrition.
        
        If there are no double bonds between carbon atoms composing a chain, then as many hydrogen atoms as possible are bonded to the carbon skeleton. The resulting fatty acid is therefore called Saturated fatty acids
        
        A fat made from saturated fatty acids is called a saturated fat. Most animal fat are saturated: The hydrocarbon chains of their fatty acid - the "tails" of the fat molecules- lack double bonds, and their flexibility allows the fat molecules to pack together tightly.
        
        A diet rich in saturated fats is one of several factors that may contribute to the cardiovascular disease known as Atherosclerosis.
        These Trans fats may contribute more than saturated fats to atherosclerosis and other problems.
        
        Unsaturated fatty acid has one or more double bonds, with one fewer hydrogen atom on each double-bonded carbon. Nearly all double bonds in naturally occurring fatty acids are cis double bonds, which causes kink in the hydrocarbon chain wherever they occur.
        
        In contrast, the fats of plants and fished are generally unsaturated, meaning they are built of one or more types of unsaturated fatty acids. The kinks where the cis double bonds are located prevent the molecules from packing together closely enough to solidify at room temperature.
        
        The major function of fat is to store energy. The hydrocarbons chains of fats are similar to gasoline molecules and just as rich in energy. A gram of fat stores more than twice as many energy as a gram of polysaccharide, such as starch.
        
        In addition to storing energy, adipose tissue also cushions such vital organs as the kidney, and a layer of fat beneath the skin insulates the body.
        Ex 1.- This subcutaneous layer is especially thick in whales, seals, and other marine life, so they can be protected from the cold water.
  - - - A Phospholipoids is similar to a fat molecule, but has only two fatty acids attached to glycerol rather than three. The third hydroxyl group of glycerol is joined to a phosphate group, which has a negative electrical charge in the cell.
        
        Two ends of the phospholipids show different behavior towards water. The hydrocarbon tails are hydrophobic and are excluded from water. When phospholipids are added to water, they self-assemble into double-layered structures called "bilayers", shielding their hydrophobic portions from water.
        
        The phospholipids are arranged in a similar bilayer. The hydrophobic tails point towards the interior of the bilayer, away from the water.
  - - - Cholesterol a type of steroid is a crucial molecule in animals. It is a common component of animal cell membranes and is also the precursor from which steroids, such as vertebrate sec hormones, are synthesized.
        
        Cholesterol is synthesized in the liver and obtained from their diets. A high level of cholesterol in the blood may contribute to atherosclerosis.
- - - - Enzymatic proteins regulate metabolism by acting as a Catalysts, chemical agents that selectively speed up chemical reactions without being consumed by the reactions.
        Because an enzyme can preform its function over and over again, these molecules can be thought of as workhorses that keep cells running by carrying out the process of life.
        
        The bonds between amino acids is called a peptide bond, so a polymer of amino acids is called Polypeptide.
        A Protein is a biologically functional molecules made up of one or more polypeptides, each folded and coiled into a specific 3-D structure.
  - - - The R group, also called the side chain, differs with each amino acid. Here the amino groups and carboxyl groups are all depicted in ionized form, the way they usually exist at the pH found in cell.
        
        The physical and chemical properties of the side chain determine the unique characteristics of a particular amino acid, thus affecting its functional role in polypeptide.
        
        One group consist of amino acids with nonpolar side chains, which are hydrophobic.
        Another group consists of amino acids with polar side chains, which are hydrophilic.
        Acidic amino acids are those with side chains that are generally negative in charge due to the presence of a carboxyl group, which is usually dissociated at cellular pH.
  - - - Repeating over and over , this process yields a polypeptide, a polymer of many amino acids linked by peptide bonds. The repeating sequence are called Polypeptide backbone.
        
        Extending from this backbone are different side chains (R groups) of the amino acids. Polypeptides range in length from a few amino acids to a thousand or more. (One end of the polypeptide chain has a free amino group, while the opposite end has a free carboxyl group.
        
        A polypeptide of any length has a single amino end (N-terminus) and a single carboxyl end (C-terminus). A polypeptide of any significant size, the side chains far outnumber the terminal groups, so the chemical nature of the molecule as a whole is determined by the kind and sequence of the side chains
        
        Immense variety of polypeptides in nature illustrates an important concept - the cells can make many different polymers by linking a limited set of monomers into divers sequences.
  - - - The person that found this out was Frederick Sanger. With the help of colleagues at Cambridge University, they worked on the hormone insulin in the late 1940s to 1950s.
        
        He used agents that break polypeptides at specific places, followed by chemical methods to determine the amino acids sequence in these small fragments. After a few years they competed amino acid sequence of insulin.
        
        A functional protein is not just a polypeptide chain, but one or more polypeptides precisely twisted, folded, and coiled into a molecule of unique shape, which can be shown in several different types of models.
        
        This folding is driven and reinforced by the formation of various bond between parts of the chain, which intern depends on the sequence of amino acids. Many proteins are roughly spherical (globular proteins), while other are shaped like long fibers ( fibrous proteins).
        
        A protein's specific structure determines how it works. In almost every case, the function of a protein depends on its ability to recognize and bind to some other molecule.
        
        Ex 1.- Morphine, heroin, and other opiate drugs are able to mimic endorphins because they all share a similar shape with endorphins and can thus fit into and bind to endorphin receptor in the brain
  - - - The Primary sequence of a protein is its sequence of amino acids. It's also like the order of letters in a very long word. (If left to chance, there would be 20^127 different ways of making a polypeptide chain 127 amino acids long.
        
        The precise primary structure of protein is determined not by the random linking of amino acids, but by the inherited genetic information. ( It dictates secondary and tertiary structure, due to the chemical nature of the backbone and the side chains (R groups) of the amino acids along the polypeptide).
      - Secondary structure is the result of hydrogen bonds between the repeating constitutes of the polypeptide backbone ( not the amino acid side chains).
        
        Within the backbone, the oxygen atoms have a partial negative charge, and the hydrogen atoms attached to the nitrogen. That has a partial positive charge; therefore, hydrogen bonds can form between these atoms.
        
        By themselves , hydrogen bonds are weak, but because there are so many of them over a relatively long region of the polypeptide chain, they can support a particular shape for that of the protein.
        
        The secondary structure is the Beta pleated sheet. This structure has two or more segments of the polypeptide backbone. (Beta pleated sheets make up the core of many globular proteins).
        
        The Alpha helix a delicate coil held together by hydrogen bonding between every fourth amino acid. (Some fibrous proteins, such as Alpha - keratin, the structural protein in hair, they have a helix structure over most of their length).
      - Tertiary structure is the overall shape of a polypeptide resulting from interactions between the side chains (R group) of the various amino acids.
        
        One type of interaction that contributes to tertiary structure is called - somewhat misleading - a Hydrophobic interactions. As a polypeptide folds into its functional shape, amino acids with hydrophobic (nonpolar) side chains usually end up in clusters at the core of the protein, out of contact with water.
        
        A "Hydrophobic interaction" is usually caused by the exclusion of nonpolar substance by water molecules. Once nonpolar amino acid side chains are close together, Van der Waals interactions help hold them together.
        
        Hydrogen bonds between polar side chains and ionic bonds between positively and negatively charged side help stabilize tertiary structure. These weak interactions help stabilize tertiary structure, but their cumulative effect helps give the protein a unique shape.
        
        Covalent bonds called disulfide bridges may further reinforce the shape of a protein. These form where two cysteine monomers, which have sulfhydryl groups (-SH) on their side chain are brought close together by the folding of the protein.
        
        The sulfer of one cysteine bonds to the sulfur of the second, and the disulfide bridge (-s-s-) rivets part of the protein together .
      - Quaternary structure is the overall protein structure that results from the aggregation of these polypeptide subunits.
        (A complete globular transthyretin protein, is made up of 4 polypeptides).
        
        An example is Collagen . ( Collagen accounts for 40% of the protein in a human body ).
        
        Hemoglobin, the oxygen-binding protein of red blood cells , is another example of a globular protein with this structure. It consists of polypeptide subunits. (Two of alpha, and two of beta).
        each subunits has a non-polypeptide component, called Heme, that has an iron atom that binds oxygen.
- - - - DNA provides directions for its own replication. DNA also directs RNA synthesis and, though RNA, it controls protein synthesis.
        (This process is called Gene expression).
        
        Dna is the genetic material that organisms inherit from their parent. Each chromosome contains one long Dna molecule, usually carrying several hundred or more genes.
        
        When a cell reproduces itself by dividing, its DNA molecules are copied and passed along from one generation of cells to the next .Encoded in the structure of DNA is the information that programs all the cell's activities.
        
        Proteins are required to implement genetic programs. The molecular hardware of the cell- the tools for biological functions- consists mostly of proteins.
      - Each gene along DNA molecule directs synthesis of a type of RNA called messanger RNA (mRNA).
        The mRNA molecule interacts with cell's protein-synthesizing machinery to direct production of a polypeptide, which folds into all or part of a protein.
        
        We can summarize the flow of genetic information as DNA> RNA> Protein. The sites of protein synthesis are cellular structures called ribosomes.
        
        In the eukaryotic cell, ribosomes are in the region between the nucleaus and the plasma membrane (the cytoplasm), but DNA resides in the nucleus.
        
        Messenger RNA conveys genetic instructions for building proteins from the nucleus to the cytoplasm. Prokaryotic cells lack nuclei but still use mRNA to convey a message from the DNA to ribosomes and other cellular equipment that translate the coded information into amino acid sequences.
  - - - A Nucleotide, is composed of three parts: a 5-carbon sugar (a pentose), a nitrogen-containing (nitrogenous) base, and one or more phosphate groups
        
        Ina polynucleotide, each monomer has only one phosphate group. The portion of a nucleotide without any phosphate groups called a nucleoside.
        
        To build a nucleotide, consider the nitrogenous base. They are called nitrogenous textbases because the nitrogen tend to take up H+ from solution, thus acting as bases.
        There are two families of nitrogenous bases: pyrimidines and purines.
        
        Pyrimidines has one 6-membered ring of carbon and nitrogen atoms. The members of the pyrimidines family are Cytosine (C), Thymine (T), and Uracil (U).
        
        Purines are larger, with 6-membered ring fused to a 5-membered ring. The purines are Adenine (A), and Guanine (G).
        
        They differ by the chemical rings attached to them. (Adenine, guanine, and cytosine are both in DNA and RNA; Thymine is only found in DNA, uracil only in RNA)
        
        In DNA the sugar is deoxyribose, in RNA it is Ribose. The only difference is that deoxyribose lacks an oxygen atom on the second carbon ion the ring .
  - - - The two free ends of the polymer are distinctly different from each other. One end has a phosphate attached to a 5'Carbon, and the other end had a hydroxyl group on a 3' Carbon.
        
        The sequence of bases along a DNA (or mRNA) polymer is unique for each gene and provides very specific information to the cell.
        
        Because genes are hundreds to thousands of nucleotides long, the number of possible base sequences in effectively limitless. A gene's meaning to the cell is encoded in its specific sequence of four DNA bases.
        
        The structures of DNA and RNA molecules.
        
        DNA molecules have two polynucleotides, or "strands", that wind around an imaginary axis, forming a Double Helix.
        The two sugar-phosphate backbones run in opposite 5'>3' direction from each other: this is called Antiparallel.
        (like a divide highways)
- - - - The linear sequence of nucleotides in DNA molecules are passed from parents to offspring's; these sequences determine the amino acid sequences of proteins
        
        Given our evolutionary view of life, we can extend this concept of " molecular genealogy" to relationships between species: We would expect two species that appear to be closely related on anatomical evidence to also share greater proportion of their DNA and protein sequences that do less closely related species.
  - - - An unplanned but profound side benefit of this project - the Human Genome Project- was the rapid development of faster and less expensive method of sequencing.
        
        Biologist often look at problems by analyzing large sets of genes or even comparing whole genomes of different species, and approach called Genomics.
        
        A similar analysis of large sets of proteins, including there sequence, is called Proteomics.
        (protein sequences can be determined either by using biochemical techniques or by translating the DNA sequences the code for them.
        
        The most significant impact of genomics and proteomics on the field of biology as a whole has been their contributions to our understanding of evolution.