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Organic Molecules Are Compounds That Have Carbon Biology Essay

Macromolecules: A big and complex molecule. For example, nucleic acids, proteins, carbohydrates, and lipids, with considerably large substantial molecular weight.

Hydrocarbons: These are organic compounds which only hydrogen and of course, carbon. The four classes consist of aromatic, alkanes, alkenes, and alkynes.

Hydrocarbons: Contain only hydrogen and carbon molecules.

Biologically-made molecules (organic molecules): Contain only carbon molecules.

Because I can’t put pictures, I will try to put the formula and I will also do my best to describe it.

Carbonyl: C-O. Two R groups (variable) attached to the Carbon while the Carbon is double bonded to Oxygen. Ex. Formaldehyde.

Hydroxyl: Chemical formula is –OH. R group attach to OH. Ex. Alcohols, Carbohydrates

Carboxyl: COOH-. R group attached to the Carbon and Carbon attaches with OH and doubled bonded to Oxygen. Ex. Amino acids, vinegar

Amino: NH2. There is an R group attached to Nitrogen and Nitrogen is attached to two Hydrogens. Ex. Ammonia.

Sulfhydryl: SH. An R group is attached to a sulfide and sulfide is attached to Hydrogen. Ex. Proteins, Rubber

Polymer: A compound which is made up of several repeating units which is usually held together by covalent bonds. The four major classes consist of carbohydrates, lipids, and nucleic acids.

The process is known as Polymerization. Monomers are combined together to form a covalent bond. This covalent bond is created through dehydration synthesis. Per monomer added to the polymer, a single water molecule is removed. When a bond is created between two monomer, each monomer contributes to the removed water molecule. One molecule provides hydrogen while another provides a hydroxyl group. Polymers are created through the repetition of this reaction as more and more monomers are added to this chain. This process is helped by enzymes.

Macromolecules are disassembled through hydrolysis. A water molecule is added. A hydrogen atom is attached to one subunit and a hydroxyl group is attached to the other subunit, which therefor breaks the covalent bond in the macromolecule.

Metabolism (otherwise known as catalysis):

Class name of protein is enzyme. It’s utilized in order to break down proteins. Ex. Proteases

Defense:

Class name of protein is Immunoglobulin. It is used to mark foreign proteins for elimination. Ex. Antibodies

Cell Recognition:

Class name of protein is Cell Surface Antigens. Used for Self recognition. Ex. MHS proteins

Transport-Throughout-Body:

Class name of protein is Globins. It is utilized to carry out O2 and CO2. Ex. Hemoglobin

Membrane Transport:

Class name is Transporters. Used for excitable membranes. Ex. Sodium potassium pump

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The amino and carboxyl groups on a pair of amino acids can undergo a condensation reaction, losing a molecule of water and forming a covalent bond. Covalent bond that attaches/links two amino acids is known as a peptide bond. The resulting of this is a protein that is composed of one or more long chains, or polypeptides, composed of amino acids linked by peptide bonds.

Primary Structure: The particular amino acid sequence of a protein is its primary structure; it is determined by the nucleotide sequence of the gene that encodes the protein itself.

Secondary structure: The two patterns of H bonding occur during this step. In one, Hydrogen bonds form along a single chain, thus linking one amino acid to another chain. This in turn tends to pull that very chain into a coil which we call ALPHA HELIX. In the OTHER pattern, hydrogen bonds occur in TWO chains, which in turn link the amino acids in one chain to those of the OTHER chain. Often parallel chains are linked forming a sheet like structure called the PLEATED BETA SHEET. The folding of the amino acid (through hydrogen bonding) into these sheets and coils is known as a protein’s SECONDARY structure.

Motifs: The elements of secondary structure tend to combine in proteins in characteristic, recurring ways which we call MOTIFS. Ex. Rossmann fold.

Tertiary Structure: Positions the various Motifs and folds nonpolar side groups towards the interior thus we have the final folded shape of a globular protein.

Domains: A domain would be each exon-encoded section of a protein. Typically 100-200 amino acids long. After folding, results in a structurally independent functional unit; Domain.

Quaternary Structure: When 2 (or more) polypeptide chains associate in order to form a functional protein, the individual single chains are called subunits of the protein. These subunits don’t need to be the same. Ex. Hemoglobin.

If a protein’s environment is altered, the protein might change its shape or unfold; DENATURATION. Proteins can be denatured when the temperature, ionic concentration, or pH of the surrounding solution is changed. During the process, polypeptide chains unravel, losing their specific shape and their function. Excessive heat can also denature proteins. Transferring from an aqueous environment to an organic solvent will in most cases denature a protein.

Protein dissocation: The normal environment of a protein is reestablished after the denaturation. A small protein might spontaneously refold towards its natural shape, motivated by internal interactions between water and nonpolar amino acids. Ex. 4 subunits of hemoglobin might dissociate into four individual molecules without denaturation of the folded globin proteins, and will readily reassume their four-subunit quarternary structure.

A polymer which consists of several nucleotide monomers is a nucleic acid. Nucleic acids are essentially blueprints for all proteins and cellular activities. They work in encoding, transmitting, and expressing genetic information. A nucleic acid is a chain of five-carbon sugars bonded together by phosphodiester bonds with an organic base protruding from each sugar. DNA and RNA are the two major classes of nucleic acid.

Nucleic acids are long polymers of repeating subunits known as nucleotides. Each subunit consists of 3 parts. A 5-carbon sugar (in RNA its ribose, but in DNA its deoxyribose), a phosphate group, and an organic base that contains nitrogen. Purines and pyrimidines are the building blocks of this.

Polymerization is the forming of large polymers. A polymer is a long molecule consisting of many similar or identical building blocks linked by covalent bonds. The repeating units that serve as the building blocks of a polymer are small molecules called monomers. The monomer of a nucleic acid is nucleotide which is made up of sugar, phosphate and a base. RNA polymerases catalyzes formation of phosphodiester bonds which actually link nucleotides to one another so that they may form a linear chain. RNA polymerase also moves along the DNA by unwinding the helix just in front of the active site for polymerization to expose a brand new region of the strand (template) for coplentary base pairing. This way, the RNA chain (which is growing) extends by one nucleotide at a time in a 5 to 3 direction. Through this process nucleotides are bonded together to create a polymer.

Cytosine and thymine are pyrimidine bases, while adenine and guanine are purine bases. The sugar and the base together are called a nucleoside. In DNA, adenine can only pair with thymine in DNA. A key feature of all nucleic acids is that they have two distinctive ends: the 5' (5-prime) and 3' (3-prime) ends. This terminology refers to the 5' and 3' carbons on the sugar.

Cytosine and thymine are pyrimidine bases, while adenine and guanine are purine bases. The sugar and the base together are called a nucleoside. In DNA, adenine can only pair with thymine in DNA or with uracil in RNA, and cytosine can only pair with guanine. RNA is very similar to DNA in that it contains four bases, however the pyrimidine base, thymine is modified because RNA lacks a methyl group and this results in uracil takes its place in base pairing. The sugar in RNA is ribose. For both DNA (shown above) and RNA, the 5' end bears a phosphate, and the 3' end a hydroxyl group.

DNA molecules in organisms exist in double chains. DNA is a double helix, in which each step is a base pair that consists of a base in one chain attracted by hydrogen bonds to a base opposite it on the other chain. DNA stores hereditary information. RNA is very similar to DNA in that it contains four bases, however the pyrimidine base, thymine is modified because RNA lacks a methyl group and this results in uracil takes its place in base pairing. The sugar in RNA is ribose. RNA molecules transcribed from DNA are typically single-stranded. RNA uses DNA’s hereditary information to specify protein.

Adenine is a vital component in Adenosine Triphosphate which is essentially the currency of energy in a cell. Nicotinamide Adenine Dinucleotide carries electrons whose energy is used to produce ATP. Flavin Adenine Dinucleotide also carries these electrons which in turn produces ATP with their substantial energy.

They are insoluble in water.

Phospholipids create the core of all biological membranes. The structure of such a molecule is a hydrophilic (attracted to water) polar head which points toward the water and the two non-polar tails point toward the hydrophobic (repulsed by water) portion.

Living organisms are capable of storing energy from certain molecules for vast extended periods of time through C-H bonds of fat. Fats contain a glycerol molecule; there are three fatty acids attached to it, one to each carbon of the glycerol backbone. Saturated: all of the internal carbon atoms in the fatty acid chains are bonded to at least two hydrogen atoms then the fatty acid is said to be saturated, because it contains the maximum possible number of hydrogen atoms. Unsaturated: if a fatty acid has double bonds between one or more pairs of successive carbon atoms, the fatty acid is said to be unsaturated. Polyunsaturated: a given fatty acid that has more that has one double bond.

Terpenes, Steroids, Prostaglandins. Terpenes are long-chained lipids that are parts of many pigments like chlorophyll and visual pigment retinal. Steroid on the other hand are another type of lipid found in membrains but are composed of carbon rings (most animal cell membranes contain the steroid cholesterol). And Prostaglandins consists of about 20 modified fatty acids with 2 non-polar tails, both of which are attached to a 5-carbon ring. They act as messengers in several vertebrate systems.

Monosaccharide: These are the simplest carbohydrates. They can contain 3 to 6 carbon atoms. Though the ones that play a huge role in energy storage have 6. Ex. Glucose

Disaccharides: It is basically two monosaccharides joined by a covalent bond. A lot of times they are vital in the role of sugar transport. Ex. Sucrose.

Polysaccharides: It is a macromolecule composed of monosaccharide subcomponents. It is used by plants to store energy and structural building. Ex. Starch, Cellulose.

Isomers: It is a 6-carbon sugar and has an empirical formula of 1:2:1 (same as above). However there are some significant differences such as the fact that isomers have arranged their atoms differently; these discrepancies lead to several functional differences too. Isomer ex. Galactose, Glucose

First 2 monosaccharides are attached to one another to make disaccharides (we call them Transport Disaccharides). Transport form sugars have differences depending which monosaccharides are linked together to actually form the disaccharide. Next through dehydration synthesis, the –OH group and the H are removed; in other words a water molecule (H2O) is removed. Thus through the synthesis a polysaccharide is formed.

Monosaccharides: They can serve as a major source of fuel for organism metabolism. It serves a vital role in both biosynthesis and also as an energy source. When cells do not require a particular monosaccharide, they tend to convert it to another form such as polysaccharides. Glucose is critical in energy storage. Fructose is another example of a monosaccharide used in energy storage (because of its 6 carbon sugar)

Polysaccharide: They can serve purposes in both structure and storage. Polysaccharides can serve storage wise through starches for plants; amylose and branched amylopectin. It can serve structural purposes as well; the polysaccharide, cellulose composes the cell wall for plants.

AP ESSAY QUESTION

Carbon = one of the most important atoms to life. It helps conceive carbonyl and carboxyl groups which are essential for the building blocks of macromolecules and molecules. It helps multicellular organisms (ex. Humans) store energy with the 6-carbon sugars like Glucose, Fructose, and Galactose. The 6-carbon are usually categorized by the 6 CH2OH group. Carbon assists carbon-based organisms create their very own protective layer (like cellulose for cell walls in plants and Chitin in arthropods). Carbon is also a vital component in the formation of the lipid bilayer; which is the biological membrane of all organisms and is only possible through the formation of cooperating carbon atoms. Carbon is critical in the formation of hydrocarbons which is important to many organisms because of the energy-rich covalent bonds between the carbon and hydrogen (in the hydrocarbon).

First off the greenhouse effect is categorized by the CO2 and a plethora of other gases trapping longer wavelengths of infrared light, or heat radiating from the earth. Fossil fuels compounds which contain carbon; when used in industrialization they produce gases that build up trapped in heat (much like a greenhouse) which warms the earth, hence the term global warming. The more carbon dioxide in the atmosphere the higher levels of ppm.

The phosphate group in Category 1 helps form phospholipids, nucleic acids, and ATP in organisms. There’s also a fatty acid group (which organisms utilize to store vital energy). All together there are 3 Alanine groups and a some nonpolar amino acids (-CH2 AND –CH3). There are also some double bonded oxygen components and hydrogen components in the edges which renders this compound POLAR. In the compound there are also carbon-sugars which are useful for energy storing. There are also a few saturated fats.

There is a Sulfhydyl (which is found in proteins) in the second group. On the right of the compound the O- makes the compound highly polar. There’s also what seems to be a fatty acid group linked to a hydrogen atom. There is also an amino group which can be found in ammonia and composes the amino acid which is responsible for DNA structure; which is the very code that makes an organism function right. This compound is also polar all around its edges.


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